bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biocomposite Thermoplastic Polyurethanes Containing Evolved Bacterial Spores as Living Fillers to Facilitate Polymer Disintegration
Authors: Kim Han Sol , Noh Myung Hyun , White Evan M. , Kandefer Michael V. , Wright Austin F. , Datta Debika , Lim Hyun Gyu , Smiggs Ethan , Locklin Jason J. , Rahman Md Arifur , Feist Adam M. , Pokorski Jonathan K. 
Published: October 2023

AbstractThe field of engineered living materials (ELMs) seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. ELMs have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication was demonstrated in which spores from polymer-degrading bacteria were incorporated into a thermoplastic polyurethane (TPU) using high-temperature melt processing. Bacteria were engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 °C. Furthermore, the overall tensile properties of spore-filled TPUs were substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitated disintegration in compost in the absence of a microbe-rich environment. Finally, spores retained a programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.
Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Complex Genotypic-Phenotypic Relationships Altering Epithelial Composition
Authors: Qin Xiaodi , Strand Siri H. , Lee Marissa R. , Saraswathibhatla Aashrith , van IJzendoorn David G. P. , Zhu ChunFang , Vennam Sujay , Varma Sushama , Hall Allison , Factor Rachel E. , King Lorraine , Simpson Lunden , Luo Xiaoke , Colditz Graham A. , Jiang Shu , Chaudhuri Ovijit , Hwang E. Shelley , Marks Jeffrey R. , Owzar Kouros , West Robert B. 
Published: October 2023

ABSTRACTTo identify mechanisms underlying the growth of ductal carcinoma in situ (DCIS) and properties that lead to progression to invasive cancer, we performed single-cell RNA-sequencing (scRNA-seq) on DCIS lesions and matched synchronous normal breast tissue. Using inferred copy number variations (CNV), we identified neoplastic epithelial cells from the clinical specimens which contained a mixture of DCIS and normal ducts. Phylogenetic analysis based on the CNVs demonstrated intratumoral clonal heterogeneity was associated with significant gene expression differences. We also classified epithelial cells into mammary cell states and found that individual genetic clones contained a mixture of cell states suggesting an ongoing pattern of differentiation after neoplastic transformation. Cell state proportions were significantly different based on estrogen receptor (ER) expression with ER-DCIS more closely resembling the distribution in the normal breast, particularly with respect to cells with basal characteristics. Using deconvolution from bulk RNA-seq in archival DCIS specimens, we show that specific alterations in cell state proportions are associated with progression to invasive cancer. Loss of an intact basement membrane (BM) is the functional definition of invasive breast cancer (IBC) and scRNA-seq data demonstrated that ongoing transcription of key BM genes occurs in specific subsets of epithelial cell states. Examining BM in archival microinvasive breast cancers and anin vitromodel of invasion, we found that passive loss of BM gene expression due to cell state proportion alterations is associated with loss of the structural integrity of the duct leading to an invasive phenotype. Our analyses provide detailed insight into DCIS biology.SIGNIFICANCESingle cell analysis reveals that preinvasive breast cancer is comprised of multiple genetic clones and there is substantial phenotypic diversity both within and between these clones. Ductal carcinoma in situ (DCIS) of the breast is a non-invasive condition commonly identified through mammographic screening. A primary diagnosis of DCIS carries little mortality risk on its own, but its presence is a risk factor for subsequent clonally related invasive breast cancer (IBC) (1–5).
Brefeldin A and M-COPA block the export of RTKs from the endoplasmic reticulum via simultaneous inactivation of ARF1, ARF4, and ARF5
Authors: Natsume Miyuki , Niwa Mariko , Ichikawa Sho , Okamoto Takuma , Tsutsui Hisazumi , Usukura Daiki , Murata Takatsugu , Abe Ryo , Shimonaka Motoyuki , Nishida Toshirou , Shiina Isamu , Obata Yuuki 
Published: October 2023

AbstractNormal receptor tyrosine kinases (RTKs) need to reach the plasma membrane (PM) for ligand-induced activation, whereas its cancer-causing mutants can be activated before reaching the PM in organelles, such as the Golgi/trans-Golgi network (TGN). Inhibitors of protein export from the endoplasmic reticulum (ER), such as brefeldin A (BFA) and 2-methylcoprophilinamide (M-COPA), can suppress the activation of mutant RTKs in cancer cells, suggesting that RTK mutants cannot initiate signaling in the ER. BFA and M-COPA block the function of ADP-ribosylation factors (ARFs) that play a crucial role in ER–Golgi protein trafficking. However, which ARFs among AFR family proteins are inhibited by BFA or M-COPA, that is, which ARFs are involved in RTKs transport from the ER, remain unclear. In this study, we showed that M-COPA blocked the export of not only KIT but also PDGFRA/EGFR/MET RTKs from the ER. ER-retained RTKs could not fully transduce anti-apoptotic signals, thereby leading to cancer cell apoptosis. Moreover, single knockdown of ARF1, ARF3, ARF4, ARF5, or ARF6 could not block ER export of RTKs, indicating that BFA/M-COPA treatment cannot be mimicked by knockdown of only one ARF member. Interestingly, simultaneous transfection of ARF1, ARF4, and ARF5 siRNAs mirrored the effect of BFA/M-COPA treatment. Consistent with these results,in vitropulldown assays showed that BFA/M-COPA blocked the function of ARF1, ARF4, and ARF5. Taken together, these results suggest that BFA/M-COPA targets at least ARF1, ARF4, and ARF5; in other words, RTKs require the simultaneous activation of ARF1, ARF4, and ARF5 for their ER export.
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Authors: Abdill Richard J. , Graham Samantha P. , Rubinetti Vincent , Albert Frank W. , Greene Casey S. , Davis Sean , Blekhman Ran 
Published: October 2023

AbstractUnderstanding the factors that shape variation in the human microbiome is a major goal of research in biology. While other genomics fields have used large, pre-compiled compendia to extract systematic insights requiring otherwise impractical sample sizes, there has been no comparable resource for the 16S rRNA sequencing data commonly used to quantify microbiome composition. To help close this gap, we have assembled a set of 168,484 publicly available human gut microbiome samples, processed with a single pipeline and combined into the largest unified microbiome dataset to date. We use this resource, which is freely available at microbiomap.org, to shed light on global variation in the human gut microbiome. We find that Firmicutes, particularly Bacilli and Clostridia, are almost universally present in the human gut. At the same time, the relative abundance of the 65 most common microbial genera differ between at least two world regions. We also show that gut microbiomes in undersampled world regions, such as Central and Southern Asia, differ significantly from the more thoroughly characterized microbiomes of Europe and Northern America. Moreover, humans in these overlooked regions likely harbor hundreds of taxa that have not yet been discovered due to this undersampling, highlighting the need for diversity in microbiome studies. We anticipate that this new compendium can serve the community and enable advanced applied and methodological research.
Population genetic analyses of longitudinal vaginal microbiome reveal racioethnic evolutionary dynamics and prevailing positive selection ofLactobacillusadhesins
Authors: Wei Xin , Tsai Ming-Shian , Liang Liang , Jiang Liuyiqi , Hung Chia-Jui , Jelliffe-Pawlowski Laura , Rand Larry , Snyder Michael , Jiang Chao 
Published: October 2023

AbstractThe vaginal microbiome is important for reproductive health and should constantly evolve in response to dynamic host-microbe interactions. The composition of the vaginal microbiome is associated with ethnicity; however, the evolutionary landscape of the vaginal microbiome, especially in the multi-ethnic context, remains under-studied. In this study, we performed a longitudinal evolutionary vaginal microbiome analysis of 351 samples from 35 pregnant women with diverse ethnic backgrounds and validated the main findings in two cohorts totaling 462 samples from 90 multi-ethnic women. Microbiome alpha diversity and community states showed strong ethnic signatures.Lactobacillaceaespecies had a significantly higher nonsynonymous/synonymous mutation ratio (pN/pS) than non-Lactobacillaceaespecies in all ethnicities. In addition, non-Lactobacillaceaeanaerobic bacteria were enriched in Black and Latino women, with significantly elevated nucleotide diversity and lower pN/pS in Black women. Intriguingly, theLactobacillaceaespecies had a large repertoire of positively selected genes, including the human mucin-binding and bacterial cell wall anchor genes, which showed independent, recurrent signatures of positive selection across multiple strains, indicating that the host-microbiome interactions directly drive microbial evolution at the molecular interface. Finally, we propose that the evolutionary metrics reflect the environmental niches of adapting microbes. Our study revealed the extensive ethnic signatures in vaginal microbial diversity, composition, community state, and evolutionary dynamics at species and gene levels, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.HighlightsExtensive ethnic signatures in the vaginal microbial diversity, composition, community state, and evolutionary dynamics were demonstrated.HealthyLactobacillaceaespecies showed lower nucleotide diversity but much more relaxed or even positive selection of genes than non-Lactobacillaceaespecies.In Black women, non-Lactobacillaceaespecies displayed higher nucleotide diversity and more stringent negative selection.Lactobacillusmucin-binding and cell wall anchor genes showed convergent signatures of positive selection across vaginal microbiomes.
Identification of residues potentially involved in optical shifts in the water-soluble chlorophyll-a binding protein through molecular dynamics simulations
Authors: Mai Martina , Zazubovich Valter , Mansbach R. A. 
Published: October 2023

AbstractReversible light- and thermally-induced spectral shifts are universally observed in a wide variety of pigment-protein complexes, at temperatures ranging from cryogenic to ambient. They can be observed either directly, in single-molecule spectroscopy experiments, or via non-photochemical spectral hole burning. These shifts are important to understand, for example, to gain a clearer picture of the primary processes of photosynthesis, or of general features of the protein energy landscapes. In this article, we have employed large-scale molecular dynamics simulations of a prototypical pigment-protein complex to better understand these shifts at a molecular scale. Although multiple mechanisms have been proposed over the years, no verification of these proposals via MD simulations has thus far been performed; our work represents the first step in this direction. The common requirement for all these mechanisms is the presence of doublewell (or multiple-well) features of the protein energy landscapes. In this work, from large-scale molecular dynamics simulations of the Water-Soluble Chlorophyll-binding Protein complex, we identified side chain rotations of certain amino acid residues as likely candidates for relevant multi-well landscape features. The protein free energy landscapes associated with side chain rotations feature energy barriers of around 1100- 1600 cm−1, in agreement with optical spectroscopy results, with the most promising residue type associated with experimental signatures being serine, which possesses a symmetric landscape and moment of inertia of a relevant magnitude.
Dynamic localization of the chromosomal passenger complex is controlled by the orphan kinesins KIN-A and KIN-B in the kinetoplastid parasiteTrypanosoma brucei
Authors: Ballmer Daniel , Akiyoshi Bungo 
Published: October 2023

AbstractThe chromosomal passenger complex (CPC) is an important regulator of cell division, which shows dynamic subcellular localization throughout mitosis, including kinetochores and the spindle midzone. In traditional model eukaryotes such as yeasts and humans, the CPC consists of the catalytic subunit Aurora B kinase, its activator INCENP, and the localization module proteins Borealin and Survivin. Intriguingly, Aurora B and INCENP as well as their localization pattern are conserved in kinetoplastids, an evolutionarily divergent group of eukaryotes that possess a unique set of kinetochore proteins and lack homologs of Borealin or Survivin. It is not understood how the kinetoplastid CPC assembles or how it is targeted to its subcellular destinations during the cell cycle. Here, we identify two orphan kinesins, KIN-A and KIN-B, as bona fide CPC proteins inTrypanosoma brucei, the causative agent of African sleeping sickness. By employing biochemical, structural, and cell biological approaches, we demonstrate that KIN-A and KIN-B serve as the scaffold for the assembly of the remaining CPC subunits. Kinetochore localization of the CPC depends on the KKT7 – KKT8 complex pathway, with the C-terminal unstructured tail of KIN-A serving as a key interaction partner for the KKT8 complex. Our data therefore show that, unlike other eukaryotes that take advantage of histone modifications for centromere recruitment, trypanosomes rely on kinetochore proteins to recruit the CPC onto kinetochores. Furthermore, the ATPase activity of KIN-A promotes chromosome alignment in prometaphase and CPC translocation to the central spindle upon anaphase onset. Thus, KIN-A constitutes a unique ‘two-in-one’ CPC localization module in complex with KIN-B, which directs the CPC to kinetochores (from S phase until metaphase) via its C-terminal tail, and to the central spindle (in anaphase) via its N-terminal kinesin motor domain. Our findings highlight the evolutionary diversity of CPC proteins and raise the possibility that kinesins may have served as the original transport vehicles for Aurora B kinases in early eukaryotes.
Structural identification of a selectivity filter in CFTR
Authors: Levring Jesper , Chen Jue 
Published: October 2023

AbstractThe cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel that regulates transepithelial salt and fluid homeostasis. CFTR dysfunction leads to reduced chloride secretion into the mucosal lining of epithelial tissues, thereby causing the inherited disease cystic fibrosis. Although several structures of CFTR are available, our understanding of the ion-conduction pathway is incomplete. In particular, the route that connects the cytosolic vestibule with the extracellular space has not been clearly defined, and the structure of the open pore remains elusive. Furthermore, although many residues have been implicated in altering the selectivity of CFTR, the structure of the “selectivity filter” has yet to be determined. In this study, we identify a chloride-binding site at the extracellular ends of transmembrane helices 1, 6, and 8, where a dehydrated chloride is coordinated by residues G103, R334, F337, T338, and Y914. Alterations to this site, consistent with its function as a selectivity filter, affect ion selectivity, conductance, and open channel block. The selectivity filter is accessible from the cytosol through a large inner vestibule and opens to the extracellular solvent through a narrow portal. The identification of a chloride-binding site at the intra- and extracellular bridging point leads us to propose a complete conductance path that permits dehydrated chloride ions to traverse the lipid bilayer.Significance statementCystic fibrosis is a fatal disease caused by inherited defects in thecftrgene. Understanding the structure and function of the CFTR protein is crucial for cystic fibrosis research. As an ion channel evolved from a family of ATP-driven active transporters, CFTR is structurally distinct from any other ion channel. This study describes the structure of CFTR’s ‘selectivity filter’, which enables us to complete the molecular description of the CFTR pore. Moreover, it enriches our broader knowledge of ion channel physiology, with a particular focus on chloride permeation mechanisms.
Larixol is not an inhibitor of Gαicontaining G proteins and lacks effect on signaling mediated by human neutrophil expressed formyl peptide receptors
Authors: Björkman Lena , Forsman Huamei , Bergqvist Linda , Dahlgren Claes , Sundqvist Martina 
Published: October 2023

AbstractNeutrophils express several G protein-coupled receptors (GPCRs) connected to intracellular Gαior Gαqcontaining G proteins for down-stream signaling. To dampen GPCR mediated inflammatory processes, several inhibitors targeting the receptors and/or their down-stream signals, have been developed. Potent and selective inhibitors for Gαqcontaining G proteins are available, but potent and specific inhibitors of Gαicontaining G proteins are lacking. Recently, Larixol, a compound extracted from the root ofEuphorbia formosana, was shown to abolish human neutrophil functions induced byN-formyl-methionyl-leucyl-phenylalanine (fMLF), an agonist recognized by formyl peptide receptor 1 (FPR1) which couple to Gαicontaining G proteins. The inhibitory effect was suggested to be due to interference with/inhibition of signals transmitted by βγ complexes of the Gαicontaining G proteins coupled to FPR1. In this study, we applied Larixol, obtained from two different commercial sources, to determine the receptor- and G protein-selectivity of this compound in human neutrophils. However, our data show that Larixol not only lacks inhibitory effect on neutrophil responses mediated through FPR1, but also on responses mediated through FPR2, a Gαicoupled GPCR closely related to FPR1. Furthermore, Larixol did not display any features as a selective inhibitor of neutrophil responses mediated through the Gαqcoupled GPCRs for platelet activating factor and ATP. Hence, our results imply that the inhibitory effects described for the root extract ofEuphorbia formosanaare not mediated by Larixol and that the search for a selective inhibitor of G protein dependent signals generated by Gαicoupled neutrophil GPCRs must continue.
State-transition Modeling of Blood Transcriptome Predicts Disease Evolution and Treatment Response in Chronic Myeloid Leukemia
Authors: Frankhouser David E. , Rockne Russell C. , Uechi Lisa , Zhao Dandan , Branciamore Sergio , O’Meally Denis , Irizarry Jihyun , Ghoda Lucy , Ali Haris , Trent Jeffery M. , Forman Stephen , Fu Yu-Hsuan , Kuo Ya-Huei , Zhang Bin , Marcucci Guido 
Published: October 2023

AbstractChronic myeloid leukemia (CML) is initiated and maintained by BCR::ABL which is clinically targeted using tyrosine kinase inhibitors (TKIs). TKIs can induce long-term remission but are also not curative. Thus, CML is an ideal system to test our hypothesis that transcriptome-based state-transition models accurately predict cancer evolution and treatment response. We collected time-sequential blood samples from tetracycline-off (Tet-Off) BCR::ABL-inducible transgenic mice and wild-type controls. From the transcriptome, we constructed a CML statespace and a three-well leukemogenic potential landscape. The potential’s stable critical points defined observable disease states. Early states were characterized by anti-CML genes opposing leukemia; late states were characterized by pro-CML genes. Genes with expression patterns shaped similarly to the potential landscape were identified as drivers of disease transition. Re-introduction of tetracycline to silence the BCR::ABL gene returned diseased mice transcriptomes to a near healthy state, without reaching it, suggesting parts of the transition are irreversible. TKI only reverted the transcriptome to an intermediate disease state, without approaching a state of health; disease relapse occurred soon after treatment. Using only the earliest time-point as initial conditions, our state-transition models accurately predicted both disease progression and treatment response, supporting this as a potentially valuable approach to time clinical intervention even before phenotypic changes become detectable.
Multiple lineages of transmissible neoplasia in the basket cockle (C. nuttallii) with repeated horizontal transfer of mitochondrial DNA
Authors: Yonemitsu Marisa A. , Sevigny Jordana K. , Vandepas Lauren E. , Dimond James L. , Giersch Rachael M. , Gurney-Smith Helen J. , Abbott Cathryn L. , Supernault Janine , Withler Ruth , Smith Peter D. , Weinandt Sydney A. , Garrett Fiona E. S. , Child Zachary J. , Sigo Robin Little Wing , Unsell Elizabeth , Crim Ryan N. , Metzger Michael J. 
Published: October 2023

ABSTRACTTransmissible cancers are clonal lineages of neoplastic cells able to infect multiple hosts, spreading through populations in the environment as an infectious disease. Transmissible cancers have been identified in Tasmanian devils, dogs, and bivalves. Several lineages of bivalve transmissible neoplasias (BTN) have been identified in multiple bivalve species. In 2019 in Puget Sound, Washington, USA, disseminated neoplasia was observed in basket cockles (Clinocardium nuttallii), a species that is important to the culture and diet of the Suquamish Tribe as well as other tribes with traditional access to the species. To test whether disseminated neoplasia in cockles is a previously unknown lineage of BTN, a nuclear locus was amplified from cockles from Agate Pass, Washington, and sequences revealed evidence of transmissible cancer in several individuals. We used a combination of cytology and quantitative PCR to screen collections of cockles from eleven locations in Puget Sound and along the Washington coastline to identify the extent of contagious cancer spread in this species. Two BTN lineages were identified in these cockles, with one of those lineages (CnuBTN1) being the most prevalent and geographically widespread. Within the CnuBTN1 lineage, multiple nuclear loci support the conclusion that all cancer samples form a single clonal lineage. However, the mitochondrial alleles in each cockle with CnuBTN1 are different from each other, suggesting mitochondrial genomes of this cancer have been replaced multiple times during its evolution, through horizontal transmission. The identification and analysis of these BTNs are critical for broodstock selection, management practices, and repopulation of declining cockle populations, which will enable continued cultural connection and dietary use of the cockles by Coast Salish Tribes.