A new approach to 'megaprimer' polymerase chain reaction mutagenesis without an intermediate gel purification step

Background  

Site-directed mutagenesis is an efficient method to alter the structure and function of genes. Here we report a rapid and efficient megaprimer-based polymerase chain reaction (PCR) mutagenesis strategy that by-passes any intermediate purification of DNA between two rounds of PCR.     

Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins

Background  

Understanding the adaptive changes that alter the function of proteins during evolution is an important question for biology and medicine. The increasing number of completely sequenced genomes from closely related organisms, as well as individuals within species, facilitates systematic detection of recent selection events by means of comparative genomics.     

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

Background  

Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes.     

Population kinetics during simultaneous infection of insect cells with two different recombinant baculoviruses for the production of rotavirus-like particles

Background  

The simultaneous production of various recombinant proteins in every cell of a culture is often needed for the production of virus-like particles (VLP) or vectors for gene therapy. A common approach for such a purpose is the coinfection of insect cell cultures with different recombinant baculoviruses, each containing one or more recombinant genes. However, scarce information exists regarding kinetics during multiple infections, and to our knowledge, no studies are available on the behavior of the different populations that arise during coinfections. Such information is useful for designing infection strategies that maximize VLP or vector yield. In this work, kinetics of cell populations expressing rotavirus GFPVP2 (infected with bacGFPVP2), VP6 (infected with bacVP6), or both proteins simultaneously (coinfected with both baculoviruses) were followed by flow cytometry.     

HIV,HBV and HCV Coinfection Prevalence in Iran - A Systematic Review and Meta-Analysis

Background

worldwide, hepatitis C and B virus infections (HCV and HCV), are the two most common coinfections with human immunodeficiency virus (HIV) and has become a major threat to the survival of HIV-infected persons. The review aimed to estimate the prevalence of HIV, HBV, HCV, HIV/HCV and HIV/HBV and triple coinfections in different subpopulations in Iran.

Method

Following PRISMA guidelines, we conducted a systematic review and meta-analysis of reports on prevalence of HIV, HBV, HCV and HIV coinfections in different subpopulations in Iran. We systematically reviewed the literature to identify eligible studies from January 1996 to March 2012 in English or Persian/Farsi databases. We extracted the prevalence of HIV antibodies (diagnosed by Elisa confirmed with Western Blot test), HCV antibodies and HBsAg (with confirmatory laboratory test) as the main primary outcome. We reported the prevalence of the three infections and coinfections as point and 95% confidence intervals.

Findings

HIV prevalence varied from %0.00 (95% CI: 0.00–0.003) in the general population to %17.25 (95% CI: 2.94–31.57) in people who inject drugs (PWID). HBV prevalence ranged from % 0.00 (95% CI: 0.00–7.87) in health care workers to % 30.9 (95% CI: 27.88–33.92) in PWID. HCV prevalence ranged from %0.19 (95% CI: 0.00–0.66) in health care workers to %51.46 (95% CI: 34.30–68.62) in PWID. The coinfection of HIV/HBV and also HIV/HCV in the general population and in health care workers was zero, while the most common coinfections were HIV/HCV (10.95%), HIV/HBV (1.88%) and triple infections (1.25%) in PWID.

Conclusions

We found that PWID are severely and disproportionately affected by HIV and the other two infections, HCV and HBV. Screenings of such coinfections need to be reinforced to prevent new infections and also reduce further transmission in their community and to others.     

Developmental dynamics of cone photoreceptors in the eel

Background  

Many fish alter their expressed visual pigments during development. The number of retinal opsins expressed and their type is normally related to the environment in which they live. Eels are known to change the expression of their rod opsins as they mature, but might they also change the expression of their cone opsins?     

Vertical distribution of zooplankton: density dependence and evidence for an ideal free distribution with costs

Background  

In lakes with a deep-water algal maximum, herbivorous zooplankton are faced with a trade-off between high temperature but low food availability in the surface layers and low temperature but sufficient food in deep layers. It has been suggested that zooplankton (Daphnia) faced with this trade-off distribute vertically according to an "Ideal Free Distribution (IFD) with Costs". An experiment has been designed to test the density (competition) dependence of the vertical distribution as this is a basic assumption of IFD theory.     

Latitudinal patterns of egg size and maternal investment trade-offs in reef corals

Aim

The aims were to test the role of temperature in latitudinal patterns of egg size and investigate maternal investment trade-offs among coral taxa.

Location

Global, from 34° S to 34° N.

Time period

1981–2020.

Major taxa studied

Reef coral species from the order Scleractinia.

Methods

We compiled a comprehensive geo-referenced global dataset of egg sizes (diameter or volume) and fecundity (number of eggs per area) for colonial corals (Scleractinia; 123 species, 5359 observations and 39 localities), substantially enhanced by new field collections (>88% of observations). We used Bayesian phylogenetic multilevel models to test for Rass' rule (a hypothesized negative relationship between egg size and temperature); we also included other environmental variables and life history traits. We also tested whether a trade-off exists between egg size and fecundity in broadcast spawning hermaphroditic corals with horizontal symbiont transmission (HHT).

Results

We found a significant relationship between coral egg size and symbiont transmission. Eggs from coral species with vertical symbiont transmission were c. 18.8% smaller than those from species with horizontal symbiont transmission. We also found non-significant relationships between egg size and sea surface temperature (SST) for broadcast spawning corals and between egg size and fecundity specifically for HHT species.

Main conclusions

Contrary to recognized latitudinal patterns of egg size across taxa, our study does not provide support for Rass' rule in corals. Additionally, our findings do not support a maternal investment trade-off between egg size and fecundity for HHT species. Our study used a phylogenetic framework that should be a standard practice when studying interspecific variation, including investigation of maternal investment and identification of the influence of multiple predictors on larval fitness (egg size), in addition to trade-offs affecting propagule influx (fecundity). Both these functional traits are vital and have direct consequences for population maintenance and connectivity in sessile organisms, such as corals.     

The generality of leaf size versus number trade-off in temperate woody species

Background and Aims

Trade-offs are fundamental to life-history theory, and the leaf size vs. number trade-off has recently been suggested to be of importance to our understanding leaf size evolution. The purpose of the present study was to test whether the isometric, negative relationship between leaf size and number found by Kleiman and Aarssen is conserved between plant functional types and between habitats.

Methods

Leaf mass, area and number, and stem mass and volume of current-year shoots were measured for 107 temperate broadleaved woody species at two altitudes on Gongga Mountain, south-west China. The scaling relationships of leaf size (leaf area and mass) vs. (mass- and volume-based) leafing intensity were analysed in relation to leaf habit, leaf form and habitat type. Trait relationships were determined with both a standardized major axis method and a phylogenetically independent comparative method.

Key Results

Significant negative, isometric scaling relationships between leaf size and leafing intensity were found to be consistently conserved across species independent of leaf habit, leaf form and habitat type. In particular, about 99 % of the variation in leaf mass across species could be accounted for by proportional variation in mass-based leafing intensity. The negative correlations between leaf size and leafing intensity were also observed across correlated evolutionary divergences. However, evergreen species had a lower y-intercept in the scaling relationships of leaf area vs. leafing intensity than deciduous species. This indicated that leaf area was smaller in the evergreen species at a given leafing intensity than in the deciduous species. The compound-leaved deciduous species were observed usually to have significant upper shifts along the common slopes relative to the simple-leaved species, which suggested that the compound-leaved species were larger in leaf size but smaller in leafing intensity than their simple counterparts. No significant difference was found in the scaling relationships between altitudes.

Conclusions

The negative, isometric scaling relationship between leaf size and number is largely conserved in plants, while the leaf size vs. number trade-off can be mediated by leaf properties. The isometry of the leaf size vs. number relationship may simply result from a biomass allocation trade-off, although a twig size constraint may provide an alternative mechanism.Key words: Allometry, trade-off, leafing intensity, leaf size, leaf habit, leaf form     

Rational design of modular circuits for gene transcription: A test of the bottom-up approach

Background  

Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR) and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design.     

Unlocking Short Read Sequencing for Metagenomics

Background

Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved.

Methodology/Principal Findings

We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.

Conclusions/Significance

This strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing.     

An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional data

Background  

Generally speaking, different classifiers tend to work well for certain types of data and conversely, it is usually not known a priori which algorithm will be optimal in any given classification application. In addition, for most classification problems, selecting the best performing classification algorithm amongst a number of competing algorithms is a difficult task for various reasons. As for example, the order of performance may depend on the performance measure employed for such a comparison. In this work, we present a novel adaptive ensemble classifier constructed by combining bagging and rank aggregation that is capable of adaptively changing its performance depending on the type of data that is being classified. The attractive feature of the proposed classifier is its multi-objective nature where the classification results can be simultaneously optimized with respect to several performance measures, for example, accuracy, sensitivity and specificity. We also show that our somewhat complex strategy has better predictive performance as judged on test samples than a more naive approach that attempts to directly identify the optimal classifier based on the training data performances of the individual classifiers.     

Individual variation evades the Prisoner's Dilemma

Background  

The Prisoner's Dilemma (PD) is a widely used paradigm to study cooperation in evolutionary biology, as well as in fields as diverse as moral philosophy, sociology, economics and politics. Players are typically assumed to have fixed payoffs for adopting certain strategies, which depend only on the strategy played by the opponent. However, fixed payoffs are not realistic in nature. Utility functions and the associated payoffs from pursuing certain strategies vary among members of a population with numerous factors. In biology such factors include size, age, social status and expected life span; in economics they include socio-economic status, personal preference and past experience; and in politics they include ideology, political interests and public support. Thus, no outcome is identical for any two different players.     

Detection and quantification of Lyme spirochetes using sensitive and specific molecular beacon probes

Background  

Lyme disease, caused by Borrelia burgdorferi, affects a large number of people in both the USA and Europe. The mouse is a natural host for this spirochete and is widely used as a model system to study Lyme pathogenesis mechanisms. Since disease manifestations often depend upon the spirochete burden in a particular tissue, it is critical to accurately measure the bacterial number in infected tissues. The current methods either lack sensitivity and specificity (SYBR Green), or require independent analysis of samples in parallel to quantitate host and bacterial DNA (TaqMan). We have developed a novel molecular beacon-based convenient multiplex real-time quantitative PCR assay to identify and detect small numbers of B. burgdorferi in infected mouse tissues.     

Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease

Background  

Genomic functional information is valuable for biomedical research. However, such information frequently needs to be extracted from the scientific literature and structured in order to be exploited by automatic systems. Natural language processing is increasingly used for this purpose although it inherently involves errors. A postprocessing strategy that selects relations most likely to be correct is proposed and evaluated on the output of SemGen, a system that extracts semantic predications on the etiology of genetic diseases. Based on the number of intervening phrases between an argument and its predicate, we defined a heuristic strategy to filter the extracted semantic relations according to their likelihood of being correct. We also applied this strategy to relations identified with co-occurrence processing. Finally, we exploited postprocessed SemGen predications to investigate the genetic basis of Parkinson's disease.     

Robust test method for time-course microarray experiments

Background  

In a time-course microarray experiment, the expression level for each gene is observed across a number of time-points in order to characterize the temporal trajectories of the gene-expression profiles. For many of these experiments, the scientific aim is the identification of genes for which the trajectories depend on an experimental or phenotypic factor. There is an extensive recent body of literature on statistical methodology for addressing this analytical problem. Most of the existing methods are based on estimating the time-course trajectories using parametric or non-parametric mean regression methods. The sensitivity of these regression methods to outliers, an issue that is well documented in the statistical literature, should be of concern when analyzing microarray data.     

Correlation analysis of life cycle impact assessment indicators measuring resource use

Introduction  

Even though the necessity of a sustainable use of natural resources is widely accepted, there is neither consensus on how “resource use” is clearly defined nor how it should be measured. Depending on the definition, it can comprise raw material consumption only or the consumption and pollution of natural resources. Consequently, lots of indicators can be applied, and the result of a life cycle assessment study aiming to quantify resource use seems to depend on the selection of impact categories. Therefore, this paper aims at analyzing life cycle impact assessment results obtained by means of several indicators to check if different indexes lead to similar results and if the number of indicators can be reduced.     

Spectrum of disease-causing mutations in protein secondary structures

Background  

Most genetic disorders are linked to missense mutations as even minor changes in the size or properties of an amino acid can alter or prevent the function of the protein. Further, the effect of a mutation is also dependent on the sequence and structure context of the alteration.     

The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families

Background -  

Enzymes that depend on vitamin B6 (and in particular on its metabolically active form, pyridoxal 5'-phosphate, PLP) are of great relevance to biology and medicine, as they catalyze a wide variety of biochemical reactions mainly involving amino acid substrates. Although PLP-dependent enzymes belong to a small number of independent evolutionary lineages, they encompass more than 160 distinct catalytic functions, thus representing a striking example of divergent evolution. The importance and remarkable versatility of these enzymes, as well as the difficulties in their functional classification, create a need for an integrated source of information about them.