Genetic Diversity and Genetic Structure of an Endangered Species, Trillium tschonoskii

The genetic diversity and genetic structure of Trillium tschonoskii (Maxim) were investigated using amplified fragment length polymorphism markers. Eight primer combinations were carried out on 105 different individuals sampled from seven populations. Of the 619 discernible DNA fragments generated, 169 (27.3%) were polymorphic. The percentage of polymorphic bands within populations ranged from 4.52 to 10.50. Genetic diversity (H_E) within populations ranged from 0.0130 to 0.0379, averaging 0.0536 at the species level. Genetic differentiation among populations was detected based on Nei's genetic diversity analysis (53.03%) and analysis of molecular variance (AMOVA) (52.43%). AMOVA indicated significant genetic differentiation among populations (52.43% of the variance) and within populations (47.57% of the variance) (p < 0.0002). Gene flow was low (0.4429) among populations. Species breeding system and limited gene flow among populations are plausible reasons for the high genetic differentiation observed for this species. We propose an appropriate strategy for conserving the genetic resources of T. tschonoskii in China.     

Genetic engineering, welfare, and accountability

Comments on the implications of genetic engineering for animal welfare. Welfare problems associated with techniques used to achieve genetic changes; Detrimental effects of genetic modifications to welfare; Modification of farm animals for biomedical products. Implications of genetic engineering for animal welfare are changing rapidly and need to be reviewed regularly. They include the welfare problems associated with techniques used to achieve genetic changes, which are similar to problems of other experimental approaches; these should be considered carefully, especially where techniques are used on a routine basis. When it comes to the genetic modifications themselves, some are detrimental to welfare, some are neutral, and some are beneficial; these results include direct effects of the intended change, side effects, and indirect effects. Currently, the two main applications are modification of farm animals for biomedical products--which appears to be largely neutral for welfare--and modification of mice as models for human disease, which results in suffering, often severe suffering. Beneficial applications are rare and still experimental or theoretical. The situation is similar with regard to the use of recombinant hormones and viruses; use of recombinant vaccines has potential for improving welfare, but may raise other ethical problems. Although few, if any, of these concerns are specific to genetic engineering, various factors combine to suggest that particular safeguards are needed in this field. These include the facts that changes can be produced rapidly and repeatedly, and that one of the driving forces behind genetic engineering is commercial exploitation of technology. In general, ethical evaluation still is done on a case-by-case basis, using the limited criteria seen as directly relevant to each case, rather than on a broader framework. There also is little public accountability, whereby the public can have confidence that such evaluation is being carried out properly. Calls for advisory “watchdog ”committees to consider ethical questions on the use of animals are endorsed by this article. Furthermore, it is essential for public confidence in the safeguarding of animal welfare that the procedures of such committees should be well-publicized.     

GeMes,Clusters of DNA Methylation under Genetic Control,Can Inform Genetic and Epigenetic Analysis of Disease

Epigenetic marks such as DNA methylation have generated great interest in the study of human disease. However, studies of DNA methylation have not established population-epigenetics principles to guide design, efficient statistics, or interpretation. Here, we show that the clustering of correlated DNA methylation at CpGs was similar to that of linkage-disequilibrium (LD) correlation in genetic SNP variation but for much shorter distances. Some clustering of methylated CpGs appeared to be genetically driven. Further, a set of correlated methylated CpGs related to a single SNP-based LD block was not always physically contiguous—segments of uncorrelated methylation as long as 300 kb could be interspersed in the cluster. Thus, we denoted these sets of correlated CpGs as GeMes, defined as potentially noncontiguous methylation clusters under the control of one or more methylation quantitative trait loci. This type of correlated methylation structure has implications for both biological functions of DNA methylation and for the design, analysis, and interpretation of epigenome-wide association studies.     

Heterochromatin, Position Effect, and Genetic Silencing

Genomes of higher eukaryotes consist of two types of chromatin: euchromatin and heterochromatin. Heterochromatin is densely packed material typically localized in telomeric and pericentric chromosome regions. Euchromatin transferred by chromosome rearrangements in the vicinity of heterochromatin is inactivated and acquires morphological properties of heterochromatin in the case of position effect variegation. One of the X chromosomes in mammal females and all paternal chromosome set in coccides become heterochromatic. The heterochromatic elements of the genome exhibit similar structural properties: genetic inactivation, compaction, late DNA replication at the S stage, and underrepresentation in somatic cells. The genetic inactivation and heterochromatin assembly are underlain by a specific genetic mechanism, silencing, which includes DNA methylation and posttranslational histone modification provided by the complex of nonhistone proteins. The state of silencing is inherited in cell generations. The same molecular mechanisms of silencing shared by all types of heterochromatic regions, be it unique or highly repetitive sequences, suggest the similar organization of these regions. No type of heterochromatin is a permanent structure as they all are formed at the strictly definite stages of early embryogenesis. Based on the bulk of evidence accumulated today, heterochromatin can be regarded as a morphological manifestation of genetic silencing.     

Genetic susceptibility, biomarker respones, and cancer

A large number of studies have reported associations between polymorphisms of xenobiotic-metabolizing enzymes (XMEs) and various cancers. However, the carcinogenic exposures behind such findings have usually been unclear. Information on susceptibility to specific carcinogens could better be obtained by examining situations where the exposure and the endpoint studied are nearer in time, i.e., by studying biomarkers of carcinogen exposure and early (genotoxic) effect in exposed humans. For example, analyses of DNA adducts and cytogenetic endpoints have indicated an increased susceptibility of glutathione S-transferase M1 (GSTM1) null genotype to genotoxicity of tobacco smoking, supporting the view that the associations of the GSTM1 null genotype with bladder and lung cancer are partly related to smoking. In vitro genotoxicity studies with human cells offer an experimental tool that can be used, within the limits of the cell systems, to predict individual sensitivity and genotype-carcinogen interactions. In vitro sensitivity to the genotoxicity of 1,2:3,4-diepoxybutane, an epoxide metabolite of 1,3-butadiene has clearly been shown to depend on GSTT1 genotype, which has also been implicated to modify, along with GSTM1 genotype, the in vitro genotoxicity of 1,2-epoxy-3-butene, another epoxide metabolite of 1,3-butadiene. These genotypes appear to modulate the excretion of 1,3-butadiene-specific mercapturic acids, and influence genotoxicity biomarker levels in 1,3-butadiene-exposed workers. The excretion of specific mercapturic acids (PHEMA) in workers exposed to styrene has clearly been shown to depend on GSTM1 genotype, and GSTT1 genotype seems to modulate the excretion of one PHEMA diastereoisomer. These genotypes have also been implicated to modulate the in vitro genotoxicity of styrene. In general, the genetic polymorphisms potentially important for biomarker response largely depend on the exposing agent, biological material examined, and ethnicity of the population under study. Individual exposure level may vary a lot, and a reliable estimate of the exposure is essential for correct interpretation of genotype-exposure interaction. Besides XME polymorphisms, any polymorphisms that affect cellular response to DNA damage could, in principle, modify individual sensitivity to genotoxins. For instance, those concerning DNA repair proteins are presently being studied by many laboratories.     

Genetic,molecular, and humoral endocycle-regulating mechanisms

The review presents data on the molecular genetic mechanisms controlling endoreduplication. The issues concerning the activity of the main cycle cell regulators, such as cyclins, cyclin-dependent kinases, and their inhibitors, under conditions of a modified cell cycle of polytene cells are considered. Specific features of regulation at the replication origin points and the role of hormones and phytohormones in the ontogenetic control of endoreduplication are analyzed.     

Kin-Aggregations Explain Chaotic Genetic Patchiness,a Commonly Observed Genetic Pattern,in a Marine Fish

The phenomenon of chaotic genetic patchiness is a pattern commonly seen in marine organisms, particularly those with demersal adults and pelagic larvae. This pattern is usually associated with sweepstakes recruitment and variable reproductive success. Here we investigate the biological underpinnings of this pattern in a species of marine goby Coryphopterus personatus. We find that populations of this species show tell-tale signs of chaotic genetic patchiness including: small, but significant, differences in genetic structure over short distances; a non-equilibrium or “chaotic” pattern of differentiation among locations in space; and within locus, within population deviations from the expectations of Hardy-Weinberg equilibrium (HWE). We show that despite having a pelagic larval stage, and a wide distribution across Caribbean coral reefs, this species forms groups of highly related individuals at small spatial scales (<10 metres). These spatially clustered family groups cause the observed deviations from HWE and local population differentiation, a finding that is rarely demonstrated, but could be more common than previously thought.     

Self-programmable,Self-assembling Two-dimensional Genetic Matter

Putative two-dimensional coding systems can beconstructed from aqueous solutions of purine andpyrimidine nucleic acid bases evaporated at moderatetemperatures on the surfaces of inorganic solids. Theresultant structures are monolayers which are formedspontaneously by molecular self-assembly and they havebeen observed with molecular resolution by scanningtunnelling microscopy (STM). When formed fromsolutions of a single base, the monolayers of adenineand uracil have crystalline characteristics and theSTM images can be interpreted in terms of thegeometrical placement of planar arranged moleculesthat interact laterally by intermolecular hydrogenbonding. When formed from solutions containing amixture of adenine and uracil, the monolayers haveaperiodic structures. Small crystalline domainswithin these monolayers can be interpreted in terms ofthe single phase configurations of the molecules andthe remaining aperiodic structures can presumably beinterpreted, geometrically, in terms of the 21theoretically possible adenine-adenine, uracil-uraciland adenine-uracil hydrogen bonding interactions. Wepropose that combinatorial arrangements of planararranged purine and pyrimidine bases could provide thenecessary complexity to act as a primitive geneticmechanism and may have relevance to the origin of life.     

Genetic essentialism,mana , and the meaning of DNA

Concerns about the commercialization of genetics have spawned a debate over the symbolic logic and meaning of DNA. The assumption is that different meanings for DNA have social and ethical consequences. Genetic essentialism as an interpretive meaning for DNA is argued to encapsulate values of materialism and autonomy that make it compatible with capital accumulation. Whether or not genetic commerce actually requires genetic essentialism is an empirical question and this study proposes that it is not difficult to find non-essentialist genetics. Two paths of inquiry are adopted. First, the history and origins of the distinction between genotype and phenotype is revisited. This history of gene theory, in particular the effort to purge vitalism, is linked to DNA and the central dogma of molecular biology. Secondly, a rather specialized debate within anthropology about the meaning of mana is introduced. An analysis of definitions for genotype and phenotype reveals a structure commensurate with the metaphysics of mana. Parallels are established between how the meaning of mana has been essentialized and the current efforts to fix the symbolic logic of DNA.     

Genetic instability of heterozygous, hybrid, natural wine yeasts

We describe a genetic instability found in natural wine yeasts but not in the common laboratory strains of Saccharomyces cerevisiae. Spontaneous cyh2(R)/cyh2(R) mutants resistant to high levels of cycloheximide can be directly isolated from cyh2(S)/cyh2(S) wine yeasts. Heterozygous cyh2(R)/cyh2(S) hybrid clones vary in genetic instability as measured by loss of heterozygosity at cyh2. There were two main classes of hybrids. The lawn hybrids have high genetic instability and generally become cyh2(R)/cyh2(R) homozygotes and lose the killer phenotype under nonselective conditions. The papilla hybrids have a much lower rate of loss of heterozygosity and maintain the killer phenotype. The genetic instability in lawn hybrids is 3 to 5 orders of magnitude greater than the highest loss-of-heterozygosity rates previously reported. Molecular mechanisms such as DNA repair by break-induced replication might account for the asymmetrical loss of heterozygosity. This loss-of-heterozygosity phenomenon could be economically important if it causes sudden phenotype changes in industrial or pathogenic yeasts and of more basic importance to the degree that it influences the evolution of naturally occurring yeast populations.     

Identification of Genetic Alterations,as Causative Genetic Defects in Long QT Syndrome,Using Next Generation Sequencing Technology

Background

Long QT Syndrome is an inherited channelopathy leading to sudden cardiac death due to ventricular arrhythmias. Despite that several genes have been associated with the disease, nearly 20% of cases remain without an identified genetic cause. Other genetic alterations such as copy number variations have been recently related to Long QT Syndrome. Our aim was to take advantage of current genetic technologies in a family affected by Long QT Syndrome in order to identify the cause of the disease.

Methods

Complete clinical evaluation was performed in all family members. In the index case, a Next Generation Sequencing custom-built panel, including 55 sudden cardiac death-related genes, was used both for detection of sequence and copy number variants. Next Generation Sequencing variants were confirmed by Sanger method. Copy number variations variants were confirmed by Multiplex Ligation dependent Probe Amplification method and at the mRNA level. Confirmed variants and copy number variations identified in the index case were also analyzed in relatives.

Results

In the index case, Next Generation Sequencing revealed a novel variant in TTN and a large deletion in KCNQ1, involving exons 7 and 8. Both variants were confirmed by alternative techniques. The mother and the brother of the index case were also affected by Long QT Syndrome, and family cosegregation was observed for the KCNQ1 deletion, but not for the TTN variant.

Conclusions

Next Generation Sequencing technology allows a comprehensive genetic analysis of arrhythmogenic diseases. We report a copy number variation identified using Next Generation Sequencing analysis in Long QT Syndrome. Clinical and familiar correlation is crucial to elucidate the role of genetic variants identified to distinguish the pathogenic ones from genetic noise.     

Advances,Problems, and Prospects of Genetic Transformation of Fungi

Advances, problems, and prospects of genetic transformation of fungi are described. Features distinguishing fungi from other organisms are analyzed. Those features should be taken into consideration while preparing genetic material for transformation. The ways to overcome problems associated with hyphae apical growth, cell wall thickness, the heterokaryotic life cycle stage, and mechanisms of immune defense are described. A comparative analysis of major methods for transformation of fungi at different stages of their life cycle was performed. Stability of genetically modified fungi and advances in transformation are discussed.     

Recent Advances of Genetic Resources,Genes and Genetic Approaches for Flooding Tolerance in Rice

Flooding is one of the most hazardous natural disasters and a major stress constraint to rice production throughout the world, which results in huge economic losses. The frequency and duration of flooding is predicted to increase in near future as a result of global climate change. Breeding of flooding tolerance in rice is a challenging task because of the complexity of the component traits, screening technique, environmental factors and genetic interactions. A great progress has been made during last two decades to find out the flooding tolerance mechanism in rice. An important breakthrough in submergence research was achieved by the identification of major quantitative trait locus (QTL) SUB1 in rice chromosomes that acts as the primary contributor for tolerance. This enabled the use of marker-assisted backcrossing (MABC) to transfer SUB1 QTL into popular varieties which showed yield advantages in flood prone areas. However, SUB1 varieties are not always tolerant to stagnant flooding and flooding during germination stage. So, gene pyramiding approach can be used by combining several important traits to develop new breeding rice lines that confer tolerances to different types of flooding. This review highlights the important germplasm/genetic resources of rice to different types of flooding stress. A brief discussion on the genes and genetic mechanism in rice exhibited to different types of flooding tolerance was discussed for the development of flood tolerant rice variety. Further research on developing multiple stresses tolerant rice can be achieved by combining SUB1 with other tolerance traits/genes for wider adaptation in the rain-fed rice ecosystems.     

Genetic Instability,DNA Damage and Atherosclerosis

We review the role of somatic mutations and genetic instability in the pathogenesis of atherosclerosis, suggesting novel therapeutic approaches.