Biology subjects

Kim, H.-s.

Publications and source records attributed to Kim, H.-s..

3 recordsLinked to original sources

bioRxiv2020

Genetic interactions among ADAMTS metalloproteases and basement membrane molecules in cell migration in Caenorhabditis elegans

During development of the Caenorhabditis elegans gonad, the gonadal leader cells, called distal tip cells (DTCs), migrate in a U-shaped pattern to form the U-shaped gonad arms. The ADAMTS (a disintegrin and metalloprotease with thrombospondin motifs) family metalloproteases MIG-17 and GON-1 are required for correct DTC migration. Mutations in mig-17 result in misshapen gonads due to the misdirected DTC migration, and mutations in gon-1 result in shortened and swollen gonads due to the premature termination of DTC migration. Although the phenotypes shown by mig-17 and gon-1 mutants are very different from one another, mutations that result in amino acid substitutions in the same basement membrane protein genes, emb-9/collagen IV a1, let-2/collagen IV a2 and fbl-1/fibulin-1, were identified as genetic suppressors of mig-17 and gon-1 mutants. To understand the roles shared by these two proteases, we examined the effects of the mig-17 suppressors on gon-1 and the effects of the gon-1 suppressors and enhancers on mig-17 gonadal defects. Some of the emb-9, let-2 and fbl-1 mutations suppressed both mig-17 and gon-1, whereas others acted only on mig-17 or gon-1. These results suggest that mig-17 and gon-1 have their specific functions as well as functions commonly shared between them for gonad formation. The levels of collagen IV accumulation in the DTC basement membrane were significantly higher in the gon-1 mutants as compared with wild type and were reduced to the wild-type levels when combined with suppressor mutations, but not with enhancer mutations, suggesting that the ability to reduce collagen IV levels is important for gon-1 suppression.

developmental biology↗

bioRxiv2020

A Trypanosoma brucei ORFeome-based Gain-of-Function Library identifies genes that promote survival during melarsoprol treatment

Trypanosoma brucei is an early branching protozoan parasite that causes human and animal African Trypanosomiasis. Forward genetics approaches are powerful tools for uncovering novel aspects of Trypanosomatid biology, pathogenesis, and therapeutic approaches against trypanosomiasis. Here we have generated a T. brucei cloned ORFeome consisting of over 90% of the targeted 7,245 genes and used it to make an inducible Gain-of-Function parasite library broadly applicable to large-scale forward genetic screens. We conducted a proof of principle genetic screen to identify genes whose expression promotes survival in melarsoprol, a critical drug of last resort. The 57 genes identified as overrepresented in melarsoprol survivor populations included the rate-limiting enzyme for the biosynthesis of an established drug target (trypanothione), validating the tool. In addition, novel genes associated with gene expression, flagellum localization, and mitochondrion localization were identified and a subset of those genes increased melarsoprol resistance upon overexpression in culture. These findings offer new insights into Trypanosomatid basic biology, implications for drugs targets, and direct or indirect drug resistance mechanisms. This study generated a T. brucei ORFeome and Gain-of-Function parasite library, demonstrated the libraries usefulness in forward genetic screening, and identified novel aspects of melarsoprol resistance that will be the subject of future investigations. These powerful genetic tools can be used to broadly advance Trypanosomatid research. IMPORTANCETrypanosomatid parasites threaten the health of over 1 billion people worldwide. Because their genomes are highly diverged from well-established eukaryotes, conservation is not always useful in assigning gene functions. However, it is precisely among the Trypanosomatid-specific genes that ideal therapeutic targets might be found. Forward genetics approaches are an effective way to identify novel gene functions. We used an ORFeome approach to clone a large percentage of Trypanosoma brucei genes and generate a Gain-of-Function parasite library. This library was used in a genetic screen to identify genes that promote resistance to the clinically significant, yet highly toxic drug, melarsoprol. Hits arising from the screen demonstrated the librarys usefulness in identifying known pathways and uncovered novel aspects of resistance mediated by proteins localized to the flagellum and mitochondrion. The powerful new genetic tools generated herein are expected to promote advances in Trypanosomatid biology and therapeutic development in the years to come.

genetics↗

bioRxiv2020

Comparative analysis of seven short-reads sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing

BackgroundMGISEQ-T7 is a new whole-genome sequencer developed by Complete Genomics and MGI utilizing DNA nanoball and combinatorial probe anchor synthesis technologies for generating short reads at a very large scale - up to 60 human genomes per day. However, it has not been objectively and systematically compared against Illumina short-read sequencers. FindingsBy using the same KOREF sample, the Korean Reference Genome, we have compared seven sequencing platforms including BGISEQ-500, MGISEQ-T7, HiSeq2000, HiSeq2500, HiSeq4000, HiSeqX10, and NovaSeq6000. We measured sequencing quality by comparing sequencing statistics (base quality, duplication rate, and random error rate), mapping statistics (mapping rate, depth distribution, and %GC coverage), and variant statistics (transition/transversion ratio, dbSNP annotation rate, and concordance rate with SNP genotyping chip) across the seven sequencing platforms. We found that MGI platforms showed a higher concordance rate of SNP genotyping than HiSeq2000 and HiSeq4000. The similarity matrix of variant calls confirmed that the two MGI platforms have the most similar characteristics to the HiSeq2500 platform. ConclusionsOverall, MGI and Illumina sequencing platforms showed comparable levels of sequencing quality, uniformity of coverage, %GC coverage, and variant accuracy, thus we conclude that the MGI platforms can be used for a wide range of genomics research fields at approximately half the cost of the Illumina platforms.

bioinformatics↗