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Articles 121 - 150 of 180
Full-Text Articles in Medical Microbiology
Construction And Characterization Of Functional Ftsa Sandwich Fusions For Studies Of Ftsa Localization And Dynamics During Escherichia Coli Cell Division, Todd A Cameron, William Margolin
Construction And Characterization Of Functional Ftsa Sandwich Fusions For Studies Of Ftsa Localization And Dynamics During Escherichia Coli Cell Division, Todd A Cameron, William Margolin
Faculty, Staff and Student Publications
FtsA, a homolog of actin, is essential for cell division of Escherichia coli and is widely conserved among many bacteria. FtsA helps to tether polymers of the bacterial tubulin homolog FtsZ to the cytoplasmic membrane as part of the cytokinetic Z ring. GFP fusions to FtsA have illuminated FtsA’s localization in live E. coli, but these fusions have not been fully functional and required the presence of the native FtsA. Here, we characterize “sandwich” fusions of E. coli FtsA to either mCherry or msfGFP that are functional for cell division and exhibit fluorescent rings at midcell that persist throughout …
Excessive Mechanotransduction In Sensory Neurons Causes Joint Contractures, Shang Ma, Adrienne E Dubin, Luis O Romero, Meaghan Loud, Alexandra Salazar, Sarah Chu, Nikola Klier, Sameer Masri, Yunxiao Zhang, Yu Wang, Alex T Chesler, Katherine A Wilkinson, Valeria Vásquez, Kara L Marshall, Ardem Patapoutian
Excessive Mechanotransduction In Sensory Neurons Causes Joint Contractures, Shang Ma, Adrienne E Dubin, Luis O Romero, Meaghan Loud, Alexandra Salazar, Sarah Chu, Nikola Klier, Sameer Masri, Yunxiao Zhang, Yu Wang, Alex T Chesler, Katherine A Wilkinson, Valeria Vásquez, Kara L Marshall, Ardem Patapoutian
Faculty, Staff and Student Publications
Distal arthrogryposis (DA) is a collection of rare disorders that are characterized by congenital joint contractures. Most DA mutations are in muscle- and joint-related genes, and the anatomical defects originate cell-autonomously within the musculoskeletal system. However, gain-of-function mutations in PIEZO2, a principal mechanosensor in somatosensation, cause DA subtype 5 (DA5) through unknown mechanisms. We show that expression of a gain-of-function PIEZO2 mutation in proprioceptive sensory neurons that mainly innervate muscle spindles and tendons is sufficient to induce DA5-like phenotypes in mice. Overactive PIEZO2 causes anatomical defects through increased activity within the peripheral nervous system during postnatal development. Furthermore, botulinum toxin …
Covidanno, Covid-19 Annotation In Human, Yuzhou Feng, Mengyuan Yang, Zhiwei Fan, Weiling Zhao, Pora Kim, Xiaobo Zhou
Covidanno, Covid-19 Annotation In Human, Yuzhou Feng, Mengyuan Yang, Zhiwei Fan, Weiling Zhao, Pora Kim, Xiaobo Zhou
Faculty, Staff and Student Publications
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 19 (COVID-19), has caused a global health crisis. Despite ongoing efforts to treat patients, there is no universal prevention or cure available. One of the feasible approaches will be identifying the key genes from SARS-CoV-2-infected cells. SARS-CoV-2-infected in vitro model, allows easy control of the experimental conditions, obtaining reproducible results, and monitoring of infection progression. Currently, accumulating RNA-seq data from SARS-CoV-2 in vitro models urgently needs systematic translation and interpretation. To fill this gap, we built COVIDanno, COVID-19 annotation in humans, available at http://biomedbdc.wchscu.cn/COVIDanno/. The aim …
Identification Of Microbiological Factors Associated With Periodontal Health Disparities, Bing-Yan Wang, Aize Cao, Meng-Hsuan Ho, Derek Wilus, Sally Sheng, Hsiu-Wan Meng, Elissa Guerra, Jianming Hong, Hua Xie
Identification Of Microbiological Factors Associated With Periodontal Health Disparities, Bing-Yan Wang, Aize Cao, Meng-Hsuan Ho, Derek Wilus, Sally Sheng, Hsiu-Wan Meng, Elissa Guerra, Jianming Hong, Hua Xie
Faculty, Staff and Student Publications
The present study aimed at identifying risk factors associated with periodontitis development and periodontal health disparities with emphasis on differential oral microbiota. The prevalence of periodontitis is recently rising dentate adults in the US, which presents a challenge to oral health and overall health. The risk of developing periodontitis is higher in African Americans (AAs), and Hispanic Americans (HAs) than in Caucasian Americans (CAs). To identify potentially microbiological determinations of periodontal health disparities, we examined the distribution of several potentially beneficial and pathogenic bacteria in the oral cavities of AA, CA, and HA study participants. Dental plaque samples from 340 …
Genome-Wide Characterization Of Trichome Birefringence-Like Genes Provides Insights Into Fiber Yield Improvement, Ziyin Li, Yuzhen Shi, Xianghui Xiao, Jikun Song, Pengtao Li, Juwu Gong, Haibo Zhang, Wankui Gong, Aiying Liu, Renhai Peng, Haihong Shang, Qun Ge, Junwen Li, Jingtao Pan, Quanjia Chen, Quanwei Lu, Youlu Yuan
Genome-Wide Characterization Of Trichome Birefringence-Like Genes Provides Insights Into Fiber Yield Improvement, Ziyin Li, Yuzhen Shi, Xianghui Xiao, Jikun Song, Pengtao Li, Juwu Gong, Haibo Zhang, Wankui Gong, Aiying Liu, Renhai Peng, Haihong Shang, Qun Ge, Junwen Li, Jingtao Pan, Quanjia Chen, Quanwei Lu, Youlu Yuan
Faculty, Staff and Student Publications
Cotton is an important fiber crop. The cotton fiber is an extremely long trichome that develops from the epidermis of an ovule. The trichome is a general and multi-function plant organ, and trichome birefringence-like (TBL) genes are related to trichome development. At the genome-wide scale, we identified TBLs in four cotton species, comprising two cultivated tetraploids (Gossypium hirsutum and G. barbadense) and two ancestral diploids (G. arboreum and G. raimondii). Phylogenetic analysis showed that the TBL genes clustered into six groups. We focused on GH_D02G1759 in group IV because it was located in a …
Research On Cloud Manufacturing Service Recommendation Based On Graph Neural Network, Minghui Li, Xiaoqiu Shi, Yuqiang Shi, Yong Cai, Xuewen Dong
Research On Cloud Manufacturing Service Recommendation Based On Graph Neural Network, Minghui Li, Xiaoqiu Shi, Yuqiang Shi, Yong Cai, Xuewen Dong
Faculty, Staff and Student Publications
There are an increasing number of manufacturing service resources appeared on the cloud manufacturing (CMfg) service platform recently, which leads to a serious information overloading problem to the enterprises that need these resources. To tackle this problem, a graph neural network-based recommendation method for CMfg service resources is proposed, which effectively overcomes some limitations of the traditional recommendation methods. Specifically, we first use different similarity calculation methods (e.g., Cosine similarity, Pearson correlation coefficient, etc.) to calculate the similarities between different resources based on the feature information of CMfg service resources. A resource graph dataset is accordingly established. A graph neural …
Advances In Flexible Graphene Field-Effect Transistors For Biomolecule Sensing, Bo Hu, Hao Sun, Jinpeng Tian, Jin Mo, Wantao Xie, Qiu Ming Song, Wenwei Zhang, Hui Dong
Advances In Flexible Graphene Field-Effect Transistors For Biomolecule Sensing, Bo Hu, Hao Sun, Jinpeng Tian, Jin Mo, Wantao Xie, Qiu Ming Song, Wenwei Zhang, Hui Dong
Faculty, Staff and Student Publications
With the increasing demand for biomarker detection in wearable electronic devices, flexible biosensors have garnered significant attention. Additionally, graphene field-effect transistors (GFETs) have emerged as key components for constructing biosensors, owing to their high sensitivity, multifunctionality, rapid response, and low cost. Leveraging the advantages of flexible substrates, such as biocompatibility, adaptability to complex environments, and fabrication flexibility, flexible GFET sensors exhibit promising prospects in detecting various biomarkers. This review provides a concise summary of design strategies for flexible GFET biosensors, including non-encapsulated gate without dielectric layer coverage and external gate designs. Furthermore, notable advancements in sensing applications of biomolecules, such …
Dysregulated Coagulation System Links To Inflammation In Diabetic Kidney Disease, Mengyun Xiao, Donge Tang, Shaodong Luan, Bo Hu, Wenyu Gong, Wolfgang Pommer, Yong Dai, Lianghong Yin
Dysregulated Coagulation System Links To Inflammation In Diabetic Kidney Disease, Mengyun Xiao, Donge Tang, Shaodong Luan, Bo Hu, Wenyu Gong, Wolfgang Pommer, Yong Dai, Lianghong Yin
Faculty, Staff and Student Publications
Diabetic kidney disease (DKD) is a significant contributor to end-stage renal disease worldwide. Despite extensive research, the exact mechanisms responsible for its development remain incompletely understood. Notably, patients with diabetes and impaired kidney function exhibit a hypercoagulable state characterized by elevated levels of coagulation molecules in their plasma. Recent studies propose that coagulation molecules such as thrombin, fibrinogen, and platelets are interconnected with the complement system, giving rise to an inflammatory response that potentially accelerates the progression of DKD. Remarkably, investigations have shown that inhibiting the coagulation system may protect the kidneys in various animal models and clinical trials, suggesting …
Common Statistical Concepts In The Supervised Machine Learning Arena, Hooman H Rashidi, Samer Albahra, Scott Robertson, Nam K Tran, Bo Hu
Common Statistical Concepts In The Supervised Machine Learning Arena, Hooman H Rashidi, Samer Albahra, Scott Robertson, Nam K Tran, Bo Hu
Faculty, Staff and Student Publications
One of the core elements of Machine Learning (ML) is statistics and its embedded foundational rules and without its appropriate integration, ML as we know would not exist. Various aspects of ML platforms are based on statistical rules and most notably the end results of the ML model performance cannot be objectively assessed without appropriate statistical measurements. The scope of statistics within the ML realm is rather broad and cannot be adequately covered in a single review article. Therefore, here we will mainly focus on the common statistical concepts that pertain to supervised ML (i.e. classification and regression) along with …
The Genetic Landscape And Clinical Implication Of Pediatric Moyamoya Angiopathy In An International Cohort, Yan-Hao Wei, Ren-Tang Bi, Yan-Mei Qiu, Chun-Lin Zhang, Jian-Zhuang Li, Ya-Nan Li, Bo Hu
The Genetic Landscape And Clinical Implication Of Pediatric Moyamoya Angiopathy In An International Cohort, Yan-Hao Wei, Ren-Tang Bi, Yan-Mei Qiu, Chun-Lin Zhang, Jian-Zhuang Li, Ya-Nan Li, Bo Hu
Faculty, Staff and Student Publications
Ischemic stroke is a highly complex systemic disease characterized by intricate interactions between the brain and gastrointestinal tract. While our current understanding of these interactions primarily stems from experimental models, their relevance to human stroke outcomes is of considerable interest. After stroke, bidirectional communication between the brain and gastrointestinal tract initiates changes in the gastrointestinal microenvironment. These changes involve the activation of gastrointestinal immunity, disruption of the gastrointestinal barrier, and alterations in gastrointestinal microbiota. Importantly, experimental evidence suggests that these alterations facilitate the migration of gastrointestinal immune cells and cytokines across the damaged blood-brain barrier, ultimately infiltrating the ischemic brain. …
Conformational Rearrangements In The Sensory Rcsf/Omp Complex Mediate Signal Transduction Across The Bacterial Cell Envelope, Sarah R Lach, Santosh Kumar, Seonghoon Kim, Wonpil Im, Anna Konovalova
Conformational Rearrangements In The Sensory Rcsf/Omp Complex Mediate Signal Transduction Across The Bacterial Cell Envelope, Sarah R Lach, Santosh Kumar, Seonghoon Kim, Wonpil Im, Anna Konovalova
Faculty, Staff and Student Publications
Timely detection and repair of envelope damage are paramount for bacterial survival. The Regulator of Capsule Synthesis (Rcs) stress response can transduce the stress signals across the multilayered gram-negative cell envelope to regulate gene expression in the cytoplasm. Previous studies defined the overall pathway, which begins with the sensory lipoprotein RcsF interacting with several outer membrane proteins (OMPs). RcsF can also interact with the periplasmic domain of the negative regulator IgaA, derepressing the downstream RcsCDB phosphorelay. However, how the RcsF/IgaA interaction is regulated at the molecular level to activate the signaling in response to stress remains poorly understood. In this …
Evolutionary Aspects Of Infections: Inflammation And Sickness Behaviors, Robert Dantzer
Evolutionary Aspects Of Infections: Inflammation And Sickness Behaviors, Robert Dantzer
Faculty, Staff and Student Publications
Sickness behavior was conceptualized initially as the behavioral counterpart of the fever response to infectious pathogens. It helps to raise body temperature to its higher setpoint and to maintain it at this new level and it has the additional benefit of enabling a weakened organism to protect itself from other dangers. The discovery of the behavioral effects of proinflammatory cytokines produced by activated immune cells provided a cellular and molecular basis to this phenomenon. The administration of cytokines or cytokine inducers like lipopolysaccharide to healthy rodents allowed to reveal the similarities and differences between inflammation-induced sickness behavior and the fever …
Sparse Tree-Based Clustering Of Microbiome Data To Characterize Microbiome Heterogeneity In Pancreatic Cancer, Yushu Shi, Liangliang Zhang, Kim-Anh Do, Robert Jenq, Christine B Peterson
Sparse Tree-Based Clustering Of Microbiome Data To Characterize Microbiome Heterogeneity In Pancreatic Cancer, Yushu Shi, Liangliang Zhang, Kim-Anh Do, Robert Jenq, Christine B Peterson
Faculty, Staff and Student Publications
There is a keen interest in characterizing variation in the microbiome across cancer patients, given increasing evidence of its important role in determining treatment outcomes. Here our goal is to discover subgroups of patients with similar microbiome profiles. We propose a novel unsupervised clustering approach in the Bayesian framework that innovates over existing model-based clustering approaches, such as the Dirichlet multinomial mixture model, in three key respects: we incorporate feature selection, learn the appropriate number of clusters from the data, and integrate information on the tree structure relating the observed features. We compare the performance of our proposed method to …
Risk Factors Associated With Severe Clostridioides Difficile Infection In Patients With Cancer, Denise Marie A Francisco, Liangliang Zhang, Ying Jiang, Adilene Olvera, Javier Adachi, Eduardo Yepez Guevara, Samuel L Aitken, Kevin W Garey, Christine B Peterson, Kim-Anh Do, Ryan Dillon, Engels N Obi, Robert Jenq, Pablo C Okhuysen
Risk Factors Associated With Severe Clostridioides Difficile Infection In Patients With Cancer, Denise Marie A Francisco, Liangliang Zhang, Ying Jiang, Adilene Olvera, Javier Adachi, Eduardo Yepez Guevara, Samuel L Aitken, Kevin W Garey, Christine B Peterson, Kim-Anh Do, Ryan Dillon, Engels N Obi, Robert Jenq, Pablo C Okhuysen
Faculty, Staff and Student Publications
INTRODUCTION: Antibiotic use is a risk factor for Clostridioides difficile infection (CDI). Few studies have correlated use of prior antibiotic classes with CDI, microbiome composition, and disease severity in patients with cancer. We hypothesized that previous antibiotic exposure and fecal microbiome composition at time of presentation are risk factors for severe CDI in patients with cancer.
METHODS: This non-interventional, prospective, cohort study examined 200 patients with cancer who had their first episode or first recurrence of CDI. C. difficile was identified using nucleic acid amplification testing. Univariate analysis was used to determine significant risk factors for severe CDI. Fecal microbiome …
Loss Of Ubiquitin-Specific Peptidase 18 Destabilizes 14-3-3Ζ Protein And Represses Lung Cancer Metastasis, Zibo Chen, Lin Zheng, Yulong Chen, Xiuxia Liu, Masanori Kawakami, Lisa Maria Mustachio, Jason Roszik, Katherine V Ferry-Galow, Ralph E Parchment, Xin Liu, Thorkell Andresson, Gerard Duncan, Jonathan M Kurie, Jaime Rodriguez-Canales, Xi Liu, Ethan Dmitrovsky
Loss Of Ubiquitin-Specific Peptidase 18 Destabilizes 14-3-3Ζ Protein And Represses Lung Cancer Metastasis, Zibo Chen, Lin Zheng, Yulong Chen, Xiuxia Liu, Masanori Kawakami, Lisa Maria Mustachio, Jason Roszik, Katherine V Ferry-Galow, Ralph E Parchment, Xin Liu, Thorkell Andresson, Gerard Duncan, Jonathan M Kurie, Jaime Rodriguez-Canales, Xi Liu, Ethan Dmitrovsky
Faculty, Staff and Student Publications
Cancer metastasis is a major cause of cancer-related mortality. Strategies to reduce metastases are needed especially in lung cancer, the most common cause of cancer mortality. We previously reported increased ubiquitin-specific peptidase 18 (USP18) expression in lung and other cancers. Engineered reduction of USP18 expression repressed lung cancer growth and promoted apoptosis. This deubiquitinase (DUB) stabilized targeted proteins by removing the complex interferon-stimulated gene 15 (ISG15). This study explores if the loss of USP18 reduced lung cancer metastasis. USP18 knock-down in lung cancer cells was independently achieved using small hairpin RNAs (shRNAs) and small interfering RNAs (siRNAs). USP18 knock-down reduced …
Clinical Significance Of Glycolytic Metabolic Activity In Hepatocellular Carcinoma, Joann Jung, Sowon Park, Yeonwoo Jang, Sung-Hwan Lee, Yun Seong Jeong, Sun Young Yim, Ju-Seog Lee
Clinical Significance Of Glycolytic Metabolic Activity In Hepatocellular Carcinoma, Joann Jung, Sowon Park, Yeonwoo Jang, Sung-Hwan Lee, Yun Seong Jeong, Sun Young Yim, Ju-Seog Lee
Faculty, Staff and Student Publications
High metabolic activity is a hallmark of cancers, including hepatocellular carcinoma (HCC). However, the molecular features of HCC with high metabolic activity contributing to clinical outcomes and the therapeutic implications of these characteristics are poorly understood. We aimed to define the features of HCC with high metabolic activity and uncover its association with response to current therapies. By integrating gene expression data from mouse liver tissues and tumor tissues from HCC patients (n = 1038), we uncovered three metabolically distinct HCC subtypes that differ in clinical outcomes and underlying molecular biology. The high metabolic subtype is characterized by poor …
Identification Of Acenkps, A Committed Common Progenitor Population Of The Ilc1 And Nk Cell Continuum, Noe Rodriguez-Rodriguez, Paula A Clark, Mayuri Gogoi, Ana C F Ferreira, Bernhard Kerscher, Alastair Crisp, Helen E Jolin, Jane E Murphy, Meera Sivasubramaniam, Luisa Pedro, Jennifer A Walker, Morgan W D Heycock, Jacqueline D Shields, Jillian L Barlow, Andrew N J Mckenzie
Identification Of Acenkps, A Committed Common Progenitor Population Of The Ilc1 And Nk Cell Continuum, Noe Rodriguez-Rodriguez, Paula A Clark, Mayuri Gogoi, Ana C F Ferreira, Bernhard Kerscher, Alastair Crisp, Helen E Jolin, Jane E Murphy, Meera Sivasubramaniam, Luisa Pedro, Jennifer A Walker, Morgan W D Heycock, Jacqueline D Shields, Jillian L Barlow, Andrew N J Mckenzie
Faculty, Staff and Student Publications
The development of innate lymphoid cell (ILC) transcription factor reporter mice has shown a previously unexpected complexity in ILC hematopoiesis. Using novel polychromic mice to achieve higher phenotypic resolution, we have characterized bone marrow progenitors that are committed to the group 1 ILC lineage. These common ILC1/NK cell progenitors (ILC1/NKP), which we call "aceNKPs", are defined as lineage-Id2+IL-7Rα+CD25-α4β7-NKG2A/C/E+Bcl11b-. In vitro, aceNKPs differentiate into group 1 ILCs, including NK-like cells that express Eomes without the requirement for IL-15, and produce IFN-γ and perforin upon IL-15 stimulation. Following reconstitution of Rag2-/-Il2rg-/- hosts, aceNKPs give rise to a spectrum of mature ILC1/NK cells …
Targeted Therapeutics And Novel Signaling Pathways In Non-Alcohol-Associated Fatty Liver/Steatohepatitis (Nafl/Nash), Dhriti Sinha, Nicholas R De Lay
Targeted Therapeutics And Novel Signaling Pathways In Non-Alcohol-Associated Fatty Liver/Steatohepatitis (Nafl/Nash), Dhriti Sinha, Nicholas R De Lay
Faculty, Staff and Student Publications
The C-terminal domain (CTD) of the major endoribonuclease RNase E not only serves as a scaffold for the central RNA decay machinery in gram-negative bacteria but also mediates coupled degradation of small regulatory RNAs (sRNAs) and their cognate target transcripts following RNA chaperone Hfq-facilitated sRNA-mRNA base pairing. Despite the crucial role of RNase E CTD in sRNA-dependent gene regulation, the contribution of particular residues within this domain in recruiting sRNAs and mRNAs upon base pairing remains unknown. We have previously shown that in Escherichia coli, the highly conserved 3'-5'-exoribonuclease polynucleotide phosphorylase (PNPase) paradoxically stabilizes sRNAs by limiting access of …
Glial Interference: Impact Of Type I Interferon In Neurodegenerative Diseases, Ethan Roy, Wei Cao
Glial Interference: Impact Of Type I Interferon In Neurodegenerative Diseases, Ethan Roy, Wei Cao
Faculty, Staff and Student Publications
No abstract provided.
Lipid Surfaces And Glutamate Anions Enhance Formation Of Dynamic Biomolecular Condensates Containing Bacterial Cell Division Protein Ftsz And Its Dna-Bound Regulator Slma, Gianfranco Paccione, Miguel Á Robles-Ramos, Carlos Alfonso, Marta Sobrinos-Sanguino, William Margolin, Silvia Zorrilla, Begoña Monterroso, Germán Rivas
Lipid Surfaces And Glutamate Anions Enhance Formation Of Dynamic Biomolecular Condensates Containing Bacterial Cell Division Protein Ftsz And Its Dna-Bound Regulator Slma, Gianfranco Paccione, Miguel Á Robles-Ramos, Carlos Alfonso, Marta Sobrinos-Sanguino, William Margolin, Silvia Zorrilla, Begoña Monterroso, Germán Rivas
Faculty, Staff and Student Publications
Dynamic biomolecular condensates formed by liquid-liquid phase separation can regulate the spatial and temporal organization of proteins, thus modulating their functional activity in cells. Previous studies showed that the cell division protein FtsZ from Escherichia coli formed dynamic phase-separated condensates with nucleoprotein complexes containing the FtsZ spatial regulator SlmA under crowding conditions, with potential implications for condensate-mediated spatiotemporal control of FtsZ activity in cell division. In the present study, we assessed formation of these condensates in the presence of lipid surfaces and glutamate ions to better approximate the E. coli intracellular environment. We found that potassium glutamate substantially promoted the …
Characterization Of Bcma Expression In Circulating Rare Single Cells Of Patients With Plasma Cell Neoplasms, Libere J Ndacayisaba, Kate E Rappard, Stephanie N Shishido, Sonia M Setayesh, Guilin Tang, Pei Lin, Nicholas Matsumoto, Ching-Ju Hsu, Rafael Nevarez, Carmen Ruiz Velasco, Amin Naghdloo, Eric Yang, Kevin Kelly, James Hicks, Jeremy Mason, Robert Z Orlowski, Elisabet E Manasanch, Peter Kuhn
Characterization Of Bcma Expression In Circulating Rare Single Cells Of Patients With Plasma Cell Neoplasms, Libere J Ndacayisaba, Kate E Rappard, Stephanie N Shishido, Sonia M Setayesh, Guilin Tang, Pei Lin, Nicholas Matsumoto, Ching-Ju Hsu, Rafael Nevarez, Carmen Ruiz Velasco, Amin Naghdloo, Eric Yang, Kevin Kelly, James Hicks, Jeremy Mason, Robert Z Orlowski, Elisabet E Manasanch, Peter Kuhn
Faculty, Staff and Student Publications
B-cell maturation antigen (BCMA), a key regulator of B-cell proliferation and survival, is highly expressed in almost all cases of plasma cell neoplasms and B-lymphoproliferative malignancies. BCMA is a robust biomarker of plasma cells and a therapeutic target with substantial clinical significance. However, the expression of BCMA in circulating tumor cells of patients with hematological malignancies has not been validated for the detection of circulating plasma and B cells. The application of BCMA as a biomarker in single-cell detection and profiling of circulating tumor cells in patients' blood could enable early disease profiling and therapy response monitoring. Here, we report …
Acute Depletion Of Human Core Nucleoporin Reveals Direct Roles In Transcription Control But Dispensability For 3d Genome Organization, Xiaoyu Zhu, Chuangye Qi, Ruoyu Wang, Joo-Hyung Lee, Jiaofang Shao, Lanxin Bei, Feng Xiong, Phuoc T Nguyen, Guojie Li, Joanna Krakowiak, Su-Pin Koh, Lukas M Simon, Leng Han, Travis I Moore, Wenbo Li
Acute Depletion Of Human Core Nucleoporin Reveals Direct Roles In Transcription Control But Dispensability For 3d Genome Organization, Xiaoyu Zhu, Chuangye Qi, Ruoyu Wang, Joo-Hyung Lee, Jiaofang Shao, Lanxin Bei, Feng Xiong, Phuoc T Nguyen, Guojie Li, Joanna Krakowiak, Su-Pin Koh, Lukas M Simon, Leng Han, Travis I Moore, Wenbo Li
Faculty, Staff and Student Publications
The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct roles remains limited. Here, by Cut&Run, we find that core NUPs display broad but also cell-type-specific association with active promoters and enhancers in human cells. Auxin-mediated rapid depletion of two NUPs demonstrates that NUP93, but not NUP35, directly and specifically controls gene transcription. NUP93 directly activates genes with high levels of RNA polymerase II loading and transcriptional elongation by facilitating full …
The Breast Cancer Microenvironment And Lipoprotein Lipase: Another Negative Notch For A Beneficial Enzyme?, Zhu-Hong Chen, Yu-Ling Cui, Jing-Ting Sun, Yu-Ting Li, Chi Zhang, Yang-Ming Zhang, Ze-Yang Li, Yu-Xuan Shang, Min-Hua Ni, Bo Hu, Lin-Feng Yan, Wen Wang
The Breast Cancer Microenvironment And Lipoprotein Lipase: Another Negative Notch For A Beneficial Enzyme?, Zhu-Hong Chen, Yu-Ling Cui, Jing-Ting Sun, Yu-Ting Li, Chi Zhang, Yang-Ming Zhang, Ze-Yang Li, Yu-Xuan Shang, Min-Hua Ni, Bo Hu, Lin-Feng Yan, Wen Wang
Faculty, Staff and Student Publications
Objectives: To quantitatively summarize the specific changes in brain structure and function in migraine patients.
Methods: A literature screening of migraine was conducted from inception to Sept 1, 2022, in PubMed, Web of Science, Cochrane Library, and Medline databases using the keyword combination of "migraine and MRI." Activation likelihood estimation (ALE) was performed to assess the differentiation of functional connectivity (FC), regional homogeneity (ReHo), and gray matter volume (GMV) of migraine patients.
Results: Eleven voxel-based morphometry (VBM) studies and 25 resting-state fMRI (rs-fMRI) studies (16 FC and 9 ReHo studies) were included in this study. ALE analysis revealed the ReHo …
Rapid Reconstruction Of Neural Circuits Using Tissue Expansion And Light Sheet Microscopy, Joshua L Lillvis, Hideo Otsuna, Xiaoyu Ding, Igor Pisarev, Takashi Kawase, Jennifer Colonell, Konrad Rokicki, Cristian Goina, Ruixuan Gao, Amy Hu, Kaiyu Wang, John Bogovic, Daniel E Milkie, Linus Meienberg, Brett D Mensh, Edward S Boyden, Stephan Saalfeld, Paul W Tillberg, Barry J Dickson
Rapid Reconstruction Of Neural Circuits Using Tissue Expansion And Light Sheet Microscopy, Joshua L Lillvis, Hideo Otsuna, Xiaoyu Ding, Igor Pisarev, Takashi Kawase, Jennifer Colonell, Konrad Rokicki, Cristian Goina, Ruixuan Gao, Amy Hu, Kaiyu Wang, John Bogovic, Daniel E Milkie, Linus Meienberg, Brett D Mensh, Edward S Boyden, Stephan Saalfeld, Paul W Tillberg, Barry J Dickson
Faculty, Staff and Student Publications
Brain function is mediated by the physiological coordination of a vast, intricately connected network of molecular and cellular components. The physiological properties of neural network components can be quantified with high throughput. The ability to assess many animals per study has been critical in relating physiological properties to behavior. By contrast, the synaptic structure of neural circuits is presently quantifiable only with low throughput. This low throughput hampers efforts to understand how variations in network structure relate to variations in behavior. For neuroanatomical reconstruction, there is a methodological gulf between electron microscopic (EM) methods, which yield dense connectomes at considerable …
Structural And Functional Diversity Of Type Iv Secretion Systems, Melissa R Cruz, Shane Cristy, Shantanu Guha, Giuseppe Buda De Cesare, Elena Evdokimova, Hiram Sanchez, Dominika Borek, Pedro Miramón, Junko Yano, Paul L Fidel, Alexei Savchenko, David R Andes, Peter J Stogios, Michael C Lorenz, Danielle A Garsin
Structural And Functional Diversity Of Type Iv Secretion Systems, Melissa R Cruz, Shane Cristy, Shantanu Guha, Giuseppe Buda De Cesare, Elena Evdokimova, Hiram Sanchez, Dominika Borek, Pedro Miramón, Junko Yano, Paul L Fidel, Alexei Savchenko, David R Andes, Peter J Stogios, Michael C Lorenz, Danielle A Garsin
Faculty, Staff and Student Publications
Fungal pathogens are a continuing challenge due to few effective antifungals and a rise in resistance. In previous work, we described the inhibition of Candida albicans virulence following exposure to the 68 amino acid bacteriocin, EntV, secreted by Enterococcus faecalis. Here, to optimize EntV as a potential therapeutic and better understand its antifungal features, an X-ray structure is obtained. The structure consists of six alpha helices enclosing a seventh 16 amino acid helix (α7). The individual helices are tested for antifungal activity using in vitro and nematode infection assays. Interestingly, α7 retains antifungal, but not antibacterial activity and is also …
The Temporal Impulse Response Function In Infantile Nystagmus, Gal Avital, Felicia Kuperwaser, Andrew W Pountain, Keenan A Lacey, Erin E Zwack, Magdalena Podkowik, Bo Shopsin, Victor J Torres, Itai Yanai
The Temporal Impulse Response Function In Infantile Nystagmus, Gal Avital, Felicia Kuperwaser, Andrew W Pountain, Keenan A Lacey, Erin E Zwack, Magdalena Podkowik, Bo Shopsin, Victor J Torres, Itai Yanai
Faculty, Staff and Student Publications
Innate immune recognition of bacterial pathogens is a key determinant of the ensuing systemic response, and host or pathogen heterogeneity in this early interaction can impact the course of infection. To gain insight into host response heterogeneity, we investigate macrophage inflammatory dynamics using primary human macrophages infected with Group B Streptococcus. Transcriptomic analysis reveals discrete cellular states within responding macrophages, one of which consists of four sub-states, reflecting inflammatory activation. Infection with six additional bacterial species—Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis, Yersinia pseudotuberculosis, Shigella flexneri, and Salmonella enterica—recapitulates these states, though at …
Oxidation Of Two Cysteines Within Yeast Hsp70 Impairs Proteostasis While Directly Triggering An Hsf1-Dependent Cytoprotective Response, Alec Santiago, Kevin A Morano
Oxidation Of Two Cysteines Within Yeast Hsp70 Impairs Proteostasis While Directly Triggering An Hsf1-Dependent Cytoprotective Response, Alec Santiago, Kevin A Morano
Faculty, Staff and Student Publications
Neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's diseases affect millions of Americans every year. One factor linked to the formation of aggregates associated with these diseases is damage sustained to proteins by oxidative stress. Management of protein misfolding by the ubiquitous Hsp70 chaperone family can be modulated by modification of two key cysteines in the ATPase domain by oxidizing or thiol-modifying compounds. To investigate the biological consequences of cysteine modification on the Hsp70 Ssa1 in budding yeast, we generated cysteine null (cysteine to serine) and oxidomimetic (cysteine to aspartic acid) mutant variants of both C264 and C303 and demonstrate …
Wellness In The Face Of Frailty Among Older Adults In First Nations Communities, Morgan Slater, Gabrielle Bruser, Roseanne Sutherland, Melissa K Andrew, Wayne Warry, Kristen M Jacklin, Jennifer D Walker
Wellness In The Face Of Frailty Among Older Adults In First Nations Communities, Morgan Slater, Gabrielle Bruser, Roseanne Sutherland, Melissa K Andrew, Wayne Warry, Kristen M Jacklin, Jennifer D Walker
Faculty, Staff and Student Publications
OBJECTIVES: First Nations people report high levels of wellness despite high rates of chronic illness. Our goal was to understand the factors associated with wellness among First Nations adults in Ontario who were considered frail.
METHODS: Using the First Nations Regional Health Survey, we created a profile of First Nations adults (aged 45+) who were categorized as "frail" (weighted sample size = 8121). We used multivariate logistic regression to determine associations between wellness (as measured by self-reported physical, emotional, mental, and spiritual balance) and determinants of health.
RESULTS: Rates of reported wellness were high among those who were frail, ranging …
Discovery Of An Orally Active Benzoxaborole Prodrug Effective In The Treatment Of Chagas Disease In Non-Human Primates, Angel M Padilla, Wei Wang, Tsutomu Akama, David S Carter, Eric Easom, Yvonne Freund, Jason S Halladay, Yang Liu, Sarah A Hamer, Carolyn L Hodo, Gregory K Wilkerson, Dylan Orr, Brooke White, Arlene George, Huifeng Shen, Yiru Jin, Michael Zhuo Wang, Susanna Tse, Robert T Jacobs, Rick L Tarleton
Discovery Of An Orally Active Benzoxaborole Prodrug Effective In The Treatment Of Chagas Disease In Non-Human Primates, Angel M Padilla, Wei Wang, Tsutomu Akama, David S Carter, Eric Easom, Yvonne Freund, Jason S Halladay, Yang Liu, Sarah A Hamer, Carolyn L Hodo, Gregory K Wilkerson, Dylan Orr, Brooke White, Arlene George, Huifeng Shen, Yiru Jin, Michael Zhuo Wang, Susanna Tse, Robert T Jacobs, Rick L Tarleton
Faculty, Staff and Student Publications
Trypanosoma cruzi, the agent of Chagas disease, probably infects tens of millions of people, primarily in Latin America, causing morbidity and mortality. The options for treatment and prevention of Chagas disease are limited and underutilized. Here we describe the discovery of a series of benzoxaborole compounds with nanomolar activity against extra- and intracellular stages of T. cruzi. Leveraging both ongoing drug discovery efforts in related kinetoplastids, and the exceptional models for rapid drug screening and optimization in T. cruzi, we have identified the prodrug AN15368 that is activated by parasite carboxypeptidases to yield a compound that targets the messenger RNA …
Characteristics Of Community-Acquired Carbapenem-Resistant Enterobacterales, Rima Shrestha, Courtney L Luterbach, Weixiao Dai, Lauren Komarow, Michelle Earley, Gregory Weston, Erica Herc, Jesse T Jacob, Robert Salata, Darren Wong, Deverick Anderson, Kirsten B Rydell, Cesar A Arias, Liang Chen, David Van Duin, Mdro Investigators
Characteristics Of Community-Acquired Carbapenem-Resistant Enterobacterales, Rima Shrestha, Courtney L Luterbach, Weixiao Dai, Lauren Komarow, Michelle Earley, Gregory Weston, Erica Herc, Jesse T Jacob, Robert Salata, Darren Wong, Deverick Anderson, Kirsten B Rydell, Cesar A Arias, Liang Chen, David Van Duin, Mdro Investigators
Faculty, Staff and Student Publications
BACKGROUND: Community-acquired carbapenem-resistant Enterobacterales (CA-CRE) are an important threat.
METHODS: In CRACKLE-2, we defined patients with CA-CRE as admitted from home, without pre-existing conditions, and a positive culture within 48 h of admission. Healthcare-associated CRE (HA-CRE) were those with the lowest likelihood of community acquisition, not admitted from home and cultured >48 h after admission. Specific genetic markers in carbapenemase-producing Klebsiella pneumoniae were evaluated through random forest modelling.
RESULTS: CA-CRE and HA-CRE were detected in 83 (10%) and 208 (26%) of 807 patients. No significant differences were observed in bacterial species or strain type distribution. K. pneumoniae (204/291, 70%) was …