Origin and Evolution of European Community-Acquired Methicillin-Resistant <named-content content-type="genus-species">Staphylococcus aureus</named-content> by Marc Stegger, Thierry Wirth, Paal S. Andersen, Robert L. Skov, Anna De Grassi, Patricia Martins Simões, Anne Tristan, Andreas Petersen, Maliha Aziz, Kristoffer Kiil, Ivana Cirković, Edet E. Udo, Rosa del Campo, Jaana Vuopio-Varkila, Norazah Ahmad, Sima Tokajian, Georg Peters, Frieder Schaumburg, Barbro Olsson-Liljequist, Michael Givskov, Elizabeth E. Driebe, Henrik E. Vigh, Adebayo Shittu, Nadjia Ramdani-Bougessa, Jean-Philippe Rasigade, Lance B. Price, Francois Vandenesch, Anders R. Larsen, Frederic Laurent

“…Moreover, the tree topology suggests a single acquisition of both the SCCmec element and a plasmid encoding the fusidic acid resistance determinant. Four canonical SNPs distinguish the derived CA-MRSA lineage and include a nonsynonymous mutation in accessory gene regulator C (agrC). …”
Get full text

Identification of ultra-rare disruptive variants in voltage-gated calcium channel-encoding genes in Japanese samples of schizophrenia and autism spectrum disorder by Chenyao Wang, Shin-ichiro Horigane, Minoru Wakamori, Shuhei Ueda, Takeshi Kawabata, Hajime Fujii, Itaru Kushima, Hiroki Kimura, Kanako Ishizuka, Yukako Nakamura, Yoshimi Iwayama, Masashi Ikeda, Nakao Iwata, Takashi Okada, Branko Aleksic, Daisuke Mori, Takashi Yoshida, Haruhiko Bito, Takeo Yoshikawa, Sayaka Takemoto-Kimura, Norio Ozaki

“…Variant filtering was applied to identify biologically relevant mutations that were not registered in the dbSNP database or that have a minor allele frequency of less than 1% in East-Asian samples from databases; and are potentially disruptive, including nonsense, frameshift, canonical splicing site single nucleotide variants (SNVs), and non-synonymous SNVs predicted as damaging by five different in silico analyses. …”
Get full text

Exome Sequencing Reveals a Putative Role for HLA-C*03:02 in Control of HIV-1 in African Pediatric Populations by Samuel Kyobe, Savannah Mwesigwa, Savannah Mwesigwa, Grace P. Kisitu, John Farirai, Eric Katagirya, Angella N. Mirembe, Lesego Ketumile, Misaki Wayengera, Fred Ashaba Katabazi, Edgar Kigozi, Edward M. Wampande, Gaone Retshabile, Busisiwe C. Mlotshwa, Lesedi Williams, Koketso Morapedi, Ishmael Kasvosve, Jacqueline Kyosiimire-Lugemwa, Betty Nsangi, Masego Tsimako-Johnstone, Chester W. Brown, Moses Joloba, Gabriel Anabwani, Lukhele Bhekumusa, Sununguko W. Mpoloka, Graeme Mardon, Graeme Mardon, Mogomotsi Matshaba, Mogomotsi Matshaba, Adeodata Kekitiinwa, Adeodata Kekitiinwa, Neil A. Hanchard

“…In one of the largest studies of HIV in Africa, we find evidence of a protective effect of canonical HLA-B alleles and a novel HLA-C association that appears to augment existing HIV-1 control alleles in pediatric populations. …”
Get full text

Bacterial Outer Membrane Polysaccharide Export (OPX) Proteins Occupy Three Structural Classes with Selective β-Barrel Porin Requirements for Polymer Secretion by Fares Saïdi, Utkarsha Mahanta, Adyasha Panda, Ahmad A. Kezzo, Nicolas Y. Jolivet, Razieh Bitazar, Gavin John, Matthew Martinez, Abdelkader Mellouk, Charles Calmettes, Yi-Wei Chang, Gaurav Sharma, Salim T. Islam

“…In the prototypic Escherichia coli Group-1-capsule biosynthesis system, eight copies of this canonical OPX protein cross the OM with an α-helix, forming a polysaccharide-export pore. …”
Get full text

Progranulin signaling in sepsis, community-acquired bacterial pneumonia and COVID-19: a comparative, observational study by Florian Brandes, Melanie Borrmann, Dominik Buschmann, Agnes S. Meidert, Marlene Reithmair, Markus Langkamp, Lutz Pridzun, Benedikt Kirchner, Jean-Noël Billaud, Nirav M. Amin, Joseph C. Pearson, Matthias Klein, Daniela Hauer, Clarissa Gevargez Zoubalan, Anja Lindemann, Alexander Choukér, Thomas W. Felbinger, Ortrud K. Steinlein, Michael W. Pfaffl, Ines Kaufmann, Gustav Schelling

“…Methods The diagnostic performance of progranulin was operationalized by calculating AUC and ROC statistics for progranulin and established biomarkers in 241 patients with sepsis, 182 patients with SIRS, 53 patients with CAP, 22 patients with COVID-19 pneumonia and 53 healthy volunteers. miRNAs and mRNAs in blood cells from sepsis patients (n = 7) were characterized by NGS and validated by RT-qPCR in an independent cohort (n = 39) to identify canonical gene networks associated with upregulated progranulin at sepsis onset. …”
Get full text

A Germline-Targeting Chimpanzee SIV Envelope Glycoprotein Elicits a New Class of V2-Apex Directed Cross-Neutralizing Antibodies by Frederic Bibollet-Ruche, Ronnie M. Russell, Wenge Ding, Weimin Liu, Yingying Li, Kshitij Wagh, Daniel Wrapp, Rumi Habib, Ashwin N. Skelly, Ryan S. Roark, Scott Sherrill-Mix, Shuyi Wang, Juliette Rando, Emily Lindemuth, Kendra Cruickshank, Younghoon Park, Rachel Baum, John W. Carey, Andrew Jesse Connell, Hui Li, Elena E. Giorgi, Ge S. Song, Shilei Ding, Andrés Finzi, Amanda Newman, Giovanna E. Hernandez, Emily Machiele, Derek W. Cain, Katayoun Mansouri, Mark G. Lewis, David C. Montefiori, Kevin J. Wiehe, S. Munir Alam, I-Ting Teng, Peter D. Kwong, Raiees Andrabi, Laurent Verkoczy, Dennis R. Burton, Bette T. Korber, Kevin O. Saunders, Barton F. Haynes, Robert J. Edwards, George M. Shaw, Beatrice H. Hahn

“…SCIV infection of RMs elicited high-titer viremia, potent autologous tier 2 neutralizing antibodies, and rapid sequence escape in the canonical V2-apex epitope. Six of seven animals also developed low-titer heterologous plasma breadth that mapped to the V2-apex. …”
Get full text

Observations and hypotheses related to low to middle free tropospheric aerosol, water vapor and altocumulus cloud layers within convective weather regimes: a SEAC⁴RS cas... by J. S. Reid, D. J. Posselt, K. Kaku, R. A. Holz, G. Chen, E. W. Eloranta, R. E. Kuehn, S. Woods, J. Zhang, B. Anderson, T. P. Bui, G. S. Diskin, P. Minnis, P. Minnis, M. J. Newchurch, S. Tanelli, C. R. Trepte, K. L. Thornhill, L. D. Ziemba

“…Using the University of Wisconsin High Spectral Resolution Lidar system at Huntsville, Alabama, USA, and the NASA DC-8 research aircraft, we investigate the altitude dependence of aerosol, water vapor and Altocumulus (Ac) properties in the free troposphere from a canonical 12 August 2013 convective storm case as a segue to a presentation of a mission-wide analysis. …”
Get full text

SURATLANT: a 1993–2017 surface sampling in the central part of the North Atlantic subpolar gyre by G. Reverdin, N. Metzl, S. Olafsdottir, V. Racapé, T. Takahashi, M. Benetti, H. Valdimarsson, A. Benoit-Cattin, M. Danielsen, J. Fin, A. Naamar, D. Pierrot, K. Sullivan, F. Bringas, G. Goni

“…The data also revealed a canonical pH decrease of −0.0021&thinsp;yr⁻¹. …”
Get full text

Histone variant MacroH2A1 is downregulated in prostate cancer and influences malignant cell phenotype by Tânia Soraia Vieira-Silva, Sara Monteiro-Reis, Daniela Barros-Silva, João Ramalho-Carvalho, Inês Graça, Isa Carneiro, Ana Teresa Martins, Jorge Oliveira, Luis Antunes, Sarah Hurtado-Bagès, Marcus Buschbeck, Rui Henrique, Carmen Jerónimo

“…A better understanding of how those mechanisms orchestrate disease might improve diagnostic and prognostic tools, allowing for improvements in treatment efficacy. Replacement of canonical histones, an epigenetic mechanism, is highly conserved among species and altered expression of histones variants (e.g., MacroH2A1) has been associated with tumorigenesis. …”
Get full text

Whole genome sequencing identifies candidate genes for familial essential tremor and reveals biological pathways implicated in essential tremor aetiology by Lorraine N. Clark, Yizhe Gao, Gao T. Wang, Nora Hernandez, Allison Ashley-Koch, Joseph Jankovic, Ruth Ottman, Suzanne M. Leal, Sandra M. Barral Rodriguez, Elan D. Louis

“…In one ET family contributing to the linkage peak on chromosome 16p13.3, we identified a likely pathogenic heterozygous canonical splice acceptor variant in exon 2 of RBFOX1 (ENST00000547372; c.4-2A>G), that co-segregated with the ET phenotype in the family. …”
Get full text

APOE alters glucose flux through central carbon pathways in astrocytes by Holden C. Williams, Brandon C. Farmer, Margaret A. Piron, Adeline E. Walsh, Ronald C. Bruntz, Matthew S. Gentry, Ramon C. Sun, Lance A. Johnson

“…One important function of astrocytes – canonically the primary source of apolipoprotein E in the brain – is to provide metabolic substrates (lactate, lipids, amino acids and neurotransmitters) to neurons. …”
Get full text

Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinomaReseach in context by Kyle T. Siebenthall, Chris P. Miller, Jeff D. Vierstra, Julie Mathieu, Maria Tretiakova, Alex Reynolds, Richard Sandstrom, Eric Rynes, Eric Haugen, Audra Johnson, Jemma Nelson, Daniel Bates, Morgan Diegel, Douglass Dunn, Mark Frerker, Michael Buckley, Rajinder Kaul, Ying Zheng, Jonathan Himmelfarb, Hannele Ruohola-Baker, Shreeram Akilesh

“…Renal cell carcinoma (RCC) is the most common malignant kidney tumor which canonically activates the hypoxia-inducible transcription factor (HIF) pathway. …”
Get full text

Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic Mice by Pingping Yang, Pingping Yang, Lu Liu, Lizhe Sun, Lizhe Sun, Pu Fang, Nathaniel Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang

“…Significantly differentially expressed (SDE) immunological genes and transcription factor (TF) were selected for functional pathways and transcriptional signaling identification.ResultsA total of 7,928 SDE genes and 46 canonical pathways derived from it were identified. …”
Get full text

Novel anti-inflammatory effects of the IL-1 receptor in kidney myeloid cells following ischemic AKI by Yanting Chen, Xiaohan Lu, Raeann L. Whitney, Raeann L. Whitney, Yu Li, Yu Li, Matthew J. Robson, Matthew J. Robson, Randy D. Blakely, Jen-Tsan Chi, Jen-Tsan Chi, Steven D. Crowley, Steven D. Crowley, Jamie R. Privratsky, Jamie R. Privratsky

“…Introduction: Acute kidney injury (AKI) is one of the most common causes of organ failure in critically ill patients. Following AKI, the canonical pro-inflammatory cytokine interleukin-1β (IL-1β) is released predominantly from activated myeloid cells and binds to the interleukin-1 receptor R1 (IL-1R1) on leukocytes and kidney parenchymal cells. …”
Get full text

MyD88 deficiency ameliorates weight loss caused by intestinal oxidative injury in an autophagy‐dependent mechanism by Ming Qi, Simeng Liao, Jing Wang, Yuankun Deng, Andong Zha, Yirui Shao, Zhijuan Cui, Tongxing Song, Yulong Tang, Bie Tan, Yulong Yin

“…Here we identify intestinal myeloid differentiation primary response gene 88 (MyD88) as a novel target for intestinal oxidative stress using canonical oxidative stress model induced by paraquat (PQ) in vitro and in vivo. …”
Get full text

The analgesic action of larixyl acetate, a potent TRPC6 inhibitor, in rat neuropathic pain model induced by spared nerve injury by Jing Wang, Ming Zhao, Peng Jia, Fang-Fang Liu, Kun Chen, Fei-Yang Meng, Jiang-Hao Hong, Ting Zhang, Xiao-Hang Jin, Juan Shi

“…Transient receptor potential canonical 6 (TRPC6) is a mechanosensitive channel that is expressed by dorsal root ganglia and glial cells. …”
Get full text

Neurofunctional differences and similarities between persistent postural-perceptual dizziness and anxiety disorder by Maximilian Maywald, Oliver Pogarell, Susanne Levai, Marco Paolini, Nadja Tschentscher, Boris Stephan Rauchmann, Daniela Krause, Sophia Stöcklein, Stephan Goerigk, Lukas Röll, Birgit Ertl-Wagner, Boris Papazov, Daniel Keeser, Susanne Karch, Agnieszka Chrobok

“…After modelling the BOLD response with a standard canonical HRF, voxel-wise t-tests between conditions (emotional-negative vs neutral stimuli) were used to generate statistical contrast maps and identify relevant brain areas (pFDR < 0.05, cluster size >30 voxels). …”
Get full text

Therapeutic Effect of Calcimimetics on Osteoclast–Osteoblast Crosslink in Chronic Kidney Disease and Mineral Bone Disease by Kuo-Chin Hung, Jia-Feng Chang, Yung-Ho Hsu, Chih-Yu Hsieh, Mai-Szu Wu, Mei-Yi Wu, I-Jen Chiu, Ren-Si Syu, Ting-Ming Wang, Chang-Chin Wu, Lie-Yee Hung, Cai-Mei Zheng, Kuo-Cheng Lu

“…Sclerostin, an inhibitor of canonical Wnt/β-catenin signaling, was decreased from 127.3 ± 102.3 pg/mL to 57.9 ± 33.6 pg/mL. …”
Get full text

Relationships between parameters of gall-bladder motility and neuroendocrine-immune complex and metabolism in men with chronic cholecystitis and pyelonephritis by Olena M Marfiyan, Walery Zukow

“…Discovered 23 neural, metabolic and immune parameters, canonical correlation which with the parameters of gall-bladder motility is very strong. …”
Get full text

Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single-cell RNA sequencing by Phillip Cohen, Emma J. DeGrace, Oded Danziger, Roosheel S. Patel, Erika A. Barrall, Tesia Bobrowski, Thomas Kehrer, Anastija Cupic, Lisa Miorin, Adolfo García-Sastre, Brad R. Rosenberg

“…After establishing a workflow that maximizes the detection of SARS-CoV-2 subgenomic mRNAs, we explore patterns of SARS-CoV-2 gene expression across cells with variable levels of total viral RNA, assess host gene expression differences between infected and bystander cells, and identify non-canonical and lowly abundant SARS-CoV-2 RNAs. The sequencing and data processing strategies developed here can enhance studies of coronavirus RNA biology at single-cell resolution and thereby contribute to our understanding of viral pathogenesis.…”
Get full text