Analysis of gene function in somatic mammalian cells using small interfering RNAs

RNA interference (RNAi) is a highly conserved gene silencing mechanism that uses double-stranded RNA (dsRNA) as a signal to trigger the degradation of homologous mRNA. The mediators of sequence-specific mRNA degradation are 21- to 23-nt small interfering RNAs (siRNAs) generated by ribonuclease III cleavage from longer dsRNAs. Twenty-one-nucleotide siRNA duplexes trigger specific gene silencing in mammalian somatic cells without activation of the unspecific interferon response. Here we provide a collection of protocols for siRNA-mediated knockdown of mammalian gene expression. Because of the robustness of the siRNA knockdown technology, genomewide analysis of human gene function in cultured cells has now become possible.     

Marker-free transgenic (MFT) near-isogenic introgression lines (NIILs) of 'golden' indica rice (cv. IR64) with accumulation of provitamin A in the endosperm tissue

We have developed near-isogenic introgression lines (NIILs) of an elite indica rice cultivar (IR64) with the genes for β-carotene biosynthesis from dihaploid (DH) derivatives of golden japonica rice (cv. T309). A careful analysis of the DH lines indicated the integration of the genes of interest [phytoene synthase ( psy ) and phytoene desaturase ( crtI )] and the selectable marker gene (hygromycin phosphotransferase, hph ) in two unlinked loci. During subsequent crossing, progenies could be obtained carrying only the locus with psy and crtI , which was segregated independently from the locus containing the hph gene during meiotic segregation. The NIILs (BC₂F₂) showed maximum similarity with the recurrent parent cultivar IR64. Further, progenies of two NIILs were devoid of any fragments beyond the left or right border, including the chloramphenicol acetyltransferase ( cat ) antibiotic resistance gene of the transformation vector. Spectrophotometric readings showed the accumulation of up to 1.06 µg total carotenoids, including β-carotene, in 1 g of the endosperm. The accumulation of β-carotene was also evident from the clearly visible yellow colour of the polished seeds.     

The interplay between environmental and host factors during an outbreak of visceral leishmaniasis in eastern Sudan

Parasitic diseases, including human visceral leishmaniasis, are multifactorial. Factors that are expected to play an important role in the parasite-human interaction are exposure, parasite "virulence" and host resistance factors. In populations exposed to Leishmania donovani most subjects do not allow the parasites to establish themselves or remain asymptomatic. Some individuals, however, fail to control parasite expansion and dissemination and develop a visceral disease. We report here the results of a longitudinal survey whose aims were to identify risk factors underlying visceral leishmaniasis (VL) susceptibility during an outbreak that occurred in a Sudanese village between 1995 and 1999. Most of the 660 subjects (90%) living in the central district were exposed to Leishmania and 20.9% (n = 138), mostly teenagers, developed VL. VL cases increased markedly in adults late in the outbreak, suggesting some changes in adult resistance status or in Leishmania "virulence" during the epidemic. Age and ethnic origin of the patients were the most important critical risk factors to account for the distribution of the VL cases that were recorded during the whole epidemic. This and the high frequency of VL in certain families suggest that host genetic factors played an important role in shaping the outbreak in this village. However, environmental factors (the presence of cows and neems in the households) that increase/decrease exposure to the parasite had significant effects on the distribution of VL cases in the village in the first phase of the outbreak.     

Visceral leishmaniasis in eastern Sudan: parasite identification in humans and dogs; host-parasite relationships

In 1996, an epidemic outbreak of visceral leishmaniasis (VL) started in Barbar el Fugara, a village in Gedarif State (eastern Sudan). From 1997 to 2000, regular epidemiological studies were carried out in the human population, as well as in mammals and sand flies. In symptomatic patients, 46/69 lymph node, 6/20 post kala-azar dermal leishmaniasis (PKDL) and 1/4 cutaneous cultures in NNN medium were positive. In 69 dogs, 23/79 lymph node cultures were positive. In other mammals (47 rodents, five donkeys, one mongoose and one monkey) spleen and/or blood cultures were negative. Characterization of isolated strains (by starch gel electrophoresis and isoelectrofocusing) identified three zymodemes of Leishmania donovani, two of L. infantum and two of L. archibaldi complexes from patient samples and three zymodemes of L. donovani, three of L. infantum and two of L. archibaldi complexes from dog samples. Five of them were present in both man and dog. For the first time, a strain from a PKDL case was identified as L. infantum, and a child had the same L. infantum zymodeme in VL and in subsequent PKDL. Blood samples from dogs were studied by immunofluorescent antibody test (IFAT). The seroprevalence in dogs was 72.5%, 74.3% and 42.9% in 1998, 1999 and 2000, respectively. By using CDC miniature light traps 12 745 sand flies were collected and then identified. Phlebotomus papatasi (7%) and P. orientalis (5%) were sympatric, mainly inside homes (85% and 75%, respectively). These results, the relative stability of seroprevalence in dogs and the intradomiciliar presence of P. orientalis, known as a vector of VL in Sudan, suggest several hypotheses: (i) man is responsible for the disease in dogs, (ii) the dog is the reservoir of VL, (iii) the dog is an intermediate host between a possible sylvatic cycle and the anthroponotic cycle. More extensive studies are needed to assess the transmission cycle of VL in this area of Sudan.     

Epidemiology of visceral leishmaniasis in Atbara River area,eastern Sudan: the outbreak of Barbar El Fugara village (1996-1997)

An outbreak of visceral leishmaniasis (VL) started in 1995 in the Atbara River area in eastern Sudan. This article reports on this outbreak and on the clinical and immunological studies that were carried out in a village, with the highest incidence of VL cases, from 1996 to 1997. A significant increase in VL incidence was recorded in a dozen villages in this area; one village, Barbar El Fugara accounted for half of the total number of cases recorded at the regional hospital. A total of 152 VL and 61 post kala-azar dermal lesion (PKDL) cases were diagnosed and treated in Barbar. Household (n = 671) and school (n = 276) surveys were performed using the leishmanin skin test (LST) and the direct agglutination test (DAT). LST positivity was 23.1 and 15.7%, whereas DAT positivity was 8.9 and 26.4% in both surveys, respectively. No gender differences were observed in either test. Unlike DAT, LST positivity was predominant in the higher age groups that also exhibited lower prevalence of VL. Few individuals were positive by both tests (1.3%, 5.2%) while the majority (68.8%, 64.8%) had no evidence of acquired immune response, suggesting either a role of innate immunity in preventing parasite establishment or, unexpectedly, lack of exposure to Leishmania. Subclinical parasitism was also demonstrated, as evidence of both acquired humoral and cellular immune responses was observed in individuals with no past history of the disease. The wide spectrum of L. donovani/human interactions may be explained by differential exposure to environmental risk factors, parasite strain polymorphisms or host genetic makeup.     

Comprehensive evaluation of canonical versus Dicer-substrate siRNA in vitro and in vivo

Since the discovery of RNA interference (RNAi), researchers have identified a variety of small interfering RNA (siRNA) structures that demonstrate the ability to silence gene expression through the classical RISC-mediated mechanism. One such structure, termed "Dicer-substrate siRNA" (dsiRNA), was proposed to have enhanced potency via RISC-mediated gene silencing, although a comprehensive comparison of canonical siRNAs and dsiRNAs remains to be described. The present study evaluates the in vitro and in vivo activities of siRNAs and dsiRNAs targeting Phosphatase and Tensin Homolog (PTEN) and Factor VII (FVII). More than 250 compounds representing both siRNA and dsiRNA structures were evaluated for silencing efficacy. Lead compounds were assessed for duration of silencing and other key parameters such as cytokine induction. We identified highly active compounds from both canonical siRNAs and 25/27 dsiRNAs. Lead compounds were comparable in potency both in vitro and in vivo as well as duration of silencing in vivo. Duplexes from both structural classes tolerated 2'-OMe chemical modifications well with respect to target silencing, although some modified dsiRNAs demonstrated reduced activity. On the other hand, dsiRNAs were more immunostimulatory as compared with the shorter siRNAs, both in vitro and in vivo. Because the dsiRNA structure does not confer any appreciable benefits in vitro or in vivo while demonstrating specific liabilities, further studies are required to support their applications in RNAi therapeutics.     

Genes and environment in susceptibility to visceral leishmaniasis

Kala azar (KA) is a lethal disease caused by Leishmania parasites (Leishmania donovani s.l.) that multiply in large numbers in deep organs such as spleen and liver. The host immunological response to these organisms is complex and experimental studies in animals have detected a large number of genetic loci involved in the control of infection and disease. We report here on a study in a human population of Sudan carried out during an outbreak of KA. The following conclusions are presented: (1) environmental factors that could have affected the distribution of the insect vector, influenced progression of KA in the initial phase of the epidemics - but they became less important later at the peak of transmission, probably after infected phlebotomies had spread to all parts of the village -; (2) Leishmania population during the epidemics was heterogeneous, suggesting a possible parasite evolution during the outbreak; (3) the incidence of KA varied markedly among age groups, families and ethnic groups. Susceptibility to KA was shown to depend on a locus on chromosomes 22q12 and on NRAMP1 on chromosome 2q35; the data also suggested a third locus in the region 2q23-q24. Overall, this study indicates complex interactions between host genes and environment in the spreading of KA in that population. It is also suspected that the large parasite diversity observed in the outbreak has contributed to disease spreading across host genetic barriers.     

The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome

U11 and U12 snRNPs bind U12-type pre-mRNAs as a preformed di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. Thus, within the U12-type prespliceosome, U11/U12 components form a molecular bridge connecting both ends of the intron. We have affinity purified human 18S U11/U12 and 12S U11 snRNPs, and identified their protein components by using mass spectrometry. U11/U12 snRNPs lack all known U1 snRNP proteins but contain seven novel proteins (i.e., 65K, 59K, 48K, 35K, 31K, 25K, 20K) not found in the major spliceosome, four of which (59K, 48K, 35K, and 25K) are U11-associated. Thus, protein-protein and protein-RNA interactions contributing to 5' splice site recognition and/or intron bridging appear to differ significantly in the minor versus major prespliceosome. The majority of U11/U12 proteins are highly conserved in organisms known to contain U12-type introns. However, homologs of those associated with U11 were not detected in Drosophila melanogaster, consistent with the presence of a divergent U11 snRNP in flies. RNAi experiments revealed that several U11/U12 proteins are essential for cell viability, suggesting they play key roles in U12-type splicing. The presence of unique U11/U12 snRNP proteins in the U12-type spliceosome provides insight into potential evolutionary relationships between the major and minor spliceosome.     

Rapid Syphilis Tests as Catalysts for Health Systems Strengthening: A Case Study from Peru

Objectives

Untreated maternal syphilis leads to adverse pregnancy outcomes. The use of point of care tests (POCT) offers an opportunity to improve screening coverage for syphilis and other aspects of health systems. Our objective is to present the experience of the introduction of POCT for syphilis in Peru and describe how new technology can catalyze health system strengthening.

Methods

The study was implemented from September 2009–November 2010 to assess the feasibility of the use of a POCT for syphilis for screening pregnant women in Lima, Peru. Outcomes measured included access to syphilis screening, treatment coverage, partner treatment, effect on patient flow and service efficiency, acceptability among providers and patients, and sustainability.

Results

Before the introduction of POCT, a pregnant woman needed 6 visits to the health center in 27 days before she received her syphilis result. We trained 604 health providers and implemented the POCT for syphilis as the “two for one strategy”, offering with one finger stick both syphilis and HIV testing. Implementation of the POCT resulted in testing and treatment on the first visit. Screening and treatment coverages for syphilis improved significantly compared with the previous year. Implementation of POCT has been scaled up nationally since the study ended, and coverages for screening, treatment and partner treatment have remained over 92%.

Conclusions

Implementation of POCT for syphilis proved feasible and acceptable, and led to improvement in several aspects of health services. For the process to be effective we highlight the importance of: (1) engaging the authorities; (2) dissipating tensions between providers and identifying champions; (3) training according to the needs; (4) providing monitoring, supervision, support and recognition; (5) sharing results and discussing actions together; (6) consulting and obtaining feedback from users; and (7) integrating with other services such as with rapid HIV testing.