The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce tree inference accuracy. It was previously proposed that filtering unreliable alignment regions can increase the accuracy of tree inference. However, it was also demonstrated that the benefit of this...
Background and objectives: The rate of evolution of drug resistance depends on the fitness of resistant pathogens. The fitness of resistant pathogens is reduced by competition with sensitive pathogens in untreated hosts and so enhanced by competitive release in drug-treated hosts. We set out to estimate the magnitude of those effects on a variety of fitness measures, hypothesizing that competitive suppression and competitive release would have larger impacts when resistance was rarer to begin with....
Data from: Cough frequency during treatment associated with baseline cavitary volume and proximity to the airway in pulmonary TBAlvaro Proaño, David P. Bui, José W. López, Nancy M. Vu, Marjory A. Bravard, Gwenyth O. Lee, Brian H. Tracey, Ziyue Xu, Germán Comina, Eduardo Ticona, Daniel J. Mollura, Jon S. Friedland, David A. J. Moore, Carlton A. Evans, Philip Caligiuri, Robert H. Gilman & Tuberculosis Working Group In Peru
Background: Cough frequency, and its duration, is a lab-free biomarker that can be used in low-resource settings and has been associated with transmission and treatment response. Radiological characteristics associated with increased cough frequency may be important in understanding transmission. The relationship between cough frequency and cavitary lung disease has never been studied. Methods: We analyzed 41 human immunodeficiency virus-negative adults with culture-confirmed, drug-susceptible pulmonary tuberculosis throughout treatment. Cough recordings were based on the Cayetano Cough...
Data from: Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosaLin Li, Xiaodong Jiao, Ilaria D’Atri, Fumihito Ono, Ralph Nelson, Chi-Chao Chan, Naoki Nakaya, Zhiwei Ma, Yan Ma, Xiaoying Cai, Longhua Zhang, Siying Lin, Abdul Hameed, Barry A. Chioza, Holly Hardy, Gavin Arno, Sarah Hull, Muhammad Imran Khan, James Fasham, V. Gaurav Harlalka, Michel Michaelides, Anthony T. Moore, Zeynep Hande Coban Akdemir, Shalini Jhangiani, James R. Lupski … & Frans P. M. Cremers
We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post...
Data from: The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific mannerCandida Bhagwandin, Erin L. Ashbeck, Michael Whalen, Joanna Bandola-Simon, Paul A. Roche, Adam Szajman, Sarah Mai Truong, Betsy C. Wertheim, Yann C. Klimentidis, Satoshi Ishido, Benjamin J. Renquist & Lonnie Lybarger
Type 2 diabetes is typified by insulin-resistance in adipose tissue, skeletal muscle, and liver, leading to chronic hyperglycemia. Additionally, obesity and type 2 diabetes are characterized by chronic low-grade inflammation. Membrane-associated RING-CH-1 (MARCH1) is an E3 ubiquitin ligase best known for suppression of antigen presentation by dendritic and B cells. MARCH1 was recently found to negatively regulate the cell surface levels of the insulin receptor via ubiquitination. This, in turn, impaired insulin sensitivity in mouse...
Data from: Dietary challenges differentially affect activity and sleep/wake behavior in mus musculus: isolating independent associations with diet/energy balance and body weightIsaac J. Perron, Brendan T. Keenan, Karthikeyani Chellappa, Nicholas F. Lahens, Nicole Y. Yohn, Keith R. Shockley, Allan I. Pack & Sigrid C. Veasey
Background and Aims: Associated with numerous metabolic and behavioral abnormalities, obesity is classified by metrics reliant on body weight (such as body mass index). However, overnutrition is the common cause of obesity, and may independently contribute to these obesity-related abnormalities. Here, we use dietary challenges to parse apart the relative influence of diet and/or energy balance from body weight on various metabolic and behavioral outcomes. Materials and Methods: Seventy male mice (mus musculus) were subjected...
Data from: Emergence and evolution of novel reassortant influenza A viruses in canines in southern ChinaYing Chen, Nídia S. Trovão, Guojun Wang, Weifeng Zhao, Ping He, Huabo Zhou, Yanning Mo, Zuzhang Wei, Kang Ouyang, Weijiang Huang, Adolfo García-Sastre, Martha I. Nelson & Weijian Huang
The capacity of influenza A viruses (IAVs) to host jump from animal reservoir species to humans presents an ongoing pandemic threat. Birds and swine are considered major reservoirs of viral genetic diversity, whereas equines and canines have historically been restricted to one or two stable IAV lineages with no transmission to humans. Here, by sequencing the complete genomes of 16 IAVs obtained from canines in southern China (Guangxi Zhuang Autonomous Region [Guangxi]) in 2013 to...
Urbanization is driving environmental change on a global scale, creating novel environments for wildlife to colonize. Through a combination of stochastic and selective processes, urbanization is also driving evolutionary change. For instance, difficulty traversing human-modified landscapes may isolate newly established populations from rural sources, while novel selective pressures, such as altered disease risk, toxicant exposure, and light pollution, may further diverge populations through local adaptation. Assessing the evolutionary consequences of urban colonization and the processes...
National Institutes of Health8
University of Arizona2
National University of San Marcos1
University of Pennsylvania1
National Institute of Environmental Health Sciences1
COMSATS Institute of Information Technology1
University of the Punjab1
University of California, San Diego1
Radboud University Nijmegen1