27 Works

Association with a novel protective microbe facilitates host adaptation to a stressful environment

Kim Hoang, Nicole Gerardo & Levi Morran
Protective symbionts can allow hosts to occupy otherwise uninhabitable niches. Despite the importance of symbionts in host evolution, we know little about how these associations arise. Encountering a microbe that can improve host fitness in a stressful environment may favor persistent interactions with that microbe, potentially facilitating a long-term association. The bacterium Bacillus subtilis protects Caenorhabditis elegans nematodes from heat shock by increasing host fecundity compared to the non-protective Escherichia coli. In this study, we...

Implementing social network analysis to understand the socio-ecology of wildlife co-occurrence and joint interactions with humans in anthropogenic environments

Krishna Balasubramaniam, Stefano Kaburu, Pascal Marty, Brianne Beisner, Eliza Bliss-Moreau, Malgorzata Arlet, Nadine Ruppert, Ahmad Ismail, Sahrul Anuar Mohd Sah, Lalith Mohan, Sandeep Rattan, Ullasa Kodandaramaiah & Brenda McCowan
1. Human population expansion into wildlife habitats has increased interest in the behavioral ecology of human-wildlife interactions. To date, however, the socio-ecological factors that determine whether, when or where wild animals take risks by interacting with humans and anthropogenic factors still remains unclear. 2. We adopt a comparative approach to address this gap, using social network analysis (SNA). SNA, increasingly implemented to determine human impact on wildlife ecology, can be a powerful tool to understand...

Construction of an immune-related lncRNA pairs model to predict prognosis and immune landscape of lung adenocarcinoma patients

Junhui Liu, Hao Wu, Zhaojia Gao, Ming Lou & Kai Yuan
The model of immune-related lncRNA pairs (IRLPs) seems to be an available predictor in lung adenocarcinoma (LUAD) patients. The aim of our study was to construct a model with IRLPs to predict the survival status and immune landscape of LUAD patients. Based on TCGA-LUAD dataset, a risk assessment model with IRLPs was established. Then, ROC curves were used to assess the predictive accuracy and effectiveness of our model. Next, we identified the difference of survival,...

Data from: Emerging experience-dependent dynamics in primary somatosensory cortex reflect behavioral adaptation

Christian Waiblinger, Megan E McDonnell, April R Reedy, Peter Y Borden & Garrett B Stanley
Behavioral experience and flexibility are crucial for survival in a constantly changing environment. Despite evolutionary pressures to develop adaptive behavioral strategies in a dynamically changing sensory landscape, the underlying neural correlates have not been well explored. Here, we use genetically encoded voltage imaging to measure signals in primary somatosensory cortex (S1) during sensory learning and behavioral adaptation in the mouse. In response to changing stimulus statistics, mice adopt a strategy that modifies their detection behavior...

An insight into SARS-CoV-2 membrane protein interaction with spike, envelope, and nucleocapsid proteins

Prateek Kumar, Amit Kumar, Neha Garg & Rajanish Giri
Intraviral protein–protein interactions are crucial for replication, pathogenicity, and viral assembly. Among these, virus assembly is a critical step as it regulates the arrangements of viral structural proteins and helps in the encapsulation of genomic material. SARS-CoV-2 structural proteins play an essential role in the self-rearrangement, RNA encapsulation, and mature virus particle formation. In SARS-CoV, the membrane protein interacts with the envelope and spike protein in Endoplasmic Reticulum Golgi Intermediate Complex (ERGIC) to form an...

Dataset: Host genetic drift and adaptation in the evolution and maintenance of parasite resistance

P. Signe White, Danial Arslan, David Kim, McKenna Penley & Levi Morran
The experiment investigates the survival of Caenorhabditis elegans host populations when exposed to a bacterial parasite, Serratia marcescens. Exposed host populations were either large (500 individuals) or small (25 or 50 individuals) and were either susceptible or resistant to the disease. Populations of C. elegans were evolved against either heat-killed or live bacteria. After 13 generations of host evolution, we exposed the worms again to the bacteria to determine whether the worms lost, gained, or...

Attenuation of porcine deltacoronavirus disease severity by porcine reproductive and respiratory syndrome virus coinfection in a weaning pig model

Xinrong Zhou, Xinna Ge, Yongning Zhang, Jun Han, Xin Guo, Yanhong Chen, Lei Zhou & Hanchun Yang
Porcine deltacoronavirus (PDCoV) is a potentially emerging zoonotic pathogen that causes severe diarrhea in young pigs, with a risk of fatal dehydration. Its pathogenicity on neonatal piglet has been previously reported, however, it is less known if the coinfection with immunosuppressive pathogens can influence PDCoV disease manifestation. Here, a coinfection model of PDCoV and porcine reproductive and respiratory syndrome virus (PRRSV), a global-spread immunosuppressive virus, was set to study their interaction. Weaning pigs in the...

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Rongsui Gao, Wenhong Zu, Yang Liu, Junhua Li, Zeyao Li, Yanling Wen, Haiyan Wang, Jing Yuan, Lin Cheng, Shengyuan Zhang, Yu Zhang, Shuye Zhang, Weilong Liu, Xun Lan, Lei Liu, Feng Li & Zheng Zhang
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’...

Asymmetric cross-strain protection for amphibians exposed to a fungal-metabolite prophylactic treatment

KM Barnett, D.J. Civitello, T.A. McMahon & S.E. Detmering
Chytridiomycosis, an infectious disease of amphibians caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), poses an imminent conservation threat. The global spread of Bd has led to mass mortality events in many amphibian species, resulting in at least 90 species’ extinctions to date. Exposure to Bd metabolites (i.e., non-infectious antigenic chemicals released by Bd) partially protects frogs during subsequent challenges with live Bd, suggesting its use as a prophylactic treatment and potential vaccine. However, we...

Data from: Genetic or toxicant-induced disruption of vesicular monoamine storage and global metabolic profiling in Caenorhabditis elegans

Vrinda Kalia, Joshua Bradner, Fion Lau, Monica Sharma, Meghan Bucher, Michelle Johnson, Merry Chen, Douglas Walker, Dean Jones & Gary Miller
The proper storage and release of monoamines contributes to a wide range of neuronal activity. Here, we examine the effects of altered vesicular monoamine transport in the nematode C. elegans. The gene cat-1 is responsible for the encoding of the vesicular monoamine transporter (VMAT) in C. elegans and is analogous to the mammalian vesicular monoamine transporter 2 (VMAT2). Our laboratory has previously shown that reduced VMAT2 activity confers vulnerability on catecholamine neurons in mice. The...

Identification of the RP11-21C4.1/SVEP1 gene pair associated with FAT2 mutations as a potential biomarker in gastric cancer

Lingshan Zhou, Yuan Yang, Min Liu, Yuling Gan, Rong Liu, Man Ren, Ya Zheng, Yuping Wang & Yongning Zhou
Gastric cancer (GC) is one of the most common malignancies worldwide. Despite rapid advances in systemic therapy, GC remains the third leading cause of cancer-related deaths. We aimed to identify a novel prognostic signature associated with FAT2 mutations in GC. We analyzed the expression levels of FAT2-mutant and FAT2-wildtype GC samples obtained from The Cancer Genome Atlas (TCGA). The Kaplan–Meier survival curve showed that patients with FAT2 mutations showed better prognosis than those without the...

Construction of an immune-related lncRNA pairs model to predict prognosis and immune landscape of lung adenocarcinoma patients

Junhui Liu, Hao Wu, Zhaojia Gao, Ming Lou & Kai Yuan
The model of immune-related lncRNA pairs (IRLPs) seems to be an available predictor in lung adenocarcinoma (LUAD) patients. The aim of our study was to construct a model with IRLPs to predict the survival status and immune landscape of LUAD patients. Based on TCGA-LUAD dataset, a risk assessment model with IRLPs was established. Then, ROC curves were used to assess the predictive accuracy and effectiveness of our model. Next, we identified the difference of survival,...

Identification of the RP11-21C4.1/SVEP1 gene pair associated with FAT2 mutations as a potential biomarker in gastric cancer

Lingshan Zhou, Yuan Yang, Min Liu, Yuling Gan, Rong Liu, Man Ren, Ya Zheng, Yuping Wang & Yongning Zhou
Gastric cancer (GC) is one of the most common malignancies worldwide. Despite rapid advances in systemic therapy, GC remains the third leading cause of cancer-related deaths. We aimed to identify a novel prognostic signature associated with FAT2 mutations in GC. We analyzed the expression levels of FAT2-mutant and FAT2-wildtype GC samples obtained from The Cancer Genome Atlas (TCGA). The Kaplan–Meier survival curve showed that patients with FAT2 mutations showed better prognosis than those without the...

Rare variant association study of Veteran twin whole-genomes links severe depression with a nonsynonymous change in the neuronal gene BHLHE22

Daniel Hupalo, Christopher Forsberg, Jack Goldberg, William S. Kremen, Michael J. Lyons, Anthony R. Soltis, Coralie Viollet, Robert J. Ursano, Murray B. Stein, Carol E. Franz, Yan V. Sun, Viola Vaccarino, Nicholas L. Smith, Clifton L. Dalgard, Matthew D. Wilkerson & Harvey B. Pollard
Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associations, but without known links to rare variation in the human genome. Here we aim to identify rare genetic variants associated with MDD using deep whole-genome sequencing data in an independent population. We report the sequencing of 1,688 whole genomes in a large sample of male-male Veteran twins. Depression status was classified based on a structured diagnostic interview according to DSM-III-R diagnostic criteria....

Prenatal medication use in a prospective pregnancy cohort by pre-pregnancy obesity status

Yassaman Vafai, Edwina H. Yeung, Rajeshwari Sundaram, Melissa M. Smarr, Nicole Gerlanc, William A. Grobman, Daniel Skupski, Edward K. Chien, Stefanie N. Hinkle, Roger B. Newman, Deborah A. Wing, Angela C. Ranzini, Anthony Sciscione, Jagteshwar Grewal, Cuilin Zhang & Katherine L. Grantz
The association between obesity (body mass index (BMI) ≥ 30 kg/m2) and pattern of medication use during pregnancy in the United States is not well-studied. Higher pre-pregnancy BMI may be associated with increases or decreases in medication use across pregnancy as symptoms (e.g. reflux) or comorbidities (e.g. gestational diabetes) requiring treatment that may be associated with higher BMI could also change with advancing gestation. To determine whether prenatal medication use, by the number and types...

Prenatal medication use in a prospective pregnancy cohort by pre-pregnancy obesity status

Yassaman Vafai, Edwina H. Yeung, Rajeshwari Sundaram, Melissa M. Smarr, Nicole Gerlanc, William A. Grobman, Daniel Skupski, Edward K. Chien, Stefanie N. Hinkle, Roger B. Newman, Deborah A. Wing, Angela C. Ranzini, Anthony Sciscione, Jagteshwar Grewal, Cuilin Zhang & Katherine L. Grantz
The association between obesity (body mass index (BMI) ≥ 30 kg/m2) and pattern of medication use during pregnancy in the United States is not well-studied. Higher pre-pregnancy BMI may be associated with increases or decreases in medication use across pregnancy as symptoms (e.g. reflux) or comorbidities (e.g. gestational diabetes) requiring treatment that may be associated with higher BMI could also change with advancing gestation. To determine whether prenatal medication use, by the number and types...

Rare variant association study of veteran twin whole-genomes links severe depression with a nonsynonymous change in the neuronal gene BHLHE22

Daniel Hupalo, Christopher W. Forsberg, Jack Goldberg, William S. Kremen, Michael J. Lyons, Anthony R. Soltis, Coralie Viollet, Robert J. Ursano, Murray B. Stein, Carol E. Franz, Yan V. Sun, Viola Vaccarino, Nicholas L. Smith, Clifton L. Dalgard, Matthew D. Wilkerson & Harvey B. Pollard
Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associations, but without known links to rare variation in the human genome. Here we aim to identify rare genetic variants associated with MDD using deep whole-genome sequencing data in an independent population. We report the sequencing of 1,688 whole genomes in a large sample of male-male Veteran twins. Depression status was classified based on a structured diagnostic interview according to DSM-III-R diagnostic criteria....

Identifying optimal capsid duplication length for the stability of reporter flaviviruses

Coleman Baker, Yang Liu, Jing Zou, Antonio Muruato, Xuping Xie & Pei-Yong Shi
Mosquito-transmitted flaviviruses cause widespread disease across the world. To provide better molecular tools for drug screens and pathogenesis studies, we report a new approach to produce stable NanoLuc-tagged flaviviruses, including dengue virus serotypes 1-4, Japanese encephalitis virus, yellow fever virus, West Nile virus, and Zika virus. Since the reporter gene is often engineered at the capsid gene region, the capsid sequence must be duplicated to flank the reporter gene; such capsid duplication is essential for...

Urinary metals and maternal circulating extracellular vesicle microRNA in the MADRES pregnancy cohort

Caitlin G. Howe, Helen B. Foley, Shohreh F. Farzan, Thomas A. Chavez, Mark Johnson, John D. Meeker, Theresa M. Bastain, Carmen J. Marsit & Carrie V. Breton
Exposure to metals increases risk for pregnancy complications. Extracellular vesicle (EV) miRNA contribute to maternal-foetal communication and are dysregulated in pregnancy complications. However, metal impacts on maternal circulating EV miRNA during pregnancy are unknown. Our objective was to investigate the impact of multiple metal exposures on EV miRNA in maternal circulation during pregnancy in the MADRES Study. Associations between urinary concentrations of nine metals and 106 EV miRNA in maternal plasma during pregnancy were investigated...

Reservoir hosts experiencing food stress alter transmission dynamics for a zoonotic pathogen

Jennifer C. Owen, Hannah R. Landwerlen, Dhruv B. Sharma, Sichao Wang, Alexander T. Ciota, Laura D. Kramer, Alan P. Dupuis & Aniruddha V. Belsare
Anthropogenic environmental change can significantly alter availability and quality of food resources for reservoir hosts and impact host-pathogen interactions in the wild. The state of the host’s nutritional reserves as time of infection is a key factor influencing infection outcomes by altering host resistance. Here we combine experimental and model-based approaches to better understand how an environmental stressor affects host resistance to West Nile virus (WNV). Using American robins (Turdus migratorius), a species considered a...

An insight into SARS-CoV-2 membrane protein interaction with spike, envelope, and nucleocapsid proteins

Prateek Kumar, Amit Kumar, Neha Garg & Rajanish Giri
Intraviral protein–protein interactions are crucial for replication, pathogenicity, and viral assembly. Among these, virus assembly is a critical step as it regulates the arrangements of viral structural proteins and helps in the encapsulation of genomic material. SARS-CoV-2 structural proteins play an essential role in the self-rearrangement, RNA encapsulation, and mature virus particle formation. In SARS-CoV, the membrane protein interacts with the envelope and spike protein in Endoplasmic Reticulum Golgi Intermediate Complex (ERGIC) to form an...

Data from: Brain functional networks associated with social bonding in monogamous voles

Sarael Alcauter, M. Fernanda López-Gutiérrez, Zeus Gracia-Tabuenca, Juan J Ortiz, Larry J Young, Francisco J Camacho, Raúl G Paredes, Nestor F. Diaz & Wendy Portillo
Previous studies have related pair bonding in Microtus ochrogaster, the prairie vole, with plastic changes in several brain regions. However, the interactions between these socially-relevant regions have yet to be described. In this study, we used resting state magnetic resonance imaging to explore bonding behaviors and functional connectivity of brain regions previously associated with pair bonding. Thirty-two male and female prairie voles were scanned at baseline, 24h and 2 weeks after the onset of cohabitation....

Attenuation of porcine deltacoronavirus disease severity by porcine reproductive and respiratory syndrome virus coinfection in a weaning pig model

Xinrong Zhou, Xinna Ge, Yongning Zhang, Jun Han, Xin Guo, Yanhong Chen, Lei Zhou & Hanchun Yang
Porcine deltacoronavirus (PDCoV) is a potentially emerging zoonotic pathogen that causes severe diarrhea in young pigs, with a risk of fatal dehydration. Its pathogenicity on neonatal piglet has been previously reported, however, it is less known if the coinfection with immunosuppressive pathogens can influence PDCoV disease manifestation. Here, a coinfection model of PDCoV and porcine reproductive and respiratory syndrome virus (PRRSV), a global-spread immunosuppressive virus, was set to study their interaction. Weaning pigs in the...

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Rongsui Gao, Wenhong Zu, Yang Liu, Junhua Li, Zeyao Li, Yanling Wen, Haiyan Wang, Jing Yuan, Lin Cheng, Shengyuan Zhang, Yu Zhang, Shuye Zhang, Weilong Liu, Xun Lan, Lei Liu, Feng Li & Zheng Zhang
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’...

Jamestown Canyon virus in Massachusetts: clinical case series and vector screening

Cormac M. Kinsella, Molly L. Paras, Sandra Smole, Samar Mehta, Vijay Ganesh, Lin H. Chen, Daniel P. McQuillen, Ruta Shah, Justin Chan, Matthew Osborne, Scott Hennigan, Frederic Halpern-Smith, Catherine M. Brown, Pardis Sabeti & Anne Piantadosi
Jamestown Canyon virus (JCV) is a neuroinvasive arbovirus that is found throughout North America and increasingly recognized as a public health concern. From 2004 to 2012, an average of 1.7 confirmed cases were reported annually in the United States, whereas from 2013 to 2018 this figure increased over seventeen-fold to 29.2 cases per year. The rising number of reported human infections highlights the need for better understanding of the clinical manifestations and epidemiology of JCV....

Registration Year

  • 2021
    27

Resource Types

  • Dataset
    27

Affiliations

  • Emory University
    27
  • Fudan University
    6
  • Central South University
    5
  • Sichuan University
    5
  • Capital Medical University
    5
  • North West Agriculture and Forestry University
    4
  • Sun Yat-sen University
    4
  • West China Second University Hospital of Sichuan University
    4
  • Jilin University
    4
  • Affiliated Hospital of Xuzhou Medical College
    4