Whole-genome sequencing and variant discovery in C. elegans

Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the reference genome to characterize the data and to evaluate coverage and representation. Massively parallel sequencing facilitates strain-to-reference comparison for genome-wide sequence variant discovery. Owing to the short-read-length sequences produced, we developed a revised approach to determine the regions of the genome to which short reads could be uniquely mapped. We then aligned Solexa reads from C. elegans strain CB4858 to the reference, and screened for single-nucleotide polymorphisms (SNPs) and small indels. This study demonstrates the utility of massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms.     

A novel test for host-symbiont codivergence indicates ancient origin of fungal endophytes in grasses

Significant phylogenetic codivergence between plant or animal hosts (H) and their symbionts or parasites (P) indicates the importance of their interactions on evolutionary time scales. However, valid and realistic methods to test for codivergence are not fully developed. One of the systems where possible codivergence has been of interest involves the large subfamily of temperate grasses (Pooideae) and their endophytic fungi (epichloae). These widespread symbioses often help protect host plants from herbivory and stresses and affect species diversity and food web structures. Here we introduce the MRCALink (most-recent-common-ancestor link) method and use it to investigate the possibility of grass-epichlo? codivergence. MRCALink applied to ultrametric H and P trees identifies all corresponding nodes for pairwise comparisons of MRCA ages. The result is compared to the space of random H and P tree pairs estimated by a Monte Carlo method. Compared to tree reconciliation, the method is less dependent on tree topologies (which often can be misleading), and it crucially improves on phylogeny-independent methods such as ParaFit or the Mantel test by eliminating an extreme (but previously unrecognized) distortion of node-pair sampling. Analysis of 26 grass species-epichlo? species symbioses did not reject random association of H and P MRCA ages. However, when five obvious host jumps were removed, the analysis significantly rejected random association and supported grass-endophyte codivergence. Interestingly, early cladogenesis events in the Pooideae corresponded to early cladogenesis events in epichloae, suggesting concomitant origins of this grass subfamily and its remarkable group of symbionts. We also applied our method to the well-known gopher-louse data set.     

Diversity and productivity of plant communities across the Inland Northwest,USA

No definitive explanation for the form of the relationship between species diversity and ecosystem productivity exists nor is there agreement on the mechanisms linking diversity and productivity across scales. Here, we examine changes in the form of the diversity–productivity relationship within and across the plant communities at three observational scales: plots, alliances, and physiognomic vegetation types (PVTs). Vascular plant richness data are from 4,760 20 m² vegetation field plots. Productivity estimates in grams carbon per square meter are from annual net primary productivity (ANPP) models. Analyses with generalized linear models confirm scale dependence in the species diversity–productivity relationship. At the plot focus, the observed diversity–productivity relationship was weak. When plot data were aggregated to a focus of vegetation alliances, a hump-shaped relationship was observed. Species turnover among plots cannot explain the observed hump-shaped relationship at the alliance focus because we used mean plot richness across plots as our index of species richness for alliances and PVTs. The sorting of alliances along the productivity gradient appears to follow regional patterns of moisture availability, with alliances that occupy dry environments occurring within the increasing phase of the hump-shaped pattern, alliances that occupy mesic to hydric environments occurring near the top or in the decreasing phase of the curve, and alliances that occupy the wettest environments having the fewest species and the highest ANPP. This pattern is consistent with the intermediate productivity theory but appears to be inconsistent with the predictions of water–energy theory.     

Plasma cortisol and beta-endorphin in horses subjected to electro-acupuncture for cutaneous analgesia

Electro-acupuncture (EA) treatment of horses to induce cutaneous analgesia also increased plasma concentrations of beta-endorphin (beta-EP) and cortisol. The magnitude of these increases did not relate consistently to the degree of EA-induced analgesia. Respiration and heart rates were also markedly increased during EA treatment. Intact female horses had higher packed cell volume and plasma beta-EP as well as lower plasma total protein than castrated male horses. Plasma cortisol, heart rate, and respiration rate did not differ significantly between sexes. None of the parameters measured before or during EA treatment provided an explanation for the differential cutaneous analgesia which depended on sex of subject and locus of stimulation as reported elsewhere.     

Human term placenta contains transforming growth factors

Growth factors of apparent molecular weights of 6,000, 10,000, 20,000 and one in excess of 30,000 daltons can be isolated from acid-ethanol extracts of human term placentas. Each size class of growth factor resembles transforming growth factor (TGF) in that it stimulates anchorage independent growth of normal rat kidney cells and competes with EGF for binding to EGF membrane receptors. The 6,000, 10,000 and 20,000 molecular weight polypeptides also resemble TGF in their acid and heat stability, and their requirement for intact disulfide bonds for growth promoting activity. By homologous radioimmunoassay, neither the 6,000 nor 10,000 dalton polypeptide is related to human epidermal growth factor (hEGF). The presence of these TGFs in ample concentrations (approximately 100 ng of EGF equivalents per term placenta for the 10,000 dalton polypeptide) indicates the usefulness of this tissue source for study of human TGFs.     

Urinary TGFs1 in neoplasia: immunoreactive TGF-alpha in the urine of patients with disseminated breast carcinoma

A tumor-associated growth factor was identified in a 22-liter pool of urine from patients with disseminated breast cancer using an isolation scheme which separates transforming growth factor-alpha (TGF-alpha) from the high level of human epidermal growth factor (hEGF) normally present in urine. Concentration of urinary proteins by adsorption onto methyl bonded microparticulate silica, selective elution by acetonitrile, and subsequent gel permeation, cation exchange, and high performance liquid chromatography, resolved an EGF-related growth factor which generated a competitive binding curve similar to that of synthetic rat TGF-alpha in radioimmunoassay. A 26-liter pool of urine from normal subjects, evaluated in the same manner as a part of another study, did not contain measureable quantities of this factor.     

Sarcocystis fayeri sp. n. from the horse.

Hearts, diaphragms, esophagi, and spinal cords from 266 horses were obtained at slaughter in Creston, Ohio. Tissues were examined microscopically for Sarcocystis in sections, digested in trypsin to obtain bradyzoites, and fed to 10 dogs and 10 cats. Intramuscular cysts were found in selections of two hearts from 57 horses and four esophagi from 107 horses. The cysts were up to 900 micron long and up to 70 micron wide. The cyst wall was 1 to 2 micron thick and cross-striated. The enclosed bradyzoites were banana-shaped, 15 to 20 by 20 to 3 micron, and contained several PAS-positive granules. Bradyzoites were found in trypsin digests of seven of 57 (13%) equine tissues (heart, diaphragm, esophagus but not spinal cord) in one experiment and 10 of 47 (21%) esophagi, eight of 47 (17%) diaphragms but none of 47 hearts and spinal cords in another experiment. All of 10 dogs shed sporulated sporocysts or oocysts in feces 12 to 15 days (12 in one, 13 in eight, and 15 days in one) after digesting tissues from 169 horses. The sporocysts were 11 to 13 (12.0 +/- 0.5) by 7 to 8.5 (7.9 +/- 0.5) micron. In histologic sections of canine small intestine the sporocysts were located in the lamina propria near the tips of the villi. The 10 cats fed tissues from 266 horses did not shed Sarcocystis. A new name, S. fayeri, is proposed for this organism. Sarcocystis fayeri sporocysts (12 by 8 micron) are shorter than those of S. betrami (15 by 10 micron), the other species of Sarcocystis from the horse. The prepatent period is 12 to 15 days for S. fayeri and 8 days for S. bertrami (synonym S. equicanis Rommel and Geisel 1975).     

Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays

Efficient construction of BAC-based human artificial chromosomes (HACs) requires optimization of each key functional unit as well as development of techniques for the rapid and reliable manipulation of high-molecular weight BAC vectors. Here, we have created synthetic chromosome 17-derived alpha-satellite arrays, based on the 16-monomer repeat length typical of natural D17Z1 arrays, in which the consensus CENP-B box elements are either completely absent (0/16 monomers) or increased in density (16/16 monomers) compared to D17Z1 alpha-satellite (5/16 monomers). Using these vectors, we show that the presence of CENP-B box elements is a requirement for efficient de novo centromere formation and that increasing the density of CENP-B box elements may enhance the efficiency of de novo centromere formation. Furthermore, we have developed a novel, high-throughput methodology that permits the rapid conversion of any genomic BAC target into a HAC vector by transposon-mediated modification with synthetic alpha-satellite arrays and other key functional units. Taken together, these approaches offer the potential to significantly advance the utility of BAC-based HACs for functional annotation of the genome and for applications in gene transfer.