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Articles by Ruby JG
Regulation of plant gene expression by tsRNAs in response to abiotic stress
Regulation of plant gene expression by tsRNAs in response to abiotic stress 1Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China 2Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China 3College of Agriculture and Biology, Zhongkai University of...
The miR-290 and miR-302 clusters are essential for reprogramming of fibroblasts to induced pluripotent stem cells
The derivation of induced pluripotent stem cells (iPSCs) from somatic cells through the introduction of exogenous factors1 has been a major boon to the scientific and medical communities, as it has enabled new and previously unimaginable advancements in disease modeling, pharmaceutical development, and regenerative medicine (reviewed in2-6).
Structural basis of endo-siRNA processing by Drosophila Dicer-2 and Loqs-PD
RNA interference (RNAi) is a highly conserved mechanism of RNA silencing that plays a pivotal role in regulating gene expression, defending against viral infections, and protecting the genome from transposon activity. This process operates at both the post-transcriptional and epigenetic levels [1, 2]. All RNAi pathways share a common effector complex, which consists of an argonaute protein paired with a short single-stranded RNA molecule.
An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters
Genes are not randomly distributed across genomes. Instead, many genes with shared functions are organized into clusters. This organizational pattern reflects the selective pressure for co-regulation and coordinated expression of functionally related genes [1, 2]. Various types of gene clusters have been discovered. For example, CRISPR clusters provides adaptive immunity against phage infections and plasmid invasions in bacteria and archaea [3].
Sida chlorotic leaf virus: a new recombinant begomovirus found in non-cultivated plants and Cucumis sativus L
Materials & Methods Sample collection and DNA extraction Leaves with typical geminivirus disease symptoms from the Sida and Malvastrum genera (Fig. 1) were collected from Colima, México (19.2209, −103.8000; 19.2049, −103.7557; 19.3086, −103.5553; 19.3335, −103.7373; 19.3618, −103.7945) during August 2018.
How genetic defects in piRNA trimming contribute to male infertility
1 INTRODUCTION Since their discovery in Drosophila melanogaster and mammals nearly two decades ago, PIWI-interacting RNAs (piRNAs) have been shown to play conserved roles in transposon silencing and germline gene regulation to ensure animal fertility.1-12 Bound to PIWI proteins, piRNAs serve as small RNA guides to regulate gametogenesis via RNA-induced silencing complexes.10, 11, 13-15 In mammals, a defective piRNA pathway in germ cells causes spermatogenic failure and male infertility.16-55...
Small RNAs in epigenetic inheritance: from mechanisms to trait transmission
Abstract Inherited information is transmitted to progeny primarily by the genome through the gametes. However, in recent years, epigenetic inheritance has been demonstrated in several organisms, including animals. Although it is clear that certain post-translational histone modifications, DNA methylation, and noncoding RNAs regulate epigenetic inheritance, the molecular mechanisms responsible for epigenetic inheritance are incompletely understood.
VGEA: an RNA viral assembly toolkit
Discussion VGEA is built on the snakemake workflow management system (BKöster & Rahmann, 2012), a workflow management system that allows the effortless deployment and execution of complex distributed computational workflows in any UNIX-based system, from local machines to high-performance computing clusters. It is a user-friendly, customizable and reproducible pipeline which can be deployed on a personal computer and which can run from start to finish with a single command.
Naked Mole-Rat mortality rates defy gompertzian laws by not increasing with age.
Elife. 2018 Jan 24;7. pii: e31157. doi: 10.7554/eLife.31157. Ruby JG1, Smith M1, Buffenstein R1. Abstract The longest-lived rodent, the naked mole-rat (Heterocephalus glaber), has a reported maximum lifespan of >30 years and exhibits delayed and/or attenuated age-associated physiological declines. We questioned whether these mouse-sized, eusocial rodents conform to Gompertzian mortality laws by experiencing an exponentially increasing risk of death as they get older.
Estimates of the Heritability of Human Longevity Are Substantially Inflated due to Assortative Mating.
Human life span is a phenotype that integrates many aspects of health and environment into a single ultimate quantity: the elapsed time between birth and death. Though it is widely believed that long life runs in families for genetic reasons, estimates of life span "heritability" are consistently low (∼15-30%). Here, we used pedigree data from Ancestry public trees, including hundreds of millions of historical persons, to estimate the heritability of human longevity.
Improving ancient DNA genome assembly
The general structure of our two-layer assembly approach is to use multiple assemblies in a first layer with different k-mers, which are then merged in a second layer assembly using an overlap-based assembly program (see Fig. 1). First the reads are preprocessed by removing sequenced adapters and clipping low-quality bases. After that, multiple de novo assemblies are generated using a de Bruijn graph approach with multiple values for k.
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