title: Cardiorespiratory fitness predicts cortical thickness of medial temporal brain areas associated with spatial cognition in young but not older adults

abstract:
Cardiorespiratory fitness (CRF) has been shown to have a potent effect on neurocognitive health. However, less is known about the impact of CRF on extrahippocampal neocortical regions in the medial temporal lobes (MTL). Specifically, it is unclear whether CRF modulates these MTL regions in young adulthood and if these brain areas are differentially related to CRF in young vs. older adults. The primary goal of the current study was to investigate if CRF predicted cortical thickness of MTL neocortical regions that, along with the hippocampus, are critical for spatial learning and memory. Additionally, given the established role of the MTL cortices in spatial navigation, we sought to determine if CRF and MTL cortical thickness would predict greater subjective sense of direction in both young and older adults. Cross-sectional data from 56 young adults (20-35 years) and 44 older adults (55-85 years) were included. Using hierarchical multiple regression analyses, we confirmed significant positive relationships between greater CRF and greater left entorhinal, left parahippocampal, and left perirhinal cortical thickness in young, but not older, adults. Left parahippocampal thickness interacted with age group to differentially predict sense of direction in young and older adults. Young adults displayed a positive, and older adults a negative, relationship between left parahippocampal thickness and sense of direction. Our findings extend previous work on the association between CRF and hippocampal subfield structure in young adulthood to left MTL neocortical regions.

HighlightsO_LICardiorespiratory fitness assessed in young and older adults using a submaximal treadmill test.
C_LIO_LISurface-based structural analysis of cortical thickness of medial temporal regions.
C_LIO_LICardiorespiratory fitness predicted left medial temporal cortical thickness in young but not older adults.
C_LIO_LILeft parahippocampal thickness differentially predicted sense of direction in young and older adults.
C_LI


title: Expression of the ACE2 virus entry protein in the nervus terminalis suggests an alternative route for brain infection in COVID-19

abstract: Previous studies suggested that the SARS-CoV-2 virus may gain access to the brain by using a route along the olfactory nerve. However, there is a general consensus that the obligatory virus entry receptor, angiotensin converting enzyme 2 (ACE2), is not expressed in olfactory receptor neurons, and the timing of arrival of the virus in brain targets is inconsistent with a neuronal transfer along olfactory projections. We determined whether nervus terminalis neurons and their peripheral and central projections should be considered as a potential alternative route from the nose to the brain. Nervus terminalis neurons in postnatal mice were double-labeled with antibodies against ACE2 and two nervus terminalis markers, gonadotropin-releasing hormone (GnRH) and choline acetyltransferase (CHAT). We show that a small fraction of CHAT-labeled nervus terminalis neurons, and the large majority of GnRH-labeled nervus terminalis neurons with cell bodies in the region between the olfactory epithelium and the olfactory bulb express ACE2 and cathepsins B and L. Nervus terminalis neurons therefore may provide a direct route for the virus from the nasal epithelium, possibly via innervation of Bowmans glands, to brain targets, including the telencephalon and diencephalon. This possibility needs to be examined in suitable animal models and in human tissues.

category: neuroscience


title: Expression of the ACE2 virus entry protein in the nervus terminalis reveals the potential for an alternative route to brain infection in COVID-19


title: An AI-guided invariant signature places MIS-C with Kawasaki disease in a continuum of host immune responses

abstract: A significant surge in cases of multisystem inflammatory syndrome in children (MIS-C, also called Pediatric Inflammatory Multisystem Syndrome - PIMS) has been observed amidst the COVID-19 pandemic. MIS-C shares many clinical features with Kawasaki disease (KD), although clinical course and outcomes are divergent. We analyzed whole blood RNA sequences, serum cytokines, and formalin fixed heart tissues from these patients using a computational toolbox of two gene signatures, i.e., the 166-gene viral pandemic (ViP) signature, and its 20-gene severe (s)ViP subset that were developed in the context of SARS-CoV-2 infection and a 13-transcript signature previously demonstrated to be diagnostic for KD. Our analyses revealed that KD and MIS-C are on the same continuum of the host immune response as COVID-19. While both the pediatric syndromes converge upon an IL15/IL15RA-centric cytokine storm, suggestive of shared proximal pathways of immunopathogenesis, they diverge in other laboratory parameters and cardiac phenotypes. The ViP signatures also revealed unique targetable cytokine pathways in MIS-C, place MIS-C farther along in the spectrum in severity compared to KD and pinpoint key clinical (reduced cardiac function) and laboratory (thrombocytopenia and eosinopenia) parameters that can be useful to monitor severity.

category: immunology


title: An AI-guided signature reveals the nature of the shared proximal pathways of host immune response in MIS-C and Kawasaki disease


title: The PD-L1 and TLR7 dual-targeting nanobody-drug conjugate exerts potent antitumor efficacy by orchestrating innate and adaptive immune responses

abstract:
A variety of tumors are insensitive to immune checkpoint blockade (ICB) therapy. We propose that ICB therapy alone is insufficient to fully reactivate antitumor T cells, while effective mobilization of antigen-presenting cells (APCs) to assist adaptive immune cell activation can lead to potent antitumor effects with broad responsiveness. The Toll-like receptor 7 (TLR7) agonist SZU-101 we developed can induce the innate immune response against tumors and increase the immunogenicity of tumors. Interestingly, SZU-101-induced upregulation of programmed death ligand 1 (PD-L1) expression in tumor tissues can further enhance the response rate of the PD-L1 antibody. In addition, PD-L1 nanobodies have better solid tumor penetration ability, and because of this ability, they can be used to precisely deliver SZU-101 to tumor tissues. Therefore, a PD-L1 and TLR7 dual-targeting nanobody-drug conjugate (NDC), a novel drug molecule, was developed. We found that TLR7 agonists and PD-L1 nanobodies act synergistically and that NDC treatment reshapes the tumor immune microenvironment, activates both innate and adaptive immune cells, and exerts antitumor effects in both "hot" and "cold" tumors primarily through CD8+ T cells and natural killer (NK) cells. Our data show that a PD-L1 and TLR7 dual-targeting NDC can exhibit potent antitumor efficacy by orchestrating innate and adaptive immune responses and shows good prospects for clinical development.

One Sentence SummaryBased on results showing that TLR7 agonists and PD-L1 nanobodies exert synergistic antitumor effects, a PD-L1 and TLR7 dual-targeting nanobody-drug conjugate that we developed shows good prospects for clinical development because it can orchestrate innate and adaptive immune responses, reshape the tumor immune microenvironment, and exert potent antitumor effects against both "hot" and "cold" tumors.


title: Legacy effect of constant and diurnally oscillating temperatures on soil respiration and microbial community structure

abstract: 1.0Laboratory incubation studies evaluating the temperature sensitivity of soil respiration often use measurements of respiration taken at a constant incubation temperature from soil that has been pre-incubated at the same constant temperature. However, such constant temperature incubations do not represent the field situation where soils undergo diurnal temperature oscillations. We investigated the effects of constant and diurnally oscillating temperatures on soil respiration and soil microbial community composition. A grassland soil from the UK was either incubated at a constant temperature of 5 {degrees}C, 10 {degrees}C, or 15 {degrees}C, or diurnally oscillated between 5 {degrees}C and 15 {degrees}C. Soil CO2 flux was measured by temporarily moving incubated soils from each of the abovementioned treatments to 5 {degrees}C, 10 {degrees}C or 15 {degrees}C, such that soils incubated at each temperature had CO2 flux measured at every temperature. We hypothesised that, irrespective of measurement temperature, CO2 emitted from the 5 {degrees}C to 15 {degrees}C oscillating incubation would be most similar to the soil incubated at 10 {degrees}C. The results showed that both incubation and measurement temperatures influence soil respiration. Incubating soil at a temperature oscillating between 5 {degrees}C and 15 {degrees}C resulted in significantly greater CO2 flux than constant incubations at 10 {degrees}C or 5 {degrees}C, but was not significantly different to the 15 {degrees}C incubation. The greater CO2 flux from soils incubated at 15 {degrees}C, or oscillating between 5 {degrees}C and 15 {degrees}C, coincided with a depletion of dissolved organic carbon and a shift in the phospholipid fatty acid profile of the soil microbial community, consistent with the thermal adaptation of microbial communities to higher temperatures. However, diurnal temperature oscillation did not significantly alter Q10. Our results suggest that daily maximum temperatures are more important than daily minimum or daily average temperatures when considering the response of soil respiration to warming.

category: microbiology


title: Comprehensive benchmarking of tools to identify phages in metagenomic shotgun sequencing data

abstract:
BackgroundAs the relevance of bacteriophages in shaping diversity in microbial ecosystems is becoming increasingly clear, the prediction of phage sequences in metagenomic datasets has become a topic of considerable interest, which has led to the development of many novel bioinformatic tools. A comprehensive comparative analysis of these tools has so far not been performed.

MethodsWe benchmarked ten state-of-the-art phage identification tools. We used artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage strains to evaluate the precision, recall and F1-scores of the tools. In addition, a set of previously simulated viromes was used to assess diversity bias in each tools output.

ResultsDeepVirFinder performed best across the datasets of artificial contigs and the mock community, with the highest F1-scores (0.98 and 0.61 respectively). Generally, machine learning-based tools performed better on the artificial contigs, while reference and machine learning based tool performed comparably on the mock community. Most tools produced a viral genome set that had similar alpha and beta diversity patterns to the original population with the notable exception of Seeker, whose metrics differed significantly from the diversity of the underlying data.

ConclusionsThis study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools.


title: Genetic Basis for Lentil Adaptation to Summer Cropping in Northern Temperate Environments

abstract:
The continued success of lentil (Lens culinaris Medik.) genetic improvement relies on the availability of broad genetic diversity and new alleles need to be identified and incorporated into the cultivated gene pool. Availability of robust and predictive markers greatly enhances the precise transfer of genomic regions from unadapted germplasm. Quantitative trait loci (QTLs) for key phenological traits in lentil were located using a recombinant inbreed line (RIL) population derived from a cross between an Ethiopian landrace (ILL 1704) and a northern temperate cultivar (CDC Robin). Field experiments were conducted at Sutherland research farm in Saskatoon and at Rosthern, Saskatchewan, Canada during 2018 and 2019. A linkage map was constructed using 21,634 SNPs located on seven linkage groups (LGs) which correspond to the seven haploid chromosomes of lentil. Eight QTL were identified for six phenological traits. Flowering related QTL were identified at two regions on LG6. FLOWERING LOCUS T (FT) genes were annotated within the flowering time QTL interval based on the lentil reference genome. Similarly, a major QTL for post-flowering developmental processes was located on LG5 with several senescence-associated genes annotated within the QTL interval. The flowering time QTL was validated in a different genetic background indicating the potential use of the identified markers for marker-assisted selection to precisely transfer genomic regions from exotic germplasm into elite crop cultivars without disrupting adaptation.

Core IdeasO_LIStable QTL were located for key phenological traits in lentil that lead to regional adaptation.
C_LIO_LIFT genes are candidates for controlling flowering time in lentil grown in temperate environments.
C_LIO_LIA major locus controlling post-flowering developmental processes was located on lentil LG5 with several senescence-associated genes annotated within the QTL interval.
C_LIO_LIMarkers identified in this study can be useful for marker-assisted selection to precisely transfer genomic regions from exotic germplasm into elite lentil cultivars without disrupting adaptation.
C_LI

category: molecular biology


title: Mutation rate dynamics reflect ecological changes in an emerging zoonotic pathogen

abstract: While mutation is often deleterious, it can also be adaptive. Mutation rates vary both within and between bacterial species, and understanding what drives this variation is essential for understanding the evolutionary dynamics of bacterial populations. In this study we investigate two factors that are predicted to influence the trade-off between the costs and benefits of mutation: ecology and genome size. To investigate the relationship between these factors and mutation rate we conducted mutation accumulation experiments on eight strains of the emerging zoonotic pathogen Streptococcus suis. Natural variation within this species allows us to compare tonsil carriage and invasive disease isolates, from both more and less pathogenic populations, with a wide range of genome sizes. We find that invasive disease isolates have repeatedly evolved mutation rates that are higher than those of closely related carriage isolates, regardless of variation in genome size. Independent of this variation in overall rate, we also observe a stronger bias towards G/C to A/T mutations in isolates from more pathogenic populations, whose genomes tend to be smaller and more AT-rich. Our results suggest that ecology is a stronger correlate of mutation rate than genome size over these timescales, and that transitions to invasive disease are consistently accompanied by rapid increases in mutation rate. These results shed light on the impact ecology can have on the adaptive potential of bacterial pathogens.

category: evolutionary biology


title: Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen


title: Activation of innate immune signalling during development predisposes to inflammatory intestine and shortened lifespan

abstract: Early-life inflammatory response is associated with risks of age-related pathologies. How transient immune signalling activity during animal development influences life-long fitness is not well understood. Using Drosophila as a model, we find that activation of innate immune pathway IMD signalling in the developing larvae increases adult starvation resistance, decreases food intake, and shortens organismal lifespan. Interestingly, lifespan is shortened by the IMD activation in the larval gut and fat body, while starvation resistance and food intake are altered by that in neurons. The adult flies developed with IMD activation show sustained IMD activity in the gut, despite complete tissue renewal during metamorphosis. The inflammatory adult gut is associated with a greater amount of Gluconobacter sp., characteristic gut microbiota increased in response to immune activation. Removing gut microbiota by antibiotics attenuates the increase of IMD activity and rescues the shortened lifespan. This study demonstrates a tissue-specific programming effect of early-life immune activation on the adult physiology and organismal lifespan.

category: genetics


title: The growth hormone gene has evolved independently in African Pygmy Mouse Mus minutoides

abstract: Mus minutoides (the African pygmy mouse) is one of the smallest mammals. We determined the nucleotide sequence of the growth hormone (Gh) gene and the sequence of the putative coding region in M. minutoides, where is predicted to be distinct in the functional and transcriptional regulatory regions between M. minutoides and Mus musculus (the House mouse). To investigate the evolutionary characteristics of Gh in M. minutoides, we constructed a phylogenetic tree based on the putative amino acid sequences of Gh in M. musculus and mammals by neighbor-joining method, suggesting that Gh diverged relatively earlier than other Mus genus and may have evolved independently in M. minutoides. Furthermore, analysis of Gh gene expression levels showed a tendency to be higher in M. minutoides than in M. musculus. Our results suggest that Gh may have evolved independently in M. minutoides and may have different functions and signaling in Mus genus.


title: Detection of conspicuous and cryptic food by marmosets (Callithrix jacchus): An evaluation of the importance of color and shape cues

abstract:
Since 19th century, the adaptive function of color vision for object identification has fascinated science. Countless articles uncovered the advantages of trichromacy (i.e., color vision expressed by most humans) in detecting yellowish/reddish targets against a background of mature green leaves. Unfortunately, the same attention was not offered to achromatic visual information, that had their physiological foundations much more explored than their possible adaptive function. So far, mostly because of studies conducted in humans, we know that achromatic cues might also play an important role in object identification, particularly when camouflage is involved. For instance, dichromacy (i.e., color vision expressed by many colorblind humans), favors the detection of camouflaged targets by exploitation of shape cues. The present study sought to evaluate the relative importance of color and shape cues on the detection of food targets by female and male marmosets (Callithrix jacchus). Animals were observed with respect to their foraging behavior and the number of food targets captured. We confirmed that females are advantageous in detecting conspicuous food against a green background and revealed that females and males rely on shape cues to segregate cryptic food. Unexpectedly, males outperformed females in cryptic food foraging. Camouflage improved males (but not females) performance.

HighlightsO_LIShape cues alone improve capture of cryptic targets by female and male marmosets.
C_LIO_LIThe sole use of color cues leads to clear-cut foraging performances between sex.
C_LIO_LIFemales outperform males when searching for orange food against a green background.
C_LIO_LIMales outperform females when searching for green food against a green background.
C_LIO_LIMales match females performance when searching for orange camouflaged food.
C_LI

category: animal behavior and cognition


title: Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling

abstract: DNA methylation microarrays can be employed to interrogate cell-type composition in complex tissues. Here, we expand reference-based deconvolution of blood DNA methylation to include 12 leukocyte subtypes (neutrophils, eosinophils, basophils, monocytes, B cells, CD4+ and CD8+ naive and memory cells, natural killer, and T regulatory cells). Including derived variables, our method provides up to 56 immune profile variables. The IDOL (IDentifying Optimal Libraries) algorithm was used to identify libraries for deconvolution of DNA methylation data both for current and retrospective platforms. The accuracy of deconvolution estimates obtained using our enhanced libraries was validated using artificial mixtures, and whole-blood DNA methylation with known cellular composition from flow cytometry. We applied our libraries to deconvolve cancer, aging, and autoimmune disease datasets. In conclusion, these libraries enable a detailed representation of immune-cell profiles in blood using only DNA and facilitate a standardized, thorough investigation of the immune system in human health and disease.

category: bioinformatics


title: Drug Sensitivity Prediction From Cell Line-Based Pharmacogenomics Data: Guidelines for Developing Machine Learning Models

abstract: The goal of precision oncology is to tailor treatment for patients individually using the genomic profile of their tumors. Pharmacogenomics datasets such as cancer cell lines are among the most valuable resources for drug sensitivity prediction, a crucial task of precision oncology. Machine learning methods have been employed to predict drug sensitivity based on the multiple omics data available for large panels of cancer cell lines. However, there are no comprehensive guidelines on how to properly train and validate such machine learning models for drug sensitivity prediction. In this paper, we introduce a set of guidelines for different aspects of training gene expression-based predictors using cell line datasets. These guidelines provide extensive analysis of the generalization of drug sensitivity predictors, and challenge many current practices in the community including the choice of training dataset and measure of drug sensitivity. Application of these guidelines in future studies will enable the development of more robust preclinical biomarkers.


title: RESIC: A tool for comprehensive adenosine to inosine RNA Editing Site Identification and Classification

abstract: Adenosine to inosine (A-to-I) RNA editing, the most prevalent type of RNA editing in metazoans, is carried out by adenosine deaminases (ADARs) in double-stranded RNA regions. Several computational approaches have been recently developed to identify A-to-I RNA editing sites from sequencing data, each addressing a particular issue. Here we present RESIC, an efficient pipeline that combines several approaches for the detection and classification of RNA editing sites. The pipeline can be used for all organisms and can use any number of RNA-sequencing datasets as input. RESIC provides 1. The detection of editing sites in both repetitive and non-repetitive genomic regions; 2. The identification of hyper-edited regions; 3. Optional exclusion of polymorphism sites to increase reliability, based on DNA, and ADAR-mutant RNA sequencing datasets, or SNP databases. We demonstrate the utility of RESIC by applying it to human, successfully overlapping and extending the list of known putative editing sites. We further tested changes in the patterns of A-to-I RNA editing, and RNA abundance of ADAR enzymes, following SARS-CoV-2 infection in human cell lines. Our results suggest that upon SARS-CoV-2 infection, compared to mock, the number of hyper editing sites is increased, and in agreement, the activity of ADAR1, which catalyzes hyper-editing, is enhanced. These results imply the involvement of A-to-I RNA editing in conceiving the unpredicted phenotype of COVID-19 disease. RESIC code is open-source and is easily extendable.


title: Vitamin C - protective role in oxidative stress conditions induced in human normal colon cells by label free Raman spectroscopy and imaging

abstract:
Colorectal cancer is the second most frequently diagnosed cancer worldwide. Conventional diagnostics methods of colorectal cancer, can detect it in advanced stage.

Spectroscopic methods, including Raman spectroscopy and imaging, are becoming more and more popular in medical applications, and allow fast, precise and unambiguous differentiation of healthy and cancerous samples. the most important advantage of Raman spectroscopy is ability to identify biomarkers that help in differentiation of healthy and cancerous cells based on biochemistry of sample and spectra typical for: lipids, proteins, DNA.

The aim of the study was to evaluate the biochemical and structural features of human colon cell lines based on Raman spectroscopy and imaging: normal cells CCD-18 Co, normal cells CCD-18 Co under oxidative stress conditions, normal cells CCD-18 Co at first treated by using tert-Butyl hydroperoxide and then supplemented by vitamin C in high concentration to show the protective role of vitamin C in micromolar concentrations against ROS by spectroscopic methods. Raman data obtained for normal cells injured by ROS were compared with spectra typical for cancerous cells.

Statistically assisted analysis has shown that normal, ROS injured and cancerous human colon cells can be distinguished based on their unique vibrational properties.

The research carried out proves that label-free Raman spectroscopy may play an important role in clinical diagnostics differentiation of normal and cancerous colon cells and may be a source of intraoperative information supporting histopathological analysis.

category: cancer biology


title: Undergraduate student interest in healthcare career in the context of COVID-19 pandemic

abstract:
ObjectivesThe healthcare profession has been long considered an excellent career choice. Pre-medical experience is documented to be important in shaping future medical landscape. In the wake of the pandemic, there has been intense media spotlight on the healthcare profession and change in academic environment, necessitating analyses of student experience. This project aims to assess change in undergraduate student interest in healthcare career using cross-sectional survey study.

MethodsThe project was approved by our Institutional Review Board. Voluntary survey collected data on demographics, socioeconomics, media exposure, academic environment, and change in interest in a healthcare profession. Survey was distributed through the university undergraduate pre-health listserv. Total of 297 responses were obtained. Descriptive statistics including Fishers exact test were applied in the analysis.

ResultsMajority of the respondents were Asians (54.9%), second generation immigrants (52.2%), and female (73.4%). Large proportion of the respondents were negatively affected by the pandemic, with losing a job or internship personally (42.1%) or a family member or a friend (62.6%). Students had mixed response to online learning environment, with 27.3% of students noting no change, 40.4% students noting increased difficulty, and 32.3% students noting decreased difficulty of classes. During the pandemic, 47.5% of students noted increased interest in pursuing healthcare career. The change in interest in healthcare career was not associated with xdemographics, economic hardship, or online learning environment.

DiscussionDespite the challenges of COVID-19 pandemic, students showed strong interest in pursuing healthcare careers.

category: scientific communication and education


title: Crystal sturctures of Scone, pseudosymmetric folding of a symmetric designer protein

abstract: Recent years have seen a raise in the development of computational proteins including symmetric ones. We recently developed a nine-fold symmetric {beta}-propeller protein named Cake. Here we wanted to further engineer this protein to a three-fold symmetric nine-bladed propeller using computational design. Two nine-bladed propeller proteins were designed, named Scone-E and Scone-R. Crystallography however revealed the structure of both designs to adopt an eight-fold conformation with distorted termini, leading to a pseudo-symmetric protein. One of the proteins could only be crystallized upon addition of a polyoxometalate highlighting the usefulness of these molecules as a crystallisation additive.

category: systems biology


title: Measuring salivary cortisol in wild carnivores

abstract:
Salivary hormone analyses provide a useful alternative to fecal and urinary hormone analyses in non-invasive studies of behavioral endocrinology. Here, we use saliva to assess cortisol levels in a wild population of spotted hyenas (Crocuta crocuta), a gregarious carnivore living in complex social groups. We first describe a novel, non-invasive method of collecting saliva from juvenile hyenas and validate a salivary cortisol assay for use in this species. We then analyze over 260 saliva samples collected from nearly 70 juveniles to investigate the relationships between cortisol and temporal and social variables in these animals. We obtain evidence of a bimodal daily rhythm with salivary cortisol concentrations dropping around dawn and dusk, times at which cub activity levels are changing substantially. We also find that dominant littermates have lower cortisol than either subordinate littermates or singletons, but that cortisol does not vary with age, sex, or maternal social rank. Finally, we examine how social behaviors such as aggression or play affect salivary cortisol concentrations. We find that inflicting aggression on others was associated with lower cortisol concentrations. We hope that the detailed description of our methods provides wildlife researchers with the tools to measure salivary cortisol in other wild carnivores.

HIGHLIGHTSO_LIWe validated methods for collecting and analyzing saliva from wild carnivores.
C_LIO_LIWe documented a bimodal daily rhythm in juvenile spotted hyena salivary cortisol.
C_LIO_LICortisol varied among juvenile hyenas based on litter size and intra-litter rank.
C_LIO_LIInflicting aggression on others was associated with lower cortisol concentrations.
C_LI

category: zoology


title: An autonomous tail-beating cycle period expressed by a region-specific swimming pattern generator in the Ciona larva

abstract:
Swimming locomotion in aquatic vertebrates, such as fish and tadpoles, is expressed through orchestrated operations of central pattern generators. These parallel neuronal circuits are ubiquitously distributed and mutually coupled along the spinal cord to express undulation patterns accommodated to efferent and afferent inputs. While such sets of schemes have been shown in vertebrates, the evolutionary origin of those mechanisms along the chordate phylogeny remains unclear. Ascidians, representing a sister group of vertebrates, give rise to tadpole larvae that freely swim in seawater. In this study, we tried to locate the swimming pattern generator in larvae of the ascidian Ciona by examining locomotor ability of segmented body fragments. Our experiments demonstrated necessary and sufficient pattern generator activity in a short region ([~]10% of the body length as the longest estimation) including the trunk-tail junction but excluding most of the trunk and tail with major sensory apparatuses therein. Moreover, we found that these "mid-piece" body fragments express periodic tail beating bursts with [~]20-s intervals without any exogenous stimuli. Comparisons among temporal patterns of tail beating bursts expressed by the mid-piece fragments and by whole larvae placed under different sensory conditions suggested that the presence of parts other than the critical mid-piece had effects to shorten swimming burst intervals, especially in the dark, and also to expand the variance in burst durations. We propose that Ciona larvae perform swimming as modified representations of autonomous and periodic pattern generator drives, which operate locally in the region of the trunk-tail junction.

Summary statementMid-piece fragments of tadpole larvae of the ascidian Ciona, lacking most of the anterior trunk and posterior tail, autonomously and periodically express tail beating bursts.


title: Naming-related spectral responses predict neuropsychological outcome after epilepsy surgery

abstract: This prospective study determined the utility of intracranially-recorded spectral responses during naming tasks in predicting neuropsychological performance following epilepsy surgery. We recruited 65 patients with drug-resistant focal epilepsy who underwent preoperative neuropsychological assessment and intracranial EEG (iEEG) recording. The Clinical Evaluation of Language Fundamentals (CELF) evaluated the baseline and postoperative language function. During extraoperative iEEG recording, we assigned patients to undergo auditory and picture naming tasks. Time-frequency analysis determined the spatiotemporal characteristics of naming-related amplitude modulations, including high gamma augmentation (HGA) at 70-110 Hz. We surgically removed the presumed epileptogenic zone based on the extent of iEEG and MRI abnormalities while maximally preserving the eloquent areas defined by electrical stimulation mapping (ESM). The multivariate regression model incorporating auditory naming-related HGA predicted the postoperative changes in Core Language Score (CLS) on CELF with r2 of 0.37 (p = 0.015) and in Expressive Language Index (ELI) with r2 of 0.32 (p = 0.047). Independently of the effects of epilepsy and neuroimaging profiles, higher HGA at the resected language-dominant hemispheric area predicted a more severe postoperative decline in CLS (p = 0.004) and ELI (p = 0.012). Conversely, the model incorporating picture naming-related HGA predicted the change in Receptive Language Index (RLI) with r2 of 0.50 (p < 0.001). Higher HGA independently predicted a more severe postoperative decline in RLI (p = 0.03). Ancillary regression analysis indicated that naming-related low gamma augmentation as well as alpha/beta attenuation likewise independently predicted a more severe CLS decline. The machine learning-based prediction model, referred to as the boosted tree ensemble model, suggested that naming-related HGA, among all spectral responses utilized as predictors, most strongly contributed to the improved prediction of patients showing a >5-point CLS decline (reflecting the lower 25 percentile among patients). We generated the model-based atlas visualizing sites, which, if resected, would lead to such a CLS decline. The auditory naming-based model predicted patients who developed the CLS decline with an accuracy of 0.80. The model indicated that virtual resection of an ESM-defined language site would have increased the relative risk of the CLS decline by 5.28 (95%CI: 3.47 to 8.02). Especially, that of an ESM-defined receptive language site would have maximized it to 15.90 (95%CI: 9.59-26.33). In summary, naming-related spectral responses predict objectively-measured neuropsychological outcome after epilepsy surgery. We have provided our prediction model as an open-source material, which will indicate the postoperative language function of future patients and facilitate external validation at tertiary epilepsy centers.


title: Tissue-resident FOLR2+ macrophages associate with tumor-infiltrating CD8+ T cells and with increased survival of breast cancer patients.

abstract: Macrophage infiltration is a hallmark of solid cancers and overall macrophage infiltration is correlated with lower patient survival and resistance to therapy. However, tumor-associated macrophages are phenotypically and functionally heterogeneous. Specific tumor-associated macrophage subsets might be endowed with antagonistic role on cancer progression and on the development of anti-tumor immunity. For instance, monocyte-derived TREM2+ tumor-associated macrophages have pro-tumorigenic and immunosuppressive functions. Here, we identify a discrete population of FOLR2+ tumor-associated macrophages positively correlating with patient survival in breast cancer. FOLR2+ macrophages are evolutionarily conserved across species and populate human and murine healthy mammary gland. Moreover, FOLR2+ macrophages co-localize with lymphoid aggregates containing CD8+ T cells in breast cancer and across ten other types of cancers. This study highlights antagonistic roles for tumor-associated macrophage subsets and paves the way for subset-specific therapeutic interventions in macrophages-based cancer therapies.


title: Public-good driven release of heterogeneous resources leads to genotypic diversification of an isogenic yeast population in melibiose.

abstract: Adaptive diversification of an isogenic population, and its molecular basis has been a subject of a number of studies in the last few years. Microbial populations offer a relatively convenient model system to study this question. In this context, an isogenic population of bacteria (E. coli, B. subtilis, and Pseudomonas) has been shown to lead to genetic diversification in the population, when propagated for a number of generations. This diversification is known to occur when the individuals in the population have access to two or more resources/environments, which are separated either temporally or spatially. Here, we report adaptive diversification in an isogenic population of yeast, S. cerevisiae, when propagated in an environment containing melibiose as the carbon source. The diversification is driven due to a public good, enzyme -galactosidase, leading to hydrolysis of melibiose into two distinct resources, glucose and galactose. The diversification is driven by a mutations at a single locus, in the GAL3 gene in the GAL/MEL regulon in the yeast.


title: Phumdis-A Promising Alternative Energy Resource

abstract: The inadequate sources of energy coupled with the increasing demands of power have necessitated the search for novel renewable energy resources.  Phumdis are one such promising alternative. Phumdis are floating mats of heterogeneous mass of vegetation, soil and organic matter found in Loktak Lake in Manipur, North Eastern India. This paper delineates the use of Phumdis as an alternative energy source. Phumdis from Loktak Lake, Manipur were processed and analyzed for their biofuel capabilities. The Results indicate that the phumdis have high calorific content, cloudpoint and flash point indicating that they are at par with other fuels.

category: developmental biology


title: Impairment of SARS-CoV-2 spike glycoprotein maturation and fusion activity by the broad-spectrum anti-infective drug nitazoxanide

abstract: SARS-CoV-2, the causative agent of COVID-19, has caused an unprecedented global health crisis. The SARS-CoV-2 spike, a surface-anchored trimeric class-I fusion-glycoprotein essential for viral entry, represents a key target for developing vaccines and therapeutics capable of blocking virus invasion. The emergence of SARS-CoV-2 spike-variants that facilitate virus spread and may affect vaccine efficacy highlights the need to identify novel antiviral strategies for COVID-19 therapy. Here we demonstrate that nitazoxanide, an antiprotozoal agent with recognized broad-spectrum antiviral activity, interferes with SARS-CoV-2 spike biogenesis, hampering its maturation at an endoglycosidase H-sensitive stage. Engineering multiple SARS-CoV-2 variant-pseudoviruses and utilizing quantitative cell-cell fusion assays, we show that nitazoxanide-induced spike modifications hinder progeny virion infectivity as well as spike-driven pulmonary cell-cell fusion, a critical feature of COVID-19 pathology. Nitazoxanide, being equally effective against the ancestral SARS-CoV-2 Wuhan-spike and different emerging variants, including the Delta variant of concern, may represent a useful tool in the fight against COVID-19 infections.


title: Impairment of SARS-CoV-2 spike-glycoprotein maturation and fusion-activity by nitazoxanide: an effect independent of spike variants emergence


title: Cascade screening following a polygenic risk score test: what is the disease risk of a sibling conditional on a high score of a proband?

abstract: Polygenic risk scores (PRSs) for predicting disease risk have become increasingly accurate, leading to rising popularity of PRS tests. Consider an individual whose PRS test has placed him/her at the top q-quantile of genetic risk. Recently, Reid et al. (Circ Genom Precis Med. 2021;14:e003262) have investigated whether such a finding should motivate cascade screening in the probands siblings. Specifically, using data from the UK biobank, Reid et al. computed the empirical probability of a sibling of the proband to also have a PRS at the top q-quantile. In this short note, I use the liability threshold model to compute this probability analytically (for either a sibling of the proband or for a more distant relative), showing excellent agreement with the empirical results of Reid et al., including that this probability is disease-independent. Further, I compute the probability of the relative of the proband to be affected, as a function of the quantile threshold q, the proportion of variance explained by the score, and the disease prevalence.


title: Cascade screening following a polygenic risk score test: what is the risk of a relative conditional on a high score of a proband?


title: Normalisr: normalization and association testing for single-cell CRISPR screen and co-expression

abstract: Single-cell RNA sequencing (scRNA-seq) provides unprecedented technical and statistical potential to study gene regulation but is subject to technical variations and sparsity. Here we present Normalisr, a linear-model-based normalization and statistical hypothesis testing framework that unifies single-cell differential expression, co-expression, and CRISPR scRNA-seq screen analyses. By systematically detecting and removing nonlinear confounding from library size, Normalisr achieves high sensitivity, specificity, speed, and generalizability across multiple scRNA-seq protocols and experimental conditions with unbiased P-value estimation. We use Normalisr to reconstruct robust gene regulatory networks from trans-effects of gRNAs in large-scale CRISPRi scRNA-seq screens and gene-level co-expression networks from conventional scRNA-seq.


title: Interactions between SARS-CoV-2 N-protein and α-synuclein accelerate amyloid formation

abstract: First cases that point at a correlation between SARS-CoV-2 infections and the development of Parkinsons disease have been reported. Currently it is unclear if there also is a direct causal link between these diseases. To obtain first insights into a possible molecular relation between viral infections and the aggregation of -synuclein protein into amyloid fibrils characteristic for Parkinsons disease, we investigated the effect of the presence of SARS-CoV-2 proteins on -synuclein aggregation. We show, in test tube experiments, that SARS-CoV-2 S-protein has no effect on -synuclein aggregation while SARS-CoV-2 N-protein considerably speeds up the aggregation process. We observe the formation of multi-protein complexes, and eventually amyloid fibrils. Microinjection of N-protein in SHSY-5Y cells disturbed the -synuclein proteostasis and increased cell death. Our results point toward direct interactions between the N-protein of SARS-CoV-2 and -synuclein as molecular basis for the observed coincidence between SARS-CoV-2 infections and Parkinsonism.

category: biophysics


title: In vivo genome-wide CRISPR screens identify SOCS1 as a major intrinsic checkpoint of CD4+ Th1 cell response

abstract: The expansion of antigen experienced CD4+ T cells is limited by intrinsic factors. Using in vivo genome-wide CRISPR-Cas9 screens, we identified SOCS1 as a non-redundant checkpoint imposing a brake on CD4+ T-cell proliferation upon rechallenge. We show here that SOCS1 is a critical node integrating both IL-2 and IFN-{gamma} signals and blocking multiple signaling pathways to abrogate CD4+ Th1 cell response. In CD8+ T-cell, SOCS1 does not impact the proliferation but rather reduces survival and effector functions. By targeting SOCS1, both murine and human CD4+ T-cell antitumor adoptive therapies exhibit a restored intra-tumor accumulation, proliferation/survival, persistence and polyfunctionality, promoting long term rejection of established tumors. These findings identify SOCS1 as a major intracellular checkpoint inhibitor of primed CD4+ T cells, opening new possibilities to optimize CAR-T cell therapies composition and efficacy.


title: Epitope profiling of coronavirus-binding antibodies using computational structural modelling

abstract: Identifying the epitope of an antibody is a key step in understanding its function and its potential as a therapeutic. It is well-established in the literature that sequence-based clonal clustering can identify antibodies with similar epitope complementarity. However, there is growing evidence that antibodies from markedly different lineages but with similar structures can engage the same epitope with near-identical binding modes. Here, we describe a novel computational method for epitope profiling based on structural modelling and clustering, and show how it can identify sequence-dissimilar antibodies that engage the same epitope. We start by searching for evidence of structural conservation across the latest solved SARS-CoV-2--binding antibody crystal structures. Despite the relatively small number of solved structures, we find numerous examples of sequence-diverse but structurally-similar coronavirus-binding antibodies engaging the same epitope. We therefore developed a high-throughput structural modeling and clustering method to identify functionally-similar antibodies across the set of thousands of coronavirus-binding antibody sequences in the Coronavirus Antibody Database (CoV-AbDab). In the resulting multiple-occupancy structural clusters, 92% bind to consistent domains based on CoV-AbDab metadata. Our approach functionally links antibodies with distinct genetic lineages, species origins, and coronavirus specificities. This indicates greater convergence exists in the immune responses to coronaviruses than would be suggested by sequence-based approaches. Our results show that applying structural analytics to large class-specific antibody databases will enable high confidence structure-function relationships to be drawn, yielding new opportunities to identify functional convergence hitherto missed by sequence-only analysis.


title: LRR protein RNH1 inhibits inflammasome activation through proteasome-mediated degradation of Caspase-1 and is associated with adverse clinical outcomes in COVID-19 patients.

abstract: Inflammasomes are cytosolic innate immune sensors of pathogen infection and cellular damage that induce caspase-1 mediated inflammation upon activation. Although inflammation is protective, uncontrolled excessive inflammation can cause inflammatory diseases and can be detrimental, such as in COVID-19. However, the underlying mechanisms that control inflammasome activation are incompletely understood. Here we report that the leucine rich repeat (LRR) protein Ribonuclease inhibitor (RNH1), which shares homology with LRRs of NLRP proteins, attenuates inflammasome activation. Deletion of RNH1 in macrophages increases IL-1{beta} production and caspase-1 activation for inflammasome stimuli. Mechanistically, RNH1 decreases pro-IL-1{beta} expression and induces proteasome-mediated caspase-1 degradation. Corroborating this, mouse models of monosodium urate (MSU)-induced peritonitis and LPS-induced endotoxemia, which are dependent on caspase-1, respectively show increased neutrophil infiltration and lethality in Rnh1-/- mice compared to WT mice. Furthermore, RNH1 protein levels are negatively correlated with inflammation and disease severity in hospitalized COVID-19 patients. We propose that RNH1 is a new inflammasome regulator with relevance to COVID-19 severity.


title: LRR protein RNH1 dampens the inflammasome activation and is associated with adverse clinical outcomes in COVID-19 patients


title: Cannabidiol (CBD) repurposing as antibacterial: promising therapy of CBD plus polymyxin B against superbugs

abstract:
Abstract

Multidrug-resistant (MDR) and extensively drug-resistant (XDR) bacteria are a major worldwide public health problem. In the last decades, resistance to last-resort antibiotics such as polymyxin B (PB) have been increasingly observed among these superbugs, compromising the effectiveness of antimicrobial therapy. The present study aimed (i) to assess the ultrapure Cannabidiol (CBD) antibacterial activity against a broad diversity of Gram-negative (GN) and Gram-positive (GP) bacteria (44 different species, 95 strains), comprising standard strains and clinical isolates, and (ii) to investigate the antibacterial activity of the combination CBD + PB against GN bacteria, including chromosomal- and plasmid-acquired PB-resistant and intrinsically PB-resistant GNB. We evaluated CBD in vitro antibacterial activity using the standard broth microdilution method, and the antibacterial activity of the combination CBD + PB was screened using the standard broth microdilution and confirmed by checkerboard assay. CBD exhibited antibacterial activity against different GP bacterial species, lipooligosaccharide (LOS)-expressing GN diplococcus (GND) (Neisseria gonorrhoeae, Neisseria meningitidis, and Moraxella catarrhalis), and Mycobacterium tuberculosis. The combination CBD + PB exhibited antibacterial activity against PB-resistant GNB (e.g., Klebsiella pneumoniae) as well as additive and/or synergistic effect against LOS-expressing GND. The antibacterial activity of the combination CBD + PB against Pseudomonas aeruginosa and plasmid-mediated colistin-resistant (MCR-1) E. coli strains could be only demonstrated in the presence of phenylalanine-arginine-{beta}-naphthylamide (PA{beta}N). In conclusion, our results show promising translational potential of the combination CBD + PB against MDR and XDR GNB, including PB-resistant K. pneumoniae, highlighting its potential as a rescue treatment for life-threatening infections caused by these superbugs.

One Sentence SummaryPromising combination of cannabidiol (CBD) + polymyxin B (PB) against superbugs (e.g., PB-resistant Gram-negative bacilli): Repurposing CBD


title: Investigating the roles of Listeria monocytogenes peroxidases in growth and virulence

abstract: Bacteria have necessarily evolved a protective arsenal of proteins to contend with peroxides and other reactive oxygen species generated in aerobic environments. Listeria monocytogenes encounters an onslaught of peroxide both in the environment and during infection of the mammalian host, where it is the causative agent of the foodborne illness listeriosis. Despite the importance of peroxide for the immune response to bacterial infection, the strategy by which L. monocytogenes protects against peroxide toxicity has yet to be illuminated. Here, we investigated the expression and essentiality of all the peroxidase-encoding genes during L. monocytogenes growth in vitro and during infection of murine cells in tissue culture. We found that chdC and kat were required for aerobic growth in vitro, and fri and ahpA were each required for L. monocytogenes to survive acute peroxide stress. Despite increased expression of fri, ahpA, and kat during infection of macrophages, only fri proved necessary for cytosolic growth and intercellular spread. In contrast, the proteins encoded by lmo0367, lmo0983, tpx, lmo1609, and ohrA were dispensable for aerobic growth, acute peroxide detoxification, and infection. Together, our results provide insight into the multifaceted L. monocytogenes peroxide detoxification strategy and demonstrate that L. monocytogenes encodes a functionally diverse set of peroxidase enzymes.


title: Effect of diet modification in intestinal 	Escherichia coli population and antimicrobial resistance

abstract: The fluctuations in the number of some intestinal bacterial lineages may be associated with increased antimicrobial resistance and disease. Adaptation to a given environment may select bacterial mutants that have reduced ability to adapt to new environments and changes in diet have been associated with alterations in microbiome taxon composition. We wanted to see the effect of diet change in linage composition and antimicrobial resistance profiles of numerically dominant E. coli. We subjected 50 chickens from an industrial operation (under corn-based diet supplemented with antimicrobials) to 2 antimicrobial-free diets; one based on corn and the other based on alfalfa. Fecal samples were obtained from all animals at arrival and after five weeks under different diets. Five E. coli colonies (from each sample) were subjected to genetic typing and antimicrobial susceptibility testing. We observed high diversity and high turnover rate of numerically dominant E. coli strains from animals from both diet groups. We did not find differences in antimicrobial resistance profiles in isolates from different diet groups. Our results suggest that there is high diversity and high turnover rate of E. coli strains in the intestines regardless of the diet. Chicken intestines seemed to contain many E. coli lineages able to thrive in different substrates. The absence of differences in antimicrobial resistance among bacteria, from animals in different diets, may indicate that the carriage of antimicrobial resistance genes does not affect the bacterial ability to adapt to different substrates.


title: Inhibition of arenavirus entry and replication by the cell-intrinsic restriction factor ZMPSTE24 is enhanced by IFITM antiviral activity

abstract:
In the absence of effective vaccines and treatments, annual outbreaks of severe human haemorrhagic fever caused by arenaviruses, such as Lassa virus, continue to pose a significant human health threat. Understanding the balance of cellular factors that inhibit or promote arenavirus infection may have important implications for the development of effective antiviral strategies. Here, we identified the cell-intrinsic zinc transmembrane metalloprotease, ZMPSTE24, as a restriction factor against arenaviruses. Notably, CRISPR-Cas9-mediated knockout of ZMPSTE24 in human alveolar epithelial A549 cells increased arenavirus glycoprotein-mediated viral entry in pseudoparticle assays and live virus infection models. As a barrier to viral entry and replication, ZMPSTE24 may act as a downstream effector of interferon-induced transmembrane protein (IFITM) antiviral function; though through a yet poorly understood mechanism. Overexpression of IFITM1, IFITM2 and IFITM3 proteins did not restrict the entry of pseudoparticles carrying arenavirus envelope glycoproteins and live virus infection, yet depletion of IFITM protein expression enhanced virus entry and replication. Furthermore, gain-of-function studies revealed that IFITMs augment the antiviral activity of ZMPSTE24 against arenaviruses, suggesting a cooperative effect of viral restriction. We show that ZMPSTE24 and IFITMs affect the kinetics of cellular endocytosis, suggesting that perturbation of membrane structure and stability is likely the mechanism of ZMPSTE24-mediated restriction and cooperative ZMPSTE24-IFITM antiviral activity. Collectively, our findings define the role of ZMPSTE24 host restriction activity in the early stages of arenavirus infection. Moreover, we provide insight into the importance of cellular membrane integrity for productive fusion of arenaviruses and highlight a novel avenue for therapeutic development.

Author SummaryIncreased human travel, virus genome evolution and expansion of the host rodent reservoir outside of endemic areas has contributed to increasing cases of the highly fatal arenaviral haemorrhagic disease, Lassa fever in Western Africa. These annual seasonal outbreaks present a serious global public health and socioeconomic burden, particularly in the absence of approved vaccines and antiviral countermeasures. Development of novel and effective therapeutic strategies against arenavirus infection is reliant on a better understanding of the molecular mechanisms of key host-virus interactions that antagonise or potentiate disease pathogenesis. We demonstrate the inhibition of arenavirus infection by the antiviral restriction factor ZMPSTE24 and describe a cooperative action with the innate immunity-stimulated family of interferon-induced transmembrane proteins (IFITMs). This work adds to our understanding of the mechanism of ZMPSTE24 and IFITM-mediated restriction of enveloped viruses and importantly suggests that these proteins may play a significant role in the pathogenesis of arenavirus infections.


title: Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe

abstract: Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive and it correlates with Pol II transcription and mRNA expression levels. While changes in Pol II occupancy were detected at only some genes in a Upf1-deficient (upf1{Delta}) strain, there is an increased Ser2 Pol II signal at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1{Delta} cells are hypersensitive to the transcription elongation inhibitor 6-azauracil and display Pol II abnormalities suggestive of Pol II hyperphosphorylation. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1{Delta}. These data envisage that by operating on the nascent transcript Upf1 might influence Pol II phosphorylation and transcription.


title: The Hippo pathway regulates density-dependent proliferation of iPSC-derived cardiac myocytes

abstract: Inducing cardiac myocytes to proliferate is considered a potential therapy to target heart disease, however, modulating cardiac myocyte proliferation has proven to be a technical challenge. The Hippo pathway is a kinase signaling cascade that regulates cell proliferation during the growth of the heart. Inhibition of the Hippo pathway increases the activation of the transcription factors YAP/TAZ, which translocate to the nucleus and upregulate transcription of pro-proliferative genes. The Hippo pathway regulates the proliferation of cancer cells, pluripotent stem cells, and epithelial cells through a cell-cell contact-dependent manner, however it is unclear if cell density-dependent cell proliferation is a consistent feature in cardiac myocytes. Here, we used cultured human iPSC-derived cardiac myocytes (hiCMs) as a model system to investigate this concept. hiCMs have a comparable transcriptome to the immature cardiac myocytes that proliferate during heart development in vivo. Our data indicate that a dense syncytium of hiCMs can regain cell cycle activity and YAP expression and activity when plated sparsely or when density is reduced through wounding. We found that combining two small molecules, XMU-MP-1 and S1P, increased YAP activity and further enhanced proliferation of low-density hiCMs. Importantly, these compounds had no effect on hiCMs within a dense syncytium. These data add to a growing body of literature that link the Hippo pathway regulation with cardiac myocyte proliferation and demonstrate that regulation is restricted to cells with reduced contact inhibition.

category: cell biology


title: Genomic loci mispositioning in Tmem120a knockout mice yields latent lipodystrophy

abstract: Little is known about the proteins that direct the highly conserved patterns of spatial genome organisation in fat. Here we report that adipocyte-specific knockout of the gene encoding nuclear envelope protein Tmem120a disrupts fat genome organisation, thus causing a novel lipodystrophy syndrome. Tmem120a deficiency broadly suppresses lipid metabolism pathway gene expression and induces myogenic gene expression by repositioning genes, enhancers and miRNA-encoding loci between the nuclear periphery and interior. Tmem120a-/- mice, particularly females, exhibit a lipodystrophy syndrome similar to human familial partial lipodystrophy FPLD2, with profound insulin resistance and metabolic defects that manifests upon exposure to an obesogenic diet. Interestingly, similar genome organisation defects occurred in cells from FPLD2 patients that harbour nuclear envelope protein laminA mutations. Our data suggest TMEM120A may mediate/instigate novel categories of adipose tissue dysfunction across the adiposity spectrum and provide a new miRNA-based mechanism possibly driving the unexplained muscle hypertrophy in human lipodystrophy.


title: Translational specialization in pluripotency by RBPMS poises future lineage-decisions

abstract: During embryonic development, translation is proposed to be uniquely specialized at the exit of pluripotency to rapidly reprogram the proteome and enable lineage commitment1-5. Yet, the fundamental role of translational specialization in programming developmental cell-fate decisions, its mediators and their mode-of-action remain elusive2,3. Here, using human embryonic stem cell-based models, we report that mesoderm commitment from pluripotency is controlled by the translational specialization factor RBPMS. RBPMS-driven translational specialization balances the abundance of cell-fate regulators to authorize accurate lineage decisions upon receiving differentiation signals. Consequently, RBPMS loss, without affecting pluripotency, selectively and severely impedes mesoderm specification and subsequent cardiogenesis. Mechanistically, direct binding of RBPMS to 3UTRs allows selective translation of developmental cell-fate regulators including integral morphogen signaling components specifying mesoderm. RBPMS loss disrupts the canonical composition of translation initiation complexes resulting in the aberrant retention of initiation factors on ribosomal complexes. Our data unveil how emerging lineage choices from pluripotency are controlled by translational specialization via ribosomal platforms acting as a regulatory nexus for developmental cell fate decisions.


title: Single cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human specific features

abstract: The spinal cord receives input from peripheral sensory neurons and controls motor output by regulating muscle innervating motor neurons. These functions are carried out by neural circuits comprising molecularly and physiologically distinct neuronal subtypes that are generated in a characteristic spatial-temporal arrangement from progenitors in the embryonic neural tube. The systematic mapping of gene expression in mouse embryos has provided insight into the diversity and complexity of cells in the neural tube. For human embryos, however, less information has been available. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions in four human embryos of Carnegie Stages (CS) CS12, CS14, CS17 and CS19 from Gestational Weeks (W) 4-7. In total we recovered the transcriptomes of 71,219 cells. Analysis of progenitor and neuronal populations from the neural tube, as well as cells of the peripheral nervous system, in dorsal root ganglia adjacent to the neural tube, identified dozens of distinct cell types and facilitated the reconstruction of the differentiation pathways of specific neuronal subtypes. Comparison with existing mouse datasets revealed the overall similarity of mouse and human neural tube development while highlighting specific features that differed between species. These data provide a catalogue of gene expression and cell type identity in the developing neural tube that will support future studies of sensory and motor control systems and can be explored at https://shiny.crick.ac.uk/scviewer/neuraltube/.


title: Reduced Shmt2 expression impairs mitochondrial folate accumulation and respiration, and leads to uracil accumulation in mouse mitochondrial DNA

abstract:
BackgroundAdequate cellular thymidylate (dTMP) pools are essential for preservation of nuclear and mitochondrial genome stability. Previous studies have indicated that disruption in dTMP synthesis in the nucleus leads to increased uracil misincorporation into DNA affecting genome stability. To date, the effects of impaired mitochondrial dTMP synthesis in non- transformed tissues have been understudied.

ObjectiveThis study aimed to determine the effects of decreased serine hydroxymethyltransferase 2 (Shmt2) expression and dietary folate deficiency on mitochondrial DNA integrity and mitochondrial function in mouse tissues.

MethodsLiver mitochondrial DNA (mtDNA) content, and uracil content in liver mtDNA was measured in Shmt2+/- and Shmt2+/+ mice weaned onto either a folate-sufficient control diet (2 mg/kg folic acid, C) or a modified diet lacking folic acid (0 mg/kg folic acid, FD) for 7 wks. Shmt2+/- and Shmt2+/+ mouse embryonic fibroblasts (MEF cells) were cultured in defined culture medium containing either 0 or 25 nM folate to assess proliferative capacity and mitochondrial function.

ResultsShmt2+/- mice exhibited 48-67% reduction in SHMT2 protein levels in tissues. Interestingly, Shmt2+/- mice consuming the folate-sufficient C diet exhibited a 25% reduction in total folate in liver mitochondria. There was also a >20-fold increase in uracil in liver mtDNA in Shmt2+/- mice consuming the C diet, and dietary folate deficiency also increased uracil content in mouse liver mtDNA from both Shmt2+/+ and Shmt2+/- mice. Furthermore, decreased Shmt2 expression in MEF cells reduced cell proliferation, mitochondrial membrane potential, and oxygen consumption rate.

ConclusionsThis study demonstrates that Shmt2 heterozygosity and dietary folate deficiency impair mitochondrial dTMP synthesis, as evidenced by the increased uracil in mtDNA. In addition, Shmt2 heterozygosity impairs mitochondrial function in MEF cells. These findings suggest that elevated uracil in mtDNA may impair mitochondrial function.

category: biochemistry


title: Modelling the impact of magnesium ions concentration on the folding of the SAM-II riboswitch

abstract:
Riboswitches are regulatory elements present in bacterial messenger RNA acting as sensors of small molecules and consequently playing a vital role in bacterial gene regulation. The SAM-II riboswitch is a class of riboswitches, that recognizes S-adenosyl methionine. It has been previously illustrated that the presence of Mg2+ ions stabilizes the pre-existing minor state of the riboswitch, which is structurally characterised by having a nucleated pseudoknot, leading to the increase of its probability. In this study, an analytical equilibrium model is developed to describe the impact of Mg2+ ions concentration on the folding of the SAM-II riboswitch, linking RNA folding and tertiary interactions energetics to ligand binding, and, hence enabling quantitative predictions. The method was used to study the role of the P1 helix sequence in determining the fraction of binding competent conformers of the SAM-II riboswitch, by simulating the Mg2+ titration curves of various mutants.

Graphical abstract

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title: Molecular determinants of phase separation for Drosophila DNA replication licensing factors

abstract: Liquid-liquid phase separation (LLPS) of intrinsically disordered regions (IDRs) in proteins can drive the formation of membraneless compartments in cells. Phase-separated structures enrich for specific partner proteins and exclude others. We have shown that the IDRs of metazoan DNA replication initiators drive DNA-dependent phase separation in vitro and chromosome binding in vivo, and that initiator condensates selectively recruit specific partner proteins. How initiator IDRs facilitate LLPS and maintain compositional specificity is unknown. Using D. melanogaster (Dm) Cdt1 as a model initiation factor, we show that phase separation results from a synergy between electrostatic DNA-bridging interactions and hydrophobic inter-IDR contacts. Both sets of interactions depend on sequence composition (but not sequence order), are resistant to 1,6- hexanediol, and do not depend on aromaticity. These findings demonstrate that distinct sets of interactions drive self-assembly and condensate specificity across different phase-separating systems and advance efforts to predict IDR LLPS propensity and specificity a priori.


title: SLIT2-ROBO signaling in tumor-associated microglia/macrophages drives glioblastoma immunosuppression and vascular dysmorphia

abstract: SLIT2 is a secreted polypeptide that guides migration of cells expressing ROBO1&2 receptors. Herein, we investigated SLIT2/ROBO signaling effects in gliomas. In patients with glioblastoma (GBM), SLIT2 expression increased with malignant progression and correlated with poor survival and immunosuppression. Knockdown of SLIT2 in mouse glioma cells and patient derived GBM xenografts reduced tumor growth and synergized with immunotherapy to prolong survival. Tumor cell SLIT2 knockdown inhibited macrophage invasion and promoted a cytotoxic gene expression profile, which improved tumor vessel function and enhanced efficacy of chemotherapy and immunotherapy. Mechanistically, SLIT2 promoted microglia/macrophage chemotaxis and tumor-supportive polarization via ROBO1&2-mediated PI3K{gamma} activation. Macrophage Robo1&2 deletion and systemic SLIT2 trap delivery mimicked SLIT2 knockdown effects on tumor growth and the tumor microenvironment (TME), revealing SLIT2 signaling through macrophage ROBOs as a novel regulator of the GBM microenvironment and a potential immunotherapeutic target for brain tumors.


title: CCR4 blockade leads to clinical activity and prolongs survival in a canine model of advanced prostate cancer

abstract:
Targeting regulatory T cell (Treg) infiltration is an emerging strategy for cancer immunotherapy. However, the efficacy of this strategy in advanced prostate cancer remains unclear. Here, we describe the therapeutic efficacy of this strategy in a canine model of advanced prostate cancer. We used dogs with naturally occurring prostate cancer to study the molecular mechanism underlying Treg infiltration into tumor tissues and the effect of anti-Treg treatment. We found that tumor-infiltrating Tregs were associated with poor prognosis in dogs bearing spontaneous prostate cancer. RNA sequencing and protein analyses showed that Treg infiltration was mediated by interaction between the tumor-producing chemokine, CCL17, and the receptor CCR4 expressed on Tregs. Dogs with advanced prostate cancer responded to mogamulizumab, a monoclonal antibody targeting CCR4, with improved survival and low incidence of clinically relevant adverse events. Exploratory analyses showed urinary CCL17 concentration and BRAFV595E mutation to be independently predictive of the response to mogamulizumab. Analysis of a publicly available transcriptomic dataset of human prostate cancer showed that the CCL17/CCR4 axis correlated with the Treg marker, Foxp3. In silico survival analyses showed that high expression of CCL17 was associated with poor prognosis. Immunohistochemistry confirmed that tumor-infiltrating Tregs expressed CCR4 in human patients with prostate cancer. These findings suggest that anti-Treg treatment through the blocking of CCR4 is a promising therapeutic approach for advanced prostate cancer.

One Sentence SummaryTargeting regulatory T cell infiltration by CCR4 blockade induces objective responses and improves survival in a canine model of prostate cancer.


title: Factors that Influence Career Choice Among Different Populations of Neuroscience Trainees

abstract: Enhancing the diversity of the scientific workforce is critical to achieving the mission of NIH: "To seek fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to enhance health, lengthen life, and reduce the burdens of illness and disability." However, specific groups have historically been, and continue to be, underrepresented in the biomedical research workforce, especially academia. Career choice is a multi-factorial process that evolves over time; among all trainees, expressed interest in faculty research careers decreases over time in graduate school, but that trend is amplified in women and members of historically underrepresented racial and ethnic groups (Fuhrmann, Halme, OSullivan, & Lindstaedt, 2011; Gibbs, McGready, Bennett, & Griffin, 2014; C. Golde & Dore, 2004; Roach & Sauermann, 2017; Sauermann & Roach, 2012). Neuroscience as a discipline has characteristics that may exacerbate the overall trends seen in the life sciences, such as a greater growth in the number of awarded neuroscience PhDs than in other life sciences fields (US National Science Foundation, 2016b). This work was designed to investigate how career interest changes over time among recent neuroscience PhD graduates, and whether differences in career interests are associated with social identity (i.e. gender and race/ethnicity), experiences in graduate school and postdoctoral training (e.g. relationship with advisor; feelings of belonging), and personal characteristics (e.g. confidence in ones potential to be an independent researcher). We report results from a survey of 1,479 PhD neuroscientists (including 16% underrepresented (UR) and 54% female scientists). We saw repeated evidence that individual preferences about careers in general, and academic careers specifically, predict current career interest. These statistically significant preferences mostly had medium to low effect size that varied by career type. These findings were mediated by social identity and experiences in graduate school and postdoctoral training. Our findings highlight the important influence of the advisor in shaping a trainees career path, and the ways in which academic culture is perceived as unwelcoming or incongruent with the values or priorities of certain groups. For women, issues of work/life balance and structural issues of academia, and for UR women in particular, lower confidence in their ability to be an independent researcher, affected their interest in academia. Both women and UR men in our study report a lower importance of autonomy in their careers. UR respondents report feeling less like they were a part of the social and intellectual community. However, they have formed beneficial relationships with faculty outside their PhD institutions that, particularly for UR women, are associated with increased interest in academia. Our findings suggest several areas for positive growth, ways to change how we think about the impact of mentorship, and policy and programmatic interventions that extend beyond trying to change or "fix" the individual and instead recognize the systemic structures that influence career choices.


title: Beneficial substrate partitioning boosts non-aqueous catalysis in de novo enzyme-alginate beads

abstract: Synthetic reactions often require solvents incompatible with biocatalysts. Here, we encapsulate a de novo heme-containing enzyme, C45, in calcium-alginate hydrogel beads to facilitate heterogeneous biocatalysis in neat organic solvents. Post-encapsulation, C45 retains activity even when the beads are suspended in organic solvents. In particular, the carbene transferase activity of C45 is enhanced when reactions are performed in aprotic, non-polar solvents such as hexane and toluene. Activity-solvent dependencies reveal that this activity boost is likely due to beneficial partitioning of the substrate into the beads from the organic phase. Furthermore, encapsulation facilitates enzyme recovery and recycling after the reaction. Such encapsulation opens up novel opportunities for biocatalysis in organic solvent systems, combining desired solvent properties of organic chemistry with enzymatic selectivity and proficiency.

category: synthetic biology


title: Critical evaluation of kinetic schemes for coagulation

abstract: Computational models of the coagulation cascade are used for a wide range of applications in bio-medical engineering such as drug and bio-medical device developments. However, a lack of robustness of numerical models has been highlighted when studying clinically relevant scenarios. In order to develop more robust models, numerical simulations need to be confronted with realistic situations relevant to clinical practice. In this work, two well-established numerical representations of the coagulation cascade initiated by the intrinsic and extrinsic systems, respectively, were compared with thrombin generation assays considering realistic pathological conditions. Proper modifications were needed to align the in vitro and in silico data, namely; adapting initial conditions to the thrombin assay system, omitting reactions irrelevant to our case study, and improving the fitting of some reaction rates. The modified models were able to capture the experimental trends of thrombin generation for a range of concentrations of factors XII, XI, and VIII for cases in which the coagulation cascade is triggered through the extrinsic and intrinsic systems. Our work emphasizes that when existing coagulation cascade models are extrapolated to experimental settings for which they were not calibrated, careful adjustments must be made. We show that the two coagulation models used in this work can predict physiological conditions, but when studying pathological conditions, proper modifications are needed to improve the numerical results.


title: Safety and efficacy of C9ORF72-repeat RNA nuclear export inhibition in amyotrophic lateral sclerosis

abstract:
BackgroundLoss of motor neurons in amyotrophic lateral sclerosis (ALS) leads to progressive paralysis and death. Dysregulation of thousands of RNA molecules with roles in multiple cellular pathways hinders the identification of ALS-causing alterations over downstream changes secondary to the neurodegenerative process. How many and which of these pathological gene expression changes require therapeutic normalisation remains a fundamental question.

MethodsHere, we investigated genome-wide RNA changes in C9ORF72-ALS patient-derived neurons and Drosophila, as well as upon neuroprotection taking advantage of our gene therapy approach which specifically inhibits the SRSF1-dependent nuclear export of pathological C9ORF72-repeat transcripts. This is a critical study to evaluate (i) the overall safety and efficacy of the partial depletion of SRSF1, a member of a protein family involved itself in gene expression, and (ii) a unique opportunity to identify neuroprotective RNA changes.

ResultsOur study demonstrates that manipulation of 362 transcripts out of 2,257 pathological changes in C9ORF72-ALS patient-derived neurons is sufficient to confer neuroprotection upon partial depletion of SRSF1. In particular, expression of 90 disease-altered transcripts is fully reverted upon neuroprotection leading to the characterisation of a human C9ORF72-ALS disease-modifying gene expression signature. These findings were further investigated in vivo in diseased and neuroprotected Drosophila transcriptomes, highlighting a list of 21 neuroprotective changes conserved with 16 human orthologues in patient-derived neurons. We also functionally validated the high therapeutic potential of one of these disease-modifying transcripts, demonstrating that inhibition of ALS-upregulated human KCNN1-3 (Drosophila SK) voltage-gated potassium channel orthologs mitigates degeneration of human motor neurons as well as Drosophila motor deficits.

ConclusionsStrikingly, manipulating the expression levels of a small proportion of RNAs is sufficient to induce a therapeutic effect, further indicating that the SRSF1-targeted gene therapy approach is safe in the above preclinical models as it does not disrupt globally gene expression. The efficacy of this intervention is also validated at genome-wide level with therapeutically-induced RNA changes involved in the vast majority of biological processes affected in C9ORF72-ALS. Finally, the identification of a characteristic signature with key RNA changes modified in both the disease state and upon neuroprotection also provides potential new therapeutic targets and biomarkers.


title: Is what you see what you get? The relationship between field observed and actual aphid parasitism rates in canola crops

abstract:
BACKGROUNDEstimating parasitoid abundance in the field can be difficult, even more so when attempting to quantify parasitism rates and the ecosystem service of biological control that parasitoids can provide. To understand how  observed parasitism rates (in-field mummy counts) of the green peach aphid, Myzus persicae (Sulzer) (Homoptera: Aphididae) translate to  actual parasitism rates (laboratory-reared parasitoid counts), field work was undertaken in Australian canola fields over a growing season. Parasitoids were reared within a controlled laboratory setting.

RESULTSTotal observed and actual parasitism rates of M. persicae varied considerably across regions, but less so on a field level. Overall, actual parasitism was on average 2.4 times higher than that observed in the field, with rates an average of 4-fold higher in South Australia. As crop growth stage progressed, the percentage of mummies observed increased. Percentage of parasitoids reared also increased with crop growth stage, averaging 3.4% during flowering and reaching 14.4% during podding/senescing. Although there was a greater diversity of reared parasitoid species at later crop growth stages, actual parasitism rate was unaffected by parasitoid species. Diaeretiella rapae was the most commonly reared parasitoid, increasing in abundance with crop growth stage.

CONCLUSIONThese findings indicate that mummy counts alone do not provide a clear representation of parasitism within fields.


title: CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens

abstract: The acquisition of antibiotic resistance genes via horizontal gene transfer is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of antibiotic resistance. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of antibiotic resistance. We analysed ~40,000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of horizontal gene transfer, and found that pathogens with a CRISPR-Cas system were less likely to carry antibiotic resistance genes than those lacking this defence system. Analysis of the mobile genetic elements targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of antibiotic resistance. These results suggest a potential "immunocompromised" state for multidrug-resistant strains that may be exploited in tailored interventions that rely on mobile genetic elements, such as phage or phagemids, to treat infections caused by bacterial pathogens.


title: Mechanism of riboregulation of p62 protein oligomerisation by vault RNA1-1 in selective autophagy

abstract: Macroautophagy ensures the clearance of intracellular substrates ranging from single ubiquitinated proteins to large proteotoxic aggregates and defective organelles. The selective autophagy receptor p62 binds these targets and recruits them to double-membrane vesicles, which fuse with lysosomes to degrade their content. We recently uncovered that p62 function is riboregulated by the small non-coding vault RNA1-1. Here, we present detailed insight into the underlying mechanism. We show that the PB1 domain and adjacent linker region of p62 (aa 1-122) are necessary and sufficient for specific vault RNA1-1 binding, and identify lysine 7 and arginine 21 as key hinges for p62 riboregulation. Chemical structure probing of vault RNA1-1 further reveals a central flexible loop within the RNA that mediates the specific p62 interaction. Our data define molecular determinants that govern mammalian autophagy via the p62-vault RNA1-1 riboregulatory pair.


title: High intensity muscle stimulation activates a systemic Nrf2-mediated redox stress response

abstract:
IntroductionHigh intensity exercise is an increasingly popular mode of exercise to elicit similar or greater adaptive responses compared to traditional moderate intensity continuous exercise. However, the molecular mechanisms underlying these adaptive responses are still unclear. The purpose of this pilot study was to compare high and low intensity contractile stimulus on the Nrf2-mediated redox stress response in mouse skeletal muscle.

MethodsAn intra-animal design was used to control for variations in individual responses to muscle stimulation by using a stimulated limb (STIM) and comparing to the contralateral unstimulated control limb (CON). High Intensity (HI - 100Hz), Low Intensity (LI - 50Hz), and Naive Control (NC - Mock stimulation vs CON) groups were used to compare these effects on Nrf2-ARE binding, Keap1 protein content, and downstream gene and protein expression of Nrf2 target genes.

ResultsMuscle stimulation significantly increased Nrf2-ARE binding in LI-STIM compared to LI-CON (p = 0.0098), while Nrf2-ARE binding was elevated in both HI-CON and HI-STIM compared to NC (p = 0.0007). The Nrf2-ARE results were mirrored in the downregulation of Keap1, where Keap1 expression in HI-CON and HI-STIM were both significantly lower than NC (p = 0.008) and decreased in LI-STIM compared to LI-CON (p = 0.015). In addition, stimulation increased NQO1 protein compared to contralateral control regardless of stimulation intensity (p = 0.019).

ConclusionsTaken together, these data suggest a systemic redox signaling exerkine is activating Nrf2-ARE binding and is intensity gated, where Nrf2-ARE activation in contralateral control limbs were only seen in the HI group. Other research in exercise induced Nrf2 signaling support the general finding that Nrf2 is activated in peripheral tissues in response to exercise, however the specific exerkine responsible for the systemic signaling effects is not known. Future work should aim to delineate these redox sensitive systemic signaling mechanisms.


title: ALS and FTD-associated missense mutations in TBK1 differentially disrupt mitophagy

abstract:
TANK-binding kinase 1 (TBK1) is a multi-functional kinase with an essential role in mitophagy, the selective clearance of damaged mitochondria. More than 90 distinct mutations in TBK1 are linked to amyotrophic lateral sclerosis (ALS) and fronto-temporal dementia (FTD), including missense mutations that disrupt the ability of TBK1 to dimerize, associate with the mitophagy receptor optineurin (OPTN), auto-activate, or catalyze phosphorylation. We investigated how ALS-associated mutations in TBK1 affect Parkin-dependent mitophagy using imaging to dissect the molecular mechanisms involved in clearing damaged mitochondria. Some mutations cause severe dysregulation of the pathway, while others induce limited disruption. Mutations that abolish either TBK1 dimerization or kinase activity were insufficient to fully inhibit mitophagy, while mutations that reduced both dimerization and kinase activity were more disruptive. Ultimately, both TBK1 recruitment and OPTN phosphorylation at S177 are necessary for engulfment of damaged mitochondra by autophagosomal membranes. Surprisingly, we find that ULK1 activity contributes to the phosphorylation of OPTN in the presense of either WT- or kinase inactive TBK1. In primary neurons, TBK1 mutants induce mitochondrial stress under basal conditions; network stress is exacerbated with further mitochondrial insult. Our study further refines the model for TBK1 function in mitophagy, demonstrating that some ALS-linked mutations likely contribute to disease pathogenesis by inducing mitochondrial stress or inhibiting mitophagic flux. Other TBK1 mutations exhibited much less impact on mitophagy in our assays, suggesting that cell-type specific effects, cumulative damage, or alternative TBK1-dependent pathways such as innate immunity and inflammation also factor into the development of ALS in affected individuals.

SIGNIFICANCE STATEMENTMissense mutations in TANK-binding kinase 1 (TBK1) have various biophysical and biochemical effects on the molecule, and are associated with the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and fronto-temporal dementia (FTD). TBK1 plays an essential role in clearing damaged mitochondria. Here, we investigate the impact of 10 ALS-linked TBK1 mutations on the critical early stage of mitophagy. We find that both TBK1 recruitment and kinase activity contribute to the clearance of the damaged mitochondria. Furthermore, in neurons, expression of TBK1 mutants alone affects mitochondrial network health. Our investigation utilizes disease-linked mutations to further refine the current model of mitophagy, identifying crosstalk between the regulatory kinases TBK1 and ULK1, and providing new insights into the roles of TBK1 in neurodegenerative pathogenesis.


title: Proteomic analysis of the role of the quality control protease LONP1 in mitochondrial protein aggregation

abstract: The mitochondrial matrix protease LONP1 is an essential part of the organellar protein quality control system. LONP1 has been shown to be involved in respiration control and apoptosis. Furthermore, a reduction in LONP1 level correlates with ageing processes. Up to now, the effects of a LONP1 defect were mostly studied by utilizing transient, siRNA-mediated knockdown approaches. We generated a new cellular model system for studying the impact of LONP1 on mitochondrial protein homeostasis by a CRISPR/Cas-mediated genetic knockdown (gKD). These cells show a stable reduction of LONP1 along with a mild phenotype characterized by absent morphological differences and only small negative effects on mitochondrial functions under normal culture conditions. To assess the consequences of a permanent LONP1 depletion on the mitochondrial proteome, we analyzed the alterations of protein levels by quantitative mass spectrometry, demonstrating small adaptive changes, in particular concerning mitochondrial protein biogenesis. In an additional proteomic analysis, we determined the temperature-dependent aggregation behavior of mitochondrial proteins and its dependence on a reduction of LONP1 activity, demonstrating the important role of the protease for mitochondrial protein homeostasis in mammalian cells. We identified a significant number of mitochondrial proteins that are affected by LONP1 activity concerning their stress-induced solubility. Taken together, our results suggest a very good applicability of the LONP1 gKD cell line as a model system for human ageing processes.


title: YTHDC2 Is Essential for Pachytene Progression and Prevents Aberrant Microtubule-Driven Telomere Clustering in Male Meiosis

abstract: Mechanisms driving the prolonged meiotic prophase I are poorly understood. The RNA helicase YTHDC2 is critical for mitosis to meiosis transition, as YTHDC2-deficient mouse germ cells initiate meiosis but arrest with mixed characteristics of mitotic and meiotic cell types. However, YTHDC2 is also highly expressed in normal pachytene cells. Here we identify an essential role for YTHDC2 in meiotic progression. Specifically, we find that YTHDC2 deficiency causes microtubule-dependent telomere clustering and apoptosis at the pachytene stage of prophase I, and thus a failure to advance to the diplotene stage. Depletion of YTHDC2 results in a massively dysregulated transcriptome in pachytene cells, with a tendency toward upregulation of genes normally expressed in mitotic germ cells and downregulation of meiotic transcripts. Dysregulation does not correlate with the m6A status of RNAs and YTHDC2-bound mRNAs are enriched in genes upregulated in mutant germ cells, revealing that YTHDC2 primarily targets its substrate mRNAs for degradation. Finally, altered transcripts in YTHDC2-deficient pachytene cells encode microtubule network proteins and inhibition of microtubule polymerization disperses clustered telomeres. Together, our results demonstrate that YTHDC2 regulates the prolonged pachytene stage of prophase I by perpetuating a meiotic transcriptome and preventing changes in the microtubule network that could lead to aberrant telomere clustering.


title: The Kinship Matrix: Inferring the Kinship Structure of a Population from its Demography

abstract: The familial structure of a population and the relatedness of its individuals are determined by its demography. There is, however, no general method to infer kinship directly from the life-cycle of a structured population. Yet this question is central to fields such as ecology, evolution and conservation, especially in contexts where there is a strong interdependence between familial structure and population dynamics. Here, we give a general formula to compute, from any matrix population model, the expected number of arbitrary kin (sisters, nieces, cousins, etc) of a focal individual ego, structured by the class of ego and of its kin. Central to our approach are classic but little-used tools known as genealogical matrices. Our method can be used to obtain both individual-based and population-wide metrics of kinship, as we illustrate. It also makes it possible to analyze the sensitivity of the kinship structure to the traits implemented in the model.

category: ecology


title: A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

abstract: Multi-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from Bacillus subtilis composed of two enzymes catalyzing opposite rather than sequential reactions ("counter-enzymes"): glutamate synthase (GltAB), and glutamate dehydrogenase (GudB), that make and break glutamate, respectively. In vivo and in vitro studies show that the primary role of complex formation is to inhibit GudBs activity as this enzyme is constitutively expressed including in glutamate-limiting conditions. Using cryo-electron microscopy, we elucidated the structure of the complex and the basis of GudBs inhibition. Finally, we show that this complex that exhibits unusual oscillatory progress curves is a necessity for planktonic growth in glutamate-limiting conditions, but is also essential for biofilm growth in glutamate-rich media, suggesting a regulatory role at fluctuating glutamate concentrations.


title: Design, Synthesis and Evaluation of WD-repeat containing protein 5 (WDR5) degraders

abstract: Histone H3K4 methylation serves as post-translational hallmark of actively transcribed genes and is introduced by histone methyltransferases (HMT) and its regulatory scaffolding proteins. One of these is the WD-repeat containing protein 5 (WDR5) that has also been associated with controlling long non-coding RNAs and transcription factors including MYC. The wide influence of dysfunctional HMTs complexes and the typically upregulated MYC levels in diverse tumor types suggested WDR5 as an attractive drug target. Indeed, protein-protein interface inhibitors for two protein interaction interfaces on WDR5 have been developed. While such compounds only inhibit a subset of WDR5 interactions, chemically induced proteasomal degradation of WDR5 might represent an elegant way to target all oncogenic function. This study presents the design, synthesis and evaluation of two diverse WDR5 degrader series based on two WIN site binding scaffolds and shows that linker nature and length strongly influence degradation efficacy.


title: Photodynamic Inactivation reduces the diversity and changes the composition of bacterial and fungal communities associated with leaf surfaces

abstract: Plant surfaces are colonized by a myriad of microorganisms including mutualistic strains and pathogens. Particularly in agricultural systems applications are required that protect the plants against pathogens without negative side effects on the environment and humans. Photodynamic Inactivation (PDI) has been demonstrated to be a promising approach to efficiently fight plant pathogens. Based on its mechanism of action, the light-induced and photosensitizer-mediated overproduction of reactive oxygen species in target cells, PDI is likely to generally inactivates microorganisms on plants irrespective of their pathogenicity. In order to prove this hypothesis we used next-generation 16S rRNA gene amplicon sequencing to characterize the bacterial and fungal communities associated with leaf surfaces of Arabidopsis thaliana before and after the photodynamic treatment using the chlorine e6 derivative B17-0024 as photoactive compound and showed that this treatment reduced the microbial richness and altered the microbial community composition. These findings may help to develop effective pathogen-control strategies and may also stimulate research on plant-microbe interactions exploiting the potential of PDI.

category: plant biology


title: Genetic Incorporation of Two Mutually Orthogonal Bioorthogonal Amino Acids That Enable Efficient Protein Dual-Labeling in Cells

abstract: The ability to site-specifically modify proteins at multiple sites in vivo will enable the study of protein function in its native environment with unprecedented levels of detail. Here, we present a versatile two-step strategy to meet this goal involving site-specific encoding of two distinct noncanonical amino acids bearing bioorthogonal handles into proteins in vivo followed by mutually orthogonal labeling. This general approach, that we call dual encoding and labeling (DEAL), allowed us to efficiently encoded tetrazine- and azide-bearing amino acids into a protein and demonstrate for the first time that the bioorthogonal labeling reactions with strained alkene and alkyne labels can function simultaneously and intracellularly with high yields when site-specifically encoded in a single protein. Using our DEAL system, we were able to perform topologically-defined protein-protein crosslinking, intramolecular stapling, and site-specific installation of fluorophores all inside living Escherichia coli cells, as well as study the DNA-binding properties of yeast Replication Protein A in vitro. By enabling the efficient dual modification of proteins in vivo, this DEAL approach provides a tool for the characterization and engineering of proteins in vivo.