title: Oncogenic mutations of PIK3CA lead to increased membrane recruitment driven by reorientation of the ABD, p85 and C-terminus

abstract: PIK3CA encoding the phosphoinositide 3-kinase (PI3K) p110 catalytic subunit is frequently mutated in cancer. The mechanisms underlying PI3K activation on membranes, and how oncogenic mutations distributed throughout p110 increase kinase activity is undefined. Using a synergy of biochemical assays and hydrogen deuterium exchange mass spectrometry (HDX-MS), we reveal unique regulatory mechanisms underlying PI3K activation. Engagement of p110 on membranes leads to disengagement of the ABD domain of p110 from the catalytic core, and the C2 domain from the iSH2 domain of the p85 regulatory subunit. PI3K activation also requires reorientation of the C-terminus, with mutations that alter the inhibited conformation of the C-terminus increasing membrane binding. Mutations at the C-terminus (M1043I/L, H1047R, G1049R, and N1068KLKR) activate p110 through distinct mechanisms, with this having important implications for mutant selective inhibitor development. This work reveals unique mechanisms underlying oncogenic mutants activate PI3K and explains how double mutants can synergistically increase PI3K activity.


title: Cryo-EM structure of the diapause chaperone artemin

abstract: The protein artemin constitutes over 10% of all protein in Artemia cysts during diapause and acts as both an RNA and protein chaperone. However, its mechanistic details remain elusive since no high-resolution structure of artemin exists. Here we report the full-length structure of artemin at 2.04 [A] resolution. The cryo-EM map contains density for an intramolecular disulfide bond between Cys22-Cys61 and resolves the entire C-terminus extending into the core of the assembled protein cage. We also provide data supporting the role of C-terminal helix F towards stabilizing the dimer form that is believed to be important for its chaperoning activity. We were able to destabilize this effect by placing a tag at the C-terminus to fully pack the internal cavity and cause limited steric hindrance.

category: biochemistry


title: Structure Of Eukaryotic Type III Glutamine Synthetase Lacking Ring-Ring Quaternary Contacts

abstract: There are three major classes of the enzyme Glutamine Synthetase (GS), denoted as GSI, GSII and GSIII in both prokaryotes and eukaryotes, that share widely conserved active-site residues but vary in average protein length, oligomeric assembly state and cofactor requirements. Key structures have been determined for all prokaryotic and eukaryotic GS classes except the GSIII class of eukaryotic origin, where even basic questions about its functional oligomeric state are unresolved. Here, we report the 3.2[A] cryo-EM structure of eukaryotic GSIII from the ancient organism of green algal lineage Ostreococcus tauri. Using a combined structural and biochemical approach, we demonstrate that O. tauri GSIII self-assembles and functions exclusively as a single hexameric ring. This is unlike most GSs in other classes, where they form double-stacked ring assemblies instead. Major structural differences in the ring-ring stacking across the classes suggest evolutionary pressure may have favored higher-order interactions that might be beneficial but are not necessarily required for the catalytic GS performance.


title: Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model

abstract: The influential hindered diffusion model postulates that the global movement of a signaling molecule through an embryo is affected by local tissue geometry and binding-mediated hindrance, but these effects have not been directly demonstrated in vivo for any signaling molecule. Nodal and Lefty are a prime example of an activator-inhibitor signaling pair whose different global diffusivities are thought to arise from differential hindrance. Here, we used single-molecule tracking of Nodal and Lefty to directly probe the tenets of the hindered diffusion model on the nanoscale. We visualized individual fluorescently-tagged Nodal and Lefty molecules in developing zebrafish embryos using reflected light-sheet microscopy. Single-particle tracking revealed molecules in three states: molecules diffusing in extracellular cavities, molecules diffusing within cell-cell interfaces, and molecules bound to cell membranes. While the diffusion coefficients of molecules were high in extracellular cavities, mobility was reduced and bound fractions were higher within cell-cell interfaces; counterintuitively, molecules nevertheless accumulated in cavities. Using agent-based simulations, we identified the geometry of the extracellular space as a key factor influencing the accumulation of molecules in cavities. For Nodal, the fraction of molecules in the bound state was larger than for Lefty, and individual Nodal molecules had binding times of tens of seconds. Together, our single-molecule measurements and simulations provide direct support for the hindered diffusion model in a developing embryo and yield unprecedented insights into the nanometer to micrometer scale transport mechanisms that together lead to macroscopic signal dispersal and gradient formation.

category: biophysics


title: Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and Global Epidemic pathovariants of Salmonella Enteritidis

abstract: Salmonella Enteritidis is the second most common serovar associated with iNTS disease in sub-Saharan Africa. Previously, genomic and phylogenetic characterisation of S. Enteritidis isolates from human bloodstream led to the discovery of the Western African and Central/Eastern African (CEAC) clades, which were distinct from the gastroenteritis- associated Global Epidemic clade (GEC). The African S. Enteritidis clades have unique genetic signatures that include genomic degradation, novel prophage repertoires and multidrug resistance, but the molecular basis for the enhanced propensity of African S. Enteritidis to cause bloodstream infection is poorly understood. We used transposon insertion sequencing to identify the genetic determinants of the GEC representative strain P125109 and the CEAC representative strain D7795 for growth in three in vitro conditions (LB or minimal NonSPI2 and InSPI2 growth media), and for survival and replication in RAW 264.7 murine macrophages. We identified 207 in vitro-required genes that were common to both S. Enteritidis strains and also required by S. Typhimurium, S. Typhi and Escherichia coli, and 63 genes that were only required by individual S. Enteritidis strains. Similar types of genes were required by both P125109 and D7795 for optimal growth in particular media. Screening the transposon libraries during macrophage infection identified 177 P125109 and 201 D7795 genes that contribute to bacterial survival and replication in mammalian cells. The majority of these genes have proven roles in Salmonella virulence. Our analysis also revealed candidate strain-specific macrophage fitness genes, some of which represent potential novel Salmonella virulence factors.

category: microbiology


title: Bps polysaccharide of Bordetella pertussis resists antimicrobial peptides by functioning as a dual surface shield and decoy and converts Escherichia coli into a respiratory pathogen.

abstract:
Infections and disease caused by the obligate human pathogen Bordetella pertussis (Bp) are increasing, despite widespread vaccinations. The current acellular pertussis vaccines remain ineffective against nasopharyngeal colonization, carriage, and transmission. In this work, we tested the hypothesis that Bordetella polysaccharide (Bps), a member of the poly-{beta}-1,6-A-acetyl-D-glucosamine (PNAG/PGA) family of polysaccharides promotes respiratory tract colonization of Bp by resisting killing by antimicrobial peptides (AMPs). Genetic deletion of the bpsA-D locus, as well as treatment with the specific glycoside hydrolase Dispersin B, increased susceptibility to AMP-mediated killing. Bps was found to be both cell surface-associated and secreted during laboratory growth and mouse infections. Addition of bacterial supernatants containing Bps and purified Bps increased B. pertussis resistance to AMPs. By utilizing ELISA, immunoblot and flow cytometry assays, we show that Bps functions as a dual surface shield and decoy by inhibiting AMP binding. Co-inoculation of C57BL/6J mice with a Bps-proficient strain enhanced respiratory tract survival of the Bps-deficient strain. In combination, the presented results highlight the critical role of Bps as a central driver of B. pertussis pathogenesis. Heterologous production of Bps in a non-pathogenic E. coli K12 strain increased AMP resistance in vitro, and augmented bacterial survival and pathology in the mouse respiratory tract. Therefore, by conferring virulence traits across bacterial genera, Bps transforms a primarily intestinal and urinary tract bacterium into a respiratory pathogen. These studies can serve as a foundation for other PNAG/PGA polysaccharides and for the development of an effective Bp vaccine that includes Bps.

Author summaryPertussis or whooping cough, caused by the obligate human pathogen Bordetella pertussis (Bp), is resurging in many countries. Currently, the mechanism by which B. pertussis subverts and resists host immunity is poorly known. In this manuscript, we examined the role of the B. pertussis polysaccharide Bps in promoting resistance to antimicrobial peptides (AMPs), a critical component of host immune defense. We show that the presence of Bps on the bacterial cell surface enhanced AMP resistance. Bps was secreted both during bacterial growth and during mouse infections. We further found that Bps functioned both as a surface shield and decoy, thereby inhibiting AMP binding. Simultaneous infection of mice with Bps-proficient and Bps- deficient strains resulted in greater survival of the Bps-deficient strain in the mouse respiratory tract. Finally, production of Bps in a non-pathogenic E. coli strain increased AMP resistance in vitro, and increased bacterial survival and heightened pathology in the mouse respiratory tract. Our study provides new insights into how B. pertussis has evolved to survive in the mammalian respiratory tract. Additionally, these studies underscore the potential of a single virulence factor to convert a non-pathogenic bacterium into a respiratory tract pathogen.


title: A multidrug-resistant Salmonella enterica serotype Typhimurium DT104 lineage circulating among humans and cattle in the United States lost the ability to produce pertussis-like toxin ArtAB in close temporal proximity to the global DT104 epidemic

abstract:
Salmonella enterica subspecies enterica serotype Typhimurium phage type DT104 (DT104) can infect both humans and animals and is often multidrug-resistant (MDR). Previous studies have indicated that, unlike most S. Typhimurium, the overwhelming majority of DT104 strains produce a pertussis-like toxin, ArtAB, via prophage-encoded artAB; however, DT104 that lack artAB have been described on occasion. Here, we identify a MDR DT104 lineage circulating among humans and cattle in the United States, which lacks artAB (i.e., the "U.S. artAB-negative major clade"; n = 41 genomes). Unlike most other bovine- and human-associated DT104 strains from the U.S. (n = 219 total genomes), which harbor artAB on prophage Gifsy-1 (n = 167), members of the U.S. artAB-negative major clade lack Gifsy-1, as well as anti-inflammatory effector gogB. The U.S. artAB-negative major clade was predicted to have lost artAB, Gifsy-1, and gogB circa 1993-1995 (95% highest posterior density interval 1989.5-1997.7), in close temporal proximity to a predicted rapid increase in the U.S. DT104 effective population size (circa 1996). When compared to DT104 genomes from other world regions (n = 752 total genomes), several additional, sporadic artAB, Gifsy-1, and/or gogB loss events among clades encompassing [≤]5 genomes were observed. In phenotypic assays that simulate conditions encountered during human and/or bovine digestion, members of the U.S. artAB-negative major clade did not differ from closely related Gifsy-1/artAB/gogB-harboring U.S. DT104 strains (ANOVA raw P > 0.05); thus, future research is needed to elucidate the roles that artAB, gogB, and Gifsy-1 play in DT104 virulence in humans and animals.

Impact StatementMulti-drug resistant (MDR) Salmonella enterica serotype Typhimurium phage type DT104 (DT104) was responsible for a global epidemic among humans and animals throughout the 1990s and continues to circulate worldwide. Previous studies have indicated that the vast majority of DT104 produce a pertussis-like toxin, ArtAB, via prophage-encoded artAB. However, here we identify a DT104 lineage circulating among cattle and humans across [≥]10 U.S. states, which lacks the ability to produce ArtAB (i.e., the "U.S. artAB-negative major clade"). The common ancestor of all U.S. artAB-negative major clade members lost the ability to produce ArtAB in close temporal proximity to the global MDR DT104 epidemic; however, the reason for this loss-of-function event within this well-established pathogen remains unclear. The role that ArtAB plays in DT104 virulence remains elusive, and phenotypic assays conducted here indicate that members of the U.S. artAB-negative major clade do not have a significant advantage or disadvantage relative to closely related Gifsy-1/artAB/gogB-harboring U.S. DT104 strains when exposed to stressors encountered during human and/or bovine digestion in vitro. However, ArtAB heterogeneity among DT104 suggest clade-specific selection for or against maintenance of ArtAB. Thus, future studies querying the virulence potential of the U.S. artAB- negative major clade are needed.

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


title: Listeria monocytogenes Co-opts Caveolin-Mediated E-cadherin Trafficking and Macropinocytosis for Epithelial Cell-to-Cell Spread

abstract: Listeria monocytogenes is an intracellular bacterial pathogen that spreads directly between adjacent host cells without exposure to the extracellular space. Recent studies have identified several host cell factors that promote L. monocytogenes cell-to-cell spread in epithelial monolayers, but details of the mechanism remain unclear. We find that the adherens junction protein, E-cadherin, promotes L. monocytogenes cell-to-cell spread at the recipient side of cell contacts. In particular, two point mutations in E-cadherins cytoplasmic domain that prevent its ubiquitination hinder bacterial cell-to-cell spread efficiency without reducing the extent of contact between neighboring cells. As ubiquitination induces E-cadherin endocytosis, we hypothesize that E-cadherin promotes protrusion engulfment, where donor cell protrusions containing L. monocytogenes are taken up by the recipient cell concurrently with E-cadherin internalization. In support of this hypothesis, we show that inhibiting caveolin-mediated membrane trafficking reduces L. monocytogenes cell-to-cell spread only under conditions where E-cadherin can be ubiquitinated. Additionally, we demonstrate that macropinocytosis also contributes to dissemination of L. monocytogenes through an epithelial monolayer.


title: Extracellular Vesicles from PRPF31+/- iPSC-Derived RPE Have a Distinct RNA Profile Compared to Those From Healthy RPE

abstract: Retinitis pigmentosa (RP) is the most common form of inherited retinal degeneration (IRD) and causes vision loss via dysfunction and death of the photoreceptor cells and retinal pigment epithelium (RPE) of the retina. Mutations in pre-mRNA processing factor 31 (PRPF31) are associated with autosomal dominant RP, and are thought to cause retinal degeneration by causing cell autonomous defects in RPE function. Genetic therapies such as adeno-associated virus (AAV) mediated gene therapy show great promise for treating IRDs, however in many cases it is challenging to measure clinical efficacy in a timely manner because IRDs progress slowly. A potential solution to this challenge is the use of additional outcome measures, such as biomarkers. Extracellular vesicles (EVs) are lipid enclosed vesicles that are secreted by cells and their RNA contents have been proposed as potential biomarkers in cancer and other diseases. We hypothesize EV RNAs can be used as biomarkers of the health status of the neural retina and RPE. To test this hypothesis for the RPE, we used PRPF31+/+ and PRPF31+/- human induced pluripotent stem cell (hiPSC)-derived RPE to investigate the RNAs contained in RPE-derived EVs, and how they change in disease. We also compared the RNA contents of RPE-EVs with the RNAs contained in the hiPSC-RPE cells themselves. We found that EVs from mutant PRPF31+/- hiPSC-RPE cells contain distinct RNAs compared to EV from the control PRPF31+/+ hiPSC-RPE cells, suggesting EV RNA contents change during disease and can potentially serve as biomarkers of retinal degeneration.

category: molecular biology


title: Sequential addition of neuronal stem cell temporal cohorts generates a feed-forward circuit in the Drosophila larval nerve cord

abstract: Understanding how circuits self-assemble starting from neuronal stem cells is a fundamental question in developmental biology. Here, we addressed how neurons from different lineages wire with each other to form a specific circuit motif. To do so, we combined developmental genetics--Twin spot MARCM, Multi-color Flip Out, permanent labeling--with circuit analysis--calcium imaging, connectomics, and network science analyses. We find many lineages are organized into temporal cohorts, which are sets of lineage-related neurons born within a tight time window, and that temporal cohort boundaries have sharp transitions in patterns of input connectivity. We identify a feed-forward circuit motif that encodes the onset of vibration stimuli. This feed-forward circuit motif is assembled by preferential connectivity between temporal cohorts from different neuronal stem cell lineages. Further, connectivity does not follow the often-cited early-to-early, late-to-late model. Instead, the feed-forward motif is formed by sequential addition of temporal cohorts, with circuit output neurons born before circuit input neurons. Further, we generate multiple new tools for the fly community. Ultimately, our data suggest that sequential addition of neurons (with outputs neurons being oldest and input neurons being youngest) could be a fundamental strategy for assembling feed-forward circuits.

category: developmental biology


title: Multiplexed promoter and gene editing in wheat using the virus-based guide RNA delivery system

abstract: The low efficiency of genetic transformation and gene editing across diverse cultivars hinders the broad application of CRISPR technology for crop improvement. The development of virus-based methods of CRISPR-Cas system delivery into the plant cells holds great promise to overcome these limitations. Here, we applied the barley stripe mosaic virus (BSMV) for delivering guide RNAs (sgRNA) into the Cas9-expressing wheat lines to create targeted deletions in the promoter of a transcription factor and to perform multiplexed editing of agronomic genes. We demonstrate that pooled BSMV-sgRNAs could be used to generate heritable targeted deletions and multiple mutations in the genome. We transferred the high-expressing allele of Cas9 into adapted spring and winter cultivars and successfully performed the BSMV-sgRNA-based editing of two agronomic genes. The strategies presented in our study could be applied to any cultivar for creating new cis-regulatory diversity or targeting multiple genes in biological pathways or QTL regions, opening possibilities for the effective engineering of crop genomes and accelerating gene discovery and trait improvement efforts.

category: genetics


title: Understanding the Spin Crossover Dynamical Effects of the Dioxygen Binding and Activation on HOD enzyme

abstract: For the cofactor-free 1-H-3-hydroxy-4-oxoquinaldine-2,4-dioxygenase (HOD), the dioxygen (O2) dependent steps are rate-limiting along with a spin state crossover to the singlet spin state. Here, the primary triplet O2 molecule activation on the 2-methyl-3-hydroxy-4(1H)-quinolone (MHQ) is investigated, and the catalytic role of the intersystem crossing effects is highlighted by directly comparing results from the Born-Oppenheimer dynamics and non-adiabatic surface hopping dynamics. This work confirms non-adiabatic dynamical effects are essential to modulate the O2 activation on the substrate MHQ. The time scale of the equilibration and conversion from triplet to singlet state should be in the range of a few hundreds of femtoseconds. We hope this work provides us a fresh look at the underlying physics of dioxygen activation reactions involving more than one spin state.


title: Understanding the Spin Crossover Dynamical Effects of the Dioxygen Binding and Activation on HOD Enzyme


title: Cell-free mutant analysis combined with structure prediction of a lasso peptide biosynthetic protein B2

abstract: Biochemical and structural analyses of purified proteins are essential for the understanding of their properties. However, many proteins are unstable and difficult to purify, hindering their characterization. The B2 proteins of the lasso peptide biosynthetic pathways are cysteine proteases that cleave precursor peptides during the maturation process. The B2 proteins are poorly soluble and no experimentally-solved structures are available. Here, we performed a rabid semi-comprehensive mutational analysis of the B2 protein from the thermophilic actinobacterium, Thermobifida fusca (TfuB2) using a cell-free transcription/translation system, and compared the results with the structure prediction by AlphaFold2. Analysis of 34 TfuB2 mutants with substitutions of hydrophobic residues confirmed the accuracy of the predicted structure, and revealed a hydrophobic patch on the protein surface, which likely serves as the binding site of the partner protein, TfuB1. Our results suggest that the combination of rapid cell-free mutant analyses with precise structure predictions can greatly accelerate structure-function research of proteins for which no structures are available.


title: Laboratory-acquired mutations fall outside the wild-type alleleome of Escherichia coli

abstract: Inexpensive DNA sequencing has led to a rapidly increasing number of whole genome sequences in the public domain. Natural sequence variation can now be assessed across a large number of sequenced strains of a bacterial species, resulting in the definition of the wild-type alleleome (the collection of alleles for every gene found in the species). Concurrently, laboratory evolution emerged as a new approach to address biological questions and to develop new phenotypic traits, and a large number of laboratory acquired mutations can be found in databases. The availability of this large-scale sequence variation data now allows for a detailed comparison of mutations fixed in natural versus laboratory evolutions. Such comparison shows that laboratory-acquired mutations are rarely found in the wild-type alleleome of Escherichia coli. The E. coli alleleome is highly conserved as most of the sequence variation is concentrated in about 2% of the coding region. We find that there are typically two alternate amino acids coded for in the variable locations, and switches between the two are found in the data sets. Finally, we find that adaptive laboratory mutations, unlike wild-type mutations, do not utilize the redundancy built into the genetic code: they are less likely to be synonymous and rely on changing a single nucleotide in a codon. However, the uniqueness of mutations fixed in laboratory evolutions bodes well for synthetic biology by revealing novel exploitable sequence space untouched by natural evolution.

category: bioengineering


title: Impact of temperature and time on DNA-free Cas9-ribonucleoprotein mediated gene editing in wheat protoplasts and immature embryos

abstract: The advancement of precision engineering for crop trait improvement is important in the face of rapid population growth, climate change, and disease. To this end, targeted double-stranded break technology using RNA-guided Cas9 has been adopted widely for genome editing in plants. Agrobacterium or particle bombardment-based delivery of plasmids encoding Cas9 and guide RNA (gRNA) is common, but requires optimization of expression and often results in random integration of plasmid DNA into the plant genome. Recent advances have described gene editing by the delivery of Cas9 and gRNA as pre-assembled ribonucleoproteins (RNPs) into various plant tissues, but with moderate efficiency in resulting regenerated plants. In this report we describe significant improvements to Cas9-RNP mediated gene editing in wheat. We demonstrate that Cas9-RNP assays in protoplasts are a fast and effective tool for rational selection of optimal gRNAs for gene editing in regenerable immature embryos (IEs), and that high temperature treatment enhances gene editing rates in both tissue types. We also show that Cas9-mediated editing persists for at least 14 days in gold particle bombarded wheat IEs. The regenerated edited wheat plants in this work are recovered at high rates in the absence of exogenous DNA and selection. With this method, we produce knockouts of a set of three homoeologous genes and two pathogenic effector susceptibility genes that result in insensitivity to corresponding necrotrophic effectors produced by Parastagonospora nodorum. The establishment of highly efficient, DNA-free gene editing technology holds promise for accelerated trait diversity production in an expansive array of crops.

category: plant biology


title: Organizing laboratory information to analyze the reproducibility of experimental workflows

abstract: Reproducibility is the cornerstone of scientific experiments. Assessing the reproducibility of an experiment requires analyzing the contribution of different factors to the variation of the observed data. Suitable data structures need to be defined prior to the data collection effort so that data associated with these factors can be recorded and associated with observations of the variable of interest. The resulting datasets can be analyzed statistically to estimate the effect of experimental factors on the observed data using ANOVA models. Custom data structures to document the execution of experimental workflows are defined in a research data management system. The data produced by multiple repetitions of a plasmid purification process and a cell culture process are analyzed using the Kruskal-Wallis H-test to identify factors contributing to their variation. Repetitions of the plasmid purification process do not lead to significant differences in extraction yields. Statistically significant differences in plasmid solution purity are identified but the differences are small enough that are not biologically relevant. The maintenance of two cell lines over many generations leads to similar datasets. However, different media preparations appear to influence the variation of cell viability and harvested cell counts in unexpected ways that may be the indirect expression of hidden effects not captured in the data structure.

category: synthetic biology


title: The purified recombinant FAT domain of the Focal Adhesion Kinase does not bind directly to recombinant Talin or MBD2 in vitro

abstract: Controlled localization and activation of the focal adhesion kinase (FAK) functionally links adhesion, migration and survival of the cell. The C-terminal focal adhesion targeting (FAT) domain of FAK is an important regulator of the localization, activation and molecular associations of FAK. Here, we aimed to investigate the structural basis for how FAK FAT binds to Talin and MBD2, which were previously reported to be cytoplasmic and nuclear ligands, respectively. Using several biophysical methods with purified recombinantly expressed protein constructs, we failed to observe measurable interactions between FAT and either the Talin FERM domain or MBD2. We conclude that the association of FAT with these proteins requires additional factors or post-translational modifications not present in bacterially produced purified proteins.


title: Host range expansion of Shigella phage Sf6 evolves through the dual roles of its tailspike

abstract: The first critical step in a viruss infection cycle is attachment to its host. This interaction is precise enough to ensure the virus will be able to productively infect the cell, but some flexibility can be beneficial to enable co-evolution and host range switching or expansion. Like many bacterial viruses, bacteriophage Sf6 utilizes a two-step process to recognize and attach to its host, Shigella flexneri. Sf6 first recognizes the lipopolysaccharide (LPS) structure of S. flexneri, then binds to either outer membrane protein (Omp) A or OmpC. This phage typically infects serotype Y strains but can also form small, turbid plaques on serotype 2a2 with greatly reduced plating efficiency, suggesting inefficient infection. To examine the interactions between Sf6 and this sub-optimal host, phage were experimentally evolved using mixed populations of S. flexneri serotypes Y and 2a2. The recovered mutants could infect serotype 2a2 with greater efficiency than the ancestral Sf6, forming clear plaques on both serotypes. All mutations mapped to two distinct regions of the tailspike protein: 1) adjacent to, but not part of, the LPS binding site near the N-terminus; and 2) at the distal, C-terminal tip of the protein. Rather than weak interactions between the Sf6 tailspike and 2a2 O-antigen, LPS of this serotype appears to inhibit infection by binding the wild-type particles more strongly, effectively removing them from the environment. These mutations reduce the inhibitory effect by either reducing electrostatic interactions with the O-antigen or increasing reliance on the Omp secondary receptors.


title: Microaerobic conditions and the complex regulation of natural competence in Staphylococcus aureus

abstract:
To perform genetic transformation, one of the three main Horizontal Gene Transfer mechanisms leading to virulence and antibiotic resistance genes acquisition, bacteria need to enter a physiological differentiated state called natural competence. Diverse environmental and cellular cues have been shown to trigger complex regulatory pathways ultimately activating central competence regulators controlling the expression of the genetic transformation genes. Interestingly, new bacteria displaying such aptitude are often discovered, and one of the latest is the human pathogen Staphylococcus aureus. However, a clear understanding of the environmental signals, regulatory pathways and central regulators involved in the development of competence in S. aureus is not yet available.

Here, using an original optimized protocol to naturally induce competence in planktonic cells, leading to improved transformation efficiencies (up to 5.10-6), we showed that the three putative central competence regulators identified in S. aureus are all essential for a complete development of competence. We also found that genes involved in genetic transformation can be divided in several classes depending on the regulators controlling their expression. In addition, we showed that oxygen availability is an important signal leading to competence development through the induction of one of the three central regulators. Our results demonstrate the complexity of competence development in S. aureus, in comparison to other historical model organisms. We anticipate our findings to be a starting point for proving the importance of natural competence and genetic transformation for S. aureus genomic plasticity. Furthermore, we also believe that our data will allow us to elucidate the environmental conditions leading to antibiotic resistance acquisitions in vivo, in this important human pathogen.

Introductory paragraphStaphylococcus aureus has become over the years an important public health concern, due to a large range of infections and the emergence of outbreaks associated to antibiotic multi-resistant strains. S. aureus remarkable adaptive powers have been acquired through the acquisition of new genetic sequences, thanks to Horizontal Gene Transfer (HGT). The recent demonstration of the capacity of S. aureus to induce natural competence for genetic transformation prompted scientists to investigate this important mode of HGT in this new model organism in the field. Few key reports have already established that the development of competence in S. aureus might be complex, involving several potential master regulators, activated in response to multiple environmental signals and regulatory pathways.

In this study, we deciphered, thanks to the design of an optimized protocol, the complexity of the regulatory pathways leading to the development of competence as well as its true potential for S. aureuss genomic plasticity in vivo. In addition, we clearly demonstrated that natural competence develops in response to oxygen limitation, a key environmental signal for a facultative anaerobe organism such as S. aureus.


title: KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin

abstract:
Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 base pair resolution and constructed a 3D KSHV genomic structural model with 2kb binning. The latent KSHV genome formed very similar genomic architectures in three different naturally infected PEL cell lines and in an experimentally infected epithelial cell line. The majority of the TAD boundaries were occupied by CTCF and SMC1, and the KSHV transactivator was recruited to these sites during reactivation. Triggering KSHV gene expression decreased pre-wired genomic loops within the regulatory unit, while contacts extending outside of regulatory borders increased, leading to formation of a larger regulatory unit with a shift from repressive to active compartments (B to A). The 3D genomic structural model proposes that the immediate-early promoter region is localized on the periphery of the 3D viral genome during latency, while highly inducible non-coding RNA regions moved toward the inner space of the structure, resembling the configuration of a "bird cage" during reactivation. The compartment-like properties of viral episomal chromatin structure and its reorganization during the transition from latency may help coordinate viral gene transcription.

ImportanceThe 3D architecture of chromatin allows for efficient arrangement, expression, and replication of genetic material. The genomes of all organisms studied to date have been found to be organized through some form of tiered domain structures. However, the architectural framework of the genomes of large double-stranded DNA viruses such as the herpesvirus family has not been reported. Prior studies with Kaposis sarcoma-associated herpesvirus (KSHV) have indicated that the viral chromatin shares many biological properties exhibited by the host cell genome, essentially behaving as a mini human chromosome. Thus, we hypothesized that the KSHV genome may be organized in a similar manner. In this report, we describe the domain structure of the latent and lytic KSHV genome at 500 base pair resolution and present a 3D genomic structural model for KSHV under each condition. These results add new insights into the complex regulation of the viral lifecycle.


title: The cytolethal distending toxin modulates cell differentiation and elicits epithelial to mesenchymal transition

abstract:
We are frequently exposed to bacterial genotoxins, such as cytolethal distending toxin (CDT), a prevalent heterotrimeric toxin whose active moiety is its CdtB subunit. CdtB triggers potent DNA damage, predisposing factors in the development of cancers, in host cells. CDT from Helicobacter hepaticus, a mouse pathogen, was shown to be directly involved in the development of murine hepatocarcinoma. Preliminary studies have shown that CDT induces certain phenotypes reminiscent of epithelial to mesenchymal transition (EMT), a process by which cells lose their epithelial characteristics in favor of mesenchymal ones, conducive to cell motility. In the present study, we investigated the different steps of EMT using liver tissues of mice infected with H. hepaticus, as well as human epithelial cell lines and xenograft mouse models following H. hepaticus CdtB expression. Most of the different steps of the EMT process were reproduced throughout the studied models. Indeed, microarray data showed a CdtB- dependent regulation of EMT-related transcripts. The key transcriptional regulators of EMT (SNAIL1 and ZEB1) and EMT markers (Vimentin, Fibronectin and 5{beta}1 integrin) were upregulated both at RNA and protein levels in response to CdtB. It also induced cell-cell junctions disassembly, causing individualization of cells and acquisition of a spindle-like morphology. CdtB activated the expression and activity of matrix metalloproteases and increased cell motility. This study demonstrated that CDT/CdtB elicits EMT process activation, supporting the idea that infection with genotoxin-producing bacteria can promote malignant transformation.

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org.highwire.dtl.DTLVardef@f94756org.highwire.dtl.DTLVardef@1ba7d59org.highwire.dtl.DTLVardef@7b80ccorg.highwire.dtl.DTLVardef@44d56d_HPS_FORMAT_FIGEXP  M_FIG C_FIG Author SummaryWe are frequently exposed to infection with genotoxin--producing bacterial from the gut microbiota, such as cytolethal distending toxin (CDT). CDT, via its active CdtB subunit, causes severe DNA damage in host cells, well-known risk factor of cancer development and progression. Chronic infection with CDT-producing bacteria is thus involved in cancer development. CDT is widespread among many bacteria and its impact in human cancer seems likely underestimated. Despite its major significance, CDT remains little studied. Here, we showed that cells exposed to CdtB are no longer cohesive, become individualized and acquire a spindle-shaped morphology known to be conducive to migration. These cells also express increased level of mesenchymal markers, as well as increased level of SNAIL1 and ZEB1, two key transcription factors orchestrating a crucial mechanism for cancer initiation and progression: epithelial to mesenchymal transition. These effects induced by CdtB were associated with increased matrix metalloproteinases degrading activity and emergence of cellular motility. Collectively, these data showed that CdB activates epithelial to mesenchymal transition, supporting the role of CDT in tumorigenesis.


title: Transformation of the symbiotic alga Oophila amblystomatis : a new toolbox for animal-algae symbiosis studies.

abstract:
The ability to conduct reverse genetic studies in symbiotic systems is enabled by transgene expression and transformation of at least one partner. The symbiotic relationship between the yellow spotted salamander, Ambystoma maculatum, and the green alga, Oophila amblystomatis, is a unique model of vertebrate-algae symbiosis. Despite over 130 years of scientific study, there are still many open questions in this symbiosis. Transgene expression in one partner will accelerate research into the symbiotic relationship. In this paper we describe a tool and method for expression of foreign DNA in, and presumed transformation of, the alga O. amblystomatis. We successfully introduced heritable antibiotic resistance to algal cultures, and observed expression of a green fluorescent reporter protein in all transfected and presumably transformed algal populations. The outcomes of this work enable genetic manipulation of the symbiotic alga Oophila amblystomatis, allowing direct testing of hypotheses derived from gene expression or genomic studies that will usher in a deeper understanding of the A. maculatum-O. amblystomatis symbiotic system.

Summary statementGenetic tools stimulate new possibilities for research in living systems. This work describes a new tool for transformation of a symbiotic alga that enters vertebrate tissues and cells.


title: Bi-phasic regulation of AIMP2 and its splice variant in PARP-1- dependent neurodegeneration

abstract: Parthanatos is a significant molecular cause of Parkinsons disease, in which AIMP2 aberrantly activates PARP-1 through a physical interaction. Interestingly, AIMP2 has an antagonistic splice variant, named DX2, which compromises AIMP2-induced apoptosis via p53 or inflammatory pathway. Here we suggested that DX2 binds to PARP-1 with a higher affinity than AIMP2, deactivating it and improving synaptic physiology. To deliver DX2 into deep brain areas, miR142 target sequence-embedded adeno-associated virus was designed to avoid unexpected expression in hematopoietic cells. RNAseq analysis revealed that DX2 selectively suppressed cell death-associated pathways, such as p53 and neuroinflammation. Upon a single intracranial injection, both behaviour and motility were mitigated in three animal models of Parkinsonism, induced by MPTP, rotenone, or 6-OHDA. Efficacy was observed in therapeutic model as well as preventive ones. Thus, AIMP2 and DX2 are suggested to act as an  ON/OFF switch for PARP-1. In particular, as cell survival properties of DX2 was exerted only when AIMP2 is accumulated abnormally, without its own additional tumorigenicity, DX2 could be a unique therapeutic tool for treating patients with Parkinsons disease.


title: Agricultural margins could enhance landscape connectivity for pollinating insects across the Central Valley of California, U.S.A.

abstract: One of the defining features of the Anthropocene is eroding ecosystem services as a function of decreases in biodiversity and overall reductions in the abundance of once-common organisms, including many insects that play innumerable roles in natural communities and agricultural systems that support human society. It is now clear that the preservation of insects cannot rely solely on the legal protection of natural areas far removed from the densest areas of human habitation. Instead, a critical challenge moving forward is to intelligently manage areas that include intensively farmed landscapes, such as the Central Valley of California. Here we attempt to meet this challenge with a tool for modeling landscape connectivity for insects (with pollinators in particular in mind) that builds on available information including lethality of pesticides and expert opinion on insect movement. Despite the massive fragmentation of the Central Valley, we find that connectivity is possible, especially utilizing the restoration or improvement of agricultural margins which (in their summed area) exceed natural areas. Finally, we highlight steps moving forward and the great many knowledge gaps that could be addressed in the field to improve future iterations of our modeling approach.

category: ecology


title: Evidence of attack deflection suggests adaptive evolution of wing tails in butterflies

abstract: Predation is a powerful selective force shaping many behavioural and morphological traits in prey species. The deflection of predator attacks from vital parts of the prey usually involves the coordinated evolution of prey body shape and colour. Here, we test the deflection effect of hindwing tails in the swallowtail butterfly Iphiclides podalirius. In this species, hindwings display long tails associated with a conspicuous colour pattern. By surveying the wings within a wild population of I. podalirius, we observed that wing damage was much more frequent on the tails. We then used a standardised behavioural assay employing dummy butterflies with real I. podalirius wings to study the location of attacks by great tits Parus major. Wing tails and conspicuous coloration of the hindwings were struck more often than the rest of the body by birds. Finally, we characterised the mechanical properties of fresh wings and found that the tail vein was more fragile than the others, suggesting facilitated escape ability of butterflies attacked at this location. Our results clearly support the deflective effect of hindwing tails and suggest that predation is an important selective driver of the evolution of wing tails and colour pattern in butterflies.

category: evolutionary biology


title: The intergenerational transmission of educational attainment: A closer look at the (interrelated) roles of paternal involvement and genetic inheritance

abstract: Numerous studies have documented a strong intergenerational transmission of educational attainment. In explaining this transmission, separate fields of research have studied separate mechanisms. To obtain a more complete understanding, the current study integrates insights from the fields of behavioural sciences and genetics and examines the extent to which factors from each field are unique underlying mechanisms, correlate with each other, and/or act as important confounders in the intergenerational transmission of educational attainment. Specifically, we focus on paternal involvement as our behavioural indicator and childrens polygenic score (PGS) for education as our genetic indicator and assess the role that fathers play in the intergenerational transmission of educational attainment. To answer our research questions, we use rich data from The National Longitudinal Study of Adolescent to Adult Health (n=4,579). Firstly, results from our mediation analyses showed that about 4 per cent of the effect of fathers educational attainment on childrens educational attainment is explained by paternal involvement, whereas a much larger share, 21 per cent, is explained by childrens education PGS. Secondly, our results showed that these genetic and behavioural influences are significantly correlated to each other. Thirdly, we found support for genetic confounding, as adding childrens education PGS to the model reduced the effect of paternal involvement by 11 per cent. Fourthly, evidence for social confounding was almost negligible (a reduction of half a per cent of the genetic effect). Our findings highlight the importance of integrating insights and data from multiple disciplines in understanding the mechanisms underlying the intergenerational transmission of inequality, as our study reveals that behavioural and genetic influences overlap, correlate, and confound each other as mechanisms underlying this transmission.


title: Novel Bruton's Tyrosine Kinase (BTK) substrates for time-resolved luminescence assays

abstract: Brutons tyrosine kinase (BTK) is a well-documented target for cancer therapeutics due to its role in B-cell signaling pathways. However, inhibitor design is hindered by lack of tools to assess kinase activity. We used in vitro phosphoproteomics to determine BTKs substrate preferences and applied this information to our updated data processing pipeline, KINATEST-ID 2.1.0. This pipeline generates a position-specific scoring matrix for BTK and a list of candidate synthetic substrates, each given a score. Characterization of selected synthetic substrates demonstrated a correlation between KINATEST-ID 2.1.0 score and biochemical performance in in vitro kinase assays. Additionally, by incorporating a known terbium-chelation motif, we adapted synthetic substrates for use in an antibody-free time-resolved terbium luminescence assay. This assay has applications in high-throughput inhibitor screening.


title: Cryo-EM reveals a mechanism of USP1 inhibition through a cryptic binding site

abstract:
Repair of DNA damage is critical to genomic integrity and frequently disrupted in cancers. USP1, a nucleus-localized deubiquitinase, lies at the interface of multiple DNA repair pathways and is a promising drug target for certain cancers. Although multiple inhibitors of this enzyme, including one in phase I clinical trials, have been established, their binding mode is unknown. Here we use cryo-Electron Microscopy to study an assembled enzyme-substrate-inhibitor complex of USP1 and the well-established inhibitor, ML323. Achieving 2.5 [A] resolution, we discover an unusual binding mode in which the inhibitor displaces part of the hydrophobic core of USP1. The consequent conformational changes in the secondary structure lead to subtle rearrangements in the active site that underlie the mechanism of inhibition. These structures provide a platform for structure-based drug design targeting USP1.

One Sentence SummaryUSP1, a cancer target, is inhibited by ML323 displacing part of the protein fold, allosterically disrupting the active site.


title: Cardiac hemodynamics and ventricular stiffness of sea-run cherry salmon (Oncorhynchus masou masou) differ critically from those of landlocked masu salmon

abstract: Ventricular diastolic mechanical properties are important determinants of cardiac function and are optimized by changes in cardiac structure and physical properties. Oncorhynchus masou masou is an anadromous migratory fish of the Salmonidae family, and several ecological studies on it have been conducted; however, the cardiac functions of the fish are not well known. Therefore, we investigated ventricular diastolic function in landlocked (masu salmon) and sea-run (cherry salmon) types at 29-30 months post fertilization. Pulsed-wave Doppler echocardiography showed that the atrioventricular inflow waveforms of cherry salmon were biphasic with early diastolic filling and atrial contraction, whereas those of masu salmon were monophasic with atrial contraction. In addition, end-diastolic pressure-volume relationship analysis revealed that the dilatability per unit myocardial mass of the ventricle in cherry salmon was significantly suppressed compared to that in masu salmon, suggesting that the ventricle of the cherry salmon was relatively stiffer (relative ventricular stiffness index; p = 0.0263). Contrastingly, the extensibility of cardiomyocytes, characterized by the expression pattern of Connectin isoforms in their ventricles, was similar in both types. Histological analysis showed that the percentage of the collagen accumulation area in the compact layer of cherry salmon increased compared with that of the masu salmon, which may contribute to ventricle stiffness. Although the heart mass of cherry salmon was about 11-fold greater than that of masu salmon, there was no difference in the morphology of the isolated cardiomyocytes, suggesting that the heart of the cherry salmon grows by cell division of cardiomyocytes, but not cell hypertrophy. The cardiac physiological function of the fish varies with differences in their developmental processes and life history. Our multidimensional analysis of the O. maosu heart may provide a clue to the process by which the heart acquires a biphasic blood-filling pattern, i.e., a ventricular diastolic suction.

category: physiology


title: Signalling speed along a key white matter tract influences memory recall ability in humans

abstract: Conduction velocity is the speed at which electrical signals travel along axons and is a crucial determinant of neural communication. Inferences about conduction velocity can now be made in vivo in humans using magnetic resonance (MR) imaging and a measure called the MR g-ratio. Here, in the first application to cognition, we found that increased MR g-ratio, and by inference faster conduction velocity, specifically in the parahippocampal cingulum bundle, which connects the hippocampus with a range of other brain areas, was associated with better memory recall ability in 217 healthy adults. Moreover, two tract features seemed to favour better memory retrieval - large inner axon diameters and coherently organised neurites, both of which facilitate speedy signalling. These results offer a new perspective on drivers of individual differences in memory recall ability. More broadly, they show that MR g-ratio can provide novel insights into how the human brain processes and integrates information.

category: neuroscience


title: A visual representation of the hand in the resting somatomotor regions of the human brain

abstract: Hands are regularly in sight in everyday life. This visibility affects motor control, perception, and attention, as visual information is integrated into an internal model of sensorimotor control. Spontaneous brain activity, i.e., ongoing activity in the absence of an active task (rest), is correlated among somatomotor regions that are jointly activated during motor tasks1. Moreover, recent studies suggest that spontaneous activity patterns do not only replay at rest task activation patterns, but also maintain a model of the statistical regularities (priors) of the body and environment, which may be used to predict upcoming behavior2-4. Here we test whether spontaneous activity in the human somatomotor cortex is modulated by visual stimuli that display hands vs. non-hand stimuli, and by the use/action they represent. We analyzed activity with fMRI and multivariate pattern analysis to examine the similarity between spontaneous (rest) activity patterns and task-evoked patterns to the presentation of natural hands, robot hands, gloves, or control stimuli (food). In the left somatomotor cortex we observed a stronger (multi-voxel) spatial correlation between resting-state activity and natural hand picture patterns, as compared to other stimuli. A trend analysis showed that task-rest pattern similarity was influenced by inferred visual and motor attributes (i.e., correlation for hand>robot>glove>food). We did not observe any task-rest similarity in the visual cortex. We conclude that somatomotor brain regions code at rest for visual representations of hand stimuli and their inferred use.


title: Auditory Language Comprehension During Saccadic Eye Movements: An Investigation Using the N400 Event-Related Brain Potential

abstract: In many situations of everyday life, it is important to quickly understand a spoken message despite distraction by an already ongoing activity. Previous dual-task studies recording the N400 component of the event-related potential (ERP) have shown that auditory language comprehension can be strongly delayed by temporally overlapping additional tasks. In the current study, we investigated whether this interference is aggravated by the need for saccadic eye movements and visuospatial attention shifts in the overlapping task. In two dual-task experiments, a synonymy judgment task for spoken words was combined with a visual discrimination task at different stimulus onset asynchronies. In half of the trials, the primary visual task required a 10{degrees} exogenous saccade towards a peripheral stimulus. The timing of semantic processing in the secondary task was assessed by recording the N400. We replicated that with increasing temporal overlap between the tasks, the N400 component was strongly delayed. However, additional saccade-related processes in the primary task had no detrimental effects on concurrent spoken language processing on their own. Unexpectedly, we also observed that a preceding saccade consistently facilitated subsequent motoric processing in the visual task (as indexed by manual reaction times and the lateralized readiness potential), suggesting that saccade execution as such can significantly enhance subsequent processing.


title: Unexpected inhibition of motor function by dopamine activation of D1/D2 co-expressing striatal neurons.

abstract:
The central function of the striatum and its dopaminergic (DA) afference in motor control and integration of cognitive and emotional processes is commonly explained by the two striatal efferent pathways characterized by striatal projection neurons (SPNs) expressing DA D1 receptor- and D2 receptor (D1-SPNs and D2-SPNs), respectively, regardless of SPNs co-expressing these two receptors (D1/D2-SPNs). Here, after developing an approach that enables to target these hybrid SPNs, we demonstrated that, although these SPNs are rare, they play a major role in guiding the motor function of the other two main populations and convey a DA-mediated antagonistic motor brake. D1/D2-SPNs project exclusively to the external globus pallidus (GPe) and have specific electrophysiological features with distinctive integration of DA signals. Optogenetic stimulation and loss-of-function experiments indicated that D1/D2-SPNs potentiate the prokinetic and antikinetic functions of D1-SPNs and D2-SPNs, respectively, and restrain the integrated motor response to psychostimulants. Overall, our findings demonstrate the essential role of this third unacknowledged population of D1/D2 co-expressing neurons, which orchestrates the fine-tuning of DA regulation in the thalamo-cortico-striatal loops.

One-Sentence SummaryD1/D2 striatal output promotes dopamine-induced motor inhibition


title: Transcriptional targets of senataxin and E2 promoter binding factors are associated with neuro-degenerative pathways during increased autophagic flux

abstract: Autophagy is an intracellular recycling process that degrades harmful molecules, maintains optimal composition of cellular organelles and enables survival during starvation. Previous studies have demonstrated how transcription factors (TFs) can increase autophagy with therapeutic potential (impaired autophagy in the ageing brain, in particular, may be an important risk factor for dementia). To investigate the transcriptional regulation of autophagy from a systems perspective, we induced autophagy by amino acid starvation and mTOR inhibition in HeLa, HEK 293 and SH-SY5Y cells and used RNA-seq to measure gene expression at three time points. We observed 453 differentially expressed (DE) genes due to starvation and 284 genes due to mTOR inhibition (PFDR < 0.05 in every cell line). Pathway analyses confirmed enrichment of genes implicated in Alzheimers (PFDR < 0.001 in SH-SY5Y and HeLa) and Parkinsons (PFDR [≤] 0.024 in SH-SY5Y and HeLa) diseases and amyotrophic lateral sclerosis (ALS, PFDR < 0.05 in 4 of 6 experiments). We then integrated Signaling Pathway Impact Analysis and TF target enrichment testing to predict which TF target genes were contributing to pathway perturbation. Differential expression of the Senataxin (SETX) target gene set was predicted to activate multiple neurodegenerative pathways (PFDR [≤] 0.04). Notably, SETX is a causal gene for a rare form of ALS. In the SH-SY5Y cells of neuronal origin, the E2F transcription family was predicted to activate Alzheimers disease pathway (PFDR [≤] 0.0065). SETX and E2F may be important mediators of transcriptional regulation of autophagy and may provide new therapeutic opportunities for neuro-degenerative conditions.

category: genomics


title: Mouse mutants in schizophrenia risk genes GRIN2A and AKAP11 show EEG abnormalities in common with schizophrenia patients

abstract:
BACKGROUNDSchizophrenia is a heterogeneous psychiatric disorder with a strong genetic basis, whose etiology and pathophysiology remain poorly understood. Exome sequencing studies have uncovered rare, loss-of-function variants that greatly increase risk of schizophrenia [1], including loss-of-function mutations in GRIN2A (aka GluN2A or NR2A, encoding the NMDA receptor subunit 2A) and AKAP11 (A-Kinase Anchoring Protein 11). AKAP11 and GRIN2A mutations are also associated with bipolar disorder [2], and epilepsy and developmental delay/intellectual disorder [1, 3, 4], respectively. Accessible in both humans and rodents, electroencephalogram (EEG) recordings offer a window into brain activity and display abnormal features in schizophrenia patients. Does loss of Grin2a or Akap11 in mice also result in EEG abnormalities?

METHODSWe monitored EEG in heterozygous and homozygous knockout Grin2a and Akap11 mutant mice compared with their wild-type littermates, at 3- and 6-months of age, across the sleep/wake cycle and during auditory stimulation protocols.

RESULTSGrin2a and Akap11 mutants exhibited increased resting gamma power, attenuated 40-50 Hz auditory steady-state responses (ASSR), and reduced responses to unexpected auditory stimuli during mismatch negativity (MMN) tests. Sleep spindle density was reduced in a gene dose-dependent manner in Akap11 mutants, whereas Grin2a mutants showed increased sleep spindle density.

CONCLUSIONSThe EEG phenotypes of Grin2a and Akap11 mutant mice show a variety of abnormal features that overlap considerably with human schizophrenia patients, reflecting systems-level changes caused by Grin2a and Akap11 deficiency. These neurophysiologic findings further substantiate Grin2a and Akap11 mutants as genetic models of schizophrenia and identify potential biomarkers for stratification of schizophrenia patients.


title: Probing different paradigms of morphine withdrawal on sleep behavior in male and female C57BL/6J mice

abstract: The opioid epidemic has increased dramatically over the last few decades resulting in many suffering from opioid use disorder (OUD). The prevalence of opioids and opioid overdose has been driven by the development of new synthetic opioids, increased availability of prescription opioids, and more recently, the COVID-19 pandemic. As we see increased in exposure to opioids, the United States has also seen increases in the frequency of instances of Narcan (naloxone) administration as a life saving measure for respiratory depression, and, thus, consequently, naloxone-precipitated withdrawal. Sleep dysregulation is one of the main symptoms of OUD and opioid withdrawal syndrome, and therefore should be a key facet of animal models of OUD. Here we examine the effect of precipitated and spontaneous morphine withdrawal on sleep behaviors in C57BL/6J. We find that morphine administration and withdrawal dysregulates sleep, however not equally across morphine exposure paradigms and not qualitatively the same across sexes. Furthermore, many environmental triggers promote relapse to drug seeking/taking behavior, and the stress of disrupted sleep may fall into that category. We find that sleep deprivation dysregulates sleep in mice that had previous opioid withdrawal experience. These data suggest that the 3-day precipitated withdrawal paradigm has the most profound effects on opioid induced sleep dysregulation, and that further validate the construct of the 3-day precipitated withdrawal model as a model for opioid dependence and OUD.


title: HOTARU: Automatic sorting system for large scale calcium imaging data

abstract: Currently, calcium imaging allows for the long-term recording of large-scale neuronal activity in diverse states. However, it remains difficult to extract neuronal dynamics from recorded imaging data. In this study, we propose an improved CNMF-based algorithm and an effective method for extracting cell shapes with fewer false positives and false negatives caused by image processing. We also showed that the values obtained during image processing can be combined and used for false positive determination of cells. For the CNMF algorithm, we combined cell-by-cell regularization and baseline shrinkage estimation, which greatly improved its stability and robustness. We applied these methods to artificial and real data and confirmed their effectiveness. Our method is simpler and faster, detects more cells with lower firing rates and signal-to-noise ratios, and enhance the quality of the extracted cell signals. These advances can improve the standard of downstream analysis and contribute to progress in neuroscience.


title: Mind the gap: Nodes of Ranvier are remodeled by chronic psychosocial stress and neuronal activity

abstract: Differential expression of myelin-related genes and changes in myelin thickness have been demonstrated in mice after chronic psychosocial stress, a risk factor for anxiety disorders. To determine whether and how stress affects structural remodeling of nodes of Ranvier, another form of myelin plasticity, we developed a 3D reconstruction analysis of node morphology in C57BL/6NCrl and DBA/2NCrl mice. We identified strain-dependent effects of chronic stress on node morphology, including elongation of paranodes in the medial prefrontal cortex (mPFC) in DBA/2NCrl mice. Furthermore, chronic chemogenetic activation of the ventral hippocampus-to-mPFC pathway resulted in increased risk assessment behavior and shortened paranodes specifically in stimulated axons, providing a direct link between anxiety-like behavior and remodeling of the nodes. Altogether, our data demonstrate genetic regulation of nodal remodeling in stress and suggest an activity-dependent regulation of paranodes in anxiety-related circuits. Nodal remodeling may thus contribute to the aberrant circuit function associated with anxiety disorders.


title: Goal-directed recruitment of Pavlovian biases through selective visual attention

abstract: Prospective outcomes bias behavior in a "Pavlovian" manner: Reward prospect invigorates action, while punishment prospect suppresses it. Theories have posited Pavlovian biases as global action "priors" in unfamiliar or uncontrollable environments. However, this account fails to explain the strength of these biases--causing frequent action slips--even in well-known environments. We propose that Pavlovian control is additionally useful if flexibly recruited by instrumental control. Specifically, instrumental action plans might shape selective attention to reward/ punishment information and thus the input to Pavlovian control. In two eye-tracking samples (N = 35/ 64), we observed that Go/ NoGo action plans influenced when and for how long participants attended to reward/ punishment information, which in turn biased their responses in a Pavlovian manner. Participants with stronger attentional effects showed higher performance. Thus, humans appear to align Pavlovian control with their instrumental action plans, extending its role beyond action defaults to a powerful tool ensuring robust action execution.


title: Population modeling with machine learning can enhance measures of mental health - Open-Data Replication

abstract: Efforts to predict trait phenotypes based on functional MRI data from large cohorts have been hampered by low prediction accuracy and/or small effect sizes. Although these findings are highly replicable, the small effect sizes are somewhat surprising given the presumed brain basis of phenotypic traits such as neuroticism and fluid intelligence. We aim to replicate previous work and additionally test multiple data manipulations that may improve prediction accuracy by addressing data pollution challenges. Specifically, we added additional fMRI features, averaged the target phenotype across multiple measurements to obtain more accurate estimates of the underlying trait, balanced the target phenotypes distribution through undersampling of majority scores, and identified data-driven subtypes to investigate the impact of between-participant heterogeneity. Our results replicated prior results from Dadi et a (2021) in a larger sample. Each data manipulation further led to small but consistent improvements in prediction accuracy, which were largely additive when combining multiple data manipulations. Combining data manipulations (i.e., extended fMRI features, averaged target phenotype, balanced target phenotype distribution) led to a three-fold increase in prediction accuracy for fluid intelligence compared to prior work. These findings highlight the benefit of several relatively easy and low-cost data manipulations, which may positively impact future work.


title: Reactivating ordinal position information from auditory sequence memory in human brains

abstract: Retaining a sequence of events in their order is a core ability of many cognitive functions, such as speech recognition, movement control, and episodic memory. Although content representations have been widely studied in working memory (WM), little is known about how ordinal position information of an auditory sequence is retained in the human brain as well as its coding characteristics. In fact, there is still a lack of an efficient approach to directly access the stored ordinal position code, since the neural activities enter a relatively  activity-silent WM state during WM retention. Here participants performed an auditory sequence WM task with their brain activities recorded using electroencephalography (EEG). We developed new triggering events that could successfully reactivate neural representations of ordinal position from the  activity-silent retention stage. Importantly, the rank reactivation is further related to recognition behavior, confirming its indexing of WM storage. Furthermore, the ordinal position code displays an intriguing  stable-dynamic format, i.e., undergoing the same dynamic neutral trajectory during both encoding and retention (whenever reactivated). Overall, our results provide an effective approach to access the behaviorally-relevant ordinal position information in auditory sequence WM and reveal its new temporal characteristics.


title: The theta paradox: 4-8 Hz EEG oscillations reflect both local sleep and cognitive control

abstract: Human brain activity generates electroencephalographic (EEG) oscillations that characterize specific behavioral and vigilance states. The frequency of these oscillations is typically sufficient to distinguish a given state, however theta oscillations (4-8 Hz) have instead been found in near-opposite conditions of drowsiness during sleep deprivation and alert cognitive control. While the latter has been extensively studied and is often referred to as "frontal midline theta", the former has been investigated far less but is considered to be a marker for local sleep during wake. In this study we investigated to what extent theta oscillations differed during cognitive tasks and sleep deprivation. We measured high-density EEG in 18 young healthy adults performing 6 tasks under 3 levels of sleep deprivation. We found both cognitive load and sleep deprivation increased theta power in medial prefrontal cortical areas, however sleep deprivation caused additional increases in theta in many other, predominantly frontal, areas. The sources of sleep deprivation theta were task-dependent, with a visual-spatial task and short-term memory task showing the most widespread effects. Notably, theta was highest in supplementary motor areas during passive music listening, and highest in the inferior temporal cortex during a spatial game. This suggests that theta caused by sleep deprivation may preferentially occur in cortical areas not involved in ongoing behavior. While our results find differences in topography from frontal midline theta, they raise the possibility that a common mechanism may underly both theta oscillations during cognition and during sleep deprivation.


title: The strength of feedback processing is associated with resistance to visual backward masking during illusory contour processing in adult humans.

abstract: Re-entrant feedback processing is a key mechanism of visual object-recognition, especially under compromised viewing conditions where only sparse information is available and object features must be interpolated. Illusory contour stimuli are commonly used in conjunction with visual evoked potentials (VEP) to study these filling-in processes, with characteristic modulation of the VEP in the ~100-150ms timeframe associated with this re-entrant processing. Substantial inter-individual variability in timing and amplitude of feedback-related VEP modulation is observed, raising the question whether this variability might underlie inter-individual differences in the ability to form strong perceptual gestalts. Backward masking paradigms have been used to study inter-individual variance in the ability to form robust object perceptions before processing of the mask interferes with object-recognition. Some individuals recognize objects when the time between target object and mask is extremely short, whereas others struggle to do so even at longer target-to-mask intervals. We asked whether timing and amplitude of feedback-related VEP modulations were associated with individual differences in resistance to backward masking. Participants (N=40) showed substantial performance variability in detecting illusory contours at intermediate target-to-mask intervals (67ms and 117ms), allowing us to use kmeans clustering to divide the population into four performance groups (poor, low-average, high-average, superior). There was a clear relationship between the amplitude (but not the timing) of feedback-related VEP modulation and illusory contour detection during backward masking. We conclude that individual differences in the strength of feedback processing in neurotypical humans lead to differences in the ability to quickly establish perceptual awareness of incomplete visual objects.


title: Analysis of non-human primate models for evaluating prion disease therapeutic efficacy

abstract: Prion disease is a fatal neurodegenerative disease caused by the conformational corruption of the prion protein (PrP), encoded by the prion protein gene (PRNP). While no disease-modifying therapy is currently available, genetic and pharmacological proofs of concept support development of therapies that lower PrP levels in the brain. In light of proposals for clinical testing of such drugs in presymptomatic individuals at risk for genetic prion disease, extensive nonclinical data are likely to be required, with extra attention paid to choice of animal models. Uniquely, the entire prion disease process can be faithfully modeled through transmission of human prions to non-human primates (NHPs), raising the question of whether NHP models should be used to assess therapeutic efficacy. Here we systematically aggregate data from N=527 prion-inoculated animals spanning six decades of research studies. Using this dataset, we assess prion strain, route of administration, endpoint, and passage number to characterize the relationship of tested models to currently prevalent human subtypes of prion disease. We analyze the incubation times observed across diverse models and perform power calculations to assess the practicability of testing prion disease therapeutic efficacy in NHPs. We find that while some models may theoretically be able to support therapeutic efficacy studies, pilot studies would be required to confirm incubation time and attack rate before pivotal studies could be designed, cumulatively requiring several years. The models with the shortest and most tightly distributed incubation times are those with smaller brains and weaker homology to humans. Our findings indicate that it would be challenging to conduct efficacy studies in NHPs in a paradigm that honors the potential advantages of NHPs over other available models, on a timeframe that would not risk unduly delaying patient access to promising drug candidates.


title: Invasion of malaria mosquitoes natural population by parasitic nematodes Dirofilaria along Ob River basin in Western Siberia

abstract: Dirofilariasis - is a dangerous disease that affects carnivores, felines, and humans. It is caused by parasitic nematodes Dirofilaria repens and D. immitis. These parasites are carried by blood-sucking mosquitoes. In recent decades the habitat of Dirofilaria in Europe has been expanding dramatically. In the present study, we investigated how malaria mosquitoes had been infected by Dirofilaria in Western Siberia (Russia) in the range between 50{degrees} 48 N (Labytnangi) and 66{degrees} 39 N (Kurota) along the Ob River. The extensiveness of parasite infection varied between 0.4 % and 5.7 %, in three species of malaria mosquitoes: Anopheles beklemishevi, An. daciae, An. messeae, which all are showed effective vectors of D. repens. The results demonstrate the significant role of malaria mosquitoes for dirofilariasis transmission in severe climate conditions of Western Siberia.


title: Lichen speciation is sparked by a substrate requirement shift and reproduction mode differentiation

abstract: We show that obligate lignicoles in lichenized Micarea are predominately asexual whereas most facultative lignicoles reproduce sexually. Our 3 loci phylogenetic analyses (ITS, mtSSU, Mcm7) together with ancestral state reconstruction show that the shift in reproduction mode has evolved independently several times within the group and that facultative and obligate lignicoles are sister species. The analyses support the assumption that the ancestor of these species was a facultative lignicole. We hypotezise that a shift in substrate requirement from bark to wood leads to differentiation in reproduction mode and becomes a driver of speciation. This is the first example of lichenized fungi where reproduction mode is linked to substrate requirement. This is also the first example where such a linkage is demonstrated to spark lichen speciation. Our main hypothesis is that obligate species on dead wood need to colonize new suitable substrata relatively fast and asexual reproduction is more effective a strategy for successful colonization. Our main hypothesis for explaining the discovered phenomenon involves the species life cycle: species on decaying wood face a significant challenge because the ecological properties of their substratum change relatively fast. When this happens, species need to colonize new suitable substrata. This may set a time limit, where asexual reproduction is a faster and more effective strategy for successful colonization.


title: The evolutionary demise of a social interaction: social partners differ in the rate at which interacting phenotypes are lost

abstract:
Phenotypic plasticity enables animals to flexibly adjust their behaviour to their social environment - sometimes through the expression of adaptive traits that have not been exhibited for several generations. We investigated how long social adaptations can usefully persist when they are not routinely expressed by using experimental evolution to document the loss of social traits associated with the supply and demand of parental care. Populations of burying beetles Nicrophorus vespilloides were evolved over 48 generations - in  Full Care populations traits associated with the supply and demand of care were expressed, whereas in  No Care populations we prevented expression of these traits experimentally. We then revived trait expression in the No Care populations at generations 24, 43 and 48 by allowing parents to supply post-hatching care, and compared these social traits with those expressed by the Full Care populations. We found that offspring demands for care decayed in the No Care populations more rapidly than a parents capacity to supply care. Furthermore, male care decayed faster than female care. We suggest that this reflects differences in the strength of selection on offspring, males and females, for the expression of alternative traits which are more likely to enhance fitness when post-hatching care is disrupted.

Impact SummarySocial interactions between animals are suggested to be increasingly vulnerable to breakdown in this changing world. Our experiments offer a rare insight into what happens next, by assessing in real time the durability of social behaviours that are no longer routinely expressed. Our results also have implications for conservation captive breeding programmes where compensatory husbandry techniques prevent trait expression and so could inadvertently induce rapid, irreversible trait loss.

We investigated how long it took populations to lose the ability to express appropriate social behaviour when they had been prevented from doing so, for many generations. We did this by evolving replicate populations of burying beetles Nicrophorus vespilloides in the laboratory for over 48 generations. The burying beetle is a common insect that is well-known for caring for its larvae, although larvae can survive in the lab without any care at all. In two populations ("Full Care"), we allowed parents and offspring to interact during the supply of post-hatching care, as usual. In two other populations ("No Care"), however, parents were removed before offspring hatched and so could not interact socially with their young.

Over the course of 48 generations of experimental evolution, we periodically revived social interactions between parents and offspring in the No Care populations. We assessed the extent to which larval begging behaviours, and parental care behaviours, had decayed by comparing their expression with those in the Full Care populations. We found that larval begging behaviour eroded rapidly in No Care populations, and more rapidly than the supply of care by parents. Furthermore, paternal care decayed to a greater extent than maternal care (which was largely unchanged relative to its expression in the Full Care populations). We suggest that these differences could be due to differences in the strength of selection on each social partner for alternative traits to enhance fitness.


title: A Genome-Wide Association Analysis of Happiness: Consistent Genetic Effects Across the Lifespan and Across Genetic Ancestries in Multiple Cohorts.

abstract:
We present a genome-wide association study of a general happiness measure in 118,851 participants from the UK Biobank. Using BOLT-LMM, we identify 3 significant loci with a heritability estimate of 0.8%. Linkage disequilibrium score regression was performed on the  big five personality traits finding significant associations with lower neuroticism and higher extraversion and conscientiousness. Using a novel approach, we construct LDpred-inf polygenic risk scores in the Adolescent Brain Cognitive Development (ABCD) cohort and the Add Health cohort. We detected nominally significant associations with several well-being measures in ABCD and significant correlations with a happiness measure in Add Health. Additionally, we tested for associations with several brain regions in a white British subsample of UK Biobank finding significant associations with several brain structure and integrity phenotypes.

We demonstrated a genetic basis for general happiness level and brain structure that appears to remain consistent throughout the lifespan and across multiple ancestral backgrounds.

Author summaryAt the genetic level, there has been little investigation into whether people may have a baseline happiness level which varies from person to person. Here we perform a genetic analysis in the UK Biobank to identify three genetic loci that associate with general happiness level and preform genetic correlations of our results with the  Big Five personality traits, identifying significant correlations with neuroticism, conscientiousness and extraversion.

We use the resulting summary statistics to create LDpred-inf polygenic risk scores in UK biobank identifying several brain metrics and regions associate with genetic loading for general happiness level. We also use a novel method to create LDpred-inf polygenic risk scores in two other cohorts, ABCD and Add Health. We found significant correlations with an independent happiness measure in Add Health and nominally significant correlations with several well-being measures in ABCD in both those of European Ancestry and all other ancestries found in these cohorts. We also attempted to replicate our UK Biobank MRi finding in ABCD.

We conclude there is evidence that individuals have a general happiness level that is in part genetic which spans across age and ancestry.


title: Doctoring Direct-to-Consumer Genetic Tests with DNA Spike-Ins

abstract: Direct-to-consumer (DTC) genetic testing companies have provided personal genotyping services to millions of customers. Customers mail saliva samples to DTC service providers to have their genotypes analyzed and receive back their raw genetic data. Both consumers and the DTC companies use the results to perform ancestry analyses, relative matching, trait prediction, and estimate predisposition to disease, often relying on genetic databases composed of the data from millions of other DTC-genotyped individuals. While the digital integrity risks to this type of data have been explored, we considered whether data integrity issues could manifest upstream of data generation through physical manipulation of DNA samples themselves, for example by adding synthetic DNA to a saliva sample ("spiked samples") prior to sample processing by a DTC company. Here, we investigated the feasibility of this scenario within the standard DTC genetic testing pipeline. Starting with the purchase of off-the-shelf DTC genetic testing kits, we found that synthetic DNA can be used to precisely manipulate the results of saliva samples genotyped by a popular DTC genetic testing service and that this method can be used to modify arbitrary single nucleotide polymorphisms (SNPs) in multiplex to create customized doctored genetic profiles. This capability has implications for the use of DTC-generated results and the outcomes of their downstream analyses.


title: Potential impact of TE-derived sRNA on gene regulation in the grassBrachypodium distachyon

abstract: In plants, the transcriptional and post-transcriptional repression of TEs involved the production of small interfering RNAs (siRNAs) that guide the de novo methylation and transcriptional silencing of TEs. Because siRNAs act via sequence complementarity, they indiscriminately target TEs and possible non-TE transcripts. TEs and their derived siRNAs might thus provide a reservoir for long-distance gene regulation. To test this hypothesis, we infected Brachypodium distachyon with Mangnaporte oryzae, the agent of Rice Blast. The infection caused the differential expression of multiple TE copies as well as a global change in gene expression. By sequencing the small RNA fraction, we identified TE-derived sRNA that are identical in sequence to motifs contained in the UTR region of differentially expressed genes. Our study opens new avenues of research to further investigate to what extent TEs may serve as a source for in trans gene regulation.


title: Genomic characteristics, virulence and antimicrobial resistance in avian pathogenic Escherichia coli MTR_BAU02 strain isolated from layer farms in Bangladesh

abstract:
BackgroundColibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting poultry worldwide. APEC is one of the leading causes of mortality and morbidity associated with significant economic losses in the poultry industry.

ObjectiveThis study was aimed to determine the genomic diversity, virulence factor genes (VFGs) and antimicrobial resistance (AMR) genes in the APEC isolated from layer chickens using whole-genome sequencing (WGS).

MethodAPEC MTR_BAU02 strain was isolated from the sick and dead birds. Genomic DNA from APEC MTR_BAU02 strain was extracted using commercial DNA extraction kit, WGS libraries were prepared using the Nextera DNA Flex Library Prep Kit, and finally, paired-end (2 x 250) WGS performed using Illumina MiSeq sequencer.

ResultsThe genome size of strain APEC MTR_BAU02 is 4,924,680 bp with a GC content of 51.1% and 4,681 protein-coding sequences. Among the annotated WGS reads, 99.71% reads mapped to Enterobacteriaceae genomes. Based on the phylogenetic analysis of the APEC MTR_BAU02 genome and 99 reference genomes of E. coli, the APEC MTR_BAU02 genome showed sequence similarities with enterotoxigenic E. coli strains isolated from infections of different clinical severity. Metabolic functional annotations detected 380 SEED subsystems including genes coding for carbohydrate metabolism (17.34%), amino acid and derivatives (14.20%), protein metabolism (10.64%), cofactors, vitamins, prosthetic groups and pigments (7.49%), respiration (4.72%), membrane transport (4.49%), stress response (4.47%), motility and chemotaxis (4.46%), and virulence, disease and defense (2.22%). We also detected 92 VFGs and 122 AMR genes in the APEC MTR_BAU02 strain.

ConclusionAssessment of these genomic features with functional genomic validation in commonly occurring serogroups of APEC will increase our understanding of the molecular pathogenesis, pave the way to early diagnosis and more effective control of colibacillosis, and improved animal welfare.


title: Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations

abstract:
Genome-wide methods offer a powerful approach to detect signatures of drug selection in parasite populations in the field. However, their application to parasitic nematodes has been limited because of both a lack of suitable reference genomes and the difficulty of obtaining field populations with sufficiently well-defined drug selection histories. Consequently, there is little information on the genomic signatures of drug selection for parasitic nematodes in the field and on how best to detect them. This study was designed to address these knowledge gaps using field populations of Haemonchus contortus with well-defined and contrasting benzimidazole-selection histories, leveraging a recently completed chromosomal-scale reference genome assembly. We generated a panel of 49,393 ddRADseq markers and used this resource to genotype 20 individual H. contortus adult worms from each of four H. contortus populations: two from closed sheep flocks that had an approximately 20-year history of frequent treatment exclusively with benzimidazole drugs, and two populations with a history of little or no drug treatment. The populations were chosen from the same geographical region to limit population structure in order to maximize the sensitivity of the approach. A clear signature of selection was detected on the left arm of chromosome I centered on the isotype-1 {beta}-tubulin gene in the benzimidazole-selected but not the unselected populations. Two additional, but weaker, signatures of selection were detected; one near the middle of chromosome I and one near the isotype-2 {beta}-tubulin locus on chromosome II. We examined genetic differentiation between populations, and nucleotide diversity and linkage disequilibrium within populations to define these two additional regions as encompassing five genes and a single gene. We also compared the relative power of using pooled versus individual worm sequence data to detect genomic selection signatures and how sensitivity is impacted by sequencing depth, worm number, and population structure.

In summary, this study used H. contortus field populations with well-defined drug selection histories to provide the first direct genome-wide evidence for any parasitic nematode that the isotype-1 {beta}-tubulin gene is the quantitatively most important benzimidazole resistance locus. It also identified two additional genomic regions that likely contain benzimidazole-resistance loci of secondary importance. Finally, this study provides an experimental framework to maximize the power of genome-wide approaches to detect signatures of selection driven by anthelmintic drug treatments in field populations of parasitic nematodes.

AUTHOR SUMMARYBenzimidazoles are important anthelmintic drugs for human and animal parasitic nematode control with [~]0.5 billion children at risk of infection treated annually worldwide. Drug resistance is common in livestock parasites and a growing concern in humans. Haemonchus contortus is the most important model parasite system used to study anthelmintic resistance and a significant livestock pathogen. It is also one of the few parasitic nematodes with a chromosomal-scale genome assembly. We have undertaken genome-wide scans using a dense RADseq marker panel on worms from natural field populations under differing levels of benzimidazole selection. We show that there is a single predominant genomic signature of selection in H. contortus associated with benzimidazole selection centred on the isotype-1 {beta}-tubulin locus. We also identify two weaker signatures of selection indicative of secondary drug resistance loci. Additionally, we assess the minimum data requirements for parameters including worm number, sequence depth, marker density needed to detect the signatures of selection and compare individual to Poolseq analysis. This work is the first genome-wide study in a parasitic nematode to provide direct evidence of the isotype-1 {beta}-tubulin locus being the single predominant benzimidazole resistance locus and provides an experimental framework for future population genomic studies on anthelmintic resistance.


title: Asynchrony rescues statistically-optimal group decisions from information cascades through emergent leaders

abstract:
It is usually assumed that information cascades are most likely to occur when an early but incorrect opinion spreads through the group. Here we analyse models of confidence-sharing in groups and reveal the opposite result: simple but plausible models of naive Bayesian decision-making exhibit information cascades when group decisions are synchronous; however, when group decisions are asynchronous, the early decisions reached by Bayesian decision makers tend to be correct, and dominate the group consensus dynamics. Thus early decisions actually rescue the group from making errors, rather than contribute to it. We explore the likely realism of our assumed decision-making rule with reference to the evolution of mechanisms for aggregating social information, and known psychological and neuroscientific mechanisms.

Significance of the studyUnderstanding the dynamics of group decision-making must combine individuals behavioural rules with a collective dynamics analysis. Here we make a parsimonious assumption that individual agents make naive-Bayesian decisions that neglect correlated social information, in order to reach group decisions in synchronous and asynchronous settings. For the synchronous case, in which there are no early decisions, decision-making is unstable and negative information cascades are observed. In the asynchronous case, however, early decisions tend to be correct and lead to positive information cascades. This observation is the opposite to the usual assumption that early decisions are erroneous and lead to negative information cascades, showing how group leaders can spontaneously emerge for the benefit of collective decisions.

category: animal behavior and cognition


title: Can the Insect Path Integration Memory be a Bump Attractor?

abstract: Many animal species are able to return to their nest after a foraging excursion without using familiar visual cues to guide them. They accomplish this by using a navigation competence known as path integration, which is vital in environments that do not have prominent visual features. To perform path integration, an animal maintains an estimate of the distance and direction to its origin as it moves. The distance and direction information needs to be maintained in memory for the duration of the trip so that the animal can return to its nest. However, the neural substrate of this memory remains unclear. A common hypothesis is that the information is maintained in a bump attractors state. We test the bump attractor hypothesis and find that its predictions do not match behavioural data from ants, thus falsifying the bump attractor hypothesis and raising the need for alternative models of path integration memory.


title: QuasiFlow: a bioinformatic tool for genetic variability analysis from next generation sequencing data

abstract: Populations of RNA and ssDNA viruses within their hosts contain a heterogeneous collection of variant genomes known as quasispecies. Large variability in mitochondrial DNA has also been found within the same organism, drawing an interesting parallel between the two situations. The advent of next-generation sequencing technologies facilitated studying genetic variation, but many open-source bioinformatic tools have to be combined in a non-trivial approach. Here it is presented QuasiFlow, a workflow based on well-stablished software that extracts reliable mutations and recombinations, even at low frequencies (~10-4), provided that at least 250 million nucleotides are analysed. Accurate prediction of mutations and recombinations has been demonstrated with synthetic reads and with in vitro rolling-circle amplification of a plant geminivirus. An in-depth analysis of viral quasispecies was performed and QuasiFlow revealed the coexistence in the plant of three virus genomes and distinct recombinations between some of them. Human mitochondrial variants were also investigated and high level of heteroplasmy (75%) was confirmed, and the relation between low-frequency heteroplasmy (0.1- 0.2%) and some human diseases, regardless of sex, was established. Hence, we propose that QuasiFlow may find use with known and emerging viruses to reveal evolutionary jumps and co-infections, with mitochondrial DNA to detect relevant heteroplasmy would otherwise be elusive, or even in other population studies such as those considering single cell sequencing.

category: bioinformatics


title: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool.

abstract: Efficient tools allowing the extraction of 2D surfaces from 3D-microscopy data are essential for studies aiming to decipher the complex cellular choreography through which epithelium morphogenesis takes place during development. Most existing methods allow for the extraction of a single and smooth manifold of sufficiently high signal intensity and contrast, and usually fail when the surface of interest has a rough topography or when its localization is hampered by other surrounding structures of higher contrast. Multiple surface segmentation entails laborious manual annotations of the various surfaces separately. As automating this task is critical in studies involving tissue-tissue or tissue-matrix interaction, we developed the Zellige software, which allows the extraction of a non-prescribed number of surfaces of varying inclination, contrast, and texture from a 3D image. The tool requires the adjustment of a small set of control parameters, for which we provide an intuitive interface implemented as a Fiji plugin. As a proof of principle of the versatility of Zellige, we demonstrate its performance and robustness on synthetic images and on four different types of biological samples, covering a wide range of biological contexts.