Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae)

Red pine (Pinus resinosa Ait.) is an ecologically and economically important forest tree species of northeastern North America and is considered one of the most genetically depauperate conifer species in the region. We have isolated and characterized 13 nuclear microsatellite loci by screening a partial genomic library with di-, tri-, and tetranucleotide repeat oligonucleotide probes. In an analysis of over 500 individuals representing 17 red pine populations from Manitoba through Newfoundland, five polymorphic microsatellite loci with an average of nine alleles per locus were identified. The mean expected and observed heterozygosity values were 0.508 and 0.185, respectively. Significant departures from Hardy-Weinberg equilibrium with excess homozygosity indicating high levels of inbreeding were evident in all populations studied. The population differentiation was high with 28–35% of genetic variation partitioned among populations. The genetic distance analysis showed that three northeastern (two Newfoundland and one New Brunswick) populations are genetically distinct from the remaining populations. The coalescence-based analysis suggests that "northeastern" and "main" populations likely became isolated during the most recent Pleistocene glacial period, and severe population bottlenecks may have led to the evolution of a highly selfing mating system in red pine

Correlation of gene expression and protein production rate - a system wide study

<p>Abstract</p> <p>Background</p> <p>Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on <it>Saccharomyces cerevisiae </it>chemostat cultivations provided the first analysis on genome wide effects of growth rate. In this work we study the filamentous fungus <it>Trichoderma reesei </it>(<it>Hypocrea jecorina</it>) that is an industrial protein production host known for its exceptional protein secretion capability. Interestingly, it exhibits a low growth rate protein production phenotype.</p> <p>Results</p> <p>We have used transcriptomics and proteomics to study the effect of growth rate and cell density on protein production in chemostat cultivations of <it>T. reesei</it>. Use of chemostat allowed control of growth rate and exact estimation of the extracellular specific protein production rate (SPPR). We find that major biosynthetic activities are all negatively correlated with SPPR. We also find that expression of many genes of secreted proteins and secondary metabolism, as well as various lineage specific, mostly unknown genes are positively correlated with SPPR. Finally, we enumerate possible regulators and regulatory mechanisms, arising from the data, for this response.</p> <p>Conclusions</p> <p>Based on these results it appears that in low growth rate protein production energy is very efficiently used primarly for protein production. Also, we propose that flux through early glycolysis or the TCA cycle is a more fundamental determining factor than growth rate for low growth rate protein production and we propose a novel eukaryotic response to this i.e. the lineage specific response (LSR).</p

Genetic variation in western red cedar (Thuja plicata Donn) seedlings

To determine whether the apparent lack of genetic variation in western red cedar (Thujaplicata Donn), as previously inferred by isozyme and terpene studies, would hold true for quantitative seedling traits, a provenance study was initiated to investigate patterns of variation in seedling growth and survival characteristics, cold temperature acclimation, and response to inbreeding. Seedlings from ten coastal and ten interior provenances, half with family structure (five families / provenance), were grown for three years at one coastal (Vancouver) and one interior (Salmon Arm) location. Twenty-three potted clones were both self-pollinated and polycrossed at Cowichan Lake; resulting progeny were monitored for growth and frost hardiness. Genetic variation could be detected from the first year, and increased annually. The narrow-sense individual heritability, assuming some inbreeding, of final heights of trees growing in Vancouver was 0.38. Height, root collar diameter, acclimation, and deacclimation exhibited mainly within-population variation, while variation in dry weight measurements, foliar nutrient content, survival at Salmon Arm, and maximum cold hardiness was evident mainly between populations. Coastal / interior differences were noted in first-year heights, branch number, height, survival, and crown dieback at Salmon Arm following a severe winter in which trees suffered major desiccation damage, and in acclimation and deacclimation. In general, adaptive traits appeared to show more between-population differences, while traits under less selective pressure showed mainly within-population variation. Provenances displaying the greatest variation at the family level were those from Vancouver Island. Between-population variability appeared to be highest in the B.C. interior, and lowest in northern B.C. populations. Elevation influenced all traits displaying provenance variation. Location effects occurred, and some genotype by environmental interactions were noted. Plasticity was evident in timing of growth initiation and cessation, timing of acclimation and deacclimation, and in depth of maximum hardiness reached per year. Early traits showed little evidence of inbreeding depression, but there seemed to be a trend towards gradual expression of inbreeding depression over time, at least in traits under selective pressure. This research showed that western red cedar is much more complex than previously believed, and substantial genetic variation exists in several traits of this species.Forestry, Faculty ofGraduat

Growth, morphology, and cold hardiness of Chamaecyparis nootkatensis seedlings originating from an abbreviated reproductive cycle

A common garden study investigated growth, morphology, and cold hardiness of yellow-cedar (Chamaecyparis nootkatensis (D. Don) Spach) seedlings originating from seed that had matured at an accelerated rate. This early maturing seed, produced at a low-elevation southern Vancouver Island seed orchard, was known to have similar germinability and seedling morphology as high-elevation normally maturing seeds. Population differences in 3-year-old seedlings were evident only in shoot harvest index (ratio of stem/shoot dry weight). The amount of stem elongation that occurred prior to the formation of secondary foliage (juvenile height) and harvest index were weakly correlated with source elevation at which maternal parents were developed. Traits that exhibited no discernable differences between progeny from early maturing seed and the control normally maturing seed included midwinter cold hardiness testing and selected measures of shoot morphology and growth. The control seedlings had significantly less height growth prior to the transition of primary foliage to secondary foliage formation than did the seedlings originating from early maturing seed

Investigation of limestone ecotypes of white spruce based on a provenance test series

Previous laboratory and field studies have presented evidence for the existence of limestone ecotypes in white spruce (Picea glauca (Moench) Voss). Remeasurements of the range-wide 410 series of provenance trials were used for further evaluation of the existence of these ecotypes. In 2001, heights were measured of 23 provenances grown at four test sites in Ontario, all located south of 46°N. Bedrock classification for test sites and provenances by limestone or non-limestone parent material was done using a 1993 data set of the Ontario Geological Survey. Analysis of variance revealed significant differences among test sites and provenances only. No significant interactions consistent with the existence of limestone ecotypes were detected. This finding is in contrast to that of an earlier field study that detected a strong interaction between test site and provenance bedrock type (p < 0.001). Examination of the relative performance of individual provenances from limestone and non-limestone bedrock types revealed differences in performance at the four different test sites but few instances supporting the existence of limestone ecotypes. Although these more recent results generally support a pattern of between-stand variation in southern Ontario, they do not disprove the existence of limestone ecotypes, owing to the nature of the 410-series test design and the classification of provenances according to bedrock type instead of actual soil analyses

Recruitment to diagnosis of urinary tract infections in young children (DUTY) study: an evaluation of the successful methods used in a primary care, prospective cohort study. [Abstract]

DUTY is a prospective cohort study to derive a clinical algorithm for diagnosis of urinary tract infections in acutely unwell children in primary care. It provides an example of successful recruitment to a complex paediatric study, requiring the collection of a urine sample from young, unwell children. The aim is to describe and evaluate factors that contributed to its success from a study management and recruiter perspective

HIV Status and Other Risk Factors for Prevalent and Incident Sexually Transmitted Infection during Pregnancy (2000-2014)

Background. Sexually transmitted infections (STIs) are associated with adverse birth outcomes. Current prenatal STI screening guidelines define “risk” without explicit consideration of HIV status. Our objective was to test the hypothesis that HIV status is associated with bacterial STI in pregnant women. Methods. We designed a retrospective cohort study to identify pregnant women with HIV who delivered at our facility during 2000-2014. HIV+ women were compared to HIV- women with matching by year of delivery. Logistic regression was used to model adjusted odds of prevalent and incident STI. Prevalent STI was defined as chlamydia (CT), gonorrhea (GC), syphilis, or trichomoniasis detected on an initial prenatal screening test and incident STI as a newly positive result following a negative prenatal test. Results. The cohort included 432 women, 210 HIV+ and 222 HIV-. Most pregnant women were screened for STI (92% of HIV+ women and 74% of HIV- women). STI rates were high and particularly elevated in HIV+ women: 29% vs 18% (p=0.02), for prevalent STI and 11% vs 2% (p<0.001) for incident STI. Risk factors for prevalent STI were as follows: HIV status (aOR 3.0, CI: 1.4-6.4), Black race (aOR 2.7, 95% CI: 1.1-6.6), and more recent delivery (2007-2014 compared to 2000-2006) (aOR 2.3, CI: 1.1-4.7). HIV status was an independent risk factor for incident STI (aOR 7.2, CI: 2.1-25.0). Conclusion. Pregnant women who delivered in our center had high STI rates. Since HIV infection was independently associated with prevalent and incident STI, prenatal screening guidelines may need to incorporate HIV status as a high-risk group for repeat testing