bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence and clinical manifestations of dengue in older patients in Bangkok Hospital for Tropical Diseases, Thailand
Authors: Chhong Lay Ngeab , Poovorawan Kittiyod , Hanboonkunupakarn Borimas , Phumratanaprapin Weerapong , Soonthornworasiri Ngamphol , Kittitrakul Chatporn , Nontprasert Apichart , Pukrittayakamee Sasithon
Published: May 2020

Background

The global incidence of dengue has increased with the ageing population. We examined the prevalence, clinical manifestations and risk factors associated with dengue severity among older patients.

Methods

A retrospective cohort study was conducted at a hospital in Thailand from 2013 to 2018. Data were collected from patient records. Older patients were those aged ≥60 y, whereas adult patients were aged at least 18 y but younger than 60 y.

Results

In total, 1822 patients were included in the study. The prevalence of older dengue was 7.96%. Older dengue patients were at a higher risk of developing dengue haemorrhagic fever (DHF) than adult dengue patients (40.69% vs 30.71%). Haematuria was significantly more frequent in older patients (24.82% vs 3.58%), whereas other clinical manifestations had similar frequencies between the groups. Multivariate logistic regression indicated that hypertension (adjusted OR [aOR]=3.549, 95% CI 1.498 to 8.407) and abdominal pain (aOR=10.904, 95% CI 1.037 to 114.710) were significantly associated with DHF among older patients.

Conclusions

Dengue is common in older adults, who also have a higher incidence of developing DHF. Older patients with dengue and comorbid hypertension and abdominal pain should be monitored for their increasing risk of DHF.
Dix-seq: An integrated pipeline for fast amplicon data analysis
Authors: wei Yongjun , Ren Tianqi , Zhang Lei
Published: May 2020

The amplicon derived from 16S rRNA genes, 18S rRNA genes, internal transcribed spacer sequences or other functional genes can be used to infer and evaluate microbial diversity or functional gene diversity. With the development of sequencing technologies, large amounts of amplicon data were generated. Several different software or pipelines had been developed for amplicon data analyses. However, most current software/pipelines require multistep and advanced programming skills. Moreover, they are often complex and time-consuming. Here, we introduced an integrated pipeline named Dix-seq for high-throughput amplicon sequence data processing (https://github.com/jameslz/dix-seq). Dix-seq integrates several different amplicon analysis algorithms and software for diversity analyses of multiple samples. Dix-seq analyzes amplicon sequences efficiently, and exports abundant visual results automatically with only one command in Linux environment. In summary, Dix-seq enables the common/advanced users to generate amplicon analysis results easily and offers a versatile and convenient tool for researchers.
Recombination in Sarbecovirus lineage and mutations/insertions in spike protein linked to the emergence and adaptation of SARS-CoV-2
Authors: Sharma Amresh Kumar , Kumari Priyanka , Som Anup
Published: May 2020

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan city, China in December 2019 and thereafter its spillover across the world has created a global pandemic and public health crisis. Researchers across the world are involved in finding the origin and evolution of SARS-CoV-2, its transmission route, molecular mechanism of interaction between SARS-CoV-2 and host cells, and the cause of pathogenicity etc. In this paper, we shed light on the origin, evolution and adaptation of SARS-CoV-2 into human systems. Our phylogenetic/evolutionary analysis supported that bat-CoV-RaTG13 is the closest relative of human SARS-CoV-2, outbreak of SARS-CoV-2 took place via inter-intra species mode of transmission, and host-specific adaptation occurred in SARS-CoV-2. Furthermore, genome recombination analysis found that Sarbecoviruses, the subgenus containing SARS-CoV and SARS-CoV-2, undergo frequent recombination. Multiple sequence alignment (MSA) of spike proteins revealed the insertion of four amino acid residues “PRRA” (Proline-Arginine-Arginine-Alanine) into the SARS-CoV-2 human strains. Structural modeling of spike protein of bat-CoV-RaTG13 also shows a high number of mutations at one of the receptor binding domains (RBD). Overall, this study finds that the probable origin of SARS-CoV-2 is the results of intra-species recombination events between bat coronaviruses belonging to Sarbecovirus subgenus and the insertion of amino acid residues “PRRA” and mutations in the RBD in spike protein are probably responsible for the adaptation of SARS-CoV-2 into human systems. Thus, our findings add strength to the existing knowledge on the origin and adaptation of SARS-CoV-2, and can be useful for understanding the molecular mechanisms of interaction between SARS-CoV-2 and host cells which is crucial for vaccine design and predicting future pandemics.
A therapeutic combination of two small molecule toxin inhibitors provides pancontinental preclinical efficacy against viper snakebite
Authors: Albulescu Laura-Oana , Xie Chunfang , Ainsworth Stuart , Alsolaiss Jaffer , Crittenden Edouard , Dawson Charlotte A. , Softley Rowan , Bartlett Keirah E. , Harrison Robert A. , Kool Jeroen , Casewell Nicholas R.
Published: May 2020

Snakebite is a medical emergency causing high mortality and morbidity in rural tropical communities that typically experience delayed access to unaffordable therapeutics. Viperid snakes are responsible for the majority of envenomings, but extensive interspecific variation in venom composition dictates that different antivenom treatments are used in different parts of the world, resulting in clinical and fiscal snakebite management challenges. Here, we show that a number of repurposed Phase 2-approved small molecules are capable of broadly neutralizing distinct viper venom bioactivitiesin vitroby inhibiting different enzymatic toxin families. Furthermore, using multiplein vivomodels of envenoming, we demonstrate that a single dose of a rationally-selected dual inhibitor combination consisting of marimastat and varespladib prevents lethality caused by venom from the most medically-important vipers of Africa, South Asia and Central America. Our findings strongly support the translation of combinations of safe and affordable enzyme inhibitors as novel broad-spectrum therapeutics for snakebite.
Metabolite profiling of experimental cutaneous leishmaniasis lesions demonstrates significant perturbations in tissue phospholipids
Authors: Parab Adwaita R. , Thomas Diane , Lostracco-Johnson Sharon , de Siqueira-Neto Jair Lage , McKerrow James , Dorrestein Pieter C. , McCall Laura-Isobel
Published: May 2020

Each year 700,000 to 1.2 million new cases of cutaneous leishmaniasis (CL) are reported and yet CL remains one of thirteen diseases classified as neglected tropical diseases (NTDs).Leishmania majoris one of several different species of that same genus that can cause CL. Current CL treatments are limited by adverse effects and rising resistance. Studying disease metabolism at the site of infection can lead to new drug targets. In this study, samples were collected from mice infected in the ear and footpad withL. majorand analyzed by untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS). Significant differences in overall metabolite profiles were noted in the ear at the site of the lesion. Interestingly, lesion-adjacent, macroscopically healthy sites also showed alterations in specific metabolites, including select phosphocholines (PCs). Host-derived PCs in the lowerm/zrange (m/z200-799) showed an increase with infection in the ear at the lesion site, while those in the higherm/zrange (m/z800-899) were decreased with infection at the lesion site. Overall, our results expanded our understanding of the mechanisms of CL pathogenesis through the host metabolism and may lead to new curative measures against infection withLeishmania.

Author summary

Cutaneous leishmaniasis (CL) is one of thirteen neglected tropical diseases in the world today. It is an infectious disease with a wide distribution spanning five continents, with increasing distribution expected due to climate change. CL manifests as skin lesions and ulcers that are disabling and stigmatized. With the current treatment options being limited, studying host-pathogen metabolism can uncover mechanisms of disease pathogenesis that may lead to new curative measures against infection. In this paper we used untargeted metabolomics to address molecular-level changes occurringin vivoin experimental skin lesions ofLeishmania major. Distinct global metabolic profiles were observed. Total phosphocholines (PCs) and those in the lowerm/zranges were significantly higher at the site of the skin lesion in the ear. In addition, specific PCs as well as PCs of variedm/zranges were also affected at healthy-appearing lesion-adjacent sites, indicating that infection-induced metabolic perturbations are not restricted to the lesion site. Ultimately, these results provide essential clues to the metabolic pathways affected by CL.
Variance lower bound on fluorescence microscopy image denoising
Authors: Li Yilun , Liu Sheng , Huang Fang
Published: May 2020

The signal to noise ratio of high-speed fluorescence microscopy is heavily influenced by photon counting noise and sensor noise due to the expected low photon budget. Denoising algorithms are developed to decrease these noise fluctuations in the microscopy data. One question arises: whether there exists a theoretical precision limit for the performance of a denoising algorithm. In this paper, combining Cramér-Rao Lower Bound with constraints and the low-pass-filter property of microscope systems, we develop a method providing a theoretical variance lower bound of microscopy image denoising. We show that this lower bound is influenced by photon count, readout noise, detection wavelength, effective pixel size and the numerical aperture of the microscope system. We demonstrate our development by comparing multiple state-of-the-art denoising algorithms to this bound. This theoretical bound provides a reference benchmark for microscopy denoising algorithms, and establishes a framework to incorporate additional prior knowledge into theoretical denoising performance limit calculation.
Passive motor learning: Oculomotor adaptation in the absence of feedback on behavioral errors
Authors: Cain Matan , Joshua Mati
Published: May 2020

Motor adaptation is commonly thought to be a trial-and-error process in which accuracy of movement improves with repetition of behavior. We challenged this view by testing whether erroneous movements are necessary for motor adaptation. In the eye movement system, the association between motor command and errors can be disentangled, since errors in the predicted stimulus trajectory can be perceived even without movements. We modified a smooth pursuit eye movement adaptation paradigm in which monkeys learn to make an eye movement that predicts an upcoming change in target direction. We trained monkeys to fixate on a target while covertly, an additional target initially moved in one direction and then changed direction after 250 ms. Monkeys showed a learned response to infrequent probe trials in which they were instructed to follow the moving target. Further experiments confirmed that probing learning or residual eye movement during fixation did not drive learning. These results show that movement is not necessary for motor adaptation and provide an animal model for studying how passive learning is implemented. The standard model assumes that the interaction between movement and error signals in the cerebellum underlies adaptive learning. Our results indicate that either sensory inputs are sufficient for driving learning in the cerebellum or that learning is implemented partly outside the cerebellum.
Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR
Authors: Akbarzadeh Arash , Houde Aimee Lee S. , Sutherland Ben J.G. , Günther Oliver P. , Miller Kristina M.
Published: May 2020

Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L−1] and hypoxia (DO = 4□5 mg L−1) in 10 and 18°C temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; p < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.
Integration of intra- and inter-sexual selection signaling
Authors: Garrison Courtney R. , Royauté Raphaël , Dochtermann Ned A.
Published: May 2020

Sexual selection can drive the evolution of dramatic morphological and behavioral signals. This selection acts on both specific components of signals and overall signals that combine multiple sources of information. By studying the structure and variability of signals and their components we can improve our understanding of how sexual selection operates. Signal integration can be understood through the lens of classical signaling hypotheses or more recently defined systems approaches. Using crickets (Acheta domesticus), we evaluated competing hypotheses about signal integration and how observed patterns of signal integration fit into both systems approaches and classic signaling hypotheses. We measured three call types of 127 male crickets multiple times for a total of 930 observations. We found evidence for an underlying integrated signaling syndrome from which both intra- and intersexual signals stemmed. This syndrome was also affected by mass, suggesting honest signaling in the species. The presence of an integrated syndrome demonstrates that intra- and intersexual signals are incorporated in a redundant signal strategy inAcheta domesticus. This support for honest and redundant signaling is also consistent with a systems framework description of signals as degenerate and functionally modular—demonstrating one way in which classic hypotheses can be integrated with modern systems approaches.
Multistability in cellular differentiation enabled by a network of three mutually repressing master regulators
Authors: Duddu Atchuta Srinivas , Sahoo Sarthak , Hati Souvadra , Jhunjhunwala Siddharth , Jolly Mohit Kumar
Published: May 2020

Identifying the design principles of complex regulatory networks driving cellular decision-making remains essential to decode embryonic development as well as enhance cellular reprogramming. A well-studied network motif involved in cellular decision-making is a toggle switch – a set of two opposing transcription factors A and B, each of which is a master regulator of a specific cell-fate and can inhibit the activity of the other. A toggle switch can lead to two possible states – (high A, low B) and (low A, high B), and drives the ‘either-or’ choice between these two cell-fates for a common progenitor cell. However, the principles of coupled toggle switches remains unclear. Here, we investigate the dynamics of three master regulators A, B and C inhibiting each other, thus forming three coupled toggle switches to form a toggle triad. Our simulations show that this toggle triad can lead to co-existence of cells into three differentiated ‘single positive’ phenotypes – (high A, low B, low C), (low A, high B, low C), and (low A, low B, high C). Moreover, the hybrid or ‘double positive’ phenotypes – (high A, high B, low C), (low A, high B, high C) and (high A, low B, high C) – can co-exist together with ‘single positive’ phenotypes. Including self-activation loops on A, B and C can increase the frequency of ‘double positive’ states. Finally, we apply our results to understand the cellular decision-making in terms of differentiation of naïve CD4+ T cells into Th1, Th2 and Th17 states, where hybrid Th1/Th2 and hybrid Th1/Th17 cells have been reported in addition to the Th1, Th2 and Th17 ones. Our results offer novel insights into the design principles of a multistable network topology and provides a framework for synthetic biology to design tristable systems.
Denitrification kinetics indicates nitrous oxide uptake is unaffected by electron competition in Accumulibacter
Authors: Samarpita Roy , Nirakar Pradhan , Yong NG How , Stefan Wuertz
Published: May 2020

Denitrifying phosphorus removal is a cost and energy efficient treatment technology that relies on polyphosphate accumulating organisms (DPAOs) utilizing nitrate or nitrite as terminal electron acceptor. Denitrification is a multistep process and many organisms do not possess the complete pathway, leading to the accumulation of intermediates such as nitrous oxide (N2O), a potent greenhouse gas and ozone depleting substance.CandidatusAccumulibacter organisms are prevalent in denitrifying phosphorus removal processes and, according to genomic analyses, appear to vary in their denitrification abilities based on their lineage. Yet, denitrification kinetics and nitrous oxide accumulation by Accumulibacter after long-term exposure to either nitrate or nitrite as electron acceptor have never been compared. We investigated the preferential use of the nitrogen oxides involved in denitrification and nitrous oxide accumulation in two enrichments of Accumulibacter and a competitor – the glycogen accumulating organismCandidatusCompetibacter. A metabolic model was modified to predict phosphorus removal and denitrification rates when nitrate, nitrite or N2O were added as electron acceptors in different combinations. Unlike previous studies, no N2O accumulation was observed for Accumulibacter in the presence of multiple electron acceptors. Electron competition did not affect denitrification kinetics or N2O accumulation in Accumulibacter or Competibacter. Despite the presence of sufficient internal storage polymers (polyhydroxyalkanoates, or PHA) as energy source for each denitrification step, the extent of denitrification observed was dependent on the dominant organism in the enrichment. Accumulibacter showed complete denitrification and N2O utilization, whereas for Competibacter denitrification was limited to reduction of nitrate to nitrite. These findings indicate that DPAOs can contribute to lowering N2O emissions in the presence of multiple electron acceptors under partial nitritation conditions.
A single dose SARS-CoV-2 simulating particle vaccine induces potent neutralizing activities
Authors: Yin Di , Ling Sikai , Tian Xiaolong , Li Yang , Xu Zhijue , Jiang Hewei , Zhang Xue , Wang Xiaoyuan , Shi Yi , Zhang Yan , Da Lintai , Tao Sheng-ce , Wang Quanjun , Xu Jianjiang , Ying Tianlei , Hong Jiaxu , Cai Yujia
Published: May 2020

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for which a vaccine is urgently needed to control its spreading. To facilitate the representation of a native-like immunogen without being infectious, here, we reported a SARS-CoV-2 vaccine candidate (designated ShaCoVacc) by incorporating spike-encoding mRNA inside and decorating spike protein on the surface of the virus simulating particles (VSPs) derived from lentiviral particles. We characterized the mRNA copy number, glycosylation status, transduction efficiency, and innate immune property of the new vaccine platform. Importantly, we showed the ShaCoVacc induced strong spike-specific humoral immune responses and potent neutralizing activities by a single injection. Additionally, we disclosed the epitopes of spike-specific antibodies using peptide microarray and revealed epitopes susceptible to specific neutralizing antibodies. These results support further development of ShaCoVacc as a candidate vaccine for COVID-19 and VSP may serve as a new vaccine platform for emerging infectious diseases.
Two mutations P/L and Y/C in SARS-CoV-2 helicase domain exist together and influence helicase RNA binding
Authors: Begum Feroza , Banerjee Arup Kumar , Tripathi Prem Prakash , Ray Upasana
Published: May 2020

RNA helicases play pivotal role in RNA replication by catalysing the unwinding of complex RNA duplex structures into single strands in ATP/NTP dependent manner. SARS coronavirus 2 (SARS-CoV-2) is a single stranded positive sense RNA virus belonging to the familyCoronaviridae. The viral RNA encodes non structural protein Nsp13 or the viral helicase protein that helps the viral RNA dependent RNA polymerase (RdRp) to execute RNA replication by unwinding the RNA duplexes. In this study we identified a novel mutation at position 541of the helicase where the tyrosine (Y) got substituted with cytosine (C). We found that Y541C is a destabilizing mutation increasing the molecular flexibility and leading to decreased affinity of helicase binding with RNA. Earlier we had reported a mutation P504L in the helicase protein for which had not performed RNA binding study. Here we report that P504L mutation leads to increased affinity of helicase RNA interaction. So, both these mutations have opposite effects on RNA binding. Moreover, we found a significant fraction of isolate population where both P504L and Y541C mutations were co-existing.
Experimental glaucoma retinal proteomics identifies mutually exclusive and overlapping molecular characteristics with human glaucoma
Authors: Mirzaei Mehdi , Gupta Vivek , Chitranshi Nitin , Deng Liting , Pushpitha Kanishka , Abbasi Mojdeh , Chick Joel , Rajput Rashi , Wu Yunqi , McKay Matthew. J. , Salekdeh Ghasem H , Gupta Veer , Haynes Paul A. , Graham Stuart L.
Published: May 2020

Current evidence suggests that exposure to chronically induced intraocular pressure (IOP) leads to neurodegenerative changes in the inner retina. This study aimed to determine retinal proteomic alterations in a rat model of glaucoma and compared findings with human retinal proteomics changes in glaucoma reported previously. We developed an experimental glaucoma rat model by subjecting the rats to increased IOP (9.3±0.1 vs 20.8±1.6 mm Hg) by weekly microbead injections into the eye (8 weeks). The retinal tissues were harvested from control and glaucomatous eyes and protein expression changes analysed using multiplexed quantitative proteomics approach. Immunofluorescence was performed for selected protein markers for data validation. Our study identified 4304 proteins in the rat retinas. Out of these, 139 proteins were downregulated (≤0.83) while expression of 109 proteins was upregulated (≥1.2-fold change) under glaucoma conditions (p≤0.05). Computational analysis revealed reduced expression of proteins associated with glutathione metabolism, mitochondrial dysfunction/oxidative phosphorylation, cytoskeleton and actin filament organisation, along with increased expression coagulation cascade, apoptosis, oxidative stress and RNA processing markers. Further functional network analysis highlighted the differential modulation of nuclear receptor signalling, cellular survival, protein synthesis, transport and cellular assembly pathways. Alterations in crystallin family, glutathione metabolism and mitochondrial dysfunction associated proteins shared similarities between the animal model of glaucoma and the human disease condition. In contrast, the activation of the classical complement pathway and upregulation of cholesterol transport proteins, were exclusive to the human glaucoma. These findings provide insights into the neurodegenerative mechanisms that are specifically affected in the retina in response to chronically elevated IOP.
Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans
Authors: Ng Kevin W. , Faulkner Nikhil , Cornish Georgina H. , Rosa Annachiara , Harvey Ruth , Hussain Saira , Ulferts Rachel , Earl Christopher , Wrobel Antoni , Benton Donald , Roustan Chloe , Bolland William , Thompson Rachael , Agua-Doce Ana , Hobson Philip , Heaney Judith , Rickman Hannah , Paraskevopoulou Stavroula , Houlihan Catherine F. , Thomson Kirsty , Sanchez Emilie , Brealey David , Shin Gee Yen , Spyer Moira J. , Joshi Dhira , O’Reilly Nicola , Walker Philip A. , Kjaer Svend , Riddell Andrew , Moore Catherine , Jebson Bethany R. , Wilkinson Meredyth G.Ll. , Marshall Lucy R. , Rosser Elizabeth C. , Radziszewska Anna , Peckham Hannah , Ciurtin Coziana , Wedderburn Lucy R. , Beale Rupert , Swanton Charles , Gandhi Sonia , Stockinger Brigitta , McCauley John , Gamblin Steve , McCoy Laura E. , Cherepanov Peter , Nastouli Eleni , Kassiotis George
Published: May 2020

Several related human coronaviruses (HCoVs) are endemic in the human population, causing mild respiratory infections1. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent of Coronavirus disease 2019 (COVID-19), is a recent zoonotic infection that has quickly reached pandemic proportions2,3. Zoonotic introduction of novel coronaviruses is thought to occur in the absence of pre-existing immunity in the target human population. Using diverse assays for detection of antibodies reactive with the SARS-CoV-2 spike (S) glycoprotein, we demonstrate the presence of pre-existing humoral immunity in uninfected and unexposed humans to the new coronavirus. SARS-CoV-2 S-reactive antibodies were readily detectable by a sensitive flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. These were predominantly of the IgG class and targeted the S2 subunit. In contrast, SARS-CoV-2 infection induced higher titres of SARS-CoV-2 S-reactive IgG antibodies, targeting both the S1 and S2 subunits, as well as concomitant IgM and IgA antibodies, lasting throughout the observation period of 6 weeks since symptoms onset. SARS-CoV-2-uninfected donor sera also variably reacted with SARS-CoV-2 S and nucleoprotein (N), but not with the S1 subunit or the receptor binding domain (RBD) of S on standard enzyme immunoassays. Notably, SARS-CoV-2-uninfected donor sera exhibited specific neutralising activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes, according to levels of SARS-CoV-2 S-binding IgG and with efficiencies comparable to those of COVID-19 patient sera. Distinguishing pre-existing and de novo antibody responses to SARS-CoV-2 will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.
Increased microclimatic variation in artificial nests does not create ecological traps for a secondary cavity breeder
Authors: Schwartz Timothée , Genouville Arnaud , Besnard Aurélien
Published: May 2020

Artificial devices are increasingly used in conservation measures to mitigate the disappearance of natural habitats. However, few studies have demonstrated their benefits for the target species, and they may pose a risk of creating ecological traps. This occurs when lower individual fitness is found in artificial habitats that are more attractive than their natural equivalents. In this study, we tested the ecological trap hypothesis on a dense population of European rollersCoracias garrulusbreeding in both natural cavities and nest-boxes. Our initial hypothesis was that the more stressful microclimatic conditions of nest-boxes would lead to reduced fitness of rollers, thus creating an ecological trap. The results showed that nest-boxes were preferred over natural cavities. Despite significantly more extreme microclimatic conditions in nest-boxes, we found similar breeding parameters between artificial and natural nest types. Our results also suggest that rollers selected the nest-boxes which best buffered the temperature, thus avoiding potential ecological traps. Overall our results lead to the conclusion that nest-boxes do not create ecological traps for rollers in this study site. However, other species may be more sensitive to microclimatic variations or less able to avoid the least favourable nest-boxes. These findings could help to inform the placement of nest-boxes in order to reduce extreme temperatures and variation in humidity rates. Future studies could compare nest types for other fitness parameters, such as juvenile body condition or survival. We also recommend the ecological trap hypothesis as a useful framework to evaluate the outcomes of artificial devices used for conservation.
A freshwater radiation of diplonemids
Authors: Mukherjee Indranil , Salcher Michaela M , Andrei Adrian-Ştefan , Kavagutti Vinicius Silva , Shabarova Tanja , Grujčić Vesna , Haber Markus , Layoun Paul , Hodoki Yoshikuni , Nakano Shin-ichi , Šimek Karel , Ghai Rohit
Published: May 2020

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Lake Biwa, Japan. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and CARD-FISH. We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to marine isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single cell genomes of marine diplonemids shows they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.
Mycobacteria inhibit neutrophil recruitment to avoid neutrophil-assisted killing by macrophages
Authors: Candel Sergio , Ramakrishnan Lalita
Published: May 2020

This article was withdrawn on 29 July 2020 after inaccuracies were identified in the experiments reported in the manuscript. The corresponding author, Professor Lalita Ramakishnan, reported concerns regarding data in the manuscript to the University of Cambridge. An investigation by the University of Cambridge concluded that data related to Alox5 -/-; mpx-/- double knockout zebrafish included in the manuscript had been fabricated. If you have any questions, please contact the corresponding author (Lalita Ramakrishnan,lr404@cam.ac.uk).
Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine
Authors: Durgan Joanne , Lystad Alf H. , Sloan Katherine , Carlsson Sven R. , Wilson Michael I. , Marcassa Elena , Ulferts Rachel , Webster Judith , Lopez-Clavijo Andrea F. , Wakelam Michael J. , Beale Rupert , Simonsen Anne , Oxley David , Florey Oliver
Published: May 2020

Autophagy is a fundamental catabolic process essential for development, homeostasis and proper immune function1. During autophagy, a cascade of ATG proteins target intracellular cargoes for lysosomal degradation and recycling2. This pathway utilises a unique post-translational modification, the conjugation of ATG8 proteins to phosphatidylethanolamine (PE) at autophagosomes, which modulates cargo selection and maturation. ATG8 lipidation also occurs during non-canonical autophagy, a parallel pathway involving Single Membrane ATG8 Conjugation (SMAC) to endolysosomal compartments, which plays a key role in phagocytosis and other processes3. It has been widely assumed that SMAC involves the same lipidation of ATG8 to PE, but this has yet to be formally tested. Here, we show that ATG8 undergoes alternative lipidation to phosphatidylserine (PS) during non-canonical autophagy/SMAC. Using mass spectrometry, we find that activation of SMAC, by pharmacological agents4,5, or during non-canonical autophagy processes such as LC3-associated phagocytosis6,7and Influenza A virus infection8, induces the covalent conjugation of ATG8 to PS, as well as PE. This alternative lipidation event is dependent on the ATG16L1 WD40 domain, and occurs at PS enriched endolysosomal membranes. Importantly, we find that the ATG8-PS and ATG8-PE adducts are differentially delipidated by isoforms of the ATG4 family, indicating significant molecular distinctions and mechanisms between these two species.

Together, these results provide an important new insight into autophagy signalling, revealing an alternative form of the hallmark ATG8-lipidation event, so widely used to define and assay autophagy. Furthermore, ATG8-PS lipidation provides a specific ‘molecular signature’ for non-canonical autophagy, uncovering a novel means of detecting and monitoring this emerging pathway.
Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments
Authors: Scott Stacey J. , Li Xiaodun , Jammula Sriganesh , Devonshire Ginny , Lindon Catherine , Fitzgerald Rebecca C. , D’Avino Pier Paolo
Published: May 2020

Polyploidy is present in many cancer types and is increasingly recognized as an important factor in promoting chromosomal instability, genome evolution, and heterogeneity in cancer cells. However, the mechanisms that trigger polyploidy in cancer cells are largely unknown. In this study, we investigated the origin of polyploidy in esophageal adenocarcinoma (EAC), a highly heterogenous cancer, using a combination of genomics and cell biology approaches in EAC cell lines, organoids, and tumors. We found the EAC cells and organoids present specific mitotic defects consistent with problems in the attachment of chromosomes to the microtubules of the mitotic spindle. Time-lapse analyses confirmed that EAC cells have problems in congressing and aligning their chromosomes, which can ultimately culminate in mitotic slippage and polyploidy. Furthermore, whole-genome sequencing, RNA-seq, and quantitative immunofluorescence analyses revealed alterations in the copy number, expression, and cellular distribution of several proteins known to be involved in the mechanics and regulation of chromosome dynamics during mitosis. Together, these results provide evidence that an imbalance in the amount of proteins implicated in the attachment of chromosomes to spindle microtubules is the molecular mechanism underlying mitotic slippage in EAC. Our findings that the likely origin of polyploidy in EAC is mitotic failure caused by problems in chromosomal attachments not only improves our understanding of cancer evolution and diversification, but may also aid in the classification and treatment of EAC and possibly other highly heterogeneous cancers.
Stress-induced translation inhibition through rapid displacement of scanning initiation factors
Authors: Bresson Stefan , Shchepachev Vadim , Spanos Christos , Turowski Tomasz , Rappsilber Juri , Tollervey David
Published: May 2020

Cellular responses to environmental stress are frequently mediated by RNA-binding proteins (RBPs). Here, we examined global RBP dynamics inSaccharomyces cerevisiaein response to glucose starvation and heat shock. Each stress induced rapid remodeling of the RNA-protein interactome, without corresponding changes in RBP abundance. Consistent with general translation shutdown, ribosomal proteins contacting the mRNA showed decreased RNA-association. Among translation components, RNA-association was most reduced for initiation factors involved in 40S scanning (eIF4A, eIF4B, and Ded1), indicating a common mechanism of translational repression. In unstressed cells, eIF4A, eIF4B, and Ded1 primarily targeted the 5′-ends of mRNAs. Following glucose withdrawal, 5’-binding was abolished within 30sec, explaining the rapid translation shutdown, but mRNAs remained stable. Heat shock induced progressive loss of 5’ RNA-binding by initiation factors over ∼16min. Translation shutoff provoked selective 5′-degradation of mRNAs encoding translation-related factors, mediated by Xrn1. These results reveal mechanisms underlying translational control of gene expression during stress.

Highlights

A quantitative proteomic approach reveals rapid stress-induced changes in RNA-binding Translation shutdown is driven by loss of mRNA binding by scanning initiation factors eIF4B and Ded1 have key but separate roles in driving the stress response Heat shock invokes rapid RNA degradation by Xrn1, selective for translation machinery
LiBis: An ultrasensitive alignment method for low-input bisulfite sequencing
Authors: Yin Yue , Li Jia , Li Jin , Lee Minjung , Zhao Sibo , Guo Linlang , Li Jianfang , Zhang Mutian , Huang Yun , Li Xiao-Nan , Sun Deqiang
Published: May 2020

The cell-free DNA (cfDNA) methylation profile in liquid biopsies has been utilized to diagnose early-stage disease and estimate therapy response. However, in typical clinical settings, only very small amounts of cfDNA can be purified. Whole-genome bisulfite sequencing (WGBS) is the gold standard to measure DNA methylation; however, WGBS using small amounts of fragmented DNA introduces a critical challenge for data analysis, namely a low mapping ratio. This, in turn, generates low sequencing depth and low coverage for CpG sites genome wide. The lack of informative CpGs has become a bottleneck for the clinical application of cfDNA-based WGBS assays. Hence, we developed LiBis (Low-input Bisulfite Sequencing), a novel method for low-input WGBS data alignment. By dynamically clipping initially unmapped reads and remapping clipped fragments, we judiciously rescued those reads and uniquely aligned them to the genome. By substantially increasing the mapping ratio by up to 88%, LiBis dramatically improved the number of informative CpGs and the precision in quantifying the methylation status of individual CpG sites. The high sensitivity and cost effectiveness afforded by LiBis for low-input samples will allow the discovery of genetic and epigenetic features suitable for downstream analysis and biomarker identification using liquid biopsy.
Expression changes in immune and epigenetic gene pathways associated with nutritional metabolites in maternal blood from pregnancies resulting in autism and atypical neurodevelopment
Authors: Zhu Yihui , Mordaunt Charles E. , Durbin-Johnson Blythe P , Caudill Marie A , Malysheva Olga V. , Miller Joshua W. , Green Ralph , James S. Jill , Melnyk Stepan B. , Fallin M. Daniele , Hertz-Picciotto Irva , Schmidt Rebecca J. , LaSalle Janine M.
Published: May 2020

Background

The prenatal period is a critical window to study factors involved in the development of autism spectrum disorder (ASD). Environmental factors, especiallyin uteronutrition, can interact with genetic risk for ASD, but how specific prenatal nutrients in mothers of children later diagnosed with ASD or non-typical development (Non-TD) associate with gestational gene expression is poorly understood. Maternal blood collected prospectively during pregnancy provides a new opportunity to gain insights into nutrition, particularly one-carbon metabolites, on gene pathways and neurodevelopment.

Methods

Genome-wide transcriptomes were measured using microarrays in 300 maternal blood samples from all three trimesters in the Markers of Autism Risk in Babies - Learning Early Signs (MARBLES) study. Sixteen different one-carbon metabolites, including folic acid, betaine, 5’-methyltretrahydrofolate (5-MeTHF), and dimethylglycine (DMG) were measured. Differential expression analysis and weighted gene correlation network analysis (WGCNA) were used to compare gene expression between children later diagnosed as typical development (TD), Non-TD and ASD, and to nutrient metabolites.

Results

Using differential gene expression analysis, six transcripts associated with four genes (TGR-AS1, SQSTM1, HLA-CandRFESD) showed genome-wide significance (FDRq< 0.05) with child outcomes. Genes nominally differentially expressed compared to TD specifically in ASD, but not Non-TD, significantly overlapped with seven high confidence ASD genes. 218 transcripts in common to ASD and Non-TD differential expression compared to TD were significantly enriched for functions in immune response to interferon-gamma, apoptosis, and metal ion transport. WGCNA identified co-expressed gene modules significantly correlated with 5-MeTHF, folic acid, DMG, and betaine. A module enriched in DNA methylation functions showed a protective association with folic acid/5-MeTHF concentrations and ASD risk. Independent of child outcome, maternal plasma betaine and DMG concentrations associated with a block of co-expressed genes enriched for adaptive immune, histone modification, and RNA processing functions.

Limitations

Blood contains a heterogeneous mixture of cell types, and many WGCNA modules correlated with cell type and/or nutrient concentrations, but not child outcome. Gestational age correlated with some co-expressed gene modules in addition to nutrients.

Conclusions

These results support the premise that the prenatal maternal blood transcriptome is a sensitive indicator of gestational nutrition and children’s later neurodevelopmental outcomes.
p53 induces ARTS to promote mitochondrial apoptosis
Authors: Hao Qian , Chen Jiaxiang , Liao Junming , Huang Yingdan , Larisch Sarit , Zeng Shelya X , Lu Hua , Zhou Xiang
Published: May 2020

ApoptosisRelated protein inTGF-βSignaling pathway (ARTS) was originally discovered in cells undergoing apoptosis in response to TGF-β, but ARTS also acts downstream of many other apoptotic stimuli. ARTS induces apoptosis by antagonizing the anti-apoptotic proteins XIAP and Bcl-2. Here, we identified the pro-apoptoticSept4/ARTSgene as a p53-responsive target gene. Ectopic p53 and a variety of p53-inducing agents increased both mRNA and protein levels of ARTS, whereas ablation of p53 reduced ARTS expression in response to multiple stress conditions. Also, γ-irradiation induced p53-dependent ARTS expression in mice. Consistently, p53 binds to the responsive DNA element on the ARTS promoter and transcriptionally activated the promoter-driven expression of a luciferase reporter gene. Interestingly, ARTS binds to and sequesters p53 at mitochondria, enhancing the interaction of the latter with Bcl-XL. Ectopic ARTS markedly augments DNA damage stress- or Nutlin-3-triggered apoptosis, while ablation of ARTS preferentially impairs p53-induced apoptosis. Altogether, these findings demonstrate that ARTS collaborates with p53 in mitochondria-engaged apoptosis.
Expression of ACE2 and TMPRSS2 proteins in the upper and lower aerodigestive tracts of rats
Authors: Sato Taku , Ueha Rumi , Goto Takao , Yamauchi Akihito , Kondo Kenji , Yamasoba Tatsuya
Published: May 2020

Objective

Patients with coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exhibit not only respiratory symptoms but also symptoms of chemo-sensitive disorders and kidney failure. Cellular entry of SARS-CoV-2 depends on the binding of its spike protein to a cellular receptor named angiotensin-converting enzyme 2 (ACE2), and the subsequent spike protein-priming by host cell proteases, including transmembrane protease serine 2 (TMPRSS2). Thus, high expression of ACE2 and TMPRSS2 are considered to enhance the invading capacity of SARS-CoV-2.

Methods

To elucidate the underlying histological mechanisms of the aerodigestive disorders caused by SARS-CoV-2, we investigated the expression of ACE2 and TMPRSS2 proteins in the aerodigestive tracts of the tongue, hard palate with partial nasal tissue, larynx with hypopharynx, trachea, esophagus, lung, and kidney of rats through immunohistochemistry.

Results

Strong co-expression of ACE2 and TMPRSS2 proteins was observed in the nasal respiratory epithelium, trachea, bronchioles, alveoli, kidney, and taste buds of the tongue. Remarkably, TMPRSS2 expression was much stronger in the peripheral alveoli than in the central alveoli. These results coincide with the reported clinical symptoms of COVID-19, such as the loss of taste, loss of olfaction, respiratory dysfunction, and acute nephropathy.

Conclusions

A wide range of organs have been speculated to be affected by SARS-CoV-2 depending on the expression levels of ACE2 and TMPRSS2. Differential distribution of TMPRSS2 in the lung indicated the COVID-19 symptoms to possibly be exacerbated by TMPRSS2 expression. This study might provide potential clues for further investigation of the pathogenesis of COVID-19.

Level of Evidence

NA
Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem
Authors: Solomon Ronnie , Wein Tanita , Levy Bar , Eshed Shahar , Dror Rotem , Reiss Veronica , Zehavi Tamar , Furman Ori , Mizrahi Itzhak , Jami Elie
Published: May 2020

Unicellular eukaryotes are an integral part of many microbial ecosystems communities where they are known to interact with their surrounding prokaryotic community – either as predators or as a mutualistic habitat. Within the rumen, one of the most complex host-associated microbial habitats, ciliate protozoa represent the main micro-eukaryotes, accounting for up to 50% of the microbial biomass. Nonetheless, the extent of the ecological effect of protozoa on the microbial community and on the rumen metabolic output remains largely understudied. To assess the role of protozoa on the rumen ecosystem, we established anex-vivosystem in which distinct protozoa sub-communities were introduced to native rumen prokaryotic community. We show that the different protozoa communities exert a strong and differential impact on the composition of the prokaryotic community, as well as its function including methane production. Furthermore, the presence of protozoa increases prokaryotic diversity with a differential effect on specific bacterial populations such as Gammaproteobacteria,Prevotellaand Spirochetes. Our results suggest that protozoa mitigate the effect of competitive exclusion between bacterial species, thereby contributing to the maintenance of prokaryotic diversity in the rumen. Our findings put forward the rumen protozoa populations as potentially important ecosystem engineers for future microbiome modulation strategies.