Genome analysis technologies: towards species identification by genotype.

Traditional identification of species has been based on phenotypic traits, although it is clear that, theoretically, genotype-based classification is more accurate. This is especially the case for microorganisms which possess less identifiable traits and are more easily influenced by environment. Therefore, technology that allows identification of species based on genotype is highly desirable. Whole genome sequencing can provide a sufficient amount of information and can be determinative for this purpose but is very impractical for routine use. Thus, a competent technology is needed that allows a reproducible reduction in the amount of information required about a whole genome, while still providing sufficiently accurate identification. It is almost imperative for such a technology to be of a high cost-performance and of easy handling. Universality and portability are also strongly desired. Based on these criteria, the current state of genome analysis technologies are reviewed. Among various methodologies discussed here, amplified fragment length polymorphism (AFLP), genome profiling (GP) and microarrays are the subject of particular attention. As species identification is a base for most fields of biology including microbiology, ecology, epidemiology and for various biotechnologies, it is of paramount importance to establish a more efficient, easily handled and more objective methodology, in parallel with conventional phenotype-based methodologies. GP is currently considered to have the most optimal nature for identification of species since it can reproducibly reduce a huge amount of genome information to a manageable size by way of random polymerase chain reaction and can extract a sufficient amount of information for species identification from the DNA fragments thus profiled by temperature gradient gel electrophoresis. The potential ability of DNA microarrays for this purpose is also discussed and promises much for the future.     

Screening for aneuploidy in twin pregnancies: maternal age- and race-specific risk assessment between 9-14 weeks.

The aim of this study was to calculate the risk for aneuploidy in twin pregnancies between 9-14 weeks utilizing maternal age, race and dizygotic twinning rates. Using previously published risks for aneuploidy in singletons and twins at the time of amniocentesis and at term, we calculated new risk estimates for twins at 9-14 weeks gestation or at the time of chorionic villus sampling. Using these tables, the risk for trisomy 21 in at least one fetus of a twin gestation in a 32-year-old at 9-14 weeks is 1/285 for Whites and for African-Americans. This is equivalent to the risk for trisomy 21 (1/265) in a 35-year-old woman with a singleton at the same gestational age. The risks for trisomies 18 and 13 also follow similar trends. In counseling women with twin pregnancies at the time of first trimester nuchal translucency screening or chorionic villus sampling, it should be noted that the maternal age-related risk for aneuploidy for a 32-year-old is equivalent to that of a 35-year-old woman with a singleton gestation.     

Molecular Analysis of tet(W) Gene-Mediated Tetracycline Resistance in Dominant Intestinal Bifidobacterium Species from Healthy Humans

tet(W) was found responsible for tetracycline resistance (MICs, 4 to ≥32 μg ml⁻¹) in dominant bifidobacterial species from the gastrointestinal tracts of healthy humans. The gene from Bifidobacterium longum H66 proved to be identical over a 2.6-kbp region to the recently described tet(W) determinant of Butyrivibrio fibrisolvens.     

Evidence for the involvement of vacuolar activity in metal(loid) tolerance: vacuolar-lacking and -defective mutants of Saccharomyces cerevisiae display higher sensitivity to chromate, tellurite and selenite

The responses of Saccharomyces cerevisiae towards the oxyanions tellurite, selenite and chromate were investigated in order to establish the involvement of the yeast vacuole in their detoxification. Three mutants of S. cerevisiae with defective vacuolar morphology and function were used; mutant JSR180D1 is devoid of any vacuolar-like structure while ScVatB and ScVatC are deficient in specific protein subunits of the vacuolar (V)-H -ATPase. All the mutant strains showed increased sensitivity to tellurite and chromate compared to their parental strains. Such sensitivity of the mutants was associated with increased accumu-lation of tellurium and chromium. These results indicate that accumulation of both tellurium and chromium occurred mainly in the cytosolic compartment of the cell, with detoxification influenced by the presence of a functionally-active vacuole which may play a role in compartmentation as well as regulation of the cytostolic compartment for optimal expression of a detoxification mechanism, e.g. reduction. In contrast, the vacuolar-lacking mutant, JSR180D1, and the defective V-H ATPase mutant ScVatB displayed lower selenium accu-mulation than their parental strains. Additionally, the mutant strain ScVatB displayed a higher tolerance to selenite than the parental strain. This result suggests that accumulation of selenium occurs mainly in the vacuolar compartment of the cell with tolerance depending on the ability of the cytosolic component to reduce selenite to elemental selenium, which might, in turn, be related to activity of the V-H -ATPase. These results are discussed in relation to vacuolar compartmentation and the significance of the vacuolar H -ATPase in cytosolic homeostasis of H both of which may affect the accumulation, reduction, and toler-ance to the tested metal(loids). © Rapid Science 1998     

Unaffected nodulation and nitrogen fixation in carbohydrate pleiotropic mutants ofRhizobium meliloti

Pleiotropic mutants were isolated fromRhizobium meliloti M5N1 with the resistance transposon Tn5. They failed to use carbohydrates as carbon source, but not dicarboxylic acids. Diauxic growth properties of the wild type and uptake assays in both M5N1 and a mutant strain 2.10 showed that the mutant was affected in the active transport of sugars. Exogenous cyclic AMP failed to affect the phenotype of the mutant, and a relatively high frequency of reversion was observed. This suggests that the mutant 2.10 was probably altered in acrp-like gene. However, its symbiotic properties remained unaffected. Thus, symbiosis does not depend on sugar utilization.     

Soil organic matter molecular composition with long-term detrital alterations is controlled by site-specific forest properties

Forest ecosystems are important global soil carbon (C) reservoirs, but their capacity to sequester C is susceptible to climate change factors that alter the quantity and quality of C inputs. To better understand forest soil C responses to altered C inputs, we integrated three molecular composition published data sets of soil organic matter (SOM) and soil microbial communities for mineral soils after 20 years of detrital input and removal treatments in two deciduous forests: Bousson Forest (BF), Harvard Forest (HF), and a coniferous forest: H.J. Andrews Forest (HJA). Soil C turnover times were estimated from radiocarbon measurements and compared with the molecular-level data (based on nuclear magnetic resonance and specific analysis of plant- and microbial-derived compounds) to better understand how ecosystem properties control soil C biogeochemistry and dynamics. Doubled aboveground litter additions did not increase soil C for any of the forests studied likely due to long-term soil priming. The degree of SOM decomposition was higher for bacteria-dominated sites with higher nitrogen (N) availability while lower for the N-poor coniferous forest. Litter exclusions significantly decreased soil C, increased SOM decomposition state, and led to the adaptation of the microbial communities to changes in available substrates. Finally, although aboveground litter determined soil C dynamics and its molecular composition in the coniferous forest (HJA), belowground litter appeared to be more influential in broadleaf deciduous forests (BH and HF). This synthesis demonstrates that inherent ecosystem properties regulate how soil C dynamics change with litter manipulations at the molecular-level. Across the forests studied, 20 years of litter additions did not enhance soil C content, whereas litter reductions negatively impacted soil C concentrations. These results indicate that soil C biogeochemistry at these temperate forests is highly sensitive to changes in litter deposition, which are a product of environmental change drivers.     

Remotely sensed localised primary production anomalies predict the burden and community structure of infection in long-term rodent datasets

The increasing frequency and cost of zoonotic disease emergence due to global change have led to calls for the primary surveillance of wildlife. This should be facilitated by the ready availability of remotely sensed environmental data, given the importance of the environment in determining infectious disease dynamics. However, there has been little evaluation of the temporal predictiveness of remotely sensed environmental data for infection reservoirs in vertebrate hosts due to a deficit of corresponding high-quality long-term infection datasets. Here we employ two unique decade-spanning datasets for assemblages of infectious agents, including zoonotic agents, in rodents in stable habitats. Such stable habitats are important, as they provide the baseline sets of pathogens for the interactions within degrading habitats that have been identified as hotspots for zoonotic emergence. We focus on the enhanced vegetation index (EVI), a measure of vegetation greening that equates to primary productivity, reasoning that this would modulate infectious agent populations via trophic cascades determining host population density or immunocompetence. We found that EVI, in analyses with data standardised by site, inversely predicted more than one-third of the variation in an index of infectious agent total abundance. Moreover, in bipartite host occupancy networks, weighted network statistics (connectance and modularity) were linked to total abundance and were also predicted by EVI. Infectious agent abundance and, perhaps, community structure are likely to influence infection risk and, in turn, the probability of transboundary emergence. Thus, the present results, which were consistent in disparate forest and desert systems, provide proof-of-principle that within-site fluctuations in satellite-derived greenness indices can furnish useful forecasting that could focus primary surveillance. In relation to the well-documented global greening trend of recent decades, the present results predict declining infection burden in wild vertebrates in stable habitats; but if greening trends were to be reversed, this might magnify the already upwards trend in zoonotic emergence.     

Timing of migration dates and detection of first wintering sites for the Turtle Dove in Northwest Africa

The identification of migration dates and wintering zones for migratory birds are key elements for the understanding of the Afro-Palearctic migration system. From 2015 to 2022, a large-scale survey of Turtle Doves Streptopelia turtur, a vulnerable species, was established in Northwest Africa, including Morocco, Algeria, and Tunisia. We monitored migration dates and wintering individuals using the line-transect method. We found that Turtle Doves arrived in the last week of March and left the North African region in mid-October. Compared with Morocco, Doves arrived significantly earlier in Algeria and Tunisia. Moreover, Doves were discovered wintering on nine Northwest African sites, from October to February, where individuals feed in groups. We found that the occurrence probability of wintering Turtle Doves decreased significantly with increasing temperature and rainfall. Birds wintered most often close to wetlands since the overwintering probability decreased with the increasing distance from the recording area to the nearest water body. These are the first and only detailed findings on the migration phenology of the globally vulnerable Turtle Dove in north western Africa.     

An analysis of the conformational paths of citrate synthase

Previous simulation studies have provided reaction pathways leading from the closed to the open form of citrate synthase. We now undertake a detailed analysis of these pathways using a variety of different tools including backbone dihedral angles, P-Curves helicoidal parameters, inter-helix geometrical parameters, and accessibility calculations. The results point to a relatively small number of residues, mostly in loop regions, which are responsible for the majority of the conformational changes observed. An important role is attributed to transient changes in the backbone which facilitate movement along the reaction coordinate. Comparisons between the two pathways show that they share many common features despite the different algorithms used to generate them. © 1993 Wiley-Liss, Inc.     

Computer-assisted sperm analysis of canine spermatozoa motility measurements

Computer-assisted sperm analysis (CASA) allows for the determination of specific motion characteristics of sperm cells in vitro. This study was designed to develop a system for the use of CASA to objectively evaluate canine sperm motility, and specifically to determine whether motility characteristics vary between individual dogs. Ejaculates from 10 dogs were collected weekly. Sperm cells were extended in a glucose-free TALP medium, placed on slides and videotaped at 200x. Videotaped samples were then analyzed by the Hamilton-Thorn Motility Analyzer, with 100 cells evaluated per slide. Two slides were made from each ejaculate. Motility characteristics that were evaluated included lateral head displacement, beat cross frequency, path velocity, path linearity, path straightness, percentage of motile cells, and percentage of progressively motile cells. Sperm cell morphology was also evaluated. Canine spermatozoa maintained good overall motility (mean +/- SD, 73 +/- 9%) during the procedure. Mean sperm motility and morphology measurements differed significantly between dogs (P<0.01). There was no difference (P>0.05) between the mean measurements of different ejaculates for an individual dog, or for different slides made from the same ejaculate. Mean motility values for the 10 dogs are reported. There was a significant but not strong correlation (r=0.44) between the percentage of progressively motile sperm cells and the percentage of sperm cells with normal morphology.