Local sequence alignments with monotonic gap penalties.

MOTIVATION: Sequence alignments obtained using affine gap penalties are not always biologically correct, because the insertion of long gaps is over-penalised. There is a need for an efficient algorithm which can find local alignments using non-linear gap penalties. RESULTS: A dynamic programming algorithm is described which computes optimal local sequence alignments for arbitrary, monotonically increasing gap penalties, i.e. where the cost g(k) of inserting a gap of k symbols is such that g(k) >/= g(k-1). The running time of the algorithm is dependent on the scoring scheme; if the expected score of an alignment between random, unrelated sequences of lengths m, n is proportional to log mn, then with one exception, the algorithm has expected running time O(mn). Elsewhere, the running time is no greater than O(mn(m+n)). Optimisations are described which appear to reduce the worst-case run-time to O(mn) in many cases. We show how using a non-affine gap penalty can dramatically increase the probability of detecting a similarity containing a long gap. AVAILABILITY: The source code is available to academic collaborators under licence.     

Effects of humidity on light-induced stomatal opening: evidence for hydraulic coupling among stomata

A mechanism for co-ordinating behaviour of stomata within an areole during patchy stomatal conductance has recently been proposed. This mechanism depends on hydraulic interactions among stomata that are mediated by transpiration-induced changes in epidermal turgor. One testable prediction that arises from this proposed mechanism is that the strength of hydraulic coupling among stomata should be proportional to evaporative demand and, therefore, inversely proportional to humidity. When a leaf is illuminated following a period of darkness, there is typically a period of time, termed the Spannungsphase, during which guard cell osmotic and turgor pressure are increasing, but the pore remains closed. If hydraulic coupling is proportional to evaporative demand, then variation among stomata in the duration of the Spannungsphase should be lower for leaves at low humidity than for leaves at high humidity. A similar prediction emerged from a computer model based on the proposed hydraulic mechanisms. These predictions were tested by measuring individual stomatal apertures on intact transpiring leaves at low and high humidity and on vacuum-infiltrated leaf pieces (to eliminate transpiration) as PFD was increased to high values from either darkness or a low value. Results showed that the range of Spannungsphasenamong stomata was reduced at low humidity compared to high humidities. Experiments that began at low PFD, rather than at darkness, showed no delay in stomatal opening. These results are discussed in the context of the proposed hydraulic coupling mechanisms.     

The tadpole of Scinax skuki (Anura: Hylidae) from the type locality,with a description of its larval skeleton

Herein, we provide external and internal morphological data of Scinax skuki tadpoles from its type locality. The benthic tadpole of S. skuki has eyes and nostrils positioned dorsally, vent tube dextral and reaching the free margin of the ventral fin, oral disk ventral with posterior margin concave when partially closed, labial tooth row formula 2/3, and the presence of nonpigmented spurs behind the lower jaw. These characters, together with the absence of a tectum parietale, and the shapes of the pars articularis quadrati and suprarostral, are useful for species identification and may be informative for systematic purposes.     

Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species

Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thus it is often unclear how many species coexist in sympatry, what are their phylogenetic relationships and their demographic history. We answer these questions using morphologically similar species of the genus Mugil that are sympatric in the largest coastal Marine Protected Area in the Tropical Southwestern Atlantic marine province. Using a sub-representation of the genome, we show that individuals are assigned to five highly differentiated genetic clusters that are coincident with five mitochondrial lineages, but discordant with morphological information, supporting the existence of five species with conserved morphology in this region. A lack of admixed individuals is consistent with strong genetic isolation between sympatric species, but the most likely species tree suggests that in one case speciation has occurred in the presence of interspecific gene flow. Patterns of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions since species formation. Together, our results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.Subject terms: Genetic variation, Phylogenetics, Speciation     

Incidence of Vibrio vulnificus in estuarine waters of the south Texas Coastal Bend region

Aims: To determine the occurrence of the human pathogen, Vibrio vulnificus, in south Texas coastal waters. Methods and Results: Coastal waters were sampled monthly between August 2006 and July 2007. Water temperature, dissolved oxygen, pH, salinity, conductivity and turbidity were measured during each sampling event. Culture‐based techniques utilizing Vibrio vulnificus agar (VVA) and membrane‐Enterococcus indoxyl‐β‐d ‐glucoside agar (mEI) were used to assess the occurrence and levels of V. vulnificus and the faecal contamination indicator group, enterococci, respectively. Vibrio vulnificus isolates were confirmed using colony‐blot hybridization with the species‐specific VVAP probe. Vibrio vulnificus was isolated at all sites throughout the year even when the water temperature dropped to 9·71°C. Significant correlations were found between concentrations of V. vulnificus and the abiotic factors, water temperature (P = 0·002) and dissolved oxygen (P = 0·028), as well as between concentrations of V. vulnificus and enterococci (P < 0·001). Conclusions: This study demonstrated the year‐round presence of V. vulnificus in coastal waters of south Texas. Significance and Impact of the Study: These findings indicate that the potential for human exposure to the pathogen, V. vulnificus, exists throughout the year. It also suggests that routinely monitored data might be used to predict the occurrence of the pathogen.     

Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome

A series of 21 multiplex (MP) polymerase chain reactions containing simple sequence repeat (SSR) markers spanning most of the apple genome has been developed. Eighty-eight SSR markers, well distributed over all 17 linkage groups (LGs), have been selected. Eighty-four of them were included in 21 different MPs while four could not be included in any MPs. The 21 MPs were then used to genotype approximately 2,000 DNA samples from the European High-quality Disease-Resistant Apples for a Sustainable agriculture project. Two SSRs (CH01d03 and NZAL08) were discarded at an early stage as they did not produce stable amplifications in the MPs, while the scoring of the multilocus (ML) SSR Hi07d11 and CN44794 was too complex for large-scale genotyping. The testing of the remaining 80 SSRs over a large number of different genotypes allowed: (1) a better estimation of their level of polymorphism; as well as of (2) the size range of the alleles amplified; (3) the identification of additional unmapped loci of some ML SSRs; (4) the development of methods to assign alleles to the different loci of ML SSRs and (5) conditions at which an SSR previously described as ML would amplify alleles of a single locus to be determined. These data resulted in the selection of 75 SSRs out of the 80 that are well suited and recommended for large genotyping projects. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The antidepressant-like effect of Ocimum basilicum in an animal model of depression

We investigated the efficacy of Ocimum basilicum (OB) essential oils for treating depression related behavioral, biochemical and histopathological changes caused by exposure to chronic unpredictable mild stress (CUMS) in mice and to explore the mechanism underlying the pathology. Male albino mice were divided into four groups: controls; CUMS; CUMS plus fluoxetine, the antidepressant administered for pharmacological validation of OB; and CUMS plus OB. Behavioral tests included the forced swim test (FST), elevated plus-maze (EPM) and the open ?eld test (OFT); these tests were performed at the end of the experiment. We assessed serum corticosterone level, protein, gene and immunoexpression of brain-derived neurotropic factor (BDNF) and glucocorticoid receptors (GRs) as well as immunoexpression of glial fibrillary acidic protein (GFAP), Ki67, caspase-3 in the hippocampus. CUMS caused depression in the mice as evidenced by prolonged immobility in the FST, prolonged time spent in the open arms during the EPM test and reduction of open field activity in the OFT. OB ameliorated the CUMS induced depressive status. OB significantly reduced the corticosterone level and up-regulated protein and gene expressions of BDNF and GR. OB reduced CUMS induced hippocampal neuron atrophy and apoptosis, and increased the number of the astrocytes and new nerve cells. OB significantly increased GFAP-positive cells as well as BDNF and GR immunoexpression in the hippocampus.