title: First comprehensive identification of proteins with increased O-GlcNAc levels during pressure overload hypertrophy.

abstract: Protein posttranslational modifications (PTMs) by O-GlcNAc globally rise during pressure-overload hypertrophy (POH). However, only a few specific proteins with altered O-GlcNAc levels during POH are known primarily because this PTM is easily lost during standard mass spectrometry (MS) conditions used for protein identification. Methodologies have recently emerged to stabilize the O-GlcNAc moiety for MS analysis. Accordingly, our goal was to determine the proteins undergoing changes in O-GlcNAc levels during POH. We used C57/Bl6 mice subjected to Sham or transverse aortic constriction (TAC) to create POH. From the hearts, we stabilized and labelled the O-GlcNAc moiety with tetramethylrhodamine azide (TAMRA) before enriching by TAMRA immunoprecipitation (IP). We used LC-MS to identify the captured O-GlcNAcylated proteins. We identified a total of 707 O-GlcNAcylated proteins in Sham and POH. Two hundred thirty-three of these proteins were significantly increased in POH over Sham whereas no proteins were significantly decreased in POH. We examined two MS identified proteins, CPT1B and PDH, to validate the MS data by immunoprecipitation. We corroborated increased O-GlcNAc levels during POH for the metabolic enzymes CPT1B and PDH. Enzyme activity assays showed higher O-GlcNAcylation increased CPT1 activity and decreased PDH activity. In summary, we generated the first comprehensive list of proteins with changes in O-GlcNAc levels during POH and, to our knowledge, the largest list for any cardiac pathology. Our results demonstrate the large number of proteins and cellular processes affected by O-GlcNAc during POH and serve as a guide for testing specific O-GlcNAc-regulated mechanisms.


title: Enhanced photosynthetic efficiency for increased carbon assimilation and woody biomass production in hybrid poplar INRA 717-1B4

abstract: Increasing CO2 levels in the atmosphere and the resulting negative impacts on climate change have compelled global efforts to achieve carbon neutrality or negativity. Most such efforts focus on carbon sequestration through chemical or physical approaches. We aim to harness the power of synthetic biology to enhance plants natural ability to draw down and sequester carbon, thereby positively affecting climate change. Past decades of scientific progress have shed light on strategies to overcome the intrinsic limitations of carbon drawdown and fixation through photosynthesis, particularly in row crops in hopes of improving agricultural productivity for food security. Incorporating a photorespiration bypass in C3 plants has shown promising results of increased biomass and grain yield. Despite their globally dominant role in atmospheric carbon flux, the drawdown rates of most trees are currently limited by their C3 photosynthetic metabolism, and efforts to improve the photosynthetic capacity of trees, such as by reducing energy loss in photorespiration, are currently lacking. Here, we selected a photorespiration bypass pathway and tested its effectiveness on photosynthetic enhancement in hybrid poplar INRA717-IB4. The design includes a RNAi strategy to reduce the transportation of the photorespiration byproduct, glycolate, out of chloroplast and a shunt pathway to metabolize the retained glycolate back to CO2 for fixation through the Calvin-Benson cycle. Molecular and physiological data collected from two repeated growth experiments indicates that transgenic plants expressing genes in the photorespiration bypass pathway have increased photosynthetic efficiency, leading to faster plant growth and elevated biomass production. One lead transgenic event accumulated 53% more above-ground dry biomass over a five month growth period in a controlled environment. Pilot projects with photosynthesis-enhanced trees in the field are in progress. Our results provide a proof-of-concept for engineering trees to help combat climate change.

category: plant biology


title: Interaction mechanism between the HSV-1 glycoprotein B and the antimicrobial peptide Amyloid-β

abstract: Unravelling the mystery of Alzheimers Disease (AD) requires urgent resolution given the worldwide increase of the aging population. There is a growing concern that the current leading AD hypothesis, the amyloid cascade hypothesis, does not stand up to validation with respect to emerging new data. Indeed, several paradoxes are being discussed in the literature, for instance, both the deposition of the Amyloid-Beta peptide (A{beta}) and the intracellular neurofibrillary tangles (NFTs) could occur within the brain without any cognitive pathology. Thus, these paradoxes suggest that something more fundamental is at play in the onset of the disease and other key and related pathomechanisms have to be investigated. The present study follows our previous investigations on the infectious hypothesis, which posits that some pathogens are linked to late onset AD. Our studies also build upon the shattering finding that A{beta} is a powerful antimicrobial agent capable of inhibiting pathogens as observed in in vitro experiments. Herein, we ask what are the molecular mechanisms in play when A{beta} neutralizes infectious pathogens? To answer this question, we probed at nanoscale lengths with FRET (Forster Resonance Energy Transfer), the interaction between A{beta} peptides and glycoprotein B (responsible of virus-cell binding) within the HSV-1 virion. We concluded that there is indeed a close interaction, likely nonspecific or semi-specific, between the two types of molecules, which participate in virus neutralization.

category: neuroscience


title: Nuclear envelope disruption triggers hallmarks of aging in lung alveolar macrophages

abstract: Aging is characterized by gradual immune dysfunction and increased risk for many diseases, including respiratory infections. Genomic instability is thought to play a central role in the aging process but the mechanisms that damage nuclear DNA in aging are insufficiently defined. Cells that migrate or reside within confined environments experience forces applied to their nucleus, leading to transient nuclear envelope (NE) ruptures. NE ruptures are associated with DNA damage, and Lamin A/C is required to limit these events. Here, we show that Lamin A/C protects lung alveolar macrophages from NE rupture and hallmarks of aging. Lamin A/C ablation in immune cells results in a selective depletion of lung alveolar macrophages (AM) and a heightened susceptibility to influenza infection. Lamin A/C-deficient AM that persist display constitutive nuclear envelope rupture marks, DNA damage and p53-dependent senescence. In wild-type mice, we found that AM migrate within constricted spaces in vivo, at heights that induce NE rupture and DNA damage. AM from aged wild-type mice and from Lamin A/C-deficient mice share an upregulated lysosomal signature with CD63 expression, and we find that CD63 is required to clear damaged DNA in macrophages. We propose that induction of genomic instability by NE disruption represents a mechanism of aging in alveolar macrophages.

category: immunology


title: modelRxiv: A platform for the distribution, computation and interactive display of models

abstract: Modeling the dynamics of biological processes is ubiquitous across the ecological and evolutionary disciplines. However, the increasing complexity of these models poses a significant challenge to the dissemination of model-derived results. With the existing standards of scientific publishing, most often only a small subset of model results are generated, presented in static figures or tables, and made available to the scientific community. Further exploration of the parameter space of a model, investigation of possible variations of a model, and validation of the results in relation to model assumptions commonly rely on local deployment of code supplied by the authors. While releasing model code is a publication requirement for most scientific journals, there are currently no standardized protocols or coding-language requirements. Deploying models locally poses a technical challenge due to the specific framework and environment in which a model was developed, and can preclude model validation and exploration by readers and reviewers. To address this issue, we developed a platform that serves as an interactive repository of biological models, called modelRxiv (https://modelrxiv.org). The platform provides a unified interface for the analysis of models developed in multiple programming languages but does not require any technical understanding of the model implementation. To reduce model computation time, the platform allows users to pool computational resources available to them, including lab workstations, clusters and cloud services. By making published models accessible, this platform promises to significantly improve the accessibility, reproducibility and validation of ecological and evolutionary models.

category: ecology


title: Bioframe: Operations on Genomic Intervals in Pandas Dataframes

abstract:
MotivationGenomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from genes, to DNA binding sites, to disease variants. Operations on genomic intervals provide a language for asking questions about relationships between features. While there are excellent interval arithmetic tools for the command line, they are not smoothly integrated into Python, one of the most popular general-purpose computational and visualization environments.

ResultsBioframe is a library to enable flexible and performant operations on genomic interval dataframes in Python. Bioframe extends the Python data science stack to use cases for computational genome biology by building directly on top of two of the most commonly-used Python libraries, numpy and pandas. The bioframe API enables flexible name and column orders, and decouples operations from data formats to avoid unnecessary conversions, a common scourge for bioinformaticians. Bioframe achieves these goals while maintaining high performance and a rich set of features.

Availability and implementationBioframe is open-source under MIT license, cross-platform, and can be installed from the Python package index. The source code is maintained by Open2C on Github at https://github.com/open2c/bioframe.

category: bioinformatics


title: Read depth correction for somatic mutations

abstract: The ability to accurately detect mutations is a function of read depth and variant allele frequency (VAF). While the read depth distribution of a sample is observable, the true VAF distribution of all mutations in a sample is uncertain when there is low coverage depth. We propose to estimate the VAF distributions that would be observed with high-depth sequencing for samples with low sequencing depth by grouping samples with similar clonality and purity and using the VAF distributions observed with the high-depth mutations that are available. With these estimated high-depth VAF distributions we then calculate what the expected VAF distributions would be at a given depth and compare against the observed VAF distributions at that depth. Using this procedure we estimate that The Cancer Genome Atlas (TCGA) MC3 dataset only reports on average 83% of the mutations in a sample which would have been detected with high-depth sequencing. These results have important implications for comparing tumor mutational burden (TMB) estimates when samples are sequenced at different depths and for modeling high-depth, gene panel-based sequencing from the TCGA MC3 dataset.


title: cLD: Rare-variant disequilibrium between genomic regions identifies novel genomic interactions

abstract: Introductory ParagraphLinkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants unanalyzed. In this work, we introduce cumulative LD (cLD), a stable statistic that captures the rare-variant LD between genetic regions and opens the door for furthering biological knowledge using rare genetic variants. In application, we find cLD reveals an increased genetic association between genes in 3D chromatin interactions, a phenomenon recently reported negatively by calculating standard LD between common variants. Additionally, we show that cLD is higher between gene pairs reported in interaction databases, identifies unreported protein-protein interactions, and reveals interacting genes distinguishing case/control samples in association studies.


title: PKD-1 Signaling Is Required for the Maintenance of CSCs with Epithelial-mesenchymal Plasticity in Pancreatic Neuroendocrine Tumors

abstract: Pancreatic neuroendocrine tumors (pNETs) are extremely heterogeneous and highly vascularized neoplasms that arise from endocrine cells in the pancreas. pNETs harbor a subpopulation of stem cell-like cancer cells (cancer stem cells/CSCs), which contribute to intratumoral heterogeneity and promote tumor maintenance and recurrence. In this study we demonstrated that CSCs in human pNETs co-expressed PKD-1 and CD44. We further identified PKD-1 signaling as a critical pathway in the regulation of CSC maintenance in pNET cells. PKD-1 signaling regulated the expression of a CSC-related gene signature and promoted CSC self-renewal. Intriguingly, pharmacological or genetic disruption of PKD-1 signaling in human pNET cells impaired lysophosphatidic acid-induced expression of genes associated with epithelial to mesenchymal transition (EMT), specifically E-cadherin and vimentin. This study indicates that PKD-1 signaling is essential for the maintenance of a subpopulation of CSCs in pNETs at an intermediate state along the epithelial-mesenchymal spectrum, thereby leading to a CSC phenotype with plasticity and partial EMT. Inhibiting the PKD-1 pathway may facilitate the elimination of CSC subpopulations to curb pNET progression, therapeutic resistance and metastasis. Given that the signaling networks associated with CSC maintenance and EMT are complex and extend across multiple levels of gene regulation, this study provides insight into signaling regulation of partial EMT in determining CSC fate and aids in developing potential therapeutic strategies that target different subsets of CSCs in a variety of cancers.

category: cancer biology


title: Cohesin mutation sensitizes cancer cells to anti-PD-1 therapy through endogenous retrovirus-mediated PD-L1 upregulation

abstract: Immune checkpoint therapy shows impressive and durable clinical responses in cancer patients, but the genetic determinants that enable cancer cells to respond to anti-PD-1 therapy are still elusive. Herein, we identified that NIPBL deficiency promotes endogenous retrovirus (ERV) expression in tumour cells, which in turn inactivates CD8+ tumour-infiltrating lymphocytes (TILs) via the PD-L1/PD-1 inhibitory checkpoint pathway. Mechanistically, NIPBL deficiency impairs DNMT1 transcription, preventing DNMT1 from suppressing ERV expression in tumour cells; ERVs stimulate PD-L1 expression by inducing the STAT2-IRF9 complex, a downstream event of double-stranded RNA (dsRNA)-MAVS-IRF3 signalling, and thereby suppress CD8 TIL-mediated immunity. An anti-PD-1 monoclonal antibody achieved remarkable therapeutic effects in Nipbl-deficient syngeneic tumour models and improved host survival by eliciting an antitumour memory immune response. Cancer patients harbouring mutations of cohesin subunits and regulators plus DNMT1 had significantly better responses to anti-PD-1 therapy than their non-mutated counterparts did. Our study reveals a novel mechanism by which cohesin complex deregulation stimulates ERV expression by impairing DNMT1 expression and fosters an immunosuppressive tumour microenvironment by activating the PD-L1/PD-1 inhibitory checkpoint.


title: Inhibiting Runx1 protects heart function after myocardial infarction

abstract:
Myocardial infarction is a major cause of death worldwide. Effective treatments are required that limit adverse cardiac remodelling and preserve cardiac contractility following myocardial infarction, with the aim of improving patient outcomes and preventing progression to heart failure. The perfused but hypocontractile myocardium bordering a newly created infarct is functionally distinct from the remote surviving myocardium; it is also a major determinant of adverse cardiac remodelling and whole heart contractility. Expression of the transcription factor RUNX1 is increased in the border zone at 1 day after myocardial infarction, suggesting potential for targeted therapeutic intervention. Here we demonstrate that RUNX1 drives reductions in cardiomyocyte contractility, sarcoplasmic reticulum-mediated calcium release, mitochondrial density, and the expression of genes important for oxidative phosphorylation.

Antagonising RUNX1 expression via short-hairpin RNA interference preserved cardiac contractile function following myocardial infarction when delivered either via direct adenoviral delivery into the border zone or via an adeno-associated virus vector administered intravenously. Equivalent effects were obtained with a small molecule inhibitor (Ro5-3335) that reduces RUNX1 function by blocking its interaction with the essential co-factor CBF{beta}. Both tamoxifen-inducible Runx1-deficient and Cbf{beta}-deficient cardiomyocyte-specific mouse models demonstrated that antagonising RUNX1 function preserves the expression of genes important for oxidative phosphorylation following myocardial infarction. Our results confirm the translational potential of RUNX1 as a novel therapeutic target in myocardial infarction, with wider opportunities for use across a range of cardiac diseases where RUNX1 drives adverse cardiac remodelling.

category: pathology


title: Deep phenotyping platform for microscopic plant-pathogen interactions

abstract:
1O_LIThe initial phases of plant-pathogen interactions are critical since they are often decisive for the successful infection. However, these early stages of interaction are typically microscopic, making it challenging to study on a large scale.
C_LIO_LIFor this reason, using the powdery mildew fungi of cereals as a model, we have developed an automated microscopy pipeline coupled with deep learning-based image analysis for the high-throughput phenotyping of plant-pathogen interactions.
C_LIO_LIThe system can quantify fungal microcolony count and density, the precise area of the secondary hyphae of each colony, and different morphological parameters. Moreover, the high throughput and sensitivity allow quantifying rare microscopic phenotypes in a large sample size. One of these phenotypes is the cryptic infection of non-adapted pathogens, marking the hidden transition stages of pathogen adaptation and breaking the nonhost barrier. Thus, our tool opens the nonhost resistance phenomenon to genetics and genomics studies.
C_LIO_LIWe have developed an open-source high-throughput automated microscopy system for phenotyping the initial stages of plant-pathogen interactions, extendable to other microscopic phenotypes and hardware platforms. Furthermore, we have validated the systems performance in disease resistance screens of genetically diverse barley material and performed Genome-wide associations scans (GWAS), discovering several resistance-associated loci, including conferring nonhost resistance.
C_LI


title: The brassinosteroid biosynthesis gene TaD11-2A controls grain size and its elite haplotype improves wheat grain yields

abstract:
Brassinosteroids (BRs) control many important agronomic traits, therefore the manipulation of BR components could improve crop productivity and performance. However, the potential effects of BR-related genes on yield-related traits and stress tolerance in wheat (Triticum aestivum L.) remain poorly understood. Here, we identified TaD11 genes in wheat (rice D11 orthologs) that encoded enzymes involved in BR biosynthesis. TaD11 genes were highly expressed in roots (Zadoks scale: Z11) and grains (Z75), while expression was significantly suppressed by exogenous BR (24-epiBL). Ectopic expression of TaD11-2A rescued the abnormal panicle structure and plant height (PH) of the cpb1 mutant, and also increased endogenous BR levels, resulting in improved grain yields and grain quality in rice. Natural variations in TaD11-2A were associated with significant differences in yield-related traits, including PH, grain width (GW), 1000-grain weight (TGW), and grain yield per plant (GYPP), and its favorable haplotype, TaD11-2A-HapI was subjected to positive selection during wheat breeding. Additionally, TaD11-2A influenced root length and salt tolerance in rice and wheat at seedling stages. These results indicated the important role of BR TaD11 biosynthetic genes in controlling grain size and root length, and also highlighted their potential in the molecular biological analysis of wheat.

HighlightThe brassinosteroid biosynthesis gene TaD11-2A regulates grain size and root length and its haplotype favorably improves grain yields and salt tolerance in wheat.


title: Identification of a small molecule, Mebendazole, as a novel ethylene signaling activator reveals a role of ethylene signaling on the regulation of lateral root angles

abstract: The lateral root angle or gravitropic set-point angle (GSA) is an important trait for root system architecture (RSA) that determines the radial expansion of the root system. The GSA therefore plays a crucial role in the ability of plants to access nutrients and water in the soil. Despite its importance, only few regulatory pathways and mechanisms that determine GSA are known, and these mostly relate to auxin and cytokinin pathways. Here, we report the identification of a small molecule that modulates GSA in Arabidopsis thaliana roots and acts via the activation of ethylene signaling. We uncover that this small molecule Mebendazole (MBZ) directly acts on the serine/threonine protein kinase CTR1, which is a negative regulator of ethylene signaling. Our study not only reveals that the ethylene signaling pathway is essential for GSA regulation, but it also identifies a small molecular modulator of RSA and the first specific activator of ethylene signaling.


title: The durability of long-lasting insecticidal nets treated with and without piperonyl butoxide (PBO) in Uganda.

abstract:
Long Lasting Insecticidal Nets (LLINs) supplemented with the synergist piperonyl butoxide have been developed in response to growing pyrethroid resistance however their durability in the field remains poorly described. A pragmatic cluster-randomised trial was embedded into Ugandas 2017-2018 distribution to compare the durability of LLINs with and without PBO

A total of 104 clusters were included with each receiving one of four LLIN products, two with pyrethroid+PBO (Olyset Plus and PermaNet 3.0) and two pyrethroid-only (Olyset Net and PermaNet 2.0). Nets were sampled at baseline, 12, and 25 months post-distribution to assess physical condition, chemical content, and bioefficacy. Physical condition was quantified using proportionate Hole Index and chemical content measured using high-performance liquid chromatography. Bioefficacy was assessed with three-minute WHO Cone and Wireball assays using pyrethroid-resistant An. gambiae, with 1hr knockdown and 24hr mortality recorded.

There was no difference in physical durability between LLIN products assessed (p=0.644). The pyrethroid content of all products remained relatively stable across timepoints but PBO content declined by 55% (p<0.001) and 58% (p<0.001) for Olyset Plus and PermaNet 3.0 respectively. Both PBO LLINs were highly effective against pyrethroid-resistant mosquitoes when new, knocking down all mosquitoes. However, bioefficacy declined over time with Olyset Plus knocking down 45.72% (95% CI: 22.84-68.62, p=0.021) and Permanet 3.0 knocking down 78.57% (95% CI: 63.57-93.58, p<0.001) after 25 months.

Here we demonstrate that both Olyset Plus and PermaNet 3.0 are as durable as their pyrethroid-only equivalents and had superior bioefficacy against pyrethroid-resistant An. gambiae. However, the superiority of PBO-LLINs decreased with operational use, correlating with a reduction in total PBO content. This decline in bioefficacy after just two years is concerning and there is an urgent need to assess the durability of PBO LLINs in other settings.

category: zoology


title: Rapid motor adaptation to bounce perturbations in online Pong game is independent from the visual tilt of the bouncing surface

abstract: Motor adaptation describes the ability of the motor system to counteract repeated perturbations in order to reduce movement errors. Most research in the field investigated adaptation in response to perturbations affecting the moving hand. Fewer studies looked at the effect of a perturbation applied to the movement target, however they used simplistic visual stimuli. In this study, we examined motor adaptation to perturbations affecting the motion of dynamic targets. In addition, we asked whether external visual cues in the environment could facilitate this process. To do so, participants were asked to play an online version of the Pong game in which they intercepted a ball bouncing off a wall using a paddle. A perturbation was applied to alter the post-bounce trajectory of the ball and the wall orientation was manipulated to be consistent or not with the ball trajectory. The "trained tilt" group (n = 34) adapted to the consistent condition and the "trained horizontal" group (n = 36) adapted to the inconsistent condition. In case participants optimally integrate external visual cues, the "trained tilt" group is expected to exhibit faster and/or more complete adaptation than the "trained horizontal" group. We found that the perturbation reduced interception accuracy. Participants showed large interception errors when the perturbation was introduced, followed by rapid error decrease and aftereffects (errors in the opposite direction) once the perturbation was removed. Although both experimental groups showed these typical markers of motor adaptation, we did not find differences in interception success rates or errors between the "trained tilt" and "trained horizontal" groups. Our results demonstrate that participants quickly adapted to the dynamics of the pong ball. However, the visual tilt of the bouncing surface did not enhance their performance. The present study highlights the ability of the motor system to adapt to external perturbations applied to a moving target in a more dynamical environment and in online settings. These findings underline the prospects of further research on sensorimotor adaptation to unexpected changes in the environment using more naturalistic and complex real-world or virtual reality tasks as well as gamified paradigms.


title: Experience-dependent learning and myelin plasticity in individuals with stroke

abstract:
BackgroundInjury to brain myelin disrupts motor performance and learning, however it is not clear if myelination is modulated by skilled motor practice or by recovery after stroke. Multi-component relaxation imaging can be used to measure water trapped between myelin bilayers which is expressed as myelin water fraction.

The purpose of this study was to examine the effect of experience-dependent learning on myelin plasticity using multi-component relaxation imaging in individuals with stroke.

MethodsThirty-two individuals with chronic stroke (>6 months) and twenty-seven healthy controls completed 4 weeks of skilled motor practice using a complex, gamified reaching task. Multi-component relaxation imaging-derived myelin water fraction was obtained before and after training. Seven brain regions associated with motor learning and sensorimotor function were investigated.

ResultsAll participants improved task-specific reaching movements after training. In individuals with stroke: 1) pre-training myelin water fraction was lower in motor brain regions but higher in the cingulum compared to controls, 2) pre-training myelin water fraction in motor and sensorimotor regions was positively associated with learning rate, and 3) myelin water fraction was increased in the ipsilesional (contralateral to the trained arm) superior longitudinal fasciculus following skilled motor practice.

ConclusionsFindings indicate that after stroke, myelin water fraction is related to measures of motor learning and modulated by 4 weeks of skilled motor practice with the paretic limb. Myelin water fraction can be enhanced in the chronic stage of stroke and may be an important target for upper-limb motor recovery.


title: Modulation of sleep by trafficking of lipids through the Drosophila blood brain barrier

abstract: Endocytosis through Drosophila glia is a significant determinant of sleep amount and occurs preferentially during sleep in glia of the blood brain barrier (BBB). To identify metabolites whose trafficking is mediated by sleep-dependent endocytosis, we conducted metabolomic analysis of flies that have increased sleep due to a block in glial endocytosis. We report that acylcarnitines, molecules that conjugate with long chain fatty acids to promote their transport, accumulate in heads of these animals. In parallel, to identify transporters and receptors whose loss contributes to the sleep phenotype caused by blocked endocytosis, we screened genes enriched in barrier glia for effects on sleep. We find that knockdown of lipid transporters LRP1&2 as well as carnitine transporters ORCT1&2 increases sleep. In support of the idea that the block in endocytosis affects trafficking through specific transporters, knockdown of LRP or ORCT transporters also increases acylcarnitines in heads. We propose that lipid species, such as acylcarnitines, are trafficked through the BBB via sleep-dependent endocytosis, and their accumulation in the brain increases the need for sleep.


title: Orthogonal Gene Engineering Enables CD8+ T Cells to Control Tumors through a Novel PD-1+ TOX-indifferent Synthetic Effector State

abstract: Adoptive immunotherapy offers opportunities to reprogram T cells and the tumor microenvironment. Orthogonal engineering of adoptively transferred T cells with an IL-2R{beta}{gamma}-binding IL-2 variant, PD1-decoy and IL-33 led to cell-autonomous T-cell expansion, T-cell engraftment and tumor control in immunocompetent hosts through reprogramming of both transferred and endogenous CD8+ cells. Tumor-infiltrating lymphocytes adopted a novel effector state characterized by TOX suppression and specific expression of multiple effector molecules, most prominently granzyme C. While the IL-2 variant promoted CD8+ T-cell stemness and persistence, and was associated with downregulation of TOX, the combination with IL-33 was necessary to trigger the novel polyfunctional effector state. Rational T-cell engineering without host lymphodepletion enables optimal reprogramming of adoptively transferred T cells as well as mobilization of endogenous immunity into new functional CD8+ states mediating tumor control.


title: Species richness and community structure of bats along a forest elevational transect in Papua New Guinea

abstract: Over the past decades, elevational gradients have become a powerful tool with which to understand the underlying cause(s) of biodiversity. The Mt. Wilhelm elevational transect is one such example, having been used to study the birds, insects, and plants of Papua New Guinea (PNG). However, a survey of mammals from this forest elevational transect was lacking. We thus aimed to investigate patterns in the community structure and species richness of bats (Chiroptera) along the transect, link the species to available regional data, and explain the observed patterns by including environmental characteristics. Bat communities were surveyed between 200 m and a timberline at 3,700 m a.s.l. at eight study sites separated by 500 m in elevation. We conducted mist-netting and acoustic surveys to detect and identify species at each site. Regional data were compiled to compare local with regional diversity. Finally, biotic (i.e., food availability, habitat features) and abiotic (i.e., mean daily temperature, available land area) factors were included in our analyses to disentangle the ecological drivers underlying bat diversity. Results revealed that species richness decreases with ascending elevation and was best explained by a corresponding decrease in both area and temperature. We also observed community turnover along the transect at local and regional scales, along with the increase of species elevational ranges. Consequently, despite that the study was restricted to one mountain in PNG, it demonstrates how basic inventory surveys can be used to address ecological questions in other similar and undisturbed tropical mountains.


title: Dense satellite data reveals landscape connectivity decline in the Andes-Amazon region

abstract: There is a complex interplay of criminal groups control over land, illicit activities, and forest cover change in the Colombian Andes-Amazon region. This area is dealing with diverse forms of conflict and peace, directly impacting landscape connectivity. While many studies have documented rapid deforestation after the peace agreement in 2016, we know little about the effect of these socio-political changes on the state of landscape connectivity. We disentangle habitat from connected habitat in forest ecosystems using the Landsat archive and landscape connectivity indices. We find that in the Andes-Amazon region during 2000-2020, connected habitat loss reached 18%, while habitat loss was 13%. This result is worrisome, because it indicates that well-connected patches are more fragmented and isolated, affecting the natural connections between the Andes and Amazon biogeographical regions and the movement ability of species. The Colombian government should conduct a strategic peacebuilding process incorporating structural changes that prevent the increase of large-scale extractive activities that are often illegal in the region. While finding a balance between extractive activities and conservation remains a big challenge, legal land tenure, census/taxation, and specific agreements with local actors can initially prevent deforestation. We discourage localized military actions and the return of aerial fumigation of coca fields, which rather than stop deforestation might exacerbate land cover change deeper into pristine forests.


title: Noninvasive sampling for comparisons of wildlife microbiomes may be more reliable than sampling trapped animals

abstract: In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for microbiome research, comparing microbiota of noninvasively collected fecal samples to those collected from trapped common cranes at the same sites over the same periods. We found significant differences in microbial composition (alpha and beta diversity), which were not accounted for by noninvasive samples exposure to soil contaminants, as manually assessed by comparing differentially abundant taxa. They could result from trapped birds exposure to sedatives. We conclude that if all samples are collected in the same manner, comparative analyses are valid, and noninvasive sampling may better represent host microbiota because there are no trapping effects. Experiments with fresh and delayed sample collection can elucidate effects of environmental exposures on microbiota. Further, stressing or sedation may unravel how trapping affects wildlife microbiota.


title: Comparison of fitness effects in the earthworm Eisenia fetida after exposure to single or multiple anthropogenic pollutants

abstract:
Terrestrial ecosystems are exposed to many anthropogenic pollutants. Non-target effects of pesticides and fertilizers have put agricultural intensification in the focus as a driver for biodiversity loss. However, other pollutants, such as heavy metals, particulate matter, or microplastic also enter the environment, e.g. via traffic and industrial activities in urban areas. As soil acts as a potential sink for such pollutants, soil invertebrates like earthworms may be particularly affected by them. Under natural conditions soil invertebrates will likely be confronted with combinations of pollutants simultaneously, which may result in stronger negative effects if pollutants act synergistically.

Within this work we study how multiple pollutants affect the soil-dwelling, substrate feeding earthworm Eisenia fetida. We compared the effects of the single stressors, polystyrene microplastic fragments, polystyrene fibers, brake dust and soot, with the combined effect of these pollutants when applied as a mixture. Endpoints measured were survival, growth, reproductive fitness, and changes in three oxidative stress markers. We found that among single pollutant treatments, brake dust imposed the strongest negative effects on earthworms in all measured endpoints including increased mortality rates. Sub-lethal effects were found for all pollutants. Exposing earthworms to all four pollutants simultaneously led to effects on mortality and oxidative stress markers that were smaller than expected by the respective null models. These antagonistic effects are likely a result of the adsorption of toxic substances found in brake dust to the other pollutants. With this study we show that effects of combinations of pollutants cannot necessarily be predicted from their individual effects and that combined effects will likely depend on identity and concentration of the pollutants.


title: Sex differences in migration timing influence the network structure of avian assemblages at a stopover site

abstract:
O_LIShifts in migration phenology aimed at minimizing possible mismatches between the timing of breeding and seasonal peaks in the availability of food resources are a well-documented phenomenon in birds. As the extent of phenological adjustments are likely to differ between species, populations, sexes and age classes, these shifts may exert a strong influence on the potential interferences among co-migrants during their journey to breeding grounds. This can be particularly true for species showing asynchronous migration driven by sex-related mechanisms (i.e., protandry), for which not only the decision on  when, but also  with whom to move might represent a way to minimize the costs associated with migrations.
C_LIO_LIHere, we used an extensive dataset from 16 years of standardized bird monitoring at the spring stopover area on the island of Ponza (Italy), to study how long-term changes in the phenology of species with protandric migration patterns affect the rewiring of potential interferences in avian assemblages.
C_LIO_LIFor each year, we reconstructed the temporal co-occurrence networks of females and males of 17 sexually dimorphic species known to exhibit phenological shifts in their migratory behaviour and measured network-specific properties related to connectivity and cohesion. We also provided a measure of  co-migration fidelity, defined as the degree to which females and males tend to follow a consistent order of association over time.
C_LIO_LICo-occurrence networks in males showed higher cohesion and lower connectivity than their females counterparts and a more clustered pattern in terms of co-migration fidelity, with species wintering in sub-Saharan Africa having a more pronounced tendency to aggregate in semi-independent groups of species characterized by common timing of migration with different foraging strategies.
C_LIO_LIThe observed differences in the rewiring of associations over time showed an increasing clustering of species having common responses to changing migration phenology in males, but not in females. This finding suggests a sex-decoupled effect of changing migration phenology on the onset of potential interferences in migratory birds, possibly influencing the global migration economy of landbirds in the Palearctic-African migration system.
C_LI


title: Call count surveys as a tool to monitor habitats occupied by Cheer Pheasants (Catreus wallichii) in Shimla, Himachal Pradesh

abstract: The vulnerable Cheer Pheasant (Catreus wallichii) is found in the western Himalayas. It prefers successional grasslands which are maintained by residents near villages. Therefore, it is prone to anthropogenic pressures which have led to local extinctions and a decline in population. We conducted five call count surveys at dusk and dawn from 15 April - 15 May 2020 in grasslands of Dharbhog panchayat, Shimla, Himachal Pradesh to assess presence of Cheer Pheasants in different habitat types. We used frequency of occurrence (number of encounters / number of visits) to determine presence or absence of Cheer Pheasant in an area of 10.5 km2 with ten established call count stations. We encountered Cheer Pheasants at six call count stations and the frequency of occurrence of the species ranged from 0 - 0.60. This survey provides an index of occupancy of the species and can be used to assess the change in habitat occupied by the species with time. The local forest department can also use these results to regulate over grazing and burning of grasslands during the breeding season in areas where we recorded the species.


title: High variation in handling times confers 35-year stability to predatorfeeding rates despite altered prey abundances and apparent diet proportions

abstract: Historical resurveys of ecological communities are important for placing the structure of modern ecosystems in context. Rarely, however, are snapshot surveys alone sufficient for providing direct insight into the rates of ecological processes that underlie how communities function, either now or in the past. In this study, I used a statistically-reasoned observational approach to estimate the feeding rates of a New Zealand intertidal predator, Haustrum haustorium, using diet surveys performed at several sites by Robert Paine in 1968-9 and by me in 2004. Comparisons between time periods reveal a remarkable consistency in H. haustoriums prey-specific feeding rates, which contrasts with the changes I observed in prey abundances, H. haustoriums body size distribution, and the proportional contributions of H. haustoriums prey to its apparent diet. Although these results imply accompanying and perhaps adaptive changes in H. haustoriums prey preferences, they are nonetheless anticipated by H. haustoriums high range of variation in prey-specific handling times that dictate not only its maximum possible feeding rates but also the probabilities with which feeding events may be detected during diet surveys. Similarly high variation in detection times (i.e. handling and digestion times) is evident in predator species throughout the animal kingdom. The potential disconnect between a predators apparent diet and its actual feeding rates suggests that much of the temporal and biogeographic variation that is perceived in predator diets and food-web structures may be of less functional consequence than currently assumed.


title: Using "identity by heterozygosity (IBH)" to detect clonemates under prevalent clonal reproduction in multicellular diploids

abstract: Clonal reproduction, the production of asexual modular units with the ability to live independently under multicellularity, is a very common life history. Genetic markers have been widely used to detect clonemates tracing back to a single sexual event. However, the currently available methods cannot work in cases where all collected samples belong to a few or even one single clone. Here we propose the concept of identity by heterozygosity (IBH), meaning that two diploid genomes are identically heterozygous at some genetic markers such as SNPs (single-nucleotide polymorphisms). Based on IBH, we develop IBH similarity (IBHs), a novel measure of genetic similarity between two diploid genomes. The core of our IBH method for detecting clonemates is to use IBHs in combination with the cutoff of 0.95. Two samples with IBHs >0.95 are considered members of the same clone, while two samples with IBHs <=0.95 are considered to represent different clones. The method requires a relatively large number of marker loci where the two target samples are identically heterozygous (i.e., NIBH, on the order of >=3,000). Another potential application of IBH is to detect possible parent-descendant pairs under selfing because this reproductive mode leads to a predictable loss of heterozygosity. Our IBH method extends the detection of clonemates to any pair of samples, and will allow the detection of clonemates in extreme cases where all collected samples belong to one single clone.

category: evolutionary biology


title: Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom

abstract: Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies, and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organisations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organisations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic and in silico reconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and inter-chromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.


title: Can imputation in a European country be improved by local reference panels? The example of France

abstract:
France has a population with extensive internal fine-structure; and while public imputation reference panels contain an abundance of European genomes, there include few French genomes. Intuitively, using a  study specific panel (SSP) for France would therefore likely be beneficial. To investigate, we imputed 550 French individuals using either the University of Michigan imputation server with the Haplotype Reference Consortium panel, or in-house using an SSP of 850 whole-genome sequenced French individuals.

With approximate geo-localization of both our target and SSP individuals we are able to pinpoint different scenarios where SSP-based imputation would be preferred over server-based imputation or vice-versa. We could also show to a high degree of resolution how the proximity of the reference panel to a target individual determined the accuracy of both haplotype phasing and genotype imputation.

Previous comparisons of different strategies have shown the benefits of combining public reference panels with SSPs. Getting the best out of both resources simultaneously is unfortunately impractical. We put forward a pragmatic solution where server-based and SSP-based imputation outcomes can be combined based on comparing posterior genotype probabilities. Such an approach can give a level of imputation accuracy markedly in excess of what could be achieved with either strategy alone.

category: genetics


title: A Model-Based Clustering via Mixture of Bayesian Hierarchical Models with Covariate Adjustment for Detecting Differentially Expressed Genes from Paired Design

abstract: The causes of many complex human diseases are still largely unknown. Genetics plays an important role in uncovering the molecular mechanisms of complex human diseases. A key step to characterize the genetics of a complex human disease is to unbiasedly identify disease-associated gene transcripts in whole-genome scale. Confounding factors could cause false positives. Paired design, such as measuring gene expression before and after treatment for the same subject, can reduce the effect of known confounding factors. Model-based clustering, such as mixtures of Bayesian hierarchical models, has been proposed to detect gene transcripts differentially expressed between paired samples. However, not all known confounding factors can be controlled in a paired/match design. To the best of our knowledge, no clustering methods have the capacity to adjust for the effects of covariates yet. In this article, we proposed a novel mixture of Bayesian hierarchical models with covariate adjustment in identifying differentially expressed transcripts using high-throughput whole-genome data from paired design. Both simulation study and real data analysis show the good performance of the proposed method

category: genomics


title: The Development and Evaluation of a Fully Automated Markerless Motion Capture Workflow

abstract: This study presented a fully automated deep learning based markerless motion capture workflow and evaluated its performance against marker-based motion capture during overground running, walking and counter movement jumping. Multi-view high speed (200 Hz) image data were collected concurrently with marker-based motion capture (criterion data), permitting a direct comparison between methods. Lower limb kinematic data for 15 participants were computed using 2D pose estimation, our 3D fusion process and OpenSim based inverse kinematics modelling. Results demonstrated high levels of agreement for lower limb joint angles, with mean differences ranging between 0.1{degrees} - 10.5{degrees} for 6 DoF hip joint rotations, and 0.7{degrees} - 3.9{degrees} for knee and ankle rotations. These differences generally fall within the documented uncertainties of marker-based motion capture, suggesting that our markerless approach could be used for appropriate biomechanics applications. We used an open-source, modular and customisable workflow, allowing for integration with other popular biomechanics tools such as OpenSim. By developing open-source tools, we hope to facilitate the democratisation of markerless motion capture technology and encourage the transparent development of markerless methods. This presents exciting opportunities for biomechanics researchers and practitioners to capture large amounts of high quality, ecologically valid data both in the laboratory and in the wild.

category: bioengineering


title: Reducing structural non-identifiabilities in upstream bioprocess models using profile-likelihood

abstract:
Process models are increasingly used to support upstream process development in the biopharmaceutical industry for process optimization, scale-up and to reduce experimental effort. Parametric unstructured models based biological mechanisms are highly promising, since they do not require large amounts of data. The critical part in the application is the certainty of the parameter estimates, since uncertainty of the parameter estimates propagates to model predictions and can increase the risk associated with those predictions. Currently Fisher-Information-Matrix based approximations or Monte-Carlo approaches are used to estimate parameter confidence intervals and regularization approaches to decrease parameter uncertainty.

Here we apply profile likelihood to determine parameter identifiability of a recent upstream process model. We have investigated the effect of data amount on identifiability and found out that addition of data reduces non-identifiability. The likelihood profiles of non-identifiable parameters were then used to uncover structural model changes. These changes effectively alleviate the remaining non-identifiabilities except for a single parameter out of 21 total parameters.

We present the first application of profile likelihood to a complete upstream process model. Profile likelihood is a highly suitable method to determine parameter confidence intervals in upstream process models and provides reliable estimates even with non-linear models and limited data.


title: Randomized gates eliminate bias in sort-seq assays

abstract: Sort-seq assays are a staple of the biological engineering toolkit, allowing researchers to profile many groups of cells based on any characteristic that can be tied to fluorescence. However, current approaches, which segregate cells into bins deterministically based on their measured fluorescence, introduce systematic bias. We describe a surprising result: one can obtain unbiased estimates by incorporating randomness into sorting. We validate this approach in simulation and experimentally, and describe extensions for both estimating group level variances and for using multi-bin sorters.


title: Photo-electrochemical Stimulation of Neurons With Organic Donor-Acceptor Heterojunctions

abstract: Recent advancements in light-responsive materials enabled the development of devices to artificially activate tissue with light, and show great potential for use in different types of therapy. Photo-stimulation based on organic semiconductors has recently attracted interest due to their unique set of properties such as biocompatibility, better mechanical match with human tissue, and strong absorption of light in the visible spectrum. Here we show the development of solution processed organic heterojunctions that are able to control the activity of primary neurons in vitro with light. The p-type polymer semiconductor PDCBT and the n-type polymer semiconductor ITIC (also known as non-fullerene acceptor) are simply spin coated on glass substrates forming a bilayer p-n junction with high photo-sensitivity in aqueous electrolytes. Photo-electrochemical measurements reveal that high photo-voltage and photo-current is produced, as a result of a charge transfer between the polymers and oxygen in the electrolyte. The biocompatibility of the proposed materials is addressed with live/dead assays on both primary mouse cortical neurons and human cell lines that are cultured on their surface. We have found that light of low intensity (i.e. 40 mW/cm2) is absorbed, and converted into a cue that triggers action potential on primary cortical neurons directly cultured on glass/PDCBT/ITIC interfaces as proven by patch clamp measurements. The activation of neurons is most likely due to photochemical reactions at the polymer/electrolyte interface that result in hydrogen peroxide, which might lead to modulation of specific ion channels on neurons membrane. Photo-thermal effects are excluded with controlled patch clamp measurements on neurons cultured on plain glass and on photoresist thin films. The profound advantages of low intensity light stimulation, simplified fabrication, and wireless operation pave the way for the integration of these interfaces in multiplex bioelectronic devices for the development of novel light therapy concepts and powerful neuroscience research tools.


title: Identification of biological processes and signaling pathways in lactate-treated cancer cells

abstract: Cancer is a complex disease that involves the alterations of metabolic pathways and tumor microenvironment. Lactate in the tumor microenvironment leads to cancer proliferation, metastasis, and angiogenesis. However, the effect of lactate on prostate cancer cells is still unclear. Here, our objective is to identify the significant molecules and biological processes by analyzing the RNA-seq data. The GSE195639 was produced by the Illumina NextSeq 500 (Homo sapiens). The KEGG and GO analyses show that Herpes simplex virus 1 infection and Rap1 signaling pathway are considered major pathways during the lactate-treated cancer cells. Furthermore, we identified the top ten essential molecules including IL6, CASP3, JUN, MAPK3, BRCA1, PIK3R1, CCNA2, TPI1, APOE, and EXO1. Therefore, our study may provide novel insights into the mechanism of prostate cancers.


title: Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data

abstract: Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of thousands of cells simultaneously and study transcriptomic changes between cells. scRNA-seq datasets increasingly include multi-subject, multi-condition experiments to investigate cell-type-specific differential states (DS) between conditions. This can be performed by first identifying the cell types in all the subjects and then by performing a DS analysis between the conditions within each cell type. Naive single-cell DS analysis methods that treat cells statistically independent are subject to false positives in the presence of variation between biological replicates, an issue known as the pseudo-replicate bias. While several methods have already been introduced to carry out the statistical testing in multi-subject scRNA-seq analysis, comparisons that include all these methods are currently lacking. Here, we performed a comprehensive comparison of 18 methods for the identification of DS changes between conditions from multi-subject scRNA-seq data. Our results suggest that the pseudo-bulk methods performed generally best. Both pseudo-bulks and mixed models that model the subjects as a random effect were superior compared with the naive single-cell methods that do not model the subjects in any way. While the naive models achieved higher sensitivity than the pseudo-bulk methods and the mixed models, they were subject to a high number of false positives. In addition, accounting for subjects through latent variable modeling did not improve the performance of the naive methods.


title: DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes

abstract: Minimizers are k-mer sampling schemes designed to generate sketches for large sequences that preserve sufficiently long matches between sequences. Despite their widespread application, learning an effective minimizer scheme with optimal sketch size is still an open question. Most work in this direction focuses on designing schemes that work well on expectation over random sequences, which have limited applicability to many practical tools. On the other hand, several methods have been proposed to construct minimizer schemes for a specific target sequence. These methods, however, require greedy approximations to solve an intractable discrete optimization problem on the permutation space of k-mer orderings. To address this challenge, we propose: (a) a reformulation of the combinatorial solution space using a deep neural network re-parameterization; and (b) a fully differentiable approximation of the discrete objective. We demonstrate that our framework, DO_SCPLOWEEPC_SCPLOWMO_SCPLOWINIMIZERC_SCPLOW, discovers minimizer schemes that significantly outperform state-of-the-art constructions on genomic sequences.


title: Choosing variant interpretation tools for clinical applications: context matters

abstract:
MotivationOur inability to solve the Variant Interpretation Problem (VIP) has become a bottleneck in the biomedical/clinical application of Next-Generation Sequencing. This situation has favored the development and use of in silico tools for the VIP. However, choosing the optimal tool for our purposes is difficult because of a fact usually ignored: the high variability of clinical context/scenarios across and within countries, and over time.

ResultsWe have developed a computational procedure, based on the use of cost models, that allows the simultaneous comparison of an arbitrary number of tools across all possible clinical scenarios. We apply our approach to a set of pathogenicity predictors for missense variants, showing how differences in clinical context translate to differences in tool ranking.

AvailabilityThe source code is available at: https://github.com/ClinicalTranslationalBioinformatics/clinical_space_partition


title: A balanced measure shows superior performance of pseudobulk methods over mixed models and pseudoreplication approaches in single-cell RNA-sequencing analysis

abstract:
Arising FromZimmerman, K. D., Espeland, M. A. & Langefeld, C. D. Nature Communications (2021). https://doi.org/10.1038/s41467-021-21038-1

SummaryRecently, Zimmerman et al.,1 proposed the use of mixed models over pseudobulk aggregation approaches, reporting improved performance on a novel simulation approach of hierarchical single-cell expression data. However, their reported results could not prove the superiority of mixed models as they are based on separate calculations of type 1 (performance of the models on non-differentially expressed genes) and type 2 error (performance on differentially expressed genes). To correctly benchmark the models, a reanalysis using a balanced measure of performance, considering both the type 1 and type 2 errors (both the differentially and non-differentially expressed genes), is necessary.

ContactAlan Murphy: a.murphy@imperial.ac.uk, Nathan Skene: n.skene@imperial.ac.uk

Code availabilityThe modified version of hierarchicell which returns the Matthews correlation coefficient performance metric as well as the type 1 error rates, uses the same simulated data across approaches and has checkpointing capabilities (so runs can continue from where they left off if aborted or crashed) is available at: https://github.com/neurogenomics/hierarchicell.

The benchmarking script along with the results are available at: https://github.com/Al-Murphy/reanalysis_scRNA_seq_benchmark.


title: Regulatory dynamics distinguishing desiccation tolerance strategies within resurrection grasses

abstract: Desiccation tolerance has evolved recurrently in grasses using two unique strategies to mitigate photooxidative damage under anhydrobiosis. The grass Oropetium thomaeum protects and retains chlorophyll, thylakoids, and the photosynthetic apparatus during desiccation (Homoiochlorophyly), while Eragrostis nindensis degrades and resynthesizes these components under desiccation and rehydration (Poikilochlorophyly). Here, we surveyed chromatin architecture and gene expression during desiccation in these two closely related species to identify regulatory dynamics underlying the distinct desiccation tolerance strategies in grasses. In both grasses, we observed a strong association between nearby chromatin accessibility and gene expression in desiccated tissues compared to well-watered, reflecting an unusual chromatin stability under anhydrobiosis. Integration of chromatin accessibility (ATACseq) and expression data (RNAseq) revealed a core desiccation response across these two grasses including many genes with binding sites for the core seed development transcription factor ABI5. O. thomaeum had a unique set of desiccation induced genes and regulatory elements associated with photoprotection, pigment biosynthesis, and response to high light, reflecting its adaptation of homoiochlorophyly. A tandem array of early light induced proteins (ELIPs) had massive shifts in gene expression and chromatin openness under desiccation in only O. thomaeum, and ELIPs acquired a novel desiccation related cis-regulatory motif, reflecting regulatory neofunctionalization during the evolution of desiccation tolerance. Together, our results highlight the complex regulatory and expression dynamics underlying desiccation tolerance in grasses.


title: Strigolactones are chemoattractants for host tropism in Orobanchaceae parasitic plants

abstract: Parasitic plants are worldwide threats that damage major agricultural crops. To initiate infection, parasitic plants have developed the ability to locate hosts and grow towards them. This ability, called host tropism, is critical for parasite survival, but its underlying mechanism remains mostly unresolved. To characterize host tropism, we used the model facultative root parasite Phtheirospermum japonicum, a member of the Orobanchaceae. Here, we show that strigolactones (SLs) function as host-derived chemoattractants. Chemotropism to SLs is also found in Striga hermonthica, a parasitic member of the Orobanchaceae, but not in non-parasites. Intriguingly, chemotropism to SLs in P. japonicum is attenuated in ammonium ion-rich conditions, where SLs are perceived, but the resulting asymmetrical accumulation of the auxin transporter PIN2 is diminished. P. japonicum encodes putative receptors that sense exogenous SLs, whereas expression of a dominant-negative form reduces its chemotropic ability. We propose a new function for SLs as navigators for parasite roots.


title: Eurasian Stone-curlews Burhinus oedicnemus breeding in Italy show a remarkable inter and intra-population variability of migratory behaviour

abstract: Migratory behaviour in birds shows a remarkable variability at species, population and individual levels. Short-distance migrants, in particular, often adopt a partial migratory strategy and tend to have a rather flexible migration schedule which allows them to respond more effectively to extreme environmental variations, like those due to climate change. Weather seasonality and environmental heterogeneity at regional and local scales have been reported as significant factors in the diversification of migratory behaviour for some species of Mediterranean migrants. Relatively few studies, however, investigated the migration patterns of non-passerine birds migrating within this area. In this study we investigated the migratory strategy of the Eurasian Stone-curlew Burhinus oedicnemus using data collected on 40 individuals tagged with geolocators and GPS-GSM tags, belonging to two continental and two Mediterranean populations of the Italian peninsula. The proportion of migrants was significantly higher in continental populations, but we observed a significant variability also within Mediterranean populations. GPS-tagged migrants traveled less than 1000 km, spending the winter within the Mediterranean basin. Continental Stone-curlews i) departed earlier in spring and later in autumn and ii) covered longer distances than those from Mediterranean areas. The speed of migration did not change between seasons for continental birds, while Mediterranean individuals tended to migrate faster in spring. The likelihood of departure for autumn migration of GPS-tagged birds significantly increased when temperatures were near or below 0 {degrees}C suggesting that Stone-curlews tend to delay departure weather conditions worsen abruptly. Thus it can be speculated that the frequency of migratory birds in the considered populations may decrease in the near future due to the effect of global warming in the Mediterranean. This could have a significant effect on the distribution of species throughout the year and should be taken into account when targeting conservation measures.


title: gamma aminobutyrate (GAB) functions as a bioenergetic and signaling gatekeeper to control T cell inflammation

abstract: {gamma}-Aminobutyrate (GAB) is the biochemical form of {gamma}-aminobutyric acid (GABA) at physiological pH and functions as an essential neurotransmitter in the vertebrates central nervous system (CNS). Growing evidence suggests that GAB may also mediate intercellular communications to shape various physiological processes, including immune response. Beyond acting as a paracrine signaling molecule, how GAB metabolism is controlled to exert many distinct functions remains elusive. By an integrated analysis of the extracellular metabolome, stable isotope traced metabolic pathway analysis, and metabolic transcriptome, we revealed that GAB is one of the most abundant metabolites produced through glutamine and arginine catabolism in CD4+ T help 17 (TH17) and induced T regulatory (iTreg) cells. GAB functions as a bioenergetic and signaling gatekeeper by reciprocally controlling pro-inflammatory TH17 cell and anti-inflammatory iTreg cell differentiation through distinct mechanisms. The expression of 4-aminobutyrate aminotransferase (ABAT) funnels GAB, as an anaplerotic substrate, into the TCA cycle to maximize carbon allocation in promoting TH17 cell differentiation. By contrast, the absence of ABAT activities in iTreg cells enables GAB exporting to the extracellular environment and acting as an autocrine signaling metabolite to promote iTreg cell differentiation. Accordingly, genetic or pharmacological ablation of ABAT activity in T cells confers protection against experimental autoimmune encephalomyelitis (EAE) pathogenic progression. Conversely, genetic ablation of GABA(A) receptor in T cells deteriorates EAE pathogenic progression. Collectively, our results suggest that the cell-autonomous control exerted by GAB on CD4+ T cell is bimodal and consists of the sequential action of two discrete processes, ABAT-dependent mitochondrial anaplerosis and the receptor-dependent autocrine signaling response, both of which are required for a properly controlled T cell-mediated inflammation.


title: Transkingdom mechanism of MAMP generation by chitotriosidase (CHIT1) feeds oligomeric chitin from fungal pathogens and allergens into TLR2-mediated innate immune sensing

abstract: Chitin is a highly abundant polysaccharide in nature and linked to immune recognition of fungal infections and asthma in humans. Ubiquitous in fungi and insects, chitin is absent in mammals and plants and, thus, represents a microbe-associated molecular pattern (MAMP). However, the highly polymeric chitin is insoluble, which potentially hampers recognition by host immune sensors. In plants, secreted chitinases degrade polymeric chitin into diffusible oligomers, which are  fed to innate immune receptors and co-receptors. In human and murine immune cells, a similar enzymatic activity was shown for human chitotriosidase (CHIT1) and oligomeric chitin is sensed via an innate immune receptor, Toll-like receptor (TLR) 2. However, a complete system of generating MAMPs from chitin and feeding them into a specific receptor/co-receptor-aided sensing mechanism has remained unknown in mammals. Here, we show that the secreted chitinolytic host enzyme, CHIT1, converts inert polymeric chitin into diffusible oligomers that can be sensed by TLR1-TLR2 co-receptor/receptor heterodimers, a process promoted by the lipopolysaccharide binding protein (LBP) and CD14. Furthermore, we observed that Chit1 is induced via the {beta}-glucan receptor Dectin-1 upon direct contact of immortalized human macrophages to the fungal pathogen Candida albicans, whereas the defined fungal secreted aspartyl proteases, Sap2 and Sap6, from C. albicans were able to degrade CHIT1 in vitro. Our study shows the existence of an inducible system of MAMP generation in the human host that enables contact-independent immune activation by diffusible MAMP ligands with striking similarity to the plant kingdom. Moreover, this study highlights CHIT1 as a potential therapeutic target for TLR2-mediated inflammatory processes that are fueled by oligomeric chitin.


abstract: Model selection aims to choose the most adequate model for the statistical analysis at hand. The model must be complex enough to capture the complexity of the data but should be simple enough to not overfit. In phylogenetics, the most common model selection scenario concerns selecting an appropriate substitution and partition model for sequence evolution to infer a phylogenetic tree. Here we explored the impact of substitution model over-parameterization in a Bayesian statistical framework. We performed simulations under the simplest substitution model, the Jukes-Cantor model, and compare posterior estimates of phylogenetic tree topologies and tree length under the true model to the most complex model, the GTR+{Gamma}+I substitution model, including over-splitting the data into additional subsets (i.e., applying partitioned models). We explored four choices of prior distributions: the default substitution model priors of MrBayes, BEAST2 and RevBayes and a newly devised prior choice (Tame). Our results show that Bayesian inference of phylogeny is robust to substitution model over-parameterization but only under our new prior settings. All three default priors introduced biases for the estimated tree length. We conclude that substitution and partition model selection are superfluous steps in Bayesian phylogenetic inference pipelines if well behaved prior distributions are applied.


title: Fisheries genomics of snapper (Chrysophrys auratus) along the western Australian coast

abstract: The efficacy of fisheries management strategies depends on stock assessment and management actions being carried out at appropriate spatial scales. This requires understanding of spatial and temporal population structure and connectivity, which is challenging in weakly structured and highly connected marine populations. We carried out a population genomics study of the heavily exploited snapper (Chrysophrys auratus) along [~]2,600 km of the Australian coastline, with a focus on Western Australia (WA). We used 10,903 filtered SNPs in 341 individuals from eight locations to characterise population structure and connectivity in snapper across WA and to assess if current spatial scales of stock assessment and management agree with evidence from population genomics. Our dataset also enabled us to investigate temporal stability in population structure as well as connectivity between WA and its nearest, eastern jurisdictional neighbor. As expected for a species influenced by the extensive ocean boundary current in the region, low genetic differentiation and high connectivity was uncovered across WA. However, we did detect strong isolation by distance and genetic discontinuities in the mid-west and south-east. The discontinuities correlate with boundaries between biogeographic regions, influenced by on-shelf oceanography, and the sites of important spawning aggregations. We also detected temporal instability in genetic structure at one of our sites, possibly due to interannual variability in recruitment in adjacent regions. Our results partly contrast with the current spatial management of snapper in WA, highlighting the need for a review. This study supports the value of population genomic surveys in informing the management of weakly-structured and wide-ranging marine fishery resources.


title: First record of anti-predator behavior in the gall-forming aphid Mordwilkoja vagabunda

abstract:
The gall-forming aphid Mordwilkoja vagabunda has been an outgroup in molecular studies of the evolution of social behavior in the Pemphigus genus, but Mordwilkoja aphids have not previously been assayed for social behavior, such as altruistic defense. This study reports experiments carried out in July in Ithaca, NY, USA, in which nymphs (immature aphids) of M. vagabunda were video recorded under a stereo microscope while they encountered pyralid moth larvae in a plastic arena. M. vagabunda nymphs of all instars used their legs to claw moth larvae while pressing their rostrums against the larvae, possibly to pierce the cuticle. Many of the attacking aphids were alatoid nymphs, rather than the specialized first instar soldiers typically observed in Pemphigus species. M. vagabunda nymphs moved in bursts that sometimes became synchronized among several aphids in the same vicinity. These synchronized, rhythmic movements may be anti-predator defense strategies comparable to the collective twitching and kicking response observed in colonies of Aphis nerii and other aphid species. Defensive behaviors by M. vagabunda nymphs may be altruistic fortress defense strategies which maximize inclusive fitness of the clone.

Open Research statementVideo data are shared publicly on a repository, Zenodo, at this DOI: https://doi.org/10.5281/zenodo.5636845

category: animal behavior and cognition


title: Nomograms of Human Hippocampal Volume Shifted by Polygenic Scores

abstract:
Nomograms are important clinical tools applied widely in both developing and aging populations. They are generally constructed as normative models identifying cases as outliers to a distribution of healthy controls. Currently used normative models do not account for genetic heterogeneity. Hippocampal Volume (HV) is a key endophenotype for many brain disorders. Here, we examine the impact of genetic adjustment on HV nomograms and the translational ability to detect dementia patients.

Using imaging data from 35,686 healthy subjects aged 44 to 82 from the UK BioBank (UKBB), we built HV nomograms using gaussian process regression (GPR), extending the application age by 20 years, including dementia critical age ranges. Using HV Polygenic Scores (HV-PGS), we built genetically adjusted nomograms from participants stratified into the top and bottom 30% of HV-PGS. This shifted the nomograms in the expected directions by [~]100 mm3 (2.3% of the average HV), which equates to 3 years of normal aging.

Clinical impact of genetically adjusted nomograms was investigated by comparing 818 subjects from the AD neuroimaging (ADNI) database diagnosed as either cognitively normal (CN), having mild cognitive impairment (MCI) or Alzheimers disease patients (AD). While no significant change in the survival analysis was found for MCI-to-AD conversion, an average of 4% decrease was found in intra-diagnostic-group variance, highlighting the importance of genetic adjustment in untangling phenotypic heterogeneity.


title: Yclon: Ultrafast clustering of B cell clones from high-throughput immunoglobulin repertoire sequencing data

abstract:
MotivationNext-generation sequencing technologies revolutionize our understanding of immunoglobulin (Ig) profile in different immune states. Clonotyping (grouping Ig sequences into B cell clones) allows the investigation of the diversity of repertoires and how they change upon antigen exposure. Despite its importance, there is no consensus on the best method for clonotyping, and the methods developed for that are computationally intractable for large sequencing datasets. This is the case of Change-O, which compares sequences through hamming distance and uses hierarchical clustering for this task.

ResultsWe propose implementing an approach to identify B cell clones from Ig repertoire data, named Yclon, that makes an alignment-free comparison of the sequences, focusing on reducing the runtime and computer memory usage. Overall, we find that a hierarchical clustering approach grouped Ig sequences into B cell clones similarly to Change-O. However, we observed that Yclon was around 35 times faster and even was able to process larger than 2 million sequences Ig repertoire, which is a critical part of repertoire studies and enables understanding antibody repertoire structure and affinity maturation.

Availability and implementationYClon is written in Python3 and is available on GitHub (https://github.com/jao321/YClon.git)

Contactjoaodgervasio@gmail.com, liza@icb.ufmg.br


title: Integrating Fossil Flowers into the Angiosperm Phylogeny using a Total Evidence Approach

abstract: Fossil flowers are essential to infer past angiosperm evolutionary processes. The assignment of fossil flowers to extant clades has traditionally relied on morphological similarity and on apomorphies shared with extant taxa. The use of explicit phylogenetic analyses to establish their affinity has so far remained limited. In this study, we built a comprehensive framework to investigate the phylogenetic placement of 24 exceptionally preserved fossil flowers. For this, we assembled a new species-level dataset of 30 floral traits for 1201 extant species that were sampled to represent the stem and crown nodes of all angiosperm families. We explored multiple analytical approaches to integrate the fossils into the phylogeny, including different phylogenetic estimation methods, topological-constrained analyses, and a total evidence approach combining molecular and morphological data of extant and fossil species. Our results were widely consistent across approaches, with minor differences in the support of fossils at different phylogenetic positions. The placement of some fossils is in agreement with previously suggested relationships, but for others, a new placement is indicated. We also identified fossils that are well constrained within particular extant families, whereas others showed high phylogenetic uncertainty. Finally, we present recommendations for future total evidence analyses, regarding the selection of fossils and appropriate methodologies, and provide some perspectives on how to integrate fossils into the investigation of divergence times and the temporal evolution of morphological traits.

category: paleontology


title: Detection and characterization of circulating microvesicles containing Shiga toxin type 2 (Stx2) in a rat model of Hemolytic Uremic Syndrome

abstract: Shiga toxin (Stx) producing Escherichia coli (STEC) are foodborne pathogens that release Stx and may develop Hemolytic Uremic Syndrome (HUS). Stx causes endothelial cell damage and leads to platelets deposition and thrombi formation within the microvasculature. It has been described that Stx activates blood cells and induces the shedding of proinflammatory and prothrombotic microvesicles (MVs) containing the toxin. In this sense, it has been postulated that MVs containing Stx2 (MVs-Stx2+) can contribute to the physiopathology of HUS, allowing Stx to reach the target organs and evading the immune system. In this work, we propose that circulating MVs-Stx2+ can be a potential biomarker for the diagnosis and prognosis of STEC infections and HUS progression. In this regard, we developed a rat HUS model by the intreperitoneal injection of a sublethal dose of Stx2 and observed: decrease in body weight, increase of creatinine and urea levels, decrease of creatinine clearance and histological renal damages. After characterization of renal damages we investigated circulating total MVs and MVs-Stx2+ by flow cytometry at different times after Stx2 injection. Additionally, we evaluated the correlation of biochemical parameters such as creatinine and urea in plasma with MVs-Stx2+. As a result, we found a significant circulation of Mvs-Stx2+ at 96 hours after Stx2 injection, nevertheless no correlation with creatinine and urea plasma levels were detected. Our results suggest that MVs-Stx2+ may be an additional biomarker for the characterization and diagnosis of HUS progression. Further analysis is required in order to validate MVs-Stx2+ as biomarker of the disease.


title: Probing stress-regulated ordering of the plant cortical microtubule array via a computational approach

abstract:
Functional properties of cells, tissues, and organs rely on predictable growth outputs. A shape change in plant cells is determined by properties of a tough cell wall that deforms anisotropically in response to high turgor pressure. This morphogenesis requires tight coordination and feedback controls among cytoskeleton-dependent wall patterning, its material properties, and stresses in the wall. Cortical microtubules bias the mechanical anisotropy of cell wall by defining the trajectories of cellulose synthase motility as they polymerize bundled microfibrils in their wake. Cortical microtubules could locally align and orient relative to cell geometry; however, the means by this orientation occurs is not known. Correlations between the microtubule orientation, cell geometry, and predicted tensile forces are strongly established, and here we simulate how different attributes of tensile force can orient and pattern the microtubule array in the cortex. We implemented a discrete model with three-state transient microtubule behaviors influenced by local mechanical stress in order to probe the mechanisms of stress-dependent patterning. We varied the sensitivity of four types of dynamic behaviors observed on the plus ends of microtubules - growth, shrinkage, catastrophe, and rescue - to local stress and then evaluated the extent and rate of microtubule alignments in a square computational domain. We optimized constitutive relationships between local stress and the plus-end dynamics and employed a biomechanically well-characterized cell wall to analyze how stress can influence the density and orientation of microtubule arrays. Our multiscale modeling approaches predict that spatial variability in stress magnitude and anisotropy mediate mechanical feedback between the wall and organization of the cortical microtubule array.

Author SummaryPlant cell growth involve multiple steps and processes. During growth, cell shape changes continuously while responding to external cues from the surroundings. Since growth is mainly driven by pressure, mechanical properties of cell wall are crucial in regulating multiple biological processes that underlie cell expansion and growth. Cell wall assembly is dynamically coupled to the remodeling of subcellular proteins. Experimental evidence has confirmed there exists potential mechanical feedback between wall assembly and protein-protein interactions. However, the actual mechanism remains unknown. In this study, we develop a computational model to study how mechanical stress could affect subcellular protein dynamics or interactions and lead to their reorganization, reminiscent of continuous changes in global pattern and cell morphology. Our results identify key parameters that can respond to external mechanical stimuli at the cellular scale. We also show that a biological stress pattern could induce protein filament organization and bundles that mimic real subcellular structure from experimental images. These computational results could benefit design of experiments for studying and discovering the potential protein candidates that underlie the mechanical feedback between multiple cellular components. In this way, a more systematic understanding about plant cell growth could be achieved, with an integrated theory that combine biology, chemistry, mechanics, and genetics.


title: Immunization with a self-assembling nanoparticle vaccine displaying EBV gH/gL protects humanized mice against lethal viral challenge

abstract: Summary/AbstractEpstein-Barr virus (EBV) is a cancer-associated pathogen responsible for 140,000 deaths per year. EBV is also the etiological agent of infectious mononucleosis and is associated with multiple sclerosis and rheumatoid arthritis. Thus, an EBV vaccine could alleviate significant morbidity and mortality. EBV is orally transmitted and has tropism for both epithelial cells and B cells which are present in the oral cavity. Therefore, a prophylactic vaccine would need to prevent infection of both cell types. Passive transfer neutralizing monoclonal antibodies targeting the viral gH/gL glycoprotein complex prevent experimental EBV infection in humanized mice and rhesus macaques, suggesting that gH/gL is an attractive vaccine candidate. Here, we produced and evaluated the immunogenicity of several nanoparticle immunogens displaying gH/gL with distinct valencies and geometries. After one or two immunizations, all nanoparticles elicited superior binding and neutralizing titers relative to monomeric gH/gL. Antibodies elicited by a computationally designed self-assembling nanoparticle that displays 60 copies of the gH/gL protein conferred protection against a lethal dose of EBV in a humanized mouse challenge model, whereas antibodies elicited by monomeric gH/gL did not. Taken together, these data motivate further development of gH/gL nanoparticle vaccine candidates for EBV.


title: Abiotic conditions shape spatial and temporal morphological variation in North American birds

abstract:
Abiotic environmental conditions play a key role in driving the size and shape of organisms. Quantifying environment-morphology relationships is important not only for understanding the fundamental processes driving phenotypic diversity within and among species (1), but also for predicting how species will respond to ongoing global change (2). Despite a clear set of expectations motivated by ecological theory (3), broad evidence in support of generalizable effects of abiotic conditions, such as temperature (4), on spatial and temporal intraspecific morphological variation has been limited. Using standardized data from over 250,000 captures of 105 landbird species, we assessed intraspecific shifts in bird morphology since 1989 while simultaneously measuring spatial morphological gradients across the North American continent. Across bird species, we found strong spatial and temporal trends in body size, with warmer temperatures associated with smaller body sizes both at more equatorial latitudes and in more recent years. The magnitude of these thermal effects varied both across and within species, with results suggesting it is the warmest, rather than the coldest, temperatures driving both spatial and temporal trends. Across elevation, we found that body size declines as relative wing length increases, likely due to the benefits that longer wings confer for flight in thin air environments. Our results provide support for both existing and new large-scale ecomorphological gradients and highlight how the response of functional tradeoffs to abiotic variation drives morphological change.

Significance StatementCharacterizing how the size and shape of organisms varies over space and time is key to understanding the processes that create ecological communities and for predicting how species will respond to climate change. Across more than 100 species of North American birds, we show that within species the size and shape of individuals varies substantially across space and time. Warmer temperatures are associated with smaller body sizes, likely due to the importance of body size for thermoregulation. As the climate continues to warm, these species will likely continue to shrink. We also provide the first large-scale evidence of an increase in wing length with elevation, a pattern that could be attributed to thinner air in high elevation environments.


title: AIscEA: Unsupervised Integration of Single-cell Gene Expression and Chromatin Accessibility via Their Biological Consistency

abstract:
Since the integrative analysis of single-cell gene expression and chromatin accessibility measurements is essential for revealing gene regulation at the single-cell resolution, integrating these two measurements becomes one of the key challenges in computational biology. Because gene expression and chromatin accessibility are measurements from different modalities, no common features can be directly used to guide their integration. Current state-of-the-art methods assume that the number of cell types across the measurements is the same. However, when cell-type heterogeneity exists, they might not generate reliable results. Furthermore, current methods do not have an effective way to select the hyper-parameter under the unsupervised setting. Therefore, applying computational methods to integrate single-cell gene expression and chromatin accessibility measurements remains difficult.

We introduce AIscEA - Alignment-based Integration of single-cell gene Expression and chromatin Accessibility - a computational method that integrates single-cell gene expression and chromatin accessibility measurements using their biological consistency. AIscEA first defines a ranked similarity score to quantify the biological consistency between cell types across measurements. AIscEA then uses the ranked similarity score and a novel permutation test to identify the cell-type alignment across measurements. For the aligned cell types, AIscEA further utilizes graph alignment to align the cells across measurements. We compared AIscEA with the competing methods on several benchmark datasets and demonstrated that AIscEA is more robust to hyper-parameters and can better handle the cell-type heterogeneity problem. Furthermore, we demonstrate that AIscEA significantly outperforms the state-of-the-art methods when integrating real-world SNARE-seq and scMultiome-seq datasets in terms of integration accuracy.


title: A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data

abstract:
BackgroundOne strategy for identifying targets of a regulatory factor is to perturb the factor and use high-throughput RNA sequencing to examine the consequences. However, distinguishing direct targets from secondary effects and experimental noise can be challenging when confounding signal is present in the background at varying levels.

ResultsHere, we present a statistical modeling strategy to identify microRNAs (miRNAs) that are primary substrates of target-directed miRNA degradation (TDMD) mediated by ZSWIM8. This method uses a bi-beta-uniform mixture (BBUM) model to separate primary from background signal components, leveraging the expectation that primary signal is restricted to upregulation and not downregulation upon loss of ZSWIM8. The BBUM model strategy retained the apparent sensitivity and specificity of the previous ad hoc approach but was more robust against outliers, achieved a more consistent stringency, and could be performed using a single cutoff of false discovery rate (FDR).

ConclusionsWe developed the BBUM model, a robust statistical modeling strategy to account for background secondary signal in differential expression data. It performed well for identifying primary substrates of TDMD and should be useful for other applications in which the primary regulatory targets are only upregulated or only downregulated. The BBUM model, FDR-correction algorithm, and significance-testing methods are available as an R package at https://github.com/wyppeter/bbum.


title: Improved pathogen and stress tolerance in tomato mutants of SET domain histone 3 lysine methyltransferases

abstract: Histone lysine methylations (HLMs) are implicated in control of gene expression in different eukaryotes. However, the role of HLMs in regulating desirable crop traits and the enzymes involved in these modifications are poorly understood. We studied the functions of tomato histone H3 lysine methyltransferases Set Domain Group 33 (SDG33) and SDG34 in biotic and abiotic stress responses. SDG33 and SDG34 mutants were altered in H3K36 and H3K4 methylations, and expression of genes involved in diverse processes and responses to biotic and abiotic stimuli. The double but not the single mutants show resistance to the fungal pathogen Botrytis cinerea. Interestingly, single mutants were tolerant to drought and the double mutant showed superior tolerance consistent with independent and additive functions. Mutants maintained higher water status during drought and improved recovery and survival after lapse of drought. Notably, diminution of H3K4 and H3K36 trimethylation and expression of negative regulators in challenged plants contributes to stress tolerance of the mutants. Mutations in SDG33 and SDG34 remove predisposition to biotic and abiotic stress by disrupting permissive transcriptional context promoting expression of negative regulatory factors. These allows improvement of stress and pathogen tolerance through modification of histone epigenetic marks.


title: Deletion of the microglial transmembrane immune signaling adaptor TYROBP ameliorates Huntington's disease mouse phenotype

abstract:
BACKGROUNDHuntingtons disease (HD) is a fatal neurodegenerative disorder caused by an expansion of the CAG trinucleotide repeat in the huntingtin gene. Immune activation is abundant in the striatum of HD patients. Detection of active microglia at presymptomatic stages suggests that microgliosis is a key early driver of neuronal dysfunction and degeneration. Recent studies showed that deletion of Tyrobp, a microglial-enriched protein, ameliorates neuronal function in Alzheimers disease amyloid and tauopathy mouse models while decreasing components of the complement subnetwork, thus raising the possibility that Tyrobp deletion can be beneficial for HD.

METHODSTo test the hypothesis that Tyrobp deficiency would be beneficial in a HD model, we placed the Q175 HD mouse model on a Tyrobp-null background. We characterized these mice with a combination of behavioral testing, immunohistochemistry, transcriptomic and proteomic profiling. Further, we evaluated the Q175 microglia-specific gene signature, with and without Tyrobp, by purifying microglia from these mice for transcriptomics.

RESULTSComprehensive analysis of publicly available transcriptomic HD human data revealed that TYROBP network is overactivated in HD putamen. The Q175 mice showed morphologic microglial activation, reduced levels of post-synaptic density-95 protein and motor deficits at 6 and 9 months of age, all of which were ameliorated on the Tyrobp-null background. Gene expression analysis revealed that lack of Tyrobp in the Q175 model does not prevent the decrease in the expression of striatal neuronal genes but reduces pro-inflammatory pathways that are specifically active in HD human brain. Integration of transcriptomic and proteomic data identified that astrogliosis and complement system pathway were reduced after Tyrobp deletion. Results were further validated by immunofluorescence analysis. Microglia-specific HD gene dysregulation, characterized by overexpression of neuronal genes, was also not corrected by Tyrobp deletion.

CONCLUSIONSOur data provide molecular and functional support demonstrating that Tyrobp deletion prevents many of the abnormalities in the Q175 HD mouse model, in the absence of correction of striatal neuronal gene expression, suggesting that the Tyrobp pathway is a potential therapeutic candidate for Huntingtons disease.