Article
Multidisciplinary Sciences
Yolandi Swart, Gerald van Eeden, Caitlin Uren, Gian van der Spuy, Gerard Tromp, Marlo Moeller
Summary: This study presents a robust method called local ancestry adjusted allelic (LAAA) analysis for discovering association signals. The researchers simulated three- and five-way admixed populations and found that the LAAA model identifies the most causal variants in most of the tested phenotypes.
Article
Multidisciplinary Sciences
Moustafa A. Shehata, Julia Contreras, Ana Martin-Hurtado, Aurane Froux, Hossam Taha Mohamed, Ahmed A. El-Sherif, Ivan Plaza-Menacho
Summary: This study investigates the structural and dynamic determinants of highly selective RET kinase inhibition, identifying a new druggable target called the post-lysine pocket. It demonstrates that second generation RET inhibitors exploit this vulnerability, providing important implications for future drug design and personalized therapies for RET-driven cancers.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Meteorology & Atmospheric Sciences
D. A. Knopf, K. R. Barry, T. A. Brubaker, L. G. Jahl, K. A. Jankowski, J. Li, Y. Lu, L. W. Monroe, K. A. Moore, F. A. Rivera-Adorno, K. A. Sauceda, Y. Shi, J. M. Tomlin, H. S. K. Vepuri, P. Wang, N. N. Lata, E. J. T. Levin, J. M. Creamean, T. C. J. Hill, S. China, P. A. Alpert, R. C. Moffet, N. Hiranuma, R. C. Sullivan, A. M. Fridlind, M. West, N. Riemer, A. Laskin, P. J. DeMott, X. Liu
Summary: The prediction of ice formation in clouds presents a significant challenge in atmospheric sciences, particularly the uncertainty in deriving INP number concentrations in cloud-resolving and climate models. The closure pilot study aims to evaluate the level of parameter details and measurement strategies needed to achieve aerosol-ice formation closure, with a focus on guiding immersion freezing schemes in models and identifying causes for INP prediction biases in climate models.
BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY
(2021)
Article
Microbiology
Carolyn R. Cornell, Ya Zhang, Daliang Ning, Liyou Wu, Pradeep Wagle, Jean L. Steiner, Xiangming Xiao, Jizhong Zhou
Summary: Land conversion for intensive agriculture has negative effects on soil ecosystems, especially soil bacterial communities. This study explored the temporal dynamics of soil bacterial communities under different disturbance intensities in a U.S. Southern Plains agroecosystem. The results showed that land use had the greatest impact on bacterial taxonomic diversity, while sampling time and its interaction with land use influenced functional diversity differences. Tillage, sampling time, and temperature were the main drivers of taxonomic diversity, while all measured factors explained similar amounts of variations in functional diversity. The findings highlight the importance of reducing agricultural disturbance to conserve soil biodiversity.
Article
Agriculture, Dairy & Animal Science
Angelique Myburgh, Helet Lambrechts, Louwrens Christiaan Hoffman
Summary: The Plains zebra, an African equine species, has the potential to be a valuable protein source in South Africa. It produces lean meat and has high dressing percentages. The study shows that the Plains zebra can be used as an alternative protein source, contributing to food security.
Article
Plant Sciences
S. F. Van Vuuren, K. E. Motlhatlego
Summary: This study reviewed the use of plant combinations in southern African traditional medicine and recorded 187 plant combinations used for various diseases. It was found that plant combinations were used to treat gastrointestinal and respiratory infections, as well as skin diseases. Additionally, combinations with non-plant derived ingredients were also commonly used.
JOURNAL OF ETHNOPHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Aisha Alnami, Raymond S. Norton, Helena Perez Pena, Shozeb Haider, Frank Kozielski
Summary: Mycobacterium tuberculosis's FtsZ protein is a potential antibacterial target, with inhibition leading to cell division arrest and eventual cell death. Research has found that a coumarin analogue can bind to novel cryptic pockets in FtsZ, revealing the molecular mechanism behind its antibacterial activity.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Geosciences, Multidisciplinary
A. L. White-Gaynor, A. A. Nyblade, R. J. Durrheim, R. Raveloson, M. van der Meijde, I Fadel, H. Paulssen, M. Kwadiba, O. Ntibinyane, N. Titus, M. Sitali
Summary: The study reveals that the southern African upper mantle exhibits high velocities at depths of 50-250 km, with the cratonic lithosphere extending to about 200-250 km depth with little difference in velocities between on-craton and off-craton regions. The upper mantle beneath the Southern African Plateau shows little thermal modification.
GEOPHYSICAL RESEARCH LETTERS
(2021)
Article
Plant Sciences
Nikita Martynenko, Evgeniy Gusev, Dmitry Kapustin, Maxim Kulikovskiy
Summary: A new species of green coccoid algae, named Mychonastes hindakii sp. nov., was discovered in the River Moscow. It was described using morphological and molecular methods and found to belong to the species group of the genus Mychonastes, characterized by spherical single cells joined with mucilaginous, irregularly shaped stalks. Comparison of DNA sequences and structures confirmed the distinctiveness of Mychonastes hindakii from other species in the genus, suggesting that molecular data is necessary for reliable identification of this cryptic species.
Article
Microbiology
Jiayao Guan, Wei Zhou, Jingyi Guo, Lin Zheng, Gejin Lu, Fuyou Hua, Mingwei Liu, Xue Ji, Yang Sun, Lingwei Zhu, Xuejun Guo
Summary: Reported here is the genetic characterization of a novel bla(VEB-1)-carrying plasmid with new insertion sequence elements from Wohlfahrtiimonas chitiniclastica, isolated from a dead zebra in China. This plasmid may enhance the pathogen's ability to survive under drug selection pressure.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Meteorology & Atmospheric Sciences
Ian N. N. Williams, Shaoyue Qiu
Summary: Doppler lidar vertical velocity retrievals were analyzed to study the scale and structure of mixed-layer turbulence over a 7-year period in the US Southern Great Plains. The study found significant variations in spectral density in the energy-production subrange and mesoscale regimes. The results showed that surface forcing and updraft size had significant effects on turbulence scale, with increasing buoyancy flux leading to narrower updrafts and cellular structures.
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES
(2022)
Article
Biodiversity Conservation
Alan Stenhouse, Tahlia Perry, Frank Grutzner, Megan Lewis, Lian Pin Koh
Summary: Short-beaked echidnas are iconic monotremes found throughout Australia, with a need for better population data. A mobile app, EchidnaCSI, has been developed to allow citizen scientists to easily record echidna sightings, improving the quantity and quality of data collected for monitoring this species.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Multidisciplinary Sciences
Tingting Li, Wenhui Xue, Qingbing Zheng, Shuo Song, Chuanlai Yang, Hualong Xiong, Sibo Zhang, Minqing Hong, Yali Zhang, Hai Yu, Yuyun Zhang, Hui Sun, Yang Huang, Tingting Deng, Xin Chi, Jinjin Li, Shaojuan Wang, Lizhi Zhou, Tingting Chen, Yingbin Wang, Tong Cheng, Tianying Zhang, Quan Yuan, Qinjian Zhao, Jun Zhang, Jason S. McLellan, Z. Hong Zhou, Zheng Zhang, Shaowei Li, Ying Gu, Ningshao Xia
Summary: The study identified two cross-neutralizing antibodies targeting the receptor-binding domain of SARS-CoV-2, which can effectively neutralize various virus variants, providing potential options for public health interventions.
NATURE COMMUNICATIONS
(2021)
Article
Electrochemistry
Fabian Aren, Rasmus Andersson, Alejandro A. Franco, Patrik Johansson
Summary: Increasing the lithium salt concentration from 1 M to 3-5 M can create highly concentrated electrolytes (HCEs), which are suggested to be a pathway towards safer and more stable lithium batteries. The unique solvation structure of HCEs with insufficient solvent to fully solvate Li+ ions is believed to contribute to their higher stability and lower volatility. However, there is still much to be understood about HCEs.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2023)
Article
Allergy
Casper-Emil Tingskov Pedersen, Anders Ulrik Eliasen, Matthias Ketzel, Jorgen Brandt, Steffen Loft, Lise Marie Frohn, Jibran Khan, Susanne Brix, Morten A. Rasmussen, Jakob Stokholm, Bo Chawes, Andreanne Morin, Carole Ober, Hans Bisgaard, Marie Pedersen, Klaus Bonnelykke
Summary: Prenatal exposure to ambient air pollution is associated with immune perturbations in early life, increasing the risk of allergic rhinitis and asthma.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Liam Quinn, Genis Garcia-Erill, Cindy Santander, Anna Bruniche-Olsen, Xiaodong Liu, Mikkel-Holger S. Sinding, Michael P. P. Heaton, Timothy P. L. Smith, Patricia Pecnerova, Laura D. D. Bertola, Kristian Hanghoj, Malthe Sebro Rasmussen, Deon de Jager, Hans R. R. Siegismund, Anders Albrechtsen, Rasmus Heller, Ida Moltke
Summary: The iconic Cape buffalo has experienced population declines attributed to multiple factors, including the rinderpest pandemic and recent human activity. This study analyzed whole genome sequencing data to assess genetic diversity in Cape buffalo populations. The results indicate that recent inbreeding and colonialism-associated events have significantly impacted the genetic diversity of the southernmost populations.
Article
Genetics & Heredity
Alida de Flamingh, Yasuko Ishida, Patricia Pecnerova, Sahara Vilchis, Hans R. Siegismund, Rudi J. van Aarde, Ripan S. Malhi, Alfred L. Roca
Summary: Non-invasive biological samples are valuable for studying rare, elusive, endangered, or dangerous species. By combining genomic techniques with computational approaches, we can improve wildlife conservation and management. In this study, we used non-invasive fecal DNA samples and easily accessible DNA preservation cards to generate genomic and metagenomic data, showcasing the utility of this approach for conservation science.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Stefanie Wagner, Andaine Seguin-Orlando, Jean-Charles Leple, Thibault Leroy, Celine Lalanne, Karine Labadie, Jean-Marc Aury, Sandy Poirier, Patrick Wincker, Christophe Plomion, Antoine Kremer, Ludovic Orlando
Summary: Whole genome characterizations based on ancient DNA have provided valuable insights into the evolutionary origins and adaptive processes of modern cultivars. However, there has been a lack of ancient genome sequences for trees, in contrast to the availability of multiple ancient reference genomes for important crops. This study generated the first ancient tree genomes, revealing the species composition and timing of leaf unfolding for ancient trees, and expanding the applications of ancient wood in enhancing our understanding of forest ecosystem responses to past changes.
Editorial Material
Multidisciplinary Sciences
Ludovic Orlando
Summary: An extensive genomic time series has been conducted on 356 humans from ice-age Europe, showing the impact of climate change on the migration patterns and cultural development of hunter-gatherer populations.
Article
Genetics & Heredity
Hong Cheng, Zhuangbiao Zhang, Jiayue Wen, Johannes A. Lenstra, Rasmus Heller, Yudong Cai, Yingwei Guo, Ming Li, Ran Li, Wenrong Li, Sangang He, Jintao Wang, Junjie Shao, Yuxuan Song, Lei Zhang, Masum Billah, Xihong Wang, Mingjun Liu, Yu Jiang
Summary: This study analyzed the whole-genome sequencing of 1,098 domestic sheep and 69 wild sheep, and found that introgression from wild sheep contributed to the morphological diversity of sheep breeds and individual variations within breeds. The frequency of introgressed fragments varied greatly among domestic breeds, indicating the role of selection and recombination in shaping genetic and phenotypic diversity.
Article
Genetics & Heredity
Rutaba Gul, Sabika Firasat, Mikkel Schubert, Asmat Ullah, Elionora Pena, Anne C. B. Thuesen, Mulazim Hussain, Frederik F. Staeger, Anette P. Gjesing, Anders Albrechtsen, Torben Hansen
Summary: The aim of this study was to identify novel genes and pathogenic variants in families from diverse regions of Pakistan with clinically diagnosed mucopolysaccharidosis type I and mucopolysaccharidosis type II. Whole genome sequencing revealed ten novel and six previously reported variants in lysosomal storage disorders-associated genes, as well as a novel candidate gene for lysosomal storage disorder-like phenotypes. The presence of multigenic inheritance in several families highlights the importance of searching for homozygous pathogenic variants in multiple genes, especially in consanguineous families.
FRONTIERS IN GENETICS
(2023)
Article
Biodiversity Conservation
Kathelijne Koops, Tatyana Humle, Peter Frandsen, Maegan Fitzgerald, Lucy D'Auvergne, Hazel A. Jackson, Claus Borsting, Hans R. Siegismund, Aly Gaspard Soumah, Christina Hvilsom
Summary: Guinea is a key habitat for western chimpanzees, but it also has high-grade iron-ore deposits. This study used genetic sampling to estimate the population size and characteristics of western chimpanzees in the Nimba Mountains, and recommended the use of genetic sampling and camera trapping for future conservation efforts.
CONSERVATION SCIENCE AND PRACTICE
(2023)
Review
Genetics & Heredity
Ninna Karsbaek Senftleber, Stina Ramne, Ida Moltke, Marit Eika Jorgensen, Anders Albrechtsen, Torben Hansen, Mette K. Andersen
Summary: Genetic variants causing loss of sucrase-isomaltase (SI) function result in malabsorption of sucrose and starch components, leading to congenital sucrase-isomaltase deficiency (CSID). The c.273_274delAG loss-of-function (LoF) variant is common in Arctic populations and may have a positive impact on metabolic health. Understanding the biological role of SI, the metabolic impact of the Arctic SI LoF variant, and the potential mechanisms linking reduced SI function to metabolic health is crucial for evaluating SI inhibition as a therapeutic target for improving cardiometabolic health.
APPLICATION OF CLINICAL GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Zilong Li, Jonas Meisner, Anders Albrechtsen
Summary: Principal component analysis (PCA) is widely used for dimensionality reduction and uncovering latent structure in statistics, machine learning, and genomics. To address the challenges of ever-growing data, this paper proposes a novel algorithm called PCAone, which achieves fast and memory-efficient PCA and outperforms existing methods in comprehensive evaluations using multiple large-scale real-world datasets.
Article
Biochemistry & Molecular Biology
Genis Garcia-Erill, Kristian Hanghoj, Rasmus Heller, Carsten Wiuf, Anders Albrechtsen
Summary: The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. We implemented maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We also developed a software, apoh, to detect recently admixed individuals or hybrids, and suggest possible admixture pedigrees.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Health Care Sciences & Services
Anne Cathrine Baun Thuesen, Frederik Filip Staeger, Alba Kaci, Marie Holm Solheim, Ingvild Aukrust, Emil Jorsboe, Cindy G. Santander, Mette K. Andersen, Zilong Li, Arthur Gilly, Sara Elizabeth Stinson, Anette Prior Gjesing, Peter Bjerregaard, Michael Lynge Pedersen, Christina Viskum Lytken Larsen, Niels Grarup, Marit E. Jorgensen, Eleftheria Zeggini, Lise Bjorkhaug, Pal Rasmus Njolstad, Anders Albrechtsen, Ida Moltke, Torben Hansen
Summary: This study aimed to identify and characterize novel variants in genes associated with MODY in the Greenlandic population. Through screening data from Greenlandic population cohorts, researchers identified a novel variant in the known MODY gene HNF1A that is specific to the Greenlandic Inuit population. The variant was found to be associated with diabetes and glucose levels, and had a significant impact on diabetes prevalence in Greenland.
LANCET REGIONAL HEALTH-EUROPE
(2023)
Article
Biochemistry & Molecular Biology
Cristina Leal Rodriguez, Shiraz A. Shah, Morten Arendt Rasmussen, Jonathan Thorsen, Ulrika Boulund, Casper-Emil Tingskov Pedersen, Josue L. Castro-Mejia, Christina Egeo Poulsen, Casper Sahl Poulsen, Ling Deng, Frej Andreas Nohr Larsen, Michael Widdowson, Yichang Zhang, Soren J. Sorensen, Sylvain Moineau, Marie-Agnes Petit, Bo Chawes, Klaus Bonnelykke, Dennis S. Nielsen, Jakob Stokholm
Summary: Components of the gut virome of 1-year-old children are associated with increased risk of development of asthma later in life, probably through direct interaction between phages and the host immune system.
Article
Allergy
Signe Kjeldgaard Jensen, Mathias Elsner Melgaard, Casper-Emil Tingskov Pedersen, Luo Yang, Nilo Vahman, Jacob P. Thyssen, Ann-Marie M. Schoos, Jakob Stokholm, Hans Bisgaard, Bo Chawes, Klaus Bonnelykke
Summary: Blood eosinophil count at 18 months was not associated with current wheezing/asthma or atopic dermatitis, while blood eosinophil count at age 6 years was associated with increased occurrence of current wheezing/asthma, atopic dermatitis, and allergic rhinitis. Blood eosinophil count at 18 months did not predict persistence or development of recurrent wheeze/asthma or atopic dermatitis at age 6 years.
PEDIATRIC ALLERGY AND IMMUNOLOGY
(2023)
