title: HelR is a helicase-like protein that protects RNA polymerase from rifamycin antibiotics.

abstract: Rifamycin antibiotics such as rifampin are widely used for the management of tuberculosis and other bacterial infections. These drugs inhibit prokaryotic RNA polymerase (RNAP) by preventing elongation of mRNA resulting in cell death. Rifamycin resistance in the clinic is manifested primarily through amino acid substitutions in RNAP that decrease target affinity for the antibiotics. In contrast, environmental bacteria possess a wide variety of highly specific rifamycin enzyme-mediated resistance mechanisms that modify and inactivate the antibiotics by glycosylation, phosphorylation, ADP-ribosylation, or hydroxylation. Expression of rifamycin resistance is controlled by a common 19bp cis-acting rifamycin associated element (RAE) upstream of inactivating genes. Guided by the presence of RAE sequences, we identify an unprecedented ATP-dependent mechanism of rifamycin resistance that acts not by antibiotic inactivation but by protecting the RNAP target. We show that Streptomyces venezuelae encodes a helicase-like protein, HelR, which confers broad spectrum rifamycin resistance. Furthermore, HelR is essential for promoting rifamycin tolerance at inhibitory concentrations, enabling bacterial evasion of the toxic properties of these antibiotics. HelR forms a complex with RNAP in vivo and rescues transcription inhibition by rifampin in vitro. We synthesized a rifamycin photoprobe and demonstrated that HelR directly displaces rifamycins from RNAP. HelR-encoding genes associated with RAEs are broadly distributed in actinobacteria, including many opportunistic Mycobacterial pathogens, which cannot currently be treated with rifamycins. This first report of an RNAP protection protein conferring antibiotic resistance and offers guidance for developing new rifamycin antibiotics that can avoid this mechanism.


title: Binding mechanism underlying FIH-1 suppression caused by the N-terminal disordered region of Mint3

abstract: Mint3 is known to enhance aerobic ATP production, known as the Warburg effect, by binding to FIH-1. Since this effect is considered to be beneficial for cancer cells, the interaction is a promising target for cancer therapy. However, previous research has suggested that the interacting region of Mint3 with FIH-1 is intrinsically disordered, which makes investigation of this interaction challenging. Therefore, we adopted a physicochemical approach that combined thermodynamic studies with structural analyses in solution, to clarify the binding mechanism. First, using a combination of CD, NMR, and hydrogen/deuterium exchange mass spectrometry (HDX-MS), we confirmed that the N-terminal half, which is the interacting part of Mint3, is mostly disordered. Next, using isothermal titration calorimetry (ITC), we revealed that the interaction of Mint3 and FIH-1 produces an enormous change in enthalpy and entropy. The profile is consistent with the model that the flexibility of disordered Mint3 is drastically reduced upon binding to FIH-1. Moreover, we performed a series of ITC experiments with several types of truncated Mint3s, an effective approach since the interacting part of Mint3 is disordered, and identified 78-88 as a novel core site for binding to FIH-1. The truncation study of Mint3 also revealed the thermodynamic contribution of each part to the interaction, where one contributes to the affinity ({Delta}G), while the other only affects enthalpy ({Delta}H), by forming non-covalent bonds. This insight can serve as a foothold for further investigation of IDRs and drug development for cancer therapy.

category: biochemistry


title: Microbiome differential abundance methods produce disturbingly different results across 38 datasets

abstract: Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods have been applied for this purpose, which are largely used interchangeably in the literature. Although it has been observed that these tools can produce different results, there have been very few large-scale comparisons to describe the scale and significance of these differences. In addition, it is challenging for microbiome researchers to know which differential abundance tools are appropriate for their study and how these tools compare to one another. Here, we have investigated these questions by analyzing 38 16S rRNA gene datasets with two sample groups for differential abundance testing. We tested for differences in amplicon sequence variants and operational taxonomic units (referred to as ASVs for simplicity) between these groups with 14 commonly used differential abundance tools. Our findings confirmed that these tools identified drastically different numbers and sets of significant ASVs, however, for many tools the number of features identified correlated with aspects of the tested study data, such as sample size, sequencing depth, and effect size of community differences. We also found that the ASVs identified by each method were dependent on whether the abundance tables were prevalence-filtered before testing. ALDEx2 and ANCOM produced the most consistent results across studies and agreed best with the intersect of results from different approaches. In contrast, several methods, such as LEfSe, limma voom, and edgeR, produced inconsistent results and in some cases were unable to control the false discovery rate. In addition to these observations, we were unable to find supporting evidence for a recent recommendation that limma voom, corncob, and DESeq2 are more reliable overall compared with other methods. Although ALDEx2 and ANCOM are two promising conservative methods, we argue that those researchers requiring more sensitive methods should use a consensus approach based on multiple differential abundance methods to help ensure robust biological interpretations.

category: bioinformatics


title: Discovery of novel ID2 antagonists from pharmacophore-based virtual screening as potential therapeutics for glioma

abstract:
Glioma, especially the most aggressive type glioblastoma multiforme, is one of the central nervous system malignant cancer with a poor prognosis. Traditional treatments are mainly surgery combined with radiotherapy and chemotherapy, which is still not satisfactory. Therefore, it is of great clinical significance to find new therapeutic agents. Served as an inhibitor of differentiation, protein ID2 (inhibitor of DNA binding 2) plays an important role in neurogenesis, neovascularization and malignant development of gliomas. It has been shown that ID2 affects the malignant progression of gliomas through different mechanisms. In this study, a pharmacophore-based virtual screening was carried out and 16 hit compounds were purchased for pharmacological evaluations on their ID2 inhibitory activities. Based on the cytotoxicity of these small-molecule compounds, two compounds were shown to effectively inhibit the viability of glioma cells in the low micromolar range. Among them, AK-778-XXMU was chosen for further study due to its better solubility in water. A SPR assay proved the high affinity between AK-778-XXMU and ID2 protein with the KD value as 129 nM. The plausible binding mode in the biding site of ID2 was studied by molecular docking. Subsequently, the cancer-suppressing potency of the compound was characterized both in vitro and in vivo. The data demonstrated that compound AK-778-XXMU is a potent ID2 antagonist which has the potential to be developed as a therapeutic agent against glioma.

HighlightsO_LITwo pharmacophores were built from the first-in-class pan-ID antagonists AGX51
C_LIO_LIA pharmacophore-based virtual screening was carried out and 16 hit compounds were purchased for pharmacological evaluations in glioma inhibition
C_LIO_LICompound AK-778-XXMU was identified to be a potent ID2 antagonist in the low submicromolar range (KD: 159 nM)
C_LI

category: cancer biology


title: Phyllosphere-inhabiting endophytic bacteria feature a stationary phase-like lifestyle

abstract: Plants are in constant association with a variety of microbes, and although much is known about how symbiotic and pathogenic microbes interact with plants, less is known about the population dynamics, adaptive traits, and transcriptional features of endophytic commensal microbes that live inside leaves. In this study, we evaluated the long-term population and transcriptional dynamics of two bacterial microbiota endophytes and compared them to those of a commensal-simulating non-pathogenic mutant of the bacterial pathogen Pseudomonas syringae. We found that population densities of all three endophytic phyllosphere bacteria remained static over a long period of time, which was caused by a continual equilibrium between bacterial multiplication and death, as evidenced by treatment of plants with antibiotics that only targeted dividing bacteria or by in planta visualization of bacteria carrying a fluorescent division reporter. Population stasis could not be explained by a lack of resources, as Arabidopsis leaves could support population densities up to 100 times higher than the normal microbiota populations, nor was population stasis reversed by significantly quenching PAMP-triggered immunity. Long-term temporal in planta transcriptomic analysis of these three bacterial endophytes revealed up-regulation of protein translation, the generation of energy, and the response to stress, and interestingly, for the microbiota strains, the longer the bacteria remained inside plants, the greater the up-regulation of some of these processes. Further transcriptomic analysis of in planta populations of commensal-simulating Pseudomonas syringae revealed a remarkable resemblance to those of in vitro bacteria in stationary phase, a metabolically active physiological state in which the production of secondary metabolites and stress responses are induced. This study provides novel insight into how endophytic bacteria survive and thrive inside plant leaves, and reshapes our current understanding of what it means to be part of the endophytic microbiota in the phyllosphere.

category: microbiology


title: Mycobacterium abscessus HelR interacts with RNA Polymerase to confer intrinsic rifamycin resistance

abstract:
Rifampicin (RIF) constitutes the frontline therapy against M. tuberculosis as well as most slow-growing non-tuberculous mycobacteria (NTM). However, RIF is completely ineffective against M. abscessus despite the absence of mutations in the rifampicin resistance determining region of Mab_rpoB. This has been attributed to the presence of an ADP-ribosyltransferase (Arr) activity that inactivates RIF. Rifabutin (RBT), a close analogue of RIF, has recently been shown to be effective against M. abscessus in vitro and in a mouse model and comprises a promising therapeutic against M. abscessus infections. Using RNA sequencing we show that exposure of M. abscessus to sublethal doses of RIF and RBT results in [~]25-fold upregulation of Mab_helR in laboratory and clinical isolates; an isogenic deletion of Mab_helR is hypersensitive to RIF and RBT, and over-expression of Mab_helR confers RIF tolerance in M. tuberculosis implying that helR constitutes a significant determinant of inducible RIF and RBT resistance. We demonstrate a preferential association of MabHelR with RNA polymerase in vivo in bacteria exposed to RIF and showed that purified MabHelR can rescue transcription inhibition in the presence of RIF in in vitro transcription assays. Furthermore, MabHelR can dissociate RNAP from RIF-stalled initiation complexes in vitro, a species we envisage accumulates upon RIF exposure. Lastly, we show that the tip of the PCh-loop of Mab_helR, in particular residues E496 and D497 that are in proximity to RIF, is critical for conferring RIF resistance without being required for RNAP dissociation from stalled complexes. This suggests that HelR may be additionally involved in displacing RIF bound to RNAP and function as an RNAP protection protein.

Significance StatementBacterial RNA polymerase is a target for the potent and broad-spectrum rifamycin group of antibiotics. Mutations within rpoB and inactivation by a diverse group of enzymes constitute the most widespread mechanisms of resistance. Herein we report an unprecedented mechanism of rifamycin resistance in M. abscessus mediated by MabHelR, a putative SF1 like helicase, that involves disassembly of RIF-stalled initiation complexes, likely followed by displacement of the antibiotic, leading to RNAP recycling. The mechanism is reminiscent of the role of HflX and ribosome protection proteins in resistance to ribosome targeting antibiotics and suggests that removal of stalled macromolecular complexes and their recycling comprises a widespread but underappreciated mechanism of antibiotic resistance. Rifampicin (RIF) is pivotal in the control of M. tuberculosis infections but ineffective against M. abscessus. Identification of inducible rifamycin resistance determinants in M. abscessus is therefore particularly crucial for informing treatment strategies and development of novel therapeutic approaches.


title: Extreme longevity of highly fecund termite queens achieved by mitochondrial and insulin upregulation without harmful lipid signatures or accumulation

abstract: Kings and queens of eusocial termites can live for decades, while queens sustain a nearly maximal fertility. To investigate the molecular mechanisms underlying their long lifespan, we carried out transcriptomics, lipidomics and metabolomics in Macrotermes natalensis on sterile short-lived workers, long-lived kings and five stages spanning twenty years of adult queen maturation. Reproductives share gene expression differences from workers in agreement with a reduction of several aging-related processes, involving upregulation of DNA damage repair and mitochondrial functions. Anti-oxidant gene expression is downregulated, while peroxidability of membranes in queens decreases. Against expectations, we observed an upregulated gene expression in fat bodies of reproductives of several components of the IIS pathway, including an insulin-like peptide, Ilp9. This pattern does not lead to deleterious fat storage in physogastric queens, while simple sugars dominate in their hemolymph and large amounts of resources are allocated towards oogenesis. Our findings support the notion that all processes causing aging need to be addressed simultaneously in order to prevent it.

category: molecular biology


title: Lifespan prolonging mechanisms and insulin upregulation without fat accumulation in long-lived reproductives of a higher termite


title: Receptor binding may directly activate the fusion machinery in coronavirus spike glycoproteins

abstract: SARS-CoV-2, the causative agent of the COVID-19 pandemic, is an enveloped RNA virus. Trimeric spike glycoproteins extend outward from the virion; these class I viral membrane fusion proteins mediate entry of the virus into a host cell and are the dominant antigen for immune response. Cryo-EM studies have generated a large number of structures for the spike either alone, or bound to the cognate receptor ACE2 or antibodies, with the three receptor binding domains (RBDs) seen closed, open, or in various combinations. Binding to ACE2 requires an open RBD, and is believed to trigger the series of dramatic conformational changes in the spike that lead to the shedding of the S1 subunit and transition of the spring-loaded S2 subunit to the experimentally observed post-fusion structure. The steps following ACE2 binding are poorly understood despite extensive characterization of the spike through X-ray, cryo-EM, and computation. Here, we use all-atom simulations, guided by analysis of 81 existing experimental structures, to develop a model for the structural and energetic coupling that connects receptor binding to activation of the membrane fusion machinery.


title: CRISPR screens for lipid regulators reveal a role for ER-bound SNX13 in lysosomal cholesterol export

abstract:
We report here two genome-wide CRISPR screens carried out to identify genes that when knocked out, alter levels of lysosomal cholesterol or bis(monoacylglycero)phosphate. In addition, these screens were also carried out under conditions of NPC1 inhibition to identify modifiers of NPC1 function in lysosomal cholesterol export. The screens confirm tight co- regulation of cholesterol and bis(monoacylglycero)phosphate levels in cells, and reveal an unexpected role for the ER-localized, SNX13 protein as a negative regulator of lysosomal cholesterol export. In the absence of NPC1 function, SNX13 knockout decreases lysosomal cholesterol, and is accompanied by triacylglycerol-rich lipid droplet accumulation and increased lysosomal bis(monoacylglycero)phosphate. These experiments provide unexpected insight into the regulation of lysosomal lipids and modification of these processes by novel gene products.

SUMMARYGenome-wide CRISPR screens carried out with and without NPC1 function identify shared pathways that coordinately control lysosomal cholesterol and bis(monoacylglycero)phosphate. ER-localized SNX13 protein plays an unexpected regulatory role in modifying NPC1 function to regulate cellular cholesterol localization.

category: cell biology


title: ALKBH5 regulates somatic cell reprogramming in a phase specific manner

abstract: Establishment of the pluripotency regulatory network in somatic cells by introducing four transcriptional factors, (Octamer binding transcription factor 4 (OCT4), SRY (sex determining region Y)-box 2 (SOX2), Kruppel - like factor 4 (KLF4), and cellular-Myelocytomatosis (c-MYC) provides a promising tool for cell-based therapies in regenerative medicine. Still, the mechanisms at play when generating induced pluripotent stem cells from somatic cells is only partly understood. Here we show that the RNA specific N6-methyladenosine (m6A) demethylase ALKBH5 regulates somatic cell reprogramming in a stage specific manner. Knockdown or knockout of Alkbh5 in the early reprogramming phase impairs the reprogramming efficiency by reducing the proliferation rate through arresting the cells at G2/M phase and decreasing the mesenchymal-to-epithelial transition (MET) rate. However, there is no significant change in reprogramming efficiency when Alkbh5 is depleted at the late phase of reprogramming. On the other hand, ALKBH5 overexpression at the earlyreprogramming phase has no significant impact on reprogramming efficiency, while overexpression at the late phase enhances the reprogramming by stabilizing Nanog transcripts resulting in upregulated Nanog expression. Our study provides mechanistic insight into the crucial dynamic role of ALKBH5 in regulating somatic cell reprogramming at the posttranscriptional level.


title: Pigment pattern morphospace of Danio fishes: evolutionary diversification and mutational effects

abstract:
Molecular and cellular mechanisms underlying differences in adult form remain largely unknown. Adult pigment patterns of fishes in the genus Danio, which includes zebrafish, D. rerio, include horizontal stripes, vertical bars, spots and uniform patterns, and provide an outstanding opportunity to identify causes of species level variation in a neural crest derived trait. Yet understanding such variation requires quantitative approaches to assess phenotypes, and such methods have been mostly lacking for pigment patterns. We introduce metrics derived from information theory that describe patterns and pattern variation in Danio fishes. We find that such metrics used singly and in multivariate combinations are suitable for distinguishing general pattern types, and can reveal even subtle phenotypic differences attributable to mutations. Our study provides new tools for analyzing pigment pattern in Danio and potentially other groups, and sets the stage for future analyses of pattern morphospace and its mechanistic underpinnings.

Summary statementWe provide quantitative metrics for studying pigment patterns of zebrafish and other species. These metrics are applicable to changes between species as well as impacts of laboratory induced mutations

category: developmental biology


title: A burst of transposon expression accompanies the activation of Y chromosome fertility genes during Drosophila spermatogenesis

abstract: Transposable elements (TEs) must replicate in germline cells to pass novel insertions to offspring. In Drosophila melanogaster ovaries, TEs can exploit specific developmental windows of opportunity to evade host silencing and increase their copy numbers. However, TE activity and host silencing in the distinct cell types of the Drosophila melanogaster testis are not well understood. We reanalyzed publicly available single-cell RNA-seq datasets to quantify TE expression in the distinct cell types of the Drosophila testis. We developed a novel method for identification of TE and host gene expression programs and find that a distinct population of early spermatocytes expresses a large number of TEs at much higher levels than other germline and somatic components of the testes. This burst of TE expression coincides with the activation of Y chromosome fertility factors and spermatocyte-specific transcriptional regulators, as well as downregulation of many components of the piRNA pathway. The TEs expressed by this cell population are enriched on the Y chromosome and depleted on the X chromosome relative to other active TEs. These data suggest that some TEs may achieve high insertional activity in males by exploiting a window of opportunity for mobilization created by the activation of spermatocyte-specific and Y-chromosome-specific transcriptional programs.

category: genomics


title: E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP

abstract: RNF213 is a giant E3 ubiquitin ligase and a major susceptibility factor of Moyamoya disease, a cerebrovascular disorder that can result in stroke or death. In the cell, RNF213 is involved in lipid droplet formation, lipotoxicity, hypoxia, and NF-{kappa}B signaling, but its exact function in these processes is unclear. Structural characterization has revealed the presence of a dynein- like ATPase module and an unprecedented but poorly understood E3 module. Here, we demonstrate that RNF213 E3 activity is dependent on ATP binding, rather than ATP hydrolysis, and is particularly responsive to the ATP/ADP/AMP ratio. Biochemical and activity-based probe analyses identify a non-canonical zinc finger domain as the E3 active site, which utilizes the strictly conserved Cys4462, not involved in zinc coordination, as the reactive nucleophile. The cryo-EM structure of the trapped RNF213:E2[~]Ub intermediate reveals RNF213 C-terminal domain as the E2 docking site, which positions the ubiquitin-loaded E2 proximal to the catalytic zinc finger, facilitating nucleophilic attack of Cys4462 on the E2[~]Ub thioester. Our findings show that RNF213 represents an undescribed type of a transthiolation E3 enzyme and is regulated by adenine nucleotide concentration via its ATPase core, possibly allowing it to react to changing metabolic conditions in the cell.


title: Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature

abstract:
BackgroundLinking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSDs provenance, scientific use, and re-use in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level.

FindingsFor this data note, we extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. Flat data tables and an data warehouse with an interactive web application were constructed to enable ad hoc exploration of NSD use and summary statistics.

ConclusionsThe extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enables scientists around the world to join literature and sequence databases in a multidimensional fashion. As a concrete use case, statistics of country clusters were visualized with respect to NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.


title: The Fluorescent Dye 1,6-Diphenyl-1,3,5-Hexatriene Binds to Amyloid Fibrils Formed by Human Amylin and Provides a New Probe of Amylin Amyloid Kinetics

abstract: The fluorescent dye 1,6-diphenyl-1,3,5-hexatriene (DPH) is widely used as a probe of membrane order. We show that DPH also interacts with amyloid fibrils formed by human amylin (also known as islet amyloid polypeptide) in solution and this results in a 100-fold increase in DPH fluorescence for a sample of 20M human amylin and 0.25 M DPH. No increase in DPH fluorescence is observed with the non-amyloidogenic rat amylin or with freshly dissolved, non-fibrillar human amylin. The time course of amyloid formation by amylin was followed by monitoring the fluorescence of added DPH as a function of time and was similar to that monitored by the standard fluorescent probe thioflavin-T. The inclusion of DPH in the buffer did not perturb the time course of amyloid formation under the conditions examined and the time course was independent of the range of DPH concentrations tested (0.25 to 5 M). Maximum final fluorescence intensity is observed at substoichiometric ratios of DPH to amylin. No significant increase in fluorescence was observed during the lag phase of amyloid formation, and the implications for the structure of amylin pre-fibril oligomers are discussed. Human amylin contains three aromatic residues. A triple aromatic to leucine mutant forms amyloid and DPH binds to the resulting fibrils, indicating that interactions with aromatic side chains are not required for DPH amylin amyloid interactions. DPH may be especially useful for studies on mutant amylins and other polypeptides in which changes in charged residues might complicate interpretation of thioflavin-T fluorescence.

category: biophysics


title: Absence of muricholic acid due to Cyp2c-deficiency protects against high fat diet-induced obesity in male mice but promotes liver damage

abstract:
ObjectiveMurine-specific muricholic acids (MCAs) are reported to protect against obesity and associated metabolic disorders. However, the response of mice with genetic depletion of MCA to an obesogenic diet has not been evaluated. We used Cyp2c-deficient (Cyp2c-/-) mice, which lack MCAs and thus have a human-like bile acid (BA) profile, to directly investigate the potential role of MCAs in diet-induced obesity.

MethodsMale and female Cyp2c-/- mice and wild-type controls were fed a standard chow diet or a high fat diet (HFD) for 18 weeks. We measured BA composition from a pool of liver, gallbladder, and intestine, as well as weekly body weight, food intake, lean and fat mass, systemic glucose homeostasis, energy expenditure, intestinal lipid absorption, fecal lipid, and energy content.

ResultsCyp2c deficiency depleted MCAs and caused other changes in BA composition, namely a decrease in the ratio of 12-hydroxylated (12-OH) BAs to non-12-OH BAs, without altering the total BA levels. While wild-type male mice became obese after HFD-feeding, Cyp2c-/- male mice were protected from obesity and associated metabolic dysfunctions. Cyp2c-/- male mice also showed reduced intestinal lipid absorption and increased lipid excretion, which was reversed by oral gavage with the 12-OH BA, taurocholic acid. Cyp2c-/- mice also showed increased liver damage, which appeared stronger in females.

ConclusionMCA does not protect against diet-induced obesity but may protect against liver injury. Reduced lipid absorption in Cyp2c-deficient male mice is potentially due to a reduced ratio of 12-OH/non-12-OH BAs.

category: physiology


title: Biohybrid Microswimmers Against Bacterial Infections

abstract: Biohybrid microswimmers exploit the natural abilities of motile microorganisms e.g. in releasing cargo on-demand with high spatial and temporal control. However, using such engineered swarms to deliver antibiotics addressing bacterial infections has not yet been realized. In the present study, a design strategy for biohybrid microswimmers is reported, which features the covalent attachment of antibiotics to the motile green algae Chlamydomonas reinhardtii via a photo-cleavable linker. The surface engineering of the algae does not rely on genetic manipulations, proceeds with high efficiency, does not impair the viability or phototactic ability of microalgae, and allows for caging of the antibiotic on the surface for subsequent release via external stimuli. Two different antibiotic classes have been separately utilized, which result in activity against both gram-positive and gram-negative strains. Guiding the biohybrid microswimmers by an external beacon, and on-demand delivery of the drugs by light with high spatial and temporal control, allowed for strong inhibition of bacterial growth in vivo. This efficient strategy could potentially allow for the selective treatment of bacterial infections by engineered algal microrobots with high precision in space and time. Overall, this work presents an operationally simple production of biohybrid microswimmers loaded with antibiotic cargo to combat bacterial infections precisely delivered in three-dimensional space.

category: synthetic biology


title: Topography of corticopontine projections is controlled by postmitotic expression of the area-mapping gene Nr2f1

abstract:
Axonal projections from layer V neurons of distinct neocortical areas are topographically organized into discrete clusters within the pontine nuclei during the establishment of voluntary movements. However, the molecular determinants controlling corticopontine connectivity are insufficiently understood. Here, we show that an intrinsic cortical genetic program driven by Nr2f1 graded expression is directly implicated in the organization of corticopontine topographic mapping. Transgenic mice lacking cortical expression of Nr2f1 and exhibiting areal organization defects were used as model systems to investigate the arrangement of corticopontine projections. Combining three-dimensional digital brain atlas tools, Cre-dependent mouse lines, and axonal tracing, we show that Nr2f1 expression in postmitotic neurons spatially and temporally controls somatosensory topographic projections, whereas expression in progenitor cells influences the ratio between corticopontine and corticospinal fibres passing the pontine nuclei. We conclude that cortical gradients of area patterning genes are directly implicated in the establishment of a topographic somatotopic mapping from the cortex onto pontine nuclei.

Summary statementCortical gradient expression of the area patterning gene Nr2f1 spatially and temporally controls corticopontine topographic connectivity in layer V projection neurons.

category: neuroscience


title: Fungi hijack a plant apoplastic endoglucanase to release a ROS scavenging β-glucan decasaccharide to subvert immune responses

abstract:
Plant pathogenic and beneficial fungi have evolved several strategies to evade immunity and cope with host-derived hydrolytic enzymes and oxidative stress in the apoplast, the extracellular space of plant tissues. Fungal hyphae are surrounded by an inner, insoluble cell wall (CW) layer and an outer, soluble extracellular polysaccharide (EPS) matrix. Here we show by proteomics and glycomics that these two layers have distinct protein and carbohydrate signatures, implicating different biological functions. The barley (Hordeum vulgare) {beta}-1,3-endoglucanase HvBGLUII, which belongs to the widely distributed apoplastic glycoside hydrolase 17 family (GH17), releases a conserved {beta}-1,3;1,6-glucan decasaccharide ({beta}-GD) from the EPS matrices of fungi with different lifestyles and taxonomic positions. This low molecular weight {beta}-GD does not activate plant immunity, is resilient to further enzymatic hydrolysis by {beta}-1,3-endoglucanases due to the presence of three {beta}-1,6-linked glucose branches and can scavenge reactive oxygen species. Additionally, exogenous application of {beta}-GD leads to enhanced fungal colonization in barley. Our data highlights the hitherto undescribed capacity of this often overseen fungal EPS layer to act as an outer protective barrier important for fungal accommodation within the hostile environment at the apoplastic plant-microbe interface.

SignificanceHere we identify and characterize a conserved {beta}-1,3;1,6-glucan decasaccharide with antioxidant activity released from the fungal extracellular polysaccharide (EPS) matrix by the activity of a plant apoplastic endoglucanase. In addition, we provide a quantitative proteomic analysis of the fungal EPS and cell wall (CW) layers.

HIGHLIGHTSO_LIThe fungal extracellular polysaccharide (EPS) matrix and the cell wall (CW) are specific layers with distinct protein and carbohydrate signatures
C_LIO_LIA conserved {beta}-1,3;1,6-glucan decasaccharide ({beta}-GD) is released from the EPS matrices of different fungi by the activity of the barley {beta}-1,3-endoglucanase BGLUII, a member of the widely distributed apoplastic GH17 family
C_LIO_LIThe {beta}-GD efficiently scavenges reactive oxygen species (ROS) and enhances fungal colonization
C_LIO_LIThe immunomodulatory potential as microbe-associated molecular pattern (MAMP) as well as the biochemical activity as ROS scavenger of soluble low molecular weight {beta}-glucans are defined by the presence of {beta}-1,6-glucose branches
C_LI


title: Orc6 at replication fork enables efficient mismatch repair

abstract:
In eukaryotes, the Origin Recognition Complex (ORC) is required for the initiation of DNA replication. The smallest subunit of ORC, Orc6, is essential for pre-replication complex (pre-RC) assembly and cell viability in yeast and for cytokinesis in metazoans. However, unlike other ORC components, the role of human Orc6 in replication remains to be resolved. Here, we identify an unexpected role for hOrc6, which is to promote S-phase progression post pre-RC assembly and DNA damage response. Orc6 localizes at the replication fork and is an accessory factor of the mismatch repair (MMR) complex. In response to oxidative damage during S-phase, often repaired by MMR, Orc6 facilitates MMR complex assembly and activity, without which the checkpoint signaling is abrogated. Mechanistically, Orc6 directly binds to MutS and enhances the chromatin-association of MutL, thus enabling efficient mismatch repair. Based on this, we conclude that hOrc6 plays a fundamental role in genome surveillance during S-phase.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/443400v1_ufig1.gif" ALT="Figure 1">
View larger version (54K):
org.highwire.dtl.DTLVardef@bfdaa8org.highwire.dtl.DTLVardef@1ac791dorg.highwire.dtl.DTLVardef@436d1corg.highwire.dtl.DTLVardef@b07689_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIHuman Orc6 is dispensable for G1 licensing, but required for S-phase progression
C_LIO_LIHuman Orc6 at the replication fork is an accessory factor for MMR complex
C_LIO_LIDepletion of hOrc6 sensitizes cells to DNA damage and impairs ATR activation
C_LIO_LIHuman Orc6 regulates MMR complex assembly and activity
C_LI


title: Single cell transcriptomics and developmental trajectories of murine cranial neural crest cell fate determination and cell cycle progression

abstract: Cranial neural crest (NC) cells migrate long distances to populate the future craniofacial regions and give rise to various tissues, including facial cartilage, bones, connective tissues, and cranial nerves. However, the mechanism that drives the fate determination of cranial NC cells remains unclear. Using single-cell RNA sequencing combined genetic fate mapping, we reconstructed developmental trajectories of cranial NC cells, and traced their differentiation in mouse embryos. We identified four major cranial NC cell lineages at different status: pre-epithelial-mesenchymal transition, early migration, NC-derived mesenchymal cells, and neural lineage cells from embryonic days 9.5 to 12.5. During migration, the first cell fate determination separates cranial sensory ganglia, the second generates mesenchymal progenitors, and the third separates other neural lineage cells. We then focused on the early facial prominences that appear to be built by undifferentiated, fast-dividing NC cells that possess similar transcriptomic landscapes, which could be the drive for the facial developmental robustness. The post-migratory cranial NC cells exit the cell cycle around embryonic day 11.5 after facial shaping is completed and initiates further fate determination and differentiation processes. Our results demonstrate the transcriptomic landscapes during dynamic cell fate determination and cell cycle progression of cranial NC lineage cells and also suggest that the transcriptomic regulation of the balance between proliferation and differentiation of the post-migratory cranial NC cells can be a key for building up unique facial structures in vertebrates.


title: An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET

abstract: With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor, to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.


title: mSWI/SNF interacts with the ribosome and its inhibition/mutations alter translation and sensitize to mTOR/PI3K inhibitors

abstract:
The chromatin remodelers mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) subunits are mutated, deleted or amplified in more than 40% of cancers. Understanding their functions in normal cells and the consequences of cancers alterations will lead to path toward new targeted therapies. Canonically, mSWI/SNF complexes regulate the structure of chromatin, however they likely have additional functions which could be relevant in carcinogenesis. Here, we highlight the substantial alteration of mSWI/SNF subunits expression in both the nucleus and cytoplasm in breast cancer cases. We demonstrate mSWI/SNF cytoplasmic localization and interaction with the translation initiation machinery. Short-term inhibition and depletion of specific subunits alter protein synthesis, implicating a direct role for these factors in translation. Inhibition and depletion of specific subunits increase sensitivity to mTOR-PI3K inhibitors, suggesting a potential therapeutic opportunity for diseases harboring mutations in these complexes. Indeed, SMARCA4 pathogenic mutations decrease protein synthesis. Furthermore, taking advantage of the DepMap studies, we demonstrate cancer cells harboring mutations of specific mSWI/SNF subunits exhibit a genetic dependency on translation factors and are particularly sensitive to translation pathway inhibitors. In conclusion, we report an unexpected cytoplasmic role for mSWI/SNF in protein synthesis, suggesting potential new therapeutic opportunities for patients afflicted by cancers demonstrating alterations in its subunits.

Statement of significanceThis study establishes direct functions for mSWI/SNF in protein synthesis. mSWI/SNF inhibition, depletion and cancer mutations alter translation and increase sensitivity to translation pathway inhibitors, illustrating the potential for new therapeutic strategies.


title: A common SEC23B missense mutation in congenital dyserythropoietic anemia type II leads to growth restriction and symptoms of chronic pancreatitis in mice

abstract: Human loss-of-function mutations in SEC23B result in congenital dyserythropoietic anemia type II (CDAII). Complete deficiency of SEC23B in mice leads to perinatal death caused by massive degeneration of professional secretory tissues. Functions of SEC23B in postnatal mice are unclear. In this study, we generated knockout (KO) mice with deletion of exons 5 and 6 of Sec23b and knockin (KI) mice with the E109K mutation, the most common CDAII missense mutation. Despite decreased SEC23B protein level, Sec23bki/ki mice showed no obvious abnormalities. Hemizygous (Sec23bki/ko) mice exhibit a partial lethal phenotype, with only half of expected mice survive past weaning. Sec23bki/ko pancreas had exocrine insufficiency and chronic pancreatitis histology, as well as increased ER stress and apoptosis. Moreover, Sec23bki/ko mice exhibited severe growth restriction accompanied by growth hormone (GH) insensitivity, reminiscent of the Laron syndrome. Growth restriction is not associated with hepatocyte-specific Sec23b deletion, suggesting non-liver origin of the phenotype. Inflammation associated with chronic pancreatic deficiency may explain GH insensitivity in Sec23bki/ko mice. Our results indicate that phenotype severities are linked to the residual functions of SEC23B, demonstrating the importance of SEC23B in pancreatic acinar function in adult mice. The Sec23bki/ko mice provide a novel model of chronic pancreatitis and growth retardation.


title: A common SEC23B missense mutation in congenital dyserythropoietic anemia type II leads to growth restriction and chronic pancreatitis in mice


title: Noise-Transfer2Clean: Denoising cryo-EM images based on noise modeling and transfer

abstract:
MotivationCryo-electron microscopy (cryo-EM) is a widely-used technology for ultrastructure determination, which constructs the three-dimensional (3D) structures of protein and macromolecular complex from a set of two-dimensional (2D) micrographs. However, limited by the electron beam dose, the micrographs in cryo-EM generally suffer from extremely low signal-to-noise ratio (SNR), which hampers the efficiency and effectiveness of downstream analysis. Especially, the noise in cryo-EM is not simple additive or multiplicative noise whose statistical characteristics are quite different from the ones in natural image, extremely shackling the performance of conventional denoising methods.

ResultsHere, we introduce the Noise-Transfer2Clean (NT2C), a denoising deep neural network (DNN) for cryo-EM to enhance image contrast and restore specimen signal, whose main idea is to improve the denoising performance by correctly discovering the noise model of cryo-EM images and transferring the statistical nature of noise into the denoiser. Especially, to cope with the complex noise model in cryo-EM, we design a contrast-guided noise and signal re-weighted algorithm to achieve clean-noisy data synthesis and data augmentation, making our method authentically achieve signal restoration based on noises true properties. To our knowledge, NT2C is the first denoising method that resolves the complex noise model in cryo-EM images. Comprehensive experimental results on simulated datasets and real datasets show that NT2C achieved a notable improvement in image denoising and specimen signal restoration, comparing with the state-of-art methods. A real-world case study shows that NT2C can improve the recognition rate on hard-to-identify particles by 19% in the particle picking task.


title: Transient exposure of a buried phosphorylation site in an autoinhibited protein

abstract: Autoinhibition is a mechanism used to regulate protein function, often by making functional sites inaccessible through the interaction with a cis-acting inhibitory domain. Such autoinhibitory domains often display a substantial degree of structural disorder when unbound, and only become structured in the inhibited state. This conformational dynamics makes it difficult to study the structural origin of regulation, including effects of regulatory post-translational modifications. Here, we study the autoinhibition of the Dbl Homology domain in the protein Vav1 by the so-called acidic inhibitory domain. We use molecular simulations to study the process by which a mostly unstructured inhibitory domain folds upon binding and how transient exposure of a key buried tyrosine residue makes it accessible for phosphorylation. We show that the inhibitory domain, which forms a helix in the bound and inhibited stated, samples helical structures already before binding and that binding occurs via a molten-globule-like intermediate state. Together, our results shed light on key interactions that enable the inhibitory domain to sample a finely-tuned equilibrium between an inhibited and a kinase-accessible state.


title: Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation

abstract: Methods that link genetic variation to steady-state gene expression levels, such as expression quantitative trait loci (eQTLs), are widely used to functionally annotate trait-associated variants, but they are limited in identifying context-dependent effects on transcription. To address this challenge, we developed the cistrome-wide association study (CWAS), a framework for nominating variants that impact traits through their effects on chromatin state. CWAS associates the genetic determinants of cistromes (e.g., the genome-wide profiles of transcription factor binding sites or histone modifications) with traits using summary statistics from genome-wide association studies (GWAS). We performed CWASs of prostate cancer and androgen-related traits, using a reference panel of 307 prostate cistromes from 165 individuals. CWAS nominated susceptibility regulatory elements or androgen receptor (AR) binding sites at 52 out of 98 known prostate cancer GWAS loci and implicated an additional 17 novel loci. We functionally validated a subset of our results using CRISPRi and in vitro reporter assays. At 28 of the 52 risk loci, CWAS identified regulatory mechanisms that are not observable via eQTLs, implicating genes with complex or context-specific regulation that are overlooked by current approaches that relying on steady-state transcript measurements. CWAS genes include transcription factors that govern prostate development such as NKX3-1, HOXB13, GATA2, and KLF5. Moreover, CWAS boosts discovery power in modestly sized GWAS, identifying novel genetic associations mediated through AR binding for androgen-related phenotypes, including resistance to prostate cancer therapy. CWAS is a powerful and biologically interpretable paradigm for studying variants that influence traits by affecting context-dependent transcriptional regulation.

category: genetics


title: Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration

abstract:
BackgroundVisual outcome of patients with neovascular age-related macular degeneration has significantly improved during the last years following the introduction of anti-vascular endothelial growth factor (VEGF) therapy. However, about one third of patients show persistent exudation and decreasing visual acuity despite recurrent anti-VEGF treatment, which implies a role of other, still unknown proangiogenic mediators.

MethodsThe present study applied transcriptional profiling of human and mouse (C57BL/6J wildtype) choroidal neovascularization (CNV) membranes each with reference to healthy control tissue to identify yet unrecognized mediators of CNV formation. Key factors were further investigated by immunohistochemistry as well as by intravitreal inhibition experiments and multiplex protein assays in the laser-induced CNV mouse model.

ResultsTranscriptional profiles of CNV membranes were characterized by enhanced activation of blood vessel development, cytoskeletal organization, and cytokine production, with angiogenesis and wound healing processes predominating in humans and activation of immune processes in mice. Besides several species-specific factors, 95 phylogenetically conserved CNV-associated genes were detected, among which fibroblast growth factor inducible-14 (FN14), a member of the tumor necrosis factor (TNF) receptor family, was identified as a key player of CNV formation. Blocking the pathway by intravitreal injection of a FN14 decoy receptor modulated the cytokine profile - most notably IL-6 - and led to a significant reduction of CNV size in vivo.

ConclusionsThis study characterizes the transcriptome of human and mouse CNV membranes in an unprejudiced manner and identifies FN14 as a phylogenetically conserved mediator of CNV formation and a promising new therapeutic target for neovascular AMD.

FundingThis study was funded by the Helmut-Ecker-Stiftung and the Volker-Homann-Stiftung.


title: A Keller-Segel model for C elegans L1 aggregation

abstract:
We describe a mathematical model for the aggregation of starved first-stage C elegans larvae (L1s). We propose that starved L1s produce and respond chemotactically to two labile diffusible chemical signals, a short-range attractant and a longer range repellent. This model takes the mathematical form of three coupled partial differential equations, one that describes the movement of the worms and one for each of the chemical signals. Numerical solution of these equations produced a pattern of aggregates that resembled that of worm aggregates observed in experiments. We also describe the identification of a sensory receptor gene, srh-2, whose expression is induced under conditions that promote L1 aggregation. Worms whose srh-2 gene has been knocked out form irregularly shaped aggregates. Our model suggests this phenotype may be explained by the mutant worms slowing their movement more quickly than the wild type.

Author summaryAmong the most complex of animal behaviors are collective behaviors, in which animals interact with each other so as to produce large-scale organization. Starved first-stage larvae of the nematode Caenorhabditis elegans exhibit such a behavior: they come together to form aggregates of several hundred worms. How and why they do this are unknown. To address these questions, we developed a mathematical model of starved L1 aggregation. This model reproduced the main features of the behavior.

category: animal behavior and cognition


title: Evolution towards increasing complexity through functional diversification in a protocell model of the RNA world

abstract: The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of  live, replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth and division through physical processes alone. Replication of RNA inside such vesicles can produce a large number of RNA strands. Yet, the impact of such replication processes on the emergence of the first ribozymes inside such protocells and on the subsequent evolution of the protocell population remains an open question. In this paper, we present a model for the evolution of protocells with functionally diverse ribozymes. Distinct ribozymes can be created with small probabilities during the error-prone RNA replication process via the rolling circle mechanism. We identify the conditions that can synergistically enhance the number of different ribozymes inside a protocell and allow functionally diverse protocells containing multiple ribozymes to dominate the population. Our work demonstrates the existence of an effective pathway towards increasing complexity of protocells that might have eventually led to the origin of life in an RNA world.


title: Multimodal Analysis Reveals Differential Immuno-Metabolic Features in Lung Squamous Cell Carcinoma and Adenocarcinoma

abstract:
BackgroundThe relationship between systemic metabolism, immune function, and lung cancer is complex and remains poorly defined. Seemingly paradoxically, overweight and obesity confer an improved response to immune checkpoint inhibition in non-small cell lung cancer (NSCLC); however, it is not known whether excess body weight or adiposity impacts the immunometabolic tumor microenvironment.

MethodsUtilizing three complementary National Cancer Institute-funded open-source databases containing 18F-fluorodeoxyglucose positron-emission tomography/computed tomography (PET-CT) images for tumor and tissue glucose uptake, adipose tissue and skeletal muscle mass, histology annotated with tumor infiltrating leukocytes, and tumor RNA sequencing, we performed a retrospective cross-sectional analysis to examine phenotypic, metabolic, and genomic intersections of adiposity and tumor immune-metabolism in patients with lung adenocarcinoma (LUAD) versus squamous cell carcinoma (LUSC).

ResultsOur data reveal distinct immunometabolomic features of LUSC as compared to LUAD: visceral fat content was negatively correlated with both tumor glucose uptake and leukocyte infiltration. Subcutaneous and visceral adiposity conferred different effects on the tumor genetic landscapes in both tumor types. LUSC tumors showed greater gene expression pathways related to pyruvate, glucose, amino acid, and lipid metabolism, in addition to significantly greater 18F-FDG uptake compared with LUAD, suggesting deeper metabolic regulation within the LUSC tumor microenvironment.

ConclusionsSeveral immunometabolomic characteristics of LUSC and LUAD differ, including tumor glucose uptake and the associated metabolic pathways in the tumor, as well as the impact of visceral adiposity on tumor metabolism. These data may highlight opportunities to advance mechanistically targeted precision medicine approaches by better understanding the interplay between metabolic, immunologic, and genomic factors in lung cancer treatment.


title: Dual G9A and EZH2 inhibition stimulates an anti-tumour immune response in ovarian high-grade serous carcinoma

abstract:
Ovarian high-grade serous carcinoma (HGSC) prognosis correlates directly with presence of intratumoral lymphocytes. However, cancer immunotherapy has yet to achieve meaningful survival benefit in patients with HGSC. Epigenetic silencing of immunostimulatory genes is implicated in immune evasion in HGSC and re-expression of these genes could promote tumour immune clearance. We discovered that simultaneous inhibition of the histone methyltransferases G9A and EZH2 activates the CXCL10-CXCR3 axis and increases homing of intratumoral effector lymphocytes and natural killer cells whilst suppressing tumour-promoting FoxP3+ CD4 T cells. The dual G9A/EZH2 inhibitor HKMTI-1-005 induced chromatin changes that resulted in the transcriptional activation of immunostimulatory gene networks, including the re-expression of elements of the ERV-K endogenous retroviral family. Importantly, treatment with HKMTI-1-005 improved the survival of mice bearing Trp53-/-null ID8 ovarian tumours and resulted in tumour burden reduction.

These results indicate that inhibiting G9A and EZH2 in ovarian cancer alters the immune microenvironment and reduces tumour growth and therefore positions dual inhibition of G9A/EZH2 as a strategy for clinical development.

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title: Subspace based Multiple Constrained Minimum Variance (SMCMV) Beamformers

abstract: In MEG and EEG brain imaging research two popular approaches are often used for spatial localization of focal task- or stimuli-related brain activations. One is a so called MUSIC approach applied in the form of RAP or TRAP MUSIC algorithms. Another one is the beamformer approach, specifically multiple constrained minimum variance (MCMV) beamformer when dealing with significantly correlated activations. Either method is using its own source localizer functions. Considering simplicity, accuracy and computational efficiency both approaches have their advantages and disadvantages. In this study we introduce a novel set of so called Subspace MCMV (or SMCMV) beamformers whose localizer functions combine MUSIC and MCMV localizers. We show that in ideal situations where forward modeling, data recording and noise measurements are error-free, SMCMV localizers allow precise identification of n arbitrarily correlated sources irrespective to their strength in just n scans of the brain volume using RAP MUSIC type algorithm. We also demonstrate by extensive computer simulations that with respect to source localization errors and the total number of identified sources SMCMV outperforms both the TRAP MUSIC and MIA MCMV (which is the most accurate MCMV algorithm to our knowledge) in non-ideal practical situations, specifically when the noise covariance cannot be estimated precisely, signal to noise ratios are small, source correlations are significant and larger numbers of sources are involved.


title: Rab35 and glucocorticoids regulate APP and BACE1 trafficking to modulate Aβ production

abstract: Chronic stress and elevated glucocorticoids (GCs), the major stress hormones, are risk factors for Alzheimers disease (AD) and promote AD pathomechanisms, including overproduction of toxic amyloid-{beta} (A{beta}) peptides and intraneuronal accumulation of hyperphosphorylated Tau protein. The latter is linked to downregulation of the small GTPase Rab35, which mediates Tau degradation via the endolysosomal pathway. Whether Rab35 is also involved in A{beta} overproduction remains an open question. Here, we find that hippocampal Rab35 levels are decreased not only by stress/GC but also by aging, another AD risk factor. Moreover, Rab35 negatively regulates A{beta} production by sorting amyloid precursor protein (APP) and {beta}-secretase (BACE1) out of the endosomal network, where they interact to produce A{beta}. Interestingly, Rab35 coordinates distinct intracellular trafficking events for BACE1 and APP, mediated by its effectors OCRL and ACAP2, respectively. Finally, we show that Rab35 overexpression prevents the amyloidogenic trafficking of APP and BACE1 induced by high GC levels. These studies identify Rab35 as a key regulator of APP processing and suggest that its downregulation may contribute to stress- and AD-related amyloidogenesis.


title: Glial Cell Responses to constant low Light exposure in Rat Retina.

abstract: Retinal damage promoted by constant illumination of low intensity resulted in a diminution in classical photoreceptors cells. Glial cells exert profound effects on neurons, vasculature and other glial cells. Macroglia and microglia with specific morphological, physiological, and antigenic characteristics may play an essential role in both the maintenance and control of retinal homeostasis, or to exert mechanisms that promote cell death. The role of glial cells and immune function in the pathogenesis promoted by low light is poorly understood. We performed glial cells characterization along the time-course of retinal degeneration induced by chronic exposure to low intensity of light in Wistar rats. We exposed the animals at constant light from 2 to 8 days and assessed the retinal glia. After 6 days of light exposure, retinas presented increased levels of GFAP, a macroglia marker and microglia markers Iba1 and CD68 displayed increased mRNA levels after 6 days. The number of Iba1 positive cells increased in the outer nuclear layer, showing ameboid morphology with thicker processes characteristic of microglial activated cells. The expression levels of immune mediators TNF-{square} and IL-6 were also significantly increased after 6 days. Finally, chemokines analysis showed that CX3CR1 and CCL2 expression levels were significantly elevated after 6 days. Hence, all the events of glial activation occurred after 5-6 days of constant light exposure, when the number of cells of the outer nuclear layer has already decreased significantly. Herein we demonstrated that glial and immune activation are secondary to neurodegeneration; in this scenario, our results suggest that photoreceptor death is an early event that may be induced by phototransduction-dependent mechanisms.


title: Mind blanking is associated with a rigid spatio-temporal profile in typical wakefulness

abstract:
Mind blanking (MB) is a waking state during which we do not report any mental content, challenging the view of a constantly thought-oriented brain. Here, we comprehensively characterize the MBs neurobehavioral profile with the aim to delineate its role during ongoing mentation. Using fMRI experience-sampling, we show that MB is reported less frequently, faster, and with low transitional dynamics among other mental states, pointing to its role as a transient mental relay. Regarding its neural underpinnings, we observe higher global signal amplitude during MB reports, indicating a distinct physiological substrate. Using the time-varying functional connectome MB reports get classified with high accuracy, suggesting that MB has a unique neural composition. Indeed, a pattern of globally positive-phase coherence shows the highest similarity to the connectivity patterns associated with MB reports. We observe that this patterns rigid signal architecture hinders content reportability due to the brains inability to differentiate signals in an informative way. Collectively, we show that MB has a unique neurobehavioural profile, indicating that non-reportable mental events can happen during wakefulness. Our results add to the characterization of spontaneous mentation and pave the way for more mechanistic investigations of MBs phenomenology.

Significance StatementThe human mind is generally assumed to be thought-oriented. Mind blanking (MB) challenges this stance because it appears as if we are derived of any particular mental content to report. We here show that, during spontaneous thinking, MB is a mental state that happens by default, it has a unique behavioural profile, and it is of a rigid neural architecture that does not permit the formulation of reportable contents. Our work essentially proposes that non-reportable mental events can happen during wakefulness, and challenges the view of the mind as a constant thought-oriented operator.


title: Mind blanking is a distinct mental state linked to a recurrent brain profile of globally positive connectivity during ongoing mentation


title: Neural codes in early sensory areas maximize fitness

abstract: It has generally been presumed that sensory information encoded by a nervous system should be as accurate as its biological limitations allow. However, perhaps counter intuitively, accurate representations of sensory signals do not necessarily maximize the organisms chances of survival. To test this hypothesis, we developed a unified normative framework for fitness-maximizing encoding by combining theoretical insights from neuroscience, computer science, and economics. Initially, we applied predictions of this model to neural responses from large monopolar cells (LMCs) in the blowfly retina. We found that neural codes that maximize reward expectation--and not accurate sensory representations--account for retinal LMC activity. We also conducted experiments in humans and find that early sensory areas flexibly adopt neural codes that promote fitness maximization in a retinotopically-specific manner, which impacted decision behavior. Thus, our results provide evidence that fitness-maximizing rules imposed by the environment are applied at the earliest stages of sensory processing.


title: Spatial and regional directory of tropical Auricularia mushrooms in Southwest, Nigeria

abstract: Bioremediation of wastelands and dumpsites in Africa is fast declining due to reduced mushroom populations. In the past, the forest of Africa was teaming with mushrooms, but nowadays; mushrooms are severely exploited, resulting in gradual drift to extinction. Mushrooms have the tendency to degrade recalcitrant wastes and absorb heavy metals (Bio-accumulation). Unless concerted efforts are made to rejuvenate or rescue the surviving mushroom population, Africa will one day be overshadowed by wastes. The mushroom diversity in Southwest, Nigeria was determined by both morphological and molecular markers, 14 primers (OPB-11, OPB-12, OPB-15, OPB-20, OPB-21, OPH-3, OPH-5, OPH-10, OPH-15, OPT-1, OPT-5, OPT-7, OPT-10 and OPT-19) produced polymorphism with the test samples under electrophoresis gel (PCR and RAPD). Using standard morphological markers, Auricularia auricula was found to be evenly distributed across 8 locations in Ekiti and Osun, 6 locations in Ogun, 5 locations in Oyo and 4 locations in Lagos. There was none identified in Ondo. Auricularia polytricha was found in abundance in all the locations in Ondo. Lagos only had 3 out of its outline Stations graced with the presence of A. polytricha, whereas, Ogun, Ekiti, Osun and Oyo had no records of A. polytricha. From the genetic dissimilarity chart, 6 clusters of mushroom, sub-characterized into 3 distinct species (Auricularia polytricha, A. auricula and an unrelated Auricularia outlier species) and 5 cultivars were obtained in the region of Southwest, Nigeria. The population of all the Auricularia mushrooms currently present in Southwest, Nigeria was effectively captioned (Location, type and identity) by this research.


title: Sexual selection and sexual size dimorphism in animals

abstract: Sexual selection is often considered as a critical evolutionary force promoting sexual size dimorphism (SSD) in animals. However, empirical evidence for a positive relationship between sexual selection on males and male-biased SSD received mixed support depending on the studied taxonomic group and on the method used to quantify sexual selection. Here, we present a meta-analytic approach accounting for phylogenetic non-independence to test how standardized metrics of the opportunity and strength of pre-copulatory sexual selection relate to SSD across a broad range of animal taxa comprising up to 102 effect sizes from 64 species. We found that SSD was correlated with the sex difference in the opportunity for sexual selection but not with the sex difference in the Bateman gradient. These findings suggest that pre-copulatory sexual selection plays a limited role for the evolution of sexual size dimorphism in a broad phylogenetic context.

category: evolutionary biology


title: Post-glacial expansion dynamics, not refugial isolation, shaped the genetic structure of a migratory bird, the Yellow Warbler (Setophaga petechia)

abstract: During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra and permafrost leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated, insular populations that persisted in disjunct regions known as refugia. According to this hypothesis, as ice sheets retreated, species recolonised the continent from these glacial refugia, and the mixing of these lineages is responsible for modern patterns of genetic diversity. However, an alternative hypothesis is that complex genetic patterns could also arise simply from heterogenous post-glacial expansion dynamics, without separate refugia. Both mitochondrial and genomic data from the North American Yellow warbler (Setophaga petechia) shows the presence of an eastern and western clade, a pattern often ascribed to the presence of two refugia. Using a climate-informed spatial genetic modelling (CISGeM) framework, we were able to reconstruct past population sizes, range expansions, and likely recolonisation dynamics of this species, generating spatially and temporally explicit demographic reconstructions. The model captures the empirical genetic structure despite including only a single, large glacial refugium. The contemporary population structure observed in the data was generated during the expansion dynamics after the glaciation and is due to unbalanced rates of northward advance to the east and west linked to the melting of the icesheets. Thus, modern population structure in this species is consistent with expansion dynamics, and refugial isolation is not required to explain it, highlighting the importance of explicitly testing drivers of geographic structure.


title: ScreenGarden: A shinyR application for fast and easy analysis of plate-based high-throughput screens

abstract: Colony growth on solid media is a simple and effective measure for high-throughput genomic experiments such as yeast-two hybrid, Synthetic Genetic Arrays and Synthetic Physical Interaction screens. The development of robotic pinning tools has facilitated the experimental design of these assays, and different imaging software can be used to automatically measure colony sizes on plates. However, comparison to control plates and statistical data analysis is often laborious and pinning issues or plate specific growth effects can lead to the detection of false positive growth defects. We have developed ScreenGarden, a shinyR application, to enable easy, quick and robust data analysis of plate-based high throughput assays.


title: Tensor P-Spline Smoothing for Spatial Analysis of Plant Breeding Trials

abstract: Large agricultural field trials may display irregular spatial trends that cannot be fully captured by a purely randomization-based analysis. For this reason, paralleling the development of analysis-of-variance procedures for randomized field trials, there is a long history of spatial modelling for field trials, starting with the early work of Papadakis on nearest neighbour analysis, which can be cast in terms of first or second differences among neighbouring plot values. This kind of spatial modelling is amenable to a natural extension using P-splines, as has been demonstrated in recent publications in the field. Here, we consider the P-spline framework, focussing on model options that are easy to implement in linear mixed model packages. Two examples serve to illustrate and evaluate the methods. A key conclusion is that first differences are rather competitive with second differences. A further key observation is that second differences require special attention regarding the representation of the null space of the smooth terms for spatial interaction, and that an unstructured variance-covariance structure is required to ensure invariance to translation and rotation of eigenvectors associated with that null space. We develop a strategy that permits fitting this model with ease, but the approach is more demanding than that needed for fitting models using first differences. Hence, even though in other areas second differences are very commonly used in the application of P-splines, our main conclusion is that with field trials first differences have advantages for routine use.


title: Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function

abstract: Deep residual learning has shown great success in protein contact prediction. In this study, a new deep residual learning-based protein contact prediction model was developed. Comparing with previous models, a new type of residual block hybridizing 1D and 2D convolutions was designed to increase the effective receptive field of the residual network, and a new loss function emphasizing the easily misclassified residue pairs was proposed to enhance the model training. The developed protein contact prediction model referred to as DRN-1D2D was first evaluated on 105 CASP11 targets, 76 CAMEO hard targets and 398 membrane proteins together with two in house-developed reference models based on either the standard 2D residual block or the traditional BCE loss function, from which we confirmed that both the dimensional hybrid residual block and the singularity enhanced loss function can be employed to improve the model performance for protein contact prediction. DRN-1D2D was further evaluated on 39 CASP13 and CASP14 free modeling targets together with the two reference models and six state-of-the-art protein contact prediction models including DeepCov, DeepCon, DeepConPred2, SPOT-Contact, RaptorX-Contact and TripleRes. The result shows that DRN-1D2D consistently achieved the best performance among all these models.


title: The sum of two halves may be different from the whole. Effects of splitting sequencing samples across lanes.

abstract:
The advances in high throughput sequencing (HTS) enabled the characterisation of biological processes at an unprecedented level of detail; the majority of hypotheses in molecular biology rely on analyses of HTS data. However, achieving increased robustness and reproducibility of results remains one of the main challenges. Although variability in results may be introduced at various stages, e.g. alignment, summarisation or detection of differences in expression, one source of variability was systematically omitted: the sequencing design which propagates through analyses and may introduce an additional layer of technical variation.

We illustrate qualitative and quantitative differences arising from splitting samples across lanes, on bulk and single-cell sequencing. For bulk mRNAseq data, we focus on differential expression and enrichment analyses; for bulk ChIPseq data, we investigate the effect on peak calling, and peaks properties. At single-cell level, we concentrate on identifying cell subpopulations. We rely on markers used for assigning cell identities; both smartSeq and 10x data are presented.

The observed reduction in the number of unique sequenced fragments reduces the level of detail on which the different prediction approaches depend. Further, the sequencing stochasticity adds in a weighting bias corroborated with variable sequencing depths and (yet unexplained) sequencing bias.


title: Therapeutic reversal of prenatal pontine ID1 signaling in DIPG

abstract:
Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive brain tumor with rare survival beyond two years. This poor prognosis is largely due to the tumors highly infiltrative and invasive nature. Previous reports demonstrate upregulation of the transcription factor ID1 with H3K27M and ACVR1 mutations, but this has not been confirmed in human tumors or therapeutically targeted. We developed an in utero electroporation (IUE) murine H3K27M-driven tumor model, which demonstrates increased ID1 expression in H3K27M- and ACVR1-mutated tumor cells. In human tumors, elevated ID1 expression is associated with H3K27M/ACVR1-mutation, brainstem location, and reduced survival. The ID1 promoter demonstrates a similar active epigenetic state in H3K27M tumor cells and murine prenatal hindbrain cells. In the developing human brain, ID1 is expressed highest in oligo/astrocyte-precursor cells (OAPCs). These ID1+/SPARCL1+ cells share a transcriptional program with astrocyte-like (AC-like) DIPG cells, and demonstrate upregulation of gene sets involved with regulation of cell migration. Both genetic and pharmacologic [cannabidiol (CBD)] suppression of ID1 results in decreased DIPG cell invasion/migration in vitro and invasion/tumor growth in multiple in vivo models. CBD reduces proliferation through reactive oxygen species (ROS) production at low micromolar concentrations, which we found to be achievable in the murine brainstem. Further, pediatric high-grade glioma patients treated off-trial with CBD (n=15) demonstrate tumor ID1 reduction and improved overall survival compared to historical controls. Our study identifies that ID1 is upregulated in DIPG through reactivation of a developmental OAPC transcriptional state, and ID1-driven invasiveness of DIPG is therapeutically targetable with CBD.

One Sentence SummaryThe transcription factor ID1 is upregulated in a subset of DIPG tumor cells, and ID1-driven invasiveness is therapeutically targetable with CBD.


title: Variation in susceptibility among three Caribbean coral species and their algal symbionts indicates the threatened staghorn coral, Acropora cervicornis, is particularly susceptible to elevated nutrients and heat stress

abstract: Coral cover is declining worldwide due to multiple interacting threats. We compared the effects of elevated nutrients and temperature on three Caribbean corals: Acropora cervicornis, Orbicella faveolata, and Siderastrea siderea. Colonies hosting different algal types were exposed to either ambient nutrients (A), elevated NH4 (N), or elevated NH4 + PO4 (N+P) at control temperatures (26 {degrees}C) for > 2 months, followed by a 3-week thermal challenge (31.5 {degrees}C). A. cervicornis hosted Symbiodinium (S. fitti) and was highly susceptible to the combination of elevated nutrients and temperature. During heat stress, A. cervicornis pre-exposed to elevated nutrients experienced 84%-100% mortality and photochemical efficiency (Fv/Fm) declines of 41-50%. In comparison, no mortality and lower Fv/Fm declines (11-20%) occurred in A. cervicornis that were heat-stressed but not pre-exposed to nutrients. O. faveolata and S. siderea response to heat stress was determined by their algal symbiont community and was not affected by nutrients. O. faveolata predominantly hosted Durusdinium trenchii or Breviolum, but only corals hosting Breviolum were susceptible to heat, experiencing 100% mortality, regardless of nutrient treatment. S. siderea colonies predominantly hosted Cladocopium C1 (C. goreaui), Cladocopium C3, D. trenchii, or variable proportions of Cladocopium C1 and D. trenchii. This species was resilient to elevated nutrients and temperature, with no significant mortality in any of the treatments. However, during heat stress, S. siderea hosting Cladocopium C3 suffered higher reductions in Fv/Fm (41-56%) compared to S. siderea hosting Cladocopium C1 and D. trenchii (17-26% and 10-16%, respectively). These differences in holobiont susceptibility to elevated nutrients and heat may help explain historical declines in A. cervicornis starting decades earlier than other Caribbean corals. Our results suggest that tackling only warming temperatures may be insufficient to ensure the continued persistence of Caribbean corals, especially A. cervicornis. Reducing nutrient inputs to reefs may also be necessary for these iconic coral species to survive.


title: Characterization of the gene repertoire and environmentally driven expression patterns in Tanner crab (Chionoecetes bairdi)

abstract: Tanner crab (Chionoecetes bairdi) are an economically important species that is threatened by ocean warming and Bitter Crab Disease, which is caused by an endoparasitic dinoflagellate, Hematodinium. Little is known about disease transmission or its link to host mortality, or how ocean warming will affect pathogenicity or host susceptibility. To provide a transcriptomic resource for the Tanner crab, we generated a suite of RNA-seq libraries encompassing pooled hemolymph samples from crab displaying differing infection statuses and maintained at different temperatures (ambient (7.5{degrees}C), elevated (10{degrees}C), or decreased (4{degrees}C)). After assembling a transcriptome and performing a multifactor differential gene expression analysis, we found genes influenced by temperature in relation to infection, and detected some of those genes over time at the individual level using RNAseq data from one crab. Biological processes associated with those genes include lipid storage, transcription, response to oxidative stress, cell adhesion, and morphogenesis. Alteration in lipid storage and transcription provide insight into how temperature impacts energy allocation in Hematodinium infected crabs. Alteration in expression patterns in genes associated with morphogenesis could suggest hemocytes were changing morphology and/or type in response to temperature. This project provides insight into how Hematodinium infection could influence crab physiology as oceans warm.


title: mRNA-decapping associated DcpS enzyme controls critical steps of neuronal development

abstract: Homozygous mutations in the gene encoding the scavenger mRNA-decapping enzyme, DcpS, have been shown to underlie developmental delay and intellectual disability. Intellectual disability is associated with both abnormal neocortical development and mRNA metabolism. However, the role of DcpS and its scavenger decapping activity in neuronal development is unknown. Here, we show that human neurons derived from patients with a DcpS mutation have compromised differentiation and neurite outgrowth. Moreover, in the developing mouse neocortex, DcpS is required for the radial migration, polarity, neurite outgrowth and identity of developing glutamatergic neurons. Collectively, these findings demonstrate that the scavenger mRNA decapping activity contributes to multiple pivotal roles in neural development, and further corroborate that mRNA metabolism and neocortical pathologies are associated with intellectual disability.


title: The type 2 diabetes factor methylglyoxal mediates axon initial segment shortening and neuronal network activity changes

abstract:
Recent evidence suggests that alteration of axon initial segment (AIS) geometry (i.e., length or position along the axon) contributes to CNS dysfunction in neurological diseases. For example, AIS length is shorter in the prefrontal cortex of type 2 diabetic mice with cognitive impairment. The key type 2 diabetes-related factor that alters AIS geometry is unknown. Here, we tested whether modifying the levels of insulin, glucose, or methylglyoxal, a reactive carbonyl species that is a metabolite of glucose, changes AIS geometry in mature cultures of dissociated postnatal mouse cortex using immunofluorescent imaging of the AIS proteins AnkyrinG and {beta}IV spectrin. Neither insulin nor glucose modification appreciably altered AIS length. Elevation of methylglyoxal produced reversible AIS shortening without cell death. Multi-electrode array recordings revealed a biphasic effect of methylglyoxal on neuronal network activity: an immediate, transient [~]300% increase in spiking and bursting rates was followed by a [~]20% reduction from baseline at 3 h. AIS length was unchanged at 0.5 h or 3 h after adding methylglyoxal, whereas development of AIS shortening at 24 h was associated with restoration of spiking to baseline levels. Immunostaining for the excitatory neuron marker Ca2+/calmodulin-dependent protein kinase II alpha revealed AIS shortening in both excitatory and inhibitory neuron populations. This suggests that complex mechanisms maintain neuronal network operation after acute exposure to the disease metabolite methylglyoxal. Importantly, our results indicate that methylglyoxal could be a key mediator of AIS shortening during type 2 diabetes.

Significance StatementSmall changes in the structure of the axon initial segment affect neuronal function and may be a key mediator of neurological complications in various disease states. However, the specific disease factors that mediate structural changes at the axon initial segment are relatively unknown. This is the first study to show that increase of methylglyoxal is sufficient to reduce axon initial segment length and modulate neuronal network function. Methylglyoxal is a disease factor implicated in a wide variety of conditions including type 2 diabetes, Alzheimers disease, and aging. Thus, these findings could significantly impact the understanding of neurological complications in several disease states and are of broad pathophysiological relevance.


title: Decentralized Brain Age Estimation using MRI Data

abstract: Recent studies have demonstrated that neuroimaging data can be used to predict brain age, as it captures information about the neuroanatomical and functional changes the brain undergoes during development and the aging process. However, researchers often have limited access to neuroimaging data because of its challenging and expensive acquisition process, thereby limiting the effectiveness of the predictive model. Decentralized models provide a way to build more accurate and generalizable prediction models, bypassing the traditional data-sharing methodology. In this work, we propose a decentralized method for brain age estimation and evaluate it on three different feature sets, including both volumetric and voxelwise structural MRI data as well as resting functional MRI data. The results demonstrate that a decentralized brain age model can achieve similar performance compared to the models trained with all the data in one location.


title: RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes

abstract:
O_LIStatistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological studies. However, as these methods grow increasingly complex, users often encounter significant challenges with summarizing, visualizing, and communicating their key results.
C_LIO_LIWe present RevGadgets, an R package for creating publication-quality figures from the results of a large variety of phylogenetic analyses performed in RevBayes (and other phylogenetic software packages).
C_LIO_LIWe demonstrate how to use RevGadgets through a set of vignettes that cover the most common use cases that researchers will encounter.
C_LIO_LIRevGadgets is an open-source, extensible package that will continue to evolve in parallel with RevBayes, helping researchers to make sense of and communicate the results of a diverse array of analyses.
C_LI

[Bayesian phylogenetics, data visualization, R, RevBayes]


title: Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity

abstract: Natural Killer (NK) cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect NK gene expression is poorly understood. We performed expression quantitative trait locus (eQTL) mapping of negatively selected NK cells from a population of healthy Europeans (n=245). We find a significant subset of genes demonstrate eQTL specific to NK cells and these are highly informative of human disease, in particular autoimmunity. An NK cell transcriptome-wide association study (TWAS) across five common autoimmune diseases identified further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor (KIR) Region, GNLY and MC1R. Our findings provide new insights into the unique biology of NK cells, demonstrating markedly different eQTL from other immune cells, with implications for disease mechanisms.


title: Frequent paternal mitochondrial inheritance and rapid haplotype frequency shifts in copepod hybrids

abstract: Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.


title: The integration of large-scale public data and network analysis uncovers molecular characteristics of psoriasis

abstract:
In recent years, a growing interest in the characterization of the molecular basis of psoriasis has been observed. However, despite the availability of a large amount of molecular data, many pathogenic mechanisms of psoriasis are still poorly understood. In this study, we performed an integrated analysis of 23 public transcriptomic datasets encompassing both lesional and uninvolved skin samples from psoriasis patients. We defined comprehensive gene co-expression network models of psoriatic lesions and uninvolved skin. Moreover, we collected, curated and exploited a wide range of functional information from multiple public sources in order to systematically annotate the inferred networks.

The integrated transcriptomics analysis of public datasets shed light on a number of genes which are frequently deregulated in the psoriatic lesion compared with the unaffected skin in a large number of studies. In particular, CRABP2, LCN2, S100A12 and PDZK1IP1 were found to be deregulated in all of the datasets analyzed.

Furthermore, the analysis of co-expression networks highlights genes showing aberrant patterns of connectivity in the lesional network as compared to the network inferred from unaffected skin samples. For instance, we identified co-expression patterns of SERPINB4, KYNU and S100A12 as being the most affected by the disease. Network analysis allowed us to identify YPEL1 and HUS1 as plausible, previously unknown, actors in the expression of the psoriasis phenotype. In addition, by exploiting topological properties of the network models, we highlighted a set of 250 non-deregulated genes, 223 of which have never been associated with the disease before, including CACNA1A, HADH, ATP5MC1 and CBARP among others.

Finally, we characterized specific communities of co-expressed genes sustaining relevant molecular functions and specific immune cell types expression signatures playing a role in the psoriasis lesion. Overall, integrating experimental driven results with curated functional information from public repositories represents an efficient approach to empower knowledge generation about psoriasis and may be applicable to other complex diseases.

category: systems biology


title: Web-based Psychoacoustics: Hearing Screening, Infrastructure, and Validation

abstract: Anonymous web-based experiments are increasingly and successfully used in many domains of behavioral research. However, online studies of auditory perception, especially of psychoacoustic phenomena pertaining to low-level sensory processing, are challenging because of limited available control of the acoustics, and the unknown hearing status of participants. Here, we outline our approach to mitigate these challenges and validate our procedures by comparing web-based measurements to labbased data on a range of classic psychoacoustic tasks. Individual tasks were created using jsPsych, an open-source javascript front-end library. Dynamic sequences of psychoacoustic tasks were implemented using Django, an open-source library for web applications, and combined with consent pages, questionnaires, and debriefing pages. Subjects were recruited via Prolific, a web-based human-subject marketplace. Guided by a meta-analysis of normative data, we developed and validated a screening procedure to select participants for (putative) normal-hearing status; this procedure combined thresholding of scores in a suprathreshold cocktail-party task with filtering based on survey responses. Headphone use was standardized by supplementing procedures from prior literature with a binaural hearing task. Individuals meeting all criteria were re-invited to complete a range of classic psychoacoustic tasks. Performance trends observed in re-invited participants were in excellent agreement with lab-based data for fundamental frequency discrimination, gap detection, sensitivity to interaural time delay and level difference, comodulation masking release, word identification, and consonant confusions. Our results suggest that web-based psychoacoustics is a viable complement to lab-based research. Source code for our infrastructure is also provided.


title: Non-Transgenic Functional Rescue of Neuropeptides

abstract: Animals constantly respond to changes in their environment and internal states via neuromodulation. Neuropeptide genes modulate neural circuits by encoding either multiple copies of the same neuropeptide or different neuropeptides. This architectural complexity makes it difficult to determine the function of discrete and active neuropeptides. Here, we present a novel genetic tool that facilitates functional analysis of individual peptides. We engineered Escherichia coli bacteria to express active peptides and fed loss-of-function Caenorhabditis elegans to rescue gene activity. Using this approach, we rescued the activity of different neuropeptide genes with varying lengths and functions: trh-1, ins-6, and pdf-1. While some peptides are functionally redundant, others exhibited unique and previously uncharacterized functions. The mechanism of peptide uptake is reminiscent of RNA interference, suggesting convergent mechanisms of gene regulation in organisms. Our rescue-by-feeding paradigm provides a high-throughput screening strategy to elucidate the functional landscape of neuropeptide genes regulating different behavioral and physiological processes.


title: Expanding the Potential Genes of Inborn Errors of Immunity through Protein Interactions

abstract: Inborn errors of immunity (IEI) are a group of genetic disorders that impair the immune system, with over 400 genes described so far, and hundreds more to be discovered. To facilitate the search for new genes, we need a way to prioritize among all the genes in the genome those most likely to play an important role in immunity. Here we identify a new list of genes by linking known IEI genes to new ones by using open-source databases of protein-protein interactions, post-translational modifications, and transcriptional regulation. We analyze this new set of 2,530 IEI-related genes for their tolerance of genetic variation and by their expression levels in various immune cell types.

category: immunology