Polymorphisms and linkage disequilibrium in the COL6A1 and COL6A2 gene cluster: novel DNA polymorphisms in the region of a candidate gene for congenital heart defects in Down's syndrome

The COL6A1 and COL6A2 (collagen VI) gene cluster on chromosome 21 is a candidate region for defects leading to congenital heart anomalies in Down's syndrome. We report a variable number of tandem repeats (VNTR) and a restriction fragment length polymorphism (RFLP) in this gene region, detected using a COL6A1 cDNA probe. Linkage disequilibrium relationships were studied among the RFLPs of this gene cluster. The RFLP reported here shows no significant linkage disequilibrium with any others in the region. It has a polymorphism information content value of 0.27, raising the informativity of the locus.     

Population density and genetic diversity are positively correlated in wild felids globally

Aim

Insights into the biological and evolutionary traits of species, and their ability to cope with global changes, can be gained by studying genetic diversity within species. A cornerstone hypothesis in evolutionary and conservation biology suggests that genetic diversity decreases with decreasing population size, however, population size is difficult to estimate in threatened species with large distribution ranges, and evidence for this is limited to few species. To address this gap, we tested this hypothesis across multiple closely related species at a global scale using population density which is a more accessible measure.

Location

Global.

Time Period

Contemporary.

Major Taxa Studied

Wild felids in their natural habitats.

Methods

We obtained data from published estimates of population density assessed via camera trap and within-population genetic diversity generated from microsatellite markers on 18 felid species across 41 countries from 354 studies. We propose a novel method to standardize population density estimates and to spatially join data using K-means clustering. Linear mixed-effect modelling was applied to account for confounding factors such as body mass, generation length and sample size used for the genetic estimates.

Results

We found a significant positive correlation between population density and genetic diversity, particularly observed heterozygosity and allelic richness. While the confounding factors did not affect the main results, long generation length and large sample size were significantly associated with high genetic diversity. Body mass had no effect on genetic diversity, likely because large-bodied species were over-represented in our data sets.

Main Conclusions

Our study emphasizes how recent demographic processes shape neutral genetic diversity in threatened and small populations where extinction vortex is a risk. Although caution is needed when interpreting the small population density effect in our findings, our methodological framework shows promising potential to identify which populations require actions to conserve maximal genetic variation.     

Quantitative Evaluation of Erotactin Secretion in Eggs of Hormosira banksii (Fucales,Phaeophyceae)

The release of the C₁₁-hydrocarbon spermatozoid attractant hormosirene by eggs of the Australian fucoid Hormosira banksii has been determined quantitatively using a closed-loop extraction technique. The eggs secrete erotactin for more than 2 weeks with an exponentially decreasing rate. The initial secretion rate was estimated to be 75 fmol h^?1 egg^?1 and the total amount of hormosirene produced per egg to be 2.35 pmol (0.35 ng). The results were used to calculate the threshold range for spermatozoid chemotaxis in the pheromone gradient around eggs.     

Evaluating perinatal mortality rates: effects of referral and case mix.

OBJECTIVE--To evaluate perinatal mortality rates as a method of auditing obstetric and neonatal care after account had been taken of transfer between hospitals during pregnancy and case mix. DESIGN--Case-control study of perinatal deaths. SETTING--Leicestershire health district. SUBJECTS--1179 singleton perinatal deaths and their selected live born controls among 114,362 singleton births to women whose place of residence was Leicestershire during 1978-87. MAIN OUTCOME MEASURE--Crude perinatal mortality rates and rates adjusted for case mix. RESULTS--An estimated 11,701 of the 28,750 women booked for delivery in general practitioner maternity units were transferred to consultant units during their pregnancy. These 11,701 women had a high perinatal mortality rate (16.8/1000 deliveries). Perinatal mortality rates by place of booking showed little difference between general practitioner units (8.8/1000) and consultant units (9.3-11.7/1000). Perinatal mortality rates by place of delivery, however, showed substantial differences between general practitioner units (3.3/1000) and consultant units (9.4-12.6/1000) because of the selective referral of high risk women from general practitioner units to consultant units. Adjustment for risk factors made little difference to the rates except when the subset of deaths due to immaturity was adjusted for birth weight. CONCLUSION--Perinatal mortality rates should be adjusted for case mix and referral patterns to get a meaningful result. Even when this is done it is difficult to compare the effectiveness of hospital units with perinatal mortality rates because of the increasingly small subset of perinatal deaths that are amenable to medical intervention.     

Identifying Mozambique's most critical areas for plant conservation: An evaluation of protected areas and Important Plant Areas

Successful protected area networks must represent biodiversity across taxonomic groups. However, too often plant species are overlooked in conservation planning, and the resulting protected areas may, as a result, fail to encompass the most important sites for plant diversity. The Mozambique Tropical Important Plant Areas project sought to promote the conservation of Mozambique's flora through the identification of Important Plant Areas (IPAs). Here, we use the Weighted Endemism including Global Endangerment (WEGE) index to identify the richest areas for rare and endemic plants in Mozambique and subsequently evaluate how well represented these hotspots are within the current protected area and IPA networks. We also examine the congruence between IPA and protected areas to identify opportunities for strengthening the conservation of plants in Mozambique. We found that high WEGE scores, representing areas rich in endemic/near-endemic and threatened species, predict the presence of IPAs in Mozambique, but do not predict the presence of protected areas. We also find that there is limited overlap between IPAs and protected areas in Mozambique. We demonstrate how IPAs could be an important tool for ensuring priority sites for plant diversity are included within protected area network expansions, particularly following the adoption of the “30 by 30” target agreed within the post-2020 Convention on Biological Diversity framework, with great potential for this method to be replicated elsewhere in the global tropics.     

Evidence of Commingling in Human Eating Behavior

This investigation tested whether distributions of certain aspects of eating behavior were consistent with the notion of a “mixture model;” that is, two or more distinct Commingled component distributions, consistent with the possibility of major gene action. Undergraduates (n=901) completed self-report trait measures of hunger, disinhibition, and dietary restraint. Variables were residualized for gender and age and transformed to remove skewness. Residualized transformed distributions were tested for departure from unimodality with Hartigan's (14) dip statistic. The distributions of all three aspects of eating behavior were significantly non-unimodal. Next, component multivariate normal distributions were estimated via maximum likelihood. Likelihood ratio tests were employed to compare nested models. A mixture of four distributions with unequal variance-covariance matrices tit significantly better than any more parsimonious model. In sum, these data strongly suggest that the distributions of several measures of eating behavior are composed of four component distributions. This finding is consistent with the possibility of major gene effects for eating behavior.     

A 610 kb YAC clone harbors 7 cM of tomato (Lycopersicon esculentum) DNA that includes themale sterile 14 gene and a hotspot for recombination

Pollen development requires both sporophytic and gametophytic gene expression. We are using a map-based cloning technique to isolate sporophytic genes which, when mutant, cause pollen abortion and a male sterile (ms) phenotype in tomato (Lycopersicon esculentum). We have genetically characterized onems locus (ms14) using RFLP analysis and identified flanking markers. High-resolution genomic physical mapping indicates that thems14 locus is located in a ～300 kb region. We have identified a YAC clone with an insert size of ～610 kb that contains thems14-linked markers, reflects the organization of the physical map and therefore most probably contains thems14 gene. In addition, we present evidence that the relationship between physical and genetic distance in this chromosomal region changes abruptly from ～105–140 kb/cM to less than 24 kb/cM, and suggest that the TG393-TG104 region is a hotspot for recombination.     

Impaired interleukin-3 (IL-3) response of the A/J mouse is caused by a branch point deletion in the IL-3 receptor alpha subunit gene.

Interleukin-3 (IL-3) alone does not support hematopoietic colony formation of bone marrow cells from the A/J mouse. To elucidate the molecular lesion in A/J mice, we examined expression of the alpha and beta subunits of the IL-3 receptor (IL-3R). While IL-3R beta was normally expressed, IL-3R alpha was not detectable on the surface of A/J-derived cells by antibody staining. Genetic linkage analysis using recombinant inbred mouse strains between A/J and IL-3-responsive C57BL/6 indicated that the IL-3R alpha gene locus was responsible for the impaired IL-3 response in A/J mice. Molecular cloning and characterization of A/J-derived IL-3R alpha cDNA revealed that it lacked the sequence corresponding to exon 8, which encodes 10 amino acid residues in the extracellular domain. The aberrant splicing was due to a 5 base pair deletion at the branch point in intron 7 and was reproduced in heterologous cells by transfecting with an IL-3R alpha minigene carrying the deleterious intron. The A/J-specific abnormal form of IL-3R alpha was localized inside the cells, but not on the cell surface, providing the molecular basis for the impaired IL-3 response in the A/J mouse.     

The application of robotics and mass spectrometry to the characterisation of the Drosophila melanogaster indirect flight muscle proteome

The rapid accumulation of sequence data generated by the various genome sequencingprojects and the generation of expressed sequence tag databases has resulted in the need forthe development of fast and sensitive methods for the identification and characterisation oflarge numbers of gel electrophoretically separated proteins to translate the sequence data intobiological function. To achieve this goal it has been necessary to devise new approaches toprotein analysis: matrix-assisted laser desorption and electrospray mass spectrometry havebecome important protein analytical tools which are both fast and sensitive. When combinedwith a robotic system for the in-gel digestion of electrophoretically separated proteins, itbecomes possible to rapidly identify many proteins by searching databases with MS data. Thepower of this combination of techniques is demonstrated by an analysis of the proteins presentin the myofibrillar lattice of the indirect flight muscle of Drosophila melanogaster. Theproteins were separated by SDS-PAGE and in-gel proteolysis was performed bothautomatically and manually. All 16 major proteins could quickly be identified by massspectrometry. Although most of the protein components were known to be present in theflight muscle, two new components were also identified. The combination of methodsdescribed offers a means for the rapid identification of large numbers of gel separatedproteins.     

Reovirus infection and tissue injury in the mouse central nervous system are associated with apoptosis.

Reovirus serotype 3 strains infect neurons within specific regions of the neonatal mouse brain and produce a lethal meningoencephalitis. Viral replication and pathology colocalize and have a predilection for the cortex, hippocampus, and thalamus. We have shown previously that infection of cultured fibroblasts and epithelial cells with reovirus type 3 Dearing (T3D) and other type 3 reovirus strains results in apoptotic cell death, suggesting that apoptosis is a mechanism of cell death in vivo. We now report that T3D induces apoptosis in infected mouse brain tissue. To determine whether reovirus induces apoptosis in neural tissues, newborn mice were inoculated intracerebrally with T3D, and at various times after inoculation, brain tissue was assayed for viral antigen by immunostaining and apoptosis was identified by DNA oligonucleosomal laddering and in situ terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling. Cells were also stained with cresyl violet to detect morphological changes characteristic of apoptosis, including chromatin condensation and cell shrinkage. DNA laddering was detected in T3D- but not in mock-infected brain tissue. Apoptotic cells were restricted to the same regions of the brain in which infected cells and tissue damage were observed. These findings suggest that virus-induced apoptosis is a mechanism of cell death, tissue injury, and mortality in reovirus-infected mice. The correlation between apoptosis and pathogenesis in vivo identifies apoptosis as a potential target for molecular and pharmacological strategies designed to curtail or prevent diseases resulting from induction of this cell death pathway.