Article
Medical Laboratory Technology
Matthijs Vynck, Friedel Nollet, Lode Sibbens, Helena Devos
Summary: The study suggests that screening at least 40 biallelic markers is necessary to achieve enough informative markers. There is room for optimization in current chimerism assays, and more effective assays can be designed through support of the introduced simulation framework.
CLINICA CHIMICA ACTA
(2022)
Article
Computer Science, Information Systems
Ziyang Lu, Yiwei Zhang
Summary: This study focuses on deletion and insertion errors in DNA-based storage and communication systems. An upper bound on the size of binary codes that can correct a (t, s)-burst error is provided, demonstrating the minimum redundancy required for such codes. An explicit construction for binary (t, s)-burst correcting codes for the case where t = 2s is also presented.
IEEE TRANSACTIONS ON INFORMATION THEORY
(2023)
Article
Medical Laboratory Technology
Lauren A. Choate, Alaa Koleilat, Kimberley Harris, Noemi Vidal-Folch, Adam Guenzel, Jessica Newman, Brenda J. Peterson, Sandra E. Peterson, Christopher S. Rice, Laura J. Train, Linda Hasadsri, Cherisse A. Marcou, Ann M. Moyer, Linnea M. Baudhuin
Summary: This study demonstrates that reportable indel variants up to 68 base pairs can be accurately assessed using NGS, even when they occur in complex regions. Depending on the complexity of the region or variant, Sanger sequence confirmation of indels is usually not necessary if the variants meet appropriate coverage and allele frequency thresholds.
CLINICAL CHEMISTRY
(2023)
Article
Genetics & Heredity
Elli-Mari Aska, Bulat Zagidullin, Esa Pitkaenen, Liisa Kauppi
Summary: Microsatellite sequences are prone to slippage during DNA replication, resulting in insertion-deletion loops. Mismatch repair is critical for maintaining microsatellite stability and its deficiency leads to microsatellite instability. By studying mouse T cells, researchers discovered different dynamics of insertions and deletions in MMR-deficient cells. Factors such as microsatellite length, nucleotide composition, gene characteristics, and replication timing were found to affect the propensity of insertions and deletions.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Rabea Ghandour, Yang Gao, Josephin Laskowski, Rouhollah Barahimipour, Stephanie Ruf, Ralph Bock, Reimo Zoschke
Summary: In plant biotechnology, the expression of transgenes in chloroplasts is common practice. However, the potential unintended effects on native chloroplast genes are often overlooked. This study examined the expression of the chloroplast genome in transplastomic tobacco plants and found that transgene insertion can lead to overexpression of downstream genes and interfere with the transcription and translation of nearby genes. The study suggests strategies to minimize unintended consequences of transgene expression on native chloroplast genes.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Computer Science, Information Systems
Yubo Sun, Yuanxiao Xi, Gennian Ge
Summary: Motivated by applications in modern storage devices, this paper studies the sequence reconstruction problem by determining the maximum intersection size between two error balls and designing reconstruction codes. It focuses on channels with single-burst-insertion/deletion errors and fully determines the maximum intersection size for both fixed-length and variable-length models. Characterizations of sequence pairs with a certain intersection size are used to design reconstruction codes and analyze their lower bounds. The results are extended to the burst-edit channel.
IEEE TRANSACTIONS ON INFORMATION THEORY
(2023)
Article
Plant Sciences
Thant Zin Maung, Ji-Min Yoo, Sang-Ho Chu, Kyu-Won Kim, Ill-Min Chung, Yong-Jin Park
Summary: The research investigated the genotypic and haplotypic variations of the GBSSI gene, identifying new functional SNPs and classifying the rice collection into different groups based on these variations. The diversity of GBSSI was found to be higher in wild rice compared to cultivated rice, with insights into the domestication process. Selective sweep signatures provided informative insights for future breeding and understanding of the evolutionary history of the gene.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Takuya Norizuki, Naoki Minamino, Miyuki Sato, Takashi Ueda
Summary: This study investigates the involvement of autophagy in the degradation and reorganization of plastids during spermiogenesis in the liverwort Marchantia polymorpha. The results show that autophagy-dependent degradation of plastids occurs during spermiogenesis and impaired autophagy leads to defective morphological changes and starch accumulation in the plastid.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Christopher James O'Grady, Vignesh Dhandapani, John K. Colbourne, Dagmar Frisch
Summary: Whole genome sequencing is crucial for studying genome variation in natural populations, and large dormant eggbanks of aquatic invertebrates provide valuable information on genomic processes over centuries. An optimized workflow for whole genome amplification (WGA) has been developed to address limited DNA amounts in single eggs, allowing successful downstream whole genome sequencing of historical eggs. Comparison of two WGA kits showed high genome coverage breadth in samples, with high recovery of genomic positions with single nucleotide polymorphisms for genotyping, and even obtaining 100% coverage of mitochondrial genomes from the oldest isolates. Mitochondrial DNA serves as an additional source for evolutionary studies of these populations.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Automation & Control Systems
Naofumi Hama, Masayoshi Mase, Art B. Owen
Summary: An important task in explainable AI is to identify the most important features behind a prediction made by a black box function. The quality of algorithms that rank pixels by importance for classification can be evaluated using insertion and deletion tests. Based on regression problems, we establish a formula to calculate the area under the curve (AUC) criteria for feature ranking. We propose an alternative area calculation for regression settings and compare different methods of computing feature importances.
JOURNAL OF MACHINE LEARNING RESEARCH
(2023)
Article
Food Science & Technology
Thant Zin Maung, Sang-Ho Chu, Yong-Jin Park
Summary: The study revealed genetic variations of the rice GBSSII gene through haplotype analysis, showing differences between cultivated and wild varieties in terms of nucleotide diversity. Tajima's D values and F-ST analysis further demonstrated the domestication and evolutionary characteristics of GBSSII.
Article
Plant Sciences
Phen Garrett, Hannes Becher, Galina Gussarova, Claude W. dePamphilis, Rob W. Ness, Shyam Gopalakrishnan, Alex D. Twyford
Summary: This study conducted a phylogenomic analysis of Euphrasia species and found extensive phylogenetic discordance at deeper and shallower nodes, with broad-scale geographic structure of genomic variation but a lack of definitive taxonomic signal.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Jong Im Kim, Bok Yeon Jo, Myung Gil Park, Yeong Du Yoo, Woongghi Shin, John M. Archibald
Summary: The Raphidophyceae is an important lineage of eukaryotic organisms that play a crucial role in marine and freshwater ecosystems. By sequencing and analyzing the plastid genomes of several species, researchers have gained insights into the evolutionary history of raphidophycean plastids. The findings suggest that lateral gene transfer from diatoms has contributed to the genetic diversity and evolution of raphidophyte plastid genomes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Virology
Lili Chu, Shengqiang Ye, Jiaying Wang, Duo Peng, Xiaoyan Wang, Yunguo Qian, Dabing Zhang
Summary: Duck adenovirus 3 (DuAdV-3; strain HB) isolated in this study is a mutant with several insertion and deletion events in its genome, demonstrating genetic variation among DuAdV-3 isolates.
ARCHIVES OF VIROLOGY
(2022)
Article
Agronomy
Kunneng Zhou, Caijuan Zhang, Jiafa Xia, Peng Yun, Yuanlei Wang, Tingchen Ma, Zefu Li
Summary: The mutant asl4 disrupts early chloroplast development and chlorophyll biosynthesis, with some genes involved in chloroplast biogenesis being up-regulated and others down-regulated. Plastid transcription is impaired in asl4 mutant tissues, leading to reduced levels of most plastid-encoded genes and proteins. The decreased contents of chloroplast rRNAs and ribosomal proteins indicate impaired chloroplast ribosome biogenesis in the asl4 mutant.