A pilot study for channel catfish whole genome sequencing and de novo assembly

<p>Abstract</p> <p>Background</p> <p>Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs. However, the average read lengths in next-generation sequencing technologies are short as compared with that of traditional Sanger sequencing. The short sequence reads pose great challenges for <it>de novo </it>sequence assembly. As a pilot project for whole genome sequencing of the catfish genome, here we attempt to determine the proper sequence coverage, the proper software for assembly, and various parameters used for the assembly of a BAC physical map contig spanning approximately a million of base pairs.</p> <p>Results</p> <p>A combination of low sequence coverage of 454 and Illumina sequencing appeared to provide effective assembly as reflected by a high N50 value. Using 454 sequencing alone, a sequencing depth of 18 X was sufficient to obtain the good quality assembly, whereas a 70 X Illumina appeared to be sufficient for a good quality assembly. Additional sequencing coverage after 18 X of 454 or after 70 X of Illumina sequencing does not provide significant improvement of the assembly. Considering the cost of sequencing, a 2 X 454 sequencing, when coupled to 70 X Illumina sequencing, provided an assembly of reasonably good quality. With several software tested, Newbler with a seed length of 16 and ABySS with a K-value of 60 appear to be appropriate for the assembly of 454 reads alone and Illumina paired-end reads alone, respectively. Using both 454 and Illumina paired-end reads, a hybrid assembly strategy using Newbler for initial 454 sequence assembly, Velvet for initial Illumina sequence assembly, followed by a second step assembly using MIRA provided the best assembly of the physical map contig, resulting in 193 contigs with a N50 value of 13,123 bp.</p> <p>Conclusions</p> <p>A hybrid sequencing strategy using low sequencing depth of 454 and high sequencing depth of Illumina provided the good quality assembly with high N50 value and relatively low cost. A combination of Newbler, Velvet, and MIRA can be used to assemble the 454 sequence reads and the Illumina reads effectively. The assembled sequence can serve as a resource for comparative genome analysis. Additional long reads using the third generation sequencing platforms are needed to sequence through repetitive genome regions that should further enhance the sequence assembly.</p

Prevalence of Grey Matter Pathology in Early Multiple Sclerosis Assessed by Magnetization Transfer Ratio Imaging

The aim of the study was to assess the prevalence, the distribution and the impact on disability of grey matter (GM) pathology in early multiple sclerosis. Eighty-eight patients with a clinically isolated syndrome with a high risk developing multiple sclerosis were included in the study. Forty-four healthy controls constituted the normative population. An optimized statistical mapping analysis was performed to compare each subject's GM Magnetization Transfer Ratio (MTR) imaging maps with those of the whole group of controls. The statistical threshold of significant GM MTR decrease was determined as the maximum p value (p<0.05 FDR) for which no significant cluster survived when comparing each control to the whole control population. Using this threshold, 51% of patients showed GM abnormalities compared to controls. Locally, 37% of patients presented abnormalities inside the limbic cortex, 34% in the temporal cortex, 32% in the deep grey matter, 30% in the cerebellum, 30% in the frontal cortex, 26% in the occipital cortex and 19% in the parietal cortex. Stepwise regression analysis evidenced significant association (p = 0.002) between EDSS and both GM pathology (p = 0.028) and T2 white matter lesions load (p = 0.019). In the present study, we evidenced that individual analysis of GM MTR map allowed demonstrating that GM pathology is highly heterogeneous across patients at the early stage of MS and partly underlies irreversible disability

GRANDMA and HXMT Observations of GRB 221009A -- the Standard-Luminosity Afterglow of a Hyper-Luminous Gamma-Ray Burst

GRB 221009A is the brightest Gamma-Ray Burst (GRB) detected in more than 50 years of study. In this paper, we present observations in the X-ray and optical domains after the GRB obtained by the GRANDMA Collaboration (which includes observations from more than 30 professional and amateur telescopes) and the Insight-HXMT Collaboration. We study the optical afterglow with empirical fitting from GRANDMA+HXMT data, augmented with data from the literature up to 60 days. We then model numerically, using a Bayesian approach, the GRANDMA and HXMT-LE afterglow observations, that we augment with Swift-XRT and additional optical/NIR observations reported in the literature. We find that the GRB afterglow, extinguished by a large dust column, is most likely behind a combination of a large Milky-Way dust column combined with moderate low-metallicity dust in the host galaxy. Using the GRANDMA+HXMT-LE+XRT dataset, we find that the simplest model, where the observed afterglow is produced by synchrotron radiation at the forward external shock during the deceleration of a top-hat relativistic jet by a uniform medium, fits the multi-wavelength observations only moderately well, with a tension between the observed temporal and spectral evolution. This tension is confirmed when using the extended dataset. We find that the consideration of a jet structure (Gaussian or power-law), the inclusion of synchrotron self-Compton emission, or the presence of an underlying supernova do not improve the predictions, showing that the modelling of GRB22109A will require going beyond the most standard GRB afterglow model. Placed in the global context of GRB optical afterglows, we find the afterglow of GRB 221009A is luminous but not extraordinarily so, highlighting that some aspects of this GRB do not deviate from the global known sample despite its extreme energetics and the peculiar afterglow evolution.Comment: Accepted to ApJL for the special issue, 37 pages, 23 pages main text, 6 tables, 13 figure

Transcriptome Sequencing of Gene Expression in the Brain of the HIV-1 Transgenic Rat

<div><p>The noninfectious HIV-1 transgenic (HIV-1Tg) rat was developed as a model of AIDs-related pathology and immune dysfunction by manipulation of a noninfectious HIV-1^gag-pol virus with a deleted 3-kb <i>Sph</i>I<i>-Msc</i>I fragment containing the 3′ -region of <i>gag</i> and the 5′ region of <i>pol</i> into F344 rats. Our previous studies revealed significant behavioral differences between HIV-1Tg and F344 control rats in their performance in the Morris water maze and responses to psychostimulants. However, the molecular mechanisms underlying these behavioral differences remain largely unknown. The primary goal of this study was to identify differentially expressed genes and enriched pathways affected by the <i>gag-pol</i>-deleted HIV-1 genome. Using RNA deep sequencing, we sequenced RNA transcripts in the prefrontal cortex, hippocampus, and striatum of HIV-1Tg and F344 rats. A total of 72 RNA samples were analyzed (i.e., 12 animals per group × 2 strains × 3 brain regions). Following deep-sequencing analysis of 50-bp paired-end reads of RNA-Seq, we used Bowtie/Tophat/Cufflinks suites to align these reads into transcripts based on the Rn4 rat reference genome and to measure the relative abundance of each transcript. Statistical analyses on each brain region in the two strains revealed that immune response- and neurotransmission-related pathways were altered in the HIV-1Tg rats, with brain region differences. Other neuronal survival-related pathways, including those encoding myelin proteins, growth factors, and translation regulators, were altered in the HIV-1Tg rats in a brain region-dependent manner. This study is the first deep-sequencing analysis of RNA transcripts associated the HIV-1Tg rat. Considering the functions of the pathways and brain regions examined in this study, our findings of abnormal gene expression patterns in HIV-1Tg rats suggest mechanisms underlying the deficits in learning and memory and vulnerability to drug addiction and other psychiatric disorders observed in HIV-positive patients.</p> </div

Percentage of mapped reads onto the regions of exons, introns, 5′ -UTRs, 3′ -UTRs, and 10-kb transcribed region upstream and downstream from coding regions in the PFC, STR, and HIP of HIV-1Tg and F344 rats.

<p>Percentage of mapped reads onto the regions of exons, introns, 5′ -UTRs, 3′ -UTRs, and 10-kb transcribed region upstream and downstream from coding regions in the PFC, STR, and HIP of HIV-1Tg and F344 rats.</p

Summary of represented genes and enriched biochemical pathways related to neurobehavioral deficits in the HIV-1Tg rat.

<p>Red represents up-regulation, whereas green represents down-regulation in mRNA expression in the PFC¹, HIP², and STR³ of HIV-1Tg rats. Numbers with strikethroughs reflect marginal significance (0.005Table S1). Abbreviations: Aspa = aspartoacylase; Camk2b = calcium/calmodulin-dependent protein kinase II beta; Ccl2 =  chemokine ligand 2; Ccl6 =  chemokine ligand 6; Chrna4 =  neuronal acetylcholine receptor subunit alpha-4; Cldn = Claudin 1; Cnp = 2,3-cyclic-nucleotide 3-phosphodiesterase; Drd4 =  D(4) dopamine receptor; Ephb1 =  EPH receptor B1; Fgf9 =  fibroblast growth factor 9; Fgf13 =  fibroblast growth factor 13; Gabbr2, Gnal = guanine nucleotide binding protein, alpha activating activity polypeptide; Grid1 =  glutamate receptor, ionotropic, delta1; Grin2a = NMDA receptor subunit epsilon-1; HDGF = hepatoma-derived growth factor; Il1rap = interleukin 1 receptor accessory protein; Insr = insulin receptor; Irak4, interleukin-1 receptor-associated kinase 4; Irf5 =  interferon regulatory factor 5; Irf7 =  interferon regulatory factor 7; Mag = myelin-associated glycoprotein; Mbp = myelin-associated glycoprotein; Mog = myelin-oligodendrocyte glycoprotein; Mpz = myelin protein P0; Npm1 =  nucleophosmin; Opalin = oligodendrocytic myelin paranodal and inner loop protein; PDGFb = platelet-derived growth factor beta polypeptide; Ppm1l = protein phosphatase 1L; Ppp1r14a = protein phosphatase 1 regulatory subunit 14A; Ppp2ca = serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform; Rl39 =  ribosomal protein L39; Rpl13 =  ribosomal protein L13; Rpl35 =  ribosomal protein L35; Rpl37 =  ribosomal protein L37; Rps8 =  ribosomal protein S8; Rps19 =  ribosomal protein S19; Rps24 =  ribosomal protein S24; Rtp4 =  receptor transporter protein 4; Slc1a7 =  glutamate transporter, member 7; Wnt5a = wingless-type MMTV integration site family, 5A; Wnt5b = wingless-type MMTV integration site family, 5B.</p