bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance of three rapid antigen tests against the SARS-CoV-2 Omicron variant
Authors: Kanjilal Sanjat , Chalise Sujata , Shah Adnan Shami , Cheng Chi-An , Senussi Yasmeen , Uddin Rockib , Thiriveedhi Vamsi , Cho Ha Eun , Carroll Seamus , Lemieux Jacob , Turbett Sarah , Walt David R
Published: February 2022

Rapid antigen detection tests (RADTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are now in widespread use in the United States. RADTs play an important role in maintaining an open society but require periodic reassessment to ensure test performance remains intact as the virus evolves. The nucleocapsid (N) protein is the target for the majority of RADTs and the SARS-CoV-2 Omicron variant has several N protein mutations that are previously uncharacterized. We sought to assess the impact of these mutations by testing 30 Omicron variant samples across a wide range of viral loads on three widely used RADTs: the iHealth COVID-19 Antigen Rapid Test, the ACON Laboratories FlowFlex COVID-19 Antigen Home Test, and the Abbott BinaxNOW COVID-19 Antigen Card, using 30 Delta variant samples as a comparator. We found no change in the analytic sensitivity of all three RADTs for detection of Omicron versus Delta, but noted differences in performance between assays. No RADT was able to detect samples with a cycle threshold (Ct) value of ≥27.5 for the envelope gene target on the Roche cobas RT-PCR assay. Epidemiologic studies are necessary to correlate these findings with their real-world performance.
GPX4-associated Sedaghatian Type Spondylometaphyseal Dysplasia: A Protein Interactome Perspective
Authors: Karunakaran Kalyani B. , Balakrishnan N. , Ganapathiraju Madhavi K.
Published: February 2022

Spondylometaphyseal dysplasia, Sedaghatian type (SMDS) is a rare and lethal skeletal dysplasia inherited in an autosomal recessive manner and caused by mutations in GPX4. In order to expand the functional landscape of this poorly studied disorder and accelerate the discovery of biologically insightful and clinically actionable targets, we constructed SMDS-centric and GPX4-centric protein-protein interaction (PPI) networks, augmented with novel protein interactors predicted by our HiPPIP algorithm. The SMDS-centric networks included those that showed the interconnections of GPX4 with other putative SMDS-associated genes and genes associated with other skeletal dysplasias. The GPX4-centric network showed the interconnections of GPX4 with genes whose perturbation has been known to affect GPX4 expression. We discovered that these networks either contained or were enriched with genes associated with specific SMDS pathophenotypes, tissue-naïve/fetus-specific functional modules and genes showing elevated expression in brain and/or testis similar to GPX4. We identified 7 proteins as novel interactors of GPX4 (APBA3, EGR4, FUT5, GAMT, GTF2F1, MATK and ZNF197) and showed their potential biological relevance to GPX4 or SMDS. Comparative transcriptome analysis of expression profiles associated with chondroplasia and immune-osseous dysplasia versus drug-induced profiles revealed 11 drugs that targeted the neighborhood network of GPX4 and other putative SMDS-associated genes. Additionally, resveratrol, which is currently being tested against a skeletal dysplasia in a clinical trial, was identified as another potential candidate based on the proximity of its targets to GPX4.
Specific attenuation of purinergic signaling during bortezomib-induced peripheral neuropathy
Authors: Holzer Anna-Katharina , Suciu Ilinca , Goj Thomas , Karreman Christiaan , Leist Marcel
Published: February 2022

Human peripheral neuropathies are poorly-understood, and the availability of experimental models limits further research. The PeriTox test uses immature dorsal root ganglia (DRG)-like neurons, derived from induced pluripotent stem cells (iPSC), to assess cell death and neurite damage. Here, we explored the suitability of matured peripheral neuron cultures for detection of sub-cytotoxic endpoints, such as altered responses of pain-related P2X receptors. A 2-step differentiation protocol, involving transient expression of ectopic neurogenin-1 (NGN1), allowed for the generation of homogeneous cultures of sensory neurons. After > 38 days-of-differentiation, they showed a robust response (Ca2+-signalling) to the P2X3 ligand α,β-methylene ATP. The clinical proteasome inhibitor bortezomib abolished the P2X3 signal at ≥ 5 nM, while 50-200 nM were required in the PeriTox test to identify neurite damage and cell death. A 24 h treatment with low nM concentrations of bortezomib led to moderate increases in resting cell intracellular [Ca2+], but signalling through transient receptor potential-V1 (TRPV1) receptors or depolarization-triggered Ca2+-influx remained unaffected. We interpret the specific attenuation of purinergic signalling as functional cell stress response. A reorganization of tubulin to dense structures around the cell somata confirmed a mild, non-cytotoxic stress triggered by low concentrations of bortezomib. The proteasome inhibitors carfilzomib, delanzomib, epoxomycin and MG-132 showed similar stress responses. Thus, the model presented here may be used for profiling of new proteasome inhibitors as to their side effect (neuropathy) potential, or for pharmacological studies on the attenuation of their neurotoxicity. P2X3 signalling proved useful as endpoint to assess potential neurotoxicants in peripheral neurons.
Fisheries genomics of snapper (Chrysophrys auratus) along the western Australian coast
Authors: Bertram Andrea , Fairclough David , Sandoval-Castillo Jonathan , Brauer Chris , Fowler Anthony , Wellenreuther Maren , Beheregaray Luciano B.
Published: February 2022

The efficacy of fisheries management strategies depends on stock assessment and management actions being carried out at appropriate spatial scales. This requires understanding of spatial and temporal population structure and connectivity, which is challenging in weakly structured and highly connected marine populations. We carried out a population genomics study of the heavily exploited snapper (Chrysophrys auratus) along ∼2,600 km of the Australian coastline, with a focus on Western Australia (WA). We used 10,903 filtered SNPs in 341 individuals from eight locations to characterise population structure and connectivity in snapper across WA and to assess if current spatial scales of stock assessment and management agree with evidence from population genomics. Our dataset also enabled us to investigate temporal stability in population structure as well as connectivity between WA and its nearest, eastern jurisdictional neighbor. As expected for a species influenced by the extensive ocean boundary current in the region, low genetic differentiation and high connectivity was uncovered across WA. However, we did detect strong isolation by distance and genetic discontinuities in the mid-west and south-east. The discontinuities correlate with boundaries between biogeographic regions, influenced by on-shelf oceanography, and the sites of important spawning aggregations. We also detected temporal instability in genetic structure at one of our sites, possibly due to interannual variability in recruitment in adjacent regions. Our results partly contrast with the current spatial management of snapper in WA, highlighting the need for a review. This study supports the value of population genomic surveys in informing the management of weakly-structured and wide-ranging marine fishery resources.
LLIN Evaluation in Uganda Project (LLINEUP) – The durability of long-lasting insecticidal nets treated with and without piperonyl butoxide (PBO) in Uganda
Authors: Mechan Frank , Katureebe Agaba , Tuhaise Violet , Mugote Martin , Oruni Ambrose , Onyige Ismail , Bumali Kawesa , Thornton Jonathan , Maxwell Kilama , Kyohere Mary , Kamya Moses R , Mutungi Peter , Kigozi Simon P , Yeka Adoke , Opigo Jimmy , Maiteki-Sebuguzi Catherine , Gonahasa Samuel , Hemingway Janet , Dorsey Grant , Reimer Lisa J , Staedke Sarah G , Donnelly Martin J , Lynd Amy
Published: February 2022

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

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

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

Here we demonstrate that both Olyset Plus and PermaNet 3.0 are as durable as their pyrethroid-only equivalents and had superior bioefficacy against pyrethroid-resistant An. gambiae. However, the superiority of PBO-LLINs decreased with operational use, correlating with a reduction in total PBO content. This decline in bioefficacy after just two years is concerning and there is an urgent need to assess the durability of PBO LLINs in other settings.
Reducing structural non-identifiabilities in upstream bioprocess models using profile-likelihood
Authors: Babel Heiko , Omar Ola , Paul Albert , Bär Joachim
Published: February 2022

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

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

We present the first application of profile likelihood to a complete upstream process model. Profile likelihood is a highly suitable method to determine parameter confidence intervals in upstream process models and provides reliable estimates even with non-linear models and limited data.
Prefrontally Modulated Vagal Tone Inhibits Inflammatory Responses to Prevent Telomere Damage in Healthy Participants
Authors: Ask Torvald F. , Sütterlin Stefan
Published: February 2022

Background

Accumulated senescent cells are proposed to be one of the main drivers of age-related pathology through disruption of tissue structure and function. We recently proposed the Neuro-Immuno-Senescence Integrative Model (NISIM; Ask et al., 2018) which relates prefrontally modulated vagal tone and subsequent balance between vagal and sympathetic input to the spleen to inflammatory responses leading to generation of reactive oxygen species and oxidative telomere damage. The NISIM is based on converging evidence and argues for the existence of a prefrontal cortex-autonomic nervous system-spleen (PAS) axis, suggesting that the inflammation that induces reactive oxygen species-generation is downstream of this axis.

Aim

In this study, we aim to assess inflammation as a mediator in the relationship between prefrontally modulated vagal tone and leukocyte telomere length to test the hypothesis that PAS axis dysregulation accelerates cellular aging. We also assess the relationship between a recently proposed index of vagal immunomodulation (vagal tone/inflammation ratio; NIM index; Gidron et al., 2018) and telomere length, and compare results between the NIM index and vagal tone as predictors of telomere length.

Methods

This study uses participant data from a large nationally representative longitudinal study since 1974 with a total of 45,000 Norwegian residents so far. A sub-sample of 1372 participants from which vagal tone, C Reactive Protein, and leukocyte telomere length could be obtained were included in the study. Relationships were analyzed with hierarchical multiple linear regression using either vagal tone and C Reactive Protein or the NIM index to predict telomere length. Sleeping problems, tobacco use status, alcohol use status, time since last meal, and symptoms of depression were included as control variables.

Results

In the mediation analysis, vagal tone was a significant positive predictor of telomere length, while C Reactive Protein was a significant negative predictor of telomere length. This relationship remained significant when individually controlling for some but not all confounding variables. The NIM index was a significant positive predictor of telomere length. This relationship remained significant when controlling for all confounding variables except one. In a reduced dataset excluding all participants where confounders were present, the NIM index remained a significant predictor of telomere length.

Conclusion

This is the first study suggesting that PAS axis activity is associated with telomere length thus supporting the NISIM. Results indicate that the NIM index is a more sensitive indicator of PAS axis activity than vagal tone and C Reactive Protein in isolation. Clinical relevance and suggestions for future research are discussed.
Genomic characterization of SARS-CoV-2 from Islamabad, Pakistan by Rapid Nanopore sequencing
Authors: Badar Nazish , Ikram Aamer , Salman Muhammad , Umair Massab , Rehman Zaira , Ahad Abdul , Mirza Hamza Ahmed , Alam Masroor , mehmood Nayab , Bashir Uzma
Published: February 2022

Since the start of COVID-19 pandemic, Pakistan has experienced four waves of pandemic. The fourth wave ended in October, 2021 while the fifth wave of pandemic starts in January, 2022. The data regarding the circulating strains after the fourth wave of pandemic from Pakistan is not available. The current study explore the genomic diversity of SARS-CoV-2 after fourth wave and before fifth wave of pandemic through whole genome sequencing. The results showed the circulation of different strains of SARS-CoV-2 during November-December, 2021. We have Omicron BA.1 (n=4), Lineage A (n=2) and delta AY.27 (n=1) variants of SARS-CoV-2 in the population of Islamabad. All the isolates harbors characteristics mutations of omicron and delta variant in the genome. The lineage A isolate harbors a nine amino acid (68-76) and a ten amino acid (679-688) deletion in the genome. The circulation of omicron in the population before the fifth wave of pandemic and subsequent upsurges of COVID-19 positive cases in Pakistan highlights the importance of genomic surveillance.
Species richness and community structure of bats along a forest elevational transect in Papua New Guinea
Authors: Sivault Elise , Amick Pita K. , Armstrong Kyle N. , Novotny Vojtech , Sam Katerina
Published: February 2022

Over the past decades, elevational gradients have become a powerful tool with which to understand the underlying cause(s) of biodiversity. The Mt. Wilhelm elevational transect is one such example, having been used to study the birds, insects, and plants of Papua New Guinea (PNG). However, a survey of mammals from this forest elevational transect was lacking. We thus aimed to investigate patterns in the community structure and species richness of bats (Chiroptera) along the transect, link the species to available regional data, and explain the observed patterns by including environmental characteristics. Bat communities were surveyed between 200 m and a timberline at 3,700 m a.s.l. at eight study sites separated by 500 m in elevation. We conducted mist-netting and acoustic surveys to detect and identify species at each site. Regional data were compiled to compare local with regional diversity. Finally, biotic (i.e., food availability, habitat features) and abiotic (i.e., mean daily temperature, available land area) factors were included in our analyses to disentangle the ecological drivers underlying bat diversity. Results revealed that species richness decreases with ascending elevation and was best explained by a corresponding decrease in both area and temperature. We also observed community turnover along the transect at local and regional scales, along with the increase of species’ elevational ranges. Consequently, despite that the study was restricted to one mountain in PNG, it demonstrates how basic inventory surveys can be used to address ecological questions in other similar and undisturbed tropical mountains.
Maximizing citizen scientists’ contribution to automated species recognition
Authors: Koch Wouter , Hogeweg Laurens , Nilsen Erlend B. , Finstad Anders G.
Published: February 2022

Technological advances and data availability have enabled artificial intelligence-driven tools that can increasingly successfully assist in identifying species from images. Especially within citizen science, an emerging source of information filling the knowledge gaps needed to solve the biodiversity crisis, such tools can allow participants to recognize and report more poorly known species. This can be an important tool in addressing the substantial taxonomic bias in biodiversity data, where broadly recognized, charismatic species are highly overrepresented. Meanwhile, the recognition models are trained using the same biased data, so it is important to consider what additional images are needed to improve recognition models. In this study, we investigated how the amount of training data influenced the performance of species recognition models for various taxa. We utilized a large Citizen Science dataset collected in Norway, where images are added independently from identification. We demonstrate that while adding images of currently under-represented taxa will generally improve recognition models more, there are important deviations from this general pattern. Thus, a more focused prioritization of data collection beyond the basic paradigm that “more is better” is likely to significantly improve species recognition models and advance the representativeness of biodiversity data.
Detection and characterization of circulating microvesicles containing Shiga toxin type 2 (Stx2) in a rat model of Hemolytic Uremic Syndrome
Authors: Sacerdoti Flavia , Gomez Fernando , Jancic Carolina , Moretton Marcela A. , Chiappetta Diego A. , Ibarra Cristina , Amaral María Marta
Published: February 2022

Shiga toxin (Stx) producing Escherichia coli (STEC) are foodborne pathogens that release Stx and may develop Hemolytic Uremic Syndrome (HUS). Stx causes endothelial cell damage and leads to platelets deposition and thrombi formation within the microvasculature. It has been described that Stx activates blood cells and induces the shedding of proinflammatory and prothrombotic microvesicles (MVs) containing the toxin. In this sense, it has been postulated that MVs containing Stx2 (MVs-Stx2+) can contribute to the physiopathology of HUS, allowing Stx to reach the target organs and evading the immune system. In this work, we propose that circulating MVs-Stx2+ can be a potential biomarker for the diagnosis and prognosis of STEC infections and HUS progression. In this regard, we developed a rat HUS model by the intreperitoneal injection of a sublethal dose of Stx2 and observed: decrease in body weight, increase of creatinine and urea levels, decrease of creatinine clearance and histological renal damages. After characterization of renal damages we investigated circulating total MVs and MVs-Stx2+ by flow cytometry at different times after Stx2 injection. Additionally, we evaluated the correlation of biochemical parameters such as creatinine and urea in plasma with MVs-Stx2+. As a result, we found a significant circulation of Mvs-Stx2+ at 96 hours after Stx2 injection, nevertheless no correlation with creatinine and urea plasma levels were detected. Our results suggest that MVs-Stx2+ may be an additional biomarker for the characterization and diagnosis of HUS progression. Further analysis is required in order to validate MVs-Stx2+ as biomarker of the disease.
The brassinosteroid biosynthesis gene TaD11-2A controls grain size and its elite haplotype improves wheat grain yields
Authors: Xu Huiyuan , Sun Han , Dong Jiajin , Ma Chengxue , Li Jingxue , Li Zhuochun , Wang Yihuan , Ji Junqi , Hu Xinrong , Wu Meihui , Zhao Chunhua , Qin Ran , Wu Jiajie , Ni Fei , Cui Fa , Wu Yongzhen
Published: February 2022

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

Highlight

The brassinosteroid biosynthesis gene TaD11-2A regulates grain size and root length and its haplotype favorably improves grain yields and salt tolerance in wheat.
Bayesian inference of phylogeny is robust to substitution model over-parameterization
Authors: Fabreti Luiza Guimarães , Höhna Sebastian
Published: February 2022

Model selection aims to choose the most adequate model for the statistical analysis at hand. The model must be complex enough to capture the complexity of the data but should be simple enough to not overfit. In phylogenetics, the most common model selection scenario concerns selecting an appropriate substitution and partition model for sequence evolution to infer a phylogenetic tree. Here we explored the impact of substitution model over-parameterization in a Bayesian statistical framework. We performed simulations under the simplest substitution model, the Jukes-Cantor model, and compare posterior estimates of phylogenetic tree topologies and tree length under the true model to the most complex model, the GTR+Γ+I substitution model, including over-splitting the data into additional subsets (i.e., applying partitioned models). We explored four choices of prior distributions: the default substitution model priors of MrBayes, BEAST2 and RevBayes and a newly devised prior choice (Tame). Our results show that Bayesian inference of phylogeny is robust to substitution model over-parameterization but only under our new prior settings. All three default priors introduced biases for the estimated tree length. We conclude that substitution and partition model selection are superfluous steps in Bayesian phylogenetic inference pipelines if well behaved prior distributions are applied.
Randomized gates eliminate bias in sort-seq assays
Authors: Trippe Brian L. , Huang Buwei , DeBenedictis Erika A. , Coventry Brian , Bhattacharya Nicholas , Yang Kevin K. , Baker David , Crawford Lorin
Published: February 2022

Sort-seq assays are a staple of the biological engineering toolkit, allowing researchers to profile many groups of cells based on any characteristic that can be tied to fluorescence. However, current approaches, which segregate cells into bins deterministically based on their measured fluorescence, introduce systematic bias. We describe a surprising result: one can obtain unbiased estimates by incorporating randomness into sorting. We validate this approach in simulation and experimentally, and describe extensions for both estimating group level variances and for using multi-bin sorters.
Experience-dependent learning and myelin plasticity in individuals with stroke
Authors: Rubino Cristina , Larssen Beverley C. , Chiu Larissa K. , Liu Hanwen , Kraeutner Sarah N. , Mahendran Niruthikha , Denyer Ronan , Lakhani Bimal , Borich Michael R. , Laule Cornelia , Boyd Lara A.
Published: February 2022

Background

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

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

Methods

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

Results

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

Conclusions

Findings indicate that after stroke, myelin water fraction is related to measures of motor learning and modulated by 4 weeks of skilled motor practice with the paretic limb. Myelin water fraction can be enhanced in the chronic stage of stroke and may be an important target for upper-limb motor recovery.
Species-Specific Formation of Paraspeckles in Intestinal Epithelium Revealed by Characterization ofNEAT1in Naked Mole-rat
Authors: Yamada Akihiro , Toya Hikaru , Tanahashi Mayuko , Kurihara Misuzu , Mito Mari , Iwasaki Shintaro , Kurosaka Satoshi , Takumi Toru , Fox Archa , Kawamura Yoshimi , Miura Kyoko , Nakagawa Shinichi
Published: February 2022

Paraspeckles are mammalian-specific nuclear bodies built on the long noncoding RNANEAT1_2. The molecular mechanisms of paraspeckle formation have been mainly studied using human or mouse cells, and it is not known if the same molecular components are involved in the formation of paraspeckles in other mammalian species. We thus investigated the expression pattern ofNEAT1_2in naked mole-rats (nNEAT1_2), which exhibit extreme longevity and lower susceptibility to cancer. In the intestine, nNEAT1_2is widely expressed along the entire intestinal epithelium, which is different from the expression of mNeat1_2, that is restricted to the cells of the distal tip in mice. Notably, the expression of FUS, a FET family RNA binding protein, essential for the formation of paraspeckles both in humans and mice, was absent in the distal part of the intestinal epithelium in naked mole-rats. Instead, mRNAs of other FET family proteins EWSR1 and TAF15 were expressed in the distal region. Exogenous expression of these proteins in Fus-deficient murine embryonic fibroblast cells rescued the formation of paraspeckles. These observations suggest that nNEAT1_2recruits different set of RNA binding proteins in a cell type-specific manner during the formation of paraspeckles in different organisms.
γ-aminobutyrate (GAB) functions as a bioenergetic and signaling gatekeeper to control T cell inflammation
Authors: Kang Siwen , Liu Lingling , Wang Tingting , Cannon Matthew , Lin Penghui , Fan Teresa W.-M. , Scott David A. , Wu Hsin-Jung Joyce , Lane Andrew N. , Wang Ruoning
Published: February 2022

γ-Aminobutyrate (GAB) is the biochemical form of γ-aminobutyric acid (GABA) at physiological pH and functions as an essential neurotransmitter in the vertebrate’s central nervous system (CNS). Growing evidence suggests that GAB may also mediate intercellular communications to shape various physiological processes, including immune response. Beyond acting as a paracrine signaling molecule, how GAB metabolism is controlled to exert many distinct functions remains elusive. By an integrated analysis of the extracellular metabolome, stable isotope traced metabolic pathway analysis, and metabolic transcriptome, we revealed that GAB is one of the most abundant metabolites produced through glutamine and arginine catabolism in CD4+ T help 17 (TH17) and induced T regulatory (iTreg) cells. GAB functions as a bioenergetic and signaling gatekeeper by reciprocally controlling pro-inflammatory TH17 cell and anti-inflammatory iTreg cell differentiation through distinct mechanisms. The expression of 4-aminobutyrate aminotransferase (ABAT) funnels GAB, as an anaplerotic substrate, into the TCA cycle to maximize carbon allocation in promoting TH17 cell differentiation. By contrast, the absence of ABAT activities in iTreg cells enables GAB exporting to the extracellular environment and acting as an autocrine signaling metabolite to promote iTreg cell differentiation. Accordingly, genetic or pharmacological ablation of ABAT activity in T cells confers protection against experimental autoimmune encephalomyelitis (EAE) pathogenic progression. Conversely, genetic ablation of GABA(A) receptor in T cells deteriorates EAE pathogenic progression. Collectively, our results suggest that the cell-autonomous control exerted by GAB on CD4+ T cell is bimodal and consists of the sequential action of two discrete processes, ABAT–dependent mitochondrial anaplerosis and the receptor-dependent autocrine signaling response, both of which are required for a properly controlled T cell-mediated inflammation.
Duplicated binding site for RIC-3 in 5-Hydroxytryptamine Receptors Subtype 3
Authors: Do Hoa Quynh , Jansen Michaela
Published: February 2022

Serotonin or 5-hydroxytryptamine receptors type 3 (5-HT3) belong to the family of pentameric ligand-gated ion channels (pLGICs), which also includes other neurotransmitter-gated ion channels such as nicotinic acetylcholine receptors (nAChRs). pLGICs have been long-standing therapeutic targets for psychiatric disorders such as anxiety, schizophrenia, and addiction, and neurological diseases like Alzheimer’s and Parkinson’s disease. Due to structural conservation and significant sequence similarities of pLGICs’ extracellular and transmembrane domains across the more than 40 subunits found in humans, clinical trials for drug candidates targeting these two domains have been largely hampered by undesired effects mediated by off-subunit modulation. With the present study, we explore the interaction interface of the 5-HT3Aintracellular domain (ICD) with the resistance to inhibitors of choline esterase (RIC-3) protein. Previously, we have shown that RIC-3 directly interacts with the ICD of 5-HT3Asubunits. Using a sequential deletion approach, we identified the L1-MX segment of the ICD fused to maltose-binding protein as sufficient for the interaction. For the present study, synthetic L1-MX-based peptides, Ala-scanning, and a pull-down assay identified positions W347, R349, and L353 as critical for binding to RIC-3. In complementary studies with full-length 5-HT3Asubunits, the identified Ala substitutions reduced the modulation of functional surface expression by co-expression of RIC-3. Additionally, we found and characterized a duplication of the binding motif at the transition between the ICD MA-helix and transmembrane segment M4. Analogous Ala substitutions at W447, R449, and L454 disrupt MAM4-peptide RIC-3 interactions and reduce modulation of functional surface expression. In summary we identify two binding sites for RIC-3 with a shared duplicated motif in 5-HT3Asubunits, one in the MX-helix and one at the MAM4-helix transition.
Contribution of spontaneous mutations to quantitative and molecular variation at the highly repetitive rDNA locus in yeast
Authors: Sharp Nathaniel P. , Smith Denise R. , Driscoll Gregory , Sun Kexin , Vickerman Catherine M. , Martin Sterling C.T.
Published: February 2022

The ribosomal DNA array inSaccharomyces cerevisiaeconsists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that un-selected mutations throughout the genome can disrupt copy number maintenance. In consequence, copy number generally declines, consistent with a model of regulation where copy number is normally increased when low. This pattern holds across ploidy levels and strains in the standard lab environment, but differs under some stressful conditions. We identify several alleles, gene categories and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself is distinct from the rest of the genome, and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.
An NKX-COUP-TFII genomic code for mucosal vascular addressins and organ morphogenesis
Authors: Dinh Thanh Theresa , Xiang Menglan , Rajaraman Anusha , Wang Yongzhi , Salazar Nicole , Roper Walter , Rhee Siyeon , Brulois Kevin , O’Hara Ed , Kiefel Helena , Dinh Truc , Bi Yuhan , Gonzalez Dalila , Bao Evan , Red-Horse Kristy , Balogh Peter , Gábris Fanni , Gaszner Balázs , Berta Gergely , Pan Junliang , Butcher Eugene C.
Published: February 2022

Immunoglobulin family and carbohydrate vascular addressins encoded byMadcam1andSt6gal1control lymphocyte homing into intestinal tissues, regulating immunity and inflammation. The addressins are developmentally programmed to decorate endothelial cells lining gut post-capillary and high endothelial venules, providing a prototypical example of organ- and segment-specific endothelial specialization. We identify conserved NKX-COUP-TFII composite elements (NCCE) in regulatory regions ofMadcam1andSt6gal1that bind intestinal homeodomain protein NKX2-3 cooperatively with venous nuclear receptor COUP-TFII to activate transcription. TheMadcam1element also integrates repressive signals from arterial/capillary Notch effectors. Pan-endothelial COUP-TFII overexpression induces ectopic addressin expression in NKX2-3+capillaries, while NKX2-3 deficiency abrogates expression by HEV. Phylogenetically conserved NCCE are enriched in genes involved in neuron migration and morphogenesis of the heart, kidney, pancreas and other organs. Our results define a genomic address code for targeted expression of mucosal vascular addressins and implicate NCCE in fundamental processes in cell specification and development.
A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data
Authors: Wang Peter Y. , Bartel David P.
Published: February 2022

Background

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

Results

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

Conclusions

We developed the BBUM model, a robust statistical modeling strategy to account for background secondary signal in differential expression data. It performed well for identifying primary substrates of TDMD and should be useful for other applications in which the primary regulatory targets are only upregulated or only downregulated. The BBUM model, FDR-correction algorithm, and significance-testing methods are available as an R package athttps://github.com/wyppeter/bbum.
Assessing Protein Homology Models with Docking Reproducibility
Authors: Plonski Alexander P. , Reed Scott M.
Published: February 2022

Results of the most recent Critical Assessment of Protein Structure (CASP) competition demonstrate that protein backbones can be predicted with very high accuracy. In particular, the artificial intelligence methods of AlphaFold 2 from DeepMind were able to produce structures that were similar enough to experimental structures that many described the problem of protein prediction solved. However, for such structures to be used for drug docking studies requires precision in the placement of side chain atoms as well. Here we built a library of 1334 small molecules and examined how reproducibly they bound to the same site on a protein using QuickVina-W, a branch of the program Autodock that is optimized for blind searches. We discovered that the higher the backbone quality of the homology model the greater the similarity between the small molecule docking to the experimental and modeled structures. Furthermore, we found that specific subsets of this library were particularly useful for identifying small differences between the best of the best modeled structures. Specifically, when the number of rotatable bonds in the small molecule increased, differences in binding sites became more apparent.
Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine
Authors: Kimura Satoshi , Srisuknimit Veerasak , McCarty Kacie , Dedon Peter C. , Kranzusch Philip J. , Waldor Matthew K.
Published: February 2022

Post-transcriptional RNA editing modulates gene expression in a condition-dependent fashion. We recently discovered C-to-Ψ editing in Vibrio cholerae tRNA. Here, we characterize the biogenesis, regulation, and functions of this previously undescribed RNA editing process. We show that an enzyme, TrcP, mediates the editing of C-to-U followed by the conversion of U to Ψ, consecutively. AlphaFold-2 predicts that TrcP consists of two globular domains, including a novel cytidine deaminase and a pseudouridylase, along with a long helical domain. The latter domain tethers tRNA substrates during both the C-to-U editing and pseudouridylation, likely enabling a substrate channeling mechanism for efficient catalysis all the way to the terminal product. C-to-Ψ editing both requires and suppresses other modifications, creating an interdependent network of modifications in the tRNA anticodon loop that facilitates coupling of tRNA modification states to iron availability. Our findings provide mechanistic insights into an RNA editing process that likely promotes environmental adaptation.
A protein semisynthesis-based strategy to probe the impact of site-specific serine ADP-ribosylation on linker histone function
Authors: Tashiro Kyuto , Mohapatra Jugal , Brautigam Chad A. , Liszczak Glen
Published: February 2022

Recently developed chemical and enzyme-based technologies to install serine ADP-ribosylation onto synthetic peptides have enabled new approaches to study PARP biology. Here, we establish a generalizable strategy to prepare ADP-ribosylated peptides that are compatible with N-terminal, C-terminal and sequential protein ligation reactions. Two unique protein-assembly routes are employed to generate full-length linker histone constructs that are homogenously ADP-ribosylated at known DNA damage-dependent modification sites. We found that serine mono-ADP-ribosylation is sufficient to alleviate linker histone-dependent chromatin compaction, and that this effect is amplified by ADP-ribose chain elongation. Our work will greatly expand the scope of ADP-ribose-modified proteins that can be constructed via semisynthesis, which is rapidly emerging as a robust approach to elucidate the direct effects that site-specific serine mono- and poly-ADP-ribosylation have on protein function.
Every single conidium in Aspergillus fumigatus caspofungin tolerant strains are intrinsically caspofungin tolerant
Authors: Valero Clara , Colabardini Ana Cristina , de Castro Patrícia Alves , Amich Jorge , Bromley Michael J. , Goldman Gustavo H.
Published: February 2022

Aspergillus fumigatus is a human fungal pathogen that causes a disease named aspergillosis. Echinocandins, such as the fungistatic drug caspofungin (CAS) are used as second-line therapy. Some A. fumigatus clinical isolates can survive and grow in higher CAS concentrations, a phenomenon known as “caspofungin paradoxical effect” (CPE). Here we investigate if CPE is due to a subpopulation of conidia produced by a CAS tolerant strain, indicative of a persistence phenotype or is caused by all the conidia which would be consistent with a tolerance phenotype. We evaluated 67 A. fumigatus clinical isolates for CPE growth and used a novel CPE Index (CPEI) classified them as CPE+ (CPEI ≥ 0.40) or CPE− (CPEI ≤ 0.20). Conidia produced by three CPE+ clinical isolates, CEA17 (CPEI=0.52), Af293 (CPEI=0.64), CM7555 (CPEI=0.58) all showed the ability to grow in high levels of CAS while all conidia produced by the CPE− isolate IFM61407 (CPEI=0.12) strain showed no evidence of tolerance. Given the importance of calcium/calcineurin/transcription factor CrzA pathway in CPE regulation, we also evaluated ΔcrzAAf293 (CPE−) and ΔcrzACEA17 (CPE+) conidia tolerance to CAS. All ΔcrzACEA17 conidia showed CPE+ while 100 % of ΔcrzAAf293 spores are CPE−. As all spores derived from an individual strain are phenotypically indistinct with respect to CPE it is likely that CPE is a genetically encoded adaptive trait that should be considered an antifungal tolerant phenotype. As the CPEI shows that the strength of the CPE is not uniform between strains we propose that the mechanisms that govern this phenomenon are multi-factorial.
Real-time monitoring of the effectiveness of six COVID-19 vaccines in Hungary in 2021 using the screening method
Authors: Krisztina Horváth J. , Ferenci Tamás , Ferenczi Annamária , Túri Gergő , Röst Gergely , Oroszi Beatrix
Published: February 2022

Several studies have reported a waning of the effectiveness of COVID-19 vaccines. We report real-life vaccine effectiveness in Hungary, estimated with the screening method, in 2021, i.e., covering the dominance of both the Alpha and the Delta variant, and including the booster roll-out. Hungary is in the unique position to use six different vaccines (including the Sputnik V and Sinopharm vaccines, for which limited evidence was available prior to the present study) in the same, relatively homogeneous population. All vaccines provided high level of protection initially which declined over time. While the picture is different in each age group, the waning of immunity is apparent for all vaccines and especially in the younger age groups and the Sinopharm, Sputnik-V and AstraZeneca vaccines, which performed similarly. This is clearly reversed by booster doses, more prominent for those vaccines, where recipients were more likely to take the booster dose (which were the aforementioned three vaccines). Booster doses were almost exclusively mRNA vaccines. Overall, two vaccines, Pfizer/BioNTech and Moderna tend to produce the best results in all age groups, and even with waning taken into account.
The effect of cytoskeleton inhibitors on coccolith morphology inCoccolithus braarudiiandScyphosphaera apsteinii
Authors: Langer Gerald , Probert Ian , Taylor Alison , Harper Glenn M. , Brownlee Colin , Wheeler Glen
Published: February 2022

The calcite platelets of coccolithophores (Haptophyta), the coccoliths, are among the most elaborate biomineral structures. How these unicellular algae accomplish the complex morphogenesis of coccoliths is still largely unknown. It has long been proposed that the cytoskeleton plays a central role in shaping the growing coccoliths. Previous studies have indicated that disruption of the microtubule network led to defects in coccolith morphogenesis inEmiliania huxleyiandCoccolithus braarudii. Disruption of the actin network also led to defects in coccolith morphology inE. huxleyi, but its impact on coccolith morphology inC. braarudiiwas less clear, as coccolith secretion was largely inhibited under the conditions used. A more detailed examination of the role of actin and microtubule networks is therefore required to address the wider role of the cytoskeleton in coccolith morphogenesis. In this study, we have examined coccolith morphology inC. braarudiiandScyphosphaera apsteiniifollowing treatment with the microtubule inhibitors vinblastine and colchicine (S. apsteiniionly) and the actin inhibitor cytochalasin B. We found that all cytoskeleton inhibitors induced coccolith malformations, strongly suggesting that both microtubules and actin filaments are instrumental in morphogenesis. By demonstrating the requirement for the microtubule and actin networks in coccolith morphogenesis in diverse species, our results suggest that both of these cytoskeletal elements are likely to play conserved roles in defining coccolith morphology.