A simple protocol for amino acid type selective isotope labeling in insect cells with improved yields and high reproducibility

An easy to use and robust approach for amino acid type selective isotope labeling in insect cells is presented. It relies on inexpensive commercial media and can be implemented in laboratories without sophisticated infrastructure. In contrast to previous protocols, where either high protein amounts or high incorporation ratios were obtained, here we achieve both at the same time. By supplementing media with a well considered amount of yeast extract, similar protein amounts as with full media are obtained, without compromising on isotope incorporation. In single and dual amino acid labeling experiments incorporation ratios are consistently ≥90% for all amino acids tested. This enables NMR studies of eukaryotic proteins and their interactions even for proteins with low expression levels. We show applications with human kinases, where protein–ligand interactions are characterized by 2D [¹⁵N, ¹H]- and [¹³C, ¹H]-HSQC spectra.     

Marine biodiversity in the Atlantic and Pacific coasts of South America: knowledge and gaps

The marine areas of South America (SA) include almost 30,000 km of coastline and encompass three different oceanic domains--the Caribbean, the Pacific, and the Atlantic--ranging in latitude from 12°N to 55°S. The 10 countries that border these coasts have different research capabilities and taxonomic traditions that affect taxonomic knowledge. This paper analyzes the status of knowledge of marine biodiversity in five subregions along the Atlantic and Pacific coasts of South America (SA): the Tropical East Pacific, the Humboldt Current,the Patagonian Shelf, the Brazilian Shelves, and the Tropical West Atlantic, and it provides a review of ecosystem threats and regional marine conservation strategies. South American marine biodiversity is least well known in the tropical subregions (with the exception of Costa Rica and Panama). Differences in total biodiversity were observed between the Atlantic and Pacific oceans at the same latitude. In the north of the continent, the Tropical East Pacific is richer in species than the Tropical West Atlantic, however, when standardized by coastal length, there is very little difference among them. In the south, the Humboldt Current system is much richer than the Patagonian Shelf. An analysis of endemism shows that 75% of the species are reported within only one of the SA regions, while about 22% of the species of SA are not reported elsewhere in the world. National and regional initiatives focusing on new exploration, especially to unknown areas and ecosystems, as well as collaboration among countries are fundamental to achieving the goal of completing inventories of species diversity and distribution.These inventories will allow accurate interpretation of the biogeography of its two oceanic coasts and latitudinal trends,and will also provide relevant information for science based policies.     

Expression of DNA Translesion Synthesis Polymerase η in Head and Neck Squamous Cell Cancer Predicts Resistance to Gemcitabine and Cisplatin-Based Chemotherapy

Purpose

The development of resistance against anticancer drugs has been a persistent clinical problem for the treatment of locally advanced malignancies in the head and neck mucosal derived squamous cell carcinoma (HNSCC). Recent evidence indicates that the DNA translesion synthesis (TLS) polymerase η (Pol η; hRad30a gene) reduces the effectiveness of gemcitabine/cisplatin. The goal of this study is to examine the relationship between the expression level of Pol η and the observed resistance against these chemotherapeutic agents in HNSCC, which is currently unknown.

Methods

Sixty-four mucosal derived squamous cell carcinomas of head and neck (HNSCC) from 1989 and 2007 at the City of Hope National Medical Center (Duarte, CA) were retrospectively analyzed. Pretreatment samples were immunostained with anti-Pol η antibody and the correlation between the expression level of Pol η and clinical outcomes were evaluated. Forty-nine cases treated with platinum (n=40) or gemcitabine (n=9) based chemotherapy were further examined for Pol η expression level for comparison with patient response to chemotherapy.

Results

The expression of Pol η was elevated in 67% of the head and neck tumor samples. Pol η expression level was significantly higher in grade 1 to grade 2 tumors (well to moderately differentiated). The overall benefit rate (complete response+ partial response) in patients treated with platinum and gemcitabine based chemotherapy was 79.5%, where low Pol η level was significantly associated with high complete response rate (p=0.03), although not associated with overall survival. Furthermore, no significant correlation was observed between Pol η expression level with gender, age, tobacco/alcohol history, tumor stage and metastatic status.

Conclusions

Our data suggest that Pol η expression may be a useful prediction marker for the effectiveness of platinum or gemcitabine based therapy for HNSCC.     

Methodology of Clinical Trials Aimed at Assessing Interventions for Cutaneous Leishmaniasis

The current evidence-base for recommendations on the treatment of cutaneous leishmaniasis (CL) is generally weak. Systematic reviews have pointed to a general lack of standardization of methods for the conduct and analysis of clinical trials of CL, compounded with poor overall quality of several trials. For CL, there is a specific need for methodologies which can be applied generally, while allowing the flexibility needed to cover the diverse forms of the disease. This paper intends to provide clinical investigators with guidance for the design, conduct, analysis and report of clinical trials of treatments for CL, including the definition of measurable, reproducible and clinically-meaningful outcomes. Having unified criteria will help strengthen evidence, optimize investments, and enhance the capacity for high-quality trials. The limited resources available for CL have to be concentrated in clinical studies of excellence that meet international quality standards.     

Homology of the Lateral Eyes of Scorpiones: A Six-Ocellus Model

Scorpions possess two types of visual organs, the median and lateral eyes. Both eyes consist of simple ocelli with biconvex lenses that differ in structure and function. There is little variation in the number of median ocelli across the order. Except for a few troglomorphic species in which the median ocelli are absent, all scorpions possess a single pair. In contrast, the number of pairs of lateral ocelli varies from zero to five across Scorpiones and may vary within species. No attempt has been made to homologize lateral ocelli across the order, and their utility in scorpion systematics has been questioned, due to the variation in number. A recent study examined the number of lateral ocelli among various Asian Buthidae C.L. Koch, 1837 and proposed a “five-eye model” for the family. This model has not been examined more broadly within Buthidae, however, nor compared with the patterns of variation observed among other scorpion families. An eyespot, referred to as an accessory lateral eye, situated ventral or posteroventral to the lateral ocelli, has also been reported in some scorpions. Analysis of its structure suggests it serves a nonvisual function. We present the first comparative study of variation in the lateral ocelli across the order Scorpiones, based on examination of a broad range of exemplar species, representing all families, 160 genera (78%), 196 species (9%), and up to 12 individuals per species. We propose a six-ocellus model for Recent scorpions with four accessory ocelli observed in various taxa, homologize the individual ocelli, and correct erroneous counts in the recent literature. We also investigate the presence of the eyespot across scorpions and discover that it is more widespread than previously recognized. Future work should investigate the genetic and developmental mechanisms underlying the formation of the lateral ocelli to test the hypotheses proposed here.     

How Far Are We from Visceral Leishmaniasis Elimination in Bangladesh? An Assessment of Epidemiological Surveillance Data

Introduction

In 2005, Bangladesh, India, and Nepal joined forces to eliminate Visceral Leishmaniasis (or kala-azar) from the region by 2015. In Bangladesh the elimination target is set at less than one new case per 10,000 population per year at upazila (sub-district) level. As the deadline approaches, we review the status of the elimination initiative in this country.

Methods

We collected all available disease surveillance data at the Disease Control Unit of the Directorate General of Health Services, Government of Bangladesh from 1994 to 2013. Additionally, we retrieved data from the Civil Surgeon Office from the Mymensingh district, one of the most heavily affected areas in Bangladesh.

Results

Between 1994 and 2013, 109,266 kala-azar cases causing 329 deaths were reported from 37 endemic districts in Bangladesh. Only 16 districts reported cases every year. The Mymensingh district was the most affected with 53,582 (49.04%) cases. Between 2008 and 2013 only 16 upazilas showed incidence rates above the elimination target in which they ranged from 1.06 to 18.25 per 10,000 people per year.

Discussion

While clear progress has been made towards eliminating VL, 16 upazilas in Bangladesh had not yet reached the target in 2013, based on official notification data that probably suffered from under-reporting bias. The elimination initiative urgently needs to establish methods to ascertain and monitor the elimination target.     

Effect of Diet Composition and Weight Loss on Resting Energy Expenditure in the POUNDS LOST Study

Weight loss reduces energy expenditure, but it is unclear whether dietary macronutrient composition affects this reduction. We hypothesized that energy expenditure might be modulated by macronutrient composition of the diet. The Prevention of Obesity Using Novel Dietary Strategies (POUNDS) LOST study, a prospective, randomized controlled trial in 811 overweight/obese people who were randomized in a 2 × 2 design to diets containing 20en% or 40en% fat and 15en% or 25en% protein (diets with 65%, 55%, 45%, and 35% carbohydrate) provided the data to test this hypothesis. Resting energy expenditure (REE) was measured at baseline, 6, and 24 months using a ventilated hood. REE declined at 6 months by 99.5 ± 8.0 kcal/day in men and 55.2 ± 10.6 kcal/day in women during the first 6 months. This decline was related to the weight loss, and there was no difference between the diets. REE had returned to baseline by 24 months, but body weight was still 60% below baseline. Measured REE at 6 months was significantly lower than the predicted (?18.2 ± 6.7 kcal/day) and was the result of significant reductions from baseline in the low‐fat diets (65% or 55% carbohydrate), but not in the high fat diet groups. By 24 months the difference had reversed with measured REE being slightly but significantly higher than predicted (21.8 ± 10.1 kcal/day). In conclusion, we found that REE fell significantly after weight loss but was not related to diet composition. Adaptive thermogenesis was evident at 6 months, but not at 24 months.     

<Emphasis Type="Italic">Membraniporopsis tubigera</Emphasis>, an invasive bryozoan in sandy beaches of southern Brazil and Uruguay

The massive irruption of the invasive bryozoan Membraniporopsis tubigera (Osburn) in sandy beaches of southern Brazil and Uruguay is reported. The species, originally described from Puerto Rico, Texas and Florida, has also been recorded for Brazilian beaches from 21°S to 26°S as well as for harbours of Australia, New Zealand and the Sea of Japan. The southward spreading rate of this bryozoan along the Brazilian and Uruguayan coasts can be estimated in approximately 183–195 km year⁻¹. The chances that this invasion could proceed southwards in the Southwest Atlantic and the possible impacts that it may be causing are discussed. The case of M. tubigera seems to be qualitatively and quantitatively different from those of other alien bryozoans previously recorded for this region, since it appeared massively in exposed sandy beaches, a habitat regarded to date as apparently free from the pervasive ecological impact of invasion by exotic species in the Southwest Atlantic.