Compression of Large genomic datasets using COMRAD on Parallel Computing Platform

The big data storage is a challenge in a post genome era. Hence, there is a need for high performance computing solutions for managing large genomic data. Therefore, it is of interest to describe a parallel-computing approach using message-passing library for distributing the different compression stages in clusters. The genomic compression helps to reduce the on disk“foot print” of large data volumes of sequences. This supports the computational infrastructure for a more efficient archiving. The approach was shown to find utility in 21 Eukaryotic genomes using stratified sampling in this report. The method achieves an average of 6-fold disk space reduction with three times better compression time than COMRAD.

Availability

The source codes are written in C using message passing libraries and are available at https:// sourceforge.net/ projects/ comradmpi/files / COMRADMPI/     

Patterns of Sperm Transfer in the Golden Orb‐Weaver Nephila edulis

Sperm competition studies typically identify copulation duration as an important predictor of paternity as it may determine the quantity of sperm transferred and thus paternity success. This study explores the relationship between copulation duration, male body size, male age and sperm transfer in the golden orb‐weaving spider, Nephila edulis. Paternity in this species is strongly associated with the relative frequency and duration of copulation, which is also influenced by male size. We determined the number of sperm transferred during copulation, by performing sperm counts in both the male copulatory organs (palps) and female sperm receptacle (spermatheca) of recently mated pairs. The total number of sperm recorded (the sum in the male palps and female spermathecae) was greater for younger males than older males, but did not vary with male body size. In general, younger males transferred more sperm and a greater proportion of their sperm supplies than older males and, among these younger males, larger individuals transferred more sperm. However, there were no significant size effects for older males. More sperm was transferred with longer copulations, but in contrast with previous studies, we found that larger males copulated for longer. The rate of sperm transferred was negatively correlated with the duration of copulation, suggesting that the variation in copulation duration in N. edulis may represent strategic investment by males to alter patterns of paternity, in addition to transferring additional sperm.     

景宁木兰花粉萌发与贮藏特性研究

以景宁木兰的花粉为试材,采用花粉离体培养法,用单因子与正交试验研究不同浓度蔗糖、H3BO3、CaCl2所组成的基本培养基对景宁木兰花粉萌发的影响,同时探讨不同贮藏条件和贮藏时间对花粉活力的影响。结果表明:景宁木兰在30 g·L-1蔗糖+200 mg·L-1H3BO3+200 mg·L-1CaCl2的液体培养基上萌发率最高(74.56%)。低温条件下有利于景宁木兰花粉生活力的保持,在-80℃条件下,花粉生活力下降较慢,并且随着贮藏时间的增加,经过硅胶干燥的花粉的活力明显高于湿润花粉的活力。     

Successful storage of protocorm-like bodies of hybrid Cymbidium (Orchidaceae) under low temperature conditions

Low temperatures result in lower metabolic cellular activity, thus slowing down cell division and growth. This is advantageous where a plant scientist might seek to store important germplasm without the risks associated with low temperature storage. In this study, two cold temperatures above freezing, namely 4 and 10 °C, were tested to assess for how long PLBs could be preserved without a significant loss in regeneration ability (i.e., the ability to form neo-PLBs). Control treatments were cultured at 25 °C on Teixeira Cymbidium (TC) medium at a 16-h photoperiod at a photosynthetic photon flux density (PPFD) of 45 μmol m⁻² s⁻¹. For the cold treatments, each was replicated in the dark and at low light intensity (12-h photoperiod and a PPFD of 10 μmol m⁻² s⁻¹). All cultures were sub-cultured six times onto fresh medium every 60 days, for approximately 1 year. On the 7th subculture, all neo-PLBs were prepared uniformly and replated onto standard TC medium under light conditions described above for the control. 45 days after the 7th subculture and just before subcultures 1–6, the number of neo-PLBs per half-PLB was measured. The number of neo-PLBs that formed under different treatments depended strongly on the temperature and light conditions with most neo-PLBs forming under control conditions, although that number dropped significantly as the temperature was dropped to 10 °C and then even more to 4 °C, the same trend being observed when explants were cultured and subcultured under dim light, with organogenesis being more strongly negatively influenced in darkness. For all low-temperature treatments, as well as the dimmed light and darkness treatments, the number of neo-PLBs increased significantly when recultured, on the 7th subculture, onto control TC medium under control environmental conditions, almost as high as the control values. In contrast, the control values decreased, with significantly fewer neo-PLBs by the 7th subculture relative to the control, indicating that new PLBs should be induced from shoot cultures at least once a year to maintain their vitality.     

The effect of relaxin supplementation of in vitro maturation medium on the development of cat oocytes obtained from ovaries stored at 4 °C

Relaxin is a member of the insulin-like family of hormones that promotes growth in a number of reproductive tissues, including the granulosa and theca cells. Cat oocytes collected from cold-stored ovaries remain capable of maturing in vitro, but the developmental ability of the oocytes decreases after 24 h of cold storage. To improve the developmental ability of cat oocytes from cold-stored ovaries, we investigated the effect of relaxin supplementation of maturation medium on their meiotic ability and subsequent development. Cat oocytes were collected from ovaries stored at 4 °C for one day and cultured in maturation medium supplemented with different concentrations (0, 10, 20, and 40 ng/ml) of relaxin for 24 h. They were then fertilized in vitro for 12 h with frozen-thawed spermatozoa. After in vitro fertilization, the zygotes were cultured in synthetic oviduct fluid medium for 8 days. There were no significant differences in the maturation rates and glutathione contents of oocytes among the groups, irrespective of relaxin supplementation. The rate of blastocyst formation from oocytes matured with 10 ng/ml relaxin (16.0%) was higher (p < 0.05) than that from oocytes matured without relaxin (5.9%). Our findings indicate that supplementation of 10 ng/ml relaxin into maturation medium may improve blastocyst formation of cat oocytes after in vitro fertilization.