title: Source range phylogenetic community structure can predict the outcome of avian introductions

abstract: Competing phylogenetic models have been proposed to explain the success of species introduced to other communities. Here, we present a study predicting the establishment success of birds introduced to Florida, Hawaii, and New Zealand using several alternative models, considering species phylogenetic relatedness to source and recipient range taxa, propagule pressure, and traits. We find consistent support for the predictive ability of source region phylogenetic structure. However, we find that the effects of recipient region phylogenetic structure vary in sign and magnitude depending on inclusion of source region phylogenetic structure, delineation of the recipient species pool, and the use of phylogenetic correction in the models. We argue that tests of alternative phylogenetic hypotheses including the both source and recipient community phylogenetic structure, as well as important covariates such as propagule pressure, are likely to be critical for identifying general phylogenetic patterns in introduction success, predicting future invasions, and for stimulating further exploration of the underlying mechanisms of invasibility.


title: Twenty-one Year Trends for Shorebirds, Waterfowl, and Other Waterbirds at Great Salt Lake, Utah

abstract: Millions of wetland-dependent birds annually depend on saline lakes and associated wetlands in the western United States. Understanding the population status and trends of birds with different life histories and habitats can guide efforts to secure water resources needed to sustain bird habitats. We used a 21-year dataset to examine population trends for 24 survey units presumed to be high-quality habitat for migratory shorebirds, waterfowl, and other waterbirds at Great Salt Lake and associated wetlands. As expected for high-quality habitats, we found stable or positive trends for 36 of 37 species or groups in fall, spring, or both seasons when considering survey units in aggregate. Despite stable or positive aggregate trends, negative trends did occur in some individual survey units. Foraging, migration distance, and taxonomic groupings were unrelated to trend direction. Research is needed to test whether survey units represent high-quality habitat. With declining regional water resources, stable and positive aggregate trends reinforce the importance of surveyed units at Great Salt Lake and associated wetlands to wetland-dependent birds. Ensuring continuation of stable and positive trends will require identifying environmental factors - including water quantity and quality - driving trends, and require coordinated regional management and monitoring of wetland-dependent birds.

category: ecology


title: Rhizome trait scaling relationships are modulated by climate and are linked to plant fitness

abstract:
Background and AimRhizomes are important organs allowing many clonal plants to persist and reproduce under stressful climates with longer rhizomes indicating enhanced ability of the plants to spread vegetatively. We do not however, know either how rhizome construction costs change with increasing length or vary with environmental conditions.

MethodsWe analysed the rhizome length vs mass scaling relationship, the plasticity in the scaling relationships, their genetic basis, and how scaling relationships are linked to plant fitness. We used data from 275 genotypes of a clonal grass Festuca rubra originating from 11 localities and cultivated under four contrasting climates. Data were analysed using standard major axis regression, mixed-effect regression models and a structural equation model.

Key ResultsRhizome construction costs increased (i.e., lower specific rhizome length) with increasing length. The trait scaling relationships were modulated by cultivation climate and its effects also interacted with the climate of origin of the experimental plants. With increasing length, increasing moisture led to a greater increase in rhizome construction costs. Plants with lower rhizome construction costs showed significantly higher fitness.

ConclusionsThis study suggests that rhizome scaling relationships are plastic, but also show genetic differentiation and are linked to plant fitness. Therefore, to persist under variable environments modulation in scaling relationships could be an important plants strategy.


title: Rhizome trait scaling relationships are modulated by growth conditions and are linked to plant fitness


title: Verification of SARS-CoV-2-Encoded small RNAs and contribution to Infection-Associated lung inflammation

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the COVID-19 pandemic. SARS-CoV-2 is a positive-stranded RNA virus belongs to Coronaviridae family. The viral genome of SARS-CoV-2 contains around 29.8 kilobase with a 5'-cap structure and 3'-poly-A tail, and shows 79.2% nucleotide identity with human SARS-CoV-1, which caused the 2002-2004 SARS outbreak. As the successor to SARS-CoV-1, SARS-CoV-2 now has circulated across the globe. There is a growing understanding of SARS-CoV-2 in virology, epidemiology, and clinical management strategies. In this study, we verified the existence of two 18-22 nt small viral RNAs (svRNAs) derived from the same precursor in human specimens infected with SARS-CoV-2, including nasopharyngeal swabs and formalin-fixed paraffin-embedded (FFPE) explanted lungs from lung transplantation of COVID-19 patients. We then simulated and confirmed the formation of these two SARS-CoV-2-Encoded small RNAs in human lung epithelial cells. And the potential pro-inflammatory effects of the splicing and maturation process of these two svRNAs in human lung epithelial cells were also explored. By screening cytokine storm genes and the characteristic expression profiling of COVID-19 in the explanted lung tissues and the svRNAs precursor transfected human lung epithelial cells, we found that the maturation of these two small viral RNAs contributed significantly to the infection associated lung inflammation, mainly via the activation of the CXCL8, CXCL11 and type I interferon signaling pathway. Taken together, we discovered two SARS-CoV-2-Encoded small RNAs and investigated the pro-inflammatory effects during their maturation in human lung epithelial cells, which might provide new insight into the pathogenesis and possible treatment options for COVID-19.

category: microbiology


title: A close-to-native structure of the synaptonemal complex

abstract: Genetic variability in sexually reproducing organisms results from an exchange of genetic material between homologous chromosomes. The genetic exchange mechanism is dependent on the synaptonemal complex (SC), a protein structure localized between the homologous chromosomes. Current structural models of the SC are based on electron microscopy, super resolution, and expansion microscopy studies using chemical fixatives and sample dehydration of gonads, which are methodologies known to produce structural artifacts. We have developed a novel electron microscopy sample-preparation approach where pachytene cells are isolated from mouse testis by FACS, followed by cryo-fixation and cryo-substitution to achieve visualization of a close-to-native structure of the SC. We found that the central region of the SC was wider than previously recognized, and the transverse filaments more densely packed in the central region. Furthermore, we identified a structure nucleating the central element of the SC.

category: cell biology


title: SARS-CoV-2 convergent evolution cannot be reliably inferred from phylogenetic analyses

abstract: A homoplasy is a trait shared between individuals that did not arise in a common ancestor, but rather is the result of convergent evolution. SARS-CoV-2 homoplasic mutations are important to characterise, because the evidence for a mutation conferring a fitness advantage is strengthened if this mutation has evolved independently and repeatedly in separate viral lineages. Yet detecting homoplasy is difficult due to insufficient variation between sequences to construct reliable phylogenetic trees. Here, we develop a method to more robustly identify confident homoplasies. We derive a maximum likelihood (ML) tree, with taxa bearing seemingly recurrent mutations dispersed across the tree, and then, for each potentially homoplasic mutation, we derive an alternative tree where the same taxa are constrained to one clade such that the mutation is no longer homoplasic. We then compare how well the two trees fit the sequence data. Applying this method to SARS-CoV-2 yields only a few instances where the constrained trees have significantly less statistical support than unconstrained tree, suggesting phylogenetics can provide limited support for homoplasy in SARS-CoV-2 and that caution is needed when inferring evidence of convergent evolution from phylogenetic methods in the absence of evidence from other sources.

category: evolutionary biology


title: Global mapping of RNA homodimers in living cells

abstract: RNA homodimerization is important for various physiological processes, including the assembly of membraneless organelles, RNA subcellular localization, and packaging of viral genomes. However, understanding of RNA homodimerization has been hampered by the lack of systematic in vivo detection methods. Here we show that PARIS, COMRADES, and other RNA proximity ligation methods can detect RNA homodimers transcriptome-wide as "overlapping" chimeric reads that contain more than one copy of the same sequence. Analysing published proximity ligation datasets, we show that RNA:RNA homodimers mediated by direct base-pairing interactions are rare across the transcriptome, but highly enriched in specific transcripts, including U8 snoRNA, U2 snRNA and a subset of tRNAs. Analysis of data from virus-infected cells reveals homodimerization of SARS-CoV-2 and Zika genomes, mediated by specific palindromic sequences located within protein-coding regions of N protein in SARS-CoV-2 and NS2A gene in Zika. We speculate that regions of viral genomes involved in homodimerization may constitute effective targets for antiviral therapies.

category: systems biology


title: LSD flattens the brain's energy landscape: evidence from receptor-informed network control theory

abstract:
Psychedelics like lysergic acid diethylamide (LSD) and psilocybin offer a powerful window into the function of the human brain and mind, by temporarily altering subjective experience through their neurochemical effects. A recent model postulates that serotonin 2a (5-HT2a) receptor agonism allows the brain to explore its dynamic landscape more readily, as reflected by more diverse (entropic) brain activity. We postulate that this increase in entropy may arise in part from a flattening of the brains control energy landscape, which can be observed using network control theory to quantify the energy required to transition between recurrent brain states measured using functional magnetic resonance imaging (fMRI) in individuals under LSD, psilocybin, and placebo conditions. We show that LSD and psilocybin reduce the amount of control energy required for brain state transitions, and, furthermore, that, across individuals, LSDs reduction in control energy correlates with more frequent state transitions and increased entropy of brain state dynamics. Through network control analysis that incorporates the spatial distribution of 5-HT2a receptors from publicly available (non-drug) positron emission tomography (PET) maps, we demonstrate the specific role of this receptor in reducing control energy. Our findings provide evidence that 5-HT2a receptor agonist compounds allow for more facile state transitions and more temporally diverse brain activity. More broadly, by combining receptor-informed network control theory with pharmacological modulation, our work highlights the potential of this approach in studying the impacts of targeted neuropharmacological manipulation on brain activity dynamics.

Significance StatementWe present a multi-modal framework for quantifying the effects of two psychedelic drugs (LSD and psilocybin) on brain dynamics by combining functional magnetic resonance imaging (fMRI), diffusion MRI (dMRI), positron emission tomography (PET) and network control theory. Our findings provide evidence that psychedelics flatten the brains control energy landscape, allowing for more facile state transitions and more temporally diverse brain activity. We also demonstrate that the spatial distribution of serotonin 2a receptors - the main target of LSD and psilocybin - is optimized for generating these effects. This approach could be used to understand how drugs act on different receptors in the brain to influence brain activity dynamics.

category: neuroscience


title: Psychedelics flatten the brain's energy landscape: evidence from receptor-informed network control theory


title: LSD and psilocybin flatten the brain's energy landscape: insights from receptor-informed network control theory


title: Broad neutralization against SARS-CoV-2 variants induced by a modified B.1.351 protein-based COVID-19 vaccine candidate

abstract: Beginning in late 2020, the emergence and spread of multiple variant SARS-CoV-2 strains harboring mutations which may enable immune escape necessitates the rapid evaluation of second generation COVID-19 vaccines, with the goal of inducing optimized immune responses that are broadly protective. Here we demonstrate in a mouse immunogenicity study that two doses of a modified B.1.351 spike (S)-Trimer vaccine (B.1.351 S-Trimer) candidate can induce strong humoral immune responses that can broadly neutralize both the original SARS-CoV-2 strain (Wuhan-Hu-1) and Variants of Concern (VOCs), including the UK variant (B.1.1.7), South African variant (B.1.351) and Brazil variant (P.1). Furthermore, while immunization with two doses (prime-boost) of Prototype S-Trimer vaccine (based on the original SARS-CoV-2 strain) induced lower levels of cross-reactive neutralization against the B.1.351 variant, a third dose (booster) administered with either Prototype S-Trimer or B.1.351 S-Trimer was able to increase neutralizing antibody titers against B.1.351 to levels comparable to neutralizing antibody titers against the original strain elicited by two doses of Prototype S-Trimer.

category: immunology


title: Structure-based design of stabilized recombinant influenza neuraminidase tetramers

abstract: Influenza virus neuraminidase (NA) is a major antiviral drug target and has recently reemerged as a key target of antibody-mediated protective immunity. Here we show that recombinant NAs across all non-bat subtypes adopt various tetrameric conformations, including a previously unreported "open" state that may help explain poorly understood variations in NA stability across viral strains and subtypes. We used homology-directed protein design to uncover the structural principles underlying these distinct tetrameric conformations and stabilize multiple recombinant NAs in the "closed" state. In addition to improving thermal stability, conformational stabilization improved affinity to protective antibodies elicited by viral infection, including antibodies targeting a quaternary epitope and the broadly conserved catalytic site. The stabilized NA proteins can also be integrated into viruses without affecting fitness. Our findings provide a deeper understanding of NA structure, stability, and antigenicity, as well as a roadmap towards structure-based discovery of NA-directed therapeutics and vaccines.


title: Moxidectin and ivermectin inhibit SARS-CoV-2 replication in Vero E6 cells but not in human primary airway epithelium cells

abstract: Antiviral therapies are urgently needed to treat and limit the development of severe COVID-19 disease. Ivermectin, a broad-spectrum anti-parasitic agent, has been shown to have anti-SARS-CoV-2 activity in Vero cells at a concentration of 5 {micro}M. These in vitro results triggered the investigation of ivermectin as a treatment option to alleviate COVID-19 disease. In April 2021, the World Health Organization stated, however, the following: "the current evidence on the use of ivermectin to treat COVID-19 patients is inconclusive". It is speculated that the in vivo concentration of ivermectin is too low to exert a strong antiviral effect. Here, we performed a head-to head comparison of the antiviral activity of ivermectin and a structurally related, but metabolically more stable, moxidectin in multiple in vitro models of SARS-CoV-2 infection, including physiologically relevant human respiratory epithelial cells. Both moxidectin and ivermectin exhibited antiviral activity in Vero E6 cells. Subsequent experiments revealed that the compounds predominantly act on a step after virus cell entry. Surprisingly, however, in human airway-derived cell models, moxidectin and ivermectin failed to inhibit SARS-CoV-2 infection, even at a concentration of 10 {micro}M. These disappointing results calls for a word of caution in the interpretation of anti-SARS-CoV-2 activity of drugs solely based on Vero cells. Altogether, these findings suggest that, even by using a high-dose regimen of ivermectin or switching to another drug in the same class are unlikely to be useful for treatment against SARS-CoV-2 in humans.


title: Glucose-dependent miR-125b is a negative regulator of β-cell function

abstract:
Impaired pancreatic {beta}-cell function and insulin secretion are hallmarks of type 2 diabetes. MicroRNAs are short non-coding RNAs that silence gene expression, vital for the development and function of {beta}-cells. We have previously shown that {beta}-cell specific deletion of the important energy sensor AMP-activated protein kinase (AMPK) results in increased miR-125b-5p levels. Nevertheless, the function of this miRNA in {beta}-cells is unclear. We hypothesized that miR-125b-5p expression is regulated by glucose and that this miRNA mediates some of the deleterious effects of hyperglycaemia in {beta}-cells. Here we show that islet miR-125b-5p expression is up-regulated by glucose in an AMPK-dependent manner and that short-term miR-125b-5p overexpression impairs glucose stimulated insulin secretion (GSIS) in the mouse insulinoma MIN6 cells and in human islets. An unbiased high-throughput screen in MIN6 cells identified multiple miR-125b-5p targets, including the transporter of lysosomal hydrolases M6pr and the mitochondrial fission regulator Mtfp1. Inactivation of miR-125b-5p in the human {beta}-cell line EndoC{beta}-H1 shortened mitochondria and enhanced GSIS, whilst mice overexpressing miR-125b-5p selectively in {beta}-cells (MIR125B-Tg) were hyperglycaemic and glucose intolerant. MIR125B-Tg {beta}-cells contained enlarged lysosomal structures and showed reduced insulin content and secretion. Collectively, we identify miR-125b as a glucose-controlled regulator of organelle dynamics that modulates insulin secretion.

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category: molecular biology


title: High level production and characterization of truncated human angiotensin converting enzyme 2 in Nicotiana benthamiana plant as a potential therapeutic target in COVID-19

abstract: The COVID-19 pandemic, which is caused by SARS-CoV-2 has rapidly spread to more than 222 countries and has put global public health at high risk. The world urgently needs safe, a cost-effective SARS-CoV-2 coronavirus vaccine, therapeutic and antiviral drugs to combat the COVID-19. Angiotensin-converting enzyme 2 (ACE2), as a key receptor for SARS-CoV-2 infections, has been proposed as a potential therapeutic target in COVID-19 patients. In this study, we report high level production (about [~]0.75 g /kg leaf biomass) of glycosylated and non-glycosylated forms of recombinant human truncated ACE2 in Nicotiana benthamiana plant. The plant produced recombinant human truncated ACE2s successfully bind to the SARC-CoV-2 spike protein, but deglycosylated ACE2 binds more strongly than the glycosylated counterpart. Importantly, both deglycosylated and glycosylated forms of AEC2 stable at elevated temperatures for prolonged periods and demonstrated strong anti-SARS-CoV-2 activity in vitro. The IC50 values of glycosylated and deglycosylated AEC2 were 0.4 and 24 g/ml, respectively, for the pre-entry infection, when incubated with 100TCID50 of SARS-CoV-2. Thus, plant produced truncated ACE2s are promising cost-effective and safe candidate as a potential therapeutic targets in the treatment of COVID-19 patients.

category: bioengineering


title: Drug-induced colorectal cancer persister cells show increased mutation rate

abstract: Compelling evidence shows that cancer persister cells limit the efficacy of targeted therapies. However, it is unclear whether persister cells are induced by anticancer drugs, and if their mutation rate quantitatively increases during treatment. Here, combining experimental characterization and mathematical modeling, we show that, in colorectal cancer, persisters are induced by drug treatment and show a 7- to 50-fold increase of mutation rate when exposed to clinically approved targeted therapies. These findings reveal that treatment may influence persistence and mutability in cancer cells and pinpoints new strategies to restrict tumor recurrence.

category: cancer biology


title: Interleukin-6 mediates PSAT1 expression and serine metabolism in TSC2-deficient cells

abstract:
Tuberous sclerosis complex (TSC) and lymphangioleiomyomatosis (LAM) are caused by aberrant mechanistic Target of Rapamycin Complex 1 (mTORC1) activation due to loss of either TSC1 or TSC2. Cytokine profiling of TSC2-deficient LAM patient-derived cells revealed striking upregulation of Interleukin-6 (IL-6). LAM patient plasma contained increased circulating IL-6 compared with healthy controls, and TSC2-deficient cells showed upregulation of IL-6 transcription and secretion compared to wildtype cells. IL-6 blockade repressed the proliferation and migration of TSC2-deficient cells and reduced oxygen consumption and extracellular acidification. U-13C glucose tracing revealed that IL-6 knockout reduced 3-phosphoserine and serine production in TSC2-deficient cells, implicating IL-6 in de novo serine metabolism. IL-6 knockout reduced expression of phosphoserine aminotransferase 1 (PSAT1), an essential enzyme in serine biosynthesis. Importantly, recombinant IL-6 treatment rescued PSAT1 expression in the TSC2-deficient, IL-6 knockout clones selectively and had no effect on wildtype cells. Treatment with anti-IL-6 (aIL-6) antibody similarly reduced cell proliferation and migration and reduced renal tumors in Tsc2+/- mice, while reducing PSAT1 expression. These data reveal a novel mechanism through which IL-6 regulates serine biosynthesis, with potential relevance to the therapy of tumors with mTORC1 hyperactivity.

ClassificationMajor category: Biological Sciences Minor category: Cell Biology

category: pathology


title: Deceleration of cell cycle underpins a switch from proliferative- to terminal division in plant stomatal lineage

abstract: Differentiation of specialized cell types from self-renewing progenitors requires precise cell cycle control. Plant stomata are generated through asymmetric divisions of a stem-cell-like precursor meristemoid followed by the single symmetric division that creates an adjustable pore surrounded by paired guard cells. The stomatal-lineage-specific transcription factor MUTE terminates the asymmetric divisions and triggers differentiation. However, the role of cell cycle machinery in this transition remains unknown. Through time-lapse imaging, we discover that the symmetric division is slower than the asymmetric division. We identify a plant-specific cyclin-dependent kinase inhibitor, SIAMESE-RELATED4 (SMR4), as a molecular brake that decelerates cell cycle during this transition. SMR4 is directly induced by MUTE and transiently accumulates in differentiating meristemoids. SMR4 physically and functionally associates with CYCD3;1 and extends G1-phase of asymmetric divisions. By contrast, SMR4 fails to interact with CYCD5;1, a MUTE-induced G1 cyclin, and permits the symmetric division. Our work unravels a molecular framework of the proliferation-to-differentiation switch within the stomatal lineage and suggests that a timely proliferative cell cycle is critical for the stomatal fate specification.

category: plant biology


title: "How do we do this at a distance?!" A descriptive study of remote undergraduate research programs during COVID-19

abstract: The COVID-19 pandemic shut down undergraduate research programs across the U.S. Twenty-three sites offered remote undergraduate research programs in the life sciences during summer 2020. Given the unprecedented offering of remote research experiences, we carried out a study to describe and evaluate these programs. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from the perspectives of participating students. Strengths included the quality of mentorship, opportunities for learning and professional development, and development of a sense of community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote REUs that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.

category: scientific communication and education


title: Synaptic targets of functionally specialized R7 and R8 photoreceptors in the central eye and dorsal rim area of Drosophila

abstract: Color and polarization provide complementary information about the world and are detected by specialized photoreceptors. However, the downstream neural circuits that process these distinct modalities are incompletely understood in any animal. Using electron microscopy, we have systematically reconstructed the synaptic targets of the photoreceptors specialized to detect color and skylight polarization in Drosophila, and we have used light microscopy to confirm many of our findings. We identified known and novel downstream targets that are selective for different wavelengths or polarized light, and followed their projections to other areas in the optic lobes and the central brain. Our results revealed many synapses along the photoreceptor axons between brain regions, new pathways in the optic lobes, and spatially segregated projections to central brain regions. Strikingly, photoreceptors in the polarization-sensitive dorsal rim area target fewer cell types, and lack strong connections to the lobula, a neuropil involved in color processing. Our reconstruction identifies shared wiring and modality-specific specializations for color and polarization vision, and provides a comprehensive view of the first steps of the pathways processing color and polarized light inputs.


title: Synaptic targets of photoreceptors specialized to detect color and skylight polarization in Drosophila


title: In mice and humans, the brain's blood vessels mature postnatally to acquire barrier and contractile properties

abstract: The brain dense vascular network is essential for distributing oxygen and nutrients to neural cells. The network develops during embryogenesis and leads to the formation of the endothelial blood-brain barrier (BBB). This barrier is surrounded by mural cells (pericytes and vascular smooth muscle cells (VSMCs)) and fibroblasts. Here, we compared the molecular and functional properties of brain vascular cells on postnatal day (P)5 vs. P15, via a transcriptomic analysis of purified mouse cortical microvessels (MVs) and the identification of vascular-cell-type-specific or -preferentially expressed transcripts. We found that endothelial cells (ECs), VSMCs and fibroblasts follow specific molecular maturation programs over this time period. In particular, ECs acquire P-glycoprotein (P-gP)-mediated efflux capacities. The arterial VSMC network expands, acquires contractile proteins (such as smooth muscle actin (SMA) and myosin heavy chain 11 (Myh11)) and becomes contractile. We also analyzed samples of human brain cortex from the early prenatal stage through to adulthood: the expression of endothelial P-gP increased at birth and Myh11 in VSMCs acts as a developmental switch (as in the mouse) at birth and up to the age of 2 of 5 years. Thus, in both mice and humans, the early postnatal phase is a critical period during which the essential properties of cerebral blood vessels (i.e. the endothelial efflux of xenobiotics and other molecules, and the VSMC contractility required for vessel tone and brain perfusion) are acquired and mature.


title: Targeted redesign of suramin analogs for novel antimicrobial lead development

abstract:
The emergence of new viral infections and drug resistant bacteria urgently necessitates expedient therapeutic development. Repurposing and redesign of existing drugs against different targets is one potential way in which to accelerate this process. Suramin was initially developed as a successful anti-parasitic drug but has also shown promising antiviral and antibacterial activities. However, due to its high conformational flexibility and negative charge, suramin is considered quite promiscuous towards positively charged sites within nucleic acid binding proteins. Although some suramin analogs have been developed against specific targets, only limited structure activity relationship (SAR) studies were performed, and virtual screening has yet to be used to identify more specific inhibitor(s) based on its scaffold. Using available structures, we investigated suramins target diversity, confirming that suramin preferentially binds to protein pockets which are both positively charged and enriched in aromatic or leucine residues. Further, suramins high conformational flexibility allows adaptation to structurally diverse binding surfaces. From this platform, we developed a framework for structure- and docking-guided elaboration of suramin analog scaffolds using virtual screening of suramin and heparin analogs against a panel of diverse therapeutically relevant viral and bacterial protein targets. Use of this new framework to design potentially specific suramin analogs is exemplified using the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and nucleocapsid protein, identifying leads that might inhibit a wide range of coronaviruses. The approach presented here establishes a computational framework for designing suramin analogs against different bacterial and viral targets and repurposing existing drugs for more specific inhibitory activity.

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title: uniForest: an unsupervised machine learning technique to detect outliers and restrict variance in microbiome studies

abstract:
Isolation Forests is an unsupervised machine learning technique for detecting outliers in continuous datasets that does not require an underlying equivariant or Gaussian distribution and is suitable for use on small datasets. While this procedure is widely used across quantitative fields, to our knowledge, this is the first attempt to solely assess its use for microbiome datasets. Here we present uniForest, an interactive Python notebook (which can be run from any desktop computer using the Google Colaboratory web service) for the processing of microbiome outliers. We used uniForest to apply Isolation Forests to the Healthy Human Microbiome project dataset and imputed outliers with the mean of the remaining inliers to maintain sample size and assessed its prowess in variance reduction in both community structure and derived ecological statistics (-diversity). We also assessed its functionality in anatomical site differentiation (pre- and postprocessing) using principal component analysis, dissimilarity matrices, and ANOSIM. We observed a minimum variance reduction of 81.17% across the entire dataset and in alpha diversity at the Phylum level. Application of Isolation Forests also separated the dataset to an extremely high specificity, reducing variance within taxa samples by a minimum of 81.33%.

It is evident that Isolation Forests are a potent tool in restricting the effect of variance in microbiome analysis and has potential for broad application in studies where high levels of microbiome variance is expected. This software allows for clean analyses of otherwise noisy datasets.


title: MiR-135-5p alleviates bone cancer pain by regulating astrocyte-mediated neuroinflammation in spinal cord through JAK2/STAT3 signaling pathway

abstract: Bone cancer pain (BCP) was associated with microRNA dysregulation. In this study, we intended to clarify the potential role of miR-135-5p in a BCP mouse model, which was established by tumor cell implantation (TCI) in the medullary cavity of the mouse femur. The BCP related behaviors were tested, including the paw withdrawal mechanical threshold (PWMT) and number of spontaneous flinches (NSF). The miRNA expression profiles in astrocytes of the sham and tumor groups were compared, and miRNA microarray and quantitative real-time PCR (qRT-PCR) assays confirmed that the amount of expression of miR-135-5p was significantly decreased in astrocytes of the tumor group. Gain- and loss-of-function studies showed that miR-135-5p could inhibit astrocytes activation and inflammation cytokines (TNF- and IL-1{beta}) expression. The relation between miR-135-5p and JAK2 was detected by bioinformatic analysis and dual luciferase reporter gene assay. By conducting in vitro experiments, it was shown that the miR-135-5P mimics lowered the level of JAK2/STAT3 proteins and inflammatory factors in astrocytes. Moreover, in vivo analysis on BCP mice model indicated that the miR-135-5p agonist could sufficiently increase PWMT and decrease NSF. Meanwhile, reduced activation of astrocytes in the spinal cord, as well as decreased expression of JAK2/STAT3 and inflammatory mediators, were found after miR-135-5p agonist treatment. Collectively, the results showed that miR-135-5p could potentially reduce BCP in mice through inhibiting astrocyte-mediated neuroinflammation and blocking of the JAK2/STAT3 signaling pathway, indicating that the upregulation of miR-135-5P could be a therapeutic focus in BCP treatment.


title: Complexities in the role of acetylation dynamics in modifying inducible gene activation parameters

abstract: High levels of histone acetylation are associated with the regulatory elements of active genes, suggesting a link between acetylation and gene activation. However, several studies have shown that histone acetylation dynamics rather than hyperacetylation per se are important determinants in gene activation, particularly at inducible genes. We revisited this model, in the context of EGF-inducible gene expression and found that rather than a simple unifying model, there are two broad classes of genes; one in which high lysine acetylation activity is required for efficient gene activation, and a second group where the opposite occurs and high acetylation activity is inhibitory. We examined the latter class in more detail using EGR2 as a model gene and found that lysine acetylation levels are critical for several activation parameters, including the timing of expression onset, and overall amplitudes of the transcriptional response. In contrast, DUSP1 responds in the canonical manner and its transcriptional activity is promoted by acetylation. Single cell approaches demonstrate heterogenous DUSP1 activation kinetics and that acetylation levels influence allele activation frequencies. Our data therefore point to a complex interplay between acetylation dynamics and target gene induction, which cannot simply be explained by a unified response to acetylation activity. Instead, acetylation level thresholds are an important determinant of transcriptional induction dynamics that are sensed in a gene-specific manner.


title: CoREST has a conserved role in facilitating SPR-5/LSD1 maternal reprogramming of histone methylation

abstract: Maternal reprogramming of histone methylation is critical for reestablishing totipotency in the zygote, but how histone modifying enzymes are regulated during maternal reprogramming is not well characterized. To address this gap, we asked whether maternal reprogramming by the H3K4me1/2 demethylase SPR-5/LSD1/KDM1A, is regulated by the co-repressor protein, SPR-1/CoREST in C. elegans and mice. In C. elegans, SPR-5 functions as part of a reprogramming switch together with the H3K9 methyltransferase MET-2. By examining germline development, fertility and gene expression in double mutants between spr-1 and met-2, we find that spr-1 mutants are partially compromised for spr-5; met-2 reprogramming. In mice, we generated a separation of function Lsd1 M448V point mutation that compromises CoREST binding, but only slightly affects LSD1 demethylase activity. When maternal LSD1 in the oocyte is derived exclusively from this allele, the progeny phenocopy the increased perinatal lethality that we previously observed when LSD1 was reduced maternally. Together, these data are consistent with CoREST having a conserved function in facilitating maternal LSD1 epigenetic reprogramming.

category: developmental biology


title: Characterization of mouse Bmp5 regulatory injury element in zebrafish wound models

abstract: Many key signaling molecules used to build tissues during embryonic development are re-activated at injury sites to stimulate tissue regeneration and repair. Bone morphogenetic proteins provide a classic example, but the mechanisms that lead to reactivation of BMPs following injury are still unknown. Previous studies have mapped a large "injury response element" (IRE) in the mouse Bmp5 gene that drives gene expression following bone fractures and other types of injury. Here we show that the large mouse IRE region is also activated in both zebrafish tail resection and mechanosensory hair cell injury models. Using the ability to test multiple constructs and image temporal and spatial dynamics following injury responses, we have narrowed the original size of the mouse IRE region by over 100 fold and identified a small 142 bp minimal enhancer that is rapidly induced in both mesenchymal and epithelial tissues after injury. These studies identify a small sequence that responds to evolutionarily conserved local signals in wounded tissues and suggest candidate pathways that contribute to BMP reactivation after injury.


title: A deleterious mutation-sheltering theory for the evolution of sex chromosomes and supergenes

abstract: Many organisms have sex chromosomes with large non-recombining regions that have expanded stepwise, generating "evolutionary strata" of differentiation. The reasons for this remain poorly understood, but the principal hypotheses proposed to date are based on antagonistic selection due to differences between sexes. However, it has proved difficult to obtain empirical evidence of a role for sexually antagonistic selection in extending recombination suppression, and antagonistic selection has been shown to be unlikely to account for the evolutionary strata observed on fungal mating-type chromosomes. There may, therefore, be other mechanisms involved in the extension of non-recombining regions. We show here, by mathematical modeling and stochastic simulation, that recombination suppression on sex chromosomes and around supergenes can expand in a stepwise manner under a wide range of parameter values simply because it shelters recessive deleterious mutations, which are ubiquitous in genomes. Permanently heterozygous alleles, such as the maledetermining allele in XY systems, protect linked chromosomal inversions against the expression of their recessive mutation load, leading to the successive accumulation of inversions around these alleles without the need for antagonistic selection. Similar results were obtained with models assuming recombination-suppressing mechanisms other than chromosomal inversions, and for supergenes other than sex chromosomes, including those without XY-like asymmetry, such as fungal mating-type chromosomes. However, inversions capturing a permanently heterozygous allele were found to be less likely to spread when the mutation load was lower (e.g. under conditions of large effective population size, low mutation rates and high dominance coefficients). This may explain why sex chromosomes remain homomorphic in some organisms but are highly divergent in others. Here, we explicitly state and model a simple and testable hypothesis explaining the existence of stepwise extensions of recombination suppression on sex chromosomes, which can also be applied to mating-type chromosomes and supergenes in general.


title: Modeling the stepwise extension of recombination suppression on sex chromosomes and other supergenes through deleterious mutation sheltering


title: Runaway evolution from male-male competition

abstract: Wondrously elaborate weapons and displays that appear to be counter to ecological optima are widespread features of male contests for mates across the animal kingdom. To understand how such diverse traits evolve, here we develop a quantitative genetic model of sexual selection for a male signaling trait that mediates aggression in male-male contests and show that an honest indicator of aggression can generate selection on itself by altering the social environment. This can cause selection to accelerate as the trait is elaborated, leading to runaway evolution. Thus, an evolving source of selection provided by the social environment is the fundamental unifying feature of runaway sexual selection driven by either male-male competition or female mate choice. However, a key difference is that runaway driven by male-male competition requires signal honesty. Our model identifies simple conditions that provide clear, testable predictions for empirical studies using standard quantitative genetic methods.


title: SMCHD1 variants may induce variegated expression in Facio Scapulo Humeral Dystophy and Bosma Arhinia and microphtalmia syndrome

abstract: An expanding number of genetic syndromes are linked to mutations in genes encoding factors that guide chromatin organization. Recently, distinct genetic syndromes have been linked to mutations in the SMCHD1 gene. However, the function of this non-canonical SMC protein remains partly defined in Human tissues. To address this question, we determined its epi-signature in type 2 Facio Scapulo Humeral Dystrophy (FSHD2) and Bosma Arhinia and Microphtalmia Syndrome (BAMS) linked to heterozygous mutations in this gene. By combining RNA-Seq, DNA methylation profiling and ChIP-Seq, we showed that SMCHD1 regulates repressed chromatin but also cis-regulatory elements and enhancers. Our results emphasize dual functions for SMCHD1, in chromatin compaction, chromatin insulation and gene regulation with variable outcomes and targets depending on tissues. We propose that altered DNA methylation and long-range chromatin organization at a number of loci required for development and tissue differentiation, trigger variegated gene expression in rare genetic diseases linked to heterozygous SMCHD1 mutations.

category: genetics


title: K-mer based prediction of Clostridioides difficile relatedness and ribotypes

abstract:
Comparative analysis of Clostridioides difficile whole-genome sequencing (WGS) data enables fine scaled investigation of transmission and is increasingly becoming part of routine surveillance. However, these analyses are constrained by the computational requirements of the large volumes of data involved. By decomposing WGS reads or assemblies into k-mers and using the dimensionality reduction technique MinHash, it is possible to rapidly approximate genomic distances without alignment. Here we assessed the performance of MinHash, as implemented by sourmash, in predicting single nucleotide differences between genomes (SNPs) and C. difficile ribotypes (RTs). For a set of 1,905 diverse C. difficile genomes (differing by 0-168,519 SNPs), using sourmash to screen for closely related genomes, at a sensitivity of 100% for pairs [≤]10 SNPs, sourmash reduced the number of pairs from 1,813,560 overall to 161,934, i.e., by 91%, with a positive predictive value of 32% to correctly identify pairs [≤]10 SNPs (maximum SNP distance 4,144). At a sensitivity of 95%, pairs were reduced by 94% to 108,266 and PPV increased to 45% (maximum SNP distance 1,009). Increasing the MinHash sketch size above 2000 produced minimal performance improvement. We also explored a MinHash similarity-based ribotype prediction method. Genomes with known ribotypes (n=3,937) were split into a training set (2,937) and test set (1,000) randomly. The training set was used to construct a sourmash index against which genomes from the test set were compared. If the closest 5 genomes in the index had the same ribotype this was taken to predict the searched genomes ribotype. Using our MinHash ribotype index, predicted ribotypes were correct in 780/1000 (78%) genomes, incorrect in 20 (2%), and indeterminant in 200 (20%). Relaxing the classifier to 4/5 closest matches with the same RT improved the correct predictions to 87%. Using MinHash it is possible to subsample C. difficile genome k-mer hashes and use them to approximate small genomic differences within minutes, significantly reducing the search space for further analysis.

Impact statementThe genetic code, or DNA, of bacteria is increasingly used to track how infection spreads and to guide infection control interventions, as similar or identical DNA sequences are expected in samples from pair of individuals related by transmission. While obtaining the DNA sequence for bacteria is increasingly straightforward, comparing thousands or even millions of sequences requires substantial computing power and time using current approaches. Here we describe how a method for summarising sequencing data, MinHash, can be used to rapidly reduce the number of possible close sequence matches in Clostridioides difficile, an important healthcare-associated pathogen. It can also be used to approximate traditional schemes used to classify C. difficile into smaller subgroups in transmission analyses, such as ribotyping.

Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

category: genomics


title: Bexarotene derivatives modify responses in acute myeloid leukemia

abstract: The retinoids all-trans retinoic acid (ATRA) and bexarotene are active in acute myeloid leukemia (AML), but responses beyond acute promyelocytic leukemia (APL) have been more modest than APL responses. To determine whether chemical modification of bexarotene might augment retinoid responses in AML, we screened a series of 38 bexarotene derivatives for activity in a mouse MLL-AF9 leukemia cell line, which exhibits strong synergistic sensitivity to the combination of ATRA and bexarotene. We found that RXRA potency correlated with anti-leukemic activity and that only one compound (103-4) with dual RARA/RXRA activity was capable of ATRA-independent anti-leukemic activity. We evaluated bioisostere and cyclohexane modifications for potential resistance to P450 metabolism and found that bioisosteres reduced potency and that bezopyran, cyclopentane, and cyclohexene modifications only modestly reduced susceptibility to metabolism. Collectively, these studies provide a map of the structure-activity relationships of bexarotene with outcomes related to RXRA and RARA activity, corepressor binding, compound stability, and anti-leukemic potential.


title: Nicotinic acetylcholine receptor partial antagonist polyamides from tunicates and their predatory sea slugs

abstract: In our efforts to discover new drugs to treat pain, we identified molleamines A-E (1-5) as major neuroactive components of the sea slug, Pleurobranchus forskalii and their prey, Didemnum molle tunicates. The chemical structures of molleamines were elucidated by spectroscopy and confirmed by the total synthesis of molleamines A (1) and C (3). Synthetic 3 completely blocked acetylcholine-induced calcium flux in peptidergic nociceptors (PNs) in the somatosensory nervous system. Compound 3 affected neither the 7 nAChR nor the muscarinic acetylcholine receptors in calcium flux assays. In addition to nociceptors, 3 partially blocked the acetylcholine-induced calcium flux in the sympathetic nervous system, including neurons from the superior cervical ganglion. Electrophysiology revealed a block of 3{beta}4 (mouse) and 6/3{beta}4 (rat) nicotinic acetylcholine receptors (nAChRs), with IC50 values of 1.4 and 3.1 {micro}M, respectively. Molleamine C (3) is a partial antagonist, reaching a maximum block of 76-82% of the acetylcholine signal and showing no partial agonist response. Molleamine C (3) may thus provide a lead compound for the development of neuroactive compounds with unique biological properties.


title: New strategy to select cross-reactivity Meningococci strains: immunization with Outer membrane vesicles of serogroup C and cationic lipid as adjuvant

abstract:
BackgroundInvasive meningococcal disease (IMD), caused by Neisseria meningitidis, is a public health problem, associated with high levels of morbidity and mortality, capable of causing outbreaks or epidemics, but preventable through vaccination. In Brazil, the main serogroups isolated are C and B. The last epidemic occurred in the  80s, in Sao Paulo, because of a B:4:P1.15 strain.

MethodsAdult Swiss mice were immunized with outer membrane vesicles (OMV) of N. meningitidis strain C:4:P1.15, adjuvanted by the cationic lipid dioctadecyldimethylammonium bromide in bilayer fragments (DDA-BF), administered via prime-booster (intranasal/subcutaneous) scheme. The humoral response was accessed by Immunoblotting and ELISA, using homologous immunization strain and a different serogroup but equal serosubtype strain, N. meningitidis B:4:P1.15.

ResultsImmunoblotting revealed the recognition of antigens associated with the molecular weight of Porin A and Opacity proteins, which are immunogenic but highly heterogeneous, and Tbp and NspA, which are more homogeneous between meningococci strains. ELISA results showed antibody production that persisted after 190 days and recognized the C:4:P1.15 and the B:4:P1.15 strains, with high avidity index. The adjuvanted group recognized antigens following the IN prime and had a higher avidity index against the heterologous strain.

ConclusionsDDA-BF improved the humoral response, but the OMV alone induced high avidity index antibodies as well. Even though these are preliminary results, we see it as a promising approach for affordable meningococcal immunization in developing countries, at outbreak or epidemic situations.


title: Reduced calcium storage blunts calcium signaling in Toxoplasma bradyzoites and impedes motility and egress

abstract: Toxoplasma gondii has evolved different developmental stages for disseminating during acute infection (i.e. tachyzoites) and for establishing chronic infection (i.e. bradyzoites). Calcium ion (Ca2+) signaling tightly regulates the lytic cycle of tachyzoites by controlling microneme secretion and motility to drive egress and cell invasion. However, the roles of Ca2+ signaling pathways in bradyzoites remain largely unexplored. Here we show that Ca2+ responses are highly restricted in bradyzoites and that they fail to egress in response to agonists. Development of dual-reporter parasites revealed dampened calcium responses and minimal microneme secretion by bradyzoites induced in vitro or harvested from infected mice and tested ex vivo. Ratiometric Ca2+ imaging demonstrated lower Ca2+ basal levels, reduced magnitude, and slower Ca2+ kinetics in bradyzoites compared with tachyzoites stimulated with agonists. Diminished responses in bradyzoites were associated with down-regulation of calcium ATPases involved in intracellular Ca2+ storage in the endoplasmic reticulum (ER) and acidocalcisomes. Once liberated from cysts by trypsin digestion, bradyzoites incubated in glucose plus calcium rapidly restored their intracellular Ca2+ and ATP stores leading to enhanced gliding. Collectively, our findings indicate that intracellular bradyzoites exhibit dampened Ca2+ signaling and lower energy levels that restrict egress, and yet upon release they rapidly respond to changes in the environment to regain motility.


title: Toxoplasma bradyzoites exhibit physiological plasticity of calcium and energy stores controlling motility and egress.


title: Plastic mulches reduce adult and larval populations of Drosophila suzukii in fall-bearing raspberry

abstract: The invasive spotted-wing drosophila, Drosophila suzukii, is a major pest of fruit crops world-wide. Management of D. suzukii relies heavily on chemical control in both organic and conventional systems, and there is a need to develop more sustainable management practices. We evaluated the efficacy of three colors of plastic mulches at reducing populations of D. suzukii in fall-bearing raspberry and assessed the mulches impacts on canopy microclimate factors relevant to D. suzukii. Black, white, and metallic plastic mulches reduced adult D. suzukii populations by 42-51% and larval populations by 52-72% compared to the grower standard. The mulches did not change canopy temperature or relative humidity, but metallic mulches increased canopy light intensity compared to the black mulch. Radiance in the visible spectrum (401-680 nm) was higher for the white and metallic mulch plots, but the black mulch plots did not differ from the control. In the UV spectrum (380-400 nm), all three plastic mulches had higher radiance than the control plots. Future studies will determine whether changes in radiance are associated with the observed reduction in D. suzukii populations. Plastic mulches are a promising cultural practice for managing D. suzukii since they can reduce adult and larval populations and could be incorporated into an integrated pest management program in both organic and conventional systems.


title: BMP signaling underlies the craniofacial heterochrony in phyllostomid bats, a hyperdiverse mammal group

abstract: The potential for variation and the capacity to evolve in response to ecological opportunity are important aspects of an adaptive radiation. Identifying the origin of phenotypic variation, in which natural selection might act upon, is a major goal of evolutionary developmental biology. The New World leaf-nosed bats (phyllostomids) are a textbook example of an adaptive radiation. Their cranial morphology is diverse along relative facial length, which is related to their diets. We previously used geometric morphometrics to reveal peramorphosis, a type of heterochrony, in the cranial evolution among phyllostomid bats. We then demonstrated that the mechanism of peramorphic diversity in phyllostomid rostrum length resulted from altered cellular proliferation. Here, we investigate the progenitors of the face, the cranial neural crest, and a key signaling pathway related to their proliferation and differentiation into mature tissues: the bone morphogenetic protein (BMP). With geometric morphometrics, immunofluorescence, and confocal imaging--in three phyllostomid species and one outgroup bat species--we show the molecular patterns that underlie the adaptive and innovative traits seen in phyllostomid bats. Then, with mouse genetics, we mimic the BMP molecular pattern observed in nectar feeding bats and recapitulate the elongated morphological variation in mice. Surprisingly, we also observe an expansion in the nose-tip of mice, akin to the expanding leaf-nose tissue in phyllostomid bats. These data, combined with the mouse genetics literature on BMP signaling, suggest the BMP developmental pathway plays a central role in shaping the craniofacial variation necessary for adaptation in bats. Further, we speculate that the BMP signaling pathway could underlie other bizarre facial phenotypes in mammals that are derived from frontonasal mesenchyme, such as the proboscis. Overall, this study combines a comparative framework to developmental data, with a genetic approach, to directly investigate the role of development on complex morphology.


title: Retention dependences support highly confident identification of lipid species in human plasma by reversed-phase UHPLC/MS

abstract: Reversed-phase ultrahigh-performance liquid chromatography q mass spectrometry (RP-UHPLC/MS) method was developed with the aim to unambiguously identify a large number of lipid species from multiple lipid classes in human plasma. The optimized RP-UHPLC/MS method employed the C18 column with sub-2 m particles with the total run time of 25 min. The chromatographic resolution was investigated with 42 standards from 18 lipid classes. The UHPLC system was coupled to high-resolution quadrupole - time-of-flight (QTOF) mass analyzer using electrospray ionization (ESI) measuring full scan and tandem mass spectra (MS/MS) in positive- and negative-ion modes with high mass accuracy. Our identification approach was based on m/z values measured with mass accuracy within 5 ppm tolerance in the full scan mode, characteristic fragment ions in MS/MS, and regularity in chromatographic retention dependences for individual lipid species, which provides the highest level of confidence for reported identifications of lipid species including regioisomeric and other isobaric forms. The graphs of dependences of retention times on the carbon number or on the number of double bond(s) in fatty acyl chains were constructed to support the identification of lipid species in homologous lipid series. Our list of identified lipid species is also compared with previous publications investigating human blood samples by various MS based approaches. In total, we have reported more than 500 lipid species representing 26 polar and nonpolar lipid classes detected in NIST Standard reference material 1950 human plasma.

category: biochemistry


title: T2R bitter taste receptors regulate apoptosis and may be associated with survival in head and neck squamous cell carcinoma

abstract: Better management of head and neck squamous cell carcinomas (HNSCCs) requires a clearer understanding of tumor biology and disease risk. Bitter taste receptors (T2Rs) have been studied in several cancers, including thyroid, salivary, and GI, but their role in HNSCC has not been explored. We found that HNSCC patient samples and cell lines expressed functional T2Rs on both the cell and nuclear membranes. Bitter compounds, including bacterial metabolites, activated T2R-mediated nuclear Ca2+ responses leading to mitochondrial depolarization, caspase activation and ultimately apoptosis. Buffering nuclear Ca2+ elevation blocked caspase activation. Furthermore, increased expression of T2Rs in HNSCCs from The Cancer Genome Atlas (TCGA) is associated with improved overall survival. This work suggests that T2Rs are potential biomarkers to predict outcomes and guide treatment selection, may be leveraged as therapeutic targets to stimulate tumor apoptosis, and may mediate tumor-microbiome crosstalk in HNSCC.


title: A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus

abstract:
The thermophilic bacterium Rhodothermus marinus has mainly been studied for its thermostable enzymes. More recently, the potential of using the species as a cell factory and in biorefinery platforms has been explored, due to the elevated growth temperature, native production of compounds such as carotenoids and EPSs, the ability to grow on a wide range of carbon sources including polysaccharides, and available genetic tools. A comprehensive understanding of the metabolism of production organisms is crucial. Here, we report a genome-scale metabolic model of R. marinus DSM 4252T. Moreover, the genome of the genetically amenable R. marinus ISCaR-493 was sequenced and the analysis of the core genome indicated that the model could be used for both strains. Bioreactor growth data was obtained, used for constraining the model and the predicted and experimental growth rates were compared. The model correctly predicted the growth rates of both strains. During the reconstruction process, different aspects of the R. marinus metabolism were reviewed and subsequently, both cell densities and carotenoid production were investigated for strain ISCaR-493 under different growth conditions. Additionally, the dxs gene, which was not found in the R. marinus genomes, from Thermus thermophilus was cloned on a shuttle vector into strain ISCaR-493 resulting in a higher yield of carotenoids.

ImportanceA biorefinery converting biomass into fuels and value-added chemicals is a sustainable alternative to fossil fuel-based chemical synthesis. Rhodothermus marinus is a bacterium that is potentially well suited for biorefineries. It possesses various enzymes that degrade biomass, such as macroalgae and parts of plants (e.g. starch and xylan) and grows at high temperatures (55-77{degrees}C) which is beneficial in biorefinery processes. In this study, we reviewed the metabolism of R. marinus and constructed a metabolic model. Such a model can be used to predict phenotypes, e.g. growth under different environmental and genetic conditions. We focused specifically on metabolic features that are of interest in biotechnology, including carotenoid pigments which are used in many different industries. We described cultivations of R. marinus and the resulting carotenoid production in different growth conditions, which aids in understanding how carotenoid yields can be increased in the bacterium.


title: Flexibility-aware graph-based algorithm improves antigen epitopes identification

abstract:
Epitopes of an antigen are the surface residues in the spatial proximity that can be recognized by antibodies. Identifying such residues has shown promising potentiality in vaccine design, drug development and chemotherapy, thus attracting extensive endeavors. Although great efforts have been made, the epitope prediction performance is still unsatisfactory. One possible issue accounting to this poor performance could be the ignorance of structural flexibility of antigens. Flexibility is a natural characteristic of antigens, which has been widely reported. However, this property has never been used by existing models. To this end, we propose a novel flexibility-aware graph-based computational model to identify epitopes. Unlike existing graph-based approaches that take the static structures of antigens as input, we consider all possible variations of the side chains in graph construction. These flexibility-aware graphs, of which the edges are highly enriched, are further partitioned into subgraphs by using a graph clustering algorithm. These clusters are subsequently expanded into larger graphs for detecting overlapping residues between epitopes if exist. Finally, the expanded graphs are classified as epitopes or non-epitopes via a newly designed graph convolutional network. Experimental results show that our flexibility-aware model markedly outperforms existing approaches and promotes the F1-score to 0.656. Comparing to the state-of-the-art, our approach makes an increment of F1-score by 16.3%. Further in-depth analysis demonstrates that the flexibility-aware strategy contributes the most to the improvement. The source codes of the proposed model is freely available at https://github.com/lzhlab/epitope.

Author summaryEpitope prediction is helpful to many biomedical applications so that dozens of models have been proposed aiming at improving prediction efficiency and accuracy. However, the performances are still unsatisfactory due to its complicated nature, particularly the noteworthy flexible structures, which makes the precise prediction even more challenging. The existing approaches have overlooked the flexibility during model construction. To this end, we propose a graph model with flexibility heavily involved. Our model is mainly composed of three parts: i) flexibility-aware graph construction; ii) overlapping subgraph clustering; iii) graph convolutional network-based subgraph classification. Experimental results show that our newly proposed model markedly outperforms the existing best ones, making an increment of F1-score by 16.3%.

category: bioinformatics


title: Metacommunity analyses show increase in ecological specialisation throughout the Ediacaran

abstract: The first animals appear during the late Ediacaran (572 - 541 Ma); an initial diversity increase was followed by a drop, interpreted as catastrophic mass extinction. We investigate the processes underlying these changes using the "Elements of Metacommunity Structure" framework. The oldest metacommunity was characterized by taxa with wide environmental tolerances, and limited specialisation and inter-taxa interactions. Structuring increased in the middle metacommunity, with groups of taxa sharing synchronous responses to environmental gradients, aggregating into distinct communities. This pattern strengthened in the youngest metacommunity, with communities showing strong environmental segregation and depth structure. Thus, metacommunity structure increased in complexity, with increased specialisation and resulting competitive exclusion, not a catastrophic environmental disaster, leading to diversity loss in the terminal Ediacaran, revealing that the complex eco-evolutionary dynamics associated with Cambrian diversification were established in the Ediacaran.

category: paleontology


title: Skeletal Muscle Transcriptome Alterations Related to Physical Function Decline in Older Mice

abstract:
One inevitable consequence of aging is the gradual deterioration of physical function and exercise capacity, driven in part by the adverse effect of age on muscle tissue. Our primary purpose was to determine the relationship between patterns of gene expression in skeletal muscle and this loss of physical function. We hypothesized that some genes changing expression with age would correlate with functional decline, or conversely with preservation of function. Male C57BL/6 mice (6-months old, 6m, 24-months, 24m, and 28+-months, 28m; all n=8) were tested for physical ability using a comprehensive functional assessment battery (CFAB). CFAB is a composite scoring system comprised of five functional tests: rotarod (overall motor function), grip strength (fore-limb strength), inverted cling (4-limb strength/endurance), voluntary wheel running (activity rate/volitional exercise), and treadmill (endurance). We then extracted total RNA from the tibialis anterior muscle, analyzed with Next Generation Sequencing RNAseq to determine differential gene expression during aging, and compared these changes to physical function. Aging resulted in gene expression differences >[boxv]1.0[boxv] log2 fold change (multiple comparison adjusted p<0.05) in 219 genes in the 24m and in 6587 genes in the 28m. Linear regression with CFAB determined 253 differentially expressed genes strongly associated (R>0.70) with functional status in the 28m, and 22 genes in the 24m. We conclude that specific age-related transcriptomic changes are associated with declines in physical function, providing mechanistic clues. Future work will establish the underlying cellular mechanisms and the physiological relevance of these genes to age-related loss of physical function.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/444371v1_ufig1.gif" ALT="Figure 1">
View larger version (36K):
org.highwire.dtl.DTLVardef@ad7362org.highwire.dtl.DTLVardef@17267e7org.highwire.dtl.DTLVardef@38600org.highwire.dtl.DTLVardef@15283a7_HPS_FORMAT_FIGEXP  M_FIG C_FIG RNA sequencing of skeletal muscle from young and old mice were compared to physical function status obtained by performing a comprehensive functional assessment battery of tests. Between adulthood (6-months) and older age (28-months), 6707 genes were differentially expressed with 253 of these genes being significantly associated with physical function. Specific age-related changes to the skeletal muscle transcriptome are associated with a decline in physical function.

category: physiology


title: Relationships between acute race-induced changes in creatine kinase activity and blood plasma myoglobin concentration and race performance in mountain bike and road cyclists

abstract: The aim of this study was to determine if the changes in plasma creatine kinase (CK) activity and myoglobin (MB) concentrations as markers of muscle damage differ between competitive road (n = 14) and mountain bike (n = 11) cyclists and if these biochemical markers show a relationship with real-world race performance. CK and MB were measured from blood samples collected 2 hours before race start and 1 hour after race completion and the change in pre- and post-race difference was calculated ({Delta}CK and {Delta}MB). An incremental exercise test was used to determine maximal oxygen uptake, maximal aerobic power, and power output at the second ventilatory threshold. Post-race CK and MB increased in the whole group of cyclists. Although the magnitude of change in CK was similar in both road and mountain bike cyclists, only the increase in road cyclists was significant. MB significantly increased only in mountain bike cyclists. Multiple regression analysis revealed a significant association between both road and mountain bike race performance and {Delta}CK and {Delta}MB. The other significant predictors for mountain bike race performance were maximal aerobic power (W{middle dot}kg-1) and power output at the second ventilatory threshold (W{middle dot}kg-1) and for road race performance both maximal oxygen uptake (l{middle dot}min-1) and power output at the second ventilatory threshold (W). In conclusion, mountain bike racing was associated with an increase in MB whereas road racing with an increase in CK, with the post-race changes in CK and MB related to race performance as high {Delta}CK and low {Delta}MB were obtained by better-performing cyclists.


title: Fluorinated oil-surfactant mixtures with the density of water: artificial cells for synthetic biology

abstract: There is a rising interest in biotechnology for the compartmentalization of biochemical reactions in water droplets. Several applications, such as the widely used digital PCR, seek to encapsulate a single molecule in a droplet to be amplified. Directed evolution, another technology with growing popularity, seeks to replicate what happens in nature by encapsulating a single gene and the protein encoded by this gene, linking genotype with phenotype. Compartmentalizing reactions in droplets also allows the experimentalist to run millions of different reactions in parallel. Compartmentalization requires a fluid that is immiscible with water and a surfactant to stabilize the droplets. While there are fluids and surfactants on the market that have been used to accomplish encapsulation, there are reported concerns with these. Span(R) 80, for example, a commonly used surfactant, has contaminants that interfere with various biochemical reactions. Similarly, synthetic fluids distributed by the cosmetic industry allow some researchers to produce experimental results that can be published, but then other researchers fail to reproduce some of these protocols due to the unreliable nature of these products, which are not manufactured with the intent of being used in biotechnology. The most reliable fluids, immiscible with water and suitable for biochemical reactions, are fluorinated fluids. Fluorinated compounds have the peculiar characteristic of being immiscible with water while at the same time not mixing with hydrophobic molecules. This peculiar characteristic has made fluorinated fluids attractive because it seems to be the basis of their being biologically inert. However, commercially available fluorinated fluids have densities between 1.4 to 1.6 g/mL. The higher-than-water density of fluorinated oils complicates handling of the droplets since these would float on the fluid since the water droplets would be less dense. This can cause aggregation and coalescence of the droplets. Here, we report the synthesis, characterization, and use of fluorinated polysiloxane oils that have densities similar to the one of water at room temperature, and when mixed with non-ionic fluorinated surfactants, can produce droplets encapsulating biochemical reactions. We show how droplets in these emulsions can host many biological processes, including PCR, DNA origami, rolling circle amplification (RCA), and Taqman(R) assays. Some of these use unnatural DNA built from an Artificially Expanded Genetic Information System (AEGIS) with six nucleotide "letters".

category: synthetic biology


title: Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages

abstract: Molecular studies of the freshwater snail Lymnaea stagnalis, a unique model organism for neurobiology research, has been severely hindered by the lack of sufficient genomic information. As part of our ongoing effort studying L. stagnalis neuronal growth and connectivity at various developmental stages, we provide the first age-specific transcriptome analysis and gene annotation of young, adult, and old L. stagnalis central nervous system (CNS). RNA sequencing using Illumina NovaSeq 6000 platform produced 56-69 millions of 150 bp paired-end reads, and 74% of these reads were mapped to the draft genome of L. stagnalis. We provide gene annotations for 32,288 coding sequences with a minimum of 100 codons, contributing to the largest number of annotated genes for the L. stagnalis genome to date. Lastly, transcriptomic analyses reveal age-specific differentially expressed genes and enriched pathways in young, adult, and old CNS. These datasets represent the largest and most updated L. stagnalis CNS transcriptomes.


title: Unsupervised learning for robust working memory

abstract:
Working memory is a core component of critical cognitive functions such as planning and decision-making. Persistent activity that lasts long after the stimulus offset has been considered a neural substrate for working memory. Attractor dynamics based on network interactions can successfully reproduce such persistent activity. However, it suffers from a fine-tuning of network connectivity, in particular, to form continuous attractors suggested for working memory encoding analog signals. Here, we investigate whether a specific form of synaptic plasticity rules can mitigate such tuning problems in two representative working memory models, namely, rate-coded and location-coded persistent activity. We consider two prominent types of plasticity rules, differential plasticity targeting the slip of instant neural activity and homeostatic plasticity regularizing the long-term average of activity, both of which have been proposed to fine-tune the weights in an unsupervised manner. Consistent with the findings of previous works, differential plasticity alone was enough to recover a graded-level persistent activity with less sensitivity to learning parameters. However, for the maintenance of spatially structured persistent activity, differential plasticity could recover persistent activity, but its pattern can be irregular for different stimulus locations. On the other hand, homeostatic plasticity shows a robust recovery of smooth spatial patterns under particular types of synaptic perturbations, such as perturbations in incoming synapses onto the entire or local populations, while it was not effective against perturbations in outgoing synapses from local populations. Instead, combining it with differential plasticity recovers location-coded persistent activity for a broader range of perturbations, suggesting compensation between two plasticity rules.

Author SummaryWhile external error and reward signals are essential for supervised and reinforcement learning, they are not always available. For example, when an animal holds a piece of information in mind for a short delay period in the absence of the original stimulus, it cannot generate an error signal by comparing its memory representation with the stimulus. Thus, it might be helpful to utilize an internal signal to guide learning. Here, we investigate the role of unsupervised learning for working memory maintenance, which acts during the delay period without external inputs. We consider two prominent classes of learning rules, namely, differential plasticity, which targets the slip of instant neural activity, and homeostatic plasticity, which regularizes the long-term average of activity. The two learning rules have been proposed to fine-tune the synaptic weights without external teaching signals. Here, by comparing their performance under various types of network perturbations, we reveal the conditions under which each rule can be effective and suggest possible synergy between them.


title: Comparative genomics reveals insights into phylogenomic taxonomy and potential algae-bacteria interactions of novel versatile Mameliella alba strain LZ-28 isolated from highly-toxic marine phycosphere

abstract: Phycosphere harbors cross-kingdom interactions with significant ecological relevance for harmful algal blooms (HAB) and phycotoxins biosynthesis. Previously, a new red-pigmented bacterium designated as strain LZ-28 was isolated from phycosphere microbiota of typical HAB dinoflagellate Alexandrium catenella LZT09 which is a vitamin B12 auxotroph and produces high levels of paralytic shellfish poisoning toxins (PST). Strain LZ-28 exhibited obvious growth-promoting activity toward its algal host, along with the production of active bioflocculanting exopolysaccharides (EPS). But the phylogenetic affiliation and genomic potential of this versatile bacterium has not yet been elucidated. In this study, we carried out combined taxonomic and phylogenomic analysis to clarify the taxonomic classification of strain LZ-28. The obtained 16S rRNA phylogeny revealed close taxonomic relationship between strain LZ-28 and other Mameliella alba members. Additional calculations of key phylogenomic parameters, average nucleotide identity (ANI), the average amino acid identity (AAI) and the digital DNA-DNA hybridization (dDDH) values based on genomes of strain LZ-28 and type strain of Mameliella alba were all exceeded the limit of species circumscription. Collectively considering the phenotypic and biochemical characterizations, strain LZ-28 was therefore identified as a new member of Mameliella alba. Furthermore, based on the genomic evidence, potential algae-bacteria interactions of strain LZ-28 with host algae LZT09 were elucidated through the associations with photosynthetic and antioxidant carotenoids, supplying of bacterial VB12 to auxotroph host, and versatile EPS serving for bacterial colonization and nutrient exchange during their interactions, along with stress response systems to defense oxidative stress and quorum sensing (QS) signals benefited survival for bacteria in the symbiotic system. Comparative genomics shed light on similar genomic features between M. alba strains, revealed potential close associations of strain LZ-28 with its algae host, and further enriched the genomic repertoire of interactions between phycosphere microbiota and algal host LZT09.

category: microbiology


title: Fusarium graminearum  DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence

abstract:
In filamentous fungi, gene silencing by RNA interference (RNAi) shapes many biological processes, including pathogenicity. Recently, fungal small RNAs (sRNAs) have been shown to act as effectors that disrupt gene activity in interacting plant hosts, thereby undermining their defence responses. We show here that the devastating mycotoxin-producing ascomycete Fusarium graminearum (Fg) utilizes DICER-like (DCL)-dependent sRNAs to target defence genes in two Poaceae hosts, barley (Hordeum vulgare Hv) and Brachypodium distachyon (Bd). We identified 104 Fg-sRNAs with sequence homology to host genes that were repressed during interactions of Fg and Hv, while they accumulated in plants infected by the DCL double knock-out (dKO) mutant PH1-dcl1/2. The strength of target gene expression correlated with the abundance of the corresponding Fg-sRNA. Specifically, the abundance of three tRNA-derived fragments (tRFs) targeting immunity-related Ethylene overproducer 1-like 1 (HvEOL1) and three Poaceae orthologues of Arabidopsis thaliana BRI1-associated receptor kinase 1 (HvBAK1, HvSERK2 and BdSERK2) was dependent on fungal DCL. Additionally, RNA-ligase-mediated Rapid Amplification of cDNA Ends (RLM-RACE) identified infection-specific degradation products for the three barley gene transcripts, consistent with the possibility that tRFs contribute to fungal virulence via targeted gene silencing.

Significance StatementFusarium graminearum is one of the most devastating fungal pathogens in cereals, while understanding the mechanisms of fungal pathogenesis is a prerequisite for developing efficient and environmentally friendly crop protection strategies. We show exploratory data suggesting that fungal small RNAs play a critical role in Fusarium virulence by suppressing plant immunity.


title: Genetic diversity and population structure of cowpea  accessions from Togo using SSR Markers

abstract: Cowpea [Vigna unguiculata (L.) Walp.] is a crop with significant agronomic and nutritional potential. I is very appreciate by local people. It is the third food habit in Togo after maize and rice. However, several accessions of cowpea cultivated in Togo are now prone to extinction, creating a risk of genetic erosion. It is therefore urgent to assess the genetic diversity of accessions in order to set up a good conservation program. To achieve this, genetic diversity and phylogenetic relationships among 70 accessions of cowpea collected in the five (5) administrative regions of Togo were assessed using Simple Sequence Repeat (SSR) molecular markers. Twenty-eight out of the thirty-two (32) primer pairs screened for polymorphism were polymorphic, and a total of 164 alleles were detected for the 28 loci with an average of 5.82 alleles per locus. Polymorphic Information Content (PIC) values ranged from 0.18 to 0.895, with an average value of 0.67. Population structure analysis using model-based revealed that the cowpea germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 85% of genetic variation existed among individuals within regions. The fixation index (Fst) value, which was 0.018, was low, indicating relatively low population differentiation. The Togolese cowpea germplasm collection was grouped into four groups independently of theirs origins. This study provides a foundation for a Togolese cowpea germplasm conservation program and can serve for the selection of parental material for further studies aimed at the genetic improvement of local germplasm.


title: An Atlas of Cortical Arealization Identifies Dynamic Molecular Signatures

abstract: The human brain is subdivided into distinct anatomical structures. The neocortex, one of these structures, enables higher-order sensory, associative, and cognitive functions, and in turn encompasses dozens of distinct specialized cortical areas. Early morphogenetic gradients are known to establish an early blueprint for the specification of brain regions and cortical areas. Furthermore, recent studies have uncovered distinct transcriptomic signatures between opposing poles of the developing neocortex1. However, how early, broad developmental patterns result in finer and more discrete spatial differences across the adult human brain remains poorly understood2. Here, we use single-cell RNA-sequencing to profile ten major brain structures and six neocortical areas during peak neurogenesis and early gliogenesis. Our data reveal that distinct cell subtypes are predominantly brain-structure specific. Within the neocortex, we find that even early in the second trimester, a large number of genes are differentially expressed across distinct cortical areas in all cell types, including radial glia, the neural progenitors of the cortex. However, the abundance of areal transcriptomic signatures increases as radial glia differentiate into intermediate progenitor cells and ultimately give rise to excitatory neurons. Using an automated, multiplexed single-molecule fluorescent in situ hybridization (smFISH) approach, we validated the expression pattern of area-specific neuronal genes and also discover that laminar gene expression patterns are highly dynamic across cortical regions. Together, our data suggest that early cortical areal patterning is defined by strong, mutually exclusive frontal and occipital gene expression signatures, with resulting gradients giving rise to the specification of areas between these two poles throughout successive developmental timepoints.


title: Defining dual-axis landscape gradients of human influence for studying ecological processes

abstract: Ecological processes are strongly shaped by human landscape modification, and understanding the reciprocal relationship between ecosystems and modified landscapes is critical for informed conservation. Single axis measures of spatial heterogeneity proliferate in the contemporary gradient ecology literature, though they are unlikely to capture the complexity of ecological responses. Here, we develop a standardized approach for defining multi-dimensional gradients of human influence in heterogeneous landscapes and demonstrate this approach to analyze landscape characteristics of ten ecologically distinct US cities. Using occupancy data of a common human-adaptive songbird collected in each of the cities, we then use our dual-axis gradients to evaluate the utility of our approach. Spatial analysis of landscapes surrounding ten US cities revealed two important axes of variation that are intuitively consistent with the characteristics of multi-use landscapes, but are often confounded in single axis gradients. These were, a hard-to-soft gradient, representing transition from developed areas to non-structural soft areas; and brown-to-green, differentiating between two dominant types of soft landscapes: agriculture (brown) and natural areas (green). Analysis of songbird data demonstrated that occupancy responds to both hard-to-soft (decreasing with development intensity) and brown-to-green gradient (increasing with more natural area). Overall, our results reveal striking consistency in the dominant sources of variation across ten geographically distinct cities and suggests that our approach advances how we relate variation in ecological responses to human influence. Our case study demonstrates this: robins show a remarkably consistent response to a gradient differentiating agricultural and natural areas, but city-specific responses to the more traditional gradient of development intensity, which would be overlooked with a single gradient approach. Managing ecological communities in human dominated landscapes is extremely challenging due to a lack of standardized approaches and a general understanding of how socio-ecological systems function, and our approach offers promising solutions.

category: ecology


title: Public attitudes towards free-roaming dogs and dog ownership practices in Bulgaria, Italy, and Ukraine

abstract: Overabundant, free-roaming dog populations are associated with risks to public health, livestock losses, wildlife conservation, and dog health and welfare. Dog population management is conducted to mitigate these issues. Assessing dog population management strategies is important to determine their effectiveness, efficiency, and long-term impact. It is essential to also determine how the behaviour and outlook of local communities may influence the efficacy of dog population management. This study aimed to determine public attitudes towards free-roaming dogs and their management and describe dog ownership practices in three European countries using an online questionnaire survey. This study found that most surveyed respondents wanted to see a reduction in free-roaming dog numbers, and felt that this should be achieved through sheltering, catch-neuter-release, and by controlling the breeding of owned dogs. This questionnaire also identified significant associations between public attitudes and dog ownership practices with gender, religious beliefs, age, education level, reason for dog ownership, previous experience with free-roaming dogs, and country of residence. Respondents who identified as: (i) being male, (ii) holding religious beliefs, (iii) owning dogs for practical reasons, (iv) being young, and (v) having no schooling or primary education had a lower probability of neutering and a higher probability of allowing dogs to roam. Respondents who identified as: (i) being female, (ii) feeling threatened by free-roaming dogs, (iii) being older, and (iv) having more education had a higher probability of answering that an increase in free-roaming dog numbers should be prevented. These findings can help to inform future dog population management interventions in these countries and highlight the importance of considering local public attitudes and dog ownership practices in the development of effective dog population management approaches. Including these social factors will ensure that both the community and organisations involved in dog population management work cohesively towards a shared goal.


title: Mass Recovery following Caloric Restriction Reverses Lipolysis and Proteolysis, but not Gluconeogenesis, in Insulin Resistant OLETF Rats

abstract: Caloric restriction (CR) is one of the most important behavioral interventions to reduce excessive abdominal adiposity, which is a risk factor for the development of insulin resistance. Previous metabolomics studies have characterized substrate metabolism during healthy conditions; however, the effects of CR and subsequent mass recovery on shifts in substrate metabolism during insulin resistance (IR) have not been widely investigated. To assess the effects of acute CR and the subsequent mass recovery on shifts in substrate metabolism, a cohort of 15-week old Long Evans Tokushima Otsuka (LETO) and Otsuka Long Evans Tokushima Fatty (OLETF) rats were calorie restricted (CR: 50% x 10 days) with or without partial body mass recovery (PR; 73% x 7 days), along with their respective ad libitum controls. End-of-study plasma samples were analyzed for primary carbon metabolites by gas chromatography (GC) time-of-flight (TOF) mass spectrometry (MS) data acquisition. Data analysis included PCA, Pearson correlation vs previously reported variables (adipose and body masses, and insulin resistance index, IRI), and metabolomics maps (MetaMapp) generated for the most significant group comparisons. All treatments elicited a significant group differentiation in at least one principal component. CR improved TCA cycle in OLETF, and increased lipolysis and proteolysis. These changes were reversed after PR except for gluconeogenesis. Plasma lipid concentrations were inversely correlated to IRI in LETO, but not OLETF. These shifts in substrate metabolism suggest that the CR-induced decreases in adipose may not be sufficient to more permanently alter substrate metabolism to improve IR status during metabolic syndrome.


title: Transcriptome-wide identification and expression profiling of the ERF gene family suggest roles as transcriptional activators and repressors of fruit ripening in durian

abstract: The involvement of the phytohormone ethylene as the main trigger of climacteric fruit ripening is well documented. However, our knowledge regarding the role of ethylene response factor (ERF) transcription factor in the transcriptional regulation of ethylene biosynthesis during fruit ripening remains limited. Here, comprehensive transcriptome analysis and expression profiling revealed 63 ERFs in durian pulps, termed DzERF1-DzERF63, of which 34 exhibited ripening-associated expression patterns at three stages (unripe, midripe, and ripe) during fruit ripening. Hierarchical clustering analysis classified 34 ripening-associated DzERFs into three distinct clades, among which, clade I consisted of downregulated DzERFs and clade III included those upregulated during ripening. Phylogenetic analysis predicted the functions of some DzERFs based on orthologs of previously characterized ERFs. Among downregulated DzERFs, DzERF6 functional prediction revealed its role as a negative regulator of ripening via ethylene biosynthetic gene repression, whereas among upregulated genes, DzERF9 was predicted to positively regulate ethylene biosynthesis. Correlation network analysis of 34 ripening-associated DzERFs with potential target genes revealed a strong negative correlation between DzERF6 and ethylene biosynthetic genes and a strong positive correlation between DzERF9 and ethylene biosynthesis. DzERF6 and DzERF9 showed differential expression patterns in association with different ripening treatments (natural, ethylene-induced, and 1-methylcyclopropene-delayed ripening). DzERF6 was downregulated, whereas DzERF9 was upregulated, during ripening and after ethylene treatment. The auxin-repressed and auxin-induced expression of DzERF6 and DzERF9, respectively, confirmed its dose-dependent responsiveness to exogenous auxin. We suggest ethylene- and auxin-mediated roles of DzERF6 and DzERF9 during fruit ripening, possibly through transcriptional regulation of ethylene biosynthetic genes.


title: Unraveling microbial interactions in the gut microbiome

abstract:
The human gut comprises trillions of microorganisms that take part in several critical functions of the body. Within this structured habitat, the microbes synergise with one another mainly mediated through metabolic exchanges. In this study, we used 52 most commonly occurring microbial species in the gut and identified the interactions between them. Using our previously developed graph-based algorithm, MetQuest, we enumerate several biosynthetic pathways, mainly involved in amino acid biosynthesis and spanning across a pair of organisms. We compute the Metabolic Support Index (MSI), which captures the extent of support/interaction between a pair of microbes, based on the incremental change in metabolic capabilities achieved in a community vis-a-vis the individual organisms. Our results from these analyses are four-fold. Firstly, we show that dependencies between the gut microorganisms largely vary with respect to the environmental conditions. We observe that few phyla such as Firmicutes, Fusobacteria and Proteobacter showed significantly higher metabolic support on DMEM conditions compared to HF medium. Secondly, we infer a microbial association network based on the MSI values and found that the gut organisms are arranged in trophic-levels, with B. bifidum and R. torques acting as central nodes with the highest betweenness centrality. Thirdly, we find that species belonging to Lactobacillus genus, especially L. mucosae and L. reuteri show an enriched amino acid synthesising ability in the presence of many other gut organisms on a minimal glucose medium. Finally, through pathway analyses, we observe that metabolic exchanges are medium-dependent, and many of the metabolites are involved in energy metabolism, nucleotide, and vitamin biosynthesis. Overall, this study sheds light on the astonishing variety of underlying interactions between microorganisms in the gut.

Author SummaryMicroorganisms are ubiquitous and exist in evolutionarily and metabolically diverse communities around us. In practically every ecosystem, microbes form complex dynamic assemblages--such as in the human gut, where they outnumber human cells. Community structure in these microbiomes is dictated by a complex web of interactions, where metabolic interactions are known to predominate. In this study, we employ computational tools to interrogate community metabolic networks and unravel the dependencies between microbes in the gut. We used 52 important and commonly occurring microbial species in the gut, as identified in previous studies. Through our analyses, we show that the dependencies between gut organisms vary in different environmental conditions. Further, we show that these organisms are arranged in multiple trophic levels, where a select few of them acting as central nodes. We also identify the metabolic interactions and demonstrate how synergistic interactions can enhance the amino acid biosynthesis in gut bacteria. These results, taken together, help us better understand the mechanism behind these interactions, which would pave the way for the rational design of pre- and pro-biotic formulations.

category: systems biology


title: A quantitative map of nuclear pore assembly reveals two distinct mechanisms

abstract: Understanding how the nuclear pore complex (NPC) assembles is of fundamental importance to grasp the mechanisms behind its essential function and understand its role during evolution of eukaryotes1-4. While we know that at least two NPC assembly pathways exist, one during exit from mitosis and one during nuclear growth in interphase, we currently lack a quantitative map of their molecular events. Here, we use fluorescence correlation spectroscopy (FCS) calibrated live imaging of endogenously fluorescently-tagged nucleoporins to map the changes in composition and stoichiometry of seven major modules of the human NPC during its assembly in single dividing cells. This systematic quantitative map reveals that the two assembly pathways employ strikingly different molecular mechanisms, inverting the order of addition of two large structural components, the central ring complex and nuclear filaments. Our dynamic stoichiometry data allows us to perform the first computational simulation that predicts the structure of postmitotic NPC assembly intermediates.

category: cell biology