The habitat function of mangroves for terrestrial and marine fauna: A review

Mangroves are defined by the presence of trees that mainly occur in the intertidal zone, between land and sea, in the (sub) tropics. The intertidal zone is characterised by highly variable environmental factors, such as temperature, sedimentation and tidal currents. The aerial roots of mangroves partly stabilise this environment and provide a substratum on which many species of plants and animals live. Above the water, the mangrove trees and canopy provide important habitat for a wide range of species. These include birds, insects, mammals and reptiles. Below the water, the mangrove roots are overgrown by epibionts such as tunicates, sponges, algae, and bivalves. The soft substratum in the mangroves forms habitat for various infaunal and epifaunal species, while the space between roots provides shelter and food for motile fauna such as prawns, crabs and fishes. Mangrove litter is transformed into detritus, which partly supports the mangrove food web. Plankton, epiphytic algae and microphytobenthos also form an important basis for the mangrove food web. Due to the high abundance of food and shelter, and low predation pressure, mangroves form an ideal habitat for a variety of animal species, during part or all of their life cycles. As such, mangroves may function as nursery habitats for (commercially important) crab, prawn and fish species, and support offshore fish populations and fisheries. Evidence for linkages between mangroves and offshore habitats by animal migrations is still scarce, but highly needed for management and conservation purposes. Here, we firstly reviewed the habitat function of mangroves by common taxa of terrestrial and marine animals. Secondly, we reviewed the literature with regard to the degree of interlinkage between mangroves and adjacent habitats, a research area which has received increasing attention in the last decade. Finally, we reviewed current insights into the degree to which mangrove litter fuels the mangrove food web, since this has been the subject of long-standing debate.     

Towards an integrated global framework to assess the impacts of land use and management change on soil carbon: current capability and future vision

Intergovernmental Panel on Climate Change (IPCC) Tier 1 methodologies commonly underpin project‐scale carbon accounting for changes in land use and management and are used in frameworks for Life Cycle Assessment and carbon footprinting of food and energy crops. These methodologies were intended for use at large spatial scales. This can introduce error in predictions at finer spatial scales. There is an urgent need for development and implementation of higher tier methodologies that can be applied at fine spatial scales (e.g. farm/project/plantation) for food and bioenergy crop greenhouse gas (GHG) accounting to facilitate decision making in the land‐based sectors. Higher tier methods have been defined by IPCC and must be well evaluated and operate across a range of domains (e.g. climate region, soil type, crop type, topography), and must account for land use transitions and management changes being implemented. Furthermore, the data required to calibrate and drive the models used at higher tiers need to be available and applicable at fine spatial resolution, covering the meteorological, soil, cropping system and management domains, with quantified uncertainties. Testing the reliability of the models will require data either from sites with repeated measurements or from chronosequences. We review current global capability for estimating changes in soil carbon at fine spatial scales and present a vision for a framework capable of quantifying land use change and management impacts on soil carbon, which could be used for addressing issues such as bioenergy and biofuel sustainability, food security, forest protection, and direct/indirect impacts of land use change. The aim of this framework is to provide a globally accepted standard of carbon measurement and modelling appropriate for GHG accounting that could be applied at project to national scales (allowing outputs to be scaled up to a country level), to address the impacts of land use and land management change on soil carbon.     

Evidence for a higher number of species of Odontotermes (Isoptera) than currently known from Peninsular Malaysia from mitochondrial DNA phylogenies

Termites of the genus Odontotermes are important decomposers in the Old World tropics and are sometimes important pests of crops, timber and trees. The species within the genus often have overlapping size ranges and are difficult to differentiate based on morphology. As a result, the taxonomy of Odontotermes in Peninsular Malaysia has not been adequately worked out. In this study, we examined the phylogeny of 40 samples of Odontotermes from Peninsular Malaysia using two mitochondrial DNA regions, that is, the 16S ribosomal RNA and cytochrome oxidase subunit I genes, to aid in elucidating the number of species in the peninsula. Phylogenies were reconstructed from the individual gene and combined gene data sets using parsimony and likelihood criteria. The phylogenies supported the presence of up to eleven species in Peninsular Malaysia, which were identified as O. escherichi, O. hainanensis, O. javanicus, O. longignathus, O. malaccensis, O. oblongatus, O. paraoblongatus, O. sarawakensis, and three possibly new species. Additionally, some of our taxa are thought to comprise a complex of two or more species. The number of species found in this study using DNA methods was more than the initial nine species thought to occur in Peninsular Malaysia. The support values for the clades and morphology of the soldiers provided further evidence for the existence of eleven or more species. Higher resolution genetic markers such as microsatellites would be required to confirm the presence of cryptic species in some taxa.     

Tophus burden reduction with pegloticase: results from phase 3 randomized trials and open-label extension in patients with chronic gout refractory to conventional therapy

Introduction

Two replicate randomized, placebo-controlled six-month trials (RCTs) and an open-label treatment extension (OLE) comprised the pegloticase development program in patients with gout refractory to conventional therapy. In the RCTs, approximately 40% of patients treated with the approved dose saw complete response (CR) of at least one tophus. Here we describe the temporal course of tophus resolution, total tophus burden in patients with multiple tophi, tophus size at baseline, and the relationship between tophus response and urate-lowering efficacy.

Methods

Baseline subcutaneous tophi were analyzed quantitatively using computer-assisted digital images in patients receiving pegloticase (8 mg biweekly or monthly) or placebo in the RCTs, and pegloticase in the OLE. Tophus response, a secondary endpoint in the trials, was evaluated two ways. Overall tophus CR was the proportion of patients achieving a best response of CR (without any new/enlarging tophi) and target tophus complete response (TT-CR) was the proportion of all tophi with CR.

Results

Among 212 patients randomized in the RCTs, 155 (73%) had ≥1 tophus and 547 visible tophi were recorded at baseline. Overall tophus CR was recorded in 45% of patients in the biweekly group (P = 0.002 versus placebo), 26% in the monthly group, and 8% in the placebo group after six months of RCT therapy. TT-CR rates at six months were 28%, 19%, and 2% of tophi, respectively. Patients meeting the primary endpoint of sustained urate-lowering response to therapy (responders) were more likely than nonresponders to have an overall tophus CR at six months (54% vs 20%, respectively and 8% with placebo).Both overall tophus CR and TT-CRs increased with treatment duration in the OLE, reaching 70% (39/56) of patients and 55% (132/238) of target tophi after one year of treatment in patients receiving pegloticase during both the RCTs and OLE. At that time point, more tophi had resolved in responders (102/145 or 70% of tophi) than nonresponders (30/93; 32%).

Conclusions

Pegloticase reduced tophus burden in patients with refractory tophaceous gout, especially those achieving sustained urate-lowering. Complete resolution of tophi occurred in some patients by 13 weeks and in others with longer-term therapy.

Trial registrations

{"type":"clinical-trial","attrs":{"text":"NCT00325195","term_id":"NCT00325195"}}NCT00325195, {"type":"clinical-trial","attrs":{"text":"NCT01356498","term_id":"NCT01356498"}}NCT01356498     

Workflow management systems for gene sequence analysis and evolutionary studies – A Review

Post ‘omic’ era has resulted in the development of many primary, secondary and derived databases. Many analytical and visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.     

Prostaglandin E1 specific binding in rhesus myometrium

Myometrial low speed supernatant prepared from non-pregnant rhesus uteri was incubated with ³H-Prostaglandin (PG) E₁ with or without addition of unlabelled prostaglandins. The uptake of ³H-PGE₁ was inhibited in a dose dependent fashion by PGE₂>PGE₁>PGA₁>PGF₂=PGA₁>PGB₁=PGB₂≥PGD₂. PGE₁ metabolites inhibited ³H-PGE₁ binding in the following order: 13,14-dihydro-PGE₁>13,14-dihydro-15-keto-PGE₁=15-keto-PGE₁. The specific binding of ³H-PGE₁ and ³H-PGF₂ was similarly affected by the temperature and time of incubation. Equilibrium binding constants determined using rhesus uteri obtained during the luteal phase of the menstrual cycle indicate the presence of high affinity PGE₁ binding sites with an average (n=3) apparent dissociation constant of 2.2 × 10⁻⁹M and a lower affinity PGE₁ binding site with a K_d 1 × 10⁻⁸M. No high affinity — low capacity ³H-PGF₂ sites could be demonstrated.

Relative uterine stimulating potencies of some natural prostaglandins and prostaglandin analogs tested after acute intravenous administration in mid-pregnant rhesus monkeys corresponded with the PGE₁ binding inhibition of the respective compound. The uterine stimulating potencies of the prostaglandin analogs tested were: (15S)-15-methyl-PGE₂=16,16-dimethyl-PGE₂>17-phenyl-18,19,20-trinor-P GE₂>16 phenoxy-17,18,19,20-tetranor-PGE₂=PGE₂=PGE₁=(15S)-15-methyl-PGE₂>PGF₂.     

Taxol binds to polymerized tubulin in vitro

Taxol, a natural plant product that enhances the rate and extent of microtubule assembly in vitro and stabilizes microtubules in vitro and in cells, was labeled with tritium by catalytic exchange with (3)H(2)O. The binding of [(3)H]taxol to microtubule protein was studied by a sedimentation assay. Microtubules assembled in the presence of [(3)H]taxol bind drug specifically with an apparent binding constant, K(app), of 8.7 x 19(-7) M and binding saturates with a calculated maximal binding ration, B(max), of 0.6 mol taxol bound/mol tubulin dimer. [(3)H]Taxol also binds and assembles phosphocellulose-purified tubulin, and we suggest that taxol stabilizes interactions between dimers that lead to microtubule polymer formation. With both microtubule protein and phosphocellulose- purified tubulin, binding saturation occurs at approximate stoichiometry with the tubulin dimmer concentration. Under assembly conditions, podophyllotoxin and vinblastine inhibit the binding of [(3)H]taxol to microtubule protein in a complex manner which we believe reflects a competition between these drugs, not for a single binding site, but for different forms (dimer and polymer) of tubulin. Steady-state microtubules assembled with GTP or with 5’-guanylyl-α,β-methylene diphosphonate (GPCPP), a GTP analog reported to inhibit microtubule treadmilling (I.V. Sandoval and K. Weber. 1980. J. Biol. Chem. 255:6966-6974), bind [(3)H]taxol with approximately the same stoichiometry as microtubules assembled in the presence of [(3)H]taxol. Such data indicate that a taxol binding site exists on the intact microtubule. Unlabeled taxol competitively displaces [(3)H]taxol from microtubules, while podophyllotoxin, vinblastine, and CaCl(2) do not. Podophyllotoxin and vinblastine, however, reduce the mass of sedimented taxol-stabilized microtubules, but the specific activity of bound [(3)H]taxol in the pellet remains constant. We conclude that taxol binds specifically and reversibly to a polymerized form of tubulin with a stoichiometry approaching unity.     

Phosphorylation and biosynthesis of high molecular weight proteins of tumor nuclear matrix

INTRODUCTIONAsearlyasin1948wehavefr8CtionatedisolatednucleifromnormalandtumorcellsbyextractionwithiMNaCIanddilutealkali[1].Thenuclearresiduewasthenstudiedmorethoroughly[2,3].Lateron,sillillarproteinousnuclearresidueswereisolatedbyotherworkers[46]andasstud…