bluuebunny/crossref_metadata_2025 huggingface dataset:
The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts
Authors: Liu Huadie , Zhai Lukai , Liu Ye , Lu Di , VanderArk Alexandra , Yang Tao , Krawczyk Connie M.
Published: February 2023

Women experience osteoporosis at higher rates than men. Aside from hormones, the mechanisms driving sex-dependent bone mass regulation are not well-understood. Here, we demonstrate that the X-linked H3K4me2/3 demethylase KDM5C regulates sex-specific bone mass. Loss of KDM5C in hematopoietic stem cells or bone marrow monocytes (BMM) increases bone mass in female but not male mice. Mechanistically, loss of KDM5C impairs the bioenergetic metabolism resulting in impaired osteoclastogenesis. Treatment with the KDM5 inhibitor reduces osteoclastogenesis and energy metabolism of both female mice and human monocytes. Our report details a novel sex-dependent mechanism for bone homeostasis, connecting epigenetic regulation to osteoclast metabolism, and positions KDM5C as a target for future treatment of osteoporosis in women.

One-Sentence Summary

KDM5C, an X-linked epigenetic regulator, controls female bone homeostasis by promoting energy metabolism in osteoclasts.
Balancing grain yield trade-offs in ‘Miracle-Wheat’
Authors: Abbai Ragavendran , Golan Guy , Longin C. Friedrich H. , Schnurbusch Thorsten
Published: February 2023

Introducing variations in inflorescence architecture, such as the ‘Miracle-Wheat’ (Triticum turgidumconvar.compositum(L.f.) Filat.) with a branching spike, has relevance for enhancing wheat grain yield. However, in the spike-branching genotypes, the increase in spikelet number is generally not translated into grain yield advantage because of reduced grains per spikelet and grain weight. Here, we investigated if such trade-offs might be a function of source-sink strength by using 385 RILs developed by intercrossing the spike-branching landrace TRI 984 and CIRNO C2008, an elite durum (T. durumL.) cultivar; they were genotyped using the 25K array. Various plant and spike architectural traits, including flag leaf, peduncle and spike senescence rate, were phenotyped under field conditions for two consecutive years. On Chr 5AL, we found a new modifier QTL for spike-branching,branched headt3(bht-A3), which was epistatic to the previously knownbht-A1locus. Besides,bht-A3was associated with more grains per spikelet and a delay in flag leaf senescence rate. Importantly, favourable allelesviz., bht-A3andgrain protein content(gpc-B1) that delayed senescence are required to improve grain number and grain weight in the spike-branching RILs. In summary, achieving a balanced source-sink relationship might minimise grain yield trade-offs in Miracle-Wheat.

HIGHLIGHT

Genetic interplay between sink number and post-anthesis source activity limits grain yield in the spike-branching ‘Miracle-Wheat’.
The Multidrug Resistance Transporter P-glycoprotein Confers Resistance to Ferroptosis Inducers
Authors: Frye William J. E. , Huff Lyn M. , González Dalmasy José M. , Salazar Paula , Carter Rachel M. , Gensler Ryan T. , Esposito Dominic , Robey Robert W. , Ambudkar Suresh V. , Gottesman Michael M.
Published: February 2023

Ferroptosis is a form of cell death caused by direct or indirect inhibition of glutathione peroxidase 4 that leads to lethal lipid peroxidation. Several small molecule ferroptosis inducers (FINs) have been reported, yet little information is available regarding resistance mechanisms, particularly their interaction with the ATP-binding cassette (ABC) transporters P-glycoprotein (P-gp, ABCB1) and ABCG2. Given the role that ABC transporters play in absorption, distribution, and excretion of many drugs, characterizing these interactions could provide information regarding oral bioavailability and brain penetration and may predict drug-drug interactions. Using ferroptosis-sensitive A673 cells transfected to express P-gp or ABCG2, we found that P-gp overexpression was able to confer resistance to FIN56 and the erastin derivatives imidazole ketone erastin and piperazine erastin. Results were confirmed with OVCAR8-derived NCI/ADR-RES cells that overexpress P-gp, where the P-gp inhibitor valspodar completely inhibited resistance to the FINs. P-gp-mediated resistance to imidazole ketone erastin and piperazine erastin was also reversed in UO-31 renal cancer cells by CRISPR-mediated knockout ofABCB1. At a concentration of 10 μM, the FINs ML-162, GPX inhibitor 26a, and PACMA31 were able to increase intracellular rhodamine 123 fluorescence over 10-fold in P-gp-expressing MDR-19 cells and GPX inhibitor 26a was able to increase intracellular purpurin-18 fluorescence over 4-fold in ABCG2-expressing R-5 cells. Expression of P-gp may reduce the efficacy of these FINs in cancers that express the transporter and may prevent access to sanctuary sites such as the brain. The ability of some FINs to inhibit P-gp and ABCG2 suggests potential drug-drug interactions.

SIGNIFICANCE STATEMENT

While several small-molecule ferroptosis inducers have been described, little work has addressed potential interactions with ABC transporters such as P-glycoprotein or ABCG2 that might limit bioavailability or brain penetration. We find that the ferroptosis inducers FIN56, imidazole ketone erastin, and piperazine erastin are substrates of P-glycoprotein. ML-162, GPX inhibitor 26a, and PACMA31 were found to inhibit P-glycoprotein, while GPX inhibitor 26a was additionally able to inhibit ABCG2, suggesting the potential for drug-drug interactions.
Spatial and Temporal Dynamics at an Actively Silicifying Hydrothermal System
Authors: Rasmussen Kalen L. , Stamps Blake W. , Vanzin Gary F. , Ulrich Shannon M. , Spear John R.
Published: February 2023

Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park, Wyoming (YNP), actively gushing silicon rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone’s outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation < 32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophileThermocrinisdominates the hydrothermal source biofilm community, and the thermophilesMeiothermusandLeptococcusdominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such asLeptococcus, Chloroflexus, andChloracidobacteriumact as primary producers for the system supporting heterotrophic growth of taxa such asRaineya, Tepidimonas, andMeiothermus. Community dynamics illustrate large changes yearly driven by abundance changes of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.
Candida albicansstimulates the formation of a multi-receptor complex that mediates epithelial cell invasion during oropharyngeal infection
Authors: Phan Quynh T. , Solis Norma V. , Cravener Max V. , Swidergall Marc , Lin Jianfeng , Huang Manning Y. , Liu Hong , Singh Shakti , Ibrahim Ashraf S. , Mazzone Massimiliano , Mitchell Aaron P. , Filler Scott G.
Published: February 2023

Fungal invasion of the oral epithelium is central to the pathogenesis of oropharyngeal candidiasis (OPC).Candida albicansinvades the oral epithelium by receptor-induced endocytosis but this process is incompletely understood. We found thatC. albicansinfection of oral epithelial cells induces c-Met to form a multi-protein complex with E-cadherin and the epidermal growth factor receptor (EGFR). E-cadherin is necessary forC. albicansto activate both c-Met and EGFR and to induce the endocytosis ofC. albicans. Proteomics analysis revealed that c-Met interacts withC. albicansHyr1, Als3 and Ssa1. Both Hyr1 and Als3 were required forC. albicansstimulation of c-Met and EGFR in oral epithelial cells in vitro and for full virulence during OPC in mice. Treating mice with small molecule inhibitors of c-Met and EGFR ameliorated OPC, demonstrating the potential therapeutic efficacy of blocking these host receptors forC. albicans.

Graphical abstract

Highlights

c-Met is an oral epithelial cell receptor forCandida albicans

C. albicansinfection causes c-Met and the epidermal growth factor receptor (EGFR) to form a complex with E-cadherin, which is required for c-Met and EGFR function

C. albicansHyr1 and Als3 interact with c-Met and EGFR, inducing oral epithelial cell endocytosis and virulence during oropharyngeal candidiasis

Dual blockade of c-Met and EGFR ameliorates oropharyngeal candidiasis
Epilepsy-associatedSCN2A(NaV1.2) Variants Exhibit Diverse and Complex Functional Properties
Authors: Thompson Christopher H. , Potet Franck , Abramova Tatiana V. , DeKeyser Jean-Marc , Ghabra Nora F. , Vanoye Carlos G. , Millichap John , George Alfred L.
Published: February 2023

Pathogenic variants in neuronal voltage-gated sodium (NaV) channel genes includingSCN2A, which encodes NaV1.2, are frequently discovered in neurodevelopmental disorders with and without epilepsy.SCN2Ais also a high confidence risk gene for autism spectrum disorder (ASD) and nonsyndromic intellectual disability (ID). Previous work to determine the functional consequences ofSCN2Avariants yielded a paradigm in which predominantly gain-of-function (GoF) variants cause epilepsy whereas loss-of-function (LoF) variants are associated with ASD and ID. However, this framework is based on a limited number of functional studies conducted under heterogenous experimental conditions whereas most disease-associatedSCN2Avariants have not been functionally annotated. We determined the functional properties of more than 30SCN2Avariants using automated patch clamp recording to assess the analytical validity of this approach and to examine whether a binary classification of variant dysfunction is evident in a larger cohort studied under uniform conditions. We studied 28 disease-associated variants and 4 common population variants using two distinct alternatively spliced forms of NaV1.2 that were heterologously expressed in HEK293T cells. Multiple biophysical parameters were assessed on 5,858 individual cells. We found that automated patch clamp recording provided a valid high throughput method to ascertain detailed functional properties of NaV1.2 variants with concordant findings for a subset of variants that were previously studied using manual patch clamp. Additionally, many epilepsy-associated variants in our study exhibited complex patterns of gain- and loss-of-function properties that are difficult to classify overall by a simple binary scheme. The higher throughput achievable with automated patch clamp enables study of a larger number of variants, greater standardization of recording conditions, freedom from operator bias, and enhanced experimental rigor valuable for accurate assessment of NaVchannel variant dysfunction. Together, this approach will enhance our ability to discern relationships between variant channel dysfunction and neurodevelopmental disorders.
In vitroandin vivoeffects of zoledronate on senescence and senescence-associated secretory phenotype markers
Authors: Samakkarnthai Parinya , Saul Dominik , Zhang Lei , Aversa Zaira , Doolittle Madison L. , Sfeir Jad G. , Kaur Japneet , Atkinson Elizabeth J , Edwards James R. , Russell R. Graham G. , Pignolo Robert J. , Kirkland James L. , Tchkonia Tamar , Niedernhofer Laura J. , Monroe David G. , LeBrasseur Nathan K. , Farr Joshua N. , Robbins Paul D. , Khosla Sundeep
Published: February 2023

In addition to reducing fracture risk, zoledronate has been found in some studies to decrease mortality in humans and extend lifespan and healthspan in animals. Because senescent cells accumulate with aging and contribute to multiple co-morbidities, the non-skeletal actions of zoledronate could be due to senolytic (killing of senescent cells) or senomorphic (inhibition of the secretion of the senescence-associated secretory phenotype [SASP]) actions. To test this, we first performedin vitrosenescence assays using human lung fibroblasts and DNA repair-deficient mouse embryonic fibroblasts, which demonstrated that zoledronate killed senescent cells with minimal effects on non-senescent cells. Next, in aged mice treated with zoledronate or vehicle for 8 weeks, zoledronate significantly reduced circulating SASP factors, including CCL7, IL-1β, TNFRSF1A, and TGFβ1 and improved grip strength. Analysis of publicly available RNAseq data from CD115+ (CSF1R/c-fms+) pre-osteoclastic cells isolated from mice treated with zoledronate demonstrated a significant downregulation of senescence/SASP genes (SenMayo). To establish that these cells are potential senolytic/senomorphic targets of zoledronate, we used single cell proteomic analysis (cytometry by time of flight [CyTOF]) and demonstrated that zoledronate significantly reduced the number of pre-osteoclastic (CD115+/CD3e-/Ly6G-/CD45R-) cells and decreased protein levels of p16, p21, and SASP markers in these cells without affecting other immune cell populations. Collectively, our findings demonstrate that zoledronate has senolytic effectsin vitroand modulates senescence/SASP biomarkersin vivo. These data point to the need for additional studies testing zoledronate and/or other bisphosphonate derivatives for senotherapeutic efficacy.
Desmosome-anchored intermediate filaments facilitate tension-sensitive RhoA signaling for epithelial homeostasis
Authors: Nanavati Bageshri Naimish , Noordstra Ivar , Verma Suzie , Duszyc Kinga , Green Kathleen J. , Yap Alpha S.
Published: February 2023

Epithelia are subject to diverse forms of mechanical stress during development and post-embryonic life. They possess multiple mechanisms to preserve tissue integrity against tensile forces, which characteristically involve specialized cell-cell adhesion junctions coupled to the cytoskeleton. Desmosomes connect to intermediate filaments (IF) via desmoplakin (DP)1,2, while the E-cadherin complex links to the actomyosin cytoskeleton in adherens junctions (AJ)3. These distinct adhesion-cytoskeleton systems support different strategies to preserve epithelial integrity, especially against tensile stress. IFs coupled to desmosomes can passively respond to tension by strain-stiffening4–10, whereas for AJs a variety of mechanotransduction mechanisms associated with the E-cadherin apparatus itself11,12, or proximate to the junctions13, can modulate the activity of its associated actomyosin cytoskeleton by cell signaling. We now report a pathway where these systems collaborate for active tension-sensing and epithelial homeostasis. We found that DP was necessary for epithelia to activate RhoA at AJ on tensile stimulation, an effect that required its capacity to couple IF to desmosomes. DP exerted this effect by facilitating the association of Myosin VI with E-cadherin, the mechanosensor for the tension-sensitive RhoA pathway at AJ12. This connection between the DP-IF system and AJ-based tension-sensing promoted epithelial resilience when contractile tension was increased. It further facilitated epithelial homeostasis by allowing apoptotic cells to be eliminated by apical extrusion. Thus, active responses to tensile stress in epithelial monolayers reflect an integrated response of the IF- and actomyosin-based cell-cell adhesion systems.
Trophic flexibility and hydrology structure alpine stream food webs: Implications for a fading cryosphere
Authors: Jorgenson Karen L. , Hotaling Scott , Tronstad Lusha M. , Finn Debra S. , Collins Sarah M.
Published: February 2023

Understanding biotic interactions and how they vary across habitats is important for assessing the vulnerability of communities to climate change. Receding glaciers in high mountain areas can lead to the hydrologic homogenization of streams and reduce habitat heterogeneity, which are predicted to drive declines in regional diversity and imperil endemic species. However, little is known about food web structure in alpine stream habitats, particularly among streams fed by different hydrologic sources (e.g., glaciers or snowfields). We used gut content and stable isotope analyses to characterize food web structure of alpine macroinvertebrate communities in streams fed by glaciers, subterranean ice, and seasonal snowpack in the Teton Range, Wyoming, USA. Specifically, we sought to: (1) assess community resource use among streams fed by different hydrologic sources; (2) explore how variability in resource use relates to feeding strategies; and (3) identify which environmental variables influenced resource use within communities. Average taxa diet differed among all hydrologic sources, and food webs in subterranean ice-fed streams were largely supported by the gold algaHydrurus. This finding bolsters a hypothesis that streams fed by subterranean ice may provide key habitat for cold-water species under climate change by maintaining a longer growing season for this high-quality food resource. While a range of environmental variables associated with hydrologic source (e.g., stream temperature) were related to diet composition, hydrologic source categories explained the most variation in diet composition models. Less variable diets within versus among streams suggests high trophic flexibility, which was further supported by high levels of omnivory. This inherent trophic flexibility may bolster alpine stream communities against future changes in resource availability as the mountain cryosphere fades. Ultimately, our results expand understanding of the habitat requirements for imperiled alpine taxa while empowering predictions of their vulnerability under climate change.
Exon 44 skipping in Duchenne muscular dystrophy: NS-089/NCNP-02, an antisense oligonucleotide with a novel connected-sequence design
Authors: Watanabe Naoki , Tone Yuichiro , Nagata Tetsuya , Masuda Satoru , Saito Takashi , Motohashi Norio , Takagaki Kazuchika , Aoki Yoshitsugu , Takeda Shin’ichi
Published: February 2023

Exon-skipping therapy mediated by antisense oligonucleotides (ASOs) is expected to provide a therapeutic option for Duchenne muscular dystrophy (DMD). ASOs for exon skipping reported so far target a single continuous sequence in or around the target exon. In the present study, we investigated ASOs for exon 44 skipping (applicable to approximately 6% of all DMD patients) to improve activity by using a novel ASO design incorporating two connected sequences. Phosphorodiamidate morpholino oligomers targeting two separate sequences in exon 44 were created to simultaneously target two splicing regulators in exon 44, and their exon 44 skipping was measured. NS-089/NCNP-02 showed the highest skipping activity among the oligomers. NS-089/NCNP-02 also induced exon 44 skipping and dystrophin protein expression in cells from a DMD patient to whom exon 44 skipping is applicable. We also assessed thein vivoactivity of NS-089/NCNP-02 by intravenous administration to cynomolgus monkeys. NS-089/NCNP-02 induced exon 44 skipping in skeletal and cardiac muscle of cynomolgus monkeys. In conclusion, NS-089/NCNP-02, an ASO with a novel connected-sequence design, showed bothin vitroandin vivoexon-skipping activity.
Mouse Embryonic Stem Cell Pluripotency Factors Regulate RNA Methylation
Authors: Sedivy Laura J. , Brandt Gabrielle , Martin Aspen L. , Abroe Hannah M. , Phiel Christopher J.
Published: February 2023

The pluripotency of embryonic stem cells (ESCs) is actively promoted by a diverse set of factors, including leukemia inhibitory factor (LIF), glycogen synthase kinase-3 (Gsk-3) and mitogen-activated protein kinase kinase (MEK) inhibitors, ascorbic acid, and α-ketoglutarate. Strikingly, several of these factors intersect with the post-transcriptional methylation of RNA (m6A), which has also been shown to play a role in ESC pluripotency. Therefore, we explored the possibility that these factors converge on this biochemical pathway to promote the retention of ESC pluripotency. Mouse ESCs were treated with various combinations of small molecules, and the relative levels of m6A RNA were measured, as well as the expression of genes marking naïve and primed ESCs. The most surprising result was the discovery that replacing glucose with high levels of fructose pushed ESCs to a more naïve state and reduced m6A RNA abundance. Our results suggest a correlation between molecules previously shown to promote the retention of ESC pluripotency and m6A RNA levels, strengthening a molecular connection between reduced m6A RNA and the pluripotent state, and provides a foundation for future mechanistic studies on the role of m6A and ESC pluripotency.
Cross-species proteomic and microRNA comparison of extracellular vesicles in human milk, cow’s milk, and infant formula products: moving towards next generation infant formula products
Authors: Turner Natalie P. , Abeysinghe Pevindu , Sadowski Pawel , Mitchell Murray D.
Published: February 2023

Milk and milk products such as infant formula (IF) play a fundamental role in serving the nutritional needs of the developing infant. Extracellular vesicles (EVs) in human (HM) and cow’s milk (CM) contain molecular cargo such as proteins and micro(mi)RNA that serve as functional messengers between cells and may be of importance to infant health. Here, we have developed a pipeline using advanced proteomics and transcriptomics to enable cross-species comparison of milk and IF EVs. EVs from HM, CM and IF were subjected to data-independent acquisition mass spectrometry and RNA-seq. Differentially abundant proteins (143) and miRNAs (514) were identified in HM and CM EVs, and CM EV proteins and miRNAs were preserved in IF EVs (∼20% protein; ∼90% miRNA). We foresee this work to be used in large scale studies to determine biologically relevant species-specific differences in milk EVs that could be leveraged to improve IF products.
Elucidation of Genome-wide Understudied Proteins targeted by PROTAC-induced degradation using Interpretable Machine Learning
Authors: Xie Li , Xie Lei
Published: February 2023

Proteolysis-targeting chimeras (PROTACs) are hetero-bifunctional molecules. They induce the degradation of a target protein by recruiting an E3 ligase to the target. The PROTAC can inactivate disease-related genes that are considered as understudied, thus has a great potential to be a new type of therapy for the treatment of incurable diseases. However, only hundreds of proteins have been experimentally tested if they are amenable to the PROTACs. It remains elusive what other proteins can be targeted by the PROTAC in the entire human genome. For the first time, we have developed an interpretable machine learning model PrePROTAC, which is based on a transformer-based protein sequence descriptor and random forest classification to predict genome-wide PROTAC-induced targets degradable by CRBN, one of the E3 ligases. In the benchmark studies, PrePROTAC achieved ROC-AUC of 0.81, PR-AUC of 0.84, and over 40% sensitivity at a false positive rate of 0.05, respectively. Furthermore, we developed an embedding SHapley Additive exPlanations (eSHAP) method to identify positions in the protein structure, which play key roles in the PROTAC activity. The key residues identified were consistent with our existing knowledge. We applied PrePROTAC to identify more than 600 novel understudied proteins that are potentially degradable by CRBN, and proposed PROTAC compounds for three novel drug targets associated with Alzheimer’s disease.

Author Summary

Many human diseases remain incurable because disease-causing genes cannot by selectively and effectively targeted by small molecules. Proteolysis-targeting chimera (PROTAC), an organic compound that binds to both a target and a degradation-mediating E3 ligase, has emerged as a promising approach to selectively target disease-driving genes that are not druggable by small molecules. Nevertheless, not all of proteins can be accommodated by E3 ligases, and be effectively degraded. Knowledge on the degradability of a protein will be crucial for the design of PROTACs. However, only hundreds of proteins have been experimentally tested if they are amenable to the PROTACs. It remains elusive what other proteins can be targeted by the PROTAC in the entire human genome. In this paper, we propose an intepretable machine learning model PrePROTAC that takes advantage of powerful protein language modeling. PrePROTAC achieves high accuracy when evaluated by an external dataset which comes from different gene families from the proteins in the training data, suggesting the generalizability of PrePROTAC. We apply PrePROTAC to the human genome, and identify more than 600 understudied proteins that are potentially responsive to the PROTAC. Furthermore, we design three PROTAC compounds for novel drug targets associated with Alzheimer’s disease.
SNP discovery and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology
Authors: Adomako Kwaku , Sovi Selorm , Kyei Bismark , Hamidu Jacob Alhassan , Olympio Oscar Simon , Aggrey Samuel E.
Published: February 2023

Indigenous and commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CC) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (21%) were in the highest PIC value range (0.45 to 0.50). Between the KNUST population and the indigenous ecotypes, pairwise FSTvalues were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies
Authors: Westfall Dylan H. , Deng Wenjie , Pankow Alec , Murrell Hugh , Chen Lennie , Zhao Hong , Williamson Carolyn , Rolland Morgane , Murrell Ben , Mullins James I.
Published: February 2023

Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciencessinglemoleculereal-time platform was used to sequence PCR amplicons derived from cDNA templates tagged withuniversalmolecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies.

Author Summary

There is a great need to understand the genetic diversity of pathogens in an accurate and timely manner, but many errors can be introduced during the sample handling and sequencing steps which may prevent accurate analyses. In some cases, the errors introduced during these steps can be indistinguishable from real genetic variation and prevent analyses from identifying true sequence variation present in the pathogen population. There are established methods which can help to prevent these types of errors, but can involve many different steps and variables, all of which must be optimized and tested together to ensure the desired effect. Here we show results from testing different methods on a set of HIV+ blood plasma samples and arrive at a streamlined laboratory protocol and bioinformatic pipeline which prevents or corrects for different types of errors that can arise in sequence datasets. These methods should be an accessible starting point for anyone wanting accurate sequencing without extensive optimizations.
Intraluminal neutrophils limit epithelium damage by reducing pathogen assault on intestinal epithelial cells duringSalmonellagut infection
Authors: Gül Ersin , Fattinger Stefan A. , Nguyen Bidong D. , Hausmann Annika , Furter Markus , Barthel Manja , Sellin Mikael E. , Hardt Wolf-Dietrich
Published: February 2023

Recruitment of neutrophils into the gut epithelium is a cardinal feature of intestinal inflammation in response to enteric infections. Previous work using the model pathogenSalmonellaTyphimurium (S. Tm) established that invasion of intestinal epithelial cells byS.Tm leads to recruitment of neutrophils into the gut lumen, where they can reduce pathogen loads transiently. Notably, a fraction of the pathogen population can survive this defense, re-grow to high density, and continue triggering enteropathy. However, the functions of intraluminal neutrophils in the defense against enteric pathogens and their effects on preventing or aggravating epithelial damage are still not fully understood. Here, we address this question via neutrophil depletion in different mouse models ofSalmonellacolitis, which differ in their degree of enteropathy. In an antibiotic pre-treated mouse model, neutrophil depletion by an anti-Ly6G antibody exacerbated epithelial damage. This could be linked to compromised neutrophil-mediated elimination and reduced physical blocking of the gut-luminalS.Tm population such that the pathogen density remained high near the epithelial surface throughout the infection. The removal of luminalS. Tm by gentamicin, an antibiotic restricted to the gut lumen, reversed the effect of neutrophil depletion on epithelial cell loss. Strikingly, when using germ-free mice and anS. TmssaVmutant capable of epithelium invasion, but attenuated for survival and growth within host tissues, neutrophil depletion caused exacerbated immune activation of the gut mucosa and a complete destruction of the epithelial barrier. Together, our data indicate that intraluminal neutrophils are central for maintaining epithelial barrier integrity during acuteSalmonella-induced gut inflammation, by limiting the sustained pathogen assault on the epithelium in a critical window of the infection.

Highlights

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After the first wave of mucosal invasion (day 1 p.i.),S. Tm maintains the assault from the lumen, triggering the continued expulsion of epithelial cells in antibiotic pre-treated mice.

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Neutrophil recruitment into the gut lumen is essential to limit this continuedSalmonellaattack on the epithelium.

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In antibiotic pre-treated SPF mice, neutrophil depletion exacerbatesS. Tm invasion, causing excessive epithelial cell loss, which compromises epithelial barrier integrity at later time points (day 2-3 p.i.).

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In germ-free mice, neutrophil depletion exacerbates epithelial responses and epithelial barrier destruction even more strongly than in streptomycin pre-treated SPF mice.

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Gentamicin treatment andssaVmutant infections indicate that neutrophils prevent epithelial damage by eliminating and physically blocking gut-luminal pathogens.
EXO1-mediated DNA repair by single-strand annealing is essential for BRCA1-deficient cells
Authors: van de Kooij B. , Schreuder A. , Pavani R.S. , Garzero V. , Van Hoeck A. , San Martin Alonso M. , Koerse D. , Wendel T.J. , Callen E. , Boom J. , Mei H. , Cuppen E. , Nussenzweig A. , van Attikum H. , Noordermeer S.M.
Published: February 2023

Deficiency for the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR) leads to chromosomal instability and diseases such as cancer. Yet, defective HR also results in vulnerabilities that can be exploited for targeted therapy. Here, we identify such a vulnerability and show that BRCA1-deficient cells are dependent on the long-range end-resection factor EXO1 for survival. EXO1 loss results in DNA replication-induced lesions decorated by poly(ADP-ribose)-chains. In cells that lack both BRCA1 and EXO1, this is accompanied by unresolved DSBs due to impaired single-strand annealing (SSA), a DSB repair process that requires the activity of both proteins. In contrast, BRCA2-deficient cells have increased SSA, also in the absence of EXO1, and hence are not dependent on EXO1 for survival. In agreement with our mechanistic data, BRCA1-mutated tumours have elevatedEXO1expression and contain more genomic signatures of SSA compared to BRCA1-proficient tumours. Collectively, our data indicate that EXO1 is a promising novel target for treatment of BRCA1-deficient tumours.
Multiviral Quartet Nanocages Elicit Broad Anti-Coronavirus Responses for Proactive Vaccinology
Authors: Hills Rory A. , Tan Tiong Kit , Cohen Alexander A. , Keeffe Jennifer R. , Keeble Anthony H. , Gnanapragasam Priyanthi N.P. , Storm Kaya N. , Hill Michelle L. , Liu Sai , Gilbert-Jaramillo Javier , Afzal Madeeha , Napier Amy , James William S. , Bjorkman Pamela J. , Townsend Alain R. , Howarth Mark
Published: February 2023

Defending against future pandemics may require vaccine platforms that protect across a range of related pathogens. The presentation of multiple receptor-binding domains (RBDs) from evolutionarily-related viruses on a nanoparticle scaffold elicits a strong antibody response to conserved regions. Here we produce quartets of tandemly-linked RBDs from SARS-like betacoronaviruses coupled to the mi3 nanocage through a SpyTag/SpyCatcher spontaneous reaction. These Quartet Nanocages induce a high level of neutralizing antibodies against several different coronaviruses, including against viruses not represented on the vaccine. In animals primed with SARS-CoV-2 Spike, boost immunizations with Quartet Nanocages increased the strength and breadth of an otherwise narrow immune response. Quartet Nanocages are a strategy with potential to confer heterotypic protection against emergent zoonotic coronavirus pathogens and facilitate proactive pandemic protection.

One Sentence Summary

A vaccine candidate with polyprotein antigens displayed on nanocages induces neutralizing antibodies to multiple SARS-like coronaviruses.
FUSDelta14 mutation impairs normal brain development and causes systemic metabolic alterations
Authors: Godoy-Corchuelo Juan M. , Ali Zeinab , Martins-Bach Aurea B. , Garcia-Toledo Irene , Fernández-Beltrán Luis C. , Nair Remya R. , Spring Shoshana , Nieman Brian J. , Jimenez-Coca Irene , Bains Rasneer S. , Forrest Hamish , Lerch Jason P. , Miller Karla , Fisher Elizabeth M.C. , Cunningham Thomas J. , Corrochano Silvia
Published: February 2023

FUS (Fused in sarcoma) is a ubiquitously expressed DNA/RNA binding protein. Mutations in FUS cause aggressive juvenile forms of amyotrophic lateral sclerosis (ALS), as in the case with the FUSDelta14 mutation. While most studies have focused on the role of FUS in motor neuron degeneration, little is known about the effect ofFUSmutations in the whole body, and the impact ofFUSmutations in the correct development of the nervous system. We studied pleiotropic phenotypes in a physiological knock-in mouse model carrying the FUSDelta14 mutation in homozygosity. RNA sequencing was conducting in six different tissues (frontal cortex, spinal cord, tibialis anterior muscle, white and brown adipose tissue and liver) to identify the genes and pathways altered by the FUSDelta14 mutant protein in the systemic transcriptome. Additionally, brain structural magnetic resonance imaging (MRI) and histological characterisation was conducted in young mice to study the role of FUS mutation in the brain development. FUS mutant protein was upregulated and mislocalised in the cytoplasm in most cells of the tissues analysed. We identified few genes commonly altered in all tissues by this mutation, although most genes and pathways affected were generally tissue-specific. Phenotypic assessment of mice revealed systemic metabolic alterations related to the pathway changes identified. MRI brain scans revealed that homozygous FUSDelta14 brains were smaller and displayed significant morphological alterations including a thinner cortex, reduced neuronal number and increased gliosis, which correlated with early cognitive impairment and fatal seizures. We demonstrated that the disease aetiology of FUS mutations can include neurodevelopmental and systemic alterations, which should be taken into consideration in the clinic.
Crystal structures of the sulfones of 2,3-diphenyl-2,3-dihydro-4H-1,3-benzothiazin-4-one and 2,3-diphenyl-2,3-dihydro-4H-pyrido[3,2-e][1,3]thiazin-4-one
Authors: Yennawar Hemant P. , Mal Tapas K. , Pacheco Carlos N. , Lagalante Anthony F. , Olsen Mark A. , Russell Michael W. , Muench Grace C. , Moyer Quentin J. , Silverberg Lee J.
Published: February 2023

The title sulfones, 2,3-diphenyl-2,3-dihydro-4H-1,3-benzothiazine-1,1,4-trione, C20H15NO3S, and 2,3-diphenyl-2,3-dihydro-4H-pyrido[3,2-e][1,3]thiazine-1,1,4-trione, C19H14N2O3S, crystallize in space group P21/n with two molecules in each of the asymmetric units and have almost identical unit cells and extended structures. In both structures, the thiazine rings exhibit a screw-boat pucker. The intermolecular interactions observed are C—H...O-type hydrogen bonds and parallel partial π–π stacking between the fused aromatic rings (benzo- or pyrido-) of the core of the molecules within each asymmetric unit, and also connecting to molecules with translational periodicity in the a-axis direction in what can be described as columns (two per asymmetric unit) of stacked molecules with alternating chirality. The pendant phenyl groups of both molecules do not participate in aromatic ring interactions.
A dynamic analysis of a prey–predator population model with a nonlinear harvesting rate
Authors: Mohdeb Nadia
Published: February 2023

Purpose

In this article, the author discusses dynamical behaviors of a prey-predator population model with nonlinear harvesting rate and offers a mathematical analysis of the model.

Design/methodology/approach

The design is by using modelization of populations interaction, qualitative theory of ordinary différential equations, bifurcations analysis, invariant center manifolds theory and Dulac's criterion.

Findings

The author studies the stability of solutions and the existence of periodic solutions in the model, and proves the existence of some invariant sets and the production of a transcritical together with a saddle-node bifurcation.

Practical implications

The author studies the effects of harvesting on the persistence and extinction properties and its influence in the perspectives of economic views.

Originality/value

The authors considers a predator–prey model with a new nonlinear form of harvesting rate. The author’s intention is to make conceptual adjustments to a well-known predator–prey model in order to incorporate the effects of harvesting.
Does environmental uncertainty drive the use of management control systems and innovation?
Authors: Luiz Thiago Tomaz , Beuren Ilse Maria
Published: February 2023

Purpose

This paper analyzes the effects of environmental uncertainty on the use of Management Control Systems (MCS) and product and process innovation.

Design/methodology/approach

The hypotheses were tested with data from a survey carried out with 140 managers of innovative Brazilian firms using structural equation modeling.

Findings

The analyzes show significant negative effects of environmental uncertainty on MCS use and non-significant ones on product and process innovation, which suggests that when environmental uncertainty increases, the MCS use decreases. In contrast, significant positive effects of MCS use on product and process innovation were found, despite environmental uncertainty permeating innovation. However, no mediating effect of the MCS use on the relationship between environmental uncertainty and innovation was observed.

Research limitations/implications

This study presents implications to the management literature grounded on the Contingency Theory by pointing out negative effects of environmental uncertainty on MCS use and product and process innovation. This encourages research on other contingency factors that might be predictors of MCS use and innovation.

Practical implications

The findings provide evidence that the analyzed organizational practices (MCS use and innovation) are conceived and implemented to disregard external stimuli, which may bring dysfunctional consequences that need to be monitored.

Originality/value

The study contributes by revealing that environmental uncertainty inhibits the MCS use and does not favor innovation. It was expected that MCS that produce information about the external environment would be valued and would have effects on the strategic planning in these firms.
Cultivating resilience among Hong Kong's underprivileged ethnic minority groups in the face of a pandemic through a social justice lens
Authors: Arat Gizem , Eryigit-Madzwamuse Suna , Hart Angie
Published: February 2023

Purpose

In this study, the authors investigated ways to cultivate resilience through a social justice lens among ethnic minorities against COVID-19 in Hong Kong.

Design/methodology/approach

A qualitative (case study) methodology was adopted to interview 15 social service providers from diverse ethnic backgrounds serving disadvantaged ethnic minority groups (South and Southeast Asian groups from low-income households, foreign domestic workers and asylum seekers/refugees).

Findings

Two major protective factors were identified, contributing to the development of resilience among diverse ethnic groups: (1) individual-based resilience (including being optimistic) and (2) socio-environmental factors (including ongoing support from strong family, peer and religious settings' support, consulates' support, on-going material and nonmaterial donations, support of young volunteers and importance of online connection and communication) using the integration of resilience and social justice frameworks.

Originality/value

This study showed that the protective factors were found to dynamically interact with each other and the environment. The present study recommends additional culturally sensitive service and policy implications for preventing the long-term impact of mass crises among Hong Kong's marginalized minorities.
A systematic literature review on mHealth related research during the COVID-19 outbreak
Authors: Alam Mohammad Zahedul , Proteek S.M. , Hoque Imranul
Published: February 2023

Purpose

Using smart mobile devices, called mobile health (mHealth), facilitates providing health services, speeds up the process and reduces the costs and complications of direct services. Also, mHealth has many capabilities and applications in epidemic and pandemic outbreaks. This study aimed to systematically review the mHealth adoption researches in epidemic/pandemic outbreaks and provide some suggestions for future research for tackling for COVID-19.

Design/methodology/approach

The results produced in this study are based on the literature analysis of 36 articles on mHealth adoption. To find the relevant studies; searches were done in PubMed, Google, Web of Science and Scopus by related keywords during 2020–2022. After selecting the studies based on the inclusion and exclusion criteria, data were collected by using PRIZMA methods for systematically reviewing the literature.

Findings

Of the 727 retrieved studies, 36 studies related to mHealth services during the pandemic situation were included. This has been performed by collecting data including demographic details, methodological details, limitations and significance of relationships between the constructs from the available articles based on the mHealth services. All studies emphasized the positive effect of mHealth for usage in epidemic/pandemic outbreaks.

Research limitations/implications

The main applications of mHealth for epidemic/pandemic outbreaks included public health aspects, data management, educational programs, diagnosis as well as treatment. mHealth is an appropriate method for encountering epidemic/pandemic outbreaks due to its extensive applications. In the pandemic outbreak of COVID-19, mHealth is one of the best choices to use in the patient-physician relationship as Tele-visits, using in fever coach, providing real-time information for healthcare providers, population monitoring and detecting the diseases based on data obtained from different locations. These findings will help the mHealth providers to design their services accordingly.

Originality/value

This study contributes to the researchers and academicians by providing relevant information regarding the mHealth during the COVID-19 pandemic. This is the first time initiative to explore the research questions and future research direction for the researchers during the COVID-19 outbreak. Based on this, we present a comprehensive and actionable research agenda and practical implications.