Accelerator Design for the CHESS-U Upgrade

During the summer and fall of 2018 the Cornell High Energy Synchrotron Source (CHESS) is undergoing an upgrade to increase high-energy flux for x-ray users. The upgrade requires replacing one-sixth of the Cornell Electron Storage Ring (CESR), inverting the polarity of half of the CHESS beam lines, and switching to single-beam on-axis operation. The new sextant is comprised of six double-bend achromats (DBAs) with combined-function dipole-quadrupoles. Although the DBA design is widely utilized and well understood, the constraints for the CESR modifications make the CHESS-U lattice unique. This paper describes the design objectives, constraints, and implementation for the CESR accelerator upgrade for CHESS-U

Survival of pacific salmons in the North Pacific in winter-spring season

Influence of several factors (water temperature, food supply, predatory, size of juveniles) on pacific salmons survival during wintering is considered on the data collected from the upper pelagic layer in surveys conducted by Pacific Fisheries Research Center (TINRO) in the North-West Pacific. There is highly unlikely that the temperature influences on fish mortality directly. There is no obvious proof of negative influence of the low temperature on food base of salmons, as well. The lowering of forage zooplankton biomass in the Subarctic Front zone in February-March is insufficient for the salmons starvation taking into account that the total abundance of planktivorous nekton is also lowered in this area and generally in the Subarctic waters in winter-spring, so the food supply cannot be considered as a crucial factor of the salmons survival. Seasonal changes with lowering of feeding intensity, lipid accumulation, and somatic growth in winter known for pacific salmons aren’t forced by poor food base but are a feature of their species-specific life strategy with cyclic changes of metabolism. Predators are not abundant in the Subarctic zone in winter, so the predatory also cannot cause the high mortality of salmons. Relationship between the size of juveniles and their mortality in winter is considered in detail for the Okhotsk Sea stocks of pink salmon and there is concluded that the size of juveniles cannot be a predictor of their year-classes return for spawning. Thus, any single factor doesn’t determine winter mortality of pacific salmons but their survival is likely determined by a complex interaction of abiotic and biotic factors

On steadyness of stereotypes in conceptions on marine ecology of pacific salmons (Oncorhynchus spp.)

Some conceptions on marine ecology of pacific salmons (Oncorhynchus spp.), established in the second half of the last century, are discussed from critical position, as overemphasizing of the sea surface temperature influence on distribution of salmons and formation of their year-classes strength, deficiency of food (particularly in winter time) and fierce competition for food, pink salmon «suppression» over other salmon species and own adjacent generations, limited carrying capacity of the Subarctic zone for salmons, distortion of the epipelagic communities structure in the North Pacific by mass artificial reproduction of chum salmon, etc. Most of these ideas have not been confirmed by the data of long-term monitoring in complex marine expeditions conducted by Pacific Fish. Res. Center (TINRO) in the Far-Eastern Seas and adjacent North Pacific waters since the 1980s till nowadays. The data show that pacific salmons are very ecologically plastic species with wide temperature range of habitat. Salmons are able to considerable vertical migrations crossing easily the temperature gradient zones and different water masses. They have wide feeding spectra. Migrating dispersed, they successfully get their ration, even in vast areas with relatively low concentration of prey (macroplankton and small nekton). Total biomass of all species of pacific salmons in the North Pacific does not exceed 4-5 million tons (1.5-2.0 million tons in the Russian waters), whereas the stocks of other mass species of nekton are hundreds of millions of tons. The salmons consume 1.0-5.0 % of the total consumption by nekton in the epipelagic layer in the western Bering Sea, 0.5-1.0 % in the Okhotsk Sea, 5.0-15.0 % at East Kamchatka, and less than 1 % in the Pacific waters at Kuril Islands, So, the role of pacific salmons in trophic nets of the Subarctic waters is rather moderate. Therefore, neither pink salmon, nor chum salmon can be seriously considered as the species responsible for reorganization of large ecosystems and fluctuating of other mass nekton species

A new approach for obtaining rapid uniformity in rice (Oryza sativa L.) via a 3x x 2x cross

A triploid (2n = 3x = 36) rice plant was obtained by screening a twin seedling population in which each seed germinated to two or three sprouts that were then crossed with diploid plants. One diploid plant was chosen among the various F1 progenies and developed into an F 2 population via self-pollination. Compared with the control variety Shanyou 63, this F 2 population had a stable agronomical performance in field trials, as confirmed by the F-test. The stability of the F 2 population was further substantiated by molecular analysis with simple sequence repeat markers. Specifically, of 160 markers assayed, 37 (covering all 12 chromosomes) were polymorphic between the parental lines. Testing the F 1 hybrid individually with these markers showed that each PCR product had only a single band instead of two bands from each parent. The bands were identical to either maternal (23 markers) or paternal (eight markers) bands or distinct from both parents (six markers). The amplified bands of all 60 randomly selected F 2 plants were uniform and identical to those of the F 1 hybrid. These results suggest that the F 1 plant is a non-segregating hybrid and that a stable F 2 population was obtained. This novel system provides an efficient means for shortening the cycle of hybrid rice seed production

Development of Genome-wide Simple Sequence Repeat Markers Using Whole-genome Shotgun Sequences of Sorghum (Sorghum bicolor (L.) Moench)

Simple sequence repeat (SSR) markers with a high degree of polymorphism contribute to the molecular dissection of agriculturally important traits in sorghum (Sorghum bicolor (L.) Moench). We designed 5599 non-redundant SSR markers, including regions flanking the SSRs, in whole-genome shotgun sequences of sorghum line ATx623. (AT/TA)n repeats constituted 26.1% of all SSRs, followed by (AG/TC)n at 20.5%, (AC/TG)n at 13.7% and (CG/GC)n at 11.8%. The chromosomal locations of 5012 SSR markers were determined by comparing the locations identified by means of electronic PCR with the predicted positions of 34 008 gene loci. Most SSR markers had a similar distribution to the gene loci. Among 970 markers validated by fragment analysis, 67.8% (658 of 970) markers successfully provided PCR amplification in sorghum line BTx623, with a mean polymorphism rate of 45.1% (297 of 658) for all SSR loci in combinations of 11 sorghum lines and one sudangrass (Sorghum sudanense (Piper) Stapf) line. The product of 5012 and 0.678 suggests that ∼3400 SSR markers could be used to detect SSR polymorphisms and that more than 1500 (45.1% of 3400) markers could reveal SSR polymorphisms in combinations of Sorghum lines

Observation of the Dynamic Beta Effect at CESR with CLEO

Using the silicon strip detector of the CLEO experiment operating at the Cornell Electron-positron Storage Ring (CESR), we have observed that the horizontal size of the luminous region decreases in the presence of the beam-beam interaction from what is expected without the beam-beam interaction. The dependence on the bunch current agrees with the prediction of the dynamic beta effect. This is the first direct observation of the effect.Comment: 9 page uuencoded postscript file, postscritp file also available through http://w4.lns.cornell.edu/public/CLNS, submitted to Phys. Rev.

Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L.

The whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequences thus obtained was 285 858 490 bp consisting of 120 586 contigs and 29 831 singlets. They accounted for ∼95% of the gene-containing regions with the average G + C content was 34.3%. A total of 40 929 complete and partial structures of protein encoding genes have been deduced. Comparison with genes of other plant species indicated that 1529 (4%) of the putative protein-encoding genes are specific to the Euphorbiaceae family. A high degree of microsynteny was observed with the genome of castor bean and, to a lesser extent, with those of soybean and Arabidopsis thaliana. In parallel with genome sequencing, cDNAs derived from leaf and callus tissues were subjected to pyrosequencing, and a total of 21 225 unigene data have been generated. Polymorphism analysis using microsatellite markers developed from the genomic sequence data obtained was performed with 12 J. curcas lines collected from various parts of the world to estimate their genetic diversity. The genomic sequence and accompanying information presented here are expected to serve as valuable resources for the acceleration of fundamental and applied research with J. curcas, especially in the fields of environment-related research such as biofuel production. Further information on the genomic sequences and DNA markers is available at http://www.kazusa.or.jp/jatropha/

Evolution and Association Analysis of Ghd7 in Rice

Plant height, heading date, and yield are the main targets for rice genetic improvement. Ghd7 is a pleiotropic gene that controls the aforementioned traits simultaneously. In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise π and θ in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs