A comparative analysis of HGSC and Celera human genome assemblies and gene sets

MOTIVATION: Since the simultaneous publication of the human genome assembly by the International Human Genome Sequencing Consortium (HGSC) and Celera Genomics, several comparisons have been made of various aspects of these two assemblies. In this work, we set out to provide a more comprehensive comparative analysis of the two assemblies and their associated gene sets. RESULTS: The local sequence content for both draft genome assemblies has been similar since the early releases, however it took a year for the quality of the Celera assembly to approach that of HGSC, suggesting an advantage of HGSC's hierarchical shotgun (HS) sequencing strategy over Celera's whole genome shotgun (WGS) approach. While similar numbers of ab initio predicted genes can be derived from both assemblies, Celera's Otto approach consistently generated larger, more varied gene sets than the Ensembl gene build system. The presence of a non-overlapping gene set has persisted with successive data releases from both groups. Since most of the unique genes from either genome assembly could be mapped back to the other assembly, we conclude that the gene set discrepancies do not reflect differences in local sequence content but rather in the assemblies and especially the different gene-prediction methodologies.     

Biogenesis of Weibel-Palade bodies

Weibel-Palade bodies (WPBs) are the lysosome-related secretory organelles of endothelial cells. Their content protein von Willebrand factor, plays a key role in haemostasis, whilst P-selectin in the membranes is critical in the initiation of inflammation. Biogenesis of these rod-shaped structures is driven by von Willebrand factor, since its heterologous expression leads to formation of organelles morphologically indistinguishable from bona fide WPBs. The two main membrane proteins of WPBs, CD63 and P-selectin, have complex itineraries controlled largely by cytoplasmic targeting signals. We are only just beginning to understand the way in which these three proteins come together to form mature WPBs.     

Sarcocystis neurona: parasitemia in a severe combined immunodeficient (SCID) horse fed sporocysts

Sarcocystis neurona was isolated from the blood of a 5-month-old Arabian foal with severe combined immunodeficiency. The foal had been inoculated approximately 3 weeks previously with 5 x 10(5) sporocysts that were isolated from the intestines of an opossum and identified by restriction enzyme analysis of PCR products as S. neurona. The isolate obtained from the blood of this foal was characterized by genetic, serologic, and morphologic methods and identified as S. neurona (WSU1). This represents the first time that S. neurona has been isolated from any tissue after experimental infection of a horse. This is also the first time a parasitemia has been detected during either natural or experimental infection. The severe combined immunodeficiency foal model provides a unique opportunity to study the pathogenesis of S. neurona infection in horses and to determine the role of the immune system in the control of infection with and development of neurologic disease.     

Plant growth inhibiting properties of diterpenes from tobacco

Certain diterpenes, isolated from various tobacco species andcultivars, inhibited the growth of wheat coleoptiles. The mostactive were sclareol, a mixture of sclareol and epi-sclareol, and rß-4,8,13-duvatriene-1,3-diol, abienol, and labdanediol. (Received December 20, 1976; )     

Classic Weinstein: tetrad analysis, genetic variation and achiasmate segregation in Drosophila and humans.

A maximum-likelihood method for the estimation of tetrad frequencies from single-spore data is presented. The multilocus exchange with interference and viability (MEIV) model incorporates a clearly defined model of exchange, interference, and viability whose parameters define a multinomial distribution for single-spore data. Maximum-likelihood analysis of the MEIV model (MEIVLA) allows point estimation of tetrad frequencies and determination of confidence intervals. We employ MEIVLA to determine tetrad frequencies among 15 X chromosomes sampled at random from Drosophila melanogaster natural populations in Africa and North America. Significant variation in the frequency of nonexchange, or E(0) tetrads, is observed within both natural populations. Because most nondisjunction arises from E(0) tetrads, this observation is quite unexpected given both the prevalence and the deleterious consequences of nondisjunction in D. melanogaster. Use of MEIVLA is also demonstrated by reanalyzing a recently published human chromosome 21 dataset. Analysis of simulated datasets demonstrates that MEIVLA is superior to previous methods of tetrad frequency estimation and is particularly well suited to analyze samples where the E(0) tetrad frequency is low and sample sizes are small, conditions likely to be met in most samples from human populations. We discuss the implications of our analysis for determining whether an achiasmate system exists in humans to ensure the proper segregation of E(0) tetrads.     

Differential expression of absorptive cation-chloride-cotransporters in the intestinal and renal tissues of the European eel (Anguilla anguilla)

Duplicate pairs of isoforms of each of the NKCC2 and the NCC absorptive cation-chloride-cotransporters have been isolated from the European eel. As with mammalian NKCC2, NKCC2alpha isoform mRNA expression was restricted to renal tissues, whereas NKCC2beta isoform expression was present in intestine and urinary bladder. Similar to mammalian NCC, NCCalpha mRNA expression was also found in the kidney, whereas, expression of NCCbeta mRNA was found at low levels in a number of tissues but particularly in intestine. Following 3 weeks of transfer of yellow or silver (adult life stages) eels from freshwater (FW) to seawater (SW), renal mRNA expression of NKCC2alpha did not change whereas NCCalpha expression was reduced although only significantly in silver eels. This suggests that any changes in renal sodium chloride re-absorption in SW-acclimated fish may be due to decreased NCCalpha cotransporter activity rather than the result of suppression of NKCCalpha cotransporter activity. Intestinal mRNA expression of NKCC2beta generally increased following SW acclimation, although maximal increases occurred later in yellow (7 days) than silver (2 days) eels. Average levels of NKCC2beta mRNA abundance in the middle intestine were 89% of those in the anterior, and this was reduced to 44% (of the level in the anterior intestine) in posterior intestine/rectum. Expression of NCCbeta was only found in the posterior intestine/rectum. Together these results suggest intestinal sodium chloride absorption may switch from occurring via NKCCbeta to NCCbeta as imbibed fluid travels down the intestine and the concentration of luminal potassium decreases.     

Organic mulches in highbush blueberries alter beetle (Coleoptera) community composition and improve functional group abundance and diversity

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