bluuebunny/crossref_metadata_2025_split huggingface dataset:
RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein structure that occur during biological processes
Authors: Hackett William Edwin , Chang Deborah , Carvalho Luis , Zaia Joseph 
Published: June 2023

AbstractMotivationGlycosylation elaborates the structures and functions of glycoproteins; glycoproteins are common post-translationally modified proteins and are heterogeneous and non-deterministically synthesized as an evolutionarily driven mechanism that elaborates the functions of glycosylated gene products. While glycoproteins account for approximately half of all proteins, their macro- and micro-heterogeneity requires specialized proteomics data analysis methods as a given glycosite can be divided into several glycosylated forms, each of which must be quantified. Sampling of heterogeneous glycopeptides is limited by mass spectrometer speed and sensitivity, resulting in missing values. In conjunction with the low sample size inherent to glycoproteomics, this necessitated specialized statistical metrics to identify if observed changes in glycopeptide abundances are biologically significant or due to data quality limitations.ResultsWe developed an R package, Relative Assessment ofm/zIdentifications by Similarity (RAMZIS), that uses similarity metrics to guide biomedical researchers to a more rigorous interpretation of glycoproteomics data. RAMZIS uses contextual similarity to assess the quality of mass spectral data and generates graphical output that demonstrates the likelihood of finding biologically significant differences in glycosylation abundance dataset. Investigators can assess dataset quality, holistically differentiate glycosites, and identify which glycopeptides are responsible for glycosylation pattern expression change. Herein RAMZIS approach is validated by theoretical cases and by a proof-of-concept application. RAMZIS enables comparison between datasets too stochastic, small, or sparse for interpolation while acknowledging these issues in its assessment. Using our tool, researchers will be able to rigorously define the role of glycosylation and the changes that occur during biological processes.Availabilityhttps://github.com/WillHackett22/RAMZISContactJoseph Zaia, Boston University Medical Campus, 670 Albany St., rm 509, Boston, MA 02118 USA, (e)jzaia@bu.edu, (v) 1-617-358-2429Supplementary informationSupplementary data are available
Role of XerCD in release of over-replicated DNA through Outer Membrane Vesicles inEscherichia coli
Authors: Mansky Johannes , Wang Hui , Wagner-Döbler Irene , Tomasch Jürgen 
Published: June 2023

AbstractOuter membrane vesicles (OMVs) are universally produced by prokaryotes and play important roles in symbiotic and pathogenic interactions. Here we show that the GammaproteobacteriumEscherichia coliproduces OMVs that contain DNA enriched for the region around the terminus of replicationter, and specifically for the recognition sequencedifof the two site-specific recombinases XerCD, similar to OMVs from the AlphaproteobacteriumDinoroseobacter shibae. In deletion mutants ofxerCorxerD, the enriched region aroundterbecomes broader while the peak directly at thedifsequence itself is reduced.ImportanceImprecise termination of replication can lead to over-replicated parts of bacterial chromosomes that have to be excised and removed from the dividing cell. The underlying mechanism is so far poorly understood. Our data suggest a conserved mechanism for repair and removal of over-replicated DNA through outer membrane vesicles and an active role of the site-specific XerCD recombinase complex therein.
Geospatially-resolved public-health surveillance via wastewater sequencing
Authors: Tierney Braden T , Foox Jonathan , Ryon Krista A , Butler Daniel , Damle Namita , Young Benjamin G , Mozsary Christopher , Babler Kristina M. , Yin Xue , Carattini Yamina , Andrews David , Solle Natasha Schaefer , Kumar Naresh , Shukla Bhavarth , Vidovic Dusica , Currall Benjamin , Williams Sion L. , Schürer Stephan C. , Stevenson Mario , Amirali Ayaaz , Beaver Cynthia C. , Kobetz Erin , Boone Melinda M. , Reding Brian , Laine Jennifer , Comerford Samuel , Lamar Walter E. , Tallon John J. , Hirschberg Jeremy Wain , Proszynski Jacqueline , Sharkey Mark E. , Church George M , Grills George S , Solo-Gabriele Helena M. , Mason Christopher E 
Published: June 2023

AbstractWastewater, which contains everything from pathogens to pollutants, is a geospatially-and temporally-linked microbial fingerprint of a given population. As a result, it can be leveraged for monitoring multiple dimensions of public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (n=1,419 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County from 2020-2022. First, we used targeted amplicon sequencing (n=966) to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with clinical caseloads from University students (N = 1,503) and Miami-Dade County hospital patients (N = 3,939 patients), as well as an 8-day earlier detection of the Delta variant in wastewater vs. in patients. Additionally, in 453 metatranscriptomic samples, we demonstrate that different wastewater sampling locations have clinically and public-health-relevant microbiota that vary as a function of the size of the human population they represent. Through assembly, alignment-based, and phylogenetic approaches, we also detect multiple clinically important viruses (e.g.,norovirus) and describe geospatial and temporal variation in microbial functional genes that indicate the presence of pollutants. Moreover, we found distinct profiles of antimicrobial resistance (AMR) genes and virulence factors across campus buildings, dorms, and hospitals, with hospital wastewater containing a significant increase in AMR abundance. Overall, this effort lays the groundwork for systematic characterization of wastewater to improve public health decision making and a broad platform to detect emerging pathogens.
Insufficient serological evidence of the association between chronic kidney disease and leptospirosis in Badulla and Kandy districts, Sri Lanka
Authors: Fonseka Regina Amanda , Senarathne Pavani , Muthusinghe Devinda Shameera , Nanayakkara Nishantha , Gunaratne Lishantha , Yoshimatsu Kumiko , Koizumi Nobuo , Gamage Chandika Damesh 
Published: June 2023

AbstractObjectiveChronic kidney disease (CKD) and chronic kidney disease of uncertain etiology (CKDu) are chronic kidney diseases that pose a significant health burden in Sri Lanka. Leptospirosis is a bacterial zoonosis that primarily damages renal tissues by colonization ofLeptospiraspp. in the renal tubules and is a suspected etiological agent of CKDu. Since Sri Lanka is an endemic for leptospirosis and outbreaks of the disease have been reported, this study aimed to determine the association between leptospirosis and chronic kidney disease in two geographically distinct regions of Sri Lanka, Badulla (CKDu endemic) and Kandy (CKDu non-endemic) districts.ResultsEighty-five patients with CKDu and 149 controls from Badulla and 49 patients with CKD and 135 controls from Kandy were serologically tested by microscopic agglutination test with a panel of 11Leptospiraserogroups. The seroprevalence rates for leptospirosis were 7.1% and 13.4% in the CKDu and control groups, respectively, in Badulla and 2.1% and 18.5% in the CKD and control groups, respectively, in Kandy. There were no statistically significant differences between demographic characteristics and leptospirosis seropositivity in the CKD and control groups in either Badulla or Kandy.
Distance sampling with vehicle-mounted cameras for the estimation of farmland bird abundance over a wide area
Authors: Kumada Nao , Fukasawa Keita , Yoshioka Akira , Tsuda Naoe , Ouchi Hirofumi 
Published: June 2023

AbstractAgricultural birds are declining due to farmland abandonment and agricultural intensification, and monitoring approaches, including efficient survey methods, are crucial for the development of effective conservation strategies. Roadside surveys (RS), especially those using vehicle-mounted video cameras, can be used to efficiently search for targets; however, they are limited by the unknown detection range. Distance sampling (DS), in which animal density or abundance is estimated from the distance between the observer and the detected individual, can provide a complimentary approach to address this limitation of RS.We developed a DS model robust to location uncertainty based on video-based RS. We integrated location errors determined by an independent field test using RS and unmanned aerial vehicles (UAVs) into a stochastic DS model. We estimated the abundance of herons and egrets in farmlands in and around the evacuation zone of the Fukushima Daiichi nuclear power plant accident by combining RS and DS.The video-based RS covered 7,031 km of roads and 24.41 km2of farmlands. All herons and egrets were observed around the evacuation zone and none were detected in the zone. The predicted abundance of herons and egrets differed substantially between areas inside (0.0158 ± 0.0174/km2) and outside of the zone (4.62 ± 5.41/km2).Integrating location uncertainty into the DS model did not affect predicted heron and egret population densities (4.62 ± 5.41 vs. 4.66 ± 5.45/km2, with or without integrating location uncertainty, respectively). Accordingly, our survey method combining RS and DS is robust to location uncertainty. The study system (i.e., herons and egrets in farmlands) and the inability of location error to exceed the size of one farmland separated by levees may contribute to the accuracy of RS in this study.Synthesis and Applications:Combining RS with vehicle-mounted cameras and DS considering location uncertainty is widely applicable to open land species and can improve the efficiency of monitoring. When large location errors are expected by conventional approaches, DS models incorporating location uncertainty determined by RS and UAVs could be effective for abundance estimation over wide areas.
Generating human neural diversity with a multiplexed morphogen screen in organoids
Authors: Amin Neal D. , Kelley Kevin W. , Hao Jin , Miura Yuki , Narazaki Genta , Li Tommy , McQueen Patrick , Kulkarni Shravanti , Pavlov Sergey , Paşca Sergiu P. 
Published: June 2023

AbstractMorphogens choreograph the generation of remarkable cellular diversity in the developing nervous system. Differentiation of stem cells toward particular neural cell fatesin vitrooften relies upon combinatorial modulation of these signaling pathways. However, the lack of a systematic approach to understand morphogen-directed differentiation has precluded the generation of many neural cell populations, and knowledge of the general principles of regional specification remain in-complete. Here, we developed an arrayed screen of 14 morphogen modulators in human neural organoids cultured for over 70 days. Leveraging advances in multiplexed RNA sequencing technology and annotated single cell references of the human fetal brain we discovered that this screening approach generated considerable regional and cell type diversity across the neural axis. By deconvoluting morphogen-cell type relationships, we extracted design principles of brain region specification, including critical morphogen timing windows and combinatorics yielding an array of neurons with distinct neuro-transmitter identities. Tuning GABAergic neural subtype diversity unexpectedly led to the derivation of primate-specific interneurons. Taken together, this serves as a platform towards anin vitromorphogen atlas of human neural cell differentiation that will bring insights into human development, evolution, and disease.
Intracellular trafficking of furin enhances cellular intoxication by recombinant immunotoxins based onPseudomonasexotoxin A
Authors: Grossman Brian D. , Sanford Jack D. , Zhu Yuyi , Zeller Cynthia B. , Weldon John E. 
Published: June 2023

AbstractFurin is a mammalian serine protease with important roles in cellular homeostasis and disease. It cleaves and activates numerous endogenous and exogenous substrates, including the SARS-CoV-2 viral spike protein and protein toxins such as diphtheria toxin andPseudomonasexotoxin A (PE). Recombinant immunotoxins (RITs) are toxin conjugates used as cancer therapeutics that connect tumor-directed antibodies with toxins for targeted cell killing. RITs based on PE have shown success in treating a variety of cancers, but often suffer from safety and efficacy concerns when used clinically. We have explored furin as a potential limiting factor in the intoxication pathway of PE-based RITs. Although the furin has widely recognized importance in RIT intoxication, its role is incompletely understood. Circumstantial evidence suggests that furin may act as a transporter for RITs in addition to its role of activation by cleavage. Here, we describe the creation of a CRISPR-engineered furin-deficient HEK293 cell line, ΔFur293. Using ΔFur293 and derivatives that express mutant forms of furin, we confirm the importance of furin in the PE RIT intoxication pathway and show that furin trafficking has a significant impact on RIT efficacy. Our data support the hypothesis that furin acts as a transporter during RIT intoxication, and suggest furin as a target to improve the effectiveness of RITs.
ACTIVATION OF CYCLIN-DEPENDENT KINASE 5 BROADENS ACTION POTENTIALS IN HUMAN SENSORY NEURONS
Authors: Tiwari Manindra Nath , Hall Bradford E. , Terse Anita , Amin Niranjana , Chung Man-Kyo , Kulkarni Ashok B. 
Published: June 2023

ABSTRACTChronic pain is one of the most devastating and unpleasant conditions, associated with many pathological conditions. Tissue or nerve injuries induce comprehensive neurobiological plasticity in nociceptive neurons, which leads to chronic pain. Recent studies suggest that cyclin-dependent kinase 5 (CDK5) in primary afferents is a key neuronal kinase that modulates nociception through phosphorylation-dependent manner under pathological conditions. However, the impact of the CDK5 on nociceptor activity especially in human sensory neurons are not known. To determine the CDK5-mediated regulation of human dorsal root ganglia (hDRG) neuronal properties, we have performed the whole-cell patch clamp recordings in neurons dissociated from hDRG. CDK5 activation induced by overexpression of p35 depolarized the resting membrane potential and reduced the rheobase currents as compared to the uninfected neurons. CDK5 activation evidently changed the shape of the action potential (AP) by increasing AP rise time, AP fall time, and AP half width. The application of a prostaglandin E2 (PG) and bradykinin (BK) cocktail in uninfected hDRG neurons induced the depolarization of RMP and the reduction of rheobase currents along with increased AP rise time. However, PG and BK applications failed to induce any further significant changes in addition to the aforementioned changes of the membrane properties and AP parameters in the p35-overexpressing group. We conclude that CDK5 activation through the overexpression of p35 in dissociated hDRG neurons broadens AP in hDRG neurons and that CDK5 may play important roles in the modulation of AP properties in human primary afferents under pathological conditions, contributing to chronic pain.
Universal features of Nsp1-mediated translational shutdown by coronaviruses
Authors: Schubert Katharina , Karousis Evangelos D. , Ban Ivo , Lapointe Christopher P. , Leibundgut Marc , Bäumlin Emilie , Kummerant Eric , Scaiola Alain , Schönhut Tanja , Ziegelmüller Jana , Puglisi Joseph D. , Mühlemann Oliver , Ban Nenad 
Published: June 2023

SummaryNonstructural protein 1 (Nsp1) produced by coronaviruses shuts down host protein synthesis in infected cells. The C-terminal domain of SARS-CoV-2 Nsp1 was shown to bind to the small ribosomal subunit to inhibit translation, but it is not clear whether this mechanism is broadly used by coronaviruses, whether the N-terminal domain of Nsp1 binds the ribosome, or how Nsp1 specifically permits translation of viral mRNAs. Here, we investigated Nsp1 from three representativeBetacoronaviruses– SARS-CoV-2, MERS-CoV, and Bat-Hp-CoV – using structural, biophysical, and biochemical assays. We revealed a conserved mechanism of host translational shutdown across the three coronaviruses. We further demonstrated that the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A binding. Structure-based biochemical experiments identified a conserved role of these inhibitory interactions in all three coronaviruses and showed that the same regions of Nsp1 are responsible for the preferential translation of viral mRNAs. Our results provide a mechanistic framework to understand howBetacoronavirusesovercome translational inhibition to produce viral proteins.
KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing
Authors: Dillingham Caleb M. , Cormaty Harshini , Morgan Ellen C. , Tak Andrew I. , Esgdaille Dakarai E. , Boutz Paul L. , Sridharan Rupa 
Published: June 2023

ABSTRACTHistone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cell (ESC) identity is characterized by a lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 family of histone demethylases removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. Acute selective degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such asDnmt3b, Tbx3andTcf12. Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.
MCAK Inhibitors Induce Aneuploidy in Triple Negative Breast Cancer Models
Authors: Smith John C. , Husted Stefan , Pilrose Jay , Ems-McClung Stephanie C. , Stout Jane R. , Carpenter Richard L. , Walczak Claire E. 
Published: June 2023

AbstractStandard of care for triple negative breast cancer (TNBC) involves the use of microtubule poisons like paclitaxel, which are proposed to work by inducing lethal levels of aneuploidy in tumor cells. While these drugs are initially effective in treating cancer, dose-limiting peripheral neuropathies are common. Unfortunately, patients often relapse with drug resistant tumors. Identifying agents against targets that limit aneuploidy may be a valuable approach for therapeutic development. One potential target is the microtubule depolymerizing kinesin, MCAK, which limits aneuploidy by regulating microtubule dynamics during mitosis. Using publicly available datasets, we found that MCAK is upregulated in triple negative breast cancer and is associated with poorer prognoses. Knockdown of MCAK in tumor-derived cell lines caused a two- to five-fold reduction in the IC50for paclitaxel, without affecting normal cells. Using FRET and image-based assays, we screened compounds from the ChemBridge 50k library and discovered three putative MCAK inhibitors. These compounds reproduced the aneuploidy-inducing phenotype of MCAK loss, reduced clonogenic survival of TNBC cells regardless of taxane-resistance, and the most potent of the three, C4, sensitized TNBC cells to paclitaxel. Collectively, our work shows promise that MCAK may serve as both a biomarker of prognosis and as a therapeutic target.Simple SummaryTriple negative breast cancer (TNBC) is the most lethal breast cancer subtype with few treatment options available. Standard of care for TNBC involves the use of taxanes, which are initially effective, but dose limiting toxicities are common, and patients often relapse with resistant tumors. Specific drugs that produce taxane-like effects may be able to improve patient quality of life and prognosis. In this study we identify three novel inhibitors of the Kinesin-13 MCAK. MCAK inhibition induces aneuploidy; similar to cells treated with taxanes. We demonstrate that MCAK is upregulated in TNBC and is associated with poorer prognoses. These MCAK inhibitors reduce the clonogenic survival of TNBC cells, and the most potent of the three inhibitors, C4, sensitizes TNBC cells to taxanes, similar to the effects of MCAK knockdown. This work will expand the field of precision medicine to include aneuploidy-inducing drugs that have the potential to improve patient outcomes.
CD4+T-cell immunity of SARS-CoV-2 patients determine pneumonia development
Authors: Naito Erika , Uchida Takahiro , Yamasaki Satoshi , Hashimoto Kosuke , Miura Yu , Shiono Ayako , Kawamura Takayuki , Mouri Atsuto , Yamaguchi Ou , Imai Hisao , Kaira Kyoichi , Nemoto Manabu , Mitsutake Kotaro , Nagata Makoto , Kagamu Hiroshi 
Published: June 2023

AbstractMost humans infected with SARS-CoV-2 will recover without developing pneumonia. A few SARS-CoV-2 infected patients, however, develop pneumonia, and occasionally develop cytokine storms. In such cases, it is assumed that there is an inadequate immune response to eliminate viral infected cells and an excessive inappropriate immune response causing organ damage, but little is known about this mechanism. In this study, we used single cell RNA sequencing and mass cytometry to analyze peripheral blood T cells from patients hospitalized with proven COVID-19 infection in order to clarify the differences in host immune status among COVID-19 pneumonia cases, non-pneumonia cases, and healthy controls. The results showed that a specific CD4+T cell cluster with chemokine receptor expression patterns, CXCR3+CCR4-CCR6+(Th1/17), was less abundant in COVID-19 pneumonia patients. Interestingly, these CD4+T-cell clusters were identical to those we have reported to correlate with antitumor immunity and predict programmed cell death (PD)-1 blockade treatment response in lung cancer. The Th1/17 cell percentages had biomarker performance in diagnosing pneumonia cases. In addition, CTLA-4 expression of type17 helper T cells (Th17) and regulatory T cells (Treg) was found to be significantly lower. This indicates that functional suppression of Th17 was less effective and Treg function was impaired in pneumonia cases. These results suggest that imbalance of CD4+T-cell immunity generates excessive immunity that does not lead to viral eradication. This might be a potential therapeutic target mechanism to prevent severe viral infections.ImportanceIn this observational study, 49 consecutive patients with SARS-CoV-2 infection confirmed by PCR testing and admitted to Saitama Medical University Hospital and Saitama Medical University International Medical Centre between December 4, 2020 and January 17, 2022 were included. Of these 49 patients, 29 were diagnosed with COVID-19 pneumonia by computed tomography (CT) scan (Table 1). The unique CD4+T-cell immunity with less abundant Th1/17 CD4+T-cell cluster and low expression of CTLA-4 in Th17 and Treg was consistently found in SARS-CoV-2 pneumonia patients on admission and 1-week of admission. The imbalance of CD4+T-cell immunity may contribute to develop pneumonia in SARS-CoV-2 virus infected patients by delaying viral clearance and resulting in an excessive immune response.