Article
Genetics & Heredity
Ulykbek Kairov, Askhat Molkenov, Aigul Sharip, Saule Rakhimova, Madina Seidualy, Arang Rhie, Ulan Kozhamkulov, Maxat Zhabagin, Jong-Il Kim, Joseph H. Lee, Joseph D. Terwilliger, Jeong-Sun Seo, Zhaxybay Zhumadilov, Ainur Akilzhanova
Summary: Kazakhstan, located along the Great Silk Road, has a rich history and a multiethnic population. By sequencing and analyzing the genomes of five ethnic Kazakhs, this study identified genetic variants associated with higher risks of diseases and demonstrated the importance of genotype-phenotype relations at the population level.
FRONTIERS IN GENETICS
(2022)
Article
Microbiology
Libo Li, Tiantian Liu, Qingchuan Wang, Yi Ding, Yajuan Jiang, Zengding Wu, Xiaoyu Wang, Huixin Dou, Yongjian Jia, Boyan Jiao
Summary: The B/Victoria influenza virus strain was the dominant virus in Jining from 2021 to 2022, with antigenic drift observed due to amino acid variations in the antigenic epitopes. Whole-genome sequencing revealed lower similarity in certain gene segments compared to the Northern Hemisphere vaccine strain, B/Washington/02/2019.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Chujie Chen, Bo Zhu, Xiangwei Tang, Bin Chen, Mei Liu, Ning Gao, Sheng Li, Jingjing Gu
Summary: By analyzing the patterns of genome-wide ROH, we found that both ancient and recent inbreeding events had varying degrees of impact on different horse breeds. However, recent inbreeding events were rare, especially among indigenous horse breeds. Therefore, the ROH-based genomic inbreeding coefficient can help monitor the level of inbreeding. Through our study on the Thoroughbred population, we identified 24 ROH islands containing 72 candidate genes associated with artificial selection traits. Our findings provide insight into horse breed characteristics and future breeding strategies.
Article
Microbiology
Yee Mey Seah, Mary K. K. Stewart, Daniel Hoogestraat, Molly Ryder, Brad T. T. Cookson, Stephen J. J. Salipante, Noah G. G. Hoffman
Summary: The identification and analysis of clinically relevant bacteria strains increasingly rely on whole-genome sequencing. However, the accuracy of variant callers for short-read sequences has seldom been validated against haploid genomes. In this study, a computational workflow was developed to introduce mutations into bacterial reference genomes and generate synthetic sequencing reads. The method was applied to three different bacterial strains, and several variant callers were evaluated using the synthetic reads as a truth set. The results showed that variant callers with high-quality soft-clipped reads and base mismatches had the highest precision and recall for identifying insertions and deletions.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Virology
Silvia Turco, Federica Gabbianelli, Carla N. Mavian, Daniele Pietrucci, Livia De Paolis, Rodolfo Gialletti, Luca Mechelli, Chiara Grazia De Ciucis, Katia Cappelli, Filippo Dell'Anno, Samanta Mecocci, Gian Guido Donato, Tiziana Nervo, Floriana Fruscione, Maria Ines Crescio, Alessandro Ghelardi, Giovanni Chillemi, Elisabetta Razzuoli
Summary: A novel Equus caballus papillomavirus (EcPV10) was identified during a survey on the fertility status of a mare using Next Generation Sequencing. The virus was confirmed through genome-walking PCR and Sanger sequencing. Preliminary studies suggest a lower incidence of EcPV10 compared to EcPV2 and EcPV9 in the same horse population.
Article
Biotechnology & Applied Microbiology
Francesca Jean, Susan Stasiuk, Tatiana Maroilley, Catherine Diao, Andrew Galbraith, Maja Tarailo-Graovac
Summary: This study demonstrates the high-throughput identification and understanding of intragenic modifiers in a clinically relevant gene by using whole genome sequencing and CRISPR/Cas9, showing that these variants are non-randomly distributed throughout the gene and that genomic context plays a crucial role in phenotypic outcomes.
Article
Genetics & Heredity
Andre E. Minoche, Ben Lundie, Greg B. Peters, Thomas Ohnesorg, Mark Pinese, David M. Thomas, Andreas Zankl, Tony Roscioli, Nicole Schonrock, Sarah Kummerfeld, Leslie Burnett, Marcel E. Dinger, Mark J. Cowley
Summary: ClinSV is a WGS-based framework for integration, annotation, prioritization, and visualization of structural variants with low false positive rates and high reproducibility. In clinical practice, ClinSV identified reportable variants that were undetectable by current clinical microarray designs in a significant percentage of cases.
Article
Genetics & Heredity
Tim H. Heupink, Lennert Verboven, Robin M. Warren, Annelies Van Rie
Summary: Improving the understanding and detection of genomic variants in Mycobacterium tuberculosis is crucial for controlling tuberculosis. The XBS bioinformatics pipeline has shown superior accuracy in identifying variants in complex genomic regions and samples with low coverage and high contamination levels, making it a valuable tool for future clinical applications and genetic studies related to drug resistance and transmission analysis.
MICROBIAL GENOMICS
(2021)
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Article
Biotechnology & Applied Microbiology
Yuanhao Li, Bo Jiang, Weijun Dai
Summary: Essential genes are crucial for bacterial viability and new drug discovery, but some false positives generated by Tn-seq may result from gene deletions by bacteria themselves. Deleting genes should be considered when evaluating essentiality, as it has been underestimated in previous studies.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Yumi Enomoto, Takayuki Yokoi, Yoshinori Tsurusaki, Hiroaki Murakami, Makiko Tominaga, Mari Minatogawa, Chihiro Abe-Hatano, Yukiko Kuroda, Ikuko Ohashi, Kazumi Ida, Shizuka Shiiya, Tatsuro Kumaki, Takuya Naruto, Jun Mitsui, Noriaki Harada, Yasuhiro Kido, Kenji Kurosawa
Summary: This study conducted comprehensive genetic analysis targeting CREBBP and EP300 genes to elucidate the underlying genetic and genomic architecture related to the RSTS phenotype. They identified various complex causative variants and utilized multiple analysis methods for their identification. Additionally, they discovered rare clinical findings, expanding our understanding of RSTS.
Article
Genetics & Heredity
Xiufang Zhi, Qi Ai, Wenchao Sheng, Yuping Yu, Jianbo Shu, Changshun Yu, Xiaoli Yu, Dong Li, Chunquan Cai
Summary: This study investigated the clinical characteristics and molecular basis of a patient with Menkes disease. The patient exhibited symptoms such as intermittent convulsions and psychomotor retardation, and a novel deep intronic variant in the ATP7A gene was identified through whole genome sequencing. Additionally, RNA sequencing confirmed the functional effect of this variant.
FRONTIERS IN GENETICS
(2022)
Article
Medicine, General & Internal
Yu Zheng, Baosheng Zhu, Jichun Tan, Yichun Guan, Cynthia C. Morton, Guangxiu Lu
Summary: This study investigated the laboratory practice, service quality, and case volumes of low-pass whole-genome sequencing (low-pass WGS) for copy number variant (CNV) analysis in Chinese tertiary hospitals. The results showed a high demand for this service in China, but there are challenges in establishing standard criteria and data reporting formats for quality control.
Article
Public, Environmental & Occupational Health
Maryam Dadar, Hanka Brangsch, Saeed Alamian, Heinrich Neubauer, Gamal Wareth
Summary: Brucellosis is a common zoonotic disease in the Middle East, causing economic losses to the livestock industry and posing a great public health concern. This study analyzed the genetic diversity and distribution of Brucella spp. in Iran using whole genome sequencing technology. The results revealed a close relationship between Iranian strains and strains from neighboring and Middle East countries, emphasizing the importance of brucellosis control measures in Iran.
Article
Immunology
Julia Hoeglund, Fatemeh Hadizadeh, Weronica E. Ek, Torgny Karlsson, Asa Johansson
Summary: This study analyzed 200,000 whole-exome sequences from the UK Biobank cohort and identified 220 genes in 55 genomic regions that are associated with eosinophil count. Among these genes, seven are driven by rare variants and two are considered novel eosinophil loci. These findings provide valuable knowledge about the effect of rare variants on eosinophil count and can aid in the identification of therapeutic targets.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Veterinary Sciences
P. Flores-Ahlschwede, S. K. Kahn, S. Ahlschwede, A. I. Bordin, N. D. Cohen
Summary: This study aimed to compare the effectiveness of transfusing 2 L and 1 L of REHIP to foals in reducing the incidence of pneumonia attributed to Rhodococcus equi. The results suggest that transfusing 2 L of REHIP may be more effective in reducing the risk of pneumonia, but the study is limited by its observational design and presumptive diagnosis methods.
EQUINE VETERINARY EDUCATION
(2022)
Article
Veterinary Sciences
Aja B. Harvey, Angela I. Bordin, Joana N. Rocha, Jocelyn M. Bray, Noah D. Cohen
Summary: The study found that opsonizing Rhodococcus equi with either equine hyperimmune plasma (HIP) or normal plasma (NP) can increase phagocytosis by alveolar macrophages and decrease the intracellular survival of the organisms. However, opsonizing Rhodococcus equi did not appear to have an enhanced effect when using HIP over NP. Other mechanisms aside from effects on alveolar macrophages may explain the clinical benefits of using HIP to decrease the incidence of Rhodococcus equi pneumonia in foals.
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2021)
Article
Veterinary Sciences
Canaan M. Whitfield-Cargile, Michelle C. Coleman, Noah D. Cohen, Ana M. Chamoun-Emanuelli, Cristobal Navas DeSolis, Taylor Tetrault, Ryan Sowinski, Amanda Bradbery, Mattea Much
Summary: The study found that phenylbutazone may cause gastrointestinal injury in horses, including impaired barrier function and gastric ulcers. Additionally, nutritional treatment could alleviate these changes.
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Chandni Praveen, Sohini S. Bhatia, Robert C. Alaniz, Robert E. Droleskey, Noah D. Cohen, Palmy R. Jesudhasan, Suresh D. Pillai
Summary: This study explores the effectiveness of electron beam-inactivated immune modulators by assessing their impact on dendritic cells and mice models. The results show that EBST has the potential as vaccine candidates, offering both the safety of a killed vaccine and the immunogenicity of an attenuated vaccine. The ability to store EBST at different temperatures without loss of potency makes it a promising new vaccine production technology.
Article
Multidisciplinary Sciences
Ellen Ruth A. Morris, Ashley G. Boyle, Miia Riihimaeki, Anna Aspan, Eman Anis, Andrew E. Hillhouse, Ivan Ivanov, Angela I. Bordin, John Pringle, Noah D. Cohen
Summary: Research using next-generation sequencing technologies found no significant or consistent differences in the genome, methylome, and transcriptome of isolates of the bacterium Streptococcus equi subsp. equi (SEE) from horses with acute clinical strangles and inapparent carrier horses. This suggests that adaptations of SEE to the host are unlikely to explain the carrier state of the pathogen. Instead, efforts to understand the carrier state of SEE should focus on host factors.
Review
Veterinary Sciences
Angela Bordin, Laura Huber, Macarena G. Sanz, Noah D. Cohen
Summary: This narrative review summarizes recent developments in the epidemiology, immune responses, treatment, and prevention of rhodococcal pneumonia in foals. Screening tests have been used for early detection and treatment, macrolide antimicrobials in combination with rifampin are recommended for treatment, and passive immunisation is the only available method to reduce incidence.
EQUINE VETERINARY JOURNAL
(2022)
Article
Microbiology
Ellen Ruth A. Morris, Jing Wu, Angela Bordin, Sara D. Lawhon, Noah D. Cohen
Summary: This study characterized the genomic and methylomic differences of multiple SEE and SEZ isolates from Texas. The results showed that genetic mobile elements in SEE and differential methylation of shared genes between SEE and SEZ might contribute to the host specificity of SEE.
MICROBIOLOGY SPECTRUM
(2022)
Article
Veterinary Sciences
Noah D. Cohen, Susanne K. Kahn, Angela Bordin, Giana M. Gonzales, Bibiana Petri da Silveira, Jocelyne M. Bray, Rebecca M. Legere, Sophia C. Ramirez-Cortez
Summary: The fecal concentration of virulent Rhodococcus equi before infection is positively associated with protection against pneumonia in foals.
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2022)
Article
Veterinary Sciences
Noah D. Cohen, Patricia Flores-Ahlschewde, Giana M. Gonzales, Susanne K. Kahn, Bibiana Petri da Silveira, Jocelyne M. Bray, Emily E. King, Caroline C. Blair, Angela Bordin
Summary: This study evaluated the accuracy of qPCR using rectal swab samples to differentiate foals with pneumonia from healthy foals of similar age in the same environment. The results showed that although the concentration of virulent R.equi in feces is significantly higher in pneumonic foals, the qPCR method lacks sufficient diagnostic accuracy for clinical use.
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2022)
Review
Veterinary Sciences
Susanne K. Kahn, Noah D. Cohen, Angela Bordin, Michelle C. Coleman, James C. Heird, Thomas H. Welsh
Summary: Rhodococcus equi bacterium causes prevalent pneumonia in foals worldwide. Transfusion of hyperimmune plasma from donor horses is widely used to reduce the incidence of pneumonia, but the effectiveness and risks are still uncertain.
EQUINE VETERINARY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Ze-Tian Fang, Rajan Kapoor, Aniruddha Datta, Shuyu Liu, Matthew A. Stull, Paige G. Seitz, Charles D. Johnson, Sakiko Okumoto
Summary: The end-use quality of wheat flour is closely related to the amount and composition of storage proteins in the endosperm. TAM 111 and TAM 112 are two popular cultivars with significantly different protein content. Transcriptome data analysis revealed differences in starch metabolism and amino acid metabolism pathways between the two cultivars, as well as variations in the potential transcription factors regulating these pathways. These findings provide valuable insights for breeders and enhance our understanding of grain development mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Green & Sustainable Science & Technology
Jessica Gilreath, Tryon Wickersham, Jason Sawyer
Summary: This study compared estimates of historical enteric methane emissions by US beef cattle using different methodologies and converted the results to carbon dioxide equivalence. The study found that the differences between methods increased over time and there were significant differences in annual and cumulative emissions metrics.
Article
Veterinary Sciences
Leslie Easterwood, Noah D. Cohen
Summary: Evaluating horse body temperature is crucial for monitoring their health and biosecurity. Although rectal thermometry is commonly used, it has safety concerns. This study compared a non-contact infrared thermometer and a rectal digital thermometer, and found that while the non-contact infrared thermometer showed good reliability, it had a large and inconsistent negative bias compared to the rectal thermometer in healthy horses. Therefore, these devices are not suitable substitutes for rectal thermometry in obtaining accurate core body temperature estimates in horses.
JOURNAL OF EQUINE VETERINARY SCIENCE
(2023)
Article
Veterinary Sciences
Kari E. E. Bevevino, Noah D. D. Cohen, Sonya G. G. Gordon, Cristobal Navas de Solis
Summary: A POCUS protocol for cardiorespiratory assessment in horses was successfully conducted using a pocket-sized ultrasound device, which was proven to be effective and capable of detecting abnormalities in different groups of horses. Further evaluation of the diagnostic accuracy and utility of the CRASH protocol is warranted.
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2023)
Article
Veterinary Sciences
Bo A. Brock, Hunter R. Greer, Clifford M. Honnas, Brad E. Gilleland, Myra F. Barrett, James N. Moore, Noah Cohen
Summary: The study of "Core Osteostixis Combined with Navicular Bursoscopy Improves Lameness in Horses with Osseous Cyst-Like Lesions: A Case Series" suggests that core osteostixis combined with navicular bursoscopy can improve lameness in horses with osseous cyst-like lesions.
VETERINARY MEDICINE-RESEARCH AND REPORTS
(2023)