Predicting potentially pathogenic effects of hRPE65 missense mutations: a computational strategy based on molecular dynamics simulations

The human retinal pigment epithelium-specific 65-kDa protein (hRPE65) plays a crucial role within the retinoid visual cycle and several mutations affecting either its expression level or its enzymatic function are associated with inherited retinal diseases such as Retinitis Pigmentosa. The gene therapy product voretigene neparvovec (Luxturna) has been recently approved for treating hereditary retinal dystrophies; however, the treatment is currently accessible only to patients presenting confirmed biallelic mutations that severely impair hRPE65 function, and many reported hRPE65 missense mutations lack sufficient evidences for proving their pathogenicity. In this context, we developed a computational approach aimed at evaluating the potential pathogenic effect of hRPE65 missense variants located on the dimerisation domain of the protein. The protocol evaluates how mutations may affect folding and conformation stability of this protein region, potentially helping clinicians to evaluate the eligibility for gene therapy of patients diagnosed with this type of hRPE65 variant of uncertain significance.     

Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses

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A role for the mismatch repair system during incipient speciation in Saccharomyces

The cause of reproductive isolation between biological species is a major issue in the field of biology. Most explanations of hybrid sterility require either genetic incompatibilities between nascent species or gross physical imbalances between their chromosomes, such as rearrangements or ploidy changes. An alternative possibility is that genomes become incompatible at a molecular level, dependent on interactions between primary DNA sequences. The mismatch repair system has previously been shown to contribute to sterility in a hybrid between established yeast species by preventing successful meiotic crossing-over leading to aneuploidy. This system could also promote or reinforce the formation of new species in a similar manner, by making diverging genomes incompatible in meiosis. To test this possibility we crossed yeast strains of the same species but from diverse historical or geographic sources. We show that these crosses are partially sterile and present evidence that the mismatch repair system is largely responsible for this sterility.     

Evolution of competitive fitness in experimental populations of E. coli: What makes one genotype a better competitor than another?

An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of Escherichia coli and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. Here, we review experiments to identify the phenotypic bases of improved competitive fitness in twelve E. coli populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate. After 10000 generations, the average fitness of the derived genotypes had increased by 50% relative to the ancestor, based on competition experiments using marked strains in the same environment. The growth kinetics of the ancestral and derived genotypes showed that the latter have a shorter lag phase upon transfer into fresh medium and a higher maximum growth rate. Competition experiments were also performed in environments where other substrates were substituted for glucose. The derived genotypes are generally more fit in competition for those substrates that use the same mechanism of transport as glucose, which suggests that enhanced transport was an important target of natural selection in the evolutionary environment. All of the derived genotypes produce much larger cells than does the ancestor, even when both types are forced to grow at the same rate. Some, but not all, of the derived genotypes also have greatly elevated mutation rates. Efforts are now underway to identify the genetic changes that underlie those phenotypic changes, especially substrate specificity and elevated mutation rate, for which there are good candidate loci. Identification and subsequent manipulation of these genes may provide new insights into the reproducibility of adaptive evolution, the importance of co-adapted gene complexes, and the extent to which distinct phenotypes (e.g., substrate specificity and cell size) are affected by the same mutations.     

Does experimental evolution reflect patterns in natural populations? E. coli strains from long-term studies compared with wild isolates

Our results show that experimental evolution mimics evolution in nature. In particular, only 1000 generations of periodic recombination with immigrant genotypes is enough for linkage disequilibrium values in experimental populations to change from a maximum linkage value to a value similar to the one observed in wild strains of E. coli. Our analysis suggests an analogy between the recombination experiment and the evolutionary history of E. coli; the E. coligenome is a patchwork of genes laterally inserted in a common backbone, and the experimental E. coli chromosome is a patchwork where some sites are highly prone to recombination and others are very clonal. In addition, we propose a population model for wild E. coli where gene flow (recombination and migration) are an important source of genetic variation, and where certain hosts act as selective sieves; i.e., the host digestive system allows only certain strains to adhere and prosper as resident strains generating a particular microbiota in each host. Therefore we suggest that the strains from a wide range of wild hosts from different regions of the world may present an ecotypic structure where adaptation to the host may play an important role in the population structure. This revised version was published online in August 2006 with corrections to the Cover Date.     

Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles

Throughout most of the mammalian genome, genetically regulated developmental programming establishes diverse yet predictable epigenetic states across differentiated cells and tissues. At metastable epialleles (MEs), conversely, epigenotype is established stochastically in the early embryo then maintained in differentiated lineages, resulting in dramatic and systemic interindividual variation in epigenetic regulation. In the mouse, maternal nutrition affects this process, with permanent phenotypic consequences for the offspring. MEs have not previously been identified in humans. Here, using an innovative 2-tissue parallel epigenomic screen, we identified putative MEs in the human genome. In autopsy samples, we showed that DNA methylation at these loci is highly correlated across tissues representing all 3 embryonic germ layer lineages. Monozygotic twin pairs exhibited substantial discordance in DNA methylation at these loci, suggesting that their epigenetic state is established stochastically. We then tested for persistent epigenetic effects of periconceptional nutrition in rural Gambians, who experience dramatic seasonal fluctuations in nutritional status. DNA methylation at MEs was elevated in individuals conceived during the nutritionally challenged rainy season, providing the first evidence of a permanent, systemic effect of periconceptional environment on human epigenotype. At MEs, epigenetic regulation in internal organs and tissues varies among individuals and can be deduced from peripheral blood DNA. MEs should therefore facilitate an improved understanding of the role of interindividual epigenetic variation in human disease.     

Parallelism in adaptive radiations of experimental Escherichia coli populations

Adaptive radiations are major contributors to species diversity. Although the underlying mechanisms of adaptive radiations, specialization and trade‐offs, are relatively well understood, the tempo and repeatability of adaptive radiations remain elusive. Ecological specialization can occur through the expansion into novel niches or through partitioning of an existing niche. To test how the mode of resource specialization affects the tempo and repeatability of adaptive radiations, we selected replicate bacterial populations in environments that promoted the evolution of diversity either through niche expansion or through niche partitioning, and in a third low‐quality single‐resource environment, in which diversity was not expected to evolve. Colony size diversity evolved equally fast in environments that provided ecological opportunities regardless of the mode of resource specialization. In the low‐quality environments, diversity did not consistently evolve. We observed the largest fitness improvement in the low‐quality environment and the smallest the glucose‐limited environment. We did not observe a change in the rate of evolutionary change in either trait or environment, suggesting that the pool of beneficial mutations was not exhausted. Overall, the mode of resource specialization did not affect the tempo or repeatability of adaptive radiations. These results demonstrate the limitations of eco‐evolutionary feedbacks to affect evolutionary outcomes.     

Haying and grazing effects on the butterfly communities of two Mediterranean-area grasslands

Grasslands are usually the most suitable environment for butterflies, but have been also traditionally used for productive activities. This paper compares the impact of mowing and grazing on butterfly biodiversity in two S Italian (Campania) grasslands, at Campo Somma (CS) and Pianoro di Prada (PP) located at an identical altitude of 850 m. These grasslands have an area of approximately 6 ha each and are at a 3 km distance from each other. They share similar climate and are both surrounded by woods, mainly of sweet chestnut. CS is managed for haying and is mown once a year, in June. PP is used for sheep and cattle grazing. Weekly transects were made from April to September in 2008 and 2009, during the butterfly flight activity. We analysed data from eight monthly transects by Kruskal–Wallis and Mann–Whitney tests. We observed 45 butterfly species at PP, and 28 at CS. Diversity indexes were significantly higher at PP, whereas evenness was similar. The monthly comparisons of species richness showed that, except for April, PP values were always significantly higher. Species abundance was significantly higher at PP in June, July and August. In all months, except in April, the Shannon–Wiener index was also significantly higher at PP, as was Simpson’s index in May, June and September. Dominance index differed significantly only in May, June and September, whereas evenness was never significantly different between the two grasslands. These data show that, as concerns butterflies, the impact of mowing was much stronger than that of grazing.     

Caesarean Delivery in South Italy: Women without Choice. A Cross Sectional Survey

Background

In spite of the World Health Organization’s recommendations to maintain caesarean delivery (CD) between 5% and 15% of total births, the rates of CD continue to rise in countries with routine access to medical services. As in Italy CD rate reached 38% in 2008, the highest at EU level, we evaluated socioeconomic and clinical correlates of “elective” and “non programmed” CD in the Country. We performed a stratified analysis in order to verify whether the effect of such correlates differed among women with an “a priori” preference for natural and caesarean delivery respectively.

Methods and Findings

We analyzed cross-sectional data from the Italian National Statistics Institute (ISTAT) survey on health condition. Socio-demographic variables, information on maternal care services use and health conditions during pregnancy, as well as maternal preferences on delivery, were available for a representative sample of 2,474 primiparous women. After an initial bivariate analysis, we used logistic regressions to evaluate factors associated to the study outcomes. Overall CD accounted for 35.5% of the total births in our sample (CI 33.6–37.4%); moreover, 30.7% (CI 28.6–32.6%) of women preferring natural delivery actually delivered with a CD. Elective CD rate is higher among women over 35 years (22.9%, CI 18.8–27.4%), and those living in the South (26.2%, CI 23.0–29.6%). The multivariate analysis showed that, even adjusting for several confounders, women in the South, receiving care in the private sector had higher chances of CD, also in case of preference for natural delivery.

Conclusion

Policy interventions are required to reduce the rate of undesired CD, e.g. increasing women knowledge regarding delivery in order to favour aware choices. An effective strategy to reduce CD rate should address the Southern Regions, as women here appear to have a very limited control over the delivery, in spite of a widespread preference for natural delivery.