Evaluation of the rrn operon copy number in Bifidobacterium using real-time PCR

AIMS: A real-time PCR-based method was developed to evaluate the Bifidobacterium rRNA operon copy number. As a result of their repetitive nature, rRNA operons are very suitable targets for chromosomal integration of heterologous genes. METHODS AND RESULTS: The rrn operon multiplicity per chromosome was determined by real-time PCR quantification of the 16S rRNA amplicons obtained from genomic DNA. The values obtained in several bifidobacterial strains of human origin ranged from 1 to 5. The reliability of the method developed was confirmed by Southern hybridization technique. CONCLUSIONS: In the Bifidobacterium genus the rrn operon copies showed variability at species and strain level. The identification of Bifidobacterium strains with high rRNA multiplicity allowed the selection of potential hosts for chromosomal integration. SIGNIFICANCE AND IMPACT OF THE STUDY: The methodology here proposed represents a rapid, reliable and sensitive new tool for the quantification of rrn operon copy number in bacteria.     

The conservation of redundancy in genetic systems: effects of sexual and asexual reproduction

The relationship between probability of survival and the number of deleterious mutations in the genome is investigated using three different models of highly redundant systems that interact with a threatening environment. Model one is a system that counters a potentially lethal infection; it has multiple identical components that act in sequence and in parallel. Model two has many different overlapping components that provide three-fold coverage of a large number of vital functions. The third model is based on statistical decision theory: an ideal detector, following an optimum decision strategy, makes crucial decisions in an uncertain world. The probability of a fatal error is reduced by a redundant sampling system, but the chance of error rises as the system is impaired by deleterious mutations. In all three cases the survival profile shows a synergistic pattern in that the probability of survival falls slowly and then more rapidly. This is different than the multiplicative or independent survival profile that is often used in mathematical models. It is suggested that a synergistic profile is a property of redundant systems. Model one is then used to study the conservation of redundancy during sexual and asexual reproduction. A unicellular haploid organism reproducing asexually retains redundancy when the mutation rate is very low (0001 per cell division), but tends to lose high levels of redundancy if the mutation rate is increased (001 to 01 per cell division). If a similar unicellular haploid organism has a sexual phase then redundancy is retained for mutation rates between 0001 and 01 per cell division. The sexual organism outgrows the asexual organism when the above mutation rates apply. If they compete for finite resources the asexual organism will be extinguished. Variants of the sexual organism with increased redundancy will outgrow those with lower levels of redundancy and the sexual process facilitates the evolution of more complex forms. There is a limit to the extent that complexity can be increased by increasing the size of the genome and in asexual organisms this leads to progressive accumulation of mutations with loss of redundancy and eventual extinction. If complexity is increased by using genes in new combinations, the asexual form can reach a stable equilibrium, although it is associated with some loss of redundancy. The sexual form, by comparison, can survive, with retention of redundancy, even if the mutation rate is above one per generation. The conservation and evolution of redundancy, which is essential for complexity, depends on the sexual process of reproduction.     

Ehd4 is required to attain normal prepubertal testis size but dispensable for fertility in male mice

The four highly homologous members of the C‐terminal EH domain‐containing (EHD) protein family (EHD1‐4) regulate endocytic recycling. To delineate the role of EHD4 in normal physiology and development, mice with a conditional knockout of the Ehd4 gene were generated. PCR of genomic DNA and Western blotting of organ lysates from Ehd4^−/− mice confirmed EHD4 deletion. Ehd4^−/− mice were viable and born at expected Mendelian ratios; however, males showed a 50% reduction in testis weight, obvious from postnatal day 31. An early (Day 10) increase in germ cell proliferation and apoptosis and a later increase in apoptosis (Day 31) were seen in the Ehd4^−/− testis. Other defects included a progressive reduction in seminiferous tubule diameter, dysregulation of seminiferous epithelium, and head abnormalities in elongated spermatids. As a consequence, lower sperm counts and reduced fertility were observed in Ehd4^−/− males. Interestingly, EHD protein expression was seen to be temporally regulated in the testis and EHD4 levels peaked between days 10 and 15. In the adult testis, EHD4 was highly expressed in primary spermatocytes and EHD4 deletion altered the levels of other EHD proteins in an age‐dependent manner. We conclude that high levels of EHD1 in the adult Ehd4^−/− testis functionally compensate for lack of EHD4 and prevents the development of severe fertility defects. Our results suggest a role for EHD4 in the proper development of postmitotic and postmeiotic germ cells and implicate EHD protein‐mediated endocytic recycling as an important process in germ cell development and testis function. genesis 48:328–342, 2010. © 2010 Wiley‐Liss, Inc.     

Key issues in achieving an integrative perspective on stress

An integrative perspective on molecular mechanisms of stress resistance requires understanding of these mechanisms not just in vitro or in the model organism in the research laboratory — but in the healthy or diseased human in society, in the cultivated plant or animal in agricultural production, and in populations and species in natural communities and ecosystems. Such understanding involves careful attention to the context in which the organism normally undergoes stress, and appreciation that biological phenomena occur at diverse levels of organization (from molecule to ecosystem). Surprisingly, three issues fundamental to achieving an integrative perspective are presently unresolved: (i) Is variation in lower-level traits (nucleotide sequences, genes, gene products) seldom, commonly, or always consequential for stress resistance? (ii) Does environmental stress reduce or enhance genetic variation, which is the raw material of evolution? (iii) Is the present distribution of organisms along natural gradients of stress largely the result of organisms living where they can, or is adaptive evolution generally sufficient to overcome stress? Effective collaboration among disciplinary specialists and meta-analysis may be helpful in resolving these issues.     

Asymmetric Karplus curves for the protein side-chain <Superscript>3</Superscript><Emphasis Type="Italic">J</Emphasis> couplings

The standard Karplus equation for calculating ³ J coupling constants from any given dihedral angle requires three empirical coefficients be determined that relate to the magnitudes of three modes of the angle dependency of ³ J. Considering cosine modes only (bimodal, unimodal and baseline component), Karplus curves are generally symmetric with respect to the sign of the angle argument. Typically, their primary and secondary maxima differ in amplitude, whereas the two minima are of equal depth. However, chiral molecular topologies, such as those surrounding the main-chain and side-chain torsions in amino-acid residues, preclude, as regards substituent positioning, exact mirror-image conformations from being formed—for any given torsion-angle value. It is therefore unlikely that ³ J couplings assume identical values for the corresponding positive and negative dihedral angles. This suggests that a better empirical fit of the torsion-angle dependency of ³ J could be obtained when removing the constraint of symmetrically identical coupling constants. A sine term added to the Karplus equation allows independent modelling of both curve minima typically located near dihedral-angle values of +90° and −90°. Revisiting an extensive ³ J coupling dataset previously recorded to determine the side-chain torsions χ₁ in the protein flavodoxin, the asymmetric Karplus model accomplishes a more accurate fit to the experimental data. Asymmetries revealed in the angle dependencies exceed the experimental precision in determining ³ J. Accounting for these effects helps improve molecular models. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

Landscape genomics is a rapidly growing field with recent advances in both genotyping efficiency and statistical analyses that provide insight towards local adaptation of populations under varying environmental and selective pressure. Chinook salmon (Oncorhynchus tshawytscha) are a broadly distributed Pacific salmon species, occupying a diversity of habitats throughout the northeastern Pacific with pronounced variation in environmental and climate features but little is understood regarding local adaptation in this species. We used a multivariate method, redundancy analysis (RDA), to identify polygenic correlations between 19 703 SNP loci and a suite of environmental variables in 46 collections of Chinook salmon (1956 total individuals) distributed throughout much of its North American range. Models in RDA were conducted on both rangewide and regional scales by hierarchical partitioning of the populations into three distinct genetic lineages. Our results indicate that between 5.8 and 21.8% of genomic variation can be accounted for by environmental features, and 566 putatively adaptive loci were identified as targets of environmental adaptation. The most influential drivers of adaptive divergence included precipitation in the driest quarter of the year (Rangewide and North Coastal Lineage, anova P = 0.002 and 0.01, respectively), precipitation in the wettest quarter of the year (Interior Columbia River Stream‐Type Lineage, anova P = 0.03), variation in mean diurnal range in temperature (South Coastal Lineage, anova P = 0.005), and migration distance (Rangewide, anova P = 0.001). Our results indicate that environmental features are strong drivers of adaptive genomic divergence in this species, and provide a foundation to investigate how Chinook salmon might respond to global environmental change.