bluuebunny/crossref_metadata_2025 huggingface dataset:
Listeria motility increases the efficiency of goblet cell invasion during intestinal infection
Authors: Wortel Inge M. N. , Kim Seonyoung , Liu Annie Y. , Ibarra Enid C. , Miller Mark J.
Published: July 2022

Listeria monocytogenes (Lm) is a food-borne pathogen that causes severe bacterial gastroenteritis, with high rates of hospitalization and mortality. Lm is ubiquitous in soil, water and livestock, and can survive and proliferate at low temperatures. Following oral ingestion of contaminated food, Lm crosses the epithelial through intestinal goblet cells in a mechanism depending on Lm InlA and host E-cadherin. Importantly, human infections typically occur with Lm growing at or below room temperature, which are flagellated and motile. Even though many important human bacterial pathogens are flagellated, little is known regarding the effect of bacterial motility on invasion and immune evasion.

Here, we used complementary imaging and computer modeling approaches to test the hypothesis that bacterial motility helps Lm locate and engage target cells permissive for invasion. Imaging explanted mouse and human intestine, we confirmed that Lm grown at room temperature uses motility to scan the epithelial surface and preferentially attach to target cells. Furthermore, we integrated quantitative parameters from our imaging experiments to construct a versatile “layered” cellular Potts model (L-CPM) that simulates host-pathogen dynamics. Simulated data are consistent with the hypothesis that bacterial motility enhances invasion by allowing bacteria to search the epithelial surface for their preferred invasion targets. Indeed, our model consistently predicts that motile bacteria have invaded ∼2-fold more at the 1-hour mark. This invasion advantage persists even in the presence of host phagocytes, with the balance between invasion and phagocytosis governed almost entirely by bacterial motility.

In conclusion, our simulations provide insight into host pathogen interactions and challenge fundamental assumptions regarding how phagocytes might limit bacterial invasion early during infection.
Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in mice
Authors: Smadja Carole M. , Loire Etienne , Caminade Pierre , Severac Dany , Gautier Mathieu , Ganem Guila
Published: July 2022

Abstract

Deciphering the genetic bases of behavioural traits is essential to understanding how they evolve and contribute to adaptation and biological diversification, but it remains a substantial challenge, especially for behavioural traits with polygenic architectures. In this study, we developed a population genomics approach coupled with functional predictions to address the evolution and genetic basis of olfactory-based assortative mate preferences in the house mouse, suspected to have evolved as a response to selection against hybridisation. We used whole genome resequencing data and theC2statistic of the program BayPass, which contrasts allele frequencies corrected for population structure, to characterize genetic differentiation between sets of populations with strong contrast in behaviour (expressing or not assortative mate preferences) and we identified some regions of the genome showing the expected significant and consistent association with behavioural divergence. A series of Olfactory and Vomeronasal Receptor genes, among the most differentiated genomic regions and in line with functional predictions, stand out as the prime candidates underlying this olfactory-based behavioural divergence. These genes form large gene clusters in the genome, with two main candidate clusters extending up to 1.8 Mb. Variant analyses indicate a potential dual role of regulatory and protein-coding changes in the evolution of choosiness. This study shows that combining expectations on the genomic patterns of divergence with functional expectations represents a promising route to unravelling the genetic architecture of complex trait variation and provides novel insights into the role of olfactory and vomeronasal receptors in mammal adaptation and speciation.
Secreted folate receptor-gamma drives fibrogenesis in nonalcoholic steatohepatitis by amplifying TGFβ signaling in hepatic stellate cells
Authors: Quinn Connor R. , Rico Mario C. , Merali Carmen , Perez-Leal Oscar , Mischley Victoria , Karanicolas John , Friedman Scott L. , Merali Salim
Published: July 2022

Hepatic fibrosis is the primary determinant of mortality in nonalcoholic steatohepatitis (NASH) patients. Antagonism of transforming growth factor β (TGFβ), a master profibrogenic cytokine, is a promising therapeutic target that has not yet been translated into an effective therapy, due in part to the lack of animal models resembling the human phenotype of NASH. Here we have identified that soluble secreted folate receptor gamma (FOLR3), expressed in humans but not rodents, is a secreted protein that is elevated in livers of NASH subjects but not in subjects with nonalcoholic fatty liver, type II diabetes, or healthy subjects. FOLR3, based on global proteomics, was the most highly expressed NASH-specific protein and positively correlated with increasing fibrosis stages, suggesting an impact on activated hepatic stellate cells (HSCs), the key fibrogenic cell in the liver. Exposure of stellate cells to exogenous FOLR3 led to elevated extracellular matrix (ECM) protein production, an effect synergistic with TGFβ1. Structurally, FOLR3 interacts with serine protease HTRA1, which downregulates TGFβ signaling through the degradation of its receptor TGFBR2. Administration of human FOLR3 to mice induced severe bridging fibrosis and an ECM pattern resembling human NASH. Our study uncovers a novel role of FOLR3 in enhancing fibrosis and identifies FOLR3 as a potential therapeutic target in NASH fibrosis.

Abstract Figure
Establishment of Measles Virus Receptor-expressing Vero Cells Lacking Functional Poliovirus Receptors
Authors: Someya Kenji , Okemoto-Nakamura Yuko , Kurata Takako , Kanbayashi Daiki , Saito Noriko , Itamochi Masae , Otsuki Noriyuki , Hanada Kentaro , Takeda Makoto
Published: July 2022

Global efforts are underway to eliminate measles and rubella and active viral surveillance is key to achieving this goal. In addition to this, the World Health Organization announced guidelines for handling materials potentially infectious for poliovirus (PV) to minimize the risk of PV reintroduction and achieve PV eradication. To support the global efforts, we have established new PV-non-susceptible cell lines useful for the isolation of measles virus (MeV) and rubella virus (RuV) (Vero ΔPVR1/2 hSLAM+). In the cell lines, MeV and RuV replicated efficiently with no concern about PV replication.
SNM1A (DCLRE1A) is crucial for efficient repair of complex DNA breaks in human cells
Authors: Swift Lonnie P. , Lagerholm B. Christoffer , Baddock Hannah T. , Henderson Lucy R. , Ratnaweera Malitha , Sengerova Blanka , Lee Sook , Cruz-Migoni Abimael , Waithe Dominic , Renz Christian , Ulrich Helle D. , Newman Joseph A. , Schofield Christopher J. , McHugh Peter J.
Published: July 2022

DNA double-strand breaks (DSBs), such as those produced by radiation and radiomimetics, are amongst the most toxic forms of cellular damage, in part because they involve extensive oxidative modifications at the break termini. Prior to completion of DSB repair, the chemically modified termini must be removed. Various DNA processing enzymes have been implicated in the processing of these ‘dirty ends’, but molecular knowledge of this process is limited. Here, we demonstrate a role for the metallo-β-lactamase fold 5ʹ-3ʹ exonuclease SNM1A in this vital process. Cells disrupted for SNM1A manifest increased sensitivity to radiation and radiomimetic agents and show defects in DSB damage repair. SNM1A is recruited and is retained at the sites of DSB damageviathe concerted action of its three highly conserved PBZ, PIP box and UBZ interaction domains, which mediate interactions with poly-ADP-ribose chains, PCNA and the ubiquitinated form of PCNA, respectively. SNM1A can resect DNA containing oxidative lesions induced by radiation damage at break termini. The combined results reveal a crucial role for SNM1A to digest chemically modified DNA during the repair of DSBs and imply that the catalytic domain of SNM1A is an attractive target for potentiation of radiotherapy.
Cardiolipin, and not monolysocardiolipin, preferentially binds to the interface of Complexes III and IV
Authors: Corey Robin A. , Harrison Noah , Stansfeld Phillip J. , Sansom Mark S.P. , Duncan Anna
Published: July 2022

The mitochondrial electron transport chain comprises a series of protein complexes embedded in the inner mitochondrial membrane that generate a proton motive force via oxidative phosphorylation, ultimately generating ATP. These protein complexes can oligomerize to form larger structures called supercomplexes. Cardiolipin (CL), a conical lipid, unique within eukaryotes to the inner mitochondrial membrane, has proven essential in maintaining the stability and function of supercomplexes. Monolysocardiolipin (MLCL) is a CL variant that accumulates in people with Barth syndrome (BTHS). BTHS is caused by defects in CL biosynthesis and characterised by abnormal mitochondrial bioenergetics and destabilised supercomplexes. However, the mechanisms by which MLCL causes pathogenesis remain unclear. Here, multiscale molecular dynamics characterise the interactions of CL and MLCL with yeast and mammalian mitochondrial supercomplexes containing Complex III (CIII) and Complex IV (CIV). Coarse-grained simulations reveal that both CL and MLCL bind to sites at the interface between CIII and CIV of the supercomplex. Free energy perturbation calculations show that MLCL interaction is weaker than that of CL and suggest that interaction with CIV drives this difference. Atomistic contact analyses show that, although interaction with CIII is similar for CL and MLCL, CIV makes more contacts with CL than MLCL, demonstrating that CL is a more successful “glue” between the two complexes. Simulations of the human CIII2CIV supercomplex show that this interface site is maintained between species. Our study suggests that MLCL accumulation in people with BTHS disrupts supercomplex stability by formation of relatively weak interactions at the interface lipid binding site.
A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation
Authors: Penny Jack , Schroeder Gunnar N. , Bengoechea José A. , Collins Ben C.
Published: July 2022

Data independent acquisition (DIA or DIA/SWATH) mass spectrometry has emerged as a primary measurement strategy in the field of quantitative proteomics. diaPASEF is a recent adaptation that leverages trapped ion mobility spectrometry (TIMS) to improve selectivity and increase sensitivity. The complex fragmentation spectra generated by co-isolation of peptides in DIA mode are most typically analyzed with reference to prior knowledge in the form of spectral libraries. The best-established method for generating libraries uses data dependent acquisition (DDA) mode, or DIA mode if appropriately deconvoluted, often including offline fractionation to increase depth of coverage. More recently strategies for spectral library generation based on gas phase fractionation (GPF), where a representative sample is injected serially using narrow DIA windows that cover different mass ranges of the complete precursor space, have been introduced that performed comparably to deep offline fractionation-based libraries for DIA data analysis. Here, we investigated whether an analogous GPF-based library building approach that accounts for the ion mobility (IM) dimension is useful for the analysis of diaPASEF data and can remove the need for offline fractionation. To enable a rapid library development approach for diaPASEF we designed a GPF acquisition scheme covering the majority of multiply charged precursors in the m/z vs 1/K0 space requiring 7 injections of a representative sample and compared this with libraries generated by direct deconvolution-based analysis of diaPASEF data or by deep offline fractionation and ddaPASEF. We found that library generation by IM-GPF outperformed direct deconvolution of the diaPASEF data and had performance approaching that of a deep offline fractionation library, when analysing diaPASEF data. This establishes the ion mobility integrated GPF scheme as a pragmatic approach to rapid library generation for the analysis of diaPASEF data.
Differential Role of GABAergic and Cholinergic Ventral Pallidal Neurons in Behavioral Despair, Conditioned Fear Memory and Active Coping
Authors: Akmese Cemal , Sevinc Cem , Halim Sahar , Unal Gunes
Published: July 2022

The ventral pallidum (VP), a core structure of the reward circuit, is well-associated with appetitive behaviors. Recent evidence suggests that this basal forebrain nucleus may have an overarching role in affective processing, including behavioral responses to aversive stimuli. We investigated this possibility by utilizing selective immunotoxin lesions and a series of behavioral tests in adult male Wistar rats. We made bilateral GAT1-Saporin, 192-IgG-Saporin or PBS (vehicle) injections into the VP to respectively eliminate GABAergic and cholinergic neurons, and tested the animals in the forced swim test (FST), open field test (OFT), elevated plus maze (EPM), Morris water maze (MWM) and cued fear conditioning. Both GAT1-Saporin and 192-IgG-Saporin injections reduced behavioral despair without altering general locomotor activity. This antidepressant-like effect was accompanied by reduced freezing and increased darting in the acquisition phase of cued fear conditioning. In the test phase, cholinergic, but not GABAergic lesions, impaired context-dependent fear memory, while both groups showed diminished conditioned freezing in a novel context. In line with this, selective cholinergic lesions impaired spatial memory in the MWM as compared to GAT1-Saporin or vehicle-injected animals. No differential effect was observed in anxiety-like behavior assessed in the OFT or EPM. These findings show that both the GABAergic and cholinergic cell groups of the VP contribute to behavioral despair and acquired fear responses by suppressing active coping. In conditioned learning, cholinergic ventral pallidal neurons contribute to the fear response in a context-independent manner, while the GABAergic population is required when the context information is missing.

Significance Statement

The ventral pallidum (VP), associated with motivation and appetitive behaviors, is tested for its role in behavioral responses to aversive stimuli. Findings show that both the GABAergic and cholinergic neuronal groups of the VP contribute to behavioral despair and acquired fear response by suppressing active coping. In conditioned learning, the cholinergic neurons are required for the acquired fear response, while the VP GABAergic population becomes necessary only when the context information is missing. These results suggest that ventral pallidal GABAergic and cholinergic projections to the amygdaloid complex may constitute therapeutic targets for affective disorders.
Molecular Underpinnings and Environmental Drivers of Spontaneous Loss of Heterozygosity in Drosophila Intestinal Stem Cells
Authors: zouabi Lara Al , Stefanutti Marine , Riddiford Nick , Rubanova Natalia , Bohec Mylène , Servant Nicolas , Bardin Allison
Published: July 2022

The genome stability of adult stem cells is of particular importance as these cells maintain long-term self-renewal capacity and can contribute extensively to adult tissues. During development and aging, genome mutation leading to loss of heterozygosity (LOH) can uncover recessive phenotypes and be propagated within tissue compartments. This phenomenon occurs in normal human tissues, and is prevalent in pathological genetic conditions and cancers. While previous studies in yeast have defined distinct DNA repair mechanisms that can promote LOH, the predominant pathways underlying LOH in complex somatic tissues of multicellular organisms arenot well understood. In addition, how environmental triggers such as pathogenic bacterial infection may impact LOH is unclear. Here, we investigate the mechanisms giving rise to LOH in adult intestinal stem cells in Drosophila. Our data indicate that infection with the enteric pathogenic bacteria, Erwinia carotovora carotovora 15 but not Pseudomonas entomophila increases LOH frequency. Using whole-genome sequencing of somatic LOH events, we demonstrate that they arise primarily via mitotic recombination. Molecular features of recombination sites and genetic evidence argue against formation via break-induced replication and instead support cross-over events arising from double Holliday junction-based repair. This study provides a mechanistic understanding of mitotic recombination in stem cells in vivo, an important mediator of LOH.
Sex differences in default mode network connectivity in healthy aging adults
Authors: Ficek-Tani Bronte , Horien Corey , Ju Suyeon , Li Nancy , Lacadie Cheryl , Shen Xilin , Scheinost Dustin , Constable R Todd , Fredericks Carolyn
Published: July 2022

Women show an increased lifetime risk of Alzheimer’s disease (AD) compared to men. Characteristic brain connectivity changes, particularly within the default mode network (DMN), have been associated with both symptomatic and preclinical AD, but the impact of sex on DMN function throughout aging is poorly understood. We investigated sex differences in DMN connectivity over the lifespan in 595 cognitively healthy participants from the Human Connectome Project - Aging cohort. We used the intrinsic connectivity distribution (a robust voxel-based metric of functional connectivity) and a seed connectivity approach to determine sex differences within the DMN and between the DMN and whole brain.

Compared with men, women demonstrated increased connectivity with age in posterior DMN nodes and decreased connectivity in the medial prefrontal cortex. Differences were most prominent in the decades surrounding menopause. Seed-based analysis revealed increased connectivity in women from the posterior cingulate to angular gyrus and parahippocampal gyrus, which correlated with neuropsychological measures of declarative memory. Taken together, we show significant sex differences in DMN subnetworks over the lifespan, including patterns in aging women that resemble changes previously seen in preclinical AD. These findings highlight the importance of considering sex in neuroimaging studies of aging and neurodegeneration.
DNA Methylation is stable after MMEJ and NHEJ double strand break repair
Authors: Bnaya Ester , Shilo Shay , Feldman Tzah , Bacharach Tal , Moskovitz Yoni , Kadam Aditee , Yedidim Paz , Azogy Hadas , Kaushansky Nathali , Chapal-Ilani Noa , Shlush Liran I.
Published: July 2022

DNA double strand breaks (DSBs) are a major source of mutations. Both non-homologous-end-joining (NHEJ) and microhomology-mediated-end-joining (MMEJ) DSB repair pathways are error prone and produce deletions, which can lead to cancer. DSBs also lead to epigenetic changes, including demethylation, which is involved in carcinogenesis. Of specific interest is the MMEJ repair pathway, as it requires methylation restoration around the break, as a result of the resection and formation of single stranded (ssDNA) intermediates. While, methylation patterns after homologous recombination (HR) have been partially studied, the methylation status after MMEJ and NHEJ remains poorly reported, and can be relevant for cancer. To study methylation patterns around DSB after NHEJ and MMEJ repair, we used targeted bisulfite-sequencing (BS-seq) to quantify methylation of dozens of single cell clones after induction of DSB by CRISPR. Each single cell clone was classified according to the sequence signature to a specific repair mechanism: NHEJ or MMEJ. Comparison of single cell clones after DSB to control cells, without DSB, demonstrated correct restoration of the methylation levels. No difference in methylation patterns was noticed when comparing NHEJ to MMEJ. Methylation levels in gene body, highly methylated CpGs (n=61, 4000 base pairs around DSB) and in low methylation CpGs (n=19), remained stable after both MMEJ and NHEJ. Gene body methylation persisted even on the background of DNMT3A R882C mutation, the most prevalent preleukemic mutation, in which the de novo methylation machinery is compromised. An exception observed in a single CpG site (ASXL1 995) which demonstrated elevated methylation rate after DSB repair only in the presence of WT DNMT3A. In summary, DNA methylation restoration demonstrated high fidelity after DSB both in methylated and unmethylated gene body, even in cases where DNA resections and deletions occurred.

Author Summary

DNA holds the genetic information. Modifications on the DNA molecule such as DNA methylation are crucial for the genetic regulation. DNA damage is harmful to the cell and needs to be repaired. Different repair mechanisms may result in mutations that can be identified according to their sequence signature. In the work presented here we examined changes in DNA methylation after different types of DNA repair, MMEJ and NHEJ. We found that DNA methylation is highly stable after DNA repair regardless to the repair mechanism and genomic context.
Live-cell imaging and mathematical analysis of the “community effect” in apoptosis
Authors: Coursier Diane , Coulette David , Leman Hélène , Grenier Emmanuel , Ichim Gabriel
Published: July 2022

As a cellular intrinsic mechanism leading to cellular demise, apoptosis was thoroughly characterized from a mechanistic perspective. Nowadays there is an increasing interest in describing the non-cell autonomous or community effects of apoptosis, especially in the context of resistance to cancer treatments. Transitioning from cell-centered to cell population-relevant mechanisms adds a layer of complexity for imaging and analyzing an enormous number of apoptotic events. In addition, the community effect between apoptotic and living cells is difficult to be taken into account for complex analysis. We describe here a robust and easy to implement method to analyze the interactions between cancer cells, while under apoptotic pressure. Using this approach we showed as proof-of-concept that apoptosis is insensitive to cellular density, while the proximity to apoptotic cells increases the probability of a given cell to undergo apoptosis.
DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts
Authors: Rimoldi Martina , Wang Ning , Zhang Jilin , Villar Diego , Odom Duncan T. , Taipale Jussi , Flicek Paul , Roller Maša
Published: July 2022

Background

DNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially correlated across the genome, typically high in repressed regions but low in transcription factor (TF) binding sites and active regulatory regions. However, the mechanisms establishing genome-wide and TF binding site methylation patterns are still unclear.

Results

We used a comparative approach to investigate the association of DNA methylation to TF binding evolution in mammals. Specifically, we experimentally profiled DNA methylation and combined this with published occupancy profiles of five distinct TFs (CTCF, CEBPA, HNF4A, ONECUT1, FOXA1) in the liver of five mammalian species (human, macaque, mouse, rat, dog). TF binding sites were lowly methylated, but they often also had intermediate methylation levels. Employing a classification and clustering approach, we extracted distinct and species conserved patterns of DNA methylation levels at TF bound regions. CEBPA, HNF4A, ONECUT1 and FOXA1 shared the same methylation patterns, while CTCF’s differed. These patterns characterize alternative functions and chromatin landscapes of TF bound regions. Leveraging our phylogenetic framework, we found DNA methylation gain upon evolutionary loss of TF occupancy, indicating coordinated evolution. Furthermore, each methylation pattern has its own evolutionary trajectory reflecting its genomic contexts.

Conclusions

Our epigenomic analyses found that specific DNA methylation profiles characterize TF binding, and are associated to their regulatory activity, chromatin contexts, and evolutionary trajectories.
Structure and host specificity ofStaphylococcus epidermidisbacteriophage Andhra
Authors: Hawkins N’Toia C. , Kizziah James L. , Hatoum-Aslan Asma , Dokland Terje
Published: July 2022

Staphylococcus epidermidisis an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. An increase in antibiotic resistance inS. epidermidisand other bacterial pathogens has led to renewed interest in the use of bacteriophages as an alternative to conventional antibiotics. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages with compact genomes that are attractive candidates for therapeutic use. Here, we report the structure of the complete virion ofS. epidermidis-infecting phage Andhra, determined using high-resolution cryo-electron microscopy, allowing atomic modeling of the capsid and tail proteins, including twelve trimers of a unique receptor binding protein, the hexameric tail knob that acts as a gatekeeper for DNA ejection, and the tail tip, which is a heterooctamer of two different lytic proteins. Our findings elucidate critical features that enable host recognition and penetration, facilitating the development of this group of phages for therapeutic applications.
Benzimidazoles cause lethality by inhibiting the function of Caenorhabditis elegans neuronal beta-tubulin
Authors: Gibson Sophia B. , Ness-Cohn Elan , Andersen Erik C.
Published: July 2022

Parasitic nematode infections cause an enormous global burden to both human and livestock populations. Resistance to the limited arsenal of anthelmintic drugs used to combat these infections is widespread, including resistance to benzimidazole (BZ) compounds commonly found in livestock parasites. Previous studies using the free-living nematode Caenorhabditis elegans to model parasitic nematode resistance have shown that loss-of-function mutations in the beta-tubulin gene ben-1 confer resistance to BZ drugs. However, the mechanism of resistance and the tissue-specific susceptibility are not well known in any nematode species. To identify in which tissue(s) ben-1 function underlies BZ susceptibility, transgenic strains that express ben-1 in different tissues, including hypodermis, muscles, neurons, intestine, and ubiquitous expression were generated. High-throughput fitness assays were performed to measure and compare the quantitative responses to BZ compounds among different transgenic lines. Significant BZ susceptibility was observed in animals expressing ben-1 in neurons, comparable to expression using the ben-1 promoter. This result suggests that ben-1 function in neurons underlies susceptibility to BZ. Subsetting neuronal expression of ben-1 based on neurotransmitter system further restricted ben-1 function in cholinergic neurons to cause BZ susceptibility. These results better inform our current understanding of the cellular mode of action of BZ and also suggest additional treatments that might potentiate the effects of BZs.

Highlights

Expressing wild-type ben-1 only in neurons restores susceptibility to benzimidazoles

Expression of ben-1 in cholinergic neurons restores susceptibility to benzimidazoles

GABAergic neurons might also play a role in benzimidazole sensitivity

Broad implications for molecular mechanisms of benzimidazole mode of action

Graphical Abstract
Optimizing targeting of pinyon-juniper management for sagebrush birds of conservation concern while avoiding imperiled pinyon jay
Authors: Reinhardt Jason R. , Tack Jason D. , Maestas Jeremy D. , Naugle David E. , Falkowski Michael J. , Doherty Kevin E.
Published: July 2022

Contemporary restoration and management of sagebrush-dominated (Artemisiaspp.) ecosystems across the intermountain west of the United States increasingly involves the removal of expanding conifer, particularly juniper (Juniperusspp.) and pinyon pine (Pinus edulis, P. monophylla). The impetus behind much of this management has been the demonstrated population benefits of sagebrush restoration via conifer removal to greater sage-grouse (Centrocercus urophasianus), a species of conservation concern. One of the challenges with scaling up from a focal-species approach to a community-level perspective, however, is balancing the habitat requirements of different species, some of which may overlap with sage-grouse and others which may have competing habitat needs. Here, we use a systematic conservation planning approach to compute spatial optimizations which prioritize areas for conifer removal across the sage-grouse range while incorporating woodland and sagebrush songbirds into decision-making. Three of the songbirds considered here, Brewer’s sparrow (Spizella breweri), green-tailed towhee (Pipilo chlorurus), and sage thrasher (Poocetes gramineus), are sagebrush-obligates, while another is a woodland-obligate, the pinyon jay (Gymnorhinus cyanocephalus). We find that the inclusion of sagebrush-obligates expands the model-selected area of consideration for conifer management, likely because habitat overlap between sagebrush-obligates is imperfect. The inclusion of pinyon jay, a woodland-obligate, resulted in substantial shifts in the distribution of model-selected priority areas for conifer removal – particularly away from pinyon jay strongholds in Nevada and east-central California. Finally, we compared the conifer optimizations created here with estimates of ongoing conifer removal efforts across the intermountain west and find that a small proportion (13-18%) of management efforts had occurred on areas predicted as being important for pinyon jay, suggesting that much of the ongoing work is already successfully avoiding critical pinyon jay habitat areas.
Physical confinement promotes mesenchymal trans-differentiation of invading transformed cells in vivo
Authors: Zulueta-Coarasa Teresa , Fadul John , Ahmed Marjana , Rosenblatt Jody
Published: July 2022

Metastasis is tightly linked with poor cancer prognosis, yet it is not clear how transformed cells become invasive carcinomas. We previously discovered that single KRasV12-transformed cells can invade directly from the epithelium by basal cell extrusion. During this process, cells de-differentiate by mechanically pinching off their epithelial determinants, but how they trans-differentiate into a migratory, mesenchymal phenotype is not known. Here, we demonstrate that basally extruded KRasV12-expressing cells become significantly deformed as they invade the zebrafish body. Decreasing the confinement that cells experience after they invade reduces the percentage of KRasV12 cells that trans-differentiate into mesenchymal cell types, while higher confinement increases this percentage. Additionally, increased confinement promotes accumulation of internal masses over time. Altogether, our results suggest that mechanical forces drive not only de-differentiation of KRasV12-transformed epithelial cells as they invade but also contribute to their re-differentiation into mesenchymal phenotypes that contribute to distant metastases.
Optimizing immunostaining of archival fish samples to enhance museum collection potential
Authors: Kwan Garfield T. , Frable Benjamin W. , Thompson Andrew R. , Tresguerres Martin
Published: July 2022

Immunohistochemistry (IHC) is a powerful biochemical technique that uses antibodies to specifically label and visualize proteins of interests within biological samples. However, fluid-preserved specimens within natural history collection often use fixatives and protocols that induce high background signal (autofluorescence), which hampers IHC as it produces low signal-to-noise ratio. Here, we explored techniques to reduce autofluorescence using sodium borohydride (SBH), citrate buffer, and their combination on fish tissue preserved with paraformaldehyde, formalin, ethanol, and glutaraldehyde. We found SBH was the most effective quenching technique, and applied this pretreatment to the gill or skin of 10 different archival fishes – including specimens that had been preserved in formalin or ethanol for up to 65 and 37 years, respectively. The enzyme Na+/K+-ATPase (NKA) was successfully immunostained and imaged using confocal fluorescence microscopy, allowing for the identification and characterization of NKA-rich ionocytes essential for fish ionic and acid-base homeostasis. Altogether, our SBH-based method facilitates the use of IHC on archival samples, and unlocks the historical record on fish biological responses to environmental factors (such as climate change) using specimens from natural history collections that were preserved decades to centuries ago.

Highlights

Sodium borohydride pretreatment reduced aldehyde-induced autofluorescence

Successfully immunostained archival samples of various fixative and fixation time

Larval fish that was formalin-fixed for 63-65 years was successfully immunostained
Fiber-Specific Structural Properties Relate to Reading Skills in Children and Adolescents
Authors: Meisler Steven Lee , Gabrieli John D.E.
Published: July 2022

Recent studies suggest that the cross-sectional relationship between reading skills and white matter microstructure, as indexed by fractional anisotropy, is not as robust as previously thought. Fixel-based analyses yield fiber-specific micro- and macrostructural measures, overcoming several shortcomings of the traditional diffusion tensor model. We ran a whole-brain analysis investigating whether the product of fiber density and cross-section (FDC) related to single-word reading skills in a large, open, quality-controlled data set of 983 children and adolescents ages 6-18. We also compared FDC between participants with (n= 102) and without (n= 570) reading disabilities. We found that FDC positively related to reading skills throughout the brain, especially in left temporoparietal and cerebellar white matter, but did not differ between reading proficiency groups. Exploratory analyses revealed that among metrics from other diffusion models - DTI, DKI, and NODDI - only the orientation dispersion and neurite density indexes from NODDI were associated (inversely) with reading skills. The present findings further support the importance of left-hemisphere dorsal temporoparietal white matter tracts in reading. Additionally, these results suggest future DWI studies of reading and dyslexia should be designed to benefit from advanced diffusion models, include cerebellar coverage, and consider continuous analyses that account for individual differences in reading skill.
Ferrous iron uptake via IRT1/ZIP evolved at least twice in green plants
Authors: Rodrigues Wenderson Felipe Costa , Lisboa Ayrton Breno P. , Lima Joni Esrom , Ricachenevsky Felipe Klein , Del-Bem Luiz-Eduardo
Published: July 2022

Iron (Fe) is an essential micronutrient for virtually all living beings, being practically irreplaceable because of its unique electrochemical properties that enable or facilitate a series of biochemical processes, including photosynthesis. Although Fe is abundant on Earth, it is generally found in the poorly soluble form Fe3+. Most extant plants have established Fe absorption strategies that involve Fe uptake in the soluble form Fe2+. The model angiosperm Arabidopsis thaliana, for example, captures Fe through a mechanism that lowers the pH through proton pumping to the rhizosphere to increase Fe3+ solubility, which is then reduced by a plasma membrane-bound reductase and transported into the cell by the ZIP family protein IRT1. ZIP proteins are transmembrane transporters of a variety of divalent metals such as Fe2+, Zn2+, Mn2+ and Cd2+. In this work, we investigate the evolution of functional homologs of IRT1/ZIP in the supergroup of photosynthetic eukaryotes Archaeplastida (Viridiplantae + Rhodophyta + Glaucophyta) using a dataset of 41 high-quality genomes of diverse lineages. Our analyses suggest that Fe is acquired through deeply divergent ZIP proteins in land plants and chlorophyte green algae, indicating that Fe2+ uptake by ZIP family proteins evolved at least twice independently during green plant evolution. Sequence and structural analyses indicate that the archetypical IRT proteins from angiosperms likely emerged in streptophyte algae before the origin of land plants and might be an important player in green plant terrestrialization, a process that involved the evolution of Fe acquisition in terrestrial subaerial settings.
Duration of BA.5 neutralization in sera and nasal swabs from SARS-CoV-2 vaccinated individuals, with or without Omicron breakthrough infection
Authors: Planas Delphine , Staropoli Isabelle , Porot Françoise , Guivel-Benhassine Florence , Handala Lynda , Prot Mathieu , Bolland William-Henry , Puech Julien , Péré Hélène , Veyer David , Sève Aymeric , Etienne-Simon-Lorière  , Bruel Timothée , Prazuck Thierry , Stefic Karl , Hocqueloux Laurent , Schwartz Olivier
Published: July 2022

Since early 2022, Omicron BA.1 has been eclipsed by BA.2, which was in turn outcompeted by BA.5, that displays enhanced antibody escape properties. Here, we evaluated the duration of the neutralizing antibody (Nab) response, up to 16 months after Pfizer BNT162b2 vaccination, in individuals with or without BA.1/BA.2 breakthrough infection. We measured neutralization of the ancestral D614G lineage, Delta and Omicron BA.1, BA.2, BA.5 variants in 291 sera and 35 nasal swabs from 27 individuals. Upon vaccination, serum Nab titers were reduced by 10-, 15-and 25-fold for BA.1, BA.2 and BA.5, respectively, compared with D614G. The duration of neutralization was markedly shortened, from an estimated period of 11.5 months post-boost with D614G to 5.5 months with BA.5. After breakthrough, we observed a sharp increase of Nabs against Omicron subvariants, followed by a plateau and a slow decline after 4-5 months. In nasal swabs, infection, but not vaccination, triggered a strong IgA response and a detectable Omicron neutralizing activity. Thus, BA.5 spread is partly due to abbreviated vaccine efficacy, particularly in individuals who were not infected with previous Omicron variants.
Years of Life Lost in the United States During the COVID-19 Pandemic, March 2020 to October 2021
Authors: Czeisler Mark É. , Czeisler Charles A.
Published: July 2022

Background

Given a downward age shift in COVID-19-involved deaths observed during the COVID-19 pandemic, we sought to estimate years of life lost (YLL) associated with leading causes of US death during the first 20 months of the pandemic.

Findings

Despite 4796 fewer COVID-19 deaths in Jan-Oct 2021 than in Mar-Dec 2020, the number of YLL due to COVID-19 increased by 1,159,761, from 4,474,186 to 5,633,947 (a 25.9% increase). YLL per COVID-19 death increased from 12.8 in 2020 to 16.3 in 2021, a 27.7% increase. YLL per death did not change by more than 2.3% for any other cause.

Interpretation

Increased YLL per COVID-19 death in 2021 result from younger-age COVID-19 mortality, contributing to a marked increase in YLL from this preventable cause of death at a later stage of the pandemic despite advancements in vaccines in treatments.
Leveraging the Elastic Deformability of Polydimethylsiloxane Microfluidic Channels for Efficient Intracellular Delivery
Authors: Alhmoud Hashim , Alkhaled Mohammed , Kaynak Batuhan E. , Hanay M. Selim
Published: July 2022

With the rapid development of microfluidic based cell therapeutics systems, the need arises for compact, modular, and microfluidics-compatible intracellular delivery platforms with small footprints and minimal operational requirements. Physical deformation of cells passing through a constriction in a microfluidic channel has been shown to create transient membrane perturbations that allow passive diffusion of materials from the outside to the interior of the cell. This mechanical approach to intracellular delivery is simple to implement and fits the criteria outlined above. However, available microfluidic platforms that operate through this mechanism are traditionally constructed from rigid channels with fixed dimensions that suffer from irreversible clogging and incompatibility with larger size distributions of cells. Here we report a flexible and elastically deformable microfluidic channel, and we leverage this elasticity to dynamically generate temporary constrictions with any given size within the channel width parameters. Additionally, clogging is prevented by increasing the size of the constriction to allow clogs to pass. By tuning the size of the constriction appropriately, we show the successful delivery of GFP-coding plasmids to the interior of three mammalian cell lines and fluorescent gold nanoparticles to HEK293 FT cells all while maintaining a high cell viability rate. This development will no doubt lead to miniaturized intracellular delivery microfluidic components that can be easily integrated into larger lab-on-a-chip systems in future cell modification devices.
Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos
Authors: Bu Guowei , Zhu Wei , Liu Xin , Zhang Jingjing , Yu Longtao , Zhou Kai , Wang Shangke , Li Zhekun , Fan Zhengang , Wang Tingting , Hu Taotao , Hu Ruifeng , Liu Zhiting , Wang Tao , Wu Linhui , Zhang Xia , Zhao Shuhong , Miao Yi-Liang
Published: July 2022

Histone modifications are critical epigenetic indicators of chromatin state associated with gene expression. Although the reprogramming patterns of H3K4me3 and H3K27me3 have been elucidated in mouse and human preimplantation embryos, the relationship between these marks and zygotic genome activation (ZGA) remains poorly understood. By ultra-low-input native chromatin immunoprecipitation and sequencing, we profiled global H3K4me3 and H3K27me3 in porcine oocytes and in vitro fertilized (IVF) embryos. We observed sharp H3K4me3 peaks in promoters of ZGA genes in oocytes, and these peaks became broader after fertilization and reshaped into sharp peaks again during ZGA. By simultaneous depletion of H3K4me3 demethylase KDM5B and KDM5C, we determined that broad H3K4me3 domain maintenance impaired ZGA gene expression, suggesting its function to prevent premature ZGA entry. In contrast, broad H3K27me3 domains underwent global removal upon fertilization, followed by a re-establishment for H3K4me3/H3K27me3 bivalency in morulae. We also found that bivalent marks were deposited at promoters of ZGA genes, and inhibiting this deposition was correlated with the activation of ZGA genes. It suggests that promoter bivalency contributes to ZGA exit in porcine embryos. Moreover, we demonstrated that aberrant reprogramming of H3K4me3 and H3K27me3 triggered ZGA dysregulation in somatic cell nuclear transfer (SCNT) embryos, whereas H3K27me3-mediated imprinting did not exist in porcine IVF and SCNT embryos. Our findings highlight two previously unknown epigenetic reprogramming modes coordinated with ZGA in porcine preimplantation embryos. Finally, the similarities observed between porcine and human histone modification dynamics suggest that the porcine embryo may also be a useful model for human embryo research.
Investigating the live streaming sales from the perspective of the ecosystem: the structures, processes and value flow
Authors: Xue Jin , Liu Matthew Tingchi
Published: July 2022

Purpose

Live streaming sales (LSS) is an emerging and flourishing practice in the retail industry. While its implementation has been pervasively attempted, there is a lack of systematic and academic exploration of the practice. Therefore, the aim of this study was to investigate the LSS ecosystem and its development through a literature review and an industry analysis. Moreover, by pinpointing the pitfalls in current practices, this paper presents the practical implications of LSS and provides recommendations and directions for future academic exploration.

Design/methodology/approach

The aim of the present study was to investigate the developing trajectory, exclusive elements (such as multi-channel networks (MCNs) and live streamers) and other critical components of the LSS ecosystem using a mixed-methods approach that comprises content analysis of newspaper articles and press releases, literature view and industry analysis.

Findings

The results of the analyses indicate the presence of several nonfungible modular components in the LSS ecosystem, including upstream suppliers, MCNs, live streamers and platforms. It was also found that inequalities and hierarchies are inherent to the LSS ecosystem as it currently exists: low-end participants in the LSS industry and small- and medium-sized enterprise owners, who constitute the majority of LSS practitioners, cannot reach the break-even point via LSS hosted by top-level live streamers or others (low-level live streamers, employees, etc.).

Originality/value

This article discusses the LSS ecosystem based on the nature of the nonfungible modules within it. In addition, it discusses the modules (roles) and relationships among them based on the theory of ecosystem developed by previous studies. Furthermore, drawing from an analysis of the pitfalls in the LSS ecosystem, this article highlights strategies for two critical e-commerce processes: 1) choosing which type of LSS to apply based on the factors of brands, products and consumers and 2) integrating LSS to optimize post-sale service and appeal to the sustainability of development.
Video compression based on zig-zag 3D DCT and run-length encoding for multimedia communication systems
Authors: Chutke Sravanthi , N.M. Nandhitha , Lendale Praveen Kumar
Published: July 2022

Purpose

With the advent of technology, a huge amount of data is being transmitted and received through the internet. Large bandwidth and storage are required for the exchange of data and storage, respectively. Hence, compression of the data which is to be transmitted over the channel is unavoidable. The main purpose of the proposed system is to use the bandwidth effectively. The videos are compressed at the transmitter’s end and reconstructed at the receiver’s end. Compression techniques even help for smaller storage requirements.

Design/methodology/approach

The paper proposes a novel compression technique for three-dimensional (3D) videos using a zig-zag 3D discrete cosine transform. The method operates a 3D discrete cosine transform on the videos, followed by a zig-zag scanning process. Finally, to convert the data into a single bit stream for transmission, a run-length encoding technique is used. The videos are reconstructed by using the inverse 3D discrete cosine transform, inverse zig-zag scanning (quantization) and inverse run length coding techniques. The proposed method is simple and reduces the complexity of the convolutional techniques.

Findings

Coding reduction, code word reduction, peak signal to noise ratio (PSNR), mean square error, compression percent and compression ratio values are calculated, and the dominance of the proposed method over the convolutional methods is seen.

Originality/value

With zig-zag quantization and run length encoding using 3D discrete cosine transform for 3D video compression, gives compression up to 90% with a PSNR of 41.98 dB. The proposed method can be used in multimedia applications where bandwidth, storage and data expenses are the major issues.