title: Oxidative respiration through the bd-I and cbb3 oxidases is required for Vibrio cholerae pathogenicity and proliferation in vivo.

abstract:
Vibrio cholerae respires both aerobically and anaerobically and, while oxygen may be available to it during infection, other terminal electron acceptors are proposed for population expansion during infection. Unlike gastrointestinal pathogens that stimulate significant inflammation leading to elevated levels of oxygen or alternative terminal electron acceptors, V. cholerae infections are not understood to induce a notable inflammatory response. To ascertain the respiration requirements of V. cholerae during infection, we used Multiplex Genome Editing by Natural Transformation (MuGENT) to create V. cholerae strains lacking aerobic or anaerobic respiration. V. cholerae strains lacking aerobic respiration were attenuated in infant mice 105-fold relative to wild type, while strains lacking anaerobic respiration had no colonization defect, contrary to earlier work suggesting a role for anaerobic respiration during infection. Using several approaches, including one we developed for this work termed Comparative Multiplex PCR Amplicon Sequencing (CoMPAS), we determined that the bd-I and cbb3 oxidases are essential for small intestinal colonization of V. cholerae in the infant mouse. The bd-I oxidase was also determined as the primary oxidase during growth outside the host, making V. cholerae the only example of a Gram-negative bacterial pathogen in which a bd-type oxidase is the primary oxidase for energy acquisition inside and outside of a host.

Author SummaryThe bacterium that causes cholera, Vibrio cholerae, can grow with or without oxygen. When growing without oxygen it may use other molecules that serve the same purpose as oxygen, acting as a terminal electron acceptor in an energy-generating process known as respiration. Given the largely anaerobic nature of the gastrointestinal tract, and the lack of significant inflammation during cholera infection, a process that can stimulate elevated levels of oxygen and other terminal electron acceptors, we sought to understand the respiratory mechanisms of V. cholerae during infection. We used a powerful genome-editing method to construct mutant strains of V. cholerae lacking some or all of the complement of proteins required for aerobic or anaerobic respiration. By analyzing these mutants in the laboratory and in intestinal colonization of infant mice, we determined that the ability to respire without oxygen is completely dispensable for V. cholerae to thrive during infection. We determined that two of the four oxygen-dependent respiration mechanisms are essential for V. cholerae to grow during infection, with the other two dispensable for wild type levels of colonization.


title: Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays

abstract:
Rapid and accurate diagnosis of infections is fundamental to individual patient care and public health management. Nucleic acid detection methods are critical to this effort, but are limited either in the breadth of pathogens targeted or by the expertise and infrastructure required. We present here a high-throughput system that enables rapid identification of bacterial pathogens, bCARMEN, which utilizes: (1) modular CRISPR-Cas13-based nucleic acid detection with enhanced sensitivity and specificity; and (2) a droplet microfluidic system that enables thousands of simultaneous, spatially multiplexed detection reactions at nanoliter volumes; and (3) a novel pre-amplification strategy that further enhances sensitivity and specificity. We demonstrate bCARMEN is capable of detecting and discriminating 52 clinically relevant bacterial species and several key antibiotic resistance genes. We further develop a proof of principle system for use with stabilized reagents and a simple workflow with optical readout using a cell phone camera, opening up the possibility of a rapid point-of-care multiplexed bacterial pathogen identification and antibiotic susceptibility testing.

Significance StatementIn this paper, we use a novel primer design method combined with droplet-based CRISPR Cas13 detection to distinguish 52 clinically relevant bacterial pathogens in a single assay. We also apply the method to detect and distinguish a panel of major antibiotic resistance genes, which is of critical importance in this era of rising antibiotic resistance. Finally, we make key advances towards making our diagnostic assay deployable at the point-of-care, with a simplified emulsion-free assay process that uses mobile phone camera for detection and reduces infrastructure/skilled labor requirements.

category: microbiology


title: An efficient and adaptable workflow for editing disease-relevant single nucleotide variants using CRISPR/Cas9

abstract:
Single nucleotide variants are the commonest genetic alterations in the human genome. At least 60,000 have been reported to be associated with disease. The CRISPR/Cas9 system has transformed genetic research, making it possible to edit single nucleotides and study the function of genetic variants in vitro. While significant advances have improved the efficiency of CRISPR/Cas9, the editing of single nucleotides remains challenging. There are two major obstacles: low efficiency of accurate editing and the isolation of these cells from a pool of cells with other editing outcomes. We present data from 85 transfections of induced pluripotent stem cells and an immortalised cell line, comparing the effects of altering CRISPR/Cas9 design and experimental conditions on rates of single nucleotide substitution. We targeted variants in TP53, which predispose to several cancers, and in TBXT which is implicated in the pathogenesis of the bone cancer, chordoma. We describe a scalable and adaptable workflow for single nucleotide editing that incorporates contemporary techniques including Illumina MiSeq sequencing, TaqMan qPCR and digital droplet PCR for screening transfected cells as well as quality control steps to mitigate against common pitfalls. This workflow can be applied to CRISPR/Cas9 and other genome editing systems to maximise experimental efficiency.

Simple SummaryCRISPR/Cas9 has revolutionised genetic research. Cas9 generates a double strand break with high efficiency which is repaired by a cells pathways. If a genetic template is provided, the damage can be accurately repaired to introduce a desired genetic alteration. However, accurate repair occurs at a low efficiency and in a small proportion of edited cells, representing the main obstacles in harnessing CRISPRs full potential. Using data from 85 CRISPR experiments for single nucleotide editing, targeting three locations in the human genome that are implicated in predisposition to cancer, we report the effect of different experimental conditions on editing efficiency. We describe current technologies that can be used to streamline the identification of accurately edited cells and synthesise these into an adaptable workflow that can be applied to CRISPR/Cas9 experiments to achieve single nucleotide editing in disease-relevant cell models.

category: molecular biology


title: The chromatin-regulating CoREST complex is animal specific and essential for development in the cnidarian Nematostella vectensis

abstract: Chromatin-modifying proteins are key players in the regulation of development and cell differentiation in animals. Many individual chromatin modifiers, however, predate the evolution of animal multicellularity and how they became integrated into the regulatory networks underlying development is unclear. Here we show that CoREST is an animal-specific protein that assembles a conserved, vertebrate-like histone-modifying complex including Lsd1 and HDAC1/2 in the sea anemone Nematostella vectensis. We further show that NvCoREST expression overlaps fully with that of NvLsd1 throughout development. NvCoREST mutants, generated using CRISPR-Cas9, reveal essential roles during development and for the differentiation of cnidocytes, thereby phenocopying NvLsd1 mutants. We also show that this requirement is cell autonomous using a cell-type-specific rescue approach. Together, this shows that the evolution of CoREST allowed the formation of a chromatin-modifying complex that was present before the last common cnidarian-bilaterian ancestor and thus represents an ancient component of the animal developmental toolkit.

category: evolutionary biology


title: Phylogenetic diversity of two common Trypanosoma cruzi lineages in the Southwestern United States

abstract: Trypanosoma cruzi is the causative agent of Chagas disease, a devastating parasitic disease endemic to Central and South America, Mexico, and the USA. We characterized the genetic diversity of T. cruzi circulating in five triatomine species (Triatoma gerstaeckeri, T. lecticularia, T. indictiva, T. sanguisuga and T. recurva) collected in Texas and Southern Arizona using nucleotide sequences from four single-copy loci (COII-ND1, MSH2, DHFR-TS, TcCLB.506529.310). All T. cruzi variants fall in two main genetic lineages: 75% of the samples corresponded to T. cruzi Discrete Typing Unit (DTU) I (TcI), and 25% to a North American specific lineage previously labelled TcIV-USA. Phylogenetic and sequence divergence analyses of our new data plus all previously published sequence data from those 4 genes collected in the USA, show that TcIV-USA is significantly different from any other previously defined T. cruzi DTUs. The significant level of genetic divergence between TcIV-USA and other T. cruzi lineages should lead to an increased focus on understanding the epidemiological importance of this lineage, as well as its geographical range and pathogenicity in humans and domestic animals. Our findings further corroborate the fact that there is a high genetic diversity of the parasite in North America and emphasize the need for appropriate surveillance and vector control programs for Chagas disease in southern USA and Mexico.


title: Interacting host modifier systems control Wolbachia-induced cytoplasmic incompatibility in a haplodiploid mite

abstract: Many reproductive parasites such as Wolbachia spread within host populations by inducing cytoplasmic incompatibility (CI). CI occurs when parasite-modified sperm fertilizes uninfected eggs. In haplodiploid hosts, CI can lead to different phenotypes depending on whether the fertilized eggs die or develop into males. Genetic conflict theories predict the evolution of host modulation of CI, which in turn strongly influences the stability of reproductive parasitism. Yet, despite the ubiquity of CI-inducing parasites in nature, there is no conclusive evidence for strong intraspecific host modulation of CI strength and phenotype. Here, we tested for intraspecific host modulation of Wolbachia-induced CI in haplodiploid Tetranychus spider mites. Using a single CI-inducing Wolbachia variant and mitochondrion, a Tetranychus urticae nuclear panel was created that consisted of infected and cured near-isogenic lines. We performed a highly replicated age-synchronized full diallel cross comprised of incompatible and compatible control crosses. We uncovered host modifier systems that strongly suppress CI strength when carried by infected T. urticae males. Interspecific crosses showed that the male modifier systems suppress CI strength across species boundaries. We also observed a continuum of CI phenotypes in our crosses and identified strong intraspecific female modulation of CI phenotype when paired with a specific male genotype. Crosses established a recessive genetic basis for the maternal effect and were consistent with polygenic Mendelian inheritance. Our findings identify spermatogenesis as an important target of selection for host suppression of CI strength and underscore the importance of maternal genetic effects for the CI phenotype. Both mechanisms interacted with the genotype of the mating partner, revealing that intraspecific host modulation of CI strength and phenotype is underpinned by complex genetic architectures.


title: MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

abstract: Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N=10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase (www.facebase.org, doi.org/10.25550/3-HXMC) and GitHub (https://github.com/jaydevine/MusMorph).

category: genetics


title: Population genomics reveal distinct and diverging populations of An. minimus in Cambodia - a widespread malaria vector in Southeast Asia

abstract: Anopheles minimus is an important malaria vector throughout its wide geographic range across Southeast Asia. Genome sequencing could provide important insights into the unique malaria transmission dynamics in this region, where many vector species feed and rest outdoors. We describe results from a study using Illumina deep whole-genome sequencing of 302 wild-caught An. minimus collected from three Cambodian provinces over several years (2010, 2014-2016) and seasons to examine the level of population structure and genetic diversity within this species. These specimens cluster into four distinct populations of An. minimus s.s., with two populations overlapping geographically. We describe the underlying genetic diversity and divergence of these populations and investigated the genetic variation in genes known to be involved in insecticide resistance. We found strong signals of selection within these An. minimus populations, most of which were present in the two Northeastern Cambodian populations and differ from those previously described in African malaria vectors. Cambodia is the focus of the emergence and spread of drug-resistant malaria parasites, so understanding the underlying genetic diversity and resilience of the vectors of these parasites is key to implementing effective malaria control and elimination strategies. These data are publicly available as part of the MalariaGEN Vector Observatory, an open access resource of genome sequence data.

category: genomics


title: Pathways to polar adaptation in fishes revealed by long-read sequencing

abstract: Long-read sequencing is driving a new reality for genome science where highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we leveraged long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Opthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance, and vision have evidence of selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: hemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the hemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage-specific loss of this cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.


title: Nanopore adaptive sampling for mitogenome sequencing and bloodmeal identification in hematophagous insects

abstract: Blood-feeding insects are important vectors for an array of zoonotic pathogens. Despite significant research focused on well-documented insect vectors of One Health importance, resources for molecular species identification of a large number of hematophagous arthropods are limited. Advancements in next-generation sequencing technologies provide opportunities for targeting mitochondrial genomes of blood-feeding insects, as well as their bloodmeal hosts. This dual approach holds great promise for elucidating complex disease transmission pathways and enhancing the molecular resources for the identification of cryptic insect species. To this end, we leveraged the newly developed Oxford Nanopore Adaptive Sampling (NAS) pipeline to dually sequence the mitogenomes of hematophagous insects and their bloodmeals. Using NAS, we sequenced the entire mitogenomes of Aedes vexans, Culex restuans, Culex territans, and Chrysops niger and successfully identified bloodmeal hosts of Chrysops niger, Culex restuans, and Aedes trivittatus. We show that NAS has the utility to simultaneously molecularly identify blood-feeding insects and characterize disease transmission pathways through bloodmeal host identification. Moreover, our data indicate NAS can facilitate a wide array of molecular systematic studies through novel  phylogenetic capture methods. We conclude the NAS approach has great potential for informing global One Health initiatives centered on the mitigation of vector-borne disease through dual vector and bloodmeal identification.


title: Scaling between DNA and cell size governs bacterial growth homeostasis and resource allocation

abstract: Bacteria maintain a stable cell size and a certain DNA content through proliferation as described by classic growth laws. How cells behave when this inherent scaling is broken, however, has rarely been interrogated. Here we engineered Escherichia coli cells with extremely low DNA contents using a tunable synthetic tool CRISPRori that temporarily inhibited chromosome replication initiation. A detailed mechanistic model coupling DNA replication, cell growth, and division revealed a fundamental DNA-centric growth law, which was validated by two observations. First, lineage dynamics were robust to large CRISPRori perturbations with division cycles rapidly restoring through a timer mechanism rather than the adder rule. Second, cellular growth transitioned into a linear regime at low DNA-cytoplasm ratios. Experiments and theory showed that in this regime, cellular resource was redirected to plasmid-borne gene expression. Together with the ability of CRISPRori to bi-directionally modulate plasmid copy numbers, these findings suggest a novel strategy for bio-production enhancement.

category: systems biology


title: PHGDH is required for germinal center formation and is a therapeutic target in MYC-driven lymphoma

abstract: The synthesis of serine from glucose is a key metabolic pathway supporting cellular proliferation in healthy and malignant cells. Despite this, the role that this aspect of metabolism plays in germinal center biology and pathology is not known. Here, we performed a comprehensive characterization of the role of the serine synthesis pathway in germinal center B cells and lymphomas derived from these cells. We demonstrate that upregulation of a functional serine synthesis pathway is a metabolic hallmark of B-cell activation and the germinal center reaction. Inhibition of phosphoglycerate dehydrogenase (PHGDH), the first and rate limiting enzyme in this pathway, leads to defective germinal formation and impaired high-affinity antibody production. In addition, overexpression of enzymes involved in serine synthesis is a characteristic of germinal center B-cell derived lymphomas, with high levels of expression being predictive of reduced overall survival in diffuse large B cell lymphoma. Inhibition of PHGDH induces apoptosis in lymphoma cells reducing disease progression. These findings establish PHGDH as a critical player in humoral immunity and a clinically relevant target in lymphoma.

category: immunology


title: Gene drives and population persistence vs elimination: the impact of spatial structure and inbreeding at low density

abstract: Synthetic gene drive constructs are being developed to control disease vectors, invasive species, and other pest species. In a well-mixed random mating population a sufficiently strong gene drive is expected to eliminate a target population, but it is not clear whether the same is true when spatial processes play a role. In species with an appropriate biology it is possible that drive-induced reductions in density might lead to increased inbreeding, reducing the efficacy of drive, eventually leading to suppression rather than elimination, regardless of how strong the drive is. To investigate this question we analyse a series of explicitly solvable stochastic models considering a range of scenarios for the relative timing of mating, reproduction, and dispersal and analyse the impact of two different types of gene drive, a Driving Y chromosome and a homing construct targeting an essential gene. We find in all cases a sufficiently strong Driving Y will go to fixation and the population will be eliminated, except in the one life history scenario (reproduction and mating in patches followed by dispersal) where low density leads to increased inbreeding, in which case the population persists indefinitely, tending to either a stable equilibrium or a limit cycle. These dynamics arise because Driving Y males have reduced mating success, particularly at low densities, due to having fewer sisters to mate with. Increased inbreeding at low densities can also prevent a homing construct from eliminating a population. For both types of drive, if there is strong inbreeding depression, then the population cannot be rescued by inbreeding and it is eliminated. These results highlight the potentially critical role that low-density-induced inbreeding and inbreeding depression (and, by extension, other sources of Allee effects) can have on the eventual impact of a gene drive on a target population.


title: Transcriptomic analyses implicate neuronal plasticity and chloride homeostasis in ivermectin resistance and recovery in a parasitic nematode

abstract:
The antiparasitic drug ivermectin plays an essential role in human and animal health globally. However, ivermectin resistance is widespread in veterinary helminths and there are growing concerns of sub-optimal responses to treatment in related helminths of humans. Despite decades of research, the genetic mechanisms underlying ivermectin resistance are poorly understood in parasitic helminths. This reflects significant uncertainty regarding the mode of action of ivermectin in parasitic helminths, and the genetic complexity of these organisms; parasitic helminths have large, rapidly evolving genomes and differences in evolutionary history and genetic background can confound comparisons between resistant and susceptible populations. We undertook a controlled genetic cross of a multi-drug resistant and a susceptible reference isolate of Haemonchus contortus, an economically important gastrointestinal nematode of sheep, and ivermectin-selected the F2 population for comparison with an untreated F2 control. RNA-seq analyses of male and female adults of all populations identified high transcriptomic differentiation between parental isolates, which was significantly reduced in the F2, allowing differences associated specifically with ivermectin resistance to be identified. In all resistant populations, there was constitutive upregulation of a single gene, HCON_00155390:cky-1, a putative pharyngeal-expressed transcription factor, in a narrow locus on chromosome V previously shown to be under ivermectin selection. In addition, we detected sex-specific differences in gene expression between resistant and susceptible populations, including constitutive upregulation of a P-glycoprotein, HCON_00162780:pgp-11, in resistant males only. After ivermectin selection, we identified differential expression of genes with roles in neuronal function and chloride homeostasis, which is consistent with an adaptive response to ivermectin-induced hyperpolarisation of neuromuscular cells. Overall, we show the utility of a genetic cross to identify differences in gene expression that are specific to ivermectin selection and provide a framework to better understand ivermectin resistance and recovery in parasitic helminths.

Author SummaryParasitic helminths (worms) infect people and animals throughout the world and are largely controlled with mass administration of anthelmintic drugs. There are a very limited number of anthelmintics available and parasitic helminths can rapidly develop resistance to these drugs. Ivermectin is a widely used anthelmintic in both humans and animals, but resistance is now widespread in the veterinary field. We crossed ivermectin resistant and ivermectin susceptible parasitic helminths and treated them with ivermectin or left them as untreated controls. This provided resistant and susceptible populations with a similar genetic background with which to study differences in gene expression associated with ivermectin resistance. We identified upregulation of a gene with no previous association with drug resistance (HCON_00155390:cky-1) in male and female worms in all resistant populations. This gene is thought to be expressed in the helminth pharynx (mouthpart) and, in mammals, plays a role in controlling nerve function and protecting nerves from damage. This is consistent with the known effects of ivermectin in inhibiting helminth feeding through pharyngeal paralysis and implicates a novel mechanism that allows resistant worms to survive treatment.


title: Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a fragmented IHHNV EVE sequence

abstract: Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements (EVEs) have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such EVEs and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of EVEs. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for one generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific EVEs identified an element comprised of a 9,045 bp stretch of repeated, inverted and jumbled genome fragments of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) bounded by a repeated 591/590 bp host sequence. As only near complete linear ~4 kb IHHNV genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear EVE types. The existence of joined inverted IHHNV genome fragments also provides a means by which hairpin dsRNAs could be expressed and processed by the shrimp RNA interference (RNAi) machinery.


title: A two-phase plant-soil feedback experiment to explore biotic influences on Phragmites australis invasion in North American wetlands

abstract: Plants can cultivate soil microbial communities that affect subsequent plant growth through a plant-soil feedback (PSF). Strong evidence indicates that PSFs can mediate the invasive success of exotic upland plants, but many of the most invasive plants occur in wetlands. In North America, the rapid spread of European Phragmites australis cannot be attributed to innate physiological advantages, thus PSFs may mediate invasion. Here we apply a two-phase fully-factorial plant-soil feedback design in which field-derived soil inocula were conditioned using saltmarsh plants and then were added to sterile soil mesocosms and planted with each plant type. This design allowed us to assess complete soil biota effects on intraspecific PSFs between native and introduced P. australis as well as heterospecific feedbacks between P. australis and the native wetland grass, Spartina patens. Our results demonstrate that native P. australis experienced negative conspecific feedbacks while introduced P. australis experienced neutral conspecific feedbacks. Interestingly, S. patens soil inocula inhibited growth in both lineages of P. australis while introduced and native P. australis inocula promoted the growth of S. patens suggestive of biotic resistance against P. australis invasion by S. patens. Our findings suggest that PSFs are not directly promoting the invasion of introduced P. australis in North America. Furthermore, native plants like S. patens seem to exhibit soil microbe mediated biotic resistance to invasion which highlights the importance of disturbance in mediating introduced P. australis invasion.

category: ecology


title: Biosorption potential and molecular characterization of metal resistant autochthonous microbes from tannery solid waste

abstract: This study encompasses isolation and screening of heavy metal-resistant fungal and bacterial strains from tannery solid waste (TSW). Twelve fungal strains and twenty-five bacterial strains were isolated from TSW. The growth of fungal strains was observed against different heavy metals ranging from 10 mg L-1 to 1050 mg L-1 and the growth of bacteria was observed in metal concentrations ranging from 10 mg L-1 to 1200 mg L-1. Five multi-metal resistant fungal isolates belonging to the genus Trichoderma and ten bacterial isolates belonging to the genus Bacillus showed good metal resistance and biosorption potential. They were identified through molecular techniques, fungi based on ITS region ribotyping, and bacteria based on 16S rRNA ribotyping. The fungal strains were characterized as T. hamatum (TSWF-06), T. harzianum (TSWF-11), T. lixii (TSWF-02) and T. pseudokoningii (TSWF-03, TSWF-10). The bacterial strains were characterized as Bacillus xiamenensis (TSW-02), B. velezensis (TSW-05), B. piscis (TSW-06), B. safensis (TSW-10), B. subtilis (TSW-14, TSW-15, TSW-17) B. licheniformis (TSW-19), B. cereus (TSW-20) and B. thuringiensis (TSW-22). The fungal strains namely, T. pseudokoningii (TSWF-03) and T. harzianum proved to be two multi-metal resistant strains with good biosorption efficiency. Unlike fungi, bacterial strains showed metal specific resistance. The strains Bacillus xiamenensis, B. subtilis (TSW-14) and B. subtilis (TSW-15) showed good biosorption efficiency against Cr, B. safensis against Cu, B. piscis and B. subtilis (TSW-17) against Pb and B. licheniformis and B. thuringiensis against Zn. The autochthonous fungal and bacterial strains can therefore be employed to clean metal contaminated environments.


title: 'Constituent length' effects in fMRI do not provide evidence for abstract syntactic processing

abstract:
How are syntactically and semantically connected word sequences, or constituents, represented in the human language system? An influential fMRI study, Pallier et al. (2011, PNAS), manipulated the length of constituents in sequences of words or pseudowords. They reported that some language regions (in the anterior temporal cortex and near the temporo-parietal junction) were sensitive to constituent length only for sequences of real words but not pseudowords. In contrast, language regions in the inferior frontal and posterior temporal cortex showed the same pattern of increased response to longer constituents--and similar overall response magnitudes-- for word and pseudoword sequences. Based on these results, Pallier et al. argued that the latter regions represent abstract sentence structure. Here we identify methodological and theoretical concerns with the Pallier et al. study and conduct a replication across two fMRI experiments. Our results do not support Pallier et al.s critical claim of distinct neural specialization for abstract syntactic representations. Instead, we find that all language regions show a similar profile of sensitivity to both constituent length and lexicality (stronger responses to real-word than pseudoword stimuli). In addition, we argue that the constituent length effect in these experiments i) is not readily grounded in established theories of sentence processing, and ii) may not actually derive from syntactic structure building, but may instead reflect the temporal receptive window of the human language system.

Significance StatementAn influential study (Pallier et al., 2011, PNAS) has been widely interpreted as evidence that inferior frontal and posterior temporal brain regions perform abstract syntactic processing during language comprehension, independent of lexical content. Here we identify theoretical, empirical, and methodological concerns with the original study and conduct a replication across two experiments. Contrary to Pallier et al. (2011), we find evidence that both syntactic and lexical processing are distributed throughout the human language network, consistent with prior arguments for a highly lexicalized and distributed human language processing system.

category: neuroscience


title: Transcriptional regulation of neonatal neural stem cells is a determinant of social behavior

abstract:
Rare gene variants confer a high level of penetrance to neurodevelopmental disorders, but their developmental origin and cellular substrates remain poorly understood. To address this limitation, we explored the role of TBX1, a gene encoded in a rare copy number variant, in cell and mouse models. Here, we report that neonatal Tbx1 deficiency contributes to defective peripubertal social behavior and impairs the proliferation of neonatal neural stem/progenitor cells. Moreover, TBX1 transcriptionally regulates genes linked to post-embryonic neurogenesis and neurodevelopmental disorders associated with other rare gene variants. Our data indicate a precise time window and cell type through which the social dimension is altered by a gene encoded in a rare CNV and provide a potential common mechanistic basis for a group of neurodevelopmental disorders.

One-Sentence SummaryTbx1, a gene affecting neonatal stem cell proliferation, influences peripubertal social behavior.


title: Cortical wiring by synapse-specific control of local protein synthesis

abstract: Neurons use local protein synthesis as a mechanism to support their morphological complexity, which requires independent control across multiple subcellular compartments including individual synapses. However, to what extent local translation is differentially regulated at the level of specific synaptic connections remains largely unknown. Here, we identify a signaling pathway that regulates the local synthesis of proteins required for the formation of excitatory synapses on parvalbumin-expressing (PV+) interneurons in the mouse cerebral cortex. This process involves the regulation of the mTORC1 inhibitor Tsc2 by the receptor tyrosine kinase ErbB4, which enables the local control of mRNA translation in a cell type-specific and synapse-specific manner. Ribosome-associated mRNA profiling reveals a molecular program of synaptic proteins that regulates the formation of excitatory inputs on PV+ interneurons downstream of ErbB4 signaling. Our work demonstrates that local protein translation is regulated at the level of specific connections to control synapse formation in the nervous system.


title: The dorsal visual pathway represents object-centered spatial relations for object recognition

abstract:
Although there is mounting evidence that input from the dorsal visual pathway is crucial for object processes in the ventral pathway, the specific functional contributions of dorsal cortex to these processes remain poorly understood. Here, we hypothesized that dorsal cortex computes the spatial relations among an objects parts - a processes crucial for forming global shape percepts - and transmits this information to the ventral pathway to support object categorization. Using fMRI with human participants (females and males), we discovered regions in the intraparietal sulcus (IPS) that were selectively involved in computing object-centered part relations. These regions exhibited task-dependent functional and effective connectivity with ventral cortex, and were distinct from other dorsal regions, such as those representing allocentric relations, 3D shape, and tools. In a subsequent experiment, we found that the multivariate response of posterior IPS, defined on the basis of part-relations, could be used to decode object category at levels comparable to ventral object regions. Moreover, mediation and multivariate effective connectivity analyses further suggested that IPS may account for representations of part relations in the ventral pathway. Together, our results highlight specific contributions of the dorsal visual pathway to object recognition. We suggest that dorsal cortex is a crucial source of input to the ventral pathway and may support the ability to categorize objects on the basis of global shape.

Significance StatementHumans categorize novel objects rapidly and effortlessly. Such categorization is achieved by representing an objects global shape structure, that is, the relations among object parts. Yet, despite their importance, it is unclear how part relations are represented neurally. Here, we hypothesized that object-centered part relations may be computed by the dorsal visual pathway, which is typically implicated in visuospatial processing. Using fMRI, we identified regions selective for the part relations in dorsal cortex. We found that these regions can support object categorization, and even mediate representations of part relations in the ventral pathway, the region typically thought to support object categorization. Together, these findings shed light on the broader network of brain regions that support object categorization.


title: Key Factors Governing Initial Stages of Lipid Droplet Formation

abstract: Lipid droplets (LDs) are neutral lipid storage organelles surrounded by a phospholipid (PL) monolayer. LD biogenesis from the endoplasmic reticulum (ER) is driven by phase separation of neutral lipids, overcoming surface tension and membrane deformation. However, the core biophysics of the initial steps of LD formation remain relatively poorly understood. Here, we use a tunable, phenomenological coarse-grained (CG) model to study triacylglycerol (TG) nucleation in a bilayer membrane. We show that PL rigidity has a strong influence on TG lensing and membrane remodeling: When membrane rigidity increases, TG clusters remain more planar with high anisotropy but a minor degree of phase nucleation. This finding is confirmed by free energy sampling simulations that calculate the potential of mean force (PMF) as a function of the degree of nucleation and anisotropy. We also show that asymmetric tension, controlled by the number of PLs on each membrane leaflet, determines the budding direction. A TG lens buds in the direction of the monolayer containing excess PLs to allow for better PL coverage of TG, consistent with reported experiments. Finally, two governing mechanisms of the LD growth, Ostwald ripening and merging, are observed. Taken together, this study characterizes the interplay between two thermodynamic quantities during the initial LD phases, the TG bulk free energy and membrane remodeling energy.

category: biophysics


title: Mechanistic insights into the enhancement or inhibition of phase separation by polyubiquitin chains of different lengths or linkages

abstract:
Ubiquitin-binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48- and K63-linked polyubiquitin chains, respectively. UBQLN2 is recruited to stress granules in cells and undergoes liquid-liquid phase separation (LLPS) in vitro. However, interactions with ubiquitin or multivalent K48-linked chains eliminate LLPS. Here, we found that, although some polyubiquitin chain types (K11-Ub4 and K48-Ub4) did generally inhibit UBQLN2 LLPS, others (K63-Ub4, M1-Ub4 and a designed tetrameric ubiquitin construct) significantly enhanced LLPS. Using nuclear magnetic resonance (NMR) spectroscopy and complementary biophysical techniques, we demonstrated that these opposing effects stem from differences in chain conformations, but not in affinities between chains and UBQLN2. Chains with extended conformations and increased accessibility to the ubiquitin binding surface significantly promoted UBQLN2 LLPS by enabling a switch between homotypically to partially heterotypically-driven phase separation. Our study provides mechanistic insights into how the structural and conformational properties of polyubiquitin chains contribute to heterotypic phase separation with ubiquitin-binding shuttles and adaptors.

HighlightsO_LIUbiquitin or short polyubiquitin chains bind to phase separation-driving stickers on UBQLN2 and inhibit its phase separation whereas longer chains provide the multivalency needed to enhance UBQLN2 phase separation.
C_LIO_LIPhase separation of UBQLN2 is promoted over a wide range of Ub:UBQLN2 ratios in the presence of extended M1- and K63-linked Ub4 chains, but not compact K11- and K48-linked Ub4 chains.
C_LIO_LIChain conformation and accessibility of the Ub interacting surface is a driving factor of UBQLN2/polyUb co-phase separation.
C_LIO_LIUBQLN2 condensates assemble during in vitro enzymatic assembly of K63-linked polyUb chains as free ubiquitin is reduced.
C_LI


title: Genome Compartmentalization with Nuclear Landmarks: Random yet Precise

abstract: The three-dimensional (3D) organization of eukaryotic genomes plays an important role in genome function. While significant progress has been made in deciphering the folding mechanisms of individual chromosomes, the principles of the dynamic large-scale spatial arrangement of all chromosomes inside the nucleus are poorly understood. We use polymer simulations to model the diploid human genome compartmentalization relative to nuclear bodies such as nuclear lamina, nucleoli, and speckles. We show that a self-organization process based on a co-phase separation between chromosomes and nuclear bodies can capture various features of genome organization, including the formation of chromosome territories, phase separation of A/B compartments, and the liquid property of nuclear bodies. The simulated 3D structures quantitatively reproduce both sequencing-based genomic mapping and imaging assays that probe chromatin interaction with nuclear bodies. Importantly, our model captures the heterogeneous distribution of chromosome positioning across cells, while simultaneously producing well-defined distances between active chromatin and nuclear speckles. Such heterogeneity and preciseness of genome organization can coexist due to the non-specificity of phase separation and the slow chromosome dynamics. Together, our work reveals that the co-phase separation provides a robust mechanism for encoding functionally important 3D contacts without requiring thermodynamic equilibration that can be difficult to achieve.


title: Optogenetic induction of appetitive and aversive taste memories in Drosophila

abstract: Tastes are typically thought to evoke innate appetitive or aversive behaviours, prompting food acceptance or rejection. However, research in Drosophila melanogaster indicates that taste responses can be modified through experience-dependent changes in mushroom body circuits. In this study, we develop a novel taste learning paradigm using closed-loop optogenetics. We find that appetitive and aversive taste memories can be formed by pairing gustatory stimuli with optogenetic activation of sensory or dopaminergic neurons associated with reward or punishment. As with olfactory memories, distinct dopaminergic subpopulations drive the parallel formation of short- and long-term appetitive memories. Long-term memories are protein synthesis-dependent and have energetic requirements that are satisfied by a variety of caloric food sources or by direct stimulation of MB-MP1 dopaminergic neurons. Our paradigm affords new opportunities to probe plasticity mechanisms within the taste system and understand the extent to which taste responses are experience dependent.


title: Myelin insulation as a risk factor for axonal degeneration in autoimmune demyelinating disease

abstract: Axonal degeneration determines the clinical outcome of multiple sclerosis (MS), and is thought to result from exposure of denuded axons to immune-mediated damage. We challenge this view after finding in MS and its mouse models that myelin itself increases the risk of axons to degenerate under inflammatory conditions. We propose a model for demyelinating diseases in which for axons that remain myelinated, and thus shielded from the extracellular milieu, dependence from oligodendroglial support turns fatal in an autoimmune disease environment.


title: PatchWarp: Corrections of non-uniform image distortions in two-photon calcium imaging data by patchwork affine transformations

abstract: Two-photon microscopy has been widely used to record the activity of populations of individual neurons at high spatial resolution in behaving animals. The ability to perform imaging for an extended period of time allows the investigation of activity changes associated with behavioral states and learning. However, imaging often accompanies shifts of the imaging field, including rapid ([~]100ms) translation and slow, spatially non-uniform distortion. To combat this issue and obtain a stable time series of the target structures, motion correction algorithms are commonly applied. However, typical motion correction algorithms are limited to full field translation of images and are unable to correct non-uniform distortions. Here, we developed a novel algorithm, PatchWarp, to robustly correct slow image distortion for calcium imaging data. PatchWarp is a two-step algorithm with rigid and non-rigid image registrations. To correct non-uniform image distortions, it splits the imaging field and estimates the best affine transformation matrix for each of the subfields. The distortion-corrected subfields are stitched together like a patchwork to reconstruct the distortion-corrected imaging field. We show that PatchWarp robustly corrects image distortions of calcium imaging data collected from various cortical areas through glass window or GRIN lens with a higher accuracy than existing non-rigid algorithms. Furthermore, it provides a fully automated method of registering images from different imaging sessions for longitudinal neural activity analyses. PatchWarp improves the quality of neural activity analyses and would be useful as a general approach to correct image distortions in a wide range of disciplines.


title: Molecular, anatomical, and functional organization of lung interoceptors

abstract: Interoceptors, sensory neurons that monitor internal organs and states, are essential for physiological homeostasis and generating internal perceptions. Here we describe a comprehensive transcriptomic atlas of interoceptors of the mouse lung, defining 10 molecular subtypes that differ in developmental origin, myelination, receptive fields, terminal morphologies, and cell contacts. Each subtype expresses a unique but overlapping combination of sensory receptors that detect diverse physiological and pathological stimuli, and each can signal to distinct sets of lung cells including immune cells, forming a local neuroimmune interaction network. Functional interrogation of two mechanosensory subtypes reveals exquisitely-specific homeostatic roles in breathing, one regulating inspiratory time and the other inspiratory flow. The results suggest that lung interoceptors encode diverse and dynamic sensory information rivaling that of canonical exteroceptors, and this information is used to drive myriad local cellular interactions and enable precision control of breathing, while providing only vague perceptions of organ states.


title: Altered brain criticality in Schizophrenia: New insights from MEG

abstract: Schizophrenia has a complex etiology and symptomatology that is difficult to untangle. After decades of research, important advancements towards a central biomarker are still lacking. One of the missing pieces is a better understanding of how non-linear neural dynamics are altered in this patient population. In this study, the resting-state neuromagnetic signals of schizophrenia patients and healthy controls were analyzed in the framework of criticality. When biological systems like the brain are in a state of criticality, they are thought to be functioning at maximum efficiency (e.g., optimal communication and storage of information) and with maximum adaptability to incoming information. Here, we assessed the self-similarity and multifractality of resting-state brain signals recorded with magnetoencephalography in patients with schizophrenia patients and in matched controls. Our analysis showed a clear ascending, rostral to caudal gradient of self-similarity values in healthy controls, and an opposite gradient for multifractality (descending values, rostral to caudal). Schizophrenia patients had similar, although attenuated, gradients of self-similarity and multifractality values. Statistical tests showed that patients had higher values of self-similarity than controls in fronto-temporal regions, indicative of more regularity and memory in the signal. In contrast, patients had less multifractality than controls in the parietal and occipital regions, indicative of less diverse singularities and reduced variability in the signal. In addition, supervised machine-learning, based on logistic regression, successfully discriminated the two groups using measures of self-similarity and multifractality as features. Our results provide new insights into the baseline cognitive functioning of schizophrenia patients by identifying key alterations of criticality properties in their resting-state brain data.


title: Stromal remodeling regulates dendritic cell abundance and activity in the tumor microenvironment

abstract:
Stimulatory dendritic cells (SDC), enriched within Batf3-DC (cDC1), engage in productive interactions with CD8+ effectors along tumor-stroma boundaries. The paradoxical accumulation of "poised" cross-presenting Batf3-DC within stromal sheets, distal to tumoral nests, is unlikely to simply reflect passive exclusion away from immunosuppressive tumor cores. Drawing parallels with embryonic morphogenesis, we hypothesized that invasive margin stromal remodeling may generate developmentally conserved cell-fate cues that regulate Batf3-DC behavior. We find that CD8+ T-cells massively infiltrate tumor matrices undergoing proteoglycan versican (VCAN) proteolysis, an essential organ-sculpting modification in development and adult tissue-plane forging. VCAN proteolysis releases a bioactive fragment (matrikine), versikine, that is necessary and sufficient for Batf3-DC accumulation. Versikine does not influence tumor-seeding pre-DC differentiation; rather, it orchestrates a distinctive activation program conferring exquisite sensitivity to DNA-sensing, coupled with survival support from atypical innate lymphoid cells. Thus, homeostatic signals from stroma invasion regulate SDC survival and activity to promote T- cell inflammation.

HIGHLIGHTSO_LITumor stroma remodeling generates cross-presenting DC survival and activation cues.
C_LIO_LIStromal-activated Batf3-DC are hypersensitive to dsDNA-sensing.
C_LIO_LIStromal signals promote atypical innate lymphoid cells (GM-CSFhi/ IFN{gamma}lo).
C_LIO_LIT-cell repriming by stroma-licensed Batf3-DC may overcome exclusion at tumor margins.
C_LI


title: Urbanization and altitude impact on gut microbiome of an Andean frog (Pristimantis unistrigatus)

abstract:
The analysis of the intestinal microbiome in amphibians provides insights of the anthropogenic environmental impact. Pristimantis unistrigatus is an Andean amphibian species whose distribution has been recorded in Ecuador and Colombia, ranging from endemic elfin forests to urban gardens. In this study, we focus on the analysis of the P. unistrigatus microbiome 16S rRNA gene sequencing. A total of 32 specimens of P. unistrigatus were collected and analyzed from 4 locations in the Valley of Quito, Ecuador, characterized by several urban environments and altitudes. The results show that the relative abundance of bacteria is significantly different amongst groups. Clostridiales are proportionally more abundant in rural and lower altitude locations, while Erysipelotrichaceae, Desulfovibrionaceae, Enterobacteriaceae, Bacteroidaceae and Lachnospiraceae are found at higher elevations. These results highlight the importance of the evolution of the microbiome as a tool of adaptation and survival of amphibians in the present-day changing ecosystems undergoing anthropogenic stresses.

ImportanceAmphibians constitutes one of the groups most vulnerable to environmental alterations. Due to their sophisticated reproductive and breeding requirements and their permeable skins to breathe, amphibians are compulsively studied as ecological indicators. The destruction of pristine habitats occurred all over the planet in recent decades has caused a catastrophic decline in amphibian populations for many species everywhere. Ecuador, being one of the most biodiverse country on Earth, hosts a huge variety of amphibians, thus offering a unique possibility of studying the biology of the amphibian species living in its ecosystems, and how they adapt to changing habitats. A direct way to diagnose the status of an amphibian population is to study the gut microbiome of the individual specimens. The gut microbiome is closely related to the hosts health and so to its ability to adapt and survive. An important output of this study is to offer indications and tools useful to conservation programs before irreversible damages are caused to the habitats and the amphibians populations still thriving in them.


title: A series of terribly unfortunate events: How environment and infection synergized to cause the Kihansi spray toad extinction

abstract: Outbreaks of emerging infectious diseases are trained by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Extinction of the Tanzanian Kihansi spray toad (Nectophrynoides asperginis) in 2004 was contemporaneous with the construction of a dam, implicating habitat modification in the loss of this species. However, high burdens of a globally emerging infection, Batrachochytrium dendrobatidis (Bd) were synchronously observed implicating infectious disease in this toads extinction. Here, by shotgun sequencing skin DNA from archived toad mortalities and assembling chytrid mitogenomes, we prove this outbreak was caused by the BdCAPE lineage and not the panzootic lineage BdGPL that is widely associated with global amphibian extinctions. Molecular dating showed an invasion of BdCAPE across Southern Africa overlapping with the timing of the extinction event. However, post-outbreak surveillance of conspecific species inhabiting this mountainous region showed widespread infection by BdCAPE yet no signs of amphibian ill-health or species decline. Our findings show that despite efforts to mitigate the environmental impact caused by dams construction, invasion of the pathogen ultimately led to the loss of the Kihansi spray toad; a synergism between emerging infectious disease and environmental change that likely heralds wider negative impacts on biodiversity in the Anthropocene.


title: Real-time alerts from AI-enabled camera traps using the Iridium satellite network: a case-study in Gabon, Central Africa

abstract:
O_LIEfforts to preserve, protect, and restore ecosystems are hindered by long delays between data collection and analysis. Threats to ecosystems can go undetected for years or decades as a result. Real-time data can help solve this issue but significant technical barriers exist. For example, automated camera traps are widely used for ecosystem monitoring but it is challenging to transmit images for real-time analysis where there is no reliable cellular or WiFi connectivity. Here, we present our design for a camera trap with integrated artificial intelligence that can send real-time information from anywhere in the world to end-users.
C_LIO_LIWe modified an off-the-shelf camera trap (Bushnell) and customised existing open-source hardware to rapidly create a  smart camera trap system. Images captured by the camera trap are instantly labelled by an artificial intelligence model and an  alert containing the image label and other metadata is then delivered to the end-user within minutes over the Iridium satellite network. We present results from testing in the Netherlands, Europe, and from a pilot test in a closed-canopy forest in Gabon, Central Africa.
C_LIO_LIResults show the system can operate for a minimum of three months without intervention when capturing a median of 17.23 images per day. The median time-difference between image capture and receiving an alert was 7.35 minutes. We show that simple approaches such as excluding  uncertain labels and labelling consecutive series of images with the most frequent class (vote counting) can be used to improve accuracy and interpretation of alerts.
C_LIO_LIWe anticipate significant developments in this field over the next five years and hope that the solutions presented here, and the lessons learned, can be used to inform future advances. New artificial intelligence models and the addition of other sensors such as microphones will expand the systems potential for other, real-time use cases. Potential applications include, but are not limited to, wildlife tourism, real-time biodiversity monitoring, wild resource management and detecting illegal human activities in protected areas.
C_LI


title: The structural determinants of intra-protein compensatory substitutions

abstract: Compensating substitutions happen when one mutation is advantageously selected because it restores the loss of fitness induced by a previous deleterious mutation. How frequent such mutations occur in evolution and what is the structural and functional context permitting their emergence remain open questions. We built an atlas of intra-protein compensatory substitutions using a phylogenetic approach and a dataset of 1,630 bacterial protein families for which high-quality sequence alignments and experimentally derived protein structures were available. We identified more than 51,000 positions coevolving by the mean of predicted compensatory mutations. Using the evolutionary and structural properties of the analyzed positions, we demonstrate that compensatory mutations are scarce (typically only a few in the protein history) but widespread (the majority of proteins experienced at least one). Typical coevolving residues are evolving slowly, are located in the protein core outside secondary structure motifs, and are more often in contact than expected by chance, even after accounting for their evolutionary rate and solvent exposure. An exception to this general scheme are residues coevolving for charge compensation, which are evolving faster than non-coevolving sites, in contradiction with predictions from simple coevolutionary models, but similar to stem pairs in RNA. While sites with a significant pattern of coevolution by compensatory mutations are rare, the comparative analysis of hundreds of structures ultimately permits a better understanding of the link between the three-dimensional structure of a protein and its fitness landscape.


title: Little heterosis found in Diploid Hybrid Potato

abstract: Hybrid potato breeding has become a novel alternative to con-ventional potato breeding allowing breeders to overcome intractable barriers (e.g. tetrasomic inheritance, masked deleterious alleles, obligate clonal propagation) with the benefit of seed-based propagule, flexible population design, and the potential of hybrid vigour. Until now, however, no formal inquiry has adequately examined the relevant genetic components for complex traits in hybrid potato populations. In this present study, we use a two-step modelling approach to estimate the relevant variance components to assess the magnitude of the general and specific combining abilities (GCA and SCA, respectively) in diploid hybrid potato (DHP). SCA effects were identified for all yield components studied here warranting evidence of non-additive genetic effects in hybrid potato yield. However, the estimated GCA effects were on average two times larger than their respective SCA quantile across all yield phenotypes. Tuber number GCAs and SCAs were found to be highly correlated with total yields genetic components. Tuber volume appearing under-selected in this population. The prominence of additive effects found for all traits presents evidence that breeders can perform hybrid potato evaluation using the mid-parent value alone. Heterotic vigour stands be useful in bolstering simpler traits but this will be very dependent on the target market of a population. This study represents the first diallel analysis of its kind in diploid potato using material derived from a commercial hybrid breeding programme.


title: Low frequency somatic copy number alterations in normal human lymphocytes revealed by large scale single-cell whole genome profiling

abstract: Genomic-scale somatic copy number alterations in healthy humans are difficult to investigate because of low occurrence rates and the structural variations stochastic natures. Using a Tn5-transposase assisted single-cell whole genome sequencing method, we sequenced over 20,000 single lymphocytes from 16 individuals. Then, with the scale increased to a few thousand single cells per individual, we found that about 7.5% of the cells had large-size copy number alterations. Trisomy 21 was the most prevalent aneuploid event among all autosomal copy number alterations, while monosomy X occurred most frequently in over-30-year-old females. In the monosomy X single cells from individuals with phased genomes and identified X-inactivation ratios in bulk, the inactive X Chromosomes were lost more often than were the active ones.


title: 3-dimensional arenas for the assessment of C. elegans behavior

abstract: C. elegans nematodes are a well-established model organism in numerous fields of experimental biology. In nature, C. elegans live in a rich 3-dimensional environment. However, their behavior has been assessed almost exclusively on the open, flat surface of NGM (Nematode Growth Medium) plates, the golden standard for C. elegans culture in the lab. We present two methods to build 3-dimensional behavioral arenas for C. elegans, by casting, and by directly 3D printing NGM hydrogel. The latter is achieved by using a highly customized fused deposition modeling (FDM) 3D-printer, modified to employ NGM hydrogel as ink. The result is the advancement of 3-dimensional complexity of behavioral assays. To demonstrate the potential of our method, we use the 3D-printed arenas to assess C. elegans physical barriers crossing. C. elegans decision to cross physical obstacles is affected by aging, physiological status (i.e., starvation), and prior experience. The 3D-printed structures can be used to spatially confine C. elegans behaviors, i.e., egg laying. We consider these findings a decisive step toward characterizing C. elegans 3-dimensional behavior, an area long overlooked due to technical constrains. We envision our method of 3D-printing NGM arenas as a powerful tool in behavioral neurogenetics, neuroethology, and invertebrate model organisms neurobiology.

category: bioengineering


title: Autonomous treatment of bacterial infections in vivo using antimicrobial micro- and nanomachines

abstract: The increasing resistance of bacteria to existing antibiotics constitutes a major public health threat globally. Most current antibiotic treatments are hindered by poor delivery to the infection site, leading to undesired off-target effects and drug resistance development and spread. Here, we describe micro- and nanomachines that effectively and autonomously deliver antibiotic payloads to the target area. The active motion and antimicrobial activity of the silica-based robots are driven by catalysis of the enzyme urease and antimicrobial peptides, respectively. These antimicrobial machines show micromolar bactericidal activity in vitro against different Gram-positive and Gram-negative pathogenic bacterial strains and act by rapidly depolarizing their membrane. Finally, they demonstrated autonomous anti-infective efficacy in vivo in a clinically relevant abscess infection mouse model. In summary, our machines combine navigation, catalytic conversion, and bactericidal capacity to deliver antimicrobial payloads to specific infection sites. This technology represents a much-needed tool to direct therapeutics to their target to help combat drug-resistant infections.


title: FEASIBILITY OF VASCULAR REMODELING PARAMETER ESTIMATION FOR ASSESSING HYPERTENSIVE PREGNANCY DISORDERS

abstract: Hypertensive pregnancy disorders, such as preeclampsia, are leading sources of both maternal and fetal morbidity in pregnancy. Non-invasive imaging, such as ultrasound and magnetic resonance imaging (MRI), is an important tool in predicting and monitoring these high risk pregnancies. While imaging can measure hemodynamic parameters, such as uterine artery pulsatility and resistivity indices, the interpretation of such metrics for disease assessment rely on ad-hoc standards, which provide limited insight to the physical mechanisms underlying the emergence of hypertensive pregnancy disorders. To provide meaningful interpretation of measured hemodynamic data in patients, advances in computational fluid dynamics can be brought to bear. In this work, we develop a patient-specific computational framework that combines Bayesian inference with a reduced-order fluid dynamics model to infer remodeling parameters, such as vascular resistance, compliance and vessel cross-sectional area, known to be related to the development of hypertension. The proposed framework enables the prediction of hemodynamic quantities of interest, such as pressure and velocity, directly from sparse and noisy MRI measurements. We illustrate the effectiveness of this approach in two systemic arterial network geometries: an aorta with carotid and a maternal pelvic arterial network. For both cases, the model can reconstruct the provided measurements and infer parameters of interest. In the case of the maternal pelvic arteries, the model can make a distinction between the pregnancies destined to develop hypertension and those that remain normotensive, expressed through the value range of the predicted absolute pressure.


title: Assembly of complete diploid phased chromosomes from draft genome sequences

abstract: De novo genome assembly is essential for genomic research. High-quality genomes assembled into phased pseudomolecules are challenging to produce and often contain assembly errors because of repeats, heterozygosity, or the chosen assembly strategy. Although algorithms that produce partially phased assemblies exist, haploid draft assemblies that may lack biological information remain favored because they are easier to generate and use. We developed HaploSync, a suite of tools that produces fully phased, chromosome-scale diploid genome assemblies, and performs extensive quality control to limit assembly artifacts. HaploSync scaffolds sequences from a draft diploid assembly into phased pseudomolecules guided by a genetic map and/or the genome of a closely related species. HaploSync generates a report that visualizes the relationships between current and legacy sequences, for both haplotypes, and displays their gene and marker content. This quality control helps the user identify misassemblies and guides Haplosyncs correction of scaffolding errors. Finally, HaploSync fills assembly gaps with unplaced sequences and resolves collapsed homozygous regions. In a series of plant, fungal, and animal kingdom case studies, we demonstrate that HaploSync efficiently increases the assembly contiguity of phased chromosomes, improves completeness by filling gaps, corrects scaffolding, and correctly phases highly heterozygous, complex regions.

category: bioinformatics


title: Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN

abstract: Microbial biosurfactants are of major interest due to their multifunctional properties, biodegradable nature and low toxicity. Agroindustrial waste, such as fruit waste, can be used as substrates for producing bacteria. In this study, six samples of fruit waste, from oranges, mangoes and mixed fruits, were self-fermented, and then subjected to short-read metagenomic sequencing, so as to allow assessment of the potential of the associated microbiota for biosurfactant production. Taxonomic analysis using the DIAMOND+MEGAN analysis pipeline shows that all six samples are dominated by Proteobacteria, in particular, a common core consisting of the genera Klebsiella, Enterobacter, Stenotrophomonas, Acinetobacter and Escherichia. To support the interactive visualization and exploration of the surfactant-related genes in such samples, we have integrated the BiosurfDB classification into MEGAN and make this available. Functional analysis indicates high similarity among samples and that a significant number of reads map to genes that are involved in the biosynthesis of lipopeptide-class biosurfactants. Gene-centric analysis reveals Klebsiella as the main assignment for genes related to putisolvins biosynthesis. This suggests that fruit waste is a promising substrate for fermentative processes because the associated microbiota may be able to produce biosurfactants that are potentially useful for the agricultural, chemical, food and pharmaceutical industries.


title: High-sensitivity pattern discovery in large, paired multi-omic datasets

abstract:
Modern biological screens yield enormous numbers of measurements, and identifying and interpreting statistically significant associations among features is essential. Here, we present a novel hierarchical framework, HAllA (Hierarchical All-against-All association testing), for structured association discovery between paired high-dimensional datasets. HAllA efficiently integrates hierarchical hypothesis testing with false discovery rate correction to reveal significant linear and non-linear block-wise relationships among continuous and/or categorical data. We optimized and evaluated HAllA using heterogeneous synthetic datasets of known association structure, where HAllA outperformed all-against-all and other block testing approaches across a range of common similarity measures. We then applied HAllA to a series of real-world multi-omics datasets, revealing new associations between gene expression and host immune activity, the microbiome and host transcriptome, metabolomic profiling, and human health phenotypes. An open-source implementation of HAllA is freely available at http://huttenhower.sph.harvard.edu/halla along with documentation, demo datasets, and a user group.

Author SummaryModern scientific datasets increasingly include multiple measurements of many complementary data types. Here, we present HAllA, a method and implementation that overcomes the statistical challenges presented by data of this type by using feature similarity within each dataset to find statistically significant groups of features between them. We applied HAllA to simulated and real datasets, showing that HAllA outperformed existing procedures and identified compelling biological relationships. HAllA is widely applicable to diverse data structures and presents the user with grouped results that are easier to interpret than traditional methods.


title: Shine: To explore specific, sensitive and conserved biomarkers from massive microbial genomic data within intrapopulations.

abstract:
BackgroundTo improve the quality of nucleic acid detection reagents, we provided a new strategy, Shine, to explore specific, sensitive and conserved biomarkers from massive microbial genomic data within intrapopulations in order to improve detection sensitivity and accuracy. It is obvious that the more comprehensive genomic data are, the more effective the detection biomarkers.

ResultsWe demonstrated that our method could detect undiscovered multicopy conserved species-specific or even subspecies-specific target fragments, according to several clinical projects. In particular, this approach was effective for any pathogenic microorganism even in incompletely assembled motifs. Based on our strategy, the detection device designed with quantitative PCR primers and probes for systematic and automated detection of pathogenic microorganisms in biological samples may cover all pathogenic microorganisms without limits based on genome annotation. On the website https://bioinfo.liferiver.com.cn, users may select different configuration parameters depending on the purpose of the project to realize routine clinical detection practices.

ConclusionsIt is recommended that our strategy is suitable to identify shared universal phylogenetic markers with few false positive or false negative errors and to automate the design of minimal primers and probes to detect pathogenic communities with cost-effective predictive power.


title: A Landmark-based Common Coordinate Framework for Spatial Transcriptomics Data

abstract: 1The increasing amount of spatial transcriptomics data prompts for means to amalgamate observations from distinct experiments, especially attractive is to cast quantities from different sources into a common coordinate frame-work (CCF) to relate signals across space. We here present a method that enables transfer of information from multiple samples to a reference representing a CCF, and show its utility by analyzing an assortment of real and synthetic data sets.


title: Secure Federated Aggregate-Count Queries on Medical Patient Databases Using Fully-Homomorphic Cryptography

abstract:
Electronic health records (EHR) are often siloed across a network of hospitals, but researchers may wish to perform aggregate count queries on said records in entirety--e.g. How many patients have diabetes? Prior work has established a strong approach to answering these queries in the form of probabilistic sketching algorithms like LogLog and HyperLogLog; however, it has remained somewhat of an open question how these algorithms should be made truly private. While many works in the computational biology community--as well as the computer science community at large--have attempted to solve this problem using differential privacy, these methods involve adding noise and still reveal some amount of non-trivial information. Here, we prototype a new protocol using fully homomorphic encryption that is trivially secured even in the setting of quantum-capable adversaries, as it reveals no information other than that which can be trivially gained from final numerical estimation. Simulating up to 16 parties on a single CPU thread takes no longer than 20 minutes to return an estimate with expected 6% approximation error; furthermore, the protocol is parallelizable across both parties and cores, so, in practice, with optimized code, we might expect sub-minute processing time for each party.

AvailibilityOur software is available at https://github.com/atleighton/rlwe-hll


title: Generalized harmonic analysis reveals a frequency modulated timer regulates mammalian hibernation

abstract: Mammalian hibernators decrease basal metabolism and body temperature (Tb) to minimize energy expenditure in harsh seasons. During hibernation, Tb drops to low temperature (<10 {degrees}C) and remains constant for days, known as deep torpor in small mammalian hibernators. Spontaneous interbout arousals interrupt torpor bouts, when Tb recovers to euthermic state ~37 {degrees}C. Torpor-interbout arousal event repeats during several months of hibernation. However, little is known about mechanisms governing Tb fluctuation across torpor-interbout arousal cycles during hibernation. Recent improvement in data-logging techniques enables us to monitor Tb for more than hundred days with high precision, opening up new avenues for quantitative analysis to address the principle governing Tb fluctuation. Here, we analyzed Tb fluctuation across torpor-interbout arousal cycle of Syrian hamster, which can hibernate in response to chronic cold and short photoperiod under a laboratory condition, using generalized harmonic analysis and discovered a model with frequency modulation quantitatively reproducing Tb fluctuation. This analysis also identified an unexpectedly longer period of 120-430 days as the period that modulates another period of several days, generating Tb fluctuation for Syrian hamster. We propose that concerted action of two endogenous periods governs torpor-interbout arousal cycles during hibernation.

category: zoology


title: Frequency modulated timer regulates mammalian hibernation


title: The use of principal component analysis to measure fundamental cognitive processes in neuropsychological data

abstract: For years, dissociation studies on neurological single cases with brain lesions were the dominant method to infer fundamental cognitive functions in neuropsychology. In contrast, the association between deficits was considered to be of less epistemological value and even misleading. Still, principal component analysis (PCA) - an associational method for dimensionality reduction - recently became popular for the identification of fundamental functions. The current study evaluated the ability of PCA and factor analysis (FA) to overcome the association problem in behavioural data of neurological patients and to identify the fundamental variables underlying a battery of measures. Synthetic data were simulated to resemble neuropsychological data with typical dissociation patterns and, thereby, typical patterns of dependence between variables. In most experiments, PCA and FA succeeded to measure the underlying target variables with high up to almost perfect precision. However, this success was fragile and relied on the success of factor rotation, which failed its intended purpose when no test scores existed that primarily measured each underlying target variable. Further, commonly used strategies to estimate the number of meaningful factors appear to underfactor neuropsychological data, thereby consistently underestimating the dimensionality of the data. Finally, simulations suggested a high potential of PCA to denoise data, with factor rotation providing an additional filter function. This can be invaluable in neuropsychology, where measures are often inherently noisy, and PCA can be superior to common compound measures, such as the arithmetic mean, in the measurement of variables with high reliability. In summary, PCA and FA appear to be powerful tools in neuropsychology that are well capable to infer fundamental cognitive functions with high precision, but the typical structure of neuropsychological data and limited informative value of associations in neuropsychology place clear limitations and a risk of a complete failure on the methods.


title: The use of principal component and factor analysis to measure fundamental cognitive processes in neuropsychological data


title: Ca2+ activity is required for injury-induced migration of microglia

abstract:
ObjectivesMicroglia are the resident immune cells in the brain. Brain injury can activate the microglia and induce its directional migration towards injury sites for exerting immune functions. While extracellular ATP released from the injury site mediates the directionality of activated microglias migration, what endows activated microglia with migration capability remains largely unexplored.

MethodsIn the present study, we used the larval zebrafish as an in vivo model to visualize the dynamics of both morphology and Ca2+ activity of microglia during its migration evoked by local brain injury.

ResultsWe found that, in response to local injury, activated microglia exhibited an immediate Ca2+ transient and later elevated Ca2+ bursts frequency during its migration towards the local injury site (P < 0.01). Furthermore, suppression of Ca2+ activities significantly retarded microglial migration (P < 0.05).

ConclusionThus, our study suggests that intracellular Ca2+ activity is required for activated microglias migration.


title: Modulation of gamma spectral amplitude and connectivity during reaching predicts peak velocity and movement duration

abstract: Voluntary movements are accompanied by increased oscillatory activity or synchronization in the gamma range (> 25.5 Hz) within the sensorimotor system. Despite the extensive literature about movement-related gamma synchronization, the specific role of gamma oscillations for movement control is still debated. In this study, we characterized movement-related gamma oscillatory dynamics and its relationship with movement characteristics based on 256-channels EEG recordings in 64 healthy subjects while performing fast and uncorrected reaching movements to targets located at three distances. We found that movement-related gamma synchronization occurred during both movement planning and execution, albeit with different gamma peak frequencies and topographies. Also, the amplitude of gamma synchronization in both planning and execution increased with target distance. Additional analysis of phase coherence revealed a gamma-coordinated long-range network involving occipital, frontal and central regions during movement execution. Gamma synchronization amplitude and phase coherence pattern reliably predicted peak velocity amplitude and timing, thus suggesting that cortical gamma oscillations play a significant role in the selection of appropriate kinematic parameters during planning and in their implementation during movement execution.


title: A dynamic clamp protocol to artificially modify cell capacitance

abstract: AO_SCPLOWBSTRACTC_SCPLOWDynamics of excitable cells and networks depend on the membrane time constant, set by membrane resistance and capacitance. Whereas pharmacological and genetic manipulations of ionic conductances are routine in electrophysiology, experimental control over capacitance remains a challenge. Here, we present capacitance clamp, an approach that allows to mimic a modified capacitance in biological neurons via an unconventional application of the dynamic clamp technique. We first demonstrate the feasibility to quantitatively modulate capacitance in a mathematical neuron model and then confirm the functionality of capacitance clamp in in vitro experiments in granule cells of rodent dentate gyrus with up to threefold virtual capacitance changes. Clamping of capacitance thus constitutes a novel technique to probe and decipher mechanisms of neuronal signaling in ways that were so far inaccessible to experimental electrophysiology.


title: α-Synuclein pre-formed fibrils induce prion-like protein aggregation and neurotoxicity in C. elegans models of Parkinson's disease

abstract: Parkinsons disease (PD) is a debilitating neurodegenerative disorder characterized by progressive motor decline and the aggregation of -synuclein protein. Growing evidence suggests that -synuclein aggregates may spread from neurons of the digestive tract to the brain in a prion-like manner. While rodent models have recapitulated gut-to-brain -synuclein transmission, animal models that are amenable to high-throughput investigations are needed to facilitate the discovery of disease mechanisms. Here we describe the first C. elegans models in which feeding with -synuclein pre-formed fibrils (PFFs) induced prion-like dopamine neuron degeneration and seeding of aggregation of human -synuclein expressed in the host. PFF acceleration of -synuclein aggregation in C. elegans muscle cells was associated with a progressive motor deficit, whereas feeding with -synuclein monomer produced much milder effects. RNAi-mediated knockdown of the C. elegans syndecan sdn-1, and enzymes involved in heparan sulfate proteoglycan biosynthesis, afforded protection from PFF-induced seeding of aggregation and toxicity, as well as dopaminergic neurodegeneration. This work offers new models by which to investigate gut-derived -synuclein spreading and propagation of disease.


title: Diverse roles of MeCP2 in the specification and maintenance of midbrain dopamine phenotype.

abstract: Midbrain dopamine (DA) neurons are associated with locomotor and psychiatric disorders. DA subtype is specified in ancestral neural precursor cells (NPCs) and maintained throughout neuronal differentiation. Here we show that endogenous expression of MeCP2 coincides with DA subtype specification in mouse mesencephalon, and premature expression of MeCP2 prevents in vitro cultured NPCs from acquiring DA subtype through interfering NURR1 transactivation of DA phenotype genes. By contrast, MeCP2 overexpression does not disturb DA subtype in DA neurons. By analyzing the dynamic change of DNA methylation along DA neuronal differentiation at the promoter of DA phenotype gene tyrosine hydroxylase (Th), we show that Th expression is determined by TET1-mediated de-methylation of NURR1 binding sites within Th promoter. Chromatin immunoprecipitation assays demonstrate that MeCP2 dominates the DNA binding of the corresponding sites thereby blocking TET1 function in DA NPCs, whereas TET1-mediated de-methylation prevents excessive MeCP2 binding in DA neurons. The significance of temporal DNA methylation status is further confirmed by targeted methylation/demethylation experiments showing that targeted de-methylation in DA NPCs protects DA subtype specification from MeCP2 overexpression, whereas targeted methylation disturbs subtype maintenance in MeCP2-overexpressed DA neurons. These findings suggest the appropriate timing of MeCP2 expression as a novel determining factor for guiding NPCs into DA lineage.


title: Premature MeCP2 Expression Disturbs the Subtype Specification of Midbrain Dopamine Neurons.


title: Structural brain connectivity predicts acute pain after mild traumatic brain injury

abstract: Mild traumatic brain injury, mTBI, is a leading cause of disability worldwide, with acute pain manifesting as one of its most debilitating symptoms. Understanding acute post-injury pain is important since it is a strong predictor of long-term outcomes. In this study, we imaged the brains of 172 patients with mTBI, following a motorized vehicle collision and used a machine learning approach to extract white matter structural and resting state fMRI functional connectivity measures to predict acute pain. Stronger white matter tracts within the sensorimotor, thalamic-cortical, and default-mode systems predicted 20% of the variance in pain severity within 72 hours of the injury. This result generalized in two independent groups: 39 mTBI patients and 13 mTBI patients without whiplash symptoms. White matter measures collected at 6-months after the collision still predicted mTBI pain at that timepoint (n = 36). These white-matter connections were associated with two nociceptive psychophysical outcomes tested at a remote body site - namely conditioned pain modulation and magnitude of suprathreshold pain-, and with pain sensitivity questionnaire scores. Our validated findings demonstrate a stable white-matter network, the properties of which determine a significant amount of pain experienced after acute injury, pinpointing a circuitry engaged in the transformation and amplification of nociceptive inputs to pain perception.


title: Dopamine depletion can be predicted by the aperiodic component of subthalamic local field potentials

abstract: Electrophysiological biomarkers reflecting the pathological activities in the basal ganglia are essential to gain an etiological understanding of Parkinsons disease (PD) and develop a method of diagnosing and treating the disease. Previous studies that explored electrophysiological biomarkers in PD have focused mainly on oscillatory or periodic activities such as beta and gamma oscillations. Emerging evidence has suggested that the nonoscillatory, aperiodic component reflects the firing rate and synaptic current changes corresponding to cognitive and pathological states. Nevertheless, it has never been thoroughly examined whether the aperiodic component can be used as a biomarker that reflects pathological activities in the basal ganglia in PD. In this study, we examined the parameters of the aperiodic component and tested its practicality as an electrophysiological biomarker of pathological activity in PD. We found that a set of aperiodic parameters, aperiodic offset and exponent, were significantly decreased by the nigrostriatal lesion. To further prove the usefulness of the parameters as biomarkers, acute levodopa treatment reverted the aperiodic offset. We then compared the aperiodic parameters with a previously established periodic biomarker of PD, beta frequency oscillation. We found a significantly low negative correlation with beta power. We showed that the performance of the machine learning-based prediction of pathological activities in the basal ganglia can be improved by using the lowly correlated parameters, beta power and aperiodic component. We suggest that the aperiodic component will provide a more sensitive measurement to early diagnosis PD and have the potential to use as the feedback parameter for the adaptive deep brain stimulation.


title: An evaluation of resonant scanning as a high-speed imaging technique for two-photon imaging of cortical vasculature

abstract: We demonstrate a simple, low-cost two-photon microscope design with both galvo-galvo and resonant-galvo scanning capabilities. We quantify and compare the signal-to-noise ratios and imaging speeds of the galvo-galvo and resonant-galvo scanning modes when used for murine neurovascular imaging. The two scanning modes perform as expected under shot-noise limited detection and are found to achieve comparable signal-to-noise ratios. Resonant-galvo scanning is capable of reaching desired signal-to-noise ratios using less acquisition time when higher excitation power can be used. Given equal excitation power and total pixel dwell time between the two methods, galvo-galvo scanning outperforms resonant-galvo scanning in image quality when detection deviates from being shot-noise limited.


title: Subiculum - BNST Structural Connectivity in Humans and Macaques

abstract: Invasive tract-tracing studies in rodents implicate a direct connection between the subiculum and bed nucleus of the stria terminalis (BNST) as a key component of neural pathways mediating hippocampal regulation of the Hypothalamic-Pituitary-Adrenal (HPA) axis. A clear characterisation of the connections linking the subiculum and BNST in humans and non-human primates is lacking. To address this, we first delineated the projections from the subiculum to the BNST using anterograde tracers injected into macaque monkeys, revealing evidence for a monosynaptic subiculum-BNST projection involving the fornix. Second, we used in vivo diffusion MRI tractography in macaques and humans to demonstrate substantial subiculum complex connectivity to the BNST in both species. This connection was primarily mediated through the fornix, with additional connectivity via the amygdala, consistent with rodent anatomy. Third, utilising the twin-based nature of our human sample, we found that microstructural properties of these tracts are moderately heritable (h2 [~] 0.5). In a final analysis, we found no evidence of any significant association between subiculum complex-BNST tract microstructure and indices of perceived stress/dispositional negativity and alcohol use, derived from principal component analysis decomposition of self-report data. We did, however, find subiculum complex-BNST tract microstructure associations with BMI, age, and sex. Our findings address a key translational gap in our knowledge of the neurocircuitry regulating stress.


title: T cells discriminate between groups C1 and C2 HLA-C

abstract: Dimorphic residues at positions 77 and 80 delineate HLA-C allotypes into two groups, C1 and C2, which associate with disease through interactions with C1 and C2-specific natural killer cell receptors. How the C1/C2 dimorphism affects T cell recognition is unknown. Using HLA-C allotypes that differ only by the C1/C2-defining residues, we found that KRAS-G12D neoantigen specific T cell receptors (TCR) discriminated groups C1 and C2 HLA-C, due to effects on peptide presentation and TCR affinity. Structural and functional experiments combined with immunopeptidomics analysis revealed that C1-HLA-C favors smaller amino acids at the peptide C-terminus minus-1 position (p{Omega}-1), and that larger p{Omega}-1 residues diminished TCR recognition of C1-HLA-C. After controlling for peptide presentation, TCRs exhibited weaker affinities for C2-HLA-C despite conserved TCR contacts. Thus, the C1/C2 dimorphism impacts peptide presentation and HLA-C restricted T cell responses, with implications in multiple disease contexts including adoptive T cell therapy targeting KRAS-G12D-induced cancers.


title: Data-Poor Ecological Risk Assessment of Multiple Stressors

abstract:
O_LIEcological Risk Assessment is a formal process widely applied to terrestrial, marine, and freshwater ecosystems to evaluate the likelihood of adverse ecological effects occurring as a result of exposure to natural or anthropogenic stressors. For many species, data is sparse and semi-quantitative methodologies provide valuable insight for ecosystem management. Recent statistical developments have improved the quality of these analyses yet a rigorous theoretical framework to assess the cumulative impact of multiple stressors is lacking.
C_LIO_LIWe present EcoRAMS, a web application and open-source software module that provides easy-to-use, statistically-robust ecological risk assessments of multiple stressors in data-poor contexts. The software receives attribute scores for two variables (e.g. exposure-sensitivity, productivity-susceptibility, severity-likelihood) via CSV templates and outputs results according to a probabilistic metric of risk.
C_LIO_LIWe demonstrate comparative results across a range of assumptions, using simulated and empirical datasets including up to five stressors. Accounting for multiple stressors even when data is limited provides a more detailed analysis of risk that may otherwise be understated in single stressor analyses.
C_LIO_LIThis application will allow quantification of risk across data-poor contexts for which statistical results have been previously unavailable. The web app format of EcoRAMS.net lowers the barrier of use for practitioners and scientists at any level of statistical training.
C_LI


title: Biocatalytic quantification of α-glucan in particulate marine organic matter

abstract:
Marine algae drive the marine carbon cycle, converting carbon dioxide into organic material. A major component of this produced biomass is a variety of glycans; and yet their chemical composition and individual involvement in production, sedimentation and bacterial uptake remain largely unknown due to a lack of analytical tools for glycan-specific quantification.

Marine -glucans include a range of storage glycans from red and green algae, bacteria, fungi and animals. Although these compounds are likely to account for a high amount of the carbon stored in the oceans they have not been quantified in marine samples so far.

Here we present a method to extract and quantify -glucans in particulate organic matter from algal cultures and environmental samples using a sequential physicochemical extraction and enzymes as -glucan-specific probes. This enzymatic assay is more specific and less susceptible to side reactions than chemical hydrolysis. Using HPAEC-PAD to detect the hydrolysis products allows for a glycan quantification in particulate marine samples even at low concentration of {approx} 2-7 {micro}g/L -glucans.

We measured -glucans (and compared their concentration with the {beta}-glucan laminarin) in three microalgae laboratory cultures as well as in marine particulate organic matter from the North Sea and western North Atlantic Ocean. While laminarin from diatoms and brown algae is an essential component of marine carbon turnover, our results further indicate the significant contribution of starch-like -glucans to marine particulate organic matter.

Henceforth, the combination of glycan-linkage-specific enzymes and chromatographic hydrolysis product detection can provide a powerful tool in the exploration of marine glycans and their role in the global carbon cycle.