bluuebunny/crossref_metadata_2025 huggingface dataset:
Aequorivita vitellina sp. nov. and Aequorivita xiaoshiensis sp. nov., isolated from marine sediment
Authors: Wang Ya-Wei , Zhang Jing , Wang Shu-Xin , Du Zong-Jun , Mu Da-Shuai
Published: March 2023

Two Gram-stain-negative, strictly aerobic, chemoheterotrophic, short-rod-shaped and non-motile strains, forming yellow colonies and designated F47161T and F64183T, were isolated from marine sediment of Xiaoshi Island, Wei Hai, PR China. Strain F47161T grew at 15–37 °C (optimally at 30 °C) and pH 6.0–9.0 (optimally at pH 7.5) and in the presence of 1–9 % (w/v) NaCl (optimally at 3 %). Strain F64183T grew at 10–37 °C (optimally at 30 °C) and pH 6.0–8.5 (optimally at pH 7.0) and in the presence of 1–8 % (w/v) NaCl (optimally at 3 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that F47161T and F64183T were related to members of the genus

Aequorivita

. The strains shared 97.4 % 16S rRNA gene sequence similarity to each other. F47161T and F64183T shared highest 16S rRNA gene sequence similarity to

Aequorivita sinensis

JCM 19789T, and the values were 97.5 % and 98.4 %, respectively. The predominant cellular fatty acids of both F64183T and F47161T were iso-C15 : 0 and iso-C17 : 0 3-OH, but the predominant fatty acids of F47161T also included anteiso-C15 : 0. The sole respiratory quinone of F47161T and F64183T was menaquinone 6 (MK-6), consistent with that observed for all related strains. Between F47161T and F64183T, the average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) values were 75.8 % and 20.5 %, respectively, and between the novel isolates (F47161T and F64183T) and

A. sinensis

JCM 19789T they were 76.0 % and 94.2 % and 20.6 % and 57.1 %, respectively. The genomic DNA G+C contents of F47161T and F64183T was 37.3 % and 34.5 %, respectively. The polar lipid profiles of F47161T and F64183T contained phosphatidylethanolamine, two aminolipids, one glycolipid, one phosphoglycolipid and two unidentified polar lipids. Differential phenotypic and genotypic characteristics of the two strains indicated that the two strains should be classified as representing two novel species of the genus Aequorivita, for which the names Aequorivita vitellina sp. nov. and Aequorivita xiaoshiensis sp. nov. are proposed. The type strains are F47161T (=MCCC 1H00509T=KCTC 92017T) and F64183T (=MCCC 1H00507T=KCTC 92016T), respectively.
Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia
Authors: Dusadeepong Rutaiwan , Delvallez Gauthier , Cheng Sokleaph , Meng Soda , Sreng Navin , Letchford Joanne , Choun Kimcheng , Teav Syna , Hardy Liselotte , Jacobs Jan , Hoang Tuyet , Seemann Torsten , Howden Benjamin P. , Glaser Philippe , Stinear Timothy P. , Vandelannoote Koen
Published: March 2023

In early 2020, the Medical Biology Laboratory of the Pasteur Institute of Cambodia isolated an unusually high number of fluoroquinolone-resistant

Salmonella enterica

subspecies

enterica

serovar Paratyphi A strains during its routine bacteriological surveillance activities in Phnom Penh, Cambodia. A public-health investigation was supported by genome sequencing of these Paratyphi A strains to gain insights into the genetic diversity and population structure of a potential outbreak of fluoroquinolone-resistant paratyphoid fever. Comparative genomic and phylodynamic analyses revealed the 2020 strains were descended from a previously described 2013–2015 outbreak of Paratyphi A infections. Our analysis showed sub-lineage 2.3.1 had remained largely susceptible to fluoroquinolone drugs until 2015, but acquired chromosomal resistance to these drugs during six separate events between late 2012 and 2015. The emergence of fluoroquinolone resistance was rapidly followed by the replacement of the original susceptible Paratyphi A population, which led to a dramatic increase of fluoroquinolone-resistant blood-culture-confirmed cases in subsequent years (2016–2020). The rapid acquisition of resistance-conferring mutations in the Paratyphi A population over a 3 year period is suggestive of a strong selective pressure on that population, likely linked with fluoroquinolone use. In turn, emergence of fluoroquinolone resistance has led to increased use of extended-spectrum cephalosporins like ceftriaxone that are becoming the drug of choice for empirical treatment of paratyphoid fever in Cambodia.
High temperatures augment inhibition of parasites by a honey bee gut symbiont
Authors: Palmer-Young Evan C , Markowitz Lindsey M , Huang Wei-Fone , Evans Jay D
Published: March 2023

Temperature affects growth, metabolism, and interspecific interactions in microbial communities. Within animal hosts, gut bacterial symbionts can provide resistance to parasitic infections. Infection can also be shaped by host body temperature. However, the effects of temperature on the antiparasitic activities of gut symbionts have seldom been explored. TheLactobacillus-rich gut microbiota of facultatively endothermic honey bees is subject to seasonal and ontogenetic changes in host temperature that could alter the effects of symbionts against parasites. We used cell cultures of aLactobacillussymbiont and an important trypanosomatid gut parasite of honey bees to test the potential for temperature to shape parasite-symbiont interactions.

We found that symbionts showed greater heat tolerance than parasites and chemically inhibited parasite growth via production of acids. Acceleration of symbiont growth and acid production at high temperatures resulted in progressively stronger antiparasitic effects across a temperature range typical of bee colonies. Consequently, the presence of symbionts reduced both peak growth rate and heat tolerance of parasites. Results suggest that the endothermic behavior of honey bees could potentiate the effectiveness of gut symbionts that limit parasites’ ability to withstand high temperature, implicating thermoregulation as a reinforcer of core symbioses and possibly microbiome-mediated antiparasitic defense.

IMPORTANCE

Two factors that shape the resistance of animals to infection are body temperature and gut microbiota. However, temperature can also alter interactions among microbes, raising the question of whether and how temperature changes the antiparasitic effects of gut microbiota. Honey bees are agriculturally important hosts of diverse parasites and infection-mitigating gut microbes. They can also socially regulate their body temperatures to an extent unusual for an insect. We show that high temperatures found in honey bee colonies augment the ability of a gut bacterial symbiont to inhibit growth of a common bee parasite and reduce the parasite’s ability to grow at high temperatures. This suggests that fluctuations in colony and body temperatures across life stages and seasons could alter the protective value of bees’ gut microbiota against parasites, and that temperature-driven changes in gut microbiota could be an underappreciated mechanism by which temperature— including endothermy and fever— alters animal infection.
HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes
Authors: Gupta Sagar , Nerli Santrupti , Kandy Sreeja Kutti , Mersky Glenn L. , Sgourakis Nikolaos G.
Published: March 2023

The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune surveillance. Accurate modeling of peptide/HLA (pHLA, the human MHC) structures has been mired by conformational diversity of the central peptide residues, which are critical for recognition by T cell receptors. Here, analysis of X-ray crystal structures within a curated database (HLA3DB) shows that pHLA complexes encompassing multiple HLA allotypes present a discrete set of peptide backbone conformations. Leveraging these representative backbones, we employ a regression model trained on terms of a physically relevant energy function to develop a comparative modeling approach for nonamer peptide/HLA structures named RepPred. Our method outperforms the top pHLA modeling approach by up to 19% in terms of structural accuracy, and consistently predicts blind targets not included in our training set. Insights from our work provide a framework for linking conformational diversity with antigen immunogenicity and receptor cross-reactivity.
Evaluation of In2Care® mosquito stations for suppression of the Australian backyard mosquito,Aedes notoscriptus
Authors: Paris Véronique , Bell Nick , Schmidt Thomas L. , Endersby-Harshman Nancy M. , Hoffmann Ary A.
Published: March 2023

Aedes notoscriptus(Skuse) is a container-inhabiting mosquito endemic to Australia that vectors arboviruses and is suspected to transmitMycobacterium ulcerans, the cause of Buruli ulcer. We evaluated the effectiveness of the In2Care® station, which suppresses mosquito populations via the entomopathogenic fungus,Beauveria bassiana, and the insect growth regulator pyriproxyfen, the latter of which is autodisseminated among larval habitats by contaminated mosquitoes. A field trial was conducted using 110 In2Care® stations in a 50,000 m2area and results were compared to four control areas that did not receive the treatment. Efficacy was evaluated by comparing egg counts and measuring larvicidal impact in surrounding breeding sites. Laboratory experiments validated the effect ofB. bassianaon adult survival. Results of this field trial indicate that, six weeks after the In2Care® stations were deployed, treatment site ovitraps contained 43% fewer eggs than control site ovitraps, and 33% fewer eggs after ten weeks, suggesting that the In2Care® station was able to reduce the egg density ofAe. notoscriptus. Population reduction remained evident for up to three weeks after In2Care® stations were removed. Treatment site ovitraps had significantly fewerAe. notoscriptuseclosing than control site ovitraps, confirming the pyriproxyfen autodissemination feature of the stations. An average reduction of 50% in adult eclosion was achieved. Exposure toB. bassianaresulted in four-times higher mortality among adult mosquitoes. Additionally, using fresh In2Care® nettings led to an 88% decrease in average survival compared to four-week-old nettings. The use of In2Care® stations has potential for suppressingAe. notoscriptusegg density.
Quantification of microvascular lesions in the central retinal field: could it predict the severity of diabetic retinopathy?
Authors: Fernández-Carneado Jimena , Almazán-Moga Ana , Ramírez-Lamelas Dolores T. , Cuscó Cristina , de la Fuente José Ignacio Alonso , Pastor Jimeno José Carlos , López-Gálvez María Isabel , Ponsati Berta
Published: March 2023

Objective

Diabetic retinopathy (DR) is a neurodegenerative disease characterized by the presence of microcirculatory lesions. Among them, microaneurysms (MAs) are the first observable hallmark of early ophthalmological changes. The present work aims at studying whether the quantification of MA, haemorrhages (Hmas) and hard exudates (HEs) in the central retinal field (CRF) could have a predictive value on DR severity.

Research Design and Methods

Retinal lesions (MAs, Hmas and HEs) were quantified in the CRF of 160 retinographies from diabetic patients from the IOBA’s reading center, previously classified by two expert readers with the 3 fields-Joslin system. Samples included different disease severity levels and excluded proliferating forms: no DR (n=30), mild non-proliferative (n=30), moderate (n=50) and severe (n=50).

Results

Quantification of MAs, Hmas, and HEs revealed an increase trend of these lesions as DR severity progresses. Differences between severity levels were statistically significant, suggesting that the analysis of the CRF provides valuable information on severity level and could be used as a valuable tool to assess DR grading in the clinical practice.

Conclusions

Even though further validation is needed, the counting of microvascular lesions in the central retinal field can be proposed as a rapid screening system to classify DR patients with different stages of severity according to the international classification.
Peripheral blood transcriptomic profiling indicates molecular mechanisms commonly regulated by binge-drinking and placebo-effects
Authors: Shetty Amol Carl , Sivinski John , Cornell Jessica , Sadzewicz Lisa , Mahurkar Anup , Wang Xing-Qun , Colloca Luana , Lin Weihong , Kane Maureen A. , Seneviratne Chamindi
Published: March 2023

Molecular changes associated with alcohol consumption arise from complex interactions between pharmacological effects of alcohol, psychological/placebo context surrounding drinking, and other environmental and biological factors. The goal of this study was to tease apart molecular mechanisms regulated by pharmacological effects of alcohol - particularly at binge-drinking, from underlying placebo effects. Transcriptome-wide RNA-seq analyses were performed on peripheral blood samples collected from healthy heavy social drinkers (N=16) enrolled in a 12-day randomized, double-blind, cross-over human laboratory trial testing three alcohol doses: Placebo, moderate (0.05g/kg (men), 0.04g/kg (women)), and binge (1g/kg (men), 0.9g/kg (women)), administered in three 4-day experiments, separated by minimum of 7-day washout periods. Effects of beverage doses on the normalized gene expression counts were analyzed within each experiment compared to its own baseline using paired-t-tests. Differential expression of genes (DEGs) across experimental sequences in which each beverage dose was administered, as well as responsiveness to regular alcohol compared to placebo (i.e., pharmacological effects), were analyzed using generalized linear mixed-effects models. The 10% False discovery rate-adjusted DEGs varied across experimental sequences in response to all three beverage doses. We identified and validated 22 protein coding DEGs potentially responsive to pharmacological effects of binge and medium doses, of which 11 were selectively responsive to binge dose. Binge-dose significantly impacted the Cytokine-cytokine receptor interaction pathway (KEGG: hsa04060) across all experimental-sequences that it was administered in, and during dose-extending placebo. Medium dose and placebo impacted pathways hsa05322, hsa04613, and hsa05034, in the first two and last experimental sequences, respectively. In summary, our findings add novel, and confirm previously reported data supporting dose-dependent effects of alcohol on molecular mechanisms and suggest that the placebo effects may induce molecular responses within the same pathways regulated by alcohol. Innovative study designs are required to validate molecular correlates of placebo effects underlying drinking.
Deep learning for quantitative MRI brain tumor analysis
Authors: Tampu Iulian Emil , Haj-Hosseini Neda , Blystad Ida , Eklund Anders
Published: March 2023

The infiltrative nature of malignant gliomas results in active tumor spreading into the peritumoral edema, which is not visible in conventional magnetic resonance imaging (cMRI) even after contrast injection. MR relaxometry (qMRI) measures relaxation rates dependent on tissue properties, and can offer additional contrast mechanisms to highlight the non-enhancing infiltrative tumor. The aim of this study is to investigate if qMRI data provides additional information compared to cMRI sequences (T1w, T1wGd, T2w, FLAIR), when considering deep learning-based brain tumor (1) detection and (2) segmentation. A total of 23 patients with histologically confirmed malignant glioma were retrospectively included in the study. Quantitative MR imaging was used to obtain R1(1/T1), R2(1/T2) and proton density maps pre- and post-gadolinium contrast injection. Conventional MR imaging was also performed. A 2D CNN detection model and a 2D U-Net were trained on transversal slices (n=528) using either cMRI or a combination of qMRI pre- and post-contrast data for tumor detection and segmentation, respectively. Moreover, trends in quantitative R1and R2rates of regions identified as relevant for tumor detection by model explainability methods were qualitatively analyzed. Tumor detection and segmentation performance for models trained with a combination of qMRI pre- and post-contrast was the highest (detection MCC=0.72, segmentation Dice=0.90), however, improvements were not statistically significant compared to cMRI (detection MCC=0.67, segmentation Dice=0.90). The analysis of the relaxation rates of the relevant regions identified using model explainability methods showed no differences between models trained on cMRI or qMRI. Relevant regions which fell outside the annotation showed changes in relaxation rates after contrast injection similar to those within the annotation, when looking at majority of the individual cases. A similar trend could not be seen when looking at relaxation trends over all the dataset. In conclusion, models trained on qMRI data obtain similar performance to those trained on cMRI data, with the advantage of quantitatively measuring brain tissue properties within the scan time (11.8 minutes for qMRI with and without contrast, and 12.2 minutes for cMRI). Moreover, when considering individual patients, regions identified by model explainability methods as relevant for tumor detection outside the manual annotation of the tumor showed changes in quantitative relaxation rates after contrast injection similar to regions within the annotation, suggestive of infiltrative tumor in the peritumoral edema.
standard-GEM: standardization of open-source genome-scale metabolic models
Authors: Anton Mihail , Almaas Eivind , Benfeitas Rui , Benito-Vaquerizo Sara , Blank Lars M. , Dräger Andreas , Hancock John M. , Kittikunapong Cheewin , König Matthias , Li Feiran , Liebal Ulf W. , Lu Hongzhong , Ma Hongwu , Mahadevan Radhakrishnan , Mardinoglu Adil , Nielsen Jens , Nogales Juan , Pagni Marco , Papin Jason A. , Patil Kiran Raosaheb , Price Nathan D. , Robinson Jonathan L. , Sánchez Benjamín J. , Suarez-Diez Maria , Sulheim Snorre , Svensson L. Thomas , Teusink Bas , Vongsangnak Wanwipa , Wang Hao , Zeidan Ahmad A. , Kerkhoven Eduard J.
Published: March 2023

The field of metabolic modelling at the genomescale continues to grow with more models being created and curated. This comes with an increasing demand for adopting common principles regarding transparency and versioning, in addition to standardisation efforts regarding file formats, annotation and testing. Here, we present a standardised template for git-based and GitHub-hosted genome-scale metabolic models (GEMs) supporting both new models and curated ones, following FAIR principles (findability, accessibility, interoperability, and reusability), and incorporating bestpractices.standard-GEMfacilitates the reuse of GEMs across web services and platforms in the metabolic modelling field and enables automatic validation of GEMs. The use of this template for new models, and its adoption for existing ones, paves the way for increasing model quality, openness, and accessibility with minimal effort.

Availability

standard-GEMis available fromgithub.com/MetabolicAtlas/standard-GEMunder the conditions of the CC BY 4.0 licence along with additional supporting material.
Transcriptomic Prediction of Breeding Values in Loblolly Pine
Authors: Festa Adam R , Whetten Ross
Published: March 2023

Phenotypic variation in forest trees can be partitioned into subsets controlled by genetic variation and by environmental factors, and heritability expressed as the proportion of total phenotypic variation attributed to genetic variation. Applied tree breeding programs can use matrices of relationships, based either on recorded pedigrees in structured breeding populations or on genotypes of molecular genetic markers, to model genetic covariation among related individuals and predict genetic values for individuals for whom no phenotypic measurements are available. This study tests the hypothesis that genetic covariation among individuals of similar genetic value will be reflected in shared patterns of gene expression. We collected gene expression data by high-throughput sequencing of RNA isolated from pooled seedlings from parents of known genetic value, and compared alternative approaches to data analysis to test this hypothesis. Selection of specific sets of transcripts increased the predictive power of models over that observed using all transcripts. Using information on presence of putative mutations in protein-coding sequences increased predictive accuracy for some traits but not for others. Known pedigree relationships are not required for this approach to modeling genetic variation, so it has potential to allow broader application of genetic covariance modeling to natural populations of forest trees.
READRetro: Natural Product Biosynthesis Planning with Retrieval-Augmented Dual-View Retrosynthesis
Authors: Lee Seul , Kim Taein , Choi Min-Soo , Kwak Yejin , Park Jeongbin , Hwang Sung Ju , Kim Sang-Gyu
Published: March 2023

Elucidating the biosynthetic pathways of natural products has been a major focus of biochemistry and pharmacy. However, predicting the whole pathways from target molecules to metabolic building blocks remains a challenge. Here we propose READRetro as a practical bio-retrosynthesis tool for planning the biosynthetic pathways of natural products. READRetro effectively resolves the tradeoff between generalizability and memorability in bio-retrosynthesis by implementing two separate modules; each module is responsible for either generalizability or memorability. Specifically, READRetro utilizes a rule-based retriever for memorability and an ensemble of two dual-representation-based deep learning models for generalizability. Through extensive experiments, READRetro was demonstrated to outperform existing models by a large margin in terms of both generalizability and memorability. READRetro was also capable of predicting the known pathways of complex plant secondary metabolites such as monoterpene indole alkaloids, demonstrating its applicability in the real-world bio-retrosynthesis planning of natural products. A website (https://readretro.net) and open-source code have been provided for READRetro, a practical tool with state-of-the-art performance for natural product biosynthesis research.
Determining the neuronal ensembles underlying sex-specific social impairments following adolescent intermittent ethanol exposure
Authors: Towner Trevor T. , Goyden Matt A. , Coleman Harper J. , Drumm Mary K. , Ritchie Isabella P. , Lieb Kayla R. , Varlinskaya Elena I. , Werner David F.
Published: March 2023

Binge drinking during adolescence can have behavioral and neurobiological consequences. We have previously found that adolescent intermittent ethanol (AIE) exposure produces a sex-specific social impairment in rats. The prelimbic cortex (PrL) regulates social behavior, and alterations within the PrL resulting from AIE may contribute to social impairments. The current study sought to determine whether AIE-induced PrL dysfunction underlies social deficits in adulthood. We first examined social stimulus-induced neuronal activation of the PrL and several other regions of interest implicated in social behavior. Male and female cFos-LacZ rats were exposed to water (control) or ethanol (4 g/kg, 25% v/v) via intragastric gavage every other day between postnatal day (P) 25 and 45 (total 11 exposures). Since cFos-LacZ rats express β-galactosidase (β-gal) as a proxy for cFos, activated cells that express of β-gal can be inactivated by Daun02. β-gal expression in most ROIs was elevated in socially tested adult rats relative to home cage controls, regardless of sex. However, differences in social stimulus-induced β-gal expression between controls and AIE-exposed rats was evident only in the PrL of males. A separate cohort underwent PrL cannulation surgery in adulthood and were subjected to Daun02-induced inactivation. Inactivation of PrL ensembles previously activated by a social stimulus led to a reduction of social behavior in control males, with no changes evident in AIE-exposed males or females. These findings highlight the role of the PrL in male social behavior and suggest an AIE-associated dysfunction of the PrL may contribute to social deficits following adolescent ethanol exposure.
Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins
Authors: Faber Gabriel P. , Hauschner Hagit , Atrash Mohammad Khaled , Bilinsky Liat , Shav-Tal Yaron
Published: March 2023

Endogenous gene knock-in using CRIPSR is becoming the standard for fluorescent tagging of endogenous proteins. Some protocols, particularly those that utilize insert cassettes that carry a fluorescent protein tag, can yield many types of cells with off-target insertions that have diffuse fluorescent signal throughout the whole cell in addition to scarce cells with on-target gene insertions that show the correct sub-cellular localization of the tagged protein. As such, when searching for cells with on-target integration using flow cytometry, the off-target fluorescent cells yield a high percentage of false positives. Here, we show that by changing the gating used to select for fluorescence during flow cytometry sorting, namely utilizing the width of the signal as opposed to the area, we can highly enrich for positively integrated cells. Reproducible gates were created to select for even minuscule percentages of correct subcellular signal, and these parameters were validated by fluorescence microscopy. This method is a powerful tool to rapidly enhance the generation of cell-lines with correctly integrated gene knock-ins encoding endogenous fluorescent proteins.
Arteries are finely tuned thermosensors regulating myogenic tone and blood flow
Authors: Phan Thieu X. , Sahibzada Niaz , Ahern Gerard P.
Published: March 2023

In response to changing blood pressure, arteries adjust their caliber to control perfusion. This vital autoregulatory property, termed vascular myogenic tone, stabilizes downstream capillary pressure. We discovered that tissue temperature critically determines myogenic tone. Heating steeply activates tone in skeletal muscle, gut, brain and skin arteries with temperature coefficients (Q10) of ∼11-20. Further, arterial thermosensitivity is tuned to resting tissue temperatures, making myogenic tone sensitive to small thermal fluctuations. Interestingly, temperature and intraluminal pressure are sensed largely independently and integrated to trigger myogenic tone. We show that TRPV1 and TRPM4 mediate heat-induced tone in skeletal muscle arteries. Variations in tissue temperature are known to alter vascular conductance; remarkably, thermosensitive tone counterbalances this effect, thus protecting capillary integrity and fluid balance. In conclusion, thermosensitive myogenic tone is a fundamental homeostatic mechanism regulating tissue perfusion.

One-Sentence Summary

Arterial blood pressure and temperature are integrated via thermosensitve ion channels to produce myogenic tone.
Parabrachial nucleus activity in nociception and pain in awake mice
Authors: Smith Jesse Andrew , Ji Yadong , Lorsung Rebecca , Breault Macauley Smith , Koenig Jeffrey , Cramer Nathan , Masri Radi , Keller Asaf
Published: March 2023

The parabrachial nuclear complex (PBN) is a nexus for aversion, and for the sensory and affective components of pain perception. We have previously shown that, during chronic pain, PBN neurons in anesthetized rodents have amplified activity. We report a method to record from PBN neurons of behaving, head-restrained mice, while applying reproducible noxious stimuli. We find that both spontaneous and evoked activity are higher in awake animals, compared to urethane anesthetized mice. Fiber photometry of calcium responses from CGRP-expressing PBN neurons demonstrates that these neurons respond to nociceptive stimuli. In both males and females with neuropathic or inflammatory pain, responses of PBN neurons remain amplified for at least 5 weeks, in parallel with increased pain metrics. We also show that PBN neurons can be rapidly conditioned to respond to innocuous stimuli, after pairing with nociceptive stimuli. Finally, we demonstrate that changes in PBN neuronal activity are correlated with changes in arousal, measured as changes in pupil diameter.

Significance Statement

The parabrachial complex is a nexus of aversion, including pain. We report a method to record from parabrachial nucleus neurons of behaving mice, while applying reproducible noxious stimuli. This allowed, for the first time, tracking the activity of these neurons over time in animals with neuropathic or inflammatory pain. It also allowed us to show that the activity of these neurons correlates with arousal states, and that these neurons can be conditioned to respond to innocuous stimuli.
Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)
Authors: Georges Arthur , Mijangos Luis , Kilian Andrzej , Patel Hardip , Aitkens Mark , Gruber Bernd
Published: March 2023

Distance measures are widely used for examining genetic structure in datasets that comprise many individuals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci.

We examine the application of distance measures to SNP genotypes and sequence tag presence-absences (SilicoDArT) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization.

Euclidean Distance is the metric of choice in many distance studies. However, other measures may be preferable because of their underlying models of divergence, population demographic history and linkage disequilibrium, because it is desirable to down-weight joint absences, or because of other characteristics specific to the data or analyses. Distance measures for SNP genotype data that depend on the arbitrary choice of reference and alternate alleles (e.g. Bray-Curtis distance) should not be used. Careful consideration should be given to which state is scored zero when applying binary distance measures to sequence tag presence-absences (e.g. Jaccard distance).

Missing values that arise in the SNP discovery process can cause displacement of affected individuals from their natural groupings and artificial inflation of confidence envelopes, leading to potential misinterpretation. Filtering on missing values then imputing those that remain avoids distortion in visual representations. Failure of a distance measure to conform to metric and Euclidean properties is important but only likely to create unacceptable outcomes in extreme cases. Lack of randomness in the selection of individuals (e.g. inclusion of sibs) and lack of independence of both individuals and loci (e.g. polymorphic haploblocks), can lead to substantial and otherwise inexplicable distortions of the visual representations and again, potential misinterpretation.
Individualized Electrode Subset Improves the Calibration Accuracy of an EEG P300-design Brain-Computer Interface for People with Severe Cerebral Palsy
Authors: Tou Si Long Jenny , Warschausky Seth A. , Karlsson Petra , Huggins Jane E.
Published: March 2023

Objective

This study examined the effect of individualized electroencephalogram (EEG) electrode location selection for non-invasive P300-design brain-computer interfaces (BCIs) in people with varying severity of cerebral palsy (CP).

Approach

A forward selection algorithm was used to select the best performing 8 electrodes (of an available 32) to construct an individualized electrode subset for each participant. BCI accuracy of the individualized subset was compared to accuracy of a widely used default subset.

Main Results

Electrode selection significantly improved BCI calibration accuracy for the group with severe CP. Significant group effect was not found for the group of typically developing controls and the group with mild CP. However, several individuals with mild CP showed improved performance. Using the individualized electrode subsets, there was no significant difference in accuracy between calibration and evaluation data in the mild CP group, but there was a reduction in accuracy from calibration to evaluation in controls.

Significance

The findings suggested that electrode selection can accommodate developmental neurological impairments in people with severe CP, while the default electrode locations are sufficient for many people with milder impairments from CP and typically developing individuals.
Single-cell transcriptomics of adult skin VE-cadherin expressing lineages during hair cycle
Authors: Chovatiya Gopal , Li Kefei Nina , Ghuwalewala Sangeeta , Tumbar Tudorita
Published: March 2023

Adult skin homeostasis involves global reorganization of dermal lineages at different stages of the mouse hair growth cycle. Vascular endothelial cadherin (VE-cadherin encoded byCdh5) expressing cells from blood and lymphatic vasculature structures are known to remodel during the adult hair cycle. Here we employ single-cell RNA-sequencing (scRNA-seq) 10x-genomics analysis of FACS-sorted VE-cadherin expressing cells marked via Cdh5-CreER genetic labeling at resting (telogen) and growth (anagen) stage of hair cycle. Our comparative analysis between the two stages uncovers a persistent Ki67+proliferative EC population and documents changes in EC population distribution and gene expression. Global gene expression changes in all the analyzed populations revealed bioenergetic metabolic changes that may drive vascular remodeling during HF growth phase, alongside a few highly restricted cluster-specific gene expression differences. This study uncovers active cellular and molecular dynamics of adult skin endothelial lineages during hair cycle that may have broad implications in adult tissue regeneration and for understanding vascular disease.
AG3D: A low-cost educational 3D printable toolkit for agarose gel electrophoresis
Authors: Barwick Matthew W , Fanucci Sidne , Mbanxa Siso , Buthelezi Khanyisile , Jukes Michael D , Abrahams Garth L , Prinsloo Earl
Published: March 2023

Access to desktop additive manufacturing is growing and the argument could be made for 3D printers to be standard laboratory equipment. The power of the printers lies in the democratisation of scientific equipment. Traditional agarose gel electrophoresis forms a cornerstone of molecular biology research, teaching and learning. Reliable electrophoresis is dependent on a number of factors which include standardized commercial equipment with respect to casting trays, combs, horizontal tanks and power supplies. The aforementioned systems come at a high initial cost; this is before factoring in the costs of standard electrophoresis grade agarose and associated reagent pricing. Here, we present a basic method for the additive manufacturing of a simple 3D printable agarose gel electrophoresis (AGE) unit with a built-in gel casting tray for standard size microscope slide-based AGE; named AG3D. The system presented was validated using different standard agarose-buffers (Tris Acetate EDTA and Tris Borate EDTA) and commercially available base-pair ladders. We provide a comparison between the AG3D and a commercial AGE system in respect to resolving power of the electrophoresis unit and discuss the overall reduction in cost afforded by the AG3D electrophoresis toolkit. The method presented has the potential for application in low resource educational environments by:

Significantly lowering costs through the reduction of reagents (agarose, buffers etc).

Allow for the use of low sample volumes.

Providing an open-source toolkit for modification whether for research or teaching & learning

Graphical abstract

Specifications table
Live cell imaging of ATP levels reveals metabolic compartmentalization within motoneurons and early metabolic changes inFUSALS motoneurons
Authors: Zimyanin Vitaly , Pielka Anne-Marie , Glaß Hannes , Japtok Julia , Martin Melanie , Deussen Andreas , Szewczyk Barbara , Deppmann Chris , Zunder Eli , Andersen Peter M. , Boeckers Tobias M. , Sterneckert Jared , Redemann Stefanie , Storch Alexander , Hermann Andreas
Published: March 2023

Motoneurons are one of the highest energy demanding cell types and a primary target in Amyotrophic lateral sclerosis (ALS), a debilitating and lethal neurodegenerative disorder without currently available effective treatments. Disruption of mitochondrial ultra-structure, transport and metabolism is a commonly reported phenotype in ALS models and can critically affect survival and proper function of motor neurons. However, how changes in metabolic rates contribute to ALS progression are not fully understood yet. Here we utilize hiPCS derived motoneuron cultures and live imaging quantitative techniques to evaluate metabolic rates in Fused in Sarcoma (FUS)-ALS model cells. We show that differentiation and maturation of motoneurons is accompanied by an overall upregulation of mitochondrial components and significant increase in metabolic rates that corresponds to their high energy-demanding state. Detailed compartment-specific live measurements using a fluorescent ATP sensor and FLIM imaging show significantly lower levels of ATP in the somas of cells carrying FUS-ALS mutations. These changes lead to the increased vulnerability of disease motoneurons to further metabolic challenges with mitochondrial inhibitors and could be due to the disruption of mitochondrial inner membrane integrity and an increase in its proton leakage. Furthermore, our measurements demonstrate heterogeneity between axonal and somatic compartments with lower relative levels of ATP in axons. Our observations strongly support the hypothesis that mutated FUS impacts metabolic states of motoneurons and makes them more susceptible to further neurodegenerative mechanisms.
Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA
Authors: Inlow Koe , Tenenbaum Debora , Friedman Larry J. , Kondev Jane , Gelles Jeff
Published: March 2023

Free-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryote Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so is unclear. We used multi-wavelength single-molecule fluorescence microscopy in vitro to examine RapA function in theE. colitranscription cycle. In our experiments, RapA at < 5 nM concentration did not appear to alter transcription initiation, elongation, or intrinsic termination. Instead, we directly observed a single RapA molecule bind specifically to the kinetically stable post-termination complex (PTC) -- consisting of core RNA polymerase (RNAP) bound to dsDNA -- and efficiently remove RNAP from DNA within seconds in an ATP-hydrolysis-dependent reaction. Kinetic analysis elucidates the process through which RapA locates the PTC and the key mechanistic intermediates that bind and hydrolyze ATP. This study defines how RapA participates in the transcription cycle between termination and initiation and suggests that RapA helps set the balance between global RNAP recycling and local transcription re-initiation in proteobacterial genomes.

SIGNIFICANCE

RNA synthesis is an essential conduit of genetic information in all organisms. After transcribing an RNA, the bacterial RNA polymerase (RNAP) must be reused to make subsequent RNAs, but the steps that enable RNAP reuse are unclear. We directly observed the dynamics of individual molecules of fluorescently labeled RNAP and the enzyme RapA as they colocalized with DNA during and after RNA synthesis. Our studies show that RapA uses ATP hydrolysis to remove RNAP from DNA after the RNA is released from RNAP and reveal essential features of the mechanism by which this removal occurs. These studies fill in key missing pieces in our current understanding of the events that occur after RNA is released and that enable RNAP reuse.
Assessing motile cilia coverage and beat frequency in mammalian in-vitro cell culture tissues
Authors: Fradique Ricardo , Causa Erika , Delahousse Clara , Kotar Jurij , Pinte Laetitia , Vallier Ludovic , Vila-Gonzalez Marta , Cicuta Pietro
Published: March 2023

Cilia density, distribution and beating frequency are important parameters lung tissues, for example in diagnostics of Primary Ciliary Dyskinesia, and in the study ofin vitromodels, e.g. derived from induced Pluripotent Stem Cells. Video microscopy can be used to characterise these parameters, but most tools available at the moment are limited in the type of information they can provide, usually only describing the ciliary beat frequency of very small areas, while requiring human intervention and training for their use. We propose a novel and open source method to fully characterise cilia beating frequency and motile cilia coverage in an automated fashion without user intervention. We demonstrate the ability to differentiate between different coverage densities, identifying even small patches of cilia in a larger field of view, and to fully characterise the cilia beating frequency of all moving areas. We also show that the method can be used to combine multiple fields of view to better describe a sample without relying on small pre-selected regions of interest. This is released with a simple graphical user interface for file handling, enabling a full analysis of individual fields of view in a few minutes on a typical personal computer.
Profiles of bacteria isolates and their antimicrobial resistance pattern among housemaids working in communal living residences in Jimma City, Ethiopia
Authors: Ango Tadele Shiwito , Teshome Tizita , Getahun Tesfalem , Mamo Girma , Byadgie Negalgn
Published: March 2023

Background

Bacterial pathogens continued to be the major causes of foodborne gastroenteritis in humans and remained public health important pathogens across the globe. As regards, housemaids operating inside a kitchen could be the source of infection and may transmit disease-inflicting pathogens through infected hands. Profiles of bacteria isolates and their antimicrobial resistance patterns among housemaids employed in dwellings in Ethiopia; particularly in the study area haven’t been underexplored yet.

Objective

A study aimed to assess the profiles of bacteria isolates and antimicrobial resistance patterns among housemaids working in communal living residences in Jimma City, Ethiopia.

Methods

Laboratory-based cross-sectional study design was employed among 230 housemaids from April-June 2022. Hand swabs samples from the dominant hand of the study participants were collected under sterile conditions for the segregation of commensal microbes following standard operating procedures. Then in the laboratory, the swabs were inoculated aseptically using streak-plating methods on mannitol salt agar, MacConkey agar, Salmonella-shigella agar, and Eosin Methylene Blue Agar. Then inoculated samples were incubated at 37°C for 24 hours for bacterial isolation. In addition, a set of biochemical tests was applied to examine bacterial species. Data was entered into Epidata version 3.1. All statistics were performed using SPSS®statistics version 26. Descriptive analyses were summarized using frequency and percentage.

Results

The response rate of respondents was 97.8%. The prevalence of bacterial contaminants in the hands of housemaids who tested positive was 72% (95%CI: 66.2-77.8%). The isolated bacterial wereStaphylococcus aureus(31.8%),Coagulase-Negative Staphylococci(0.9%),Escherichia coli(21.5%),Salmonella(1.3%),Shigella(6.7%),Klebsiella species(23.3%) andProteus species(14.8%). The isolation rate of bacteria was significantly associated with the removal watch, ring, and bracelet during hand washing. Most isolated bacteria were sensitive to Chloramphenicol while the majority of them were resistant to Tetracycline, Gentamycin, Vancomycin, and Ceftazidime.

Conclusions

Hands of housemaids are important potential sources of disease-causing bacterial pathogens that would result in the potential risk of foodborne diseases. Most isolated bacteria were resistant to tested antimicrobial drugs. Everybody responsible should work practice of good hand hygiene.
Obesity and Smoking: A Tale of 2 Risk Factors with Implications for the Next Pandemic
Authors: Adams Mary L.
Published: March 2023

Background

In 1990, two risk factors that would figure prominently in the COVID-19 pandemic were on divergent paths in the US. The smoking rate was 23.5% and dropped to 13.5% in 2021, while the obesity rate was 11.5% and increased 186% to 33.0%.

Objective

The study objective was to compare the global impact of those risk factors on COVID deaths to help prepare the US for future pandemics.

Methods

Stata and Excel were used to regress global COVID deaths on obesity and smoking before and after vaccines were available, and US deaths/day were compared pre-and post-vaccines.

Results

Obesity was associated with global COVID deaths, with R2as high as 0.87 for cumulative data with slightly lower R2and coefficients for post-vaccines. For 9 regressions of deaths on obesity, all P values (overall and coefficients) were <0.05 while for regressions on smoking, no P values were < 0.05. Of the 1.1 million US deaths, the death rate/day post-vaccines was 59% of that pre-vaccines. If the US obesity rate had remained 11.5%, estimates suggest 800,000+ lives could have been saved. US smoking rate was reduced 42% by multiple strategies using support from a 1998 multi-billion-dollar settlement between states and tobacco companies.

Conclusion

Vaccines have limited ability to reduce total COVID deaths, with obesity remaining a key factor in death rates. Results suggest that lower obesity rates are needed to further reduce US COVID deaths, potentially saving thousands of lives in future pandemics. Lessons from reducing smoking rates might prove useful.
Targeted and selective knockout of the TLQP-21 neuropeptide unmasks its unique role in energy homeostasis
Authors: Sahu Bhavani S. , Razzoli Maria , McGonigle Seth , Pallais Jean Pierre , Nguyen Megin E. , Sadahiro Masato , Jiang Cheng , Lin Wei-Jye , Kelley Kevin A. , Rodriguez Pedro , Mansk Rachel , Cero Cheryl , Caviola Giada , Palanza Paola , Rao Loredana , Beetch Megan , Alejandro Emilyn , Sham Yuk Y. , Frontini Andrea , Salton Stephen R. , Bartolomucci Alessandro
Published: March 2023

Pro-peptide precursors are processed into biologically active peptide hormones or neurotransmitters, each playing an essential role in physiology and disease. Genetic loss of function of a pro-peptide precursor results in the simultaneous ablation of all biologically-active peptides within that precursor, often leading to a composite phenotype that can be difficult to align with the loss of specific peptide components. Due to this biological constraint and technical limitations, mice carrying the selective ablation of individual peptides encoded by pro-peptide precursor genes, while leaving the other peptides unaffected, have remained largely unaddressed. Here, we developed and characterized a mouse model carrying the selective knockout of the TLQP-21 neuropeptide (ΔTLQP-21) encoded by theVgfgene. To achieve this goal, we used a knowledge-based approach by mutating a codon in theVgfsequence leading to the substitution of the C-terminal Arginine of TLQP-21, which is the pharmacophore as well as an essential cleavage site from its precursor, into Alanine (R21→A). We provide several independent validations of this mouse, including a novel in-gel digestion targeted mass spectrometry identification of the unnatural mutant sequence, exclusive to the mutant mouse. ΔTLQP-21 mice do not manifest gross behavioral and metabolic abnormalities and reproduce well, yet they have a unique metabolic phenotype characterized by a temperature-dependent resistance to diet-induced obesity and activation of the brown adipose tissue.