Article
Biochemical Research Methods
Pedro G. Nachtigall, Felipe G. Grazziotin, Inacio L. M. Junqueira-de-Azevedo
Summary: MITGARD is an automated pipeline that reliably recovers mitochondrial genomes from RNA-seq data of various sources. The tool can reconstruct mitogenomes across different species and sequencing schemes, demonstrating its effectiveness even in scenarios of low-sequencing depth. Additionally, MITGARD's use of phylogenetically related references allows for the recovery of entire mitogenomes or most mitochondrial genes, making it valuable for biodiversity projects and evolutionary studies.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Mariya A. Kusliy, Nadezhda V. Vorobieva, Alexey A. Tishkin, Alexey I. Makunin, Anna S. Druzhkova, Vladimir A. Trifonov, Tumur-O. Iderkhangai, Alexander S. Graphodatsky
Summary: The study of ancient Mongolian horse samples revealed genetic continuity and close phylogenetic relationships with horses from regions such as the Middle East, China, and Italy. Despite 3000 years of Mongolian peoples' migrations, the mitochondrial haplogroup composition of Mongolian horse populations remains almost unchanged.
Article
Ecology
Leonardo Dapporto, Mattia Menchetti, Raluca Voda, Cecilia Corbella, Sylvain Cuvelier, Imed Djemadi, Martin Gascoigne-Pees, Joan C. Hinojosa, Nok Ting Lam, Maria Serracanta, Gerard Talavera, Vlad Dinca, Roger Vila
Summary: This article introduces four new resources for Western Palaearctic butterflies, including an updated species checklist, mitochondrial COI sequences, intraspecific genetic variation indexes, and species-level distribution maps. These resources will facilitate comparative studies, integrative taxonomy, and conservation strategies.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Article
Multidisciplinary Sciences
Marco Tigano, Danielle C. Vargas, Samuel Tremblay-Belzile, Yi Fu, Agnel Sfeir
Summary: The study reveals that mtDSBs activate a type-I interferon response, leading to the phosphorylation of STAT1 and activation of interferon-stimulated genes. After breaks in mtDNA, herniation mediated by BAX and BAK releases mitochondrial RNA into the cytoplasm and triggers a RIG-I-MAVS-dependent immune response.
Article
Genetics & Heredity
Renkui Bai, Hong Cui, Joseph M. Devaney, Katrina M. Allis, Amanda M. Balog, Xinyue Liu, Rhonda E. Schnur, Faye L. Shapiro, Ariel Brautbar, Juvianee Estrada-Veras, Laurel Hochstetler, Allyn McConkie-Rosell, Marie T. McDonald, Benjamin D. Solomon, Sean Hofherr, Gabriele Richard, Sharon F. Suchy
Summary: Reports questioning the traditional belief of exclusive maternal transmission of human mtDNA have sparked debates, with recent findings suggesting a potential biparental transmission mode. The observed paternal origin of mitochondrial haplogroups is likely due to rare coamplification of nuclear mtDNA segments during testing. Further research is needed to clarify the clinical significance of these findings.
GENETICS IN MEDICINE
(2021)
Article
Ecology
Thomas F. Duda
Summary: The study demonstrated variation in estimates of mu (m)/mu (n) among gastropod groups, with the Bradybaenidae family showing a significantly higher mutation rate compared to other groups. Data sets containing sequences of recently diverged species tended to exhibit higher values of mu (m)/mu (n).
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Duilio Iamonico, Olga De Castro, Emanuela Di Iorio, Gianluca Nicolella, Mauro Iberite
Summary: This study investigates four endemic species from the Tyrrhenian coast of central Italy and the Ponziane Archipelago using molecular and morphometric analyses. The results provide new information about the taxonomy of these species and suggest that they should be considered as a single species entity.
Article
Plant Sciences
Olga De Castro, Gianluigi Bacchetta, Salvatore Brullo, Emanuele Del Guacchio, Emanuela Di Iorio, Carole Piazza, Paolo Caputo
Summary: This study investigates the morphological variability and native status of Genista etnensis, a tree endemic to Sicily, Sardinia, and Corsica. The results suggest strong isolation between populations in different biogeographical provinces and a possible origin in the middle Pleistocene.
Article
Multidisciplinary Sciences
James de Villiers, Rensu Theart
Summary: This paper presents a novel method using neural networks to predict the occurrence and locations of mitochondrial fission, fusion, and depolarisation events in 3D. The accuracy achieved by the neural networks in predicting these events is relatively low, but it indicates their potential usefulness in the absence of time-lapse sequences. The results of this paper can serve as a baseline for future research in this area.
Review
Biochemistry & Molecular Biology
Liying Xue, Jesse D. Moreira, Karan K. Smith, Jessica L. Fetterman
Summary: Nuclear-mitochondrial DNA segments (NUMTs) are fragments of mtDNA that have been inserted into the nuclear genome. They can contaminate mtDNA sequencing results and introduce false positive variants. This review discusses their prevalence, mechanisms of de novo insertion, and approaches for minimizing contamination. Both wet lab-based and computational methods can be used to filter NUMTs, and multiple approaches should be applied for effective identification.
Article
Biochemistry & Molecular Biology
Sung-Ik Cho, Seonghyun Lee, Young Geun Mok, Kayeong Lim, Jaesuk Lee, Ji Min Lee, Eugene Chung, Jin-Soo Kim
Summary: Mitochondrial DNA editing is crucial for modeling mitochondrial genetic disorders and potential future treatments. This study presents a new editing enzyme called TALEDs, which efficiently induce A-to-G editing in human mitochondria.
Article
Genetics & Heredity
Xuejing Li, Dan Xu, Beilei Cheng, Yunlian Zhou, Zhimin Chen, Yingshuo Wang
Summary: A new mutation in the CD40LG gene was found in a X-HIGM patient, caused by de novo nuclear mitochondrial DNA sequences (NUMTs), highlighting a novel mechanism for X-HIGM.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2021)
Review
Biochemistry & Molecular Biology
Cristina Mazzaccara, Bruno Mirra, Ferdinando Barretta, Martina Caiazza, Barbara Lombardo, Olga Scudiero, Nadia Tinto, Giuseppe Limongelli, Giulia Frisso
Summary: Mitochondrial Cardiomyopathy is a common manifestation of multi-organ Mitochondrial Diseases, presenting diagnostic complexities due to clinical and genetic heterogeneity. Molecular screening plays a crucial role in MD management and identifying disease genes can aid in developing targeted gene panels for accurate diagnosis of patients with clinical suspect of mitochondrial cardiomyopathies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Forestry
Meng Dang, Hui-Juan Zhou, Keith E. Woeste, Ming Yue, Yi Zhang, Gui-Fang Zhao, Shuo-Xin Zhang, Peng Zhao
Summary: The study found that even when sympatric, walnut species rarely introgress, indicating strong hybridization barriers between them. The two species occupy distinct ecological niches, and sympatric populations may be the result of recent postglacial population expansion.
TREES-STRUCTURE AND FUNCTION
(2021)
Article
Cardiac & Cardiovascular Systems
Ruipeng Wei, Ying Ni, Peter Bazeley, Sneha Grandhi, Janet Wang, Samuel T. Li, Stanley L. Hazen, W. H. Wilson Tang, Thomas LaFramboise
Summary: This study found associations between mtDNA copy number and cardiovascular disease patient phenotypes, as well as a potential protective role for rare inherited mtDNA variants. The results suggest that mtDNA content and abundance may serve as biomarkers in heart disease, valid across diverse ancestries.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2021)
Article
Biochemistry & Molecular Biology
Yu-Chi Chen, Masoud Nazarizadeh, Fu-Min Lei, Xiao-Jun Yang, Cheng-Te Yao, Feng Dong, Lu Dong, Fa-Sheng Zou, Sergei V. Drovetski, Yang Liu, Chun-Cheng Huang, Chih-Ming Hung
Article
Biochemistry & Molecular Biology
Hung N. Nguyen, Chia-Wei Lu, Jui-Hua Chu, Larry Lee Grismer, Chih-Ming Hung, Si-Min Lin
Article
Multidisciplinary Sciences
Marko Rakovic, Julio M. Neto, Ricardo J. Lopes, Evgeniy A. Koblik, Igor V. Fadeev, Yuriy V. Lohman, Sargis A. Aghayan, Giovanni Boano, Marco Pavia, Yoav Perlman, Yosef Kiat, Amir Ben Dov, J. Martin Collinson, Gary Voelker, Sergei V. Drovetski
Article
Biochemical Research Methods
Chun-Cheng Huang, Yi-Ying Chen, Yi-Ting Fang, Yu-Chi Chen, Chih-Ming Hung
JOURNAL OF NEUROSCIENCE METHODS
(2019)
Article
Biochemistry & Molecular Biology
Nicholas J. Clark, Sergei Drovetski, Gary Voelker
Article
Ornithology
Tiago M. Rodrigues, Edward H. Miller, Sergei V. Drovetski, Robert M. Zink, Jon Fjeldsa, David Goncalves
Summary: The study looked at phenotypic differentiation in two shorebird species, finding that while there were no significant differences in skeletal variables between the species, there were significant differences in plumage traits. These differences suggest a more rapid divergence in socially selected traits between the species than in traits related to resource use.
Article
Ornithology
Yi-Ting Fang, Cheng-Te Yao, Yu-Cheng Hsu, Chih-Ming Hung
Summary: Environment plays a key role in the evolution of bird plumage coloration, with mountains exhibiting different ecological conditions that may cause intraspecific plumage divergence. The study on Rufous-capped Babblers in Taiwan shows that birds in montane habitats have higher UV-reflectance and brightness compared to lowland birds, likely due to differences in UV intensity between the habitats. Additionally, there is significant sexual dichromatism in plumage coloration, with females exhibiting brighter or stronger UV-associated coloration than males, suggesting minimal impact of sexual selection on babbler plumage.
Article
Environmental Sciences
Jhih-Syuan Wang, Mao-Ning Tuanmu, Chih-Ming Hung
Summary: The study found that ALAN had a positive impact on the reproductive success of barn swallows, especially in their first brood. Parent birds in nests with higher ALAN intensity had higher feeding rates and extended feeding time past sunset, likely due to increased begging behavior of their chicks. Night-feeding behavior might contribute to increased fledging success.
ENVIRONMENTAL POLLUTION
(2021)
Article
Biochemistry & Molecular Biology
Chia-Wei Lu, Cheng-Te Yao, Chih-Ming Hung
Summary: This study examined the domestication history of a recently domesticated species, the society finch, and its parent species, the white-rumped munia, through genomic analyses and Sequentially Markov Coalescent models. The results showed that domestication of the society finch likely originated from inbreeding rather than hybridization. Surprisingly, the use of Sequentially Markov Coalescent models revealed a distorted population trajectory in the society finch, emphasizing the need for caution and multiple analyses when interpreting histories of recently domesticated species.
Article
Ecology
Chih-Ming Hung, Shu-Han Tsao, Pei-Lin Chiang, Shang-Ping Wu, Mao-Ning Tuanmu, Jia-Yang Juang
Summary: This study reveals the functional connection between bird nests and eggshells, suggesting that birds produce stiffer eggs in response to higher collision risk in unstable or enclosed nests. Results indicate that the evolution of eggshell stiffness is more likely to be influenced by nest characters. The study also highlights the trade-off between competing for established nesting niches and exploring new territories for birds.
Article
Ecology
Jing-Chia Guo, Jo-Szu Tsai, Jhih-Syuan Wang, Ya-Wen Lin, Pei-Jen Lee Shaner, Chih-Ming Hung
Summary: A facilitative species interaction between Asian house martins and russet sparrows was discovered in a montane farming area of Taiwan, where the use of house martin nests improved the reproductive success of the endangered russet sparrows, suggesting that man-made structures can be used as a conservation tool.
ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Chia-Wei Lu, Shih-Ting Huang, Shun-Jen Cheng, Chen-Tau Lin, Yu-Cheng Hsu, Cheng-Te Yao, Feng Dong, Chih-Ming Hung, Hao-Chih Kuo
Summary: The rufous-capped babbler in Taiwan split from its sister group in mainland China around 1-2 million years ago and colonized mountain habitats at least twice around 0.03-0.22 million years ago. Gene flow occurred between montane and lowland populations, indicating strong selection related to different elevations. The study identified genes COL9A1 and SOX11 as candidates underlying beak size changes. Altitudinally divergent mutations were found to regulate genes related to various functions and morphological traits. These findings enhance our understanding of genomic mechanisms underlying adaptation to high elevation environments.
Article
Evolutionary Biology
Yu-Chi Chen, Hao-Chih Kuo, Wen-Sui Lo, Chih-Ming Hung
BMC EVOLUTIONARY BIOLOGY
(2020)
Article
Microbiology
Gary R. Graves, Kenan O. Matterson, Christopher M. Milensky, Brian K. Schmidt, Michael J. O'Mahoney, Sergei Drovetski
Article
Microbiology
Sergei Drovetski, Michael J. O'Mahoney, Kenan O. Matterson, Brian K. Schmidt, Gary R. Graves