bluuebunny/crossref_metadata_2025 huggingface dataset:
Host related factors determine co-occurrence patterns between pathogenic bacteria, protozoa, and helminths in populations of the multimammate mouse, Mastomys natalensis
Authors: Mariën Joachim , Vanden Broecke Bram , Tafompa Pamela Jones June , Bernaerts Lisse , Ribas Alexis , Mnyone Ladslaus L. , Mulugu Loth S. , Leirs Herwig
Published: January 2022

Advances in experimental and theoretical work increasingly suggest that parasite interactions within a single host can affect the spread and severity of wildlife diseases. Yet empirical data to support predicted co-infection patterns are limited due to the practical challenges of gathering convincing data from animal populations and the stochastic nature of parasite transmission. Here, we investigated co-infection patterns between micro- (bacteria and protozoa) and macroparasites (gastrointestinal helminths) in natural populations of the multimammate mouse (Mastomys natalensis). Fieldwork was performed in Morogoro (Tanzania), where we trapped 211 individual M. natalensis and tested their behavior using a modified open-field arena. All animals were checked on the presence of helminths in their gastrointestinal tract, three bacteria (Anaplasma, Bartonella, and Borrelia) and two protozoan genera (Piroplasma and Hepatozoon). Besides the presence of eight different helminth genera (reported earlier), we found that 21% of M. natalensis were positive for Anaplasma, 13% for Bartonella, and 2% for Hepatozoon species. Hierarchical modelling of species communities was used to investigate the effect of the different host-related factors on these parasites’ infection probability and community structure. Our results show that the infection probability of Anaplasma and Bartonella was higher in adults than juveniles. We also observed that females and less explorative individuals had a higher infection probability with Bartonella. We found limited support for within-host interactions between micro-and macroparasites, as only animals infected with Bartonella were significantly more likely to be infected with Protospirura, Trichuris, and Trichostrongylidae helminths.
Probabilistic machine learning ensures accurate ambient denoising in droplet-based single-cell omics
Authors: Sheng Caibin , Lopes Rui , Li Gang , Schuierer Sven , Waldt Annick , Cuttat Rachel , Dimitrieva Slavica , Kauffmann Audrey , Durand Eric , Galli Giorgio G. , Roma Guglielmo , de Weck Antoine
Published: January 2022

Droplet-based single-cell omics, including single-cell RNA sequencing (scRNAseq), single-cell CRISPR perturbations (e.g., CROP-seq), and single-cell protein and transcriptomic profiling (CITE-seq) hold great promise for comprehensive cell profiling and genetic screening at the single-cell resolution. However, these technologies suffer from substantial noise, among which ambient signals present in the cell suspension may be the predominant source. Current models to address this issue are highly technology-specific and relatively scRNAseq-centric. while a universal model to describe the noise across these technologies may reveal this common source, improving the denoising accuracy. To this end, we explicitly examined these unexpected signals in multiple datasets across droplet-based technologies, summarised a predictable pattern, and developed single-cell Ambient Remover (scAR) – a hypothesis-driven machine learning model to predict and remove ambient signals (including mRNA counts, protein counts, and sgRNA counts) at the molecular level. We benchmarked scAR on three technologies – single-cell CRISPR screens, CITE-seq, and scRNAseq along with the state-of-the-art single-technology-specific approaches. scAR showed high denoising accuracy for each type of dataset.
The RNA-binding landscape of HAX1 protein indicates its involvement in ribosome biogenesis and translation
Authors: Balcerak Anna , Macech-Klicka Ewelina , Wakula Maciej , Tomecki Rafal , Goryca Krzysztof , Rydzanicz Malgorzata , Chmielarczyk Mateusz , Szostakowska-Rodzos Malgorzata , Wisniewska Marta , Lyczek Filip , Helwak Aleksandra , Tollervey David , Kudla Grzegorz , Grzybowska Ewa A.
Published: January 2022

HAX1 is a human protein with no known homologues or structural domains, mutations in which cause severe congenital neutropenia through mechanisms that are poorly understood. Previous studies reported RNA-binding capacity of HAX1, but the role of this binding in physiology and pathology remains unexplained. Here we report transcriptome-wide characterization of HAX1 RNA targets using RIP-seq and CRAC, indicating that HAX1 binds transcripts involved in ribosome biogenesis and rRNA processing. Using CRISPR knockouts we find that RNA targets of HAX1 partially overlap with transcripts downregulated inHAX1KO, implying a role in mRNA stabilization. Gene ontology analysis demonstrated that genes differentially expressed inHAX1KO (including genes involved in ribosome biogenesis and translation) are also enriched in a subset of genes whose expression correlates withHAX1expression in four analyzed neoplasms. Functional connection to ribosome biogenesis was also demonstrated by gradient sedimentation ribosome profiles, which revealed differences in the small subunit:monosome ratio inHAX1WT/KO. We speculate that changes in HAX1 expression may be important for the etiology of HAX1-linked diseases through dysregulation of translation.
Caffeine and MDMA (ecstasy) exacerbate ER stress triggered by hyperthermia
Authors: Trychta Kathleen A. , Harvey Brandon K.
Published: January 2022

Drugs of abuse can cause local and systemic hyperthermia, a known trigger of endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). Another trigger of ER stress and UPR is ER calcium depletion which causes ER exodosis, the secretion of ER resident proteins. Club drugs such as 3,4-methylenedioxymethamphetamine (MDMA, ‘ecstasy’) can create hyperthermic conditions in the brain and cause toxicity that is affected by the environmental temperature and the presence of other drugs, such as caffeine. Here we examine the secretion of ER resident proteins and activation of the UPR under combined exposure to MDMA and caffeine in a cellular model of hyperthermia. We show that hyperthermia triggers the secretion of normally ER resident proteins and that this aberrant protein secretion is potentiated by the presence of MDMA, caffeine, or a combination of the two drugs. Hyperthermia activates the UPR but the addition of MDMA or caffeine does not alter canonical UPR gene expression despite the drug effects on ER exodosis of UPR-related proteins. One exception was increased BiP/Grp78 mRNA levels in MDMA-treated cells exposed to hyperthermia. These findings suggest that club drug use under hyperthermic conditions exacerbates disruption of ER proteostasis contributing to cellular toxicity.

Highlights

ER resident proteins are redistributed into the extracellular space in response to hyperthermia and caffeine and MDMA further enhance this secretion.

Stabilizing ER calcium and overexpressing KDEL receptors reduces ER resident protein secretion following hyperthermia.

Hyperthermia triggers a UPR response with MDMA augmenting BiP expression in hyperthermic conditions.
Role of the circadian clock “Death-Loop” in the DNA damage response underpinning cancer treatment resistance
Authors: Vainshelbaum Ninel Miriam , Salmina Kristine , Gerashchenko Bogdan I. , Lazovska Marija , Zayakin Pawel , Cragg Mark S. , Pjanova Dace , Erenpreisa Jekaterina
Published: January 2022

The Circadian Clock (CC) drives the normal cell cycle and reciprocally regulates telomere elongation. However, it can be deregulated in cancer, embryonic stem cells (ESC), and the early embryo. Here, its role in the resistance of cancer cells to genotoxic treatments was assessed in relation to whole-genome duplication (WGD) and telomere regulation. We first evaluated the DNA damage response of polyploid cancer cells and observed a similar impact on the cell cycle to that seen in ESC - overcoming G1/S, adapting DNA damage checkpoints, tolerating DNA damage, and coupling telomere erosion to accelerated cell senescence, favouring transition by mitotic slippage into the ploidy cycle (reversible polyploidy). Next, we revealed a positive correlation between cancer WGD and deregulation of CC assessed by bioinformatics on 11 primary cancer datasets (rho=0.83; p<0.01). As previously shown, the cancer cells undergoing mitotic slippage cast off telomere fragments with TERT, restore the telomeres by recombination and return their depolyploidised mitotic offspring to TERT-dependent telomere regulation. Through depolyploidisation and the CC “death loop” the telomeres and Hayflick limit count are thus again renewed. This mechanism along with similar inactivity of the CC in early embryos support a life-cycle (embryonic) concept of cancer.
Modeling predicts differences in CAR T cell signaling due to biological variability
Authors: Tserunyan Vardges , Finley Stacey D.
Published: January 2022

In recent decades, chimeric antigen receptors (CARs) have been successfully used to generate engineered T cells capable of recognizing and eliminating cancer cells. The structure of CARs frequently includes costimulatory domains, which enhance the T cell response upon antigen encounter. However, it is not fully known how the CAR co-stimulatory domains influence T cell activation in the presence of biological variability. In this work, we used mathematical modeling to elucidate how the inclusion of one such co-stimulatory molecule, CD28, impacts the response of a population of engineered T cells under different sources of variability. Particularly, our simulations demonstrate that CD28-bearing CARs mediate a faster and more consistent population response under both target antigen variability and kinetic rate variability. We identify kinetic parameters that have the most impact on mediating cell activation. Finally, based on our findings, we propose that enhancing the catalytic activity of lymphocyte-specific protein tyrosine kinase (LCK) can result in drastically reduced and more consistent response times among heterogeneous CAR T cell populations.
Identification of a transcriptional signature found in multiple models of ASD and related disorders
Authors: Thudium Samuel , Palozola Katherine , L’Her Eloise , Korb Erica
Published: January 2022

Epigenetic regulation plays a critical role in many neurodevelopmental disorders, including Autism Spectrum Disorder (ASD). In particular, many such disorders are the result of mutations in genes that encode chromatin modifying proteins. However, while these disorders share many features, it is unclear whether they also share gene expression disruptions resulting from the aberrant regulation of chromatin. We examined 5 chromatin modifiers that are all linked to ASD despite their different roles in regulating chromatin. Specifically, we depleted Ash1L, Chd8, Crebbp, Ehmtl, and Nsd1 in parallel in a highly controlled neuronal culture system. We then identified sets of shared genes, or transcriptional signatures, that are differentially expressed following loss of multiple ASD-linked chromatin modifiers. We examined the functions of genes within the transcriptional signatures and found an enrichment in many neurotransmitter transport genes and activity-dependent genes. In addition, these genes are enriched for specific chromatin features such as bivalent domains that allow for highly dynamic regulation of gene expression. The downregulated transcriptional signature is also observed within multiple mouse models of neurodevelopmental disorders that result in ASD, but not those only associated with intellectual disability. Finally, the downregulated transcriptional signature can distinguish between neurons generated from iPSCs derived from healthy donors and idiopathic ASD patients through RNA-deconvolution, demonstrating that this gene set is relevant to the human disorder. This work identifies a transcriptional signature that is found within many neurodevelopmental syndromes, helping to elucidate the link between epigenetic regulation and the underlying cellular mechanisms that result in ASD.
Mitochondrial and redox modifications in early stages of Huntington’s disease
Authors: Lopes Carla , Luísa Ferreira I. , Maranga Carina , Beatriz Margarida , Mota Sandra I. , Sereno José , Castelhano João , Abrunhosa Antero , Oliveira Francisco , De Rosa Maura , Hayden Michael , Laço Mário N. , Januário Cristina , Branco Miguel Castelo , Rego A. Cristina
Published: January 2022

Defects in mitochondrial function and mitochondrial-related redox deregulation have been attributed to Huntington’s disease (HD), a genetic neurodegenerative disorder largely affecting the striatum. However, whether these changes occur in early stages of the disease and can be detected in vivo is still unclear. Thus, in the present study, we analyzed changes in mitochondrial function and overreduced states associated with production of reactive oxygen species (ROS) at early stages and along disease progression. Studies were performed in vivo in human brain using positron emission tomography (PET) using [64Cu]-ATSM and ex vivo in human skin fibroblasts of premanifest and prodromal (Pre-M) and manifest HD patients; in vivo brain [64Cu]-ATSM PET and isolated mitochondria derived from striatum and cortex were also analyzed in YAC128 transgenic mouse at pre-symptomatic (3 month-old, mo) and symptomatic (6 to 12 mo) stages. Oxygen consumption rates were assessed by Seahorse analysis, hydrogen peroxide levels were determined using fluorescent probes and mitochondrial morphology by transmission electron microscopy in human skin fibroblasts and mouse striatal and cortical isolated mitochondria. Pre-M HD carriers exhibited enhanced whole-brain (with exception of caudate) [64Cu]-ATSM labelling, correlating with CAG repeat number. Fibroblasts from Pre-M showed enhanced basal and maximal respiration, proton (H+) leak and increased hydrogen peroxide levels, the later progressing to manifest HD; mitochondria from fibroblasts of Pre-M HD carriers also showed reduced roundness, while higher number of mitochondrial DNA copies correlated with maximal respiratory capacity. In vivo animal PET analysis showed increased accumulation of [64Cu]-ATSM in YAC128 mouse striatum. Pre-symptomatic YAC128 mouse striatal isolated mitochondria exhibited a rise in basal and maximal mitochondrial respiration and in ATP production, along with increased complex II and III activities; mouse HD mitochondria also showed enhanced mitochondrial hydrogen peroxide levels and roundness, as revealed by brain ultrastructure analysis, and defects in Ca2+ handling, supporting increased striatal susceptibility in YAC128 mouse brain. Data demonstrate both human and mouse mitochondrial overactivity and altered morphology at early HD stages, facilitating redox unbalance, the latter extending over manifest disease stages.
Multisite Phosphorylation and Binding Alter Conformational Dynamics of the 4E-BP2 Protein
Authors: Smyth Spencer , Zhang Zhenfu , Bah Alaji , Tsangaris Thomas E. , Dawson Jennifer , Forman-Kay Julie D. , Gradinaru Claudiu C.
Published: January 2022

Intrinsically disordered proteins (IDPs) play critical roles in regulatory protein interactions, but detailed structural/dynamics characterization of their ensembles remain challenging, both in isolation and they form dynamic ‘fuzzy’ complexes. Such is the case for mRNA cap-dependent translation initiation, which is regulated by the interaction of the predominantly folded eukaryotic initiation factor 4E (eIF4E) with the intrinsically disordered eIF4E binding proteins (4E-BPs) in a phosphorylation-dependent manner. Single-molecule Förster resonance energy transfer showed that the conformational changes of 4E-BP2 induced by binding to eIF4E are non-uniform along the sequence; while a central region containing both motifs that bind to eIF4E expands and becomes stiffer, the C-terminal region is less affected. Fluorescence anisotropy decay revealed a nonuniform segmental flexibility around six different labelling sites along the chain. Dynamic quenching of these fluorescent probes by intrinsic aromatic residues measured via fluorescence correlation spectroscopy report on transient intra- and inter-molecular contacts on ns-μs timescales. Upon hyperphosphorylation, which induces folding of ~40 residues in 4E-BP2, the quenching rates decreased at most labelling sites. The chain dynamics around sites in the C-terminal region far away from the two binding motifs significantly increased upon binding to eIF4E, suggesting that this region is also involved in the highly dynamic 4E-BP2:eIF4E complex. Our time-resolved fluorescence data paint a sequence-level rigidity map of three states of 4E-BP2 differing in phosphorylation or binding status and distinguish regions that form contacts with eIF4E. This study adds complementary structural and dynamics information to recent studies of 4E-BP2, and it constitutes an important step towards a mechanistic understanding of this important IDP via integrative modelling.
Phase Separation of Shell Protein and Enzyme: An Insight into the Biogenesis of a Prokaryotic Metabolosome
Authors: Kumar Gaurav , Sinha Sharmistha
Published: January 2022

Bacterial microcompartments are substrate specific metabolic modules that are conditionally expressed in certain bacterial species. These all protein structures have size in the range of 100-150 nm and are formed by the self-assembly of thousands of protein subunits, all encoded by genes belonging to a single operon. The operon contains genes that encode for both enzymes and shell proteins. The shell proteins self-assemble to form the outer coat of the compartment and enzymes are encapsulated within. A perplexing question in MCP biology is to understand the mechanism which governs the formation of these small yet complex assemblages of proteins. In this work we use 1,2-propanediol utilization microcompartments (PduMCP) as a paradigm to identify the factors that drive the self-assembly of MCP proteins. We find that a major shell protein PduBB’ tend to self-assemble under macromolecular crowded environment and suitable ionic strength. Microscopic visualization and biophysical studies reveal phase separation to be the principle mechanism behind the self-association of shell protein in the presence of salts and macromolecular crowding. The shell protein PduBB’ interacts with the enzyme diol-dehydratase PduCDE and co-assemble into phase separated liquid droplets. The co-assembly of PduCDE and PduBB’ results in the enhancement of catalytic activity of the enzyme. A combination of spectroscopic and biochemical techniques shows the relevance of divalent cation Mg2+in providing stability to intact PduMCPin vivo. Together our results suggest a combination of protein-protein interactions and phase separation guiding the self-assembly of Pdu shell protein and enzyme in solution phase.

Significance Statement

Present work shows how surrounding environment modulates the self-assembly behavior of a major shell protein of 1,2-propanediol utilization microcompartment (PduMCP). Appropriate ionic strength and macromolecular crowding bring about liquid-liquid phase separation of the shell protein. Under crowded environment Mg2+displayed unique property to drive the formation of shell protein liquid condensates. The co-phase separation of a native enzyme along with the shell protein enables it to outperform the enzyme in isolation. This adds on to the existing concept of phase separation being the underlying principle behind the genesis of lipid free organelles in prokaryotes. Further, our results indicate that the divalent metal ion Mg2+plays an intricate role in the outfitting of the structure-function integrity of PduMCPs.

Graphical Abstract
Sustained correction of hippocampal neurogenic and cognitive deficits after a brief treatment by Nutlin-3 in a mouse model of Fragile X Syndrome
Authors: Javadi Sahar , Li Yue , Sheng Jie , Zhao Lucy , Fu Yao , Wang Daifeng , Zhao Xinyu
Published: January 2022

Background

Fragile X syndrome (FXS), the most prevalent inherited intellectual disability and one of the most common monogenic form of autism, is caused by a loss of FMRP translational regulator 1 (FMR1). We have previously shown that FMR1 represses the levels and activities of ubiquitin ligase MDM2 in young adult FMR1-deficient mice and treatment by a MDM2 inhibitor Nutlin-3 rescues both hippocampal neurogenic and cognitive deficits in FMR1-deficient mice when analyzed shortly after the administration. However, it is unknown whether Nutlin-3 treatment can have long-lasting therapeutic effects.

Methods

We treated 2-month-old young adult FMR1-deficient mice with Nutlin-3 for 10 days and then assessed the persistent effect of Nutlin-3 on both cognitive functions and adult neurogenesis when mice were 6-month-old mature adults. To investigate the mechanisms underlying persistent effects of Nutlin-3, we analyzed proliferation and differentiation of neural stem cells isolated from these mice and assessed the transcriptome of the hippocampal tissues of treated mice.

Results

We found that transient treatment with Nutlin-3 of 2-month-old young adult FMR1-deficient mice prevents the emergence of neurogenic and cognitive deficits in mature adult FXS mice at 6-month of age. We further found that the long-lasting restoration of neurogenesis and cognitive function might not be mediated by changing intrinsic properties of adult neural stem cells. Transcriptomic analysis of the hippocampal tissue demonstrated that transient Nultin-3 treatment leads to significant expression changes in genes related to extracellular matrix, secreted factors, and cell membrane proteins in FMR1-deficient hippocampus.

Conclusions

Our data indicates that transient Nutlin-3 treatment in young adults leads to long-lasting neurogenic and behavioral changes through modulating adult neurogenic niche rather than intrinsic properties of adult neural stem cells. Our results demonstrate that cognitive impairments in FXS may be prevented by an early intervention through Nutlin-3 treatment.
Allogeneic gene-edited HIV-specific CAR-T cells secreting PD-1 blocking scFv enhance anti-HIV activity in vitro
Authors: Pan Hanyu , Wang Jing , Liang Huitong , Jiang Zhengtao , Zhao Lin , Wang Yanan , Yang Xinyi , Liang Zhiming , Shen Xiaoting , Lin Qinru , Liang Yue , Yang Jinglong , Lu Panpan , Zhu Yuqi , Xiang Weirong , Li Min , Wang Pengfei , Zhu Huanzhang
Published: January 2022

HIV-specific chimeric antigen receptor (CAR) T cells have been developed to target latently infected CD4+ T cells that express virus either spontaneously or after intentional latency reversal. However, the T-cell exhaustion and the patient-specific autologous paradigm of CAR-T hurdled the clinical application. Here, we created HIV-specific CAR-T cells using human peripheral blood mononuclear cells and a 3BNC117-E27 CAR (3BE CAR) construct that enables the expression of PD-1 blocking scFv E27 and the single-chain variable fragment of the HIV-1-specific broadly neutralizing antibody 3BNC117 to target native HIV envelope glycoprotein (Env). In comparison with T cells expressing 3BNC117-CAR alone, 3BE CAR-T cells showed greater anti-HIV potency with stronger proliferation capability, higher killing efficiency (up to ~75%) and enhanced cytokine secretion in the presence of HIV envelope glycoprotein-expressing cells. Furthermore, our approach achieved high levels (over 97%) of the TCR-deficient 3BE CAR-T cells with the functional inactivation of endogenous TCR to avoid graft-versus-host disease without compromising their antiviral activity relative to standard anti-HIV CAR-T cells. These data suggest that we have provided a feasible approach to large-scale generation of “off-the-shelf” anti-HIV CAR-T cells in combination with antibody therapy of PD-1 blockade, which can be a powerful therapeutic candidate for the functional cure of HIV.
Dickeya colocasiae sp. nov. isolated from wetland taro, Colocasia esculentum
Authors: Boluk Gamze , Dobhal Shefali , Arizala Dario , Alvarez Anne M. , Arif Mohammad
Published: January 2022

Bacterial pathogens identified as Dickeya sp. have recently been associated with a corm rot of wetland taro on Oahu, Hawaii, but the species designation of these strains was unclear. A Gram-negative, pectinolytic bacterial strain PL65T isolated from an infected taro corm was subjected to polyphasic analysis to determine its genomic and phenotypic characteristics. Multi-locus sequence analyses (MLSA) based on five housekeeping genes (dnaA, gapA, gyrB, atpD, and purA) revealed that Dickeya zeae and D. oryzae, were the closest relatives. Phylogenetic analysis based on 463 core gene sequences clearly showed two potentially new species within Dickeya oryzae. In silico DNA– DNA hybridization value of strain PL65T with 12 Type strains of Dickeya species was <68%. Average nucleotide identity (ANI) analysis revealed that PL65T was at the margin of the species delineation cut-off values with a 96% ANI value. The metabolic profile of strain PL65T using BIOLOG differentiated it from the type strains of all other known species of Dickeya. Based on the results of genome-to-genome comparisons and phenotypic data presented in this report, we propose establishment of a new species, Dickeya colocasiae sp. nov. with strain PL65T as the type strain (ICMP 24361T).
Population genomic evidence of selection on structural variants in a natural hybrid zone
Authors: Zhang Linyi , Chaturvedi Samridhi , Nice Chris C. , Lucas Lauren K. , Gompert Zachariah
Published: January 2022

Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between twoLycaeidesbutterfly taxa (L. melissaand Jackson HoleLycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviating from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson HoleLycaeidesancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average then SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess introgression from Jackson HoleLycaeides.Excess Jackson HoleLycaeidesancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might contribute disproportionately to hybrid fitness and thus (partial) reproductive isolation.
Gene regulatory evolution in cold-adapted fly populations neutralizes plasticity and may undermine genetic canalization
Authors: Huang Yuheng , Lack Justin B. , Hoppel Grant T. , Pool John E.
Published: January 2022

The relationships between adaptive evolution, phenotypic plasticity, and canalization remain incompletely understood. Theoretical and empirical studies have made conflicting arguments on whether adaptive evolution may enhance or oppose the plastic response. Gene regulatory traits offer excellent potential to study the relationship between plasticity and adaptation, and they can now be studied at the transcriptomic level. Here we take advantage of three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. We measure the transcriptome-wide plasticity in gene expression levels and alternative splicing (intron usage) between warm and cold laboratory environments. We find that suspected adaptive changes in both gene expression and alternative splicing tend to neutralize the ancestral plastic response. Further, we investigate the hypothesis that adaptive evolution can lead to decanalization of selected gene regulatory traits. We find strong evidence that suspected adaptive gene expression (but not splicing) changes in cold-adapted populations are more vulnerable to the genetic perturbation of inbreeding than putatively neutral changes. We find some evidence that these patterns may reflect a loss of genetic canalization accompanying adaptation, although other processes including hitchhiking recessive deleterious variants may contribute as well. Our findings augment our understanding of genetic and environmental effects on gene regulation in the context of adaptive evolution.

Significance Statement

It is unclear whether adaptive evolution is concordant or discordant with regulatory plasticity, especially for splicing plasticity which is rarely studied. Here we analyzed RNA-seq data from three pairs of natural fly populations that represent separate adaptive evolution to cold climate. We found that adaptive evolution is generally discordant with the ancestral plasticity between cold and warm temperatures for gene expression abundance and splicing. We also investigate the hypothesis that adaptation leads to decanalization of the selected traits. By comparing the expression variance between inbred and outbred samples, we found evidence that adaptation may lead to genetic decanalization for expression abundance but not for splicing. Our study reveals the relationship between adaptation, plasticity and canalization in three instances in nature.
FRET monitoring of transcription factor activities in living bacteria
Authors: Wang Pengchao , Zhang Guangming , Xu Zeling , Chen Zhe , Liu Xiaohong , Wang Chenyin , Zheng Chaogu , Wang Jiangyun , Zhang Hongmin , Yan Aixin
Published: January 2022

Bacteria adapt to the constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor the in situ TF-promoter interactions in living bacteria are lacking. Herein, we developed a whole-cell TF-promoter binding assay based on the intermolecular Förster resonance energy transfer (FRET) between a fluorescent unnatural amino acid CouA which is genetically encoded into defined sites in TFs and the live cell fluorescent nucleic acid stain SYTO 9. We show that this new FRET pair monitors the intricate TF-promoter interactions elicited by various types of signal transduction systems with specificity and sensitivity. Furthermore, the assay is applicable to identify novel modulators of the regulatory systems of interest and monitor TF activities in bacteria colonized inC. elegans. In conclusion, we established a tractable and sensitive TF-promoter binding assay in living bacteria which not only complements currently available approaches for DNA-protein interactions but also provides novel opportunities for functional annotation of bacterial signal transduction systems and studies of the bacteria-host interface.
THE EFFECT OF HAND HYGIENE INTERVENTION ON THE KNOWLEDGE AND SKILLS LEVEL OF SCHOOL CHILDREN
Authors: Mufida Nurlela , Rumambo Pandin Moses Glorino
Published: January 2022

Background

Hand washing is an alternative, effective and inexpensive method that can be used to prevent infectious diseases. Washing hands with soap can improve children’s health. The purpose of this study was to determine the effect of hand hygiene intervention on the level of knowledge and skills of elementary school students. The method used to conduct this research is a critical review, namely by reviewing articles from databases such as Google Scholar, Pubmed, Direct, Medline. The search keywords used were: quantitative studies on delivery, intervention, hand hygiene, skills, children, and primary school. The selected articles are articles that meet the standard writing criteria, which were published between 2017-2021, both in English and Indonesian. Based on these evaluation criteria, 20 (twenty) studies were obtained. From the results of a literature search, several studies on the use of intervention strategies to provide hand hygiene health education found that although there were other intervention strategies to improve hand hygiene, there were significant differences in both knowledge and skills after being given the intervention.
A prospective, single-center study to evaluate the clinical performance of Meril ABFind in individuals vaccinated against COVID-19
Authors: Shastri Jayanthi , Agrawal Sachee , Chatterjee Nirjhar , Gupta Harsha
Published: January 2022

Background

Accurate rapid antibody detection kits requiring minimum infrastructure are beneficial in detecting post-vaccination antibodies in large populations. ChAdOx1-nCOV (COVISHIELD™) and BBV-152 (Covaxin™) vaccines are primarily used in India.

Methods

In this single-centre prospective study, performance of Meril ABFind was investigated by comparing with Abbott SARS-CoV-2 IgG II Quant (Abbott Quant), GenScript cPass SARS-CoV-2 neutralization antibody detection kit (GenScript cPass), and COVID Kawach MERILISA (MERILISA) in 62 vaccinated health care workers (HCW) and 40 pre-pandemic samples.

Results

In the vaccinated subjects, Meril ABFind kit displayed high sensitivity of 93.3% (CI, 89.83%-96.77%), 94.92% (CI, 91.88%-97.96%), and 90.3% (CI, 86.20%-94.4%) in comparison to Abbott Quant, MERILISA, and GenScript cPass respectively. The results of the Meril ABFind in the COVISHIELD-vaccinated group were excellent with 100% sensitivity in comparison to the other three kits. In the Covaxin-vaccinated group, Meril ABFind displayed sensitivity ranging from 80% to 88.9%. In control samples, there were no false positives detected by Meril ABFind, while Abbott Quant, MERILISA, and GenScript cPass reported 2.5%, 10.0%, and 12.5% false positives, respectively. In the pre-pandemic controls, specificity of Meril ABFind was 100%, Abbott Quant 97.5%, MERILISA 90%, and GenScript cPass 87.5%.

Conclusion

The Meril ABFind kit demonstrated satisfactory performance when compared with the three commercially available kits and was the only kit without false positives in the pre-pandemic samples. This makes it a viable option for rapid diagnosis of post vaccination antibodies.
Using Mobile Phone-based Text Message to Recruit Representative Samples: Assessment of a Cross-Sectional Survey about the COVID-19 Vaccine Hesitation
Authors: Sartorao Filho C.I. , Sartorao Neto C.I. , Sartorao A.L.V. , Terribile D.C. , Mello R. , Mello B.B. , Zoqui M.C. , Duarte D.O. , Cachoni L.E.G. , Bisseto V.C.Q. , Ribeiro E.A.C.
Published: January 2022

Background

Limited research has examined mobile phone-based platforms for survey recruitment, especially during the COVID-19 pandemic in Brazil. Our objective was to investigate the feasibility and representativeness of mobile phone-based advertisement during a preliminary study about COVID-19 vaccine hesitation in Brazil. Moreover, we evaluate whether the older population can be reached through mobile phone-based platforms of the survey.

Methods

We conducted a study in December 2021 based on a preliminary survey about the COVID-19 vaccine hesitation in Assis, Brazil, Sao Paulo state. From a list of the adult population hesitant for the second dose of the COVID-19 vaccine, we sent a mobile phone-based advertisement inviting the participants to answer the survey for one week. The respondent’s data were collected in a Google form platform. The comparison between the target population and the respondents was made using the Chi-squared test and the Welch’s test, using a P-value of .05 as significative.

Results

The response rate was 9.99% after one week. The mean age of the respondent group was 33.97 (SD 14.99) and 35.05 (SD 14.19) of the population, with a P-value of .192 and a Cohen’s d coefficient of 0.0754, corresponding to a small effect size between groups. We demonstrate that the mobile phone-based survey is a feasible and representative strategy during the pandemics in Brazil. Moreover, the older population respondent was representative.

Conclusion

We achieved a representative sample of respondents using the mobile phone-based survey in Brazil. Furthermore, it was representative in all sociodemographic and health characteristics assessed. Finally, these findings suggest the method is a highly feasible and economical means of recruiting for survey research.
Implementation of a Rapid RT-LAMP Saliva-based SARS-CoV-2 Testing Program in the Workplace
Authors: Cook Bradley W.M. , Kobasa Kaitlyn , Tamayo Marielou , Theriault Natasha , Pappas Diane Gordon , Theriault Steven S.
Published: January 2022

Rising SARS-CoV-2 cases, testing delays and the risk of pre-symptomatic and asymptomatic transmission provided the impetus for an in-house rapid testing program. Employees and their household contacts were encouraged to self-collect saliva samples which were pooled for routine testing using an established colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. In brief, individual or a maximum of four saliva samples were pooled, heat-inactivated to render microorganisms, especially SARS-CoV-2, non-infectious prior to being added to RT-LAMP assay tubes containing either human sample control gene, RNase P or a region of the SARS-CoV-2 gene, ORF1ab. During the second wave of SARS-CoV-2 infections in November 2020, two samples from an employee and a member of their household tested positive via RT-LAMP within two days of each other. A delayed clinical qRT-PCR test confirmation of both individuals 5 days later underscores the power of routine rapid testing with with-in-the-hour turnaround times. Workplace rapid testing programs using RT-LAMP are flexible in their design, have a reduced cost compared to qRT-PCR, may involve non-invasive self-saliva collection for increased safety for the testing personnel, and can be performed with minimal training.
Waning COVID-19 Vaccine Effectiveness for BNT162b2 and CoronaVac in Malaysia: An Observational Study
Authors: Suah Jing Lian , Husin Masliyana , Keng Tok Peter Seah , Tng Boon Hwa , Thevananthan Thevesh , Low Ee Vien , Appannan Maheshwara Rao , Zin Faizah Muhamad , Zin Shahanizan Mohd , Yahaya Hazlina , Peariasamy Kalaiarasu M. , Sivasampu Sheamini
Published: January 2022

Background

Evaluation of vaccine effectiveness over time against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or coronavirus disease 2019 (COVID-19) is important. Evidence on effectiveness over time for the CoronaVac vaccine is lacking despite its widespread use globally. In Malaysia, a diverse set-up of COVID-19 vaccines was rolled out nationwide, and the waning of vaccine protection is a concern. We aimed to investigate and compare waning vaccine effectiveness against COVID-19 infections, COVID-19 related ICU admission and COVID-19 related deaths for BNT162b2 and CoronaVac vaccines.

Methods

In this observational study, we consolidated nationally representative data on COVID-19 vaccination and patients’ outcomes. Data on all confirmed COVID-19 cases from 1 to 30 September 2021 were used to compare vaccine effectiveness between the ‘early’ group (fully vaccinated in April to June 2021) and the ‘late’ group (fully vaccinated in Jul to Aug 2021). We used a negative binomial regression model to estimate vaccine effectiveness against COVID-19 infections for both ‘early’ and ‘late’ groups, by comparing the rates of infection for individuals vaccinated in the two different periods relative to the unvaccinated. Among confirmed COVID-19 cases, we used logistic regression to estimate and compare vaccine effectiveness against ICU admission and deaths between the two different periods.

Findings

For BNT162b2, vaccine effectiveness against COVID-19 infections declined from 90.8% (95% CI 89.4, 92.0) in the late group to 79.1% (95% CI 75.8, 81.9) in the late group. Vaccine effectiveness for BNT162b2 against ICU admission and deaths were comparable between the two different periods. For CoronaVac, vaccine effectiveness waned against COVID-19 infections from 74.4% in the late group (95% CI 209 70.4, 77.8) to 30.0% (95% CI 18.4, 39.9) in the early group. It also declined significantly against ICU admission, dropping from 56.1% (95% CI 51.4, 60.2) to 29.9% (95% CI 13.9, 43.0). For deaths, however, CoronaVac’s effectiveness did not wane after three to five months of full vaccination.

Interpretation

Vaccine effectiveness against COVID-19 infections waned after three to five months of full vaccination for both BNT162b2 and CoronaVac in Malaysia. Additionally, for CoronaVac, protection against ICU admission declined as well. Evidence on vaccine effectiveness over time informs evolving policy decisions on vaccination.
Frequency of Hematologic and Solid Malignancies in the Family History of Patients with Myeloid Neoplasms
Authors: Ali Alaa , Yassin Batool , Almothaffar Ali
Published: January 2022

Background

Studies demonstrated that there are several germline mutations that lead to a familial predisposition for acute myeloid leukemia and Myelodysplastic syndrome. According to the American Society of Clinical Oncology ,the minimum cancer family history was defined as including first- and second-degree family history, type of primary cancer, and age at diagnosis.

The current study aimed to estimate the frequency of positive family history for hematologic and solid malignancies in patients with Myeloid Neoplasms / Aplastic anemia.

Patients and Methods

A cross section study was carried out at the Center of Blood Diseases, Medical City Campus during the period from March-December 2020. A purposeful sample of all adult patients with Myeloid Neoplasms [Acute Myeloid Leukemia, Myelodysplastic Syndrome, Chronic Myeloid Leukemia and Aplastic Anemia] were included in the study. A data collection form was prepared, based on the Hereditary Hematopoietic Malignancies Screening form adopted by the University of Chicago, and modified by the researchers; The data were collected by direct interview with the patients. Patients with hematologic malignancy and one or more first-degree relatives, or ≥2 second-degree relatives, with hematologic malignancies and individuals with Myelodysplastic Syndrome or Acute Myeloid Leukemia and two first or second-degree relatives with a diagnosis of solid tumor malignancy were considered potential carriers of such genetic predisposition.

Results

A total of 153 patients were included; males were nearly equal to females with a male to female ratio of nearly 1:1. Acute Myeloid Leukemia was found in 57.5%, Aplastic Anemia was found in 19%, Chronic Myeloid Leukemia in 17% and only four patients (6.5%) were known cases of Myelodysplastic Syndrome. Nine patients (5.9%) reported family history of hematological malignancies, 29 (19.0%) reported family history of solid malignancies and only one patient reported family history of both hematological and solid malignancies.

Regarding the official medical reports of the patients, no patient had been interviewed properly about this crucial point.

Conclusion

Positive family history for hematological and solid malignancies in Iraqi patients with myeloid neoplasms is prevalent. Our current approach to this critical issue in Iraq needs to be re-considered.
Prevalence and determinants of oral and cervicogenital HPV infection: baseline analysis of the MHOC cohort study
Authors: Brouwer Andrew F. , Campredon Lora P. , Walline Heather M. , Marinelli Brittany M. , Goudsmit Christine M. , Thomas Trey B. , Delinger Rachel L. , Lau Yan Kwan , Andrus Emily C. , Yost Monica L. , McCloskey Jodi K. , Sullivan Taylor S. , Mortensen Alex S. , Huang Suiyuan , Murphy Keith , Cheng Bonnie , Stanek Kayla , Nair Thankam , Carey Thomas E. , Meza Rafael , Eisenberg Marisa C.
Published: January 2022

We determined baseline oral and cervicogenital human papillomavirus (HPV) prevalence and determinants of infection in the Michigan HPV and Oropharyngeal Cancer (MHOC) study. We enrolled 394 college-age and older-adult participants of both sexes in Ann Arbor, Michigan and the surrounding area. All participants provided an oral sample at baseline, and 130 females provided a cervicogenital sample. Samples were tested for 18 HPV genotypes using polymerase chain reaction (PCR) MassArray. Participants filled out sociodemographic and behavioral questionnaires. Prevalence ratios for HPV oral or cervicogenital prevalence by predictor variables were estimated in univariable log-binomial models. Analysis was conducted 2018–20. In the full cohort, baseline oral HPV prevalence was 10.0% for any detected genotype (among the 338 valid oral tests at baseline) and 6.5% for high-risk types, and cervicogenital prevalence was 20.0% and 10.8%, respectively (among the 130 first valid cervicogenital tests). Oral HPV prevalence did not vary by sex, with 10.5% of women and 9.0% of men having an infection. We found a high prevalence of oral and cervicogenital HPV infection among those reporting no recent sexual partners compared to those with a single recent sexual partner, but prevalence increased with the number of recent partners for most sexual behaviors. We observed an ecological fallacy masking the direction of impact of vaccination on HPV prevalence in the full cohort compared to the college-aged and older-adult populations considered separately. Substance use was not significantly associated with oral or cervicogenital HPV infection. Many studies report substantially higher oral HPV infection prevalence in men than in women. That difference may not be uniform across populations in the US.
Characterizing the Progression of Pulmonary Edema Severity: Can Pairwise Comparisons in Radiology Reports Help?
Authors: Hu Stephanie M. , Horng Steven , Berkowitz Seth J. , Liao Ruizhi , Krishnan Rahul G. , Lehman Li-wei H. , Mark Roger G.
Published: January 2022

Accurately assessing the severity of pulmonary edema is critical for making treatment decisions in congestive heart failure patients. However, the current scale for quantifying pulmonary edema based on chest radiographs does not have well-characterized severity levels, with substantial inter-radiologist disagreement. In this study, we investigate whether comparisons documented in radiology reports can provide accurate characterizations of pulmonary edema progression. We propose a rules-based natural language processing approach to assess the change in a patient’s pulmonary edema status (e.g. better, worse, no change) by performing pairwise comparisons of consecutive radiology reports, using regular expressions and heuristics derived from clinical knowledge. Evaluated against ground-truth labels from expert radiologists, our labeler extracts comparisons describing the progression of pulmonary edema with 0.875 precision and 0.891 recall. We also demonstrate the potential utility of comparison labels in providing additional fine-grained information over noisier labels produced by models that directly estimate severity level.