bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning
Authors: Mitrovic Darko , Comas Sarah Mc , Alleva Claudia , Bonaccorsi Marta , Drew David , Delemotte Lucie 
Published: September 2022

AbstractSugar porters represent the largest group of secondary-active transporters. Some members, such as the glucose (GLUT) transporters, are well-known for their role in maintaining blood glucose homeostasis in mammals, with their expression upregulated in many types of cancers. Because only a few sugar porter structures have been determined, mechanistic models have been constructed by piecing together structural states of distantly related proteins. Current GLUT transport models are predominantly descriptive and oversimplified. Here, we have combined coevolution analysis and comparative modeling, to predict structures of the entire sugar porter superfamily in each state of the transport cycle. We have analysed the state-specific contacts inferred from coevolving residue pairs and shown how this information can be used to rapidly generate free-energy landscapes consistent with experimental estimates, as illustrated here for the mammalian fructose transporter GLUT5. By comparing many different sugar porter models and scrutinizing their sequence, we have been able to define the molecular determinants of the transport cycle, which are conserved throughout the sugar porter superfamily. We have also been able to highlight differences leading to the emergence of proton-coupling, validating, and extending the previously proposed latch mechanism. Our computational approach is transferable to any transporter, and to other protein families in general.
Impact of clonal architecture on clinical course and prognosis in patients with myeloproliferative neoplasms
Authors: Luque Paz Damien , Bader Michael S. , Nienhold Ronny , Rai Shivam , Almeida Fonseca Tiago , Stetka Jan , Hao-Shen Hui , Mild-Schneider Gabi , Passweg Jakob R. , Skoda Radek C. 
Published: September 2022

AbstractMyeloproliferative neoplasms (MPNs) are caused by a somatic gain-of-function mutation in one of three “disease driver” genes JAK2, MPL or CALR. About half of MPN patients also carry additional somatic mutations that modify the clinical course. The order of acquisition of these gene mutations has been proposed to influence the phenotype and evolution of the disease. We studied 50 JAK2-V617F-positive MPN patients who carried at least one additional somatic mutation and determined the clonal architecture of their hematopoiesis by sequencing DNA from single cell derived colonies. In 22 of these patients we also side-by-side applied Tapestri single-cell DNA sequencing (scDNAseq) with cells from the same blood sample. The clonal architectures derived by the two methods showed good overall concordance. scDNAseq showed higher sensitivity for mutations with low variant allele fraction, but had more difficulties distinguishing between heterozygous and homozygous mutations. By unsupervised analysis of clonal architecture data from all 50 MPN patients we defined 4 distinct clusters that differed by the order of acquisition of the mutations, and the complexity of the subclonal structure. Cluster 4, characterized by more complex subclonal structure without a preferred order of acquisition, correlated with reduced overall survival, and in multivariate analysis represented a risk factor independent of the MPN subtype or the age at diagnosis. Our results suggest that deciphering the clonal architecture in patients with MPN that carry multiple gene mutations can improve the molecular prognostic stratification that until now was primarily based on the number and type of gene mutations.
Analysis of sex differential genes at whole genome level reveals their organ-and chromosome-dependent expressions, regulations, and interactions
Authors: Ma Jiamin , Wang Lishi , Yuan Gang , Fernando Chrishan , Yao Lan , Dong Wei , Tian Cheng , Bukiya Anna , Jablonski Monica M. , Feng Helin , Li Daniel Z. , Lu Lu , Jiao Yan , Ji Jiafu , Wang Gang , Gu Weikuan 
Published: September 2022

AbstractMales and females possess genomes that are almost identical but differ in morbidity, prevalence, severity, response to therapies and mortality of many diseases. We comprehensively analyzed gene expression data in seven tissues from BXD recombinant inbred (RI) mouse strains. We found that there were considerable differences in the numbers and functions among different tissues and between autosomal and sex chromosomes. Among sex differential genes, those on autosomal chromosomes mainly function to regulate metabolic pathways related to their host organs, while those on sex chromosomes mainly regulate nuclear proteins required for DNA replication or transcription during early development. Kidney possessed the fewest sex differential genes on sex chromosomes. The sexually dimorphic genes expressed on X chromosomes were all related to perception, while genes on the autosomal chromosomes were related to metabolism. These patterns of gene expression do not translate into similarity of protein structures, rather they are grouping with function.
Gene regulatory changes underlie developmental plasticity in respiration and aerobic performance in highland deer mice
Authors: Schweizer Rena M. , Ivy Catherine M. , Natarajan Chandrasekhar , Scott Graham R. , Storz Jay F. , Cheviron Zachary A. 
Published: September 2022

AbstractPhenotypic plasticity can play an important role in the ability of animals to tolerate environmental stress, but the nature and magnitude of plastic responses are often specific to the developmental timing of exposure. Here, we examine changes in gene expression in the diaphragm of highland deer mice (Peromyscus maniculatus) in response to hypoxia exposure at different stages of development. In highland deer mice, developmental plasticity in diaphragm function may mediate changes in several respiratory traits that influence aerobic metabolism and performance under hypoxia. We generated RNAseq data from diaphragm tissue of adult deer mice exposed to 1) life-long hypoxia (before conception to adulthood), 2) post-natal hypoxia (birth to adulthood), 3) adult hypoxia (6-8 weeks only during adulthood), or 4) normoxia. We found five suites of co-regulated genes that are differentially expressed in response to hypoxia, but the patterns of differential expression depend on the developmental timing of exposure. We also identified four transcriptional modules that are associated with important respiratory traits. Many of the genes in these transcriptional modules bear signatures of altitude-related selection, providing an indirect line of evidence that observed changes in gene expression may be adaptive in hypoxic environments. Our results demonstrate the importance of developmental stage in determining the phenotypic response to environmental stressors.
Protection of homologous and heterologous boosters after primary schemes of rAd26-rAd5, ChAdOx1 nCoV-19 and BBIBP-CorV during the Omicron outbreak in adults of 50 years and older in Argentina: a test-negative case-control study
Authors: González Soledad , Olszevicki Santiago , Gaiano Alejandra , Salazar Martín , Regairaz Lorena , Varela Baino Ana Nina , Barkel Erika , Varela Teresa , González Martínez Veronica V. , Pesci Santiago , Marín Lupe , Irassar Juan Ignacio , Ceriani Leticia , Garcia Enio , Kreplak Nicolás , Estenssoro Elisa , Marsico Franco 
Published: September 2022

ABSTRACTObjectivesTo estimate the protection against laboratory-confirmed SARS-CoV-2 infection, hospitalisations, and death after homologous or heterologous third-dose (booster) in individuals with primary vaccination schemes with rAd26-rAd5, ChAdOx1nCoV-19, BBIBP-CorV or heterologous combinations, during the period of Omicron BA.1 predominance.DesignRetrospective, test-negative, case-control study, with matched analysis.SettingProvince of Buenos Aires, Argentina, between 12/1/21-4/1/21.Participants422,144 individuals ≥50 years who had received two or three doses of COVID-19 vaccines and were tested for SARS-CoV-2.Main outcome measures: Odds ratios of confirmed SARS-CoV-2 infection, hospitalisations and death after administering different boosters, compared to a two-dose primary scheme.ResultsOf 221,933(52.5%) individuals with a positive test, 190,884(45.2%) had received a two-dose vaccination scheme and 231,260(54.8%) a three-dose scheme. The matched analysis included 127,014 cases and 180,714 controls.The three-dose scheme reduced infections (OR 0.81[0.80-0.83]) but after 60 days protection dropped (OR 1.04[1.01-1.06]). The booster dose decreased the risk of hospitalisations and deaths after 15-59 days (ORs 0.28[0.25-0.32] and 0.25[0.22-0.28] respectively), which persisted after administration for 75[66-89] days.Administration of a homologous booster after a primary scheme with vectored-vaccines provided low protection against infections (OR 0.94[0.92-0.97] and 1.05[1.01-1.09] before and after 60 days). Protection against hospitalisations and death was significant (OR 0.30[0.26-0.35] and 0.29[0.25-0.33] respectively) but decreased after 60 days (OR 0.59[0.47-0.74] and 0.51[0.41- 0.64] respectively).The inoculation of a heterologous booster after a primary course with ChAdOx1 nCoV-19, rAd26-rAd5, BBIBP-CorV, or heterologous schemes, offered some protection against infection (OR 0.70[0.68-0.71]), which decreased after 60 days (OR 1.01[0.98-1.04]). The protective effect against hospitalisations and deaths (OR 0.26[0.22-0.31] and 0.22[0.18-0.25] respectively) was clear and persisted after 60 days (OR 0.43[0.35-0.53] and 0.33[0.26-0.41]).ConclusionsThis study shows that, during Omicron predominance, heterologous boosters provide an enhanced protection and longer effect duration against COVID-19-related hospitalisations and death in individuals older than 50, compared to homologous boosters.
Separation of the effects of small intestinal microbiome-diet interactions on human gut hormone secretion
Authors: Rienzi Sara C. Di , Danhof Heather A. , Huerta Juan , Britton Robert A. 
Published: September 2022

SummaryMicrobial regulation of gut hormones is a potential mechanism by which the gut microbiome acts on systemic physiology. However, there are limited systems that permit study of how small intestinal microbes and diet modulate gut hormone secretion. Here we present the platformCulturing andApplication ofMicrobes onIntestinalOrganoids (CAMIO) and demonstrate its usage in studying the effects of diet and microbes on gut hormones. We validate that CAMIO supports long-term cultivation of a small intestinal microbiome in different dietary sugars and show that CAMIO permits measurement of gut hormones released from jejunal organoids in response to products of the small intestinal communities. In doing so, we observe differential secretion of ghrelin, PP, and PYY according to whether the microbial communities were grown in glucose-fructose versus sucrose or trehalose. We expect CAMIO to be useful in mechanistically understanding how diet and microbes collectively regulate gut hormones.
Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes
Authors: Zhu Han , Wang Gaowei , Nguyen-Ngoc Kim-Vy , Kim Dongsu , Miller Michael , Goss Georgina , Kovsky Jenna , Harrington Austin R. , Saunders Diane , Melton Rebecca , Powers Alvin C. , Preissl Sebastian , Spagnoli Francesca M. , Gaulton Kyle J. , Sander Maike 
Published: September 2022

AbstractPancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and pancreas from childhood and adult donors for comparison. We delineate major cell types, define their regulomes, and describe spatiotemporal gene regulatory relationships between transcription factors. CDX2 emerged as a regulator of enterochromaffin-like cells, which we show resemble a transient, previously unrecognized, CDX2+ pre-β-cell population in fetal pancreas, arguing against a proposed non-pancreatic origin. Furthermore, we observe insufficient activation of signal-dependent transcriptional programs during in vitro β-cell maturation and identify sex hormones as drivers of β-cell proliferation in childhood. Altogether, our analysis provides a comprehensive understanding of cell fate acquisition in stem cell-derived islets and a framework for manipulating cell identities and maturity.
Biophysical and Structural Characterization of a Viral Genome Packaging Motor
Authors: Prokhorov Nikolai S. , Davis Christal R. , Maruthi Kashyap , Yang Qin , Woodson Michael , White Mark A. , Miller Lohra M. , Jarrold Martin F. , Catalano Carlos E. , Morais Marc C. 
Published: September 2022

AbstractLike many dsDNA viruses, bacteriophage λ replicates its genome as a concatemer consisting of multiple copies of covalently linked dsDNA genomes. To encapsidate a single genome within a nascent procapsid, λ must: 1) find its own dsDNA amongst the multitude of host nucleic acids; 2) identify the genomic start site; 3) cut the DNA; 4) bring the excised DNA to a procapsid; 5) translocate DNA into the capsid; 6) cut DNA again at a packaging termination site, 7) disengage from the newly filled capsid; and 8) bring the remainder of the genomic concatemer to fill another empty procapsid. These disparate genome processing tasks are carried out by a single virus-encoded enzyme complex called terminase. While it has been shown that λ terminase initially forms a tetrameric complex to cut DNA, it is not clear whether the same configuration translocates DNA. Here, we describe biophysical and initial structural characterization of a λ terminase translocation complex. Analytical ultracentrifugation (AUC) and small angle X-ray scattering (SAXS) indicate that between 4 and 5 protomeric subunits assemble a cone-shaped terminase complex with a maximum dimension of ∼230 and radius of gyration of ∼72 Å. Two-dimensional classification of cryoEM images of λ terminase are consistent with these dimensions and show that particles assume a preferred orientation in ice. The orientations appear to be end-on, as terminase rings resemble a starfish with approximate pentameric symmetry. While ∼5-fold symmetry is apparent, one of the five “arms” appears partially displaced with weaker more diffuse density in some classes, suggesting flexibility and/or partial occupancy. Charge detection mass spectrometry (CDMS) is consistent with a pentameric complex, with evidence that one motor subunit is weakly bound. Kinetic analysis indicates that the complex hydrolyzes ATP at a rate comparable to the rates of other phage packaging motors. Together with previously published data, these results suggest that λ terminase assembles conformationally and stoichiometrically distinct complexes to carry out different genome processing tasks. We propose a “symmetry resolution” pathway to explain how terminase transitions between these structurally and functionally distinct states.
Cell cycle dynamics and window of MUTE action during the terminal division of stomata and ramification of its loss-of-function on the cell cycle of an uncommitted precursor
Authors: Zuch Daniel T. , Herrmann Arvid , Kim Eun-Deok , Torii Keiko U. 
Published: September 2022

ABSTRACTPlants develop in the absence of cell migration. As such, cell division and differentiation need to be coordinated for functional tissue formation. Cellular valves on the plant epidermis, stomata, are generated through a stereotypical sequence of cell division and differentiation events. In Arabidopsis, three master-regulatory transcription factors, SPEECHLESS (SPCH), MUTE, and FAMA sequentially drive initiation, proliferation, and differentiation of stomata. Among them, MUTE switches the cell cycle mode from proliferative asymmetric division to terminal symmetric division and orchestrates the execution of the single symmetric division event. However, it remains unclear to what extent MUTE regulates the expression of cell cycle genes through the symmetric division and whether MUTE accumulation itself is gated by the cell cycle. Here, we show that MUTE directly upregulates the expression of cell cycle components throughout the terminal cell cycle phases of a stomatal precursor, not only the core cell cycle engines but also checkpoint regulators. Time-lapse live imaging using the multi-color cell cycle indicator PlaCCI revealed that MUTE accumulates up to the early G2 phase, whereas its successor and direct target, FAMA, accumulates at late G2 through terminal mitosis. In the absence of MUTE, meristemoids fail to differentiate, and their G1 phase elongates as they reiterate asymmetric divisions. Combined, our work provides the framework of cell cycle and master regulatory transcription factors to coordinate a single symmetric cell division, and suggests a mechanism for the eventual cell cycle arrest of an uncommitted stem-cell-like precursor at the G1 phase.
Synchronization of oscillatory growth prepares fungal hyphae for fusion
Authors: Wernet Valentin , Kumpost Vojtech , Mikut Ralf , Hilbert Lennart , Fischer Reinhard 
Published: September 2022

Communication is crucial for organismic interactions, from bacteria, to fungi, to humans. Humans may use the visual sense to monitor the environment before starting acoustic interactions. In comparison, fungi lack a visual system, instead, hyphae use a cell-to-cell dialogue based on secreted signaling molecules to orchestrate cell fusion and establish hyphal networks. Hyphae alternate roles as signal-sender and signal-receiver, as can be visualized via the putative signaling protein, Soft, which is recruited in an oscillatory manner to the respective cytoplasmic membrane of interacting hyphae. Here, we show that signal oscillations already occur in single hyphae of Arthrobotrys flagrans in the absence of a potential fusion partner. They occurred in the same phase as growth oscillations. Once two fusion partners came into each other’s vicinity, their oscillation frequencies slowed down (entrainment phase) and transit into anti-phasic synchronization of the two cells’ oscillations with frequencies of 130 +/-20 sec. Single-cell oscillations, transient entrainment, and anti-phasic oscillations were reproduced by a mathematical model where nearby hyphae can absorb and secrete a limited molecular signaling component into a shared extra-cellular space. We show that intracellular Ca2+ concentrations oscillate in two approaching hyphae, and depletion of Ca2+ in the surrounding affected vesicle-driven extension of the hyphal tip, abolished single-cell molecular oscillations and the anti-phasic synchronization of two hyphae. Our results suggest that single hyphae engage in a “monologue” that may be used for exploration of the environment and can dynamically shift their extra-cellular signaling systems into a “dialogue” to initiate hyphal fusion.Significance statementCommunication at the cellular level often relies on chemical signal exchange. One prominent example is the fusion of fungal hyphae to form complex hyphal networks. As opposed to mating-type dependent cell fusion, cell-fusion events described here occur in genetically identical cells. Relying only on one chemical signaling channel raises the question of how communication is initiated. We discovered that individual hyphae constantly perform signal oscillations, comparable to a cellular “monologue” until they meet another hypha with which they then coordinate signal oscillations in a cell-to-cell dialogue. We also show that signal oscillations are mechanistically interlinked with calcium-dependent growth oscillations. Although the signaling molecule(s) has not been identified yet, it is highly likely linked to the hyphal growth machinery.
Separate roles of LMAN1 and MCFD2 in ER-to-Golgi trafficking of factor V and factor VIII
Authors: Zhang Yuan , Liu Zhigang , Zhang Bin 
Published: September 2022

AbstractMutations in LMAN1 and MCFD2 cause the combined deficiency of FV and FVIII (F5F8D). LMAN1 and MCFD2 form a protein complex that transport FV and FVIII from the endoplasmic reticulum to the Golgi. Although both proteins are required for the cargo receptor function, little is known about specific roles of LMAN1 and MCFD2 in transporting FV/FVIII. We used different LMAN1 and MCFD2 deficient cell lines to investigate the LMAN1/MCFD2-dependent FV/FVIII secretion pathway. LMAN1 deficiency led to more profound decreases in FV/FVIII secretion in HEK293T and HepG2 cells than in HCT116 cells, suggesting regulation of cargo transport by the LMAN1/MCFD2 pathway varies in different cell types. Using these cell lines, we developed functional assays to accurately assess pathogenicity of recently reported potential LMAN1 and MCFD2 missense mutations. LMAN1 with mutations abolishing carbohydrate binding can still partially rescue FV/FVIII secretion, suggesting that N-glycan binding is not absolutely required for FV/FVIII transport. Surprisingly, overexpression of either WT or mutant MCFD2 is sufficient to rescue FV/FVIII secretion defects in LMAN1 deficient cells. These results suggest that cargo binding and transport are carried out by MCFD2 and that LMAN1 primarily serves as a shuttling carrier of MCFD2. Finally, overexpression of both LMAN1 and MCFD2 does not further increase FV/FVIII secretion, suggesting that the amount of the LMAN1-MCFD2 receptor complex is not a rate-limiting factor in ER-Golgi transport of FV/FVIII. This study provides new insight into the molecular mechanism of F5F8D and intracellular trafficking of FV and FVIII.Key PointsEfficient ER-to-Golgi transport of FV and FVIII requires the LMAN1-MCFD2 cargo receptor complex.MCFD2 functions as a primary interacting partner of FV/FVIII cargo and LMAN1 primarily serves as a shuttling carrier of MCFD2.
Retrotransposons hijack alt-EJ DNA repair process for mobilization and eccDNA biogenesis
Authors: Yang Fu , Su Weijia , Chung Oliver W. , Tracy Lauren , Wang Lu , Ramsden Dale A. , Zhang ZZ Zhao 
Published: September 2022

AbstractParasitic retrotransposons populate in the genome to rewrite the hosts’ genetic code. How retrotransposons use the host factors to achieve their propagation remains largely unclear. Here we report retrotransposons hijack the alternative end-joining (alt-EJ) DNA repair process to accomplish mobilization cycle. We applied Nanopore sequencing to examine the fates of replicated retrotransposon DNA, and found that only 10% of them achieve integration, while 90% exist as extrachromosomal circular DNA (eccDNA). Using eccDNA production as a readout, further genetic screens identified factors from alt-EJ as essential for retrotransposon replication. alt-EJ drives the 2nd-strand synthesis of the retrotransposon DNA via a circularization process, thus is necessitated for eccDNA production and integrations. Our study reveals a conserved function of alt-EJ in promoting selfish element propagation, which potentially causes disease or drives evolution.