Aortic valve opening and closure: the clover dynamics.

Background: Systolic aortic root expansion is reported to facilitate valve opening, but the precise dynamics remain unknown. A sonometric study with a high data sampling rate (200 to 800 Hz) was conducted in an acute ovine model to better understand the timing, mechanisms, and shape of aortic valve opening and closure. Methods: Eighteen piezoelectric crystals were implanted in 8 sheep at each annular base, commissures, sinus of Valsalva, sinotubular junction, nodulus of Arantius, and ascending aorta (AA). Geometric changes were time related to pressures and flows. Results: The aortic root was hemodynamically divided into left ventricular (LV) and aortic compartments situated, respectively, below and above the leaflets. During isovolumetric contraction (IVC), aortic root expansion started in the LV compartment, most likely due to volume redistribution in the LV outflow tract below the leaflets. This expansion initiated leaflet separation prior to ejection (2.1%±0.5% of total opening area). Aortic compartment expansion was delayed toward the end of IVC, likely related to volume redistribution above the leaflets due to accelerating aortic backflow toward the aortic valve and coronary flow reduction due to myocardial contraction. Maximum valve opening during the first third of ejection acquired a truncated cone shape [leaflet free edge area smaller than annular base area (-41.5%±5.5%)]. The distal orifice became clover shaped because the leaflet free edge area is larger than the commissural area by 16.3%±2.0%. Conclusions: Aortic valve opening is initiated prior to ejection related to delicate balance between LV, aortic root, and coronary dynamics. It is clover shaped at maximum opening in systole. A better understanding of these mechanisms should stimulate more physiological surgical approaches of valve repair and replacement

Towards the Understanding of Complex Traits in Rice: Substantially or Superficially?

Completion of the genome analysis followed by extensive comprehensive studies on a variety of genes and gene families of rice (Oryza sativa) resulted in rapid accumulation of information concerning the presence of many complex traits that are governed by a number of genes of distinct functions in this most important crop cultivated worldwide. The genetic and molecular biological dissection of many important rice phenotypes has contributed to our understanding of the complex nature of the genetic control with respect to these phenotypes. However, in spite of the considerable advances made in the field, details of genetic control remain largely unsolved, thereby hampering our exploitation of this useful information in the breeding of new rice cultivars. To further strengthen the field application of the genome science data of rice obtained so far, we need to develop more powerful genomics-assisted methods for rice breeding based on information derived from various quantitative trait loci (QTL) and related analyses. In this review, we describe recent progresses and outcomes in rice QTL analyses, problems associated with the application of the technology to rice breeding and their implications for the genetic study of other crops along with future perspectives of the relevant fields

Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars

To dissect the genetic factors controlling naturally occurring variation of heading date in Asian rice cultivars, we performed QTL analyses using F2 populations derived from crosses between a japonica cultivar, Koshihikari, and each of 12 cultivars originating from various regions in Asia. These 12 diverse cultivars varied in heading date under natural field conditions in Tsukuba, Japan. Transgressive segregation was observed in 10 F2 combinations. QTL analyses using multiple crosses revealed a comprehensive series of loci involved in natural variation in flowering time. One to four QTLs were detected in each cross combination, and some QTLs were shared among combinations. The chromosomal locations of these QTLs corresponded well with those detected in other studies. The allelic effects of the QTLs varied among the cross combinations. Sequence analysis of several previously cloned genes controlling heading date, including Hd1, Hd3a, Hd6, RFT1, and Ghd7, identified several functional polymorphisms, indicating that allelic variation at these loci probably contributes to variation in heading date. Taken together, the QTL and sequencing results indicate that a large portion of the phenotypic variation in heading date in Asian rice cultivars could be generated by combinations of different alleles (possibly both loss- and gain-of-function) of the QTLs detected in this study

How the oxygen tolerance of a [NiFe]-hydrogenase depends on quaternary structure

‘Oxygen-tolerant’ [NiFe]-hydrogenases can catalyze H(2) oxidation under aerobic conditions, avoiding oxygenation and destruction of the active site. In one mechanism accounting for this special property, membrane-bound [NiFe]-hydrogenases accommodate a pool of electrons that allows an O(2) molecule attacking the active site to be converted rapidly to harmless water. An important advantage may stem from having a dimeric or higher-order quaternary structure in which the electron-transfer relay chain of one partner is electronically coupled to that in the other. Hydrogenase-1 from E. coli has a dimeric structure in which the distal [4Fe-4S] clusters in each monomer are located approximately 12 Å apart, a distance conducive to fast electron tunneling. Such an arrangement can ensure that electrons from H(2) oxidation released at the active site of one partner are immediately transferred to its counterpart when an O(2) molecule attacks. This paper addresses the role of long-range, inter-domain electron transfer in the mechanism of O(2)-tolerance by comparing the properties of monomeric and dimeric forms of Hydrogenase-1. The results reveal a further interesting advantage that quaternary structure affords to proteins

Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4+ concentrations in hydroponic conditions

Root system development is an important target for improving yield in cereal crops. Active root systems that can take up nutrients more efficiently are essential for enhancing grain yield. In this study, we attempted to identify quantitative trait loci (QTL) involved in root system development by measuring root length of rice seedlings grown in hydroponic culture. Reliable growth conditions for estimating the root length were first established to renew nutrient solutions daily and supply NH4+ as a single nitrogen source. Thirty-eight chromosome segment substitution lines derived from a cross between ‘Koshihikari’, a japonica variety, and ‘Kasalath’, an indica variety, were used to detect QTL for seminal root length of seedlings grown in 5 or 500 μM NH4+. Eight chromosomal regions were found to be involved in root elongation. Among them, the most effective QTL was detected on a ‘Kasalath’ segment of SL-218, which was localized to the long-arm of chromosome 6. The ‘Kasalath’ allele at this QTL, qRL6.1, greatly promoted root elongation under all NH4+ concentrations tested. The genetic effect of this QTL was confirmed by analysis of the near-isogenic line (NIL) qRL6.1. The seminal root length of the NIL was 13.5–21.1% longer than that of ‘Koshihikari’ under different NH4+ concentrations. Toward our goal of applying qRL6.1 in a molecular breeding program to enhance rice yield, a candidate genomic region of qRL6.1 was delimited within a 337 kb region in the ‘Nipponbare’ genome by means of progeny testing of F2 plants/F3 lines derived from a cross between SL-218 and ‘Koshihikari’

Biosynthesis of Salmonella enterica [NiFe]-hydrogenase-5 : probing the roles of system-specific accessory proteins

A subset of bacterial [NiFe]-hydrogenases have been shown to be capable of activating dihydrogen-catalysis under aerobic conditions; however, it remains relatively unclear how the assembly and activation of these enzymes is carried out in the presence of air. Acquiring this knowledge is important if a generic method for achieving production of O2-resistant [NiFe]-hydrogenases within heterologous hosts is to be developed. Salmonella enterica serovar Typhimurium synthesizes the [NiFe]-hydrogenase-5 (Hyd-5) enzyme under aerobic conditions. As well as structural genes, the Hyd-5 operon also contains several accessory genes that are predicted to be involved in different stages of biosynthesis of the enzyme. In this work, deletions in the hydF, hydG, and hydH genes have been constructed. The hydF gene encodes a protein related to Ralstonia eutropha HoxO, which is known to interact with the small subunit of a [NiFe]-hydrogenase. HydG is predicted to be a fusion of the R. eutropha HoxQ and HoxR proteins, both of which have been implicated in the biosynthesis of an O2-tolerant hydrogenase, and HydH is a homologue of R. eutropha HoxV, which is a scaffold for [NiFe] cofactor assembly. It is shown here that HydG and HydH play essential roles in Hyd-5 biosynthesis. Hyd-5 can be isolated and characterized from a ΔhydF strain, indicating that HydF may not play the same vital role as the orthologous HoxO. This study, therefore, emphasises differences that can be observed when comparing the function of hydrogenase maturases in different biological systems

Rice-Map: a new-generation rice genome browser

<p>Abstract</p> <p>Background</p> <p>The concurrent release of rice genome sequences for two subspecies (<it>Oryza sativa </it>L. ssp. <it>japonica </it>and <it>Oryza sativa </it>L. ssp. <it>indica</it>) facilitates rice studies at the whole genome level. Since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively.</p> <p>Description</p> <p>More than one hundred annotation tracks (81 for <it>japonica </it>and 82 for <it>indica</it>) have been compiled and loaded into Rice-Map. These pre-computed annotations cover gene models, transcript evidences, expression profiling, epigenetic modifications, inter-species and intra-species homologies, genetic markers and other genomic features. In addition to these pre-computed tracks, registered users can interactively add comments and research notes to Rice-Map as User-Defined Annotation entries. By smoothly scrolling, dragging and zooming, users can browse various genomic features simultaneously at multiple scales. On-the-fly analysis for selected entries could be performed through dedicated bioinformatic analysis platforms such as WebLab and Galaxy. Furthermore, a BioMart-powered data warehouse "Rice Mart" is offered for advanced users to fetch bulk datasets based on complex criteria.</p> <p>Conclusions</p> <p>Rice-Map delivers abundant up-to-date <it>japonica </it>and <it>indica </it>annotations, providing a valuable resource for both computational and bench biologists. Rice-Map is publicly accessible at <url>http://www.ricemap.org/</url>, with all data available for free downloading.</p