Klebsiella Species Associated with Bovine Mastitis in Newfoundland

Klebsiella spp. is a common cause of bovine mastitis, but information regarding its molecular epidemiology is lacking from many parts of the world. On using mass spectrometry and partial sequencing of the rpoB gene, it was found that over a one year study, K. variicola and Enterobacter cloacae were misidentified as K. pneumoniae in a small number of clinical mastitis (CM) cases from Newfoundland. Results suggest that the currently used standard biochemical/phenotypic tests lack the sensitivity required to accurately discriminate among the three mentioned Gram negative bacteria. In addition, a single strain of K. variicola was associated with CM from one farm in the study as demonstrated by Random Amplified Polymorphic DNA (RAPD) PCR. To the best of our knowledge, K. variicola, which is normally found in the environment, has not been isolated previously from milk obtained from cows with CM. Therefore, it is possible that K. variicola was not detected in milk samples in the past due to the inability of standard tests to discriminate it from other Klebsiella species.     

Purifying Selection in Deeply Conserved Human Enhancers Is More Consistent than in Coding Sequences

Comparison of polymorphism at synonymous and non-synonymous sites in protein-coding DNA can provide evidence for selective constraint. Non-coding DNA that forms part of the regulatory landscape presents more of a challenge since there is not such a clear-cut distinction between sites under stronger and weaker selective constraint. Here, we consider putative regulatory elements termed Conserved Non-coding Elements (CNEs) defined by their high level of sequence identity across all vertebrates. Some mutations in these regions have been implicated in developmental disorders; we analyse CNE polymorphism data to investigate whether such deleterious effects are widespread in humans. Single nucleotide variants from the HapMap and 1000 Genomes Projects were mapped across nearly 2000 CNEs. In the 1000 Genomes data we find a significant excess of rare derived alleles in CNEs relative to coding sequences; this pattern is absent in HapMap data, apparently obscured by ascertainment bias. The distribution of polymorphism within CNEs is not uniform; we could identify two categories of sites by exploiting deep vertebrate alignments: stretches that are non-variant, and those that have at least one substitution. The conserved category has fewer polymorphic sites and a greater excess of rare derived alleles, which can be explained by a large proportion of sites under strong purifying selection within humans – higher than that for non-synonymous sites in most protein coding regions, and comparable to that at the strongly conserved trans-dev genes. Conversely, the more evolutionarily labile CNE sites have an allele frequency distribution not significantly different from non-synonymous sites. Future studies should exploit genome-wide re-sequencing to obtain better coverage in selected non-coding regions, given the likelihood that mutations in evolutionarily conserved enhancer sequences are deleterious. Discovery pipelines should validate non-coding variants to aid in identifying causal and risk-enhancing variants in complex disorders, in contrast to the current focus on exome sequencing.     

Accelerated Active Case Detection of Visceral Leishmaniasis Patients in Endemic Villages of Bangladesh

Background

The visceral leishmaniasis (VL) elimination program in Bangladesh is in its attack phase. The primary goal of this phase is to decrease the burden of VL as much as possible. Active case detection (ACD) by the fever camp method and an approach using past VL cases in the last 6–12 months have been found useful for detection of VL patients in the community. We aimed to explore the yield of Accelerated Active Case Detection (AACD) of non-self reporting VL as well as the factors that are associated with non-self reporting to hospitals in endemic communities of Bangladesh.

Methods

Our study was conducted in the Trishal sub-district of Mymensingh, a highly VL endemic region of Bangladesh. We used a two-stage sampling strategy from 12 VL endemic unions of Trishal. Two villages from each union were selected at random. We looked for VL patients who had self-reported to the hospital and were under treatment from these villages. Then we conducted AACD for VL cases in those villages using house-to-house visit. Suspected VL cases were referred to the Trishal hospital where diagnosis and treatment of VL was done following National Guidelines for VL case management. We collected socio-demographic information from patients or a patient guardian using a structured questionnaire.

Results

The total number of VL cases was 51. Nineteen of 51 (37.3%) were identified by AACD. Poverty, female gender and poor knowledge about VL were independent factors associated with non self-reporting to the hospital.

Conclusion

Our primary finding is that AACD is a useful method for early detection of VL cases that would otherwise go unreported to the hospital in later stage due to poverty, poor knowledge about VL and gender inequity. We recommend that the National VL Program should consider AACD to strengthen its early VL case detection strategy.     

Identification and analysis of cis-regulatory elements in development using comparative genomics with the pufferfish, Fugu rubripes

The control of vertebrate development is facilitated by cis-regulatory sequences hardwired into the genome. Given that many developmental processes are strikingly similar across all backboned animals, it is reasonable to expect these sequences to be conserved at the nucleotide level, their potential for mutation being constrained by their function. Comparison between the genomes of highly divergent organisms allows such sequences to be identified and some of the most successful approaches have compared regions from the pufferfish, Fugu rubripes, with its distant mammalian relatives, rodents and humans. This review describes progress made in this kind of comparison, from small regions of individual genes, to whole genome alignments.     

Ironic fate: can a banned drug control metal heavies in neurodegenerative diseases?

In this issue of Neuron, Kaur et al. demonstrate that iron chelation by ferritin transgene or the metal chelator clioquinol prevent oxidative damage and MPTP toxicity in mice. This raises the issue of specific iron chelators or clioquinol for control of oxidative damage in Parkinson's, Alzheimer's, and other neurodegenerative diseases, but not without safety concerns.     

Proteomic characterization of protein phosphatase complexes of the mammalian nucleus

Our knowledge of the serine/threonine protein phosphatases of the mammalian nucleus is limited compared with their cytosolic counterparts. Microcystin-Sepharose chromatography and mass spectrometry were utilized to affinity purify and identify protein phosphatase-associated proteins from isolated rat liver nuclei. Far Western analysis with labeled protein phosphatase 1 (PP1) showed that many more PP1 binding proteins exist in the nucleus than were previously demonstrated. Mass spectrometry confirmed the presence in the nucleus of the mammalian PP1 isoforms alpha1, alpha2, beta, and gamma1, plus the Aalpha and several of the B and B' subunits that are complexed to PP2A. Other proteins enriched on the microcystin matrix include the spliceosomal proteins known as the U2 snRNPs SAP145 and SAP155 and the U5 snRNPs p116 and p200, myosin heavy chain, and a nuclear PP1 myosin-targeting subunit related to M110. The putative RNA binding protein ZAP was also established as a nuclear PP1 binding protein using the criteria of co-purification with PP1 on microcystin-Sepharose, co-immunoprecipation, binding PP1 in an overlay assay, and presence of a putative PP1 binding site (KKRVRWAD). These results further support a key role for protein phosphatases in several nuclear functions, including the regulation of pre-mRNA splicing.     

A review of the leishmanin skin test: A neglected test for a neglected disease

The leishmanin skin test (LST) has been used for decades to detect exposure and immunity to the parasite Leishmania, the causative agent of the neglected tropical disease leishmaniasis. In the LST, Leishmania antigen (leishmanin) is intradermally injected into the forearm. In an individual who has been previously infected, a delayed-type hypersensitivity (DTH) reaction results in a measurable induration at the site of the injection, indicating that previous exposure to Leishmania has resulted in the development of cell-mediated immunity. LST positivity is associated with long-lasting protective immunity against reinfection, most notably as reported for visceral leishmaniasis (VL). Despite efforts over the past few decades, leishmanin antigen is no longer produced under good manufacturing practice (GMP) conditions anywhere in the world. Consequently, the use of the LST in epidemiological studies has declined in favor of serological and molecular tests. In this review, we provide a historical overview of the LST and justification for the reintroduction of leishmanin. A GMP-grade leishmanin can be used to detect immunity in vivo by the LST and can be investigated for use in an interferon-γ release assay (IGRA), which may serve as an in vitro version of the LST. The LST will be a valuable tool for surveillance and epidemiological studies in support of the VL elimination programs and as a surrogate marker of immunity in vaccine clinical trials.MethodsA review of the literature was conducted using PubMed as the primary database, with MeSH terms “leishmanin skin test” OR “Montenegro test” OR “Montenegro skin test.” Articles written in English that describe the history or standardization of leishmanin, the use of leishmanin in an IGRA, or the use of the LST in epidemiological studies or vaccine trials were prioritized in our appraisal of the literature.     

Functional Profiling of Live Melanoma Samples Using a Novel Automated Platform

Aims

This proof-of-concept study was designed to determine if functional, pharmacodynamic profiles relevant to targeted therapy could be derived from live human melanoma samples using a novel automated platform.

Methods

A series of 13 melanoma cell lines was briefly exposed to a BRAF inhibitor (PLX-4720) on a platform employing automated fluidics for sample processing. Levels of the phosphoprotein p-ERK in the mitogen-activated protein kinase (MAPK) pathway from treated and untreated sample aliquots were determined using a bead-based immunoassay. Comparison of these levels provided a determination of the pharmacodynamic effect of the drug on the MAPK pathway. A similar ex vivo analysis was performed on fine needle aspiration (FNA) biopsy samples from four murine xenograft models of metastatic melanoma, as well as 12 FNA samples from patients with metastatic melanoma.

Results

Melanoma cell lines with known sensitivity to BRAF inhibitors displayed marked suppression of the MAPK pathway in this system, while most BRAF inhibitor-resistant cell lines showed intact MAPK pathway activity despite exposure to a BRAF inhibitor (PLX-4720). FNA samples from melanoma xenografts showed comparable ex vivo MAPK activity as their respective cell lines in this system. FNA samples from patients with metastatic melanoma successfully yielded three categories of functional profiles including: MAPK pathway suppression; MAPK pathway reactivation; MAPK pathway stimulation. These profiles correlated with the anticipated MAPK activity, based on the known BRAF mutation status, as well as observed clinical responses to BRAF inhibitor therapy.

Conclusion

Pharmacodynamic information regarding the ex vivo effect of BRAF inhibitors on the MAPK pathway in live human melanoma samples can be reproducibly determined using a novel automated platform. Such information may be useful in preclinical and clinical drug development, as well as predicting response to targeted therapy in individual patients.     

Effects of 2-nitrooxy ethyl 2-amino 3-methylbutanoate gel on resistance exercise performance and blood nitrate/nitrite in resistance trained men

Nitric oxide dietary supplements are popular within the sport community. Our recent work involving the oral intake of 2-nitrooxy ethyl 2-amino 3-methylbutanoate demonstrated an approximately 6.7% increase in circulating nitrate/nitrite. However, no measures of exercise performance were obtained. The present study used a topical form of this molecule to determine the impact on exercise performance and blood nitrate/nitrite. Fourteen resistance trained men (24 ± 1 years old) reported to the laboratory on 2 occasions to undergo exercise testing, which consisted of arm curl isometric force and muscular endurance (3 sets to fatigue using 80, 65, and 50% of 1 repetition maximum [1RM]: total of 9 sets). The gel (2-nitrooxy ethyl 2-amino 3-methylbutanoate; mixed in tea tree oil) or placebo (tea tree oil) was applied topically by the subjects for 7 days before each test day, with 7-10 days separating the randomly ordered conditions. Blood samples, arm circumference, and perceived "muscle pump" were taken before and immediately after exercise on both test days. The heart rate and perceived exertion were measured after each set. No statistically significant differences were noted between conditions for performance variables (p > 0.05). However, when using a load of 50% of 1RM, 6.2% more repetitions were performed when using the gel as compared with when using the placebo; 19.9% more repetitions were performed by 8 subjects noted to be "responders" to gel treatment. Blood lactate and muscle pump significantly increased with exercise (p < 0.0001) but were not different between conditions (p > 0.05). Minimal change was noted in nitrate/nitrite, and the heart rate and perceived exertion were nearly identical between conditions (p > 0.05). These findings indicate that 2-nitrooxy ethyl 2-amino 3-methylbutanoate gel has a modest (6.2%), nonstatistically significant effect on exercise performance, in particular when using a load of 50% 1RM-with greater benefit noted in selected individuals. Studies inclusive of a larger sample size are needed to extend these initial findings.     

Learning and discrimination of cuticular hydrocarbons in a social insect

Social insect cuticular hydrocarbon (CHC) mixtures are among the most complex chemical cues known and are important in nest-mate, caste and species recognition. Despite our growing knowledge of the nature of these cues, we have very little insight into how social insects actually perceive and discriminate among these chemicals. In this study, we use the newly developed technique of differential olfactory conditioning to pure, custom-designed synthetic colony odours to analyse signal discrimination in Argentine ants, Linepithema humile. Our results show that tri-methyl alkanes are more easily learned than single-methyl or straight-chain alkanes. In addition, we reveal that Argentine ants can discriminate between hydrocarbons with different branching patterns and the same chain length, but not always between hydrocarbons with the same branching patterns but different chain length. Our data thus show that biochemical characteristics influence those compounds that ants can discriminate between, and which thus potentially play a role in chemical signalling and nest-mate recognition.