title: Phenotypic heterogeneity is adaptive for microbial populations under starvation

abstract:
To persist in variable environments populations of microorganisms have to survive periods of starvation and be able to restart cell division in nutrient-rich conditions. Typically, starvation signals initiate a transition to a quiescent state in a fraction of individual cells, while the rest of the cells remain non-quiescent. It is widely believed that, while quiescent cells (Q) help the population to survive long starvation, the non-quiescent cells (NQ) are a side effect of imperfect transition. We analysed regrowth of starved monocultures of Q and NQ cells compared to mixed, heterogeneous cultures in simple and complex starvation environments. Our experiments, as well as mathematical modelling, demonstrate that Q monocultures benefit from better survival during long starvation, and from a shorter lag phase after resupply of rich medium. However, when the starvation period is very short, the NQ monocultures outperform Q and mixed cultures, due to their short lag phase. In addition, only NQ monocultures benefit from complex starvation environments, where nutrient recycling is possible. Our study suggests that phenotypic heterogeneity in starved populations could be a form of bet hedging, which is adaptive when environmental determinants, such as the length of the starvation period, the length of the regrowth phase, and the complexity of the starvation environment vary over time.

ImportanceNon-genetic cell heterogeneity is present in glucose starved yeast populations in the form of quiescent (Q) and nonquiescent (NQ) phenotypes. There is evidence that Q cells help the population to survive long starvation. However, the role of the NQ cell type is not known, and it has been speculated that the NQ phenotype is just a side effect of imperfect transition to the Q phenotype. Here we show that, in contrast, there are ecological scenarios in which NQ cells perform better than monocultures of Q cells or naturally occuring mixed populations containing both Q and NQ. NQ cells benefit when the starvation period is very short and environmental conditions allow nutrient recycling during starvation. Our experimental and mathematical modeling results suggest a novel hypothesis: the presence of both Q and NQ phenotypes within starved yeast populations may reflect a form of bet hedging, where different phenotypes provide fitness advantages depending on environmental conditions.


title: Exploiting Family History in Aggregation Unit-based Genetic Association Tests

abstract: The development of sequencing technology calls for new powerful methods to detect disease associations and lower the cost of sequencing studies. Family history (FH) contains information on disease status of relatives, adding valuable information about the probands health problems and risk of diseases. Incorporating data from FH is a cost-effective way to improve statistical evidence in genetic studies, and moreover, overcomes limitations in study designs with insufficient cases or missing genotype information for association analysis. We proposed family history aggregation unit-based test (FHAT) and optimal FHAT (FHAT-O) to exploit available FH for rare variant association analysis. Moreover, we extended liability threshold model of case-control status and FH (LT-FH) method in aggregated unit-based methods and compared that with FHAT and FHAT-O. The computational efficiency and flexibility of the FHAT and FHAT-O were demonstrated through both simulations and applications. We showed that FHAT, FHAT-O and LT-FH method offer reasonable control of the type I error unless case/control ratio is extremely unbalanced, in which case they result in smaller inflation than that observed with conventional methods excluding FH. We also demonstrated that FHAT and FHAT-O are more powerful than LT-FH method and conventional methods in many scenarios. By applying FHAT and FHAT-O to the analysis of all cause dementia and hypertension using the exome sequencing data from the UK Biobank, we showed that our methods can improve significance for known regions. Furthermore, we replicated the previous associations in all cause dementia and hypertension and detected novel regions through the exome-wide analysis.

category: genetics


title: Millisecond Mix-and-Quench Crystallography (MMQX) Enables Time-Resolved Studies of PEPCK With Remote Data Collection

abstract: Time-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and complex experimental infrastructure required remain serious obstacles to widespread application. We have developed Millisecond Mix-and-Quench crystallography (MMQX), which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase is observed with a time resolution of 40 ms. MMQX, by lowering the entry barrier to time-resolved crystallography, should enable broad expansion in structural studies of protein dynamics.

category: biochemistry


title: GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser

abstract: Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.

category: bioinformatics


title: In Silico Analysis and Characterization of Differentially Expressed Genes to Distinguish Glioma Stem Cells from Normal Neural Stem Cells

abstract: Glioblastoma multiforme (GBM) is a heterogeneous, invasive primary brain tumor that develops chemoresistance post therapy. Theories regarding the aetiology of GBM focus on transformation of normal neural stem cells (NSCs) to a cancerous phenotype or tumorigenesis driven via glioma stem cells (GSCs). Comparative RNA-Seq analysis of GSCs and NSCs can provide a better understanding of the origin of GBM. Thus, in the current study, we performed various bioinformatics analyses on transcriptional profiles of a total 40 RNA-seq samples including 20 NSC and 20 GSC, that were obtained from the NCBI-SRA (SRP200400). First, differential gene expression (DGE) analysis using DESeq2 revealed 348 significantly differentially expressed genes between GSCs and NSCs (padj. value <0.05, log2fold change [≥] 3.0 (for GSCs) and [≤] -3.0 (for NSCs)) with 192 upregulated and 156 downregulated genes in GSCs in comparison to NSCs. Subsequently, exploratory data analysis using principal component analysis (PCA) based on key significant genes depicted the clear separation between both the groups. Further, Hierarchical clustering confirmed the distinct clusters of GSC and NSC samples. Eventually, the biological enrichment analysis of the significant genes showed their enrichment in tumorigenesis pathways such as Wnt-signalling, VEGF-signalling and TGF-{beta}-signalling pathways. Conclusively, our study depicted significant differences in the gene expression patterns between NSCs and GSCs. Besides, we also identified novel genes and genes previously unassociated with gliomagenesis that may prove to be valuable in establishing diagnostic, prognostic biomarkers and therapeutic targets for GBM.

category: cancer biology


title: Investigating the mechanisms of indocyanine green (ICG) cellular uptake in sarcoma

abstract:
IntroductionIndocyanine green (ICG) is a near infrared (NIR) dye which has been used clinically for over 50 years and has recently been utilised for fluorescence guided surgery in a number of cancer types, including sarcoma. ICG is taken up and retained by sarcoma tumours to a greater extent than normal tissue, demonstrating its potential to aid in visualisation of tumour margins. However, the mechanisms surrounding preferential ICG uptake in tumours are poorly understood.

MethodsIn vitro ICG cellular uptake studies were performed across a panel of four sarcoma cell lines and one breast cancer cell line, exhibiting varying proliferation rates and phenotypes. The effects of ICG concentration, incubation time, inhibition of clathrin mediated endocytosis and cell line proliferation rate on the cellular uptake of ICG were investigated using fluorescence microscopy and flow cytometry. The spatial orientation of ICG was also assessed in a patient specimen.

ResultsThe level of ICG cellular uptake was dependent on ICG concentration and incubation time. Cell line proliferation rate correlated significantly to ICG uptake within 30 minutes (Rs= 1, p<0.001), whilst retention of ICG after 24hrs did not (Rs= 0.3, p=0.624). From our data, the primary mechanism of ICG uptake in sarcoma cells is via clathrin mediated endocytosis. Following the resection of a grade 3 leiomyosarcoma, ICG signal was detectable macroscopically and on 3m sections, whilst being negative on the muscle control.

ConclusionsThe use of ICG for tumour detection in sarcoma surgery may demonstrate higher utility in high grade tumours compared to low grade tumours, due to the observation of higher ICG uptake in more proliferative cell lines. It is likely that the enhanced permeability and retention (EPR) effect plays a significant role in the retention of ICG within tumours. Future work on the detection of ICG at the cellular level within human tissue sections is required, with the aid of purpose built NIR microscopes.


title: Constrained G4 structures unveil topology specificity of known and new G4 binding proteins

abstract:
G-quadruplexes (G4) are non-canonical secondary structures consisting in stacked tetrads of hydrogen-bonded guanines bases. An essential feature of G4 is their intrinsic polymorphic nature, which is characterized by the equilibrium between several conformations (also called topologies) and the presence of different types of loops with variable lengths. In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures. In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins. Using G-rich single-stranded oligonucleotides that adopt non-controlled G4 conformations, a large number of G4-binding proteins have been identified in vitro, but their specificity towards G4 topology remained unknown.

Constrained G4 structures are biomolecular objects based on the use of a rigid cyclic peptide scaffold as a template for directing the intramolecular assembly of the anchored oligonucleotides into a single and stabilized G4 topology. Here, using various constrained RNA or DNA G4 as baits in human cell extracts, we establish the topology preference of several well-known G4-interacting factors. Moreover, we identify new G4-interacting proteins such as the NELF complex involved in the RNA-Pol II pausing mechanism, and we show that it impacts the clastogenic effect of the G4-ligand pyridostatin.


title: Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia

abstract:
AO_SCPLOWBSTRACTC_SCPLOWIncreased complexity of engineered microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases of metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent strains must be robustly controlled to achieve desired circuit behaviors. Here, we address these challenges with a modeling-based investigation of emergent spatiotemporal population dynamics that result from cell-length control of monolayer, two-strain bacterial consortia. We demonstrate that with dynamic control of a strains division length, nematic cell alignment in close-packed monolayers can be destabilized. We found this destabilization conferred an emergent, competitive advantage on smaller-length strains--but by mechanisms that differed depending on the spatial patterns of the population. We used complementary modeling approaches to elucidate underlying mechanisms: an agent-based model to simulate detailed mechanical and signaling interactions between the competing strains and a reductive, stochastic lattice model to represent cell-cell interactions with a single rotational parameter. Our modeling suggests that spatial strain-fraction oscillations can be generated when cell-length control is coupled to quorum-sensing signaling in negative feedback topologies. Our research employs novel methods of population control and points the way to programming strain fraction dynamics in consortial synthetic biology.

Engineered microbial collectives are more versatile and robust than single strain populations. However, the function of such collectives is sensitive to their spatiotemporal organization. Here, we demonstrate control of the spatiotemporal composition of synthetic microbial consortia by dynamically modulating the average cell length of constituent strains. Such modulation confers an emergent "mechanical fitness" advantage upon the shorter length strain. We used both a biophysically realistic agent-based model to test the impact of cell shape on spatiotemporal dynamics and a conceptually simpler stochastic lattice model to explain the essential mechanisms driving the dynamics.

category: biophysics


title: "Multi-Agent" Screening Improves the Efficiency of Directed Enzyme Evolution

abstract:
Enzyme evolution has enabled numerous advances in biotechnology. However, directed evolution programs can still require many iterative rounds of screening to identify optimal mutant sequences. This is due to the sparsity of the fitness landscape, which in turn, is due to "hidden" mutations that only offer improvements synergistically in combination with other mutations. These "hidden" mutations are only identified by evaluating mutant combinations, necessitating large combinatorial libraries or iterative rounds of screening. Here, we report a multi-agent directed evolution approach that incorporates diverse substrate analogues in the screening process. With multiple substrates acting like multiple agents navigating the fitness landscape, we are able to identify "hidden" mutant residues that impact substrate specificity without a need for testing numerous combinations. We initially validate this approach in engineering a malonyl-CoA synthetase for improved activity with a wide variety of non-natural substrates. We found that "hidden" mutations are often distant from the active site, making them hard to predict using popular structure-based methods. Interestingly, many of the "hidden" mutations identified in this case are expected to destabilize interactions between elements of tertiary structure, potentially affecting protein flexibility. This approach may be widely applicable to accelerate enzyme engineering. Lastly, multi-agent system inspired approaches may be more broadly useful in tackling other complex combinatorial search problems in biology.

Highlights- "Multi-agent" screening improves directed evolution.
- The incorporation of multiple substrates leads to the identification of "hidden" mutations, which can be hard to identify through one substrate.
- "Hidden" mutations are often remote from the active site and are expected to interrupt stabilizing side-chain interactions, thus increasing enzyme flexibility.

category: synthetic biology


title: Nuclear dengue virus NS5 antagonizes expression of PAF1-dependent immune response genes

abstract:
Dengue virus (DENV) disruption of the innate immune response is critical to establish infection. DENV non-structural protein 5 (NS5) plays a central role in this disruption, such as antagonism of STAT2. We recently found that DENV serotype 2 (DENV2) NS5 interacts with Polymerase associated factor 1 complex (PAF1C). The primary members of PAF1C are PAF1, LEO1, CTR9 and CDC73. This nuclear complex is an emerging player in the immune response. It promotes the expression of many genes, including genes related to the antiviral, antimicrobial and inflammatory responses, through close association with the chromatin of these genes. Our previous work demonstrated that NS5 antagonizes PAF1C recruitment to immune response genes. However, it remains unknown if NS5 antagonism of PAF1C is complementary to its antagonism of STAT2. Here, we show that knockout of PAF1 enhances DENV2 infectious virion production. By comparing gene expression profiles in PAF1 and STAT2 knockout cells, we find that PAF1 is necessary to express immune response genes that are STAT2-independent. Finally, we mapped the viral determinants for the NS5-PAF1C protein interaction. We found that NS5 nuclear localization and the C-terminal region of the methyltransferase domain are required for its interaction with PAF1C. Mutation of these regions rescued the expression of PAF1-dependent immune response genes that are antagonized by NS5. In sum, our results support a role for PAF1C in restricting DENV2 replication that NS5 antagonizes through its protein interaction with PAF1C.

Author summaryDengue virus (DENV) is a pathogen that infects nearly 400 million people a year and thus represents a major challenge for public health. Productive infection by DENV relies on the effective evasion of intrinsic antiviral defenses and is often accomplished through virus-host protein interactions. Here, we investigate the recently discovered interaction between DENV non-structural protein 5 (NS5) and the transcriptional regulator Polymerase associated factor 1 complex (PAF1C). Our work demonstrates PAF1C member PAF1 acts as an antiviral factor and inhibits DENV replication. In parallel, we identified immune response genes involved in intrinsic antiviral defense that depend on PAF1 for expression. We further identified the regions of NS5 required for the protein interaction with PAF1C. Breaking the NS5-PAF1C protein interaction restores the expression of PAF1-dependent immune response genes. Together, our work establishes the antiviral role of PAF1C in DENV infection and NS5 antagonism of PAF1-dependent gene expression through a virus-host protein interaction.

category: microbiology


title: Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses

abstract: Defining the unique properties of SARS-CoV-2 protein sequences, has potential to explain the range of Coronavirus Disease 2019 (COVID-19) severity. To achieve this we compared proteins encoded by all Sarbecoviruses using profile Hidden Markov Model similarities to identify protein features unique to SARS-CoV-2. Consistent with previous reports, a small set of bat and pangolin-derived Sarbecoviruses show the greatest similarity to SARS-CoV-2 but unlikely to be the direct source of SARS-CoV-2. Three proteins (nsp3, spike and orf9) showed differing regions between the bat Sarbecoviruses and SARS-CoV-2 and indicate virus protein features that might have evolved to support human infection and/or transmission. Spike analysis identified all regions of the protein that have tolerated change and revealed that the current SARS-CoV-2 variants of concern (VOCs) have sampled only a fraction (~31%) of the possible spike domain changes which have occurred historically in Sarbecovirus evolution. This result emphasises the evolvability of these coronaviruses and potential for further change in virus replication and transmission properties over the coming years.

category: evolutionary biology


title: Genetic and phenotypic heterogeneity in PNPT1, MYO15A, PTPRQ and SLC12A2 variants detected among hearing impaired assortative mating families in Southern India

abstract: Exome analysis was used to resolve the etiology of hearing loss (HL) in four South Indian assortative mating families. Six variants, including three novel ones, were identified in four genes: PNPT1 p.Ala46Gly and p.Asn540Ser, MYO15A p.Leu1485Pro and p.Tyr1891*, PTPRQ p.Gln1336*, and SLC12A2 p.Pro988Ser. Compound heterozygous PNPT1 variants were associated with prelingual profound sensorineural hearing loss (SNHL), vestibular dysfunction and unilateral progressive vision loss in one family. In the second family, MYO15A variants in the myosin motor domain, including a novel variant, were found to be associated with prelingual profound SNHL. A novel PTPRQ variant was associated with postlingual progressive sensorineural/mixed HL and vestibular dysfunction in the third family, with mastoid bone hypopneumatization observed in one family member. In the fourth family, the SLC12A2 novel variant was found to segregate with severe-to-profound HL causing DFNA78, across three generations. Our results suggest a high level of allelic, genotypic and phenotypic heterogeneity of HL in these families. This study is the first to report the association of PNPT1, PTPRQ and SLC12A2 variants with HL in the Indian population.


title: Extensive OMICS resource for Sf21 and Tni cell lines

abstract: Insect-derived cell lines, from Spodoptera frugiperda (Sf21) and from Trichoplusia ni (Tni), are the two most widely used cell lines for recombinant protein expression in combination with the Baculoviral Expression Vector System (BEVS). Genomic sequences and annotations are still incomplete for Sf21 and absent for Tni. In this study, we present an approach using different sequencing data types, including short-read sequencing, long synthetic and Oxford Nanopore reads, to build genomes. The Sf21 and Tni assemblies contain 4,020 scaffolds of 463 Mb in size with N50 of 364 Kb and 2,954 scaffolds of 332 Mb in size with N50 of 326 Kb, respectively. Furthermore, we built a new gene prediction workflow, which integrates transcriptome and proteome information using pre-existing tools. Using this approach, we predicted 21,506 Sf21 and 14,159 Tni genes, generated and integrated proteomic datasets to validate predicted genes and could identify 5577 and 4919 proteins in the Sf21 and Tni cell lines respectively. This integrative approach could be theoretically applied to any uncharacterized genome and result in valuable new resources. With this information available, Sf21 and Tni cells will become even better tools for protein expression and could be used in a wider range of applications, from promoter identification to genome engineering and editing.

category: genomics


title: Target identification of drug candidates with machine-learning algorithms: how to choose negative examples for training

abstract: (1) Background:Identification of hit molecules protein targets is essential in the drug discovery process. Target prediction with machine-learning algorithms can help accelerate this search, limiting the number of required experiments. However, Drug-Target Interactions databases used for training present high statistical bias, leading to a high number of false positive predicted targets, thus increasing time and cost of experimental validation campaigns. (2) Methods: To minimize the number of false positive predicted proteins, we propose a new scheme for choosing negative examples, so that each protein and each drug appears an equal number of times in positive and negative examples. We artificially reproduce the process of target identification for 3 particular drugs, and more globally for 200 approved drugs. (3) Results: For the detailed 3 drugs examples, and for the larger set of 200 drugs, training with the proposed scheme for the choice of negative examples improved target prediction results: the average number of false positive among the top ranked predicted targets decreased and overall the rank of the true targets was improved. (4) Conclusion: Our method enables to correct databases statistical bias and reduces the number of false positive predictions, and therefore the number of useless experiments potentially undertaken.


title: Rapid Kinetic Fingerprinting of Single Nucleic Acid Molecules by a FRET-based Dynamic Nanosensor

abstract: Biofluids contain cell-free nucleic acids such as microRNAs (miRNAs) and circulating tumor-derived DNAs (ctDNAs) that have emerged as promising disease biomarkers. Conventional detection of these biomarkers by digital PCR and next generation sequencing, although highly sensitive, requires time-consuming extraction and amplification steps that increase the risk of sample loss and cross-contamination, respectively. To achieve the direct, rapid detection of miRNAs and ctDNAs with near-perfect specificity and single-molecule level sensitivity, we herein describe an accelerated amplification-free single-molecule kinetic fingerprinting. This approach, termed intramolecular single-molecule recognition through equilibrium Poisson sampling (iSiMREPS), exploits a dynamic DNA nanosensor comprising a surface anchor and a pair of fluorescent detection probes: one probe captures individual target molecules onto the surface, while the other transiently interrogates them to generate kinetic fingerprints by intramolecular single-molecule Forster resonance energy transfer (smFRET). Formamide is used to further accelerate the kinetics of probe-target interactions and fingerprinting, while background signals are reduced by removing non-target-bound probes from the surface using toehold-mediated strand displacement. We show that iSiMREPS can detect in as little as 10 seconds two distinct, promising cancer biomarkers--miR-141 and a common EGFR exon 19 deletion--reaching a limit of detection (LOD) of ~3 fM and a mutant allele fraction among excess wild-type as low as 1 in 1 million, or 0.0001%. We anticipate that iSiMREPS will find utility in research and clinical diagnostics based on its features of rapid detection, high specificity, sensitivity, and generalizability.


title: Murine monoclonal antibodies against RBD of SARS-CoV-2 neutralize authentic wild type SARS-CoV-2 as well as B.1.1.7 and B.1.351 viruses and protect in vivo in a mouse model in a neutralization dependent manner

abstract:
After first emerging in December 2019 in China, severe acute respiratory syndrome 2 (SARS-CoV-2) has since caused a pandemic leading to millions of infections and deaths worldwide. Vaccines have been developed and authorized but supply of these vaccines is currently limited. With new variants of the virus now emerging and spreading globally, it is essential to develop therapeutics that are broadly protective and bind conserved epitopes in the receptor binding domain (RBD) or the whole spike of SARS-CoV-2. In this study, we have generated mouse monoclonal antibodies (mAbs) against different epitopes on the RBD and assessed binding and neutralization against authentic SARS-CoV-2. We have demonstrated that antibodies with neutralizing activity, but not non-neutralizing antibodies, lower viral titers in the lungs when administered in a prophylactic setting in vivo in a mouse challenge model. In addition, most of the mAbs cross-neutralize the B.1.351 as well as the B.1.1.7 variants in vitro.

ImportanceCrossneutralization of SARS-CoV-2 variants by RBD-targeting antibodies is still not well understood and very little is known about the potential protective effect of non-neutralizing antibodies in vivo. Using a panel of mouse monoclonal antibodies, we investigate both of these aspects.


title: Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis

abstract: The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) symptoms. We asked whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n=30) and healthy control (n=16) were collected during hospitalization. Plasma microbiome was analyzed using 16S rRNA sequencing, metatranscriptomic analysis, and gut permeability markers including FABP-2, PGN and LPS in both patient cohorts. Almost 65% (9 out 14) COVID-19 patients showed abnormal presence of gut microbes in their bloodstream. Plasma samples contained predominately Proteobacteria, Firmicutes, and Actinobacteria. The abundance of gram-negative bacteria (Acinetobacter, Nitrospirillum, Cupriavidus, Pseudomonas, Aquabacterium, Burkholderia, Caballeronia, Parabhurkholderia, Bravibacterium, and Sphingomonas) was higher than the gram-positive bacteria (Staphylococcus and Lactobacillus) in COVID-19 subjects. The levels of plasma gut permeability markers FABP2 (1282{+/-}199.6 vs 838.1{+/-}91.33; p=0.0757), PGN (34.64{+/-}3.178 vs 17.53{+/-}2.12; p<0.0001), and LPS (405.5{+/-}48.37 vs 249.6{+/-}17.06; p=0.0049) were higher in COVID-19 patients compared to healthy subjects. These findings support that the intestine may represent a source for bacteremia and may contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.


title: Limits to resilience of Afroalpine vegetation to grazing and burning: a case study of grasses from the Drakensberg Mountain Centre, southern Africa

abstract:
O_LIHigh-elevation Afroalpine ecosystems of the Drakensberg Mountain Centre (DMC) of Lesotho and South Africa, renowned for their high endemism and key ecosystem services, are socio-ecological systems that have seen human activity for millennia. However, their responses to land management practices are understudied. Controversy over their natural state has also led to conflicting policies and management emphases.
C_LIO_LIFocusing on the crucial ecosystem-modulating component, grasses (Poaceae), we evaluate the response of DMC Afroalpine vegetation to human impact through grazing and burning. Grass species associations were recorded from grassland, shrubland and wetland-riparian-seep ecotypes across a range of grazing and fire regimes to document relationships between abiotic conditions, disturbance, and taxonomic diversity and composition.
C_LIO_LICCA of grass community composition retrieved a large cluster of plots of mixed grazing and burning regimes with no particular environmental vector correlated with them. Other smaller groups of plots separated from these were associated to heavy grazing, bioclimatic variables, slope gradient, and aspect. Indicator species analyses found DMC endemic grasses were associated to low grazing, while alien grasses were associated to heavy grazing. GLMs found little difference between ecotype-disturbance categories with regards plant species richness, mean alpha hull=2 range-size of native and sub-Saharan endemic grasses, and site-level Sorensen beta diversity ({beta}sor). Some differences were noted, including the highest cover and proportion of DMC endemics being found in low-grazed grassland, and highest cover and proportion of alien grasses and highest plot-level {beta}sor being found in heavily grazed ecotypes. Relative importance analyses found grazing regime to be the main influence on cover and proportion of DMC endemic and alien grasses. Partial Mantel tests found mean annual temperature and grazing regime to be the main influence on plot-level {beta}sor.
C_LIO_LISynthesis: Taxonomic diversity and composition of DMC Afroalpine grasslands was relatively unaffected by moderate grazing and intense burning, although heavy grazing had a largely detrimental impact, with its ubiquity across the DMC a major cause for concern. High levels of endemism, coupled with the above data emphasizing the robustness of DMC grasslands to disturbance, also supports Afroalpine grasslands as a natural component of the DMC. This research reinforces the natural grass-dominated nature of the DMC as a social-ecological system where sustainable management is possible thanks to its resilience to grazing and burning, although current widespread overgrazing requires urgent attention.
C_LI

category: ecology


title: A novel approach to partitioning evapotranspiration into evaporation and transpiration in flooded ecosystems

abstract: Reliable partitioning of micrometeorologically measured evapotranspiration (ET) into evaporation (E) and transpiration (T) would greatly enhance our understanding of the water cycle and its response to climate change. While some methods on ET partitioning have been developed, their underlying assumptions make them difficult to apply more generally, especially in sites with large contributions of E. Here, we report a novel ET partitioning method using Artificial Neural Networks (ANN) in combination with a range of environmental input variables to predict daytime E from nighttime ET measurements. The study uses eddy covariance data from four restored wetlands in the Sacramento-San Joaquin Delta, California, USA, as well as leaf-level T data for validation. The four wetlands vary in structure from some with large areas of open water and little vegetation to very densely vegetated wetlands, representing a range of ET conditions. The ANNs were built with increasing complexity by adding the input variable that resulted in the next highest average value of model testing R2 across all sites. The order of variable inclusion (and importance) was: vapor pressure deficit (VPD) > gap-filled sensible heat flux (H_gf) > air temperature (Tair) > friction velocity (u*) > other variables. Overall, 36 ANNs were analyzed. The model using VPD, H_gf, Tair, and u* (F11), showed an average testing R2 value across all sites of 0.853. In comparison with the model that included all 10 variables (F36), F11 generally performed better during validation with independent data. In comparison to other methods described in the literature, the ANN method generated more consistent T/ET partitioning results especially for more complex sites with large E contributions. Our method improves the understanding of T/ET partitioning. While it may be particularly suited to flooded ecosystems, it can also improve T/ET partitioning in other systems, increasing our knowledge of the global water cycle.


title: The males of the parasitoid wasp, Nasonia vitripennis, can identify which fly hosts contain females.

abstract: The reproductive success of a male is limited by the number of females it can mate with. Thus, males deploy elaborate mate-finding strategies to maximize access to females. In the haplodiploid wasp genus, Nasonia, which are parasitoids of cyclorrhaphous flies, mate-finding is restricted to the natal patch, where males compete for access to females. This study investigates whether there are any additional mate finding strategies of males, especially, whether they can identify the presence of adult females which are still inside the fly host. Results reveal that only one out of the four species, N. vitripennis, can distinguish which hosts specifically have adult female wasps indicating a species-specific unique mate-finding capability. Behavioral assays revealed that the cues used by N. vitripennis males are olfactory in nature and not auditory or visual. GC-MS analyses show that these olfactory cues are female-specific cuticular hydrocarbons (CHCs), possibly emanating from within the fly puparium. Further assays indicated that N. vitripennis males can also detect differences in the concentrations of compounds to identify female-specific cues from male-specific ones. This study, therefore, uncovers a previously unknown mate-finding strategy in one of the most widely studied parasitoid wasp.


title: Can Deep Convolutional Neural Networks Learn Same-Different Relations?

abstract: Same-different visual reasoning is a basic skill central to abstract combinatorial thought. This fact has lead neural networks researchers to test same-different classification on deep convolutional neural networks (DCNNs), which has resulted in a controversy regarding whether this skill is within the capacity of these models. However, most tests of same-different classification rely on testing on images that come from the same pixel-level distribution as the testing images, yielding the results inconclusive. In this study we tested relational same-different reasoning DCNNs. In a series of simulations we show that DCNNs are capable of visual same-different classification, but only when the test images are similar to the training images at the pixel-level. In contrast, even when there are only subtle differences between the testing and training images, the performance of DCNNs could drop to chance levels. This is true even when DCNNs training regime included a wide distribution of images or when they were trained in a multi-task setup in which training included an additional relational task with test images from the same pixel-level distribution.

category: animal behavior and cognition


title: High-Potency Polypeptide-based Interference for Coronavirus Spike Glycoproteins

abstract: Specific manipulation of proteins post-translationally remains difficult. Here we report results of a general approach that uses a partial sequence of a protein to efficiently modulate the expression level of the native protein. When applied to coronavirus, human immunodeficiency virus, Ebolavirus, respiratory syncytial virus and influenza virus, polypeptides containing highly conserved regions of the viral glycoproteins potently diminished expression of the respective native proteins. In the cases of coronavirus and influenza virus where multiple strains were tested, the polypeptides were equally effective against glycoproteins of other coronavirus and influenza strains with sequence identity as low as 27%, underscoring their high insensitivity to mutations. Thus, this method provides a platform for developing high-efficacy broad-spectrum anti-viral inhibitors, as well as a new way to alter expression of essentially any systems post-translationally.


title: High-Potency Polypeptide-based Inhibition of Enveloped-virus Glycoproteins


title: Integrative structural modelling of macromolecular complexes using Assembline

abstract: Integrative modelling enables structure determination of macromolecular complexes by combining data from multiple experimental sources such as X-ray crystallography, electron microscopy (EM), or crosslinking mass spectrometry (XL-MS). It is particularly useful for complexes not amenable to high-resolution EM--complexes that are flexible, heterogenous, or imaged in cells with cryo-electron tomography. We have recently developed an integrative modelling protocol that allowed us to model multi-megadalton complexes as large as the nuclear pore complex. Here, we describe the Assembline software package, which combines multiple programs and libraries with our own algorithms in a streamlined modelling pipeline. Assembline builds ensembles of models satisfying data from atomic structures or homology models, EM maps and other experimental data, and provides tools for their analysis. Comparing to other methods, Assembline enables efficient sampling of conformational space through a multi-step procedure, provides new modeling restraints, and includes a unique configuration system for setting up the modelling project. Our protocol achieves exhaustive sampling in less than 100 - 1,000 CPU-hours even for complexes in the megadalton range. For larger complexes, resources available in institutional or public computer clusters are needed and sufficient to run the protocol. We also provide step-by-step instructions for preparing the input, running the core modelling steps, and assessing modelling performance at any stage.


title: ADNKA overcomes SARS-CoV2-mediated NK cell inhibition through non-spike antibodies

abstract: The outcome of infection is dependent on the ability of viruses to manipulate the infected cell to evade immunity, and the ability of the immune response to overcome this evasion. Understanding this process is key to understanding pathogenesis, genetic risk factors, and both natural and vaccine-induced immunity. SARS-CoV-2 antagonises the innate interferon response, but whether it manipulates innate cellular immunity is unclear. An unbiased proteomic analysis determined how cell surface protein expression is altered on SARS-CoV-2-infected lung epithelial cells, showing downregulation of activating NK ligands B7-H6, MICA, ULBP2, and Nectin1, with minimal effects on MHC-I. This correlated with a reduction in NK cell activation, identifying a novel mechanism by which SARS-CoV2 antagonises innate immunity. Later in the disease process, strong antibody-dependent NK cell activation (ADNKA) developed. These responses were sustained for at least 6 months in most patients, and led to high levels of pro-inflammatory cytokine production. Depletion of spike-specific antibodies confirmed their dominant role in neutralisation, but these antibodies played only a minor role in ADNKA compared to antibodies to other proteins, including ORF3a, Membrane, and Nucleocapsid. In contrast, ADNKA induced following vaccination was focussed solely on spike, was weaker than ADNKA following natural infection, and was not boosted by the second dose. These insights have important implications for understanding disease progression, vaccine efficacy, and vaccine design.

category: immunology


title: Ageing impairs the airway epithelium defence response to SARS-CoV-2

abstract: Age-dependent differences in the clinical response to SARS-CoV-2 infection is well-documented1-3 however the underlying molecular mechanisms involved are poorly understood. We infected fully differentiated human nasal epithelium cultures derived from healthy children (1-12 years old), young adults (26-34 years old) and older adults (56-62 years old) with SARS-COV-2 to identify age-related cell-intrinsic differences that may influence viral entry, replication and host defence response. We integrated imaging, transcriptomics, proteomics and biochemical assays revealing age-related changes in transcriptional regulation that impact viral replication, effectiveness of host responses and therapeutic drug targets. Viral load was lowest in infected older adult cultures despite the highest expression of SARS-CoV-2 entry and detection factors. We showed this was likely due to lower expression of hijacked host machinery essential for viral replication. Unlike the nasal epithelium of young adults and children, global host response and induction of the interferon signalling was profoundly impaired in older adults, which preferentially expressed proinflammatory cytokines mirroring the "cytokine storm" seen in severe COVID-194,5. In silico screening of our virus-host-drug network identified drug classes with higher efficacy in older adults. Collectively, our data suggests that cellular alterations that occur during ageing impact the ability for the host nasal epithelium to respond to SARS-CoV-2 infection which could guide future therapeutic strategies.


title: Hda1C restricts the transcription initiation frequency to limit divergent non-coding RNA transcription

abstract: Nucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA Polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA, and a divergent non-coding (DNC) transcript with an unclear purpose. Here, we characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast. We identified the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC in high-throughput reverse genetic screens based on quantitative single-cell fluorescence measurements. Nascent transcription profiling showed a genome-wide role of Hda1C in DNC repression. Live-cell imaging of transcription revealed that Hda1C reduced the frequency of DNC transcription. Hda1C contributed to decreased acetylation of histone H3 in DNC regions, supporting DNC repression by histone deacetylation. Our data support the interpretation that DNC results as a consequence of the NDR-based architecture of eukaryotic promoters, but that it is governed by locus-specific repression to maintain genome fidelity.


title: Genomic and phenotypic characterization of finger millet indicates a complex diversification history

abstract:
Advances in sequencing technologies mean that insights into crop diversification aiding future breeding can now be explored in crops beyond major staples. For the first time, we use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the sub-genome level. A set of 8,778 SNPs and 13 agronomic traits characterizing a broad panel of 423 landrace accessions from Africa and Asia suggested the crop has undergone complex, context-specific diversification consistent with a long domestication history. Both Principal Component Analysis and Discriminant Analysis of Principal Components of SNPs indicated four groups of accessions that coincided with the principal geographic areas of finger millet cultivation. East Africa, the considered origin of the crop, appeared the least genetically diverse. A Principal Component Analysis of phenotypic data also indicated clear geographic differentiation, but different relationships among geographic areas than genomic data. Neighbour-joining trees of sub-genomes A and B showed different features which further supported the crops complex evolutionary history. Our genome-wide association study indicated only a small number of significant marker-trait associations. We applied then clustering to marker effects from a ridge regression model for each trait which revealed two clusters of different trait complexity, with days to flowering and threshing percentage among simple traits, and finger length and grain yield among more complex traits. Our study provides comprehensive new knowledge on the distribution of genomic and phenotypic variation in finger millet, supporting future breeding intra- and inter-regionally across its major cultivation range.

Core ideasO_LI8,778 SNPs and 13 agronomic traits characterized a panel of 423 finger millet landraces.
C_LIO_LI4 clusters of accessions coincided with major geographic areas of finger millet cultivation.
C_LIO_LIA comparison of phenotypic and genomic data indicated a complex diversification history.
C_LIO_LIThis was confirmed by the analysis of allotetraploid finger millets separate sub-genomes.
C_LIO_LIComprehensive new knowledge for intra- and inter-regional breeding is provided.
C_LI


title: Universal prediction of cell cycle position using transfer learning

abstract:
BackgroundThe cell cycle is a highly conserved, continuous process which controls faithful replication and division of cells. Single-cell technologies have enabled increasingly precise measurements of the cell cycle both as a biological process of interest and as a possible confounding factor. Despite its importance and conservation, there is no universally applicable approach to infer position in the cell cycle with high-resolution from single-cell RNA-seq data.

ResultsHere, we present tricycle, an R/Bioconductor package, to address this challenge by leveraging key features of the biology of the cell cycle, the mathematical properties of principal component analysis of periodic functions, and the use of transfer learning. We estimate a cell cycle embedding using a fixed reference dataset and project new data into this reference embedding; an approach that overcomes key limitations of learning a dataset dependent embedding. Tricycle then predicts a cell-specific position in the cell cycle based on the data projection. The accuracy of tricycle compares favorably to gold-standard experimental assays, which generally require specialized measurements in specifically constructed in vitro systems. Using internal controls which are available for any dataset, we show that tricycle predictions generalize to datasets with multiple cell types, across tissues, species and even sequencing assays.

ConclusionsTricycle generalizes across datasets, is highly scalable and applicable to atlas-level single-cell RNA-seq data.


title: Activation of the autophagy pathway affects Dengue virus infection in Aedes aegypti

abstract:
Mosquito-borne Dengue virus (DENV) has caused major disease worldwide, impacting 50 to 100 million people every year, and is spread by the major mosquito vector Aedes aegypti. Understanding mosquito physiology and developing new control strategies becomes an important issue to eliminate DENV. We focused on autophagy, a pathway suggested as having a positive influence on virus replication in humans, as a potential anti-viral target in the mosquito. To understand the role played by autophagy in Ae. aegypti, we examined the expression of the pathway in vitro (Aag-2 cell) and in vivo (Ae. aegypti). The results indicated that DENV infection in Aag-2 cells caused the microtubule-associated protein light chain 3-phosphatidylethanolamine conjugate (LC3-II) protein levels to increase which indicated the activation of the autophagy pathway. Rapamycin and 3-Methyladenine were used to activate or suppress the autophagy pathway, respectively. Rapamycin treatment decreased the virus titer in the Aag-2 cells, but the 3-Methyladenine treatment did not affect DENV titer. In Ae. aegypti, microinjected rapamycin increased the DENV titer after one-day infection and was significantly different compared to the control group titer. Two ATG genes, ATG4 and ATG12, were expressed differentially under the rapamycin treatments. Although the results differed between in vitro and in vivo studies, findings from both support the interaction between autophagy and DENV. Our studies revealed the activation of the autophagy pathway through rapamycin could be related to DENV infection in the mosquito. The possibility of autophagy being associated with different antiviral mechanisms at different extrinsic incubation times and tissues in Ae. aegypti is discussed.

Author SummaryDengue virus (DENV) has been a great threat to public health and has not developed an efficient method to stop the transmission. To understand the complex interaction between virus and mosquito, we investigate the autophagy pathway and its role during the infection process. We noticed the induction of autophagy pathways from DENV infection in Aag-2 cells and blood meal from Ae. aegypti. Moreover, activation of the autophagy pathway from rapamycin could alter the DENV titer. Our results indicated the autophagy pathway is associated with DENV and could be crucial during the DENV infection. Furthermore, we proved the practicality of small molecules in altering the autophagy pathway in mosquitoes, and thus the usage of small molecules as possible mosquito pathogen vaccines should be evaluated.

category: molecular biology


title: Altered drug metabolism and increased susceptibility to fatty liver disease in an inducible liver-specific mouse model of myotonic dystrophy

abstract: Myotonic Dystrophy type 1 (DM1) is multi-systemic muscular dystrophy, affecting 1 in 3000 people, characterized by muscle wasting, myotonia, cardiac and gastrointestinal abnormalities and cognitive impairment, among other symptoms. DM1 is caused by a (CTG)n repeat expansion in the 3 UTR of the ubiquitously expressed gene DMPK. The (CUG)n containing RNAs resulting from the transcription of this diseased DMPK gene aggregate in the nucleus, forming foci which sequester muscleblind-like (MBNL) family proteins, a group of splicing factors that play significant roles in the juvenile-to-adult development of many tissues. Recent studies show that DM1 patients have increased susceptibility toward glucose intolerance, non-alcoholic fatty liver disease (NAFLD), and metabolic syndrome. Furthermore, DM1 patients are abnormally sensitive to a wide range of analgesics and anesthetics, with complications ranging from prolonged anesthesia recovery to heightened pulmonary dysfunction. These findings suggest a predisposition for liver damage and dysfunction in DM1 patients; however, this possibility has gone uninvestigated. To understand the effects of DM1 in the liver, we generated a hepatocyte-specific DM1 mouse model in which we can induce the expression of CUG containing RNA, specifically in the liver. Through these mice, we demonstrate that the expression of the toxic RNA in hepatocytes sequesters MBNL proteins, causing a reduction in mature hepatocellular activity, however, we find that, in contrast to other tissues, loss of MBNL1 activity only reproduces a small portion of the transcriptome changes in DM1 afflicted hepatocytes. We characterized the transcriptomic changes driven by DM1 in the liver and show that these lead to changes in hepatocellular morphology, inflammation, and necrosis, as well as excessive lipid accumulation and fatty liver disease. We further demonstrate that DM1 mice livers are defective in drug metabolism and clearance, and when challenged, exhibit marked impairment against zoxazolamine-induced paralysis and acetaminophen-induced hepatotoxicity. Together, these results reveal that the expression of CUG repeat containing RNA disrupts the normal hepatic functions and predisposes the liver to injury, fatty liver disease, and drug clearance pathologies that may jeopardize the health of DM1 patients and complicate the treatment of DM1.


title: Comprehensive Proteomic Quantification of Bladder Stone Progression in a Cystinuric Mouse Model Using Data-Independent Acquisitions

abstract: Cystinuria is one of various disorders that cause biomineralization in the urinary system, including bladder stone formation in humans. It is most prevalent in children and adolescents and more aggressive in males. There is no cure, and only limited disease management techniques help to solubilize the stones. Recurrence, even after treatment, occurs frequently. Other than a buildup of cystine, little is known about factors involved in the formation, expansion, and recurrence of these stones. This study sought to define the growth of bladder stones, guided by micro-computed tomography imaging, and to profile dynamic stone proteome changes in a cystinuria mouse model. After bladder stones developed in vivo, they were harvested and separated into four developmental stages (sand, small, medium and large stone), based on their size. Data-dependent and data-independent acquisitions allowed deep profiling of stone proteomics. The proteomic signatures and pathways illustrated major changes as the stones grew. Stones initiate from a small nidus, grow outward, and show major enrichment in ribosomal proteins and factors related to coagulation and platelet degranulation, suggesting a major dysregulation in specific pathways that can be targeted for new therapeutic options.

category: cell biology


title: The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)

abstract: Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for designing new approaches in crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species are able to revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.


title: Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia

abstract: During pre-mRNA processing, the poly(A) signal is recognized by a protein complex that ensures precise cleavage and polyadenylation of the nascent transcript. The location of this cleavage event establishes the length and sequence of the 3' UTR of an mRNA, thus determining much of its post-transcriptional fate. Here, using long-read sequencing, we characterize the polyadenylation signal and related sequences surrounding Giardia lamblia cleavage sites for over 2600 genes. We find that G. lamblia uses a AGURAA poly(A) signal, which differs from the mammalian AAUAAA. We also describe how G. lamblia lacks common auxiliary elements found in other eukaryotes, along with the proteins that recognize them. Further, we identify 133 genes that show evidence of alternative polyadenylation. These results suggest that despite pared down cleavage and polyadenylation machinery, 3' end formation still appears to be an important regulatory step for gene expression in G. lamblia.


title: Identification of decondensed large-scale chromatin regions by TSA-seq and their localization to a subset of chromatin domain boundaries

abstract: Large-scale chromatin compaction is nonuniform across the human genome and correlates with gene expression and genome organization. Current methodologies for assessing large-scale chromatin compaction are indirect and largely based on assays that probe lower levels of chromatin organization, primarily at the level of the nucleosome and/or the local compaction of nearby nucleosomes. These assays assume a one-to-one correlation between local nucleosomal compaction and large-scale compaction of chromosomes that may not exist. Here we describe a method to identify interphase chromosome regions with relatively high levels of large-scale chromatin decondensation using TSA-seq, which produces a signal proportional to microscopic-scale distances relative to a defined nuclear compartment. TSA-seq scores that change rapidly as a function of genomic distance, detected by their higher slope values, identify decondensed large-scale chromatin domains (DLCDs), as then validated by 3D DNA-FISH. DLCDs map near a subset of chromatin domain boundaries, defined by Hi-C, which separate active and repressed chromatin domains and correspond to compartment, subcompartment, and some TAD boundaries. Most DLCDs can also be detected by high slopes of their Hi-C compartment score. In addition to local enrichment in cohesin (RAD21, SMC3) and CTCF, DLCDs show the highest local enrichment to super-enhancers, but are also locally enriched in transcription factors, histone-modifying complexes, chromatin mark readers, and chromatin remodeling complexes. The localization of these DLCDs to a subset of Hi-C chromatin domain boundaries that separate active versus inactive chromatin regions, as measured by two orthogonal genomic methods, suggests a distinct role for DLCDs in genome organization.


title: Metabolic function in aging retina and retinal pigment epithelium remains robust despite vision loss

abstract:
PurposeCharacterize how metabolic function in the murine retina and retinal pigment epithelium-choroid-sclera (eyecup) complex is impacted by natural aging.

MethodsWe examined scotopic and photopic visual function of young (3-6 months) and aged (23-26 months) C57Bl/6J mice using electroretinograms (ERGs). Metabolic changes in retina and eyecup explants were characterized by measuring uptake and usage of U-13C-glucose or U-13C-glutamine at different timepoints by gas chromatography-mass spectrometry (GC-MS), measuring oxygen consumption rate (OCR) using a perifusion apparatus, and determining ATP levels with a bioluminescence assay.

ResultsScotopic and photopic ERG responses declined in aged mice. Glucose metabolism, glutamine metabolism, OCR, and ATP pools in retinal explants were mostly unaffected by the age of the mouse. In eyecups, glutamine usage in the Krebs Cycle decreased while glucose metabolism, OCR, and ATP pools remained stable.

ConclusionsThe ex vivo approach in our study to examine aging glucose and glutamine metabolism in retina and RPE showed negligible impact of age on retina and an impairment of glutamine anaplerosis in eyecups. The surprising metabolic stability of these tissues ex vivo suggests age-related metabolic alterations in these tissues may not be intrinsic. Future experiments should focus on determining whether external factors including nutrient supply, oxygen availability, or other structural changes influence ocular metabolism in vivo.


title: Altered O-glycosylation Level of SARS-CoV-2 Spike Protein by Host O-glycosyltransferase Strengthens Its Trimeric Structure

abstract: The trimeric spike protein (S) mediates host-cell entry and membrane fusion of SARS-CoV-2. S protein is highly glycosylated, whereas its O-glycosylation is still poorly understood. Herein, we site-specifically examine the O-glycosylation of S protein through a mass spectrometric approach with HCD-triggered-ETD model. We identify 15 high-confidence O-glycosites and at least 10 distinct O-glycan structures on S protein. Peptide microarray assays prove that human ppGalNAc-T6 actively participates in O-glycosylation of S protein. Importantly, the upregulation of ppGalNAc-T6 expression can profoundly enhance the O-glycosylation level by generating new O-glycosites and increasing both O-glycan heterogeneity and intensities. Further molecular dynamics simulations reveal that the O-glycosylation on the protomer-interface regions, which are mainly modified by ppGalNAc-T6, can potentially stabilize the trimeric S protein structure. Our work provides deep molecular insights of how viral infection harnesses the host O-glycosyltransferases to dynamically regulate the O-glycosylation level of the viral envelope protein responsible for membrane fusion.


title: Fast slow folding of an Outer Membrane Porin

abstract: In comparison to globular proteins, the spontaneous folding and insertion of {beta}-barrel membrane proteins is surprisingly slow, typically occurring on the order of minutes. Using single-molecule Forster Resonance Energy Transfer to report on the folding of fluorescently-labelled Outer Membrane Protein G we measured the real-time insertion of a {beta}-barrel membrane protein from an unfolded state. Folding events were rare, and fast (<20 ms); occurring immediately upon arrival at the membrane. This combination of infrequent, but rare, folding resolves this apparent dichotomy between slow ensemble kinetics, and the typical timescales of biomolecular folding.


title: The mechanism of activation of monomeric B-Raf V600E

abstract: Oncogenic mutations in the serine/threonine kinase B-Raf, particularly the V600E mutation, are frequent in cancer, making it a major drug target. Although much is known about B-Rafs active and inactive states, questions remain about the mechanism by which the protein changes between these two states. Here, we utilize molecular dynamics to investigate both wild-type and V600E B-Raf to gain mechanistic insights into the impact of the Val to Glu mutation. The results show that the wild-type and mutant follow similar activation pathways involving an extension of the activation loop and an inward motion of the C-helix. The V600E mutation, however, destabilizes the inactive state by disrupting hydrophobic interactions present in the wild-type structure while the active state is stabilized through the formation of a salt bridge between Glu600 and Lys507. Additionally, when the activation loop is extended, the C-helix is able to move between an inward and outward orientation as long as the DFG motif adopts a specific orientation. In that orientation Phe595 rotates away from the C-helix, allowing the formation of a salt bridge between Lys483 and Glu501. These mechanistic insights have implications for the development of new Raf inhibitors.


title: Preliminary in silico experiments: Towards new cancer treatments?

abstract: We present some "in silico" experiments to design combined chemo- and immunotherapy treatment schedules. We introduce a new framework by combining flatness-based control along with model-free control. The flatness property of the used mathematical model yields straightforward reference trajectories. They provide us with the nominal open-loop control inputs. Closing the loop via model-free control allows to deal with the uncertainties on the injected drug doses. Several numerical simulations illustrating different case studies are displayed. We show in particular that the considered health indicators are driven to the safe region, even for critical initial conditions. Furthermore, in some specific cases there is no need to inject chemotherapeutic agents.


title: Effects of  imidacloprid and thiamethoxam at LC30 and LC50 on the life table of soybean aphid Aphis glycines (Hemiptera: Aphididae)

abstract: The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), is a main pests of soybean that poses a serious threat to its production. Studies were conducted to understand effects of the different concentrations of the insecticides (imidacloprid and thiamethoxam) on the life table of A. glycines to provide vital information for its effective management. We found that the mean generation time, adult and total pre-oviposition periods in A. glycines specimens exposed to LC50 imidacloprid and thiamethoxam were significantly longer than those in the control group. However, when exposed to LC30 imidacloprid and thiamethoxam, the adult pre-ovipositional period was significantly shorter than that in the control group. The mean fecundity per female adult, net reproductive rate, intrinsic rate of increase, and finite rate of increase were significantly decreased in individuals exposed to LC30 and LC50 concentrations of imidacloprid and thiamethoxam, respectively (P < 0.05). Both insecticides produce stress effects on A. glycines, and specimens treated with LC50 concentrations of the two insecticides exhibited a significant decrease in their growth rates than those treated with LC30 concentrations. This study provides data that can be used as a reference to predict the effect of imidacloprid and thiamethoxam on the population dynamics in the field, and agricultural producers could attach importance to prevent stimulation the reproduction made by low-lethal concentrations during actually applying pesticides.

category: pharmacology and toxicology


title: Effects of potassium fertilizer on dry matter accumulation and potassium absorption characteristics of maize (Zea mays L.) inbred lines with different yield types

abstract: In this experiment, 20 different maize inbred lines were used as basic materials, which were divided into high-yield type, middle-yield type and low-yield type by yield cluster analysis. A 3-year long-term positioning field experiment (2016-2018) was carried out to assess the effects of potassium fertilizer on dry matter, potassium absorption and potassium absorption efficiency of maize inbred lines with different yield types. The results showed that the dry matter, potassium absorption and potassium absorption efficiency of leaf, stem, bract, rachis and grain of maize inbred lines have been significantly increased with potassium application in comparison with no potassium application. Potassium fertilizer could improve the dry matter accumulation capacity and potassium absorption characteristics of maize, promote the potassium absorption by maize plants, influence the growth and development of maize, and then improve the maize yield. The decrease of dry matter, potassium absorption and potassium absorption efficiency of high-yield maize inbred lines was smaller under low potassium stress. The high-yield maize inbred lines had stronger ability to maintain higher dry matter accumulation and potassium absorption characteristics under low potassium stress. The study provided a theoretical basis for the breeding of potassium-efficient maize materials.

category: plant biology


title: Heritable Variation in Locomotion, Reward Sensitivity, and Impulsive Action, Choice, and Waiting in a Genetically Diverse Inbred Mouse Panel

abstract: Drugs of abuse, including alcohol and stimulants like cocaine, produce effects that are subject to individual variability, and genetic variation accounts for at least a portion of those differences. Notably, research in both animal models and human subjects point towards reward sensitivity and impulsivity as being trait characteristics that predict relatively greater positive subjective responses to stimulant drugs. Here we describe use of the eight Collaborative Cross (CC) founder strains and multiple CC strains to examine the heritability of reward sensitivity and impulsivity traits, as well as genetic correlations between these measures and existing addiction-related phenotypes. Methods. Strains were all tested for activity in an open field and reward sensitivity (intake of chocolate BOOST(R)). Mice were then divided into two counterbalanced groups and underwent reversal learning (impulsive action and waiting impulsivity) or delay discounting (impulsive choice). Results. CC and founder mice demonstrate significant heritability for impulsive action, impulsive choice, waiting impulsivity, locomotor activity, and reward sensitivity, with each impulsive phenotype determined to be non-correlating, independent traits. This research was conducted within the broader, inter-laboratory effort of the Center for Systems Neurogenetics of Addiction (CSNA) to characterize CC and DO mice for multiple, cocaine abuse related traits. These data will facilitate the discovery of genetic correlations between predictive traits, which will then guide discovery of genes and genetic variants that contribute to addictive behaviors.

category: neuroscience


title: Heritable variation in locomotion, reward sensitivity and impulsive behaviors in a genetically diverse inbred mouse panel


title: Extracting temporal relationships between weakly coupled peptidergic and motoneuronal signaling: application to Drosophila ecdysis behavior

abstract:
Neuromodulators, such as neuropeptides, can regulate and reconfigure neural circuits to alter their output, affecting in this way animal physiology and behavior. The interplay between the activity of neuronal circuits, their modulation by neuropeptides, and the resulting behavior, is still poorly understood. Here, we present a quantitative framework to study the relationships between the temporal pattern of activity of peptidergic neurons and of motoneurons during Drosophila ecdysis behavior, a highly stereotyped motor sequence that is critical for insect growth. We analyzed, in the time and frequency domains, simultaneous intracellular calcium recordings of peptidergic CCAP (crustacean cardioactive peptide) neurons and motoneurons obtained from isolated central nervous systems throughout fictive ecdysis behavior induced ex vivo by Ecdysis triggering hormone. We found that the activity of both neuronal populations is tightly coupled in a cross-frequency manner, suggesting that CCAP neurons modulate the faster oscillation of motoneurons. To explore this idea further, we used a probabilistic logistic model to show that calcium dynamics in CCAP neurons can predict the oscillation of motoneurons, both in a simple model and in a conductance-base model capable of simulating many of the observed neural dynamics features. Finally, we developed an algorithm to quantify the motor behavior observed in videos of pupal ecdysis, and compared their features to the patterns of neuronal calcium activity recorded ex vivo. We found that the motor activity of the intact animal is more regular than the motoneuronal activity recorded from the ex vivo preparations during fictive ecdysis behavior; the analysis of movement patterns also allowed us to identify a new post-ecdysis phase.

Author SummaryRepetitive movements such as walking, swimming, and flying are controlled by networks of neurons known as central patter generators. In many cases, the exact pattern of activity is modulated by neuropeptides, which are small signaling molecules that, unlike neurotransmitters, are broadly released within regions of the nervous system. Because of this mode of action, it can be difficult to discern the relationship between the temporal pattern of firing of peptidergic neurons and the timing of the resulting motor behavior. Here, we developed methods to analyze the patterns of activity of such weakly coupled systems as applied to ecdysis, the stereotyped sequence of behaviors used by insects to shed the remains of their old exoskeleton at the end of every molt. Key actors in this process are motoneurons (MN) and a set of neurons expressing the neuropeptide, Crustacean Cardioactive Peptide (CCAP). Combining real-time calcium imaging, frequency analysis, computational simulations, and image processing, we determined the relationships between the activity of CCAP neurons and the resulting motor output during pupal ecdysis in the fruit fly, Drosophila melanogaster. We found that several temporal features of the activity of CCAP neurons are highly coupled to the patter of activity motoneuronal pattern, suggesting an active role of CCAP neurons during ecdysis. We also developed quantitative approaches that allowed us to identify a new ecdysis sub-phase.


title: Pre-diabetes increases tuberculosis disease severity, while high body fat without impaired glucose tolerance is protective

abstract: Type 2 diabetes (T2D) is a well-known risk factor for tuberculosis (TB), but little is known about pre-diabetes and the relative contribution of impaired glucose tolerance vs. obesity towards susceptibility to TB. Here, we developed a preclinical model of pre-diabetes and TB. Mice fed a high fat diet (HFD) for 12 weeks presented with impaired glucose tolerance and hyperinsulinemia compared to mice fed normal chow diet (NCD). Infection with M. tuberculosis (Mtb) H37Rv after the onset of dysglycemia was associated with significantly increased lung pathology, lower concentrations of TNF-a, IFN-g, IFN-{beta} and IL-10 and a trend towards higher bacterial burden at 3 weeks post infection. To determine whether the increased susceptibility of pre-diabetic mice to TB is reversible and is associated with dysglycemia or increased body fat mass, we performed a diet reversal experiment. Pre-diabetic mice were fed a NCD for 10 additional weeks (HFD/NCD) at which point glucose tolerance was restored, but body fat mass remained higher compared to control mice that consumed NCD throughout the entire experiment (NCD/NCD). Upon Mtb infection HFD/NCD mice had significantly lower bacterial burden compared to NCD/NCD mice and this was accompanied by restored IFN-{gamma} responses. Our findings demonstrate that pre-diabetes increases susceptibility to TB, but a high body mass index without dysglycemia is protective. This murine model offers the opportunity to further study the underlying immunological, metabolic and endocrine mechanisms of this association.


title: Antibody Activities in Hyperimmune Plasma Against the Rhodococcus equi Virulence -Associated Protein A or Poly-N-Acetyl Glucosamine are Associated with Protection of Foals Against Rhodococcal Pneumonia

abstract: The efficacy of transfusion with hyperimmune plasma (HIP) for preventing pneumonia caused by Rhodococcus equi remains ill-defined. Quarter Horse foals at 2 large breeding farms were randomly assigned to be transfused with 2 L of HIP from adult donors hyperimmunized either with R. equi (RE HIP) or a conjugate vaccine eliciting antibody to the surface polysaccharide {beta}-1[->]6-poly-N-acetyl glucosamine (PNAG HIP) within 24 hours of birth. Antibody activities against PNAG and the rhodococcal virulence-associated protein A (VapA), and to deposition of complement component 1q (C1q) onto PNAG were determined by ELISA, and then associated with either clinical pneumonia at Farm A (n=119) or subclinical pneumonia at Farm B (n=114). Data were analyzed using multivariable logistic regression. Among RE HIP-transfused foals, the odds of pneumonia were approximately 6-fold higher (P = 0.0005) among foals with VapA antibody activity [≤] the population median. Among PNAG HIP-transfused foals, the odds of pneumonia were approximately 3-fold (P = 0.0347) and 11-fold (P = 0.0034) higher for foals with antibody activities [≤] the population median for PNAG or C1q deposition, respectively. Results indicated that levels of activity of antibodies against R. equi antigens are correlates of protection against both subclinical and clinical R. equi pneumonia in field settings. Among PNAG HIP-transfused foals, activity of antibodies with C1q deposition (an indicator of functional antibodies) were a stronger predictor of protection than was PNAG antibody activity alone. Collectively, these findings suggest that the amount and activity of antibodies in HIP (i.e., plasma volume and/or antibody activity) is positively associated with protection against R. equi pneumonia in foals.


title: Shared and Unique Evolutionary Trajectories to Ciprofloxacin Resistance in Gram-negative Bacterial Pathogens

abstract:
The resistance to broad-spectrum antibiotic ciprofloxacin is detected in high rates for a wide range of bacterial pathogens. To investigate dynamics of ciprofloxacin resistance development we proposed a comparative resistomics workflow for three clinically relevant species of Gram-negative bacteria: Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. We combined experimental evolution in a morbidostat with deep sequencing of evolving bacterial populations in time series that reveals both shared and unique aspects of evolutionary trajectories patterns. Representative clone characterization by sequencing and MIC measurements enabled direct assessment of mutations impact on the extent of acquired drug resistance. In all three species we observed a two-stage evolution: (1) early ciprofloxacin resistance reaching 4-16-fold of wildtype MIC commonly as a result of single mutations in DNA gyrase target genes (gyrA or gyrB) and (2) additional genetic alterations affecting transcriptional control of drug efflux machinery or secondary target genes (DNA topoisomerase parC or parE).

ImportanceThe challenge of spreading antibiotic resistance calls for systematic efforts to develop more "irresistible" drugs based on deeper understanding of dynamics and mechanisms of antibiotic resistance acquisition. To address this challenge, we have established a comparative resistomics approach which combines experimental evolution in a continuous culturing device, the morbidostat, with ultradeep sequencing of evolving microbial populations to identify evolutionary trajectories (mutations and genome rearrangements) leading to antibiotic resistance over a range of target pathogens. Here we report the comparative resistomics study of three Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa), which revealed shared and species-specific aspects of the evolutionary landscape leading to robust resistance against the clinically important antibiotic ciprofloxacin. In addition to specific findings, the impact of this study is in highlighting the anticipated utility of a morbidostat-based comparative genomic approach to guide rational optimization of treatment regimens for current antibiotics and development of novel antibiotics with minimized resistance propensities.


title: Highly-potent, synthetic APOBEC3s restrict HIV-1 through deamination-independent mechanisms

abstract:
The APOBEC3 (A3) genes encode cytidine deaminase proteins with potent antiviral and anti-retroelement activity. This locus is characterized by duplication, recombination, and deletion events that gave rise to the seven A3s found in primates. These include three single deaminase domain A3s (A3A, A3C, and A3H) and four double deaminase domain A3s (A3B, A3D, A3F, and A3G). The most potent of the A3 proteins against HIV-1 is A3G. However, it is not clear if double deaminase domain A3s have a generalized functional advantage to restrict HIV-1. In order to test whether superior restriction factors could be created by genetically linking single A3 domains into synthetic double domains, we combined A3C and A3H single domains in novel combinations. We found that A3C/A3H double domains acquired enhanced antiviral activity that is at least as potent, if not better than, A3G. These synthetic double domain A3s have more efficiency of packaging into budding virions than their respective single domains, but this does not fully explain their gain of antiviral potency. The antiviral activity is conferred both by cytidine-deaminase dependent and independent mechanisms, with the latter correlating to an increase in RNA binding affinity. T cell lines expressing this A3C-A3H super restriction factor are able to control replicating HIV-1{Delta}Vif infection to similar levels as A3G. Together, these data show that novel combinations of A3 domains are capable of gaining potent antiviral activity to levels similar to the most potent genome-encoded A3s, via a primarily non-catalytic mechanism.

Author SummaryAntiviral genes are encoded by all organisms to help protect them from viral infections, including proteins encoded by primates to protect them from viruses similar to HIV-1. These antiviral proteins are also called "restriction factors". Some restriction factors are broadly acting, while others are very specific. During the course of evolution, some of these genes have expanded into multiple copies and rearranged in different versions to give them new activities. However, not all versions of these genes have been sampled in nature. In this paper, we validated the hypothesis that one particular antiviral gene family, called the APOBEC3 family, has the capability of making novel combinations of antiviral genes with as great, or greater, potency against HIV-1 as the most potent natural member of this family. By combining parts of the APOBEC3 proteins into novel combinations, we created potent antiviral versions that act through a mechanism distinct from existing APOBEC3 proteins.


title: Host Factor Rab11a is Critical for Efficient Assembly of Influenza A Virus Genomic Segments

abstract: It is well documented that influenza A viruses selectively package 8 distinct viral ribonucleoprotein complexes (vRNPs) into each virion; however, the role of host factors in genome assembly is not completely understood. To evaluate the significance of cellular factors in genome assembly, we generated a reporter virus carrying a tetracysteine tag in the NP gene (NP-Tc virus) and assessed the dynamics of vRNP localization with cellular components by fluorescence microscopy. At early time points, vRNP complexes were preferentially exported to the MTOC; subsequently, vRNPs associated on vesicles positive for cellular factor Rab11a and formed distinct vRNP bundles that trafficked to the plasma membrane on microtubule networks. In Rab11a deficient cells, however, vRNP bundles were smaller in the cytoplasm with less co-localization between different vRNP segments. Furthermore, Rab11a deficiency increased the production of non-infectious particles with higher RNA copy number to PFU ratios, indicative of defects in specific genome assembly. These results indicate that Rab11a+ vesicles serve as hubs for the congregation of vRNP complexes and enable specific genome assembly through vRNP:vRNP interactions, revealing the importance of Rab11a as a critical host factor for influenza A virus genome assembly.


title: Nuclear RNA-acetylation can be erased by the deacetylase SIRT7

abstract: A large number of RNA modifications are known to affect processing and function of rRNA, tRNA and mRNA 1. The N4-acetylcytidine (ac4C) is the only known RNA acetylation event and is known to occur on rRNA, tRNA and mRNA 2,3. RNA modification by acetylation affects a number of biological processes, including translation and RNA stability 2. For a few RNA methyl modifications, a reversible nature has been demonstrated where specific writer proteins deposit the modification and eraser proteins can remove them by oxidative demethylation 4-6. The functionality of RNA modifications is often mediated by interaction with reader proteins that bind dependent on the presence of specific modifications 1. The NAT10 acetyltransferase has been firmly identified as the main writer of acetylation of cytidine ribonucleotides, but so far neither readers nor erasers of ac4C have been identified 2,3. Here we show, that ac4C is bound by the nucleolar protein NOP58 and deacetylated by SIRT7, for the first time demonstrating reversal by another mechanism than oxidative demethylation. NOP58 and SIRT7 are involved in snoRNA function and pre-ribosomal RNA processing 7-10, and using a NAT10 deficient cell line we can show that the reduction in ac4C levels affects both snoRNA sub-nuclear localization and pre-rRNA processing. SIRT7 can deacetylate RNA in vitro and endogenous levels of ac4C on snoRNA increase in a SIRT7 deficient cell line, supporting its endogenous function as an RNA deacetylase. In summary, we identify the first eraser and reader proteins of the RNA modification ac4C, respectively, and suggest an involvement of RNA acetylation in snoRNA function and pre-rRNA processing.


title: Exercise and training regulation of autophagy markers in human and rodent skeletal muscle.

abstract: Autophagy is a key intracellular mechanism by which cells degrade old or dysfunctional proteins and organelles. In skeletal muscle, evidence suggests that exercise increases autophagosome content and autophagy flux. However, the exercise-induced response seems to differ between rodents and humans, and little is known about how different exercise prescription parameters may affect these results. The present study utilised skeletal muscle samples obtained from four different experimental studies using rats and humans. Here we show that following exercise, in the soleus muscle of Wistar rats, there is an increase in LC3B-I protein levels (+ 109%) immediately after exercise, and a subsequent increase in LC3B-II protein levels (+ 97%) 3 hours into the recovery. Conversely, in human skeletal muscle, there is an immediate exercise-induced decrease in LC3B-II protein levels (- 24%), independent of whether exercise is performed below or above the maximal lactate steady state, which returns to baseline 3.5 hours following recovery, while no change in LC3B-I protein levels is observed. p62 protein levels did not change in neither rats nor humans following exercise. By employing an ex vivo autophagy flux assay previously used in rodents we demonstrate that the exercise-induced decrease in LC3B-II protein levels in humans does not reflect a decreased autophagy flux. Instead, effect size analyses suggest a modest-to-large increase in autophagy flux following exercise that lasts up to 24 hours. Our findings suggest that exercise-induced changes in autophagosome content markers differ between rodents and humans, and that exercise-induced decrease in LC3B-II protein levels do not reflect autophagy flux level.


title: Resurrecting self-cleaving mini-ribozymes from 40-million-year-old LINE-1 elements in human genome

abstract: Long Interspersed Nuclear Element (LINE) retrotransposons play an important role in genomic innovation as well as genomic instability in many eukaryotes including human. Random insertions and extinction through mutational inactivation make them perfectly time-stamped "DNA fossils". Here, we investigated the origin of a self-cleaving ribozyme in 5 UTR of LINE-1. We showed that this ribozyme only requires 35 nucleotides for self-cleavage with a simple but previously unknown secondary-structure motif that was determined by deep mutational scanning and covariation analysis. Structure-based homology search revealed the existence of this mini-ribozyme in anthropoids but not in prosimians. In human, the most homologs of this mini-ribozyme were found in lineage L1PA6-10 but essential none in more recent L1PA1-2 or more ancient L1PA13-15. We resurrected mini-ribozymes according to consensus sequences and confirmed that mini-ribozymes were active in L1PA10 and L1PA8 but not in L1PA7 and more recent lineages. The result paints a consistent picture for the emergence of the active ribozyme around 40 million years ago, just before the divergence of the new world monkeys (Platyrrhini) and old-world monkeys (Catarrhini). The ribozyme, however, subsequently went extinct after L1PA7 emerged around 30 million years ago with a deleterious mutation. This work uncovers the rise and fall of the mini-LINE-1 ribozyme recorded in the "DNA fossils" of our own genome. More importantly, this ancient, naturally trans-cleaving ribozyme (after removing the non-functional stem loop) may find its modern usage in bioengineering and RNA-targeting therapeutics.


title: Tubular ERGIC (t-ERGIC): a SURF4-mediated expressway for ER-to-Golgi transport

abstract: The endoplasmic reticulum (ER)-to-Golgi transport is critical to protein secretion and intracellular sorting. Cargo carriers mediating the ER-to-Golgi transport are morphologically diverse, but it remains unclear whether this diversity arises from different cargo receptors, or whether it could lead to differential transport kinetics. Here we report a tubular ER-Golgi intermediate compartment (t-ERGIC) that is induced by the cargo receptor SURF4 and selectively expedites the ER-to-Golgi transport of SURF4 cargoes. Lacking the canonical ERGIC marker ERGIC-53 yet positive for the small GTPase Rab1, the t-ERGIC is further distinct from the stereotypical vesiculo-tubular cluster (VTC) ERGIC by its extremely elongated shape (~10 m long with <30 nm diameter). With its exceptional surface-to-volume ratio and en bloc cargo packaging, high (~2 m/s) intracellular traveling speeds, and ER-Golgi recycling capability, the t-ERGIC provides an efficient means for trafficking SURF4-bound cargoes. The biogenesis and cargo selectivity of t-ERGIC both depend on SURF4, which recognizes the N-terminus of soluble cargoes and co-clusters with the selected cargoes to expand the ER exit site. At the steady state, the t-ERGIC-mediated fast ER-to-Golgi transport is antagonized by retrograde transport based on the cargo C-terminal ER retrieval signal: we thus demonstrate the fine-tuning of protein trafficking and localization via its primary structure. Together, our results argue that specific cargo-receptor interactions give rise to distinct transport carriers, which in turn regulate the ER-to-Golgi trafficking kinetics.


title: The TNF Egr participates in signaling during cell competition in the absence of a requirement for JNK

abstract: Numerous signaling pathways have been implicated in the elimination of cells in cell competition. Here we explore the relative contributions of two of them, the recently discovered CCSM and the conserved JNK stress pathway, using a series of genetic interactions tests. We demonstrate that the expression of the TNF Eiger (Egr), and the TNFR adaptor protein Traf4, are specifically up-regulated in the wild-type "loser" cell population during Myc-mediated cell competition. We find that the absence of Egr or its receptor Grindelwald (grnd) robustly prevents elimination of the loser cells in genetic cell competition assays. In contrast, although canonical JNK signaling is activated downstream of these adaptors, loss of either of the JNK effectors Tak1/JNKK or Hemipterous/JNK is not sufficient to prevent loser cell elimination in the competitive context. Our results instead suggest that Egr/Grnd influences the Rel activator Dredd in carrying out the cells competitive death and elimination. Our experiments thus provide evidence that although Egr/Grnd signaling activates two parallel pathways in Myc cell competition, only the CCSM is sufficient to remove the wild-type loser cells from the tissue.

category: developmental biology


title: Uneven growth of SARS-CoV-2 clones evidenced by more than 500,000 whole-genome sequences

abstract: We have computed the frequencies of the alleles of the "UK variant" (B.1.1.7) and "South Africa variant" (B.1.351) of SARS-CoV-2 from the large GISAID repository. We find that the frequencies of the mutations in UK variant overall rose towards the end of 2020, as widely reported in the literature and in the general press. However, we also find that these frequencies vary in different patterns rather than in concert. For South Africa variant we find a more complex scenario with frequencies of some mutations rising and some remaining close to zero. Our results point to that what is generally reported as one variant is in fact a collection of variants with different genetic characteristics.


title: Morphology of migration: Associations between wing shape, bill morphology, and migration in kingbirds (Tyrannus)

abstract: Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb-morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviors also interact with diet, such that migratory animals tend to be dietary generalists, while sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and limb and bill morphology across kingbirds, a pan-American genus of birds with migratory, partially migratory, and sedentary taxa. Migratory kingbirds had longer wings, in agreement with expectations if selection favors improved aerodynamics for long-distance migration. We also found an association between migratory status and bill shape, such that more migratory taxa had wider, deeper, and shorter bills compared to sedentary taxa. However, there was no difference in intraspecific morphological variation among migrants, partial migrants, and residents, suggesting that dietary specialization has evolved independently of migration strategy. The evolutionary links between migration, diet, and morphology in kingbirds uncovered here further strengthen ecomorphological associations that underlie long-distance seasonal movements in animals.


title: Morphology of migration: Associations between wing, and bill morphology and migration in kingbirds (Tyrannus)


title: Linkage disequilibrium and population structure in a core collection of Brassica napus (L.)

abstract: Estimation of genetic diversity in rapeseed/canola is important for sustainable breeding program to provide an option for the development of new breeding lines. The objective of this study was to elucidate the patterns of genetic diversity within and among different structural groups, and measure the extent of linkage disequilibrium (LD) of 383 globally distributed rapeseed/canola germplasm using 8,502 single nucleotide polymorphism (SNP) markers. The germplasm accessions were divided into five subpopulations (P1 to P5) with obvious geographic and growth habit-related patterns. All subpopulations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.24) between most of the combinations. The rutabaga type showed highest divergence with spring and winter types. Higher divergence was also found between winter and spring types. Overall, mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 45 kb distance for whole genome. The LD decay was slower in C genome (< 93 kb), relative to the A genome (< 21 kb) which was confirmed by availability of larger haplotype blocks in C genome than A genome. To maximize genetic gain, hybridization between rutabaga and other types are potentially the best option. Hybridization between spring and winter, semi-winter type is also helpful to maximize the diversity in subsequent populations. Low genetic differentiation between both spring type subpopulations (P4 and P3) will accelerate favorable allele accumulation for specific traits in elite lines. The Neighbor-Joining tree and kinship matrix will assist to identify distantly related genotypes from subpopulations to utilize in hybridization. The low levels of LD and population structure make the core collection an important resource for association mapping efforts to identify genes useful in crop improvement as well as for selection of parents for hybrid breeding.


title: Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNA

abstract: The primary objective of the FDA-led Sequencing and Quality Control Phase 2 (SEQC2) project is to develop standard analysis protocols and quality control metrics for use in DNA testing to enhance scientific research and precision medicine. This study reports a targeted next generation sequencing (NGS) method that enables more accurate detection of actionable mutations in circulating tumor DNA (ctDNA) clinical specimens. This advancement was enabled by designing a synthetic internal standard spike-in for each actionable mutation target, suitable for use in NGS following hybrid-capture enrichment and unique molecular index (UMI) or non-UMI library preparation. When mixed with contrived ctDNA reference samples, internal standards enabled calculation of technical error rate, limit of blank, and limit of detection for each variant at each nucleotide position, in each sample. True positive mutations with variant allele fraction too low for detection by current practice were detected with this method, thereby increasing sensitivity.