title: SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease

abstract: The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets and at the facioscapulohumeral muscular dystrophy associated macro-array, D4Z4. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against another epigenetic regulator complex, PRC2, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1s role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.

category: molecular biology


title: Selective recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules

abstract: Stress granules (SGs) are membraneless organelles composed of mRNAs and RNA binding proteins which undergo assembly in response to stress-induced inactivation of translation initiation. The biochemical criteria for mRNA recruitment into SGs are largely unknown. In general, SG recruitment is limited to a subpopulation of a given mRNA species and RNA-seq analyses of purified SGs revealed that signal sequence-encoding (i.e. endoplasmic reticulum (ER)-targeted) transcripts are significantly under-represented, consistent with prior reports that ER-localized mRNAs are excluded from SGs. Using translational profiling, cell fractionation, and single molecule mRNA imaging, we examined SG biogenesis during the unfolded protein response (UPR) and report that UPR-elicited SG formation is gene selective. Combined immunofluorescence-smFISH studies demonstrated that UPR-induced mRNA granules co-localized with SG protein markers and were in close physical proximity to or directly associated with the ER membrane. mRNA recruitment into ER-associated SGs required stress-induced translational inhibition, though translational inhibition was not solely predictive of mRNA accumulation in SGs. SG formation in response to UPR activation or arsenite addition was blocked by the transcriptional inhibitors actinomycin D or triptolide, suggesting a functional link between gene transcriptional state and SG biogenesis. These data demonstrate that ER-targeted mRNAs can be recruited into SGs and identify the ER as a subcellular site of SG assembly. On the basis of the transcriptional inhibitor studies, we propose that newly transcribed mRNAs undergoing nuclear export during conditions of suppressed translation initiation are key substrates for SG biogenesis.

category: cell biology


title: Dynein light chain-dependent dimerization of Egalitarian is essential for maintaining oocyte fate in Drosophila.

abstract: Egalitarian (Egl) is an RNA adaptor for the Dynein motor and is thought to link numerous, perhaps hundreds, of mRNAs with Dynein. Dynein, in turn, is responsible for the transport and localization of these mRNAs. Studies have shown that efficient mRNA binding by Egl requires the protein to dimerize. We recently demonstrated that Dynein light chain (Dlc) is responsible for facilitating the dimerization of Egl. Mutations in Egl that fail to interact with Dlc do not dimerize, and as such, are defective for mRNA binding. Consequently, this mutant does not efficiently associate with BicaudalD (BicD), the factor responsible for linking the Egl/mRNA complex with Dynein. In this report, we tested whether artificially dimerizing this Dlc-binding mutant using a leucine zipper would restore mRNA binding and rescue mutant phenotypes in vivo. Interestingly, we found that although artificial dimerization of Egl restored BicD binding, it only partially restored mRNA binding. As a result, Egl-dependent phenotypes, such as oocyte specification and mRNA localization, were only partially rescued. We hypothesize that Dlc-mediated dimerization of Egl results in a three-dimensional conformation of the Egl dimer that is best suited for mRNA binding. Although the leucine zipper restores Egl dimerization, it likely does not enable Egl to assemble into the conformation required for maximal mRNA binding activity.


title: Live-Cell Imaging of (p)ppGpp with RNA-based Fluorescent Sensors

abstract: Guanosine tetra- and pentaphosphate, (p)ppGpp, are important alarmone nucleotides that regulate bacterial survival in stressful environment. A direct detection of (p)ppGpp in living cells is critical for our understanding of the mechanism of bacterial stringent response. However, it is still challenging to directly image and measure cellular (p)ppGpp. Here, we report a type of RNA-based fluorescent sensors for live-cell imaging of (p)ppGpp. Our sensor is engineered by conjugating a recently identified (p)ppGpp-specific riboswitch with a fluorogenic RNA aptamer, Broccoli. These sensors can be genetically encoded and enable direct monitoring of cellular (p)ppGpp accumulation. Unprecedented information on cell-to-cell variation and cellular dynamics of (p)ppGpp levels can now be obtained under different nutritional conditions. We predict that these RNA-based sensors will be broadly adapted to study bacterial stringent response.


title: A Method for Rapid Flow-cytometric Isolation of Endothelial Nuclei and RNA from Archived Frozen Brain Tissue

abstract: Endothelial cells are important contributors to brain development, physiology, and disease. Although RNA sequencing has contributed to the understanding of brain endothelial cell diversity, bulk analysis and single-cell approaches have relied on fresh tissue digestion protocols for the isolation of single endothelial cells and flow cytometry-based sorting on surface markers or transgene expression. These approaches are limited in the analysis of the endothelium in human brain tissues, where fresh samples are difficult to obtain. Here, we developed an approach to examine endothelial RNA expression by using an endothelial-specific marker to isolate nuclei from abundant archived frozen brain tissues. We show that this approach rapidly and reliably extracts endothelial nuclei from frozen mouse brain samples, and importantly, from archived frozen human brain tissues. Furthermore, isolated RNA transcript levels are closely correlated with expression in whole cells from tissue digestion protocols and are enriched in endothelial markers and depleted of markers of other brain cell types. As high-quality RNA transcripts could be obtained from as few as 100 nuclei in archived frozen human brain tissues, we predict that this approach should be useful for both bulk analysis of endothelial RNA transcripts in human brain tissues as well as single-cell analysis of endothelial sub-populations.


title: Inferring kinetic parameters of oscillatory gene regulation from single cell time series data

abstract: Gene expression dynamics, such as stochastic oscillations and aperiodic fluctuations, have been associated with cell fate changes in multiple contexts, including development and cancer. Single cell live imaging of protein expression with endogenous reporters is widely used to observe such gene expression dynamics. However, the experimental investigation of regulatory mechanisms underlying the observed dynamics is challenging, since these mechanisms include complex interactions of multiple processes, including transcription, translation, and protein degradation. Here, we present a Bayesian method to infer kinetic parameters of oscillatory gene expression regulation using an auto-negative feedback motif with delay. Specifically, we use a delay-adapted nonlinear Kalman filter within a Metropolis-adjusted Langevin algorithm to identify posterior probability distributions. Our method can be applied to time series data on gene expression from single cells and is able to infer multiple parameters simultaneously. We apply it to published data on murine neural progenitor cells and show that it outperforms alternative methods. We further analyse how parameter uncertainty depends on the duration and time resolution of an imaging experiment, to make experimental design recommendations. This work demonstrates the utility of parameter inference on time course data from single cells and enables new studies on cell fate changes and population heterogeneity.

category: developmental biology


title: Complex introgression among three diverged largemouth bass lineages

abstract: Hybrid zones between diverged lineages offer an unique opportunity to study evolutionary processes related to speciation. Natural and anthropogenic hybridization in the black basses (Micropterus spp.) is well documented, including an extensive intergrade zone between the widespread northern Largemouth Bass (M. salmoides) and the Florida Bass (M. floridanus). Phenotypic surveys have identified an estuarine population of Largemouth Bass (M. salmoides) in the Mobile-Tensaw Delta, with larger relative weight and smaller adult size compared to inland populations, suggesting a potential third lineage of largemouth bass. To determine the evolutionary relationships between these Mobile Delta bass populations, M. salmoides, and M. floridanus, putative pure and intergrade populations of all three groups were sampled across the eastern United States. Phylogenetic analyses of 8,582 nuclear SNPs derived from genotype-by-sequencing and the ND2 mitochondrial gene determined that Delta bass populations stem from a recently diverged lineage of Largemouth Bass. Using a novel quantitative pipeline, a panel of 73 diagnostic SNPs was developed for the three lineages, evaluated for accuracy, and then used to screen 881 samples from 52 sites for genetic integrity and hybridization on the Agena MassARRAY platform. These results strongly support a redrawing of native ranges for both the intergrade zone and M. floridanus, which has significant implications for current fisheries management. Furthermore, Delta bass ancestry was shown to contribute significantly to the previously described intergrade zone between northern Largemouth Bass and Florida Bass, suggesting a more complex pattern of secondary contact and introgression among these diverged Micropterus lineages.

category: evolutionary biology


title: <underline>Genome-wide Imputation Using the Practical Haplotype Graph in the Heterozygous Crop Cassava</underline>

abstract: Genomic applications such as genomic selection and genome-wide association have become increasingly common since the advent of genome sequencing. Genotype imputation makes it possible to infer whole genome information from limited input data, making large sampling for genomic applications more feasible, especially in non-model species where resources are less abundant. Imputation becomes increasingly difficult in heterozygous species where haplotypes must be phased. The Practical Haplotype Graph is a recently developed tool that can accurately impute genotypes, using a reference panel of haplotypes. The Practical Haplotype Graph is a haplotype database that implements a trellis graph to predict haplotypes using minimal input data. Genotyping information is aligned to the database and missing haplotypes are predicted from the most likely path through the graph. We showcase the ability of the Practical Haplotype Graph to impute genomic information in the highly heterozygous crop cassava (Manihot esculenta). Accurately phased haplotypes were sampled from runs of homozygosity across a diverse panel of individuals to populate the graph, which proved more accurate than relying on computational phasing methods. At 1X input sequence coverage, the Practical Haplotype Graph achieves a high concordance between predicted and true genotypes (R=0.84), as compared to the standard imputation tool Beagle (R=0.69). This improved accuracy was especially visible in the prediction of rare and heterozygous alleles. We validate the Practical Haplotype Graph as an accurate imputation tool in the heterozygous crop cassava, showing its potential for application in heterozygous species.

category: genomics


title: A catalog of transcription start sites across 115 human tissue and cell types

abstract: Accurate transcription start site (TSS) annotations are essential for understanding transcriptional regulation and its role in human disease. Gene collections such as GENCODE contain annotations for tens of thousands of TSSs, but not all of these annotations are experimentally validated nor do they contain information on cell type-specific usage. Therefore, we sought to generate a collection of experimentally validated TSSs by integrating RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression (RAMPAGE) data from 115 cell and tissue types, which resulted in a collection of approximately 50 thousand representative RAMPAGE peaks. These peaks were primarily proximal to GENCODE-annotated TSSs and were concordant with other transcription assays. Because RAMPAGE uses paired-end reads, we were then able to connect peaks to transcripts by analyzing the genomic positions of the 3 ends of read mates. Using this paired-end information, we classified the vast majority (37 thousand) of our RAMPAGE peaks as verified TSSs, updating TSS annotations for 20% of GENCODE genes. We also found that these updated TSS annotations were supported by epigenomic and other transcriptomic datasets. To demonstrate the utility of this RAMPAGE rPeak collection, we intersected it with the NHGRI/EBI GWAS catalog and identified new candidate GWAS genes. Overall, our work demonstrates the importance of integrating experimental data to further refine TSS annotations and provides a valuable resource for the biological community.


title: TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

abstract:
BackgroundTopologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs was shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing led to the discovery of cohesin-independent TAD-like structures, also known as single-cell domains -- highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Recent computational modeling studies suggest that epigenetic interactions may underlie the formation of the single-cell domains.

ResultsHere we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components did not significantly affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains.

ConclusionsIn sum, this study suggests that single-cell domains are genome architecture building blocks independent of the tested major epigenetic components.


title: Universal amyloidogenicity of patient-derivedimmunoglobulin light chains

abstract: The deposition of immunoglobulin light chains (IgLCs) in the form of amorphous aggregates or amyloid fibrils in different tissues of patients can lead to severe and potentially fatal organ damage, requiring transplantation in some cases. There has been great interest in recent years to elucidate the origin of the very different in vivo solubilities of IgLCs, as well as the molecular determinants that drive either the formation of ordered amyloid fibrils or disordered amorphous aggregates. It is commonly thought that the reason of this differential aggregation behaviour is to be found in the amino acid sequences of the respective IgLCs, i.e. that some sequences display higher intrinsic tendencies to form amyloid fibrils. Here we perform in depth Thermodynamic and Aggregation Fingerprinting (ThAgg-Fip) of 9 multiple myeloma patient-derived IgLCs, the amino acid sequences of all of which we have solved by de novo protein sequencing with mass spectrometry. The latter technique was also used for one IgLc from a patient with AL amyloidosis. We find that all samples also contain proteases that fragment the proteins under physiologically relevant mildly acidic pH conditions, leading to amyloid fibril formation in all cases. Our results suggest that while every pathogenic IgLC has a unique ThAgg fingerprint, all sequences have comparable amyloidogenic potential. Therefore, extrinsic factors, in particular presence of, and susceptibility to, proteolytic cleavage is likely to be a strong determinant of in vivo aggregation behaviour. The important conclusion, which is corroborated by systematic analysis of our sequences, as well as many sequences of IgLCs from amyloidosis patients reported in the literature, challenges the current paradigm of the link between sequence and amyloid fibril formation of pathogenic light chains.

category: biophysics


title: Single-Cell Stochastic Modeling of the Action of Antimicrobial Peptides on Bacteria

abstract: Antimicrobial peptides (AMPs) produced by multi-cellular organisms as their immune systems defense against microbes are actively considered as natural alternatives to conventional antibiotics. Although a substantial progress has been achieved in studying the AMPs, the microscopic mechanisms of their functioning remain not well understood. Here, we develop a new theoretical framework to investigate how the AMPs are able to efficiently neutralize the bacteria. In our minimal theoretical model, the most relevant processes, AMPs entering into and the following inhibition of the single bacterial cell, are described stochastically. Using complementary master equations approaches, all relevant features of bacteria clearance dynamics by AMPs, such as the probability of inhibition and the mean times before the clearance, are explicitly evaluated. It is found that both processes, entering and inhibition, are equally important for the efficient functioning of AMPs. Our theoretical method naturally explains a wide spectrum of efficiencies of existing AMPs and their heterogeneity at the single-cell level. Theoretical calculations are also consistent with existing single-cell measurements. Thus, the presented theoretical approach clarifies some microscopic aspects of the action of AMPs on bacteria.


title: Neural cell injury pathology due to high-rate mechanical loading

abstract:
Successful detection and prevention of brain injuries relies on the quantitative identification of cellular injury thresholds associated with the underlying pathology. Here, by combining a recently developed inertial microcavitation rheology technique with a 3D in vitro neural tissue model, we quantify and resolve the structural pathology and critical injury strain thresholds of neural cells occurring at high loading rates such as encountered in blast, cavitation or directed energy exposures. We find that neuronal dendritic spines characterized by MAP2 displayed the lowest physical failure strain at 7.3%, whereas microtubules and filamentous actin were able to tolerate appreciably higher strains (14%) prior to injury. Interestingly, while these critical injury thresholds were similar to previous literature values reported for moderate and lower strain rates (< 100 1/s), the pathology of primary injury reported here was distinctly different by being purely physical in nature as compared to biochemical activation during apoptosis or necrosis.

TeaserControlled microcavitation enables quantitative identification of injury thresholds in neural cells.


title: Mice lacking the cAMP effector protein POPDC1 show enhanced hippocampal synaptic plasticity

abstract: Extensive research has uncovered diverse forms of synaptic plasticity and a wide array of molecular signaling mechanisms that act as positive or negative regulators. Specifically, cAMP-dependent signaling pathways have been crucially implicated in long-lasting synaptic plasticity. In this study, we examine the role of POPDC1 (or BVES), a cAMP effector protein expressed in brain, in modulating hippocampal synaptic plasticity. Unlike other cAMP effectors, such as PKA and EPAC, POPDC1 is membrane-bound and the sequence of the cAMP-binding cassette differs from canonical cAMP-binding domains. These properties suggest that POPDC1 may have a unique role in cAMP-mediated signaling underlying synaptic plasticity. Our results show that POPDC1 is enriched in hippocampal synaptoneurosomes. Acute hippocampal slices from Popdc1 knockout (KO) mice exhibit enhanced long-term potentiation (LTP) induced by a variety of stimulation paradigms, particularly in response to weak stimulation paradigms that in slices from wildtype mice induce only transient LTP. Furthermore, Popdc1 KO mice did not display any further enhancement in forskolin-induced LTP observed following inhibition of phosphodiesterases (PDEs), suggesting a possible modulation of cAMP-PDE signaling by POPDC1. Taken together, these data reveal POPDC1 as a novel player in the regulation of hippocampal synaptic plasticity and as a potential target for cognitive enhancement strategies.

category: neuroscience


title: IL-31 uncouples skin inflammation from itch sensation in allergic dermatitis

abstract: Despite a robust literature associating IL-31 with pruritic inflammatory skin diseases, its influence on cutaneous inflammation and on the interplay between inflammatory and neurosensory pathways remain unmapped. Here, we examined the effects of IL-31 and its receptor IL31RA on both inflammation and pruritus in mouse models of dermatitis, including chronic topical house dust mite (HDM) exposure. Unexpectedly, Il31 deficiency increased cutaneous adaptive type 2 cytokine-producing cells and serum IgE. In addition, M2-like macrophages capable of fueling feedforward pro-inflammatory loops were selectively enriched in Il31ra-deficient skin. Thus, IL-31 is not strictly a pro-inflammatory cytokine, but rather an immunoregulatory factor that limits the magnitude of allergic skin inflammation. In contrast, Il31-deficient mice displayed a deficit in HDM-induced scratching. Itch reduction occurred despite intact - and in some cases increased - responsiveness of sensory neurons to other pruritogens released during HDM challenge, highlighting the non-redundant contribution of IL-31-receptive sensory afferents to pruritus in environmental allergen-induced dermatitis. When present, therefore, IL-31 uncouples circuits driven by sensory neurons and immune cells that converge in inflamed skin.

category: immunology


title: Thrombopoietin from hepatocytes promotes hematopoietic stem cell regeneration after myeloablation

abstract: The bone marrow niche plays a critical role in hematopoietic recovery and hematopoietic stem cell (HSC) regeneration after myeloablation. However, it is not clear whether systemic factors beyond the local niche are required for these essential processes in vivo. Thrombopoietin (TPO) is a critical cytokine promoting hematopoietic rebound after myeloablation and its transcripts are expressed by multiple cellular sources. The upregulation of bone marrow-derived TPO has been proposed to be crucial for hematopoietic recovery and HSC regeneration after stress. Nonetheless, the cellular source of TPO in stress has never been investigated genetically. We assessed the functional sources of TPO following two common myeloablative perturbations: 5-fluorouracil (5-FU) administration and irradiation. Using a Tpo translational reporter, we found that the liver but not the bone marrow is the major source of TPO protein after myeloablation. Mice with conditional Tpo deletion from osteoblasts or bone marrow stromal cells showed normal recovery of HSCs and hematopoiesis after myeloablation. In contrast, mice with conditional Tpo deletion from hepatocytes showed significant defects in HSC regeneration and hematopoietic rebound after myeloablation. Thus, systemic TPO from the liver is necessary for HSC regeneration and hematopoietic recovery in myeloablative stress conditions.


title: Nerve recovery from treatment with a vascularized nerve graft compared to an autologous non-vascularized nerve graft in animal models: a systematic review and meta-analysis

abstract:
BackgroundTreatment of nerve injuries proves to be a worldwide clinical challenge. Vascularized nerve grafts are suggested to be a promising alternative for bridging a nerve gap to the current gold standard, an autologous non-vascularized nerve graft. However, there is no adequate clinical evidence for the beneficial effect of vascularized nerve grafts and they are still disputed in clinical practice.

ObjectiveTo systematically review whether vascularized nerve grafts give a superior nerve recovery compared to non-vascularized nerve autografts regarding histological and electrophysiological outcomes in animal models.

Material and methodsPubMed and Embase were systematically searched. The inclusion criteria were as follows: 1) the study was an original full paper which presented unique data; 2) a clear comparison between a vascularized and a non-vascularized autologous nerve transfer was made; 3) the population study were animals of all genders and ages. A standardized mean difference and 95% confidence intervals for each comparison was calculated to estimate the overall effect. Subgroup analyses were conducted on graft length, species and time frames.

ResultsFourteen articles were included in this review and all of them were included in the meta-analyses. A vascularized nerve graft resulted in a significantly larger diameter, higher nerve conduction velocity and axonal count compared to an autologous non-vascularized nerve

graft. However, during sensitivity analysis the effect on axonal count disappeared. No significant difference was observed in muscle weight.

ConclusionTreating a nerve gap with a vascularized graft results in superior nerve recovery compared to non-vascularized nerve autografts in three out of four outcome measurements. However, this conclusion needs to be taken with some caution due to the inherent limitations of this meta-analysis. We recommend future studies to be performed under conditions more closely resembling human circumstances and to use long nerve defects.


title: Rotational remapping between differently prioritized representations in visual working memory

abstract:
How does the brain prioritize among the contents of working memory (WM) to appropriately guide behavior? Using inverted encoding modeling (IEM), previous work (Wan et al., 2020) showed that unprioritized memory items (UMI) are actively represented in the brain but in a "flipped", or opposite, format compared to prioritized memory items (PMI). To gain insight into the mechanisms underlying the UMI-to-PMI representational transformation, we trained recurrent neural networks (RNNs) with an LSTM (long short-term memory) architecture to perform a 2-back working memory task. Although visualization of LSTM hidden layer activity using Principal Component Analysis (PCA) suggested that stimulus representations undergo a smooth rotational transformation across the trial, demixed (d)PCA of the same data decomposed this pattern into a cascade of multiple trajectories, each with a different time course, unfolding within UMI and PMI subspaces. The application of the same analyses to the EEG dataset of Wan et al. (2020) indicated that an items trajectory through the UMI subspace closely mirrored that of the RNN, but that its trajectory through the PMI subspace differed markedly from the RNN. It may be a general principle that, at the level of the representational code, information held in WM undergoes priority-based transformations that allow for its retention while preventing it from interfering with concurrent behavior. Implementational details of this process may vary across model systems.

Author SummaryHow is information held in working memory (WM) but outside the current focus of attention? Motivated by previous neuroimaging studies, we trained recurrent neural networks (RNNs) to perform a 2-back WM task that entails shifts of an items priority status. Dimensionality reduction of the resultant activity in the hidden layer of the RNN allowed us to characterize how a stimulus items representation follows a transformational trajectory through high-dimensional representational space as its priority status changes from memory probe to unprioritized to prioritized. This work illustrates the value of artificial neural networks for assessing and refining hypotheses about mechanisms for information processing in the brain.


title: Priority-based transformations of stimulus representation in visual working memory


title: Allele imputation for the Killer cell Immunoglobulin-like Receptor KIR3DL1/S1

abstract:
Highly polymorphic interactions of KIR3DL1 and KIR3DS1 with HLA class I ligands modulates the effector functions of natural killer (NK) cells and some T cells. This genetically determined diversity affects severity of infections, immune-mediated diseases, and some cancers, and impacts the course of cancer treatment, including transplantation. KIR3DL1 is an inhibitory receptor, and KIR3DS1 is an activating receptor encoded by the KIR3DL1/S1 gene that has more than 200 diverse and divergent alleles. Determination of KIR3DL1/S1 genotypes for medical application is hampered by complex sequence and structural variation that distinguishes individuals and populations, requiring targeted approaches to generate and analyze high-resolution allele data. To overcome these obstacles, we developed and optimized a model for imputing KIR3DL1/S1 alleles at high-resolution from whole-genome SNP data, and designed to represent a substantial component of human genetic diversity. We show that our Global model is effective at imputing KIR3DL1/S1 alleles with an accuracy ranging from 89% in Africans to 97% in East Asians, with mean specificity of 99.8% and sensitivity of 99% for named alleles >1% frequency. We used the established algorithm of the HIBAG program, in a modification named Pulling Out Natural killer cell Genomics (PONG). Because HIBAG was designed to impute HLA alleles also from whole-genome SNP data, PONG allows combinatorial diversity of KIR3DL1/S1 and HLA-A and B to be analyzed using complementary techniques on a single data source. The use of PONG thus negates the need for targeted sequencing data in very large-scale association studies where such methods might not be tractable. All code, imputation models, test data and documentation are available at https://github.com/NormanLabUCD/PONG.

Author SummaryNatural killer (NK) cells are cytotoxic lymphocytes that identify and kill infected or malignant cells and guide immune responses. The effector functions of NK cells are modulated through polymorphic interactions of KIR3DL1/S1 on their surface with the human leukocyte antigens (HLA) that are found on most other cell types in the body. KIR3DL1/S1 is highly polymorphic and differentiated across human populations, affecting susceptibility and course of multiple immune-mediated diseases and their treatments. Genotyping KIR3DL1/S1 for direct medical application or research has been encumbered by the complex sequence and structural variation, which requires targeted approaches and extensive domain expertise to generate and validate high-resolution allele calls. We therefore developed Pulling Out Natural Killer Cell Genomics (PONG) to impute KIR3DL1/S1 alleles from whole genome SNP data, and which we implemented as an open-source R package. We assessed imputation performance using data from five broad population groups that represent a substantial portion of human genetic diversity. We can impute KIR3DL1/S1 alleles with an accuracy ranging from 89% in Africans and South Asians to 97% in East Asians. Globally, imputation of KIR3DL1/S1 alleles having frequency >1% has a mean sensitivity of 94% and specificity of 99.8%. Thus, the PONG method both enables highly sensitive individual-level calling and makes large scale medical genetic studies of KIR3DL1/S1 possible.


title: Cell-to-cell transmission of HSV1 in human keratinocytes in the absence of the major entry receptor, nectin1

abstract:
Herpes simplex virus 1 (HSV1) infects the stratified epithelia of the epidermis, oral or genital mucosa, where the main cell type is the keratinocyte. Here we have used nTERT human keratinocytes to generate a CRISPR-Cas9 knockout (KO) of the primary candidate HSV1 receptor, nectin1, resulting in a cell line that is refractory to HSV1 entry. Nonetheless, a small population of KO cells was able to support infection, and strikingly at later times, those cells originally resistant to HSV1 infection had also been infected. Appearance of this later population was blocked by inhibition of virus genome replication, or infection with a{Delta} UL34 virus defective in capsid export to the cytoplasm, while newly formed GFP-tagged capsids were detected in cells surrounding the initial infected cell, suggesting that virus was spreading following replication in the original susceptible cells. Neutralizing human serum failed to block virus transmission in KO cells, which was dependent on the cell-to-cell spread glycoproteins gI and gE, indicating that virus was spreading by direct cell-to-cell transmission. In line with these results, both HSV1 and HSV2 formed plaques on nectin1 KO cells, albeit at a reduced titre, confirming that once the original cell population was infected, the virus could spread into all other cells in the monolayer. Additional siRNA depletion of the second major HSV1 receptor HVEM, or PTP1B, a cellular factor shown elsewhere to be involved in cell-to-cell transmission, had no effect on virus spread in the absence of nectin1. We conclude that although nectin1 is required for extracellular entry in to the majority of human keratinocytes, it is dispensable for direct cell-to-cell transmission.

Author SummaryHerpes simplex virus 1 (HSV1) infects the epithelia of the epidermis, oral or genital mucosa to cause cold sores, genital herpes, or more serious outcomes such as keratitis and neonatal herpes. Like many viruses, HSV1 can spread through the extracellular environment or by direct cell-to-cell transmission, with the latter mechanism being important for avoiding antibody responses in the host. Here we have studied HSV1 entry and transmission in the human keratinocyte, the main cell type in the target epithelia, by generating a CRISPR-Cas9 knockout of the primary candidate virus receptor, nectin1. While HSV1 was unable to infect the majority of nectin1 knockout keratinocytes, a small population of these nectin1 KO cells remained susceptible to virus entry, and once infected, the virus was able to spread unhindered into the rest of the monolayer. This spread continued in the presence of neutralising serum which blocks extracellular virus, and required the glycoproteins gE and gI which are known to be involved in cell-to-cell spread. Hence, while nectin1 is required for virus entry into the majority of human keratinocyte cells, it is dispensable for cell-to-cell transmission of the virus. These data have implications for the mechanism of HSV1 epithelial spread and pathogenesis.

category: microbiology


title: Microtubule inhibitors enhance DNA transfection efficiency through autophagy receptor p62/SQSTM1

abstract: Ectopic gene expression is an indispensable tool in biology and medicine, but is often limited by the low efficiency of DNA transfection. We previously reported that depletion of the autophagy receptor p62/SQSTM1 enhances DNA transfection efficiency by preventing the degradation of transfected DNA. Therefore, p62 is a potential target for drugs to increase transfection efficiency. To identify such drugs, a non-biased high-throughput screening was applied to over 4,000 compounds from the Osaka University compound library, and their p62-dependency was evaluated. The top-scoring drugs were mostly microtubule inhibitors, such as colchicine and vinblastine, and all of them showed positive effects only in the presence of p62. To understand the p62-dependent mechanisms, the time required for p62-dependent ubiquitination, which is required for autophagosome formation, was examined using polystyrene beads that were introduced into cells as materials that mimicked transfected DNA. Microtubule inhibitors caused a delay in ubiquitination. Furthermore, the level of phosphorylated p62 at S405 was markedly decreased in the drug-treated cells. These results suggest that microtubule inhibitors inhibit p62-dependent autophagosome formation. Our findings demonstrate for the first time that microtubule inhibitors suppress p62 activation as a mechanism for increasing DNA transfection efficiency and provide solutions to increase efficiency.


title: Microtubule inhibitors identified through non-biased screening enhance DNA transfection efficiency by delaying p62-dependent ubiquitin recruitment


title: Microgravity effect on murine T cells exposed to suborbital flight aboard Blue Origins New Shepard vehicle

abstract: Numerous scientific experiments have been conducted in space. However, the precise mechanisms mediating successful human body adaption to the hostile space environment are still not delineated. The cost and logistic challenges of sending biological payloads to International Space Station are forcing scientists to find alternative research platforms. In this study, we investigated whether brief exposure to microgravity during the suborbital flight aboard Blue Origins New Shepard rocket modulated the behavior of the gravity-sensitive murine T cells. We assessed the effect of suborbital environment on different T cell subsets, activation markers, functionality, and cytokine secretion capabilities. Thus, to optimize the potential response of T cells, we cultured them in interleukin IL-2 alone or combined with IL-12. We found that exposure to microgravity decreased the expression of T cells with CD4+ cells being more sensitive to suborbital flight as compared to CD8+ cells. Our data indicate that the functional capabilities of flown T cells were reduced. Also, our findings suggest that supplementing cells with IL-2 and IL-12 cytokines may restore microgravity-mediated cellular alterations. Finally, our study provides insights on the microgravity effect on the murine T cells by utilizing a novel suborbital research platform.


title: Regulators of the secretory pathway have distinct inputs into single-celled branching morphogenesis and seamless tube formation in the Drosophila trachea

abstract: Biological tubes serve as conduits through which gas, nutrients and other important fluids are delivered to tissues. Most biological tubes consist of multiple cells connected by epithelial junctions. Unlike these multicellular tubes, seamless tubes are unicellular and lack junctions. Seamless tubes are present in various organ systems, including the vertebrate vasculature, C.elegans excretory system, and Drosophila tracheal system. The Drosophila tracheal system is a network of air-filled tubes that delivers oxygen to all tissues. Specialized cells within the tracheal system, called terminal cells, branch extensively and form seamless tubes. Terminal tracheal tubes are polarized; the lumenal membrane has apical identity whereas the outer membrane exhibits basal characteristics. Although various aspects of membrane trafficking have been implicated in terminal cell morphogenesis, the precise secretory pathway requirements for basal and apical membrane growth have yet to be elucidated. In the present study, we demonstrate that anterograde trafficking, retrograde trafficking and Golgi-to-plasma membrane vesicle fusion are each required for the complex branched architecture of the terminal cell, but their inputs during seamless lumen formation are more varied. The COPII subunit, Sec 31, and ER exit site protein, Sec16, are critical for subcellular tube architecture, whereas the SNARE proteins Syntaxin 5, Syntaxin 1 and Syntaxin15 are required for seamless tube growth and maintenance. These data suggest that distinct components of the secretory pathway have differential contributions to basal and apical membrane growth and maintenance during terminal cell morphogenesis.


title: Sex differences in microRNA expression in first and third trimester human placenta

abstract:
Maternal and fetal pregnancy outcomes related to placental function vary based on fetal sex, which may be the result of sexually dimorphic epigenetic regulation of RNA expression. We identified sexually dimorphic miRNA expression throughout gestation in human placentae. Next-generation sequencing was used to identify miRNA expression profiles in first and third trimester uncomplicated pregnancies using tissue obtained at chorionic villous sampling (n=113) and parturition (n=47). Sequencing and differential expression (DE) analysis identified 432 mature miRNAs expressed in the first trimester female, 425 in the first trimester male, 400 in the third trimester female, and 508 in the third trimester male placenta (baseMean >10). Of these, 11 sexually dimorphic (FDR<0.05, baseMean >10) miRNAs were identified in the first and 4 miRNAs were identified in the third trimester, including miR-361-5p, significant in both trimesters, all upregulated in females. Across gestation, 207 miRNAs were DE across gestation, common to both females and males, miR-4483, the most DE across gestation. There were twice as many female-specific differences across gestation as male-specific (44 miRNAs vs 21 miRNAs), indicating that miRNA abundance across human gestation is sexually dimorphic. Pathway enrichment analysis identified significant pathways that were differentially regulated in first and third trimester as well as across gestation. This work provides the normative sex dimorphic miRNA atlas in first and third trimester, as well as the sex independent and sex specific placenta miRNA atlas across gestation which may be used to identify biomarkers of placental function and direct functional studies investigating placental sex differences.

Summary SentenceSex dimorphism in miRNA expression is more pronounced in first compared to third trimester placenta, and there are twice as many female-specific gestational differences, indicating miRNA abundance across human gestation is also sexually dimorphic.


title: Origami: Single-cell oriented 3D shape dynamics of folding epithelia from fluorescence microscopy images

abstract: A common feature of morphogenesis is the formation of three-dimensional structures from the folding of two-dimensional epithelial sheets aided by spatio-temporal cell shape changes at the cellular-level. Studying cell shape dynamics and polarised processes that underpin them, requires orienting cells within the epithelial sheet. In epithelia with highly curved surfaces, assigning cell orientation can be difficult to automate in silico. We present  Origami, a MATLAB-based image analysis pipeline to compute oriented cell shape-features. Our automated method accurately computed cell orientation in regions with opposing curvature in synthetic epithelia and fluorescence images of zebrafish embryos. As proof of concept, we identified different cell shape signatures in the developing zebrafish inner ear, where the epithelium deforms in opposite orientations to form different structures. Origami is designed to be user-friendly and is generally applicable to fluorescence images of curved epithelia.


title: Alkaline intracellular pH activates AMPK-mTORC2 signaling to promote cell survival during growth factor limitation

abstract:
mTORC2 controls cell metabolism and promotes cell survival, yet its upstream regulation by diverse cellular cues remains poorly defined. While considerable evidence indicates that mTORC1 but not mTORC2 responds dynamically to amino acid levels, several studies reported activation of mTORC2 signaling by amino acids, a paradox that remains unresolved. Following amino acid starvation, we noted that addition of a commercial amino acid solution but not re-feeding with DMEM containing amino acids increased mTORC2 signaling. Interestingly, the pH of the amino acid solution was [~] 10. These key observations enabled us to discover that alkaline intracellular pH (pHi) represents a previously unknown activator of mTORC2. Using a fluorescent pH-sensitive dye (cSNARF-1-AM) coupled to live-cell imaging, we demonstrate that alkaline extracellular pH (pHe) increases intracellular pHi, which increases mTORC2 catalytic activity and downstream signaling to Akt. Alkaline pHi also activates AMPK, a sensor of energetic stress. Functionally, alkaline pHi attenuates apoptosis caused by growth factor withdrawal, which requires AMPK in part and mTOR in full. Collectively, these findings reveal that alkaline pHi increases AMPK-mTORC2 signaling to promote cell survival during growth factor limitation. As elevated pHi represents an under-appreciated hallmark of cancer cells, alkaline pH sensing by AMPK-mTORC2 may contribute to tumorigenesis.

One Sentence SummaryAlkaline intracellular pH activates mTORC2

category: cancer biology


title: A gap-filling algorithm for prediction of metabolic interactions in microbial communities

abstract:
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.

Author summaryMicrobes compose the most abundant form of life on our planet and they are almost never found in isolation, as they live in close association with one another and with other organisms. The metabolic capacity of individual microbial species dictates their ways of interaction with other species as well as with their environment. The metabolic interactions among microorganisms have been recognised as the driving force for the emergence of the properties of microbial communities. For this reason, understanding the effect of microbial metabolism on interspecies metabolic interactions is detrimental for the study of microbial communities. This study can be benefited by metabolic modeling and the insights offered by constraint-based methods which have been developed for interrogating metabolic models. In this paper, we present an algorithm that predicts cooperative and competitive metabolic interactions between species, while it resolves metabolic gaps in their metabolic models in a computationally efficient way. We use our community gap-filling algorithm to study microbial communities with interesting environmental and health-related applications.

category: systems biology


title: Variable brain wiring through scalable and relative synapse formation in Drosophila

abstract:
Variability of synapse numbers and partners despite identical genes reveals limits of genetic determinism. Non-genetic perturbation of brain wiring can therefore reveal to what extent synapse formation is precise and absolute, or promiscuous and relative. Here, we show the role of relative partner availability for synapse formation in the fly brain through perturbation of developmental temperature. Unexpectedly, slower development at lower temperatures substantially increases axo-dendritic branching, synapse numbers and non-canonical synaptic partnerships of various neurons, while maintaining robust ratios of canonical synapses. Using R7 photoreceptors as a model, we further show that scalability of synapse numbers and ratios is preserved when relative availability of synaptic partners is changed in a DIP{gamma} mutant that ablates R7s preferred synaptic partner. Behaviorally, movement activity scales inversely with synapse numbers, while movement precision and relative connectivity are congruently robust. Hence, the fly genome encodes scalable relative connectivity to develop functional, but not identical, brains.

One-Sentence SummaryNon-identical connectivity and behavior result from temperature-dependent synaptic partner availability in Drosophila.


title: Truncating Tau Reveals Different Pathophysiological Actions of Oligomers in Single Neurons

abstract: Tau protein is involved in maintaining neuronal structure. In Alzheimers disease, small numbers of tau molecules can aggregate to forms oligomers. However, how these oligomers produce changes in neuronal function remains unclear. Previously, oligomers made from full-length human tau were found to have multiple effects on neuronal properties. Here we have cut the tau molecule into two parts: the first 123 amino acids and the remaining 124-441 amino acids. These truncated tau molecules had specific effects on neuronal properties, allowing us to assign the actions of full-length tau to different regions of the molecule. We identified one key target for the effects of tau, the voltage gated sodium channel, which could account for the effects of tau on the action potential. By truncating the tau molecule, we have probed the mechanisms that underlie tau dysfunction, and this increased understanding of taus pathological actions, will build towards developing future tau-targeting therapies.


title: Mechanistic of Rac and Cdc42 synchronization at the cell edge by ARHGAP39-dependent signaling nodules and the impact on protrusion dynamics

abstract: Compartmentalization of GTPase regulators into signaling nodules dictates the GTPase pathways selected. Rac and Cdc42 are synchronized at the cell edge for effective protrusion in motile cells but how their activity is coordinated remains elusive. Here, we discovered that ARHGAP39, a Rac and Cdc42 GTPase-activating protein, sequentially interacts with WAVE and mDia2 to control Rac/lamellipodia and Cdc42/filopodia protrusions, respectively. Mechanistically, ARHGAP39 binds to WAVE and, upon phosphorylation by Src kinase, inactivates Rac to promote Cdc42-induced filopodia formation. With our optimized FRET biosensor, we detected active Cdc42 at the filopodia tips that controls filopodia extension. ARHGAP39 is transported to filopodia tips by Myosin-X where it binds mDia2 and inactivates Cdc42 leading to filopodia retraction. Failure in lamellipodia to filopodia switch by defective ARHGAP39 impairs cell invasion and metastasis. Our study reveals that compartmentalization of ARHGAP39 within Rac/Cdc42 signaling nodules orchestrates the synchronization of lamellipodia/filopodia crosstalk and highlights the intricate regulation of leading edge dynamics in migrating cells.


title: Microfluidic Streptomyces Cultivation for Whole Lifecycle Characterization and Phenotypic Assays Enabled by Nanogap-stabilized Air-Water Interface

abstract:
Streptomyces is a model filamentous prokaryote to study multicellular differentiation and a rich reservoir for antibiotics discovery. In their natural conditions, Streptomyces grows at the interface of porous soil, air, and water. The morphological development of Streptomyces is traditionally performed on agar plates and mostly studied at the population levels. However, the detailed lifecycle of Streptomyces has not been well studied due to its complexity and lack of research tools which can mimic their natural conditions in the soil. Here, we developed a simple assembled microfluidic device for cultivation and the entire lifecycle observation of Streptomyces development from single-cell level. The microfluidic device composed of a microchannel for loading samples and supplying nutrients, microwell arrays for seeding and growth of single spores, and air-filled chambers aside of the microwells that facilitate growth of aerial hyphae and spores. A unique feature of this device is that each microwell is surrounded by a 1.5 {micro}m gap connected to an air-filled chamber which provide stabilized water-air interface. We used this device to observe the development of single Streptomyces spores and found that unlike those in bulk liquid culture, Streptomyces can differentiate at water-air interfaces in microscale liquid culture. Finally, we demonstrated that phenotypic A-Factor assay can be performed at defined time point of its lifecycle. This microfluidic device could become a robust tool for studying Streptomyces multi-cellular differentiation and interaction at single cell level.

IMPORTANCEWe describe a microfluidic device that mimics the natural porous environment for the growth and development of Streptomyces, the model system for bacterial multicellularity. The microfluidic device is used for cultivation and the entire lifecycle observation of Streptomyces development from single-cell level, including growth of aerial filaments. The aerial hyphae development of Streptomyces at the water-air interface was observed at real time in the microfluidic device. The early growth, opportunistic transformation (in the gap), and merging of aerial hyphae of Streptomyces in the microfluidic device were observed for the first time. It will play an important role in finding single-cell heterogeneity to study secondary metabolites related to the complex lifecycle of Streptomyces.


title: Data Independent Acquisition Mass Spectrometry of the Human Lens Enhances Spatiotemporal Measurement of Fiber Cell Aging

abstract: The ocular lens proteome undergoes post-translational and progressive degradation as fiber cells age. The oldest fiber cells and the proteins therein are present at birth and are retained through death. Transparency of the lens is maintained in part by the high abundance crystallin family proteins (up to 300 mg/mL), which establishes a high dynamic range of protein abundance. As a result, previous Data Dependent Analysis (DDA) measurements of the lens proteome are less equipped to identify the lowest abundance proteins. In an attempt to probe more deeply into the lens proteome, we measured the insoluble lens proteome of an 18-year-old human with DDA and newer Data Independent Analysis (DIA) methods. By applying library free DIA search methods, 4,564 protein groups, 48,474 peptides and 5,577 deamidation sites were detected: significantly outperforming the quantity of identifications in using DDA and Pan-Human DIA library searches. Finally, by segmenting the lens into multiple fiber cell-age related regions, we uncovered cell-age resolved changes in proteome composition and putative function.

category: biochemistry


title: Distinct developmental mechanisms influence sexual dimorphisms in the milkweed bug Oncopeltus fasciatus

abstract: Sexual dimorphism is common in animals. The most complete model of sex determination comes from Drosophila melanogaster, where the relative dosage of autosomes and X chromosomes leads indirectly to sex-specific transcripts of doublesex. Female Dsx interacts with a mediator complex protein encoded by intersex to activate female development. In males the transcription factor encoded by fruitless promotes male-specific behavior. The genetics of sex determination have been examined in a small number of other insects, yet several questions remain about the pleisomorphic state. Is doublesex required for female and male development? Is fruitless conserved in male behavior or morphology? Are other components such as intersex functionally conserved? To address these questions, we report expression and functional tests of doublesex, intersex and fruitless in the hemipteran Oncopeltus fasciatus, characterizing three sexual dimorphisms. doublesex prevents intersex phenotypes in all sexes and dimorphic traits in the milkweed bug. intersex and fruitless are expressed across the body, in females and males. fruitless and intersex also affect the genitalia of both sexes, but have effects limited to different dimorphic structures in different sexes. These results reveal roles for intersex and fruitless distinct from other insects, and demonstrate distinct development mechanisms in different sexually dimorphic structures.


title: Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches

abstract:
The basic reproduction number (R0) of an infection determines the impact of its control. For many endemic infections, R0 is often estimated from appropriate country-specific seroprevalence data. Studies sometimes pool estimates from the same region for settings lacking seroprevalence data, but the reliability of this approach is unclear. Plausibly, indicator-based approaches could predict R0 for such settings. We calculated R0 for rubella for 98 settings and correlated its value against 66 demographic, economic, education, housing and health-related indicators. We also trained a random forest regression algorithm using these indicators as the input and R0 as the output. We used the mean-square error to compare the performances of the random forest, simple linear regression and a regional averaging method in predicting R0 using 4-fold cross validation. R0 was <5, 5-10 and >10 for 81, 14 and 3 settings respectively, with no apparent regional differences and in the limited available data, it was usually lower for rural than urban areas. R0 was most correlated with educational attainment, and household indicators for the Pearson and Spearman correlation coefficients respectively and with poverty-related indicators followed by the crude death rate considering the Maximum Information Coefficient, although the correlation for each was relatively weak (Pearson correlation coefficient: 0.4, 95%CI: (0.24,0.48) for educational attainment). A random forest did not perform better in predicting R0 than simple linear regression, depending on the subsets of training indicators and studies, and neither out-performed a regional averaging approach. R0 for rubella is typically low and using indicators to estimate its value is not straightforward. A regional averaging approach may provide as reliable an estimate of R0 for settings lacking seroprevalence data as one based on indicators. The findings may be relevant for other infections and studies estimating the disease burden and the impact of interventions for settings lacking seroprevalence data.

Author SummaryThe basic reproduction number (R0) of an infection, defined as the average number of secondary infectious people resulting from the introduction of an infectious person into a totally susceptible, determines how easily the infection can be controlled. For many established endemic infections, R0 is estimated using data describing the presence of antibodies in a population obtained prior to the introduction of vaccination in that population (prevaccination seroprevalence data). For countries lacking such data the estimation is often done by pooling estimates from their geographical region. We estimated R0 for rubella for 98 settings with existing prevaccination seroprevalence data and we investigated the effectiveness of using simple machine learning regression methods to predict R0 from 66 demographic, economic, education, housing and health-related indicators in those same settings. Our results suggest that the indicator data and prediction methods under investigation do not perform better than regional pooling. We discuss possible ways of improving the prediction accuracy. Since research on predicting R0 using socio-economic data is very scarce, our findings may also be relevant to estimating the disease burden and the impact of interventions in other pathogens.

category: bioinformatics


title: STING mediates immune responses in a unicellular choanoflagellate

abstract: Animals have evolved unique repertoires of innate immune genes and pathways that provide their first line of defense against pathogens. To reconstruct the ancestry of animal innate immunity, we have developed the choanoflagellate Monosiga brevicollis, one of the closest living relatives of animals, as a model for studying mechanisms underlying pathogen recognition and immune response. We found that M. brevicollis is killed by exposure to Pseudomonas aeruginosa bacteria. Moreover, M. brevicollis expresses STING, which, in animals, activates innate immune pathways in response to cyclic dinucleotides during pathogen sensing. M. brevicollis STING increases the susceptibility of M. brevicollis to P. aeruginosa-induced cell death and is required for responding to the cyclic dinucleotide 23 cGAMP. Furthermore, similar to animals, autophagic signaling in M. brevicollis is induced by 23 cGAMP in a STING-dependent manner. This study provides evidence for a pre-animal role for STING in antibacterial immunity and establishes M. brevicollis as a model system for the study of immune responses.


title: STING mediates immune responses in the closest living relatives of animals


title: A chemically-defined growth medium to support Lactobacillus-Acetobacter community analysis

abstract: Lactobacilli and acetobacters are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in the digestive tract of Drosophila melanogaster fruit flies. Communities of these bacteria are widespread and prolific, despite numerous strain-specific auxotrophies, suggesting they have evolved nutrient interdependencies that regulate their growths. The use of a chemically-defined medium (CDM) supporting the growth of both groups of bacteria would greatly facilitate identification of the precise metabolic interactions between these two groups of bacteria. While numerous such media have been developed that support specific strains of lactobacilli and acetobacters, there has not been a medium formulated to support both genera. We developed such a medium, based on a previous Lactobacillus CDM, by modifying the nutrient abundances to improve growth of both groups of bacteria. We further simplified the medium by substituting casamino acids for individual amino acids and the standard Wolfes vitamins and mineral stocks for individual vitamins and minerals, resulting in a reduction from 40 to 8 stock solutions. The new CDM and variations of it support robust growth of lactobacilli and acetobacters. We provide the composition and an example of its use to measure nutritional interactions.


title: Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations

abstract: CRISPR/Cas9 systems provide a highly efficient and flexible genome editing technology with numerous potential applications in areas ranging from gene therapy to population control. Some proposed applications involve CRISPR/Cas9 endonucleases integrated into an organisms genome, which raises questions about potentially harmful effects to the transgenic individuals. One application where this is particularly relevant are CRISPR-based gene drives, which promise a mechanism for rapid genetic alteration of entire populations. The performance of such drives can strongly depend on fitness costs experienced by drive carriers, yet relatively little is known about the magnitude and causes of these costs. Here, we assess the fitness effects of genomic CRISPR/Cas9 expression in Drosophila melanogaster cage populations by tracking allele frequencies of four different transgenic constructs, designed to disentangle direct fitness costs due to the integration, expression, and target-site activity of Cas9 from costs due to potential off-target cleavage. Using a maximum likelihood framework, we find a moderate level of fitness costs due to off-target effects but do not detect significant direct costs. Costs of off-target effects are minimized for a construct with Cas9HF1, a high-fidelity version of Cas9. We further demonstrate that using Cas9HF1 instead of standard Cas9 in a homing drive achieves similar drive conversion efficiency. Our results suggest that gene drives should be designed with high-fidelity endonucleases and may have implications for other applications that involve genomic integration of CRISPR endonucleases.


title: HASTER is a transcriptional stabilizer of HNF1A

abstract: The biological purpose and disease relevance of long noncoding RNAs (lncRNAs) is poorly understood. We examined HASTER, a lncRNA antisense to HNF1A. Haploinsufficient mutations in HNF1A, encoding a homeodomain transcription factor, cause diabetes mellitus. Using mouse and human models, we show that HASTER maintains HNF1A at cell-specific physiological concentrations through positive and negative feedback loops. Haster mutant pancreatic {beta} cells thus showed variegated HNF1A overexpression or silencing, causing insulin-deficiency and diabetes. We demonstrate that the HASTER promoter acts in cis to prevent HNF1A overexpression and silencing, and link HASTER-dependent inhibition to local remodelling of 3D chromatin architecture. We further show that HASTER negative feedback ensures that HNF1A creates open chromatin at appropriate cell-specific genome regions. Our studies expose a cis-regulatory element that is unlike enhancers or silencers, and instead stabilizes expression levels of a pioneer transcription factor. They also show that disruption of a mammalian lncRNA can cause diabetes mellitus.


title: Dynamical Origin for Winner-Take-All Competition in A Biological Network of The Hippocampal Dentate Gyrus

abstract:
We consider a biological network of the hippocampal dentate gyrus (DG). The DG is a pre-processor for pattern separation which facilitates pattern storage and retrieval in the CA3 area of the hippocampus. The main encoding cells in the DG are the granule cells (GCs) which receive the input from the entorhinal cortex (EC) and send their output to the CA3. We note that the activation degree of GCs is so low (~ 5%). This sparsity has been thought to enhance the pattern separation. We investigate the dynamical origin for winner-take-all (WTA) competition which leads to sparse activation of the GCs. The whole GCs are grouped into lamellar clusters. In each GC cluster, there is one inhibitory (I) basket cell (BC) along with excitatory (E) GCs. There are three kinds of external inputs into the GCs; the direct excitatory EC input, the indirect inhibitory EC input, mediated by the HIPP (hilar perforant path-associated) cells, and the excitatory input from the hilar mossy cells (MCs). The firing activities of the GCs are determined via competition between the external E and I inputs. The E-I conductance ratio [Formula] (given by the time average of the external E to I conductances) may represents well the degree of such external E-I input competition. It is thus found that GCs become active when their [Formula] is larger than a threshold [Formula], and then the mean firing rates of the active GCs are strongly correlated with [Formula]. In each GC cluster, the feedback inhibition of the BC may select the winner GCs. GCs with larger [Formula] than the threshold [Formula] survive, and they become winners; all the other GCs with smaller [Formula] become silent. In this way, WTA competition occurs via competition between the firing activity of the GCs and the feedback inhibition from the BC in each GC cluster. In this case, the hilar MCs are also found to play an essential role of enhancing the WTA competition in each GC cluster by exciting both the GCs and the BC.

PACS numbers: 87.19.lj, 87.19.lm, 87.19.lv


title: Structural heterogeneity of cellular K5/K14 filaments as revealed by cryo-electron microscopy

abstract: Keratin intermediate filaments are an essential and major component of the cytoskeleton in epithelial cells. They form a stable yet dynamic filamentous network extending from the nucleus to the cell periphery. Keratin filaments provide cellular resistance to mechanical stresses, ensure cell and tissue integrity in addition to regulatory functions. Mutations in keratin genes are related to a variety of epithelial tissue diseases that mostly affect skin and hair. Despite their importance, the molecular structure of keratin filaments remains largely unknown. In this study, we analyzed the structure of keratin 5/keratin 14 filaments within ghost keratinocytes by cryo-electron microscopy and cryo-electron tomography. By averaging a large number of keratin segments, we have gained insights into the helical architecture of the filaments. Interestingly, two-dimensional classification revealed profound variations in the diameter of keratin filaments and their subunit organization. Reconstitution of filaments of substantial length from keratin segments uncovered a high degree of internal heterogeneity along single filaments, which can contain regions of helical symmetry, regions with less symmetry and regions with significant diameter fluctuations. Cross section views of filaments revealed that keratins form hollow cylinders consisting of multiple protofilaments, with an electron dense core located in the center of the filament. These findings shed light on the complex architecture of keratin filaments, which demonstrate a remarkable degree of heterogeneity, suggesting that they are highly flexible, dynamic cytoskeletal structures.


title: Polygene control and trait dominance in death-feigning syndrome in the red flour beetle Tribolium castaneum

abstract: Death-feigning behavior is an anti-predator behavior in a wide range of animal taxa, and it often correlates with the movement (i.e. death-feigning syndrome). In the present study, we performed reciprocal crossing among strains with genetically longer (L strain) and shorter (S strain) duration of death feigning, and investigated related heritable factors in the F1 and F2 populations. We also investigated moving activity which negatively responded to artificial selection for death feigning in T. castaneum. Our results showed that death feigning occurred more frequently and for shorter periods in the F1 population. In the F2 population, death feigning and movement showed continuous segregation. The distribution of each trait value in the F2 generation was different from the distribution of trait values in the parental generation, and no individuals transgressing the distribution of trait values in the parental generation emerged in the F2 generation. Chi-square analysis of the observed death feigning and movement of F1 and F2 progenies rejected the hypothesis of mono-major gene inheritance. These results suggest that death-feigning syndrome is controlled in a polygenic manner. Our study indicated that reciprocal crossing experiments are useful in assessing the quantitative inheritance of behavioral traits.


title: Generalizability in White Blood Cells' Classification Problem

abstract: Counting and classifying white blood cells (WBCs) in blood samples helps the early diagnosis of the disease. Many works have been done to develop machine learning-based methods to count WBCs. However, most of these works have low generalizability, and their accuracy decreases sharply as the dataset changes. In this paper, a new method is presented that helps to increase the generalization power. In this method, first, the WBCs nucleus is segmented, and then its convex hull is obtained. By subtracting the nucleus from the convex hull, a new image is created called the representative of the convex hull (ROC). Then, by Training a convolutional neural network (CNN) with the cells RGB image as well as the binary images of the nucleus and ROC, the generalization power is increased. The proposed method was first trained on the Raabin-WBC dataset, then its performance was evaluated on the LISC dataset without retraining. The proposed methods accuracy on the Raabin-WBC and LISC datasets is 93.97% and 51.57 %, respectively. Besides, the generalization power of four well-known CNNs named VGG16, ResNext50, MobileNet-V2, and MnasNet1 was investigated. It was found that VGG16 has more generalization power among these models.

category: bioengineering


title: Rapid Estimation of SNP Heritability using Predictive Process approximation in Large scale Cohort Studies

abstract: With the advent of high throughput genetic data, there have been attempts to estimate heritability from genome-wide SNP data on a cohort of distantly related individuals using linear mixed model (LMM). Fitting such an LMM in a large scale cohort study, however, is tremendously challenging due to its high dimensional linear algebraic operations. In this paper, we propose a new method named PredLMM approximating the aforementioned LMM motivated by the concepts of genetic coalescence and gaussian predictive process. PredLMM has substantially better computational complexity than most of the existing LMM based methods and thus, provides a fast alternative for estimating heritability in large scale cohort studies. Theoretically, we show that under a model of genetic coalescence, the limiting form of our approximation is the celebrated predictive process approximation of large gaussian process likelihoods that has well-established accuracy standards. We illustrate our approach with extensive simulation studies and use it to estimate the heritability of multiple quantitative traits from the UK Biobank cohort.


title: Direct Reconstruction of Gene Regulatory Networks underlying Cellular state Transitions without Pseudo-time Inference

abstract: Nowadays the advanced technology for single-cell transcriptional profiling enables people to routinely generate thousands of single-cell expression data, in which data from different cell states or time points are derived from different samples. Without transferring such time-stamped cross-sectional data into pseudo-time series, we propose COSLIR (COvariance restricted Sparse LInear Regression) for directly reconstructing the gene regulatory networks (GRN) that drives the cell-state transition. The differential gene expression between adjacent cell states is modeled as a linear combination of gene expressions in the previous cell state, and the GRN is reconstructed through solving an optimization problem only based on the first and second moments of the sample distributions. We apply the bootstrap strategy as well as the clip threshold method to increase the precision and stability of the estimation. Simulations indicate the perfect accuracy of COSLIR in the oracle case as well as its good performance and stability in the sample case. We apply COSLIR separately to two cell lineages in a published single-cell qPCR dataset during mouse early embryo development. Nearly half of the inferred gene-gene interactions have already been experimentally reported and some of them were even discovered during the past decade after the dataset was published, indicating the power of COSLIR. Furthermore, COSLIR is also evaluated on several single-cell RNA-seq datasets, and the performance is comparable with other methods relying on the pseudo-time reconstruction.


title: An Explainable Deep Learning Approach for Multimodal Electrophysiology Classification

abstract: In recent years, more biomedical studies have begun to use multimodal data to improve model performance. As such, there is a need for improved multimodal explainability methods. Many studies involving multimodal explainability have used ablation approaches. Ablation requires the modification of input data, which may create out-of-distribution samples and may not always offer a correct explanation. We propose using an alternative gradient-based feature attribution approach, called layer-wise relevance propagation (LRP), to help explain multimodal models. To demonstrate the feasibility of the approach, we selected automated sleep stage classification as our use-case and trained a 1-D convolutional neural network (CNN) with electroencephalogram (EEG), electrooculogram (EOG), and electromyogram (EMG) data. We applied LRP to explain the relative importance of each modality to the classification of different sleep stages. Our results showed that across all samples, EEG was most important, followed by EOG, and EMG. For individual sleep stages, EEG and EOG had higher relevance for classifying awake and non-rapid eye movement 1 (NREM1). EOG was most important for classifying REM, and EEG was most relevant for classifying NREM2-NREM3. Also, LRP gave consistent levels of importance to each modality for correctly classified samples across folds and inconsistent levels of importance for incorrectly classified samples. Our results demonstrate the additional insight that gradient-based approaches can provide relative to ablation methods and highlight their feasibility for explaining multimodal electrophysiology classifiers.


title: Deep protein representations enable recombinant protein expression prediction

abstract: A crucial process in the production of industrial enzymes is recombinant gene expression, which aims to induce enzyme overexpression of the genes in a host microbe. Current approaches for securing overexpression rely on molecular tools such as adjusting the recombinant expression vector, adjusting cultivation conditions, or performing codon optimizations. However, such strategies are time-consuming, and an alternative strategy would be to select genes for better compatibility with the recombinant host. Several methods for predicting soluble expression are available; however, they are all optimized for the expression host Escherichia coli and do not consider the possibility of an expressed protein not being soluble. We show that these tools are not suited for predicting expression potential in the industrially important host Bacillus subtilis. Instead, we build a B. subtilis-specific machine learning model for expressibility prediction. Given millions of unlabelled proteins and a small labeled dataset, we can successfully train such a predictive model. The unlabeled proteins provide a performance boost relative to using amino acid frequencies of the labeled proteins as input. On average, we obtain a modest performance of 0.64 area-under-the-curve (AUC) and 0.2 Matthews correlation coefficient (MCC). However, we find that this is sufficient for the prioritization of expression candidates for high-throughput studies. Moreover, the predicted class probabilities are correlated with expression levels. A number of features related to protein expression, including base frequencies and solubility, are captured by the model.


title: Genetic diversity at putatively adaptive but not neutral loci in Primula veris responds to recent habitat change in semi-natural grasslands

abstract: Recent habitat change in semi-natural grasslands due to a lack of management has been shown to affect the genetic diversity of grassland plants. However, it is unknown how a change in local environment affects genetic diversity at adaptive loci. We applied RADseq (restriction-site associated DNA sequencing) to extract > 3,000 SNPs across 568 individuals from 32 Estonian populations of Primula veris, a plant species common to semi-natural grasslands. We evaluated the effect of recent grassland overgrowth following management abandonment on the genetic diversity at putatively neutral and adaptive loci, which we distinguished by applying three methods, i.e., linear and categorical environmental association analyses, and an FST outlier test. For validation, we randomised the genotype to sample assignments. Effects of recent habitat change on genetic diversity differed between neutral and adaptive SNP sets. Genetic diversity assessed at putatively neutral loci was similar in open and overgrown habitats but showed a significant difference between these habitat types at putatively adaptive loci: overgrown (i.e. newly established) habitats exhibited higher genetic diversity at putatively adaptive loci than open (i.e. old) habitats, likely due to the exertion of novel selection pressures imposed by new habitat conditions. This increase in genetic diversity at putatively adaptive loci in the new environment points to currently ongoing selection processes where genetic adaptation to the old habitat is potentially lost through altered allele frequencies. Our study suggests that a recent change in local habitat conditions may not be reflected in neutral loci whereas putatively adaptive loci can inform about potential selection processes.

category: plant biology


title: The effect of recent habitat change on genetic diversity at putatively adaptive and neutral loci in Primula veris in semi-natural grasslands


title: A Genome-Scale TF-DNA Interaction Network of Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism

abstract: In single-celled microbes, transcriptional regulation by single transcription factors is sufficient to shift primary metabolism. Corresponding genome-level transcriptional regulatory maps of metabolism reveal the underlying design principles responsible for these shifts as a model in which master regulators largely coordinate specific metabolic pathways. Relative to individual microbes, plant metabolism is more complex. Primary and specialized metabolism occur within innumerable cell types, and their reactions shift depending on internal and external cues. Given the importance of plants and their metabolites in providing humanity with food, fiber and medicine, we set out to develop a genome-scale transcriptional regulatory map of Arabidopsis metabolic genes. A comprehensive set of protein-DNA interactions between Arabidopsis thaliana transcription factors and promoters of primary metabolism and specialized metabolism were mapped. To demonstrate the utility of this resource, we identified and functionally validated regulators of the TCA cycle. The resulting network suggests that plant metabolic design principles are distinct from that of microbes. Instead, metabolism appears to be transcriptionally coordinated via developmental- and stress-conditional processes that can coordinate across primary and specialized metabolism. These data represent the most comprehensive resource of interactions between TFs and metabolic genes in plants.


title: nGauge: Integrated and extensible neuron morphology analysis in Python

abstract: The study of neuron morphology requires robust and comprehensive methods to quantify the differences between neurons of different subtypes and animal species. Several software packages have been developed for the analysis of neuron tracing results stored in the standard SWC format. However, providing relatively simple quantifications and their non-extendable architecture prohibit their use for advanced data analysis and visualization. We developed nGauge, a Python toolkit to support the parsing and analysis of neuron morphology data. As an application programming interface (API), nGauge can be referenced by other popular open-source software to create custom informatics analysis pipelines and advanced visualizations. nGauge defines an extendable data structure that handles volumetric constructions (e.g. soma), in addition to the SWC linear reconstructions, while remaining light-weight. This greatly extends nGauges data compatibility.


title: PEN receptor GPR83 in anxiety-like behaviors: differential regulation in global vs amygdalar knockdown

abstract: Anxiety disorders are prevalent across the United States and result in a large personal and societal burden. Currently, numerous therapeutic and pharmaceutical treatment options exist. However, drugs to classical receptor targets have shown limited efficacy and often come with unpleasant side effects, highlighting the need to identify novel targets involved in the etiology and treatment of anxiety disorders. GPR83, a recently deorphanized receptor activated by the abundant neuropeptide PEN, has also been identified as a glucocorticoid regulated receptor (and named GIR) suggesting that this receptor may be involved in stress-responses that underlie anxiety. Consistent with this, GPR83 null mice have been found to be resistant to stress-induced anxiety. However, studies examining the role of GPR83 within specific brain regions or potential sex differences have been lacking. In this study, we investigate anxiety-related behaviors in male and female mice with global knockout and following local GPR83 knockdown in female mice. We find that a global knockdown of GPR83 has minimal impact on anxiety-like behaviors in female mice and a decrease in anxiety-related behaviors in male mice. In contrast, a local GPR83 knockdown in the basolateral amygdala leads to more anxiety-related behaviors in female mice. Local GPR83 knockdown in the central amygdala or nucleus accumbens showed no significant effect on anxiety-related behaviors. Finally, dexamethasone administration leads to a significant decrease in receptor expression in the amygdala and nucleus accumbens of female mice. Together, our studies uncover a significant, but divergent role for GPR83 in different brain regions in the regulation of anxiety-related behaviors, which is furthermore dependent on sex.


title: LaminaRGeneVis: a tool to visualize gene expression across the laminar architecture of the human neocortex

abstract:
Application of RNA sequencing has enabled the characterization of genome-wide gene expression in the human brain, including distinct layers of the neocortex. Neuroanatomically, the molecular patterns that underlie the laminar organization of the neocortex can help link structure to circuitry and function. To advance our understanding of cortical architecture, we created LaminaRGeneVis, a web application that displays across-layer cortical gene expression from multiple datasets. These datasets were collected using bulk, single-nucleus, and spatial RNA sequencing methodologies and these data were harmonized to facilitate comparisons between datasets. The online resource facilitates single- and multi-gene analyses by providing figures and statistics for user-friendly assessment of laminar gene expression patterns in the adult human neocortex.

Availability and implementationLaminaRGeneVis is available at https://ethanhkim.shinyapps.io/laminargenevis. The source code and data is accessible at https://github.com/ethanhkim/laminargenevis.


title: Temporal Dynamics of Neural Processing of Facial Expressions and Emotions

abstract: Emotion processing has been a focus of research in psychology and neuroscience for some decades. While the evoked neural markers in human brain activations in response to different emotions have been reported, the temporal dynamics of emotion processing has received less attention. Differences in processing speeds, that depend on emotion type, have not been determined. Furthermore, behavioral studies have found that the right side of the human face expresses emotions more accurately than the left side. Therefore, accounting for both the content of the emotion and the visual angle of presentation from the perspective of the viewer, here we have investigated variability in the discrimination of happy and sad faces when the visual angle of presentation was Positive (right side of the face) compared to Negative (left side of the face). Furthermore, the temporal dynamics involved in processing happy and sad emotions have been compared. Regardless of visual angle, happy emotions were processed faster than sad emotions. However, the evoked response to sad emotions significantly increased in amplitude compared to that for happy emotions, when faces were presented at Positive visual angles only. Source reconstruction from sensor-level ERFs show localized activities in ventral and dorsal stream, including fusiform gyrus, lingual gyrus, putamen and Pre and Post central gyrus. Multivariate pattern analysis (MVPA) confirmed these findings - demonstrating successful decoding of happy and sad emotions only occurred when the facial expression was viewed from a positive visual angle, and that happy emotions were processed faster than sad emotions.


title: T cell receptor (TCR) repertoire analysis reveals a highly conserved TCR repertoire in a bilateral tumor mouse model

abstract:
Temporal analysis of the T cell receptor (TCR) repertoire has been used to monitor treatment-induced changes in antigen-specific T cells in patients with cancer. However, the lack of experimental models that allow temporal analysis of the TCR repertoire in the same individual in a homogeneous population limits the understanding of the causal relationship between changes in TCR repertoire and antitumor responses. A bilateral tumor model, where tumor cells were inoculated bilaterally into the backs of mice, could be used for temporal analysis of the TCR repertoire. This study examined the prerequisite for this strategy: the TCR repertoire is conserved between bilateral tumors with the same growth rate. Bilateral tumors with equivalent size and draining lymph nodes (dLNs) were collected 13 days after tumor inoculation to analyze the TCR repertoire of CD4+ and CD8+ T cells. The tumor-infiltrating T cell clones were highly conserved between the bilateral tumors, and the extent of clonal expansion was equivalent. In addition, the similarity between the bilateral tumors was equivalent to heterogeneity on one side of the tumor. The similarity of the TCR repertoire in the bilateral dLNs was markedly lower than that in the tumor, suggesting that tumor-reactive T cell clones induced independently in each dLN integrated during recirculation and then infiltrated the tumor. These findings suggest that our bilateral tumor model is suitable for temporal monitoring of the TCR repertoire to evaluate temporal and treatment-induced changes in tumor-reactive T cell clones.

Significance StatementThe bilateral subcutaneous tumor model, where tumor cells were inoculated bilaterally into the backs of mice, is a promising model for temporal analysis of the antitumor response in cancer immunotherapy. This study demonstrated a highly conserved TCR repertoire in bilateral tumors and provided the basis for using a bilateral tumor model for evaluating temporal and treatment-induced changes in tumor-responsive T cell clones in individual mice. In humans, accurate statistical analysis is hampered by various background factors, including cancer type and stage and history of treatment. Moreover, temporal tumor biopsy in patients is highly invasive. Our bilateral tumor model overcomes these clinical issues and is expected to be a valuable tool for the development of novel immune monitoring and therapeutic strategies.


title: Predicted the impacts of climate change and extreme-weather events on the future distribution of fruit bats in Australia

abstract:
AimFruit bats (Megachiroptera) are important pollinators and seed dispersers whose distribution might be affected by climate change and extreme-weather events. We assessed the potential impacts of those changes, particularly more frequent and intense heatwaves, and drought, on the future distribution of fruit bats in Australia. We also focus a case study on Tasmania, the southernmost island state of Australia, which is currently devoid of fruit bats but might serve as a future climate refugium.

LocationAustralia (continental-scale study) and Tasmania.

MethodsSpecies distribution modelling was used to predict the occurrence of seven species of fruit bats, using an ensemble of machine-learning algorithms. Predictors included extreme-weather events (heatwave and drought), vegetation (as a proxy for habitat) and bioclimatic variables. Predictions were made for the current-day distribution and future (2050 and 2070) scenarios using multiple emission scenarios and global circulation models.

ResultsChanges in climate and extreme-weather events are forecasted to impact all fruit-bat species, with the loss and gain of suitable areas being predominantly along the periphery of a species current distribution. A higher emission scenario resulted in a higher loss of areas for Grey-headed flying fox (Pteropus poliocephalus) and Spectacled flying fox (P. conspicillatus) but a higher gain of areas for the Northern blossom bat (Macroglossus minimus). The Grey-headed flying fox (Pteropus poliocephalus) is the only study species predicted to potentially occur in Tasmania under future scenarios.

Main conclusionsFruit bats are likely to respond to climate change and extreme weather by migrating to more suitable areas, including regions not historically inhabited by those species such as Tasmania--possibly leading to human-wildlife conflicts. Conservation strategies (e.g., habitat protection) should focus on areas we found to remain suitable under future scenarios, and not be limited by state-political boundaries.

category: ecology


title: Homogeneous environmental selection overturns distance-decay relationship of soil prokaryotic community

abstract: Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biomes on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4,000 km in both alpine and temperate biomes. Surprisingly, prokaryotic similarities increased with geographic distance after tipping points of 1,760 - 1,920 km, overturning the well-accepted distance-decay relationship and generating a significant U-shape pattern. Such U-shape pattern was likely due to decreased disparities in environmental heterogeneity along with geographic distance when across biomes, as homogeneous environmental selection dominated prokaryotic assembly based on {beta}NTI analysis. Consistently, short-term environmental heterogeneity also followed the U-shape pattern spatially, mainly attributed to dissolved nutrients. In sum, these results demonstrate that homogeneous environmental selection via dissolved nutrients overwhelmed the "distance" effect when across biomes, subverting the previously well-accepted geographic pattern for microbes on a large scale.


title: The Origin of Bladder Cancer from Mucosal Field Effects

abstract: We used whole-organ mapping to study loco-geographic molecular changes in evolution of human bladder cancer from mucosal field effects. The integrative multi-platform analyses based on genome-wide RNA sequencing, methylation, copy number variations, and whole exome sequencing identified over 100 dysregulated canonical pathways involving immunity, tissue differentiation and transformation as initiators of bladder carcinogenesis. Widespread dysregulation of interleukin signaling was the dominant change signifying the important role of inflammation and immunity in the incipient phases of urothelial carcinogenesis. The analyses of mutational patterns identified three types of mutations based on their geographic distribution and variant allele frequencies. The most common were low frequency subclonal mutations restricted to individual mucosal samples which were the progeny of their respective uroprogenitor cells. The two additional types of mutations were associated with clonal expansion and involved large areas of bladder mucosa. The first group referred to as  mutations, showed a low mutational frequency across the mucosa. The second group referred to as {beta} mutations increased in their frequencies with disease progression and a large proportion of them represented mutated transcriptional regulators controlling proliferation. Time modeling revealed that bladder carcinogenesis is spanning 10-15 years and can be divided into dormant and progressive phases. The progressive phase lasted 1-2 years and was primarily driven by {beta} mutations with high proliferative advantage. This is the first detailed molecular characterization of mucosal field effects initiating bladder carcinogenesis on the whole-organ scale. It provides novel insights into incipient phases of bladder carcinogenesis and biomarkers for early detection of bladder cancer as well as targets for preventive therapies.