title: DNA damage-induced phosphorylation of histone H2A at serine 15 is linked to DNA end resection

abstract: The repair of DNA double-strand breaks (DSBs) occurs in chromatin and several histone post-translational modifications have been implicated in the process. Modifications of histone H2A N-terminal tail has also been linked to DNA damage response, through acetylation or ubiquitination of lysine residues that regulate repair pathway choice. Here, we characterize a new DNA damage-induced phosphorylation on chromatin, at serine 15 of H2A in yeast. We show that this SQ motif functions independently of the classical S129 C-terminal site ({gamma}H2A) and mutant mimicking constitutive phosphorylation increases cell sensitivity to DNA damage. H2AS129ph is induced by Tel1ATM and Mec1ATR, and loss of Lcd1ATRIP or Mec1 signaling decreases {gamma}H2A spreading distal to the DSB. In contrast, H2AS15ph is completely dependent on Lcd1ATRIP, indicating that this modification only happens when end resection is engaged. This is supported by an increase of RPA and a decrease in DNA signal near the DSB in the H2AS-15E phosphomimic mutant, indicating higher resection. This serine is replaced by a lysine in mammals (H2AK15), which undergoes an acetyl-monoubiquityl switch to regulate binding of 53BP1 and resection. This regulation seems functionally conserved with budding yeast H2AS15 and 53BP1-homolog Rad9, using different post-translational modifications between organisms but achieving the same function.

category: molecular biology


title: Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing

abstract: TNRC6 is a scaffolding protein that bridges interactions between small RNAs, argonaute (AGO) protein, and effector proteins to control gene expression. There are three paralogs in mammalian cells, TNRC6A, TNRC6B, and TNRC6C. These paralogs have ~40% amino acid sequence identity and the extent of their unique or redundant functions is unclear. Here, we use knockout cell lines, enhanced crosslinking immunoprecipitation (eCLIP), and high-throughput RNA sequencing (RNAseq) to explore the roles of TNRC6 paralogs in RNA-mediated control of gene expression. We find that that the paralogs are largely functionally redundant and changes in levels of gene expression are well-correlated with those observed in AGO knockout cell lines. Splicing changes observed in AGO knockout cell lines are observed in TNRC6 knockout cells. These data further define the roles of the TNRC6 isoforms as part of the RNA interference (RNAi) machinery.


title: An algal symbiont (Breviolum psygmophilum) responds more strongly to chronic high temperatures than its facultatively symbiotic coral host (Astrangia poculata)

abstract: Scleractinian corals form the foundation of coral reefs by secreting skeletons of calcium carbonate. Their intracellular algal symbionts (Symbiodiniaceae) translocate a large proportion of photosynthate to the coral host, which is required to maintain high rates of calcification. Global warming is causing dissociation of coral host and algal symbiont, visibly presented as coral bleaching. Despite decades of study, the precise mechanisms of coral bleaching remain unknown. Separating the thermal stress response of the coral from the algal symbiont is key to understanding bleaching in tropical corals. The facultatively symbiotic northern star coral, Astrangia poculata, naturally occurs as both symbiotic and aposymbiotic (lacking algal symbionts) polyps - sometimes on the same coral colony. Thus, it is possible to separate the heat stress response of the coral host alone from the coral in symbiosis with its symbiont Breviolum psygmophilum. Using replicate symbiotic and aposymbiotic ramets of A. poculata, we conducted a chronic heat stress experiment to increase our understanding of the cellular mechanisms resulting in coral bleaching. Sustained high temperature stress resulted in photosynthetic dysfunction in B. psygmophilum, including a decline in maximum photosynthesis rate, maximum photochemical efficiency, and the absorbance peak of chlorophyll a. Interestingly, the metabolic rates of symbiotic and aposymbiotic corals were differentially impacted. RNAseq analysis revealed more differentially expressed genes between heat-stressed and control aposymbiotic colonies than heat-stressed and control symbiotic colonies. Notably, aposymbiotic colonies increased the expression of inflammation-associated genes such as nitric oxide synthases. Unexpectedly, the largest transcriptional response was observed between heat-stressed and control B. psygmophilum, including genes involved in photosynthesis, response to oxidative stress, and meiosis. Thus, it appears that the algal symbiont suppresses the immune response of the host, potentially increasing the vulnerability of the host to pathogens. The A. poculata-B. psygmophilum symbiosis provides a tractable model system for investigating thermal stress and immune challenge in scleractinian corals.

category: ecology


title: Evolution of gene-rich germline restricted chromosomes in black-winged fungus gnats through introgression (Diptera: Sciaridae)

abstract: Germline restricted DNA has evolved in diverse animal taxa, and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline restricted DNA has evolved, especially in flies, in which three diverse families, Chironomidae, Cecidomyiidae, and Sciaridae exhibit germline restricted chromosomes (GRCs). We conducted a genomic analysis of germline restricted chromosomes in the fungus gnat Bradysia (Sciara) coprophila (Diptera: Sciaridae), which carries two large germline restricted "L" chromosomes. We sequenced and assembled the genome of B. coprophila, and used differences in sequence coverage and k-mer frequency between somatic and germ tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs in B. coprophila are large, gene-rich, and have many genes with paralogs on other chromosomes in the genome. We also found that the GRC genes are extraordinarily divergent from their paralogs, and have sequence similarity to another Dipteran family (Cecidomyiidae) in phylogenetic analyses, suggesting that these chromosomes have arisen in Sciaridae through introgression from a related lineage. These results suggest that the GRCs may have evolved through an ancient hybridization event, raising questions about how this may have occurred, how these chromosomes became restricted to the germline after introgression, and why they were retained over time.

category: evolutionary biology


title: Nse5/6 inhibits the Smc5/6 ATPase to facilitate DNA substrate selection.

abstract: Eukaryotic cells employ three SMC complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA repair and in preventing the accumulation of deleterious DNA junctions. To elucidate how specific features of Smc5/6 govern these functions, we reconstituted the yeast holo-complex. We found that the Nse5/6 sub-complex strongly inhibited the Smc5/6 ATPase by preventing productive ATP binding. This inhibition was relieved by plasmid DNA binding but not by short linear DNA, while opposing effects were observed without Nse5/6. We uncovered two binding sites for Nse5/6 on Smc5/6, based on an Nse5/6 crystal structure and cross-linking mass spectrometry data. One binding site is located at the Smc5/6 arms and one at the heads, the latter likely exerting inhibitory effects on ATP hydrolysis. Cysteine cross-linking demonstrated that the interaction with Nse5/6 anchored the ATPase domains in a non-productive state, which was destabilized by ATP and DNA. Under similar conditions, the Nse4/3/1 module detached from the ATPase. Altogether, we show how DNA substrate selection is modulated by direct inhibition of the Smc5/6 ATPase by Nse5/6.

category: biochemistry


title: Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression

abstract: The SARS-CoV-2 pandemic has challenged humankinds ability to quickly determine the cascade of health effects caused by a novel infection. Even with the unprecedented speed at which vaccines were developed and introduced into society, identifying therapeutic interventions and drug targets for patients infected with the virus remains important as new strains of the virus may evolve, or future coronaviruses may emerge, that are resistant to current vaccines. The application of transcriptomic RNA sequencing of infected samples may shed new light on the pathways involved in viral mechanisms and host responses. We describe the application of "dual RNA-seq" analysis to consider both the host and pathogen transcriptomes simultaneously, to investigate for the first time the co-regulation of human and SARS-CoV-2 genes. Together with differential expression analysis, we describe the tissue specificity of SARS-CoV-2 expression, an inferred lipopolysaccharide response, and co-regulation of CXCLs, SPRRs, S100s with SARS-CoV-2 expression. Lipopolysaccharide response pathways in particular offer promise for future therapeutic research and the prospect of subgrouping patients based on chemokine expression that may help explain the vastly different reactions patients have to infection. Taken together these findings illuminate previously unappreciated SARS-CoV-2 expression signatures, identify new therapeutic considerations, and contribute a pipeline for studying multi-transcriptome systems.

category: bioinformatics


title: Mechanistic underpinning of nonuniform collective motions in swarming bacteria

abstract: Self-propelled bacteria can exhibit a large variety of non-equilibrium self-organized phenomena. Swarming is one such fascinating dynamical scenario where a number of motile individuals grouped into clusters and move in synchronized flows and vortices. While precedent investigations in rod-like particles confirm that increased aspect-ratio promotes alignment and order, recent experimental studies in bacteria Bacillus subtilis show a non-monotonic dependence of cell-aspect ratio on their swarming motion. Here, by computer simulations of an agent-based model of selfpropelled, mechanically interacting, rod-shaped bacteria in overdamped condition, we explore the collective dynamics of bacterial swarm subjected to a variation of cell-aspect ratio. When modeled with an identical self-propulsion speed across a diverse range of cell aspect ratio, simulations demonstrate that both shorter and longer bacteria exhibit slow dynamics whereas the fastest speed is obtained at an intermediate aspect ratio. Our investigation highlights that the origin of this observed non-monotonic trend of bacterial speed and vorticity with cell-aspect ratio is rooted in the cell-size dependence of motility force. The swarming features remain robust for a wide range of surface density of the cells, whereas asymmetry in friction attributes a distinct effect. Our analysis identifies that at an intermediate aspect ratio, an optimum cell size and motility force promote alignment, which reinforces the mechanical interactions among neighboring cells leading to the overall fastest motion. Mechanistic underpinning of the collective motions reveals that it is a joint venture of the short-range repulsive and the size-dependent motility forces, which determines the characteristics of swarming.

category: biophysics


title: Exosomes from COVID-19 patients carry tenascin-C and fibrinogen-β in triggering inflammatory signals in distant organ cells

abstract:
SARS-CoV-2 infection causes cytokine storm and overshoot immunity in humans; however, it remains to be determined whether genetic material of SARS-CoV-2 and/or virus induced soluble mediators from lung epithelial cells as natural host are carried out by macrophages or other vehicles at distant organs causing tissue damage. We speculated that exosomes as extracellular vesicles are secreted from SARS-CoV-2 infected cells may transport messages to other cells of distant organs leading to pathogenic consequences. For this, we took an unbiased proteomic approach for analyses of exosomes isolated from plasma of healthy volunteers and SARS-CoV-2 infected patients. Our results revealed that tenascin-C (TNC) and fibrinogen-{beta} (FGB) are highly abundant in exosomes from SARS-CoV-2 infected patients plasma as compared to that of healthy normal controls. Since TNC and FGB stimulate pro-inflammatory cytokines via NF-{kappa}B pathway, we examined the status of TNF-, IL-6 and CCL5 expression upon exposure of hepatocytes to exosomes from COVID-19 patients and observed significant increase when compared with that from healthy subjects. Together, our results demonstrated that soluble mediators, like TNC and FGB, are transported through plasma exosomes in SARS-CoV-2 infected patients and trigger pro-inflammatory cytokine expression in cells of distant organs in COVID-19 patients.

ImportanceExosomes play an important role in intercellular communication by inducing physiological changes in recipient cells by transferring bioactive proteins. Little is known about exosomes from SARS-CoV-2 infected cells and their role in pathogenesis. Here, we have carefully examined and analyzed this aspect of SARS-CoV-2 infection. Our results uncovered the potential mechanisms by which SARS-CoV-2 communicates with other cells of distant organs and promotes pathogenesis. We expect to detect whether other factors are modulated in the presence of COVID-19 exosomes. Our exosomes related proteomic experiments prioritize after initial verification to further examine their role in SARS-CoV-2 associated other pathogenic mechanisms to target for therapeutic modalities.

category: physiology


title: A unified model of amino acid homeostasis in mammalian cells

abstract: Homeostasis is one of the fundamental concepts in physiology. Despite remarkable progress in our molecular understanding of amino acid transport, metabolism and signalling, it remains unclear by what mechanisms cytosolic amino acid concentrations are maintained. We propose that amino acid transporters are the primary determinants of intracellular amino acid levels. We show that a cells endowment with amino acid transporters can be deconvoluted by a logical series of experiments. This was used to computationally simulate amino acid translocation across the plasma membrane. For two different cancer cell lines and human myotubes, transport simulation generates cytosolic amino acid concentrations that are close to those observed in vitro. Perturbations of the system were replicated in silico and could be applied to systems where only transcriptomic data are available. The methodology developed in this study is widely applicable to other transport processes and explain amino acid homeostasis at the systems-level.

category: systems biology


title: Transcriptome signature of cell viability predicts drug response and drug interaction for Tuberculosis

abstract: The treatment of tuberculosis (TB), which kills 1.8 million each year, remains difficult, especially with the emergence of multidrug resistant strains of Mycobacterium tuberculosis (Mtb). While there is an urgent need for new drug regimens to treat TB, the process of drug evaluation is slow and inefficient owing to the slow growth rate of the pathogen, the complexity of performing bacteriologic assays in a high-containment facility, and the context-dependent variability in drug sensitivity of the pathogen. Here, we report the development of "DRonA" and "MLSynergy", algorithms to perform rapid drug response assays and predict response of Mtb to novel drug combinations. Using a novel transcriptome signature for cell viability, DRonA accurately detects bacterial killing by diverse mechanisms in broth culture, macrophage infection and patient sputum, providing an efficient, and more sensitive alternative to time- and resource-intensive bacteriologic assays. Further, MLSynergy builds on DRonA to predict novel synergistic and antagonistic multi-drug combinations using transcriptomes of Mtb treated with single drugs. Together DRonA and MLSynergy represent a generalizable framework for rapid monitoring of drug effects in host-relevant contexts and accelerate the discovery of efficacious high-order drug combinations.

category: microbiology


title: Population density affects the outcome of competition in co-cultures of Gardnerella species isolated from the human vaginal microbiome

abstract: Negative frequency-dependent selection is one possible mechanism for maintenance of rare species in communities, but the selective advantage of rare species may be checked at lower overall population densities where resources are abundant. Gardnerella spp. belonging to cpn60 subgroup D, are detected at low levels in vaginal microbiomes and are nutritional generalists relative to other more abundant Gardnerella spp., making them good candidates for negative frequency-dependent selection. The vaginal microbiome is a dynamic environment and the resulting changes in density of the microbiota may explain why subgroup D never gains dominance. To test this, we co-cultured subgroup D isolates with isolates from the more common and abundant subgroup C. Deep amplicon sequencing of rpoB was used to determine proportional abundance of each isolate at 0 h and 72 h in 152 co-cultures, and to calculate change in proportion. D isolates had a positive change in proportional abundance in most co-cultures regardless of initial proportion. Initial density affected the change in proportion of subgroup D isolates either positively or negatively depending on the particular isolates combined, suggesting that growth rate, population density and other intrinsic features of the isolates influenced the outcome. Our results demonstrate that population density is an important factor influencing the outcome of competition between Gardnerella spp. isolated from the human vaginal microbiome.


title: Atomic structure of human sapovirus capsid by single particle cryo-electron microscopy

abstract: Sapovirus is a cause of acute gastroenteritis in humans and animals. Infants and younger children have the greatest disease burden. Although it shares many similarities with norovirus, the lack of detailed structural information has hampered the development of vaccines and therapeutics. Here, we investigated the human sapovirus VLP by single particle cryo-electron microscopy and are the first to report the atomic structure of the capsid at 2.9 [A] resolution. The atomic model revealed the domain interactions of the capsid protein and functionally important amino acid residues. The extended loop from the P1 subdomain was involved in interactions in the P2 domain, forming unique arch-like dimeric protrusions of capsid proteins. All hypervariable regions that are important candidates for immune response or receptor binding, formed a large cluster at the top of the P domain. These results pave the way for developing vaccines, antiviral drugs, and diagnostic systems for this infectious disease.


title: A transferrable and integrative type I-F Cascade for heterologous genome editing and transcription modulation

abstract: The Class 1 type I CRISPR-Cas systems represent the most abundant and diverse CRISPR systems in nature. However, their applications for generic genome editing have been hindered by difficulties of introducing the class-specific, multi-component effectors in heterologous hosts for functioning. Here we established a transferrable Cascade system that enables stable integration and expression of a complete and highly active I-F Cascade in the notoriously recalcitrant and diverse P. aeruginosa genomes by conjugation. The transferred Cascade displayed substantially higher DNA interference activity and greater editing capacity than the Cas9 system in diverse genetic backgrounds, including removal of the large (21-kb) integrated cassette with efficiency and simplicity. An advanced {lambda}red-I-F system enabled editing in genotypes with poor homologous recombination capacity, clinical isolates lacking sequence information, and cells containing anti-CRISPR elements Acrs. Lastly, an  all-in-one I-F Cascade-mediated CRISPRi platform was developed for transcription modulation by simultaneous introduction of the Cascade and the mini-CRISPR array expressing desired crRNA in one-step. This study provides a framework for expanding the diverse type I Cascades for widespread, heterologous genome editing and establishment of editing techniques in non-model isolates of pathogens.


title: Argonaute Binding within Human Nuclear RNA and its Impact on Alternative Splicing

abstract: Mammalian RNA interference (RNAi) is often linked to the regulation of gene expression in the cytoplasm. Synthetic RNAs, however, can also act through the RNAi pathway to regulate transcription and splicing. While nuclear regulation by synthetic RNAs can be robust, a critical unanswered question is whether endogenous functions for nuclear RNAi exist in mammalian cells. Using enhanced crosslinking immunoprecipitation (eCLIP) in combination with RNA sequencing (RNAseq) and multiple AGO knockout cell lines, we mapped AGO2 protein binding sites within nuclear RNA. The strongest AGO2 binding sites were mapped to micro RNAs (miRNAs). The most abundant miRNAs were distributed similarly between cytoplasm and nucleus, providing no evidence for mechanisms that facilitate localization of miRNAs in one compartment versus the other. Beyond miRNAs, most statistically-significant AGO2 binding was within introns. Splicing changes were confirmed by RT-PCR and were recapitulated by synthetic duplex RNAs and miRNA mimics complementary to the sites of AGO2 binding. These data support the hypothesis that miRNAs can control gene splicing. While nuclear RNAi proteins have the potential to be a natural regulatory mechanism, careful study will be necessary to identify critical RNA drivers of normal physiology and disease.


title: Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses

abstract: Molecular clock dating is widely used to estimate timescales of phylogenetic histories and to infer rates at which species evolve. One of the major challenges with inferring rates of molecular evolution is the observation of a strong correlation between estimated rates and the timeframe of their measurements. Recent empirical analysis of virus evolutionary rates suggest that a power-law rate decay best explains the time-dependent pattern of substitution rates and that the same pattern is observed regardless of virus type (e.g. groups I-VII in the Baltimore classification). However there exists no explanation for this trend based on molecular evolutionary mechanisms. We provide a simple predictive mechanistic model of the time-dependent rate phenomenon, incorporating saturation and host constraints on the evolution of some sites. Our model recapitulates the ubiquitous power-law rate decay with a slope of -0.65 (95% HPD: -0.72, -0.52) and can satisfactorily account for the variation in inferred molecular evolutionary rates over a wide range of timeframes. We show that once the saturation of sites starts - typically after hundreds of years in RNA viruses and thousands of years in DNA viruses - standard substitution models fail to correctly estimate divergence times among species, while our model successfully re-creates the observed pattern of rate decay. We apply our model to re-date the diversification of genotypes of hepatitis C virus (HCV) to 396,000 (95% HPD: 326,000 - 425,000) years before present, a time preceding the dispersal of modern humans out of Africa, and also showed that the most recent common ancestor of sarbecoviruses dates back to 23,500 (95% HPD: 21,100 - 25,300) years ago, nearly thirty times older than previous estimates. This not only creates a radical new perspective for our understanding the origins of HCV but also suggests a substantial revision of evolutionary timescales of other viruses can be similarly achieved.


title: Mutation bias implicates RNA editing in a wide range of mammalian RNA viruses

abstract:
The rapid evolution of RNA viruses has been long considered to result from a combination of high copying error frequencies during RNA replication, short generation times and the consequent extensive fixation of neutral or adaptive changes over short periods. While both the identities and sites of mutations are typically modelled as being random, recent investigations of sequence diversity of SARS coronavirus 2 (SARS-CoV-2) have identified a preponderance of C->U transitions, potentially driven by an APOBEC-like RNA editing process. The current study investigated whether this phenomenon could be observed in the more genetically diverse datasets of other RNA viruses. Using a 5% divergence filter to infer directionality, 18 from 32 datasets of aligned coding region sequences from a diverse range of mammalian RNA viruses (including Picornaviridae, Flaviviridae, Matonaviridae, Caliciviridae and Coronaviridae) showed a >2-fold base composition normalised excess of C->U transitions compared to U->C (range 2.1x-7.5x). C->U transitions showed a weak favoured 5 U upstream context consistent with previous analyses of APOBEC-mediated RNA targeting. Amongst several genomic compositional and structural parameters, the presence of genome scale RNA secondary structure (GORS) was associated with C->U/U->C transition asymmetries (p < 0.001), potentially reflecting the documented structure dependence of APOBEC-mediated RNA editing. Using the association index metric, C->U changes were specifically over-represented at phylogenetically uninformative sites, consistent with extensive homoplasy documented in SARS-CoV-2. Excess C->U substitutions accounted for 15-20% of standing sequence variability of HCV and other RNA viruses; RNA editing may therefore represent a potent driver of RNA virus sequence diversification and longer term evolution.

Author SummaryThe rapid evolution of RNA viruses is thought to arise from high mutation frequencies during replication and the rapid accumulation of genetic changes over time in response to its changing environments. This study describes an additional potent factor that contributes to the evolution of RNA infecting mammals, the deliberate mutation of the viral genome by host antiviral pathways active within the cell when it becomes infected. This so called "genome editing" by one or more APOBEC enzymes leads to characteristic C->U mutations that damage the viruss ability to replicate. While this pathway is well characterised as an antiviral defence against HIV and other retroviruses, this study provides evidence for its activity against a wide range of human and veterinary viruses, including HCV and foot and mouth disease virus. APOBEC-driven mutations accounted for 15-20% of standing sequence variability of RNA virus groups, representing a potent driver of RNA virus sequence diversification.

category: genomics


title: The protection of Gαz-null NOD mice from hyperglycemia is sexually dimorphic and only partially β-cell autonomous

abstract: The mechanisms that underlie the {beta}-cell pathophysiology of Type 1 Diabetes (T1D) are not fully understood. Our group has defined the unique heterotrimeric G protein alpha-subunit, Gz, as a key negative regulator of {beta}-cell signal transduction pathways. Non-obese diabetic (NOD) mice lacking Gz throughout the body are protected from developing T1D-like hyperglycemia. To determine whether this phenotype is {beta}-cell autonomous, we generated and validated a {beta}-cell-specific Gz knockout ({beta}KO) on the NOD background and characterized the phenotype of female and male cohorts. Long-term hyperglycemia incidence was lower in Gz {beta}KO mice as compared to wild-type (WT) controls, but, unlike global Gz knockout mice, this protection was incomplete. While young male and female Gz {beta}KO NOD mice had improved glucose tolerance, WT NOD males were significantly less glucose tolerant than females, and only female Gz {beta}KO mice retained improved glucose tolerance at 28-29 weeks of age. Conversely, {beta}-cell-specific Gz loss only influenced insulitis in 28-29-week old male NOD mice, a phenotype correlating directly with body burden of glucose during oral glucose challenge. Using surrogates for {beta}-cell function and apoptosis, the partial penetrance of euglycemia in Gz {beta}KO NOD was best explained by an early failure to up-regulate {beta}-cell proliferation. We conclude {beta}-cell Gz is an important regulator of the sexually-dimorphic T1D-like phenotype of NOD mice. Yet, other factors must be important in imparting full protection from the disease.


title: Intranasal type I interferon treatment is beneficial only when administered before clinical signs onset in the SARS-CoV-2 hamster model

abstract:
Impaired type I interferons (IFNs) production or signaling have been associated with severe COVID-19, further promoting the evaluation of recombinant type I IFNs as therapeutics against SARS-CoV-2 infection. In the Syrian hamster model, we show that intranasal administration of IFN- starting one day pre-infection or one day post-infection limited weight loss and decreased viral lung titers. By contrast, intranasal administration of IFN- starting at the onset of symptoms three days post-infection had no impact on the clinical course of SARS-CoV-2 infection. Our results provide evidence that early type I IFN treatments are beneficial, while late interventions are ineffective, although not associated with signs of enhanced disease.

One Sentence SummaryThe timing of type I interferon treatment is a critical determinant of its efficacy against SARS-CoV-2 infection.


title: A Human 3D neural assembloid model for SARS-CoV-2 infection

abstract: Clinical evidence suggests the central nervous system (CNS) is frequently impacted by SARS-CoV-2 infection, either directly or indirectly, although mechanisms remain unclear. Pericytes are perivascular cells within the brain that are proposed as SARS-CoV-2 infection points1. Here we show that pericyte-like cells (PLCs), when integrated into a cortical organoid, are capable of infection with authentic SARS-CoV-2. Prior to infection, PLCs elicited astrocytic maturation and production of basement membrane components, features attributed to pericyte functions in vivo. While traditional cortical organoids showed little evidence of infection, PLCs within cortical organoids served as viral  replication hubs, with virus spreading to astrocytes and mediating inflammatory type I interferon transcriptional responses. Therefore, PLC-containing cortical organoids (PCCOs) represent a new  assembloid model2 that supports SARS-CoV-2 entry and replication in neural tissue, and PCCOs serve as an experimental model for neural infection.


title: homeRNA: A self-sampling kit for the collection of peripheral blood and stabilization of RNA

abstract: Gene expression analysis (e.g., targeted gene panels, transcriptomics) from whole blood can elucidate mechanisms of immune function and aid in the discovery of biomarkers. Conventional venipuncture offers only a small snapshot of our broad immune landscape as immune responses may occur outside of the time and location parameters available for conventional venipuncture. A self-operated method that enables flexible sampling of liquid whole blood coupled with immediate stabilization of cellular RNA is instrumental in facilitating capture and preservation of acute or transient immune fluxes. To this end, we developed homeRNA: a kit for self-collection of peripheral blood ([~]0.5 mL) and immediate stabilization of cellular RNA, using the Tasso- SST blood collection device with a specially designed stabilizer tube containing RNAlater. To assess the feasibility of homeRNA for self-collection and stabilization of whole blood RNA, we conducted a pilot study (n = 47 participants) where we sent homeRNA to participants aged 21-69, located across 10 US states (94% successful blood collections, n = 61/65). Among participants who successfully collected blood, 93% reported no or minimal pain/discomfort using the kit (n = 39/42), and 79% reported very easy/somewhat easy stabilization protocol (n = 33/42). Total RNA yield from the stabilized samples ranged between 0.20 {micro}g and 5.99 {micro}g (mean = 1.51 {micro}g), and all but one RNA Integrity Number (RIN) values were above 7.0 (mean = 8.1), indicating limited RNA degradation. Results from this study demonstrate the self-collection and RNA stabilization of whole blood with homeRNA by participants themselves, in their own home.

category: bioengineering


title: Elucidating the patterns of seed-to-seedling transmission of Xanthomonas citri pv. malvacearum, the causal agent of cotton bacterial blight

abstract: Cotton bacterial blight (CBB) was a major disease of cotton in the United States in the early part of the 20th century. The recent reemergence of CBB, caused by Xanthomonas citri pv. malvacearum (Xcm) revealed many gaps in our understanding of this important disease. In this study, we employed a field isolate of Xcm from Georgia USA (WT) to generate a non- pathogenic, hrcV mutant lacking a functional Type III Secretion System (T3SS-). We tagged the WT and T3SS- strains with an auto-bioluminescent Tn7 reporter and compared colonization patterns of susceptible and resistant cotton seedlings using macroscopic image analysis and bacterial load enumeration. Wildtype and T3SS- Xcm strains colonized cotton cotyledons of resistant and susceptible cotton cultivars. However, Xcm populations were significantly higher in susceptible seedlings inoculated with the WT strain. Additionally, WT and T3SS- Xcm strains systemically colonized true leaves, although at different rates. Finally, we observed that seed-to-seedling transmission of Xcm may involve systemic spread through the vascular tissue of cotton plants. These findings yield novel insights into potential Xcm reservoirs for CBB outbreaks.

category: plant biology


title: A linguistic representation in the visual system underlies successful lipreading

abstract: There is considerable debate over how visual speech is processed in the absence of sound and whether neural activity supporting lipreading occurs in visual brain areas. Surprisingly, much of this ambiguity stems from a lack of behaviorally grounded neurophysiological findings. To address this, we conducted an experiment in which human observers rehearsed audiovisual speech for the purpose of lipreading silent versions during testing. Using a combination of computational modeling, electroencephalography, and simultaneously recorded behavior, we show that the visual system produces its own specialized representation of speech that is 1) well-described by categorical linguistic units ("visemes") 2) dissociable from lip movements, and 3) predictive of lipreading ability. These findings contradict a long-held view that visual speech processing co-opts auditory cortex after early visual processing stages. Consistent with hierarchical accounts of visual and audiovisual speech perception, our findings show that visual cortex performs at least a basic level of linguistic processing.

category: neuroscience


title: A refinement to gene editing in Atlantic salmon using asymmetrical oligonucleotide donors

abstract: Selective breeding programs in aquaculture are limited by the heritability of the trait and long generation time in most fish species. New breeding technology (NBT) using CRISPR/Cas9-induced homology directed repair (HDR) have the potential to expedite genetic improvement in aquaculture, but the method requires optimization. Here we show that asymmetrical oligonucleotide (ODN) donors induce highly efficient and precise edits in individual Atlantic salmon founder animals. We performed single nucleotide replacement (SNR) in dnd with up to 59.2% efficiency, and inserted FLAG elements into slc45a2 and dnd, with up to 36.7 % and 32.7% efficiency, respectively. We found HDR efficiency to be dependent on template concentration, but a trade-off with respect to toxicity was observed. Using this NBT in salmon we demonstrate that precise modification of the genome can be achieved in a single generation, allowing efficient introgression of favorable alleles and bypassing challenges associated with traditional selective breeding.


title: Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction

abstract: Stratified squamous epithelium of the esophagus is comprised of basal keratinocytes that execute a terminal differentiation program in overlying suprabasal and superficial cell layers. Although morphologic progression coupled with expression of specific molecular markers has been characterized along the esophageal epithelial differentiation gradient, the molecular heterogeneity within the cell types along this trajectory has yet to be classified at the level of single cell resolution. To explore the molecular characteristics of esophageal keratinocytes along the squamous differentiation continuum, we performed single cell RNA-Sequencing transcriptomic profiling of 7,972 cells from murine esophageal epithelial sheets. We identified 8 distinct cell clusters in esophageal epithelium, unveiling an unexpected level of diversity, particularly among basal cells. We further mapped the cellular pathways and lineage trajectories within basal, suprabasal, and superficial clusters as well as within the heterogeneous basal cell populations, providing a comprehensive molecular view of esophageal epithelial cells in the context of squamous differentiation. Finally, we explored the impact of tissue aging upon esophageal epithelial cell clusters and demonstrated that mitochondrial dysfunction is a feature of aging in normal esophageal epithelium. These studies provide an unparalleled molecular perspective on murine esophageal keratinocytes that will serve as a valuable resource for dissecting cell type-specific roles in esophageal biology under conditions of homeostasis, aging, and tissue pathology.


title: Improving germline transmission efficiency in chimeric chickens using a multi-stage injection approach

abstract: Although different strategies have been developed to generate transgenic poultry, low efficiency of germline transgene transmission has remained a challenge in poultry transgenesis. Herein, we developed an efficient germline transgenesis method using a lentiviral vector system in chickens through multiple injections of transgenes into embryos at different stages of development. The embryo chorioallantoic membrane (CAM) vasculature was successfully used as a novel route of gene transfer into germline tissues. We established a new method of eggshell windowing for embryo manipulation at different developmental stages. Compared to the other routes of viral vector administration, the embryos bloodstream at Hamburger-Hamilton (HH) stages 14-15 achieved the highest rate of germline transmission (GT), 7.7%. Single injection of viral vectors into the CAM vasculature resulted in a GT efficiency of 2.7%, which was significantly higher than the 0.4% obtained by injection into embryos at the blastoderm stage. Double injection of viral vectors into the bloodstream at HH stages 14-15 and through CAM was the most efficient method for producing germline chimeras, giving a GT rate of 13.6%. The authors suggest that the new method described in this study could be efficiently used to produce transgenic poultry in virus-mediated gene transfer systems.

category: developmental biology


title: Yield Maintenance Under Drought is Orchestrated by the qDTY12.1-Encoded DECUSSATE Gene of Rice Through a Network With Other Flowering-Associated Genes Across the Genetic Background

abstract:
Introgression of major-effect QTLs is an important component of rice breeding for yield-retention under drought. While largely effective, the maximum potentials of such QTLs have not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background could either enhance or undermine the QTL effects. To elucidate the molecular underpinnings of such interaction, we dissected qDTY12.1 synergy with numerous peripheral genes in context of network rewiring effects. By integrative transcriptome profiling and network modeling, we identified the DECUSSATE (OsDEC) within qDTY12.1 as the core of the synergy and shared by two sibling introgression lines in IR64 genetic background, i.e., LPB (low-yield penalty) and HPB (high-yield penalty). OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway, which are lacking in HPB. Results further support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. We propose that the functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the depletion of photosyntate needed for reproductive growth due to drought. Its impact on yield-retention is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought.

Author summaryWhile the Green Revolution of the 1960s significantly increased rice grain yields through the creation of high-yielding varieties for high input systems, current marginal climates pose a significant challenge for providing consistent yield. In rice growing regions of the world, drought affects the livelihood of small-scale and subsistence farmers by inflicting significant yield penalties to their production systems. Breeding of next-generation rice varieties with optimal balance of survivability and productivity traits will be key to providing consistent yields year to year. Within this paradigm, the use of large effect QTLs such as qDTY12.1 to improve yield retention under drought have been largely successful. By integrating the use of high resolution transcriptome datasets with a focused biological interrogation of agronomic results from this and previous studies, we uncovered a putative functional genetic network, anchored by the DECUSSATE gene (OsDEC) within qDTY12.1, that effectively minimizes drought penalties to yield by driving cellular processes that culminate in timely flowering that maximizes the use of photosynthetic sources for efficient reproduductive transition and ultimately seed development. Our study further illuminates the qDTY12.1 function and speaks to the misconception that qDTY introgression alone is sufficient for providing consistently large positive effects to yield retention under reproductive stage drought.

category: genetics


title: Relative brain size and cognitive equivalence in fishes

abstract: There are two well-established facts about vertebrate brains: brains are physiologically costly organs, and both absolute and relative brain size varies greatly between and within the major vertebrate clades. While the costs are relatively clear, scientists struggle to establish how larger brains translate into higher cognitive performance. Part of the challenge is that intuitively larger brains are needed to control larger bodies without any changes in cognitive performance. Therefore, body size needs to be controlled to establish the slope of cognitive equivalence between animals of different sizes. Potentially, intraspecific slopes provide the best available estimate of how an increase in body size translates into an increase in brain size without changes in cognitive performance. Here, we provide the first evaluation of this hypothesis for fishes. First, a dataset of 51 species that included only samples of [≥] ten wild-caught individuals yielded a mean brain-body slope of 0.46 (albeit with a large range of 0.26 to 0.79). This mean slope is similar to the encephalisation quotients for ectotherm higher taxa, i.e. teleost fishes, amphibians and reptiles ([~] 0.5). However, the slope is much higher than what has been found in endotherm vertebrate species ([~] 0.3). Second, we provide slope estimates for brain-body sizes and for cognition-body sizes in wild-caught cleaner fish Labroides dimidiatus as a case study. Brain-body slopes from two datasets gave the values of 0.58 (MRI scans data) and 0.47 (dissection data). Furthermore, we have cognitive performance data from 69 individuals tested in four different cognitive tasks that estimated learning, numerical, and inhibitory control abilities. In all four tasks, the cognitive performance did not correlate significantly with body size. These results suggest that the brain-body slopes represent estimates of intraspecific cognitive equivalence for this species. While subject to further studies on various species, our results suggest that endo- and ectotherm brain organisations and resulting cognitive performances are fundamentally different.

category: animal behavior and cognition


title: Checkpoint proteins in patients with precancer and cervical cancer

abstract:
The efficiency of immuno-oncological drugs in treatment cervical cancer is not high. The research of new immunological targets in cervical cancer is actual.

The aim was to study the local level of checkpoint proteins of immune cycle in patients with cervical cancer of different stages (sCD25, 4-1BB, B7.2, TGF-b1, CTLA-4, PD-L1, PD-1, Tim-3, LAG-3, Galectin-9, sCD27, PD-L2).

Materials and research methods. The objects of study were the patients with precancer (n=13) and cervical cancer (n=49). The control group consisted of 13 gynecologically healthy women. The material of study was cervical epithelium obtained by cervical brush. The research method was flow cytometry. Test parameters: sCD25, 4-1BB, B7.2, TGF-b1, CTLA-4, PD-L1, PD-1, Tim-3, LAG-3, Galectin-9, sCD27, PD-L2. Statistical analysis of the data was carried out using nonparametric statistics using the Mann - Whitney U-test. The results of the study.

The levels of sCD25, B7.2, PDL1, Tim-3, sCD27, PD-L2 were increased in the comparison groups relation to the control (p <0.05). The differential criterion for invasive cervical cancer may be an increase in the level of LAG-3 in the cervical epithelium by 43% (p <0.05).The levels of PD-L1, PD-1, sCD27 and PD-L2 were increased opposite the levels LAG-3 and Galectin-9 were decreased in patients with metastatic cervical cancer(p <0.05).

category: cancer biology


title: Interspecies activation correlations reveal functional correspondences between marmoset and human brain areas

abstract: The common marmoset has enormous promise as a nonhuman primate model of human brain functions. While resting-state functional magnetic resonance imaging (fMRI) has provided evidence for a similar organization of marmoset and human cortices, the technique cannot be used to map the functional correspondences of brain regions between species. This limitation can be overcome by movie-driven fMRI (md-fMRI), which has become a popular tool for non-invasively mapping the neural patterns generated by rich and naturalistic stimulation. Here, we used md-fMRI in marmosets and humans to identify whole-brain functional correspondences between the two primate species. In particular, we describe functional correlates for the well-known human face, body, and scene patches in marmosets. We find that these networks have a similar organization in both species, suggesting a largely conserved organization of higher-order visual areas between New World marmoset monkeys and humans. However, while face patches in humans and marmosets were activated by marmoset faces, only human face patches responded to the faces of other animals. Together, the results demonstrate that md-fMRI is a powerful tool for interspecies functional mapping and characterization of higher-order visual functions.


title: Wing structure and neural encoding jointly determine sensing strategies in insect flight

abstract: Animals rely on sensory feedback to generate accurate, reliable movements. In many flying insects, strain-sensitive neurons on the wings provide rapid feedback that enables stable flight control. While the impacts of wing structure on aerodynamic performance have been widely studied, the impacts of wing structure on sensing remain unexplored. In this paper, we show how the structural properties of the wing and encoding by mechanosensory neurons interact to jointly determine optimal sensing strategies and performance. Specifically, we examine how neural sensors can be placed effectively over a flapping wing to detect body rotation about different axes, using a computational wing model with varying flexural stiffness inspired by the hawkmoth Manduca sexta. A small set of mechanosensors, conveying strain information at key locations with a single action potential per wingbeat, permit accurate detection of body rotation. Optimal sensor locations are concentrated at either the wing base or the wing tip, and they transition sharply as a function of both wing stiffness and neural threshold. Moreover, the sensing strategy and performance is robust to both external disturbances and sensor loss. Typically, only five sensors are needed to achieve near-peak accuracy, with a single sensor often providing accuracy well above chance. Our results show that small-amplitude, dynamic signals can be extracted efficiently with spatially and temporally sparse sensors in the context of flight. The demonstrated interaction of wing structure and neural encoding properties points to the importance of their joint evolution.


title: Synaptotagmin 7 is enriched at the plasma membrane to promote vesicle docking and control synaptic plasticity

abstract:
Synaptotagmin (SYT) 7 has emerged as key regulator of presynaptic function, but its localization and precise function in the synaptic vesicle cycle remain unclear. Here, we used iGluSnFR to optically and directly interrogate glutamate release, at the single bouton level, in SYT7 KO dissociated mouse hippocampal neurons. We analyzed asynchronous release, paired pulse facilitation, and synaptic vesicle replenishment, and found that SYT7 contributes to each of these processes to different degrees.  Zap-and-freeze electron microscopy revealed that loss of SYT7 impairs the docking of synaptic vesicles after a stimulus and the recovery of depleted synaptic vesicles after a stimulus train. To execute these functions, SYT7 must be targeted to the plasma membrane via {gamma}-secretase-mediated cleavage of the amino terminus, followed by palmitoylation. The complex sorting itinerary of SYT7 endows this Ca2+-sensor with the ability to control crucial forms of synaptic function and plasticity.

O_LISYT7 mediated asynchronous release, paired pulse facilitation, and synaptic vesicle replenishment was observed optically at individual hippocampal synapses
C_LIO_LILocalization, trafficking, and stability of SYT7 is dependent on processing by {gamma}-secretase
C_LIO_LIShort term plasticity defects arise in SYT7KOs due to decreased docking of synaptic vesicles after stimulation
C_LIO_LISYT7 promotes paired-pulse facilitation and asynchronous release via distinct mechanisms
C_LI


title: Reward enhances online participants' engagement with a demanding auditory task

abstract: Online recruitment platforms are increasingly utilized for experimental research. Crowdsourcing is associated with numerous benefits but also notable constraints, including lack of control over participants environment and engagement. In the context of auditory experiments, these limitations may be particularly detrimental to threshold-based tasks that require effortful listening. Here, we ask whether incorporating a performance-based monetary bonus will improve speech reception performance of online participants. In two experiments, participants performed an adaptive matrix-type speech-in-noise task (where listeners select two key words out of closed sets). In Experiment 1, our results revealed worse performance in online (N = 49) compared with in-lab (N = 81) groups. Specifically, relative to the in-lab cohort, significantly fewer participants in the online group achieved very low (< -17dB) thresholds. In Experiment 2 (N = 200), we show that a monetary reward improved listeners threshold to levels similar to those observed in the lab setting. Overall the results suggest that providing a small performance-based bonus increases participants task-engagement, facilitating a more accurate estimation of auditory ability under challenging listening conditions.


title: Linking Labs: Interconnecting Experimental Environments

abstract: We introduce the concept of LabLinking: a technology-based interconnection of experimental laboratories across institutions, disciplines, cultures, languages, and time zones - in other words experiments without borders. In particular, we introduce LabLinking levels (LLL), which define the degree of tightness of empirical interconnection between labs. We describe the technological infrastructure in terms of hard- and software required for the respective LLLs and present examples of linked laboratories along with insights about the challenges and benefits. In sum, we argue that linked labs provide a unique platform for a continuous exchange between scientists and experimenters, thereby enabling a time synchronous execution of experiments performed with and by decentralized user and researchers, improving outreach and ease of subject recruitment, allowing to establish new experimental designs and to incorporate a panoply of complementary biosensors, devices, hard- and software solutions.


title: High expression of CD38 and MHC class II on CD8+ T cells during severe influenza disease reflects bystander activation and trogocytosis

abstract:
Although co-expression of CD38 and HLA-DR on CD8+ T cells reflects activation during influenza, SARS-CoV-2, Dengue, Ebola and HIV-1 viral infections, high and prolonged CD38+HLA-DR+ expression can be associated with severe and fatal disease outcomes. As the expression of CD38+HLA-DR+ is poorly understood, we used mouse models of influenza A/H7N9, A/H3N2 and A/H1N1 infection to investigate the mechanisms underpinning CD38+MHC-II+ phenotype on CD8+ T-cells. Our analysis of influenza-specific immunodominant DbNP366+CD8+ T-cell responses showed that CD38+MHC-II+ co-expression was detected on both virus-specific and bystander CD8+ T-cells, with increased numbers of both CD38+MHC-II+CD8+ T-cell populations observed in the respiratory tract during severe infection. To understand the mechanisms underlying CD38 and MHC-II expression, we also used adoptively-transferred transgenic OT-I CD8+ T-cells recognising the ovalbumin-derived KbSIINFEKL epitope and A/H1N1-SIINKEKL infection. Strikingly, we found that OT-I cells adoptively-transferred into MHC-II-/- mice did not display MHC-II after influenza virus infection, suggesting that MHC-II was acquired via trogocytosis in wild-type mice. Additionally, detection of CD19 on CD38+MHC II+ OT-I cells further supports that MHC-II was acquired by trogocytosis, at least partially, sourced from B-cells. Our results also revealed that co-expression of CD38+MHC II+ on CD8+ T-cells was needed for the optimal recall ability following secondary viral challenge. Overall, our study provides evidence that both virus-specific and bystander CD38+MHC-II+ CD8+ T-cells are recruited to the site of infection during severe disease, and that MHC-II expression occurs via trogocytosis from antigen-presenting cells. Our findings also highlight the importance of the CD38+MHC II+ phenotype for CD8+ T-cell memory establishment and recall.

SummaryCo-expression of CD38 and MHC-II on CD8+ T cells is recognized as a classical hallmark of activation during viral infections. High and prolonged CD38+HLA-DR+ expression, however, can be associated with severe disease outcomes and the mechanisms are unclear. Using our established influenza wild-type and transgenic mouse models, we determined how disease severity affected the activation of influenza-specific CD38+MHC-II+CD8+ T cell responses in vivo and the antigenic determinants that drive their activation and expansion. Overall, our study provides evidence that both virus-specific and bystander CD38+MHC-II+ CD8+ T-cells are recruited to the site of infection during severe disease, and that MHC-II expression occurs, at least in part, via trogocytosis from antigen-presenting cells. Our findings also highlight the importance of the CD38+MHC II+ phenotype for CD8+ T-cell memory establishment and recall.

category: immunology


title: Streptococcus pyogenes forms serotype and local environment-dependent inter-species protein complexes

abstract: Streptococcus pyogenes is known to cause both mucosal and systemic infections in humans. In this study, we used a combination of quantitative and structural mass spectrometry techniques to determine the composition and structure of the interaction network formed between human plasma proteins and the surface of different S. pyogenes serotypes. Quantitative network analysis revealed that S. pyogenes form serotype-specific interaction networks that are highly dependent on the domain arrangement of the surface-attached M protein. Subsequent structural mass spectrometry analysis and computational modelling on one of the M proteins, M28 revealed that the network structure changes across different host microenvironments. We report that M28 binds secretory IgA via two separate binding sites with high affinity in saliva. During vascular leakage mimicked by increasing plasma concentrations in saliva, the binding of secretory IgA was replaced by binding of monomeric IgA and C4BP. This indicates that an upsurge of C4BP in the local microenvironment due to damage of the mucosal membrane drives binding of C4BP and monomeric IgA to M28. The results suggest that S. pyogenes has evolved to form microenvironment-dependent host-pathogen protein complexes to combat the human immune surveillance during both mucosal and systemic infections.


title: New exon ignites accelerated evolution of placental gene Nrk in the ancestral lineage of eutherians

abstract: Accelerated evolution is often driven by the interaction between environmental factors and genes. However, it remains unclear whether accelerated evolution can be ignited. Here, we focused on adaptive events during the emergence of chorioallantoic placenta. We scanned the chromosome X and identified eight accelerated regions in the ancestral lineage of eutherian mammals. Five of these regions (P = 5.61 x 10-11 ~ 9.03 x 10-8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Moreover, a eutherian-specific exogenous exon lack of splice variant was found to be conserved. Structure modelling of NRK suggests that the accelerated exons and the eutherian-specific exon could change the enzymatic activity of eutherian NRK. Since the eutherian-specific exon was surrounded by accelerated exons, it indicates that the accelerated evolution of Nrk may be ignited by the emergence of the new exon in the ancestral lineage of eutherian mammals. The new exon might shift the function of Nrk and provide a new fitness landscape for eutherian species to explore. Although multiple exons were accelerated in both of the Nrk catalytic and regulatory domains, positive selection can only be revealed on the regulatory domain if the branch specific nonsynonymous and synonymous rate test was performed by PAML. Thus, it may be important to detect accelerated evolution when studying positive selection on coding regions. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection. Identifying positively selected placental genes provides insights into how eutherian mammals gain benefits from the invasive chorioallantoic placenta to form one of the most successful groups among terrestrial vertebrates.


title: Motor Sequences - Separating The Sequence From The Motor. A longitudinal rsfMRI Study

abstract: In motor learning, sequence-specificity, i.e. the learning of specific sequential associations, has predominantly been studied using task-based fMRI paradigms. However, offline changes in resting state functional connectivity after sequence-specific motor learning are less well understood. Previous research has established that plastic changes following motor learning can be divided into stages including fast learning, slow learning and retention. A description of how resting state functional connectivity after sequence-specific motor sequence learning (MSL) develops across these stages is missing. This study aimed to identify plastic alterations in whole-brain functional connectivity after learning a complex motor sequence by contrasting an active group who learned a complex sequence with a control group who performed a control task matched for motor execution. Resting state fMRI and behavioural performance were collected in both groups over the course of 5 consecutive training days and at follow-up after 12 days to encompass fast learning, slow learning, overall learning and retention. Between-group interaction analyses showed sequence-specific decreases in functional connectivity during overall learning in the right supplementary motor area (SMA). We found that connectivity changes in key regions of the motor network including the superior parietal cortex (SPC) and primary motor cortex (M1) were not a result of sequence-specific learning but were instead linked to motor execution. Our study confirms the sequence-specific role of SMAthat has previously been identified in online task-based learning studies, and extends it to resting state network changes after sequence-specific MSL.


title: Chloroplast redox state changes indicate cell-to-cell signalling during the hypersensitive response

abstract: Hypersensitive response (HR)-conferred resistance is associated with an induction of programmed cell death (PCD) and pathogen spread restriction in its proximity. While the pivotal role of salicylic acid (SA) in the restriction of pathogen spread during HR has been confirmed, the exact role of chloroplastic reactive oxygen species and the link between SA signalling and chloroplast redox state during HR remain unexplained. To unravel these relationships, we performed detailed spatiotemporal analysis of chloroplast redox response to potato virus Y (PVY) infection in resistant Ny-1-gene-bearing potato and its transgenic counterpart with impaired SA accumulation and compromised resistance. We found that the chloroplasts are highly oxidized in the cells adjacent to the cell death zone at different stages after virus inoculation in both genotypes. Moreover, we detected individual cells with moderately oxidized chloroplasts, which we call "signalling cells", in close proximity as well as farther from the cell death zone. These are relatively rare in SA-deficient plants, suggesting their role in signalling for HR-conferred resistance. This hypothesis is further supported by highly induced formation of stroma filled tubules that extend from chloroplasts (stromules) in the cells adjacent to signalling cells. Unexpectedly, the cells with the highest occurrence of stromules have chloroplasts in more reduced state than the adjacent ones. In addition, we show that stromules are induced also at the edge of PVY multiplication zone. We conclude that chloroplast redox state and stromule formation are tightly spatiotemporally regulated by SA-signalling which leads to effective HR response.


title: Neuromesodermal progenitor origin of trunk neural crest in vivo

abstract: Neural crest (NC) is a vertebrate-specific population of multipotent embryonic cells predisposed to diverse derivatives along the anteroposterior (A-P) axis. Only cranial NC progenitors give rise to ectomesenchymal cell types, whereas trunk NC is biased for neuronal cell fates. By integrating multimodal single-cell analysis, we provide evidence for divergent embryonic origins of cranial vs. trunk NC that explain this dichotomy. We show that the NC regulator foxd3 is heterogeneously expressed across the A-P axis and identify its specific cranial and trunk autoregulatory enhancers. Whereas cranial-specific enhancer is active in the bona fide NC, the trunk foxd3 autoregulatory element surprisingly marked bipotent tailbud neuromesodermal progenitors (NMps). We integrated NMp single cell epigemomics and trasncriptomics data and for the first time reconstructed anamniote NMp gene regulatory network. Moreover, using pseudotime and developmental trajectory analyses of NMps and NC during normal development and in foxd3 mutants, we demonstrate an active role for foxd3 in balancing non-cranial NC and NMp fates during early embryonic development. Strikingly, we show that a portion of posterior NC in the developing zebrafish embryo is derived from the pro-neural NMps. This suggests a common embryonic origin of trunk NC and NM progenitors that is distinct from cranial NC anlage, and elucidates pro-neural bias of trunk NC.


title: The foraging gene affects alcohol sensitivity, metabolism and memory in Drosophila

abstract: The genetic basis of alcohol use disorder (AUD) is complex. Understanding how natural genetic variation contributes to alcohol phenotypes can help identify mechanisms underlying the genetic contribution of AUD. Recently, a single nucleotide polymorphism in the human foraging (for) gene ortholog, Protein Kinase cGMP-Dependent 1 (PRKG1), was found to be associated with stress-induced risk for alcohol abuse. However, the mechanistic role that PRKG1 plays in AUD is not well understood. We use natural variation in the Drosophila for gene to describe how variation of cGMP-dependent protein kinase (PKG) activity modifies ethanol-induced phenotypes. We found that variation in for affects ethanol-induced increases in locomotion and memory of the appetitive properties of ethanol intoxication. Further, these differences may stem from the ability to metabolize ethanol. Together, this data suggests that natural variation in PKG modulates cue reactivity for alcohol, and thus could influence alcohol cravings by differentially modulating metabolic and behavioral sensitivities to alcohol.


title: Assessing evolutionary and developmental transcriptome dynamics in homologous cell types

abstract:
BackgroundDuring development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built - largely - by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear.

ResultsHere, using a paradigm of morphological diversification, the tetrapod limb, and singlecell RNA-sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. We developed a user-friendly bioinformatics workflow to detect gene co-expression modules and test for their conservation across developmental stages and species boundaries. Using mouse limb data as reference, we identified 19 gene co-expression modules with varying tissue or cell type-restricted activities. Testing for co-expression conservation revealed modules with high evolutionary turnover, while others seemed maintained - to different degrees, in module make-up, density or connectivity - over developmental and evolutionary timescales.

ConclusionsWe present an approach to identify evolutionary and developmental dynamics in gene co-expression modules during patterning-relevant stages of homologous cell type specification.


title: Customized de novo mutation detection for any variant calling pipeline: SynthDNM

abstract:
MotivationAs sequencing technologies and analysis pipelines evolve, DNM calling tools must be adapted. Therefore, a flexible approach is needed that can accurately identify de novo mutations from genome or exome sequences from a variety of datasets and variant calling pipelines.

ResultsHere, we describe SynthDNM, a random-forest based classifier that can be readily adapted to new sequencing or variant-calling pipelines by applying a flexible approach to constructing simulated training examples from real data. The optimized SynthDNM classifiers predict de novo SNPs and indels with robust accuracy across multiple methods of variant calling.

AvailabilitySynthDNM is freely available on Github (https://github.com/james-guevara/synthdnm)

Contactjsebat@ucsd.edu

Supplementary informationSupplementary data are available at Bioinformatics online.


title: Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer

abstract: Prostate cancer is profoundly heterogeneous and patients would benefit from methods that stratify clinically indolent from more aggressive forms of the disease. We employed single-cell assay for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide. In doing so, we identified pre-existing and treatment-persistent cell subpopulations that possess transcriptional stem-like features and regenerative potential when subjected to treatment. We found distinct chromatin landscapes associated with enzalutamide treatment and resistance that are linked to alternative transcriptional programs. Transcriptional profiles characteristic of persistent stem-like cells were able to stratify the treatment response of patients. Ultimately, we show that defining changes in chromatin and gene expression in single-cell populations from pre-clinical models can reveal hitherto unrecognized molecular predictors of treatment response. This suggests that high analytical resolution of pre-clinical models may powerfully inform clinical decision-making.


title: Reversible blood-brain barrier opening utilizing the membrane active peptide melittin in vitro and in vivo

abstract: The blood-brain barrier (BBB) tightly controls entry of molecules and cells into the brain, restricting the delivery of therapeutics. Blood-brain barrier opening (BBBO) utilizes reversible disruption of cell-cell junctions between brain microvascular endothelial cells to enable transient entry into the brain. Development of BBBO techniques has been hindered by a lack of physiological models for in vitro study. Here, we utilize an in vitro tissue-engineered microvessel model to demonstrate that melittin, a membrane active peptide present in bee venom, supports BBBO. From endothelial and neuronal viability studies, we identify the accessible concentration range for BBBO. We then use a tissue-engineered model of the human BBB to optimize dosing and elucidate the mechanism of opening. Melittin and other membrane active variants transiently increase paracellular permeability via disruption of cell-cell junctions. In mice, we demonstrate a minimum clinically effective intra-arterial dose of 3 M{middle dot}min melittin, which is reversible within one day and neurologically safe. Melittin-induced BBBO represents a novel platform for delivery of therapeutics into the brain.


title: Patient-specific cell communication networks associate with disease progression in cancer

abstract: The maintenance and function of tissues in health and disease depends on cell-cell communication. This work shows how high-level features, representing cell-cell communication, can be defined and used to associate certain signaling  axes with clinical outcomes. Using cell-sorted gene expression data, we generated a scaffold of cell-cell interactions and define a probabilistic method for creating per-patient weighted graphs based on gene expression and cell deconvolution results. With this method, we generated over 9,000 graphs for TCGA patient samples, each representing likely channels of intercellular communication in the tumor microenvironment. It was shown that particular edges were strongly associated with disease severity and progression, in terms of survival time and tumor stage. Within individual tumor types, there are predominant cell types and the collection of associated edges were found to be predictive of clinical phenotypes. Additionally, genes associated with differentially weighted edges were enriched in Gene Ontology terms associated with tissue structure and immune response. Code, data, and notebooks are provided to enable the application of this method to any expression dataset (https://github.com/IlyaLab/Pan-Cancer-Cell-Cell-Comm-Net).


title: ACE: Explaining cluster from an adversarial perspective

abstract: A common workflow in single-cell RNA-seq analysis is to project the data to a latent space, cluster the cells in that space, and identify sets of marker genes that explain the differences among the discovered clusters. A primary drawback to this three-step procedure is that each step is carried out independently, thereby neglecting the effects of the nonlinear embedding and inter-gene dependencies on the selection of marker genes. Here we propose an integrated deep learning framework, Adversarial Clustering Explanation (ACE), that bundles all three steps into a single work-flow. The method thus moves away from the notion of "marker genes" to instead identify a panel of explanatory genes. This panel may include genes that are not only enriched but also depleted relative to other cell types, as well as genes that exhibit differences between closely related cell types. Empirically, we demonstrate that ACE is able to identify gene panels that are both highly discriminative and nonredundant, and we demonstrate the applicability of ACE to an image recognition task. 1


title: On the application of BERT models for nanopore methylation detection

abstract:
MotivationDNA methylation is a common epigenetic modification, which is widely associated with various biological processes, such as gene expression, aging, and disease. Nanopore sequencing provides a promising methylation detection approach through monitoring abnormal signal shifts for detecting modified bases in target motif regions. Recently, model-based approaches, especially those with deep learning models, have achieved significant performance improvements on nanopore methylation detection. In this work, we explore using bidirectional encoder representations from transformers (BERT) for doing the task, which can provide non-recurrent neural structures for fast parallel computation.

ResultsWe find original BERT architecture does not work as well as the bidirectional recurrent neural network (biRNN) on the nanopore methylation prediction task. Through further analysis, we observe recurrent patterns of positional-signal-shift in the context window surrounding target 5-methylcytosine (5mC) and N6-methyladenine (6mA) motifs. We propose a refined BERT with relative position representation and center hidden units concatenation, which takes account of task-specific characters into modeling. We perform systematic evaluations in-sample and cross-sample. The experiment results show that the refined BERT model can achieve competitive or even better results than the state-of-the-art biRNN model, while the model inference speed is about 6x faster. Besides, on the cross-sample evaluation of datasets from the different research groups, BERT models demonstrate a good generalization performance.

AvailabilityThe source code and data are available at https://github.com/yaozhong/methBERT

Contactyaozhong@ims.u-tokyo.ac.jp


title: A comparative study of genomic adaptations to low nitrogen availability in Genlisea aurea

abstract: Genlisea aurea is a carnivorous plant that grows on nitrogen-poor waterlogged sandstone plateaus and is thought to have evolved carnivory as an adaptation to very low nitrogen levels in its habitat. The carnivorous plant is also unusual for having one of the smallest genomes among flowering plants. Genomic DNA is known to have a high nitrogen content and yet, to the authors knowledge, no published study has linked nitrogen starvation of G. aurea with genome size reduction. This comparative study of the carnivorous plant G. aurea, the model organism Arabidopsis thaliana (Brassicaceae) and the nitrogen fixing Trifolium pratense (Fabaceae) attempts to investigate whether the genome, transcriptome and proteome of G. aurea showed evidence of adaptations to low nitrogen availability. It was found that although G. aureas genome, CDS and non-coding DNA were much lower in nitrogen than the genome of T. pratense and A. thaliana this was solely due to the length of the genome, CDS and non-coding sequences rather than the composition of these sequences.


title: Diet High in Soybean Oil Increases Susceptibility to Colitis in Mice

abstract: Soybean oil (SO), the most prevalent cooking oil in the United States, consists primarily of linoleic acid (LA, C18:2 omega-6), a polyunsaturated fatty acid positively linked to the development of ulcerative colitis (UC) in humans. Here, we show that dietary SO increases intestinal epithelial barrier permeability and susceptibility to colitis in mice. It also disrupts the balance of isoforms encoded by the UC susceptibility gene Hepatocyte Nuclear Factor 4 (HNF4), which in turn impacts barrier function and IBD susceptibility. The SO diet causes gut dysbiosis, including an increased abundance of an adherent, invasive Escherichia coli (AIEC) which can use LA as a carbon source. Metabolomic analysis indicates that gut bacteria and the SO diet can alter levels of LA and its oxylipin and endocannabinoid metabolites in the gut. Our results suggest that an SO-enriched diet increases susceptibility to colitis due to effects on intestinal HNF4, microbiota and LA metabolites.


title: Serum and sputum MMP-9/TIMP-1 in winter sports athletes and swimmers: relationships with airway function

abstract:
IntroductionCross-country skiers and swimmers present characteristics of airway inflammation and remodeling of the extracellular matrix similar to what is observed in mild asthma. We aimed to compare serum and sputum MMP-9/TIMP-1 levels, to assess the balance between airway fibrogenesis and inflammation process in both categories of athletes, and to observe its seasonal variations in winter sports athletes.

MethodsCompetitive winter sports athletes (n=41), swimmers (n=25) and healthy nonathletes (n=10) had blood sampling, lung function measurement, skin prick tests, eucapnic voluntary hyperpnea challenge, methacholine inhalation test (MIT), and induced sputum analysis. Twelve winter sport athletes performed the test during both summer and winter. Serum and sputum MMP-9 and TIMP-1 were measured by ELISA.

ResultsNo significant difference in serum or sputum MMP-9/TIMP-1 ratio was observed between groups, nor relationship with airway function or responsiveness. Serum MMP-9/TIMP-1 ratio was significantly higher during the summer in winter sport athletes compared with winter season (median [Interquartile range]: 3.65 [2.47-4.03] ng.ml-1 and 1.27 [0.97-1.62] ng.ml-1, respectively, p=0.005). Sputum MMP-9 correlated with Methacholine PC20 and serum CC16/SP-D ratio.

ConclusionMMP-9/TIMP-1 ratio in sputum or serum may fluctuate with training or environment but does not correlate with airway lung function or responsiveness in competitive athletes.


title: Resting-state brain activity can predict target-independent aptitude in fMRI-neurofeedback training

abstract: Neurofeedback (NF) aptitude, which refers to an individuals ability to change its brain activity through NF training, has been reported to vary significantly from person to person. The prediction of individual NF aptitudes is critical in clinical NF applications. In the present study, we extracted the resting-state functional brain connectivity (FC) markers of NF aptitude independent of NF-targeting brain regions. We combined the data in fMRI-NF studies targeting four different brain regions at two independent sites (obtained from 59 healthy adults and six patients with major depressive disorder) to collect the resting-state fMRI data associated with aptitude scores in subsequent fMRI-NF training. We then trained the regression models to predict the individual NF aptitude scores from the resting-state fMRI data using a discovery dataset from one site and identified six resting-state FCs that predicted NF aptitude. Next we validated the prediction model using independent test data from another site. The result showed that the posterior cingulate cortex was the functional hub among the brain regions and formed predictive resting-state FCs, suggesting NF aptitude may be involved in the attentional mode-orientation modulation systems characteristics in task-free resting-state brain activity.


title: Feedforward and feedback interactions between visual cortical areas use different population activity patterns

abstract: Brain function relies on the coordination of activity across multiple, recurrently connected, brain areas. For instance, sensory information encoded in early sensory areas is relayed to, and further processed by, higher cortical areas and then fed back. However, the way in which feedforward and feedback signaling interact with one another is incompletely understood. Here we investigate this question by leveraging simultaneous neuronal population recordings in early and midlevel visual areas (V1-V2 and V1-V4). Using a dimensionality reduction approach, we find that population interactions are feedforward-dominated shortly after stimulus onset and feedback-dominated during spontaneous activity. The population activity patterns most correlated across areas were distinct during feedforward- and feedback-dominated periods. These results suggest that feedforward and feedback signaling rely on separate "channels", such that feedback signaling does not directly affect activity that is fed forward.


title: In vivo optogenetic stimulation of the primate retina activates the visual cortex after long-term transfection

abstract:
Over the last 15 years, optogenetics has changed fundamental research in neuroscience, and is now reaching toward therapeutic applications. Vision restoration strategies using optogenetics are now at the forefront of these new clinical opportunities. But applications to human patients suffering from retinal diseases leading to blindness rise important concerns on the long-term functional expression of optogenes and the efficient signal transmission to higher visual centers. Here we demonstrate in non-human primates, continued expression and functionality at the retina level [~]20 months after delivery of our construct. We also performed in-vivo recordings of visually evoked potentials in the primary visual cortex of anaesthetized animals. Using synaptic blockers, we isolated the in-vivo cortical activation resulting from the direct optogenetic stimulation of primate retina.

In conclusion, our work indicates long-term transgene expression and transmission of the signal generated in the macaque retina to the visual cortex, two important features for future clinical applications.


title: In vivo optogenetic stimulation of the primate retina activates the visual cortex after long-term transduction


title: Effects of treatment with three antibiotics, vancomycin, neomycin, and AVNM on gut microbiome in C57BL/6 mice

abstract: Higher organisms, especially mammals, harbor diverse microbiota in the gut that plays a major role in maintaining health and physiological homeostasis. Perturbation of gut flora helps identifying their roles. Antibiotics are potent perturbing agents of microbiome. Select antibiotics like vancomycin, neomycin, and AVNM (an antibiotic cocktail containing ampicillin, vancomycin, neomycin, and metronidazole) were used to perturb the gut microbiota of C57BL/6 male mice to understand their roles in host immunity and metabolism. The current study revealed that the resulting gut microbial composition was different, and diversity (at the phylum and genus level) was reduced differentially following each antibiotic treatment. Vancomycin treatment caused a significant increase in Verrucomicrobia and Proteobacteria phyla. The treatment with neomycin yielded an increase in the Bacteroidetes phylum, while the treatment with AVNM led to an increase in Proteobacteria phylum with lowest diversity of microbiome in the gut. The current results also revealed that the different antibiotics treatment caused variation in the cecal index, expression of immune genes (TNF-, IL-10, IFN-{gamma}) in the colon, and short-chain fatty acids (SCFA) level in the blood of mice. A strong correlation was observed for antibiotic-induced differential dysbiosis patterns of gut microbiota and the altered immune and SCFA profile of the host. The outcome of the present study could be clinically important.


title: Establishment of a reverse genetic system from a bovine derived Influenza D virus isolate.

abstract: The ruminant-associated Influenza D virus (IDV) has a broad host tropism and was shown to have zoonotic potential. To identify and characterize molecular viral determinants influencing the host spectrum of IDV, a reverse genetic system is required. For this, we first performed 5' and 3' rapid amplification of cDNA ends (RACE) of all seven genomic segments, followed by assessment of the 5' and 3' NCR activity prior to constructing the viral genomic segments of a contemporary Swiss bovine IDV isolate (D/CN286) into the bidirectional pHW-2000 vector. The bidirectional plasmids were transfected in HRT-18G cells followed by viral rescue on the same cell type. Analysis of the segment specific 5' and 3' non-coding regions (NCR) highlighted that the terminal 3' end of all segments harbours an Uracil instead of a Cytosine nucleotide, similar to other Influenza viruses. Subsequent analysis on the functionality of the 5' and 3' NCR in a minireplicon assay revealed that these sequences were functional and that the variable sequence length of the 5' and 3' NCR influences reporter gene expression. Thereafter, we evaluated the replication efficiency of the reverse genetic clone on conventional cell lines of human, swine and bovine origin by use of an in vitro model recapitulating the natural replicate site of IDV in bovine and swine. This revealed that the reverse genetic clone D/CN286 replicates efficiently in all cell culture models. Combined, these results demonstrate the successful establishment of a reverse genetic system from a contemporary bovine IDV isolate that can be used for future identification and characterization of viral determinants influencing the broad host tropism of IDV.


title: Does the ratio of β-1,4-glucosidase (BG) to β-1,4-N-acetylglucosaminidase (NAG) indicate the relative resource allocation of soil microbes to C and N acquisition?

abstract: The ratio of {beta}-1,4-glucosidase (BG) to {beta}-1,4-N-acetylglucosaminidase (NAG) activity (BG:NAG ratio) is often used as an indicator of the relative resource allocation of soil microbes to C acquisition compared with N. An increasing number of recent studies have used this index to assess the nutrient status of microbes. However, the validity of this index for assessing the nutrient status of microbes is not well tested. In this study, we collected published data and tested that validity by investigating whether N fertilization elevated the BG:NAG ratio, assuming that microbes reduce their allocation to the N-acquiring enzyme (NAG) under N-enriched conditions. Of the data points, 54% (82/151) did not support the hypothesis because those studies showed lower BG:NAG ratios in N-enriched soils than under ambient conditions, especially when the ambient BG:NAG ratio was higher than 2.0 (77%, 59/77). This suggests that the BG:NAG ratio does not always indicate the microbial status for C or N limitation. Rather, we hypothesized that the decomposition stage explained the variation in BG:NAG because N addition accelerates decomposition, and the BG:NAG ratio is lower at later stages of decomposition due to the dominance of NAG-targeting C (chitin or peptidoglycan). A negative correlation of BG:NAG ratio with polyphenol oxidase activity, which increases with decomposition, supported our hypothesis.

category: ecology


title: Harmful Algal Bloom-Forming Organism Responds to Nutrient Stress Distinctly From Model Phytoplankton

abstract:
O_LIResources such as nitrogen (N) and phosphorus (P) play an important role in primary production and constraining phytoplankton bloom dynamics. Models to predict bloom dynamics require mechanistic knowledge of algal metabolic shifts in response to resource limitation. For well-studied model phytoplankton like diatoms, this information is plentiful. However, for less-studied groups such as the raphidophytes, there remain significant gaps in understanding metabolic changes associated with nutrient limitation.
C_LIO_LIUsing a novel combination of metabolomics and transcriptomics, we examined how the harmful algal bloom-forming raphidophyte Heterosigma akashiwo shifts its metabolism under N- and P-stress. We chose H. akashiwo because of its ubiquity within estuarine environments worldwide, where bloom dynamics are influenced by N and P availability.
C_LIO_LIOur results show that each stress phenotype is distinct in both the allocation of carbon and the recycling of macromolecules. Further, we identified biomarkers of N- and P-stress that may be applied in situ to help modelers and stakeholders manage, predict, and prevent future blooms.
C_LIO_LIThese findings provide a mechanistic foundation to model the metabolic traits and trade-offs associated with N- and P-stress in H. akashiwo, and evaluate the extent to which these metabolic responses can be inferred in other phytoplankton groups.
C_LI


title: How to count your bugs?

abstract: Ability to estimate local population density of an insect is critical in many fields, from pest management to conservation. No method currently exists that reliably connects trap catch with the insect population density, including the corresponding uncertainty. Here we report a simple and universal predictive relationship for a probability of catching an insect located a given distance away from the trap. This relationship allows to estimate, from a single catch, the most likely population density along with its statistical upper and lower bounds. To test the generality of this equation we used 10 distinct trapping data sets collected on insects from 5 different orders and major trapping methods: chemical-baited and light. For all of the datasets the equation faithfully [Formula] describes the relationship between location of an insect and probability to catch it. The ability to estimate absolute population density from a single trap catch will significantly improve our understanding of insect population dynamics and allow for more effective research, management, and conservation programs.


title: Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes

abstract: The deep-sea remains among the most unknown ecosystems on Earth despite its relevant role in carbon sequestration and increasing threat due to interest by fishing and mining industries. This, together with the recent discovery that the upper layer of this ecosystem (mesopelagic zone) harbors about 90% of the fish biomass on Earth, claims for a deeper understanding of the deep-sea so that the foundations for a sustainable use of its resources can be established. The analysis of environmental DNA (eDNA) collected from the water column emerges as an alternative to traditional methods to acquire this elusive information, but its application to the deep ocean is still incipient. Here, we have amplified and sequenced the fish eDNA contained in vertical profile samples (from surface to 2000 m depth) collected during day and night-time throughout the Bay of Biscay. We found that eDNA-derived deep-sea fish richness and abundance follow a day-night pattern that is consistent with the diel migratory behavior of many mesopelagic species, and that eDNA can reveal species-specific distribution and movement through the water column. These results highlight the potential of eDNA-based studies to improve our knowledge on the species inhabiting the dark ocean before this still pristine ecosystem is exploited.


title: Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels

abstract: Proteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host-pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions associated with particular structural or functional characteristics across the genome, since many proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis of Drosophila protein-coding genes. We found that protein sequence adaptation is more relevant to function-related rather than structure-related properties. Interestingly, intermolecular interactions contribute significantly to protein adaptation. We further showed that intermolecular interactions, such as physical interactions may play a role in the co-adaptation of fast-adaptive proteins. We found that strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. This strongly indicates that a number of adaptive sites tend to be repeatedly mutated and selected in evolution, in the past, present, and maybe future. Our results highlight the important roles of intermolecular interactions and co-adaptation in the adaptive evolution of proteins both at the species and population levels.

category: evolutionary biology


title: Complex introgression history of the erato-sara clade of Heliconius butterflies

abstract: AO_SCPLOWBSTRACTC_SCPLOWIntrogressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species makes estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood analysis methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ full-likelihood methods under the multispecies coalescent (MSC) model with and without gene flow to analyze the genomic data from six members of the erato-sara clade of Heliconius butterflies and infer the species phylogeny and cross-species introgression events. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the sara clade and an ancestral population of H. telesiphe, a likely hybrid speciation origin for H. hecalesia, and gene flow between sister species H. erato and H. himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the multispecies coalescent makes it possible to extract rich historical information of species divergence and gene flow from genomic data.


title: Full-likelihood analysis of genomic data clarifies a complex history of species divergence and introgression in the erato-sara group of Heliconius butterflies


title: Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies


title: Cardiopharyngeal deconstruction and ancestral tunicate sessility

abstract: A key problem in understanding chordate evolution has been the origin of sessility of ascidians, and whether the appendicularian free-living style represents a primitive or derived condition of tunicates. To address this problem, we performed comprehensive developmental and genomic comparative analyses of the cardiopharyngeal gene regulatory network (GRN) between appendicularians and ascidians. Our results reveal that the cardiopharyngeal GRN has suffered a process of evolutionary deconstruction with massive ancestral losses of genes (Mesp, Ets1/2, Gata4/5/6, Mek1/2, Tbx1/10, and RA- and FGF-signaling related genes) and subfunctions (e.g. FoxF, Islet, Ebf, Mrf, Dach and Bmp signaling). These losses have led to the deconstruction of two modules of the cardiopharyngeal GRN that in ascidians are related to early and late multipotent state cells involved in lineage fate determination towards first and secondary heart fields, and siphon muscle. Our results allow us to propose an evolutionary scenario, in which the evolutionary deconstruction of the cardiopharyngeal GRN has had an adaptive impact on the acceleration of the developmental cardiac program, the redesign of the cardiac architecture into an open-wide laminar structure, and the loss of pharyngeal muscle. Our findings, therefore, provide evidence supporting that the ancestral tunicate had a sessile ascidian-like lifestyle, and points to the deconstruction of the cardiopharyngeal GRN in appendicularians as a key event that facilitated the evolution of their pelagic free-living style connected to the innovation of the house.