Detection of Phanerochaete chrysosporium in soil by PCR and restriction enzyme analysis.

A nonradioactive method to detect Phanerochaete chrysosporium grown in a soil matrix was developed. This method involved DNA extraction, PCR amplification, and restriction enzyme analysis. Amplification of ligninase H8 DNA from pure cultures of P. chrysosporium was not as sensitive as amplification of the internal transcribed spacer (ITS) of the highly repetitive nuclear ribosomal DNA. Amplified ITS DNA was digested with restriction enzymes for analysis. The restriction enzyme pattern of PCR-amplified ITS DNA of P. chrysosporium was unique compared with those of unrelated fungi. Two strains of Phanerochaete chrysosporium and two strains of Phanerochaete sordida were indistinguishable by restriction enzyme analysis, while a third strain of P. chrysosporium had an unique pattern. These results were confirmed by sequence information and indicate that species designations of Phanerochaete spp. should be reexamined. The restriction enzyme pattern of DNA extracted and PCR amplified from P. chrysosporium grown in soil was identical to that from P. chrysosporium grown in pure culture. The ITS sequence was detected in 14 ng of the 100 micrograms of total DNA extracted from 1 g of soil.     

Monitoring attributes for ecological restoration in Latin America and the Caribbean region

Ecological restoration is becoming mainstreamed worldwide but target ecosystems' responses to restorative interventions are not sufficiently monitored, in terms of the wide range of ecological, social, and economic attributes available. In order to highlight and better understand this problem, we conducted a literature review of the ecological, social, and economic attributes cited in the scientific literature used for monitoring the success of ecological restoration projects in Latin America and the Caribbean region, where no regional study of this kind has previously been conducted. In 84 of the 91 articles retained for the study, ecological indicators were evaluated, while only seven articles included measurements of socioeconomic indicators. Regarding the Society for Ecological Restoration Primer attributes of restored ecosystems, we only found indicators measuring attributes 1–6, with attribute 1 (species assemblages) predominating (73%), followed by physical conditions (54%) and ecological functions (51%). Brazil was the country in the region where most monitoring was being carried out (51% of the articles), and tropical rainforest (33%) and tropical dry forest (25%) were the ecosystem types where ecological restoration was most frequently monitored. Highly vulnerable ecosystems such as mangroves and paramos were underrepresented. Attributes related to ecosystem stability or to governance and education of communities were not monitored at all. More real long‐term monitoring, instead of chronosequences, is needed, especially where understanding socioeconomic implications of, and barriers to, effective ecological restoration is a top priority.     

Progress towards eliminating canine rabies: policies and perspectives from Latin America and the Caribbean

Human rabies transmitted by dogs is considered a neglected disease that can be eliminated in Latin America and the Caribbean (LAC) by 2015. The aim of this paper is to discuss canine rabies policies and projections for LAC regarding current strategies for achieving this target and to critically review the political, economic and geographical factors related to the successful elimination of this deadly disease in the context of the difficulties and challenges of the region. The strong political and technical commitment to control rabies in LAC in the 1980s, started with the regional programme coordinated by the Pan American Health Organization. National and subnational programmes involve a range of strategies including mass canine vaccination with more than 51 million doses of canine vaccine produced annually, pre- and post-exposure prophylaxis, improvements in disease diagnosis and intensive surveillance. Rabies incidence in LAC has dramatically declined over the last few decades, with laboratory confirmed dog rabies cases decreasing from approximately 25 000 in 1980 to less than 300 in 2010. Dog-transmitted human rabies cases also decreased from 350 to less than 10 during the same period. Several countries have been declared free of human cases of dog-transmitted rabies, and from the 35 countries in the Americas, there is now only notification of human rabies transmitted by dogs in seven countries (Bolivia, Peru, Honduras, Haiti, Dominican Republic, Guatemala and some states in north and northeast Brazil). Here, we emphasize the importance of the political commitment in the final progression towards disease elimination. The availability of strategies for rabies control, the experience of most countries in the region and the historical ties of solidarity between countries with the support of the scientific community are evidence to affirm that the elimination of dog-transmitted rabies can be achieved in the short term. The final efforts to confront the remaining obstacles, like achieving and sustaining high vaccination coverage in communities that are most impoverished or in remote locations, are faced by countries that struggle to allocate sufficient financial and human resources for rabies control. Continent-wide cooperation is therefore required in the final efforts to secure the free status of remaining countries in the Americas, which is key to the regional elimination of human rabies transmitted by dogs.     

Cross-sectional analysis of late HAART initiation in Latin America and the Caribbean: late testers and late presenters

Background

Starting HAART in a very advanced stage of disease is assumed to be the most prevalent form of initiation in HIV-infected subjects in developing countries. Data from Latin America and the Caribbean is still lacking. Our main objective was to determine the frequency, risk factors and trends in time for being late HAART initiator (LHI) in this region.

Methodology

Cross-sectional analysis from 9817 HIV-infected treatment-naïve patients initiating HAART at 6 sites (Argentina, Chile, Haiti, Honduras, Peru and Mexico) from October 1999 to July 2010. LHI had CD4⁺ count ≤200cells/mm³ prior to HAART. Late testers (LT) were those LHI who initiated HAART within 6 months of HIV diagnosis. Late presenters (LP) initiated after 6 months of diagnosis. Prevalence, risk factors and trends over time were analyzed.

Principal Findings

Among subjects starting HAART (n = 9817) who had baseline CD4⁺ available (n = 8515), 76% were LHI: Argentina (56%[95%CI:52–59]), Chile (80%[95%CI:77–82]), Haiti (76%[95%CI:74–77]), Honduras (91%[95%CI:87–94]), Mexico (79%[95%CI:75–83]), Peru (86%[95%CI:84–88]). The proportion of LHI statistically changed over time (except in Honduras) (p≤0.02; Honduras p = 0.7), with a tendency towards lower rates in recent years. Males had increased risk of LHI in Chile, Haiti, Peru, and in the combined site analyses (CSA). Older patients were more likely LHI in Argentina and Peru (OR 1.21 per +10-year of age, 95%CI:1.02–1.45; OR 1.20, 95%CI:1.02–1.43; respectively), but not in CSA (OR 1.07, 95%CI:0.94–1.21). Higher education was associated with decreased risk for LHI in Chile (OR 0.92 per +1-year of education, 95%CI:0.87–0.98) (similar trends in Mexico, Peru, and CSA). LHI with date of HIV-diagnosis available, 55% were LT and 45% LP.

Conclusion

LHI was highly prevalent in CCASAnet sites, mostly due to LT; the main risk factors associated were being male and older age. Earlier HIV-diagnosis and earlier treatment initiation are needed to maximize benefits from HAART in the region.     

Diagnosis of mycobacterial infections by PCR and restriction enzyme digestion

A method for the diagnosis of mycobacterial infections by PCR amplification followed by selective restriction enzyme digestion of the PCR product was developed. The amplified DNA sequence used in this study occurs within the gene encoding for the mycobacterial 65 kDa heat shock protein (Hance et al. 1989), which is found in all mycobacteria. However, there are minute differences in the amplified sequence from the Mycobacterium tuberculosis complex compared with the corresponding sequence from the Mycobacterium avium complex. These differences made it possible to rapidly identify to which mycobacterial complex a particular sample belonged by restriction enzyme digestion of the PCR product. A total of 66 samples were tested and all of them were correctly identified. This and similar methods should provide a sensitive, specific and rapid (within 12 h) way of diagnosing mycobacterial infections to the species level.     

On the Margin of the Periphery: Culture and Race in Latin America and the Caribbean

Blackness in Latin America and the Caribbean, volume 1. Norman E. Whitten. Jr. and Arlene Torres, eds. Bloomington: Indiana University Press, 1998. 520 pp.
Blackness in Latin America and the Caribbean, volume 2. Norman E. Whitten. Jr. and Arlene Torres, eds. Bloomington: Indiana University Press, 1998. 557 pp.     

Good news from Latin America and the Caribbean: national and international restoration networks are moving ahead

Degradation of ecosystems is ongoing in Latin America but there is also a strong upswing in conservation and restoration efforts. SIACRE – the Ibero‐American and Caribbean Society for Ecological Restoration – is playing a key role in coordinating and promoting this trend at international, national, and subnational levels. In October 2014, SIACRE members organized the first national seminar on ecological restoration in Chile, with participants representing both academic and non‐academic sectors. This seminar served as the catalyst for this essay and was an historic event at the national level. Much work has been underway in the science and practice of restoration in Chile, but until now it has been fragmented. This first national seminar enabled helped the principal strengths and challenges that Chile has and must face in the transdisciplinary domain of ecological restoration. Since 2004, various meetings have been organized in the region, in order to communicate the importance of restoration, especially in Mexico, Cuba, Colombia, Brazil, and more recently in Chile and Argentina. Here we trace the history of national and subnational restoration networks in Latin America and the Caribbean, and of SIACRE, and then outline some goals and challenges for the coming years.     

Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet)

Bioinformatics is increasingly recognised as a crucial field for research and development in the biological sciences, and forms an integral part of genomics, proteomics and modern biotechnology. Worldwide participation is important, and scientists in developing countries can contribute to this field. Regional networks for bioinformatics are highly beneficial for capacity strengthening and cooperation, and for establishing productive interactions between scientists in the fields of biological and informatics sciences. Such a network (LACBioNet) is being organised for Latin America and the Caribbean. Its immediate goals include the organisation and extension of nodes and services, information and communication, research and development in different specialty fields of bioinformatics, and training and human resource development.     

Characteristics of Randomized Trials Published in Latin America and the Caribbean According to Funding Source

Introduction

Few studies have assessed the nature and quality of randomized controlled trials (RCTs) in Latin America and the Caribbean (LAC).

Methods and Findings

The aims of this systematic review are to evaluate the characteristics (including the risk of bias assessment) of RCT conducted in LAC according to funding source. A review of RCTs published in 2010 in which the author''s affiliation was from LAC was performed in PubMed and LILACS. Two reviewers independently extracted data and assessed the risk of bias. The primary outcomes were risk of bias assessment and funding source. A total of 1,695 references were found in PubMed and LILACS databases, of which 526 were RCTs (N = 73.513 participants). English was the dominant publication language (93%) and most of the RCTs were published in non-LAC journals (84.2%). Only five of the 19 identified countries accounted for nearly 95% of all RCTs conducted in the region (Brazil 70.9%, Mexico 10.1%, Argentina 5.9%, Colombia 3.8%, and Chile 3.4%). Few RCTs covered priority areas related with Millennium Development Goals like maternal health (6.7%) or high priority infectious diseases (3.8%). Regarding children, 3.6% and 0.4% RCT evaluated nutrition and diarrhea interventions respectively but none pneumonia. As a comparison, aesthetic and sport related interventions account for 4.6% of all trials. A random sample of RCTs (n = 358) was assessed for funding source: exclusively public (33.8%); private (e.g. pharmaceutical company) (15.3%); other (e.g. mixed, NGO) (15.1%); no funding (35.8%). Overall assessments for risk of bias showed no statistically significant differences between RCTs and type of funding source. Statistically significant differences favoring private and others type of funding was found when assessing trial registration and conflict of interest reporting.

Conclusion

Findings of this study could be used to provide more direction for future research to facilitate innovation, improve health outcomes or address priority health problems.     

Random amplified polymorphic DNA and restriction enzyme analysis of PCR amplified rDNA in taxonomy: two identification techniques for food-borne yeasts

The random amplified polymorphic DNA (RAPD) assay and the restriction enzyme analysis of PCR amplified rDNA are compared for the identification of the common spoilage yeasts Zygosaccharomyces bailii, Z. rouxii, Saccharomyces cerevisiae, Candida valida and C. lipolytica. Both techniques proved to be adequate tools for yeast identification. Since the RAPD does provide less stable patterns than restriction enzyme analysis of PCR amplified rDNA, and a large amount of data had to be compared without data reduction, Principal Component Analysis (PCA) was applied successfully for clustering the RAPD patterns. The success of PCA is highly influenced by the primer used in RAPD and the amount of reference samples. A large amount of reference samples improves the performance of clustering in PCA. The primer of choice was shown to be important with respect to the discriminatory power of the RAPD method. Some primers used enabled discrimination on the subspecies level. The results collected with both typing methods justify the conclusion that the present typing system can be applied for taxonomical purposes.     

Levels of spending and resource allocation to HIV programs and services in Latin America and the Caribbean

Background

An estimated 1.86 million people are living with HIV in Latin America and the Caribbean (LAC). The region is comprised of mainly middle-income countries with steady economic growth while simultaneously there are enormous social inequalities and several concentrated AIDS epidemics. This paper describes HIV spending patterns in LAC countries including analysis of the levels and patterns of domestic HIV spending from both public and international sources.

Methods and Findings

We conducted an extensive analysis of the most recently available data from LAC countries using the National AIDS Spending Assessment tool. The LAC countries spent a total of US$ 1.59 billion on HIV programs and services during the latest reported year. Countries providing detailed information on spending showed that high percentages are allocated to treatment and care (75.1%) and prevention (15.0%). Domestic sources accounted for 93.6 percent of overall spending and 79 percent of domestic funds were directed to treatment and care. International funds represented 5.4 percent of total HIV funding in the region, but they supplied the majority of the effort to reach most-at-risk-populations (MARPs). However, prevalence rates among men who have sex with men (MSM) still reached over 25 percent in some countries.

Conclusions

Although countries in the region have increasingly sustained their response from domestic sources, still there are future challenges: 1) The growing number of new HIV infections and more people-living-with-HIV (PLWH) eligible to receive antiretroviral treatment (ART); 2) Increasing ART coverage along with high prices of antiretroviral drugs; and 3) The funding for prevention activities among MARPs rely almost exclusively on external donors. These threats call for strengthened actions by civil society and governments to protect and advance gains against HIV in LAC.     

Deforestation and Reforestation of Latin America and the Caribbean (2001–2010)

Forest cover change directly affects biodiversity, the global carbon budget, and ecosystem function. Within Latin American and the Caribbean region (LAC), many studies have documented extensive deforestation, but there are also many local studies reporting forest recovery. These contrasting dynamics have been largely attributed to demographic and socio‐economic change. For example, local population change due to migration can stimulate forest recovery, while the increasing global demand for food can drive agriculture expansion. However, as no analysis has simultaneously evaluated deforestation and reforestation from the municipal to continental scale, we lack a comprehensive assessment of the spatial distribution of these processes. We overcame this limitation by producing wall‐to‐wall, annual maps of change in woody vegetation and other land‐cover classes between 2001 and 2010 for each of the 16,050 municipalities in LAC, and we used nonparametric Random Forest regression analyses to determine which environmental or population variables best explained the variation in woody vegetation change. Woody vegetation change was dominated by deforestation (?541,835 km²), particularly in the moist forest, dry forest, and savannas/shrublands biomes in South America. Extensive areas also recovered woody vegetation (+362,430 km²), particularly in regions too dry or too steep for modern agriculture. Deforestation in moist forests tended to occur in lowland areas with low population density, but woody cover change was not related to municipality‐scale population change. These results emphasize the importance of quantitating deforestation and reforestation at multiple spatial scales and linking these changes with global drivers such as the global demand for food.     

Use of multiplex PCR and PCR restriction enzyme analysis for detection and exploration of the variability in the free-living amoeba Naegleria in the environment

A multiplex PCR was developed to simultaneously detect Naegleria fowleri and other Naegleria species in the environment. Multiplex PCR was also capable of identifying N. fowleri isolates with internal transcribed spacers of different sizes. In addition, restriction fragment length polymorphism analysis of the PCR product distinguished the main thermophilic Naegleria species from the sampling sites.