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

ALMA Observations of the IRDC Clump G34.43+00.24 MM3: DNC/HNC Ratio

We have observed the clump G34.43+00.24 MM3 associated with an infrared dark cloud in DNC $J$=3--2, HN$^{13}$C $J$=3--2, and N$_2$H$^+$ $J$=3--2 with the Atacama Large Millimeter/submillimeter Array (ALMA). The N$_2$H$^+$ emission is found to be relatively weak near the hot core and the outflows, and its distribution is clearly anti-correlated with the CS emission. This result indicates that a young outflow is interacting with cold ambient gas. The HN$^{13}$C emission is compact and mostly emanates from the hot core, whereas the DNC emission is extended around the hot core. Thus, the DNC and HN$^{13}$C emission traces warm regions near the protostar differently. The DNC emission is stronger than the HN$^{13}$C emission toward most parts of this clump. The DNC/HNC abundance ratio averaged within a $15^{\prime\prime} \times 15^{\prime\prime}$ area around the phase center is higher than 0.06. This ratio is much higher than the value obtained by the previous single-dish observations of DNC and HN$^{13}$C $J$=1--0 ($\sim$0.003). It seems likely that the DNC and HNC emission observed with the single-dish telescope traces lower density envelopes, while that observed with ALMA traces higher density and highly deuterated regions. We have compared the observational results with chemical-model results in order to investigate the behavior of DNC and HNC in the dense cores. Taking these results into account, we suggest that the low DNC/HNC ratio in the high-mass sources obtained by the single-dish observations are at least partly due to the low filling factor of the high density regions.Comment: accepted to Ap

Coexistence of malignant phyllodes tumor and her2-positive locally advanced breast cancer in distinct breasts: A case report

AbstractIntroductionPhyllodes tumor of the breast is a rare biphasic neoplasm, accounting for less than 1% of all breast tumors. Coexistence of phyllodes tumor and breast cancer in distinct breasts is extremely rare.Case presentationA 47-year-old Japanese woman presented with bilateral breast lumps. A HER2-positive, unresectable invasive carcinoma in the right breast and fibroadenoma in the left were diagnosed via core needle biopsy. During chemotherapy with anti-HER2 therapy, the breast cancer shrank quickly, while the left breast lump suddenly enlarged. Under a diagnosis of malignant neoplasm of the breast, left mastectomy was performed. Malignant phyllodes tumor was diagnosed by postoperative histological examination and recurred in multiple areas as early as 2 months after surgery.DiscussionOnly 10 cases of coexisting phyllodes tumor and breast cancer in distinct breasts have been reported in the English literature. Phyllodes tumor associated with breast cancer in distinct breasts tends to be malignant. This is the first case of phyllodes tumor rapidly enlarging during anti-HER2 chemotherapy for locally advanced HER2-positive breast cancer.ConclusionEven during effective treatment of advanced or recurrent breast cancer, attention should also be paid to the contralateral breast for the possible association of a second malignancy such as phyllodes tumor

The Magnetic Tape System of the Kyoto University Digital Computer KDC-I

This paper describes the details of the magnetic tape system of the Kyoto University Digital Computer KDC-I with emphasis on the design features and problems. The system was developed and built in collaboration with Hitachi, Ltd., and was attached to the main part of the computer in October 1960. The tape is used only as a secondary memory and not as an input/output medium at present. The tape system includes magnetic tape handlers and a magnetic tape control unit which contains a high speed magnetic core memory. The main features of the tape system are :-concurrent operations of the tape and of the main part of the computer, a new block number system which was named a variable block number system, an instruction system which enables a simple treatment of the drop-out problem of magnetic tape, noise suppression and the correction of time displacement error by using the KDC-I basic logic circuits, and so on. In spite of difficulties at the time of the design of the system, the completed tape system satisfies the required functions and is utilized almost daily at the Kyoto University Computation Center

On the Design of the Kyoto University Digital Computer KDC-I

This paper describes the outline, the design features and design problems of the KDC-I, Kyoto University Digital Computer I, which has been developed and built in collaboration with Hitachi, Ltd. and put into operation since August 1960 at the computation center of the University. Emphasis is laid on the computer instructions. On other subjects only main design features are given. The KDC-I is a serial-parallel decimal computer using transistor dynamic flip-flop circuits operating at 230kc per second. A magnetic core and magnetic drum memory constitute the main internal memory of the computer, while magnetic tape memory is used as an external memory. Both fixed-point and floating-point operations are feasible in the computer. The concurrent operations of the output and of the magnetic tape units with the central processing unit increase the processing speed of the computer. The programming group at the University has already completed a fairly extensive library of subroutines and some very useful assemblers such as SYCS-1. Moreover a KDC ALGOL 60 Compiler is now under program test. The KDC-I has already performed a vast amount of calculations on various problems, which have been submitted by the staff and students of the University. With two years of operating experience, satisfactory results are being obtained from this computer