title: A bacterium-like particle vaccine displaying Zika virus prM-E induces systemic immune responses in mice

abstract:
The emergence of Zika virus (ZIKV) infection, which is an unexpectedly associated with congenital defects, has prompted the development of safe and effective vaccines. The gram-positive enhancer matrix-protein anchor (GEM-PA) display system has emerged as a versatile and highly effective platform for delivering target proteins for vaccines. In this article, we developed a bacterium-like particle vaccine ZI-{Delta}-PA-GEM based on the GEM-PA system. The fusion protein ZI-{Delta}-PA, which contains the prM-E-{Delta} protein of ZIKV (with a stem-transmembrane region deletion) and the protein anchor PA3, was expressed. The fusion protein was successfully displayed on the GEM surface, forming ZI-{Delta}-PA-GEM. Moreover, when BALB/c mice were immunized intramuscularly with ZI-{Delta}-PA-GEM combined with 201 VG and poly(I:C) adjuvants, durable ZIKV-specific IgG and protective neutralizing antibody responses were induced. Potent B cell/DC activation was also be stimulated early after immunization. Remarkably, splenocyte proliferation, the secretion of multiple cytokines, T/B cell activation and central memory T cell responses were elicited. These data indicate that ZI-{Delta}-PA-GEM is a promising bacterium-like particle vaccine candidate for ZIKV.

Author summaryBecause Zika virus (ZIKV) infection is considered as an example of "disease X", the development of a safe and effective ZIKV vaccine is essential. The gram-positive enhancer matrix-protein anchor (GEM-PA) display system has been used in many vaccine studies due to its advantages. In this study, prM-E-{bigtriangleup} protein of ZIKV (with a stem-transmembrane region deletion) and the protein anchor PA3 was fusion expressed, termed ZI-{bigtriangleup}-PA. Then the fusion protein ZI-{bigtriangleup}-PA could be displayed on the surface of GEM, forming ZI-{bigtriangleup}-PA-GEM. The author evaluated the immunogenicity of ZI-{bigtriangleup}-PA-GEM with the 201 VG and poly(I:C) adjuvants. The study demonstrates that ZI-{bigtriangleup}-PA-GEM induced mice to produce neutralizing antibody and specific cellular immune responses. The author believe that the bacterium-like particle vaccine ZI-{bigtriangleup}-PA-GEM has the potential to be used as the ZIKV vaccine.


title: Metabolomics and Transcriptomics unravel the mechanism of browning resistance in  Agaricus bisporus

abstract: Agaricus bisporus is widely used on the world market. The easy browning of mushroom surface is one of the most intuitive factors affecting consumer purchase. A certain cognition on browning mechanism have been made after years of research. At present, people slow down the browning of mushrooms mainly by improving preservation methods. In addition, breeding is also a reliable way. In the production practice, we have identified some browning resistant varieties,and we selected a browning-resistant variety to compare with ordinary variety to reveal the resistance mechanism. Using transcriptomics and metabolomics, the differences in gene expression and metabolite levels were revealed, respectively. The results showed that differentially expressed genes (DEGs) like AbPPO4, AbPPO3 and AbPPO2 were differently expressed and these DEGs involved in many pathways that related to browning. The expression of AbPPO expression play an important role in the browning of A. bisporus and multiple PPO family members are involved in the regulation of browning. However, the resistance to browning cannot be judged only by the expression level of AbPPOs. Formetabolomics, most of the different metabolites were organic acids. These organic acids had a higher level in anti-browning (BT) than easy-browning varieties (BS), although the profile was very heterogeneous. On the contrary, the content of trehalose in BS was significantly higher than that in BT. Higher organic acids decreased pH and further inhibited PPO activity. In addition, the BS had a higher content of trehalose, which might play roles in maintain the activity of PPO. The difference of browning resistance between BS and BT is mainly due to the differential regulation mechanism of PPO.

category: microbiology


title: Production and control of a Brazilian tailor-made meningococcal B vaccineShort title: Brazilian meningococcal B vaccine production

abstract: Meningococcal disease has been a public health problem in Brazil since the serogroups A and C epidemics occurred in the 1970s. The Oswaldo Cruz Foundation in Brazil has been working to develop a serogroup B meningococcal vaccine composed of detergent-treated outer membrane vesicles (OMV) and detoxified endotoxin (dLOS) from Neisseria meningitidis serogroup B prevalent strains. Experimental vaccine were produced in a pilot-scale under Good Manufacturing Practice condition (GMP). Physicochemical and biological controls were established based on what has been reported previously for OMV vaccines. The developed vaccine contained the main class 1, 2, 3, and 5 proteins, some minor iron-regulated proteins, and 5-10% residual lipopolysaccharide related to total protein content. The dLOS was added, as a vaccine component, in half of the total protein amount. The pyrogenicity of the final products, based on the residual LOS in OMVs, varied from 1.01 to 2.24 ng LOS/kg rabbit. Three experimental vaccines, were highly immunogenic in mice with better performance using higher antigen concentrations.


title: Antimicrobial interactions between the phytoextracts of Callistemon citrinus and Eriobotrya japonica against Streptococcus mutans

abstract: Streptococcus mutans is a gram-positive bacterium in the oral cavity that is most implicated in the dental caries progression. The condition is very expensive to manage and the most commonly used products such as fluoride tooth pastes and alcohol-based mouth washes are associated with many side effects. The current study therefore focused on providing a scientific evidence to guide the use of a combination of Eriobotrya japonica (EJ) and Callistemon citrinus (CC) as actives in development of an effective and cheaper herbal formulation for management of dental caries. The objective of this study was to determine antimicrobial interactions of Eriobotrya japonica and Callistemon citrinus phytoextracts proportions against Streptococcus mutans bacteria. The leaves of both plants (EJ and CC) were shade-dried and pulverized into a coarse powder which were then cold macerated using ethanol (60 %) for 24 h. Phytochemical screening was conducted for the two dry extracts obtained after fan drying before they were mixed in to five different proportions (1:0, 3:1, 1:1, 1:3 and 0:1). Minimum inhibitory concentrations (MIC) and minimum bactericidal concentration (MBC) assays against Streptococcus mutans were done for all the proportions above with ciprofloxacin and 2.5 % Dimethyl sulfoxide (DMSO) as the positive and negative controls respectively. Antimicrobial interactions between the two extracts were also evaluated using Fractional Inhibitory and Bacterial Concentration Indices (FICI/FBCI). Results showed that EJ and CC had percentage yields of 20.05 % and 15.45 % respectively. All the extracts showed similar phytochemical profiles. They also demonstrated an inhibitory effect on Streptococcus mutans with MIC and MBC values ranging from 521 to 3333 g/ml and 1042 to 3667 g/ml respectively. However, CC: EJ (1:0) had the lowest MIC and MBC comparable to that of the standard drug at P <0.05. The FICI/FBCI were between 1.5 and 3.917. Therefore, CC: EJ (1:0) proportion markedly demonstrated better antimicrobial activity against the test organism and there are no beneficial antimicrobial interactions between the two plant extracts to inform their combination as actives for dental caries product formulation.


title: microRNA Expression Levels Change in Neonatal Patients During and After Exposure to Cardiopulmonary Bypass

abstract:
ObjectivesThe systemic inflammation that occurs after exposure to cardiopulmonary bypass (CPB), which is especially severe in neonatal patients, is associated with poorer outcomes and is not well understood. In order to gain deeper insight into how exposure to bypass activates inflammatory responses in circulating leukocytes, we studied changes in microRNA (miRNA) expression during and after exposure to bypass. miRNAs are small non-coding RNAs that have important roles in modulating protein levels and function of cells.

MethodsWe performed miRNA-Sequencing on leukocytes isolated from neonatal cardiopulmonary bypass patients (N=5) at 7 timepoints during the process of CPB, including prior to the initiation of bypass, during bypass, and at three time points during the first 24 hours after weaning from bypass. We identified significant differentially expressed miRNAs using generalized linear regression models, and miRNAs were defined as statistically significant using an FDR adjusted p <0.05. We identified gene targets of these miRNAs using the Targetscan database, and identified significantly enriched biological pathways for these gene targets.

ResultsWe identified 54 miRNAs with differential expression during and after CPB. These miRNAs clustered into 3 groups, including miRNAs that were increased during and after CPB (3 miRNAs), miRNAs that decreased during and after CPB (10 miRNAs), and miRNAs that decreased during CPB but then increased 8-24 hours after CPB. 38.9% of the target genes of these miRNAs were significantly differentially expressed in our previous study. miRNAs with altered expression levels are predicted to significantly modulate pathways related to inflammation and signal transduction.

ConclusionsThe unbiased profiling of the miRNA changes that occur in the circulating leukocytes of bypass patients provides deeper insight into the mechanisms that underpin the systemic inflammatory response that occurs in patients after exposure to cardiopulmonary bypass. These data will help the development of novel treatments and biomarkers for bypass associated inflammation.

category: developmental biology


title: "Playing mysterious": occurrence of Bio-duck calls in Brazil reveals a complex acoustic behaviour for the Antarctic minke whale (Balaenoptera bonaerensis)

abstract: Acoustic methods can provide important data on the occurrence and distribution of migratory species. Information about Antarctic Minke whale (Balaenoptera bonaerensis) occurrence in the winter breeding grounds is scarce, mostly limited to old records from whaling stations before 1960s international moratory, such as Costinha Station in Northeastern Brazil (6{degrees} S / 34{degrees} W). This work describes the occurrence of the Antarctic minke whale (AMW) through Bio-duck acoustic detections in the Santos Basin, South-Southeastern Brazil (22{degrees} and 28{degrees} S / 42{degrees} and 48{degrees} W), registered between November 12 and December 19, 2015. AMW calls were detected for 12 days. We detected and classified 9 different Bio-duck calls in Brazilian coast waters, evidencing a high diverse acoustic behaviour for the minke whale breeding ground. This is the first study to describe the acoustic diversity of AMW vocalizations in lower latitudes, constituting important information to the conservation and management of cetaceans and their habitat. Therefore, our study presents the foremost acoustic evidence of the Antarctic minke whale in Brazil, utilizing high technological passive acoustic methods, such as autonomous underwater vehicle (SeaGlider) sampling.

category: animal behavior and cognition


title: Judgement Bias During Pregnancy In Domestic Pigs

abstract: In humans and rats, changes in mood and affect are known to occur during pregnancy, however it is unknown how gestation may influence mood in other non-human mammals. This study assessed changes in pigs judgment bias as a measure of affective state throughout gestation. Pigs were trained to complete a spatial judgement bias task with reference to positive and negative locations. We tested gilts before mating, and during early and late pregnancy, by assessing their responses to ambiguous probe locations. Pigs responded increasingly negatively to ambiguous probes as pregnancy progressed and there were consistent inter-individual differences in baseline optimism. This suggests that the pigs affective state may be altered during gestation, although as a non-pregnant control group was not tested, an effect of learning cannot be ruled out. These results suggest that judgement bias is altered during pregnancy in domestic pigs, consequently raising novel welfare considerations for captive multiparous species.


title: Modeling toes contributes to realistic stance knee mechanics in three-dimensional predictive simulations of walking

abstract: Physics-based predictive simulations have been shown to capture many salient features of human walking. Yet they often fail to produce realistic stance knee mechanics and terminal stance ankle plantarflexion. While the influence of the performance criterion on the predicted walking pattern has been previously studied, the influence of the mechanics has been less explored. Here, we investigated the influence of two mechanical assumptions on the predicted walking pattern: the complexity of the foot segment and the stiffness of the Achilles tendon. We found, through three-dimensional muscle-driven predictive simulations of walking, that modeling the toes and metatarsophalangeal joints, and thus using two-segment instead of single-segment foot models, contributed to robustly eliciting physiological stance knee flexion angles, knee extension torques, and knee extensor activity. Yet modeling toe joints did not improve ankle kinematics, nor did decreasing the Achilles tendon stiffness. The lack of predicted terminal stance ankle plantarflexion thereby remains an open question. Overall, this simulation study shows that not only the performance criterion but also mechanical assumptions affect predictive simulations of walking. Improving the realism of predictive simulations is required for their application in clinical contexts. Here, we suggest that using complex models is needed to yield such realism.

category: bioengineering


title: CureSCi Metadata Catalog - Making sickle cell studies findable

abstract:
ObjectivesTo adopt the FAIR principles (Findable, Accessible, Interoperable, Reusable) to enhance data sharing, the Cure Sickle Cell Initiative (CureSCi) MetaData Catalog (MDC) was developed to make Sickle Cell Disease (SCD) study datasets more Findable by curating study metadata and making them available through an open-access web portal.

MethodsStudy metadata, including study protocol, data collection forms, and data dictionaries, describe information about study patient-level data. We curated key metadata of 16 SCD studies in a three-tiered conceptual framework of category, subcategory, and data element using ontologies and controlled vocabularies to organize the study variables. We developed the CureSCi MDC by indexing study metadata to enable effective browse and search capabilities at three levels: study, Patient-Reported Outcome (PRO) Measures, and data element levels.

ResultsThe CureSCi MDC offers several browse and search tools to discover studies by study level, PRO Measures, and data elements. The "Browse Studies," "Browse Studies by PRO Measures," and "Browse Studies by Data Elements" tools allow users to identify studies through pre-defined conceptual categories. "Search by Keyword" and "Search Data Element by Concept Category" can be used separately or in combination to provide more granularity to refine the search results. This resource helps investigators find information about specific data elements across studies using public browsing/search tools, before going through data request procedures to access controlled datasets. The MDC makes SCD studies more Findable through browsing/searching study information, PRO Measures, and data elements, aiding in the reuse of existing SCD data.

category: bioinformatics


title: Novel murine models of post-implantation and midgestional malaria-induced preterm birth

abstract: Despite major advances made in malaria treatment and control over recent decades, the development of new models for studying disease pathogenesis remains a vital part of malaria research efforts. The study of malaria infection during pregnancy is particularly reliant on mouse models, as a means of circumventing many challenges and costs associated with pregnancy studies in endemic human populations. Here, we introduce three novel murine models that will further our understanding of how post-implantation and midgestional malaria infection affects pregnancy outcomes. When C57BL/6J (B6) mice are infected with Plasmodium chabaudi chabaudi AS on either embryonic day (E) 6.5, 8.5, or 10.5, preterm birth occurs in all animals by E16.5, E17.5, or E18.5 respectively, with no evidence of intrauterine growth restriction. We found that the time to delivery, placental inflammatory and antioxidant transcript upregulation, and the relationships between parasitemia and transcript expression prior to preterm birth are different based on the embryonic day of infection. On the day before preterm delivery, E6.5 infected mice did not experience significant upregulation of the inflammatory or antioxidant gene transcripts examined; however, parasitemia correlated positively with Il1{beta}, Cox1, and Hmox1 placental transcript abundance. E8.5 infected mice had elevated transcripts for Ifn{gamma}, Tnf, Il10, Cox1, Cox2, Sod1, Sod2, Cat, and Nrf2, while Sod3 was the only transcript that correlated with parasitemia. Finally, E10.5 infected mice had elevated transcripts for Ifn{gamma} only, with a tendency for Tnf transcripts to correlate with parasitemia. Tumor necrosis factor deficient (TNF-/-) and TNF receptor 1 deficient (TNFR1-/-) mice infected on E8.5 experienced preterm birth at the same time as B6 controls. Further characterization of these models is necessary to discover new and/or existing mechanism(s) or trigger(s) responsible for malaria-driven preterm birth that is determined by gestational age upon maternal infection, parasite-host dynamics, or both.

category: physiology


title: Accounting for heterogeneity in wild adult samples to measure insecticide resistance in Anopheles malaria vectors

abstract:
BackgroundSystematic, long-term, and spatially representative monitoring of insecticide resistance in mosquito populations is urgently needed to quantify its impact on malaria transmission, and to combat failing interventions when resistance emerges. Resistance assays on wild-caught adult mosquitoes (known as adult-capture) offer an alternative to the current protocols, and can be done cheaply, in a shorter time frame, and in the absence of an insectary. However, quantitative assessments of the performance of these assays relative to the gold standard, which involves rearing larvae in an insectary, are lacking.

Methodology/Principal findingsWe developed a discrete-time deterministic mosquito lifecycle model to simulate insecticide resistance assays from adult-captured mosquito collection in a heterogeneous environment compared to the gold standard larval capture methods, and to quantify possible biases in the results. We incorporated non-lethal effects of insecticide exposure that have been demonstrated in laboratory experiments, spatial structure, and the impact of multiple exposure to insecticides and natural ageing on mosquito death rates during the assay. Using output from this model, we compared the results of these assays to true resistance as measured by the presence of the resistance allele. In simulated samples of 100 test mosquitoes, reflecting WHO-recommended sample sizes, we found that compared to adult-captured assays (MSE = 0.0059), larval-captured assays were a better measure of true resistance (MSE = 0.0018). Using a correction model, we were able to improve the accuracy of the adult-captured assay results (MSE = 0.0038). Bias in the adult-capture assays was dependent on the level of insecticide resistance rather than coverage of bed nets or spatial structure.

Conclusions/SignificanceUsing adult-captured mosquitoes for resistance assays has logistical advantages over the standard larval-capture collection, and may be a more accurate sample of the mosquito population. These results show that adult-captured assays can be improved using a simple mathematical approach and used to inform resistance monitoring programs.

Author SummaryGrowing insecticide resistance in the mosquitoes that transmit malaria necessitates more widespread monitoring. Conducting assays on mosquitoes captured as adults is logistically simpler than raising them from eggs or larvae, the current recommended practice. However, this method is not widely used because survival when exposed to insecticide is known to depend on age and history of previous history as well as genetic resistance-factors that cannot be controlled when testing wild-caught adults. Here, we developed a mathematical model to quantify the difference in resistance measured via adult-capture assays compared to the gold standard larval-capture assays. We find that adult-capture assay results can be easily corrected using a formula based only on the measured resistance. This result has the potential to expand access to monitoring by reducing the time and infrastructure required to conduct these tests.

category: evolutionary biology


title: Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

abstract: Genome-scale metabolic network reconstructions (GENREs) are valuable tools for understanding microbial community metabolism. The process of automatically generating GENREs includes identifying metabolic reactions supported by sufficient genomic evidence to generate a draft metabolic network. The draft GENRE is then gapfilled with additional reactions in order to recapitulate specific growth phenotypes as indicated with associated experimental data. Previous methods have implemented absolute mapping thresholds for the reactions automatically included in draft GENREs; however, there is growing evidence that integrating annotation evidence in a continuous form can improve model accuracy. There is a need for flexibility in the structure of GENREs to better account for uncertainty in biological data, unknown regulatory mechanisms, and context specificity associated with data inputs. To address this issue, we present a novel method that provides a framework for quantifying combined genomic, biochemical, and phenotypic evidence for each biochemical reaction during automated GENRE construction. Our method, Constraint-based Analysis Yielding reaction Usage across metabolic Networks (CANYUNs), generates accurate GENREs with a quantitative metric for the cumulative evidence for each reaction included in the network. The structure of a CANYUN GENRE allows for the simultaneous integration of three data inputs while maintaining all supporting evidence for biochemical reactions that may be active in an organism. CANYUNs is designed to maximize the utility of experimental and annotation datasets and to ultimately assist in the curation of the reference datasets used for the automatic reconstruction of metabolic networks. We validated CANYUNs by generating an E. coli K-12 model and compared it to the manually curated reconstruction iML1515. Finally, we demonstrated the use of CANYUNs to build a model by generating an E. coli Nissle CANYUN GENRE using novel phenotypic data that we collected. This method may address key challenges for the procedural construction of metabolic networks by leveraging uncertainty and redundancy in biological data.

category: systems biology


title: Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

abstract: Recent years have seen a revolution in single-cell technologies, particularly single-cell RNA-sequencing (scRNA-seq). As the number, size and complexity of scRNA-seq datasets continue to increase, so does the number of computational methods and software tools for extracting meaning from them. Since 2016 the scRNA-tools database has catalogued software tools for analysing scRNA-seq data. With the number of tools in the database passing 1000, we take this opportunity to provide an update on the state of the project and the field. Analysis of five years of analysis tool tracking data clearly shows the evolution of the field, and that the focus of developers has moved from ordering cells on continuous trajectories to integrating multiple samples and making use of reference datasets. We also find evidence that open science practices reward developers with increased recognition and help accelerate the field.


title: Vesalius: Tissue anatomy from spatial transcriptomic data.

abstract: Characterization of tissue architecture promises to deliver insights into development, cell communication and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high-resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain.

category: genomics


title: Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis


title: Trichoderma asperellum: First report in Bangladesh

abstract:
The experiment was conducted at four laboratory, Bangladesh Agricultural University, Mymensingh to identify T. asperellum and its characterization was obtained from the rhizosphere of 49 different crops in 109 different locations of 36 districts in Bangladesh. Fifteen isolates of 88 isolates in T. asperellum were characterized on morphological and physiological features. All of the isolates were produced at 35 {degrees}C, but only TR27 and TR45 were grown and sporulate at 40 {degrees}C. Mycelial growth of all the isolates was reduced with the increasing of pH value. Molecular characterization in four isolates of TR27, TR45, TR70 and TR85 were studied at ITS and TEF region nucleotide sequencing among 15 isolates of T. asperellum and the morphological characterization at ITS and tef1 nucleotide sequencing was assimilated with molecular characterization. The isolates of TR45, TR70 and TR85 were found with 98% homology and TR27 exhibited 88% against their respective closest isolate. The isolates of TR27 and TR85 marked their respective nearest homology at 96%, while TR45 showed 99%, and 93% homology was signified with TR70 in TEF sequences. Three isolates (TR45, TR70 and TR85) were identified as T. asperellum of 100% bootstrap value and TR27 isolate was also recognized with 72% bootstrap value in phylogenetic tree. In phylogenetic analysis, tef1 extended better differentiation among the Trichoderma isolates within and among the groups of closely related species than the rDNA of the ITS region in reflecting wider variability in the isolates while a higher transversion ratio and evolutionary divergence were defined. Moreover the exploring of scientific and useful diversification of Trichoderma isolates on physiological and molecular traits has deemed in research fields.

IMPORTANCETrichoderma is an important genus in different aspect of uses as biofertilizer and bioremediation in agriculture. Specific identification in physiological and molecular characterization has also foremost attention with genome sequences as stored in databases. The diversity and genetic distances were ascertained among the isolates in phylogenetic analysis with the sequence data of the ITS region and tef1 of known Trichoderma strains was found in GenBank. Consequently, the databases of Trichoderma asperellum in molecular characterization can be frequently studied in the beneficial scope of agriculture. Trichoderma isolates of Rhizosphere soil in 4 locations with crops of (TR27) Sadar, Moulvibazar (Rice), (TR45) Sadar, Mymensingh (Sweet gourd), (TR70) Chapra, Chapai Nawabganj (Sesame) and (TR85) Nayanpur, Lalmonirhat (Maize) were found to be substantiated as Trichoderma asperellum strain in Bangladesh that were confirmed on physiological and molecular characters, and utilization of this strain can run faster in invasive technologies to control crop diseases.

category: molecular biology


title: Dynamics of maternal gene expression in Rhodnius prolixus

abstract: The study of the developmental processes in Rhodnius prolixus has recently advanced with the sequencing of the genome. In this work, we study maternal gene expression driving oogenesis and early embryogenesis in R. prolixus. We analyze the transcriptional profile of mRNAs to establish the genes expressed across the ovary, unfertilized eggs and different embryonic stages of R. prolixus until the formation of the germ band anlage (0, 12, 24, and 48 hours post egg laying). We identified 81 putative maternal and ovary-related genes and validated their expression by qRT-PCR. Consistent with a role in oogenesis and early development of R. prolixus, we show that parental RNAi against Rp-BicD results in embryos that did not show any distinguishable embryonic structure. In this framework we propose three hierarchies of maternal genes that affect early and late oogenesis, and embryonic patterning.


title: Seven-CpG DNA Methylation Age determined by Single Nucleotide Primer Extension and Illumina's Infinium MethylationEPIC array provide highly comparable results

abstract:
DNA methylation age (DNAm age, epigenetic clock) is a novel and promising biomarker of aging. It is calculated from the methylation fraction of specific cytosine phosphate guanine sites (CpG sites) of genomic DNA. Several groups have proposed epigenetic clock algorithms and these differ mostly regarding the number and location of the CpG sites considered and the method used to assess the methylation status. Most epigenetic clocks are based on a large number of CpGs, e.g. as measured by DNAm microarrays. We have recently evaluated an epigenetic clock based on the methylation fraction of seven CpGs that were determined by methylation-sensitive single nucleotide primer extension (MS-SNuPE). This method is more cost-effective when compared to array-based technologies as only a few CpGs need to be examined. However, there is only little data on the correspondence in epigenetic age estimation using the 7-CpG clock and other algorithms.

To bridge this gap, in this study we measured the 7-CpG DNAm age using two methods, via MS-SNuPE and via the MethylationEPIC array, in a sample of 1,058 participants of the Berlin Aging Study II (BASE-II), assessed as part of the GendAge study. On average, participants were 75.6 years old (SD: 3.7, age range: 64.9 - 90.0, 52.6% female). Agreement between methods was assessed by Bland-Altman plots. DNAm age was highly correlated between methods (Pearsons r=0.9) and Bland-Altman plots showed a difference of 3.1 years. DNAm age by the 7-CpG formula was 71.2 years (SD: 6.9 years, SNuPE) and 68.1 years (SD: 6.4 years, EPIC array). The mean of difference in methylation fraction between methods for the seven individual CpG sites was between 0.7 and 13 percent. To allow direct conversion between methods we developed an adjustment formula with a randomly selected training set of 529 participants using linear regression. After conversion of the Illumina data in a second and independent validation set, the adjusted DNAm age was 71.44 years (SD: 6.1 years, n=529). In summary, we found the results of DNAm clocks to be highly comparable. Furthermore, we developed an adjustment formula that allows for direct conversion of estimates between methods and enables one singular clock to be used in studies that employ either the Illumina or the SNuPE method.

category: genetics


title: Cardiomyocyte BRAF and type 1 RAF inhibitors promote cardiomyocyte and cardiac hypertrophy in mice in vivo

abstract: The extracellular signal-regulated kinase 1/2 (ERK1/2) cascade promotes cardiomyocyte hypertrophy and is cardioprotective, with the three RAF kinases forming a node for signal integration. Our aims were to determine if BRAF is relevant for human heart failure, if BRAF promotes cardiomyocyte hypertrophy, and if Type 1 RAF inhibitors developed for cancer (that paradoxically activate ERK1/2 at low concentrations: the "RAF paradox") may have the same effect. BRAF was upregulated in heart samples from patients with heart failure compared with normal controls. We assessed the effects of activated BRAF in the heart using mice with tamoxifen-activated Cre for cardiomyocyte-specific knock-in of the activating V600E mutation into the endogenous gene. We used echocardiography to measure cardiac dimensions/function. Cardiomyocyte BRAFV600E induced cardiac hypertrophy within 10 d, resulting in increased ejection fraction and fractional shortening over 6 weeks. This was associated with increased cardiomyocyte size without significant fibrosis, consistent with compensated hypertrophy. The experimental Type 1 RAF inhibitor, SB590885, and/or encorafenib (a RAF inhibitor used clinically) increased ERK1/2 phosphorylation in cardiomyocytes, and promoted hypertrophy, consistent with a "RAF paradox" effect. Both promoted cardiac hypertrophy in mouse hearts in vivo, with increased cardiomyocyte size and no overt fibrosis. In conclusion, BRAF potentially plays an important role in human failing hearts, activation of BRAF is sufficient to induce hypertrophy, and Type 1 RAF inhibitors promote hypertrophy via the "RAF paradox". Cardiac hypertrophy resulting from these interventions was not associated with pathological features, suggesting that Type 1 RAF inhibitors may be useful to boost cardiomyocyte function.

category: biochemistry


title: Cannabinoids differentially modulate behavioral and developmental responses to ethanol in Drosophila

abstract: Prolonged prenatal or adult exposure to ethanol is detrimental to mental and physical well-being, resulting in developmental abnormalities, progressive addiction and ultimate death. A growing number of studies have shown the therapeutic potential of cannabinoids in ethanol-related behaviors in mammals. However, the potential pharmacological actions of cannabinoids in ethanol responses have not been examined in the model organism Drosophila melanogaster. Here, we systematically investigated the effects of various cannabinoids on ethanol preference, ethanol sensitivity and tolerance, and ethanol-induced developmental defect in Drosophila. We showed that treatment with the phytocannabinoid cannabidiol (CBD) displayed a significant decrease in preference for consuming ethanol in adult flies. Interestingly, cannabinoids exhibited differential roles in short- and long-term ethanol tolerance in flies. Although cannabinoids had no detectable effects on short-term ethanol tolerance, CBD and the endocannabinoid anandamide (AEA) suppressed long-term tolerance to ethanol. Moreover, ethanol exposure delayed larval-to-pupal development and increased larval/pupal size. Unexpectedly, treatment with CBD or endocannabinoids did not attenuate ethanol-induced developmental delay, instead, exacerbated its detrimental effect. Thus, our systematical study reveals, for the first time, a differential role of the cannabinoids in the modulation of ethanol-related responses in Drosophila.

category: pharmacology and toxicology


title: Using Oxford Nanopore Technology direct RNA sequencing to identify depurination events induced by ricin and other ribosome inactivating proteins

abstract: Depurination is a frequent modification to both DNA and RNA, in DNA causing point mutations through misincorporation, in RNA, disabling ribosomes and halting protein synthesis. Some modifications of nucleic acids can be determined by direct sequencing using Oxford Nanopore Technologies (ONT). However, the identification of modifications is often limited by noise and their variety and number. Ricin is a toxin which enters cells and depurinates an adenine base in the sarcin-ricin loop of the large ribosomal subunit. This leaves only a ribose backbone, thus inhibiting protein translation. In humans, biological threat agents and ribosome inactivating proteins, such as ricin and saporin, depurinate base 4605 on the 28S rRNA providing a single defined target to try and identify. We postulated that the depurination event could be detected using ONT direct RNA sequencing through a change in charge in the ricin loop. A software tool was developed, RIPpore, that quantified the adenine modification from direct RNA sequencing data of ribosomal RNA purified from respiratory epithelial cells exposed to ricin. This provided a novel method of directly identifying ricin exposure and a basis for ONTs utility in detecting lesions in nucleic acids caused by depurination events.


title: Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in failing murine heart

abstract: Advancements of cross-linking mass spectrometry (XL-MS) for structural analysis of proteins bridges the gap between purified systems and native tissue environments. Here, isobaric quantitative protein interaction reporter technology (iqPIR) was utilized to further extend XL-MS to the first system-wide comparative study of mitochondrial proteins from healthy and diseased murine hearts. The failing heart interactome includes 602 statistically significant cross-linked peptide pairs altered in the disease condition. Structural insight into ketone oxidation metabolons, OXPHOS machinery, and nucleotide transporter hybrid-conformations, support mitochondrial remodeling in failing heart while bringing forth new hypotheses for pathological mechanisms. Application of quantitative cross-linking technology in tissue provides molecular-level insight to complex biological systems difficult to model in cell culture, thus providing a valuable resource for study of human diseases.


title: Cortical hyperexcitability drives dying forward ALS symptoms and pathology in mice

abstract: Amyotrophic lateral sclerosis (ALS) is a progressive fatal disorder caused by degeneration of motor neurons in the cortex and spinal cord. The origin of ALS in the central nervous system is unclear, however cortical hyperexcitability appears as an early and intrinsic feature of ALS and has been linked to degeneration of spinal motor neurons via a dying-forward mechanism. Here, we implement chemogenetics to validate the dying forward hypothesis of ALS in mice. We show that chronic hyperexcitability of corticomotoneurons induced by excitatory chemogenetics results in motor symptoms and core neuropathological hallmarks of ALS, including corticomotoneuron loss, corticospinal tract degeneration and reactive gliosis. Importantly, corticomotoneuron loss was sufficient to drive degeneration of spinal motor neurons and neuromuscular junctions (NMJs), associated with cytoplasmic TAR DNA binding protein 43 (TDP-43) pathology. These findings establish a cortical origin of ALS mediated by neuronal hyperexcitability, consistent with a dying forward mechanism of neurodegeneration.

category: neuroscience


title: FLARIM v2.0, an improved method to quantify transcript-ribosome interactions in vivo in the adult Drosophila brain

abstract: Neural injury triggers striking immune reactions from glial cells, including significant transcriptional and morphological changes, but it is unclear how these events are coordinated to mount an effective immune response. Here, we present a new variant of the Fluorescence assay to detect ribosome interactions with mRNA (FLARIM), which we term FLARIM v2.0, to visualize single immune gene transcripts and association with ribosomes in glia responding to neurodegeneration. Specifically, using an in vivo axotomy assay in Drosophila, we show that matrix metalloproteinase-1 (Mmp-1) mRNAs and associated ribosomes are detected in distal processes of reactive glia where they are actively engulfing degenerating axonal material, suggesting that local translation is an important component of the glial immune response to axotomy. This work also validates our enhanced FLARIM assay as a promising tool to investigate mechanisms of mRNA transport and translation in a wide range of in vitro and in vivo paradigms.


title: Maternal γδ T Cells Shape Offspring Pulmonary Type-2 Immunity In A Microbiota-Dependent Manner

abstract: Immune system development is greatly influenced by vertically transferred cues. However, beyond antibody-producing B cells, little is known about the role of other cell subsets of the maternal immune system in regulating offspring immunity. We reasoned {gamma}{delta} T cells to be attractive candidates based on their tissue distribution pattern: abundant in the skin, mammary glands and female reproductive tract. Here we found that mice born from {gamma}{delta} T cell-deficient (TCR{delta}-/-) dams display, early after birth, a pulmonary milieu selectively enriched in type-2 cytokines such as IL-33, IL-4, IL-5, and IL-13, and type-2-polarized immune cells, when compared to the progeny of {gamma}{delta} T cell-sufficient dams. In addition, upon helminth infection, mice born from TCR{delta}-/- dams sustained an increased type-2 inflammatory response. Critically, this was independent of the genotype of the pups. Despite similar levels of circulating antibodies in mothers and progeny, the intestinal microbiota in the offspring of TCR{delta}-/- and TCR{delta}+/- dams harbored distinct bacterial communities acquired during birth and fostering. These differences were accompanied by changes in the intestinal short-chain fatty acids (SCFA) profile. Importantly, antibiotic treatment abrogated the differences observed in the pulmonary milieu, and exogenous SCFA supplementation suppressed first-breath- and infection-induced inflammation. In summary, maternal {gamma}{delta} T cells control the establishment of a neonatal gut-lung axis by conditioning the postnatal microbial colonization of the off-spring and bacterial-derived metabolite availability; ultimately impacting on the development of pulmonary type-2 immunity in the offspring.

category: immunology


title: NLRP1B and NLRP3 control the host response following colonization by the commensal protist Tritrichomonas musculis.

abstract:
Commensal intestinal protozoa, unlike their pathogenic relatives, are neglected members of the mammalian microbiome. These microbes have a significant impact on the hosts intestinal immune homeostasis, typically by elevating anti-microbial host defense. Tritrichomonas musculis (T. mu), a protozoan gut commensal, strengthens the intestinal host defense against enteric Salmonella infections through Asc- and Il1r1-dependent Th1 and Th17 cell activation. However, the underlying inflammasomes mediating this effect remain unknown. Here, we report that colonization with T. mu results in an increase in luminal extracellular ATP, elevated levels of IL-1{beta}, and increased numbers of IL-18 receptor-expressing Th1 and Th17 cells in the colon. Mice deficient in either Nlrp1b or Nlrp3 failed to display these protozoan-driven immune changes and lost resistance to enteric Salmonella infections even in the presence of T. mu. These findings demonstrate that T. mu-mediated host protection requires sensors of extra and intracellular ATP to confer resistance to enteric Salmonella infections.

KEY POINTSO_LIIntestinal colonization with the commensal Tritrichomonas musculis elevates luminal ATP levels
C_LIO_LINLRP1B and NLRP3 activation is required for Tritrichomonas musculis-driven Th cell response.
C_LI


title: Overlap of expression and alignment of diurnal and circadian rhythmicity in the human blood transcriptome with organ and tissue specific rhythmicity in a non-human primate

abstract:
BACKGROUNDTwenty-four-hour rhythmicity in transcriptomes of tissues and organs is driven by local circadian oscillators, systemic factors, the central circadian pacemaker, and light-dark cycles. This rhythmicity is to some extent organ- and tissue-specific such that the sets of rhythmic transcripts or their timing are different across tissues/organs. Monitoring rhythmicity of tissues and organs holds promise for circadian medicine, but in humans most tissues and organs are not easily accessible. To investigate the extent to which rhythmicity in the human blood transcriptome reflects rhythmicity in tissues and organs, we compared the overlap and timing of rhythmic transcripts in human blood and rhythmic transcripts in 64 tissues/organs of the baboon.

METHODSRhythmicity in the transcriptomes of humans and baboons were compared using set logic, circular cross-correlation, circular clustering, functional enrichment analyses and partial least squares regression.

RESULTSOf the 759 orthologous genes that were rhythmic in human blood, 652 (86%) were also rhythmic in at least one baboon tissue. Most of these genes were associated with basic processes such as transcription and protein homeostasis. 109 (17%) of the 652 overlapping rhythmic genes were reported as rhythmic in only one baboon tissue or organ and several of these genes have tissue/organ-specific functions. Analysis of the alignment between baboon and human transcriptomes showed that in these diurnal species, rhythmicity is aligned with the onset, rather than midpoint or end of light period. In both species, the timing of rhythmic transcripts displayed prominent  night and  day clusters, with genes in the dark cluster associated with translation. The timing of human and baboon transcriptomes was significantly correlated in 25 tissue/organs with an average earlier timing of 3.21 h (SD 2.47 h) in human blood.

CONCLUSIONSThe human blood transcriptome contains sets of rhythmic genes that overlap with rhythmic genes of tissues/organs, some of which are tissue/organ-specific, in the baboon. The rhythmic sets vary across tissues/organs but the timing of most rhythmic genes is similar across human blood and baboon tissues/organs. These results have implications for our understanding of the regulation of rhythmicity across tissues/organs and species and development of blood transcriptome-based biomarkers for rhythmicity in tissues and organs.


title: Partial endothelial-to-mesenchymal transition (EndMT) contributes to lumen re-organization after carotid arteryligation

abstract: Endothelial-to-mesenchymal transition (EndMT) is a fundamental process in vascular remodeling. Carotid artery ligation is commonly used for induction of neointima formation and vessel stenosis; however, the precise regulatory mechanism of vascular remodeling is not entirely understood. In this study, we showed that resident endothelial cells (ECs) are the origin of neointima cells and ECs transiently expressed CD45 in the early stage of neointima formation accompanied by increased expression of EndMT markers. In vitro, CD45-positive EndMT was induced by stabilization of HIF-1 with cobalt chloride or VHL inhibitor in human primary ECs, which mimicked the hypoxic condition of ligated artery, and promoted the formation of integrin 11-SHARPIN complex. Notably, a CD45 phosphatase inhibitor disrupted this complex, thereby destabilizing cell-cell junctions. These results suggest that the CD45 activity is required for the retention of an EC phenotype and cell-cell junctions during EndMT (termed "partial EndMT"). We thus propose a novel mechanism of partial EndMT that contributes to lumen re-organization during vascular injury.


title: Crystalline deposits reveal caste identity of late embryos and larvae of the ant Cardiocondyla obscurior

abstract: Social insects are interesting models for the study of anticipatory developmental plasticity because of the striking differentiation into reproductive queens and functionally sterile workers. A few ant genera, including Cardiocondyla, represent the pinnacle of social evolution in the Hymenoptera, where workers have completely lost their reproductive organs, minimizing reproductive conflicts between queens and workers. Here we show that late embryos and larvae of queens of the ant C. obscurior can be identified by the appearance of urate deposits around the forming ovaries. The discovery of caste-specific urate patterns in C. obscurior and three additional Cardiocondyla species will facilitate future studies of developmental plasticity in ants.


title: Severe inbreeding and gene loss in the historical and extant population of the critically endangered Devils Hole pupfish

abstract: Small populations with limited geographic distributions are predicted to be threatened by inbreeding and lack of genetic diversity, both of which may negatively impact fitness and exacerbate population decline. One of the most extreme natural examples is the Devils Hole pupfish (Cyprinodon diabolis), an iconic and critically endangered species with the smallest known habitat range of any vertebrate. This imperiled species has experienced severe declines in population size over the last thirty years and suffered major, repeated bottlenecks in 2007 and 2013, when the population sunk to 38 and 35 individuals, respectively. Here we sequenced contemporary and historical genomes of Devils Hole and neighboring Death Valley and Ash Meadows desert pupfishes to examine the genomic consequences of small population size. We found extreme inbreeding (FROH = 0.71 - 0.82) and increased genetic load in the Devils Hole pupfish. We also document unique fixed loss-of-function (LOF) alleles and deletions in genes associated with sperm motility, stress, and hypoxia within the extant Devils Hole pupfish population that likely reduce fitness. Comparisons between contemporary samples (2008 - 2012) and a genome sequenced from a 1980 formalin-fixed museum specimen suggest that inbreeding has increased 6% as the population has declined, but that many putatively deleterious variants have been segregating in the population since at least 1980. This includes a fixed early stop codon in cfap43 (n = 8/8 samples), which is associated with sperm flagellum defects and causes infertility in humans and mice. Out of ninety-four unique deletions, fifteen were detected within 2 kb of annotated genes. Five have roles in physiological responses to hypoxia and mitochondrial activity, such as redd1 (n = 7/7 samples), suggesting impaired hypoxia tolerance in this species despite the low oxygen concentrations of Devils Hole. We thus document one of the most extreme inbreeding events in a natural population and a set of candidate deleterious variants to inform management and potential genetic rescue in this conservation icon.


title: The first chromosome-level gecko genome reveals dynamic sex chromosomes in Neotropical leaf-litter geckos (Sphaerodactylidae: Sphaerodactylus)

abstract: Sex chromosomes have evolved many times across eukaryotes, indicating both their importance and their evolutionary flexibility. Some vertebrate groups, such as mammals and birds, have maintained a single, conserved sex chromosome system across long evolutionary time periods. By contrast, many reptiles, amphibians, and fish have undergone frequent sex chromosome transitions, most of which remain to be catalogued. Among reptiles, gecko lizards (infraorder Gekkota) have shown an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However--across geckos--information about sex chromosome linkage is expressly lacking, leaving large gaps in our understanding of the evolutionary processes at play in this system. To address this gap, we assembled the first chromosome-level genome for a gecko and use this linkage information to survey six Sphaerodactylus species using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species of Sphaerodactylus geckos. We expand upon that work to identify between two and four sex chromosome cis-transitions (XY to XY) within the genus. Interestingly, we confirmed two linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus 3 and Gallus 18/30/33). We highlight the increasing evidence that most (if not all) linkage groups will likely be identified as a sex chromosome in future studies given thorough enough sampling.


title: Machine-learning-guided library design cycle for directed evolution of enzymes: the effects of training data composition on sequence space exploration

abstract: Machine learning (ML) is becoming an attractive tool in mutagenesis-based protein engineering because of its ability to design a variant library containing proteins with a desired function. However, it remains unclear how ML guides directed evolution in sequence space depending on the composition of training data. Here, we present a ML-guided directed evolution study of an enzyme to investigate the effects of a known "highly positive" variant (i.e., variant known to have high enzyme activity) in training data. We performed two separate series of ML-guided directed evolution of Sortase A with and without a known highly positive variant called 5M in training data. In each series, two rounds of ML were conducted: variants predicted by the first round were experimentally evaluated, and used as additional training data for the second-round prediction. The improvements in enzyme activity were comparable between the two series, both achieving enzyme activity 2.2-2.5 times higher than 5M. Intriguingly, the sequences of the improved variants were largely different between the two series, indicating that ML guided the directed evolution to the distinct regions of sequence space depending on the presence/absence of the highly positive variant in the training data. This suggests that the sequence diversity of improved variants can be expanded not only by conventional ML using the whole training data, but also by ML using a subset of the training data even when it lacks highly positive variants. In summary, this study demonstrates the importance of regulating the composition of training data in ML-guided directed evolution.


title: In vitro reconstitution demonstrates the amyloid-beta mediated myelin membrane deformation

abstract: Amyloid-beta (A{beta}) aggregation mediated neuronal membrane deformation, although poorly understood, is implicated in Alzheimers Disease (AD). Particularly, whether A{beta} aggregation can induce neuronal demyelination remains unknown. Here we show that A{beta}-40 binds and induces extensive tubulation in the myelin membrane in vitro. The binding of A{beta}-40 depends predominantly on the lipid packing defect densities and electrostatic interactions and results in rigidification of the myelin membrane in the early time scales. Furthermore, elongation of A{beta}-40 into higher oligomeric and fibrillar species leads to eventual fluidization of the myelin membrane followed by extensive membrane tubulation observed in the late phase. Taken together, our results capture mechanistic insights into snapshots of temporal dynamics of A{beta}-40 - myelin membrane interaction and demonstrate how short timescale, local phenomena of binding, and fibril mediated load generation manifests into long timescale, global phenomena of myelin tubulation and demonstrates the ability of A{beta}-40 to demyelinate.

category: biophysics


title: Gpnmb inhibits oligodendrocyte differentiation of adult neural stem cells by amplifying TGFβ1 signaling

abstract: Gli1 expressing neural stem cells, in the subventricular zone of the adult mammalian brain, respond to demyelination injury by differentiating into oligodendrocytes. We have identified Gpnmb as a novel regulator of oligodendrogenesis in Gli1 neural stem cells, whose expression is induced by TGF{beta}1 signaling via Gli1, in response to a demyelinating injury. Upregulation of Gpnmb further activates the TGF{beta}1 pathway by increasing the expression of the TGF{beta}1 binding receptor subunit, TGF{beta}R2. Thus the TGF{beta}1[->]Gli1[->]Gpnmb[->]TGF{beta}R2 signaling pathway forms a feed forward loop for sustained activation of TGF{beta}1 signaling in Gli1 neural stem cells, resulting in inhibition of their differentiation into mature oligodendrocytes following demyelination.


title: Host cell amplification of nutritional stress contributes to persistence in Chlamydia trachomatis

abstract: Persistence, a viable, but non-replicating state has been implicated in diseases caused by Chlamydia trachomatis. Multiple nutritional stressors produce a superficially similar "persistent" state, yet no systematic comparison has been made to determine their likeness. We employed host-pathogen dual RNA-sequencing under both iron- and tryptophan-starved conditions to gain insight into chlamydial persistence and identify contributions by the host cell. Analysis of the transcriptome of iron- or tryptophan-starved Chlamydia revealed a common "core" component and a stress-specific "accessory" subset. Despite the overall transcriptomic differences of host cells starved for either iron or tryptophan, both stressors induced persistence. A common metabolic consequence of the stressors was a reduction in intracellular GTP levels. Mizoribine inhibition of IMDPH1, which catalyzes the rate-limiting step in de novo guanine nucleotide synthesis reproduced to a similar extent GTP depletion, and inhibited chlamydial growth as expected for a pathogen that is auxotrophic for GTP. Thus, the reduction of guanine nucleotide synthesis manifests amplification of either iron or tryptophan starvation contributing to persistence. These findings illustrate that a nutritionally stressed host cell remains effective in arresting growth of Chlamydia by targeting metabolic pathways required by the pathogen.


title: Mycorrhizal inoculation and treatment with biochar and compost from pruning waste improve the qualitative properties of a calcareous soil under wheat cultivation

abstract: Most calcareous soils have relatively low levels of organic matter. To address this issue and improve the qualitative properties of calcareous soils, soils can be treated with mycorrhizal fungi and/or exogenous organic material such as biochar or compost derived from tree pruning waste. To evaluate the effect of pruning waste biochar (PWB) and pruning waste compost (PWC) derived from apple and grape trees combined with arbuscular mycorrhizal fungi (AMF) on the biological indices of calcareous soils, a rhizobox study on wheat plants using a completely randomized design was conducted under greenhouse conditions. The studied factors included the source of the type of organic material applied (PWB, PWC, and control), the nature of the microbial inoculation (inoculation with AMF or no inoculation), and the zone to which the treatments were applied (rhizosphere and non-rhizosphere soil). At the end of the plant growth period, organic carbon (OC), microbial biomass carbon (MBC), microbial biomass phosphorous (MBP), microbial respiration (BR), substrate-induced respiration (SIR), alkaline (ALP), acid (ACP) phosphatase enzyme activities in the rhizosphere and non-rhizosphere soils, and root mycorrhizal colonization were determined. Simultaneous application of a source of organic matter and AMF inoculation significantly increased the OC and biological indices of soil relative to those observed when applying organic matter without AMF inoculation. Additionally, MBC, MBP, ACP and ALP - enzymes activities in the rhizosphere zone were significantly higher than in the non-rhizosphere. AMF increased BR and SIR levels in the rhizosphere by 13.06% and 7.95% compared to non-rhizosphere, respectively. It can be concluded that in calcareous soils with low organic carbon contents, organic amendments such as PWC and PWB can improve soil biological properties by increasing microbial activity and changing the properties of the rhizosphere.


title: Target Enrichment Enhances the Sensitivity of Sanger Sequencing for BRAF V600 Mutation Detection

abstract: BRAF is a serine/threonine protein kinase whose mutations lead to unregulated cell growth and cause different types of cancers. Since V600E is a major BRAF mutation and V600E detection as a companion diagnostic test (CDx) is stipulated in the labeling of the BRAF V600 inhibitors. Traditional Sanger sequencing cannot accurately detect mutations lower than 15% variant allele frequency (VAF) due to its limited sensitivity. Here we applied our patented XNA molecular clamping technology to modify Sanger sequencing template preparation by enriching the mutation population. We found that the use of our mutation-enriched template enhanced the analytical sensitivity of Sanger sequencing to 0.04% VAF. The method is verified to detect V600E, V600K, and V600R mutants and is validated for the known BRAF mutation status in clinical samples. Our streamlined protocol can be used for easy validation of the highly sensitive target-enrichment method for detecting BRAF V600 mutations using Sanger sequencing in clinical labs. In addition to BRAF V600 mutations, this method can be extended to the detection of other clinically important actionable mutations for cancer diagnostics.


title: Response of Posidonia oceanica (L.) Delile and its associated N2 fixers to different combinations of temperature and light levels

abstract: Ocean warming and water turbidity are threats for the persistence of seagrass meadows and their effects on the productivity of seagrasses and the functioning of their associated microorganisms have not been studied extensively. The purpose of this study was to assess the effects of different light levels and temperatures on Posidonia oceanica, the endemic seagrass species in the Mediterranean Sea, and their N2 fixing community, which contributes importantly to the nitrogen requirements and high productivity of the plants. Aquarium experiments were conducted in winter when the plants are more vulnerable to changes in temperature, subjecting them to short-term exposures to ambient (15.5 {degrees}C) and elevated temperatures (ambient+5.5 {degrees}C) and at limited (13 mol photons m-2 s-1) and saturating light conditions (124 mol photons m-2 s-1). Primary production, chlorophyll content, reactive oxygen species production, polyphenols content, the nifH gene expression, N2 fixation and alkaline phosphatase activities were measured in different plant tissues. Plants incubated at ambient temperature and high light exhibited enhanced total chlorophyll production and significantly higher gross and net primary production, which were approximately two-fold compared to the rest of the treatments. The oxidative stress analyses revealed increased production of reactive oxygen species in young leaves incubated at ambient temperature and saturating light, while the polyphenols content in top leaves was considerably higher under elevated temperatures. In contrast, N2 fixation and alkaline phosphatase rates were significantly higher under elevated temperature and low light levels. The presence of the N2 fixing phylotypes UCYN-A, -B and -C was detected through genetic analyses, with UCYN-B demonstrating the highest nifH gene transcription levels at elevated temperatures. These findings emphasize the significant role of irradiance on the productivity of P. oceanica and the temperature dependence of the N2 fixation process in winter.

category: ecology


title: Identification and targeting of G-quadruplex structures in MALAT1 long non-coding RNA

abstract: RNA G-quadruplexes (rG4s) have functional roles in many cellular processes in diverse organisms. While a number of rG4 examples have been reported in coding messenger RNAs (mRNA), so far only limited works have studied rG4s in non-coding RNAs (ncRNAs), especially in long non-coding RNAs (lncRNAs) that are of emerging interest and significance in biology. Herein, we report that MALAT1 lncRNA contains conserved rG4 motifs, forming thermostable rG4 structures with parallel topology. We also show that rG4s in MALAT1 lncRNA can interact with NONO protein with high specificity and affinity in vitro and in nuclear cell lysate, and we provide in vivo data to support that NONO protein recognizes MALAT1 lncRNA via rG4 motifs. Notably, we demonstrate that rG4s in MALAT1 lncRNA can be targeted by rG4-specific small molecule, peptide, and L-aptamer, leading to the dissociation of MALAT1 rG4-NONO protein interaction. Altogether, this study uncovers new and important rG4s in MALAT1 lncRNAs, reveals their specific interactions with NONO protein, offers multiple strategies for targeting MALAT1 and its RNA-protein complex via its rG4 structure, and illustrates the prevalence and significance of rG4s in ncRNAs.


title: Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation

abstract:
Because of the continuous rise of foodborne illnesses caused by the consumption of raw fruits and vegetables, effective post-harvest anti-microbial strategies are needed. This study evaluated the dose x time effects on the anti-microbial action of ozone (O3) gas against the Gram-negative Escherichia coli O157:H7 and Gram-positive Listeria monocytogenes, which are common contaminants in fresh produce. The study on non-host tomato environment correlated the dose x time aspects of xenobiosis by examining the correlation between bacterial survival in terms of log-reduction and defense responses at the level of gene expression. In E. coli, low (1 g O3/g of fruit) and moderate (2 g O3/g of fruit) doses caused insignificant reduction in survival, while high dose (3 g/g of fruit) caused significant reduction in survival in a time-dependent manner. In L. monocytogenes, moderate dose caused significant reduction even with short-duration exposure. Distinct responses to O3 xenobiosis between E. coli and L. monocytogenes are likely related to differences in membrane and cytoplasmic structure and components.

Transcriptome profiling by RNA-Seq showed that primary defenses in E. coli were attenuated after exposure to a low dose, while the responses at moderate dose were characterized by massive upregulation of pathogenesis and stress-related genes, which implied the activation of defense responses. More genes were downregulated during the first hour at high dose, with a large number of such genes getting significantly upregulated after 2 hr and 3 hr. This trend suggests that prolonged exposure led to potential adaptation. In contrast, massive downregulation of genes was observed in L. monocytogenes regardless of dose and exposure duration, implying a mechanism of defense distinct from that of E. coli. The nature of bacterial responses revealed by this study should guide the selection of xenobiotic agents for eliminating bacterial contamination on fresh produce without overlooking the potential risks of adaptation.

category: microbiology


title: Evolutionary dynamics of sex-biased gene expression in a young XY system: Insights from the brown algae

abstract: The sex-dependent regulation of gene expression is considered to be an underlying cause of often extensive, sexually dimorphic traits between males and females. Although the nature and degree of sex-biased gene expression has been well-documented in several animal and plant systems, far less is known about the commonality, conservation, recruitment mechanisms and evolution of sex-biased genes in more distant eukaryotic groups. Brown algae are of particular interest for empirical studies on the evolution of sex-biased gene expression, as they have been evolving independently from animals and plants for over one billion years. Here we focus on two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. Using RNA-seq, we study sex-biased gene expression and discuss different evolutionary forces responsible for the evolution of sex-biased genes. We find that both species evolved masculinized transcriptomes, with sex-biased genes allocated mainly to male reproductive tissue, but virtually absent in vegetative tissues. Conserved male-biased genes were enriched in functions related to gamete production, along with sperm competition and include two flagellar proteins under positive selection. In contrast to female-biased genes, which show high turnover rates, male-biased genes reveal remarkable conservation of bias and expression levels between the two species. As observed in other XY systems, male-biased genes also display accelerated rates of coding sequence evolution compared to female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels. Similar to evolutionarily distant plant and animal lineages, sex-biased gene expression in Fucus evolved during the transition to dioecy to resolve intra-locus sexual conflict arising from anisogamy.


title: Evolutionary dynamics of sex-biased gene expression in a young XY system: Insightsfrom the brown alga genus Fucus


title: Clock genes Period1 and Period2 in the hippocampal CA1 mediate depression-like behaviors and rapid antidepressant response

abstract:
Accumulated reports have indicated that circadian rhythm is closely related to the pathogenesis of major depressive disorder (MDD). Recently, adenosine has been identified to modulate circadian clock via adenosine A1 and A2A receptor signaling pathways. Cyclic AMP-response element binding protein (CREB) is a convergent point that plays a critical role in the pathogenesis of depression and is a downstream molecule of adenosine A1 receptor signaling pathway as an endpoint that can regulate the expression of circadian genes Period1 (Per1) and Period2 (Per2). However, whether Per mediates the development of MDD via CREB has not been elucidated. We used chronic unpredictable stress (CUS) to induce depression-like behaviors and found that it could induce decrease in p-CREB and PER1 levels in the hippocampal CA1 region in rats. Both depression-like behaviors and the decreased protein levels could be rapidly rescued by the administration of adenosine A1 receptor agonist 2-Choro-N6-cyclopentyladenosine (CCPA). Furthermore, knockdown of Per1 in hippocampal CA1 region could also induce depression-like behaviors, which could also be rescued by CCPA. Interestingly, Per2 knockdown in hippocampal CA1 region resulted in potential antidepressant-like effect. In addition, knockout of CRE sequence in the promoter regions of either Per1 or Per2 led to depression-like behaviors, which could not be rescued by CCPA. These results indicated that clock genes Per1 and Per2 play critical roles in the pathophysiology of depression and CRE sequences in the promoter regions of Per1 and Per2 may be a critical antidepressant target.

HighlightsO_LICUS induces both depression-like behaviors and decreases in the expression of p-CREB and PER1 levels in the hippocampal CA1 region in rats, which can be rapidly rescued by 2-Choro-N6-cyclopentyladenosine (CCPA).
C_LIO_LIKnockdown of clock gene Per1 in the hippocampal CA1 brain region leads to depression-like behaviors in rats, which can be also rescued by CCPA.
C_LIO_LIKnockdown of clock gene Per2 in the hippocampal CA1 brain region may have potential antidepressant-like effect.
C_LIO_LIKnockout of the CRE sequence on the promoter region of the clock genes Per1 and Per2 produces depression-like behaviors, which cannot be rescued by CCPA.
C_LI


title: Quantifying predator functional responses under field conditions reveals interactive effects of temperature and interference with sex and stage.

abstract:
O_LIPredator functional responses describe predator feeding rates and are a core component of predator-prey theory. Although originally defined as the relationship between predator feeding rates and prey densities, it is now well known that predator functional responses are shaped by a multitude of factors. Unfortunately, how these factors interact with one another remains unclear, as widely used laboratory methods for measuring functional responses are generally logistically constrained to examining a few factors simultaneously. Furthermore, it is also often unclear whether laboratory derived functional responses translate to field conditions.
C_LIO_LIOur goal was to apply an observational approach for measuring functional responses to understand how sex/stage differences, temperature, and predator interference interact to influence the functional response of zebra jumping spiders on midges under natural conditions.
C_LIO_LIWe used field feeding surveys of jumping spiders to infer spider functional responses. We applied a Bayesian model averaging approach to estimate differences among sexes and stages of jumping spiders in their feeding rates and their dependencies on midge densities, temperature, and predator interference.
C_LIO_LIWe find that females exhibit the steepest functional responses on midges, followed by juveniles, and then males, despite males being larger than juveniles. We also find that sexes and stages differ in the temperature dependence of their space clearance (aka attack) rates. We find little evidence of temperature dependence in females, whereas we find some evidence for an increase in space clearance rate at high temperatures in males and juveniles. Interference effects on feeding rates were asymmetric with little effect of interference on male feeding rates, and effects of interference on females and juveniles depending on the stage/sex from which the interference originates.
C_LIO_LIOur results illustrate the multidimensional nature of functional responses in natural settings and reveal how factors influencing functional responses can interact with one another through behavior and morphology. Further studies investigating the influence of multiple mechanisms on predator functional responses under field conditions will provide an increased understanding of the drivers of predator-prey interaction strengths and their consequences for communities and ecosystems.
C_LI


title: Local overfishing patterns have regional effects on health of coral, and economic transitions can promote its recovery

abstract: Overfishing has the potential to severely disrupt coral reef ecosystems worldwide, while harvesting at more sustainable levels instead can boost fish yield without damaging reefs. The dispersal abilities of reef species mean that coral reefs form highly connected environments, and the viability of reef fish populations depends on spatially explicit processes such as the spillover effect and unauthorized harvesting inside marine protected areas. However, much of the literature on coral conservation and management has only examined overfishing on a local scale, without considering how different spatial patterns of fishing levels can affect reef health both locally and regionally. Here, we simulate a coupled human-environment model to determine how coral and herbivorous reef fish respond to overfishing across multiple spatial scales. We find that coral and reef fish react in opposite ways to habitat fragmentation driven by overfishing, and that a potential spillover effect from marine protected areas into overfished patches helps coral populations far less than it does reef fish. We also show that ongoing economic transitions from fishing to tourism have the potential to revive fish and coral populations over a relatively short timescale, and that large-scale reef recovery is possible even if these transitions only occur locally. Our results show the importance of considering spatial dynamics in marine conservation efforts, and demonstrate the ability of economic factors to cause regime shifts in human-environment systems.


title: A Driven Disordered Systems Approach to Biological Evolution in Changing Environments

abstract: Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly understood. We study a particular model of antibiotic resistance evolution in bacteria where the antibiotic concentration is an environmental parameter and the fitness landscapes incorporate tradeoffs between adaptation to low and high antibiotic concentration. With evolutionary dynamics that follow fitness gradients, the evolution of the system under slowly changing antibiotic concentration resembles the athermal dynamics of disordered physical systems under quasistatic external drives. Specifically, our model can be described as a system with interacting hysteretic elements, and it exhibits effects such as hysteresis loops and memory formation under antibiotic concentration cycling. Using methods familiar from studies in this field, we derive a number of analytical and numerical results. Our approach provides a general framework for studying motifs of evolutionary dynamics in biological systems in a changing environment.


title: Estimating tumor mutational burden from RNA-sequencing without a matched-normal sample

abstract: Detection of somatic point mutations using patients sequencing data has many clinical applications, including the identification of cancer driver genes, detection of mutational signatures, and estimation of tumor mutational burden (TMB). In a recent work we developed a tool for detection of somatic mutations using tumor RNA and matched-normal DNA. Here, we further extend it to detect somatic mutations from RNA sequencing data without a matched-normal sample. This is accomplished via a machine learning approach that classifies mutations as either somatic or germline based on various features. When applied to RNA-sequencing of >450 melanoma samples high precision and recall are achieved, and both mutational signatures and driver genes are correctly identified. Finally, we show that RNA-based TMB is significantly associated with patient survival, with similar or superior performance to DNA-based TMB. Our pipeline can be utilized in many future applications, analyzing novel and existing datasets where only RNA is available.


title: Third Generation Cytogenetic Analysis (TGCA): diagnostic application of long-read sequencing.

abstract:
Unbalanced Structural Variants (uSVs) play important roles in the pathogenesis of several genetic syndromes. Traditional and molecular karyotyping are considered the first-tier diagnostic tests to detect macroscopic and cryptic deletions/duplications. However, their time-consuming and laborious experimental protocols protract diagnostic times from three to fifteen days. Long read sequencing approaches, such as Oxford Nanopore Technologies (ONT), have the ability to reduce time to results for the detection of uSVs with the same resolution of current state-of-the-art diagnostic tests.

Here we compared ONT to molecular karyotyping for the detection of pathogenic uSVs of 7 patients with previously diagnosed causative CNVs of different sizes and allelic fractions. Larger chromosomal anomalies included trisomy 21 and mosaic tetrasomy 12p. Among smaller CNVs we tested two reciprocal genomic imbalances in 7q11.23 (1.367 Mb), a 170 kb deletion encompassing NRXN1 and mosaic 6q27 (1.231 Mb) and 2q23.1 (408 kb) deletions. DNA libraries were prepared following ONT standard protocols and sequenced on the GridION device for 48 h. Data generated during runs were analysed in online mode, using NanoGLADIATOR.

We were capable to identify all pathogenic CNVs with detection time inversely proportional to size and allelic fraction. Aneuploidies were called after only 30 minutes of sequencing, while 30 hours were needed to call CNVs < 500 kb also in mosaic state (44%). These results demonstrate the clinical utility of our approach that allows the molecular diagnosis of genomic disorders within a 30 minutes to 30 hours time-frame.


title: The ability of bumblebees Bombus terrestris (Hymenoptera: Apidae) to detect floral humidity is dependent upon environmental humidity

abstract: Flowers produce local humidity that is often greater than that of the surrounding environment, and studies have shown that insect pollinators may be able to use this humidity difference to locate and identify suitable flowers. However, environmental humidity is highly heterogeneous, and is likely to affect the detectability of floral humidity, potentially constraining the contexts in which it can be used as a salient communication pathway between plants and their pollinators. In this study, we use differential conditioning techniques on bumblebees Bombus terrestris audax (Harris) to explore the detectability of an elevated floral humidity signal when presented against different levels of environmental noise. Artificial flowers were constructed that could be either dry or humid, and individual bumblebees were presented with consistent rewards in either the humid or dry flowers presented in an environment with four levels of constant humidity, ranging from low ([~]20% RH) to highly saturated ([~]95% RH). Ability to learn was dependent upon both the rewarding flower type and the environment: the bumblebees were able to learn rewarding dry flowers in all environments, but their ability to learn humid rewarding flowers was dependent on the environmental humidity, and they were unable to learn humid rewarding flowers when the environment was highly saturated. This suggests that floral humidity might be masked from bumblebees in humid environments, suggesting that it may be a more useful signal to insect pollinators in arid environments.


title: AngioPlate - Biofabrication of perfusable complex tissues in multi-well plates with 4D subtractive manufacturing

abstract: Organ-on-a-chip systems that recapitulate tissue-level functions have been proposed to improve in vitro-in vivo correlation in drug development. Significant progress has been made to control the cellular microenvironment with mechanical stimulation and fluid flow. However, it has been challenging to introduce complex 3D tissue structures due to the physical constraints of microfluidic channels or membranes in organ-on-a-chip systems. Although this problem could be addressed with the integration of 3D bioprinting, it is not an easy task because the two technologies have fundamentally different fabrication processes. Inspired by 4D bioprinting, we develop a 4D subtractive manufacturing technique where a flexible sacrificial material can be patterned on a 2D surface, change shape when exposed to aqueous hydrogel, and subsequently degrade to produce perfusable networks in a natural hydrogel matrix that can be populated with cells. The technique is applied to fabricate organ-specific vascular networks, vascularized kidney proximal tubules, and terminal lung alveoli in a customized 384-well plate and then further scaled to a 24-well plate format to make a large vascular network, vascularized liver tissues, and for integration with ultrasound imaging. This biofabrication method eliminates the physical constraints in organ-on-a-chip systems to incorporate complex ready-to-perfuse tissue structures in an open-well design.


title: Changes in resting state functional connectivity associated with dynamic adaptation of wrist movements

abstract:
Dynamic adaptation is an error-driven process of adjusting planned motor actions to changes in task dynamics (1). Adapted motor plans are consolidated into motor memories that contribute to better performance on re-exposure to the same dynamic condition. In parallel, dynamic perturbations can be compensated for by alternate motor control processes, such as co-contraction, that contribute to error reduction (2). Whether these control strategies share the same neural resources for memory formation is unclear. To address this gap in knowledge, we used a novel fMRI-compatible wrist robot, the MR-SoftWrist (3), to identify neural processes specific to dynamic adaptation and subsequent memory formation. Using the MR-SoftWrist, we acquired fMRI during a motor performance and a dynamic perturbation task to localize brain networks of interest. Resting state fMRI scans were acquired immediately before and after task performance to quantify changes in resting state functional connectivity (rsFC) within these networks. Twenty-four hours later, we assessed behavioral retention of training. A variance decomposition analysis was used to isolate behavior associated with adaptation versus alternate error reduction strategies. Immediately after the dynamic perturbation task, rsFC significantly increased within the corticothalamic-cerebellar network of the trained wrist and decreased interhemispherically within the cortical sensorimotor network. These changes were associated to behavioral measures of initial acquisition and retention, indicative of memory formation. Variance decomposition analysis revealed that increases within the cortico-thalamic-cerebellar network were associated with adaptation, while interhemispheric decreases in rsFC within the sensorimotor network were associated with alternate error reduction processes.

Significance StatementMotor memory formation processes have been studied using resting state functional connectivity (rsFC) before and after exposure to adaptation tasks. However, due to technical limitations, previous studies have not investigated rsFC within brain regions localized during task execution, nor quantified rsFC within minutes after task performance. The present study used an fMRI-compatible wrist robot to localize relevant brain regions during dynamic adaptation within the cortico-thalamic-cerebellar network and bilateral sensorimotor network. Immediately following dynamic adaptation, we measured significant changes in rsFC within these networks, that were associated with adaptation behavior and with gains in behavior assessed 24 hours later, indicative of memory formation. Variance decomposition analysis identified distinct rsFC networks associated with adaptation specific processes, and with alternate motor control strategies.


title: Data-driven Discovery of Mathematical and Physical Relations in Oncology Data using Human-understandable Machine Learning

abstract: For decades, researchers have used the concepts of rate of change and differential equations to model and forecast neoplastic processes. This expressive mathematical apparatus brought significant insights in oncology by describing the unregulated proliferation and host interactions of cancer cells, as well as their response to treatments. Now, these theories have been given a new life and found new applications. With the advent of routine cancer genome sequencing and the resulting abundance of data, oncology now builds an "arsenal" of new modeling and analysis tools. Models describing the governing physical laws of tumor-host-drug interactions can be now challenged with biological data to make predictions about cancer progression. Our study joins the efforts of the mathematical and computational oncology community by introducing a novel machine learning system for data-driven discovery of mathematical and physical relations in oncology. The system utilizes computational mechanisms such as competition, cooperation, and adaptation in neural networks to simultaneously learn the statistics and the governing relations between multiple clinical data covariates. Targeting an easy adoption in clinical oncology, the solutions of our system reveal human-understandable properties and features hidden in the data. As our experiments demonstrate, our system can describe nonlinear conservation laws in cancer kinetics and growth curves, symmetries in tumors phenotypic staging transitions, the pre-operative spatial tumor distribution, and up to the nonlinear intracellular and extracellular pharmacokinetics of neoadjuvant therapies. The primary goal of our work is to enhance or improve the mechanistic understanding of cancer dynamics by exploiting heterogeneous clinical data. We demonstrate through multiple instantiations that our system is extracting an accurate human-understandable representation of the underlying dynamics of physical interactions central to typical oncology problems. Our results and evaluation demonstrate that using simple - yet powerful - computational mechanisms, such a machine learning system can support clinical decision making. To this end, our system is a representative tool of the field of mathematical and computational oncology and offers a bridge between the data, the modeler, the data scientist, and the practising clinician.


title: scAgeCom: a murine atlas of age-related changes in intercellular communication inferred with the package scDiffCom

abstract: Dysregulation of intercellular communication is a well-established hallmark of aging. To better understand how this process contributes to the aging phenotype, we built scAgeCom, a comprehensive atlas presenting how cell-type to cell-type interactions vary with age in 23 mouse tissues. We first created an R package, scDiffCom, designed to perform differential intercellular communication analysis between two conditions of interest in any mouse or human single-cell RNA-seq dataset. The package relies on its own list of curated ligand-receptor interactions compiled from seven established studies. We applied this tool to single-cell transcriptomics data from the Tabula Muris Senis consortium and the Calico murine aging cell atlas. All the results can be accessed online, using a user-friendly, interactive web application (https://scagecom.org). The most widespread changes we observed include upregulation of immune system processes, inflammation and lipid metabolism, and downregulation of extracellular matrix organization, growth, development and angiogenesis. More specific interpretations are also provided.


title: Scoring Protein Sequence Alignments Using Deep Learning

abstract:
BackgroundA high-quality sequence alignment (SA) is the most important input feature for accurate protein structure prediction. For a protein sequence, there are many methods to generate a SA. However, when given a choice of more than one SA for a protein sequence, there are no methods to predict which SA may lead to more accurate models without actually building the models. In this work, we describe a method to predict the quality of a proteins SA.

MethodsWe created our own dataset by generating a variety of SAs for a set of 1,351 representative proteins and investigated various deep learning architectures to predict the local distance difference test (lDDT) scores of distance maps predicted with SAs as the input. These lDDT scores serve as indicators of the quality of the SAs.

ResultsUsing two independent test datasets consisting of CASP13 and CASP14 targets, we show that our method is effective for scoring and ranking SAs when a pool of SAs is available for a protein sequence. With an example, we further discuss that SA selection using our method can lead to improved structure prediction.


title: Deciphering Multi-way Interactions in the Human Genome

abstract: Chromatin architecture, a key regulator of gene expression, can be inferred using chromatin contact data from chromosome conformation capture, or Hi-C. However, classical Hi-C does not preserve multi-way contacts. Here we use long sequencing reads to map genome-wide multi-way contacts and investigate higher order chromatin organization in the human genome. We use hypergraph theory for data representation and analysis, and quantify higher order structures in neonatal fibroblasts, biopsied adult fibroblasts, and B lymphocytes. By integrating multi-way contacts with chromatin accessibility, gene expression, and transcription factor binding, we introduce a data-driven method to identify cell type-specific transcription clusters. We provide transcription factor-mediated functional building blocks for cell identity that serve as a global signature for cell types.


title: Can foot placement during gait be trained? Adaptations in stability control when ankle moments are constrained

abstract: Accurate coordination of mediolateral foot placement, relative to the center of mass kinematic state, is one of the mechanisms which ensures mediolateral stability during human walking. Previously, we found that shoes constraining ankle moments decreased the degree of foot placement control with respect to the center of mass kinematic state. As such, ankle moment constraints can be seen as a perturbation of foot placement. Direct mechanical perturbations of the swing leg trajectory can improve the degree of foot placement control as an after-effect. Here, we asked whether constrained ankle moments could have a similar effect. If confirmed, this would offer a simple training tool for individuals with impaired foot placement control. Participants walked in three conditions; normal (baseline) while wearing shoes constraining ankle moments (training) and normal again (after-effects). The degree of foot placement control was calculated as the percentage of variance in foot placement that could be predicted based on the center of mass kinematic state in the preceding swing phase. During training, the degree of foot placement control decreased initially compared to baseline, but it gradually improved over time. In the after-effect condition, it was higher than during baseline, yet not significantly so. During training, we observed increased step width, decreased stride time and reduced local dynamic stability. In conclusion, constraining ankle moment control deteriorates the degree of foot placement control. A non-significant trend towards an improved degree of foot placement control after prolonged exposure to constrained ankle moments, allows for speculation on a training potential.


title: RAPPPID: Towards Generalisable Protein Interaction Prediction with AWD-LSTM Twin Networks

abstract:
MotivationComputational methods for the prediction of protein-protein interactions, while important tools for researchers, are plagued by challenges in generalising to unseen proteins. Datasets used for modelling protein-protein predictions are particularly predisposed to information leakage and sampling biases.

ResultsIn this study, we introduce RAPPPID, a method for the Regularised Automatic Prediction of Protein-Protein Interactions using Deep Learning. RAPPPID is a twin AWD-LSTM network which employs multiple regularisation methods during training time to learn generalised weights. Testing on stringent interaction datasets composed of proteins not seen during training, RAPPPID outperforms state-of-the-art methods. Further experiments show that RAPPPIDs performance holds regardless of the particular proteins in the testing set and its performance is higher for biologically supported edges. This study serves to demonstrate that appropriate regularisation is an important component of overcoming the challenges of creating models for protein-protein interaction prediction that generalise to unseen proteins. Additionally, as part of this study, we provide datasets corresponding to several data splits of various strictness, in order to facilitate assessment of PPI reconstruction methods by others in the future. Availability and Implementation: Code and datasets are freely available at https://github.com/jszym/rapppid.

Contactamin.emad@mcgill.ca

Supplementary InformationOnline-only supplementary data is available at the journals website.


title: Inference and Validation of the Structure of Lotka-Volterra Models

abstract:
For close to a century, Lotka-Volterra (LV) models have been used to investigate interactions among populations of different species. For a few species, these investigations are straightforward. However, with the arrival of large and complex microbiomes, unprecedently rich data have become available and await analysis. In particular, these data require us to ask which microbial populations of a mixed community affect other populations, whether these influences are activating or inhibiting and how the interactions change over time. Here we present two new inference strategies for interaction parameters that are based on a new algebraic LV inference (ALVI) method. One strategy uses different survivor profiles of communities grown under similar conditions, while the other pertains to time series data. In addition, we address the question of whether observation data are compliant with the LV structure or require a richer modeling format.

The code and data used in this manuscript are available at "https://github.com/LBSA-VoitLab/Inference_and_Validation_of_the_Structure_of_Lotka_Volterra_Models".


title: Integration of transcriptomics and network analysis reveals co-expressed genes in Frankliniella occidentalis larval guts that respond to tomato spotted wilt virus infection

abstract:
BackgroundThe arthropod gut is the first barrier to infection by viruses that are internally borne and transmitted persistently by arthropod vectors to plant and animal hosts. Tomato spotted wilt virus (TSWV), a plant-pathogenic virus, is transmitted exclusively by thrips vectors in a circulative-propagative manner. Frankliniella occidentalis (western flower thrips), the principal thrips vector of TSWV, is transmission-competent only if the virus is acquired by young larvae. To begin to understand the larval gut response to TSWV infection and accumulation, a genome- assisted, transcriptomic analysis of F. occidentalis gut tissues of first (early L1) and second (early L2 and late L2) instar larvae was conducted using RNA-Seq to identify differentially-expressed transcripts (DETs) in response to TSWV compared to non- exposed cohorts.

ResultsThe larval gut responded in a developmental stage-dependent manner, with the majority of DETs (71%) associated with the early L1 stage at a time when virus infection is limited to the midgut epithelium. Provisional annotations of these DETs inferred roles in digestion and absorption, insect innate immunity, and detoxification. Weighted gene co-expression network analysis using all assembled transcripts of the gut transcriptome revealed eight gene modules that distinguish the larval development. Intra-module interaction network analysis of three most DET- enriched modules revealed ten central hub genes. Droplet digital PCR-expression analyses of select network hub and connecting genes revealed temporally-dynamic changes in gut expression during and post exposure to TSWV.

ConclusionThese findings expand our understanding of the developmentally-mediated interaction between thrips vectors and orthotospoviruses, and provide opportunities for probing pathways for biomarkers of thrips vector competence.