title: Phodopus roborovskii SH101 as a systemic infection model of SARS-CoV-2

abstract:
Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is currently causing a worldwide threat with its unusually high transmission rates and rapid evolution into diverse strains. Unlike typical respiratory viruses, SARS-CoV-2 frequently causes systemic infection by breaking the boundaries of the respiratory systems. The development of animal models recapitulating the clinical manifestations of COVID-19 is of utmost importance not only for the development of vaccines and antivirals but also for understanding the pathogenesis. However, there has not been developed an animal model for systemic infection of SARS-CoV-2 representing most aspects of the clinical manifestations of COVID-19 with systemic symptoms. Here we report that a hamster strain of Phodopus roborovskii SH101, a laboratory inbred hamster strain of P. roborovskii, displayed most symptoms of systemic infection upon SARS-CoV-2 infection as in the case of the human counterpart, unlike current COVID-19 animal models. P. roborovskii SH101 post-infection of SARS-CoV-2 represented most clinical symptoms of COVID-19 such as snuffling, dyspnea, cough, labored breathing, hunched posture, progressive weight loss, and ruffled fur, in addition to high fever following shaking chills. Histological examinations also revealed a serious right-predominated pneumonia as well as slight organ damages in the brain and liver, manifesting systemic COVID-19 cases. Considering the merit of a small animal as well as its clinical manifestations of SARS-CoV-2 infection in human, this hamster model seems to provide an ideal tool to investigate COVID-19.

Author summaryAlthough the current animal models supported SARS-CoV-2 replication and displayed varying degrees of illness after SARS-CoV-2 infection, the infections of SARS-CoV-2 were mainly limited to the respiratory systems of these animals, including hACE2 transgenic mice, hamsters, ferrets, fruit bats, guinea pigs, African green monkey, Rhesus macaques, and Cynomolgus macaques. While these animal models can be a modest model for the respiratory infection, there is a clear limit for use them in the study of COVID-19 that also displays multiple systemic symptoms. Therefore, the development of an animal model recapitulating COVID-19-specific symptoms such as the right-predominated pneumonia would be the utmost need to overcome the imminent threat posed by COVID-19. We identified a very interesting hamster strain, Phodopus roborovskii SH101, which mimics almost all aspects of the clinical manifestations of COVID-19 upon SARS-CoV-2 infection. Unlike the current animal models, SARS-CoV-2-infected P. roborovskii SH101 not only displayed the symptoms of respiratory infection but also clinical manifestations specific to human COVID-19 such as high fever following shaking chills, serious right-predominated pneumonia, and minor organ damages in the brain and liver.


title: Release, rescue and recycling: termination of translation in mammalian mitochondria

abstract: The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single particle cryo-EM as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondria release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present near-atomic models detailing the process of mitochondrial ribosome recycling, to explain how a dedicated elongation factor, mtEFG2, has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process. (134 words)

category: molecular biology


title: Rapid characterization of complex genomic regions using Cas9 enrichment and Nanopore sequencing

abstract: Long-read sequencing approaches have considerably improved the quality and contiguity of genome assemblies. Such platforms bear the potential to resolve even extremely complex regions, such as multigenic families and repetitive stretches of DNA. Deep sequencing coverage, however, is required to overcome low nucleotide accuracy, especially in regions with high homopolymer density, copy number variation, and sequence similarity, such as the MHC and KIR gene clusters of the immune system. Therefore, we have adapted a targeted enrichment protocol in combination with long-read sequencing to efficiently annotate complex genomic regions. Using Cas9 endonuclease activity, segments of the complex KIR gene cluster were enriched and sequenced on an Oxford Nanopore Technologies platform. This provided sufficient coverage to accurately resolve and phase highly complex KIR haplotypes. Our strategy facilitates rapid characterization of large and complex multigenic regions, including its epigenetic footprint, in multiple species, even in the absence of a reference genome.


title: Co-chaperone involvement in knob biogenesis implicates host-derived chaperones in malaria virulence

abstract:
The pathology associated with malaria infection is largely due to the ability of infected human erythrocytes to adhere to a number of receptors on endothelial cells within tissues and organs. This phenomenon is driven by the export of parasite-encoded proteins to the host cell, the exact function of many of which is still unknown. Here we inactivate the function of one of these exported proteins, PFA66, a member of the J-domain protein family. Although parasites lacking this protein were still able to grow in cell culture, we observed severe defects in normal host cell modification, including aberrant morphology of surface knobs, disrupted presentation of the cytoadherence molecule PfEMP1, and a total lack of cytoadherence, despite the presence of the knob associated protein KAHRP. Complementation assays demonstrate that an intact J-domain is required for recovery to a wild-type phenotype and suggest that PFA66 functions in concert with a HSP70 to carry out host cell modification. Strikingly, this HSP70 is likely to be of host origin.

Taken together, our data reveal a role for PFA66 in host cell modification, implicate human HSP70 as also being essential in this process, and uncover a KAHRP-independent mechanism for correct knob biogenesis. Our observations open up exciting new avenues for the development of new anti-malarials.

category: cell biology


title: A quantitative landscape of cell fate transitions identifies principles of cellular decision-making

abstract: Fate decisions in developing tissues involve cells transitioning between a set of discrete cell states, each defined by a distinct gene expression profile. Geometric models, often referred to as Waddington landscapes, in which developmental paths are given by the gradient and cell states by the minima of the model, are an appealing way to describe differentiation dynamics and developmental decisions. To construct and validate accurate dynamical landscapes, quantitative methods based on experimental data are necessary. To this end we took advantage of the differentiation of neural and mesodermal cells from pluripotent mouse embryonic stem cells exposed to different combinations and durations of signalling factors. We developed a principled statistical approach using flow cytometry data to quantify differentiating cell states. Then, using a framework based on Catastrophe Theory and approximate Bayesian computation, we constructed the corresponding dynamical landscape. The result was a quantitative model that accurately predicted the proportions of neural and mesodermal cells differentiating in response to specific signalling regimes. Analysis of the geometry of the landscape revealed two distinct ways in which cells make a binary choice between one of two fates. We discuss the biological relevance of these mechanisms and suggest that they represent general archetypal designs for developmental decisions. Taken together, the approach we describe is broadly applicable for the quantitative analysis of differentiation dynamics and for determining the logic of developmental cell fate decisions.

category: developmental biology


title: One pair of motor neurons provokes early spontaneous motor behavior through periodic bursting in the chordate ascidian embryo

abstract: Vertebrate rhythmic motor behaviour is generated by the central pattern generator (CPG) located in the spinal cord. However, the development of the CPG has not been elucidated at the single-neuron level. We found that a single pair of motor neurons (A10.64/MN2) constitutes the CPG and regulates rhythmic early motor behaviour in the proto-chordate, Ciona. This pair of cells exhibited Ca2+ oscillation with an 80-sec interval at the mid-tailbud stage and 25 sec at the late tailbud stage. The Ca2+ oscillation occurred independently in a dissociated single cell. In the late tailbud stage, the Ca2+ oscillation began to coincide in phase with the ipsilateral tail muscle contraction, which corresponds to rhythmic early motor behaviour. Interestingly, the number and frequency of tail muscle contractions gradually coincided with spikes in the burst of membrane potential as the embryos developed toward late tailbud stage. Photoablation of A10.64/MN2 abolished the rhythmic early motor behaviour. These findings indicate that the early spontaneous rhythmic motor behaviour of Ciona is directly regulated by A10.64/MN2 as an essential component of the CPG. Our findings shed light on the development and evolution of chordate rhythmic behaviours.


title: A single motor neuron determines the rhythm of early motor behaviour in Ciona

category: neuroscience


title: Permissive epigenetic landscape facilitates distinct transcriptional signatures of activating transcription factor 6 in the liver

abstract: Proteostatic stress initiates a transcriptional response that is unique to the stress condition, yet the regulatory mechanisms underlying the distinct gene expression patterns observed in stressed cells remains unknown. Using a functional genomic approach, we investigated how activating transcription factor 6 (ATF6), a key transcription factor in the unfolded protein response (UPR), regulates target genes. We first designed a computational strategy to define Atf6 target genes based on the evolutionary conservation of predicted ATF6 binding in gene promoters, identifying 652 conserved putative Atf6 target (CPAT) genes. CPATs were overrepresented for genes functioning in the UPR, however, the majority functioned in cellular processes unrelated to proteostasis, including small molecule metabolism and development. Functional studies of stress-independent and toxicant based Atf6 activation in zebrafish livers showed that the pattern of CPAT expression in response to Atf6 overexpression, alcohol and arsenic was unique. Only 34 CPATs were differentially expressed in all conditions, indicating that Atf6 is sufficient to regulate a small subset of CPATs. Blocking Atf6 using Ceapins in zebrafish demonstrated that Atf6 is necessary for activation of these genes in response to arsenic. We investigated CPAT during physiologically mediated hepatocyte stress using liver regeneration in mice as a model. Over half of all CPATs were differentially expressed during this process. This was attributed to the permissive chromatin environment in quiescent livers on the promoters of these genes, characterized by the absence of H3K27me3 and enrichment of H3K4me3. Taken together, these data uncover a complex transcriptional response to Atf6 activation and implicate a permissive epigenome as a mechanism by which distinct transcriptional responses are regulated by Atf6.

category: genomics


title: Characterization and Heterotic Grouping of Traditional Assam rice (Oryza sativa L.)

abstract: Parents of heterotic hybrids are derived from different heterotic groups with high genetic divergence. Classification of traditional Assam rice germplasm in divergent pools will be advantageous to maximize the heterosis and thereby to ensure food security. In the present investigation, a group of 60 upland rice genotypes were characterized using 53 polymorphic simple sequence repeats (SSR) markers out of 83 molecular markers. The genetic divergence study using unweighted Neighbour-joining (UNJ) method clustered the 60 genotypes into 3 major clusters. The eleven most divergent genotypes identified were crossed in half diallel fashion to determine the mid-parent and better-parent heterosis values for the objective of heterotic grouping. No correlation between heterosis and genetic distance can be attributable to the use of a subset of markers not linked to yield or concerned. In genetic distance based heterotic grouping, the intra-group hybrids were recorded a higher frequency of crosses, grain yield per plant, specific combining ability effect, mid parent heterosis, better parent heterosis and standard parent heterosis value than those of inter-group hybrids. Overall, sn extensive choice of parents with attractive traits constellation leading to increased yield of the hybrids for much better complementation must be stressed along with a substantial hereditary distance for augmentation of yield heterosis.


title: Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications

abstract: Mutations in the SARS-CoV-2 Membrane (M) gene are relatively uncommon. The M gene encodes the most abundant viral structural protein, and is implicated in multiple viral functions, including initial attachment to the host cell via heparin sulfate proteoglycan, viral protein assembly in conjunction with the N and E genes, and enhanced glucose transport. We have identified a recent spike in the frequency of reported SARS-CoV-2 genomes carrying M gene mutations. This is associated with emergence of a new sub-B.1 clade defined by the previously unreported M:I82T mutation within TM3, the third of three membrane spanning helices implicated in glucose transport. The frequency of this mutation increased in the USA from 0.014% in October 2020 to 1.62% in February 2021, a 116-fold change. While constituting 0.7% of the isolates overall, M:I82T sub-B.1 lineage accounted for 14.4% of B.1 lineage isolates in February 2021, similar to the rapid initial increase previously seen with the B.1.1.7 and B.1.429 lineages, which quickly became the dominant lineages in Europe and California over a period of several months. A similar increase in incidence was also noted in another related mutation, V70L, also within the TM2 transmembrane helix. The rapid emergence of this sub-B.1 clade with recurrent I82T mutation suggests that this M gene mutation is more biologically fit, perhaps related to glucose uptake during viral replication, and should be included in ongoing genomic surveillance efforts and warrants further evaluation for potentially increased pathogenic and therapeutic implications.


title: A conserved BAH module within mammalian BAHD1 connects H3K27me3 to Polycomb gene silencing

abstract:
Trimethylation of histone H3 lysine 27 (H3K27me3) is important for gene silencing and imprinting, (epi)genome organization and organismal development. In a prevalent model, the functional readout of H3K27me3 in mammalian cells is achieved through the H3K27me3-recognizing chromodomain harbored within the chromobox (CBX) component of canonical Polycomb repressive complex 1 (cPRC1), which induces chromatin compaction and gene repression. Here, we report that binding of H3K27me3 by a Bromo Adjacent Homology (BAH) domain harbored within BAH domain-containing protein 1 (BAHD1) is required for overall BAHD1 targeting to chromatin and for optimal repression of the H3K27me3-demarcated genes in mammalian cells. Disruption of direct interaction between BAHD1BAH and H3K27me3 by point mutagenesis leads to chromatin remodeling, notably, increased histone acetylation, at its Polycomb gene targets. Mice carrying an H3K27me3-interaction-defective mutation of Bahd1BAH causes marked embryonic lethality, showing a requirement of this pathway for normal development. Altogether, this work demonstrates an H3K27me3-initiated signaling cascade that operates through a conserved BAH "reader" module within BAHD1 in mammals.

Key PointsO_LIBAHD1BAH is a functionally validated mammalian "reader" of H3K27me3, mediating BAHD1 targeting for gene silencing.
C_LIO_LIBAHD1BAH connects H3K27me3 together with histone deacetylation, an integral step of gene silencing.
C_LIO_LIBAHD1BAH-mediated functional readout of H3K27me3 is essential for organismal development.
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Graphic abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/435004v2_ufig1.gif" ALT="Figure 1">
View larger version (11K):
org.highwire.dtl.DTLVardef@1e072a4org.highwire.dtl.DTLVardef@86a86borg.highwire.dtl.DTLVardef@9b1354org.highwire.dtl.DTLVardef@111fa5d_HPS_FORMAT_FIGEXP  M_FIG A mammalian H3K27me3-transduction pathway operates through an H3K27me3-specific reader module (BAH) of BAHD1, which assembles a complex with corepressors (HDACs and others) for suppressing histone acetylation and repressing expression at Polycomb target genes.

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category: biochemistry


title: Functional characterization of a DNA-dependent AAA ATPase in SimranZ1, a F cluster mycobacteriophage

abstract: Mycobacteriophages are viruses of Mycobacterium spp. with promising diagnostic and therapeutic potential. Phage genome exploration and characterization of their proteomes are essential to gain a better understanding of their role in phage biology. So far, about 2014 mycobacteriophages have been genomically defined and 1563 phage protein families (phamilies) are identified. However, the function of only a fraction (about 15%) is known and a majority of ORFs in phage genomes are hypothetical proteins. In this study, from the annotated genome of a F1 cluster mycobacteriophage SimranZ1, a putative AAA ATPase (Gp65, Pham 9410) is characterized as a DNA-dependent ATPase. Sequence-based functional annotation predicted Gp65 to belong to the P-loop NTPase superfamily, having AAA_24 and RecA/RadA domains which are known to be involved in ATP-dependent DNA repair/maintenance mechanism. On molecular docking, Gly21 and Ser23 of Gp65 showed specific binding with ATP. Using a microtiter plate assay, ATPase activity of Gp65 was experimentally verified which was found to increase in the presence of dsDNA. Gel electrophoresis under non-denaturing condition showed the oligomeric states of Gp65 and Transmission Electron Microscopy revealed it to exist as a hexamer having a prominent central pore with a diameter of 1.9 nm. In summary, functional characterization of Gp65 as a DNA dependent AAA ATPase indicates its role in DNA repair/maintenance mechanism in mycobacteriophages.


title: Coordination of -1 Programmed Ribosomal Frameshifting by Transcript and Nascent Chain Features Revealed by Deep Mutational Scanning

abstract: Programmed ribosomal frameshifting (PRF) is a translational recoding mechanism that enables the synthesis of multiple polypeptides from a single transcript. In the alphavirus structural polyprotein, -1PRF is coordinated by a "slippery" sequence in the transcript, an RNA stem-loop, and a conformational transition in the nascent polypeptide chain. To characterize each of these effectors, we measured the effects of 4,530 mutations on -1PRF by deep mutational scanning. While most mutations within the slip-site and stem-loop disrupt -1PRF, mutagenic effects upstream of the slip-site are far more variable. Molecular dynamics simulations of polyprotein biogenesis suggest many of these mutations alter stimulatory forces on the nascent chain through their effects on translocon-mediated cotranslational folding. Finally, we provide evidence suggesting the coupling between cotranslational folding and -1PRF depends on the translation kinetics upstream of the slip-site. These findings demonstrate how -1PRF is coordinated by features within both the transcript and nascent chain.


title: A small fraction of progenitors differentiate into mature adipocytes due to constraints on the cell structure change

abstract: Differentiating 3T3-L1 pre-adipocytes are a mixture of non-identical culture cells. It is vital to identify the cell types that respond to the induction stimulus to understand the pre-adipocyte potential and the mature adipocyte behavior. To test this hypothesis, we deconvoluted the gene expression profiles of the cell culture of MDI-induced 3T3-L1 cells. Then we estimated the fractions of the sub-populations and their changes in time. We characterized the sub-populations based on their specific expression profiles. Initial cell cultures comprised three distinct phenotypes. A small fraction of the starting cells responded to the induction and developed into mature adipocytes. Unresponsive cells were probably under structural constraints or were committed to differentiating into alternative phenotypes. Using the same population gene markers, similar proportions were found in induced human primary adipocyte cell cultures. The three sub-populations had diverse responses to treatment with various drugs and compounds. Only the response of the maturating sub-population resembled that estimated from the profiles of the mixture. We then showed that even at a low division rate, a small fraction of cells could increase its share in a dynamic two-populations model. Finally, we used a cell cycle expression index to validate that model. To sum, pre-adipocytes are a mixture of different cells of which a limited fraction become mature adipocytes.

category: bioinformatics


title: Facilitated Dissociation of Nucleoid Associated Proteins from DNA in the Bacterial Confinement

abstract: Transcription machinery depends on the temporal formation of protein-DNA complexes. Recent experiments demonstrated that lifetime of the complex can also affect transcription. In parallel, in vitro single-molecule studies showed that nucleoid-associated proteins (NAPs) leave the DNA rapidly as the bulk concentration of the protein increases via facilitated dissociation (FD). Never-theless, whether such concentration-dependent mechanism is functional in a bacterial cell, in which NAP levels and the 3D chromosomal structure are often coupled, is not clear a priori. Here, by using extensive coarse-grained molecular simulations, we model the unbinding of specific and nonspecific dimeric NAPs from a high-molecular-weight circular DNA molecule in a cylindrical structure mimicking the cellular confinement of a bacterial chromosome. Our simulations show that physiologically relevant peak protein levels (tens of micromolar) lead to highly compact chromosomal structures. This compaction results in rapid off rates (shorter DNA-residence times) but only for specifically DNA-binding NAPs such as the factor for inversion stimulation (Fis). Contrarily, for nonspecific NAPs, the off rates decrease as the protein levels increase, suggesting an inverse FD pattern. The simulations with restrained chromosome models reveal that this inverse response is due to DNA-segmental fluctuations, and that chromosomal compaction is in favor of faster protein dissociation. Overall, our results indicate that cellular-concentration level of a structural DNA-binding protein can be highly intermingled with its DNA-residence time.

category: biophysics


title: Immunity Depletion, Telomere Imbalance, and Cancer-associated Metabolism Pathway Aberrations in Intestinal Mucosa upon Caloric Restriction

abstract: Systematic analysis of calorie restriction (CR) mechanisms and pathways in cancer biology has not been carried out, leaving therapeutic benefits unclear. Using a systems biology approach and metadata analysis, we studied gene expression changes in the response of normal mouse duodenum mucosa (DM) to short-term (2-weeks) 25% CR as a biological model. We found a high similarity of gene expression profiles in human and mouse DM tissues. Surprisingly, 26% of the 467 CR responding differential expressed genes (DEGs) in mice consist of cancer-associated genes--most never studied in CR contexts. The DEGs were enriched with over-expressed cell cycle, oncogenes, and metabolic reprogramming pathways (MRP) that determine tissue-specific tumorigenesis, cancer, and stem cell activation; tumor suppressors and apoptosis genes were under-expressed. DEG enrichments suggest a misbalance in telomere maintenance and activation of metabolic pathways playing dual (anti-cancer and pro-oncogenic) roles. Immune system genes (ISGs) consist of 37% of the total DEGs; the majority of ISGs are suppressed, including cell-autonomous immunity and tumor immune evasion controls. Thus, CR induces MRP suppressing multiple immune mechanics and activating oncogenic pathways, potentially driving pre-malignant and cancer states. These findings change the paradigm regarding the anti-cancer role of CR and may initiate specific treatment target development.

category: cancer biology


title: Gene expression shapes the patterns of parallel evolution of herbicide resistance in the agricultural weed Monochoria vaginalis

abstract: The evolution of herbicide resistance in weeds is an example of parallel evolution, through which genes encoding herbicide target proteins are repeatedly represented as evolutionary targets. The number of herbicide target-site genes differs among species, and little is known regarding the effects of duplicate gene copies on the evolution of herbicide resistance. We investigated the evolution of herbicide resistance in Monochoria vaginalis, which carries five copies of sulfonylurea target-site acetolactate synthase (ALS) genes. Suspected resistant populations collected across Japan were investigated for herbicide sensitivity and ALS gene sequences, followed by functional characterisation and ALS gene expression analysis. We identified over 60 resistant populations, all of which carried resistance-conferring amino acid substitutions exclusively in MvALS1 or MvALS3. All MvALS4 alleles carried a loss-of-function mutation. Although the enzymatic properties of ALS encoded by these genes were not markedly different, the expression of MvALS1 and MvALS3 was prominently higher among all ALS genes. The higher expression of MvALS1 and MvALS3 is the driving force of the biased representation of genes during the evolution of herbicide resistance in M. vaginalis. Our findings highlight that gene expression is a key factor in creating evolutionary hotspots.

category: plant biology


title: The Induction of Pyrenoid Synthesis by Hyperoxia and its Implications for the Natural Diversity of Photosynthetic Responses in Chlamydomonas

abstract: In algae, it is well established that the pyrenoid, a component of the carbon-concentrating mechanism (CCM), is essential for efficient photosynthesis at low CO2. However, the signal that triggers the formation of the pyrenoid has remained elusive. Here, we show that, in Chlamydomonas reinhardtii, the pyrenoid is strongly induced by hyperoxia, even at high CO2 or bicarbonate levels. These results suggest that the pyrenoid can be induced by a common product of photosynthesis specific to low CO2 or hyperoxia. Consistent with this view, the photorespiratory by-product, H2O2, induced the pyrenoid, suggesting that it acts as a signal. Finally, we show evidence for linkages between genetic variations in hyperoxia tolerance, H2O2 signaling, and pyrenoid morphologies.


title: Biofoundry-assisted expression and characterisation of plant proteins

abstract: Many goals in synthetic biology, including the elucidation and refactoring of biosynthetic pathways and the engineering of regulatory circuits and networks, require knowledge of protein function. In plants, the prevalence of large gene families means it can be particularly challenging to link specific functions to individual proteins. However, protein characterisation has remained a technical bottleneck, often requiring significant effort to optimise expression and purification protocols. To leverage the ability of biofoundries to accelerate design-built-test-learn cycles, we present a workflow for automated DNA assembly and cell-free expression of plant proteins that accelerates optimisation and enables rapid progression to characterisation. First, we developed a phytobrick-compatible Golden Gate DNA assembly toolbox containing plasmid acceptors for cell-free expression using E. coli or wheat germ lysates as well as a set of N- and C-terminal tag parts for detection, purification, and improved expression/folding. We next optimised automated assembly of miniaturised cell-free reactions using an acoustic liquid handling platform and then compared tag configurations to identify those that increase expression. We additionally developed a luciferase-based system for rapid quantification that requires a minimal 11 aa tag and demonstrate facile removal of tags following synthesis. Finally, we show that several functional characterisation experiments can be performed with cell-free protein synthesis reactions without the need for protein purification. Together, the combination of automated assembly of DNA parts and cell-free expression reactions should significantly increase the throughput of experiments to test and understand plant protein function and enable the direct reuse of DNA parts in downstream plant engineering workflows.

category: synthetic biology


title: Regulatory B cells (Bregs) inhibit osteoclastogenesis and prevent bone loss in osteoporotic mice model

abstract: Increasing evidences in recent years have suggested that regulatory B cells (Bregs) are crucial modulator in various inflammatory disease conditions. However, the role of Bregs in case of postmenopausal osteoporosis remains unknown. Also, no study till date have ever investigated the significance of Bregs in modulating osteoclastogenesis. In the present study, we for the first time examined the anti-osteoclastogenic potential of Bregs under in vitro conditions and we observed that Bregs suppressed RANKL mediated osteoclastogenesis in bone marrow cells in a dose dependent manner. We further elucidated the mechanism behind the suppression of osteoclasts differentiation by Bregs and found that Bregs inhibit osteoclastogenesis via IL-10 production. To further confirm the bone health modulating potential of Bregs we employed post-menopausal osteoporotic mice model. Remarkably, our in vivo data clearly suggest a significant reduction (p < 0.01) in both CD19+IL-10+ and CD19+CD1dhiCD5+IL-10+ B10 Bregs in case of osteoporotic mice model. Moreover, our serum cytokine data further confirms the significant reduction of IL-10 levels in osteoporotic mice. Taken together, the present study for the first time unravels and establish the unexplored role of regulatory B cells in case of osteoporosis and provide new insight into Bregs biology in the context of post-menopausal osteoporosis.

category: immunology


title: ChAdOx1 nCoV-19 (AZD1222) protects against SARS-CoV-2 B.1.351 and B.1.1.7

abstract: We investigated ChAdOx1 nCoV-19 (AZD1222) vaccine efficacy against SARS-CoV-2 variants of concern (VOCs) B.1.1.7 and B.1.351 in Syrian hamsters. We previously showed protection against SARS-CoV-2 disease and pneumonia in hamsters vaccinated with a single dose of ChAdOx1 nCoV-19. Here, we observed a 9.5-fold reduction of virus neutralizing antibody titer in vaccinated hamster sera against B.1.351 compared to B.1.1.7. Vaccinated hamsters challenged with B.1.1.7 or B.1.351 did not lose weight compared to control animals. In contrast to control animals, the lungs of vaccinated animals did not show any gross lesions. Minimal to no viral subgenomic RNA (sgRNA) and no infectious virus was detected in lungs of vaccinated animals. Histopathological evaluation showed extensive pulmonary pathology caused by B.1.1.7 or B.1.351 replication in the control animals, but none in the vaccinated animals. These data demonstrate the effectiveness of the ChAdOx1 nCoV-19 vaccine against clinical disease caused by B.1.1.7 or B.1.351 VOCs.

category: microbiology


title: ChAdOx1 nCoV-19 (AZD1222) protects hamsters against SARS-CoV-2 B.1.351 and B.1.1.7 1 disease


title: ChAdOx1 nCoV-19 (AZD1222) protects Syrian hamsters against SARS-CoV-2 B.1.351 and B.1.1.7 1 disease


title: A PX-BAR protein Mvp1/SNX8 and a dynamin-like GTPase Vps1 drive endosomal recycling

abstract:
Membrane protein recycling systems are essential for maintenance of the endosome-lysosome system. In yeast, retromer and Snx4 coat complexes are recruited to the endosomal surface where they recognize cargos. They sort cargo and deform the membrane into recycling tubules that bud from the endosome and target to the Golgi. Here, we reveal that the SNX-BAR protein, Mvp1, mediates an endosomal recycling pathway which is mechanistically distinct from the retromer and Snx4 pathways. Mvp1 deforms the endosomal membrane and sorts cargos containing a specific sorting motif into a membrane tubule. Subsequently, Mvp1 recruits the dynamin-like GTPase Vps1 to catalyze membrane scission and release of the recycling tubule. Similarly, SNX8, the human homolog of Mvp1, which has been also implicated in Alzheimers disease, mediates formation of an endosomal recycling tubule. Thus, we present evidence for a novel endosomal retrieval pathway that is conserved from yeast to humans.

In BriefPX-BAR Mvp1 and dynamin-like GTPase Vps1 drive retromer independent endosomal recycling.

HighlightsO_LIRetromer- and Snx4-independent endosomal recycling pathway discovered
C_LIO_LISNX-BAR Mvp1 and dynamin-like GTPase Vps1 mediate cargo sorting into recycling tubules/vesicles in the absence of retromer function
C_LIO_LIMvp1 together with retromer and Snx4 complexes contribute to proper endosome function
C_LIO_LIMvp1 mediated recycling is evolutionary conserved from yeast to humans
C_LIO_LICharacters: 43,934/45,000 (including spaces and main figure legends but excluding STAR Methods text, supplemental item legends, and References section)
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title: Integrin α6 upregulation in nucleus pulposus cell under high oxygen tension attenuates intervertebral disc degeneration

abstract: The destruction of low oxygen microenvironment played critical roles in the pathogenesis of intervertebral disk degeneration (IVDD). In this study, high oxygen tension (HOT) treatment upregulated integrin 6(ITG 6) expression, which could be alleviated by blocking PI3K/AKT signaling pathway. And the levels of ITG 6 expression were increased in the NP tissue from IVDD patients and IVDD rat model with mild degeneration, which were reduced as degeneration degree increases. Further studies found that ITG 6 could protect NP cells against HOT-induced apoptosis and oxidative stress, and protect NP cells from HOT-inhibited ECM proteins synthesis. ITG 6 upregulation by HOT contributed to maintain a NP tissue homeostasis through the interaction with hypoxia inducible factor-1 (HIF-1). Furthermore, silencing of ITG 6 in vivo could obviously accelerate puncture-induced IVDD. Taken together, ITG 6 upregulation by HOT in NP cells might be a protective factor in IVDD as well as restore NP cell function.


title: Winter rye cover cropping changes squash (Cucurbita pepo) phyllosphere microbiota and reduces Pseudomonas syringae symptoms

abstract: Cover cropping is a soil conservation practice that may reduce the impacts of the economically important pathogen Pseudomonas syringae on crops including squash (Cucurbita pepo). To date, no studies have directly quantified the effect of rye cover crops on P. syringae populations, nor on the bacterial community of squash leaves. In this work, we tested the hypothesis that the protective effects of cover cropping on squash may be mediated by cover cropping effects on the plants microbiota that in turn protects against P. syringae. Using combined 16S sequencing and culture-based approaches, we showed that rye cover cropping protects squash against P. syringae, by decreasing pathogen population size on squash leaves and increasing fruit health and marketability at harvest. We also found evidence of a strong effect of rye cover crops on bacterial communities of the squash phyllosphere. Those findings were more striking early in the growing season. Finally, we identified numerous phyllosphere bacteria belonging to the genera Sphingomonas, Methylobacterium and Pseudomonas that were promoted by rye cover crops. Overall, our findings suggest cover cropping is effective for the sustainable management of P. syringae on squash and may provide a reservoir of potential microbial biocontrol agents colonizing the phyllosphere.

category: ecology


title: A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians

abstract: The mitochondrial genome encodes core subunits of the oxidative phosphorylation machinery, and it is expected that these mitochondria-encoded polypeptides would be shaped by bioenergetic needs corresponding to diverse diets and environments. Here, we have developed a robust and effective method for highlighting phylogenetic tree edges with unexpectedly rapid, and likely efficacious, mitochondrial protein evolution. Further, our approach allows detection of those discrete protein substitutions likely to alter enzyme performance. A survey of mammalian taxonomic groups performed using our method supports the idea that widely conserved residues in mitochondria-encoded proteins are more likely to rapidly mutate within specific clades. Intriguingly, primates share a substitution profile with a number of mammals characterized by low mass-specific rates of metabolism. Our data suggest low metabolic performance and activity of ancestral simians, as well as reduced cellular metabolism across many extant primates.

category: evolutionary biology


title: Normalization and De-noising of Single-cell Hi-C Data with BandNorm and 3DVI

abstract: Single-cell high-throughput chromatin conformation capture methodologies (scHi-C) enable profiling long-range genomic interactions at the single-cell resolution; however, data from these technologies are prone to technical noise and bias that, when unaccounted for, hinder downstream analysis. Here we developed a fast band normalization approach, BandNorm, and a deep generative modeling framework, 3DVI, to explicitly account for scHi-C specific technical biases. We present robust performances of BandNorm and 3DVI compared to existing state-of-the-art methods. BandNorm is effective in separating cell types, identification of interaction features, and recovery of cell-cell relationship, whereas de-noising by 3DVI successfully enables 3D compartments and domains recovery, especially for rare cell types.


title: Single-cell transcriptome reveals a testis-specific expression profile of TCEA in human spermatogenesis

abstract: Transcription elongation factor A (TCEA) is a eukaryotic transcriptional molecule, required for a formation of initiation and elongation of gene transcription-mediated RNA polymerase II (RNAPII) complex, to promote transcription-coupled nucleotide excision repair (TC-NER) after RNAPII backtracking recovery. TCEA shares three isoforms in which TCEA1 is ubiquitously expressed among all eukaryotic cells. We found a spermatogenesis TCEA1 and TCEA2 expression profile has a unique transcriptional programme, compared with embryogenesis. Moreover, the testis-specific TCEA2 profile correlates with gene transcription, whereas TCEA1 specifically correlates with genes transcribed for Nuclear excision repair (NER) during human spermatogenesis. We also found that the expression activation of RNF20, a TCEA1 inhibitor, leads to expressional TCEA1 reduction, but having no direct impact on TCEA2 expression, implying the potential RNF20-dependent transcriptional switching of TCEA2 in transcriptional regulation during spermatogenesis. Our analysis defined a transcriptional bursting event where transcription-coupled repair (both Base excision repair and Nuclear excision repair) is a major pathway highly expressed in early spermatogenesis, supporting the transcriptional scanning hypothesis of which mutation of transcribed genes is effectively repaired as proposed by Xia B., et al. (2020).


title: how are we stranded here: Quick determination of RNA-Seq strandedness

abstract: Quality control checks are the first step in RNA-Sequencing analysis, which enable the identification of common issues that occur in the sequenced reads. Checks for sequence quality, contamination, and complexity are commonplace, and allow users to implement steps downstream which can account for these issues. Strand-specificity of reads is frequently overlooked and is often unavailable even in published data, yet when unknown or incorrectly specified can have detrimental effects on the reproducibility and accuracy of downstream analyses. We present how_are_we_stranded_here, a Python library that helps to quickly infer strandedness of paired-end RNA-Sequencing data.


title: Divergence in Population Coding for Space between Dorsal and Ventral CA1

abstract:
Molecular, anatomic, and behavioral studies show that the hippocampus is structurally and functionally heterogeneous, with dorsal hippocampus implicated in mnemonic processes and spatial navigation and ventral hippocampus involved in affective processes. By performing electrophysiological recordings of large neuronal populations in dorsal and ventral CA1 in head-fixed mice navigating a virtual environment, we found that this diversity resulted in different strategies for population coding of space. We found that the populations of neurons in dorsal CA1 had a higher dimensionality and showed more complex patterns of activity, translating to more information being encoded, as compared ensembles in vCA1. Furthermore, a pairwise maximum entropy model was better at predicting the structure of global patterns of activity in ventral CA1 as compared to dorsal CA1. Taken together, we uncovered different coding strategies that likely emerge from anatomical and physiological differences along the longitudinal axis of hippocampus and that may, in turn, underpin the divergent ethological roles of dorsal and ventral CA1.

HighlightsO_LINo differences in dCA1 and vCA1 place field size in recordings of neuronal populations in mice navigating a virtual environment
C_LIO_LIdCA1 has higher single-neuron and population-level spatial information compared to vCA1 due to differences in the sparsity of firing.
C_LIO_LIPopulation activity of dCA1 has higher entropy and is higher dimensional than vCA1
C_LIO_LIPairwise maximum entropy models are better at predicting population activity in vCA1 compared to dCA1
C_LI


title: Rapid tissue-specific screening of Wolbachia, Cardinium and Rickettsia in Flies (Diptera: Sepsidae; Drosophilidae)

abstract: Maternally transmitted endosymbionts can negatively influence the reproduction of their arthropod hosts (e.g. male-killing, cytoplasmic incompatibility). However, such infections are rarely assessed in insect models such as Sepsidae or Drosophilidae that are routinely used in sexual selection studies. To detect infection and bacterial localisation in the host, we developed and optimised a tissue-specific multiplex screening protocol for Wolbachia, Cardinium and Rickettsia that can be completed in a day. The robustness of the protocol was tested with the screening of multiple species and populations of flies commonly used in reproductive studies (N=147 flies; n=426 tissues). With triplex PCRs and more effective duplex PCRs, we detected both single and co-infections in most individuals from both families (Drosophilidae | Sepsidae; Single infection: 51.4% | 62.7%; Dual infection: 29.2% | 9.3%; Triple infection: 4.2% | 0%). Surprisingly, we documented the presence of all three reproductive bacteria in 32 wild-caught drosophilids from Singapore. Also, we note that most sepsid populations (19 out of 22) tested positive for Cardinium. We found that the Rickettsia infection was overall low, but it was predominantly detected in the gastrointestinal tract instead of the reproductive tract, suggesting a potential horizontal transmission. Finally, we found that amplicon sequences of equivalent sizes between the three tissues from the same individuals share at least 98.8% identity, which suggests that the same endosymbiont strain inhabits within the whole arthropod. Overall, we believe this protocol is effective in detecting co-infections and understanding the transmission of various reproductive endosymbionts. It can also be used to assess endosymbiont infections in other insects.


title: Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia)

abstract: The iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our results establish a genetic link between iris and plumage color, two traits that were long known by pigeon breeders to co-occur, and demonstrate the importance of gene duplicates in establishing possibilities and constraints in the evolution of color and color pattern among vertebrates.

category: genetics


title: A meta-analysis of effects of feeding seaweed on beef and dairy cattle performance and methane yield

abstract: There has been considerable interest in the use of red seaweed, and in particular Asparagopsis taxiformis, to increase production of cattle and to reduce greenhouse gas emissions. We hypothesized that feeding seaweed or seaweed derived products would increase beef or dairy cattle performance as indicated by average daily gain (ADG), feed efficiency measures, milk production, and milk constituents, and reduce methane emissions. We used meta-analytical methods to evaluate these hypotheses. A comprehensive search of Google Scholar, Pubmed and ISI Web of Science produced 14 experiments from which 23 comparisons of treatment effects could be evaluated. Red seaweed (A. taxiformis) and brown seaweed (Ascophyllum nodosum) were the dominant seaweeds used. There were no effects of treatment on ADG or dry matter intake (DMI). There was an increase in efficiency for feed to gain by 0.41 {+/-} 0.22 kg per kg [standardized mean difference (SMD) = 0.70 {+/-} 0.35; P = 0.001], but not for gain to feed (P = 0.215), although the direction of the change was for improved efficiency. The type of seaweed used was not a significant covariable for ADG and DMI. Milk production was increased with treatment on weighted mean difference (WMD; 1.35 {+/-} 0.44 kg/d; P <0.001); however, the SMD of 0.45 was not significant (P = 0.111). Extremely limited data suggest the possibility of increased percentages of milk fat (P = 0.040) and milk protein (P = 0.001) on DerSimonian and Laird (D&L) WMD evaluation. The limited data available indicate dietary supplementation with seaweed produced a significant and substantial reduction in methane yield by 5.28 {+/-} 3.5 g/kg DMI (P = 0.003) on D&L WMD evaluation and a D&L SMD of -1.70 (P = 0.001); however, there was marked heterogeneity in the results (I2 > 80%). In one comparison, methane yield was reduced by 97%. We conclude that while there was evidence of potential for benefit from seaweed use to improve production and reduce methane yield more in vivo experiments are required to strengthen the evidence of effect and identify sources of heterogeneity in methane response, while practical applications and potential risks are evaluated for seaweed use.

category: scientific communication and education


title: Information flows from hippocampus to cortex during replay of verbal working memory items.

abstract:
The maintenance of items in working memory relies on a widespread network of cortical areas and hippocampus where synchronization between electrophysiological recordings reflects functional coupling.

We investigated the direction of information flow between auditory cortex and hippocampus while participants heard and then mentally replayed strings of letters in working memory by activating their phonological loop. We recorded LFP from the hippocampus, reconstructed beamforming sources of scalp EEG, and - additionally in 3 participants - recorded from subdural cortical electrodes. When analyzing Granger causality, the information flow was from auditory cortex to hippocampus with a peak in the 4-8 Hz range while participants heard the letters. This flow was subsequently reversed during maintenance while participants maintained the letters in memory. The functional interaction between hippocampus and the cortex and the reversal of information flow provide a physiological basis for the encoding of memory items and their active replay during maintenance.


title: Identifying regions in prefrontal cortex related to working memory improvement: a novel meta-analytic method using electric field modeling

abstract:
Altering cortical activity using transcranial direct current stimulation (tDCS) has been shown to improve working memory (WM) performance. Due to large inter-experimental variability in the tDCS montage configuration and strength of induced electric fields, results have been mixed. Here, we present a novel meta-analytic method relating behavioral effect sizes to electric field strength to identify brain regions underlying largest tDCS-induced WM improvement. Simulations on 69 studies targeting left prefrontal cortex showed that tDCS electric field strength in lower dorsolateral prefrontal cortex (Brodmann area 45/47) relates most strongly to improved WM performance. This region explained 7.8% of variance, equaling a medium effect. A similar region was identified when correlating WM performance and electric field strength of right prefrontal tDCS studies (n = 18). Maximum electric field strength of five previously used tDCS configurations were outside of this location. We thus propose a new tDCS montage which maximizes the tDCS electric field strength in that brain region. Our findings can benefit future tDCS studies that aim to affect WM function.

Highlights- We summarize the effect of 87 tDCS studies on working memory performance
- We introduce a new meta-analytic method correlating tDCS electric fields and performance
- tDCS-induced electric fields in lower DLPFC correlate significantly with improved working memory
- The lower DLPFC was not maximally targeted by most tDCS montages and we provide an optimized montage


title: Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

abstract: Body hair is a defining mammalian characteristic, but several mammals, such as whales, naked mole-rats, and humans, have notably less hair than others. To find the genetic basis of reduced hair quantity, we used our evolutionary-rates-based method, RERconverge, to identify coding and noncoding sequences that evolve at significantly different rates in so-called hairless mammals compared to hairy mammals. Using RERconverge, we performed an unbiased, genome-wide scan over 62 mammal species using 19,149 genes and 343,598 conserved noncoding regions to find genetic elements that evolve at significantly different rates in hairless mammals compared to hairy mammals. We show that these rate shifts resulted from relaxation of evolutionary constraint on hair-related sequences in hairless species. In addition to detecting known and potential novel hair-related genes, we also discovered hundreds of putative hair-related regulatory elements. Computational investigation revealed that genes and their associated noncoding regions show different evolutionary patterns and influence different aspects of hair growth and development. Many genes under accelerated evolution are associated with the structure of the hair shaft itself, while evolutionary rate shifts in noncoding regions also included the dermal papilla and matrix regions of the hair follicle that contribute to hair growth and cycling. Genes that were top-ranked for coding sequence acceleration included known hair and skin genes KRT2, KRT35, PKP1, and PTPRM that surprisingly showed no signals of evolutionary rate shifts in nearby noncoding regions. Conversely, accelerated noncoding regions are most strongly enriched near regulatory hair-related genes and microRNAs, such as mir205, ELF3, and FOXC1, that themselves do not show rate shifts in their protein-coding sequences. Such dichotomy highlights the interplay between the evolution of protein sequence and regulatory sequence to contribute to the emergence of a convergent phenotype.


title: Notch signaling via Hey1 and Id2b regulates Müller glia's regenerative response to retinal injury

abstract: Zebrafish Muller glia (MG) respond to retinal injury by suppressing Notch signaling and producing progenitors for retinal repair. A certain threshold of injury-derived signal must be exceeded in order to engage MG in a regenerative response (MGs injury-response threshold). Pan-retinal Notch inhibition expands the zone of injury-responsive MG at the site of focal injury, suggesting that Notch signaling regulates MGs injury-response threshold. We found that Notch signaling enhanced chromatin accessibility and gene expression at a subset of regeneration-associated genes in the uninjured retina. Two Notch effector genes, hey1 and id2b, were identified that reflect bifurcation of the Notch signaling pathway, and differentially regulate MGs injury-response threshold and proliferation of MG-derived progenitors. Furthermore, Notch signaling component gene repression in the injured retina suggests a role for Dll4, Dlb, and Notch3 in regulating Notch signaling in MG and epistasis experiments confirm that the Dll4/Dlb-Notch3-Hey1/Id2b signaling pathway regulates MGs injury-response threshold and proliferation.


title: Notch signaling via Hey1 and Id2b regulates Muller glia's regenerative response to retinal injury


title: Early mechanisms of whisker development: Prdm1 and its regulation in whisker development and evolutionary loss

abstract: Whiskers (vibrissae) are miniaturized organs that are designed for tactile sensing. Extremely conserved among mammals, they underwent a reduction in primates and disappeared in the human lineage. Furthermore, whiskers are highly innervated and their mechanoceptors signal to the primary somatosensory cortex, where a column of neurons called "barrel" represents each of them. This structure, known as barrel cortex, occupies a large portion of the somatosensory cortex of the rodent brain. Strikingly, Prdm1 conditional knockout mice are one of the rare transgenic strains that do not develop whisker hair follicles while still displaying a pelage (Robertson et al. 2007). Here we show that Prdm1 is expressed early on during whisker development, more precisely in clusters of mesenchymal cells before placode formation. Its conditional knockout leads to the loss of expression of Bmp2, Shh, Bmp4, Krt17, Edar, Gli1 though leaving the {beta}-catenin driven first dermal signal intact. Furthermore, we prove that Prdm1 expressing cells not only act as a signaling center but also as a multipotent progenitor population contributing to the formation of the dermal papilla, dermal sheath and pericytes of the vascular sinuses of vibrissae. We confirm by genetic ablation experiments that the absence of motile vibrissae (macro vibrissae) formation reverberates on the organization of nerve wiring in the mystacial pads and organization of the barrel cortex. We prove that Lef1 acts upstream of Prdm1 and identify a potential enhancer (named Leaf) that might be involved in the evolutionary process that led to the progressive reduction of snout size and vibrissae in primates.


title: mTOR-activating mutations in RRAGD cause kidney tubulopathy and cardiomyopathy (KICA) syndrome

abstract:
BackgroundOver the last decaces, advances in genetic techniques have resulted in the identification of rare hereditary disorders of renal magnesium and salt handling. Nevertheless, {+/-}20% of all tubulopathy patients remain without genetic diagnosis. Here, we explore a large multicentric patient cohort with a novel inherited salt-losing tubulopathy, hypomagnesemia and dilated cardiomyopathy (DCM).

MethodsWhole exome and genome sequencings were performed with various subsequent functional analyses of identified RRAGD variants in vitro.

ResultsIn 8 children from unrelated families with a tubulopathy characterized by hypomagnesemia, hypokalemia, salt-wasting, and nephrocalcinosis, we identified heterozygous missense variants in RRAGD that mostly occurred de novo. Six of these patients additionally suffered from DCM requiring heart transplantation in 3 of them. An additional dominant variant in RRAGD was simultaneously identified in eight members of a large family with a similar renal phenotype. RRAGD encodes GTPase RagD mediating amino acid signaling to the mechanistic target of rapamycin complex 1 (mTORC1). RagD expression along the mammalian nephron include the thick ascending limb and the distal convoluted tubule. The identified RRAGD variants were shown to induce a constitutive activation of mTOR signaling in vitro,

ConclusionsOur findings establish a novel disease phenotype combining kidney tubulopathy and cardiomyopathy (KICA) caused by an activation of mTOR signaling suggesting a critical role of Rag GTPase D for renal electrolyte handling and cardiac function.

SIGNIFICANCE STATEMENTHere, we report on heterozygous variants in RRAGD in patients with profound hypomagnesemia, renal salt wasting, nephrocalcinosis, and dilated cardiomyopathy. The identified RagD variants induce a constitutive activation of mTOR signaling in vitro. These findings not only establish a novel monogenic disorder of the kidney tubule, but demonstrate the essential role of mTOR signaling for distal tubular electrolyte handling and cardiac function.


title: Probable omnigenic effect and evolutionary insights of aerobic adaptation allele OsNCED2T on qDTY12.1 effecting grain yield under reproductive stage drought stress in rice

abstract: Yield associated quantitative trait loci (qDTY) under drought stress provides significant advantage for grain yield in rice. The major, stable qDTY12.1 was identified in a mapping population developed from upland cultivars Vandana and Way Rarem. Further, introgression line comprising of qDTY12.1 genomic region was characterized to have multiple genes (NAM, DECUSSATE) regulating the drought tolerance under severe drought stress substantiated through recently proposed omnigenic model for complex traits. Recently, plastid localized NCED2T allele present within the qDTY12.1 genomic region was characterized for conferring aerobic adaptation in lowland varieties. Since, NCED2T is evolutionary fixed in upland cultivars and Vandana was found to have the favorable allele of NCED2T, we hypothesized that this favorable allele might confer omnigenic effect on qDTY12.1 genes. Our evolutionary analysis using non synonymous SNPs present in genes namely NCED, NAM, and DECUSSATE and qDTY12.1 genomic regions showed specific grouping of Vandana with upland cultivars only for NCED gene and its adjoining genomic regions. However, non synonymous SNPs in NAM and DECUSSATE genes and its adjoining genomic regions of drought tolerant varieties were closely related and grouped together in the phylogenetic analysis. Moreover, ecotype specific differentiation and greater nucleotide difference with wild relatives was also observed for DECUSSATE gene in rice. This finding indicates differential evolution of qDTY12.1 regions for upland and drought tolerance and omnigenic effect of NCED2T gene in qDTY12.1. Further, we propose a breeding model for enhancing genetic gain for yield under severe drought stress by incorporation of NCEDT, qDTY12.1 and other drought tolerant QTLs for membrane stability in rice.


title: Interferons Reshape the 3D Conformation and Accessibility of Macrophage Chromatin

abstract: Engagement of macrophages in innate immune responses is directed and enhanced by type I and type II interferons. An essential component of IFN activity is the use of JAK-STAT signal transduction for the transcriptional control of interferon-stimulated genes (ISG). Here, we study the immediate early nuclear response to type I IFN and IFN-{gamma} in murine macrophages. Despite their distinct immunological activities, both IFN types triggered highly overlapping epigenomic and transcriptional changes. These changes included a rapid rearrangement of the 3D chromatin organization and an increase of DNA accessibility at ISG loci. ISGF3, the major transcriptional regulator of ISG, controlled homeostatic as well as induced-state DNA accessibility at a subset of ISG. Increases in DNA accessibility correlated with the appearance of activating histone marks at surrounding nucleosomes. Collectively our data emphasize changes in the three-dimensional nuclear space and epigenome as an important facet of transcriptional control by the IFN-induced JAK-STAT pathway.


title: Alpha satellite insertions and the evolutionary landscape of centromeres

abstract: Human centromeres are mainly composed of alpha satellite DNA hierarchically organized as higher-order repeats (HORs). Alpha satellite dynamics is shown by sequence homogenization in centromeric arrays and by its transfer to other centromeric locations, for example during the maturation of new centromeres. We identified during prenatal aneuploidy diagnosis by FISH a de novo insertion of alpha satellite DNA from the centromere of chromosome 18 (D18Z1) into cytoband 15q26. Although bound by CENP-B, this locus did not acquire centromeric functionality as demonstrated by lack of constriction and absence of CENP-A binding. The insertion was associated with a 2.8 kbp deletion and likely occurred in the paternal germline. The site was enriched in long terminal repeats (LTRs) and located ~10 Mbp from the location where a centromere was ancestrally seeded and became inactive in the common ancestor of humans and apes 20-25 million years ago. Long read mapping to the T2T-CHM13 human genome assembly revealed that the insertion derives from a specific region of chromosome 18 centromeric 12-mer HOR array in which the monomer size follows a regular pattern. The rearrangement did not directly disrupt any gene or predicted regulatory element and did not alter the methylation status of the surrounding region, consistent with the absence of phenotypic consequences in the carrier. This case demonstrates a likely rare but new class of structural variation that we name  alpha satellite insertion. It also expands our knowledge on alphoid DNA dynamics and conveys the possibility that alphoid arrays can relocate near vestigial centromeric sites.


title: Alpha satellite insertion close to an ancestral centromeric region


title: Pathogenic MAST3 variants in the STK domain are associated with epilepsy

abstract:
ObjectiveThe MAST family of microtubule-associated serine-threonine kinases (STK) have distinct expression patterns in the developing and mature human and mouse brain. To date, only MAST1 has been associated with neurological disease, with de novo variants in individuals with a neurodevelopmental disorder, including a mega corpus callosum.

MethodsUsing exome sequencing we identify MAST3 missense variants in individuals with epilepsy. We also assess the effect of these variants on the ability of MAST3 to phosphorylate the target gene product ARPP-16 in HEK293T cells.

ResultsWe identify de novo missense variants in the STK domain in 11 individuals, including two recurrent variants p.G510S (n=5) and p.G515S (n=3). All 11 individuals had Developmental and epileptic encephalopathy, with 8 having normal development prior to seizure onset at < 2 years of age. All patients developed multiple seizures types, while 9/11 had seizures triggered by fever and 9/11 had drug-resistant seizures. In vitro analysis of HEK293T cells transfected with MAST3 cDNA carrying a subset of these patient-specific missense variants demonstrated variable but generally lower expression, with concomitant increased phosphorylation of the MAST3 target, ARPP-16, compared to wildtype. These findings suggest the patient-specific variants may confer MAST3 gain-of-function. Moreover, single-nuclei RNA sequencing and immunohistochemistry shows that MAST3 expression is restricted to excitatory neurons in the cortex late in prenatal development and postnatally.

InterpretationIn summary, we describe MAST3 as a novel epilepsy-associated gene with a potential gain-of-function pathogenic mechanism that may be primarily restricted to excitatory neurons in the cortex.


title: Genomic Prediction in Family Bulks Using Different Traits and Cross-Validations in Pine

abstract: Genomic prediction (GP) integrates statistical, genomic and computational tools to improve the estimation of breeding values and increase genetic gain. Due to the broad diversity in biology, breeding scheme, propagation method, and unit of selection, no universal GP approach can be applied in all crops. In a genome-wide family prediction (GWFP) approach, the family bulk is the basic unit of selection. We tested GWFP in two loblolly pine (Pinus taeda L.) datasets: a breeding population composed of 63 full-sib families (5-20 individuals per family), and a simulated population with the same pedigree structure. In both populations, phenotypic and genomic data was pooled at the family level in silico. Marker effects were estimated to compute genomic estimated breeding values at the individual (GEBV) and family (GWFP) levels. Less than six individuals per family produced inaccurate estimates of family phenotypic performance and allele frequency. Tested across different scenarios, GWFP predictive ability was higher than those for GEBV in both populations. Validation sets composed of families with similar phenotypic mean and variance as the training population yielded predictions consistently higher and more accurate than other validation sets. Results revealed potential for applying GWFP in breeding programs whose selection unit are family bulks, and for systems where family can serve as training sets. The GWFP approach is well suited for crops that are routinely genotyped and phenotyped at the plot-level, but it can be extended to other breeding programs. Higher predictive ability obtained with GWFP would motivate the application of GP in these situations.


title: Interaction of micropatterned topographical and biochemical cues to direct neurite growth from spiral ganglion neurons

abstract: Functional outcomes with neural prosthetic devices, such as cochlear implants, are limited in part due to physical separation between the stimulating elements and the neurons they stimulate. One strategy to close this gap aims to precisely guide neurite regeneration to position the neurites in closer proximity to electrode arrays. Here, we explore the ability of micropatterned biochemical and topographic guidance cues, singly and in combination, to direct the growth of spiral ganglion neuron (SGN) neurites, the neurons targeted by cochlear implants. Photopolymerization of methacrylate monomers was used to form unidirectional topographical features of ridges and grooves in addition to multidirectional patterns with 90{degrees} angle turns. Microcontact printing was also used to create similar uni- and multi-directional patterns of peptides on polymer surfaces. Biochemical cues included peptides that facilitate (laminin, LN) or repel (EphA4-Fc) neurite growth. On flat surfaces, SGN neurites preferentially grew on LN-coated stripes and avoided EphA4-Fc-coated stripes. LN or EphA4-Fc was selectively adsorbed onto the ridges or grooves to test the neurite response to a combination of topographical and biochemical cues. Coating the ridges with EphA4-Fc and grooves with LN lead to enhanced SGN alignment to topographical patterns. Conversely, EphA4-Fc coating on the grooves or LN coating on the ridges tended to disrupt alignment to topographical patterns. SGN neurites respond to combinations of topographical and biochemical cues and surface patterning that leverages both cues enhance guided neurite growth.

category: bioengineering


title: Sequence features around cleavage sites are highly conserved among different species and a critical determinant for RNA cleavage position across eukaryotes

abstract: RNA degradation is critical for control of gene expression, and endonucleolytic cleavage- dependent RNA degradation is conserved among eukaryotes. Some cleavage sites are secondarily capped in the cytoplasm and identified using the CAGE method. Although uncapped cleavage sites are widespread in eukaryotes, comparatively little information has been obtained about these sites using CAGE-based degradome analysis. Previously, we developed the truncated RNA-end sequencing (TREseq) method in plant species and used it to acquire comprehensive information about uncapped cleavage sites; we observed G-rich sequences near cleavage sites. However, it remains unclear whether this finding is general to other eukaryotes. In this study, we conducted TREseq analyses in fruit flies (Drosophila melanogaster) and budding yeast (Saccharomyces cerevisiae). The results revealed specific sequence features related to RNA cleavage in D. melanogaster and S. cerevisiae that were similar to sequence patterns in Arabidopsis thaliana. Although previous studies suggest that ribosome movements are important for determining cleavage position, feature selection using a random forest classifier showed that sequences around cleavage sites were major determinant for cleaved or uncleaved sites. Together, our results suggest that sequence features around cleavage sites are critical for determining cleavage position, and that sequence-specific endonucleolytic cleavage-dependent RNA degradation is highly conserved across eukaryotes.


title: On the generality and cognitive basis of base-rate neglect

abstract: Base rate neglect refers to peoples apparent tendency to underweight or even ignore base rate information when estimating posterior probabilities for events, such as the probability that a person with a positive cancer-test outcome actually does have cancer. While often replicated, almost all evidence for the phenomenon comes from studies that used problems with extremely low base rates, high hit rates, and low false alarm rates. It is currently unclear whether the effect generalizes to reasoning problems outside this "corner" of the entire problem space. Another limitation of previous studies is that they have focused on describing empirical patterns of the effect at the group level and not so much on the underlying strategies and individual differences. Here, we address these two limitations by testing participants on a broader problem space and modelling their responses at a single-participant level. We find that the empirical patterns that have served as evidence for base-rate neglect generalize to a larger problem space, albeit with large individual differences in the extent with which participants "neglect" base rates. In particular, we find a bi-modal distribution consisting of one group of participants who almost entirely ignore the base rate and another group who almost entirely account for it. This heterogeneity is reflected in the cognitive modeling results: participants in the former group were best captured by a linear-additive model, while participants in the latter group were best captured by a Bayesian model. We find little evidence for heuristic models. Altogether, these results suggest that the effect known as "base-rate neglect" generalizes to a large set of reasoning problems, but varies largely across participants and may need a reinterpretation in terms of the underlying cognitive mechanisms.

category: animal behavior and cognition


title: Osteoarthritis Early-, Mid- and Late-Stage Progression in the Rat Medial Meniscus Transection Model

abstract: Osteoarthritis is a degenerative disease of synovial joints affecting all tissues, including the articular cartilage and underlying subchondral bone. Osteoarthritis animal models can recapitulate aspects of human disease progression and are commonly used to test the development of drugs, biomaterials, and cell therapies for treatment. The rat medial meniscus transection (MMT) model is a surgically induced post-traumatic osteoarthritis model and is one of the most commonly used models for therapeutic development; however, it is typically used to evaluate the efficacy of therapies to prevent disease development rather than testing the treatment of disease progression in already established disease. We describe herein, the qualitative and quantitative changes to articular cartilage, subchondral bone, and formation of osteophytes in rats at early-(3-weeks post-surgery), mid-(6-weeks post-surgery) and late-(12-weeks post-surgery) stages of osteoarthritis progression. Tibiae of MMT-operated animals showed loss of proteoglycan and fibrillation formation on articular cartilage surfaces as early as 3-weeks post-surgery. Using a contrast-enhanced CT technique, quantitative, 3-dimensional analysis of the tibiae showed that the articular cartilage initially thickened at 3- and 6-weeks post-surgery and then decreased at 12-weeks post-surgery. This decrease in cartilage thickness corresponded with increased lesions in the articular cartilage, including fully degraded surfaces down to the subchondral bone layer. In this rat MMT model, subchondral bone thickening was significant at 6-weeks post-surgery and seem to follow cartilage damage. Osteophytes were found at 3-weeks post-surgery, which coincided with articular cartilage degradation. Cartilaginous osteophytes preceded mineralization suggesting that these marginal tissue growths most likely occurred through endochondral ossification. The use of the rat MMT model has predominantly been used out to 3-weeks, and most studies determine the effect of therapies to delay or prevent the onset of osteoarthritis. We provide evidence that an extension of the rat MMT model out to 6 and 12 weeks resembled more severe phenotypes of human osteoarthritis. The mid- to late-stages of rat MMT model can be used to evaluate the therapeutic efficacy of novel treatments to treat the progression of established disease -- since patients typically present in the clinic when the disease is established and becomes symptomatic, thus evaluating the efficacy of new treatments at the late stage will be important for eventual clinical translation.

category: pathology


title: Systems-level network modeling deciphers the master regulators of phenotypic plasticity and heterogeneity in melanoma

abstract: Phenotypic (i.e. non-genetic) heterogeneity in melanoma drives dedifferentiation, recalcitrance to targeted therapy and immunotherapy, and consequent tumor relapse and metastasis. Various markers or regulators associated with distinct phenotypes in melanoma have been identified, but, how does a network of interactions among these regulators give rise to multiple "attractor" states and phenotypic switching remains elusive. Here, we inferred a network of transcription factors (TFs) that act as master regulators for gene signatures of diverse cell-states in melanoma. Dynamical simulations of this network predicted how this network can settle into different "attractors" (TF expression patterns), suggesting that TF network dynamics drives the emergence of phenotypic heterogeneity. These simulations can recapitulate major phenotypes observed in melanoma and explain de-differentiation trajectory observed upon BRAF inhibition. Our systems-level modeling framework offers a platform to understand trajectories of phenotypic transitions in the landscape of a regulatory TF network and identify novel therapeutic strategies targeting melanoma plasticity.

category: systems biology


title: Bidirectional modulation of pain-related behaviors in the zona incerta

abstract: Central amygdala neurons expressing protein kinase C-delta (CeA-PKC{delta}) are sensitized following nerve injury and promote pain-related responses in mice. The neural circuits underlying modulation of pain-related behaviors by CeA-PKC{delta} neurons, however, remain unknown. In this study, we identified a functional monosynaptic inhibitory neural circuit that originates in CeA-PKC{delta} neurons and terminates in the ventral region of the zona incerta (ZI), a subthalamic structure previously linked to pain processing. Behavioral experiments further show that chemogenetic inhibition of GABAergic ZI neurons is sufficient to induce bilateral hypersensitivity in uninjured mice as well as contralateral hypersensitivity after nerve injury. In contrast, chemogenetic activation of GABAergic ZI neurons reverses nerve injury-induced hypersensitivity, demonstrating that silencing of the ZI is required for injury-induced behavioral hypersensitivity. Our results identify a previously unrecognized inhibitory efferent pathway from CeA-PKC{delta} neurons to the ZI and demonstrate that ZI-GABAergic neurons can bidirectionally modulate pain-related behaviors in mice.

category: neuroscience


title: Single-trial-based Temporal Principal Component Analysis on Extracting Event-related Potentials of Interest for an Individual Subject

abstract: Temporal principal component analysis (t-PCA) has been widely used to extract event-related potentials (ERPs) at the group level of multiple subjects ERP data. The t-PCA is, however, poorly employed to isolate ERPs from single-trial data of an individual subject. Additionally, the effects of varied trial numbers on the yields of t-PCA have not been systematically examined. To fill both gaps, in an emotional experiment (22 subjects), we use t-PCA and Promax rotation to extract interesting P2/N2 from single-trial data of each subject with consecutive increasingly trial numbers (from 10 to 42) and all trials, respectively. Besides, time-domain analysis and other two group t-PCA strategies (trial-averaged and single-trial) are also employed to isolate ERPs of interest from all subjects. The results indicate that the proposed technique produces the internal consistent measure of N2 from few trials (i.e., 19) as from all trials compared with the other three approaches (more than 30 trials). As for P2, all approaches yield internal-subject consistent effect after approximately 33 trials are included in the average, but Cronbachs alpha values for the proposed technique are higher than the other two group PCA strategies over varied trials. Combined, the yields provide evidence that the proposed approach may efficiently temporally filter the data to extract more reliable and stable ERPs for an individual subject.


title: Bayesian Multivariate Growth Mixture Modeling of Longitudinal Data: An Application to Alzheimer's Disease Study

abstract: Alzheimers disease (AD) studies often collect longitudinal biomarker measures of multiple cohorts at different stages of disease and follow these biomarkers with a relatively short period of time. The heterogeneity of the longitudinal patterns of biomarkers can be ubiquitous across both individual trajectories and cognitive domains. We propose a flexible Bayesian multivariate growth mixture model to identify distinct longitudinal patterns of data from the Alzheimers Disease Neuroimaging Initiative (ADNI) study. A Gibbs sampling is implemented for achieving the Bayesian inference. We perform a simulation study to demonstrate the adequate performance of our proposed approach and apply the model to identify three latent cognitive decline patterns among patients from the ADNI study.


title: Forced swim stress dynamically alters neural activity and bi-directionally modulates NMDA receptors in the prefrontal cortex

abstract: Repeated exposure to stress results in progressively divergent effects on cognitive behaviors that are dependent on the integrity of networks in the medial prefrontal cortex (mPFC). To investigate molecular mechanisms responsive to variable repetition of mild stress, we measured persistent neural activity, in vitro, from mPFC slices in mice that had been repetitively exposed to 10 minutes of forced swim stress for 3-10 days. 3-day short-term stress facilitated persistent neural activity by increasing event duration while 10 days suppressed event duration and amplitude. These dynamic changes were accompanied by a similar bi-directional modulation of the NMDA/AMPA receptor current ratio, an important synaptic mechanism for sustaining the persistency of neural activity. Specifically, short-term stress led to potentiated NMDA currents with slower decay kinetics, and extended stress produced smaller currents with faster decay. The inhibitory action of ifenprodil, a specific blocker of NR2B-containing NMDA receptors, was more effective in NMDA current suppression following light stress and less effective after longer stress compared to naive controls. Persistent activity and glutamate receptor balance in the neocortex have been linked to working memory and impulse control. Therefore, these results could provide insight for generating therapeutic strategies to prevent or reverse stress-induced cognitive deficits.


title: The dynamics of decision making and action during active sampling

abstract: Embodied Cognition Theories (ECTs) propose that the decision process continues to unfold during the execution of choice actions, and its outcome manifests itself in these actions. Scenarios where actions not only express choice but also help sample information can provide a valuable test of this framework. Remarkably almost no studies so far have addressed this scenario. Here, we present a study testing just this paradigmatic situation with humans. On each trial, subjects categorized a central object image, blurred to different extents (2AFC task) by moving a cursor toward the left or right of the display. Upward cursor movements, orthogonal with respect to choice options, reduced the image blur and could be freely used to actively sample information. Thus, actions for decision and actions for sampling were made orthogonal to each other. We analyzed response trajectories to test a central prediction of ECTs; whether information-sampling movements co-occurred with the ongoing decision process. Trajectory data revealed were bimodally distributed, with one kind being direct towards one response option (non-sampling trials), and the other kind containing an initial upward component before veering off towards an option (sampling trials). This implies that there was an initial decision at the early stage of a trial whether to sample information or not. Importantly, the trajectories in sampling trials were not purely upward, but rather had a significant horizontal deviation that was visible early on in the movement. This result suggests that movements to sample information exhibit an online interaction with the decision process. The finding that decision processes interact with actions to sample information supports the ECT under novel, ecologically relevant constrains.


title: A rapid and efficient learning rule for biological neural circuits

abstract: The dominant view in neuroscience is that changes in synaptic weights underlie learning. It is unclear, however, how the brain is able to determine which synapses should change, and by how much. This uncertainty stands in sharp contrast to deep learning, where changes in weights are explicitly engineered to optimize performance. However, the main tool for doing that, backpropagation, is not biologically plausible, and networks trained with this rule tend to forget old tasks when learning new ones. Here we introduce the Dendritic Gated Network (DGN), a variant of the Gated Linear Network [1, 2], which offers a biologically plausible alternative to backpropagation. DGNs combine dendritic "gating" (whereby interneurons target dendrites to shape neuronal response) with local learning rules to yield provably efficient performance. They are significantly more data efficient than conventional artificial networks and are highly resistant to forgetting, and we show that they perform well on a variety of tasks, in some cases better than backpropagation. The DGN bears similarities to the cerebellum, where there is evidence for shaping of Purkinje cell responses by interneurons. It also makes several experimental predictions, one of which we validate with in vivo cerebellar imaging of mice performing a motor task.


title: Human primary visual cortex shows larger population receptive fields for binocular disparity-defined stimuli

abstract: 1The visual perception of 3D depth is underpinned by the brains ability to combine signals from the left and right eyes to produce a neural representation of binocular disparity for perception and behavior. Electrophysiological studies of binocular disparity over the past two decades have investigated the computational role of neurons in area V1 for binocular combination, while more recent neuroimaging investigations have focused on identifying specific roles for different extrastriate visual areas in depth perception. Here we investigate the population receptive field properties of neural responses to binocular information in striate and extrastriate cortical visual areas using ultra-high field fMRI. We measured BOLD fMRI responses while participants viewed retinotopic-mapping stimuli defined by different visual properties: contrast, luminance, motion, correlated and anti-correlated stereoscopic disparity. By fitting each condition with a population receptive field model, we compared quantitatively the size of the population receptive field for disparity-specific stimulation. We found larger population receptive fields for disparity compared with contrast and luminance in area V1, the first stage of binocular combination, which likely reflects the binocular integration zone, an interpretation supported by modelling of the binocular energy model. A similar pattern was found in region LOC, where it may reflect the role of disparity as a cue for 3D shape. These findings provide insight into the binocular receptive field properties underlying processing for human stereoscopic vision.


title: Paradoxical relationship between speed and accuracy in olfactory figure-background segregation

abstract: In natural settings, many stimuli impinge on our sensory organs simultaneously. Parsing these sensory stimuli into perceptual objects is a fundamental task faced by all sensory systems. Similar to other sensory modalities, increased odor backgrounds decrease the detectability of target odors by the olfactory system. The mechanisms by which background odors interfere with the detection and identification of target odors are unknown. Here we utilized the framework of the Drift Diffusion Model (DDM) to consider possible interference mechanisms in an odor detection task. We consider effects of background odors on both signal and noise in the decision-making dynamics, and show that these produce different predictions about decision accuracy and speed. To test these predictions, we trained mice to detect target odors that are embedded in random background mixtures in a two-alternative choice task. Trial duration was independent of behavioral reaction times to avoid motivating rapid responses. We found that the behavioral data is most consistent with background odors acting by adding noise to the decision-making dynamics. The added noise decreases the correct rate, but also decreases decision times, thereby creating a paradoxical relationship between speed and accuracy of target detection, where mice make faster and less accurate decisions in the presence of background odors.


title: Transient Kinetic Proofreading

abstract: We propose a new stochastic model for understanding the transient kinetic proofreading mechanism in a T-cell. Our model indicates that a stochastic version of absolute ligand discrimination is a consequence of the finite number of receptors on the cell surface; thus, pointing to receptor number control as being critical to T-cell activation. We propose four different metrics to characterize the performance of kinetic proofreading mechanisms. We explore the numerical experiments that explore the trade-offs between speed, specificity, sensitivity, and robustness of T-cell activation as a function of the model parameters. We also consider the impact of receptor clustering on these trade-offs.


title: A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk

abstract: Wolbachia are the most widespread bacterial endosymbionts in animals. Within arthropods, these maternally-transmitted bacteria can selfishly hijack host reproductive processes to increase the relative fitness of their transmitting females. One such form of reproductive parasitism called male killing, or the selective killing of infected males, is recapitulated to degrees by transgenic expression of the WO-mediated killing (wmk) gene. Here, we characterize the genotype-phenotype landscape of wmk-induced male killing in D. melanogaster using transgenic expression. While phylogenetically distant wmk homologs induce no sex-ratio bias, closely-related homologs exhibit complex phenotypes spanning no death, male death, or death of all hosts. We demonstrate that alternative start codons, synonymous codons, and notably a single synonymous nucleotide in wmk can ablate killing. These findings reveal previously unrecognized features of transgenic wmk-induced killing and establish new hypotheses for the impacts of post-transcriptional processes in male killing variation. We conclude that synonymous sequence changes are not necessarily silent in nested endosymbiotic interactions with life-or-death consequences.

category: genomics


title: MR-APSS: a unified approach to Mendelian Randomization accounting for pleiotropy and sample structure using genome-wide summary statistics

abstract: Mendelian Randomization (MR) is a valuable tool for inferring causal relationships among a wide range of traits using summary statistics from genome-wide association studies (GWASs). Existing summary-level MR methods often rely on strong assumptions, resulting in many false positive findings. To relax MR assumptions, ongoing research has been primarily focused on accounting for confounding due to pleiotropy. Here we show that sample structure is another major confounding factor, including population stratification, cryptic relatedness, and sample overlap. We propose a unified MR approach, MR-APSS, which (i) accounts for pleiotropy and sample structure simultaneously by leveraging genome-wide information; and (ii) allows to include more genetic variants with moderate effects as instrument variables (IVs) to improve statistical power without inflating type I errors. We first evaluated MR-APSS using comprehensive simulations and negative controls, and then applied MR-APSS to study the causal relationships among a collection of diverse complex traits. The results suggest that MR-APSS can better identify plausible causal relationships with high reliability. In particular, MR-APSS can perform well for highly polygenic traits, where the IV strengths tend to be relatively weak and existing summary-level MR methods for causal inference are vulnerable to confounding effects.


title: Mendelian Randomization for causal inference accounting for pleiotropy and sample structure using genome-wide summary statistics


title: Single Cell Transcriptomic Landscape of Diabetic Foot Ulcers

abstract: To understand the diabetic wound healing microenvironment, we profiled 174,962 single cells from foot, forearm, and PBMCs using single-cell RNA sequencing (scRNASeq) approach. Our analysis shows enrichment of a unique population of fibroblasts overexpressing MMP1, MMP3, MMP11, HIF1A, CHI3L1, and TNFAIP6 genes and M1 macrophage polarization in the DFU patients with healing wounds. Further, scRNASeq of spatially separated samples from same patient and spatial transcriptomics (ST) revealed preferential localization of these healing associated fibroblasts toward deep wound/ulcer bed as compared to wound edge or non-wounded skin. ST also validated our findings of higher enrichment of M1 macrophages in healers and M2 macrophages in non-healers. Our analysis provides deep insights into the wound healing microenvironment, identifying cell types that could be critical in promoting DFU healing, and may inform novel therapeutic approaches for DFU treatment.


title: 3D soft hydrogels induce human mesenchymal stem cells "deep" quiescence

abstract:
Human mesenchymal stem/stromal cells (hMSCs) present a great opportunity for tissue regeneration due to their multipotent capacity. However, when cultured on 2D tissue culture polystyrene (TCPS) plates, hMSCs lose their differentiation capacity and clinical potential. It has been reported that cells need a more physiologically relevant micro-environment that allows them to maintain their phenotype. Here, we have developed a 3D alginate hydrogel functionalized with the Arg-Gly-Asp (RGD) sequence and having low mechanical stiffness that mimics the mechanical properties (>5 KPa) of bone marrow. hMSCs cultured in these hydrogels appeared to be halted in G1 phase of the cell cycle and to be non-proliferative, as shown by flow cytometry and 5-Ethynyl-2-deoxyuridine (EdU) staining, respectively. Their quiescent state was characterized by an upregulation of enhancer of zeste homolog 1 (EZH1) at the gene level, forkhead box O3 (FoxO3) and cyclin-dependent kinase inhibitor 1B (p27) at the gene and protein levels compared to hMSCs grown in 2D TCPS. Comparative studies in 3D hydrogels of alginate-RGD presenting higher concentration of the peptide or in collagen hydrogels revealed that independently of the concentration of RGD or the chemistry of the adhesion motives, hMSCs cultured in 3D presented a similar phenotype.

This quiescent phenotype was exclusive of 3D cultures. In 2D, even when cells were starved of fetal bovine serum (FBS) and became also non-proliferative, the expression of these markers was not observed. We propose that this difference may be the result of mammalian target of rapamycin complex 1 (mTORC1) being downregulated in hMSCs cultured in 3D hydrogels, which induces cells to be in "deep" quiescence and be kept alive ex vivo for a long period of time. Our results represent a step forward towards understanding hMSCs quiescence and its molecular pathways, providing more insight for hMSCs cell therapies.


title: The mutational signatures of formalin fixation on the human genome

abstract:
BackgroundFormalin fixation and paraffin embedding (FFPE) of patient material remains standard practice in clinical pathology labs around the world. Clinical archives of patient material near-exclusively consist of FFPE blocks. The ability to perform high quality genome sequencing on FFPE-derived DNA would accelerate a broad spectrum of medical research. However, formalin is a recognised mutagen and sequencing of DNA derived from FFPE material is known to be riddled with artefactual mutations.

ResultsHere we derive genome-wide mutational signatures caused by formalin fixation, and provide a computational method to correct mutational profiles for these formalin-induced artefacts. We show that the FFPE-signature is dominated by C>T transitions caused by cytosine deamination, and has very high similarity to COSMIC signature SBS30 (base excision repair deficiency due to inactivation mutations in NTHL1). Further, we demonstrate that chemical repair of formalin-induced DNA lesions, a process that is routinely performed as part of sequencing library preparation, leads to a signature highly similar to COSMIC signature SBS1 (spontaneous deamination of methylated cytosine). Next, we design FFPEsig, a computational method to remove the formalin-induced artefacts from mutational counts. We prove the efficacy of this method by generating synthetic FFPE samples using 2,780 cancer genomes from the Pan-Cancer Analysis of Whole Genome (PCAWG) project, and via analysis of FFPE-derived genome sequencing data from colorectal cancers.

ConclusionsFormalin fixation leaves a predictable mutational footprint across the genome. The application of our FFPEsig software corrects the mutational profile for the influence of formalin, enabling robust mutational signature analysis in FFPE-derived patient material.

category: bioinformatics


title: Exponentiating pixel values for data augmentation to improve deep learning image classification in chest X-rays

abstract: A previous study reported that exponentiating pixel values of a medical can be used for DA through enhancing contrast of the image. However, it is still unclear whether exponentiating pixel values of CXR images can be used for DA with CNN. The aim of this study is to evaluate the effectiveness of exponentiating pixel values for DA using CNN in the task of classifying normal and abnormal CXR images. In constructing an image for DA, each pixel value of the original images was exponentiated by the exponent ranging from 1 to 10, incrementing by 0.5. We call this image as exponentiated image (EI). For each exponent (1.0, 1.5, 1.5, 2.0,..., 10.0), the CNN model was trained using the original training dataset and EI for 40 epochs. Test accuracy was calculated at the end of each epoch using the test dataset. The maximum test accuracy (MTA) among the 40 test accuracies was saved for statistical analysis. This process was repeated 50 times for each exponent (1.0, 1.5, 1.5, 2.0,..., 10.0). The mean MTA for each exponent (1.5, 1.5, 2.0,..., 10.0) was compared using Students t-test, to that of 1.0. The mean MTA when the exponent was 1.0 was 0.749 (reference). The mean MTA was higher than the reference at exponent values 4.5(MTA=0.762, p-value=0.014), 5.0(0.762, 0.019), 5.5(0.772, 2.9 x 10-5), and 6.5(0.763, 0.010). Exponentiating pixel values can be used for DA with CNN to classify normal and abnormal CXR images.