Survival Probability of Beneficial Mutations in Bacterial Batch Culture

The survival of rare beneficial mutations can be extremely sensitive to the organism’s life history and the trait affected by the mutation. Given the tremendous impact of bacteria in batch culture as a model system for the study of adaptation, it is important to understand the survival probability of beneficial mutations in these populations. Here we develop a life-history model for bacterial populations in batch culture and predict the survival of mutations that increase fitness through their effects on specific traits: lag time, fission time, viability, and the timing of stationary phase. We find that if beneficial mutations are present in the founding population at the beginning of culture growth, mutations that reduce the mortality of daughter cells are the most likely to survive drift. In contrast, of mutations that occur de novo during growth, those that delay the onset of stationary phase are the most likely to survive. Our model predicts that approximately fivefold population growth between bottlenecks will optimize the occurrence and survival of beneficial mutations of all four types. This prediction is relatively insensitive to other model parameters, such as the lag time, fission time, or mortality rate of the population. We further estimate that bottlenecks that are more severe than this optimal prediction substantially reduce the occurrence and survival of adaptive mutations.     

Expansion of a novel endogenous retrovirus throughout the pericentromeres of modern humans

BackgroundApproximately 8% of the human genome consists of sequences of retroviral origin, a result of ancestral infections of the germ line over millions of years of evolution. The most recent of these infections is attributed to members of the human endogenous retrovirus type-K (HERV-K) (HML-2) family. We recently reported that a previously undetected, large group of HERV-K (HML-2) proviruses, which are descendants of the ancestral K111 infection, are spread throughout human centromeres.ResultsStudying the genomes of certain cell lines and the DNA of healthy individuals that seemingly lack K111, we discover new HERV-K (HML-2) members hidden in pericentromeres of several human chromosomes. All are related through a common ancestor, termed K222, which is a virus that infected the germ line approximately 25 million years ago. K222 exists as a single copy in the genomes of baboons and high order primates, but not New World monkeys, suggesting that progenitor K222 infected the primate germ line after the split between New and Old World monkeys. K222 exists in modern humans at multiple loci spread across the pericentromeres of nine chromosomes, indicating it was amplified during the evolution of modern humans.ConclusionsCopying of K222 may have occurred through recombination of the pericentromeres of different chromosomes during human evolution. Evidence of recombination between K111 and K222 suggests that these retroviral sequences have been templates for frequent cross-over events during the process of centromere recombination in humans.     

Isolation and characterization of four di-<Emphasis Type="Italic">n</Emphasis>-butyl phthalate (DBP)-degrading <Emphasis Type="Italic">Gordonia</Emphasis> sp<Emphasis Type="Italic">.</Emphasis> strains and cloning the 3,4-phthalate dioxygenase gene

Four aerobic bacterial strains capable of utilizing di-n-butyl phthalate (DBP) as the sole source of carbon and energy were isolated from river sediments. Based on the morphology, biochemical characterization, and 16S rRNA gene sequence analysis, they were identified as Gordonia sp. The optimal conditions for DBP degradation by these strains were found to be pH 7.0, 30°C, and stirring at 175 rpm. These four strains could degrade, respectively, 96, 98, 98, and 78% of DBP (400 mg l⁻¹) as well as dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-octyl phthalate (DOP), di-isooctyl phthalate (DIOP), and di-isononyl phthalate (DINP). Furthermore, partial sequences of the gene for 3,4-phthalate dioxygenase were obtained from all four strains. To our knowledge, this is the first time that the 3,4-phthalate dioxygenase gene has been successfully cloned from Gordonia sp.     

Lizard species richness patterns in China and its environmental associations

Many ecological hypotheses have been widely used to explain species richness variation across the globe. We investigated lizard species richness patterns in China, and identified areas of high species richness. Furthermore, we tested hypotheses concerning the relationships between lizard richness and environmental variables. A large data including 30,902 records of point locality data for 151 lizard species occurring in China were retrieved from Herpetology museums of CIB/CAS and other museums through HerpNET, and published sources, and then predicted distributions maps were generated using ecological niche modeling. We overlaid all species prediction maps into a composite map to describe species richness patterns. A multiple regression analysis using eigenvector-based spatial filtering (SEVM) was performed to examine the best environmental predictors of species richness. Richness peaked mainly in southern China located in the Oriental realm. Our best multiple regression models explained a total of 80.1% variance of lizard richness (r² = 0.801; F = 203.47; P < 0.001). Among related factors in shaping species richness distribution, the best environmental predictors of species richness were: frost-day frequency, elevation, vegetation, and wet-day frequency. Based on models selection, our results revealed that underlying mechanisms related to different ecological hypotheses might work together and best explain lizard richness in China. We are in an initial step to develop a large data set on species richness, and provide the necessary conservation implications from habitat loss. Additional studies that test species richness at different geographical scale are required to better understand the factors that may influence the species richness distribution in East Asia.     

Effects of iron deficiency and iron overload on angiogenesis and oxidative stress-a potential dual role for iron in breast cancer

Estrogen alone cannot explain the differences in breast cancer (BC) recurrence and incidence rates in pre- and postmenopausal women. In this study, we have tested a hypothesis that, in addition to estrogen, both iron deficiency due to menstruation and iron accumulation as a result of menstrual stop play important roles in menopause-related BC outcomes. We first tested this hypothesis in cell culture models mimicking the high-estrogen and low-iron premenopausal condition or the low-estrogen and high-iron postmenopausal condition. Subsequently, we examined this hypothesis in mice that were fed iron-deficient and iron-overloaded diets. We show that estrogen only slightly up-regulates vascular endothelial growth factor (VEGF), an angiogenic factor known to be important in BC recurrence. It is, rather, iron deficiency that significantly promotes VEGF by stabilizing hypoxia-inducible factor-1α. Conversely, high iron levels increase oxidative stress and sustain mitogen-activated protein kinase activation, which are mechanisms of known significance in BC development. Taken together, our results suggest, for the first time, that an iron-deficiency-mediated proangiogenic environment could contribute to the high recurrence of BC in young patients, and iron-accumulation-associated pro-oxidant conditions could lead to the high incidence of BC in older women.     

A water-soluble 1,8-naphthalimide-based 'turn on' fluorescent chemosensor for selective and sensitive recognition of mercury ion in water

A water-soluble 1,8-naphthalimide-based fluorescent chemosensor 1, bearing two acetic carboxylic moieties, exhibited high selectivity and sensitivity for recognition of Hg(2+) ion in water over other heavy and transition metal (HTM) ions with fluorescent enhancement. An increase in the fluorescent intensity at 562 nm was due to the formation of a 1:1 1-Hg(2+) inclusion complex.