Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis

<p>Abstract</p> <p>Background</p> <p>Rice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. Wild rice is expected to provide useful genetic resources that could improve the present cultivated species. However, the quantity and quality of these unexplored resources remain unclear. Recent accumulation of the genomic information of both cultivated and wild rice species allows for their comparison at the molecular level. Here, we compared the genome sequence of <it>Oryza sativa </it>ssp. <it>japonica </it>with sets of bacterial artificial chromosome end sequences (BESs) from two wild rice species, <it>O. rufipogon </it>and <it>O. nivara</it>, and an African rice species, <it>O. glaberrima</it>.</p> <p>Results</p> <p>We found that about four to five percent of the BESs of the two wild rice species and about seven percent of the African rice could not be mapped to the <it>japonica </it>genome, suggesting that a substantial number of genes have been lost in the <it>japonica </it>rice lineage; however, their close relatives still possess their counterpart genes. We estimated that during evolution, <it>O. sativa </it>has lost at least one thousand genes that are still preserved in the genomes of the other species. In addition, our BLASTX searches against the non-redundant protein sequence database showed that disease resistance-related proteins were significantly overrepresented in the close relative-specific genomic portions. In total, 235 unmapped BESs of the three relatives matched 83 non-redundant proteins that contained a disease resistance protein domain, most of which corresponded to an NBS-LRR domain.</p> <p>Conclusion</p> <p>We found that the <it>O. sativa </it>lineage appears to have recently experienced massive gene losses following divergence from its wild ancestor. Our results imply that the domestication process accelerated large-scale genomic deletions in the lineage of Asian cultivated rice and that the close relatives of cultivated rice have the potential to restore the lost traits.</p

Effects of Choto-san (Diao-Teng-San) on microcirculation of bulbar conjunctiva and hemorheological factors in patients with asymptomatic cerebral infarction

In this study, the effects of Choto-san ( 釣藤散 ) on the microcirculation of bulbar conjunctiva in 16 patients with asymptornatic cerebral infarction were investigated with a video-microscopic system. After the administration of Choto-san for four weeks, variables of microcirculatory flow of the bulbar conjunctiva, that is, the internal diameter of vessels, flow velocity and flow volume rate were increased (p<0.05) . Erythrocyte aggregability, evaluated by measuring the maximum diameter of a column of intravascular erythrocyte aggregation, was also improved (p<0.05) . Simultaneously, hemorheological factors such as whole blood viscosity, plasrna viscosity, erythrocyte deformability and leukocyte deformability were examined. Choto-san improved deformability of both erythrocytes and leukocytes (p<0.05) , but not blood viscosity. These results suggest that Choto-san may have favorable effects on cerebrovascular disorders through changes in microcirculatory flow, erythrocyte aggregability and blood cell deformability. 今回,無症候性脳梗塞患者16名を対象に,眼球結膜微小循環に及ぼす釣藤散の効果をビデオ顕徴鏡システムを用いて検討した。釣藤散を4週間投与後,眼球結膜微小循環の血管内径,血流速度,血流量が増加した(p<0.05)。血管内赤血球集合現象を認める血管の最大内径で評価ざれる赤血球集合能も改善した(p<0.05)。同時に,血液レオロジー因子である全血粘度,血漿粘度,赤血球変形能,白血球変形能も検討したところ,釣藤散は赤血球と白血球の変形能を改善したが(p<0.05),血液粘度は改善しなかった。以上の結果から,釣藤散は徴小循環血流や赤血球集合能,血球変形能を改善することで,脳血管障害に好影響を与える可能性が示唆された

Combined analysis of microstructures within an annual ring of Douglas fir (Pseudotsuga menziesii) by dynamic mechanical analysis and small angle X-ray scattering

Dynamic mechanical analysis (DMA) and small angle X-ray scattering (SAXS) measurements of water-saturated wood of Douglas fir (Pseudotsuga menziesii) in the temperature range of 0 ℃ to 100 ℃ were focused to clarify microstructural changes within an annual ring. The following results were obtained. Thermal softening behavior caused by micro-Brownian motion of lignin was observed in both earlywood and latewood. The peaks of tanδ were found at around 95 ℃ for earlywood and at around 90 ℃ for latewood. These results suggested that the structures of lignin in the cell wall were different between earlywood and latewood. SAXS measurements of water-saturated earlywood and latewood in water were performed with precise temperature control. The scattering intensity increased with increasing temperature, indicating that the density of the matrix was reduced at higher temperature. One-dimensional SAXS intensity at the equator, which approximately represents cellulose microfibrils arrangement in the matrix, was intensively analyzed using the WoodSAS model. The result of this model fitting showed that the cellulose microfibril diameter of latewood was higher than that of earlywood. In addition, the value of interfibrillar distance decreased monotonically in the earlywood, while it decreased rapidly in the latewood from 60 ℃ to 90 ℃. The changes in the cellulose microfibril (CMF) diameter and the interfibrillar distance with increasing temperature between earlywood and latewood by SAXS measurement were different. The differences in CMF diameter and inter-fibril distance between earlywood and latewood measured by SAXS also support the hypothesis that lignin structure differs between earlywood and latewood based on the results of DMA measurements

Role of premature leptin surge in obesity resulting from intrauterine undernutrition

SummaryIntrauterine undernutrition is closely associated with obesity related to detrimental metabolic sequelae in adulthood. We report a mouse model in which offspring with fetal undernutrition (UN offspring), when fed a high-fat diet (HFD), develop pronounced weight gain and adiposity. In the neonatal period, UN offspring exhibited a premature onset of neonatal leptin surge compared to offspring with intrauterine normal nutrition (NN offspring). Unexpectedly, premature leptin surge generated in NN offspring by exogenous leptin administration led to accelerated weight gain with an HFD. Both UN offspring and neonatally leptin-treated NN offspring exhibited an impaired response to acute peripheral leptin administration on a regular chow diet (RCD) with impaired leptin transport to the brain as well as an increased density of hypothalamic nerve terminals. The present study suggests that the premature leptin surge alters energy regulation by the hypothalamus and contributes to “developmental origins of health and disease.

A novel superior factor widely controlling the rice grain quality

Synthesis of storage starch and protein accumulation is the main action of endosperm organogenesis in term of the economic importance of rice. This event is strongly disturbed by abiotic stresses such as high temperature; thus, the upcoming global warming will cause a crisis with a great impact on food production^1,2^. The enzymes for the protein storage and starch synthesis pathway should work in concert to carry out the organogenesis of rice endosperm^3-5^, but the regulatory mechanism is largely unknown. Here we show that a novel regulatory factor, named OsCEO1, acts as the conductor of endosperm organogenesis during the rice grain filling stage. The physiological properties of _floury-endosperm-2_ (_flo2_) mutants showed many similarities to symptoms of grains developed under high-temperature conditions, suggesting important roles of the responsible gene in sensitivity to high-temperature stress. Our map-based cloning identified the responsible gene for the _flo2_ mutant, _OsCEO1_, which has no homology to any genes of known function. The _OsCEO1_ belongs to a novel conserved gene family and encodes a protein composed of 1,720 amino acid residues containing a TPR (tetratricopeptide repeat) motif, which is considered to mediate a protein-protein interaction. The yeast two-hybrid analysis raised an unknown protein showing homology to a late embryogenesis abundant protein and a putative basic helix-loop-helix protein as candidates for the direct interactor for _OsCEO1_, whereas no enzyme genes for the synthesis of storage substances were detected. The _flo2_ mutant exhibited reduced expression of several genes for putative regulatory proteins as well as many enzymes involved in storage starch and proteins. These results suggest that _OsCEO1_ is a superior conductor of the novel regulatory cascade of endosperm organogenesis and may have important roles in the response to high-temperature stress

Membrane-Type 1 Matrix Metalloproteinase Cleaves Cd44 and Promotes Cell Migration

Migratory cells including invasive tumor cells frequently express CD44, a major receptor for hyaluronan and membrane-type 1 matrix metalloproteinase (MT1-MMP) that degrades extracellular matrix at the pericellular region. In this study, we demonstrate that MT1-MMP acts as a processing enzyme for CD44H, releasing it into the medium as a soluble 70-kD fragment. Furthermore, this processing event stimulates cell motility; however, expression of either CD44H or MT1-MMP alone did not stimulate cell motility. Coexpression of MT1-MMP and mutant CD44H lacking the MT1-MMP–processing site did not result in shedding and did not promote cell migration, suggesting that the processing of CD44H by MT1-MMP is critical in the migratory stimulation. Moreover, expression of the mutant CD44H inhibited the cell migration promoted by CD44H and MT1-MMP in a dominant-negative manner. The pancreatic tumor cell line, MIA PaCa-2, was found to shed the 70-kD CD44H fragment in a MT1-MMP–dependent manner. Expression of the mutant CD44H in the cells as well as MMP inhibitor treatment effectively inhibited the migration, suggesting that MIA PaCa-2 cells indeed use the CD44H and MT1-MMP as migratory devices. These findings revealed a novel interaction of the two molecules that have each been implicated in tumor cell migration and invasion

Application of Japanese guidelines for gestational weight gain to multiple pregnancy outcomes and its optimal range in 101,336 Japanese women

This study was performed to investigate whether the Japanese guidelines for gestational weight gain (GWG) can be used to determine the risks of multiple pregnancy outcomes and estimate optimal GWG in 101,336 women with singleton pregnancies in 2013. Multivariable logistic regression analyses indicated that the risks associated with low birth weight, small for gestational age, and preterm birth increased significantly with weight gain below the Japanese guidelines, and the risks of macrosomia and large for gestational age increased with weight gain above the guidelines regardless of Asian-specific pre-pregnancy body mass index (BMI). The GWG cutoff points estimated from the adjusted area under the receiver operating characteristics curve >0.6 corresponded to 10-13.8 kg in underweight women with pre-pregnancy BMI = 30 kg/m(2). The optimal GWG ranges proposed by the present study are slightly higher than those recommended by the current Japanese guidelines

A large cavernous malformation of the third ventricle floor: A case report

Suprasellar and third ventricular region cavernous malformations originating from the floor of the third ventricle are extremely rare. We report a case of third ventricular cavernous malformation arising from the ventricle floor in a 24-year-old woman who presented with short-term memory loss and disorientation. Computed tomography revealed a suprasellar mass with calcification in the posterior chiasmatic region. T2-weighted magnetic resonance imaging revealed a mass with heterogeneous intensity and without hydrocephalus. The mass was slightly enhanced subsequent to gadolinium infusion. Using a basal interhemispheric translamina terminalis approach and a neuroendoscope, we confirmed that the tumor was located at the floor of the third ventricle and removed it. Histopathological examination confirmed the diagnosis of cavernous malformation. The postoperative course was uneventful, but the patient's short-term memory loss persisted. Despite its rarity, cavernous malformation should be suspected when a tumor is detected in the vicinity of the third ventricle floor. It is treatable through surgical resection

Involvement of TRPV3 and TRPM8 ion channel proteins in induction of mammalian cold-inducible proteins

Cold-inducible RNA-binding protein (CIRP), RNA-binding motif protein 3 (RBM3) and serine and arginine rich splicing factor 5 (SRSF5) are RNA-binding proteins that are transcriptionally upregulated in response to moderately low temperatures and a variety of cellular stresses in mammalian cells. Induction of these cold-inducible proteins (CIPs) is dependent on transient receptor potential (TRP) V4 channel protein, but seems independent of its ion channel activity. We herein report that in addition to TRPV4, TRPV3 and TRPM8 are necessary for the induction of CIPs. We established cell lines from the lung of TRPV4-knockout (KO) mouse, and observed induction of CIPs in them by western blot analysis. A TRPV4 antagonist RN1734 suppressed the induction in wild-type mouse cells, but not in TRPV4-KO cells. A TRPV3 channel blocker S408271 and a TRPM8 channel blocker AMTB as well as siRNAs against TRPV3 and TRPM8 suppressed the CIP induction in mouse TRPV4-KO cells and human U-2 OS cells. A TRPV3 channel agonist 2-APB induced CIP expression, but camphor did not. Neither did a TRPM8 channel agonist WS-12. These results suggest that TRPV4, TRPV3 and TRPM8 proteins, but not their ion channel activities are necessary for the induction of CIPs at 32 °C. Identification of proteins that differentially interact with these TRP channels at 37 °C and 32 °C would help elucidate the underlying mechanisms of CIP induction by hypothermia

Cisterna magna meningiomas without dural attachment: Report of two cases

Meningiomas within the cisterna magna without dural attachment are extremely rare. To the best of our knowledge, only three cases of meningiomas within the cisterna magna have been reported in the literature. The authors present two cases of patient with the cisterna magna meningioma without dural attachment. (Case 1) A 36-year-old female presented with a 10-month history of numbness in the left hand. Magnetic resonance imaging (MRI) disclosed the presence of a contrast-enhanced tumor in the posterior fossa. A suboccipital craniectomy was performed, and the tumor located within the cisterna magna with no attachment to the dura. Diagnosis is made as clear cell meningioma. The postoperative course was uneventful, and a recurrence has not been observed for three years. (Case 2) A 58-year-old man presented with a well-circumscribed mass in the posterior fossa. At surgery, the tumor located within the cisterna magna with a connection to the right tenia. The tumor was totally removed without neurological deficits. At a 7-year follow-up, no evidence of a recurrence was observed. It is quite difficult to preoperatively diagnose as a cisterna magna meningioma without dural attachment. However, complete removal of the tumor should be achieved