Study of inter species diversity and population structure by molecular genetic method in Iranian Artemia

Artemia is a small crustacean that adapted to live in brine water and has been seen in different brine water sources in Iran. Considering the importance of genetic studies manifest inter population differences in species, to estimate genetic structure, detect difference at molecular level and separate different Artemia populations of Iran, also study of phylogenic relationships among them, samples of Artemia were collected from nine region: Urmia lake in West Azerbaijan, Shoor and Inche-Borun lakes in Golestan, Hoze-Soltan and Namak lakes in Qom, Maharloo and Bakhteghan lakes in Fars, Nough pool in Kerman and Mighan pool in Markazi and DNA extracted by phenol-chloroform method. Primers designed on a ribosomal fragment (16s rRNA) of mt DNA sequence and PCR was done. Digestion of the 1566 bp segment PCR product by 10 restriction endonuclease (Alu I, EcoR I, Eco47 I, Hae III, Hind III, Hinf I, Mbo I, Msp I, Rsa I, TaqI) showed 25 different haplotypes: 9 in Urmia, 4 in Shoor and Inche- Borun, 1 in Namak and Hoze-Soltan, 3 in Mighan, 1 in Bakhtegan Maharlo, 3 in Maharloo and 4 in Nough. Measurement of haplotype and nucleotide diversity intra population and nucleotide diversity and divergence inter populations and evolutionary distance between haplotypes showed a high diversity in mitochondrial genome of Artemia in studied regions whose results are similar to those explained for highly geographic expansion organism. In addition, results showed considerable heterogeneity between different populations and there are enough evidences in haplotypic level for separation of studied samples and division of Iranian Artemia to seven populations including Urmia, Shoor and Inche-Borun, Hoze-Soltan and Namak, Maharloo, Bakhteghan, Nough and Mighan. Phylogenetic analysis of the 16S rRNA data set resulted strict consensus and neighbor joining distance trees, demonstrated that all samples were monophyletic and parthenogenetic form derivation from bisexual populations and genetically high resemblance to those of A. urmiana. Study of 270 specimens from different region showed the genus Artemia in Iran clustered into three clades including: 1- Shoor, Inche-Burun, Hoze-Soltan, Namak, Bakhtegan and Maharloo 2- Nough and Mighan 3- Urmia. Totally, obtained results indicated to ability of used techniques for study of inter species diversity, population structure, reveal of phylogenic relationship and dividing of different populations of Artemia in Iran.

Ecological impact of Mahshahr petrochemical activities on abundance and diversity of macrobenthic fauna in Zangi Creek (Persian Gulf)

The Moosa Creek extends from its opening into the Persian Gulf, with some sub narrow creeks leading to it. Zangi creek is one of the main branches of Moosa creek. The creek contains numerous sources of organic pollution, including sewage outlet flows and boat waste. After establishing the Petrochemical special Economic Zone (PETZONE) in 1997 near to the Zangi Creek, the pipelines, streets and railway made it distinct from eastern and western parts of this creek. Industrial activities have released sludge and effluents in this creek along these years. A survey of the Zangi creek was performed, assessing water properties, organic pollution, and the population density, distribution and diversity of macrobenthic fauna through bi-monthly sampling from July 2006 to September 2007. Samples were collected from water near the bottom and sediment at 7 stations include 2 stations inside the distinct Zangi creek and 4 stations along a transect with 1 km distances between them in eastern free part and one reference station located at the Persian Gulf entrance to the Moosa creek. The environmental parameters such as temperature, salinity, pH, dissolved oxygen, COD, turbidity, EC and heavy metals include Hg, Cd, Pb, Ni as well as percentage silt-clay and total organic matter of the sediment were measured. The faunal population density and their distribution are discussed in relation to the environmental changes. Results showed spatial heterogeneity in faunal distribution of the Zangi creek. Nine groups of macrofauna were identified out of distinct zangi creek. Polychaets formed the dominant group (48%) followed by bivalves (13%), gastropods (10%), Decapods (2%), Tanaids (5%), and all other groups (22%). The distinct creek was heavily polluted without any macrofauna communities probably as a consequence of the high pH, COD, low salinity and heavy metals contamination specially Cd and Pb. The other stations near to the disposal site were found with macrofauna communities commonly tolerant to organic pollution, At 3 km east of the disposal site, macrofauna is comparable to the surrounded creek, whereas macrofauna still indicate environmental degradation. Farther a way, faunal density decreases and equilibrium taxa gradually replace opportunistic species, while the other stations were far from polluted area contained lower pollution and relatively healthy macrofauna. The mean biomass of macrobenthic fauna were estimated for the whole studied area. The results are considered in Minimum density and biomass in surrounded creek and maximum density and biomass in 3 km of surrounded area. Biodiversity Indices were low in surrounded creek. The Shanon-weaver information index was used to describe the spatially variations in diversity. Macrofauna density, shanon and simpson index were significantly variable between surrounded and free parts of Zangi creek (p<0.05). The numerical abundance of macrobenthose varied from 221. m-2 in polluted area to 4346 m-2 in free part of Zangi creek. The Shanon-weaver information index varied from 0.4 in distinct area to 2.9 in reference station. The physico- chemical changes between distinct and free creeks showed significant variations such as pH, salinity and EC. Salinity and EC were significantly positive correlate to macrofauna density, whereas pH and TOM percentage indicated significantly negative correlation to density. Heavy metals concentrations in sediments were higher than water samples. Concentration pattern of heavy metals in sediments and water samples were Ni>Pb>Cd>Hg. Salinity and pH were significantly correlated to metals in sediments (p<0.01). No significant correlation were found between Macrofauna density and heavy metals (p<0.05).

Report of the socio-economic baseline assessment dissemination meeting, Yangon, Myanmar, 28 January, 2015

The Data Dissemination Stakeholder Meeting was was a means of disseminating data from a socio-economic baseline study undertaken in 2014 (Schneider at al 2014). Implications included: the importance of heterogeneity of communities; population structure and migration trends; livelihoods diversity and vulnerability; and stakeholder mobilisation.

Studies on distribution, diversity and production of macrobenthic fauna in the Chahbahar Bay

The population density, distribution, diversity and secondry production of macrobenthic fauna of the inner Chahbahar Bay were studied through bi-monthly sampling from April 1995 to March 1996. Samples were collected from water near the bottom and sediment at 14 stations inside the Bay and one reference station located outside at the entrance to the Bay. The environmental parameters Such as temperature, water depth, salinity, pH and dissolved oxygen as well as percentage silt-clay and total organic matter of the sediment were measured. The faunal population density and their distribution is discussed in relation to the environmental changes. results obtained indicated both spatial and temporal heterogeneity in faunal distribution of the Chahbahar Bay. The total of 18 groups of macrofauna were identified in all samples. Amphipods formed the dominant group (21%) followed by polychaetes (19%), gastropods (15.7%) bivalves (10.6%) and all other groups (33.7%). Seasonal changes in faunal density is shown in relation to Indian Ocean southwest monsoon,the result of which indicated lower population density during monsoon (June to September) than that of the premonsoon (February to May) and post monsoon (October to January) periods. The numerical abundance of macrobenthos varied from 10260.m2 before monsoon to 5190 m2 during monsoon season. Three dominant groups of macrofauna including polychaetes, gastropods, and bivalves were identified in all collected samples. Indices of diversity, richness and evenness were calculated for these three dominant groups. The Shannon-Weaver information index was used to describe the spatially and temporally variation in diversity of these three major faunal groups. The results exhibited lower faunal diversity during monsoon period. The annual production of two dominant macrofauna species including a species of bivalve, Nuculana acuta and a species of Cephalochordata, Branchiostoma lanceolatum were measured by using age group determination. Furthermore the mean biomass and total annual production of macrobenthic fauna were estimated for the whole studied area. The potential yield of demersal fishery resources (fish and crustacean) then estimated and worked out to be 15360 tons/year asuming 10% ecological efficiency of hypothetical pyramid from 3rd to 4th marine trophic level. Accordingly the annual exploitable demersal fishery resources for the entire Chahbahar Bay was estimated to be 7600 to 8500 tons/year by taking 50 to 55% of the total estimated potential in to account.

Optimal design of Functionally Graded Materials using a procedural model and Particle Swarm Optimization

A new method for the optimal design of Functionally Graded Materials (FGM) is proposed in this paper. Instead of using the widely used explicit functional models, a feature tree based procedural model is proposed to represent generic material heterogeneities. A procedural model of this sort allows more than one explicit function to be incorporated to describe versatile material gradations and the material composition at a given location is no longer computed by simple evaluation of an analytic function, but obtained by execution of customizable procedures. This enables generic and diverse types of material variations to be represented, and most importantly, by a reasonably small number of design variables. The descriptive flexibility in the material heterogeneity formulation as well as the low dimensionality of the design vectors help facilitate the optimal design of functionally graded materials. Using the nature-inspired Particle Swarm Optimization (PSO) method, functionally graded materials with generic distributions can be efficiently optimized. We demonstrate, for the first time, that a PSO based optimizer outperforms classical mathematical programming based methods, such as active set and trust region algorithms, in the optimal design of functionally graded materials. The underlying reason for this performance boost is also elucidated with the help of benchmarked examples. © 2011 Elsevier Ltd. All rights reserved.

An Online Expectation-Maximization Algorithm for Changepoint Models

Changepoint models are widely used to model the heterogeneity of sequential data. We present a novel sequential Monte Carlo (SMC) online Expectation-Maximization (EM) algorithm for estimating the static parameters of such models. The SMC online EM algorithm has a cost per time which is linear in the number of particles and could be particularly important when the data is representable as a long sequence of observations, since it drastically reduces the computational requirements for implementation. We present an asymptotic analysis for the stability of the SMC estimates used in the online EM algorithm and demonstrate the performance of this scheme using both simulated and real data originating from DNA analysis.

An Online Expectation-Maximization Algorithm for Changepoint Models

Changepoint models are widely used to model the heterogeneity of sequential data. We present a novel sequential Monte Carlo (SMC) online Expectation-Maximization (EM) algorithm for estimating the static parameters of such models. The SMC online EM algorithm has a cost per time which is linear in the number of particles and could be particularly important when the data is representable as a long sequence of observations, since it drastically reduces the computational requirements for implementation. We present an asymptotic analysis for the stability of the SMC estimates used in the online EM algorithm and demonstrate the performance of this scheme using both simulated and real data originating from DNA analysis.

SynGAP isoforms exert opposing effects on synaptic strength.

Alternative promoter usage and alternative splicing enable diversification of the transcriptome. Here we demonstrate that the function of Synaptic GTPase-Activating Protein (SynGAP), a key synaptic protein, is determined by the combination of its amino-terminal sequence with its carboxy-terminal sequence. 5' rapid amplification of cDNA ends and primer extension show that different N-terminal protein sequences arise through alternative promoter usage that are regulated by synaptic activity and postnatal age. Heterogeneity in C-terminal protein sequence arises through alternative splicing. Overexpression of SynGAP α1 versus α2 C-termini-containing proteins in hippocampal neurons has opposing effects on synaptic strength, decreasing and increasing miniature excitatory synaptic currents amplitude/frequency, respectively. The magnitude of this C-terminal-dependent effect is modulated by the N-terminal peptide sequence. This is the first demonstration that activity-dependent alternative promoter usage can change the function of a synaptic protein at excitatory synapses. Furthermore, the direction and degree of synaptic modulation exerted by different protein isoforms from a single gene locus is dependent on the combination of differential promoter usage and alternative splicing.

Entrepreneurial innovation problems associated with the dynamic growth of university spin-outs in China: A capabilities perspective

This research aims to develop a capabilities-based conceptual framework in order to study the stage-specific innovation problems associated with the dynamic growth process of university spin-outs (hereafter referred to as USOs) in China. Based on the existing literature, pilot cases and five critical cases, this study attempts to explore the interconnections between the entrepreneurial innovation problems and the configuration of innovative capabilities (that acquire, mobilise and re-configure the key resources) throughout the lifecycle of a firm in four growth phases. This paper aims to contribute to the literature in a holistic manner by providing a theoretical discussion of USOs' development through adding evidence from a rapid growth emerging economy. To date, studies that have investigated the development of USOs in China recognised the heterogeneity of USOs in terms of capabilities still remain sparse. Addressing this research gap will be of great interest to entrepreneurs, policy makers and venture investors. © Copyright 2010 Inderscience Enterprises Ltd.

Long-term performance of cement-bentonite containment wall

The paper presents hydraulic conductivity, unconfined compression strength (UCS) and triaxial test results of an 11 year old slag-cement-bentonite (CB) cut-off wall material and identifies factors affecting their long-term performance. The laboratory tests were performed on three types of CB samples ranging from contaminated block field samples to uncontaminated laboratory cast samples. The results showed that hydraulic conductivity reduces till 3 years and UCS increases till 90 days, but there after it remains constant till 11 years of age. The mean hydraulic conductivity and UCS values of block field samples are inferior and have large variability than laboratory cured samples. Such variations are mainly because of heterogeneity caused by aggressive environment and impurities within the specimen. Consolidated undrained triaxial test found that under an effective confining pressure of less than 200 kPa, tension failure occurred since the minor principal stress dropped to zero value at failure. The research outcome is useful for understanding future liability of CB wall and improving their design. © 2009 IOS Press.

Quantification of the effects of antibodies on the extra- and intracellular dynamics of Salmonella enterica.

Antibodies are known to be essential in controlling Salmonella infection, but their exact role remains elusive. We recently developed an in vitro model to investigate the relative efficiency of four different human immunoglobulin G (IgG) subclasses in modulating the interaction of the bacteria with human phagocytes. Our results indicated that different IgG subclasses affect the efficacy of Salmonella uptake by human phagocytes. In this study, we aim to quantify the effects of IgG on intracellular dynamics of infection by combining distributions of bacterial numbers per phagocyte observed by fluorescence microscopy with a mathematical model that simulates the in vitro dynamics. We then use maximum likelihood to estimate the model parameters and compare them across IgG subclasses. The analysis reveals heterogeneity in the division rates of the bacteria, strongly suggesting that a subpopulation of intracellular Salmonella, while visible under the microscope, is not dividing. Clear differences in the observed distributions among the four IgG subclasses are best explained by variations in phagocytosis and intracellular dynamics. We propose and compare potential factors affecting the replication and death of bacteria within phagocytes, and we discuss these results in the light of recent findings on dormancy of Salmonella.

Large scale heterogeneous networks, the Davis-Wielandt shell, and graph separation

We consider a large scale network of interconnected heterogeneous dynamical components. Scalable stability conditions are derived that involve the input/output properties of individual subsystems and the interconnection matrix. The analysis is based on the Davis-Wielandt shell, a higher dimensional version of the numerical range with important convexity properties. This can be used to allow heterogeneity in the agent dynamics while relaxing normality and symmetry assumptions on the interconnection matrix. The results include small gain and passivity approaches as special cases, with the three dimensional shell shown to be inherently connected with corresponding graph separation arguments. © 2012 Society for Industrial and Applied Mathematics.

Does precision decrease with set size?

The brain encodes visual information with limited precision. Contradictory evidence exists as to whether the precision with which an item is encoded depends on the number of stimuli in a display (set size). Some studies have found evidence that precision decreases with set size, but others have reported constant precision. These groups of studies differed in two ways. The studies that reported a decrease used displays with heterogeneous stimuli and tasks with a short-term memory component, while the ones that reported constancy used homogeneous stimuli and tasks that did not require short-term memory. To disentangle the effects of heterogeneity and short-memory involvement, we conducted two main experiments. In Experiment 1, stimuli were heterogeneous, and we compared a condition in which target identity was revealed before the stimulus display with one in which it was revealed afterward. In Experiment 2, target identity was fixed, and we compared heterogeneous and homogeneous distractor conditions. In both experiments, we compared an optimal-observer model in which precision is constant with set size with one in which it depends on set size. We found that precision decreases with set size when the distractors are heterogeneous, regardless of whether short-term memory is involved, but not when it is homogeneous. This suggests that heterogeneity, not short-term memory, is the critical factor. In addition, we found that precision exhibits variability across items and trials, which may partly be caused by attentional fluctuations.

Independence is elusive: set size effects on encoding precision in visual search.

Looking for a target in a visual scene becomes more difficult as the number of stimuli increases. In a signal detection theory view, this is due to the cumulative effect of noise in the encoding of the distractors, and potentially on top of that, to an increase of the noise (i.e., a decrease of precision) per stimulus with set size, reflecting divided attention. It has long been argued that human visual search behavior can be accounted for by the first factor alone. While such an account seems to be adequate for search tasks in which all distractors have the same, known feature value (i.e., are maximally predictable), we recently found a clear effect of set size on encoding precision when distractors are drawn from a uniform distribution (i.e., when they are maximally unpredictable). Here we interpolate between these two extreme cases to examine which of both conclusions holds more generally as distractor statistics are varied. In one experiment, we vary the level of distractor heterogeneity; in another we dissociate distractor homogeneity from predictability. In all conditions in both experiments, we found a strong decrease of precision with increasing set size, suggesting that precision being independent of set size is the exception rather than the rule.

Explicitly coupled thermal flow mechanical formulation for gas-hydrate sediments

This paper presents an explicit time-marching formulation for the solution of the coupled thermal flow mechanical behavior of gas- hydrate sediment. The formulation considers the soil skeleton as a deformable elastoplastic continuum, with an emphasis on the effect of hydrate (and its dissociation) on the stress-strain behavior of the soil. In the formulation, the hydrate is assumed to deform with the soil and may dissociate into gas and water. The formulation is explicitly coupled, such that the changes in temperature because of energy How and hydrate dissociation affect the skeleton stresses and fluid (water and gas) pressures. This, in return, affects the mechanical behavior. A simulation of a vertical well within a layered soil is presented. It is shown that the heterogeneity of hydrate saturation causes different rates of dissociation in the layers. The difference alters the overall gas production and also the mechanical-deformation pattern, which leads to loading/ unloading shearing along the interfaces between the layers. Copyright © 2013 Society of Petorlleum Engineers.