Susceptibility of south Indian strains of Mycobacterium tuberculosis to tuberactinomycin

A total of 114 strains of Mycobacterium tuberculosis isolated from sputum samples of 114 patients of pulmonary tuberculosis in south India, were coded and tested for their in vitro susceptibility to tuberactinomycin (Tum) incorporated in Lowenstein-Jensen (LJ) medium. Of these strains, 95 (83.3%) and 15 (13.2%) were susceptible to Tum at 25 and 50 mg/l respectively. Only 4 (3.5%) strains were inhibited at 100 mg/l or more. Of the 37 drug sensitive strains, 2 (5.4%) were not susceptible to Tum at 25 mg/l compared to 17 (22.1%) of 77 strains-resistant to one or more of antituberculosis drugs (P <0.02). The drug susceptibility pattern of the strains revealed that there was no significant association of resistance between Tum and streptomycin or rifampicin or ethambutol or ethionamide or isoniazid. However, 15 (53.6%) of 28 kanamycin (K) resistant strains were not susceptible to Tum at 25 mg/l. This cross resistance between Tum and K was further studied in 24 and 15 K sensitive and resistant strains respectively, by correlating their proportion resistance at 16 mg/l and it was found to have a significant positive correlation (r = 0.55; X0.01)

Use of cetylpyridinium chloride for the storage of sputum samples and isolation of M. tuberculosis

Of 220 sputum specimens collected from pulmonary tuberculosis patients, 85 were culture positive when the sputum aliquots were stored with cetypyridinium chloride (CPC) and processed on 7th day (CPC method), whereas only 70 were culture positive when the aliquots of the same specimens were stored without CPC and processed by sodium hydroxide (NaOH) method. The difference in the culture positivity was statistically significant. The number of positive, cultures obtained by the CPC method (85) was comparable to that obtained by the NaOH method before storage (95) and the difference was not statistically significant

Damage function for historic paper. Part I: Fitness for use

Background In heritage science literature and in preventive conservation practice, damage functions are used to model material behaviour and specifically damage (unacceptable change), as a result of the presence of a stressor over time. For such functions to be of use in the context of collection management, it is important to define a range of parameters, such as who the stakeholders are (e.g. the public, curators, researchers), the mode of use (e.g. display, storage, manual handling), the long-term planning horizon (i.e. when in the future it is deemed acceptable for an item to become damaged or unfit for use), and what the threshold of damage is, i.e. extent of physical change assessed as damage. Results In this paper, we explore the threshold of fitness for use for archival and library paper documents used for display or reading in the context of access in reading rooms by the general public. Change is considered in the context of discolouration and mechanical deterioration such as tears and missing pieces: forms of physical deterioration that accumulate with time in libraries and archives. We also explore whether the threshold fitness for use is defined differently for objects perceived to be of different value, and for different modes of use. The data were collected in a series of fitness-for-use workshops carried out with readers/visitors in heritage institutions using principles of Design of Experiments. Conclusions The results show that when no particular value is pre-assigned to an archival or library document, missing pieces influenced readers/visitors’ subjective judgements of fitness-for-use to a greater extent than did discolouration and tears (which had little or no influence). This finding was most apparent in the display context in comparison to the reading room context. The finding also best applied when readers/visitors were not given a value scenario (in comparison to when they were asked to think about the document having personal or historic value). It can be estimated that, in general, items become unfit when text is evidently missing. However, if the visitor/reader is prompted to think of a document in terms of its historic value, then change in a document has little impact on fitness for use

Lytic Efficiency of Mycobacteriophages

Abstract: Mycobacteriophages D29 and TM4 are the two virulent phages widely used for the study of mycobacterial genetics. Both the phages are capable of killing Mycobacterium tuberculosis but the efficiency of these phages in killing has not been evaluated and compared. There are reports based on codon usage analysis where TM4 is predicted to be a better killing phage over D29 which corroborated with the whole genome in silico analysis. In addition a kill assay using 5 wild type virulent mycobacteriophages viz. D29, TM4, I3, Che7 and Che11 was performed to study the killing efficiency of these phages using LRP assay. Based on the results, D29 was found to infect all the 10 clinical strains of M. tuberculosis and significantly reduced RLU at 3 hours and this effect continued up to 24 hours. Thus, D29 is found to have better killing efficiency than TM4 contradicting the earlier predictions. In silico analysis of holin and lysin genes of TM4 and D29 substantiated our findings

Quality indicators in a mycobacteriology laboratory supporting clinical trials for pulmonary tuberculosis

AbstractBackgroundDocumentation of structured quality indicators for mycobacteriology laboratories supporting exclusively controlled clinical trials in pulmonary tuberculosis (PTB) is lacking.ObjectiveTo document laboratory indicators for a solid (Lowenstein–Jensen medium) culture system in a mycobacteriology laboratory for a period of 4years (2007–2010).MethodsThe sputum samples, collected from PTB suspects/patients enrolled in clinical trials, were subjected to fluorescence microscopy, culture and drug sensitivity testing (DST). Data was retrospectively collected from TB laboratory registers and computed using pre-formulated Microsoft Office Excel. Laboratory indicators were calculated and analyzed.ResultsThe number of samples processed in a calendar year varied from 6261 to 10,710. Of the samples processed in a calendar year, specimen contamination (4.8–6.9%), culture positives (78.4–85.1%) among smear positives, smear positives (71.8–79.0%) among culture positive samples, smear negatives among culture negative samples (95.2–96.7%), and average time to report DST results (76–97days) varied as shown in parentheses.ConclusionValues of quality indicators in mycobacteriology laboratories supporting exclusively clinical trials of PTB have to be defined and used for meaningful monitoring of laboratories

Novel Molecular Targets of Azadirachta indica Associated with Inhibition of Tumor Growth in Prostate Cancer

Advanced prostate cancer has significant long-term morbidity, and there is a growing interest in alternative and complimentary forms of therapy that will improve the outcomes of patients. Azadirachta indica (common name: neem) contains multiple active compounds that have potent anti-inflammatory and anticancer properties. The present study investigates the novel targets of the anticancer activity of ethanol extract of neem leaves (EENL) in vitro and evaluates the in vivo efficacy in the prostate cancer models. Analysis of the components in the EENL by mass spectrometry suggests the presence of 2′,3′-dehydrosalannol, 6-desacetyl nimbinene, and nimolinone. Treatment of C4-2B and PC-3M-luc2 prostate cancer cells with EENL inhibited the cell proliferation. Genome-wide expression profiling, using oligonucleotide microarrays, revealed genes differentially expressed with EENL treatment in prostate cancer cells. Functional analysis unveiled that most of the up-regulated genes were associated with cell death, and drug metabolism, and the down-regulated genes were associated with cell cycle, DNA replication, recombination, and repair functions. Quantitative PCR confirmed significant up-regulation of 40 genes and immunoblotting revealed increase in the protein expression levels of HMOX1, AKR1C2, AKR1C3, and AKR1B10. EENL treatment inhibited the growth of C4-2B and PC-3M-luc2 prostate cancer xenografts in nude mice. The suppression of tumor growth is associated with the formation of hyalinized fibrous tumor tissue and the induction of cell death by apoptosis. These results suggest that EENL-containing natural bioactive compounds could have potent anticancer property and the regulation of multiple cellular pathways could exert pleiotrophic effects in prevention and treatment of prostate cancer

GOLPH2 protein expression as a novel tissue biomarker for prostate cancer: implications for tissue-based diagnostics

GOLPH2 is coding the 73-kDa type II Golgi membrane antigen GOLPH2/GP73. Upregulation of GOLPH2 mRNA has been recently reported in expression array analyses of prostate cancer. As GOLPH2 protein expression in prostate tissues is currently unknown, this study aimed at a comprehensive analysis of GOLPH2 protein in benign and malignant prostate lesions. Immunohistochemically detected GOLPH2 protein expression was compared with the basal cell marker p63 and the prostate cancer marker α-methylacyl-CoA racemase (AMACR) in 614 radical prostatectomy specimens. GOLPH2 exhibited a perinuclear Golgi-type staining pattern and was preferentially seen in prostatic gland epithelia. Using a semiquantitative staining intensity score, GOLPH2 expression was significantly higher in prostate cancer glands compared with normal glands (P<0.001). GOLPH2 protein was upregulated in 567 of 614 tumours (92.3%) and AMACR in 583 of 614 tumours (95%) (correlation coefficient 0.113, P=0.005). Importantly, GOLPH2 immunohistochemistry exhibited a lower level of intratumoral heterogeneity (25 vs 45%). Further, GOLPH2 upregulation was detected in 26 of 31 (84%) AMACR-negative prostate cancer cases. These data clearly suggest GOLPH2 as an additional ancillary positive marker for tissue-based diagnosis of prostate cancer

Chemical Characterization of Selected Benchmark Spots for C Sequestration in the Semi-Arid Tropics, India. Global Theme on Agroecosystems Report no. 32

Soil organic carbon (SOC) plays an important role as a source of plant nutrients and in maintaining the soil integrity. Any land use management that increases SOC by removing CO2 from the atmosphere by storing it in the soil, is termed as carbon sequestration. This study was conducted to learn about the role of various agricultural practices on soil nutrient dynamics and its relationship with SOC in various land use systems of semi-arid tropics (SAT). The study area covered 28 SAT benchmark spots, 21 out of which were on black soils and 7 on red soils, covering areas of 15.29 m ha and 6.34 m ha, respectively. Soils were sampled from the benchmark sites/pedons during 2000–03 and processed for chemical analysis. It was observed that irrespective of bioclimatic zones, land use under horticultural and agricultural systems in general, and paddy systems in particular, had maximum content of organic carbon and total N. The soil parameter viz. clay fraction also influenced the total N and total P, and hence organic carbon in black and red soils showed significant positive correlation with total N and P. Results indicated that perennials could sequester carbon better when compared to annual crops. The nutrient stocks and soil organic C and N ratio (carbon/nitrogen C:N), and carbon/phosphorus (C:P) were computed in addition to SOC for the purpose of identifying the maintained soil quality. It was observed that the C:N ratio varied from 16:1 to 22:1 under different zones and it was highest under semi-arid (moist) zones in black soils. Similarly C:P ratio of soils under various bioclimatic zones revealed that it was highest under sub-humid (moist), followed by arid zone and lowest under semiarid zones. The C:N ratio of studied soils under various systems was wider than commonly accepted values reported for other tropical soils. The mean total N content of black soils was 0.042% and in case of red soils it was 0.052%, which corresponds to a minimum threshold level of 0.063% and 0.078% for black and red soils, respectively. Thus within the defined range of C:N ratios, those soils having SOC content of above values was considered along with minimum threshold values of total nitrogen stocks (Mg ha-1) to arrive at the better systems. The minimum values of TN stocks was calculated with the established equation and the values for the corresponding levels of SOC was found to be 1.95 Mg ha-1 for black soils and 2.30 Mg ha-1 for red soils (both the soils types having an average bulk density of 1.5 Mg m-3). Thus the soil total N stocks of systems that were found above the minimum threshold values are considered as better production systems. The nutrient stocks and nutrient ratio in addition to soil organic carbon was used as the main criteria to develop the soil C:N index. The index varied between 0.27 and 0.87 with an average of 0.57 under the various systems spread over different bioclimatic zones and soil types. The variation of soil C:N index in different soil types showed that, the fertility status of red soils in terms of SOC and soil nutrient stocks in majority of the pedons was higher as compared to black soils. The variation in the soil C: N index due to bioclimatic zones in black and red soils, showed that semiarid (moist) zone in black soils had the highest soil C: N index while the lowest was observed in sub-humid (moist) zone. As the MAR decreased from 1200 mm to 850 mm, the index increased from 0.30 to 0.38. Thus among the zones, the semi-arid moist was found to sequester more carbon. The variation in soil C:N index in different land use based systems such as horticultural (0.50) and forest systems (0.40) had better C:N index as compared to agricultural system in black soils. In red soils, forest system (0.76) had better C:N index as compared to agricultural system dominated by annual crops. Another significant observation was that permanent fallow land also had the potential to sequester carbon based on the magnitude of soil C:N index. The variation in the soil C:N index with the three major crop based systems studied showed that cereal based cropping systems sequester more carbon as compared to cotton and soybean based systems and can be promoted

Chemical Characterization of Selected Benchmark Spots for C Sequestration in the Semi-Arid Tropics, India

Soil organic carbon (SOC) plays an important role as a source of plant nutrients and in maintaining the soil integrity. Any land use management that increases SOC by removing CO2 from the atmosphere by storing it in the soil, is termed as carbon sequestration. This study was conducted to learn about the role of various agricultural practices on soil nutrient dynamics and its relationship with SOC in various land use systems of semi-arid tropics (SAT). The study area covered 28 SAT benchmark spots, 21 out of which were on black soils and 7 on red soils, covering areas of 15.29 m ha and 6.34 m ha, respectively. Soils were sampled from the benchmark sites/pedons during 2000–03 and processed for chemical analysis. It was observed that irrespective of bioclimatic zones, land use under horticultural and agricultural systems in general, and paddy systems in particular, had maximum content of organic carbon and total N. The soil parameter viz. clay fraction also influenced the total N and total P, and hence organic carbon in black and red soils showed significant positive correlation with total N and P. Results indicated that perennials could sequester carbon better when compared to annual crops. The nutrient stocks and soil organic C and N ratio (carbon/nitrogen C:N), and carbon/phosphorus (C:P) were computed in addition to SOC for the purpose of identifying the maintained soil quality. It was observed that the C:N ratio varied from 16:1 to 22:1 under different zones and it was highest under semi-arid (moist) zones in black soils. Similarly C:P ratio of soils under various bioclimatic zones revealed that it was highest under sub-humid (moist), followed by arid zone and lowest under semiarid zones. The C:N ratio of studied soils under various systems was wider than commonly accepted values reported for other tropical soils. The mean total N content of black soils was 0.042% and in case of red soils it was 0.052%, which corresponds to a minimum threshold level of 0.063% and 0.078% for black and red soils, respectively. Thus within the defined range of C:N ratios, those soils having SOC content of above values was considered along with minimum threshold values of total nitrogen stocks (Mg ha-1) to arrive at the better systems. The minimum values of TN stocks was calculated with the established equation and the values for the corresponding levels of SOC was found to be 1.95 Mg ha-1 for black soils and 2.30 Mg ha-1 for red soils (both the soils types having an average bulk density of 1.5 Mg m-3). Thus the soil total N stocks of systems that were found above the minimum threshold values are considered as better production systems. The nutrient stocks and nutrient ratio in addition to soil organic carbon was used as the main criteria to develop the soil C:N index. The index varied between 0.27 and 0.87 with an average of 0.57 under the various systems spread over different bioclimatic zones and soil types. The variation of soil C:N index in different soil types showed that, the fertility status of red soils in terms of SOC and soil nutrient stocks in majority of the pedons was higher as compared to black soils. The variation in the soil C: N index due to bioclimatic zones in black and red soils, showed that semiarid (moist) zone in black soils had the highest soil C: N index while the lowest was observed in sub-humid (moist) zone. As the MAR decreased from 1200 mm to 850 mm, the index increased from 0.30 to 0.38. Thus among the zones, the semi-arid moist was found to sequester more carbon. The variation in soil C:N index in different land use based systems such as horticultural (0.50) and forest systems (0.40) had better C:N index as compared to agricultural system in black soils. In red soils, forest system (0.76) had better C:N index as compared to agricultural system dominated by annual crops. Another significant observation was that permanent fallow land also had the potential to sequester carbon based on the magnitude of soil C:N index. The variation in the soil C:N index with the three major crop based systems studied showed that cereal based cropping systems sequester more carbon as compared to cotton and soybean based systems and can be promoted

Inferring the conservative causal core of gene regulatory networks

<p>Abstract</p> <p>Background</p> <p>Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically.</p> <p>Results</p> <p>In this paper, we introduce a novel gene regulatory network inference (GRNI) algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from <it>E. coli </it>that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently.</p> <p>Conclusions</p> <p>For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results.</p