bluuebunny/crossref_metadata_2025 huggingface dataset:
Environmental Surface Monitoring as a Noninvasive Method for SARS-CoV-2 Surveillance in Community Settings: Lessons from a University Campus Study
Authors: Ali Sobur , Cella Eleonora , Johnston Catherine , Deichen Michael , Azarian Taj
Published: July 2023

Environmental testing of high-touch objects is a potential noninvasive approach for monitoring population-level trends of SARS-CoV-2 and other respiratory viruses within a defined setting. We aimed to determine the association between SARS-CoV-2 contamination on high-touch environmental surfaces, community level case incidence, and university student health data. Environmental swabs were collected from January 2022 to November 2022 from high-touch objects and surfaces from five locations on a large university campus in Florida, USA. RT-qPCR was used to detect and quantify viral RNA, and a subset of positive samples was analyzed by viral genome sequencing to identify circulating lineages. During the study period, we detected SARS-CoV-2 viral RNA on 90.7% of 162 tested samples. Levels of environmental viral RNA correlated with trends in community-level activity and case reports from the student health center. A significant positive correlation was observed between the estimated viral gene copy number in environmental samples and the weekly confirmed cases at the university. Viral sequencing data from environmental samples identified lineages contemporaneously circulating in the local community and state based on genomic surveillance data. Further, we detected emerging variants in environmental samples prior to their identification by clinical genomic surveillance. Our results demonstrate the utility of viral monitoring on high-touch environmental surfaces for SARS-CoV-2 surveillance at a community level. In communities with delayed or limited testing facilities, immediate environmental surface testing may considerably inform epidemic dynamics.

Graphical Abstract
Booster dose of self-amplifying SARS-CoV-2 RNA vaccine vs. mRNA vaccine: a phase 3 comparison of ARCT-154 with Comirnaty®
Authors: Oda Yoshiaki , Kumagai Yuji , Kanai Manabu , Iwama Yasuhiro , Okura Iori , Minamida Takeshi , Yagi Yukihiro , Kurosawa Toru , Greener Benjamin , Zhang Ye , Walson Judd L.
Published: July 2023

Background

Licensed mRNA vaccines demonstrated initial effectiveness against COVID-19 but require booster doses to broaden the anti-SARS-CoV-2 response. There is an unmet need for novel highly immunogenic and broadly protective vaccines. We compared immunogenicity and tolerability of ARCT-154, a novel self-amplifying mRNA vaccine with the mRNA vaccine, Comirnaty®.

Methods

We compared immune responses to ARCT-154 and Comirnaty booster doses in healthy 18– 77-year-old Japanese adults initially immunised with two doses of mRNA COVID-19 vaccine (Comirnaty or Spikevax®) then a third dose of Comirnaty at least 3 months previously. Neutralising antibodies were measured before and 28 days after booster vaccination. The primary objective was to demonstrate non-inferiority of the immune response against Wuhan-Hu-1 SARS-CoV-2 virus as geometric mean titre (GMT) ratios and seroresponse rates (SRR) of neutralising antibodies; key secondary endpoints included the immune response against the Omicron BA.4/5 variant and vaccine tolerability assessed using participant-completed electronic diaries.

Findings

Between December 13, 2022 and February 25, 2023 we enrolled 828 participants randomised 1:1 to receive ARCT-154 (n = 420) or Comirnaty (n = 408) booster doses. Four weeks after boosting, ARCT-154 induced higher Wuhan-Hu-1 neutralising antibodies GMTs than Comirnaty (5641 [95% CI: 4321, 7363] and 3934 [2993, 5169], respectively), a GMT ratio of 1·43 (95% CI: 1·26–1·63), with SRR of 65·2% (60·2–69·9) and 51·6% (46·4–56·8) meeting the non-inferiority criteria. Respective anti-Omicron BA.4/5 GMTs were 2551 (1687–3859) and 1958 (1281–2993), a GMT ratio of 1·30 (95% CI: 1·07–1·58), with SRR of 69·9% (65·0–74·4) and 58·0% (52·8–63·1), meeting the superiority criteria for ARCT-154 over Comirnaty. Booster doses of either ARCT-154 or Comirnaty were equally well-tolerated with no causally-associated severe or serious adverse events; 94·8% and 96·8% of ARCT-154 and Comirnaty vaccinees reported local reactions and 65·7% and 62·5% had solicited systemic adverse events. Events were mainly mild in severity, occurring and resolving within 3–4 days of vaccination.

Interpretation

Immune responses four weeks after an ARCT-154 booster dose in mRNA-immunised adults were higher than after a Comirnaty booster, meeting non-inferiority criteria against the prototype Wuhan-Hu-1 virus, and superiority criteria against the Omicron BA.4/5 variant.

Funding

The study was funded by the Japanese Ministry of Health, Labour, and Welfare following a public invitation to bid for an urgent improvement project for vaccine manufacturing systems, fourth invitation, Grant number: 1212-3.

Clinical Trials registration and identifier

The study was registered on the Japan Registry for Clinical Trials (jRCT 2071220080).
On the limitations of large language models in clinical diagnosis
Authors: Reese Justin T , Danis Daniel , Caufield J Harry , Groza Tudor , Casiraghi Elena , Valentini Giorgio , Mungall Christopher J , Robinson Peter N
Published: July 2023

Objective

Large Language Models such as GPT-4 previously have been applied to differential diagnostic challenges based on published case reports. Published case reports have a sophisticated narrative style that is not readily available from typical electronic health records (EHR). Furthermore, even if such a narrative were available in EHRs, privacy requirements would preclude sending it outside the hospital firewall. We therefore tested a method for parsing clinical texts to extract ontology terms and programmatically generating prompts that by design are free of protected health information.

Materials and Methods

We investigated different methods to prepare prompts from 75 recently published case reports. We transformed the original narratives by extracting structured terms representing phenotypic abnormalities, comorbidities, treatments, and laboratory tests and creating prompts programmatically.

Results

Performance of all of these approaches was modest, with the correct diagnosis ranked first in only 5.3-17.6% of cases. The performance of the prompts created from structured data was substantially worse than that of the original narrative texts, even if additional information was added following manual review of term extraction. Moreover, different versions of GPT-4 demonstrated substantially different performance on this task.

Discussion

The sensitivity of the performance to the form of the prompt and the instability of results over two GPT-4 versions represent important current limitations to the use of GPT-4 to support diagnosis in real-life clinical settings.

Conclusion

Research is needed to identify the best methods for creating prompts from typically available clinical data to support differential diagnostics.
Automated Pipeline for Comparing Protein Conformational States in the PDB to AlphaFold2 Predictions
Authors: Ellaway Joseph I. J. , Anyango Stephen , Nair Sreenath , Zaki Hossam A. , Nadzirin Nurul , Powell Harold R. , Gutmanas Aleksandras , Varadi Mihaly , Velankar Sameer
Published: July 2023

Proteins, as molecular machines, are necessarily dynamic macromolecules that carry out essential cellular functions. Recognising their stable conformations is important for understanding the molecular mechanisms of disease. While AI-based computational methods have enabled protein structure prediction, the prediction of protein dynamics remains a challenge. Here, we present a deterministic pipeline that clusters experimentally determined protein structures to comprehensively recognise conformational states across the Protein Data Bank. Our approach clusters protein chains based on a GLObal CONformation (GLOCON) difference score, which is computed from pairwise C-alpha distances. By superposing the clustered structures, differences and similarities in conformational states can be observed. Additionally, we offer users the ability to superpose predicted models from the AlphaFold Database to the clusters of PDB structures. This clustering pipeline significantly advances researchers’ ability to explore the conformational landscape within the PDB. All clustered and superposed models can be viewed in Mol* on the PDBe Knowledge Base website, or accessed in as raw annotations via our GraphAPI and FTP server. The clustering package is made available as an open-source Python3 package under the Apache-2.0 license.
The Endogenous Opioid Met-Enkephalin Modulates Thalamo-Cortical Excitation Inhibition Balance in a Medial Thalamus-Anterior Cingulate Cortex Circuit
Authors: Arias Hervert Erwin , Birdsong William
Published: July 2023

Activation of opioid receptors in the anterior cingulate cortex (ACC) mediates aspects of analgesia induced by both exogenous and endogenous opioids. We have previously shown that opioid signaling disrupts both afferent excitatory and indirect inhibitory synaptic transmission from the medial thalamus (MThal) to the ACC, but the effects of endogenous opioids within this circuit remain poorly understood. The goal of the current study was to understand how the endogenous opioid, [Met]5-enkephalin (ME), modulates thalamic-driven excitatory and inhibitory synaptic transmission onto layer V pyramidal neurons in the ACC. We used pharmacology, brain slice electrophysiology and optogenetic stimulation to study opioid-mediated modulation of optically evoked glutamatergic and GABAergic transmission. The results revealed that ME inhibited both AMPA-mediated excitatory and GABA-mediated inhibitory synaptic transmission in the ACC. However, inhibitory transmission was more potently inhibited than excitatory transmission by ME. This preferential reduction in GABAA-mediated synaptic transmission was primarily due to the activation of delta opioid receptors by ME and resulted in a net disinhibition of MThal-ACC excitatory pathway. These results suggest that moderate concentrations of ME can lead to net excitation of ACC circuitry and that analgesia may be associated with disinhibition rather than inhibition of ACC subcircuits.
A simulation framework for modeling the within-patient evolutionary dynamics of SARS-CoV-2
Authors: Terbot John W , Cooper Brandon S. , Good Jeffrey M. , Jensen Jeffrey D.
Published: July 2023

The global impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to considerable interest in detecting novel beneficial mutations and other genomic changes that may signal the development of variants of concern (VOCs). The ability to accurately detect these changes within individual patient samples is important in enabling early detection of VOCs.

Such genomic scans for positive selection are best performed via comparison of empirical data to simulated data wherein evolutionary factors, including mutation and recombination rates, reproductive and infection dynamics, and purifying and background selection, can be carefully accounted for and parameterized. While there has been work to quantify these factors in SARS-CoV-2, they have yet to be integrated into a baseline model describing intra-host evolutionary dynamics. To construct such a baseline model, we develop a simulation framework that enables one to establish expectations for underlying levels and patterns of patient-level variation. By varying eight key parameters, we evaluated 12,096 different model-parameter combinations and compared them to existing empirical data. Of these, 592 models (∼5%) were plausible based on the resulting mean expected number of segregating variants. These plausible models shared several commonalities shedding light on intra-host SARS-CoV-2 evolutionary dynamics: severe infection bottlenecks, low levels of reproductive skew, and a distribution of fitness effects skewed towards strongly deleterious mutations. We also describe important areas of model uncertainty and highlight additional sequence data that may help to further refine a baseline model. This study lays the groundwork for the improved analysis of existing and future SARS-CoV-2 within-patient data.

Significance Statement

Despite its tremendous impact on human health, a comprehensive evolutionary baseline model has yet to be developed for studying the within-host population genomics of SARS-CoV-2. Importantly, such modeling would enable improved analysis and provide insights into the key evolutionary dynamics governing SARS-CoV-2 evolution. Given this need, we have here quantified a set of plausible baseline models via large-scale simulation. The commonly shared features of these relevant models - including severe infection bottlenecks, low levels of progeny skew, and a high rate of strongly deleterious mutations - lay the foundation for sophisticated analyses of SARS-CoV-2 evolution within patients using these baseline models.
LactoSpanks: a collection of IPTG inducible promoters for the commensal lactic acid bacteriaLactobacillus gasseri
Authors: Fristot Elsa , Cambray Guillaume , Bonnet Jerome
Published: July 2023

Lactic acid bacteria (LAB) are important for many biotechnological applications, such as bioproduction and engineered probiotics for therapy. Inducible promoters are key gene expression control elements, yet those available in LAB are mainly based on bacteriocin systems and have many drawbacks, including large gene clusters, costly inducer peptides and little portability toin vivosettings. UsingLactobacillus gasseri, a model commensal bacteria from the human gut, we report the engineering of Lactospanks promoters (Pls), a collection of variable strength inducible promoters controlled by theLacIrepressor fromB. subtilisand induced by isopropyl β-D-1-thiogalactopyranoside (IPTG). We first show that the Phyper-spank promoter fromBacillus subtilisis functional inL. gasseri, albeit with substantial leakage. We then construct and screen a semi-rational library of Phyper-spank variants to select a set of four IPTG-inducible promoters that span a range of expression levels and exhibit reduced leakages and operational dynamic ranges (from ca. 9 to 28 fold-change). With their low genetic footprint and simplicity of use, Lactospanks will support many applications inL. gasseri, and potentially other lactic acid and gram-positive bacteria.
Lipid nanoparticle-mediated delivery of mRNA into the mouse and human retina and other ocular tissues
Authors: Chambers Cheri Z. , Soo Gillian L. , Engel Abbi L. ,   Birth Defects Research Laboratory (BDRL), Glass Ian A. , Frassetto Andrea , Martini Paolo G. V. , Cherry Timothy J.
Published: July 2023

Structured Abstract

Purpose

Lipid nanoparticles (LNPs) show promise in their ability to introduce mRNA to drive protein expression in specific cell types of the mammalian eye. Here, we examined the ability of mRNA encapsulated in lipid nanoparticles (LNPs) with two distinct formulations to drive gene expression in mouse and human retina and other ocular tissues.

Methods

We introduced mRNA carrying LNPs into two biological systems. Intravitreal injections were tested to deliver LNPs into the mouse eye. Human retinal pigment epithelium (RPE) and retinal explants were used to assess mRNA expression in human tissue. We analyzed specificity of expression using histology, immunofluorescence, and imaging.

Results

In mice, mRNAs encoding GFP and ciliary neurotrophic factor (CNTF) were specifically expressed by Müller glia and retinal pigment epithelium (RPE). Acute inflammatory changes measured by microglia distribution (Iba-1) or interleukin-6 (IL-6) expression were not observed 6 hours post-injection. Human RPE also expressed high levels of GFP. Human retinal explants expressed GFP in cells with apical and basal processes consistent with Müller glia and in perivascular cells consistent with macrophages.

Conclusions

We demonstrated the ability to reliably transfect subpopulations of retinal cells in mice eye tissuesin vivoand in human ocular tissues. Of significance, intravitreal injections were sufficient to transfect the RPE in mice. To our knowledge we demonstrate delivery of mRNA using LNPs in human ocular tissues for the first time.

Translational Relevance

Ocular gene-replacement therapies using non-viral vector methods are of interest as alternatives to adeno-associated virus (AAV) vectors. Our studies show that mRNA LNP delivery can be used to transfect retinal cells in both mouse and human tissues without inducing significant inflammation. This promising methodology could be used to transfect retinal cell lines, tissue explants, mice, or potentially as gene-replacement therapy in a clinical setting in the future.
Four-dimensional omics data reveals ribosome heterogeneity, regulation of translation efficacy, and nonsense-mediated decay in the differentiation of spermatocyte to round spermatid
Authors: Lee Szu-Shuo , Kung Ying-Chih , Jou Yuh-Shan
Published: July 2023

A protein expression is regulated by transcription, translation, and sequential processing. However, well correlated RNA and protein abundance just only proportionate 40%, and even poorer when cell was stressed, differentiated, or tumorigenic transformed. Here, we discovered spermatocyte (SP) differentiated to round spermatid (RS) had equal regulation extent which may related to ribosomal behavior alteration. The change of ribosome occupancy was related to SP and RS specific function in spermatogenesis. Interactome of functional ribosome in SP and RS revealed the activated ribosome in SP but stalled and nonsense-mediated decay (NMD) associated ribosome in RS. Functional ribosomes of RS occupied 5’untranslated regions (5’UTR) of SP specific transcripts and correlated its’ RNA and protein downregulation. These findings suggested a branched NMD pathway was activated in RS to eliminate SP specific transcripts and keep them from being translated. Our discovery suggested the heterogeneity of ribosomal interactome may play an important role in spermatogenesis.
Chronic cisplatin exposure does not affect epimutations inC. elegansbut induces fluctuations in tRNA-derived small non-coding RNAs
Authors: Fallet Manon , Wilson Rachel , Sarkies Peter
Published: July 2023

The individual lifestyle and environment of an organism can influence its phenotype and potentially the phenotype of its offspring. The different genetic and non-genetic components of the inheritance system and their mutual interactions are key mechanisms to generate inherited phenotypic changes. Epigenetic changes can be transmitted between generations independently from changes in DNA sequence. InC. elegans, epigenetic differences, i.e., epimutations, mediated by small non-coding RNAs, particularly 22G-RNAs, as well as chromatin have been identified and their average persistence is 3 to 5 generations. In addition, previous research showed that some epimutations had a longer duration and concerned genes that were enriched for multiple components of xenobiotic response pathways. These results raise the possibility that environmental stresses might change the rate at which epimutations occur, with potential significance for adaptation. In this work, we explore this question by propagatingC. eleganslines either in control conditions or in moderate or high doses of cisplatin, which introduces genotoxic stress by damaging DNA. Our results show that cisplatin has a limited effect on global small non-coding RNAs epimutations and epimutations in gene expression levels. However, cisplatin exposure leads to increased fluctuations in the levels of small non-coding RNAs derived from tRNA cleavage. We show that changes in tRNA-derived small RNAs may be associated with gene expression changes. Our work shows that epimutations are not substantially altered by cisplatin exposure but identifies transient changes in tRNA-derived small RNAs as a potential source of transcriptional variation induced by genotoxic stress.
Peptriever: A Bi-Encoder approach for large-scale protein-peptide binding search
Authors: Gurvich Roni , Markel Gal , Tanoli Ziaurrehman , Meirson Tomer
Published: July 2023

Motivation

In peptide therapeutics, the successful interaction between a designed peptide and a specific receptor is crucial, while minimizing interactions with other receptors is equally essential. Current computational methods excel at estimating the probability of the former but estimating the latter requires excessive computational resources, making it challenging.

Results

In this study, we propose transformers-based protein embeddings that can quickly identify and rank millions of interacting proteins. Furthermore, the proposed approach outperforms existing sequence- and structure-based methods, with a mean AUC-ROC and AUC-PR of 0.73.

Availability

Training data, scripts, and fine-tuned parameters are available athttps://github.com/RoniGurvich/Peptriever. A live demonstration of the application can be found athttps://peptriever.app/.

Contact

tomermrsn@gmail.comandzia.rehman@helsinki.fi
Inconsistencies of empirical ecological network inference are governed by considerations of statistical approaches and dimensions of input data
Authors: Kusch Erik , Bimler Malyon D. , Blanchet F. Guillaume , Lutz James A. , Ordonez Alejandro
Published: July 2023

Identifying the most suitable method of ecological network inference in line with individual research considerations is a non-trivial task, which significantly hinders adoption of network approaches to forest management applications. To advance the study of ecological networks and better guide their use in managing forest ecosystems, we propose a framework that aligns pairwise species-association inference methods with specific research questions, biological interaction types, data availability, and spatial scales of study. We motivate the adoption of this framework through an empirical comparison of multiple inference methods, highlighting substantial inconsistencies that arise across scales and methodologies. Using data on species distributions and attributes at local, regional, and continental scales for temperate conifer forests in North America, we show that network inference varies significantly depending on whether occurrence, abundance, or performance data are used and the degree to which confounding factors are accounted for. Across four widely used and/or cutting-edge inference methods (COOCCUR, NETASSOC, HMSC, NDD-RIM), we find notable disparities in both whole-network metrics and pairwise species associations, particularly at continental scales. These findings underscore that no single method is likely to universally outperforms others across scales, emphasizing the importance of choosing an inference approach that aligns with specific ecological and spatial contexts. Our framework aids in interpreting network topologies and interactions in light of these method- and datatype-driven variances, providing a structured approach to more reliably infer ecological associations and address complex network dynamics in forest management practices.
Geomagnetic orientation in subterranean mole crickets during burrowing
Authors: Endo Tsubasa , Ando Noriyasu
Published: July 2023

While many terrestrial animals use celestial and terrestrial cues for orientation, subterranean animals lack access to these cues. The geomagnetic field serves as a reliable alternative cue for underground navigation. Subterranean mammals use the geomagnetic field to burrow and navigate within their nests; however, whether subterranean insects possess magnetoreception remains unclear. Here, we investigated the influence of magnetic fields on burrowing directions in subterranean mole crickets (Gryllotalpa orientalis). Under an intact magnetic field, mole crickets predominantly burrow in the north-south direction. However, when the magnetic field was rotated by 90°, the preferred burrowing direction shifted to the east-west axis. Notably, when the horizontal component of the geomagnetic field was reduced to near 0 µT, no preferred direction was observed. These results suggest that mole crickets have a magnetic sense and they align the direction at the beginning of burrowing. The study enhances our comprehension of underground orientation mechanisms in subterranean insects and reveals convergent evolution between insects and mammals in utilizing the geomagnetic field as a navigational cue.
Enhancing sensitivity and versatility of Tn5-based single cell omics
Authors: Seufert Isabelle , Sant Pooja , Bauer Katharina , Syed Afzal P. , Rippe Karsten , Mallm Jan-Philipp
Published: July 2023

The analysis of chromatin features in single cells centers around Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the assay for transposase-accessible chromatin in single cells (scATAC-seq) to map open chromatin regions. However, a current limitation is the sparse coverage of open chromatin loci that are detected in a given single cell by droplet-based methods. Thus, enhancing Tn5 activity to improve genomic coverage of scATAC-seq or facilitating multi-omics readouts of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell by targeting Tn5 to antibody-bound chromatin epitopes. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.
Spatiotemporal dynamics and emergent ordering in a mixture of morphologically distinct bacteria having different cell motility
Authors: Mondal Kaustav , Bera Palash , Ghosh Pushpita
Published: July 2023

Microbial communities exhibit complex behaviors driven by species interactions and individual characteristics. In this study, we delve into the dynamics of a mixed bacterial population comprising two distinct species with different morphology and motility aspects. Employing agent-based modeling and computer simulations, we analyze the impacts of size ratios and packing fractions on dispersal patterns, aggregate formation, clustering, and spatial ordering. Notably, we find that motility and anisotropy of elongated bacteria significantly influence the distribution and spatial organization of nonmotile spherical species. Passive spherical cells display superdiffusive behavior, particularly at smaller size ratios, while active rod-like cells exhibit normal diffusive behavior in the diffusion regime. As the size ratio increases, clustering of passive cells is observed, accompanied by enhanced alignment and closer packing of active cells in the presence of higher passive cell area fractions. As the size ratio increases, clustering of passive cells is observed, accompanied by enhanced alignment and closer packing of active cells in the presence of higher passive cell area fractions. Additionally, we identify the pivotal role of passive cell area fraction in influencing the response of active cells toward nematicity, with its dependence on size ratio. These findings shed light on the significance of morphology and motility in shaping the collective behavior of microbial communities, providing valuable insights into complex microbial behaviors with implications for ecology, biotechnology, and bioengineering.
Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome relative to a standardized biological variable
Authors: Gustafson K.L. , McAdams Z.L. , Russell A.L. , Dorfmeyer R.A. , Turner G.M. , Ericsson A.C.
Published: July 2023

Background

While murine fecal collection is central to microbiome research, there are a number of practical considerations that may vary during fecal sample collection, including time to sample storage, time of day the sample is collected, and position within the colon during terminal collections. While the need to control these factors is recognized, the relative effect on microbial community of duration at room temperature, time of day, and hindgut position, in the context of a known biological variable, is unclear. To answer these questions, and assess reproducibility of results across different microbiome compositions, parallel experiments were performed to investigate the effect of those factors on the microbiome of age- and sex-matched isogenic mice colonized with two different vendor-origin microbiomes.

Results

16S rRNA amplicon sequencing data from flash-frozen fecal samples showed no statistical difference in alpha or beta diversity compared to samples incubated for 1, 2, 3, 4, 6, and 9 hours at room temperature. Overall, samples collected in the AM period showed greater richness and alpha-diversity compared to samples collected in the PM period. While a significant effect of time was detected in all hindgut regions, the effect increased from cecum to distal colon. When using two vendor-origin microbiomes as a biological variable, its effect size vastly outweighed the effect size of the time samples spent at room temperature, the time of day samples were collected, and the position within the colon from which samples were collected.

Conclusions

This study has highlighted multiple scenarios encountered in microbiome research that may affect outcome measures of microbial diversity and composition. Unexpectedly, delayed time to sample cold storage up to nine hours did not affect the alpha or global beta diversity of fecal sample. We then presented evidence of location- and time-dependent effects within the hindgut on microbial richness, diversity, and composition. We finally demonstrated a relatively low effect size of these technical factors when compared to a primary experimental factor with large intergroup variability.
Chromatin states contribute to coordinated allelic transcriptional bursting to drive iPSC reprogramming
Authors: Parichitran A , Naik HC , Naskar AJ , Bammidi LS , Gayen S
Published: July 2023

Molecular mechanisms behind the reprogramming of somatic cells to induced pluripotent stem cells (iPSC) remain poorly understood. While dynamic changes in gene expression are considered to drive reprogramming, the contribution of individual alleles of genes to reprogramming remains unexplored. It is thought that two alleles of a gene can transcribe independently or coordinatedly, which in turn can lead to temporal expression heterogeneity with potentially distinct impacts on cell fate. Here, we profiled genome-wide transcriptional burst kinetics with an allelic resolution during the reprogramming of mouse embryonic fibroblast (MEF) to iPSC. We show that many genes involved in iPSC reprogramming pathways exhibit bursty expression and contribute to dynamic autosomal random monoallelic expression (aRME). Moreover, we find that the degree of coordination of allelic bursting differs among genes and changes dynamically during iPSC reprogramming. Importantly, we show that alleles of many reprogramming-related genes burst in a highly coordinated fashion. ATAC-seq analysis revealed that coordination of allelic bursting is linked to allelic chromatin accessibility. Consistently, we show that highly coordinated genes are enriched with chromatin accessibility regulators such as H3K36me3, H3K27ac, histone variant H3.3 and BRD4. Collectively, our study demonstrates that chromatin states contribute to coordinated allelic bursting to fine-tune the expression of genes involved in iPSC reprogramming and provides insights into the implications of allelic bursting coordination in cell fate specification.

Abstract Figure
A singular PpaA/AerR-like protein inRhodospirillum rubrumrules beyond the boundaries of photosynthesis in response to the intracellular redox state
Authors: Godoy Manuel S. , de Miguel Santiago R. , Prieto M. Auxiliadora
Published: July 2023

Photosynthesis (PS) in Purple Non-Sulphur Bacteria (PNSB) is strictly controlled to avoid energy consumption and to prevent oxidative stress when oxygen is present. PpsR, a transcriptional repressor codified in the Photosynthetic Gene Cluster (PGC), is one of the main players in the regulation of PS related genes. In some cases, PpsR do not sense the environmental cue by itself but delegates this task to another protein like PpaA/AerR anti-repressors, which can ultimately affect PpsR affinity to some promoter regions. In this work, the effects of locus Rru_A0625 product (HP1) on PS regulation ofRhodospirillum rubrum, were studied by mutation/complementation and transcriptomic strategies. Rru_A0625 is located next toppsRgene, just like other PpaA/AerR members, and its deletion annuls pigment synthesis in dark micro/anaerobic growth conditions. HP1 shows similarity to PpaA/AerR anti-repressors family, although it does not possess their typical cobalamin binding domain. A transcriptomic analysis of Rru_A0625 deletion mutant showed that HP1 not only has effects on bacterioclorophyll and carotenoid biosynthesis, but also many other biological processes in the cell. The most notorious is the impact on the transcription of the nitrogenase complex components and some accessory proteins. Our results suggest that this new member of the PpaA/AerR family has evolved losing the canonical cobalamin binding domain, but not the redox sensing capability, conserving a not fully understood mechanism of PS regulation.

IMPORTANCE

Rhodospirillum rubrumvast metabolic versatility places it as a remarkable model bacterium and an excellent biotechnological chassis. The key component of PS studied in this work (HP1) stands out among the other members of PpaA/AerR anti-repressors family since it lacks the most conserved motif they all share: the cobalamin B-12 binding motif. Even with a minimized and barely recognizable aminoacidic sequence, HP1 stills controls PS as the other members of the family, allowing a fast response to changes in the redox state of the cell. This work also shows that HP1 absence affects genes form relevant biological processes other than PS, including nitrogen fixation and stress response. From a biotechnological perspective, HP1 could be manipulated in approaches where PS is not necessary, such hydrogen or polyhydroxyalkanoates production, to suppress unnecessary energy burden.
Intracellular sphingolipid sorting drives membrane phase separation in the yeast vacuole
Authors: Kim Hyesoo , Budin Itay
Published: July 2023

The yeast vacuole membrane can phase separate into ordered and disordered domains, a phenomenon that is required for micro-lipophagy under nutrient limitation. Here we report that sorting of sphingolipids (SLs) into the vacuole membrane controls this process. We first developed a vacuole isolation method to identify lipidome changes during the onset of phase separation in early stationary stage cells. We found that phase separated vacuoles are characterized by increases in lipid raft-forming components not found in the whole cell, including a dramatic change in SL composition. Sorting of both SLs and ergosterol into the vacuole membrane is dependent on Npc2, the yeast homologue of the Niemann-Pick Type C2 lipid transporter. Genetic dissection of SL biosynthesis revealed that the composition of vacuole SLs modulates membrane phase separation and micro-lipophagy under glucose restriction. These results show that lipid trafficking can drive membrane phase separationin vivoand identify SLs as key mediators of this process in yeast.
Monitoring integrated stress response in liveDrosophila
Authors: Lidsky Peter V. , Yuan Jing , Lashkevich Kseniya A. , Dmitriev Sergey E. , Andino Raul
Published: July 2023

Cells exhibit stress responses to various environmental changes. Among these responses, the integrated stress response (ISR) plays a pivotal role as a crucial stress signaling pathway. While extensive ISR research has been conducted on cultured cells, our understanding of its implications in multicellular organisms remains limited, largely due to the constraints of current techniques that hinder our ability to track and manipulate the ISR in vivo. To overcome these limitations, we have successfully developed an internal ribosome entry site (IRES)-based fluorescent reporter system. This innovative reporter enables us to label Drosophila cells, within the context of a living organism, that exhibit eIF2 phosphorylation-dependent translational shutoff – a characteristic feature of the ISR and viral infections. Through this methodology, we have unveiled tissue- and cell-specific regulation of stress response in Drosophila flies and have even been able to detect stressed tissues in vivo during virus and bacterial infections. To further validate the specificity of our reporter, we have engineered ISR-null eIF2αS50A mutant flies for stress response analysis. Our results shed light on the tremendous potential of this technique for investigating a broad range of developmental, stress, and infection-related experimental conditions. Combining the reporter tool with ISR-null mutants establishes Drosophila as an exceptionally powerful model for studying the ISR in the context of multicellular organisms.
Multiple embryonic sources converge to form the pectoral girdle skeleton in zebrafish
Authors: Kuroda Shunya , Lalonde Robert L. , Mansour Thomas A. , Mosimann Christian , Nakamura Tetsuya
Published: July 2023

The morphological transformation of the pectoral/shoulder girdle is fundamental to the water-to-land transition in vertebrate evolution. Although previous studies have resolved the embryonic origins of the tetrapod shoulder girdle, those of the fish pectoral girdle remain uncharacterized, creating a gap in the understanding of girdle transformation mechanisms from fish to modern tetrapods. Here, we identified the embryonic origins of the pectoral girdle of zebrafish (Danio rerio), including the cleithrum as an ancestral pectoral girdle element lost in extant tetrapods. Our combinatorial approach of photoconversion and genetic cell lineage tracing mapped that cleithrum development combines three adjoining embryonic populations: cranial neural crest cells and lateral plate mesoderm-derivatives (trunk lateral plate mesoderm and cardiopharyngeal mesoderm-associated cells). The topographical position of the cleithrum at the head/trunk interface is a shared characteristic among cleithrum-bearing fish, thus its multiple embryonic origins are likely a conserved feature. Moreover, a comparison of the pectoral girdle progenitors between aquatic fish and extant amniotes suggests that cleithrum loss is associated with the disappearance of its unique developmental environment by the insertion of the neck lateral plate mesoderm into the head/trunk interface. Overall, our study establishes an embryological framework for pectoral/shoulder girdle formation and their evolutionary trajectories from their origin in water to diversification on land.
Hif-2αprogrammes oxygen chemosensitivity in chromaffin cells
Authors: Prange-Barczynska Maria , Jones Holly A. , Sugimoto Yoichiro , Cheng Xiaotong , Lima Joanna D. C. C. , Ratnayaka Indrika , Douglas Gillian , Buckler Keith J. , Ratcliffe Peter J. , Keeley Thomas P. , Bishop Tammie
Published: July 2023

The study of transcription factors that determine specialised neuronal functions has provided invaluable insights into the physiology of the nervous system. Peripheral chemoreceptors are neurone-like electro-physiologically excitable cells that link the oxygen content of arterial blood to the neuronal control of breathing. In the adult, this oxygen chemosensitivity is exemplified by the Type I cells of the carotid body and recent work has revealed one isoform of the transcription factor HIF, HIF-2α, to have a non-redundant role in the development and function of that organ. Here we show that the activation of HIF-2α, including isolated overexpression alone, is sufficient to induce oxygen chemosensitivity in the otherwise unresponsive adult adrenal medulla. This phenotypic change in the adrenal medulla was associated with retention of extra-adrenal paraganglioma-like tissues that resemble the foetal organ of Zuckerkandl and also manifest oxygen chemosensitivity. Acquisition of chemosensitivity was associated with changes in the adrenal medullary expression of classes of genes that are ordinarily characteristic of the carotid body, including G-protein regulators and atypical subunits of mitochondrial cytochrome oxidase. Overall, the findings suggest that, at least in certain tissues, HIF-2α acts as a phenotypic driver for cells that display oxygen chemosensitivity, providing a route to mechanistic understanding.
SpeckleNN: a unified embedding for real-time speckle pattern classification in X-ray single-particle imaging with limited labeled examples
Authors: Wang Cong , Florin Eric , Chang Hsing-Yin , Thayer Jana , Yoon Chun Hong
Published: July 2023

With X-ray free-electron lasers (XFELs), it is possible to determine the three-dimensional structure of noncrystalline nanoscale particles using X-ray single-particle imaging (SPI) techniques at room temperature. Classifying SPI scattering patterns, or `speckles', to extract single-hits that are needed for real-time vetoing and three-dimensional reconstruction poses a challenge for high-data-rate facilities like the European XFEL and LCLS-II-HE. Here, we introduce SpeckleNN, a unified embedding model for real-time speckle pattern classification with limited labeled examples that can scale linearly with dataset size. Trained with twin neural networks, SpeckleNN maps speckle patterns to a unified embedding vector space, where similarity is measured by Euclidean distance. We highlight its few-shot classification capability on new never-seen samples and its robust performance despite having only tens of labels per classification category even in the presence of substantial missing detector areas. Without the need for excessive manual labeling or even a full detector image, our classification method offers a great solution for real-time high-throughput SPI experiments.
Safety risk assessment of aircraft EWIS based on the improved combined weight and cloud model
Authors: Sang YiQin , Li Huang , Ge Hongjuan , Gao Cong , Hu Yinxiao , Jin Hui
Published: July 2023

Purpose

This study aims to conduct the aircraft electrical wiring interconnection system (EWIS) safety risk assessment process abundantly and hierarchically and establish the assessment index system considering the weights and interrelationships of different levels of indices.

Design/methodology/approach

Due to the failure of EWIS being multifactorial, hidden and diverse, this paper divides the factors influencing the failure of EWIS into 3 primary indices, 13 secondary indices and 38 tertiary indices. Taking open circuit failure (OCF) and short circuit failure (SCF) as examples, calculate the weights of assessment indices based on the triangular fuzzy number analytic hierarchy process (TFNAHP) and triangular fuzzy number decision-making trial and evaluation laboratory (TFNDEMATEL). The cloud model (CM) divides the risk levels and obtains the safety risk assessment results. The comparative analyses of different weight calculation methods, different failure modes and different aircraft EWIS zones verify the effectiveness and practicability of the proposed method.

Findings

The results show that the proposed method aligns more with the actual situation than other methods. Also, the results identify key focus objects in EWIS safety risk assessment, such as the surrounding environmental factors among the primary indices having the most significant influence on OCF and SCF, the risk level of SCF being higher than that of OCF, etc.

Originality/value

This paper proposes a safety risk assessment index system for aircraft EWIS based on the cable parameters, surrounding environmental factors, installation and protection methods. The weight assignment is added to the assessment index system, and the safety risk assessment model is constructed by combining TFNAHP, TFNDEMATEL and CM.
Determination of heavy metals in cow's and buffalo's fresh raw milk from different areas of Pakistan
Authors: Abid Kanza , Shams Zafar Iqbal , Tahir Muhammad Suleman , Zubair Arif
Published: July 2023

Purpose

The presence of heavy metals in milk causes many acute and chronic physiological dysfunctions in human organs. The present study aims to investigate the heavy metals in cow's and buffalo's milk of two major cities, Karachi and Gujranwala, Pakistan to estimate metal intake by humans from this source.

Design/methodology/approach

In total, 48 milk samples from 2 cities were drawn from animals' udder to avoid contamination. Each sample was digested with nitric acid at 105 oC (degree Celsius) on a pre-heated electric hot plate to investigate the metals by atomic absorption spectroscopy (flame type). Air-acetylene technique analyzed chromium, cadmium and lead, and the hydride method analyzed arsenic in the milk samples.

Findings

The results revealed the highest mean lead concentration (19.65 ± 43.86 ppb) in the milk samples, followed by chromium (2.10 ± 2.33 ppb) and arsenic (0.48 ± 0.73 ppb). Cadmium was not detected in any sample, assuming cadmium's occurrence was below the detection level. The concentrations of all the metals in the samples of the two cities do not differ statistically. Lead concentrations in the buffalo's milk were higher than in cow's milk (p < 0.05). However, the concentrations of arsenic and chromium between buffalo's and cow's milk do not differ statistically. The present study reveals a lower level of metals in the milk than those conducted elsewhere. The mean concentrations of all the metals met the World Health Organization's (WHO) safety guidelines (1993).

Research limitations/implications

Although cadmium causes toxicity in the human body, cadmium could not be measured because cadmium's concentration was below the detection level, which is 1 ppb.

Practical implications

This study will help reduce the toxic metals in our environment, and the sources of heavy metals, particularly from the industrial sector could be identified. The feed and water consumed by the milking animals could be carefully used for feeding them.

Social implications

This study will help reduce the diseases and malfunction of human organs and organ systems since these heavy metals cause toxicity and carcinogenicity in humans. Arsenic and chromium cause cancer while lead causes encephalopathy (a brain disease).

Originality/value

The study reports heavy metal concentrations in the two attributes of four independent variables of raw milk samples that were scarcely reported from Pakistan.