bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic and Transcriptional Dysregulation in CD4+ T cells of Patients with Atopic Dermatitis
Authors: Eapen Amy A. , Parameswaran Sreeja , Forney Carmy , Edsall Lee E. , Miller Daniel , Donmez Omer , Dunn Katelyn , Lu Xiaoming , Granitto Marissa , Rowden Hope , Magier Adam Z. , Pujato Mario , Chen Xiaoting , Kaufman Kenneth , Bernstein David I , Devonshire Ashley L. , Rothenberg Marc E. , Weirauch Matthew T. , Kottyan Leah 
Published: December 2021

ABSTRACTAtopic dermatitis (AD) is one of the most common skin disorders in children. Disease etiology involves genetic and environmental factors, with the 29 independent AD risk loci enriched for risk allele-dependent gene expression in the skin and CD4+ T cell compartments. We investigated epigenetic mechanisms that may account for genetic susceptibility in CD4+ T cells. To understand gene regulatory activity differences in peripheral blood T cells in AD, we measured chromatin accessibility (ATAC-seq), NFKB1 binding (ChIP-seq), and gene expression (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD and age-matched, non-allergic controls. Open chromatin regions in stimulated CD4+ T cells were highly enriched for AD genetic risk variants, with almost half of AD risk loci overlapping with AD-dependent ATAC-seq peaks. AD-specific open chromatin regions were strongly enriched for NFκB DNA binding motifs. ChIP-seq identified hundreds of NFKB1-occupied genomic loci that were AD-specific or Control-specific. As expected, the AD-specific ChIP-seq peaks were strongly enriched for NFκB DNA binding motifs. Surprisingly, Control-specific NKFB1 ChIP-seq peaks were not enriched for NFKB1 motifs, instead containing motifs for other classes of human TFs, suggesting a mechanism involving altered indirect NFKB1 binding. Using DNA sequencing data, we identified 63 instances of genotype-dependent chromatin accessibility at 36 AD risk variants (30% of AD risk loci) that could lead to genotype-dependent expression at these loci. We propose that CD4+ T cells respond to stimulation in an AD-specific manner, resulting in disease and genotype-dependent chromatin accessibility involving NFKB binding.AUTHOR SUMMARYStimulated CD4+ T cells from patients with atopic dermatitis have disease-dependent regulation of how gene expression is regulated. This regulation is disease dependent and the way the DNA is accessible and the transcription factor NFKB1 binds is enriched for genetic risk variants. Clinically, the CD4+ T cells in the peripheral blood of patients with AD respond to stimulation in a disease and genotype-dependent manner.
Harzianic Acid has multi-target antimicrobial activity against Gram-Positive Bacteria
Authors: Ouyang Xudong , Hoeksma Jelmer , Beenker Wouter A.G. , van der Beek Samantha , den Hertog Jeroen 
Published: December 2021

AbstractThe thermophilic fungus Oidiodendron flavum is a saprobe that is commonly isolated from soil. Here, we identified a Gram-positive bacteria-selective antimicrobial secondary metabolite from this fungal species, harzianic acid (HA). Using Bacillus subtilis strain 168 combined with several assays, we found that HA targeted the cell membrane, though only at high concentrations. To further study the antimicrobial activity of HA, we isolated an HA-resistant strain, Bacillus subtilis strain M9015, and discovered that the mutant has more translucent colonies, has cross resistance to rifampin, and harbors five mutations in the coding region of four distinct genes. Further analysis of these genes indicated that the mutation in atpE might be responsible for the translucency of the colony, and mutation in yusO for resistance to both HA and rifampin. We conclude that HA is a multi-target antimicrobial agent against Gram-positive bacteria.
Lateral plate mesoderm cell-based organoid system for NK cell regeneration from human pluripotent stem cells
Authors: Huang Dehao , Li Jianhuan , Hu Fangxiao , Weng Qitong , Wang Tongjie , Peng Huan , Wu Bingyan , Xia Chengxiang , Wu Hongling , Xiong Jiapin , Lin Jiali , Lin Yunqing , Wang Yao , Zhang Qi , Liu Xiaofei , Liu Lijuan , Zheng Xiujuan , Qiu Haiyan , Geng Yang , Du Xin , Wang Lei , Hao Jie , Wang Jinyong 
Published: December 2021

ABSTRACTHuman pluripotent stem cell (hPSC)-induced NK (iNK) cells are a promising “off-the-shelf” cell product for universal immune therapy. Conventional methods for iNK cell regeneration from hPSCs include embryonic body-formation and feeder-based expansion steps, which bring instability, time-consuming, and high costs for manufacture. In this study, we develop an embryonic body-free, organoid aggregate method for NK cell regeneration from hPSCs. In a short time window of 27-day induction, millions of hPSC input can produce over billions of iNK cells without the necessity of NK cell-expansion feeders. The iNK cells highly express classical toxic granule proteins, apoptosis-inducing ligands, as well as abundant activating and inhibitory receptors. Functionally, the iNK cells eradicate human tumor cells by mechanisms of direct cytotoxity, apoptosis, and antibody-dependent cellular cytotoxicity. This study provides a reliable scale-up method for regenerating human NK cells from hPSCs, which promotes the universal availability of NK cell products for immune therapy.
A wipe-based stool collection and preservation kit for microbiome community profiling
Authors: Hua Hui , Meydan Cem , Afshin Evan E. , Lili Loukia , D’Adamo Christopher R. , Dudley Joel , Price Nathan D. , Zhang Bodi , Mason Christopher E. 
Published: December 2021

AbstractWhile a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. Future studies will be needed to further explore sample processing options and their applications in non-healthy subjects, particularly patients with irritable bowel syndrome, inflammatory bowel disease, and colorectal cancer, but these data suggest the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.
A dynamic antibacterial T6SS in Pantoea agglomerans pv. betae delivers a lysozyme-like effector to antagonize competitors
Authors: Carobbi Andrea , Di Nepi Simone , Fridman Chaya M. , Dar Yasmin , Ben-Yaakov Rotem , Barash Isaac , Salomon Dor , Sessa Guido 
Published: December 2021

ABSTRACTThe type VI secretion system (T6SS) is deployed by numerous Gram-negative bacteria to deliver toxic effectors into neighboring cells. The genome of Pantoea agglomerans pv. betae (Pab) phytopathogenic bacteria contains a gene cluster (T6SS1) predicted to encode a complete T6SS. Using secretion and competition assays, we found that T6SS1 in Pab is a functional antibacterial system that allows this pathogen to outcompete rival plant-associated bacteria found in its natural environment. Computational analysis of the T6SS1 gene cluster revealed that antibacterial effector and immunity proteins are encoded within three dynamic genomic islands that harbor arrays of orphan immunity genes or toxin and immunity cassettes. Functional analysis demonstrated that the specialized antibacterial effector VgrG contains a C-terminal catalytically active glucosaminidase domain that is used to degrade prey peptidoglycan. Moreover, we confirmed that a bicistronic unit at the end of the T6SS1 cluster encodes a novel antibacterial T6SS effector and immunity pair. Together, these results demonstrate that Pab T6SS1 is an antibacterial system delivering a lysozyme-like effector to eliminate competitors, and indicate that this bacterium contains novel T6SS effectors.Significance StatementIn this work, we describe the identification of a Pantoea agglomerans T6SS as an antibacterial determinant used by this phytopathogen to outcompete bacterial rivals. Furthermore, we provide an in-depth analysis of the T6SS gene cluster and the putative effector and immunity genes that comprise it, and we propose explanations for its dynamic evolution and effector diversification in Pantoea strains. Lastly, we experimentally validate two predicted effector and immunity pairs, and we demonstrate that one is a potent lysozyme-like toxin.
c-MAF maintains the transcriptional program of enterocyte zonation and the balance of absorptive/intestinal secretory cell types
Authors: González-Loyola Alejandra , Wyss Tania , Munoz Olivia , Prat-Luri Borja , Delorenzi Mauro , Verdeil Gregory , Petrova Tatiana V. 
Published: December 2021

AbstractSmall intestinal villi are structural and functional units uniquely adapted to the nutrient absorption in higher vertebrates. Villus enterocytes are organized in spatially resolved “zones” dedicated to specialized tasks such anti-bacterial protection, and absorption of amino-acids, carbohydrates and lipids. The molecular mechanisms specifying villus zonation are incompletely understood. We report that inactivation of transcription factor c-MAF, highly expressed in mature lower and mid-villus enterocytes, perturbed the entire villus zonation program, by increasing the expression of regulators of carbohydrate and bile acid metabolism and transport, while suppressing genes related to amino acid and lipid absorption. Maf inactivation under homeostatic conditions expanded tuft cells and led to compensatory gut lengthening, preventing body weight loss. However, delayed enterocyte maturation in the absence of Maf impaired body weight recovery after acute intestinal injury, resulting in reduced survival. Our results identify c-MAF as a novel regulator of small intestinal villus zonation program, while highlighting the importance of coordination between stem/progenitor and differentiation programs for intestinal regeneration.Summaryc-MAF is expressed in differentiated enterocytes. c-MAF loss alters enterocyte zonation leading to a compensatory gut remodelling and tuft cell expansion. Upon acute intestinal injury mice deficient for c-MAF cannot recover due to lack of nutrient transport and compensatory lengthening.
The structure of HiSiaQM defines the architecture of tripartite ATP-independent periplasmic (TRAP) transporters
Authors: Peter Martin F. , Depping Peer , Schneberger Niels , Severi Emmanuele , Gatterdam Karl , Tindall Sarah , Durand Alexandre , Heinz Veronika , Koenig Paul-Albert , Geyer Matthias , Ziegler Christine , Thomas Gavin H. , Hagelueken Gregor 
Published: December 2021

SummaryTripartite ATP-independent periplasmic (TRAP) transporters are widespread in bacteria and archaea and provide important uptake routes for many metabolites 1–3. They consist of three structural domains, a soluble substrate-binding protein (P-domain), and two transmembrane domains (Q- and M-domains) that form a functional unit 4. While the structures of the P-domains are well-known, an experimental structure of any QM-domain has been elusive. HiSiaPQM is a TRAP transporter for the monocarboxylate sialic acid, which plays a key role in the virulence of pathogenic bacteria 5. Here, we present the first cryo-electron microscopy structure of the membrane domains of HiSiaPQM reconstituted in lipid nanodiscs. The reconstruction reveals that TRAP transporters consist of 15 transmembrane helices and are structurally related to elevator-type transporters, such as GltPh and VcINDY 6, 7. Whereas the latter proteins function as multimers, the idiosyncratic Q-domain of TRAP transporters enables the formation of a monomeric elevator architecture. Structural and mutational analyses together with an AlphaFold 8 model of the tripartite (PQM) complex reveal the structural and conformational coupling of the substrate-binding protein to the transporter domains. Furthermore, we characterize high-affinity VHHs that bind to the periplasmic side of HiSiaQM and inhibit sialic acid uptake in vivo. Thereby, they also confirm the orientation of the protein in the membrane. Our study provides the first structure of any binding-protein dependent secondary transporter and provides starting points for the development of specific inhibitors.
Characterization of the hepatitis E virus replicase
Authors: Metzger Karoline , Bentaleb Cyrine , Hervouet Kévin , Alexandre Virginie , Montpellier Claire , Saliou Jean-Michel , Ferrié Martin , Camuzet Charline , Rouillé Yves , Lecoeur Cécile , Dubuisson Jean , Cocquerel Laurence , Aliouat-Denis Cécile-Marie 
Published: December 2021

AbstractHepatitis E virus (HEV) is the major cause of acute hepatitis worldwide. HEV is a positive-sense RNA virus expressing 3 open reading frames (ORFs). ORF1 encodes the ORF1 non– structural polyprotein, the viral replicase which transcribes the full-length genome and a subgenomic RNA that encodes the structural ORF2 and ORF3 proteins. The present study is focused on the replication step with the aim to determine whether the ORF1 polyprotein is processed during the HEV lifecycle and to identify where the replication takes place inside the host cell. As no commercial antibody recognizes ORF1 in HEV-replicating cells, we aimed at inserting epitope tags within the ORF1 protein without impacting the virus replication efficacy. Two insertion sites located in the hypervariable region were thus selected to tolerate the V5 epitope while preserving HEV replication efficacy. Once integrated into the infectious full-length Kernow C-1 p6 strain, the V5 epitopes did neither impact the replication of genomic nor the production of subgenomic RNA. Also, the V5-tagged viral particles remained as infectious as the wildtype particles to Huh-7.5 cells. Next, the expression pattern of the V5-tagged ORF1 was compared in heterologous expression and replicative HEV systems. A high molecular weight protein (180 kDa) that was expressed in all 3 systems and that likely corresponds to the unprocessed form of ORF1 was detected up to 25 days after electroporation in the p6 cell culture system. Additionally, less abundant products of lower molecular weights were detected in both in cytoplasmic and nuclear compartments. Concurrently, the V5-tagged ORF1 was localized by confocal microscopy inside the cell nucleus but also as compact perinuclear substructures in which ORF2 and ORF3 proteins were detected. Importantly, using in situ hybridization (RNAScope®), positive and negative-strand HEV RNAs were localized in the perinuclear substructures of HEV-producing cells. Finally, by simultaneous detection of HEV genomic RNAs and viral proteins in these substructures, we identified candidate HEV factories.
A spatiotemporally resolved single cell atlas of the Plasmodium liver stage
Authors: Afriat Amichay , Zuzarte-Luís Vanessa , Halpern Keren Bahar , Buchauer Lisa , Marques Sofia , Lahree Aparajita , Amit Ido , Mota Maria M. , Itzkovitz Shalev 
Published: December 2021

AbstractMalaria infection involves an obligatory, yet clinically silent liver stage1,2. Hepatocytes operate in repeating units termed lobules, exhibiting heterogeneous gene expression patterns along the lobule axis3, but the effects of hepatocyte zonation on parasite development have not been molecularly explored. Here, we combine single-cell RNA sequencing4 and single-molecule transcript imaging5 to characterize the host’s and parasite’s temporal expression programs in a zonally-controlled manner for the rodent malaria parasite Plasmodium berghei ANKA. We identify differences in parasite gene expression in distinct zones, and a sub-population of periportally-biased hepatocytes that harbor abortive infections associated with parasitophorous vacuole breakdown. These ‘abortive hepatocytes’ up-regulate immune recruitment and key signaling programs. They exhibit reduced levels of Plasmodium transcripts, perturbed parasite mRNA localization, and may give rise to progressively lower abundance of periportal infections. Our study provides a resource for understanding the liver stage of Plasmodium infection at high spatial resolution and highlights heterogeneous behavior of both the parasite and the host hepatocyte.
Ubiquitin Ligase SmDDA1b of Eggplant (Solanum melongena) Enhances Bacterial Wilt Resistance via SmNAC Degradation
Authors: Wang Yixi , Yan Shuangshuang , Yu Bingwei , Gan Yuwei , Lei Jiangjun , Chen Changming , Zhu Zhangsheng , Qiu Zhengkun , Cao Bihao 
Published: December 2021

AbstractBacterial wilt (BW) is a soil-borne disease that severely impacts plant growth and productivity globally. Ubiquitination plays a crucial role in disease resistance. Our previous research indicated that NAC transcription factor SmNAC negatively regulates BW resistance in eggplant (Solanum melongena). However, whether the ubiquitin/26S proteasome system (UPS) participates in this regulation is unknown.This study used SmNAC as a bait to screen eggplant cDNA library and obtained SmDDA1b, an E3 ubiquitin ligase. Subcellular location and bimolecular fluorescence complementation assays revealed that SmDDA1b could interact with SmNAC in the nucleus. The in vivo and in vitro ubiquitination experiments indicated that SmDDA1b can degrade SmNAC through UPS. However, the discovery of negative regulation of SmDDA1b expression by SmNAC showed that there was a negative feedback loop between SmNAC and SmDDA1b in eggplant.The SmDDA1b-overexpressed lines showed a higher BW resistance associated with high expression levels of salicylic acid (SA)-related genes and SA content than the wild-type lines. However, SmDDA1b-silencing lines showed the opposite results, indicating that SmDDA1b is a positive regulatory gene for BW resistance.This study provides a candidate gene that can enhance BW resistance in eggplants. In addition, it provides insight into a mechanism that promotes plant disease resistance via the SmDDA1b-SmNAC-SA pathway.
Plasmodium SAS4/CPAP is a flagellum basal body component during male gametogenesis, but is not essential for parasite transmission
Authors: Zeeshan Mohammad , Brady Declan , Markus Robert , Vaughan Sue , Ferguson David , Holder Anthony A. , Tewari Rita 
Published: December 2021

AbstractThe centriole/basal body (CBB) is an evolutionarily conserved organelle acting as a microtubule organising centre (MTOC) to nucleate cilia, flagella and the centrosome. SAS4/CPAP is a conserved component associated with BB biogenesis in many model flagellated cells. Plasmodium, a divergent unicellular eukaryote and causative agent of malaria, displays an atypical closed mitosis with an MTOC, reminiscent of the acentriolar MTOC, embedded in the nuclear membrane at most proliferative stages. Mitosis during male gamete formation is accompanied by flagellum formation: within 15 minutes, genome replication (from 1N to 8N) and three successive rounds of mitosis without nuclear division occur, with coordinated axoneme biogenesis in the cytoplasm resulting in eight flagellated gametes. There are two MTOCs in male gametocytes. An acentriolar MTOC located with the nuclear envelope and a centriolar MTOC (basal body) located within the cytoplasm that are required for flagellum assembly. To study the location and function of SAS4 during this rapid process, we examined the spatial profile of SAS4 in real time by live cell imaging and its function by gene deletion. We show its absence during asexual proliferation but its presence and coordinated association and assembly of SAS4 with another basal body component, kinesin8B, which is involved in axoneme biogenesis. In contrast its separation from the nuclear kinetochore marker NDC80 suggests that SAS4 is part of the basal body and outer centriolar MTOC residing in the cytoplasm. However, deletion of the SAS4 gene produced no phenotype, indicating that it is not essential for male gamete formation or parasite transmission through the mosquito.
LINE-1 activation in the cerebellum drives ataxia
Authors: Takahashi Takehiro , Kudo Eriko , Song Eric , Carvalho Fernando , Yasumoto Yuki , Kong Yong , Park Annsea , Stoiljkovic Milan , Gao Xiao-Bing , Shanabrough Marya , Szigeti-Buck Klara , Liu Zhong-Wu , Zhang Yalan , Sulkowski Parker , Glazer Peter M. , Kaczmarek Leonard K. , Horvath Tamas L. , Iwasaki Akiko 
Published: December 2021

ABSTRACTPrevious studies have revealed that dysregulation of long interspersed nuclear element 1 (LINE-1), a dominant class of transposable elements in the human genome, correlates with neurodegeneration1–3. Yet whether LINE-1 dysregulation is causal to disease pathogenesis has not been proven directly. Here, we demonstrate that expression of evolutionarily younger LINE-1 families is elevated in the cerebella of ataxia telangiectasia (AT) patients, which was correlated with extensive downregulation of epigenetic silencers. To examine whether LINE-1 activation causes neurologic disease, we established an approach to directly target and activate the promoter of a young family of LINE-1 in mice. LINE-1 activation in the cerebellum was sufficient to lead to robust progressive ataxia. Purkinje cells in the diseased mice exhibited marked electrophysiological dysfunctions and degeneration with a significant accumulation of cytoplasmic ribonucleoprotein LINE-1Orf1p aggregates, endoplasmic reticulum (ER) stress, and DNA damage. Treatment with lamivudine, a nucleoside reverse transcriptase inhibitor, blunted the disease progression by reducing DNA damage, attenuating gliosis and interferon gene signature, and recovering the loss of key functional molecules for calcium homeostasis in Purkinje cells. This study provides direct evidence that young LINE-1 activation drives ataxia phenotype, and points to its pleiotropic effects leading to DNA damage, inflammation, and dysfunction and degeneration of neurons.
Drosophila renal stem cells enhance fitness by delayed remodeling of adult Malpighian tubules
Authors: Wang Chenhui , Spradling Allan C. 
Published: December 2021

AbstractDrosophila renal stem cells (RSCs) contradict the common expectation that stem cells maintain tissue homeostasis. RSCs are abundant, quiescent and confined to the peri-ureter region of the kidney-like Malpighian tubules (MTs). Although derived during pupation like intestinal stem cells, RSCs initially remodel the larval MTs only near the intestinal junction. However, following adult injury to the ureter by xanthine stones, RSCs remodel the damaged region in a similar manner. Thus, RSCs represent stem cells encoding a developmental redesign. The remodeled tubules have a larger luminal diameter and shorter brush border, changes linked to enhanced stone resistance. However, RSC-mediated modifications also raise salt sensitivity and reduce fecundity. Our results suggest that RSCs arose by arresting developmental progenitors to preserve larval physiology until a time in adulthood when it becomes advantageous to complete development by RSC activation.One-Sentence SummaryActivated Drosophila renal stem cells rebuild the adult Malphigian tubules using a less efficient but more stone-resistant design.