RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse

Eukaryotic genomes contain many nongenic elements that function in gene regulation, chromosome organization, recombination, repair or replication, and mutation of those elements can affect genome function and cause disease. While numerous epigenomic studies provide high coverage of gene regulatory regions, those data are not usually exposed in traditional genome annotation, and can be difficult to access and interpret without field-specific expertise. The National Center for Biotechnology Information (NCBI) therefore provides RefSeq Functional Elements (RefSeqFEs), which represent experimentally validated human and mouse nongenic elements derived from the literature. The curated dataset is comprised of richly annotated sequence records, descriptive records in the NCBI Gene database, reference genome feature annotation, and activity-based interactions between nongenic regions, target genes and each other. The dataset provides succinct functional details and transparent experimental evidence, leverages data from multiple experimental sources, is readily accessible and adaptable, and utilizes a flexible data model. The data have multiple uses for basic functional discovery, bioinformatics studies, genetic variant interpretation, as known positive controls for epigenomic data evaluation, and as reference standards for functional interactions. Comparisons to other gene regulatory datasets show that the RefSeqFE dataset includes a wider range of feature types representing more areas of biology, but it is comparatively smaller and subject to data selection biases. RefSeqFEs thus provide an alternative and complementary resource for experimentally assayed functional elements, with future dataset growth expected.

Optimization of CRISPR/Cas System for Improving Genome Editing Efficiency in Plasmodium falciparum

Studies of molecular mechanisms and related gene functions have long been restricted by limited genome editing technologies in malaria parasites. Recently, a simple and effective genome editing technology, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system, has greatly facilitated these studies in many organisms, including malaria parasites. However, due to the special genome feature of malaria parasites, the manipulation and gene editing efficacy of the CRISPR/Cas system in this pathogen need to be improved, particularly in the human malaria parasite, Plasmodium falciparum. Herein, based on the CRISPR/Cas9 system, we developed an integrating strategy to generate a Cas9i system, which significantly shortened the time for generation of transgenic strains in P. falciparum. Moreover, with this Cas9i system, we have successfully achieved multiplexed genome editing (mutating or tagging) by a single-round transfection in P. falciparum. In addition, we for the first time adapted AsCpf1 (Acidaminococcus sp. Cpf1), an alternative to Cas9, into P. falciparum parasites and examined it for gene editing. These optimizations of the CRISPR/Cas system will further facilitate the mechanistic research of malaria parasites and contribute to eliminating malaria in the future.

A Novel Partitivirus in the Hypovirulent Isolate QT5-19 of the Plant Pathogenic Fungus Botrytis cinerea

A pink isolate (QT5-19) of Botrytis cinerea was compared with three gray isolates of B. cinerea for growth and morphogenesis on potato dextrose agar (PDA), and for pathogenicity on tobacco. A double-stranded (ds) RNA mycovirus infecting QT5-19 was identified based on its genome feature and morphology of the virus particles. The results showed that QT5-19 grew rapidly and established flourishing colonies as the gray isolates did. However, it is different from the gray isolates, as it failed to produce conidia and sclerotia asthe gray isolates did. QT5-19 hardly infected tobacco, whereas the gray isolates aggressively infected tobacco. Two dsRNAs were detected in QT5-19, dsRNA 1 and dsRNA 2, were deduced to encode two polypepetides with homology to viral RNA-dependent RNA polymerase (RdRp) and coat protein (CP), respectively. Phylogenetic analysis of the amino acid sequences of RdRp and CP indicated that the two dsRNAs represent the genome of a novel partitivirus in the genus Alphapartitivirus, designated here as Botrytis cinerea partitivirus 2 (BcPV2). BcPV2 in QT5-19 was successfully transmitted to the three gray isolates through hyphal contact. The resulting BcPV2-infected derivatives showed rapid growth on PDA with defects in conidiogenesis and sclerogenesis, and hypovirulence on tobacco. This study suggests that BcPV2 is closely associated with hypovirulence of B. cinerea.

Exploring human genome feature for improving genetic algorithm performance

Genetic algorithm (i.e., GA) has longtermly obtained an extensive recognition for solving the optimization problem. Its pipelines process, which involves several operations, has been applied in many NP-hard problems, including the transportation network design problem (i.e., TNDP). As part of evolutionary computation methods, GA is inspired by Darwinian evolution, which is relied on the genetic operators (i.e., recombination, and mutation). On other side, the considerably achievement has been acquired by the genome researches, which offers an opportunity to deeply explore the recombination and mutation processes. This paper then presents variants of GA, which are inspired by the recent genome evidence of genetic operators. This exploration expectantly extends the benefit of evolution-based algorithm, which has been shown by the previous finding of GA. For examining the performance of proposed GA, the numerical experiment is involved for solving the TNDP. The performance comparisons show that the variation of crossover rate within a certain group of population provide better result than the standard GA.