Article
Urology & Nephrology
Jose Lazaro-Guevara, Julio Fierro-Morales, A. Hunter Wright, River Gunville, Christopher Simeone, Scott G. Frodsham, Melissa H. Pezzolesi, Courtney A. Zaffino, Laith Al-Rabadi, Nirupama Ramkumar, Marcus G. Pezzolesi
Summary: This study investigated the genetic basis of nondiabetic kidney disease (NDKD) and diabetic kidney disease (DKD) through targeted NGS, finding rare diagnostic variants consistent with clinical diagnoses in 19% of NDKD patients and in 22% of DKD patients. Additionally, genetic variants suggestive of NDKD were detected in 3% of diabetic patients. These findings suggest that rare variants in kidney disease-related genes may contribute to the pathogenesis of DKD and NDKD in patients with diabetes.
AMERICAN JOURNAL OF NEPHROLOGY
(2021)
Article
Clinical Neurology
Jakub Scaber, Alexander G. Thompson, Lucy Farrimond, Emily Feneberg, Malcolm Proudfoot, Lynn Ossher, Martin R. Turner, Kevin Talbot
Summary: This study demonstrates that expanding genetic testing to all patients diagnosed with ALS can enhance recruitment potential for clinical trials, but also has significant resource implications for genetic counseling.
EUROPEAN JOURNAL OF NEUROLOGY
(2023)
Article
Physiology
Agnes Bloch-Zupan, Tristan Rey, Alexandra Jimenez-Armijo, Marzena Kawczynski, Naji Kharouf, Muriel de La Dure-Molla, Emmanuelle Noirrit, Magali Hernandez, Clara Joseph-Beaudin, Serena Lopez, Corinne Tardieu, Beatrice Thivichon-Prince, Tatjana Dostalova, Milan Macek Jr, Mustapha El Alloussi, Leila Qebibo, Supawich Morkmued, Patimaporn Pungchanchaikul, Blanca Urzua Orellana, Marie-Cecile Maniere, Benedicte Gerard, Isaac Maximiliano Bugueno, Virginie Laugel-Haushalter
Summary: In this study, next-generation sequencing was used to analyze a cohort of Amelogenesis imperfecta (AI) patients, revealing more than 70 genes associated with AI. The findings showed that 73% of the cases were non-syndromic AI and 27% were syndromic AI. The genetic diagnosis provided important insights for the diagnosis and treatment of AI. This study demonstrated the potential of next-generation sequencing in AI research and provided new insights into the classification and treatment of AI.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Plant Sciences
Peng Zhou, Jiao Li, Jing Huang, Fei Li, Qiang Zhang, Min Zhang
Summary: In this study, the genome features of Ilex chinensis were analyzed using next-generation sequencing technology. The results showed that the I. chinensis genome is complex with high heterozygosity and few repeated sequences. Additionally, a large number of microsatellite motifs were detected, providing basic molecular markers for further research.
Article
Biochemistry & Molecular Biology
Kang Huang, Wenkai Li, Bing Yang, Dan Wang, Shujun He, Yujia Shen, Jincuo Ao, Yuhang Li, Yunxia Cui, Yuchen Kong, Wei Li, Nianlong Li, Derek W. Dunn, Baoguo Li
Summary: Polyploid plants are important for studying evolution, molecular ecology, and agriculture. However, their unique genetic inheritance requires specific software for population genetic analysis.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Medical Laboratory Technology
Lisa A. Lansdon, Maxime Cadieux-Dion, John C. Herriges, Jeffrey Johnston, Byunggil Yoo, Joseph T. Alaimo, Isabelle Thiffault, Neil Miller, Ana S. A. Cohen, Elena A. Repnikova, Lei Zhang, Midhat S. Farooqi, Emily G. Farrow, Carol J. Saunders
Summary: The study validated the clinical effectiveness of the laboratory's migration from GRCh37 to GRCh38, and identified some important differences between the two genome versions, including discrepancies leading to protein coding sequence variants and discrepancies resolved in coding regions.
CLINICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Se-Won Chun, Jei-Wan Lee, Ji-Young Ahn
Summary: This study developed and characterized novel microsatellite markers of Tilia amurensis, and characterized three populations in Korea, demonstrating the significance of these markers for genetic diversity studies.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Urology & Nephrology
Vuthy Ea, Anne Bergougnoux, Pascal Philibert, Nadege Servant-Fauconnet, Alice Faure, Jean Breaud, Laura Gaspari, Charles Sultan, Francoise Paris, Nicolas Kalfa
Summary: The study evaluated the clinical utility of NGS for patients with hypospadias and found that even mild cases can benefit from advanced sequencing techniques. Some variants of unknown significance (VUSs) were identified, but most cases remain unexplained.
Article
Genetics & Heredity
Susan Rojahn, Tina Hambuch, Jessika Adrian, Erik Gafni, Alex Gileta, Hannah Hatchell, Britt Johnson, Ben Kallman, Kate Karfilis, Curtis Kautzer, Michael Kennemer, Lloyd Kirk, Daniel Kvitek, Jessica Lettes, Fenner Macrae, Fernando Mendez, Joshua Paul, Maurizio Pellegrino, Ronny Preciado, Jan Risinger, Matthew Schultz, Lindsay Spurka, Sajani Swamy, Rebecca Truty, Nathan Usem, Andrea Velenich, Swaroop Aradhya
Summary: By customizing next-generation sequencing (NGS) methods, technically challenging genetic variants can be detected with high sensitivity, providing a scalable and cost-effective approach to identifying all clinically relevant variants within a single sample.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2022)
Article
Plant Sciences
Yue-Hong Jiang, Ting-Jun Jiang, Xiao-Feng Lv, Xiao-Fei Yu, Wei-Qun Chi
Summary: Three new mexicanolide limonoids were isolated from the seeds of Khaya senegalensis, with structures elucidated through spectroscopic analysis. In vitro testing showed that compounds 1-3 exhibited antimicrobial activity against Gram negative bacteria, particularly at concentrations below 40 mu g/ml.
JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH
(2022)
Article
Gastroenterology & Hepatology
Toky Ratovomanana, Romain Cohen, Magali Svrcek, Florence Renaud, Pascale Cervera, Aurelie Siret, Quentin Letourneur, Olivier Buhard, Pierre Bourgoin, Erell Guillerm, Coralie Dorard, Remy Nicolle, Mira Ayadi, Mehdi Touat, Franck Bielle, Marc Sanson, Philippe Le Rouzic, Marie-Pierre Buisine, Guillaume Piessen, Ada Collura, Jean-Francois Flejou, Aurelien de Reynies, Florence Coulet, Francois Ghiringhelli, Thierry Andre, Vincent Jonchere, Alex Duval
Summary: This study evaluated the performance of NGS in identifying MSI in CRC, especially dMMR mCRC treated with ICI, and proposed a new algorithm called MSICare. The results showed that MSICare performed more accurately in detecting MSI in all testing modes, making it a potential reference method for NGS-based testing of MSI in CRC, especially in mCRC requiring ICI treatment.
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Ophthalmology
Marta Del Pozo-Valero, Rosa Riveiro-Alvarez, Inmaculada Martin-Merida, Fiona Blanco-Kelly, Saoud Swafiri, Isabel Lorda-Sanchez, Maria Jose Trujillo-Tiebas, Ester Carreno, Belen Jimenez-Rolando, Blanca Garcia-Sandoval, Marta Corton, Almudena Avila-Fernandez, Carmen Ayuso
Summary: This study utilized next-generation sequencing technologies to analyze the genetic landscape of 1036 families diagnosed with either autosomal recessive or sporadic macular dystrophies. The study discovered the mutational spectrum and identified ABCA4 as the most commonly mutated gene. Furthermore, the study found associations between other genes and different types of dystrophies.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Multidisciplinary Sciences
Laurel A. Keefer, James R. White, Derrick E. Wood, Kelly M. R. Gerding, Kenneth C. Valkenburg, David Riley, Christopher Gault, Eniko Papp, Christine M. Vollmer, Amy Greer, James Hernandez, Paul M. McGregor, Adriana Zingone, Brid M. Ryan, Kristen Deak, Shannon J. McCall, Michael B. Datto, James L. Prescott, John F. Thompson, Gustavo C. Cerqueira, Sian Jones, John K. Simmons, Abigail McElhinny, Jennifer Dickey, Samuel Angiuoli, Luis A. Diaz, Victor E. Velculescu, Mark Sausen
Summary: This study describes a comprehensive genomic profiling assay with high analytical performance and provides validation of its accuracy and reliability using clinically and biologically relevant samples.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Romane H. Cristescu, Riana Gardiner, Julien Terraube, Kye McDonald, Dan Powell, Alexis L. Levengood, Celine H. Frere
Summary: The 2019-2020 Australian bushfires had a significant impact on koala habitat and population density. While koala density decreased in most fire-affected sites, there was unexpectedly a higher density observed in one of the sites. This highlights the importance of monitoring koalas in fire-affected areas for several months after the fires.
Correction
Multidisciplinary Sciences
K. Strickland, A. Levengood, V. Foroughirad, J. Mann, E. Krzyszczyk, C. H. Frere
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Behavioral Sciences
Alexis L. Levengood, Kasha Strickland, Vivienne Foroughirad, Janet Mann, Romane H. Cristescu, Ewa Krzyszczyk, Celine H. Frere
Summary: The competition for resources and differences in habitat affect the social interactions and relationships of individual dolphins, with variations seen between males and females. These findings highlight the influence of environmental conditions on long-term social relationships of individuals.
BEHAVIORAL ECOLOGY
(2022)
Article
Ecology
Nicola Jackson, Bethan L. Littleford-Colquhoun, Kasha Strickland, Barbara Class, Celine H. Frere
Summary: Oceanic archipelagos and cities have similarities in terms of evolutionary and ecological processes, and city parks can be studied as archipelagos for rapid evolution.
Article
Behavioral Sciences
Vivienne Foroughirad, Molly McEntee, Anna M. Kopps, Alexis Levengood, Celine Frere, Janet Mann
Summary: Mothers are easily identifiable in most mammals due to extended parental care, but fathers can be absent. In a community of dolphins, twice as many mothers as fathers were detected with random genetic sampling. Our study found that the bias in parentage assignment can be explained by differences in reproductive timing.
BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY
(2022)
Article
Biodiversity Conservation
Riana Gardiner, Julien Terraube, Celine Frere, Romane Cristescu
Summary: This study surveyed 959 sites to determine the occurrence of koalas in secondary eucalyptus forests. The results showed that koalas were less likely to be found in secondary forests compared to primary forests. However, the distance to major roads and the water area had interactive effects on koala occurrence, with greater distances and larger water areas predicting increased koala presence. This highlights the importance of considering the landscape context when protecting secondary eucalyptus forests for koala conservation.
BIODIVERSITY AND CONSERVATION
(2023)
Article
Behavioral Sciences
Vivienne Foroughirad, Celine H. Frere, Alexis L. Levengood, Anna M. Kopps, Ewa Krzyszczyk, Janet Mann
Summary: This study investigates the effects of family size on female sociality in the Indo-Pacific bottlenose dolphins in Shark Bay, Australia. The results show that females have strong preferences for affiliations with both matrilineal and nonmatrilineal kin, but family size has only a small impact on individual social position. Individual foraging ecology has a stronger and more consistent effect on sociality.
Article
Behavioral Sciences
J. Tacey, B. Class, C. Delme, D. Powell, C. H. Frere
Summary: This study investigated the impact of fungal infection on the social behavior of urban eastern water dragons. The results showed that dragons with severe infections avoided diseased individuals, but the infection status did not affect their social interactions with healthy conspecifics.
Article
Behavioral Sciences
Kaitlin E. Barham, Cameron J. Baker, Craig E. Franklin, Hamish A. Campbell, Celine H. Frere, Terri R. Irwin, Ross G. Dwyer
Summary: In species with costly conflict, individuals use alternative movement tactics to minimize competitive interactions. This study investigated how the behavior of male estuarine crocodiles shifted over an 11-year period in relation to ontogeny, body condition, and physical injuries. Results showed that males sorted into different movement classes, with larger males maintaining confined territories, while smaller males adopted high movement or low movement tactics. Our study provides insights into the mechanisms and costs of movement tactics in wild crocodile populations.
BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY
(2023)
Article
Behavioral Sciences
Sarah Ball, Dominique A. Potvin, Barbara Class, Celine H. Frere
Summary: Agonistic and movement behaviors, which are associated with territoriality, showed individual repeatability but were not found to be correlated. This suggests that aggression and movement may be independent traits and territoriality may not drive shared selective pressures for both.
BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY
(2023)
Article
Entomology
Shirin Christensen (nee Roohigohar), Chloe A. van Der Burg, Anthony R. Clarke, Peter J. Prentis
Summary: The Queensland fruit fly is a major pest in Australia, causing damage to a wide range of fruits and vegetables. By analyzing the transcriptome of fruit fly larvae feeding on different stages of tomato fruit, it was found that larval survival is poor in immature fruit due to the presence of toxins. The immature fruit inhibits larval development and basic cellular functions, while fully ripe fruit promotes larval growth and detoxification processes.
JOURNAL OF APPLIED ENTOMOLOGY
(2023)
Article
Biochemistry & Molecular Biology
C. H. Frere, G. D. O'Reilly, K. Strickland, A. Schultz, K. Hohwieler, J. Hanger, D. de Villiers, R. Cristescu, D. Powell, W. Sherwin
Summary: The genetic consequences of population subdivision in human-impacted landscapes are significant for long-term evolution. This study analyzes the effects of population subdivision on genetic diversity using koala population data and proposes a method to evaluate mitigation measures.
Article
Multidisciplinary Sciences
Andy C. W. Lui, Kah Chee Pow, Nan Lin, Lydia Pui Ying Lam, Guoquan Liu, Ian D. Godwin, Zhuming Fan, Chen Jing Khoo, Yuki Tobimatsu, Lanxiang Wang, Quan Hao, Clive Lo
Summary: The study reveals that sorghum and wild sugarcane accumulate different types of O-methylated stilbenes due to major differences in catalytic regioselectivities of O-methyltransferases. This research reports the inherent ability of two Saccharinae grasses to produce regioselectively O-methylated stilbenes. The findings have important implications for the bioengineering synthesis of O-methylated stilbenes.
NATURE COMMUNICATIONS
(2023)
Article
Food Science & Technology
Hayden L. Smith, Peter J. Prentis, Scott E. Bryan, Raymond S. Norton, Daniel A. Broszczak
Summary: The venom delivery system of Phylum Cnidaria is unique, consisting of individual organelles known as nematocysts. Acontia, found in a limited number of sea anemone species, are packed with large nematocysts used for defense. This study identified the venom profile of acontia in Calliactis polypus, revealing limited toxin diversity and a novel toxin with two ShK-like domains. This research provides a foundation for further investigating the function of acontial toxins in sea anemones.
Article
Plant Sciences
Albert Chern Sun Wong, Erik J. van Oosterom, Ian D. Godwin, Andrew K. Borrell
Summary: Plant architecture modification through gene-editing technologies like PIN auxin efflux carriers can be used as an adaptive strategy in crop breeding to address climate uncertainties. Stay-green trait plays an important role in enabling plants to remain photosynthetically active and delay senescence during grain filling under post-anthesis drought stress. Sorghum serves as a model crop for researching the potential of using PIN auxin efflux carriers to modulate plant architecture for climate-resilient crops.
