Article
Oncology
Muthiah Bose, Jan Benada, Jayashree Vijay Thatte, Savvas Kinalis, Bent Ejlertsen, Finn Cilius Nielsen, Claus Storgaard Sorensen, Maria Rossing
Summary: The study established a dynamic database of curated breast cancer genes, identifying chromosomes 17 and 19 with the highest density of breast cancer loci. Functional enrichment analysis revealed steroid metabolism and DNA repair pathways as predominant among breast cancer genes.
BREAST CANCER RESEARCH AND TREATMENT
(2022)
Article
Biochemistry & Molecular Biology
Claudio Lo Giudic, Federico Zambelli, Matteo Chiara, Giulio Pavesi, Marco Antonio Tangaro, Ernesto Picardi, Graziano Pesole
Summary: UTRdb 2.0 is a database containing a extensive collection of eukaryotic 5' and 3' UTR sequences, enriched with functional annotations. It provides a flexible web interface for selecting and retrieving specific subsets of UTRs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ying-Ying Zhang, Wen-Ya Zhang, Xiao-Hong Xin, Pu-Feng Du
Summary: Long non-coding RNAs (lncRNAs) have important roles in biological processes, with some being essential for cell survival or reproduction. Existing databases lack comprehensive records of essential non-coding genes, particularly essential lncRNAs. The creation of the dbEssLnc database fills this gap by providing a user-friendly platform for browsing, searching, visualizing, and blast searching essential lncRNA records.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Justin Wagner, Nathan D. Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Arkarachai Fungtammasan, Yih-Chii Hwang, Richa Gupta, Aaron M. Wenger, William J. Rowell, Ziad M. Khan, Jesse Farek, Yiming Zhu, Aishwarya Pisupati, Medhat Mahmoud, Chunlin Xiao, Byunggil Yoo, Sayed Mohammad Ebrahim Sahraeian, Danny E. Miller, David Jaspez, Jose M. Lorenzo-Salazar, Adrian Munoz-Barrera, Luis A. Rubio-Rodriguez, Carlos Flores, Giuseppe Narzisi, Uday Shanker Evani, Wayne E. Clarke, Joyce Lee, Christopher E. Mason, Stephen E. Lincoln, Karen H. Miga, Mark T. W. Ebbert, Alaina Shumate, Heng Li, Chen-Shan Chin, Justin M. Zook, Fritz J. Sedlazeck
Summary: The repetitive and complex nature of medically relevant genes poses challenges for accurate analysis, but a haplotype-resolved whole-genome assembly can help overcome these challenges. By characterizing 273 challenging genes, a curated benchmark set is obtained, which reports a large number of gene variations and can improve the accuracy of variant detection.
NATURE BIOTECHNOLOGY
(2022)
Article
Chemistry, Physical
Benjamin S. Lazarus, Rachel K. Luu, Samuel Ruiz-Perez, Josiane D. V. Barbosa, Iwona Jasiuk, Marc A. Meyers
Summary: Periodic microcomputed tomography scans are used to observe the temporal behavior of the hoof's meso and microstructures during compression, fracture, and relaxation. The study reveals the structural anisotropy of the hoof wall and the behavior of the hollow tubules in different scenarios. Several fracture phenomena, including tubule interfaces, tubule bridging, tubule arresting, and fiber bridging, are elucidated. Relaxation tests demonstrate the recovery of tubule cavities after compression.
Article
Engineering, Environmental
Shaojing Wang, Yuan Yun, Xuefeng Tian, Zhaoying Su, Zitong Liao, Guoqiang Li, Ting Ma
Summary: The investigation of hydrocarbon degradation potential of environmental microorganisms is crucial for understanding global carbon cycle and remediating oil pollution. To facilitate the process, a professional gene database called HMDB was developed, which includes 38 genes encoding 11 monooxygenases responsible for the hydroxylation of 8 hydrocarbons. Validations showed high sensitivity and low false positive rate for HMDB.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Cell Biology
Xiaohua Jiang, Daren Zhao, Asim Ali, Bo Xu, Wei Liu, Jie Wen, Huan Zhang, Qinghua Shi, Yuanwei Zhang
Summary: MeiosisOnline is a comprehensive database containing known functional genes and potential candidates, providing a wealth of information and classification related to meiosis. 165 mouse genes were predicted as potential candidates for meiosis. The database's search tools and user-friendly interface greatly assist researchers in studying meiosis efficiently and easily.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Genetics & Heredity
Elena V. Ignatieva, Alexander V. Osadchuk, Maxim A. Kleshchev, Anton G. Bogomolov, Ludmila V. Osadchuk
Summary: Genetic causes of global decline in male fertility are a hot topic in reproductive genetics research, with factors including genetics and diseases. Lower semen quality is often associated with subfertility or infertility and can be caused by various diseases, genetic factors, and other factors.
FRONTIERS IN GENETICS
(2021)
Article
Biology
Jorge Rojas-Vargas, Hugo G. Castelan-Sanchez, Liliana Pardo-Lopez
Summary: Researchers have presented a curated database, HADEG, of hydrocarbon aerobic degradation enzymes and genes. This database, based on experimental evidence, includes proteins and genes involved in the degradation of alkanes, alkenes, aromatics, and plastics, as well as biosurfactant production in bacteria and fungi.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2023)
Article
Engineering, Biomedical
Cheng-Shen (Andrew) Shiang, Christian Bonney, Benjamin Lazarus, Marc Meyers, Iwona Jasiuk
Summary: This study predicted the effective elastic moduli of substructures within an equine hoof wall, revealing a decrease in elastic modulus with increasing scale due to the hierarchical structure of the hoof wall.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
Summary: MyGeneset.info provides an API for integrated annotations for gene sets, allowing users to import gene sets from commonly-used resources and create their own sets. It offers a means for managing and utilizing gene sets in a more FAIR manner.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Physics, Multidisciplinary
Zhu Wang, Xu-Tao Zeng, Yuanchuan Biao, Zhongbo Yan, Rui Yu
Summary: This study reports the experimental realization of a long-sought-after Hopf insulator in a 3D circuit system, which confirms the bulk-boundary correspondence of the Hopf insulator.
PHYSICAL REVIEW LETTERS
(2023)
Article
Mathematical & Computational Biology
Asma Sindhoo, Saima Sipy, Abbas Khan, Gurudeeban Selvaraj, Abdulrahman Alshammari, Mark Earl Casida, Dong-Qing Wei
Summary: This study developed a dynamic database called ESOMIR, which provides comprehensive information on the relationship between esophageal cancer and miRNA. The database allows users to easily access relevant information by searching for miRNA, target genes, sequences, chromosomal positions, and associated signaling pathways. It also provides information on network interactions, signaling pathways, and region information of chromosomes, among others.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Multidisciplinary Sciences
Luis Pedro Coelho, Renato Alves, Alvaro Rodriguez del Rio, Pernille Neve Myers, Carlos P. Cantalapiedra, Joaquin Giner-Lamia, Thomas Sebastian Schmidt, Daniel R. Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia K. Forslund, Supriya Khedkar, Oleksandr M. Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjorn Nielsen, Jaime Huerta-Cepas, Peer Bork
Summary: The majority of microbial genes are specific to a single habitat, with a small fraction found in multiple habitats enriched in antibiotic-resistance genes and markers for mobile genetic elements. A small fraction of protein families contain the majority of genes, with most genetic variability observed within the families being neutral or nearly neutral.
Article
Agriculture, Dairy & Animal Science
Xinwei Xiong, Yousheng Rao, Jinge Ma, Zhangfeng Wang, Qin He, Jishang Gong, Wentao Sheng, Jiguo Xu, Xuenong Zhu, Yuwen Tan, Yanbei Yang
Summary: This study constructed a catalog of microbial genes and genomes in the quail gut using deep metagenomic sequencing. The results showed that the gut microbiome composition and function differed between the two quail breeds. These findings provide an important resource for further research on the quail gut microbiome.
Article
Agriculture, Dairy & Animal Science
Tosso Leeb, Danika Bannasch, Jeffrey J. Schoenebeck
Summary: Advances in DNA sequencing and other technologies have made it easier to identify genetic risk factors for inherited diseases in dogs. Researchers have reviewed recent technological developments in canine disease genetics and suggest that identifying disease-causing variants in dogs with monogenic diseases may become a widely used diagnostic approach in veterinary medicine. The study also discusses the challenges posed by diseases with complex modes of inheritance and provides insights on interpreting sequence variants based on developments in human clinical genetics.
ANNUAL REVIEW OF ANIMAL BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Eric W. Sayers, Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Catherine M. Farrell, Michael Feldgarden, Anna M. Fine, Kathryn Funk, Eneida Hatcher, Sivakumar Kannan, Christopher Kelly, Sunghwan Kim, William Klimke, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Adriana Malheiro, Aron Marchler-Bauer, Terence D. Murphy, Lon Phan, Shashikant Pujar, Sanjida H. Rangwala, Valerie A. Schneider, Tony Tse, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry
Summary: The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. NCBI offers search and retrieval operations through 35 distinct databases, most of which are accessed through the E-utilities programming interface. Recent additions to the resources include the Comparative Genome Resource (CGR) and the BLAST ClusteredNR database. Significant updates have been made to resources such as PubMed, PMC, Bookshelf, IgBLAST, GDV, and RefSeq in the past year.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Agriculture, Dairy & Animal Science
Sarah Kiener, Susanne Ahman, Vidhya Jagannathan, Sara Soto, Tosso Leeb
Article
Agriculture, Dairy & Animal Science
Matthias Christen, Odette Ludwig-Peisker, Vidhya Jagannathan, Udo Hetzel, Ulrike Schoenball, Tosso Leeb
Summary: This study reports a case of primary ciliary dyskinesia in an Australian Shepherd dog, characterized by impaired movement of respiratory cilia. Whole genome sequencing and RT-PCR analysis revealed a mutation in the STK36 gene as the most likely candidate variant for the disease. These findings have important implications for understanding the pathogenesis of the disease and breeding strategies.
Article
Agriculture, Dairy & Animal Science
Sarah Kiener, Ching Yang, Naomi Rich, Vidhya Jagannathan, Elizabeth A. A. Mauldin, Tosso Leeb
Summary: Darier disease is a skin disorder caused by genetic variants in the ATP2A2 gene, leading to calcium signaling defects and characteristic skin lesions. A study identified a heterozygous missense variant in the ATP2A2 gene in a Shih Tzu dog with erythematous papules and ear nodules. These findings confirm the diagnosis of canine Darier disease and demonstrate the potential of genetic analysis as a diagnostic approach in veterinary medicine.
Article
Agriculture, Dairy & Animal Science
Sarah Kiener, Eloy Castilla, Vidhya Jagannathan, Monika Welle, Tosso Leeb
Summary: This study investigated a 9-month-old Chihuahua with non-epidermolytic ichthyosis. A genetic defect was identified in the SDR9C7 gene, which is involved in the production of a functional corneocyte lipid envelope. This is the first report of a spontaneous SDR9C7 variant in domestic animals.
Article
Biochemistry & Molecular Biology
Stephanie Hilton, Matthias Christen, Thomas Bilzer, Vidhya Jagannathan, Tosso Leeb, Urs Giger
Summary: This study describes a clinically mild and slowly progressive muscular dystrophy in a family of Maine Coon crossbred cats. The cats exhibit marked structural changes in their muscles, but protein modeling suggests that the identified gene variant may not have a major impact on protein function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Ricardo Di Lazzaro Filho, Guilherme Lopes Yamamoto, Tiago J. Silva, Leticia A. Rocha, Bianca D. W. Linnenkamp, Matheus Augusto Araujo Castro, Deborah Bartholdi, Andre Schaller, Tosso Leeb, Samantha Kelmann, Claudia Y. Utagawa, Carlos E. Steiner, Leandra Steinmetz, Rachel Sayuri Honjo, Chong Ae Kim, Lisa Wang, Raphael Abourjaili-Bilodeau, Philippe Campeau, Matthew Warman, Maria Rita Passos-Bueno, Nicolas C. Hoch, Debora Romeo Bertola
Summary: Rothmund-Thomson syndrome (RTS) is a rare autosomal recessive genodermatosis characterized by poikiloderma. We reported on six Brazilian probands and two siblings of Swiss/Portuguese ancestry with severe short stature, widespread poikiloderma, and congenital ocular anomalies. Genomic and functional analysis revealed compound heterozygosity for a deep intronic splicing variant in trans with loss of function variants in DNA2, expanding the phenotypical spectrum of DNA2 mutations.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Genetics & Heredity
Michaela Drogemuller, Nadine Klein, Rikke Lill Steffensen, Miriam Keiner, Vidhya Jagannathan, Tosso Leeb
Summary: A female Lagotto Romagnolo dog and her offspring with polycystic kidney disease (PKD) were studied. The affected dogs showed no clinical symptoms but had renal cysts detected by sonography. Whole genome sequencing analysis revealed a de novo heterozygous nonsense variant in the PKD1 gene, which is predicted to truncate the wild-type PKD1 protein. The finding suggests that this mutation is the cause of PKD in the affected dogs and may serve as an animal model for similar diseases in humans.
Article
Cell Biology
Sophia Jenni, Odette Ludwig-Peisker, Vidhya Jagannathan, Sandra Lapsina, Martina Stirn, Regina Hofmann-Lehmann, Nikolay Bogdanov, Nelli Schetle, Urs Giger, Tosso Leeb, Anna Bogdanova
Summary: This study describes the clinical, pathophysiological, and molecular genetic features of a cat with hereditary methemoglobinemia. Genetic analyses revealed a single homozygous base exchange in the CYB5R3 gene, resulting in a splice defect and expression of two mutant CYB5R3 transcripts. The affected cat showed characteristics such as increased red blood cell fragility and deformability, glutathione overload, and morphological alterations typical for stress erythropoiesis associated with methemoglobinemia.
Article
Veterinary Sciences
Diletta Dell'Apa, Martina Fumeo, Antonella Volta, Marco Bernardini, Francesca Fidanzio, Valentina Buffagni, Matthias Christen, Vidhya Jagannathan, Tosso Leeb, Ezio Bianchi
Summary: Two boxer dogs from the same litter presented with urinary and fecal incontinence at 3 months of age. They both had an abnormal tail, atonic anal sphincter, and absent perineal reflex and sensation. Radiology and CT scan revealed sacral agenesis with abnormalities in the spine.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Genetics & Heredity
Matthias Christen, Isabel Zdora, Michael Leschnik, Vidhya Jagannathan, Christina Puff, Enrice Huenerfauth, Holger A. Volk, Wolfgang Baumgaertner, Tessa C. Koch, Wencke Schaefer, Miriam Kleiter, Tosso Leeb
Summary: There are several genetically distinct forms of cerebellar ataxia in Belgian shepherd dogs. In this study, two puppies from a litter developed cerebellar ataxia and showed clinical signs that stabilized but remained visible into adulthood. Through genetic analysis, a homozygous deletion in exon 35 of the RALGAPA1 gene was identified as the likely causative defect for the observed phenotype.
Article
Genetics & Heredity
Sarah Kiener, Heather Troyer, Daniel Ruvolo, Paula Grest, Sara Soto, Anna Letko, Vidhya Jagannathan, Tosso Leeb, Elizabeth A. Mauldin, Ching Yang, Ana Rostaher
Summary: Epidermolysis bullosa (EB) is a heterogeneous disease characterized by defective adhesion of the epidermis to the dermis. This study identified COL17A1 gene variants as the cause of EB in two cats, providing new insights into the diagnosis and genotype-phenotype correlation of this disease.
Article
Genetics & Heredity
Barbara Brunetti, Barbara Bacci, Jessica Maria Abbate, Giorgia Tura, Orlando Paciello, Emanuela Vaccaro, Francesco Prisco, Gualtiero Gandini, Samuel Okonji, Andrea di Paola, Anna Letko, Cord Drogemuller, Vidhya Jagannathan, Maria Elena Turba, Tolulope Grace Ogundipe, Luca Lorenzini, Marco Rosati, Dimitra Psalla, Tosso Leeb, Michaela Drogemuller
Summary: An 8-month-old Lagotto Romagnolo dog was diagnosed with a rare form of muscular dystrophy based on pathological and genetic analysis. The gene variant associated with this disease is rare in the breeding population of this breed.
Editorial Material
Genetics & Heredity
Tosso Leeb
Summary: Wolves were the first animals to be domesticated by humans, and thousands of generations of dog breeding have resulted in more than 350 recognized breeds with distinct morphological, behavioral, and disease predisposition differences. The domestication and breeding of dogs can be seen as a significant genetic experiment for humans, providing unique research opportunities. This special issue, titled Canine Genetics 2, focuses on the importance of canine genetics and includes reports on genetic diseases in dogs, as well as research on wild canids, genetic diversity, and canine morphology.
