bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hemophagocytic Lymphohistiocytosis Secondary to Juvenile Myelomonocytic Leukemia: A Case Report and Review of the Literature
Authors: Zheng Fangyuan , Jia Yueping , Zhang Leping , Qin Jiong 
Published: December 2021

Rationale:
Juvenile myelomonocytic leukemia (JMML) is a rare hematopoietic disorder, which is more rarely accompanied by monosomy 5 or deletion of the long arm of chromosome 5q (−5/5q−) or monosomy 5 (5q−/−5), and hemophagocytic lymphohistiocytosis (HLH) is a rare, uncontrolled hyperinflammation condition, which is more rarely secondary to JMML. Up to now, only a few cases of JMML with −5/5q− and HLH secondary to JMML were described. Here we described an extremely rare case of HLH second to JMML with 5q−.

Patient Concerns:
The patient had multiple cafe-au-lait-spots at birth and was found that NF1 gene mutation was positive. At his 6 years old, he developed hepatosplenomegaly, anemia, thrombocytopenia, monocyte count 4.12×109/L in peripheral blood, 13% blasts in peripheral blood, and 11% blasts in bone marrow, without BCR/ABL rearrangement, combining with positive NF1 gene mutation, he was diagnosed as JMML. In the bone marrow, there was chromosomal abnormalities with −5/5q−. In the treatment, HLH occurred.

Diagnoses:
The patient was diagnosed as secondary HLH to JMML.

Interventions:
The patient received the chemotherapy treatment of the improved diffuse alveolar hemorrhage protocol, and meanwhile, he prepared for hematopoietic stem cell transplantation. Then on the basis of anti-infection, symptomatic and supportive therapy, he was commenced the treatment according to the HLH-2004 protocol.

Outcomes:
He had a partial response, manifesting that his fever resolved, but the blood coagulation function did not improve, and the severe thrombocytopenia remained. Then, the parents refused the continual treatment, and the child died of intracranial hemorrhage 3 months after the diagnosis of JMML.

Lessons:
JMML and HLH were relatively easy to diagnose based on clinical and laboratory results. Due to the low incidence of JMML with −5/5q− and HLH secondary to JMML, no clinical practice guidelines for the treatment of the disease have been established yet. The clinical data of a case of HLH secondary to JMML with 5q− were analyzed, and relevant studies were studied.
Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn's disease
Authors: Lee Jae-Yun , Kang Woorim , Shin Na-Ri , Hyun Dong-Wook , Kim Pil Soo , Kim Hyun Sik , Lee June-Young , Tak Euon Jung , Sung Hojun , Bae Jin-Woo 
Published: December 2021

Cultivation and isolation of gut bacteria are necessary for understanding their role in the intestinal ecosystem. We isolated a novel bacterium, designated strain BG01T, from the faeces of a patient with Crohn's disease. Strain BG01T was a strictly anaerobic, rod-shaped, Gram-variable and endospore-forming bacterium. Strain BG01T possessed C12 : 0, C18 : 0 dimethyl aldehyde (DMA) and C18 : 1
ω9c DMA as predominant cellular fatty acids and meso-diaminopimelic acid as a diagnostic diamino acid. Strain BG01T grew at 15–45 °C (optimum, 37 °C), with 0–4 % (w/v) NaCl (optimum, 0–1 %), at pH 6–10 (optimum, pH 7) and was resistant to bile salt, but not to ampicillin, metronidazole, vancomycin and cefoperazone. Butyrate, propionate, oxalacetate and fumarate were produced as fermentation end products from Gifu anaerobic medium broth. Strain BG01T showed 97.7 % 16S rRNA gene sequence similarity, and 92.0 and 48.5 % of average nucleotide identity and digital DNA–DNA hybridization values, respectively, with

Anaerostipes caccae

KCTC 15019T. Genomic analysis indicated that strain BG01T had a butyrate-producing pathway. The genomic G+C content of the strain was 43.5 mol%. Results of the phenotypic, phylogenetic and genotypic analyses indicated that strain BG01T represents a novel butyrate-producing species of the genus

Anaerostipes

, for which the name Anaerostipes hominis sp. nov. is proposed. The type strain is BG01T (=KCTC 15617T=JCM 32275T).
Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches
Authors: Thornlow Bryan , Kramer Alexander , Ye Cheng , De Maio Nicola , McBroome Jakob , Hinrichs Angie S. , Lanfear Robert , Turakhia Yatish , Corbett-Detig Russell 
Published: December 2021

AbstractPhylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 datasets do not fit this mould. There are currently over 10 million sequenced SARS-CoV-2 genomes in online databases, with tens of thousands of new genomes added every day. Continuous data collection, combined with the public health relevance of SARS-CoV-2, invites an “online” approach to phylogenetics, in which new samples are added to existing phylogenetic trees every day. The extremely dense sampling of SARS-CoV-2 genomes also invites a comparison between likelihood and parsimony approaches to phylogenetic inference. Maximum likelihood (ML) methods are more accurate when there are multiple changes at a single site on a single branch, but this accuracy comes at a large computational cost, and the dense sampling of SARS-CoV-2 genomes means that these instances will be extremely rare because each internal branch is expected to be extremely short. Therefore, it may be that approaches based on maximum parsimony (MP) are sufficiently accurate for reconstructing phylogenies of SARS-CoV-2, and their simplicity means that they can be applied to much larger datasets. Here, we evaluate the performance of de novo and online phylogenetic approaches, and ML and MP frameworks, for inferring large and dense SARS-CoV-2 phylogenies. Overall, we find that online phylogenetics produces similar phylogenetic trees to de novo analyses for SARS-CoV-2, and that MP optimizations produce more accurate SARS-CoV-2 phylogenies than do ML optimizations. Since MP is thousands of times faster than presently available implementations of ML and online phylogenetics is faster than de novo, we therefore propose that, in the context of comprehensive genomic epidemiology of SARS-CoV-2, MP online phylogenetics approaches should be favored.
Drug repurposing screening identified tropifexor as a SARS-CoV-2 papain-like protease inhibitor
Authors: Ma Chunlong , Wang Yuyin , Choza Juliana , Wang Jun 
Published: December 2021

AbstractThe global COVID-19 pandemic underscores the dire need of effective antivirals. Encouraging progress has been made in developing small molecule inhibitors targeting the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and main protease (Mpro). However, the development of papain-like protease (PLpro) inhibitors faces several obstacles. Nevertheless, PLpro represents a high-profile drug target given its multifaceted roles in viral replication. PLpro is involved in not only the cleavage of viral polyprotein but also modulation of host immune response. In this study, we conducted a drug-repurposing screening of PLpro against the MedChemExpress bioactive compound library and identified three hits, EACC, KY-226, and tropifexor, as potent PLpro inhibitors with IC50 values ranging from 3.39 to 8.28 µM. The three hits showed dose-dependent binding to PLpro in the thermal shift assay. In addition, tropifexor inhibited the cellular PLpro activity in the FlipGFP assay with an IC50 of 10.6 µM. Gratifyingly, tropifexor showed antiviral activity against SARS-CoV-2 in Calu-3 cells with an EC50 of 4.03 µM, a 7.8-fold increase compared to GRL0617 (EC50 = 31.4 µM). Overall, tropifexor represents a novel PLpro inhibitor that can be further developed as SARS-CoV-2 antivirals.
Genetic insights into the management and conservation of Arctic charr in North Wales
Authors: Beck Samantha V. , Carvalho Gary R. , McCarthy Ian , Hanks Walter , Evans Robert , Edwards Robert , Taylor Martin , de Bruyn Mark 
Published: December 2021

AbstractAquatic species throughout the world are threatened by extinction in many parts of their range, particularly in their most southerly distributions. Arctic charr (Salvelinus alpinus) is a Holarctic species with a distribution that includes the glacial lakes of North Wales, towards it southern limit. To date, no genetic studies have been conducted to determine the genetic health of the three remaining native Arctic charr populations in North Wales, despite exposure to stocking and adverse environmental and ecological conditions. We used seven microsatellite loci to determine whether: 1) genetic differentiation existed between native populations; 2) translocated populations from Llyn Peris were genetically similar to the historically connected Llyn Padarn population; and 3) hatchery supplementation negatively impacted genetic diversity in Llyn Padarn. All three native populations retained their genetic integrity, with Llyn Bodlyn showing high levels of divergence (FST= 0.26 ± 0.02SD) as well as low genetic diversity (HO0.30) compared to remaining populations (HO0.64 ± 0.14SD). Although evidence suggests that stocking increased the effective population size of Llyn Padarn in the short term without impacting genetic diversity, the long term effects of such practices are yet to be seen. Results provide baseline data for conservation management, and highlight the need for protection of small isolated populations that are being negatively impacted by the processes of genetic drift due to escalating anthropogenic pressures. Continual monitoring of both Arctic charr and their habitats using a combination of methods will increase the likelihood that these threatened and iconic populations will persist in the future.
Multimodal Analyses of Stable Vitiligo Skin Identify Tissue Interactions That Control Disease Persistence
Authors: Shiu Jessica , Zhang Lihua , Lentsch Griffin , Flesher Jessica L , Jin Suoqin , Polleys Christopher , Jo Seong Jin , Mizzoni Craig , Mobasher Pezhman , Kwan Jasmine , Ruis-Diaz Francisca , Tromberg Bruce J , Georgakoudi Irene , Nie Qing , Balu Mihaela , Ganesan Anand K 
Published: December 2021

AbstractVitiligo is an autoimmune skin disease that is characterized by the progressive destruction of melanocytes by autoreactive CD8+ T cells. Melanocyte destruction in active vitiligo is mediated by CD8+ T cells but why white patches in stable disease persist is poorly understood. The interaction between immune cells, melanocytes, and keratinocytes in situ in human skin has been difficult to study due to the lack of proper tools. Here, we combine non-invasive multiphoton microscopy (MPM) imaging and single-cell RNA sequencing (scRNA-seq) to identify distinct subpopulations of keratinocytes in lesional skin of stable vitiligo patients. We show that these keratinocytes are enriched in lesional vitiligo skin and differ in metabolism, an observation corroborated by both MPM and scRNA-seq. Systematic investigation of cell-cell communication show that CXCL is the prominent signaling change in this small population of keratinocytes, which secrete CXCL9 and CXCL10 to create local inflammatory cytokine loops with T cells to drive stable vitiligo persistence. Pseudotemporal dynamics analyses predict an alternative keratinocyte differentiation trajectory that generates this new population of keratinocytes in vitiligo skin. In summary, we couple advanced imaging with transcriptomics and bioinformatics to discover cellcell communication networks and keratinocyte cell states that perpetuate inflammation and prevent repigmentation.One Sentence SummaryCommunication between keratinocytes, immune cells, and melanocytes maintain depigmented patches in stable vitiligo.
ABCC1/MRP1 exports cGAMP and modulates cGAS-dependent immunity
Authors: Maltbaek Joanna H. , Snyder Jessica M. , Stetson Daniel B. 
Published: December 2021

AbstractThe DNA sensor cyclic GMP-AMP synthase (cGAS) is important for antiviral and anti-tumor immunity. cGAS generates cyclic GMP-AMP (cGAMP), a diffusible cyclic dinucleotide that activates the antiviral response through the adapter protein Stimulator of Interferon Genes (STING). cGAMP is negatively charged and cannot passively cross cell membranes, but recent advances have established a role for extracellular cGAMP as an “immunotransmitter” that can be imported into cells. However, the mechanism by which cGAMP exits cells remains unknown. Here, we identify ABCC1/MRP1 as an ATP-dependent cGAMP exporter that influences STING signaling and type I interferon production. We demonstrate that ABCC1 deficiency exacerbates cGAS-dependent autoimmunity in theTrex1-/-mouse model of Aicardi-Goutières syndrome. These studies identify ABCC1-mediated cGAMP export as a key regulatory mechanism of the cGAS-STING pathway.
Regulation with cell size ensures mitochondrial DNA homeostasis during cell growth
Authors: Seel Anika , Padovani Francesco , Finster Alissa , Mayer Moritz , Bureik Daniela , Osman Christof , Klecker Till , Schmoller Kurt M. 
Published: December 2021

AbstractTo maintain stable DNA concentrations, proliferating cells need to coordinate DNA replication with cell growth. For nuclear DNA, eukaryotic cells achieve this by coupling DNA replication to cell cycle progression, ensuring that DNA is doubled exactly once per cell cycle. By contrast, mitochondrial DNA replication is typically not strictly coupled to the cell cycle, leaving the open question of how cells maintain the correct amount of mitochondrial DNA during cell growth. Here, we show that in budding yeast, mitochondrial DNA copy number increases with cell volume, both in asynchronously cycling populations and during G1 arrest. Our findings suggest that cell-volume-dependent mitochondrial DNA maintenance is achieved through nuclear encoded limiting factors, including the mitochondrial DNA polymerase Mip1 and the packaging factor Abf2, whose amount increases in proportion to cell volume. By directly linking mitochondrial DNA maintenance to nuclear protein synthesis, and thus cell growth, constant mitochondrial DNA concentrations can be robustly maintained without a need for cell-cycle-dependent regulation.
Unconventional secretion of unglycosylated ORF8 is critical for the cytokine storm during SARS-CoV-2 infection
Authors: Lin Xiaoyuan , Fu Beibei , Xiong Yan , Xing Na , Xue Weiwei , Guo Dong , Zaky Mohamed Y. , Pavani Krishna Chaitanya , Kunec Dusan , Trimpert Jakob , Wu Haibo 
Published: December 2021

AbstractCoronavirus disease 2019 is a respiratory infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Evidence on the pathogenesis of SARS-CoV-2 is accumulating rapidly. In addition to structural proteins such as Spike and Envelope, the functional roles of non-structural and accessory proteins in regulating viral life cycle and host immune responses remain to be understood. Here, we show that open reading frame 8 (ORF8) acts as messenger for inter-cellular communication between alveolar epithelial cells and macrophages during SARS-CoV-2 infection. Mechanistically, ORF8 is a secretory protein that can be secreted by infected epithelial cells via both conventional and unconventional secretory pathways. The unconventionally secreted ORF8 recognizes the IL17RA receptor of macrophages and induces cytokine release. However, conventionally secreted ORF8 cannot bind to IL17RA due to N-linked glycosylation. Furthermore, we found that Yip1 interacting factor homolog B (YIF1B) is a channel protein that translocates unglycosylated ORF8 into vesicles for unconventional secretion. Blocking the unconventional secretion of ORF8 via a YIF1B knockout in hACE2 mice attenuates inflammation and yields delayed mortality following SARS-CoV-2 challenge.
Loquacious Modulates Flaviviral RNA Replication in Mosquito Cells
Authors: Shivaprasad Shwetha , Weng Kuo-Feng , Ooi Yaw Shin , Belk Julia , Carette Jan E. , Flynn Ryan , Sarnow Peter 
Published: December 2021

AbstractArthropod-borne viruses infect both mosquito and mammalian hosts. While much is known about virus-host interactions that modulate viral gene expression in their mammalian host, much less is known about the interactions that involve inhibition, subversion or avoidance strategies in the mosquito host. A novel RNA-Protein interaction detection assay was used to detect proteins that directly or indirectly bind to dengue viral genomes in infected mosquito cells. Membrane-associated mosquito proteins SEC61A1 and Loquacious (Loqs) were found to be in complex with the viral RNA. Depletion analysis demonstrated that both SEC61A1 and Loqs have pro-viral functions in the dengue viral infectious cycle. Co-localization and pull-down assays showed that Loqs interacts with viral protein NS3 and both full-length and subgenomic viral RNAs. While Loqs coats the entire positive-stranded viral RNA, it binds selectively to the 3’ end of the negative-strand of the viral genome. In-depth analyses showed that the absence of Loqs did not affect translation or turnover of the viral RNA but modulated viral replication. Loqs also displayed pro-viral functions for several flaviviruses in infected mosquito cells, suggesting a conserved role for Loqs in flavivirus-infected mosquito cells.Author SummaryThere is a wealth of information that dictates virus-host interactions in flavivirus-infected mammalian cells, yet there is only sparse information on the mechanisms that modulate viral gene expression in the mosquito host. Using a novel RNA-protein detection assay, the interactions of SEC61A1 and Loqs with the dengue viral genome were found to have proviral functions in infected mosquito cells. In particular, Loqs forms complexes with the positive-strand of the viral RNA and the very 3’ end of the negative-strand viral RNA. Further analyses showed that Loqs modulates viral RNA replication of dengue virus and gene amplification of several other flaviviral genomes. These findings argue that Loqs is an essential proviral host factor in mosquitos.
An unusual trafficking domain in MSRP6 defines a complex needed for Maurer’s clefts anchoring and maintenance inP. falciparuminfected red blood cells
Authors: Blancke Soares Alexandra , Stäcker Jan , Schwald Svenja , Hoijmakers Wieteke , Metwally Nahla Galal , Cronshagen Jakob , Schoeler Hanno , Flemming Sven , Höhn Katharina , Fröhlke Ulrike , Mesén-Ramírez Paolo , Bergmann Bärbel , Khosh-Naucke Melissa , Bruchhaus Iris , Bártfai Richárd , Spielmann Tobias 
Published: December 2021

AbstractIntracellular malaria blood stage parasites remodel their host cell, a process essential for parasite survival and a cause of pathology in malaria infections. Host cell remodeling depends on the export of different classes of exported parasite proteins into the infected red blood cell (RBC). Here we show that members of a recently discovered group of difficult to predict exported proteins harbor an N-terminal export domain, similar to other classes of exported proteins, indicating that this is a common theme among all classes of exported proteins. For one such protein, MSRP6 (MSP-7 related protein 6), we identified a second, untypical export-mediating domain that corresponded to its MSP7-like region. In addition to its function in export, this domain also mediated attachment to the Maurer’s clefts, prominent parasite-induced structures in the host cell where MSRP6 is located. Using BioID with the Maurer’s clefts attachment domain of MSRP6 to identify interactors and compartment neighbors in live parasites we discovered a novel complex of proteins at the Maurer’s clefts. We show that this complex is necessary for the anchoring and maintaining the structural integrity of the Maurer’s clefts. The Maurer’s clefts are believed to be involved in the transport of the major virulence factor PfEMP1 to the host cell surface where it mediates cytoadherence of infected RBCs to endothelial cells, a main reason for the importance of host cell modifications for parasite virulence in the human host. Taking advantage of MSRP6 complex mutants and IT4 parasites that we modified to express only one specific PfEMP1 we find that abolishing Maurer’s clefts anchoring was neither needed for PfEMP1 transport to the host cell surface nor for cytoadherence. Altogether, this work reveals parasite proteins involved in Maurer’s clefts anchoring and maintenance and unexpectedly finds that these functions seem to be dispensable for virulence factor transport and surface display.
DExCon, DExogron, LUXon: on-demand expression control of endogenous genes reveals differential dynamics of Rab11 family members
Authors: Gemperle Jakub , Harrison Thomas , Flett Chloe , Adamson Antony , Caswell Patrick 
Published: December 2021

CRISPR technology has made generation of gene knockouts widely achievable in cells. However, once inactivated, their reactivation remains difficult, especially in diploid cells. Here, we present DExCon (Doxycycline-mediated endogenous gene Expression Control), DExogron (DExCon combined with auxin-mediated targeted protein degradation) and LUXon (light responsive DExCon), approaches which combine one-step CRISPR-Cas9 mediated targeted knock-in of fluorescent proteins with an advanced Tet-inducible TRE3GS promoter. These approaches combine blockade of active gene transcription with the ability to reactivate transcription on demand, including activation of silenced genes. Systematic control can be exerted using doxycycline or spatiotemporally by light, and we demonstrate functional knockout/rescue in the closely related Rab11 family of vesicle trafficking regulators. Fluorescent protein knock-in results in bright signals compatible with low-light live microscopy from monoallelic modification, the potential to simultaneously image different alleles of the same gene and bypasses the need to work with clones. Protein levels are easily tunable to correspond with endogenous expression through cell sorting (DExCon), timing of light illumination (LUXon) or by exposing cells to different levels of auxin (DExogron). Furthermore, our approach allowed us to quantify previously unforeseen differences in vesicle dynamics, expression kinetics and protein stability among highly similar endogenous Rab11 family members and their colocalization in triple knock-in cells.GRAPHICAL ABSTRACTIN BRIEFWe describe development of DExCon, LUXon and DExogron approaches, where a single CRIPR/Cas9-mediated gene editing event can block endogenous gene expression, with the ability to reactivate expression encoded such that even silent genes can be expressed. Expression can be controlled systematically using doxycycline, or spatiotemporally by light, allowing fluorescent tagging of endogenous proteins and quantification of expression kinetics, protein dynamics and stability for highly similar genes such as members of the Rab11 family.