A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings

Background

In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have evaluated the discriminatory power and clustering concordance of a novel and simple genotyping approach, combining spoligotyping with pncA sequencing (SpoNC), against two well-established methods: IS6110-RFLP and 24-loci MIRU-VNTR.

Methods

A total of 216 MDR-TB isolates collected from January to June 2010 from the NHLS Central TB referral laboratory in Braamfontein, Johannesburg, representing a diversity of strains from South Africa, were included. The isolates were submitted for genotyping, pncA sequencing and analysis to the Centre for Tuberculosis in South Africa and the Public Health Research Institute Tuberculosis Center at Rutgers University in the United States. Clustering rates, Hunter-Gaston Discriminatory Indexes (HGI) and Wallace coefficients were compared between the methods.

Results

Overall clustering rates were high by both IS6110-RFLP (52.8%) and MIRU-VNTR (45.8%), indicative of on-going transmission. Both 24-loci MIRU-VNTR and IS6110-RFLP had similar HGI (0.972 and 0.973, respectively), with close numbers of unique profiles (87 vs. 70), clustered isolates (129 vs. 146), and cluster sizes (2 to 26 vs. 2 to 25 isolates). Spoligotyping alone was the least discriminatory (80.1% clustering, HGI 0.903), with 28 unique types. However, the discriminatory power of spoligotyping was improved when combined with pncA sequencing using the SpoNC approach (61.8% clustering, HGI 0.958). A high proportion of MDR-TB isolates had mutations in pncA (68%, n = 145), and pncA mutations were significantly associated with clustering (p = 0.007 and p = 0.0013 by 24-loci MIRU-VNTR and IS6110-RFLP, respectively), suggesting high rates of resistance to pyrazinamide among all MDR-TB cases and particularly among clustered cases.

Conclusion

We conclude that SpoNC provides good discrimination for MDR-TB surveillance and early identification of outbreaks in South Africa, with 24-loci MIRU-VNTR applied for pncA wild-type strains as needed.     

How Physical Disturbance and Nitrogen Addition Affect the Soil Carbon Decomposition?

The decomposition of soil organic carbon (SOC) plays a critical role in regulating atmospheric CO₂ concentrations and climate dynamics. However, the mechanisms and factors controlling SOC decomposition are still not fully understood. Here, we conducted a 60 days incubation experiment to test the effects of physical disturbance and nitrogen (N) addition on SOC decomposition. N addition increased the concentration of NO₃^- by 51% in the soil, but had little effect on the concentration of NH₄⁺. N addition inhibited SOC decomposition, but such an effect differed between disturbed and undisturbed soils. In disturbed and undisturbed soils, application of N decreased SOC decomposition by 37% and 15%, respectively. One possible explanation is that extra N input suppressed microbial N mining and/or increased the stability of soil organic matter by promoting the formation of soil aggregates and incorporating part of the inorganic N into organic matter, and consequently decreased microbial mineralization of soil organic matter. Physical disturbance intensified the inhibition of N on SOC decomposition, likely because physical disturbance allowed the added N to be better exposed to soil microbes and consequently increased the availability of added N. We conclude that physical disturbance and N play important roles in modulating the stability of SOC.     

G-protein gamma subunit GNG11 strongly regulates cellular senescence

GNG11 is a member of the gamma subunit family of heteromeric G-protein, but its function is entirely unknown. Here, we successfully characterized its specific role in cellular senescence. We have found that overexpression of GNG11 immediately induces cellular senescence in normal human fibroblasts, and its down-regulation by antisense cDNA extends their lifespan. Surprisingly, this gene is very rapidly induced by senescence-inducing agents such as H(2)O(2). Furthermore, overexpression of GNG11 activated ERK1/2 of the MAP kinase family, but did not Ras. Collectively, these results suggest a novel senescence pathway mediated by GNG11 in response to environmental cues.     

Aberrant promoter methylation and reduced expression of p16 gene in esophageal squamous cell carcinoma from Kashmir valley: a high-risk area

Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent cancer in Jammu and Kashmir region of India and has multi-factorial etiology involving dietary habits, genetic factors, and gene environmental interactions. Inactivation of the p16 gene expression by aberrant promoter methylation plays an important role in the progression of esophageal carcinoma. In the present investigation, we have studied the role of p16 promoter methylation in 69 histopathologically confirmed ESCC tissues and compared it with corresponding normal adjacent tissues for DNA methylation in the CpG island in the p16 promoter region by methylation-specific polymerase chain reaction (MSP) and p16 protein expression by immunoblotting. The results showed loss of p16 expression in 67% (46/69) of tumor tissues compared to only 3% in control tissues (2/69). Promoter methylation was observed in 52% (36/69) of tumor tissues and it gradually increased with the increasing severity of histological grades of the cancer (P = 0.0001). Loss of p16 expression with promoter methylation was observed in 26 of 36 cases (72%). Analysis of patients dietary habits revealed a strong association between promoter methylation and high consumption of hot salted tea (P < 0.05) which is a most favourite drink commonly consumed by Kashmiri people.     

Some results on translation invariance in the human visual system

Four experiments were conducted to study the nature of visual translation invariance in humans. In all the experiments, subjects were trained to discriminate between a previously unknown target and two non-target distractors presented at a fixed retinal location to one side of the fixation point. In a subsequent test phase, this performance was compared with the performance when the patterns were presented either centrally at the fixation point or at a location on the other side of the fixation point, opposite to the location where the patterns were learned, but where acuity was identical to what it was at the learned location. Two different experimental paradigms were used. One used an eye movement control device (Experiment 1) to ensure the eye could not move relative to the patterns to be learned. In the other three experiments, presentation duration of the patterns was restricted to a short enough period to preclude eye movements. During the training period in Experiments 1 and 2, presentation location of the patterns was centered at 2.4 deg in the periphery, whereas in Experiments 3 and 4 presentation eccentricity was reduced to 0.86 and 0.49 deg. In all four experiments performance dropped when the pattern had to be recognized at new test positions. This result suggests that the visual system does not apply a global transposition transformation to the retinal image to compensate for translations. We propose that, instead, it decomposes the image into simple features which themselves are more-or-less translation invariant. If in a given task, patterns can be discriminated using these simple features, then translation invariance will occur. If not, then translation invariance will fail or be incomplete.     

Salinity tolerance of Gambusia affinis (Baird & Girard) and Heteropneustes fossilis (Bloch)

The present paper describes the results of a study on the salinity tolerance of two freshwater fishes, Gambusia affinis (Baird & Girard) and Heteropneustes fossilis (Bloch). The two species were treated with various concentrations of sea water and three most common salts found in the saline waters of Iraq, namely sodium chloride, calcium chloride and potassium chloride. The mortality rates following these treatments were recorded. Both species showed the highest degree of resistance for sea water and sodium chloride, and the lowest degree of tolerance to potassium chloride. Gambusia affinis was more resistant to these salts and sea water than H. fossilis .     

Cloning and characterization of SK2 channel from chicken short hair cells

In the inner ear of birds, as in mammals, reptiles and amphibians, acetylcholine released from efferent neurons inhibits hair cells via activation of an apamin-sensitive, calcium-dependent potassium current. The particular potassium channel involved in avian hair cell inhibition is unknown. In this study, we cloned a small-conductance, calcium-sensitive potassium channel (gSK2) from a chicken cochlear library. Using RT-PCR, we demonstrated the presence of gSK2 mRNA in cochlear hair cells. Electrophysiological studies on transfected HEK293 cells showed that gSK2 channels have a conductance of approximately 16 pS and a half-maximal calcium activation concentration of 0.74±0.17 M. The expressed channels were blocked by apamin (IC₅₀=73.3±5.0 pM) and d-tubocurarine (IC₅₀=7.6±1.0 M), but were insensitive to charybdotoxin. These characteristics are consistent with those reported for acetylcholine-induced potassium currents of isolated chicken hair cells, suggesting that gSK2 is involved in efferent inhibition of chicken inner ear. These findings imply that the molecular mechanisms of inhibition are conserved in hair cells of all vertebrates.     

Syntax at Hand: Common Syntactic Structures for Actions and Language

Evidence that the motor and the linguistic systems share common syntactic representations would open new perspectives on language evolution. Here, crossing disciplinary boundaries, we explore potential parallels between the structure of simple actions and that of sentences. First, examining Typically Developing (TD) children displacing a bottle with or without knowledge of its weight prior to movement onset, we provide kinematic evidence that the sub-phases of this displacing action (reaching + moving the bottle) manifest a structure akin to linguistic embedded dependencies. Then, using the same motor task, we reveal that children suffering from specific language impairment (SLI), whose core deficit affects syntactic embedding and dependencies, manifest specific structural motor anomalies parallel to their linguistic deficits. In contrast to TD children, SLI children performed the displacing-action as if its sub-phases were juxtaposed rather than embedded. The specificity of SLI’s structural motor deficit was confirmed by testing an additional control group: Fragile-X Syndrome patients, whose language capacity, though delayed, comparatively spares embedded dependencies, displayed slower but structurally normal motor performances. By identifying the presence of structural representations and dependency computations in the motor system and by showing their selective deficit in SLI patients, these findings point to a potential motor origin for language syntax.