The genome sequence and structure of rice chromosome 1

The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.     

Birth of parthenogenetic mice that can develop to adulthood

Only mammals have relinquished parthenogenesis, a means of producing descendants solely from maternal germ cells. Mouse parthenogenetic embryos die by day 10 of gestation. Bi-parental reproduction is necessary because of parent-specific epigenetic modification of the genome during gametogenesis. This leads to unequal expression of imprinted genes from the maternal and paternal alleles. However, there is no direct evidence that genomic imprinting is the only barrier to parthenogenetic development. Here we show the development of a viable parthenogenetic mouse individual from a reconstructed oocyte containing two haploid sets of maternal genome, derived from non-growing and fully grown oocytes. This development was made possible by the appropriate expression of the Igf2 and H19 genes with other imprinted genes, using mutant mice with a 13-kilobase deletion in the H19 gene as non-growing oocytes donors. This full-term development is associated with a marked reduction in aberrantly expressed genes. The parthenote developed to adulthood with the ability to reproduce offspring. These results suggest that paternal imprinting prevents parthenogenesis, ensuring that the paternal contribution is obligatory for the descendant.     

Effect of reduction roasting by using bio-char derived from empty fruit bunch on the magnetic properties of Malaysian iron ore

Beneficiation of Malaysian iron ore is becoming necessary as iron resources are depleting. However, the upgrading process is challenging because of the weak magnetic properties of Malaysian iron ore. In this study, bio-char derived from oil palm empty fruit bunch (EFB) was utilized as an energy source for reduction roasting. Mixtures of Malaysian iron ore and the bio-char were pressed into briquettes and subjected to reduction roasting processes at 873–1173 K. The extent of reduction was estimated on the basis of mass loss, and the magnetization of samples was measured using a vibrating sample magnetometer (VSM). When reduced at 873 K, the original goethite-rich ore was converted into hematite. An increase in temperature to 1073 K caused a significant conversion of hematite into magnetite and enhanced the magnetic susceptibility and saturation magnetization of samples. The magnetic properties diminished at 1173 K as the iron ore was partially reduced to wustite. This reduction roasting by using the bio-char can assist in upgrading the iron ore by improving its magnetic properties.     

Sound velocities of majorite garnet and the composition of the mantle transition region

The composition of the mantle transition region, characterized by anomalous seismic-wave velocity and density changes at depths of approximately 400 to 700 km, has remained controversial. Some have proposed that the mantle transition region has an olivine-rich 'pyrolite' composition, whereas others have inferred that it is characterized by pyroxene- and garnet-rich compositions ('piclogite'), because the sound velocities in pyrolite estimated from laboratory data are substantially higher than those seismologically observed. Although the velocities of the olivine polymorphs at these pressures (wadsleyite and ringwoodite) have been well documented, those of majorite (another significant high-pressure phase in the mantle transition region) with realistic mantle compositions have never been measured. Here we use combined in situ X-ray and ultrasonic measurements under the pressure and temperature conditions of the mantle transition region to show that majorite in a pyrolite composition has sound velocities substantially lower than those of earlier estimates, owing to strong nonlinear decreases at high temperature, particularly for shear-wave velocity. We found that pyrolite yields seismic velocities more consistent with typical seismological models than those of piclogite in the upper to middle parts of the region, except for the potentially larger velocity jumps in pyrolite relative to those observed at a depth of 410 km. In contrast, both of these compositions lead to significantly low shear-wave velocities in the lower part of the region, suggesting possible subadiabatic temperatures or the existence of a layer of harzburgite-rich material supplied by the subducted slabs stagnant at these depths.     

Asa Issie, Aramis and the origin of Australopithecus

The origin of Australopithecus, the genus widely interpreted as ancestral to Homo, is a central problem in human evolutionary studies. Australopithecus species differ markedly from extant African apes and candidate ancestral hominids such as Ardipithecus, Orrorin and Sahelanthropus. The earliest described Australopithecus species is Au. anamensis, the probable chronospecies ancestor of Au. afarensis. Here we describe newly discovered fossils from the Middle Awash study area that extend the known Au. anamensis range into northeastern Ethiopia. The new fossils are from chronometrically controlled stratigraphic sequences and date to about 4.1-4.2 million years ago. They include diagnostic craniodental remains, the largest hominid canine yet recovered, and the earliest Australopithecus femur. These new fossils are sampled from a woodland context. Temporal and anatomical intermediacy between Ar. ramidus and Au. afarensis suggest a relatively rapid shift from Ardipithecus to Australopithecus in this region of Africa, involving either replacement or accelerated phyletic evolution.     

Odorant receptor gene choice is reset by nuclear transfer from mouse olfactory sensory neurons

Of the approximately 1,000 odorant receptor (OR) genes in the mouse genome, an olfactory sensory neuron (OSN) is thought to express one gene, from one allele. This is reminiscent of immunoglobulin and T-cell receptor genes, which undergo DNA rearrangements in lymphocytes. Here, we test the hypothesis that OR gene choice is controlled by DNA rearrangements in OSNs. Using permanent genetic marking, we show that the choice by an OSN to express an allele of the OR gene M71 is irreversible. Using M71-expressing OSNs as donors for nuclear transfer, we generate blastocysts, embryonic stem (ntES) cell lines and clonal mice. DNA analysis of these cell lines, whose genome is clonally derived from an M71-expressing OSN, does not reveal DNA rearrangements or sequence alterations at the M71 locus. OSNs that differentiate from ntES cells after injection into blastocysts are not restricted to expression of M71 but can express other OR genes. Thus, M71 gene choice is irreversible but is reset upon nuclear transfer, and is not accompanied by genomic alterations.     

A genome-wide association study identifies three new risk loci for Kawasaki disease

We performed a genome-wide association study (GWAS) of Kawasaki disease in Japanese subjects using data from 428 individuals with Kawasaki disease (cases) and 3,379 controls genotyped at 473,803 SNPs. We validated the association results in two independent replication panels totaling 754 cases and 947 controls. We observed significant associations in the FAM167A-BLK region at 8p22-23 (rs2254546, P = 8.2 × 10(-21)), in the human leukocyte antigen (HLA) region at 6p21.3 (rs2857151, P = 4.6 × 10(-11)) and in the CD40 region at 20q13 (rs4813003, P = 4.8 × 10(-8)). We also replicated the association of a functional SNP of FCGR2A (rs1801274, P = 1.6 × 10(-6)) identified in a recently reported GWAS of Kawasaki disease. Our findings provide new insights into the pathogenesis and pathophysiology of Kawasaki disease.     

Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations

Chronic kidney disease (CKD), impairment of kidney function, is a serious public health problem, and the assessment of genetic factors influencing kidney function has substantial clinical relevance. Here, we report a meta-analysis of genome-wide association studies for kidney function-related traits, including 71,149 east Asian individuals from 18 studies in 11 population-, hospital- or family-based cohorts, conducted as part of the Asian Genetic Epidemiology Network (AGEN). Our meta-analysis identified 17 loci newly associated with kidney function-related traits, including the concentrations of blood urea nitrogen, uric acid and serum creatinine and estimated glomerular filtration rate based on serum creatinine levels (eGFRcrea) (P < 5.0 × 10(-8)). We further examined these loci with in silico replication in individuals of European ancestry from the KidneyGen, CKDGen and GUGC consortia, including a combined total of ～110,347 individuals. We identify pleiotropic associations among these loci with kidney function-related traits and risk of CKD. These findings provide new insights into the genetics of kidney function.     

Treatment of diabetes and atherosclerosis by inhibiting fatty-acid-binding protein aP2

Adipocyte fatty-acid-binding protein, aP2 (FABP4) is expressed in adipocytes and macrophages, and integrates inflammatory and metabolic responses. Studies in aP2-deficient mice have shown that this lipid chaperone has a significant role in several aspects of metabolic syndrome, including type 2 diabetes and atherosclerosis. Here we demonstrate that an orally active small-molecule inhibitor of aP2 is an effective therapeutic agent against severe atherosclerosis and type 2 diabetes in mouse models. In macrophage and adipocyte cell lines with or without aP2, we also show the target specificity of this chemical intervention and its mechanisms of action on metabolic and inflammatory pathways. Our findings demonstrate that targeting aP2 with small-molecule inhibitors is possible and can lead to a new class of powerful therapeutic agents to prevent and treat metabolic diseases such as type 2 diabetes and atherosclerosis.