Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases

Genome-wide association studies (GWASs) have identified hundreds of susceptibility genes, including shared associations across clinically distinct autoimmune diseases. We performed an inverse χ(2) meta-analysis across ten pediatric-age-of-onset autoimmune diseases (pAIDs) in a case-control study including more than 6,035 cases and 10,718 shared population-based controls. We identified 27 genome-wide significant loci associated with one or more pAIDs, mapping to in silico-replicated autoimmune-associated genes (including IL2RA) and new candidate loci with established immunoregulatory functions such as ADGRL2, TENM3, ANKRD30A, ADCY7 and CD40LG. The pAID-associated single-nucleotide polymorphisms (SNPs) were functionally enriched for deoxyribonuclease (DNase)-hypersensitivity sites, expression quantitative trait loci (eQTLs), microRNA (miRNA)-binding sites and coding variants. We also identified biologically correlated, pAID-associated candidate gene sets on the basis of immune cell expression profiling and found evidence of genetic sharing. Network and protein-interaction analyses demonstrated converging roles for the signaling pathways of type 1, 2 and 17 helper T cells (TH1, TH2 and TH17), JAK-STAT, interferon and interleukin in multiple autoimmune diseases

Chemotherapy Agents Alter Plasma Lipids in Breast Cancer Patients and Show Differential Effects on Lipid Metabolism Genes in Liver Cells.

Cardiovascular complications have emerged as a major concern for cancer patients. Many chemotherapy agents are cardiotoxic and some appear to also alter lipid profiles, although the mechanism for this is unknown. We studied plasma lipid levels in 12 breast cancer patients throughout their chemotherapy. Patients received either four cycles of doxorubicin and cyclophosphamide followed by weekly paclitaxel or three cycles of epirubicin, cyclophosphamide and 5'-fluorouracil followed by three cycles of docetaxel. Patients demonstrated a significant reduction (0.32 mmol/L) in high density lipoprotein cholesterol (HDL-C) and apolipoprotein A1 (apoA1) levels (0.18 g/L) and an elevation in apolipoprotein B (apoB) levels (0.15 g/L) after treatment. Investigation of the individual chemotherapy agents for their effect on genes involved in lipoprotein metabolism in liver cells showed that doxorubicin decreased ATP binding cassette transporter A1 (ABCA1) via a downregulation of the peroxisomal proliferator activated receptor γ (PPARγ) and liver X receptor α (LXRα) transcription factors. In contrast, ABCA1 levels were not affected by cyclophosphamide or paclitaxel. Likewise, apoA1 levels were reduced by doxorubicin and remained unaffected by cyclophosphamide and paclitaxel. Doxorubicin and paclitaxel both increased apoB protein levels and paclitaxel also decreased low density lipoprotein receptor (LDLR) protein levels. These findings correlate with the observed reduction in HDL-C and apoA1 and increase in apoB levels seen in these patients. The unfavourable lipid profiles produced by some chemotherapy agents may be detrimental in the longer term to cancer patients, especially those already at risk of cardiovascular disease (CVD). This knowledge may be useful in tailoring effective follow-up care plans for cancer survivors

Disease reaction to Rhizoctonia solani and yield losses in soybean

Seedling blight and root rot caused by Rhizoctonia solani are important constraints to the expansion of soybean (Glycine max) production in Alberta, Canada. The reaction of 21 soybean genotypes to R. solani was assessed in inoculated field trials in Alberta in 2014â 2016. Inoculation with R. solani resulted in a significant reduction in stand, nodulation and yield and a significant increase in root rot severity for all of the soybean genotypes. The genotype P001T34R had lower reductions in stand establishment compared with NSC Portage RR, TH29002RR, TH27005RR, or LS003R22, and there were inconsistent variations in yield loss among the genotypes in two of the three site-years. No significant variation in disease severity or nodulation was observed among the genotypes. Stability analysis showed the soybean genotypes P001T34R, 23-60RY, NSC VitoRR, and NSC TilstonRR2Y had higher and more stable stand establishment, while 900Y01, 23-60RY, P001T34R and P002T04R had higher and more stable seed yield in comparison with the other genotypes in this study. The study also revealed that R. solani caused a loss of 48% in stand establishment and 52% in seed yield. Root rot severity ranged from 0.38â 2.36 on a scale of 0-4 among the genotypes, but it was not consistent over the trials. Root rot severity and yield loss increased with increasing inoculum density, while stand establishment, nodulation and seed yield declined. Regression analysis showed that stand establishment, nodulation, and yield were strongly positively correlated, but strongly negatively correlated with root rot severity.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Identification of anthracnose races in Manitoba and Ontario from 2005 to 2015 and their reactions on Ontario dry bean cultivars

Anthracnose, caused by the fungus Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, is one of the most destructive diseases of dry bean (Phaseolus vulgaris L.) in the world. Between 2005 and 2015, commercial fields of dry beans in Manitoba and Ontario were surveyed to determine the frequency of occurrence of races of the anthracnose fungus. Throughout the study, race 73 was most prevalent in Manitoba and Ontario. However, three anthracnose races not previously reported in Canada also were identified. These three new races and four previously identified anthracnose races were used to screen 52 dry bean cultivars, as well as a mung bean and azuki bean cultivar from Ontario, for their seedling reactions to determine their patterns of race resistance. The dry bean cultivars were classified into a total of 19 resistance spectra based on the pattern of seedling reactions to the seven anthracnose races. The most common resistance spectrum was susceptible to the majority of the anthracnose races and no cultivar was resistant to all of the races. Many bean cultivars produced intermediate anthracnose ratings to races 31 and 105 and tests of 16 dry bean cultivars against those races indicated that all cultivars with intermediate ratings to a specific race were segregating in their seedling reactions and none of the cultivars produced plants with only intermediate anthracnose severity ratings. This study provides new information on the anthracnose reactions of common bean cultivars in Canada, which should be useful for the development of new bean cultivars with durable resistance.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Effects of Fusarium avenaceum and Rhizoctonia solani on growth of soybean in saline soils

Soybean (Glycine max) acreage on the Canadian prairies has increased rapidly in recent years. Production has expanded into semiarid regions where irrigation and drainage problems often result in the accumulation of salts in the soil. Fusarium avenaceum and Rhizoctonia solani are the two dominant pathogens in the disease complex that cause root and seedling blight of soybean on the Canadian prairies. The effects of F. avenaceum or R. solani in combination with soil salinity on soybean root rot were evaluated under greenhouse and mini-plot conditions. As expected, inoculation with F. avenaceum or R. solani consistently reduced seedling emergence and increased root rot severity on soybean. At high soil EC values, adverse the effects of the two pathogens were even stronger than at low salinity values. Twenty soybean cultivars were evaluated for their reactions to inoculation with F. avenaceum or R. solani in a saline soil (21.1 dS/m). High seedling emergence was observed in cultivars 900Y61, P002T04R, 900Y01, TH27005RR, P001T34R, and 900Y81 in the non-inoculated control, and for P002T04R and 900Y61 in the F. avenaceum treatment, and for 900Y61, 900Y81 and 900Y71 in the R. solani treatment. Root rot severity was low for cultivars NSC Portage and 900Y61 in the non-inoculated control and P002T004R in the F. avenaceum treatment. The cultivar 900Y61 also consistently had lower disease severity over the trials in the mini-plot test.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Plasma lipoprotein analysis by FPLC.

<p>Plasma samples of breast cancer patients at baseline and final point of treatment were subjected to Fast Protein Liquid Chromatography (FPLC) to fractionate plasma lipoproteins. Cholesterol content in each fraction was measured by enzymatic assay. Representative FPLC profiles of three different breast cancer patient samples are shown (A, B, C).</p

Doxorubicin and paclitaxel increase apoB levels whereas cyclophosphamide did not affect apoB levels in HepG2 cells.

<p>HepG2 cells were treated with of doxorubicin (DOX) or paclitaxel (TAX) at 2.5 nM, 10 nM and 25 nM concentration or 1 μg/ml, 10 μg/ml and 100 μg/ml cyclophosphamide (CPA) for 24 hours at 37°C. ApoB protein (A, B, C) and LDLR protein (D, E, F) levels were determined after treatment by western blot after normalizing against actin (see inset). Protein levels are expressed relative to that of untreated control cells. Results are expressed as mean ± S.E for two experiments performed in triplicate for western blots. *, p< 0.05 **, p< 0.01 ***, p< 0.001 compared with control.</p

Cyclophosphamide and Paclitaxel did not affect ABCA1 or apoA1 levels.

<p>HepG2 cells were treated with 1 μg/ml, 10 μg/ml and 100 μg/ml cyclophosphamide (CPA) or 2.5 nM, 10 nM and 25 nM paclitaxel (TAX) for 24 hours at 37°C. ABCA1 and apoA1 protein levels after cyclophosphamide (A, B) and paclitaxel (D, E) treatment were determined by western blotting and expressed relative to that of untreated cells after normalisation against actin (see inset). HepG2 cells were loaded with [³H] cholesterol for 48 hours prior to treatment and cells were incubated with apoA1 acceptor after treatment for 2 hours. ApoA1 mediated cholesterol efflux was calculated after cyclophosphamide (C) and paclitaxel (F) treatment. Results are expressed as two experiments performed in triplicate for protein quantification and triplicate experiments for cholesterol efflux assays. *, p< 0.05 **, p< 0.01 ***, p< 0.001 compared with untreated control.</p

Doxorubicin reduces PPARγ and LXRα levels in HepG2 cells.

<p>HepG2 cells were treated with 2.5 nM, 10 nM and 25 nM doxorubicin (DOX) for 24 hours at 37°C. mRNA and protein levels of PPARγ (A, B) and LXRα (C, D) were determined. mRNA levels were quantified by RT-PCR after normalising against β2-microglobulin and RPL27 mRNA. Protein levels were quantified by western blotting after normalising to actin (see inset). All results are expressed relative to that of the untreated control. Results are expressed as mean ± S.E for three experiments performed in triplicates for RT-PCR and at least two experiments performed in duplicate for protein quantification. *, p< 0.05 **, p< 0.01 ***, p< 0.001 compared with untreated control.</p