A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani

Visceral leishmaniasis or kala azar is the most severe form of leishmaniasis and is caused by the protozoan parasite Leishmania donovani. There is no published report on L. donovani genome sequence available till date, although the genome sequences of three related Leishmania species are already available. Thus, we took a proteogenomic approach to identify proteins from two different life stages of L. donovani. From our analysis of the promastigote (insect) and amastigote (human) stages of L. donovani, we identified a total of 22,322 unique peptides from a homology-based search against proteins from three Leishmania species. These peptides were assigned to 3711 proteins in L. infantum, 3287 proteins in L. major, and 2433 proteins in L. braziliensis. Of the 3711 L. donovani proteins that were identified, the expression of 1387 proteins was detectable in both life stages of the parasite, while 901 and 1423 proteins were identified only in promastigotes and amastigotes life stages, respectively. In addition, we also identified 13 N-terminally and one C-terminally extended proteins based on the proteomic data search against the six-frame translated genome of the three related Leishmania species. Here, we report results from proteomic profiling of L. donovani, an organism with an unsequenced genome.     

Discovery and use of single nucleotide polymorphic (SNP) markers in Jatropha curcas L.

Various programs for genetic improvement in oil yield of the biofuel plant Jatropha curcas L. are currently in progress worldwide. In order to develop strategies for genetic improvement, it is important to estimate the degree of diversity at the genetic level among various genotypes of J. curcas. High-throughput sequencing of complexity-reduced nuclear genomic DNA of J. curcas coupled with computational analysis discovered 2,482 informative single nucleotide polymorphisms (SNPs). Genotyping of selective SNPs among 148 global collections of J. curcas lines and further diversity analysis through NTSYS-pc, DARwin and Structure?2.0 software revealed that a narrow level of genetic diversity existed among the indigenous genotypes as compared to the exotic genotypes of J. curcas. The level of marker informativeness along with distance-based and Bayesian clustering revealed grouping of the accession from Togo (Africa) with various Indian accessions at K?=?4 and K?=?5 values (where K represents the number of populations). The diverse accessions identified in the study will be of further use in genetic improvement of J. curcas through quantitative trait loci and association mapping.     

Improved Recovery of Bacillus Spores from Nonporous Surfaces with Cotton Swabs over Foam,Nylon, or Polyester,and the Role of Hydrophilicity of Cotton in Governing the Recovery Efficiency

Evaluating different swabbing materials for spore recovery efficiency (RE) from steel surfaces, we recorded the maximum RE (71%) of 10⁷ Bacillus subtilis spores with Tulips cotton buds, followed by Johnson''s cotton buds and standard Hi-Media cotton, polyester, nylon, and foam (23%) swabs. Among cotton swabs, instant water-absorbing capacity or the hydrophilicity index appeared to be the major indicator of RE, as determined by testing three more brands. Tulips swabs worked efficiently across diverse nonporous surfaces and on different Bacillus spp., registering 65 to 77% RE.     

Modeling of ferrous iron oxidation by a Leptospirillum ferrooxidans-dominated chemostat culture

The objective of this study was to evaluate a direct classical bioengineering approach to model data generated from continuous bio-oxidation of Fe(2+) by a Leptospirillum ferrooxidans-dominated culture fed with either 9 g or 18 g Fe(2+) L(-1) under chemostat conditions (dilution rates were between 0.051 and 0.094 h(-1)). The basic Monod and Pirt equations have successfully been integrated in an overall mass balance procedure, which has not been previously presented in this detail for Fe(2+) oxidation. To ensure chemostat conditions, it was found that the range of the dilution rates had to be limited. A too long retention time might cause starvation or non-negligible death rate whereas, a too short retention time may cause a significant alteration in solution chemistry and culture composition. Modeling of the experimental data suggested that the kinetic- and yield parameters changed with the overall solution composition. However, for respective feed solutions only minor changes of ionic strength and chemical speciation can be expected within the studied range of dilution rates, which was confirmed by thermodynamic calculations and conductivity measurements. The presented model also suggests that the apparent Fe(3+) inhibition on specific Fe(2+) utilization rate was a direct consequence of the declining biomass yield on Fe(2+) due to growth uncoupled Fe(2+) oxidation when the dilution rate was decreased. The model suggested that the maintenance activities contributed up to 90% of the maximum specific Fe(2+) utilization rate, which appears close to the critical dilution rate. Biotechnol. Bioeng. 2008;99: 378-389. (c) 2007 Wiley Periodicals, Inc.     

An enhanced sensitivity methyl <Superscript>1</Superscript>H triple-quantum pulse scheme for measuring diffusion constants of macromolecules

We present a pulse scheme that exploits methyl ¹H triple-quantum (TQ) coherences for the measurement of diffusion rates of slowly diffusing molecules in solution. It is based on the well-known stimulated echo experiment, with encoding and decoding of TQ coherences. The size of quantifiable diffusion coefficients is thus lowered by an order of magnitude with respect to single-quantum (SQ) approaches. Notably, the sensitivity of the scheme is high, approximately ¾ that of the corresponding single quantum experiment, neglecting relaxation losses, and on the order of a factor of 4 more sensitive than a previously published sequence for AX₃ spin systems (Zheng et al. in JMR 198:271–274, 2009) for molecules that are only ¹³C labeled at the methyl carbon position. Diffusion coefficients measured from TQ- and SQ-based experiments recorded on a range of protein samples are in excellent agreement. We present an application of this technique to the study of phase-separated proteins where protein concentrations in the condensed phase can exceed 400 mg/mL, diffusion coefficients can be as low as ~10^?9 cm²s^?1 and traditional SQ experiments fail.     

Metabolic basis of HIV-lipodystrophy syndrome

Human immunodeficiency virus (HIV)-lipodystrophy syndrome (HLS) is characterized by hypertriglyceridemia, low high-density lipoprotein-cholesterol, lipoatrophy, and central adiposity. We investigated fasting lipid metabolism in six men with HLS and six non-HIV-infected controls. Compared with controls, HLS patients had lower fat mass (15.9 +/- 1.3 vs. 22.3 +/- 1.7 kg, P < 0.05) but higher plasma glycerol rate of appearance (R(a)), an index of total lipolysis (964.71 +/- 103.33 vs. 611.08 +/- 63.38 micromol x kg fat(-1) x h(-1), P < 0.05), R(a) palmitate, an index of net lipolysis (731.49 +/- 72.36 vs. 419.72 +/- 33.78 micromol x kg fat(-1) x h(-1), P < 0.01), R(a) free fatty acids (2,094.74 +/- 182.18 vs. 1,470.87 +/- 202.80 micromol x kg fat(-1) x h(-1), P < 0.05), and rates of intra-adipocyte (799.40 +/- 157.69 vs. 362.36 +/- 74.87 micromol x kg fat(-1) x h(-1), P < 0.01) and intrahepatic fatty acid reesterification (1,352.08 +/- 123.90 vs. 955.56 +/- 124.09 micromol x kg fat(-1) x h(-1), P < 0.05). Resting energy expenditure was increased in HLS patients (30.51 +/- 2.53 vs. 25.34 +/- 1.04 kcal x kg lean body mass(-1) x day(-1), P < 0.05), associated with increased non-plasma-derived fatty acid oxidation (139.04 +/- 24.17 vs. 47.87 +/- 18.81 micromol x kg lean body mass(-1) x min(-1), P < 0.02). The lipoatrophy observed in HIV lipodystrophy is associated with accelerated lipolysis. Increased hepatic reesterification promotes the hypertriglyceridemia observed in this syndrome.