bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultra-fast protein structure prediction to capture effects of sequence variation in mutation movies
Authors: Weissenow Konstantin , Heinzinger Michael , Steinegger Martin , Rost Burkhard 
Published: November 2022

AbstractTop protein three-dimensional (3D) structure predictions require evolutionary information from multiple-sequence alignments (MSAs) and deep, convolutional neural networks and appear insensitive to small sequence changes. Here, we describeEMBER3Dusing embeddings from the pre-trained protein language model (pLM) ProtT5 to predict 3D structure directly from single sequences. Orders of magnitude faster than others, EMBER3D predicts average-length structures in milliseconds on consumer-grade machines. Although not nearly as accurate asAlphaFold2, the speed of EMBER3D allows a glimpse at future applications such as the almost real-time rendering of deep mutational scanning (DMS) movies that visualize the effect of all point mutants on predicted structures. This also enables live-editing of sequence/structure pairs. EMBER3D is accurate enough for highly sensitive rapid remote homology detection byFoldseekidentifying structural similarities. Overall, our use cases suggest that speed can complement accuracy, in particular when accessible through consumer-grade machines. EMBER3D is free and publicly available:https://github.com/kWeissenow/EMBER3D.
Subset-specific mitochondrial and DNA damage shapes T cell responses to fever and inflammation
Authors: Heintzman Darren R. , Elasy Joel , Chi Channing , Ye Xiang , Krystoviak Evan S. , Khan Wasay , Olson Lana , Jones Angela , Voss Kelsey , Patterson Andrew R. , Sugiura Ayaka , Mason Frank M. , Hong Hanna S. , Bass Lindsay , Beier Katherine L. , Deng Wentao , Lyssiotis Costas A. , Bick Alexander G. , Rathmell W. Kimryn , Rathmell Jeffrey C. 
Published: November 2022

AbstractHeat is a cardinal feature of inflammation. Despite temperature variability and dependence of enzymes and complexes, how heat and fever affect immune cells remains uncertain. We found that heat broadly increased inflammatory activity of CD4+T cell subsets and decreased Treg suppressive function. Th1 cells, however, also selectively developed mitochondrial dysfunction with high levels of ROS production and DNA damage. This led Th1 cells to undergoTp53-dependent death, which was required to minimize the accumulation of mutations in heat and inflammation. Th1 cells with similar DNA damage signatures were also detected in Crohn’s disease and rheumatoid arthritis. Fever and inflammation-associated heat thus selectively induce mitochondrial stress and DNA damage in activated Th1 cells that requires p53 to maintain genomic integrity of the T cell repertoire.One Sentence SummaryFever temperatures augment CD4+T cell-mediated inflammation but induce differential metabolic stress and DNA damage in T cell subsets, with Th1 cells selectively sensitive and dependent on p53 to induce apoptosis and maintain genomic integrity.
Controlled Hydrogen Sulfide Delivery to Enhance Cell Survival in Bone Tissue Engineering
Authors: Ghavimi Soheila Ali Akbari , Faulkner Trent J. , Tata Rama Rao , Lungren Ethan S. , Zhang Rui , Bumann Erin E. , Ulery Bret D. 
Published: November 2022

ABSTRACTThe increased local concentration of calcium ions (Ca2+) and phosphate (Pi), a natural body process for bone healing and remodeling, as well as local delivery of these ions as signaling molecules by synthetic bone graft substitutes, may lead to cytotoxic ion levels that can result in Ca2+/ Pimitochondria overload, oxidative stress, and cell death. In this research, the effect of H2S as a cytoprotective signaling molecule to increase the tolerance of mesenchymal stem cells (MSCs) in the presence of cytotoxic level of Ca2+/Piwas evaluated. Different concentrations of sodium hydrogen sulfide (NaSH), a fast-releasing H2S donor, were exposed to cells in order to evaluate the influence of H2S on MSC proliferation. The results suggested that a range of NaSH (i.e., 0.25 - 4 mM NaSH) was non-cytotoxic and could improve cell proliferation and differentiation in the presence of cytotoxic levels of Ca2+(32 mM) and/or Pi(16 mM). To controllably deliver H2S over time, a novel donor molecule in thioglutamic acid (GluSH) was synthesized and evaluated for its H2S release profile. Excitingly, GluSH successfully maintained cytoprotective level of H2S over 7 days. Furthermore, MSCs exposed to cytotoxic Ca2+/Piconcentrations in the presence of GluSH were able to thrive and differentiate into osteoblasts. These findings suggest that the incorporation of a sustained H2S donor such as GluSH into CaP-based bone substitutes can facilitate considerable cytoprotection making it an attractive option for complex bone regenerative engineering applications.
Optimizing bioink composition for human chondrocyte expression of lubricin
Authors: Martyniak Kari , Kennedy Sean , Cruz Maria A. , Karimzadeh Makan , Jeon Oju , Alsberg Eben , Kean Thomas J. 
Published: November 2022

AbstractThe surface zone of articular cartilage is the first area impacted by cartilage defects, commonly resulting in osteoarthritis. Chondrocytes in the surface zone of articular cartilage synthesize and secrete lubricin, a proteoglycan that functions as a lubricant protecting the deeper layers from shear stress. 3D bioprinting is a tissue engineering technique that uses cells encapsulated in biomaterials to fabricate 3D constructs. Gelatin methacrylate (GelMA) is a frequently used biomaterial for 3D bioprinting cartilage. Oxidized methacrylated alginate (OMA) is a chemically modified alginate designed for its tunable degradation rate and mechanical properties. To determine an optimal combination of GelMA and OMA for lubricin expression, we used our novel high-throughput human articular chondrocyte reporter system. Primary human chondrocytes were transduced withPRG4(lubricin) promoter-drivenGaussialuciferase, allowing for temporal assessment of lubricin expression. A lubricin expression driven Design of Experiment screen and subsequent validation identified 14% GelMA/2% OMA for further study. Therefore, 14% GelMA/2% OMA, 14% GelMA and 16% GelMA were 3D bioprinted. The combination of lubricin protein expression and shape retention over the 22 days in culture, determined the 14% GelMA/2%OMA to be the optimal formulation for lubricin secretion.
Standards needed? An Exploration of Qualifying Exams from a Literature Review and Website Analysis of University-Wide Policies
Authors: McLaughlin Jacqueline E. , Morbitzer Kathryn , Meilhac Margaux , Poupart Natalie , Layton Rebekah L. , Jarstfer Michael B. 
Published: November 2022

ABSTRACTPurposeWhile known by many names, qualifying exams function as gatekeepers to graduate student advancement to PhD Candidacy, yet there has been little formal study on best qualifying exam practices particularly in biomedical and related STEM PhD programs. The purpose of this study was to examine the current state of qualifying exams through an examination of the literation and exploration of university policies.Design/methodology/approachWe conducted a literature review of studies on qualifying exams and completed an external evaluation of peer institutions’ and internal institutional qualifying exam requirements to inform our discussion of common practices of qualifying exams in doctoral training at a research-intensive institutions.FindingsOur research identified the need for more evidence-based research on qualifying exams, which are nearly universal as a major doctoral training milestone across US institutions of higher education. Our findings indicate a wide variety of qualifying exam formats, often lacking the establishment of explicit expectations and evidence for specific formats. This lack of understanding of best practices coupled with insufficient clarity has a real potential to disadvantage doctoral students, particularly first generation, underrepresented minority, international, and/or other trainees who are not privileged or socialized to navigate training environments with vague landmarks such as the qualifying exams.OriginalityThere are very few studies that evaluate qualifying exams in US doctoral education, particularly in STEM fields, and to our knowledge, there has been no analysis of campus wide policies on qualifying exams reported. The lack of evidence for best practices and the need for to evaluate the implementation and effectiveness of qualifying exams are discussed.
Investigations into hydrogen sulfide-induced suppression of neuronal activity in vivo and calcium dysregulation in vitro
Authors: Kim Dong-Suk , Pessah Isaac N. , Santana Cristina M , Purnell Benton , Li Rui , Buchanan Gordon F , Rumbeiha Wilson K. 
Published: November 2022

AbstractAcute exposure to high concentrations of hydrogen sulfide (H2S) leads to sudden death and, if survived, lingering neurological disorders. Clinical signs include seizures, loss of consciousness, and dyspnea. The proximate mechanisms underlying H2S-induced acute toxicity and death have not been clearly elucidated. We investigated electrocerebral, cardiac and respiratory activity during H2S exposure using EEG, EKG and plethysmography. H2S suppressed electrocerebral activity and disrupted breathing. Cardiac activity was comparatively less affected. To test whether Ca2+dysregulation contributes to H2S-induced EEG suppression, we developed an in vitro real-time rapid throughput assay measuring patterns of spontaneous synchronized Ca2+oscillations in cultured primary cortical neuronal (PCN) networks loaded with the indicator Fluo-4 using the fluorescent imaging plate reader (FLIPR-Tetra®). Sulfide >5 ppm dysregulated SCO patterns in a dose-dependent manner. Inhibitors of NMDA and AMPA receptors magnified H2S-induced SCO suppression. Inhibitors of L-type voltage gated Ca2+channels (VGCC) and transient receptor potential (TRP) channels prevented H2S-induced SCO suppression. Inhibitors of T-type VGCC, ryanodine receptors, and sodium channels had no measurable influence on H2S-induced SCO suppression. Exposures to >5 ppm sulfide also suppressed neuronal electrical activity in PCN measured by multi-electrode array (MEA), an effect alleviated by pretreatment with the nonselective TRP inhibitor 2-APB. The TRP inhibitor also reduced PCN cell death from sulfide exposure. These results improve our understanding of the role of different Ca2+channels in acute H2S-induced neurotoxicity and identify TRP channel modulators as novel structures with potential therapeutic benefits.
Misaligned plastic and evolutionary responses of lifespan to novel carbohydrate diets
Authors: Narayan Vikram P. , Wasana Nidarshani , Wilson Alastair J. , Chenoweth Stephen F. 
Published: November 2022

AbstractDiet elicits varied effects on longevity across a wide range of animal species. For example, diets low in protein and high in carbohydrate typically extend lifespan while diets high in protein tend to reduce it. Although studies have also shown that diet-induced lifespan changes can persist through transgenerational plasticity, whether such changes lead to evolutionary shifts in lifespan remains unclear. In this study we combine experimental evolution and phenotypic plasticity assays to address this gap. UsingDrosophila serrata, we investigated the evolutionary potential of lifespan in response to four novel diets spanning a carbohydrate-protein gradient. We also examined developmental plasticity effects using a set of control populations that were raised on the four novel environments. Our results show that although lifespan evolved in response to changes in dietary carbohydrate concentration, the plastic responses for lifespan differed from the evolved responses. The direction of the evolved response (increased lifespan) observed on low carbohydrate diets was in the opposite direction to the plastic response (decreased lifespan). Our results imply that plastic responses to low carbohydrates can be maladaptive for lifespan and misaligned with the evolved responses, laying the groundwork for future investigations of carbohydrate contributions to evolved and plastic effects on lifespan.
Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport
Authors: Gustafsson Johan , Robinson Jonathan L. , Zetterberg Henrik , Nielsen Jens 
Published: November 2022

AbstractEnergy metabolism of the brain is poorly understood partly due to the complex morphology of neurons. Here we used metabolic models that estimate costs of enzyme usage per pathway, enzyme utilization over time, and enzyme transport to evaluate a paradigm that suggests that brain energy metabolism is optimized to minimize enzyme synthesis and transportation costs. Our models recapitulate known metabolic behaviors and provide explanation for the astrocyte-neuron lactate shuttle theory.
A complex evolutionary history of genetic barriers to gene flow in hybridizing warblers
Authors: Wang Silu , Coop Graham 
Published: November 2022

AbstractTheSetophagawarbler sister species in western North America,Setophaga occidentalisandS. townsendiprovide a rare opportunity to explore how the accumulation of genetic barriers to gene flow contributes to speciation. These sister species are at the very early stages of speciation, as their genome-wide divergence is limited, and they hybridize extensively upon secondary contact. However, there are several well-characterized loci involved in speciation. There is a plumage difference between the species controlled by mutations close to the agouti signaling protein (ASIP), which generates underdominance due to compromised hybrid territorial signaling. A second large region (~2Mb) on chromosome 5 encodes many mitochondrial-interacting genes and coevolves with the mitochondrial genome. Here we reconstructed the ancestral recombination graphs of these genomic regions relative to the genome-wide background to learn about the evolutionary history of these barriers. We find signatures of long-lasting barrier effects that lasted for ~190 K generations, and recent selective sweeps in chr5 mitonuclear genetic block in both species within the past 60 K generations ago. We further observed heterogeneity within the long-lasting mitonuclear barrier with localized signals of much more recent selective sweeps unique one of the species. The divergence of ASIP is elevated by a species-specific selective sweep withinS. occidentalisthat occurred 21 K generations ago. However, the signature of long-lasting barrier effect is much weaker at ASIP suggesting that it may have arisen later than the mitonuclear system. Associating the evolutionary history of these genetic barriers with Pleistocene climate change history sheds light on the intrinsic and extrinsic reciprocity underlying the origin of species.
A dynamic Campylobacterales epibiont community associated with the bone eating wormOsedax
Authors: Goffredi Shana , Panossian Balig , Brzechffa Camille , Field Naomi , King Chad , Moggioli Giacomo , Rouse Greg W. , Martín-Durán José M. , Henry Lee 
Published: November 2022

AbstractOsedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, that help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-year study, we reveal a dynamic, yet persistent, succession of Campylobacterales integrated into the epidermis ofOsedax, that change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species ofOsedax, which comprise 67% of the bacterial community on the trunk, are initially dominated by the genusArcobacter(at early time points < 24 months), theSulfurospirillumat intermediate stages (~ 50 months), and theSulfurimonasat later stages (>140 months) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests a transition from heterotrophy to autotrophy along the successional gradient, and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free living relatives, theOsedaxepibionts were highly enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms
Interleukin-2 immunotherapy reveals human regulatory T cell subsets with distinct functional and gatekeeper features
Authors: Raeber Miro E. , Caspar Dominic , Zurbuchen Yves , Guo Nannan , Schmid Jonas , Michler Jan , Steiner Urs C. , Moor Andreas E. , Koning Frits , Boyman Onur 
Published: November 2022

ABSTRACTDue to its stimulatory potential for immunomodulatory CD4+regulatory T (Treg) cells, low-dose interleukin-2 (IL-2) immunotherapy has recently gained considerable attention for treatment of various autoimmune diseases. Although early-stage clinical trials have correlated expansion of circulating Treg cells with clinical response to IL-2 treatment, detailed mechanistic data on responding Treg cell subsets are lacking. In this investigator-initiated phase-2 clinical trial of low-dose IL-2 immunotherapy in systemic lupus erythematosus (SLE) patients, we performed an in-depth study of circulating and cutaneous Treg cell subsets by imaging mass cytometry, high-parameter spectral flow cytometry, bulk and single-cell RNA sequencing with cellular indexing, and targeted serum proteomics. Low-dose IL-2 stimulated circulating Treg cells with skin-homing properties that appeared in the skin of SLE patients in close interaction with endothelial cells, suggestive of a gatekeeper function. Analysis of surface proteins and transcriptomes detected different IL-2-driven Treg cell programs, including highly proliferative CD38+HLA-DR+, activated gut-homing CD38+, and skin-homing HLA-DR+Treg cells. These data identify distinct and functionally characteristic Treg cell subsets in human blood and skin, including the Treg cell subsets most responsive to IL-2 immunotherapy, thus providing unprecedented insight into Treg cell biology during IL-2 treatment.
Latent tuberculosis and depressive symptoms in household contacts of persons with active TB: A cohort study
Authors: Galea Jerome , Chu Alexander L. , Sweetland Annika , Jimenez Judith , Yataco Rosa , Calderón Roger , Zhang Zibiao , Huang Chuan-Chin , Lecca Leonid , Murray Megan 
Published: November 2022

ABSTRACTBackgroundDepression is common among persons with TB and associated with poor clinical outcomes. However, little is known about the relationship between latent TB infection (LTBI) and depression. Here, we assessed the association between LTBI and depressive symptoms among household contacts (HHCs) of patients receiving TB treatment.MethodsWe enrolled 1,009 HHCs of 307 patients receiving TB treatment in Lima, Peru, 2016-2018. We assessed HHC LTBI status at enrollment using interferon gamma release assay (IGRA). Depressive symptoms were assessed at baseline and 12 months later using the Patient Health Questionnaire-9 (PHQ-9) using a cutoff of ≥5. We used logistic regression to estimate the odds ratio for PHQ-9 ≥5 comparing HHCs with and without baseline LTBI.ResultsAmong 921 HHCs, 378 (41.0%) had LTBI at baseline, and 70 (12.4%) of 563 HHCs had PHQ-9 ≥5. Compared to HHCs without LTBI at enrollment, those with LTBI had almost two times the odds of PHQ-9 ≥5 at follow-up after controlling for potential confounders (adjusted OR, 1.93, 95% CI, 1.09-3.39); this association was driven by greater severities of depressive symptoms.ConclusionHHCs with LTBI had increased odds of depressive symptoms one year later. This at-risk population may benefit from mental health screening and interventions integrated within TB programs.
Longitudinal analysis of retinal ganglion cell damage at individual axon bundle level in mice using visible-light optical coherence tomography fibergraphy
Authors: Grannonico Marta , Miller David A. , Gao Jingyi , McHaney Kara M. , Liu Mingna , Krause Michael , Netland Peter A. , Zhang Hao F. , Liu Xiaorong 
Published: November 2022

AbstractWe developed a new analytic tool based on visible-light optical coherence tomography fibergraphy (vis-OCTF) to longitudinally track individual axon bundle transformation following acute optic nerve crush injury (ONC) in mice. We analyzed four parameters: lateral bundle width, axial bundle height, cross-sectional area, and the shape of individual bundles. We showed that axon bundles became wider and thicker at 3-days post ONC. The bundle swelling at 3-days post-ONC has correlated with about 15% retinal ganglion cell (RGC) soma loss. At 6-days post-ONC, axon bundles showed a significant reduction in lateral width and cross-sectional area, followed by a reduction in bundle height at 9-days post-ONC. Bundle shrinking at 9-days post-ONC has correlated with about 68% RGC soma loss. Both experimental and simulated results suggested that the cross-sectional area of individual RGC axon bundles is more sensitive than the bundle width and height to indicate RGC soma loss. This study is the first to track and quantify individual RGC axon bundlesin vivofollowing ONC injury and establish the correlation between the morphological changes of RGC axon bundles and RGC soma loss.
Inflammation durably imprints memory CD4+ T cells
Authors: Gray-Gaillard Sophie L. , Solis Sabrina , Chen Han M. , Monteiro Clarice , Ciabattoni Grace , Samanovic Marie I. , Cornelius Amber R. , Williams Tijaana , Geesey Emilie , Rodriguez Miguel , Ortigoza Mila Brum , Ivanova Ellie N. , Koralov Sergei B. , Mulligan Mark J. , Herati Ramin Sedaghat 
Published: November 2022

SummaryAdaptive immune responses are induced by vaccination and infection, yet little is known about how CD4+ T cell memory differs when primed in these two contexts. Notably, viral infection is generally associated with higher levels of systemic inflammation than is vaccination. To assess whether the inflammatory milieu at the time of CD4+ T cell priming has long-term effects on memory, we compared Spike-specific memory CD4+ T cells in 22 individuals around the time of the participants’ third SARS-CoV-2 mRNA vaccination, with stratification by whether the participants’ first exposure to Spike was via virus or mRNA vaccine. Multimodal single-cell profiling of Spike-specific CD4+ T cells revealed 755 differentially expressed genes that distinguished infection- and vaccine-primed memory CD4+ T cells. Spike-specific CD4+ T cells from infection-primed individuals had strong enrichment for cytotoxicity and interferon signaling genes, whereas Spike-specific CD4+ T cells from vaccine-primed individuals were enriched for proliferative pathways by gene set enrichment analysis. Moreover, Spike-specific memory CD4+ T cells established by infection had distinct epigenetic landscapes driven by enrichment of IRF-family transcription factors, relative to T cells established by mRNA vaccination. This transcriptional imprint was minimally altered following subsequent mRNA vaccination or breakthrough infection, reflecting the strong bias induced by the inflammatory environment during initial memory differentiation. Together, these data suggest that the inflammatory context during CD4+ T cell priming is durably imprinted in the memory state at transcriptional and epigenetic levels, which has implications for personalization of vaccination based on prior infection history.One Sentence SummarySARS-CoV-2 infection versus SARS-CoV-2 mRNA vaccination prime durable transcriptionally and epigenetically distinct Spike-specific CD4+ T cell memory landscapes.