Article
Multidisciplinary Sciences
Stephanie Gamez, Duverney Chaverra-Rodriguez, Anna Buchman, Nikolay P. Kandul, Stelia C. Mendez-Sanchez, Jared B. Bennett, Hector M. C. Sanchez, Ting Yang, Igor Antoshechkin, Jonny E. Duque, Philippos A. Papathanos, John M. Marshall, Omar S. Akbari
Summary: This study explores the use of CRISPR technology for sex selection and gene drive by developing a transgenic line of Drosophila melanogaster expressing Cas9 from the Y chromosome. The results demonstrate the high efficiency of this transgenic line for population control.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Lefan Pu, Farhan Goher, Mengke Zeng, Dongsheng Wu, Qingdong Zeng, Dejun Han, Chunlian Li
Summary: This study identified and evaluated the resistance source to crown rot disease in wheat using genetic diversity. Six varieties were classified as resistant and 79 varieties as moderately resistant. Genome-wide association analysis identified 33 significant SNPs associated with seedling resistance to crown rot. These findings provide a theoretical foundation for genetic improvement and breeding for crown rot resistance in wheat.
Article
Biochemistry & Molecular Biology
Olga V. Andreenkova, Olga D. Shishkina, Alexandra I. Klimenko, Aleksandra E. Korenskaia, Margarita A. Bobrovskikh, Natalja V. Shatskaya, Gennady V. Vasiliev, Nataly E. Gruntenko
Summary: Several methods for extracting Wolbachia DNA from insect hosts have been described, but the low quantity of the bacteria made these techniques labor-intensive. This paper proposes a simplified and accelerated method for isolating high-purity Wolbachia DNA from Drosophila melanogaster, using centrifugation, filtration, and a modified version of the Livak buffer protocol. The proportion of Wolbachia DNA in total DNA was quantified using sequencing and bioinformatic analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Ecology
Weihao Dou, Yunheng Miao, Jinhua Xiao, Dawei Huang
Summary: Research has shown that Wolbachia affects various biological processes in Drosophila melanogaster adult testes, with genes related to carbohydrate metabolism, lysosomal degradation, proteolysis, lipid metabolism, and immune response being upregulated in the presence of Wolbachia. In contrast, genes associated with cutin and wax biosynthesis, and peroxisome pathways were downregulated. No differentially expressed genes related to spermatogenesis were found in the datasets.
Article
Biochemistry & Molecular Biology
Monika Mokrzycka, Stefan Stojalowski, Miroslaw Tyrka, Przemyslaw Matysik, Barbara Zmijewska, Rafal Marcinkowski, Urszula Wozna-Pawlak, Roza Martofel, Michal Rokicki, Monika Rakoczy-Trojanowska, Pawel Krajewski
Summary: This study identified markers associated with wheat agronomic traits using genome-wide association analysis. The study also investigated the effects of markers on heterosis and their linkage disequilibrium grouping. The results revealed a large number of single nucleotide polymorphisms with significant effects, predominantly influencing protein translation modification. These findings provide valuable insights for developing new wheat varieties with desirable properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Yuying Fan, Yue Wang, Gregory A. Korfanty, Meagan Archer, Jianping Xu
Summary: Aspergillus fumigatus is a common causative agent of aspergillosis, with triazoles being the common first-line drugs for treatment. However, triazole resistance in A. fumigatus is increasing, with a large number of novel mutations potentially associated with triazole resistance.
Article
Genetics & Heredity
Wan Song, Ram Podicheti, Douglas B. Rusch, William Daniel Tracey
Summary: Pseudouridine (Psi) is a common post-transcriptional modification of RNA. It is found in various types of RNA, including rRNA, snRNA, snoRNA, tRNA, non-coding RNA, and recently discovered on mRNA. This study focused on the transcriptome-wide detection of Psi in Drosophila melanogaster and identified thousands of Psi modifications in the female fly head transcriptome. The presence of Psi was found in both cellular and mitochondrial rRNAs, as well as in mRNAs. The study also highlighted the importance of pseudouridylation for ribosome and mitochondrial function, as many Psi sites were found in genes encoding ribosomal proteins and mitochondrial encoded RNAs. The study also identified specific RNAs enriched with Psi, such as the non-coding RNA 7SLRNA and highly expressed yolk protein mRNAs. Additionally, the study compared the pseudouridine profiles in the RluA-2 mutant and the control genotype, revealing potential RluA-2 targets. The loss of RluA-2 was found to have a major impact on the ribosome and translational machinery, as shown by the differential gene expression analysis of the mutant transcriptome.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Venkata Rami Reddy Yannam, Marlon Caicedo, Rosa Ana Malvar, Bernardo Ordas
Summary: The study used GWAS and genome-wide association analysis to elucidate the genetic characteristics of senescence and its impact on agronomic traits. Core senescence genes could serve as crucial candidates for future gene editing and breeding purposes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Ronald D. Smith, Joshua R. Puzey, Gregory D. Conradi Smith
Summary: In an empirical analysis, it was found that transposable element count in natural populations of Mimulus guttatus and Drosophila melanogaster showed a surprisingly high variance. This variance is likely due to copy-and-paste proliferation dynamics rather than purifying selection on total element load.
Article
Biochemistry & Molecular Biology
Alexandru Al Ecovoiu, Alexandru Marian Bologa, David Ioan Mihail Chifiriuc, Andrei Mihai Ciuca, Nicoleta Denisa Constantin, Iulian Constantin Ghionoiu, Iulian Cristian Ghita, Attila Cristian Ratiu
Summary: This study presents the new functions of GA_v2 tool for mapping and annotation of transposons and demonstrates its applicability in the genome of D. melanogaster. The results indicate that GA_v2 is a reliable and autonomous tool for transposon mapping and annotation in genomes sequenced by long sequencing technology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Zhiyu Hao, Jin Gao, Yuxin Song, Runqing Yang, Di Liu
Summary: In this study, a hierarchical mixed model (Hi-LMM) was proposed to estimate genomic breeding values and infer the association between genotypes and phenotypes, effectively correcting confounding factors and improving the statistical power of association analysis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Fisheries
Zhen Xi Zhang, Zhi Yong Wang, Ming Fang, Kun Ye, Xin Tang, Dong Ling Zhang
Summary: A genome-wide association study identified 14 SNPs correlated with disease resistance in large yellow croaker, with candidate genes involved in the NF-kappa B signaling pathway. This suggests a complex polygenic architecture for resistance against the parasite scuticociliate in large yellow croaker and provides a valuable foundation for future marker-assisted selection breeding.
Article
Genetics & Heredity
Jiaqi Li, Jingjing Wang, Peijing Zhang, Renying Wang, Yuqing Mei, Zhongyi Sun, Lijiang Fei, Mengmeng Jiang, Lifeng Ma, E. Weigao, Haide Chen, Xinru Wang, Yuting Fu, Hanyu Wu, Daiyuan Liu, Xueyi Wang, Jingyu Li, Qile Guo, Yuan Liao, Chengxuan Yu, Danmei Jia, Jian Wu, Shibo He, Huanju Liu, Jun Ma, Kai Lei, Jiming Chen, Xiaoping Han, Guoji Guo
Summary: This study generated single-cell whole-body expression landscapes of zebrafish, Drosophila, and earthworm using Microwell-seq. By integrating cell landscapes from eight representative species, the researchers developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory programs. Conserved genetic regulation in vertebrates and invertebrates were revealed through comparison of cell-type-specific transcription factors. This work provides a valuable resource and a new strategy for studying regulatory grammar in diverse biological systems.
Article
Plant Sciences
Hao Tang, Zhi Tan, Xiangxiang Wang, Lisheng Yang, Guoyue Chen, Hua Yu, Zhien Pu, Qiantao Jiang, Maolian Li, Mengping Cheng, Pengfei Qi, Wei Li, Yujiao Liu, Jirui Wang
Summary: Black point (BP) disease is a significant problem in China, affecting wheat grain quality. This study evaluated 272 Chinese wheat landraces for their BP reaction and identified 11 QTLs for BP resistance, along with novel molecular markers that can aid molecular breeding efforts for developing resistant cultivars.
Article
Food Science & Technology
Guocai Zhang, Xianjun Dai
Summary: Anthocyanin extracts from bilberry (BANCs) have been found to effectively prolong the lifespan of flies, improve reproductive capacity and antioxidant capacity. This is achieved by altering the growth cycle, sex ratio, and ROS levels in the offspring's fat bodies, as well as reducing the expression levels of antioxidant and autophagy-related genes in UV-treated flies.
CURRENT RESEARCH IN FOOD SCIENCE
(2022)
Article
Behavioral Sciences
Zhengyang Zhou, Hung-Chih Ku, Sydney E. Manning, Ming Zhang, Chao Xing
Summary: This study presents a flexible statistical procedure to detect gene-environment interaction (GxE) regardless of whether the underlying relationship is linear or not. By modeling the joint genetic and GxE effects as a varying-coefficient function of the environmental factor, the proposed model is able to capture dynamic trajectories of GxE. A likelihood ratio test with a fast Monte Carlo algorithm is employed for hypothesis testing. Simulations and real data analysis demonstrate the validity and power of the proposed model in various settings, especially for nonlinear GxE.
Article
Multidisciplinary Sciences
Sydney Manning, Hung-Chih Ku, Douglas Dluzen, Chao Xing, Zhengyang Zhou
Summary: Identification of new genetic signals associated with susceptibility to complex human diseases is crucial for disease diagnosis, prevention, and treatment. This study compares the power of the Jonckheere-Terpstra (JT) trend test and the Cochran-Armitage (CA) trend test under different scenarios, and shows that the JT trend test outperforms the CA trend test in terms of statistical power in certain circumstances, especially when the sample size is small and the minor allele frequency is low. Overall, the JT trend test is a valuable alternative to the CA trend test for better detection of genetic signals and a finer understanding of their genetic architecture.
Article
Radiology, Nuclear Medicine & Medical Imaging
Zhenyu Xiong, Yuncheng Zhong, Thomas I. Banks, Robert Reynolds, Tsuicheng Chiu, Jun Tan, You Zhang, David Parsons, Yulong Yan, Andrew Godley, Strahinja Stojadinovic
Summary: This study presents data from the clinical commissioning of an Xstrahl 150 x-ray unit used for superficial radiotherapy. The measured characteristics of the machine were within specifications, and the PDD data showed excellent agreement with published values.
BIOMEDICAL PHYSICS & ENGINEERING EXPRESS
(2023)
Article
Microbiology
Maikke B. Ohlson, Jennifer L. Eitson, Alexandra I. Wells, Ashwani Kumar, Seoyeon Jang, Chunyang Ni, Chao Xing, Michael Buszczak, John W. Schoggins
Summary: Viruses rely on host ribosomes for protein synthesis, but the specific factors involved in translation of viral RNAs are not fully understood. Through a CRISPR screen, researchers identified multiple host factors, including 60S ribosome biogenesis proteins, that are required for viral protein synthesis. In addition, the study revealed the importance of SBDS and SPATA5 in viral replication for a wide range of viruses.
Article
Chemistry, Medicinal
Leah S. Imlay, Aloysus K. Lawong, Suraksha Gahalawat, Ashwani Kumar, Chao Xing, Nimisha Mittal, Sergio Wittlin, Alisje Churchyard, Hanspeter Niederstrasser, Benigno Crespo-Fernandez, Bruce A. Posner, Francisco-Javier Gamo, Jake Baum, Elizabeth A. Winzeler, Benoit Laleu, Joseph M. Ready, Margaret A. Phillips
Summary: Current malaria treatments face drug resistance and there is an urgent need for new drugs. Through a screening process, we discovered (S)-SW228703 ((S)-SW703), a tyrosine amide with activity against asexual blood and liver stages of malaria and a fast-killing profile. Resistance to (S)-SW703 is associated with mutations in the Plasmodium falciparum cyclic amine resistance locus (Pf CARL) and P. falciparum acetyl CoA transporter (PfACT), similar to other compounds with fast and liver-stage activity. The exact mechanism of action or binding mode of these compounds, which are thought to act in the endoplasmic reticulum (ER), remains unknown. (S)-SW703 provides a new chemical series with broad activity against multiple life-cycle stages and a fast-killing mechanism of action, which can be further optimized for the development of new malaria treatments.
ACS INFECTIOUS DISEASES
(2023)
Article
Chemistry, Medicinal
Michael L. Neugent, Neha Hulyalkar, Ashwani Kumar, Chao Xing, Philippe E. Zimmern, Vladimir Shulaev, Nicole J. De Nisco
Summary: Glycosaminoglycans (GAGs) are linear polysaccharides with negative charges, composed of uronic acid and amino sugars. The bladder epithelium is covered by a layer of GAGs, which are believed to serve as a protective barrier and potential interaction site for the urinary microbiome. This study investigated urinary GAG composition in postmenopausal women and found that chondroitin sulfate (CS) is the major GAG. The study also identified an elevation of urinary CS in women with active recurrent urinary tract infection (rUTI). Additionally, the study revealed associations between urinary GAGs and urobiome composition, including specific bacterial species associated with different GAG types and vaginal dysbiosis.
ACS INFECTIOUS DISEASES
(2023)
Article
Biochemistry & Molecular Biology
Matthew B. McDougal, Anthony M. De Maria, Maikke B. Ohlson, Ashwani Kumar, Chao Xing, John W. Schoggins
Summary: Interferons control viral infection by inducing the expression of antiviral effector proteins encoded by interferon-stimulated genes (ISGs). Using CRISPR-based loss-of-function screens, this study identified a limited set of ISGs that mediate interferon-mediated suppression of Venezuelan equine encephalitis virus (VEEV). Combinatorial gene targeting revealed that three antiviral effectors, ZAP, IFIT3, and IFIT1, together constitute the majority of interferon-mediated restriction of VEEV, while accounting for < 0.5% of the interferon-induced transcriptome. These findings suggest a refined model of the antiviral interferon response.
Article
Multidisciplinary Sciences
Martyna Kosno, Simon L. Currie, Ashwani Kumar, Chao Xing, Michael K. Rosen
Summary: In this study, the formation of biomolecular condensates by the oncogenic fusion protein BRD4-NUT and its associated histone acetyltransferase p300 were investigated. The researchers found that a minimal fragment of NUT fused with BRD4 is sufficient to bind p300 and form condensates. The results suggest a model for condensate formation involving positive feedback and phase separation, and identify different regions of p300 that contribute to condensate formation and transcriptional regulation.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Widler Casy, Irvin T. Garza, Xin Chen, Thomas Dong, Yuhui Hu, Mohammed Kanchwala, Cynthia B. Trygg, Charles Shyng, Chao Xing, Bruce A. Bunnell, Stephen E. Braun, Steven J. Gray
Summary: The use of AAV capsid libraries with selection strategies has successfully generated novel AAVs with enhanced features. However, the inability to sequence the complete capsid gene in a high-throughput manner has limited capsid engineering. To overcome this limitation, AAV capsid shuffled libraries were generated and directed evolution was applied in mice and non-human primates to yield AAVs compatible for translational applications. The use of single molecule real-time sequencing and nuclei-enrichment step provided insights for variant identification in the central nervous system.
Article
Genetics & Heredity
Fieke W. Hoff, Chao Xing, Vinaya Simha, Anil K. Agarwal, Xunzhi Zhang, Leena Lekkala, Madhumati S. Vaishnav, Frank Vuitch, Abhimanyu Garg
Summary: Through a study on an Asian Indian family, it was found that 4 family members had Werner's syndrome instead of the common types of diabetes. The research suggests that the diagnosis of Werner's syndrome should be considered in cases with consanguinity, dysmorphic features, and malignancy.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2023)
Article
Ophthalmology
Bogale Aredo, Ashwani Kumar, Bo Chen, Chao Xing, Rafael L. Ufret-Vincenty
Summary: In this study, the fundus camera-delivered light-induced retinal degeneration model was used to analyze cell type-specific responses to retinal oxidative injury. It was found that a subpopulation of Muller glia cells plays a crucial role in the cellular recovery process. These findings may contribute to the development of therapeutic approaches for minimizing damage and promoting recovery.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2023)
Article
Ophthalmology
Brian C. Leonard, Sangwan Park, Soohyun Kim, Laura J. Young, Iman Jalilian, Krista Cosert, Xunzhi Zhang, Jessica M. Skeie, Hanna Shevalye, Nayeli Echeverria, Vanessa Rozo, Xin Gong, Chao Xing, Christopher J. Murphy, Mark A. Greiner, V. Vinod Mootha, Vijay Krishna Raghunathan, Sara M. Thomasy
Summary: This study examines the role of Wwtr1 in murine ocular structure and function, and its relationship with FECD. The results suggest that Wwtr1 deficient mice exhibit phenotypic abnormalities similar to FECD-affected patients, indicating that they could serve as a murine model for late-onset FECD.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2023)
Article
Medicine, Research & Experimental
Chunhui Jiang, Ashwani Kumar, Ze Yu, Tracey Shipman, Yong Wang, Renee M. McKay, Chao Xing, Lu Q. Le
Summary: Neurofibromatosis type 1 (NF1) is a common tumor-predisposing genetic disorder characterized by the development of benign neurofibromas. This study explored the mechanism of extracellular matrix (ECM) deposition during neurofibroma development and treatment response. The researchers found that basement membrane (BM) proteins, rather than major collagen isoforms, were upregulated in the ECM during plexiform neurofibroma (pNF) development. They also identified TGF-β1 signaling as a key regulator of ECM dynamics and demonstrated that TGF-β1 overexpression promoted pNF progression. The findings suggest that BM proteins could serve as biomarkers for diagnosing and monitoring the treatment response of NF1.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Chemistry, Medicinal
Leah S. Imlay, Aloysus K. Lawong, Suraksha Gahalawat, Ashwani Kumar, Chao Xing, Nimisha Mittal, Sergio Wittlin, Alisje Churchyard, Hanspeter Niederstrasser, Benigno Crespo-Fernandez, Bruce A. Posner, Francisco-Javier Gamo, Jake Baum, Elizabeth A. Winzeler, Benoit Laleu, Joseph M. Ready, Margaret A. Phillips
Summary: Current malaria treatments face the threat of drug resistance, necessitating the development of new drugs. Through a screening process, (S)-SW228703 ((S)-SW703) was identified as a potential antimalarial with activity against asexual blood and liver stages and a fast-killing profile. Resistance to (S)-SW703 is associated with mutations in the Plasmodium falciparum cyclic amine resistance locus (Pf CARL) and P. falciparum acetyl CoA transporter (PfACT). The discovery of (S)-SW703 offers a new chemical series with broad activity for multiple life-cycle stages and a fast-killing mechanism, which can be further optimized for malaria treatment.
ACS INFECTIOUS DISEASES
(2023)
Article
Cell Biology
Islam Oguz Tuncay, Darlene Devries, Ashlesha Gogate, Kiran Kaur, Ashwani Kumar, Chao Xing, Kimberly Goodspeed, Leah Seyoum-Tesfa, Maria H. Chahrour
Summary: This study investigates the genetics of autism spectrum disorder (ASD) in an East African population, revealing a higher prevalence of ASD and decreased genetic heterogeneity. The findings highlight the importance of African genetic variation and admixture analysis in understanding the genetic architecture of complex disorders.
