Fast algorithms for computing sequence distances by exhaustive substring composition

The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reconstruction. Such needs are hardly fulfilled by the more traditional measures of sequence similarity and distance, like string edit and gene rearrangement, due to a mixture of epistemological and computational problems. Alternative measures, based on the subword composition of sequences, have emerged in recent years and proved to be both fast and effective in a variety of tested cases. The common denominator of such measures is an underlying information theoretic notion of relative compressibility. Their viability depends critically on computational cost. The present paper describes as a paradigm the extension and efficient implementation of one of the methods in this class. The method is based on the comparison of the frequencies of all subwords in the two input sequences, where frequencies are suitably adjusted to take into account the statistical background.     

Male-Driven Differences in Chimpanzee (<Emphasis Type="Italic">Pan troglodytes</Emphasis>) Population Genetic Structure Across Three Habitats in Cameroon and Nigeria

Complex ecological pressures affect the social dynamics of many primate species, but it is unclear how they affect primate speciation. Molecular tools are often used to answer questions about the evolutionary histories and social systems of primates. Mitochondrial DNA (mtDNA), in particular, is frequently used to answer many of these questions, but because it is passed from mothers to offspring it reveals only the histories of females. In many species, including chimpanzees, females generally disperse from their natal groups while males are philopatric, and thus differences in dispersal patterns likely leave different signatures in the genome. We previously analyzed samples from 187 unrelated male and female chimpanzees in Nigeria and Cameroon using 21 autosomal microsatellites and mtDNA sequences. Here, we examine the contributions of males and females in shaping the genetic history of these chimpanzees by genotyping a subset of 56 males at 12 Y-chromosome microsatellites. We found that Y-chromosome population structure differed from the results of analysis of mtDNA haplotypes. The results also revealed that males in rainforest habitats (Guinean and Congolian rainforests) are more closely related to one another than those inhabiting the savanna-woodland mosaic ecotone in central Cameroon. In contrast, the pattern of female relatedness did not differ across habitats. We hypothesize that these differences in population structure and patterns of relatedness among males in different habitat types may be due to differences in the community dynamics of chimpanzees in the ecotone vs. rainforests, and that these factors contribute to making Cameroon an engine of diversification for chimpanzees. Broadly, these results demonstrate the importance of habitat variation in shaping social systems, population genetics, and primate speciation.     

Do MCF7 cells cope with metformin treatment under energetic stress in low glucose conditions?

There is a growing body of evidence about metformin being effective in cancer therapy. Despite controversies about the ways of its effectiveness, several ongoing clinical trials are evaluating the drug when used as an adjuvant or a neo-adjuvant agent. We aimed to investigate metformin’s effects on proliferation, metastasis, and hormone receptor expressions in breast cancer cell line MCF-7 incubated in two different glucose conditions. MCF-7 cells were incubated in high or low glucose media and treated with various doses of metformin. The cell viability was studied using MTT test. The Ki-67, estrogen and progesterone receptor expression were evaluated by ICC and galectin-3 expression was evaluated by ELISA or spectrophotometrically. The cell viability following consecutive metformin doses in either glucose condition for 24 and 48 h represented a significant decrease when compared to control. The proliferation detected in low glucose medium following metformin at doses < 20 mM was found significantly decreased when compared to high glucose medium at 48 h. In terms of galectin-3 levels, the increase in high glucose medium treated with metformin and the decrease in low glucose medium were found statistically significant when compared to control. Progesterone receptor staining demonstrated a significant increase in low glucose medium. Our findings represent better outcomes for cancer lines incubated in low glucose medium treated with metformin in terms of viability, receptor expression and metastatic activity, and highlight the potential benefit of metformin especially in restraining the cancer cell’s ability to cope energetic stress in low glucose conditions.     

‘Cool’ adaptations to cold environments: globins in Notothenioidei (Actynopterygii,Perciformes)

Notothenioidei, the taxonomic group of teleosts that dominates the Southern Ocean and dwell in the Ross Sea at large, provide an example of marine species that underwent unique adaptations to life at low temperatures and high oxygen concentrations, resulting in morphological, physiological, genomic, and biochemical peculiarities in comparison with warm-water fish. Global Warming raises concerns over the fate of these stenothermal fish, as their adaptation has been accompanied by irreversible genomic losses, which suggest a poor genetic potential to adapt to warmer climates. Specifically, this review focuses on adaptation of proteins belonging to the globin superfamily, which include the respiratory proteins hemoglobin and myoglobin and the non-respiratory proteins neuroglobin and cytoglobin. Here, we describe their molecular adaptations to cold temperatures in the framework of the physiology of oxygen transport and management of oxidative stress in fish species largely populating the Ross Sea.     

When the same is not the same: phenotypic variation reveals different plant ecological strategies within species occurring in distinct Neotropical savanna habitats

Variations in abiotic characteristics such as soil water availability and fertility impose different selective pressures on plant populations. This may produce intraspecific variability in functional traits, even at a fine spatial scale. We investigated whether functional traits related to water-use efficiency, resource-retention strategy, soil nutrient acquisition, and fire tolerance differ in species that occur in two different habitats of Brazilian Cerrado: rocky savannas and savanna woodlands. Rocky savannas occur over sandstone, quartzite outcrops and have shallow nutrient-poor and low-moisture rocky soils, while savanna woodlands occur over well-drained and deep soils with frequent fire regimes. We measured nine functional traits of 40 tree species that occur in both habitats. Rocky savanna individuals exhibited a greater water-use efficiency strategy. The resource-retention strategy in rocky savanna individuals was corroborated by lower adult maximum height. However, despite the lower nutrient availability in rocky savanna soils, we only detected lower leaf phosphorus content in individuals from this habitat. Furthermore, individuals from both habitats had equally thick bark, suggesting that the fire-defense strategy is related to a stable, rather than plastic trait. Overall, our results highlight the central role of contrasting soil water availability patterns in driving phenotypic plasticity within species. We conclude that savanna species are responding to water and nutrient availabilities, via plasticity in traits related to the resource-retention strategy, and preparing for future fires, via uniformly thick bark. Wide plant distribution in contrasting habitats is possible for species that can shift ecological strategies to survive in nutrient- and water-limited habitats such as rocky savannas.     

Is ADHD a valid diagnosis in older adults?

ADHD is a neurodevelopmental syndrome that often persists into adulthood. It is possible that different criteria are necessary for older adults than younger adults: the manifestations of ADHD could change with age; other conditions with onset in later life share presenting symptoms with ADHD; different contextual challenges and patterns of compensatory support may exist. For these reasons, we reviewed evidence for the validity of DSM ADHD criteria in adulthood for individuals over the age of 50. Specifically, we evaluated evidence that the DSM criteria for ADHD identify a valid syndrome in older adults based on clinical presentation, laboratory or testing findings, absence of alternate diagnosis to explain symptoms, course of the syndrome, or familial presence of the condition. We found evidence that various ADHD criteria identify subjects with clinical presentations similar to that seen in younger adults, but only 92 well-described cases have been reported in the literature. ADHD traits also may be less common in the general population of older adults than in younger adults, suggesting that the threshold for an atypical burden of ADHD traits may be lower in older populations. Future research can establish a richer basis for validity of diagnostic criteria for ADHD in older adults.     

Simplified approaches for the development of an ELISA to detect circulating autoantibodies to p53 in cancer patients

Background  

The recognition that human tumors stimulate the production of autoantibodies has initiated the use of this immune response as serological markers for the early diagnosis and management of cancer. The enzyme-linked immunosorbent assay (ELISA) is the most common method used in detecting autoantibodies, which involves coating the microtiter plate with the tumor associated antigen (TAA) of interest and allowing serum antibodies to bind. The patient's sample is directly in contact with the coating antigen so the protein used for coating must be pure to avoid non-specific binding. In this study, a simplified method to selectively and specifically immobilize TAAs onto microtiter plates in order to detect circulating autoantibodies in cancer patients without prior purification process was described. Wild type full-length p53 protein was produced in fusion with biotin carboxyl carrier peptide (BCCP) or hexahistidine [(His)6] using pAK400 and pET15b(+) vectors, respectively. The recombinant p53 fusion protein produced was then subjected to react with either a commercial p53 monoclonal antibody (mAb) or sera from lung cancer patients and healthy volunteers in an enzyme-linked immunosorbent assay (ELISA) format.