CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems

CRISPR/Cas and CRISPR/Cmr immune machineries of archaea and bacteria provide an adaptive and effective defence mechanism directed specifically against viruses and plasmids. Present data suggest that both CRISPR/Cas and Cmr modules can behave like integral genetic elements. They tend to be located in the more variable regions of chromosomes and are displaced by genome shuffling mechanisms including transposition. CRISPR loci may be broken up and dispersed in chromosomes by transposons with the potential for creating genetic novelty. Both CRISPR/Cas and Cmr modules appear to exchange readily between closely related organisms where they may be subjected to strong selective pressure. It is likely that this process occurs primarily via conjugative plasmids or chromosomal conjugation. It is inferred that interdomain transfer between archaea and bacteria has occurred, albeit very rarely, despite the significant barriers imposed by their differing conjugative, transcriptional and translational mechanisms. There are parallels between the CRISPR crRNAs and eukaryal siRNAs, most notably to germ cell piRNAs which are directed, with the help of effector proteins, to silence or destroy transposons. No homologous proteins are identifiable at a sequence level between eukaryal siRNA proteins and those of archaeal or bacterial CRISPR/Cas and Cmr modules.

Executive function and attention span in euthymic patients with bipolar 1 disorder

This is a cross sectional comparison study to assess executive function and attention span in euthymic patients with bipolar 1 disorder. It compares the performance of these two cognitive domains in 40 patients with bipolar 1 disorder to that of 40 healthy normal subjects using Trail Making (TMT), Digit Span (Forward and Backward) and Verbal Fluency (VF) tests. The association between demographic, clinical characteristics and performance in all tests were examined. Patients with bipolar illness showed significant impairment with moderate to large effect sizes (VF = 0.67, TMT A = 0.52, TMT B = 0.81, Digit Forward = 0.97, Digit backward = 1.10) in all tasks of executive and attention functioning. These impairments are observed in the absence of active mood symptoms while duration and severity of illness are not found to have an effect on both cognitive domains. Medications received by patients with bipolar disorder have significant association with performance on executive tasks. The results of this study add on to the existing global evidence of cognitive impairment in bipolar illness despite its cross cultural differences. Its presence in the absence of mania, depression or mixed episode indicates that cognitive impairment is stable even after symptoms recovery.

Collective diffusion in colloid-polymer suspensions: relative role of thermodynamics and hydrodynamics

Theories such as the mode coupling theory (MCT) have seen recent success in predicting the kinetic arrest boundaries and resultant flow properties of colloidal suspensions. A key assumption of such theories is that interparticle forces and equilibrium structure control slow dynamics and gelation, not long-time many-body hydrodynamics. Here we report measurements of short-time collective diffusivities of colloid-polymer suspensions aimed at elucidating the relative contributions of hydrodynamics and thermodynamics as a phase transition or gelation boundary is approached. The experimental system is a hard sphere octadecyl silica suspension to which nonadsorbing polystyrene is added. Two different polymer molecular weights are chosen such that they give rise to a liquid-liquid or a gel transition as the colloid volume fraction or polymer concentration is increased. The short-time diffusivities are measured for each polymer molecular weight as a function of polymer concentration and colloid volume fraction. At a fixed polymer molecular weight and concentration, the colloid volume fraction is varied from dilute to concentrated and near the phase separation boundary. It is found for all measured colloid volume fractions that the diffusivities decrease linearly with increasing strength of the polymer-mediated depletion attraction at a fixed polymer molecular weight. Comparisons are made with theoretical predictions in the dilute limit. When the effects of thermodynamics are normalized out by multiplying the measured diffusivities with the suspension structure factor, it is found that the hydrodynamic effects are essentially those of hard spheres independent of the range and strength of depletion attraction.

Four newly isolated fuselloviruses from extreme geothermal environments reveal unusual morphologies and a possible interviral recombination mechanism

Spindle-shaped virus-like particles are abundant in extreme geothermal environments, from which five spindle-shaped viral species have been isolated to date. They infect members of the hyperthermophilic archaeal genus Sulfolobus, and constitute the Fuselloviridae, a family of double-stranded DNA viruses. Here we present four new members of this family, all from terrestrial acidic hot springs. Two of the new viruses exhibit a novel morphotype for their proposed attachment structures, and specific features of their genome sequences strongly suggest the identity of the host-attachment protein. All fuselloviral genomes are highly conserved at the nucleotide level, although the regions of conservation differ between virus-pairs, consistent with a high frequency of homologous recombination having occurred between them. We propose a fuselloviral specific mechanism for interviral recombination, and show that the spacers of the Sulfolobus CRISPR antiviral system are not biased to the highly similar regions of the fusellovirus genomes.

High-risk behaviours among juvenile prison inmates in Pakistan

OBJECTIVES

To assess the sexual- and drug-use-related risk behaviours of male juvenile detainees in Karachi, Pakistan.

DESIGN

Cross-sectional study.

METHODS

A cross-sectional study was conducted of prison inmates aged 15-21 years in Karachi Juvenile Prison in 2002. In total, 321 inmates were interviewed about sexual orientation and behaviours, and knowledge about human immunodeficiency virus (HIV) and sexually transmitted infections (STIs). Urine specimens were collected and tested for Chlamydia trachomatis and Neisseria gonorrhoeae using ligase chain reaction.

RESULTS

A substantial proportion (n=111, 34.6%) of the participants were sexually active. Sixty-two (19%) and 67 (21%) had had sex with a male or female before incarceration, respectively. Twenty-seven (8.4%) participants had an STI, and 50% of the 109 sexually active participants had had multiple sexual partners. Use of addictive substances was associated with sexual activity. The mean knowledge score computed from the sum of 16 items was 4.7, with a median of 2.9. A large proportion (40%) of participants knew about condoms, but very few (3.4%) had ever used one. The mean+/-standard deviation risk score from nine items was 2.4+/-1.7. On the basis of behavioural and biological markers, 117 (36.4%) participants had high-risk behaviour. In multivariate logistic regression analysis, knowledge, risk perception and age were predictive of higher risk.

CONCLUSIONS

HIV risk behaviours are common among adolescent inmates. Although inmates do have knowledge about modes of transmission and condom use, the use of condoms is significantly low. Interventions are needed for behavioural change among this group.

Recurrent multifocal primary amyloidosis of urinary bladder

Primary localized amyloidosis of bladder is rare. We report a case of recurrence of multifocal primary amyloidosis of urinary bladder. Cystoscopy revealed a diffuse left lateral wall lesion with normal surrounding mucosa. Histopathological examination of the specimen revealed urinary bladder amyloidosis with negative surgical margins. Recurrent urinary bladder amyloidosis was confirmed 3 months after the first resection. Close follow-up is recommended.

Syndromic management training for non-formal care providers in Pakistan improves quality of care for sexually transmitted diseases STD care: a randomized clinical trial

We conducted a randomized, controlled, three-armed trial to assess whether training in syndromic management, with provision of packets, could improve the quality of STD services provided among non-formal care providers. The quality of STD case management service, observed by "incognito patients" in both intervention groups, improved substantially compared to the control group (p < 0.05). The training-and-packets group performed better in service delivery, HIV-testing referral, and condom provision when compared to the training-only group (all p < 0.05). The training-and-packets group also retained more knowledge and practiced more skillfully at six months post-intervention when compared to the training-only group (p < 0.05). Exit interviews of clients suggested that 81% of providers in the intervention groups offered advice on condom use when compared to none of those in the control group (p < 0.001). Syndromic management training and free syndrome packets for non-formal providers had a positive impact on the quality of STD care among the trained providers.

Reduced mortality with right-lobe living donor compared to deceased-donor liver transplantation when analyzed from the time of listing

Right lobe living donor liver transplantation (RLDLT) is not yet a fully accepted therapy for patients with end-stage liver failure in the Western hemisphere because of concerns about donor safety and inferior recipient outcomes. An outcome analysis from the time of listing for all adult patients who were listed for liver transplantation (LT) at our center was performed. From 2000 to 2006, 1091 patients were listed for LT. One hundred fifty-four patients (LRD; 14%) had suitable live donors and 153 (99%) underwent RLDLT. Of the remaining patients (DD/Waiting List; n = 937), 350 underwent deceased donor liver transplant (DDLT); 312 died or dropped off the waiting list; and 275 were still waiting at the time of this analysis. The LRD group had shorter mean waiting times (6.0 months vs. 9.8 months; p < 0.001). Although medical model for end-stage liver disease (MELD) scores were similar at the time of listing, MELD scores at LT were significantly higher in the DD/Waiting List group (15.4 vs. 19.5; p = 0.002). Patients in Group 1 had a survival advantage with RLDLT from the time of listing (1-year survival 90% vs. 80%; p < 0.001). To our knowledge, this is the first report to document a survival advantage at time of listing for RLDLT over DDLT.

Cadaveric Renal Transplantation: Our Experience at the Institute of Kidney Diseases & Research Centre, Institute of Transplantation Sciences, Ahmedabad

In a developing country such as India, cadaveric renal transplantation accounts for only less than 1% of total renal transplantations. The reasons for such a low rate of cadaveric transplantation are many, ranging from lack of awareness to socioeconomic reasons. Our institute conducted a statewide public awareness program and initiated an intercity organ harvesting program. This doubled the cadaveric renal transplantations in the last 2 years. We performed 38 cadaveric transplantations among 190 renal transplantations in the last year (August 2005 to July 2006). We retrieved kidneys from 21 donors, of whom 9 were outside our city. From 21 donors we transplanted 38 recipients; out of whom 3 received dual kidneys and one kidney was discarded. The Mean age of the donors was 41.4 +/- 18.2 years with a mean cold ischemia time of 6.9 +/- 3.8 hours. Sixty-eight percent had delayed graft function. At the last follow-up, which was 190 +/- 98 days, patient survival rate was 90%: 4 patients died, including 2 due to bacterial sepsis and 2 due to cytomegalovirus (CMV) disease. The Graft survival rate was 85%, and the death-censored graft survival rate was 90%. Mean serum creatinine value at the last follow-up was 1.2 +/- 0.3 mg%. There were 5 episodes of acute rejection in 31 patients during first 3 months (16% acute rejection rate). The increase in cadaveric transplantations was associated with satisfactory patient and graft survival despite the high incidence of delayed graft function.

Selective use of older adults in right lobe living donor liver transplantation

Many centers are reluctant to use older donors (>44 years) for adult right-lobe living donor liver transplantation (RLDLT) due to concerns about possible increased morbidity in donors and poorer outcomes in recipients. Since 2000, 130 adult RLDLTs have been performed at our institution. Recipients were divided into those who received a right lobe graft from a donor </=age 44 (n = 89, 68%; median age 30) and those who received a liver graft from a donor age >44 (n = 41, 32%; mean age 52). The two donor and recipient populations had similar demographic and operative profiles. With a median follow-up of 29 months, the severity and number of complications in older donors were similar to those in younger donors. No living donor died. Older donor allografts had initial allograft dysfunction compared to younger donors. Complication rates were similar among recipients in both groups but there was a higher bile duct stricture rate with older donor grafts (27% vs. 12%; p = 0.04). One-year recipient graft survival was 86% for older donors and 85% for younger donors (p = 0.95). Early experience with the use of selected older adults (>44 years) for RLDLT is encouraging, but may be associated with a higher rate of biliary complications in the recipient.

Biliary strictures in 130 consecutive right lobe living donor liver transplant recipients: results of a Western center

Biliary strictures remain the most challenging aspect of adult right lobe living donor liver transplantation (RLDLT). Between 04/2000 and 10/2005, 130 consecutive RLDLTs were performed in our center and followed prospectively. Median follow-up was 23 months (range 3-67) and 1-year graft and patient survival was 85% and 87%, respectively. Overall incidence of biliary leaks (n = 19) or strictures (n = 22) was 32% (41/128) in 33 patients (26%). A duct-to-duct (D-D) or Roux-en-Y (R-Y) anastomosis were performed equally (n = 64 each) with no difference in stricture rate (p = 0.31). The use of ductoplasty increased the number of grafts with a single duct for anastomosis and reduced the biliary complication rate compared to grafts >/=2 ducts (17% vs. 46%; p = 0.02). Independent risk factors for strictures included older donor age and previous history of a bile leak. All strictures were managed nonsurgically initially but four patients ultimately required conversion from D-D to R-Y. Ninety-six percent (123/128) of patients are currently free of any biliary complications. D-D anastomosis is safe after RLDLT and provides access for future endoscopic therapy in cases of leak or stricture. When presented with multiple bile ducts, ductoplasty should be considered to reduce the potential chance of stricture.

HIV-infected workers deported from the Gulf States: impact on Southern Pakistan

HIV prevalence is still very low in Pakistan, but its south Asian location and subgroups with recognized lifestyle risk factors suggest that Pakistan will experience expanded diffusion of HIV. We report the frequency of HIV infections identified by the AIDS Control Programme in the Sindh province of Pakistan. Most HIV positive cases currently reported to the Sindh AIDS Control Programme are found among Pakistani workers deported from the Gulf States and among foreigners. The 58 returned workers with HIV represent 61 to 86% of reported cases in any given year during the 1996-1998 period. Five wives of returning workers have been identified with HIV. Expatriate workers in the Gulf States are tested for HIV routinely, unlike other subgroups in Pakistan. Considering the risk of HIV/AIDS due to regular introduction of HIV from returned workers, and the limited awareness surrounding sexual health and HIV/STD transmission issues in Pakistan, intervention programmes targeted at overseas workers need to be implemented to control the expansion of the HIV epidemic in Pakistan (Int J STD AIDS 1999;10:812-14).

Analysis of long-term gene expression in neurons of the hippocampal subfields following traumatic brain injury in rats

After experimental traumatic brain injury (TBI), widespread neuronal loss is progressive and continues in selectively vulnerable brain regions, such as the hippocampus, for months to years after the initial insult. To clarify the molecular mechanisms underlying secondary or delayed cell death in hippocampal neurons after TBI, we compared long-term changes in gene expression in the CA1, CA3 and dentate gyrus (DG) subfields of the rat hippocampus at 24 h and 3, 6, and 12 months after TBI with changes in gene expression in sham-operated rats. We used laser capture microdissection to collect several hundred hippocampal neurons from the CA1, CA3, and DG subfields and linearly amplified the nanogram samples of neuronal RNA with T7 RNA polymerase. Subsequent quantitative analysis of gene expression using ribonuclease protection assay revealed that mRNA expression of the anti-apoptotic gene, Bcl-2, and the chaperone heat shock protein 70 was significantly downregulated at 3, 6 (Bcl-2 only), and 12 months after TBI. Interestingly, the expression of the pro-apoptotic genes caspase-3 and caspase-9 was also significantly decreased at 3, 6 (caspase-9 only), and 12 months after TBI, suggesting that long-term neuronal loss after TBI is not mediated by increased expression of pro-apoptotic genes. The expression of two aging-related genes, p21 and integrin beta3 (ITbeta3), transiently increased 24 h after TBI, returned to baseline levels at 3 months and significantly decreased below sham levels at 12 months (ITbeta3 only). Expression of the gene for the antioxidant glutathione peroxidase-1 also significantly increased 6 months after TBI. These results suggest that decreased levels of neuroprotective genes may contribute to long-term neurodegeneration in animals and human patients after TBI. Conversely, long-term increases in antioxidant gene expression after TBI may be an endogenous neuroprotective response that compensates for the decrease in expression of other neuroprotective genes.

Study of dust pollution caused by traffic in Aligarh city

In the present study the dust pollution caused by vehicles in Aligarh city was estimated. Four major national roads viz. Anoopshahar road, Delhi road, Agra road and Kanpur road of Aligarh city were selected. The dust pollution was maximum on Kanpur road (46.44 gm/m2/ month) followed by Agra road (38.94 gm/m2/month) and Delhi road (34.52 gm/m2/month). The least dust pollution was recorded on Anoopshahar road (20.10gm/m2/month). In general, the dust fall rate per unit area was highest at 3 km inside city (38.66 gm/m2/month) closely followed by starting point (37.27gm/m2/month) and least at 3 km outside city (29.09 gm/m2/ month). The average dust fall rate per unit area was estimated to be about 35 gm/m2/month in Aligarh city.