title: GAGAM: a genomic annotation-based enrichment of scATAC-seq data for Gene Activity Matrix

abstract: Single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) is rapidly becoming a powerful technology to assess the epigenetic landscape of thousands of cells. However, the current great sparsity of the resulting data poses significant challenges to their interpretability and informativeness. Different computational methods are available, proposing ways to generate significant features from accessibility data and process them to obtain meaningful results. In particular, the most common way to interpret the raw scATAC-seq data is through peak-calling, generating the peaks as features. Nevertheless, this method is dataset-dependent because the peaks are related to the given dataset and can not be directly compared between different experiments. For this reason, this study wants to improve on the concept of the Gene Activity Matrix (GAM), which links the accessibility data to the genes, by proposing a Genomic-Annotated Gene Activity Matrix (GAGAM), which aims to label the peaks and link them to the genes through functional annotation of the whole genome. Using genes as features solves the problem of the feature dataset dependency allowing for the link of gene accessibility and expression. The latter is crucial for gene regulation understanding and fundamental for the increasing impact of multi-omics data. Results confirm that our method performs better than the previous GAMs.


title: Multi-omics analysis combining pyroptosis-related signatures for building a prognosis prediction model in hepatocellular carcinoma

abstract: Hepatocellular carcinoma (HCC) is a major cause of cancer-related death worldwide and has a poor prognosis. Pyroptosis, which is programmed cell necrosis mediated by gasdermin, participates in the progression of tumors. Recently, multiple omics analysis has been applied frequently to provide comprehensive and more precise conclusions. However, multiomics analysis combining pyroptosis-related signatures in HCC and their correlations with prognosis remain unclear. Here, we identified 42 pyroptosis genes that were differentially expressed between HCC and normal hepatocellular tissues. According to these differentially expressed genes (DEGs), all HCC cases could be divided into two heterogeneous subtypes. Then, we evaluated the prognostic value of differential pyroptosis-related genes to construct a multigene model using The Cancer Genome Atlas (TCGA) cohort. A 22-gene model was built and classified HCC patients in the TCGA cohort into low-risk and high-risk groups by the least absolute shrinkage and selection operator (LASSO) Cox regression method. HCC patients belonging to the low-risk group had significantly higher survival possibilities than those belonging to the high-risk group (p<0.001). Furthermore, the related genes and two groups were analyzed with multiple omics in different molecular layers. The pyroptosis-related gene model was validated with HCC patients from the Gene Expression Omnibus (GEO) cohort, and the low-risk group in GEO showed increased overall survival (OS) time (P=0.018). The risk score was an independent factor for predicting the OS of HCC patients. In conclusion, pyroptosis-related genes in HCC are correlated with tumor immunity and could be used to predict the prognosis of HCC patients.

category: cancer biology


title: The Effect of Ethanolic Extract of Acacia Seyal Bark on Induced Diabetic rats

abstract:
BackgroundDiabetes mellitus Type 2 is a chronic metabolic disorder characterized by insulin insensitivity that leads to a decrease in glucose transport into the other cells. Many drugs are being developed, while no cure is available regarding to this disease although, there are limitations due to high cost and certain side effects. The Traditional Medicines are preferred due to lesser side effects and low cost. Acacia species have wide traditional medicinal using as anti-diabetic, antimicrobial, and anti-inflammatory activities.

ObjectiveThe study aimed to examine the effect of ethanolic extract of Acacia Seyal bark in induced diabetic rats.

Materials and methodsAcacia Seyal bark was extracted in ethanol 80%. The Ethanolic extract was analyzed for phytochemicals screening tests using standard methods. To investigate the effect of the extract thirty induced diabetic albino rats introduced by injection of glucose 2g\kg were divided to 5 groups equally; Group 1 was treated with 10mg\kg of glibenclamide, group 2 left as control treated with distilled water 10mg\kg, Group 3 was treated with 200mg of plant extract, Group 4 was treated with 400mg of plant extract, and Group 5 was treated with 800mg of plant extract. The Glucose Tolerant Test were done after 1 hour, 2 hour and 4 hour to determine blood glucose level of rats. Estimation of in vitro glucose uptake by rat diaphragm experiment was done to evaluate the glucose utilization capacity of extract.

ResultsThe effect of different concentration of ethanolic extract of Acacia Seyal bark on the blood glucose level of diabetic induced rats is significantly different (0.05 p 0.01 <p). The phytochemical screening of extract indicated the presence of Saponin, Tannins Steroids, Triterpens, and Anthraquinone, While the absence of flavonoids. In vitro glucose consumption by diaphragm study the level of utilized glucose from the media is 69.4% in the presence of extract compared to control group.

ConclusionStudy concluded that the ethanolic bark extract of A. seyal showed significant anti-diabetic activity. This results might have a great potential for translation to humans and the obtained data might set the stage for clinical trials investigating the effects of anti-diabetic effect in patients with diabetes mellitus type2. In the best of our knowledge, this is the first study that has conducted to study the anti-diabetics effect of ethanolic extract of Acacia Seyal bark in diabetic rats.

category: pharmacology and toxicology


title: The Hyaloperanospora arabidopsidis effector HaRxL77 is hypermobile between cells and manipulates host defence

abstract:
Multicellular organisms require dynamic communication between cells, tissues and organs to integrate responses to external and internal signals. In plants, cell-to-cell communication relies in part on plasmodesmata, which connect adjacent cells and allow the exchange of signals and resources. Upon infection by pathogens, plants act to isolate infected cells from non-infected cells by closing plasmodesmata but pathogens can suppress this defence and maintain plasmodesmata in an open state. To address the question of what a pathogen might gain from keeping plasmodesmata open, we screened effectors from the biotrophic Arabidopsis pathogen Hyaloperonospora arabidopsidis (Hpa) for the ability to move cell-to-cell via plasmodesmata in plant tissues. We quantified the mobility of cytoplasmic effectors and identified six that were hypermobile, i.e., can move further than expected for a protein of that size. Of these, HaRxL77 indirectly modifies plasmodesmatal permeability to facilitate hypermobility and suppresses the flg22-induced ROS burst, suggesting that cell-to-cell mobility of effectors allows defence manipulation ahead of the infection front. Thus, this study provides novel insights into how Hpa exploits plasmodesmata-mediated intercellular connectivity to promote infection, characterising a poorly explored element of plant-pathogen interaction.

Author SummaryDuring infection, pathogens secrete effectors into host cells to manipulate them for their benefit. Plant cells are connected via plasmodesmata, and pathogen effectors can use these connections to reach uninfected cells. We asked what a pathogen might gain by having effectors that can travel between cells and thus screened Arabidopsis downy mildew effectors for this capability. We found downy mildew produces many cell-to-cell mobile effectors, and that some of these can move further than we might expect. One  hypermobile effector, HaRxL77, can open plasmodesmata to allow this increased mobility, although how it does this is not clear. HaRxL77 interferes with several host defence mechanisms, suggesting that cell- to-cell mobility allows effectors to perturb host defence ahead of the infection front.

category: plant biology


title: Integrating Math Modeling, Coding, and Biology in aCURE Lab

abstract: The development of mathematical and quantitative skills is increasingly critical for biology students. Literacy in coding, statistics, and mathematical modeling enables students to engage in systems-thinking and the analysis of large data sets. Here we present a flexible tool illustrating concepts in mathematical modeling, coding, and biology for integration into both traditional  cookbook and inquiry-driven labs for freshmen biology students. We developed simple and complex mathematical models of potato catechol oxidase, a popular system to teach enzyme kinetics in undergraduate biology labs. We integrated both models into a freely-available web app for simulation and parameter estimation. The models are usable even if experimental details are unknown or poorly controlled, so that even novice students can work through the problem. We illustrate this by estimating the kinetic parameters of catechol oxidase in the complex model using data obtained from two sections of a course-based undergraduate research experience (CURE) freshman biology lab. Worksheets with questions motivating model building and simulation comprehension are provided. The effect of these exercises on students opinions of math, biology, and coding are evaluated using pre- and post-test surveys and student feedback. Our results show that these tools illustrate enzyme kinetics mathematically, students are not intimidated by the degree of math or coding involved, and in some cases are interested to do more, despite being unaware of the focus of the lab when signing up.

category: scientific communication and education


title: Mathematical Modeling of Thyroid Homeostasis: Implications for the Allan-Herndon-Dudley Syndrome

abstract:
ObjectiveA mathematical model of the pituitary-thyroid feedback loop is extended to deepen the understanding of the Allan-Herndon-Dudley syndrome (AHDS).

BackgroundThe AHDS is characterized by unusual thyroid hormone concentrations and a mutation in the SLC16A2 gene encoding for the monocarboxylate transporter 8 (MCT8). This mutation leads to a loss of thyroid hormone transport activity. One hypothesis to explain the unusual hormone concentrations of AHDS patients is that due to the loss of thyroid hormone transport activity, thyroxine (T4) is partially retained in thyroid cells.

MethodsThis hypothesis is investigated by extending a mathematical model of the pituitary-thyroid feedback loop to include a model of the net effects of membrane transporters such that the thyroid hormone transport activity can be considered. Two modeling approaches of the membrane transporters are employed: on the one hand a nonlinear approach based on the Michaelis-Menten kinetics and on the other hand its linear approximation. The unknown parameters are identified through a constrained parameter optimization.

ResultsIn dynamic simulations, damaged membrane transporters result in a retention of T4 in thyroid cells and ultimately in the unusual hormone concentrations of AHDS patients. The two different modeling approaches lead to similar results.

ConclusionThe results support the hypothesis that a partial retention of T4 in thyroid cells represents one mechanism responsible for the unusual hormone concentrations of AHDS patients. Moreover, our results suggest that the retention of T4 in thyroid cells could be the main reason for the unusual hormone concentrations of AHDS patients.

category: systems biology


title: Lysophosphatidic acid, a CSF marker in posthemorrhagic hydrocephalus that drives CSF accumulation via TRPV4-induced hyperactivation of NKCC1

abstract: A range of neurological pathologies can cause secondary hydrocephalus. For decades, treatment has been limited to surgical CSF diversion, as still no pharmacological options exist due to the elusive molecular nature of the CSF secretion apparatus and its regulatory properties. We have now identified phospholipid lysophosphatidic acid (LPA) as a biomarker for posthemorrhagic hydrocephalus (PHH) in patients with subarachnoid hemorrhage (SAH) and mimicked our results in an animal model of intraventricular hemorrhage (IVH). Intraventricular administration of LPA caused elevated brain water content and ventriculomegaly in experimental rats, via its action as an agonist of the choroidal transient receptor potential vanilloid 4 (TRPV4) channel. TRPV4 was revealed as a novel regulator of ICP in experimental rats via its ability to modulate the CSF secretion rate through its direct activation of the Na+, K+, 2Cl- cotransporter (NKCC1) implicated in CSF secretion. Together, our data reveal that a biomarker present in brain pathologies with hemorrhagic events promotes CSF hypersecretion and ensuing brain water accumulation via its direct action on TRPV4 and its downstream regulation of NKCC1. TRPV4 may therefore be a promising future pharmacological target for pathologies involving disturbed brain fluid dynamics.

category: neuroscience


title: A retroviral origin of vertebrate myelin

abstract: Myelin, the insulating sheath that surrounds neuronal axons, is produced by oligodendrocytes in the central nervous system (CNS). This evolutionary innovation, which first appears in jawed vertebrates, enabled rapid transmission of nerve impulses, more complex brains and greater morphological diversity. Here we report that RNA level expression of RNLTR12-int, a retrotransposon of retroviral origin, is essential for myelination. We show RNLTR12-int-encoded non-coding RNA binds to the transcription factor SOX10 to regulate transcription of myelin basic protein (Mbp, the major constituent of myelin). RNLTR12-int like sequences (which we name RetroMyelin) are found in all jawed-vertebrates and also regulate myelination in zebrafish, suggesting retroviral endogenization as a key step in the emergence of vertebrate myelin.


title: Impact of decision and action outcomes on subsequent decision and action behaviors

abstract: In general, speed-accuracy tradeoff adjustments in decision-making have been studied separately from those in motor control. In the wild however, animals coordinate their decision and action, freely investing time in choosing versus moving given specific contexts. Recent behavioral studies support this view, indicating that humans can trade decision time for movement time to maximize their reward rate at the level of entire experimental sessions. Besides, it is established that choice outcomes largely impact subsequent decisions. Crucially though, whether and how a decision also influences the subsequent motor behavior, and whether and how a motor error influences the next decision is currently unknown. Here we address these questions by analyzing trial-to-trial changes of choice and motor behaviors in humans instructed to perform successive perceptual decisions expressed with reaching movement whose duration was either bounded or unconstrained in separate tasks. Results indicate that after a bad decision, subjects who were not constrained in their action duration decided more slowly and more accurately. Interestingly, they also shortened their subsequent movement duration by moving faster. Conversely, we found that movement errors not only influenced the speed and the accuracy of the following movement, but those of the decision as well. If the movement had to be slowed down, the decision that precedes that movement was accelerated, and vice versa. Together, these results indicate that from one trial to the next, humans are primarily concerned about determining a behavioral duration as a whole instead of optimizing each of the decision and action speed-accuracy trade-offs independently of each other.


title: Host Chitinase 3-like-1 is a Universal Therapeutic Target for the Delta, Omicron and Other SARS-CoV-2 Viral Variants in COVID 19

abstract: COVID 19 is the disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2; SC2) which has caused a world-wide pandemic with striking morbidity and mortality. Evaluation of SC2 strains demonstrated impressive genetic variability and many of these viral variants are now defined as variants of concern (VOC) that cause enhanced transmissibility, decreased susceptibility to antibody neutralization or therapeutics and or the ability to induce severe disease. Currently, the delta ({delta}) and omicron (o) variants are particularly problematic based on their impressive and unprecedented transmissibility and ability to cause break through infections. The delta variant also accumulates at high concentrations in host tissues and has caused waves of lethal disease. Because studies from our laboratory have demonstrated that chitinase 3-like-1 (CHI3L1) stimulates ACE2 and Spike (S) priming proteases that mediate SC2 infection, studies were undertaken to determine if interventions that target CHI3L1 are effective inhibitors of SC2 viral variant infection. Here we demonstrate that CHI3L1 augments epithelial cell infection by pseudoviruses that express the alpha, beta, gamma, delta or omicron S proteins and that the CHI3L1 inhibitors anti-CHI3L1 and kasugamycin inhibit epithelial cell infection by these VOC pseudovirus moieties. Thus, CHI3L1 is a universal, VOC-independent therapeutic target in COVID 19.

category: immunology


title: Host Chitinase 3-like-1 is a Universal Therapeutic Target for SARS-CoV-2 Viral Variants in COVID 19


title: SARS-CoV-2 Omicron variant virus isolates are highly sensitive to interferon treatment

abstract: Recently, we have shown that SARS-CoV-2 Omicron virus isolates are less effective at inhibiting the host cell interferon response than Delta viruses. Here, we present further evidence that reduced interferon-antagonising activity explains at least in part why Omicron variant infections are inherently less severe than infections with other SARS-CoV-2 variants. Most importantly, we here also show that Omicron variant viruses display enhanced sensitivity to interferon treatment, which makes interferons promising therapy candidates for Omicron patients, in particular in combination with other antiviral agents.

category: microbiology


title: Lack of Ronapreve (REGN-CoV; casirivimab and imdevimab) virological efficacy against the SARS-CoV 2 Omicron variant (B.1.1.529) in K18-hACE2 mice

abstract: The Omicron variant (B.1.1.529) of SARS-CoV-2 has placed enormous strain on global healthcare systems since it was first identified by South African researchers in late 2021. Omicron has >50 mutations which mainly occur in the surface spike protein and this has led to rapid assessment of monoclonal antibodies to assess the impact on virus neutralisation. Ronapreve has shown potential application in post-exposure prophylaxis, mild/moderate disease and in seronegative patients with severe COVID19, but several early reports of loss of in vitro neutralisation activity have been documented. Here, the virological efficacy of Ronapreve was assessed in K18-hACE2 mice to provide an in vivo outcome. Ronapreve reduced sub-genomic RNA in lung and nasal turbinate for the Delta variant but not the Omicron variant of SARS-CoV-2 at doses 2-fold higher than those shown to be active against previous variants of the virus. These data add to the growing evidence that the effectiveness of Ronapreve is compromised for the Omicron variant.


title: Chemical-induced degradation of PreS2 mutant surface antigen reverses HBV- mediated hepatocarcinogenesis

abstract:
Naturally evolved immune-escape PreS2 mutant is an oncogenic caveat of liver cirrhosis and hepatocellular carcinoma (HCC) during chronic hepatitis B virus (HBV) infection. Notably, PreS2 mutants is prevalent in above 50% of patients with HCC. Intrahepatic expression of PreS2 mutant large surface antigen (PreS2-LHBS) induces endoplasmic reticulum stress, mitochondria dysfunction, cytokinesis failure and subsequent chromosome hyperploidy. In this study, we ask if long-term inhibition of PreS2-LHBS may act to reverse HBV-mediated hepatocarcinogenesis. We set up a stability reporter platform and identified ABT199 as an inhibitor of PreS2-LHBS from a library of 1068 FDA-approved drugs. Treatment of ABT199 induced PreS2-LHBS degradation without affecting the general cell viability, as shown in hepatoma and immortalized hepatocyte cell lines. We found that ABT199 induced the recruitment of PreS2-LHBS to ring-shaped structures in close proximity to lysosomal marker Lamp1 and multivesicular body marker Rab7. Simultaneously, inhibitions of lysosomal degradation or microautophagy restored the expression of PreS2-LHBS. Specifically, a 24-hr treatment of ABT199 reduced DNA damages and cytokinesis failure induced by PreS2-LHBS. Persistent treatment of ABT199 for 3 weeks reversed chromosome hyperploidy in PreS2-LHBS cells and suppressed anchorage-independent growth of HBV-positive hepatoma cell line. Together, we showed that ABT199 provoked selective degradation of PreS2-LHBS through the induction of microautophagy, and a long-term treatment of ABT199 reversed oncogenic mechanisms induced by HBV. Our results indicate that long-term degradation of PreS2-LHBS may serve as a novel therapeutic strategy to constrain HBV-mediated hepatocarcinogenesis.

Graphical abstract

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View larger version (16K):
org.highwire.dtl.DTLVardef@1720c85org.highwire.dtl.DTLVardef@943121org.highwire.dtl.DTLVardef@1257a22org.highwire.dtl.DTLVardef@1756348_HPS_FORMAT_FIGEXP  M_FIG C_FIG Author summaryHBV PreS2 mutant large surface antigen (PreS2-LHBS) is an oncoprotein that induces liver cirrhosis and liver cancer. This study identified ABT199 as a potential inhibitor of PreS2-LHBS. We found that ABT199 could trigger the degradation of PreS2-LHBS through the induction of microautophagy. Moreover, a long-term treatment of ABT199 significantly reversed LHBS-induced oncogenic events including DNA damage, mitotic failure, chromosome hyperploidy, and anchorage-independent growth. This study not only identifies a specific inhibitor of PreS2-LHBS but also highlights a plausible strategy to constrain HBV-mediated hepatocarcinogenesis through targeting the degradation of PreS2-LHBS.


title: Bacteriophage-derived dsRNA exerts anti-SARS-CoV-2 activity in vitro and in Golden Syrian hamsters in vivo

abstract:
PurposeBacteriophage-derived dsRNA, also known as Larifan, is nationally well-known broad-spectrum antiviral medication. The goal of this study was to ascertain the antiviral activity of Larifan against the novel SARS-CoV-2.

MethodsThe antiviral activity of Larifan against SARS-CoV-2 in vitro was measured in human lung adenocarcinoma (Calu3) and primary human small airway epithelial cells (HSAEC) using cytopathic effect assay, viral RNA copy number detection by digital droplet PCR (ddPCR) and infectious virus titration in cells supernatants in Vero E6 cells by end-point titration method. The antiviral effect of Larifan in vivo was detected in SARS-CoV-2 infection model in Golden Syrian hamsters. Larifan (5 mg/kg) was administered either subcutaneously or intranasally twice before and after virus infection with a 24-hour interval between doses. The viral RNA copies and infectious virus titre were detected in animal lungs at day three and five post-infection using ddPCR and end-point titration in Vero E6 cells, respectively. Histopathology of lungs was analysed as well.

ResultsLarifan inhibited SARS-CoV-2 replication in Calu3 cells both after the drug addition pre- and post-infection with a substantial drop in the supernatant viral RNA copy numbers from eight (p = 0.0013) to twenty (p = 0.0042) times, respectively. Similarly, infectious virus titre in Vero E6 cells dropped by 3.6log10 TCID50 and 2.8log10 TCID50 after the drug addition pre- and post-infection, respectively. In HSAEC, Larifan inhibited SARS-CoV-2 replication at the similar level. Larifan also markedly reduced virus numbers in the lungs of infected hamsters (p = 0.0032) both at day three and five post-infection with a more pronounced effect after intranasal administration reaching a drop by 2.7log10 at day three and 2.0log10 at day five. The administration of Larifan also reduced the amount of infections virus titer in lungs (p = 0.0039) by 4.3log10 TCID50 and 2.8log10 TCID50 at day three and five post-infection, respectively. Improvements in the infection-induced pathological lesion severity in the lungs of animals treated with Larifan were also demonstrated by histological analyses.

ConclusionsThe inhibition of SARS-CoV-2 replication in vitro and the reduction of the viral load in the lungs of infected hamsters treated with Larifan alongside the improved lung histopathology, suggests a potential use of Larifan in controlling the COVID-19 disease in humans.


title: Global success in oyster reef restoration despite ongoing recovery debt

abstract: Habitat destruction and biodiversity loss from exploitation of ecosystems have led to increased restoration and conservation efforts worldwide. Disturbed ecosystems accumulate a recovery debt - the accumulated loss of ecosystem services - and quantifying this debt presents a valuable tool to develop better ecosystem restoration practices. Here, we quantified the ongoing recovery debt following structural restoration of oyster habitats, one of the most degraded marine ecosystems worldwide. We found that whilst restoration initiates a rapid increase in biodiversity and abundance of 2- to 5-fold relative to unrestored habitat, recovery rate decreases substantially within a few years post-restoration and accumulated global recovery debt persists at >35% per annum. Therefore, while efficient restoration methods will produce enhanced recovery success and minimise recovery debt, potential future coastal development should be weighed up against not just the instantaneous damage to ecosystem functions and services but also the potential for generational loss of services and long-term recovery.

category: ecology


title: Does the impact of cultivar mixtures on virulence dynamics in Zymoseptoria tritici populations persist after interseason sexual reproduction?

abstract: This study follows on from a previous study showing that binary mixtures of wheat cultivars affect the evolution of Zymoseptoria tritici populations within a field epidemic from the beginning (t1) to the end (t2) of a growing season. Here, we focused on the impact of interseason sexual reproduction on this evolution. We studied mixtures of susceptible and resistant cultivars (carrying Stb16q, a recently broken-down resistance gene) in proportions of 0.25, 0.5 and 0.75, and their pure stands. We determined the virulence status of 1440 ascospore-derived strains collected from residues of each cultivar by phenotyping on seedlings. Virulence frequencies were lower in mixtures than in pure stands of the resistant cultivar, as at t2, revealing that the impact of mixtures persisted until the beginning of the next epidemic (t3). The frequency of virulence was lower in the offspring population on the susceptible cultivar and, more surprisingly, the frequency of avirulence on the resistant cultivar increased after sexual reproduction. Our findings highlight two epidemiological processes in mixtures: selection within the local pathogen population between t1 and t2 driven by asexual cross-contamination between cultivars (previous study) and sexual crosses between avirulent and virulent strains between t2 and t3 driven by changes in the probabilities of physical encounters (this study). Mixtures therefore appear to be a promising strategy for the deployment of qualitative resistances, not only to limit the intensity of Septoria tritici blotch epidemics, but also to reduce the erosion of resistances by managing evolution of the pathogen population at a pluriannual scale.


title: ArtSeg: Rapid Artifact Segmentation and Removal in Brightfield Cell Microscopy Images

abstract: Brightfield cell microscopy is a foundational tool in life sciences. The acquired images are prone to contain visual artifacts that hinder downstream analysis, and automatically removing them is therefore of great practical interest. Deep convolutional neural networks are state-of-the-art for image segmentation, but require pixel-level annotations, which are time-consuming to produce. Here, we propose ScoreCAM-U-Net, a pipeline to segment artifactual regions in brightfield images with limited user input. The model is trained using only image-level labels, so the process is faster by orders of magnitude compared to pixel-level annotation, but without substantially sacrificing the segmentation performance. We confirm that artifacts indeed exist with different shapes and sizes in three different brightfield microscopy image datasets, and distort downstream analyses such as nuclei segmentation, morphometry and fluorescence intensity quantification. We then demonstrate that our automated artifact removal ameliorates this problem. Such rapid cleaning of acquired images using the power of deep learning models is likely to become a standard step for all large scale microscopy experiments.

category: bioinformatics


title: The N764K and N856K mutations in SARS-CoV-2 Omicron S protein generate potential cleavage sites for SKI-1/S1P protease

abstract: Spike (S) protein is a key protein in coronaviruses life cycle. SARS-CoV-2 Omicron BA.1 variant of concern (VoC) presents an exceptionally high number of 30 substitutions, 6 deletions and 3 insertions in the S protein. Recent works revealed major changes in the SARS-CoV-2 Omicron biological properties compared to earlier variants of concern (VoCs). Here, these major changes could be explained, at least in part, by the mutations N764K and/or N856K in S2 subunit. These mutations were not previously detected in other VoCs. N764K and N856K generate two potential cleavage sites for SKI-1/S1P serine protease, known to cleave viral envelope glycoproteins. The new sites where SKI-1/S1P could cleave S protein might impede the exposition of the internal fusion peptide for membrane fusion and syncytia formation. Based on the human protein atlas, SKI-1/S1P protease is not found in lung tissues (alveolar cells type I/II and endothelial cells), but present in bronchus and nasopharynx. This may explain why Omicron has change of tissue tropism. Viruses have evolved to use several host proteases for cleavage/activation of envelope glycoproteins. Mutations that allow viruses to change of protease may have a strong impact in host range, cell and tissue tropism, and pathogenesis.


title: The N764K and N856K mutations in SARS-CoV-2 Omicron BA.1 S protein generate potential cleavage sites for SKI-1/S1P protease


title: Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment

abstract: We computationally investigated the role of the Omicron RBD mutations on its structure and interactions with ACE2. Our results suggest that, compared to the WT and Delta, the mutations in the Omicron RBD facilitate a more efficient RBD opening and ACE2 attachment. These effects, combined with antibody evasion, may contribute to its dominance over Delta. While the Omicron RBD escapes most antibodies from prior infections, epitope analysis shows that it harbors sequences with significantly improved antigenicity compared to other variants, suggesting more potent Omicron-specific neutralizing antibodies.

category: biophysics


title: Differences in durability of PARP inhibition by clinically approved PARP inhibitors: implications for combinations and scheduling

abstract:
Five PARP inhibitors (PARPi) are approved for cancer treatment, they exploit cancer-specific defects in homologous recombination repair (HRR) to selectively kill tumour cells. Continuous PARP inhibition is required for single-agent anticancer activity. PARPi are also being investigated with ATR inhibitors clinically. We previously showed rucaparib caused prolonged PARP inhibition. Here we aimed to determine if this property was unique to rucaparib or common to other PARPis and the implications for scheduling with an ATR inhibitor (VE-821). Durability of PARP inhibition was determined at 0, 1, 24, 48 and 72 h after a 1 h pulse of 1M of rucaparib, olaparib, niraparib, talazoparib or pamiparib in IGROV-1 (human ovarian cancer) cells. Inhibition of PARP was sustained to a variable degree with all inhibitors, but reduced with time. Rucaparib caused the most persistent inhibition of PARP activity, which was maintained at [≥]75% for 72 h after drug withdrawal. In contrast, only 12% inhibition remained at this time with talazoparib and pamiparib and no detectable inhibition with olaparib and niraparib. Rucaparib enhanced VE-821 cytotoxicity to a similar extent in a sequential schedule as in co-exposure studies (PF50: 2.6 vs. 2.7) and there was even an approx. 2-fold enhancement after a 24 h delay between rucaparib and VE-821. Olaparib and niraparib produced similar enhancement of VE-821 cytotoxicity if co-exposed but were ineffective in sequential exposures. These data have clinical implications for both schedules of current PARPi monotherapy and the scheduling of PARPi in combination with ATRi and other cytotoxic drugs.

Novelty and ImpactPARPi are a new class of anticancer agent. We demonstrate for the first time that 5 PARPi continue to suppress cellular PARP activity after drug removal to a variable extent. Rucaparib caused the most durable PARP inhibition, olaparib and niraparib the least. Rucaparib enhanced ATR inhibitor cytotoxicity in sequential and co-exposures, olaparib and niraparib were only active in co-exposure settings. These data have implications for the clinical use of PARPi, particularly in combination with other drugs.


title: Becoming metrics literate: An analysis of brief videos that teach about the h-index

abstract:
IntroductionAcademia uses scholarly metrics, such as the h-index, to make hiring, promotion, and funding decisions. These high-stakes decisions require that those using scholarly metrics be able to recognize, interpret, critically assess and effectively and ethically use them. This study aimed to characterize educational videos about the h-index to understand available resources and provide recommendations for future educational initiatives.

MethodsThe authors analyzed videos on the h-index posted to YouTube. Videos were identified by searching YouTube and were screened by two authors. To code the videos the authors created a coding sheet, which assessed content and presentation style with a focus on the videos educational quality based on Cognitive Load Theory. Two authors coded each video independently with discrepancies resolved by group consensus.

ResultsThirty-one videos met inclusion criteria. Twenty-one videos (68%) were screencasts and seven used a "talking head" approach. Twenty-six videos defined the h-index (83%) and provided examples of how to calculate and find it. The importance of the h-index in high-stakes decisions was raised in 14 (45%) videos. Sixteen videos (52%) described caveats about using the h-index, with potential disadvantages to early researchers the most prevalent (n=7; 23%). All videos incorporated various educational approaches with potential impact on viewer cognitive load. Most videos (n=21; 68%) displayed amateurish production quality.

DiscussionThe videos featured content with potential to enhance viewers metrics literacies such that many defined the h-index and described its calculation, providing viewers with skills to recognize and interpret the metric. However, less than half described the h-index as an author quality indicator, which has been contested, and caveats about h-index use were inconsistently presented, suggesting room for improvement. While most videos integrated practices to facilitate balancing viewers cognitive load, few (32%) were of professional production quality. Some videos missed opportunities to adopt particular practices that could benefit learning.


title: A bite force database of 654 insect species

abstract: Bite force is a decisive performance trait in animals because it plays a role for numerous life history components such as food consumption, inter- and intraspecific interactions, and reproductive success. Bite force has been studied across a wide range of vertebrate species, but only for 20 species of insects, the most speciose animal lineage. Here we present the insect bite force database with bite force measurements for 654 insect species covering 111 families and 13 orders with body lengths ranging from 4.2 - 180.1 mm. In total we recorded 1906 bite force series from 1290 specimens, and, in addition, present basal head, body, and wing metrics. As such, the database will facilitate a wide range of studies on the characteristics, predictors, and macroevolution of bite force in the largest clade of the animal kingdom and may serve as a basis to further our understanding of macroevolutionary processes in relation to bite force across all biting metazoans.

category: zoology


title: Nasally-delivered interferon-{lambda} protects mice against upper and lower respiratory tract infection of SARS-CoV-2 variants including Omicron

abstract: Although vaccines and monoclonal antibody countermeasures have reduced the morbidity and mortality associated with SARS-CoV-2 infection, variants with constellations of mutations in the spike gene threaten their efficacy. Accordingly, antiviral interventions that are resistant to further virus evolution are needed. The host-derived cytokine IFN-{lambda} has been proposed as a possible treatment based on correlative studies in human COVID-19 patients. Here, we show IFN-{lambda} protects against SARS-CoV-2 B.1.351 (Beta) and B.1.1.529 (Omicron)variants in three strains of conventional and human ACE2 transgenic mice. Prophylaxis or therapy with nasally-delivered IFN-{lambda}2 limited infection of historical or variant (B.1.351 and B.1.1.529) SARS-CoV-2 strains in the upper and lower respiratory tracts without causing excessive inflammation. In the lung, IFN-{lambda} was produced preferentially in epithelial cells and acted on radio-resistant cells to protect against of SARS-CoV-2 infection. Thus, inhaled IFN-{lambda} may have promise as a treatment for evolving SARS-CoV-2 variants that develop resistance to antibody-based countermeasures.


title: Ligand-independent modulation of GIPR signaling by splice variants

abstract: Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a potential drug target for metabolic disorders. It works with glucagon-like peptide-1 receptor (GLP-1R) and glucagon receptor (GCGR) in humans to maintain glucose homeostasis. Unlike the other two receptors, GIPR has at least 7 reported (EMBL-EBI, 2022; NCBI, 2022a, 2022b) splice variants (SVs) with previously undefined functions. To explore their roles in endogenous peptide mediated GIPR signaling, we investigated the outcome of co-expressing each of the four SVs in question with GIPR in terms of ligand binding, cAMP accumulation, Gs activation, {beta}-arrestin recruitment and cell surface localization. The effects of these SVs on intracellular cAMP responses modulated by receptor activity-modifying proteins (RAMPs) were also studied. It was found that while SVs of GIPR neither bound to the hormone nor affected its signal transduction per se, they differentially regulated GIPR-mediated cAMP and {beta}-arrestin responses. Specifically, SV1 and SV4 were preferable to Gs signaling, SV3 was biased towards {beta}-arrestin recruitment, whereas SV2 was inactive on both pathways. In the presence of RAMPs, only SV1 and SV4 synergized the repressive action of RAMP3 on GIP-elicited cAMP production. The results suggest a new form of signal bias that is constitutive and ligand-independent, thereby expanding our knowledge of biased signaling beyond pharmacological manipulation (i.e., ligand specific) as well as constitutive and ligand-dependent (e.g., SV1 of the growth hormone-releasing hormone receptor).

category: molecular biology


title: Evolutionary conserved aspects of animal nutrient uptake and transport in sea anemone vitellogenesis

abstract: Vitellogenesis, the accumulation of egg yolk, relies on the transport of dietary nutrients from the gut to the ovary through the circulatory system in many bilaterians (e.g. vertebrates, arthropods). How these dietary nutrients and yolk precursors are absorbed and transported in cnidarians (e.g. corals, sea anemones, jellyfish), which are bi-layered and lack a circulatory system, is however only poorly understood. Here, we studied the tissues and molecules that facilitate the uptake and transport of dietary nutrients, especially lipids, towards the oocytes in the sea anemone Nematostella vectensis to better understand the evolution of systemic nutrient transport in animals. We identified the somatic gonad epithelium as one of several gastrodermal tissues specialized in phagocytosis, micropinocytosis and intracellular digestion. We showed more specifically that dietary fatty acids are absorbed by the ApolipoproteinB- and Vitellogenin-expressing somatic gonad epithelium. Their subsequent, rapid transport into the extracellular matrix (ECM) and endocytosis into oocytes is likely mediated by an evolutionary conserved Vitellogenin (Vtg)-Very Low-Density Lipoprotein Receptor (VLDLR) ligand/receptor pair. We propose that ECM-based, Vtg/VLDLR-mediated lipoprotein transport during vitellogenesis predates the cnidarian-bilaterian split and provided a mechanistic basis to evolve sophisticated circulatory systems in bilaterians.

category: evolutionary biology


title: Proteostasis is differentially modulated by inhibition of translation initiation or elongation

abstract: Recent work has revealed an increasingly important role for mRNA translation in maintaining proteostasis. Inhibiting translation protects from various proteostatic insults, including heat, expression of aggregation-prone proteins, or aging. However, multiple studies have come to differing conclusions about the mechanisms underlying the protective effects of translation inhibition. Here, we systematically lower translation either by pharmacologically inhibiting translation initiation or elongation and show that each step activates distinct protective responses in Caenorhabditis elegans. Targeting initiation triggers an HSF-1 dependent mechanism that protects from heat and age-associated protein misfolding but not from proteotoxicity caused by proteasome dysfunction. Conversely, targeting elongation triggers an HSF-1 independent mechanism that protects from heat and proteasome dysfunction but not from age-associated protein aggregation. Furthermore, while inhibiting translation initiation increases lifespan in wild-type worms, inhibiting translation elongation only extends lifespan when the animals exhibit preexisting proteotoxic stress--either as a result of aggregation-prone protein expression or hsf-1 deficiency. Together our findings suggest that organisms evolved complementary mechanisms that the mRNA translation machinery can trigger to restore proteostasis.

category: biochemistry


title: Crystal structure of an RNA/DNA strand exchange junction

abstract: Short segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types--an RNA:DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-5/DNA-3 strand exchange junction at an anisotropic resolution of 1.6 to 2.2 [A]. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events.


title: Reactive Oxygen Species-induced Protein Carbonylation Promotes Deterioration of Physiological Activity of Wheat Seeds

abstract: During the seed aging process, reactive oxygen species (ROS) can induce the carbonylation of proteins, which changes their functional properties and affects seed vigor. However, the impact and regulatory mechanisms of protein carbonylation on wheat seed vigor are still unclear. In this study, we investigated the changes in wheat seed vigor, carbonyl protein content, ROS content and embryo cell structure during an artificial aging process, and we analyzed the correlation between protein carbonylation and seed vigor. During the artificial wheat-seed aging process, the activity levels of antioxidant enzymes and the contents of non-enzyme antioxidants decreased, leading to the accumulation of ROS and an increase in the carbonyl protein content, which ultimately led to a decrease in seed vigor, and there was a significant negative correlation between seed vigor and carbonyl protein content. Moreover, transmission electron microscopy showed that the contents of protein bodies in the embryo cells decreased remarkably. We postulate that during the wheat seed aging process, an imbalance in ROS production and elimination in embryo cells leads to the carbonylation of proteins, which plays a negative role in wheat seed vigor.

category: physiology


title: The sowing date changed the temperature and light conditions in the field modified the cadmium content of brown rice (Oryza sativa L.) by regulating the expression of Cd-related genes

abstract: Cadmium (Cd) contamination in rice is a potential health hazard when ingested through the food chain worldwide. Reducing the Cd content in rice through agronomic measures is an effective way to reduce the risk of Cd contamination to human health. In order to clarify the correlation between temperature and light conditions and Cd accumulation (Cd-A) and Cd content of brown rice (CdBR) during the field growth period (FGP) of rice, consequently provide a theoretical basis for the selection of sowing date (SD) for "Low-Cd-Rice" production, field experiment with different SDs was carried out by using two rice varieties with different Cd accumulation characteristics (Luliangyou 996, V1, a high Cd accumulation variety; Zhuliangyou 819, V2, a low Cd accumulation variety). The results showed that the temperature and light factors such as mean soil temperature (ST), mean air temperature (AT), soil accumulation temperature (SAT), air accumulation temperature (AAT), ultraviolet radiation accumulation (UR), photosynthetic radiation accumulation (PR), light intensity accumulation (I) and sunshine hours accumulation (SH) varied to different degrees under different SDs; The difference in CdBR in two varieties could be up to 2.82 and 8.48 times respectively among SDs, with the CdBR of S4 and S5 of V2 being lower than the national standard of 0.2 mg/kg. The relative expression of OsIRT1 in the root system was significantly positively correlated with ST, SAT, AT, AAT, and SH, while OsNramp5, OsNramp1, and OsHMA3 showed significant negative correlations with ST, SAT, AT, AAT, and SH in relative expression in the root system; OsIRT1 expressed in the roots of V1 was significantly negatively correlated with CdBR, while OsHMA3 expression was significantly positively correlated with CdBR; OsLCD, OsNramp1, and OsHMA3 expression in the roots of V2 were significantly positively correlated with Cd-A and CdBR, while OsIRT1 in the roots of V2 and OsLCT1 in the leaves were significantly negatively correlated with Cd-A; The expression of OsNramp5 in roots was significantly negatively correlated with Cd-A and CdBR in both V1 and V2. Bias correlation analysis showed that ST, SAT, AT, and AAT were significantly negatively correlated with both Cd-A and CdBR; SH was significantly negatively correlated with CdBR in V1. Summarily, the temperature and light conditions during the FGP of rice and their regulation of the expression levels of related genes could be changed by sowing selection, so as to achieve safe production of rice under Cd-contaminated fields.


title: Initial assessment of the spatial learning, reversal, and sequencing task capabilities of knock-in rats with humanizing mutations in the Ass-coding region of App

abstract: Model organisms mimicking the pathogenesis of human diseases are useful for identifying pathogenic mechanisms and testing therapeutic efficacy of compounds targeting them. Models of Alzheimers disease and related dementias aim to reproduce the brain pathology associated with these neurodegenerative disorders. Transgenic models, which involve random insertion of disease-causing genes under the control of artificial promoters, are efficient means of doing so. There are confounding factors associated with transgenic approaches, however, including target gene overexpression, dysregulation of endogenous gene expression at transgenes integration sites, and limitations in mimicking loss-of-function mechanisms. Furthermore, the choice of species is important, and there are anatomical, physiological, and cognitive reasons for favoring the rat over the mouse, which has been the standard for models of neurodegeneration and dementia. We report an initial assessment of the spatial learning, reversal, and sequencing task capabilities of knock-in Long-Evans rats with humanizing mutations in the A{beta}-coding region of App, which encodes amyloid precursor protein (Apph/h rats), using the IntelliCage, an automated operant social home cage system, at 6-8 weeks of age, then again at 4-5 months of age. These rats were previously generated as control organisms for studies on neurodegeneration involving other knock-in rat models from our lab. Apph/h rats of either sex can acquire place learning and reversal tasks. They can also acquire a diagonal sequencing task by 6-8 weeks of age, but not a more advanced serial reversal task involving alternating diagonals, even by 4-5 months of age.


title: Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla)

abstract:
BackgroundMacadamia is a true dicotyledonous plant that thrives in a mild, humid, low wind environment. It is cultivated and traded internationally due to its high-quality nuts thus, has significant development prospects and scientific research value. However, information on the genetic resources of Macadamia spp. remains scanty.

ResultsThe mitochondria (mt) genomes of three economically important Macadamia species, Macadamia integrifolia, M. ternifolia and M. tetraphylla, were assembled through the Illumina sequencing platform. The results showed that each species has 71 genes, including 42 protein-coding genes, 26 tRNAs, and 3 rRNAs. Repeated sequence analysis, RNA editing site prediction, and analysis of genes migrating from chloroplast (cp) to mt were performed in the mt genomes of the three Macadamia species. Phylogenetic analysis based on the mt genome of the three Macadamia species and 35 other species was conducted to reveal the evolution and taxonomic status of Macadamia. Furthermore, the characteristics of the plant mt genome, including genome size and GC content, were studied through comparison with 36 other plant species. The final non-synonymous (Ka) and synonymous (Ks) substitution analysis showed that most of the protein-coding genes in the mt genome underwent negative selections, indicating their importance in the mt genome.

ConclusionThe findings of this study provide a better understanding of the Macadamia genome and will inform future research on the genus.

category: genomics


title: Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon

abstract: Single Nucleotide Polymorphisms (SNPs) are now popular for a myriad of applications in animal and plant species including, ancestry assignment, conservation genetics, breeding, and traceability of animal products. The objective of this study was to develop a customized cost-effective SNP panel for genetic characterisation of Macrobrachium species in Cameroon. The SNPs identified in a previous characterization study were screened as viable candidates for the reduced panel. Starting from a full set of 1,814 SNPs, a total of 72 core SNPs were chosen using conventional approaches: a) allele frequency differentials, minor allele frequency (MAF) profiles, and Wrights Fst statistics. The discriminatory power of reduced set of informative SNPs were then tested using the admixture analysis, principal component analysis (PCA), and discriminant analysis of principal components (DAPC). The panel of prioritised SNP markers (i.e., N = 72 SNPs) distinguished Macrobrachium species with 100% accuracy. However, large sample size is needed to identify more informative SNPs for discriminating genetically closely related species, including M. macrobrachion versus M. vollenhovenii and M. sollaudii versus M. dux. Overall, the findings in this study show that we can accurately characterise Macrobrachium using a small set of core SNPs which could be useful for commercial breeding operations, conservation, and species assignment of this economically important species in Cameroon. Given the results obtained in this study, a larger independent validation sample set will be needed to confirm the discriminative capacity of this SNP panel for wider commercial and research applications.


title: Morphological analysis of human and mouse dendritic spines reveals a morphological continuum and differences across ages and species

abstract: Dendritic spines have diverse morphologies, with a wide range of head and neck sizes, and these morphological differences likely generate different synaptic and functional properties. To explore how this morphological diversity differs across species we analyzed 3D confocal reconstructions of ~8,000 human spines and ~1,700 mouse spines, labeled by intracellular injections in fixed tissue. Using unsupervised machine-learning algorithms, we computationally separated spine heads and necks and systematically measured morphological features of spines in apical and basal dendrites from cortical pyramidal cells. Human spines had unimodal distributions of parameters, without any evidence of morphological subtypes. Their spine necks were longer and thinner in apical than in basal spines, and spine head volumes of an 85-years-old individual were larger than those of a 40-years-old individual. Human spines overall had longer and thicker necks and bigger head volumes than mouse spines. Our results indicate that human spines form part of a morphological continuum, are larger and longer than those of mice, and become larger with increasing adult age. These morphological differences in spines across species could generate functional differences in biochemical and electrical spine compartmentalization, or in synaptic properties, across species and ages.


title: Predictive coding in ASD: inflexible weighting of prediction errors when switching from stable to volatile environments

abstract: Individuals with autism spectrum disorder (ASD) have been widely reported to show atypicalities in predictive coding, though there remains a controversy regarding what causes such atypical processing. Suggestions range from overestimation of volatility to rigidity in the reaction to environmental changes. Here, we tested two accounts directly using duration reproduction of volatile and non-volatile interval sequences. Critically, both sequences had the same set of intervals but differed in their stimulus presentation orders. Comparing individuals with ASD vs. their matched controls, we found both groups to respond to the volatility in a similar manner, albeit with a generally reduced prior in the ASD group. Interestingly, though, relative to the control group, the ASD group exhibited a markedly reduced trust in the prior in the volatile trial session when this was performed after the non-volatile session, while both groups performed comparably in the reverse session order. Our findings suggest that it is not the learning of environmental volatility that is compromised in ASD. Rather, it is their response to a change of the volatility regimen from stable to volatile, which causes a highly inflexible weighting of prediction errors.


title: Forecasted trends of the new COVID-19 epidemic due to the Omicron variant in Thailand, 2022

abstract:
BackgroundThe introduction of the Omicron variant is of significant concern to the Thai Government due to the possibility of a new wave of the COVID-19 epidemic, which may cause a huge strain to the countrys health system. This study aims to forecast the trends of COVID-19 cases and deaths given the advent of the Omicron variant in Thailand.

MethodsWe used a compartmental susceptible-exposed-infectious-recovered model in combination with a system dynamics model. We developed four scenarios according to differing values of the production number (R) and varying vaccination rates.

ResultsThe findings indicated that in the most pessimistic scenario (R = 7.5 and base vaccination rate), the number of incident cases reached a peak of 49,523 (95% CI: 20,599 to 99,362) by day 73 and the peak daily deaths enlarged to 270 by day 50 (95% CI: 124 to 520). The predicted cumulative cases and deaths at the end of the wave (day 120) were approximately 3.7 million and 22,000 respectively. In the most optimistic assumption (with R = 4.5 and a speedy vaccination rate [tripled the base rate]), the peak of the incident cases was about one third of the most pessimistic assumption (15,650, 95% CI: 12,688 to 17,603). The corresponding daily fatalities were 72 (95% CI: 54 to 84) and the prevalent intubated cases numbered 572 (95% CI: 429 to 675).

ConclusionsIn the coming months, Thailand may face a new wave of the COVID-19 epidemic due to the Omicron variant. The case toll due to the Omicron wave is likely to outnumber the earlier Delta wave, but the death toll is proportionately lower. Despite the immune-escape characteristic of the Omicron variant, the vaccination campaign for the booster dose should be expedited as an effective way of preventing severe illness and death.


title: A human DNA methylation atlas reveals principles of cell type-specific methylation and identifies thousands of cell type-specific regulatory elements

abstract:
DNA methylation is a fundamental epigenetic mark that governs chromatin organization, cell identity, and gene expression. Here we describe a human methylome atlas, based on deep whole-genome bisulfite sequencing allowing fragment-level analysis across thousands of unique markers for 39 cell types sorted from 207 healthy tissue samples.

Replicates of the same cell-type are >99.5% identical, demonstrating robustness of cell identity programs to genetic variation and environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny, and identifies methylation patterns retained since gastrulation. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely hyper-methylated loci are rare and are enriched for CpG islands, polycomb targets, and CTCF binding sites, suggesting a novel role in shaping cell type-specific chromatin looping. The atlas provides an essential resource for interpretation of disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies.

Summary paragraphDNA methylation, a fundamental epigenetic mark, governs chromatin organization and gene expression1, thus defining the molecular identity of cells and providing a window into developmental processes with wide-ranging physiologic and clinical ramifications. Current DNA methylation datasets have limitations, typically including only a fraction of methylation sites, many from cell lines that underwent massive changes in culture or from tissues containing unspecified mixtures of cells2-6.

We present a human methylome atlas based on deep whole-genome bisulfite sequencing of 39 sorted, primary cell types and use this dataset to address fundamental questions in developmental biology, physiology and pathology. Biological replicates are >99.5% identical, demonstrating unappreciated robustness to genetic variation and environmental perturbations. Clustering recapitulates key elements of tissue ontogeny, identifying methylation patterns retained since gastrulation. Loci uniquely unmethylated in individual cell types identify novel transcriptional enhancers and are enriched for tissue-specific transcription factors binding motifs. In contrast, loci uniquely hyper-methylated in specific cell types are rare, enriched for CpG islands and polycomb targets, and overlap CTCF binding sites, suggesting a novel role in shaping cell-type-specific chromatin looping. Finally, the atlas facilitates fragment-level deconvolution of tissue and plasma methylomes across thousands of cell-type specific regions to quantify their individual components at unprecedented resolution.

The human cell-type-specific methylation atlas provides an essential resource for studying gene regulation by defining cell-type-specific distal enhancers and regulators of 3D organization, for identifying pathological changes in DNA methylation, and for the interpretation of methylation-based liquid biopsies.

O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

O_LIA deep methylation atlas of 39 human cell types, sorted from healthy samples
C_LIO_LIMethylomes record developmental history of cells
C_LIO_LIThousands of novel cell type-specific methylation markers
C_LIO_LIHypo-methylation uncovers cell type-specific regulatory map of distal enhancers
C_LIO_LIHyper-methylation across CTCF sites
C_LIO_LICell type-specific biomarkers facilitate fragment-level deconvolution of tissues and cfDNA
C_LI


title: Structural and mechanistic basis of σ-dependent transcriptional pausing

abstract: In {sigma}-dependent transcriptional pausing, the transcription initiation factor {sigma}, translocating with RNA polymerase (RNAP), makes sequence-specific protein-DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in {sigma}-dependent pausing, the RNAP active center can access off-pathway "backtracked" states that are substrates for the transcript-cleavage factors of the Gre family, and on-pathway "scrunched" states that mediate pause escape. Here, using site-specific protein-DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of {sigma} relative to DNA at the{lambda} PR promoter, we show directly that {sigma}-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2-4 bp, and that {sigma}-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2-3 bp. Analogous experiments with a library of 47 ([~]16,000) transcribed-region sequences show that the state scrunched by 2-3 bp--and only that state--is associated with the consensus sequence, T-3N-2Y-1G+1, (where -1 corresponds to the position of the RNA 3 end), which is identical to the consensus for pausing in initial transcription, and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T-3 resides in the DNA nontemplate strand. A cryo-EM structure of a complex engaged in {sigma}-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T-3 of the consensus sequence exerts its effects by facilitating scrunching.


title: Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins

abstract: Peripheral membrane-associated proteins are known to accumulate on the surface of biomembranes as result of membrane-mediated interactions. For a pair of rotationally-symmetric curvature-inducing proteins, membrane mechanics at the low-temperature limit predicts pure repulsion. On the other hand, temperature-dependent entropic forces arise between pairs of stiff-binding proteins suppressing membrane fluctuations. These Casimir-like interactions have thus been suggested as candidates for attractive force leading to aggregation. With dense assemblies of peripheral proteins on the membrane, both these abstractions encounter multi-body complications. Here, we make use of a particle-based membrane model augmented with flexible peripheral proteins to quantify purely membrane-mediated interactions and investigate their underlying nature. We introduce a continuous reaction coordinate corresponding to the progression of protein aggregation. We obtain free energy and entropy landscapes for different surface concentrations along this reaction coordinate. In parallel, we investigate time-dependent estimates of membrane entropy corresponding to membrane undulations and coarse-grained tilt field and how they also change dynamically with protein aggregation. Congruent outcomes of the two approaches point to the conclusion that for low surface concentrations, interactions with an entropic nature may drive the aggregation. But at high concentrations, energetic contributions due to concerted membrane deformation by protein clusters are dominant.


title: Structure of ATP synthase under strain during catalysis

abstract: ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F1 motor and a proton-translocation-driven FO motor. The F1 and FO motors oppose each others action on a shared rotor subcomplex and are held stationary relative to each other by a peripheral stalk. Structures of resting mitochondrial ATP synthases revealed a left-handed curvature of the peripheral stalk even though rotation of the rotor, driven by either ATP hydrolysis in F1 or proton translocation through FO, would apply a right-handed bending force to the stalk. We used cryoEM to image yeast mitochondrial ATP synthase under strain during ATP-hydrolysis-driven rotary catalysis, revealing a large deformation of the peripheral stalk. The structures show how the peripheral stalk opposes the bending force and suggests that proton translocation during ATP synthesis causes accumulation of strain in the stalk, which relaxes by driving the relative rotation of the rotor through six sub-steps within F1, leading to catalysis.


title: Harringtonine has the effects of double blocking SARS-CoV-2 membrane fusion

abstract: Fusion with host cell membrane is the main mechanism of infection of SARS-CoV-2. Here, we propose a new strategy to double block SARS-CoV-2 membrane fusion by using Harringtonine (HT), a small-molecule antagonist. By using cell membrane chromatography (CMC), we found that HT specifically targeted the SARS-CoV-2 S protein and host cell TMPRSS2, and then confirmed that HT can inhibit pseudotyped virus membrane fusion. Furthermore, HT successfully blocked SARS-CoV-2 infection, especially in the delta and Omicron mutant. Since HT is a small-molecule antagonist, it is minimally affected by the continuous variation of SARS-CoV-2. Our findings show that HT is a potential small-molecule antagonist with a new mechanism of action against SARS-CoV-2 infection, and thus HT mainly targets the S protein, and thus, greatly reduces the damage of the S proteins autotoxicity to the organ system, has promising advantages in the clinical treatment of COVID-19.


title: The m6A writer FIONA1 methylates the 3'UTR of FLC and controls flowering in Arabidopsis

abstract: Adenosine bases of RNA can be transiently modified by the deposition of a methyl-group to form N6-methyladenosine (m6A). This adenosine-methylation is an ancient process and the enzymes involved are evolutionary highly conserved. A genetic screen designed to identified suppressors of late flowering transgenic Arabidopsis plants overexpressing the miP1a microProtein yielded a new allele of the FIONA1 (FIO1) m6A-methyltransferase. To characterize the early flowering phenotype of fio1 mutant plants we employed an integrative approach of mRNA-seq, Nanopore direct RNA-sequencing and meRIP-seq to identify differentially expressed transcripts as well as differentially methylated mRNAs. We provide evidence that FIO1 is the elusive methylase responsible for the 3-end methylation of the FLOWERING LOCUS C (FLC) transcript. Furthermore, our genetic and biochemical data suggest that 3-methylation stabilizes FLC mRNAs and non-methylated FLC is a target for rapid degradation.


title: Manganese excess and deficiency affects photosynthesis and metabolism in Marchantia polymorpha

abstract: Manganese is an essential metal for plant growth. The most important Mn-containing enzyme is the Mn4CaO5 cluster that catalyses water oxidation in Photosystem II. Mn deficiency primarily affects photosynthesis, while Mn excess is generally toxic. Mn excess and deficiency were studied in the liverwort Marchantia polymorpha, an emerging model ideally suited for analysis of metal stress since it accumulates rapidly toxic substances due to the absence of well-developed vascular and radicular systems and a reduced cuticle. We established growth conditions for Mn excess and deficiency, performed analysis of metal content in thalli and isolated chloroplasts and determined metabolites. Metabolome analysis revealed a strong accumulation of N-methylalanine upon exposure to Mn excess and a different response of Marchantia to heavy metal stress than that known for higher plants. We investigated photosynthetic performance by chlorophyll fluorescence at room temperature and at 77K, P700 absorption and by studying the susceptibility of thalli to photoinhibition. In vivo super-resolution fluorescence microscopy was used to visualize changes in the organization of the thylakoid membrane under Mn excess and deficiency. Non-optimal Mn concentrations changed the ratio of photosystem I to photosystem II and altered the organisation of thylakoid membranes. Mn deficiency seems to favour cyclic electron flow around photosystem I protecting thereby photosystem II against photoinhibition.


title: Correction of the scientific production: publisher performance evaluation using a dataset of 4844 PubMed retractions.

abstract:
BackgroundWithdrawal of problematic scientific articles after publication is one of the mechanisms for correcting the literature available to publishers, especially in the conditions of the ever-increasing trend of publishing activity in the medical field. The market volume and the business model justify publishers involvement in the post-publication quality control(QC) of scientific production. The limited information about this subject determined us to analyze retractions and the main retraction reasons for publishers with many withdrawn articles. We also propose a score to measure the evolution of their performance. The data set used for this article consists of 4844 PubMed retracted papers published between 1.01.2009 and 31.12.2020.

MethodsWe have analyzed the retraction notes and retraction reasons, grouping them by publisher. To evaluate performance, we formulated an SDTP score whose calculation formula includes several parameters: speed (article exposure time(ET)), detection rate (percentage of articles whose retraction is initiated by the editor/publisher/institution without the authors participation), transparency (percentage of retracted articles available online and clarity of retraction notes), precision (mention of authors responsibility and percentage of retractions for reasons other than editorial errors).

ResultsThe 4844 withdrawn articles were published in 1767 journals by 366 publishers, the average number of withdrawn articles/journal being 2.74. Forty-five publishers have more than ten withdrawn articles, holding 88% of all papers and 79% of journals. Combining our data with data from another study shows that less than 7% of PubMed journals withdrew at least one article. Only 10.5% of the withdrawal notes included the individual responsibility of the authors. Nine of the top 11 publishers had the largest number of articles withdrawn in 2020, in the first 11 places finding, as expected, some big publishers. Retraction reasons analysis shows considerable differences between publishers concerning the articles ET: median values between 9 and 43 months (mistakes), 9 and 73 months (images), 10 and 42 months (plagiarism & overlap).

The SDTP score shows, between 2018 and 2020, an improvement in QC of four publishers in the top 11 and a decrease in the gap between 1st and 11th place. The group of the other 355 publishers also has a positive evolution of the SDTP score.

ConclusionsPublishers have to get involved actively and measurably in the post-publication evaluation of scientific products. The introduction of reporting standards for retraction notes and replicable indicators for quantifying publishing QC can help increase the overall quality of scientific literature.


title: LMM-MQM time series mapping - An application in a murine advanced intercross line identifies novel growth QTLs

abstract:
The Berlin Fat Mouse Inbred line 860 (BFMI860) is a mouse model for juvenile obesity. Previously, a recessive major effect locus (jObes1) was identified on chromosome 3 explaining around 26% of the body weight variance in an BFMI860xC57BL/6NCrl advanced intercross line. The aim of this study was to discover additional QTL.

Time series body weight data were modeled using linear mixed models (LMM), while a multiple QTL mapping (MQM) approach compensated for the jObes1 locus effect. LMM-MQM identified five additional loci significantly associated with body weight. Variance explained by the jObes1 locus increased to 38.1% when using LMM-MQM mapping, while the additional loci explained between 2.0% and 3.9% of the body weight variance. Several positional candidate genes within the novel QTL regions were found in KEGG pathways for insulin signaling and insulin resistance. Strong distortion with preference for the BFMI allele was observed within a newly identified QTL containing the well-known Foxo1 regulator of adipocyte differentiation.

Here, we present a novel method for QTL detection in time series data: LMM-MQM time series mapping. We show that our method is more powerful in detecting QTLs compared to single timepoint mapping approaches. Thus, the time series structure should be considered for optimal detection of small effect QTLs. LMM-MQM time series mapping can be used to find genetic determinants of all kind of "phenotypes over time" be it lactation curves in cattle, plant biomass, drug clearance in human clinical trials, or cognitive decline during disease.

category: genetics


title: Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA

abstract: Methylation of carbon-5 of cytosines (m5C) is a post-transcriptional nucleotide modification of RNA with widespread distribution across organisms. m5C has been shown to participate in mRNA transport and maintain mRNA stability through its recognition by the reader proteins ALYREF and YBX1, respectively. We recently showed that m5C is required for Caenorhabditis elegans development and fertility under heat stress. To contribute to the understanding of how m5C and its oxidative derivatives mediate their functions, we developed RNA baits bearing modified cytosines in diverse structural contexts to pulldown potential readers in C. elegans. Our mass spectrometry analyses reveal unique binding proteins for each of the modifications. We validate our dataset by demonstrating that the nematode ALYREF homologues ALY-1 and ALY-2 preferentially bind m5C in vitro. The dataset presented here serves as an important scientific resource that will support the discovery of new functions of m5C and its derivatives.


title: Rubisco forms a lattice inside alpha-carboxysomes

abstract: Bacteria employ microcompartments to sequester enzymatic processes, either for purposes of protecting cellular contents from reactive intermediates or as a way of increasing reaction efficiency. In these structures, a cargo of enzymes and accessory proteins is encased within a semi-permeable protein shell that permits passage of substrates and products but restricts movement of intermediates. In addition to their importance as a component of many bacterial species metabolisms, microcompartments have recently become a target of protein engineering. The shells can be reassembled from purified proteins, and the full operons can be functionally expressed outside their native prokaryotes and can remain functional following purification. Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo electron tomography to image -carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo in situ, and determined a novel arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 M. This characterization of Rubisco cargo inside the -carboxysome provides new insight into the balance between order and disorder in microcompartment organization.


title: Post-embryonic maturation of the C. elegans motor circuit

abstract:
During development, animals can maintain behavioral output even as the underlying circuits structurally remodel. After hatching, C. elegans undergoes substantial motor neuron expansion and synapse re-wiring while the animal continuously moves with an undulatory pattern. To understand how the circuit transitions from its juvenile to mature configuration without disrupting functional output, we reconstructed the C. elegans motor circuit by electron microscopy across larval development. We observed: 1) Embryonic motor neurons transiently interact with the developing post-embryonic motor neurons prior to remodeling of their juvenile wiring; 2) Post-embryonic neurons initiate synapse development with their future partners as their neurites navigate through the juvenile nerve cords; 3) Embryonic and post-embryonic neurons sequentially build structural machinery needed for the adult circuit before the embryonic neurons relinquish their roles to post-embryonic neurons; 4) This transition is repeated region by region along the body in an anterior to posterior sequence, following the birth order of post-embryonic neurons. Through this orchestrated, programmed and gradual rewiring, the motor circuit transforms from asymmetric to symmetric wiring. These maturation strategies support the continuous maintenance of motor patterns as the juvenile circuit develops into the adult configuration.

HighlightsO_LIPost-embryonic motor circuit maturation was reconstructed by synapse-resolution serial EM.
C_LIO_LIMotor patterns are maintained as the circuit matures from asymmetric to symmetric configuration.
C_LIO_LIProgrammed rewiring gradually and sequentially transforms the circuit structure.
C_LIO_LIPreparatory and communicative wiring-rewiring allows maturation without functional disruption.
C_LI


title: The geometry of hippocampal CA2 representations enables abstract coding of social familiarity and identity

abstract: Social recognition memory encompasses two distinct processes: familiarity - the ability to rapidly distinguish a novel from familiar individual - and recollection, the recall of detailed episodic memories of prior encounters with familiar individuals (1). Although it is clear that the hippocampus is important for different forms of episodic memory (2), including spatial memory (3) and social recognition memory (4-7), whether and how neural activity in this single brain region may be able to encode both social familiarity and social recollection remains unclear (8-13). We addressed such questions using microendoscopic calcium imaging from pyramidal neurons in the dorsal CA2 region of the hippocampus (dCA2), an area crucial for social recognition memory (6, 14, 15) that encodes social and spatial information (16-18), as mice explored novel and familiar conspecifics. Here we demonstrate that the geometry of dCA2 representations in neural activity space enables social familiarity, social identity, and spatial information to be readily disentangled. Importantly, highly familiar littermates were encoded in higher-dimensional neural representations compared to novel individuals. As a result of this coding strategy, dCA2 neural activity was able to both provide an abstract, low-dimensional representation of social familiarity that could readily distinguish a novel from familiar individual and encode detailed episodic memories associated with familiar individuals.


title: Variability in sampling of cortex-wide neural dynamics explains individual differences in functional connectivity and behavioral phenotype

abstract: Individual differences in behavior are associated with changes in the correlation of neural activity between brain areas. Such differences in  functional connectivity are thought to reflect individual differences in brain structure that alter the flow of neural activity between regions. Here, in contrast, we show that individual differences in functional connectivity and behavior can be explained by differences in how frequently an individual expresses distinct cortex-wide spatiotemporal patterns of neural activity. This suggests variability in sampling of cortex-wide neural dynamics may underlie individuals unique behavioral phenotypes.


title: Hippocampal fear engrams modulate ethanol-induced maladaptive contextual generalization in mice.

abstract: The compounding symptomatology of comorbid alcohol use disorder (AUD) and post-traumatic stress disorder (PTSD) gives rise to an interaction of maladaptive neurobiological processes, the etiology of which remains elusive. Here, we devised an optogenetic strategy aimed at rescuing maladaptive responses to fearful stimuli in male c57BL/6 mice following chronic ethanol administration and forced abstinence. In the first experiment, we confirmed that fear acquisition and maladaptive contextual generalization was potentiated in ethanol-exposed mice during fear conditioning and exposure to a novel environment, respectively. In the second experiment, using an activity-dependent tet-tag system, we labeled and artificially inhibited the neural ensemble selectively activated by contextual fear conditioning in the dorsal hippocampus to attenuate behavioral dysfunctions resulting from ethanol exposure. We found that acute optogenetic inhibition during exposure to a novel environment suppressed maladaptive generalization in ethanol-exposed mice. These results provide further evidence for a crucial link between ethanol exposure and impaired fear memory processing by providing cellular and behavioral insights into the neural circuitry underlying AUD and PTSD comorbidity.


title: Multilevel Development of Cognitive Abilities in an Artificial Neural Network

abstract: Several neuronal mechanisms have been proposed to account for the formation of cognitive abilities through postnatal interactions with the physical and socio-cultural environment. Here, we introduce a three-level computational model of information processing and acquisition of cognitive abilities. We propose minimal architectural requirements to build these levels and how the parameters affect their performance and relationships. The first sensorimotor level handles local nonconscious processing, here during a visual classification task. The second level or cognitive level globally integrates the information from multiple local processors via long-ranged connections and synthesizes it in a global, but still nonconscious manner. The third and cognitively highest level handles the information globally and consciously. It is based on the Global Neuronal Workspace (GNW) theory and is referred to as conscious level. We use trace and delay conditioning tasks to, respectively, challenge the second and third levels. Results first highlight the necessity of epigenesis through selection and stabilization of synapses at both local and global scales to allow the network to solve the first two tasks. At the global scale, dopamine appears necessary to properly provide credit assignment despite the temporal delay between perception and reward. At the third level, the presence of interneurons becomes necessary to maintain a self-sustained representation within the GNW in the absence of sensory input. Finally, while balanced spontaneous intrinsic activity facilitates epigenesis at both local and global scales, the balanced excitatory-inhibitory ratio increases performance. Finally, we discuss the plausibility of the model in both neurodevelopmental and artificial intelligence terms.


title: A sparse set of spikes corresponding to reliable correlations is highly informative of visual stimulus on single trials

abstract: Spike trains in cortical neuronal populations vary in number and timing trial-to-trial, rendering a viable single trial coding scheme for sensory information elusive. Correlations between pairs of neocortical neurons can be segmented into either sensory or noise according to their stimulus specificity. Here we show that pairs of spikes, corresponding to reliable sensory correlations in imaged populations in layer 2/3 of mouse visual cortex are particularly informative of visual stimuli. This set of spikes is sparse and exhibits comparable levels of trial-to-trial variance relative to the full spike train. Despite this, correspondence of pairs of spikes to a specific set of sensory correlations identifies spikes that carry more information per spike about the visual stimulus than the full set or any other matched set of spikes. Moreover, this sparse subset is more accurately decoded, regardless of the decoding algorithm employed. Our findings suggest that consistent pairwise correlations between neurons, rather than first-order statistical features of spike trains, may be an organizational principle of a single trial sensory coding scheme.


title: Hippocampal delta oscillations entrain neuronal activity, modulate gamma amplitude and convey information about running speed on a treadmill

abstract:
Locomotion has long been associated with rhythmic oscillations in the rat hippocampus. Running speed and acceleration affect the spectral density at the theta (6-10 Hz) and gamma (30-150 Hz) bands and the rhythmic entrainment of neuronal activity. However, less is known about other oscillatory rhythms. Recent studies have shown that oscillatory activity in the delta (1-4 Hz) band also relates to locomotion in stationary conditions, such as running on a treadmill or in a running wheel. To further investigate the effects of stationary running on hippocampal oscillations, we recorded CA1 local field potentials and neuronal activity while rats ran at different speed protocols on a treadmill. We found a remarkable oscillatory activity at 2 Hz that was strongly modulated by running speed. Delta power and peak frequency were highest at the fastest running speed, both in constant and progressively increasing speed protocols. Delta and theta oscillations co-occurred and showed independent relationships in their instantaneous power and frequency. Moreover, the delta phase modulated the amplitude of low-gamma (20-50 Hz) oscillations and the spiking activity of putative pyramidal neurons in a speed-dependent manner. Finally, spectral components in the delta frequency range, but not theta, predicted running speed using a naive Bayes classifier. In summary, our study shows that locomotion-related delta oscillations convey information about stationary running speed and coordinate hippocampal rhythmic activity in a speed-dependent manner.

Statement of significanceTheta and gamma oscillations are hallmarks of rhythmic activity in the rat hippocampus during locomotion and exploratory behaviors, but less is known about other oscillatory rhythms. This study shows the emergence of delta ([~]2 Hz) oscillations in the dorsal CA1 of rats running on a treadmill. Locomotion-related delta oscillations are independent of the concomitant theta activity and convey information about running speed. Delta waves modulate low-gamma oscillations and the spiking activity of pyramidal neurons in a speed-dependent way. These results suggest that oscillatory activity in the delta band aids rhythmic coordination during stationary locomotor behaviors.


title: Broad-Spectrum Antimicrobial Potential of Crassula ovata

abstract: This study investigates the antimicrobial properties of Crassula ovata (C. ovata) against both gram-positive and gram-negative bacteria. About 1-3g samples of C. Ovata leaf samples were extracted with 95 % ethanol and the extract infused into paper discs by soaking and drying. The dried discs were screened against various strains of bacteria and the antimicrobial effects of the infused agents determined by measuring zones of inhibition due to the agents infused into the discs. By the zones of inhibition, C. ovata showed antimicrobial activity against the following gram-negative bacteria: E. coli (14 mm mean zone of clearing), P. vulgaris (13 mm mean zone of clearing), E. cloacae (16 mm mean zone of clearing), and K. pneumoniae (13 mm mean zone of clearing). C. ovata showed antimicrobial activity against the following gram-positive bacteria: S. aureus (22 mm mean zone of clearing) and S. agalactiae (8 mm mean zone of clearing). C. ovata did not show antimicrobial activity against S. pyogenes. By its antimicrobial activity against gram-positive and gram-negative bacteria, C. ovata displayed broad spectrum antimicrobial activity against E. coli, S. aureus, S. agalactiae, P. vulgaris, E. cloacae, and K. pneumoniae. C. ovata may have the potential to serve as a broad-spectrum antimicrobial in the future. Further testing should be done to investigate the toxicities and side effects of C. ovata. Further testing must also be done with C. ovata against drug-resistant strains of bacteria.


title: A system-wide quantitative map of RNA and protein subcellular localisation dynamics

abstract: Existing methods to analyse RNA localisation are constrained to specific RNAs or subcellular niches, precluding the cell-wide mapping of RNA. We present Localisation of RNA (LoRNA), which maps, at once, RNAs to membranous (nucleus, ER and mitochondria) and membraneless compartments (cytosol, nucleolus and phase-separated granules). Simultaneous interrogation of all RNA locations allows the system-wide quantification of RNA proportional distribution and the comprehensive analysis of RNA subcellular dynamics. Moreover, we have re-engineered the LOPIT (Localisation Of Proteins by Isotope Tagging) method, enabling integration with LoRNA, to jointly map RNA and protein subcellular localisation. Applying this framework, we obtain a global re-localisation map for 31839 transcripts and 5314 proteins during the unfolded protein response, uncovering that ER-localised transcripts are more efficiently recruited to stress granules than cytosolic RNAs, and revealing eIF3d is key to sustain cytoskeletal function. Overall, we provide the most exhaustive map to date of RNA and protein subcellular dynamics.

category: cell biology


title: USH2A gene mutations in rabbits lead to progressive retinal degeneration and hearing loss

abstract: Mutations in USH2A gene are responsible for the greatest proportion of hearing and vision loss among individuals with Usher Syndrome (USH) and for autosomal recessive non-syndromic retinitis pigmentosa. Mutations on USH2A exon 13 account for more than 35% of the disease causing USH2A variants including the most prevalence point mutation, c.2299delG, a frameshift mutation. The lack of a clinically relevant animal model has been a bottleneck for the development of therapeutics for USH2A related vision loss. Using CRSPR/Cas9 technology, this study establishes a rabbit line carrying an USH2A frameshift mutation on exon12 (equivalent to human USH2A Exon 13) as a novel mammalian animal model of USH2A. The bi-allelic mutant rabbits exhibit hyper reflective signals in FAF indicating RPE damage and OCT changes indicating photoreceptor degeneration as early as 4 months of age. ERG signals of both rod and cone function were reduced in the USH2A mutant rabbits starting from 7 months old and further decreased at 15-22 months old, indicating progressive retinal photoreceptor degeneration, which is further confirmed by retinal histopathology examination. ABR examination showed moderate to server hearing loss in the USH2A mutant rabbits. These results indicated that disruption of USH2A gene in rabbits is sufficient to induce hearing loss and progressive photoreceptor degeneration. To our knowledge, this is the first mammalian animal model of USH2 which closely recapitulates the phenotype of retinitis pigmentosa in human patients. This study supports the use of rabbits as a clinically relevant animal model to understand the pathogenesis and to develop novel therapeutics for Usher Syndrome.

category: developmental biology


title: Cullin-5 regulates nuclear positioning and reveals insights on the sensing of the nuclear-to-cytoplasmic ratio in Drosophila embryogenesis

abstract: In most metazoans, early embryonic development is characterized by rapid division cycles which pause before gastrulation at the mid-blastula transition (MBT).1 These early cleavage divisions are accompanied by cytoskeletal rearrangements which ensure proper nuclear positioning. Yet, the molecular mechanisms controlling nuclear positioning are not fully elucidated. In Drosophila, early embryogenesis unfolds in a multinucleated syncytium, and nuclei rapidly move across the anterior-posterior (AP) axis at cell cycles 4-6 in a process driven by actomyosin contractility and cytoplasmic flows.2,3 Previously, shackleton (shkl) mutants were identified in which this axial spreading is impaired.4 Here, we show that shkl mutants carry mutations in the cullin-5 (cul-5) gene. Live imaging experiments show that Cul-5 is downstream of the cell cycle but required for cortical actomyosin contractility. The nuclear spreading phenotype of cul-5 mutants can be rescued by reducing Src activity genetically, suggesting that a major target of Cul-5 is Src kinase. cul-5 mutants display gradients of nuclear density across the AP axis at the MBT which we exploit to study cell cycle control as a function of the N/C ratio. We found that the N/C ratio is sensed collectively in neighborhoods of about 100m and such collective sensing is required for a precise MBT in which all the nuclei in the embryo pause their division cycle. Moreover, we found that the response to the N/C ratio is slightly graded along the AP axis. These two features can be linked to the spatiotemporal regulation of Cdk1 activity. Collectively, our results reveal a new pathway controlling nuclear spreading and provide a quantitative dissection of how nuclear cycles respond to the N/C ratio.


title: "Holey" niche! Finding holes in niche hypervolumesusing persistence homology

abstract:
O_LIHutchinsons niche hypervolume concept has enabled significant progress in our understanding of species ecological needs and distributions across environmental gradients. Nevertheless, the properties of Hutchinsons n-dimensional hypervolumes can be challenging to calculate and several methods have been proposed to extract meaningful measurements of hypervolumes properties (e.g., volume).
C_LIO_LIOne key property of hypervolumes are holes, which provide important information about the ecological occupancy of species. However, to date, current methods rely on volume estimates and set operations to identify holes in hypervolumes. Yet, this approach can be problematic because in high-dimensions, the volume of region enclosing a hole tends to zero.
C_LIO_LIHere, we propose the use of the topological concept of persistence homology (PH) to identify holes in hypervolumes and in ecological datasets more generally. PH allows for the estimates of topological properties in n-dimensional niche hyper-volumes and is independent of the volume estimates of the hypervolume. We demonstrate the application of PH to canonical datasets and to the identification of holes in the hypervolumes of five vertebrate species with diverse niches, highlighting the potential benefits of this approach to gain further insights into animal ecology.
C_LIO_LIOverall, our approach enables the study of an yet unexplored property of Hutchinsons hypervolumes (i.e., holes), and thus, have important implications to our understanding of animal ecology.
C_LI