The influence of reduced oxygen availability on gene expression in laboratory (H37Rv) and clinical strains (S7 and S10) of Mycobacterium tuberculosis

Mycobacterium tuberculosis has the ability to persist within the host in a dormant stage. One important condition believed to contribute to dormancy is reduced access to oxygen known as hypoxia. However, the response of M. tuberculosis to such hypoxia condition is not fully characterized. Virtually all dormant models against tuberculosis tested in animals used laboratory strain H37Rv or Erdman strain. But major outbreaks of tuberculosis (TB) occur with the strains that have widely different genotypes and phenotypes compared to H37Rv. In this study, we used a custom oligonucleotide microarray to determine the overall transcriptional response of laboratory strain (H37Rv) and most prevalent clinical strains (S7 and S10) of M. tuberculosis from South India to hypoxia. Analysis of microarray results revealed that a total of 1161 genes were differentially regulated (>= 1.5 fold change) in H37Rv, among them 659 genes upregulated and 502 genes down regulated. Microarray data of clinical isolates showed that a total of 790 genes were differentially regulated in S7 among which 453 genes were upregulated and 337 down regulated. Interestingly, numerous genes were also differentially regulated in S10 (total 2805 genes) of which 1463 genes upregulated and 1342 genes down regulated during reduced oxygen condition (Wayne's model). One hundred and thirty-four genes were found common and upregulated among all three strains (H37Rv, S7, and S10) and can be targeted for drug/vaccine development against TB. (C) 2015 Published by Elsevier B.V.

An in vitro transposon system for highly regulated gene expression: construction of Escherichia coli strains with arabinose-dependent growth at low temperatures.

Placing a gene of interest under the control of an inducible promoter greatly aids the purification, localization and functional analysis of proteins but usually requires the sub-cloning of the gene of interest into an appropriate expression vector. Here, we describe an alternative approach employing in vitro transposition of Tn Omega P(BAD) to place the highly regulable, arabinose inducible P(BAD) promoter upstream of the gene to be expressed. The method is rapid, simple and facilitates the optimization of expression by producing constructs with variable distances between the P(BAD) promoter and the gene. To illustrate the use of this approach, we describe the construction of a strain of Escherichia coli in which growth at low temperatures on solid media is dependent on threshold levels of arabinose. Other uses of the transposable promoter are also discussed.

Performance of low density parity check codes as a function of actual and assumed noise levels

We investigate how sensitive Gallager's codes are, when decoded by the sum-product algorithm, to the assumed noise level. We have found a remarkably simple function that fits the empirical results as a function of the actual noise level at both high and low noise levels. © 2004 Elsevier B.V.

Performance of low density parity check codes as a function of actual and assumed noise levels

We investigate how sensitive Gallager's codes are, when decoded by the sum-product algorithm, to the assumed noise level. We have found a remarkably simple function that fits the empirical results as a function of the actual noise level at both high and low noise levels. ©2003 Published by Elsevier Science B. V.

Accommodation of large plastic strains and defect accumulation in nanocrystalline Ni grains

A transmission electron microscopy (TEM) study has been carried out to uncover how dislocations and twins accommodate large plastic strains and accumulate in very small nanocrystalline Ni grains during low-temperature deformation. We illustrate dislocation patterns that suggest preferential deformation and nonuniform defect storage inside the nanocrystalline grain. Dislocations are present in individual and dipole configurations. Most dislocations are of the 60 degrees type and pile up on (111) slip planes. Various deformation responses, in the forms of dislocations and twinning, may simultaneously occur inside a nanocrystalline grain. Evidence for twin boundary migration has been obtained. The rearrangement and organization of dislocations, sometimes interacting with the twins, lead to the formation of subgrain boundaries, subdividing the nanograin into mosaic domain structures. The observation of strain (deformation)-induced refinement contrasts with the recently reported stress-assisted grain growth in nanocrystalline metals and has implications for understanding the stability and deformation behavior of these highly nonequilibrium materials.

Local stresses and strains in axially cracked cylindrical shells

A perturbation solution is obtained for the local stress-strain fields in an axially cracked cylindrical shell. The tenth-order differential equations are used that take into account the transverse shear deformation. The perturbation of a curvature parameter, λ, is employed, where . The stress intensity factors for finite size cylindrical shells subjected to bending and internal pressure are evaluated. Sufficient accuracy can be obtained without using fine mesh sizes in regions near the crack tip. Also analyzed are the influence of cylinder diameter and shearing stiffness on bulging.

Comparative Response of Two Hydrilla Strains to Fluridone

Experiments were conducted in a controlled-environmental growth chamber to evaluate the response of two strains of the invasive submersed plant Hydrilla verticillata (L.f.) Royle to fluridone (1-methyl-3-phenyl-5-[3-trifluoromethyl)phenyl]- 4(1H)-pyridinone). (PDF has 6 pages.)

Policies on release of improved fish strains in China

Since 1991, the certification, release and maintenance of new species for aquaculture have become part of the national policy in China. During the past 15 years, this policy has been conducted and improved and has begun to show its significant role in Chinese fisheries. This paper describes the updated system of certification, release and maintenance of new species for aquaculture in China.

Maintaining the "public good" nature of improved fish strains: dissemination of knowledge and materials

Many sources of information that discuss currents problems of food security point to the importance of farmed fish as an ideal food source that can be grown by poor farmers, (Asian Development Bank 2004). Furthermore, the development of improved strains of fish suitable for low-input aquaculture such as Tilapia, has demonstrated the feasibility of an approach that combines “cutting edge science” with accessible technology, as a means for improving the nutrition and livelihoods of both the urban poor and poor farmers in developing countries (Mair et al. 2002). However, the use of improved strains of fish as a means of reducing hunger and improving livelihoods has proved to be difficult to sustain, especially as a public good, when external (development) funding sources devoted to this area are minimal1. In addition, the more complicated problem of delivery of an aquaculture system, not just improved fish strains and the technology, can present difficulties and may go explicitly unrecognized (from Sissel Rogne, as cited by Silje Rem 2002). Thus, the involvement of private partners has featured prominently in the strategy for transferring to the public technology related to improved Tilapia strains. Partnering with the private sector in delivery schemes to the poor should take into account both the public goods aspect and the requirement that the traits selected for breeding “improved” strains meet the actual needs of the resource poor farmer. Other dissemination approaches involving the public sector may require a large investment in capacity building. However, the use of public sector institutions as delivery agents encourages the maintaining of the “public good” nature of the products.

Use of genetic data to assess the uncertainty in stock assessments due to the assumed stock structure: the case of albacore (Thunnus alalunga) from the Atlantic Ocean

Stock assessments can be problematic because of uncertainties associated with the data or because of simplified assumptions made when modeling biological processes (Rosenberg and Restrepo, 1995). For example, the common assumption in stock assessments that stocks are homogeneous and discrete (i.e., there is no migration between the stocks) is not necessarily true (Kell et al., 2004a, 2004b).

Progress toward a global genealogy of common carp (Cyprinus carpio L.) strains using mitochondrial nucleotide sequences data

As part of a study of genetic variation in the Vietnamese strains of the common carp (Cyprinus carpio L.) using direct DNA sequencing of mitochondrial control and ATPase6/8 gene regions, samples from a number of other countries were analyzed for comparison. Results show that the levels of sequence divergence in common carp is low on a global scale, with the Asian carp having the highest diversity while Koi and European carp are invariant. A genealogical analysis supports a close relationship among Vietnamese, Koi, Chinese Color and, to a lesser extent, European carp. Koi carp appear to have originated from a strain of Chinese red carp. There is considerable scope to extend this research through the analysis of additional samples of carp from around the world, especially from China, in order to generate a comprehensive global genealogy of common carp strains.