title: VTA MC3R neurons control feeding in an activity and sex-dependent manner in mice

abstract: Increasing evidence indicates that the melanocortin and mesolimbic dopamine systems interact to regulate feeding and body weight. Because melanocortin-3 receptors (MC3R) are highly expressed in the ventral tegmental area (VTA), we tested whether VTA neurons expressing these receptors (VTA MC3R neurons) control feeding and body weight in vivo. We also tested whether there were sex differences in the ability of VTA MC3R neurons to control feeding, as MC3R -/- mice show sex-dependent alterations in reward feeding and dopamine levels, and there are clear sex differences in multiple dopamine-dependent behaviors and disorders. DREADD receptors were used to acutely activate and inhibit VTA MC3R neurons and changes in food intake and body weight were measured. Acutely altering the activity of VTA MC3R neurons decreased feeding in an activity- and sex-dependent manner, with acute activation decreasing feeding, but only in females, and acute inhibition decreasing feeding, but only in males. These differences did not appear to be due to sex differences in the number of VTA MC3R neurons, the ability of hM3Dq to activate VTA MC3R neurons, or the proportion of VTA MC3R neurons expressing tyrosine hydroxylase (TH). These studies demonstrate an important role for VTA MC3R neurons in the control of feeding and reveal important sex differences in behavior, whereby opposing changes in neuronal activity in male and female mice cause similar changes in behavior.


title: ER exit sites in Drosophila display abundant ER-Golgi vesicles and pearled tubes but no megacarriers

abstract: Secretory cargos are collected at ER exit sites (ERES) before transport to the Golgi apparatus. Decades of research have provided many details of the molecular events underlying ER-Golgi exchanges. Essential questions, however, remain about the organization of the ER-Golgi interface in cells and the type of membrane structures mediating traffic from ERES. To investigate these, we used transgenic tagging in Drosophila flies, 3D-SIM and FIB-SEM to characterize ERES-Golgi units in collagen-producing fat body, imaginal discs and imaginal discs overexpressing ERES determinant Tango1. We found in front of ERES a pre-cis-Golgi region involved in both anterograde and retrograde transport. This pre-cis-Golgi is continuous with the rest of the Golgi, not a separate intermediate compartment or collection of large carriers, for which we found no evidence. We found, however, many vesicles, as well as pearled tubules connecting ERES and Golgi.

category: cell biology


title: Structural dynamics of cytochrome P450 3A4 in the presence of substrates and cytochrome P450 reductase

abstract: Cytochrome P450 3A4 (CYP3A4) is the most important drug-metabolizing enzyme in humans and has been associated with harmful drug interactions. The activity of CYP3A4 is known to be modulated by several compounds, as well as by the electron transfer partner, cytochrome P450 reductase (CPR). The underlying mechanism of these effects however is poorly understood. We have used hydrogen-deuterium exchange mass spectroscopy (HDX-MS) to investigate the impact of CPR and three different substrates (7-benzyloxy-4-trifluoromethyl-coumarin, testosterone and progesterone) on the conformational dynamics of CYP3A4. Here, we report that interaction of CYP3A4 with substrates or with the oxidized or reduced form of CPR leads to a global rigidification of the CYP3A4 structure. This was evident from a suppression of deuterium exchange in several regions of CYP3A4, including those known to be involved in protein-protein interactions (C-helix) as well as substrate binding and specificity (B-, E-helices and K/{beta}1-loop). Furthermore, the bimodal isotopic distributions observed for some CYP3A4-derived peptides were drastically impacted by CPR and/or substrates, suggesting the existence of stable CYP3A4 conformational populations that are perturbed by ligand/CPR binding. The results have implications for understanding the mechanisms of allostery, ligand binding, and catalysis in CYP enzymes.

category: biochemistry


title: Endothelial Pannexin 1-TRPV4 channel signaling lowers pulmonary arterial pressure

abstract: Pannexin 1 (Panx1) is an ATP-efflux channel that controls endothelial function in the systemic circulation. However, the roles of endothelial Panx1 in resistance-sized pulmonary arteries (PAs) are unknown. Extracellular ATP dilates PAs through activation of endothelial TRPV4 (transient receptor potential vanilloid 4) ion channels. We hypothesized that endothelial Panx1-ATP- TRPV4 channel signaling promotes vasodilation and lowers pulmonary arterial pressure (PAP). Endothelial, but not smooth muscle, knockout of Panx1 or TRPV4 increased PA contractility and raised PAP. Panx1-effluxed extracellular ATP signaled through purinergic P2Y2 receptor (P2Y2R) to activate protein kinase C (PKC), which in turn activated endothelial TRPV4 channels. Finally, caveolin-1 provided a signaling scaffold for endothelial Panx1, P2Y2R, PKC, and TRPV4 channels in PAs, promoting their spatial proximity and enabling signaling interactions. These results indicate that endothelial Panx1-P2Y2R-TRPV4 channel signaling, facilitated by caveolin-1, reduces PA contractility and lowers PAP.


title: Selective and reversible disruption of mitochondrial inner membrane protein complexes by lipophilic cations

abstract:
Mitochondria represent an attractive drug target in the treatment of many diseases. One of the most commonly used approaches to deliver therapeutics specifically into mitochondria is their conjugation to the triphenylphosphonium (TPP) moiety. While the TPP molecule is often regarded as biologically inert, there is evidence that the moiety itself has a significant impact on the activity of mitochondrial respiratory chain complexes.

We studied the impact of a subchronic exposure of C2C12 mouse myoblasts to a set of TPP derivatives. Our results show that the alkyl-TPP cause dose- and hydrophobicity-dependent alterations of mitochondrial morphology and a selective decrease in the amounts of mitochondrial inner membrane (but not outer membrane) proteins including structural subunits of the respiratory chain complexes (such as MT-CO1 of complex IV or NDUFB8 of complex I), as well as components of the mitochondrial calcium uniporter complex (MCUC). The treatment with alkyl-TPP additionally resulted in OPA1-cleavage. Both the structural and functional effects of alkyl-TPP were found to be reversible. A similar effect was observed with the mitochondria-targeted antioxidant MitoQ. We further show that this effect on protein levels cannot be explained solely by a decrease in mitochondrial membrane potential.

We conclude that TPP derivatives negatively affect mitochondrial structure and function at least in part through their effect on selective mitochondrial membrane protein levels via a reversible controlled process.


title: Optimizing mechanostable anchor points of engineered lipocalin in complex with CTLA-4

abstract: We used single-molecule AFM force spectroscopy (AFM-SMFS) to screen residues along the backbone of a non-antibody protein binding scaffold (lipocalin/anticalin), and determine the optimal anchor point that maximizes binding strength of the interaction with its target (CTLA-4). By incorporating non-canonical amino acids into anticalin, and using click chemistry to attach an Fg{beta} peptide at internal sequence positions, we were able to mechanically dissociate anticalin from CTLA-4 by pulling from eight different anchoring residues using an AFM cantilever tip. We found that pulling on the anticalin from residue 60 or 87 resulted in significantly higher rupture forces and a decrease in koff by 2-3 orders of magnitude over a force range of 50-200 pN. Five of the six internal pulling points tested were significantly more stable than N- or C-terminal anchor points, rupturing at up to 250 pN at loading rates of 0.1-10 nN sec-1. Anisotropic network modelling and molecular dynamics simulations using the G[o]-MARTINI approach explained the mechanism underlying the geometric dependency of mechanostability. These results suggest that optimization of attachment residue position for therapeutic and diagnostic cargo can provide large improvements in binding strength, allowing affinity maturation without requiring genetic mutation of binding interface residues.

category: biophysics


title: Functional basis of electron transport within photosynthetic complex I

abstract: Photosynthesis and respiration rely upon a proton gradient to produce ATP. In photosynthesis, the Respiratory Complex I homologue, Photosynthetic Complex I (PS-CI) is proposed to couple ferredoxin oxidation and plastoquinone reduction to proton pumping across thylakoid membranes, and is fundamental to bioenergetics in photosynthetic bacteria and some higher plant cell types. However, little is known about the PS-CI molecular mechanism and attempts to understand its function have previously been frustrated by its large size and high lability. Here, we overcome these challenges by pushing the limits in sample size and spectroscopic sensitivity, to determine arguably the most important property of any electron transport enzyme - the reduction potentials of its cofactors, in this case the iron-sulphur clusters of PS-CI, and unambiguously assign them to the structure using double electron-electron resonance (DEER). We have thus determined the bioenergetics of the electron transfer relay and provide insight into the mechanism of PS-CI, laying the foundations for understanding of how this important bioenergetic complex functions.


title: Sub-stoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of a yeast prion protein

abstract: The prion-like self-perpetuating conformational conversion is involved in both transmissible neurodegenerative diseases and non-Mendelian inheritance traits. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins. To provide the mechanistic underpinning of the generation and persistence of prefibrillar amyloid seeds that are critical for the prion-like propagation, we studied the effect of Hsp104 disaggregase on the assembly mechanism of a yeast prion determinant of Saccharomyces cerevisiae Sup35. At low sub-stoichiometric concentrations, Hsp104 exhibits a dual role and considerably accelerates the formation of seeding-competent prefibrillar amyloids by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into matured fibers. Hsp104-mediated amyloid species comprise a more ordered packing and display an enhanced autocatalytic self-templating ability compare to amyloids formed without Hsp104. Our findings underscore the key functional and pathological roles of sub-stoichiometric chaperones in prion-like propagation.


title: Entropic pressure controls oligomerization of Vibrio cholerae ParD2 antitoxin

abstract: ParD2 is the antitoxin component of the parDE2 toxin-antitoxin module from Vibrio cholerae and consists of an ordered DNA binding domain followed by an intrinsically disordered ParE-neutralizing domain. In absence of the C-terminal IDP domain, VcParD2 crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open 10-mer or 12-mer, likely as a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows for an extended operator to wrap around the VcParD2 oligomer.


title: Sortilin-related receptor is a druggable therapeutic target in breast cancer

abstract: In breast cancer, the currently approved anti-receptor tyrosine-protein kinase erbB-2 (HER2) therapies do not fully meet the expected clinical goals due to therapy resistance. Identifying alternative HER2-related therapeutic targets could offer means to overcome these resistance mechanisms. We have previously demonstrated that an endosomal sorting protein, sortilin-related receptor (SorLA), regulates the traffic and signaling of HER2 and HER3, thus promoting resistance to HER2-targeted therapy in breast cancer. This study aims to assess the feasibility of targeting SorLA using a monoclonal antibody. Our results demonstrate that anti-SorLA antibody (SorLA ab) alters the resistance of breast cancer cells to HER2 monoclonal antibody trastuzumab in vitro and in ovo. We found that SorLA ab and trastuzumab combination therapy also inhibits tumor cell proliferation and tumor cellularity in a mouse xenograft model of HER2-positive breast cancer. In addition, SorLA ab inhibits the proliferation of breast cancer patient-derived explant three-dimensional cultures. These results provide for the first time proof-of-principle that SorLA is a druggable target in breast cancer.

category: cancer biology


title: Cancer drug discovery as a low rank tensor completion problem

abstract: The heterogeneity of cancer necessitates developing a multitude of targeted therapies. We propose the view that cancer drug discovery is a low rank tensor completion problem. We implement this vision by using heterogeneous public data to construct a tensor of drug-target-disease associations. We show the validity of this approach computationally by simulations, and experimentally by testing drug candidates. Specifically, we show that a novel drug candidate, SU11652, controls melanoma tumor growth, including BRAFWT melanoma. Independently, we show that another molecule, TC-E 5008, controls tumor proliferation on ex vivo ER+ human breast cancer. Most importantly, we identify these chemicals with only a few computationally selected experiments as opposed to brute-force screens. The efficiency of our approach enables use of ex vivo human tumor assays as a primary screening tool. We provide a web server, the Cancer Vulnerability Explorer (accessible at https://cavu.biohpc.swmed.edu), to facilitate the use of our methodology.


title: A Scalable Screening of E. coli Strains for Recombinant Protein Expression

abstract: Structural biology projects are highly dependent on the large-scale expression of soluble protein and, for this purpose, heterologous expression using bacteria or yeast as host systems is usually employed. In this scenario, some of the parameters to be optimized include (i) those related to the protein construct, such as the use of a fusion protein, the choice of an N-terminus fusion/tag or a C-terminus fusion/tag; (ii) those related to the expression stage, such as the concentration and selection of inducer agent and temperature expression and (iii) the choice of the host system, which includes the selection of a prokaryotic or eukaryotic cell and the adoption of a strain. The optimization of some of the parameters related to protein expression, stage (ii), is straightforward. On the other hand, the determination of the most suitable parameters related to protein construction requires a new cycle of gene cloning, while the optimization of the host cell is less straightforward. Here, we evaluated a scalable approach for the screening of host cells for protein expression in a structural biology pipeline. We evaluated four Escherichia coli strains looking for the best yield of soluble heterologous protein expression using the same strategy for protein construction and gene cloning and comparing it to our standard strain, Rosetta 2 (DE3). Using a liquid handling device (robot), E. coli pT-GroE, Lemo21(DE3), Arctic Express (DE3), and Rosetta Gami 2 (DE3) strains were screened for the maximal yield of soluble heterologous protein recovery. For the genes used in this experiment, the Arctic Express (DE3) strain resulted in better yields of soluble heterologous proteins. We propose that screening of host cell/strain is feasible, even for smaller laboratories and the experiment as proposed can easily be scalable to a high-throughput approach.

category: molecular biology


title: Destruction of DNA-binding proteins by programmable O'PROTAC: Oligonucleotide-based PROTAC

abstract: DNA-binding proteins including transcription factors (TFs) play essential roles in gene transcription and DNA replication and repair during normal organ development and pathogenesis of diseases such as cancer, cardiovascular disease and obesity, deeming to be a large repertoire of attractive therapeutic targets. However, this group of proteins are generally considered undruggable as they lack an enzymatic catalytic site or a ligand binding pocket. PROteolysis-TArgeting Chimera (PROTAC) technology has been developed by engineering a bifunctional small molecule chimera to bring a protein of interest (POI) to the proximity of an E3 ubiquitin ligase, thus inducing the ubiquitination of POI and further degradation through proteasome pathway. Here we report the development of Oligonucleotide-based PROTAC (OPROTACs), a class of noncanonical PROTACs in which a TF-recognizing double-stranded oligonucleotide is incorporated as a binding moiety of POI. We demonstrate that OPROTACs of ERG and LEF1, two highly cancer-related transcription factors selectively promote degradation of these proteins and inhibit their transcriptional activity in cancer cells. The programmable nature of OPROTACs indicates that this approach is applicable to destruct other TFs. OPROTACs not only can serve as a research tool, but also can be harnessed as a therapeutic arsenal to target DNA binding proteins for effective treatment of diseases such as cancer.


title: Boundary convection during velocity sedimentation in the Optima analytical ultracentrifuge

abstract: Analytical ultracentrifugation (AUC) provides the most widely applicable, precise and accurate means for characterizing solution hydrodynamic and thermodynamic properties. In recent times AUC has found broad application in the biopharmaceutical industry as a first-principle means for quantitatively characterizing biopharmaceuticals. Boundary sedimentation velocity AUC (SV-AUC) analysis is widely used to assess protein aggregation, fragmentation and conformational variants in the same solvents used during drug development and production. SV-AUC is especially useful for the analysis of drug substance, drug product and dosing solution, where other techniques may exhibit solvent matrix issues or concentration limitations. Recently, the only manufacturer of the analytical ultracentrifuge, released its newest (third generation) analytical ultracentrifuge, the Optima, in early 2017 to replace its aging 2nd generation XL series ultracentrifuges. However, SV-AUC data from four Optima units used in conducting characterization work on adeno-associated virus (AAV) has shown evidence of sample convection. Further investigation reveals that this problem arises from the temperature control system design, which is prone to producing destabilizing temperature induced density gradients that can lead to density inversions. The observed convection impacts both the qualitative and quantitative data generated by the Optima. The problem is intermittent and variable in severity within a given Optima unit and between Optima units. This convection appears to be mainly associated with low rotor speeds and dilute samples in dilute solvents, such as AAV samples in formulation buffers containing relatively low concentrations of salts, sugars, etc. Under these conditions it is found that a sufficiently robust stabilizing density gradient is not always present during sedimentation, making the sample susceptible to convection by localized density inversions. Because SV-AUC is used as an analytical tool in making critical decisions in the development and quality control of biotherapeutics, it is imperative to alert users about this potential problem. In general special attention to data quality needs to be made by those researchers working with very large biopharmaceutical particles (e.g. gene therapy products that involve viral vectors or nanoparticles), where the conditions leading to convection are most likely to occur. It is important to note that the XL series analytical ultracentrifuges do not suffer from this problem, indicating that this problem is unique to the Optima. Attributes that reveal the presence of this problem and strategies for its elimination or minimization are provided.


title: A viral genome packaging ring-ATPase is a flexibly coordinated pentamer

abstract: Multi-subunit ring-ATPases carry out a myriad of biological functions, including genome packaging in viruses. Though the basic structures and functions of these motors have been well-established, the mechanisms of ATPase firing and motor coordination are poorly understood. Here, by direct counting using single-molecule fluorescence, we have determined that the active bacteriophage T4 DNA packaging motor consists of five subunits of gp17. By systematically doping motors with an ATPase-defective subunit and selecting single motors containing a precise count of active/inactive subunit(s), we found, unexpectedly, that the packaging motor can tolerate an inactive sub-unit. However, motors containing an inactive subunit(s) exhibit fewer DNA engagements, a higher failure rate in encapsidation, reduced packaging velocity, and increased pausing. These findings suggest a new packaging model in which the motor, by re-adjusting its grip on DNA, can skip an inactive subunit and resume DNA translocation, contrary to the prevailing notion of strict coordination amongst motor subunits of other packaging motors.


title: Metabolic breakdown of non-small cell lung cancers by mitochondrial HSPD1 targeting

abstract:
The identification of novel targets is of paramount importance to develop more effective drugs and improve the treatment of non-small cell lung cancer (NSCLC), the leading cause of cancer-related deaths worldwide. Since cells alter their metabolic rewiring during tumorigenesis and along cancer progression, targeting key metabolic players and metabolism-associated proteins represents a valuable approach with a high therapeutic potential. Metabolic fitness relies on the functionality of heat shock proteins (HSPs), molecular chaperones that facilitate the correct folding of metabolism enzymes and their assembly in macromolecular structures. Here, we show HSPD1 (HSP60) as a survival gene ubiquitously expressed in NSCLC and associated with poor patients prognosis. HSPD1 knockdown or its chemical disruption by the small molecule KHS101 induces a drastic breakdown of oxidative phosphorylation, and suppresses cell proliferation both in vitro and in vivo. By combining drug profiling with transcriptomics and through a whole-genome CRISPR/Cas9 screen, we demonstrate that HSPD1-targeted anti-cancer effects are dependent on OXPHOS and validated molecular determinants of KHS101 sensitivity, in particular, the creatine-transporter SLC6A8 and the subunit of the cytochrome c oxidase complex COX5B. These results highlight mitochondrial metabolism as an attractive target and HSPD1 as a potential theranostic marker for developing therapies to combat NCSLC.

SignificanceHSPD1 elimination or disruption interferes with NSCLC metabolic activity causing a strong OXPHOS-dependent energetic breakdown, which the cancer cells fail to overcome, highlighting HSPD1 as a potential theranostic marker for improving lung cancer therapy.


title: Multiphasic value biases in fast-paced decisions

abstract: Perceptual decisions are biased toward higher-value options when overall gains can be improved. When stimuli demand immediate reactions, the neurophysiological decision process dynamically evolves through distinct phases of growing anticipation, detection and discrimination, but how value biases are exerted through these phases remains unknown. Here, by parsing motor preparation dynamics in human electrophysiology, we uncovered a multiphasic pattern of countervailing biases operating in speeded decisions. Anticipatory preparation of higher-value actions began earlier, conferring a "starting point"-advantage at stimulus onset, but the delayed preparation of lower-value actions was steeper, conferring a value-opposed buildup rate bias. This, in turn, was countered by a transient deflection toward the higher value action evoked by stimulus detection. A neurally-constrained process model featuring anticipatory urgency, biased detection, and accumulation of growing stimulus-discriminating evidence, successfully captured both behavior and motor preparation dynamics. Thus, an intricate interplay of distinct biasing mechanisms serves to prioritise time-constrained perceptual decisions.

category: neuroscience


title: Optimal Time Lags from Causal Prediction Model Help Stratify and Forecast Nervous System Pathology

abstract: Traditional clinical approaches diagnose disorders of the nervous system using standardized observational criteria. Although aiming for homogeneity of symptoms, this method often results in highly heterogeneous disorders. A standing question thus is how to automatically stratify a given random cohort of the population, such that treatment can be better tailored to each clusters symptoms, and severity of any given group forecasted to provide neuroprotective therapies. In this work we introduce new methods to automatically stratify a random cohort of the population composed of healthy controls of different ages and patients with different disorders of the nervous systems. Using a simple walking task and measuring micro-fluctuations in their biorhythmic motions, we combine non-linear causal network connectivity analyses in the temporal and frequency domains with stochastic mapping. The methods define a new type of internal motor timings. These are amenable to create personalized clinical interventions tailored to self-emerging clusters signaling fundamentally different types of gait pathologies. We frame our results using the principle of reafference and operationalize them using causal prediction, thus renovating the theory of internal models for the study of neuromotor control.


title: Chimpanzee pant-hoots encode information about individual but not group differences

abstract: Vocal learning, the ability to voluntarily modify the acoustic structure of vocalizations based on social cues, is a fundamental feature of speech in humans (Homo sapiens). While vocal learning is common in taxa such as songbirds and whales, the vocal learning capacities of nonhuman primates appear more limited. Intriguingly, evidence for vocal learning has been reported in chimpanzees (Pan troglodytes), for example in the form of regional variation ( dialects) in the  pant-hoot calls. This suggests that some capacity for vocal learning may be an ancient feature of the Pan-Homo clade. Nonetheless, reported differences have been subtle, with inter-community variation representing only a small portion of the total acoustic variation. To gain further insights into the extent of regional variation in chimpanzee vocalizations, we performed an analysis of pant-hoots from chimpanzees in the neighboring Kasekela and Mitumba communities at Gombe National Park, Tanzania, and the geographically distant Kanyawara community at Kibale National Park, Uganda. We observed group differences only among the geographically isolated communities and did not find any differences between the neighboring communities at Gombe. Furthermore, we found differences among individuals in all communities. Hence, the variation in chimpanzee pant-hoots reflected individual differences, rather than group differences. The limited evidences for vocal learning in Pan suggest that extensive vocal learning emerged in the human lineage after the divergence from Pan.

category: animal behavior and cognition


title: Climate fluctuations drive the recruitment and growth of temperate grassland plants

abstract: Recent climate warming is associated with the increasing magnitude and frequency of extreme events, including heatwaves and drought periods worldwide. Such events can have major effects on the species composition of plant communities, hence on biodiversity and ecosystem functioning. Here we studied responses of Central European dry grassland plants to fluctuating temperature and precipitation over the last thirty years with monthly temporal resolution. We assessed the seasonal and annual dynamics of plant recruitment and growth based on the analysis of annual growth rings from the root collar. Although most studies so far applied such methods to trees and shrubs, we focused on typical grassland plants, two forbs and two chamaephytes. We related the recruitment and annual growth to monthly and annual precipitation, temperature and aridity between 1991 and 2019. We revealed species-specific responses, namely the (i) recruitment of deep-rooted, heavy-seeded species was positively affected by precipitation in both late winter-early spring and summer, whereas recruitment of shallow-rooted, light-seeded species was weakly influenced by climate fluctuations; (ii) growth of shallow-rooted species was more adversely affected by high summer temperature and drought than the growth of deep-rooted species. The population age structure of all the studied species was affected by the climate of the past decades. Most individuals established in the wet period of the 2000s, fewer in the precipitation-poorer 1990s, and the establishment was considerably reduced in the dry and warm period of the 2010s. Our findings indicate that the change towards warmer and drier climate has a profound effect even on drought-adapted ecosystems such as temperate dry grasslands. However, plant responses to various climatic extremes are species-specific, depending on their characteristics, such as life form or rooting depth. Consequently, the ongoing and anticipated climate warming will likely result in complex changes in species composition and other ecosystem properties of temperate grasslands

category: ecology


title: immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires

abstract: Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. To date, widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency, and interoperability. immuneML (immuneml.uio.no) addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows. To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. We demonstrate the broad applicability of immuneML by (i) reproducing a large-scale study on immune state prediction, (ii) developing, integrating, and applying a novel method for antigen specificity prediction, and (iii) showcasing streamlined interpretability-focused benchmarking of AIRR ML.

category: bioinformatics


title: High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe

abstract: The dia-PASEF technology exploits ion mobility separation for high-sensitivity analysis of complex proteomes. Here, we demonstrate neural network-based processing of the ion mobility data, which we implement in the DIA-NN software suite. Using spectral libraries generated with the MSFragger-based FragPipe computational platform, the DIA-NN analysis of dia-PASEF raw data increases the proteomic depth by up to 69% compared to the originally published dia-PASEF workflow. For example, we quantify over 5200 proteins from 10ng of HeLa peptides separated with a 95-minute nanoflow gradient, and over 5000 proteins from 200ng using a 4.8-minute separation with an Evosep One system. In complex samples, featuring a mix of human and yeast lysates, the workflow detects over 11700 proteins in single runs acquired with a 100-minute nanoflow gradient, while demonstrating quantitative precision. Hence, the combination of FragPipe and DIA-NN provides a simple-to-use software platform for dia-PASEF data analysis, yielding significant gains in high-sensitivity proteomics.


title: Palynofacies, environments, and climate changes in the Magdalena River Basin

abstract:
Four environments (swamp, shallow lake, alluvial flood plain, and lagoon) from the Lower Magdalena River Basin were studied for palynofacies quantitative characterization. Each environment has been described based on four criteria: palynomorph assemblage, organic matter concentration, organic matter palynological composition, and organic particle morphology.

Shallow lakes palynological assemblages are dominated by composite and grass pollen. The POM (particulate organic matter) morphology is characterized by a maximum at {Phi} 5 class (silt), and it has a sphericity histogram with bimodal distribution (peaks at 0.1 and 0.5/0.6). From a composition point of view, POM is mainly opaque amorphous materials. POM concentration is usually lower than 0.1%.

Swamp environments palynological assemblages are dominated by grass pollen with a slightly smaller amount of composite pollen. The POM is dominated by finely dispersed amorphous and indeterminate "other" types (organo-mineral gel ?), depending on the oxidation degree. The swamp concentration of organic matter a few centimeters below the water-sediment interface varies between 0.1% and 0.3%. Below that, organic concentration is usually lower than 0.1%.

Lagoon assemblages are rich in species and specimens, but assemblages are highly variable. Main components are either finely dispersed amorphous or plant cuticular/epidermal or amorphous homogeneous and heterogeneous or fungal remains. Peat lithology is rich in mangrove pollen, while clay assemblages are dominated by composites, grass, and water plants together with Botryococcus algal remains. Lagoon sediments are the richest in POM concentration, with values between 0.13% and 1% (excluding peats). Regarding particle size and shape, in this environment, they show a trend to decrease in grain size from {Phi} 1 to {Phi} 2 class (sand) dominated assemblages to {Phi} 5 to {Phi} 6 class (silt) dominated assemblages from base to top. Elongated shapes are abundant, with 30% to 50% of particles in the tabloid to elongated tabloid classes.

Alluvial - fluvial flood basin samples are often barren in palynomorphs and organic matter. Occasionally present grass pollen and fungal remains. The POM, when present, is mainly of organo-mineral gel type and has a bimodal grain size distribution, with a minor peak at {Phi} 7 class (v.f.silt) and a major peak at {Phi} 4 to {Phi} 2 class (c. silt to f. sand).

Significant changes in quantitative palynofacies occur within the top few meters of the cores, representing the last 1000 yr of sedimentation in the area. These changes are related to shifts in climate, from colder to warmer conditions or from dry to wet periods, most probably linked with E.N.S.O. A short dry and cold period related to the "Little Ice Age" was identified in the Ayapel and Cienaga de El Medio cores.

category: paleontology


title: A novel nitrogen concentrating mechanism in the coral-algae symbiosome

abstract:
Coral algal symbionts are hosted inside the symbiosome of gastrodermal cells, an intracellular compartment that isolates algae from the external environment and allows host cells to control the delivery of metabolites to their symbionts. However, the underlying molecular mechanisms are largely unknown. Here, we report the diel trafficking of NH3-transporting Rhesus (Rh) channels between the cytoplasm and the symbiosome membrane in the coral Acropora yongei, which matches established patterns of nitrogen delivery to endosymbionts. Heterologous expression in Xenopus oocytes established that A. yongei Rh (ayRhp1) is a channel that facilitates NH3 diffusion across membranes following its partial pressure gradient. Immunostaining revealed ayRhp1 is widely distributed throughout coral tissues and most abundantly present in oral ectodermal cells, desmocytes, and gastrodermal cells. In the latter, ayRhp1 was observed in the symbiosome membrane of alga-containing cells. Together with V-type H+-ATPases that make the symbiosome highly acidic (pH~4), ayRhp1 constitutes an NH4+-trapping mechanism analogous to that in mammalian renal tubule. Remarkably, ayRhp1 presence in the symbiosome membrane was higher during the day than the night. This indicates a regulatory mechanism that facilitates NH4+ delivery to alga during the day, likely to sustain high turnover rates of photosynthetic proteins, while restricting NH4+ delivery at night to maintain the endosymbiotic algae in a nitrogen-limited stage that stagnates their growth. The dynamic trafficking of proteins to and away from the symbiosome membrane is a previously unknown mechanism that contributes to metabolic regulation between symbiotic partners.

Significance StatementThe endosymbiotic relationship between corals and algae relies on the coordinated exchange of metabolites. Disruption of these metabolic exchanges can result in interruption of the symbiosis; however, the underlying molecular mechanisms are poorly understood. Here we report that Acropora yongei coral host cells express ammonia-transporting channel proteins (ayRhp1), which traffic to and away from the symbiosome membrane surrounding the endosymbiotic algae. In conjunction with the acidic symbiosome microenvironment, this mechanism allows host cells to regulate nitrogen delivery to endosymbionts sustaining essential functions while restricting growth. This work provides novel mechanistic information about metabolic regulation of animal-algae symbioses, and advances our understanding of physiological mechanisms that might determine coral local adaptation, resilience, and vulnerability to environmental stress including climate change.

category: physiology


title: Laminar-specific interhemispheric connectivity mapping with bilateral line-scanning fMRI

abstract:
Despite extensive studies detecting blood-oxygen-level-dependent (BOLD) fMRI signals across two hemispheres to present cognitive processes in normal and diseased brains, the role of corpus callosum (CC) to mediate interhemispheric functional connectivity remains controversial. Several studies show maintaining low-frequency fluctuation of resting-state (rs)-fMRI signals in homotopic brain areas of acallosal humans and post-callosotomy animals, raising the question: how can we specify the circuit-specific rs-fMRI signal fluctuation from other sources? To address this question, we have developed a bilateral line-scanning fMRI (BiLS) method to detect bilateral laminar BOLD fMRI signals from symmetric cortical regions with high spatial (100 m) and temporal (100 ms) resolution in rodents under anesthesia. In addition to ultra-slow oscillation (0.01-0.02 Hz) patterns across all cortical layers, a layer-specific bilateral coherence pattern was observed with a peak at Layer (L)2/3, where callosal projection neurons are primarily located and reciprocal transcallosal projections are received. In particular, the L2/3-specific coherence pattern showed a peak at 0.05 Hz based on the stimulation paradigm, depending on the interhemispheric CC activation. Meanwhile, the L2/3-specific rs-fMRI coherence was peaked at 0.08-0.1Hz which was independent of the varied ultra-slow oscillation patterns (0.01-0.02 Hz) presumably involved with global neuromodulation. This work provides a unique laminar fMRI mapping scheme to characterize the CC-mediated evoked fMRI and frequency-dependent rs-fMRI responses, presenting crucial evidence to distinguish the circuit-specific fMRI signal fluctuations across two hemispheres.

Significance statementLaminar fMRI is a promising method to better understand neuronal circuit contribution to functional connectivity (FC) across cortical layers. Here, we developed a bilateral line-scanning fMRI method, allowing the detection of laminar-specific BOLD-fMRI signals from homologous cortical regions in rodents with high spatial and temporal resolution. Laminar coherence patterns of both evoked and rs-fMRI signals revealed that CC-dependent interhemispheric FC is significantly strong at Layer 2/3, where callosal projection neurons are primarily located. The Layer 2/3-specific rs-fMRI coherence is independent of ultra-slow oscillation based on global neuromodulation, distinguishing the circuit-specific rs-fMRI signal fluctuation from different regulatory sources.


title: Allopregnanolone mediates affective switching through modulation of oscillatory states in the basolateral amygdala

abstract: Brexanolone (allopregnanolone), was recently approved by the FDA for the treatment of post-partum depression, demonstrating long-lasting antidepressant effects. Despite our understanding of the mechanism of action of neurosteroids as positive allosteric modulators (PAMs) of GABAO_SCPLOWAC_SCPLOW receptors, we still do not fully understand how allopregnanolone exerts these persistent antidepressant effects. Here, we demonstrate that allopregnanolone and similar synthetic neuroactive steroid analogs, SGE-516 (tool-compound) and zuranolone (SAGE-217, investigational-compound), are capable of modulating oscillatory states across species, which we propose may contribute to long-lasting changes in behavioral states. We identified a critical role for interneurons in generating oscillations in the basolateral amygdala (BLA) and a role for delta-containing GABAO_SCPLOWAC_SCPLOWRs in mediating the ability of neurosteroids to modulate network and behavioral states. Actions of allopregnanolone in the BLA is sufficient to alter behavioral states and enhance BLA high-theta oscillations (6-12Hz) through delta-containing GABAO_SCPLOWAC_SCPLOW receptors, a mechanism distinct from other GABAO_SCPLOWAC_SCPLOW PAMs, such as benzodiazepines. Moreover, treatment with the allopregnanolone analog SGE-516 induces long-lasting protection from chronic stress-induced disruption of network states, which correlates with improved behavioral outcomes. Our findings demonstrate a novel molecular and cellular mechanism mediating the well-established anxiolytic and antidepressant effects of neuroactive steroids.


title: Variability of EEG electrode positions and their underlying brain regions: visualising gel artifacts from a simultaneous EEG-fMRI dataset

abstract: We investigated the between-subject variability of EEG electrode placement from a simultaneously recorded EEG-fMRI dataset. Neuro-navigation software was used to localise electrode positions in xyz and MNI space, made possible by the gel artifacts present in the structural MRI images. To assess variation in the brain regions directly underneath each electrode, we used both raw MNI coordinates and labels from the Harvard-Oxford Cortical atlas. In a sample of 20 participants, the mean standard deviation of electrode placement was 3.94 mm in x, 5.55 mm in y, and 7.17 mm in z, with the largest variation in parietal and occipital electrodes. In addition, the brain regions covered by electrode pairs was not always consistent; for example, the mean location of electrode P07 was mapped to BA18, whereas P08 was closer to BA19. Further, electrode C1 was mapped to the left primary motor cortex, whereas C2 was closer to right pre-motor cortex. Overall, the results emphasise the variation in electrode positioning that can be found even in a fixed cap, potentially caused by between-subject differences in brain morphology. We present a relatively simple method for approximating the location of electrodes in a simultaneous EEG-fMRI data set with accompanying analysis code, and suggest that researchers check the regions underlying their EEG ROIs to improve the generalisability and reliability of their neuroimaging results.


title: Multimodal image fusion via deep generative models

abstract:
Recently, it has become progressively more evident that classic diagnostic labels are unable to accurately and reliably describe the complexity and variability of several clinical phenotypes. This is particularly true for a broad range of neuropsychiatric illnesses such as depression and anxiety disorders or behavioural phenotypes such as aggression and antisocial personality. Patient heterogeneity can be better described and conceptualized by grouping individuals into novel categories, which are based on empirically-derived sections of intersecting continua that span both across and beyond traditional categorical borders. In this context, neuroimaging data carry a wealth of spatiotemporally resolved information about each patients brain. However, they are usually heavily collapsed a priori through procedures which are not learned as part of model training, and consequently not optimized for the downstream prediction task. This is due to the fact that every individual participant usually comes with multiple whole-brain 3D imaging modalities often accompanied by a deep genotypic and phenotypic characterization, hence posing formidable computational challenges.

In this paper we design and validate a deep learning architecture based on generative models rooted in a modular approach and separable convolutional blocks (which result in a 20-fold decrease in parameter utilization) in order to a) fuse multiple 3D neuroimaging modalities on a voxel-wise level, b) efficiently convert them into informative latent embeddings through heavy dimensionality reduction, c) maintain excellent generalizability and minimal information loss. As proof of concept, we test our architecture on the well characterized Human Connectome Project database (n=974 healthy subjects), demonstrating that our latent embeddings can be clustered into easily separable subject strata which, in turn, map to extremely different phenotypical information (including organic, neuropsychological, personality variables) which was not included in the embedding creation process.

The ability to extract meaningful and separable phenotypic information from brain images alone can aid in creating multi-dimensional biomarkers able to chart spatio-temporal trajectories which may correspond to different pathophysiological mechanisms unidentifiable to traditional data analysis approaches. In turn, this may be of aid in predicting disease evolution as well as drug response, hence supporting mechanistic disease understanding and also empowering clinical trials.


title: Exposure to sevoflurane results in changes of transcription factor occupancy in sperm and inheritance of autism

abstract:
One in 54 children in the U.S. is diagnosed with Autism Spectrum Disorder (ASD). De novo germline and somatic mutations cannot account for all cases of ASD, suggesting that epigenetic alterations triggered by environmental exposures may be responsible for a subset of ASD cases. Human and animal studies have shown that exposure of the developing brain to general anesthetic (GA) agents can trigger neurodegeneration and neurobehavioral abnormalities but the effects of general anesthetics on the germ line have not been explored in detail. We exposed pregnant mice to sevoflurane during the time of embryonic development when the germ cells undergo epigenetic reprogramming and found that more than 38% of the directly exposed F1 animals exhibit impairments in anxiety and social interactions. Strikingly, 44-47% of the F2 and F3 animals, which were not directly exposed to sevoflurane, show the same behavioral problems. We performed ATAC-seq and identified more than 1,200 differentially accessible sites in the sperm of F1 animals, 69 of which are also present in the sperm of F2 animals. These sites are located in regulatory regions of genes strongly associated with ASD, including Arid1b, Ntrk2, and Stmn2. These findings suggest that epimutations caused by exposing germ cells to sevoflurane can lead to ASD in the offspring, and this effect can be transmitted through the male germline inter and trans-generationally.

Summary sentencePregnant mouse F0 females exposed to sevoflurane give rise to F1 males with sociability and anxiety defects. These behaviors are transmitted to F2 and F3 males. Their sperm show changes in transcription factor occupancy in genes implicated in autism.


title: Characterizing neural phase-space trajectories via Principal Louvain Clustering

abstract:
BackgroundWith the growing size and richness of neuroscience datasets in terms of dimension, volume, and resolution, identifying spatiotemporal patterns in those datasets is increasingly important. Multivariate dimension-reduction methods are particularly adept at addressing these challenges.

New MethodIn this paper, we propose a novel method, which we refer to as Principal Louvain Clustering (PLC), to identify clusters in a low-dimensional data subspace, based on time-varying trajectories of spectral dynamics across multisite local field potential (LFP) recordings in awake behaving mice. Data were recorded from prefrontal cortex, hippocampus, and parietal cortex in eleven mice while they explored novel and familiar environments.

ResultsPLC-identified subspaces and clusters showed high consistency across animals, and were modulated by the animals ongoing behavior.

ConclusionsPLC adds to an important growing literature on methods for characterizing dynamics in high-dimensional datasets, using a smaller number of parameters. The method is also applicable to other kinds of datasets, such as EEG or MEG.


title: The extracellular milieu of Toxoplasma-s lytic cycle drives lab-adaptation and promotes changes in lipid metabolism primarily driven by transcriptional reprogramming

abstract: To map host-independent in vitro virulence traits of Toxoplasma gondii, evolve and resequencing (E&R) during the lab-adaption was applied. Phenotypic assessments of the lytic cycle revealed that only traits needed in the extracellular milieu evolved. Surprisingly, only non-synonymous mutations in a P4 flippase fixed in two populations. However, dramatic changes in the transcriptional signature of extracellular parasites revealed a "pro-tachyzoite" profile as well as upregulation of fatty acid biosynthesis (FASII) pathway genes. More general, a set of 300 genes which expression profile changes during evolution mapped to specific traits. Validation of a select number of genes in this set by knock-outs indeed confirmed their role in lab-adaptation. Finally, assembly of an ApiAP2 and Myb transcription factor network revealed the transcriptional program underlying the adapting extracellular state. Overall, E&R is a new genomic tool successfully applied to map the development of polygenic traits underlying in vitro virulence of T. gondii.

category: microbiology


title: A Tail Fiber Protein and a Receptor-Binding Protein Mediate ICP2 Bacteriophage Interactions with Vibrio cholerae OmpU

abstract:
ICP2 is a virulent bacteriophage (phage) that preys on Vibrio cholerae. ICP2 was first isolated from cholera patient stool samples. Some of these stools also contained ICP2-resistant isogenic V. cholerae strains harboring missense mutations in the trimeric outer membrane porin protein OmpU, identifying it as the ICP2 receptor. In this study, we identify the ICP2 proteins that mediate interactions with OmpU by selecting for ICP2 host-range mutants within infant rabbits infected with a mixture of wild type and OmpU mutant strains. ICP2 host-range mutants had missense mutations in putative tail fiber gene gp25 and putative adhesin gp23. Using site-specific mutagenesis we show that single or double mutations in gp25 are sufficient to generate the host-range mutant phenotype. However, at least one additional mutation in gp23 is required for robust plaque formation on specific OmpU mutants. Mutations in gp23 alone were insufficient to give a host-range mutant phenotype. All ICP2 host-range mutants retained the ability to plaque on wild type V. cholerae cells. The strength of binding of host-range mutants to V. cholerae correlated with plaque morphology, indicating that the selected mutations in gp25 and gp23 restore molecular interactions with the receptor. We propose that ICP2 host-range mutants evolve by a two-step process where, first, gp25 mutations are selected for their broad host-range, albeit accompanied by low level phage adsorption. Subsequent selection occurs for gp23 mutations that further increase productive binding to specific OmpU alleles, allowing for near wild type efficiencies of adsorption and subsequent phage multiplication.

ImportanceConcern over multidrug-resistant bacterial pathogens, including Vibrio cholerae, has led to a renewed interest in phage biology and their potential for phage therapy. ICP2 is a genetically unique virulent phage isolated from cholera patient stool samples. It is also one of three phages in a prophylactic cocktail shown to be effective in animal models of infection and the only one of the three that requires a protein receptor (OmpU). This study identifies a ICP2 tail fiber and a receptor binding protein and examines how ICP2 responds to the selective pressures of phage-resistant OmpU mutants. We found that this particular co-evolutionary arms race presents fitness costs to both ICP2 and V. cholerae.


title: Stromal inflammation is a targetable driver of hematopoietic aging

abstract: Hematopoietic aging is marked by a loss of regenerative capacity and skewed differentiation from hematopoietic stem cells (HSC) leading to dysfunctional blood production. Signals from the bone marrow (BM) niche dynamically tailor hematopoiesis, but the effect of aging on the niche microenvironment and the contribution of the aging niche to blood aging still remains unclear. Here, we characterize the inflammatory milieu in the aged marrow cavity that drives both stromal and hematopoietic remodeling. We find decreased numbers and functionality of osteogenic mesenchymal stromal cells (MSC) at the endosteum and expansion of pro-inflammatory perisinusoidal MSCs with deterioration of sinusoidal endothelium in the central marrow, which together create a degraded and inflamed old niche. Molecular mapping at single cell resolution confirms disruption of cell identities and enrichment of inflammatory response genes in niche populations. Niche inflammation, in turn, drives chronic activation of emergency myelopoiesis pathways in old HSCs and multipotent progenitors (MPP), which promotes myeloid differentiation at the expense of lymphoid and erythroid commitment and hinders hematopoietic regeneration. Remarkably, niche deterioration, HSC dysfunction and defective hematopoietic regeneration, can be improved by blocking inflammatory IL-1 signaling. Our results demonstrate that targeting niche inflammation is a tractable strategy to restore blood production during aging.


title: Ecosystem size and complexity dictate riverine biodiversity

abstract:
Larger ecosystems support more species; this ubiquitous pattern is the foundation of current conservation schemes. However, many ecosystems possess a complex spatial structure that cannot be represented by area, and the role of such complexity in scaling biodiversity is largely unknown. Here, we use theory and extensive fish community data from two distinct geographic regions (Japan and United States) to show that ecosystem size and complexity dictate riverine biodiversity. We found that larger and more branched  complex river networks harbored greater species richness due to increased space and environmental heterogeneity. The complexity effect was comparable to the size effect, and this pattern has emerged regardless of ecological contexts. The dual control of biodiversity may be a pervasive feature that has far-reaching implications for biodiversity conservation.

One sentence summaryThis study provides the first evidence that ecosystem size and complexity play comparable roles in regulating biodiversity.


title: Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet

abstract: Conservation strategies centred around species habitat protection rely on species dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus). Traditional microhistological analysis of crop contents or faeces and/or direct observations are time-consuming and at low taxonomic resolution. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trondelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 {+/-} 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis F5,86= 11.01, p <0.05) and seasons (adonis F2,03= 0.64, p <0.05). Dietary composition also differed between sexes at each location (adonis F1,47 = 2.77, p <0.05), although not significant for all data combined. In total, 35 taxa (36.84% of taxa recorded) were new capercaillie food items compared to existing knowledge. The non-invasive molecular dietary analysis applied in this study provides new ecological understanding of capercaillies diet which can have real conservation implications. The broad variety of diet items indicates that vegetation does not limit food intake. This plasticity in diet suggests that other factors including disturbed mating grounds and not diet could be the main threat to their survival.


title: Underwater photo-identification of marine megafauna: an identity card catalogue of sperm whales (Physeter macrocephalus) off Mauritius Island

abstract:
The long-term monitoring of long-lived animal populations often requires individual identification. For cetacean populations, this identification is mostly based on morphological characters observable from a boat such as shape, spots and cuts of the back, caudal and dorsal fins. This is well suited for species easily displaying their caudal fins, such as the humpback whales Megaptera novaeangliae, or those whose skin pigmentation patterns enable individual identification.

However, for elusive or shier species such as the sperm whales Physeter macrocephalus, this approach may be more challenging as individuals display a rather uniform skin pigmentation. They also do not show very often their caudal fin that must be photographed perpendicularly to the water surface, vertically and fully emerged, uneasing the individual identification from a boat. Immature sperm whales that usually have a caudal fin without any distinctive marks may sometimes be excluded from photo-identification catalogues.

Within the framework of the Maubydick project, focusing on the long-term monitoring of sperm whales in Mauritius, passive underwater observation and video recording were used to identify long-lasting body markers (e.g., sex, ventral white markings, cut outs of fins) to improve individual identification. A catalogue of individual identity cards was developed and 38 individuals were recorded (six adult males, 18 adult females and 14 immatures). This catalogue was used in the field and enabled observers to record some nearly-daily and yearly recaptures. Advantages and disadvantages of this method are presented here.

Such catalogues represent a robust baseline for conducting behavioural, genetic and acoustic studies in marine megafauna social species. Benefits of such newly acquired knowledge are of first importance to implement relevant conservation plans in the marine realm.


title: Sexual conflict promotes species coexistence through negative frequency dependence

abstract:
A major challenge in community ecology is to understand the mechanisms promoting stable local coexistence. A necessary feature of local coexistence is that species show negative frequency dependence, rescuing rare species from exclusion. However, most studies have focused on ecological differences driving negative frequency dependence, ignoring non-ecological mechanisms such as reproductive interactions. Here, we combined field studies with behavioural and mesocosm experiments to investigate how reproductive interactions within and between species promote coexistence. Our results indicate that the intensity of male mating harassment and sexual conflict increases as species become more common, reducing female productivity and leading to negative frequency dependence. Moreover, field surveys reveal that negative frequency dependence operates in natural settings, consistent with our experimental results. These results suggest that sexual conflict can promote local coexistence and highlights the importance of studying reproductive interactions together with ecological differences to better understand the mechanisms promoting species coexistence.

Significance statementResearch on the mechanisms promoting local species coexistence have focused on canonical ecological differences that increase intraspecific over interspecific competition. However, one intrinsic factor of species that can promote coexistence are the reproductive interactions. We performed a series of behavioural and mesocosm experiments manipulating species frequencies together with field observations and show that sexual conflict can decrease female fitness when species are common and promote local coexistence. Our results suggest that reproductive interactions are an understudied mechanism that can promote species coexistence even when species are ecologically equivalent.


title: Comparative phylogeography of the freshwater mussels of the southeastern United States: reconstructing historic drainages using molecular data

abstract: Knowledge of species ages and their distribution enhance our understanding of processes that create and maintain species diversity at both local and regional levels. The largest family of freshwater mussels (Unionidae), reach their highest species diversity in drainages of the southeastern united states. By sequencing multiple loci from mussel species distributed throughout the drainages in this region, we attempt to uncover historical patterns of divergence and determine the role of vicariance events on the species formation in mussels and extend our hypothesis to freshwater animals in general. We analyzed 346 sequences from five genera encompassing 37 species. Species were sampled across 12 distinct drainages ending either in the Atlantic Ocean or the Gulf of Mexico. Overall the topologies of the different genera returned phylogenetic trees that were congruent with geographically contiguous drainages. The most common pattern was the grouping between the Atlantic slope and gulf coast drainages, however the Tennessee drainage was often the exception to this pattern grouping with the Atlantic slope. Most mussel species find a most recent common ancestor within a drainage before finding an ancestor between drainages. This supports the hypothesis of allopatric divergence followed by later burst of speciation within a drainage. Our estimated divergence times for the Atlantic-Gulf split agree with other studies estimating vicariance in fish species of the Atlantic and gulf coast.

category: evolutionary biology


title: Transposon-induced inversions activate gene expression in Maize pericarp

abstract: Chromosomal inversions can have considerable biological and agronomic impacts including disrupted gene function, change in gene expression and inhibited recombination. Here we describe the molecular structure and functional impact of six inversions caused by Alternative Transpositions between p1 and p2 genes responsible for floral pigmentation in maize. In maize line p1-wwB54, the p2 gene is expressed in anther and silk but not in pericarp, making the kernels white. We identified inversions in this region caused by transposition of Ac and fractured Ac (fAc) transposable elements. These inversions change the position of a p1 enhancer and activate the expression of p2 in the kernel pericarp, resulting in red kernel color. We hypothesize that these inversions place the p2 gene promoter near a p1 gene enhancer, thereby activating p2 expression in kernel pericarp.

category: genetics


title: Identification of putative causal loci in whole-genome sequencing data via knockoff statistics

abstract: The analysis of whole-genome sequencing studies is challenging due to the large number of rare variants in noncoding regions and the lack of natural units for testing. We propose a statistical method to detect and localize rare and common risk variants in whole-genome sequencing studies based on a recently developed knockoff framework. It can (1) prioritize causal variants over associations due to linkage disequilibrium thereby improving interpretability; (2) help distinguish the signal due to rare variants from shadow effects of significant common variants nearby; (3) integrate multiple knockoffs for improved power, stability and reproducibility; and (4) flexibly incorporate state-of-the-art and future association tests to achieve the benefits proposed here. In applications to whole-genome sequencing data from the Alzheimers Disease Sequencing Project (ADSP) and COPDGene samples from NHLBI Trans-Omics for Precision Medicine (TOPMed) Program we show that our method compared with conventional association tests can lead to substantially more discoveries.


title: Distributed Brain Co-Processor for Neurophysiologic Tracking and Adaptive Stimulation: Application to Drug Resistant Epilepsy

abstract: Early implantable epilepsy therapy devices provided open-loop electrical stimulation without brain sensing, computing, or an interface for synchronized behavioral inputs from patients. Recent epilepsy stimulation devices provide brain sensing but have not yet developed analytics for accurately tracking and quantifying behavior and seizures. Here we describe a distributed brain co-processor providing an intuitive bi-directional interface between patient, implanted neural stimulation and sensing device, and local and distributed computing resources. Automated analysis of continuous streaming electrophysiology is synchronized with patient reports using a hand-held device and integrated with distributed cloud computing resources for quantifying seizures, interictal epileptiform spikes, and patient symptoms during therapeutic electrical brain stimulation. The classification algorithms for interictal epileptiform spikes and seizures were developed and parameterized using long-term ambulatory data from 9 humans and 8 canines with epilepsy, and then implemented prospectively in out-of-sample testing in 2 pet canines and 4 humans with drug resistant epilepsy living in their natural environments.

category: bioengineering


title: Distributed brain co-processor for tracking electrophysiology and behavior during electrical brain stimulation


title: Estimating Ectopic Beat Probability with Simplified Statistical Models that Account for Experimental Uncertainty

abstract:
Ectopic beats (EBs) are cellular arrhythmias that can trigger lethal arrhythmias. Simulations using biophysically-detailed cardiac myocyte models can reveal how model parameters influence the probability of these cellular arrhythmias, however such analyses can pose a huge computational burden. Here, we develop a simplified approach in which logistic regression models (LRMs) are used to define a mapping between the parameters of complex cell models and the probability of EBs (P(EB)). As an example, in this study, we build an LRM for P(EB) as a function of diastolic cytosolic Ca2+ concentration ([Ca2+]i), sarcoplasmic reticulum (SR) Ca2+ load, and kinetic parameters of the inward rectifier K+ current (IK1) and ryanodine receptor (RyR). This approach, which we refer to as arrhythmia sensitivity analysis, allows for evaluation of the relationship between these arrhythmic event probabilities and their associated parameters. This LRM is also used to demonstrate how uncertainties in experimentally measured values determine the uncertainty in P(EB). In a study of the role of [Ca2+]SR uncertainty, we show a special property of the uncertainty in P(EB), where with increasing [Ca2+]SR uncertainty, P(EB) uncertainty first increases and then decreases. Lastly, we demonstrate that IK1 suppression, at the level that occurs in heart failure myocytes, increases P(EB).

Author summaryAn ectopic beat is an abnormal cellular electrical event which can trigger dangerous arrhythmias in the heart. Complex biophysical models of the cardiac myocyte can be used to reveal how cell properties affect the probability of ectopic beats. However, such analyses can pose a huge computational burden. We develop a simplified approach that enables a highly complex biophysical model to be reduced to a rather simple statistical model from which the functional relationship between myocyte model parameters and the probability of an ectopic beat is determined. We refer to this approach as arrhythmia sensitivity analysis. Given the efficiency of our approach, we also use it to demonstrate how uncertainties in experimentally measured myocyte model parameters determine the uncertainty in ectopic beat probability. We find that, with increasing model parameter uncertainty, the uncertainty in probability of ectopic beat first increases and then decreases. In general, our approach can efficiently analyze the relationship between cardiac myocyte parameters and the probability of ectopic beats and can be used to study how uncertainty of these cardiac myocyte parameters influences the ectopic beat probability.


title: Leveraging omic features with F3UTER enables identification of unannotated 3'UTRs for synaptic genes

abstract: There is growing evidence for the importance of 3 untranslated region (3UTR) dependent regulatory processes. However, our current human 3UTR catalogue is incomplete. Here, we developed a machine learning-based framework, leveraging both genomic and tissue-specific transcriptomic features to predict previously unannotated 3UTRs. We identify unannotated 3UTRs associated with 1,513 genes across 39 human tissues, with the greatest abundance found in brain. These unannotated 3UTRs were significantly enriched for RNA binding protein (RBP) motifs and exhibited high human lineage-specificity. We found that brain-specific unannotated 3UTRs were enriched for the binding motifs of important neuronal RBPs such as TARDBP and RBFOX1, and their associated genes were involved in synaptic function and brain- related disorders. Our data is shared through an online resource F3UTER (https://astx.shinyapps.io/F3UTER/). Overall, our data improves 3UTR annotation and provides novel insights into the mRNA-RBP interactome in the human brain, with implications for our understanding of neurological and neurodevelopmental diseases.


title: Latent representation of the human pan-celltype epigenome through a deep recurrent neural network

abstract: The availability of thousands of assays of epigenetic activity necessitates compressed representations of these data sets that summarize the epigenetic landscape of the genome. Until recently, most such representations were celltype specific, applying to a single tissue or cell state. Recently, neural networks have made it possible to summarize data across tissues to produce a pan-celltype representation. In this work, we propose Epi-LSTM, a deep long short-term memory (LSTM) recurrent neural network autoencoder to capture the long-term dependencies in the epigenomic data. The latent representations from Epi-LSTM capture a variety of genomic phenomena, including gene-expression, promoter-enhancer interactions, replication timing, frequently interacting regions and evolutionary conservation. These representations outperform existing methods in a majority of cell-types, while yielding smoother representations along the genomic axis due to their sequential nature.


title: APPTEST is an innovative new method for the automatic prediction of peptide tertiary structures

abstract: Good knowledge of a peptides tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational method that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works for both linear and cyclic peptides of 5-40 natural amino acids. APPTEST is computationally efficient, returning predicted structures within a number of minutes. APPTEST performance was evaluated on a set of 356 test peptides; the best structure predicted for each peptide deviated by an average of 1.9[A] from its experimentally determined backbone conformation, and a native or near-native structure was predicted for 97% of the target sequences. A comparison of APPTEST performance with PEP-FOLD, PEPstrMOD and Peplook across benchmark datasets of short, long and cyclic peptides shows that on average APPTEST produces structures more-native than the existing methods in all three categories. This innovative, cutting-edge peptide structure prediction method is available as an online web server at https://research.timmons.eu/apptest, facilitating in silico study and design of peptides by the wider research community.


title: The carbon footprint of bioinformatics

abstract: Bioinformatic research relies on large-scale computational infrastructures which have a non-zero carbon footprint. So far, no study has quantified the environmental costs of bioinformatic tools and commonly run analyses. In this study, we estimate the bioinformatic carbon footprint (in kilograms of CO2 equivalent units, kgCO2e) using the freely available Green Algorithms calculator (www.green-algorithms.org). We assess (i) bioinformatic approaches in genome-wide association studies (GWAS), RNA sequencing, genome assembly, metagenomics, phylogenetics and molecular simulations, as well as (ii) computation strategies, such as parallelisation, CPU (central processing unit) vs GPU (graphics processing unit), cloud vs. local computing infrastructure and geography. In particular, for GWAS, we found that biobank-scale analyses emitted substantial kgCO2e and simple software upgrades could make GWAS greener, e.g. upgrading from BOLT-LMM v1 to v2.3 reduced carbon footprint by 73%. Switching from the average data centre to a more efficient data centres can reduce carbon footprint by ~34%. Memory over-allocation can be a substantial contributor to an algorithms carbon footprint. The use of faster processors or greater parallelisation reduces run time but can lead to, sometimes substantially, greater carbon footprint. Finally, we provide guidance on how researchers can reduce power consumption and minimise kgCO2e. Overall, this work elucidates the carbon footprint of common analyses in bioinformatics and provides solutions which empower a move toward greener research.


title: HERMES: a molecular formula-oriented method to target the metabolome

abstract: Comprehensive metabolome analyses are hampered by low identification rates of metabolites due to suboptimal strategies in MS and MS2 acquisition, and data analysis. Here we present a molecular formula-oriented and peak detection-free method, HERMES, that improves sensitivity and selectivity for metabolite profiling in MS and structural annotation in MS2. An analysis of environmental water, E. coli, and human plasma extracts by HERMES showed increased biological specificity of MS2 scans, leading to improved mass spectral similarity scoring and identification rates when compared to iterative data-dependent acquisition (DDA). HERMES is available as an R package with a user-friendly graphical interface to allow data analysis and interactive tracking of compound annotations.


title: Make Interactive Complex Heatmaps in R

abstract: Heatmap is a powerful visualization method on two-dimensional data to reveal patterns shared by subsets of rows and columns. In R, there are many packages that make heatmaps. Among them, ComplexHeatmap provides rich tools for constructing highly customizable heatmaps. It can easily establish connections between information from multiple sources by automatically concatenating and adjusting multiple heatmaps as well as complex annotations, which makes it widely applied in data analysis in various fields, especially in Bioinformatics. Nevertheless, the limit of ComplexHeatmap still exists. It only generates static plots which restricts deeper inspections on complex heatmaps, e.g., to look into a subset of rows and columns when a specific pattern of interest is observed from the heatmap. In this work, we described a new R/Bioconductor package InteractiveComplexHeatmap that brings interactivity to ComplexHeatmap. InteractiveComplexHeatmap is designed with an easy-to-use interface where static complex heatmaps can be directly exported to an interactive Shiny web application only with one extra line of code. The interactive application contains comprehensive tools for manipulating heatmaps. Besides common tools as supported in other interactive heatmap packages, InteractiveComplexHeatmap additionally supports, e.g., selecting over multiple heatmaps and searching heatmaps via row or column labels. Also, InteractiveComplexHeatmap provides methods for exporting static heatmaps from other popular heatmap functions, e.g., heatmap.2() or pheatmap(), to interactive heatmap applications. Finally, InteractiveComplexHeatmap provides flexible functionalities for integrating interactive heatmap widgets into other Shiny applications. InteractiveComplexHeatmap provides a user interface for self-defining response to the selection events on heatmaps, which helps to implement more complex Shiny web applications.


title: Silkworm spinning: the programmed self-assembly from natural silk fibroin to superfibre

abstract: Silkworm silk is one of the best natural protein fibers spun by the silkworm at ambient temperature and pressure using aqueous silk protein solution. It is a great challenge to reproduce high-performance artificial fibers comparable to natural silk by bionics for the incomplete understanding of silkworm spinning mechanism, especially the structure and assembly of natural silk fibroin (NSF) in the silk gland. Here, we studied the structure and assembly of NSF with the assistance of amphipol and digitonin. Our results showed NSFs were present as nanofibrils primarily composed of random coils in the silk gland. Metal ions were vital for the formation of NSF nanofibrils. The successive decrease in pH from posterior silk gland (PSG) to anterior silk gland (ASG) resulted in a gradual increase in NSF hydrophobicity. NSF nanofibrils were randomly arranged from PSG to ASG-1, and then self-assembled into herringbone-like patterns near the spinneret (ASG-2) ready for silkworm spinning. Our study reveals the mechanism by which silkworms cleverly utilize metal ions and pH gradient in the silk gland to drive the programmed self-assembly of NSF from disordered nanofibrils to anisotropic liquid crystalline spinning dope (herringbone-like patterns) for silkworm spinning, thus providing novel insights into silkworm/spider spinning mechanism and bionic creation of high-performance fibers.

category: zoology


title: Snapshot of the Atlantic Forest canopy: surveying arboreal mammals in a biodiversity hotspot

abstract: The Atlantic Forest of South America supports some of the greatest terrestrial biodiversity on our planet but is now reduced to only a small extent of its original forest cover. It hosts a large number of endemic mammalian species but our knowledge on arboreal mammal ecology and conservation has been hindered by the challenges of observing arboreal species from ground level. Camera trapping has proven to be an effective tool in terrestrial mammal monitoring, but the technique has rarely been used for arboreal species. Here we generated data on the arboreal mammal community based on canopy camera trapping for the first time in the Atlantic Forest, focusing on Caparao National Park, Brazil. We placed 24 infrared camera traps in the forest canopy distributed in seven areas within the Park, operating continuously from January 2017 to June 2019. In this time, they accumulated 4,736 camera-days and generated 2,256 sets of pictures and 30 second videos of vertebrates. Canopy camera traps were able to detect arboreal mammals spanning a wide variety of body sizes. The local mammal assemblage comprised of 15 identifiable species, including the critically endangered northern muriqui (Brachyteles hypoxanthus) and the buffy-headed marmoset (Callithrix flaviceps), and other rare, nocturnal and inconspicuous species. For the first time, we confirmed the occurrence of the thin-spined porcupine (Chaetomys subspinosus) in the Park. Species richness varied across sampling areas and forest types. Our findings demonstrate the potential of canopy camera trapping for future surveying efforts to better inform conservation strategies for mammals.


title: Spike-frequency dependent coregulation of multiple ionic conductances in fast-spiking cells forces a metabolic tradeoff

abstract: High-frequency action potentials (APs) allow rapid information acquisition and processing in neural systems, but create biophysical and metabolic challenges for excitable cells. The electric fish Eigenmannia virescens images its world and communicates with high-frequency (200-600 Hz) electric organ discharges (EODs) produced by synchronized APs generated at the same frequency in the electric organ cells (electrocytes). We cloned three previously unidentified Na+-activated K+ channel isoforms from electroctyes (eSlack1, eSlack2, and eSlick1). In electrocytes, mRNA transcript levels of the rapidly-activating eSlick, but not the slower eSlack1 or eSlack2, correlated with EOD frequency across individuals. In addition, transcript levels of an inward-rectifier K+ channel, a voltage-gated Na+ channel, and Na+,K+-ATPases also correlated with EOD frequency while a second Na+ channel isoform did not. Computational simulations showed that maintaining electrocyte AP waveform integrity as firing rates increase requires scaling conductances in accordance with these mRNA expression correlations, causing AP metabolic costs to increase exponentially.


title: The neural basis of creative production: A cross-modal ALE meta-analysis

abstract: One of the central questions about the cognitive neuroscience of creativity is the extent to which creativity depends on either domain-specific or domain-general mechanisms. To address this question, we carried out two parallel activation likelihood estimation meta-analyses of creativity: 1) a motoric analysis that combined studies across five domains of creative production (verbalizing, music, movement, writing, and drawing), and 2) an analysis of the Alternate Uses divergent-thinking task. All experiments contained a contrast between a creative task and a matched non-creative or less-creative task that controlled for the sensorimotor demands of task performance. The activation profiles of the two meta-analyses were non-overlapping, but both pointed to a domain-specific interpretation in which creative production is, at least in part, an enhancement of sensorimotor brain areas involved in non-creative production. The most concordant areas of activation in the motoric meta-analysis were high-level motor areas such as the pre-supplementary motor area and inferior frontal gyrus that interface motor planning and executive control, suggesting a means of uniting domain-specificity and -generality in creative production.


title: Self-Healing Neural Codes

abstract:
As an adaptive system, the brain must retain a faithful representation of the world while continuously integrating new information. Recent experiments have measured population activity in cortical and hippocampal circuits over many days, and found that patterns of neural activity associated with fixed behavioral variables and percepts change dramatically over time. Such "representational drift" raises the question of how malleable population codes can interact coherently with stable long-term representations that are found in other circuits, and with relatively rigid topographic mappings of peripheral sensory and motor signals. We explore how known plasticity mechanisms can allow single neurons to reliably read out an evolving population code without external error feedback. We find that interactions between Hebbian learning and single-cell homeostasis can exploit redundancy in a distributed population code to compensate for gradual changes in tuning. Recurrent feedback of partially stabilized readouts could allow a pool of readout cells to further correct inconsistencies introduced by representational drift. This shows how relatively simple, known mechanisms can stabilize neural tuning in the short term, and provides a plausible explanation for how plastic neural codes remain integrated with consolidated, long-term representations.

SignificanceThe brain is capable of adapting while maintaining stable long-term memories and learned skills. Recent experiments show that neural responses are highly plastic in some circuits, while other circuits maintain consistent responses over time, raising the question of how these circuits interact coherently. We show how simple, biologically motivated Hebbian and homeostatic mechanisms in single neurons can allow circuits with fixed responses to continuously track a plastic, changing representation without reference to an external learning signal.


title: Self-healing neural codes: Hebbian and homeostatic mechanisms can track evolving neural representations


title: Self-healing codes: how stable neural populations can track continually reconfiguring neural representations


title: Bilateral symmetry of linear streptomycete chromosomes

abstract: Here we characterise an uncommon set of telomeres from Streptomyces rimosus ATCC 10970, the parental strain of a lineage of one of the earliest-discovered antibiotic-producers. Following the closure of its genome sequence, we then compared unusual telomeres from this organism with the other five classes of replicon ends found amongst streptomycetes. Closed replicons of streptomycete chromosomes were organised with respect to their phylogeny and physical orientation, which demonstrated that different telomeres were not associated with particular clades and were likely shared amongst different strains by plasmid-driven horizontal gene transfer. Furthermore, we identified a ~50 kb origin island with conserved synteny that is located at the core of all streptomycete chromosomes and forms an axis around which symmetrical chromosome inversions can take place. Despite this chromosomal bilateral symmetry, a bias in parS sites to the right of oriC is maintained across the family Streptomycetaceae and suggests that the formation of ParB/parS nucleoprotein complexes on the right replichore is a conserved feature in streptomycetes. Consequently our studies reveal novel features of linear bacterial replicons that, through their manipulation, may lead to improvements in growth and productivity of this important industrial group of bacteria.


title: High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System

abstract:
Viruses belonging to the Nucleocytoviricota phylum are globally-distributed and include members with notably large genomes and complex functional repertoires. Recent studies have shown that these viruses are particularly diverse and abundant in marine systems, but the magnitude of actively replicating Nucleocytoviricota present in ocean habitats remains unclear. In this study, we compiled a curated database of 2,431 Nucleocytoviricota genomes and used it to examine the gene expression of these viruses in a 2.5-day metatranscriptomic time-series from surface waters of the California Current. We identified 145 viral genomes with high levels of gene expression, including 90 Imitervirales and 49 Algavirales viruses. In addition to recovering high expression of core genes involved in information processing that are commonly expressed during viral infection, we also identified transcripts of diverse viral metabolic genes from pathways such as glycolysis, the TCA cycle, and the pentose phosphate pathway, suggesting that virus-mediated reprogramming of central carbon metabolism is common in oceanic surface waters. Surprisingly, we also identified viral transcripts with homology to actin, myosin, and kinesin domains, suggesting that viruses may use them to manipulate host cytoskeletal dynamics during infection. We performed phylogenetic analysis on the virus-encoded myosin and kinesin proteins, which demonstrated that most belong to deep-branching viral clades, but that others appear to have been acquired from eukaryotes more recently. Our results highlight a remarkable diversity of active Nucleocytoviricota in a coastal marine system and underscore the complex functional repertoires expressed by these viruses during infection.

ImportanceThe discovery of giant viruses has transformed our understanding of viral complexity. Although viruses have traditionally been viewed as filterable infectious agents that lack metabolism, giant viruses can reach sizes rivalling cellular lineages and possess genomes encoding central metabolic processes. Recent studies have shown that giant viruses are widespread in aquatic systems, but the activity of these viruses and the extent to which they reprogram host physiology in situ remains unclear. Here we show that numerous giant viruses consistently express central metabolic enzymes in a coastal marine system, including components of glycolysis, the TCA cycle, and other pathways involved in nutrient homeostasis. Moreover, we found expression of several viral-encoded actin, myosin, and kinesin genes, indicating viral manipulation of the host cytoskeleton during infection. Our study reveals a high activity of giant viruses in a coastal marine system and indicates they are a diverse and underappreciated component of microbial diversity in the ocean.


title: Glucose decoration on wall-teichoic acid is required for phage adsorption and InlB-mediated virulence in Listeria ivanovii

abstract:
Listeria ivanovii (Liv) is an intracellular Gram-positive pathogen that primarily infects ruminants, but also occasionally causes enteric infections in humans. Albeit rare, this bacterium possesses the capacity to cross the intestinal epithelium of humans, similar to its more frequently pathogenic cousin, Listeria monocytogenes (Lmo). Recent studies in Lmo have shown that specific glycosyl modifications on the cell wall-associated glycopolymers (termed wall-teichoic acid, or WTA) of Lmo are responsible for bacteriophage adsorption and retention of the major virulence factor, Internalin B (InlB). However, the relationship between InlB and WTA in Liv remains unclear. Here, we report the identification of the unique gene, liv1070 that encodes a putative glucosyltransferase in the polycistronic WTA gene cluster of the Liv WSLC 3009 genome. We found that in-frame deletion of liv1070 led to loss of the glucose substitution on WTA, as revealed by UPLC-MS analysis. Interestingly, the glucose-deficient mutant became resistant to phage B025 infection due to an inability of the phage to adsorb to the bacterial surface, a binding process mediated by the receptor-binding protein B025_Gp17. As expected, deletion of liv1070 led to loss of InlB retention to the bacterial cell wall, which corresponded to a drastic decrease in cellular invasion. Genetic complementation of liv1070 restored the characteristic phenotypes, including glucose decoration, phage adsorption, and cellular invasion. Taken together, our data demonstrate that an interplay between phage, bacteria, and host cells also exists in Listeria ivanovii, suggesting the trade-off between phage resistance and virulence attenuation may be a general feature in the Listeria genus.

ImportanceListeria ivanovii is a Gram-positive bacterial pathogen known to cause enteric infection in rodents and ruminants, and occasionally in immunocompromised humans. Recent investigations revealed that, in its better-known cousin Listeria monocytogenes, strains develop resistance to bacteriophage attack due to loss of glycosylated surface receptors, which subsequently resulting in disconnection of one of the bacteriums major virulence factors, InlB. However, the situation in L. ivanovii remains unclear. Here, we show that L. ivanovii acquires phage resistance following deletion of a unique glycosyltransferase. This deletion also leads to dysfunction of InlB, making the resulting strain unable to invade host cells. Overall, this study suggests that the interplay between phage, bacteria and the host may be a feature common to the Listeria genus.


title: Ultra-small cells and DPANN genome unveiled inside an extinct vent chimney

abstract: Chemosynthetic organisms flourish around deep-sea hydrothermal vents where energy-rich fluids are emitted from metal sulfide chimneys. In contrast to actively venting chimneys, the nature of microbial life in extinct chimneys without fluid venting remains largely unknown. Here, the occurrence of ultra-small cells in silica-filled grain boundaries inside an extinct chimney is demonstrated by high-resolution bio-signature mapping. The ultra-small cells are associated with extracellularly precipitated Cu2O nanocrystals. Single-gene analysis shows that the chimney interior is dominated by a member of Pacearchaeota known as a major phylum of DPANN. Genome-resolved metagenomic analysis reveals that the chimney Pacearchaeota member is equipped with a nearly full set of genes for fermentation-based energy generation from nucleic acids, in contrast to previously characterized Pacearchaeota members lacking many genes for nucleic acid fermentation. We infer that the ultra-small cells associated with silica and extracellular Cu2O nanocrystals in the grain boundaries are Pacearchaeota, on the basis of the experimentally demonstrated capability of silica to concentrate nucleic acids from seawater and the presence of Cu-exporting genes in a reconstructed Pacearchaeota genome. Given the existence of ~3-billion-year-old submarine hydrothermally deposited silica, proliferation of microbial life using silica-bound nucleic acids might be relevant to the primitive vent biosphere.


title: A simple method to separate birds and insects in single-pol weather radar data

abstract: Recent and archived data from weather radar networks are extensively used for quantification of continent-wide bird migration pattern. While discriminating birds from weather signals is well established, insect contamination is still a problem. We present a simple method combining two doppler radar products within a single Gaussian-mixture model to estimate the proportions of birds and insects within a single measurement, as well as the density and speed of birds and insects. The method can be applied to any existing archives of vertical bird profiles, such as the ENRAM repository (enram.eu) with no need to recalculate the huge amount of original polar volume data, which often are not available.


title: Post-2020 Kunming 30% target can easily protect all endemic sharks and rays in the Western Indian Ocean and more

abstract:
Sharks and rays are possibly the most threatened Class of marine fishes and their declines can be halted if protected areas are optimised to benefit these species. We identify spatial priorities for all 63 endemic sharks and rays in the marine biodiversity hotspot, the Western Indian Ocean (WIO). Collectively, while the WIO nations currently surpass the 10% Aichi ocean protection target, this amounts to a dismal protection of only 1.57% of each species distribution range. We show that the entire ranges of all endemics can be achieved by protecting 11% of EEZs of WIO nations, well within reach of the new 30% of oceans by 2030 target. Regional management bodies exist, which if taken advantage of to implement shark and ray management, provide opportunities to implement more efficient management across the region. We recommend key management actions to implement and explicit incentivisation of international cooperation in the post-2020 biodiversity framework.

Science for SocietyThe past decade has seen massive growth in the establishment of marine protected areas (MPAs), driven by the Aichi biodiversity target of protecting 10% of all ocean areas. This expansion of MPAs, however, has largely occurred in areas residual to extractive uses, often coinciding with less threatened areas of lower conservation value. This coming decade will see a further push to ensure 30% of the oceans are protected by 2030. It is important to understand how existing and future MPAs should be placed to benefit threatened biodiversity. Currently this is unclear for sharks and rays, comprising a species group that is the most evolutionarily distinct vertebrate radiation in the world and also one of the most threatened. We identify both regional and national conservation priorities for expanding marine protected areas to benefit all 63 endemic sharks and rays occurring in the Western Indian Ocean region. We find that the region has already exceeded the 10% ocean protection target, but this amounts to an average of only 1.57% protection of the distribution ranges of these species. We show that protecting the top 10% priority sites will conserve almost half of the geographic range of each species yet require only 1.16% of the total EEZ - a tiny fraction of the 30% by 2030 target. We also show that regional collaboration among all nations can result in more spatially efficient conservation priorities. We recommend that the post-2020 biodiversity framework needs to explicitly incentivise regional cooperation between nations to efficiently achieve urgent targets and maximise benefits to biodiversity.