A chromosome conformation capture ordered sequence of the barley genome.

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

Analysis of the Efficacy and Safety of Teriparatide and Alendronate in the Treatment of Osteoporosis After Renal Transplantation.

INTRODUCTION: Both teriparatide and alendronate were used in the treatment of osteoporosis after renal transplantation. However, there are few studies comparing their application after renal transplant surgeries. This study was carried out to compare the effect of alendronate and teriparatide on bone mineral density in the treatment of osteoporosis after renal transplantation. METHODS: This is a retrospective cohort study of 153 patients who were diagnosed with osteoporosis after receiving renal transplantation, and received either alendronate or teriparatide treatment. The demographic patient information, changes in patients' quality of life, mobility and pain scores, serum biochemical markers and bone density of lumbar spine, hip and femoral neck were measured and compared between groups a year after treatment. RESULTS: there were no significant differences between the two groups concerning patient demographics such as age, gender and BMI. After a year of treatment, there were no significant differences between the two groups in biochemical markers such as serum calcium, phosphorus, creatinine and 25-OH Vitamin D (P > .05). BMD of lumbar spine, hip and femoral neck after the treatment was significantly higher in the teriparatide group than alendronate group (P < .05), while the incidence of adverse effects was higher in the teriparatide group than alendronate group (P < .05). CONCLUSION: teriparatide can be more effective than the alendronate in the treatment of osteoporosis in renal transplant patients, while having more adverse effects. DOI: 10.52547/ijkd.6475.

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. 'Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

Genetic Control over mtDNA and Its Relationship to Major Depressive Disorder.

Control over the number of mtDNA molecules per cell appears to be tightly regulated, but the mechanisms involved are largely unknown. Reversible alterations in the amount of mtDNA occur in response to stress suggesting that control over the amount of mtDNA is involved in stress-related diseases including major depressive disorder (MDD). Using low-coverage sequence data from 10,442 Chinese women to compute the normalized numbers of reads mapping to the mitochondrial genome as a proxy for the amount of mtDNA, we identified two loci that contribute to mtDNA levels: one within the TFAM gene on chromosome 10 (rs11006126, p value = 8.73 × 10(-28), variance explained = 1.90%) and one over the CDK6 gene on chromosome 7 (rs445, p value = 6.03 × 10(-16), variance explained = 0.50%). Both loci replicated in an independent cohort. CDK6 is thus a new molecule involved in the control of mtDNA. We identify increased rates of heteroplasmy in women with MDD, and show from an experimental paradigm using mice that the increase is likely due to stress. Furthermore, at least one heteroplasmic variant is significantly associated with changes in the amount of mtDNA (position 513, p value = 3.27 × 10(-9), variance explained = 0.48%) suggesting site-specific heteroplasmy as a possible link between stress and increase in amount of mtDNA. These findings indicate the involvement of mitochondrial genome copy number and sequence in an organism's response to stress.