Article
Biochemistry & Molecular Biology
Hong You, Johannes U. Mayer, Rebecca L. Johnston, Haran Sivakumaran, Shiwanthi Ranasinghe, Vanessa Rivera, Olga Kondrashova, Lambros T. Koufariotis, Xiaofeng Du, Patrick Driguez, Juliet D. French, Nicola Waddell, Mary G. Duke, Wannaporn Ittiprasert, Victoria H. Mann, Paul J. Brindley, Malcolm K. Jones, Donald P. McManus
Summary: CRISPR/Cas9-mediated genome editing has shown great potential for genetic modification of helminth parasites, as demonstrated by successful gene knock-in in Schistosoma mansoni eggs. This study confirmed the utility of CRISPR/Cas9 for functional genomics in schistosomes through combining CRISPR/Cas9 with single-stranded oligodeoxynucleotides (ssODNs).
Article
Plant Sciences
Yahui Lei, Ling Yang, Shengchang Duan, Siqi Ning, Dawei Li, Zijun Wang, Guisheng Xiang, Ling Yang, Chunping Wang, Shiyu Zhang, Shuangyan Zhang, Shuang Ye, Ling Kui, Pratiksha Singh, Jun Sheng, Yang Dong
Summary: This study conducted population genomic analysis of tea populations in eight main tea-producing areas in Lincang, Yunnan through whole-genome resequencing, revealing the origin centers of Lincang tea and observing low genetic differentiation between geographical tea populations.
FRONTIERS IN PLANT SCIENCE
(2022)
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
Health Care Sciences & Services
Eun-Ju Lee, Joohon Sung, Hyung-Lae Kim, Han-Na Kim
Summary: Based on a study of blood microbiota in healthy individuals, this research found that Proteobacteria accounts for more than 95% of the blood microbiota. Different age groups showed significant differences in the types and abundance of bacteria present in the blood, with the elderly group having higher levels of certain bacteria and lower levels of others. These findings provide meaningful evidence for the association between chronic diseases related to aging and metabolic endotoxemia and chronic inflammation.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Biology
Raphael T. F. Coimbra, Sven Winter, Arthur Muneza, Stephanie Fennessy, Moses Otiende, Domnic Mijele, Symon Masiaine, Jenna Stacy-Dawes, Julian Fennessy, Axel Janke
Summary: Through analyzing the genomes of wild giraffes, the study found evidence of historical gene flow between Nubian and reticulated giraffes. However, contemporary gene flow between these two lineages is minimal. The study also observed a decline in effective population sizes of Nubian and reticulated giraffes. Overall, the findings suggest that these three giraffe lineages have maintained their reproductive isolation.
Article
Microbiology
Sabino Pacheco, Isabel Gomez, Marcos Chinas, Jorge Sanchez, Mario Soberon, Alejandra Bravo
Summary: Bacillus thuringiensis (Bt) are soil bacteria that produce insecticidal proteins used for pest control. Genomic characterization of Bt strains provides valuable pesticidal protein resources with potential biotechnological applications. The sequenced Bt GR007 strain contains multiple genes coding for pesticidal proteins and virulent factors, which show differential toxicity against different insect larvae.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Virology
Carlos Padilla-Rojas, Victor Jimenez-Vasquez, Veronica Hurtado, Orson Mestanza, Iris S. Molina, Luis Barcena, Sandra Morales Ruiz, Steve Acedo, Wendy Lizarraga, Henri Bailon, Omar Caceres, Marco Galarza, Nancy Rojas-Serrano, Natalia Vargas-Herrera, Priscila Lope-Pari, Joseph Huayra, Lely Solari
Summary: The pandemic caused by SARS-Cov-2 has hit South America hard, with new variants raising concerns over evasion of vaccine protection, increased transmissibility, or higher virulence. Genomic surveillance in Peru revealed a significant rise of the lambda lineage, becoming predominant from January to April 2021, warranting close monitoring for potential variant of concern status.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Medicine, General & Internal
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
Summary: This study analyzed whole genome sequence data to identify novel candidate genes and pathways associated with essential tremor. The findings provide new insights into the genetic architecture of the disease and can guide future genetic and functional studies.
Article
Infectious Diseases
Julien Kincaid-Smith, Alan Tracey, Ronaldo de Carvalho Augusto, Ingo Bulla, Nancy Holroyd, Anne Rognon, Olivier Rey, Cristian Chaparro, Ana Oleaga, Santiago Mas-Coma, Jean-Francois Allienne, Christoph Grunau, Matthew Berriman, Jerome Boissier, Eve Toulza
Summary: The article describes the occurrence of schistosomiasis and the genetic admixture of hybrid schistosomes, as well as their compatibility with snail vectors. The results indicate that the hybrid is strongly introgressed genetically, with ancient hybridization events and subsequent backcrosses with the human-specific species. The study also highlights the discrepancy between egg morphology and genetic composition of schistosomes, emphasizing the importance of genetic testing for accurate hybrid identification.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Genetics & Heredity
Marilena Melas, Esko A. Kautto, Samuel J. Franklin, Mari Mori, Kim L. McBride, Theresa Mihalic Mosher, Ruthann B. Pfau, Maria Elena Hernandez-Gonzalez, Sean D. McGrath, Vincent J. Magrini, Peter White, Julie Balch Samora, Daniel C. Koboldt, Richard K. Wilson
Summary: Synpolydactyly 1, or syndactyly type II (SDTY2), is a genetic limb malformation characterized by polydactyly with syndactyly. The study identified heterozygous alterations in the HOXD13 gene associated with the disease, and highlighted the value of long-read whole-genome sequencing in elucidating the molecular etiology of congenital limb malformation disorders.
Article
Multidisciplinary Sciences
Jyh-Ming Jimmy Juang, Tzu-Pin Lu, Ming-Wei Su, Chien-Wei Lin, Jenn-Hwai Yang, Hou-Wei Chu, Chien-Hsiun Chen, Yi-Wen Hsiao, Chien-Yueh Lee, Li-Mei Chiang, Qi-You Yu, Chuhsing Kate Hsiao, Ching-Yu Julius Chen, Pei-Ei Wu, Chien-Hua Pai, Eric Y. Chuang, Chen-Yang Shen
Summary: This study established the first genomic database for Han Chinese in Taiwan, identifying hypertension and hyperlipidemia-associated variants and developing prediction models. Additionally, an online database for exploring racial differences in the important cardiac gene SCN5A was created, and population-specific SNVs in genes related to drug metabolism and blood clotting were discovered.
JOURNAL OF ADVANCED RESEARCH
(2021)
Article
Microbiology
Shunshi Ji, Zexuan Song, Lijuan Luo, Yiqian Wang, Lingling Li, Pan Mao, Changyun Ye, Yan Wang
Summary: This study investigated the genomic characteristics and evolutionary relationship of foodborne L. monocytogenes in China. Five serogroups, 35 sequence types, and four lineages were identified. The study also found evidence of persistent and/or cross-contamination in Chinese markets. Additionally, antibiotic resistance genes and a strain carrying Listeria Pathogenicity Island 3 were discovered.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Limiao Hu, Xi Zeng, Qi Ai, Caijuan Liu, Xiaotuan Zhang, Yajun Chen, Logen Liu, Guo-Qing Li
Summary: In this study, the authors investigated the antibiotic resistance pattern of H. pylori in a Chinese medical center. The results showed high rates of resistance to clarithromycin, metronidazole, and levofloxacin. The study also compared short-read- and long-read-based whole-genome sequencing methods for identifying genotypes and found that both methods were effective in predicting antibiotic resistance. Furthermore, the study discovered the heterozygous status of the 23S rRNA gene in H. pylori strains, which is important for clarithromycin resistance. Overall, the study provides important evidence for empirical treatment of H. pylori and demonstrates the potential of Nanopore sequencing in predicting clarithromycin resistance.
MICROBIOLOGY SPECTRUM
(2023)
Article
Agronomy
Anna Marzec-Grzadziel, Anna Galazka
Summary: The isolation of new bacterial strains from the natural environment can lead to the detection of microorganisms with potential practical importance. The characterization of such microorganisms can be carried out using classical microbiological and molecular biology methods, as well as sequencing techniques. This study focused on the sequencing and analysis of the genome of Achromobacter sp. 77Bb1, a bacterium isolated from the maize crop rhizosphere. The obtained genome contained genes related to xenobiotics biodegradation and metabolisms, suggesting its potential application in natural bioremediation methods.
Article
Biochemistry & Molecular Biology
Maulik Upadhyay, Elisabeth Kunz, Edson Sandoval-Castellanos, Andreas Hauser, Stefan Krebs, Alexander Graf, Helmut Blum, Arsen Dotsev, Innokentiy Okhlopkov, Alexey Shakhin, Vugar Bagirov, Gottfried Brem, Ruedi Fries, Natalia Zinovieva, Ivica Medugorac
Summary: Snow sheep, adapted to cold and alpine habitats, play a crucial role in their ecosystem and show potential for adaptation to climate change. Genomic analysis revealed low heterozygosity possibly due to isolation and bottlenecks, with introgression involving other wild sheep species indicating past genetic interactions. Adaptive introgression was found to target genes related to immunity, adipogenesis, and morphology, with selection on genes for mitochondrial function and thermogenesis underlying cold adaptation in snow sheep.
Article
Immunology
Jessica Clark, Moses Arinaitwe, Andrina Nankasi, Christina L. Faust, Adriko Moses, Diana Ajambo, Fred Besigye, Alon Atuhaire, Aidah Wamboko, Lauren Carruthers, Rachel Francoeur, Edridah M. Tukahebwe, Joaquin M. Prada, Poppy H. L. Lamberton
Summary: The impact of treatment for schistosomiasis in high-endemicity settings is short-lived due to less efficacy than expected and rapid reinfection. Current surveillance methods may underestimate infection prevalence, and improved diagnostics such as POC-CCA+ test may provide more accurate estimates of reinfection rate but face interpretation challenges. Frequent sampling is necessary to understand the clearance and reinfection dynamics post-treatment.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Parasitology
Suzan C. M. Trienekens, Christina L. Faust, Fred Besigye, Lucy Pickering, Edridah M. Tukahebwa, Janet Seeley, Poppy H. L. Lamberton
Summary: This study aims to understand the variation in water contact locations, behaviors, and infection risk in school-aged children in a region with persistent high endemicity of schistosomiasis in Uganda. The findings suggest that children with reinfection have more high-risk water contact behaviors and come into contact with water sources that have higher snail abundance, indicating that specific water contact behaviors interact with environmental features to explain the variation in risk within these areas. Targeted behavior change, vector control, and safe water supplies could reduce reinfection in school-aged children in such settings.
PARASITES & VECTORS
(2022)
Article
Infectious Diseases
Meng-Tao Sun, Man-Man Gu, Jie-Ying Zhang, Qiu-Fu Yu, Poppy H. L. Lamberton, Da-Bing Lu
Summary: PCR techniques show satisfactory performance for diagnosing S. japonicum infections in humans in endemic areas, with both high sensitivity and specificity. Further research on diagnostic techniques, especially targeting low endemicity areas and detecting dual-sex and single-sex infections, is needed.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Infectious Diseases
Tushabe John Vianney, Duncan J. Berger, Stephen R. Doyle, Geetha Sankaranarayanan, Joel Serubanja, Prossy Kabuubi Nakawungu, Fred Besigye, Richard E. Sanya, Nancy Holroyd, Fiona Allan, Emily L. Webb, Alison M. Elliott, Matthew Berriman, James A. Cotton
Summary: This study aims to understand the impact of praziquantel (PZQ) treatment on the genetics of schistosomes. The authors obtained whole-genome sequence data from 174 individual miracidia collected from fishing communities in Uganda and investigated the genetic variation and genomic signatures of natural selection in pre- and post-treatment parasite populations. The study found higher genetic diversity in pre-treatment parasite populations and identified genes with evidence of recent positive selection in post-treatment and intensively treated parasites that could be related to reduced susceptibility to PZQ treatment.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Public, Environmental & Occupational Health
Chanika Worasith, Phattharaphon Wongphutorn, Kulthida Y. Kopolrat, Chutima Homwong, Anchalee Techasen, Raynoo Thanan, Chompunoot Wangboon, Chatanun Eamudomkarn, Jiraporn Sithithaworn, Thomas Crellen, Paiboon Sithithaworn
Summary: In this study, the daily and long-term variability of Opisthorchis viverrini antigen concentrations in urine for the diagnosis of opisthorchiasis was investigated. The results showed that there was no significant change in antigen-positive rate and antigen concentration over 30 days, indicating the reliability of urine assay for diagnosis of opisthorchiasis. The consistency of urine antigen concentration over a 10-month follow-up period further supported the accuracy of the urine assay.
AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE
(2023)
Article
Biology
Thomas Crellen, Melissa Haswell, Paiboon Sithithaworn, Somphou Sayasone, Peter Odermatt, Poppy H. L. Lamberton, Simon E. F. Spencer, T. Deirdre Hollingsworth
Summary: A study on opisthorchiasis found that parasite fecundity varies between populations and the relationship between routine diagnostics and true prevalence is influenced by parasite aggregation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Parasitology
Gregory Colin Milne, Joanne P. Webster, Martin Walker
Summary: Several studies have suggested a decline in the incidence of congenital toxoplasmosis due to decreasing seroprevalence of Toxoplasma gondii. However, the consistency of this trend across different populations and its implications for prenatal screening programs remain unclear. This study explores how the changing epidemiology of the parasite may affect trends in congenital toxoplasmosis incidence and emphasizes the importance of updating cost-effectiveness estimates of screening programs to account for neuropsychiatric sequelae.
TRENDS IN PARASITOLOGY
(2023)
Review
Parasitology
Isobel L. Gabain, Anouschka S. Ramsteijn, Joanne P. Webster
Summary: Globally, approximately 149.2 million children under the age of 5 are affected by stunting, but the underlying causes and mechanisms are still unclear, leading to limited treatment and prevention strategies. The direct link between parasites and stunting is often lacking due to the complex nature of stunting and a lack of interdisciplinary research. Based on existing studies, this paper presents potential pathways by which parasitic infection in mothers and/or infants may lead to childhood stunting. The need for future multidisciplinary longitudinal studies and clinical trials to identify influential factors and develop effective solutions is highlighted.
TRENDS IN PARASITOLOGY
(2023)
Article
Infectious Diseases
Nicholas Ngwili, Derrick N. Sentamu, Max Korir, Moses Adriko, Prudence Beinamaryo, Michel M. Dione, Joyce Moriku Kaducu, Alfred Mubangizi, Pauline Ngina Mwinzi, Lian F. Thomas, Matthew A. Dixon
Summary: A mapping study conducted in Uganda revealed high-risk areas for the zoonotic cestode Taenia solium, indicating the need for urgent control efforts to achieve the World Health Organization's milestones.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Biology
Anna Borlase, Joaquin M. Prada, Thomas Crellen
Summary: Reducing the morbidities caused by neglected tropical diseases (NTDs) is important, but the association between infection and long-term pathology is complex and often poorly quantified. Mathematical modelling has been used for understanding the transmission dynamics of infectious diseases, but long-term morbidities are generally not considered. This study explores the complexities and challenges of incorporating long-term morbidity into NTD transmission models.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
Elias Kabbas-Pinango, Moses Arinaitwe, Govert J. J. van Dam, Adriko Moses, Annet Namukuta, Andrina Barungi Nankasi, Nicholas Khayinja Mwima, Fred Besigye, Joaquin M. Prada, Poppy H. L. Lamberton
Summary: Schistosomiasis affects over 240 million people worldwide. Detecting the parasite eggs using Kato-Katz method is specific but not sensitive, while the urine-based POC-CCA test is more sensitive but has specificity issues and interpretation challenges. This study explores the variation in test results and suggests different thresholds for accurate diagnosis and prevalence monitoring.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jennifer D. Noonan, Robin N. Beech
Summary: Previous studies showed that some N-AChRs require RIC-3 in heterologous expression systems, while others do not. By constructing chimeric and mutant ACR-16 receptors between A. suum and D. medinensis, two amino acid residues (R/K159 and I504) were identified as crucial for determining the requirement of RIC-3.
Article
Infectious Diseases
Eun Seok Kim, Moses Adriko, Wamboko Aidah, Kabarangira Christine Oseku, David Lokure, Kalpana Sabapathy, Emily Webb
Summary: This study aimed to evaluate the efficacy of dual-dose albendazole compared to single-dose albendazole for treating hookworm infection in Mayuge district, Uganda. The results showed that dual-dose albendazole improved the cure rate of hookworm, but co-administration with fatty food did not significantly improve the treatment efficacy.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Microbiology
Aya Hefnawy, Gabriel Negreira, Marlene Jara, James A. Cotton, Ilse Maes, Erika D'Haenens, Hideo Imamura, Bart Cuypers, Pieter Monsieurs, Christina Mouchtoglou, Hans De Winter, Isabel Pintelon, Jean-Pierre Timmermans, Matt Berriman, Mandy Sanders, Julio Martin, Geraldine de Muylder, Jean-Claude Dujardin, Yann G-J Sterckx, Malgorzata Anna Domagalska
Summary: The study demonstrates the importance of prospective drug resistance (DR) studies for neglected tropical diseases (NTDs) using Leishmania donovani as a paradigm. By experimentally selecting resistance to a promising compound for visceral leishmaniasis and characterizing resistant parasites, a new DR mechanism involving LdoDLP1 was discovered. This highlights the practical relevance of prospective DR studies.