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PubMed2005

The PIN-domain toxin-antitoxin array in mycobacteria.

PIN-domains (homologues of the pilT N-terminal domain) are small protein domains of approximately 140 amino acids. They are found in a diverse range of organisms and recent evidence from bioinformatics, biochemistry, structural biology and microbiology suggest that the majority of the prokaryotic PIN-domain proteins are the toxic components of toxin-antitoxin (TA) operons. Several microorganisms have a large cohort of these operons. For example, the genome of Mycobacterium tuberculosis encodes 48 PIN-domain proteins, of which 38 are thought to be involved in TA interactions. This large array of PIN-domain TA operons raises questions as to their evolutionary origin and contemporary functional significance. We suggest that the evolutionary origin of genes encoding mycobacterial PIN-domain TA operons is linked to the mobile gene pool, but that TA operons can become resident within the chromosome of host cells from where they might be recruited to fulfil a variety of roles associated with retardation of cell growth and persistence in stressful environments.

Adenosine Triphosphatases↗
PubMed2004

Vaccine-induced protection against anthrax in cheetah (Acinonyx jubatus) and black rhinoceros (Diceros bicornis).

Institution of a policy of vaccination in endangered species with a vaccine not previously administered to it cannot be undertaken lightly. This applies even more in the case of cheetah (Acinonyx jubatus) with their unusually monomorphic gene pool and the potential restrictions this places on their immune responses. However, the recently observed mortalities from anthrax in these animals in the Etosha National Park, Namibia, made it imperative to evaluate vaccination. Black rhinoceros (Diceros bicornis), another endangered species in the park, have been vaccinated for over three decades but the effectiveness of this has never been evaluated. Passive protection tests in A/J mice using sera from 12 cheetahs together with enzyme immunoassay indicated that cheetah are able to mount seemingly normal primary and secondary humoral immune responses to the Sterne 34F2 live spore livestock vaccine. Overall protection rates in mice injected with the sera rose and fell in concert with rises and declines in antibody titres, although fine analysis showed that the correlation between titre and protection was complex. Once a high level of protection (96% of mice 1 month after a second booster in the cheetahs) had been achieved, the duration of substantial protection appeared good (60% of the mice 5 months after the second booster). Protection conferred on mice by sera from three of four vaccinated rhino was almost complete, but, obscurely, none of the mice receiving serum from the fourth rhino were protected. Sera from three park lions with naturally acquired high antibody titres, included as controls, also conferred high levels of protection. For the purposes of wildlife management, the conclusions were that vaccination of cheetah with the standard animal anthrax vaccine causes no observable ill effect in the animals and does appear to confer protective immunity. At least one well-separated booster does appear to be desirable. Vaccination of rhino also appears to be justified from the limited data obtained.

Acinonyx↗
PubMed2006

Chronological and geographical variations in the small RNA segment of the teratogenic Akabane virus.

Characterization of the small RNA segment of the teratogenic Akabane virus was performed to define the genetic heterogeneity and molecular epidemiology of the virus. The nucleotide and amino acid sequences were highly conserved among the Akabane virus isolates, irrespective of the year of isolation and geographical origin, except for a Kenyan strain MP496. On the basis of the nucleocapsid gene sequences of the segment, 170 field isolates were grouped into four distinct phylogenetic lineages. The Japanese isolates were divided into two major clusters, one containing the prototype strain JaGAr39 and strains isolated in the 1970s, 1988-1989, 1991, and 1994-1999, and the other containing strains isolated from 1982 to 1987, 1990, 1993, 1998, and 2000 to 2003 together with the Taiwanese and Israeli strains. The Asian strains seemed to have evolved in a common gene pool. The Australian and Kenyan strains were placed in the independent third and fourth clusters of the phylogenetic tree, respectively. No consecutive mutations have occurred on the small RNA segment of the Japanese isolates, indicating that the various genotypes of the virus might invade continuously from an exotic source and that certain viruses adaptable to the Japanese environment might spread transiently.

Animals↗
PubMed2006

Circumpolar phylogeography of Juncus biglumis (Juncaceae) inferred from AFLP fingerprints, cpDNA sequences, nuclear DNA content and chromosome numbers.

We explored the circumpolar phylogeographic history of the arctic-alpine Juncus biglumis using amplified fragment length polymorphisms (AFLPs), sequences of cpDNA, relative nuclear DNA content and chromosome numbers. The analyses of the AFLP and cpDNA data gave congruent results and revealed three distinct clades. One of them, represented by a single population from the Taymyr peninsula in northern Siberia, had approximately fourfold larger genome size than the other samples and produced an AFLP pattern that was too aberrant to be analysed together with the rest of the data set. The two other clades represented different ploidy levels (2n = 60 and 120) as judged from chromosome counts of selected populations but differed only in c. 6% relative DNA content. Based on the AFLP and partly also on the cpDNA data, each of the two main clades was further subdivided into two well-supported subgroups. Three of the subgroups were widespread and exhibited largely overlapping distribution patterns. The fourth subgroup seems to be absent from the North Atlantic region and from western Siberia. We suggest that the four subgroups diverged during isolation in different glacial refugia during the Quaternary. Interestingly, individuals of both main clades were encountered in geographically close populations in eastern Greenland and even within a single population from Svalbard, indicating that both areas were colonised at least twice. The different genome sizes and ploidy levels strongly suggest that the three main clades represent distinct gene pools and act as cryptic species.

Asia↗
PubMed2006

Species boundaries and phylogeography of the "Euscorpius carpathicus complex" (Scorpiones: Euscorpiidae) in Italy.

Euscorpius tergestinus (C.L. Koch, 1837), Euscorpius concinnus (C.L. Koch, 1837) and Euscorpius sicanus (C.L. Koch, 1837), three presumed closely related species belonging to the "carpathicus group", occur in the Italian peninsula with a largely parapatric distribution and some zones of range overlap. These areas of sympatry represent interesting opportunities to investigate species boundaries in natural populations. Here we report on a study exploring genetic variation in sympatric populations of the three species from central Tuscany. Additional collecting sites, from different localities across Italy, were also included in the analysis in order to explore the phylogeographic structure of the group. Species boundaries and evolutionary relationships were examined by sequence comparison of mitochondrial 16S rRNA and nuclear ITS-1 rRNA gene fragments. DNA sequence data show no evidence of genetic introgression between different evolutionary lineages from the area of range overlap, suggesting the absence of either past or ongoing inter-specific gene flow. It is therefore probable that reproductive barriers exist, preventing gene pools from amalgamating. Furthermore, our results support the recent morphological distinction of E. tergestinus, as traditionally classified, into two different species: E. tergestinus and E. concinnus. Both mitochondrial and nuclear sequence data clearly indicate that the two taxa represent well-supported and deeply divergent lineages. Euscorpius sicanus seems to represent a monophyletic taxon, but the high genetic variability observed within this taxon calls for future investigation. The present distribution patterns across the Italian peninsula were mainly interpreted as the consequence of climatic oscillations.

Animals↗
PubMed1998

The etiology of obesity: relative contribution of metabolic factors, diet, and physical activity.

Three major factors modulate body weight: metabolic factors, diet, and physical activity, each influenced by genetic traits. Despite recent advances in these areas, the prevalence of obesity in Westernized societies has increased. In contrast to monogenic animal models and rare human genetic syndromes, predisposition to common forms of obesity is probably influenced by numerous susceptibility genes, accounting for variations in energy requirements, fuel utilization, muscle metabolic characteristics, and taste preferences. Although recent increases in obesity prevalence cannot be explained by changes in the gene pool, previously "silent" genetic variants may now play important permissive roles in modern societies. Available data suggest that variations in resting energy expenditure, thermic effect of food, and fuel utilization exist but, by themselves, are unlikely to explain the onset of obesity. Regarding diet, the best available trend survey data indicate that fat and energy intake have fallen, in this and other Westernized countries. Diverging trends of decreasing energy intake and increasing body weight suggest that reduced physical activity may be the most important current factor explaining the rising prevalence of obesity. Subsistence in modern societies requires extreme adaptations in previously useful energy-conserving diet and exercise behaviors. Recognizing the difficulties in sustaining energy-restricted diets in the presence of fast foods and social feasts, the current trend toward increasing body weight is not likely to be reversed solely through recommendations for further reductions in energy intake. In all likelihood, activity levels will have to increase in response to an environment engineered to be more physically demanding.

Appetite↗
PubMed1981

Cancers of the breast and female genital system: search for recessive genetic factors through analysis of human isolate.

To investigate the importance of recessive genes in female breast and genital cancers, we have conducted investigations in the Hutterites, a highly inbred genetic isolate in North America. The homogeneous life style of this group, which lives on communal farms, also facilitates distinction between shared environmental and genetic factors. We ascertained 177 cases of cancer (all organ systems) through Canadian and United States cancer registries, field trips, and searches of death certificates. Breast cancer and endometrial cancer mortalities were those expected for 1970 United States whites, but no deaths due to squamous cervical carcinoma were ascertained in this monogamous population. Inbreeding coefficients (F) for cases were higher than means for matched controls for each of the four cases of breast cancers that occurred in younger women (less than 45 years of age), for four of five cases of endometrial cancer, and for the single cases of uterine leiomyosarcoma, dysgerminoma, and ovarian adenocarcinoma. By contrast, in cases of breast cancer that occurred in women 45 years of age or older, only four of 15 F's were above those for controls. There is a significant difference between the two breast cancer age groups with respect to the likelihood that the F of cases was higher than the F of controls (chi 2 = 6.99, p less than 0.01). However, grouping cases by type, none of the F distributions were significantly different from those of their matched controls. These preliminary genetic investigations thus conform certain concepts concerning breast and female genital cancer but also suggest the desirability of further studies to elucidate the role of genetic factors in premenopausal breast cancer.

Adult↗
PubMed2001

Energy expenditure, physical activity, and obesity in children.

Although there are physiologic and genetic influences on the various components of energy metabolism and body weight regulation, and a major portion of individual differences in body weight can be explained by genetic differences, it seems unlikely that the increased global prevalence of obesity has been driven by a dramatic change in the gene pool. It is more likely and more reasonable that acute changes in behavior and environment have contributed to the rapid increase in obesity and that genetic factors may be important in the deferring individual susceptibilities to these changes. The most striking behavioral changes that have occurred have been an increased reliance on high-fat and energy-dense "fast foods," with larger portion sizes, coupled with an ever-increasing sedentary lifestyle. The more sedentary lifestyle is caused by an increased reliance on technology and labor-saving devices, which has reduced the need for physical exertion for everyday activities. Examples of energy-saving devices that have resulted in a secular decline in physical activity include: Increased use of automated transport rather than walking or biking Central heating and use of automated equipment, such as washing machines, in the household. Reduction in physical activity in the workplace because of computers, automated equipment, and electronic mail. Increased use of television and computers for entertainment and leisure activities. Use of elevators and escalators rather than stairs. Increased concern for crime, which has reduced the likelihood of outdoor playing. Poor urban planning that does not provide adequate biking paths or even sidewalks in some communities. Thus, the increasing prevalence, numerous health risks, and astounding economic costs of obesity clearly justify widespread efforts toward prevention efforts. These prevention efforts should begin in childhood because the behaviors are learned and continue through the lifetime.

Adolescent↗
PubMed1996

Differential survival and natural selection: their impact upon aging and cancer mortality.

Evidence for natural selection is often presented from the perspective of evolution. However, evolution is not the purpose of natural selection. Natural selection might also impact upon the manifestation of senescence via differential survival. The relationship between age-specific cancer mortality rates and corresponding age group population size in the USA from 1951 to 1989 for age groups over age 45 was examined. Rising age-specific cancer mortality rates among elderly men were increasingly correlated with growing age group population size with increasing age. This relationship was not observed in women. Since an age-specific rate should be independent of age group population size, this finding suggests that successive cohorts of elderly USA men were not comparable with respect to their susceptibility to cancer mortality. Differential survival, which effects men more than women, and its selective culling effect upon the surviving gene pool in an aging population may account for some of the observed increasing cancer mortality rates among elderly men. If so, evidence of natural selection can also be presented from the perspective of manifestation rates for some disorders associated with senescence.

Age Distribution↗
PubMed2005

Use of AFLP markers in surveys of plant diversity.

The collection of the available range of genetic variation in a gene pool, usually made of the cultivated species and their undomesticated relatives, is referred to as a germplasm collection. Increasingly, discriminator data generated using molecular genetic markers are either complementing or completely replacing those from morphological characters (known as descriptors) in surveys of genetic diversity. In addition to highlighting the state of knowledge on the specific applications of amplified fragment length polymorphisms (AFLPs) in surveys of plant genetic diversity, an attempt at a brief description and comparison of the different marker systems in use has also been made in this chapter. We have also attempted a description of the AFLP marker technology, its strengths and weaknesses, methodologies for generating reliable AFLP data, available resources (hardware, software, consumables); the kinds of questions for which AFLP data provide valid answers; and data management options. This chapter also highlights salient considerations that would guide decisions on the adoption of molecular marker assays.

DNA, Complementary↗
PubMed2002

Development of gonadotropin-releasing hormone-1 neurons.

Gonadotropin releasing hormone-1 (GnRH-1) neurons, critical for reproduction, are derived from the nasal placode and migrate into the brain during prenatal development. Once within the brain, GnRH-1 cells become integral components of the CNS-pituitary-gonadal axis, essential for reproductive maturation and maintenance of reproductive function in adults. This review focuses on the lineage and development of the GnRH-1 neuroendocrine system. Although the migration of these cells from nose to brain has been well documented in a variety of species, many questions remain concerning the melecules and cues directing GnRH-1 cell differentiation, migration, axon targeting, and establishment and control of GnRH-1 secretion. These process most likely involve multiple and redundant cues because if these mechanisms fail, reproduction dysfunction will ensue and guarantee that this defect does not remain in the gene pool.

Animals↗
PubMed2003

The cryopreservation of ovarian tissue: uses and indications in veterinary medicine.

Animal experiments have shown that cryopreservation of the ovarian cortex, containing primordial follicles, could be used to preserve gametes thereby restoring fertility in humans and animals. During the last 100 years, many hundreds of species have been lost, and a third of the breeding animals are threatened with extinction. To preserve genetic diversity, notably for the conservation of endangered species, it is essential to conserve female and male gametes. Today, biotechnologies such as artificial insemination and embryo transfer are used in breeding programs and are well developed. However, even using these advanced techniques, there are problems due to the limited number of individuals used as the source of gametes, so that the risk of inbreeding is high, even in large populations. To preserve genetic diversity, it is necessary to create gene banks of male and female gametes and embryos, using a very large number of individual donors. Cryopreservation of ovarian tissue could present a means for enlarging the gene pool. Cryopreserved ovarian tissue could be used in auto- or xenografts, or for in vitro maturation (IVM) of primordial follicles. In this review, we describe the processes for cryopreservation of ovarian tissue and the various possibilities for using it.

Animals↗
PubMed2001

Frequency of CCR5 gene 32-basepair deletion in Chilean HIV-1 infected and non-infected individuals.

A 32-basepair deletion polymorphism in the CCR5 chemokine receptor gene (CCR5Delta32) has been identified and shown to have functional significance in determining susceptibility to infection by human immunodeficiency virus type 1 (HIV-1) and possibly in influencing disease progression in HIV-1 positive individuals. These findings led to an interest in studies of DeltaCCR5 allele geographical distribution in human population, for complete understanding of the role of CCR5 in HIV-1 epidemiology. Inter-population variation in CCR5Delta32 frequency may be a significant factor in the prediction of AIDS endemicity. In this report we assessed the frequency of DeltaCCR5 in a Chilean population (63 HIV-1 infected and 62 non-infected individuals). No homozygous CCR5Delta32 individual was identified, and no significant difference was observed between HIV-1 infected (3/63) and non-infected (3/62) individuals for the heterozygote CCR5Delta32 state. This is the first evidence of the contribution of DeltaCCR5 allele to the genetic background of the Chilean population, which is characterized by intense ethnic admixture and by gene flow from the European Spanish gene pool.

Chile↗
PubMed2000

Genetic diversity of RNA segments 5, 7 and 9 of the Palyam serogroup orbiviruses from Japan, Australia and Zimbabwe.

Reverse transcriptase-polymerase chain reaction (RT-PCR) methods, based on the sequences of RNA segments 5, 7 and 9 of Chuzan virus, were established for specific detection and molecular characterization of the Palyam serogroup orbiviruses. Nucleotide sequences obtained from the amplified cDNA fragments of these three genes of 24 isolates were analyzed and compared individually to determine the intra-serogroup phylogenetic relationship of Japanese, Australian and Zimbabwean isolates. It seems that Chuzan virus isolates in Japan are genetically stable. Interestingly, mutations have occurred almost simultaneously on these three genes of Chuzan virus. In all cases, isolates from the same geographical area were closely related to each other at the molecular level, irrespective of serotype. The data suggested that the Palyam serogroup viruses can be differentiated into geographically distinct groups and that the viruses evolve independently in the different gene pools. A strain KY-115 was considered to be produced by reassortment of genome segments between different groups. Restriction fragment length polymorphism (RFLP) analysis of these PCR products is useful for rapid discrimination of isolates and for detection of genetic mutations.

Animals↗
PubMed1997

Antigenic diversity of Akabane virus detected by monoclonal antibodies.

The antigenic properties of 21 Japanese field isolates and two Australian strains of Akabane (AKA) virus (Simbu serogroup, bunyavirus) isolated from 1959 to 1990 were compared by enzyme-linked immunosorbent assay (ELISA), plaque-reduction neutralization (PRNT) and hemagglutination inhibition (HI) tests using monoclonal antibodies (Mabs) to the OBE-1 strain of AKA virus. Sixteen Mabs were established by fusing P3X63Ag8U1 mouse myeloma cells and spleen cells from BALB/c mice immunized with the OBE-1 strain. Of the 16 clones, 13 produced immunoglobulin (Ig) which precipitated glycoprotein G1 and three produced Ig which precipitated nucleoprotein (N). Twelve out of 13 Mabs had both NT and HI activities to not only the homologous OBE-1 strain but also the other isolates. By the competitive binding assay, at least five antigenic regions for G1, and two for N were defined. Some of the anti-G1 Mabs which reacted to the same antigenic region had unique reactivity while anti-N Mabs recognizing the same epitope reacted with almost the same degree to all of the isolates. Finally, nine epitopes of the G1 protein in five different antigenic regions have been identified. There was no striking correlation between isolation date and place of the isolates and their reactivity to Mabs. A most interesting result is that three isolates collected in the same place over a three week period had different reactivity patterns detected by ELISA, showing great antigenic variation of the virus. AKA virus may be a single gene pool consisting of different genotypes in the field.

Animals↗
PubMed1987

Impact of plasmids and genetic change on the numerical classification of staphylococci.

Newly isolated bacterial strains often contain extrachromosomal DNA as plasmid DNA. These accessory components of the DNA gene pool confer additional phenotypic properties on their host but, despite this, little attention has been paid to the impact of plasmid-mediated characters on bacterial classification. In the present study, the effect of antibiotic resistance plasmids on the classification of representative staphylococci was determined using numerical phenetic techniques. Over sixty percent of the eighty-one test strains contained one or more plasmids which varied in molecular weight from 1.4 to 36 Mdal. Antibiotic resistance phenotypes were eliminated from strains of S. aureus, S. chromogenes, S. cohnii, S. hyicus and S. xylosus, and from a laboratory isolate, to give sixteen derivative strains. Fourteen had lost one or more plasmids and two had deleted plasmids. In addition three further derivative strains were isolated which showed no plasmid loss but exhibited gross phenotypic changes. The test and derivative strains were the subject of numerical phenetic analyses based on seventy-eight unit characters. Data were examined using the simple matching, Jaccard and pattern coefficients and clustering achieved using the unweighted pair group method with arithmetic averages algorithm. Cluster composition was not markedly affected by the statistics used or by test error, estimated at 1.02%. Numerically circumscribed clusters and subclusters were equated with the established species S. aureus, S. chromogenes, S. cohnii, S. hyicus, S. lentus, S. intermedius, S. sciuri and S. xylosus. The sixteen derivative strains with either lost or delected plasmids were recovered in the same cluster or subcluster as their corresponding parent indicating that the removal of plasmid-expressed characters had little effect on the structure of the numerical classification. In contrast, two of the three strains of S. xylosus with genomically-derived phenotypic variation formed a cluster that separated from their parent strain at the 70% similarity level in the SSM, UPGMA analysis.

Animals↗
PubMed1999

The role of cultural and social factors in the cause of addictive disorders.

For many centuries, generations of young people were protected from the early onset of addictive disorders. Although addiction to drugs and alcohol had been well known for centuries, widespread addiction has occurred only in recent centuries. Because the human gene pool or human biochemistry did not likely change suddenly to produce this result, social and cultural factors likely have produced widespread addiction. From another perspective, the sociocultural factors that once protected our societies against widespread addiction may have become weakened or inoperative. Our social institutions--our families, schools, religions, neighborhoods, and governments--no longer protect us and our young from addiction as they once did. The failure of traditional social institutions to protect us from addiction does not mean that we must seek drug panaceas only in nonsocietal venues, such as medications and psychotherapies. Rather, we should look to those elements of our institutions that have failed us and seek to bolster them. A gradually evolving body of literature on this topic demonstrates that institutional changes can serve to reduce widespread addiction among us. Moreover, these changes can be implemented at many levels: within our families, schools, friendship groups, workplaces, churches, neighborhoods, and legislatures.

Adolescent↗
PubMed2000

Identical marker alleles in Podolic cattle (Bos taurus) and Indian zebu (Bos indicus).

In the context of biochemical marker research and in order to add new information on native breeds, the present work focuses on a local Southern Italy cattle, namely Italian Podolic. We provide the complete structural characterisation of alpha-lactalbumins and beta-globin chains isolated from Podolic cattle (Bos taurus). Given the unavailability of the complete sequence for alpha-lactalbumin A of taurine cattle in the literature, we intended to check its structure in order to ascertain the absence of any possible silent mutation. Screening the Podolic cattle, we found a new beta-globin variant not detectable by conventional methods. The presence of such a new variant might be helpful in the study of the Podolic population genetic structure and for a better knowledge of the gene pool per se, and in comparison with the other breeds. Structural analyses showed that the new beta-globin Podolic variant exhibited the same sequence as beta-globin Azebu. The alpha-lactalbumin A was the same as that isolated from zebu cattle (Bos indicus). The results are discussed in relation to the possible involvement of the two markers in the debate on the origin of the Podolic breed.

Alleles↗