Article
Biochemical Research Methods
Shangru Jia, Artem Lysenko, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda
Summary: Cell-type annotation is a critical step in analyzing scRNA-seq data. Most current methods use unsupervised clustering algorithms, resulting in rough classification. To address this issue, we propose scDeepInsight, a supervised annotation method that performs manifold assignments, data integration, supervised training, outlier detection, and cell-type annotation. It can also identify active genes related to cell-types.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Agriculture, Multidisciplinary
Nam-Yeon Kim, Hyo-Jeong Lee, Hong-Sup Kim, Su-Heon Lee, Jae-Sun Moon, Rae-Dong Jeong
Summary: This study investigated the viral populations infecting a major pear cultivar in Korea and identified ASGV and ASPV as the dominant viruses in 'Singo.' The research described the virome of the cultivar and provided insights into the diversity of viral communities, offering valuable information on the genetic variability of viruses infecting pear trees.
PLANT PATHOLOGY JOURNAL
(2021)
Article
Infectious Diseases
Silvana Sosa Portugal, Marti Cortey, Montserrat Tello, Carlos Casanovas, Susana Mesonero-Escuredo, Sergio Barrabes, Pilar Pineda, Silke Wacheck, Gerard Martin-Valls, Enric Mateu
Summary: This study aimed to assess the diversity of influenza A viruses in pig farms in the Iberian Peninsula, finding that IAV is a common agent in respiratory disease outbreaks in Spanish pig farms. The genetic diversity of the virus is continuously expanding with clear changes in the predominant subtypes and lineages in relatively short periods of time.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Kai Fu, Qianhui Wu, Ning Jiang, Sijia Hu, Hongyan Ye, Yi Hu, Lei Li, Tao Li, Zhengxi Sun
Summary: This study investigated the role of small interfering RNAs (siRNAs) in the interaction between wheat and Fusarium head blight (FHB), a fungal disease that poses a threat to wheat production. The researchers sequenced siRNAs from FHB-resistant and FHB-susceptible wheat varieties and analyzed their expression patterns. They found that F. graminearum, the fungus causing FHB, suppressed the expression of siRNAs, leading to the upregulation of disease resistance genes and enhanced resistance to F. graminearum infection. This study provides new insights into the function of siRNAs in wheat-F. graminearum interaction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Pradeep Sawant, Abhijeet Kulkarni, Rajkumar Mane, Renu Patil, Mallika Lavania
Summary: This study investigated the RNA virome in RVA-infected diarrheic piglets and calves from India, and found viral genomes belonging to Astroviridae, Reoviridae, and Picornaviridae. Astroviruses were predominant in both species, with the identification of a potential porcine-human reassortant and recombinant viruses. This study provides insights into the diverse RNA virome in Indian piglets and calves for the first time.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
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)
Review
Microbiology
Amy H. Fitzpatrick, Agnieszka Rupnik, Helen O'Shea, Fiona Crispie, Sinead Keaveney, Paul Cotter
Summary: This review assesses and recommends approaches for targeted and agnostic High Throughput Sequencing of RNA viruses, highlighting the challenges and biases that method choice can impart to sequencing results. Methodology choices from RNA extraction to library preparation have a significant impact on the detection or characterization of RNA viruses.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ayesha Imtiaz
Summary: Autosomal recessive non-syndromic hearing loss (ARNSHL) is a common hereditary deafness with high genetic heterogeneity. The molecular basis of ARNSHL is still unresolved in many cases, and techniques used to identify gene mutations vary. Various methods including homozygosity mapping, linkage studies, candidate gene approach, and position-independent approaches have been used to identify the gene mutations associated with ARNSHL.
MOLECULAR GENETICS AND GENOMICS
(2022)
Article
Biology
Daniel Crespo-Piazuelo, Herve Acloque, Olga Gonzalez-Rodriguez, Mayrone Mongellaz, Marie-Jose Mercat, Marco C. A. M. Bink, Abe E. Huisman, Yuliaxis Ramayo-Caldas, Juan Pablo Sanchez, Maria Ballester
Summary: Genome-wide association studies on pigs have identified millions of significant associations between genetic polymorphisms and the expression of genes in the duodenum, liver, and muscle. These findings shed light on the regulatory variations that shape end-trait phenotypes and provide valuable insights into molecular mechanisms.
Article
Virology
Hang Yin, Zheng Dong, Xulong Wang, Shuhao Lu, Fei Xia, Annihaer Abuduwaili, Yang Bi, Yongqiang Li
Summary: Various viruses infecting marigold plants were identified, including marigold mosaic virus and marigold cryptic virus, through deep sequencing. Genetic and phylogenetic analysis revealed the relationships between these viruses and other known viruses, enriching our understanding of viral infections in marigolds.
Article
Veterinary Sciences
Aiyou Wen, Wei Zhang, Jingen Xu, Kunping Wang, Hong Hu
Summary: The study found that eccDNAs and ecDNAs are present in both Wei pig (WP) and Large White pig (LP), and they both have sizes large enough to carry one or several partial or complete genes. These findings have expanded our understanding of circular DNA in pigs and will serve as a reference for using pigs as a medical model and discovering new genetic markers for selecting high-quality breeds.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Gastroenterology & Hepatology
Liuyang Zhao, Yu Shi, Harry Cheuk-Hay Lau, Weixin Liu, Guangwen Luo, Guoping Wang, Changan Liu, Yasi Pan, Qiming Zhou, Yanqiang Ding, Joseph Jao-Yiu Sung, Jun Yu
Summary: Through ultra-deep metagenomic sequencing, we discovered 1058 novel human gut viruses, including some viral genomes longer than the largest bacteriophage found in humans. Our study also demonstrated that a biomarker panel of 14 novel viruses can differentiate patients with colorectal cancer from controls in a training cohort.
Article
Plant Sciences
Na-Kyeong Kim, Hyo-Jeong Lee, Sang-Min Kim, Rae-Dong Jeong
Summary: This study identified three different virus species infecting oats in six different geographical locations in Korea using RNA-sequencing and bioinformatics analyses. The dominant virus infecting winter oats was barley yellow dwarf virus (BYDV), while rice black-streaked dwarf virus (RBSDV) was identified in only one region. The genetic variations and phylogenetic analyses provided insights into the characteristics and origins of these viruses.
Article
Pharmacology & Pharmacy
Xinyue Hu, Zhuang Li, Mingliang Ji, Yucheng Lin, Yuzhi Chen, Jun Lu
Summary: This study systematically analyzed the immunogenicity and biological function of chondrocytes in Osteoarthritis (OA), and identified the subtypes and biomarkers involved in the development of the disease. It was found that effector chondrocytes and fibrocartilage chondrocytes play a crucial role in promoting OA, and they exhibit stronger immunogenicity compared to other chondrocytes.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tao Zhou, Shidong Zhou, Yong Chen, Jun Wang, Ruina Zhang, Huan Xiang, Zihao Xia, Mengnan An, Xiuxiang Zhao, Yuanhua Wu
Summary: This study identified major plant viruses affecting cigar and flue-cured tobacco in Sichuan through deep sequencing and molecular techniques, and developed a fast detection method for these viruses.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Environmental Sciences
Mykhailo Savin, Gabriele Bierbaum, Ricarda Maria Schmithausen, Celine Heinemann, Judith Kreyenschmidt, Silvia Schmoger, Inna Akbaba, Annemarie Kaesbohrer, Jens Andre Hammerl
Summary: Klebsiella strains isolated from poultry and pig slaughterhouses' wastewater exhibit high resistance, with poultry slaughterhouses showing the highest colistin resistance rate and carbapenem-resistant strains only detected in wastewater treatment plant samples. The diversity of resistance genes was highest in Klebsiella spp. from wastewater treatment plants, with no carbapenemase-encoding genes detected.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Jens Andre Hammerl, Andrea Barac, Anja Bienert, Aslihan Demir, Niklas Drueke, Claudia Jaeckel, Nina Matthies, Jin Woo Jun, Mikael Skurnik, Juliane Ulrich, Stefan Hertwig
Summary: This study found that Yersinia pseudotuberculosis phages with a broad host range can be easily isolated from zoo animals, especially birds.
FRONTIERS IN MICROBIOLOGY
(2022)
Editorial Material
Microbiology
Jens Andre Hammerl
Article
Chemistry, Medicinal
Silvia Wuerstle, Jana Stender, Jens Andre Hammerl, Kilian Vogele, Kathrin Rothe, Christian Willy, Joachim Jakob Bugert
Summary: This study aims to establish an efficient personalized phage delivery pipeline and provide guidelines and evaluation tools. By adjusting the components and set points of the pipeline, the efficiency of the process was successfully improved. This is of great importance for treating critically ill patients with multidrug-resistant Gram-negative bacterial infections.
Article
Biology
Tobias Lienen, Arne Schnitt, Jens Andre Hammerl, Sven Maurischat, Bernd-Alois Tenhagen
Summary: This study investigated the antimicrobial resistance potential of mammaliicocci isolates from German dairy farms. The findings showed that these isolates carry multiple antimicrobial resistance genes and exhibit resistance to various antibiotics. These mammaliicocci may play a significant role in the transmission of antimicrobial resistance genes.
Article
Biotechnology & Applied Microbiology
Katharina Juraschek, Janina Malekzadah, Burkhard Malorny, Annemarie Kaesbohrer, Stefan Schwarz, Diana Meemken, Jens Andre Hammerl
Summary: This study investigated the occurrence and genetic basis of the fluoroquinolone resistance enhancing determinant qnrB in ESBL-/non-ESBL-producing E. coli. The qnrB-carrying E. coli were found to be highly heterogenic in their multilocus sequence types (STs) and their phenotypic resistance profiles.
Article
Biotechnology & Applied Microbiology
Agnes Perrin-Guyomard, Sophie A. Granier, Jannice Schau Slettemeas, Muna Anjum, Luke Randall, Manal AbuOun, Natalie Pauly, Alexandra Irrgang, Jens Andre Hammerl, Jette Sejer Kjeldgaard, Anette Hammerum, Alessia Franco, Magdalena Skarzynska, Ewelina Kaminska, Dariusz Wasyl, Cindy Dierikx, Stefan Borjesson, Yvon Geurts, Marisa Haenni, Kees Veldman
Summary: This study evaluated the performance of a screening protocol to detect and isolate mcr-positive Escherichia coli and Salmonella spp. from animal caecal content and meat samples. The results showed that the combined method was effective in detecting and isolating E. coli or Salmonella spp. strains harboring different mcr genes, and could potentially be used as a harmonized protocol for screening mcr genes in food-producing animals and food products in Europe.
LETTERS IN APPLIED MICROBIOLOGY
(2022)
Article
Microbiology
Jens A. Hammerl, Andrea Barac, Claudia Jaeckel, Julius Fuhrmann, Ashish Gadicherla, Stefan Hertwig
Summary: Phage vB_YenS_P400 is a virulent siphovirus of Y. enterocolitica with a narrow host range and specific growth conditions, providing insight into the diversity of Yersinia phages.
Article
Infectious Diseases
Mirjam Grobbel, Jens A. Hammerl, Katja Alt, Alexandra Irrgang, Annemarie Kaesbohrer, Bernd-Alois Tenhagen
Summary: Resistance rates of Escherichia coli were compared between organic and conventional poultry in Germany. The study found that organic farming had lower resistance rates in E. coli compared to conventional farming, with broilers showing more pronounced differences.
Article
Virology
Christian Willy, Joachim J. Bugert, Annika Y. Classen, Li Deng, Anja Duechting, Justus Gross, Jens A. Hammerl, Imke H. E. Korf, Christian Kuehn, Simone Lieberknecht-Jouy, Christine Rohde, Markus Rupp, Maria J. G. T. Vehreschild, Kilian Vogele, Sarah Wienecke, Martin Witzenrath, Silvia Wuerstle, Holger Ziehr, Karin Moelling, Felix Broecker
Summary: Bacteriophage therapy shows promise in addressing global and German antibiotic resistance crises. The current situation in Germany regarding phage therapy and research is outlined. Critical shortcomings include a lack of clinical trials, regulation, and phages for clinical use. Phage therapy is being used on a limited number of patients as individual treatment trials.
Article
Microbiology
Dorothee Serian, Yury Churin, Jens Andre Hammerl, Manfred Rohde, Arne Jung, Anja Mueller, Min Yue, Corinna Kehrenberg
Summary: In this study, seven Bordetella avium phages were isolated and characterized, showing broad host range and strong bacteriolytic activity. These phages used lipopolysaccharides as host receptors and exhibited a myovirus structure. Although phenotypically thought to be lytic, these phages were found to undergo a lysogenic phase, but infection did not confer stable host superinfection immunity. These findings are important for potential phage therapy against avian bordetellosis.
MICROBIOLOGY SPECTRUM
(2023)
Article
Virology
Julia Anabell Braeuer, Jens Andre Hammerl, Sabrin El-Mustapha, Julius Fuhrmann, Andrea Barac, Stefan Hertwig
Summary: Telomere phages are a small group of temperate phages that replicate as linear plasmids and have a specific host specificity. Their unique characteristics make them important in research.
Article
Microbiology
Ulrike Binsker, Kathrin Oelgeschlaeger, Bernd Neumann, Guido Werner, Annemarie Kaesbohrer, Jens A. Hammerl
Summary: The mcr-1.26 gene, carried by E. coli isolated from poultry samples in Germany, was found to be mainly transmitted through plasmids. The genetic sequences of the plasmids in poultry and human isolates were highly similar, suggesting that poultry husbandry is the primary source of mcr-1.26.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Quantao Zhang, Thomas Alter, Eckhard Strauch, Jens Andre Hammerl, Keike Schwartz, Maria Borowiak, Carlus Deneke, Susanne Fleischmann
Summary: This study characterized the virulence potential of NOVC strains isolated from retail seafood at both genotypic and phenotypic levels. The results showed differences in the virulence potential among the analyzed strains, which may have implications for future seafood monitoring and risk assessment.
Review
Microbiology
Ulrike Binsker, Annemarie Kaesbohrer, Jens A. Hammerl
Summary: The global rise of MDR and XDR Enterobacterales in human medicine has led to the reintroduction of colistin as a last-resort drug. However, the use of colistin in veterinary medicine has resulted in a steadily increasing prevalence of resistant isolates in livestock and meat-based food. The transmission of resistant isolates from animals to humans, acquiring resistance through food, and exposure to colistin in clinical settings have contributed to the increased prevalence of colistin-resistant Enterobacterales in humans. This study focuses on the understanding of chromosomal-mediated resistance mechanisms in Enterobacterales, providing an overview of the genes involved in colistin resistance and the global situation of colistin-resistant Enterobacterales.
FEMS MICROBIOLOGY REVIEWS
(2022)