Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single-stranded nucleic acids.

The three-dimensional structure of the homodimeric single-stranded DNA binding protein encoded by the filamentous Pseudomonas bacteriophage Pf3 has been determined using heteronuclear multidimensional NMR techniques and restrained molecular dynamics. NMR experiments and structure calculations have been performed on a mutant protein (Phe36 --> His) that was successfully designed to reduce the tendency of the protein to aggregate. The protein monomer is composed of a five-stranded antiparallel beta-sheet from which two beta-hairpins and a large loop protrude. The structure is compared with the single-stranded DNA binding protein encoded by the filamentous Escherichia coli phage Ff, a protein with a similar biological function and DNA binding properties, yet quite different amino acid sequence, and with the major cold shock protein of Escherichia coli, a single-stranded DNA binding protein with an entirely different sequence, biological function and binding characteristics. The amino acid sequence of the latter is highly homologous to the nucleic acid binding domain (i.e. the cold shock domain) of proteins belonging to the Y-box family. Despite their differences in amino acid sequence and function, the folds of the three proteins are remarkably similar, suggesting that this is a preferred folding pattern shared by many single-stranded DNA binding proteins.     

The intertidal mudflats of Barr Al Hikman,Sultanate of Oman,as feeding,reproduction and nursery grounds for brachyuran crabs

Brachyuran crabs are an important ecological and economical, yet often unstudied aspect of intertidal mudflats of the Arabian Peninsula. Here we provide baseline density estimates of crabs at the relatively pristine intertidal mudflats of Barr Al Hikman (Sultanate of Oman) and provide information on their life cycle and habitat preference. Across the winters of 2012–2015 crabs were sampled on a grid covering the entire intertidal depth gradient. 29 species were found and average densities varied between 12 and 54 crabs/m². Deposit-feeding and herbivorous crabs were the most abundant species across all winters. Size frequency data and the presence of ovigerous females show that most crabs species reproduce in the intertidal area. P. segnis, the most important crab for local fisheries, was found to use the intertidal area as a nursery ground. We analysed the relationships between the two most abundant crab species, Macrophthalmus sulcatus and Thalamita poissonii and the environmental variables: seagrass density, tidal elevation, median grain size and sediment depth using Random Forest models. The predictive capacity of the models and the relative importance of the environmental predictors varied between years, but crab densities in general were positively associated with seagrass density, presumably because seagrass offers feeding habitat.

     

Investigating Incipient Speciation in Arabidopsis lyrata from Patterns of Transmission Ratio Distortion

Our understanding of the development of intrinsic reproductive isolation is still largely based on theoretical models and thorough empirical studies on a small number of species. Theory suggests that reproductive isolation develops through accumulation of epistatic genic incompatibilities, also known as Bateson–Dobzhansky–Muller (BDM) incompatibilities. We can detect these from marker transmission ratio distortion (TRD) in hybrid progenies of crosses between species or populations, where TRD is expected to result from selection against heterospecific allele combinations in hybrids. TRD may also manifest itself because of intragenomic conflicts or competition between gametes or zygotes. We studied early stage speciation in Arabidopsis lyrata by investigating patterns of TRD across the genome in F₂ progenies of three reciprocal crosses between four natural populations. We found that the degree of TRD increases with genetic distance between crossed populations, but also that reciprocal progenies may differ substantially in their degree of TRD. Chromosomes AL6 and especially AL1 appear to be involved in many single- and two-locus distortions, but the location and source of TRD vary between crosses and between reciprocal progenies. We also found that the majority of single- and two-locus TRD appears to have a gametic, as opposed to zygotic, origin. Thus, while theory on BDM incompatibilities is typically illustrated with derived nuclear alleles proving incompatible in hybrid zygotes, our results suggest a prominent role for distortions emerging before zygote formation.     

Effective and Low-Cost Saccharification of Pineapple Peel by <Emphasis Type="Italic">Trichoderma viride</Emphasis> Crude Extract with Enhanced β-Glucosidase Activity

Efficient, low-cost enzymatic hydrolysis of lignocellulosic biomass is essential for cost-effective production of bioethanol. The aim of this study was to establish a fungal fermentation-based strategy for the economic enzymatic conversion of pineapple peel into fermentable sugars. Trichoderma viride was grown on passion fruit peel in order to improve its β-glucosidase production, and a crude extract was then used to hydrolyze pineapple peel. The effects of medium pH, cultivation time, and passion fruit peel concentration on β-glucosidase production were evaluated using a central composite rotational design (CCRD) combined with response surface methodology (RSM). Optimal β-glucosidase activity of 2.40 U mL^?1 was found after 6.5 days of cultivation in medium at pH 6.0, containing 2.0 % passion fruit peel. Saccharification of pineapple peel was also optimized by RSM and CCRD with respect to pH, temperature, β-glucosidase concentration, and reaction time and proceeded optimally at pH 4.0, 55 °C, with a β-glucosidase loading of 31.25 U g^?1 dry feedstock and 75 h of reaction. Under these conditions, T. viride crude extract hydrolyzed pineapple peel with a glucose yield of 65.3 %. This study therefore presents passion fruit peel as an attractive raw material for the production of β-glucosidases. In addition, it describes an improved, effective, and low-cost enzymatic method for the production of fermentable sugars from pineapple peel, an abundant and inexpensive agro-industrial waste.     

Acceleration of newborn rats’ development with the use of photobiomodulation and the near possibility of application in human premature babies

Photobiomodulation was explored to find evidence of stimulation during the development of newborn rats. A light chamber device was used, and rat pups were divided into groups after birth. Investigation of the process’ security was performed before the full experiment. Following a protocol of alternating illumination and mother's presence during the first 13 days, we observed that, in the group that received photobiomodulation, the pups opened their eyes faster, indicating earlier achievement of maturity. The rate of weight gain also indicates faster metabolic activity in the group that was photostimulated. This study is the first step toward the use of photobiomodulation for premature newborn human babies.     

Testing for equal rates of cladogenesis in diverse taxa

Taxa differ widely in numbers of species, which may be due either to chance alone or to factors that cause differences in speciation and extinction rates between taxa. To test whether an observed distribution of species over taxa differs from the distribution expected from chance alone, one must take into account that neither speciation nor extinction rates are known. This paper introduces a way to estimate speciation and extinction probabilities from the distribution of extant species over families and to test whether the observed distribution is different from expected. Application of this procedure to the distributions of bird, hexapod, primate, and angiosperm species over taxa provides statistical evidence of differences in rates of cladogenesis between taxa.     

Serotonergic mechanisms of the lateral parabrachial nucleus and cholinergic-induced sodium appetite

Central cholinergic mechanisms are suggested to participate in osmoreceptor-induced water intake. Therefore, central injections of the cholinergic agonist carbachol usually produce water intake (i.e., thirst) and are ineffective in inducing the intake of hypertonic saline solutions (i.e., the operational definition of sodium appetite). Recent studies have indicated that bilateral injections of the serotonin receptor antagonist methysergide into the lateral parabrachial nucleus (LPBN) markedly increases salt intake in models involving the activation of the renin-angiotensin system or mineralocorticoid hormones. The present studies investigated whether sodium appetite could be induced by central cholinergic activation with carbachol (an experimental condition where only water is typically ingested) after the blockade of LPBN serotonergic mechanisms with methysergide treatment in rats. When administered intracerebroventricularly in combination with injections of vehicle into both LPBN, carbachol (4 nmol) caused water drinking but insignificant intake of hypertonic saline. In contrast, after bilateral LPBN injections of methysergide (4 microg), intracerebroventricular carbachol induced the intake of 0.3 M NaCl. Water intake stimulated by intracerebroventricular carbachol was not changed by LPBN methysergide injections. The results indicate that central cholinergic activation can induce marked intake of hypertonic NaCl if the inhibitory serotonergic mechanisms of the LPBN are attenuated.     

Development,characterization, validation,and mapping of SSRs derived from <Emphasis Type="Italic">Theobroma cacao</Emphasis> L.<Emphasis Type="Italic">–Moniliophthora perniciosa</Emphasis> interaction ESTs

In this study, we report results of the detection and analysis of SSR markers derived of cacao–Moniliophthora perniciosa expressed sequence tags (ESTs) in relation to cacao resistance to witches’ broom disease (WBD), and we compare the polymorphism of those ESTs (EST-simple sequence repeat (SSR)) with classical neutral SSR markers. A total of 3,487 ESTs was used in this investigation. SSRs were identified in 430 sequences: 277 from the resistant genotype TSH 1188 and 153 from the susceptible one Catongo, totalizing 505 EST-SSRs with three types of motifs: dinucleotides (72.1%), trinucleotides (27.3%), and tetranucleotides (0.6%). EST-SSRs were classified into 16 main categories; most of the EST-SSRs belonged to “Unknown function” and “No homology” categories (45.82%). A high frequency of SSRs was found in the 5’UTR and in the ORF (about 27%) and a low frequency was observed in the 3’UTR (about 8%). Forty-nine EST-SSR primers were designed and evaluated in 21 cacao accessions, 12 revealed polymorphism, having 47 alleles in total, with an average of 3.92 alleles per locus. On the other hand, the 11 genomic SSR markers revealed a total of 47 alleles, with an average of 5.22 alleles per locus. The association of EST-SSR with the genomic SSR enhanced the analysis of genetic distance among the genotypes. Among the 12 polymorphic EST-SSR markers, two were mapped on the F₂ Sca 6 × ICS 1 population reference for WBD resistance.     

Random processes and geographic species richness patterns: why so few species in the north?

In response to the suggestion that the latitudinal gradient in species richness is the result of stochastic processes of species distributions, we created a computer simulation program that enabled us to study random species distributions over irregularly shaped areas. Our model could not explain latitudinal variation in species richness of New World mammals and created species richness patterns that differed dramatically from previous stochastic models. The interplay of speciation and species migration in our simulation generated the highest species richness in the middle of a landmass, not in the middle of its latitudinal stretch as was found in previous one-dimensional models. The discrepancy between the results of this study and previous empirical studies suggests that the effect of randomness in species-richness distribution is on a continental scale restricted by other, dominant determinants that limit the effect of chance.