Large-scale identification of polymorphic microsatellites using an <Emphasis Type="Italic">in silico</Emphasis> approach

Background  

Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. In silico approaches have become a practicable and relatively inexpensive alternative during the last decade, although testing putative SSR markers still is time consuming and expensive. In many species only a relatively small percentage of SSR markers turn out to be polymorphic. This is particularly true for markers derived from expressed sequence tags (ESTs). In EST databases a large redundancy of sequences is present, which may contain information on length-polymorphisms in the SSR they contain, and whether they have been derived from heterozygotes or from different genotypes. Up to now, although a number of programs have been developed to identify SSRs in EST sequences, no software can detect putatively polymorphic SSRs.     

POCUS: mining genomic sequence annotation to predict disease genes

Here we present POCUS (prioritization of candidate genes using statistics), a novel computational approach to prioritize candidate disease genes that is based on over-representation of functional annotation between loci for the same disease. We show that POCUS can provide high (up to 81-fold) enrichment of real disease genes in the candidate-gene shortlists it produces compared with the original large sets of positional candidates. In contrast to existing methods, POCUS can also suggest counterintuitive candidates.     

Bateson's two Toronto addresses, 1921: 2. Evolutionary faith

William Bateson's plenary address to the American Association for the Advancement of Science meeting in Toronto in 1921 was titled "Evolutionary Faith and Modern Doubts." In it he expressed his deep-seated skepticism about the causes of evolution (and in particular, his dissatisfaction with Darwinian natural selection) while reaffirming his belief in the reality of evolution itself. The address led to controversy at both the scientific and popular levels. Scientific criticism centered on Bateson's rejection of natural selection; popular controversy, as evidenced by contemporary newspaper clippings, was very widespread, not least because religious fundamentalists misrepresented Bateson in their campaign against evolution. I draw attention to the forgotten case of F.E. Dean, a superintendent of schools at Fort Sumner, New Mexico, who in 1922 was forced to resign his post for merely challenging a resolution of the local school board banning the teaching of evolution in schools. Dean deserves to be remembered, along with John T. Scopes, as an early hero of the continuing fight for the right to teach evolution in U.S. schools.     

Platelet-activating factor and serum components from oestrous mice co-operate to mimic the activity of 'early pregnancy factor' in the rosette inhibition assay

When male mouse spleen cells were incubated with a combination of platelet activating factor (PAF, 1-0-alkyl-2-acetyl-sn-glycero-3-phosphocholine) and sera from female mice in oestrus, the cells displayed a markedly increased rosette inhibition titre (RIT) when subsequently tested in the rosette inhibition assay. Neither PAF nor oestrous mouse sera alone could induce this effect, the combined action was required. Lyso-PAF could not substitute for the PAF, nor could male mouse sera nor the sera from females in dioestrus or metoestrus substitute for the oestrous mouse serum requirement. Pro-oestrous mouse sera could replace oestrous mouse sera but were less effective in their dose-responses. Studies on the mechanism of action of the PAF and oestrous mouse serum components suggested that the PAF stimulated the production and release of soluble factors (termed S2 factors) which by themselves could induce increased RIT values when applied to fresh spleen cells. The PAF-stimulated cell populations were rendered refractory to the action of these S2 factors and did not display increased RIT values, unless oestrous mouse serum was added. This serum acted to reverse the refractory state, allowing the S2 factors to exert their effect, and so cells treated with PAF and oestrous mouse serum displayed increased RIT values.     

Risk of HIV infection from transfusion with blood negative for HIV antibody in a west African city.

OBJECTIVE--To estimate the risk of infection with HIV (HIV 1 or HIV 2, or both) from transfusion of a screened unit of blood in a high prevalence area in west Africa. DESIGN--Retrospective cohort study for January-July 1991. SETTING--National Blood Transfusion Centre, Abidjan, Côte d''Ivoire. SUBJECTS--Repeat donors (5831 units of blood) and first time donors (5076 units) in the first five months of 1991. MAIN OUTCOME MEASURES--Prevalence and estimated incidence of HIV infection in repeat and first time donors; estimated rate of potentially infected, HIV antibody negative units; and rate of (false negative) potentially infected units assuming a laboratory test sensitivity of 99%. RESULTS--Overall HIV prevalence was 11.0% in first time donors and 2.1% in repeat donors. In the first seven months of 1991, 29 HIV antibody positive (27 HIV 1, 1 HIV 2, 1 dually reactive) donors with a seronegative unit of blood earlier in the year were identified; 26 had donated blood eight weeks or less before their estimated dates of seroconversion and may have been infectious (minimum rate 26/5831 (4.5/1000 potentially infected units)). Estimated incidence of infection in repeat donors was 1.2-2.5%. Laboratory test insensitivity would result in an estimated 1.1/1000 false negative units from first time donors and 0.2/1000 units from regular donors. The overall rate of potentially infected units (all donors, seroconversions, and errors) was estimated at 5.4-10.6/1000. CONCLUSIONS--The risk of HIV infection from a single unit of blood remains substantial (5.4-10.6/1000 units). To prevent infection from blood transfusion in areas of high incidence and prevalence of HIV all but absolutely essential transfusions should be avoided, and donors with low incidence of HIV infection should be selected.     

Repair of UV-induced pyrimidine dimers in the individual genes Gart, Notch and white from Drosophila melanogaster cell lines.

The excision repair of UV-induced pyrimidine dimers was investigated in three genes: Gart, Notch and white in a permanent Drosophila cell line Kc, derived from wild type Drosophila melanogaster embryonic cells. In this cell line Gart and Notch are actively transcribed, whereas white is not expressed. In all three genes UV-induced pyrimidine dimers were removed with the same rate and to the same extent: 60% removal within 16 hours, up to 80-100% in 24 hours after irradiation with 10 or 15 J/m2 UV. These kinetics are similar to the time course of dimer removal measured in the genome overall. No difference in repair of the inactive white locus compared to the active Gart and Notch genes was found. Similar results were obtained using a different wild type cell line, SL2, although repair appeared to be somewhat slower in this cell line. The results are discussed with respect to the data found for gene specific repair in other eukaryotic systems.     

Stomatal response to air humidity and its relation to stomatal density in a wide range of warm climate species

The gas exchange of 19 widely different warm climate species was observed at different leaf to air vapour pressure deficits (VPD). In all species stomata tended to close as VPD increased resulting in a decrease in net photosynthesis. The absolute reduction in leaf conductance per unit increase in VPD was greatest in those species which had a large leaf conductance at low VPDs. This would be expected even if stomata of all species were equally sensitive. However the percentage reduction in net photosynthesis (used as a measure of the relative sensitivity of stomata of the different species) was also closely related to the maximal conductance at low VPD. Similarily the relative sensitivity of stomata to changes in VPD was closely related to the weighted stomatal density or crowding index.The hypothesis is presented that stomatal closure at different VPDs is related to peristomatal evaporation coupled with a high resistance between the epidermis and the mesophyll and low resistance between the stomatal apparatus and the epidermal cells. This hypothesis is consistent with the greater relative sensitivity of stomata on leaves with a high crowding index.The results and the hypothesis are discussed in the light of selection, for optimal productivity under differing conditions of relative humidity and soil water availablility, by observation of stomatal density and distribution on the two sides of the leaf.Visiting scientist, plant physiologist and research assitant of the Cassava Program