Methods for monitoring for the population consequences of disturbance in marine mammals : a review

This work was sponsored by the Office of Naval Research: Marine Mammal Biology Program, under award N000141612858.Assessing the non-lethal effects of disturbance and their population-level consequences is a significant ecological and conservation challenge, because it requires extensive baseline knowledge of behavioral patterns, life-history and demography. However, for many marine mammal populations, this knowledge is currently lacking and it may take decades to fill the gaps. During this time, undetected population declines may occur. In this study we identify methods that can be used to monitor populations subject to disturbance and provide insights into the processes through which disturbance may affect them. To identify and address the knowledge gaps highlighted above, we reviewed the literature to identify suitable response variables and methods for monitoring these variables. We also used existing models of the population consequences of disturbance (PCoD) to identify demographic characteristics (e.g., the proportion of immature animals in the population, or the ratio of calves/pups to mature females) that may be strongly correlated with population status and therefore provide early warnings of future changes in abundance. These demographic characteristics can be monitored using established methods such as visual surveys combined with photogrammetry, and capture-recapture analysis. Individual health and physiological variables can also inform PCoD assessment and can be monitored using photogrammetry, remote tissue sampling, hands-on assessment and individual tracking. We then conducted a workshop to establish the relative utility and feasibility of all these approaches for different groups of marine mammal species. We describe how future marine mammal monitoring programs can be designed to inform population-level analysis.Publisher PDFPeer reviewe

Directed evolution and targeted mutagenesis to murinize listeria monocytogenes internalin A for enhanced infectivity in the murine oral infection model

BACKGROUND: Internalin A (InlA) is a critical virulence factor which mediates the initiation of Listeria monocytogenes infection by the oral route in permissive hosts. The interaction of InlA with the host cell ligand E-cadherin efficiently stimulates L. monocytogenes entry into human enterocytes, but has only a limited interaction with murine cells. RESULTS: We have created a surface display library of randomly mutated InlA in a non-invasive heterologous host Lactococcus lactis in order to create and screen novel variants of this invasion factor. After sequential passage through a murine cell line (CT-26), multiple clones with enhanced invasion characteristics were identified. Competitive index experiments were conducted in mice using selected mutations introduced into L. monocytogenes EGD-e background. A novel single amino acid change was identified which enhanced virulence by the oral route in the murine model and will form the basis of further engineering approaches. As a control a previously described EGD-InlA(m) murinized strain was also re-created as part of this study with minor modifications and designated EGD-e InlA(m)*. The strain was created using a procedure that minimizes the likelihood of secondary mutations and incorporates Listeria-optimized codons encoding the altered amino acids. L. monocytogenes EGD-e InlA(m)* yielded consistently higher level murine infections by the oral route when compared to EGD-e, but did not display the two-fold increased invasion into a human cell line that was previously described for the EGD-InlA(m) strain. CONCLUSIONS: We have used both site-directed mutagenesis and directed evolution to create variants of InlA which may inform future structure-function analyses of this protein. During the course of the study we engineered a murinized strain of L. monocytogenes EGD-e which shows reproducibly higher infectivity in the intragastric murine infection model than the wild type, but does not display enhanced entry into human cells as previously observed. This murinized L. monocytogenes strain will provide a useful tool for the analysis of the gastrointestinal phase of listeriosis

The (1RS,2RS,7RS,8RS)- and (1RS,2SR,7SR,8RS)-diastereoisomers of 8,9,11,12-tetrachloro-N-ethyltricyclo[6.2.2.0²,⁷]dodeca-9,11-diene-1,10-dicarboximide

Two racemic diastereoisomers, C₁₆H₁₅Cl₄NO₂, of the title 1,4-photoadduct of N-ethyltetrachlorophthalimide with cyclohexene have been isolated and their stereostructures determined

Development of multiple strain competitive index assays for Listeria monocytogenes using pIMC; a new site-specific integrative vector

The foodborne, gram-positive pathogen, Listeria monocytogenes, is capable of causing lethal infections in compromised individuals. In the post genomic era of L. monocytogenes research, techniques are required to identify and validate genes involved in the pathogenicity and environmental biology of the organism. The aim here was to develop a widely applicable method to tag L. monocytogenes strains, with a particular emphasis on the development of multiple strain competitive index assays

Development of multiple strain competitive index assays for Listeria monocytogenes using pIMC; a new site-specific integrative vector

<p>Abstract</p> <p>Background</p> <p>The foodborne, gram-positive pathogen, <it>Listeria monocytogenes</it>, is capable of causing lethal infections in compromised individuals. In the post genomic era of <it>L. monocytogenes </it>research, techniques are required to identify and validate genes involved in the pathogenicity and environmental biology of the organism. The aim here was to develop a widely applicable method to tag <it>L. monocytogenes </it>strains, with a particular emphasis on the development of multiple strain competitive index assays.</p> <p>Results</p> <p>We have constructed a new site-specific integrative vector, pIMC, based on pPL2, for the selection of <it>L. monocytogenes </it>from complex samples. The pIMC vector was further modified through the incorporation of IPTG inducible markers (antibiotic and phenotypic) to produce a suite of four vectors which allowed the discrimination of multiple strains from a single sample. We were able to perform murine infection studies with up to four EGDe isolates within a single mouse and showed that the tags did not impact upon growth rate or virulence. The system also allowed the identification of subtle differences in virulence between strains of <it>L. monocytogenes </it>commonly used in laboratory studies.</p> <p>Conclusion</p> <p>This study has developed a competitive index assay that can be broadly applied to all <it>L. monocytogenes </it>strains. Improved statistical robustness of the data was observed, resulting in fewer mice being required for virulence assays. The competitive index assays provide a powerful method to analyse the virulence or fitness of <it>L. monocytogenes </it>in complex biological samples.</p

A Pilot Survey for the H2_2O Southern Galactic Plane Survey (HOPS)

We describe observations with the Mopra radiotelescope designed to assess the feasibility of the H$_2$O maser southern Galactic plane survey (HOPS). We mapped two one-square-degree regions along the Galactic plane using the new 12 mm receiver and the UNSW Mopra spectrometer (MOPS). We covered the entire spectrum between 19.5 and 27.5 GHz using this setup with the main aims of finding out which spectral lines can be detected with a quick mapping survey. We report on detected emission from H$_2$O masers, NH$_3$ inversion transitions (1,1), (2,2) and (3,3), HC$_3$N (3-2), as well as several radio recombination lines.Comment: accepted by PAS

Isolation and characterisation of actinomycin D producing Streptomyces spp. from Sudanese soil

Sudanese soil is an unexplored source of antibiotic-producing microorganisms. Here, we reported the screening of soil samples from Sudan for actinomycetes that have antibacterial activity. Two isolates, AH11.4 and AH47, displaying a broad antimicrobial spectrum were selected for further study. Morphological, physiological and biochemical studies indicated that the two isolates are Streptomyces spp. 16S rDNA sequencing confirmed that the closest matches were to other Streptomyces, but phylogenetic analysis demonstrated that the Sudanese strains were on a different node to previously identified strains. The antibiotic activity was isolated by preparative High-performance liquid chromatography (HPLC) and determined to be primarily actinomycin D on the basis of UV, 1H- and 13CNMR, and MS analyses. One strain also produced actinomycin X2 and aB. These strains are distinct from the known producers of actinomycin, thus are new sources of these antibiotics.Keywords: Screening, antibiotic, antitumour, identificationAfrican Journal of Biotechnology Vol. 12(19), pp. 2624-263

Remote real-time monitoring of subsurface landfill gas migration

The cost of monitoring greenhouse gas emissions from landfill sites is of major concern for regulatory authorities. The current monitoring procedure is recognised as labour intensive, requiring agency inspectors to physically travel to perimeter borehole wells in rough terrain and manually measure gas concentration levels with expensive hand-held instrumentation. In this article we present a cost-effective and efficient system for remotely monitoring landfill subsurface migration of methane and carbon dioxide concentration levels. Based purely on an autonomous sensing architecture, the proposed sensing platform was capable of performing complex analytical measurements in situ and successfully communicating the data remotely to a cloud database. A web tool was developed to present the sensed data to relevant stakeholders. We report our experiences in deploying such an approach in the field over a period of approximately 16 months

Transcutaneous electrical nerve stimulation using an LTP-like repetitive stimulation protocol for patients with upper limb complex regional pain syndrome: A feasibility study

Introduction This feasibility study aimed to (i) develop a clinical protocol using a long-term potentiation-like repetitive stimulation protocol for transcutaneous electrical nerve stimulation in patients with upper limb complex regional pain syndrome and (ii) develop a research protocol for a single-blind randomised controlled trial investigating the efficacy of transcutaneous electrical nerve stimulation for complex regional pain syndrome. Methods This small-scale single-blind feasibility randomised-controlled trial planned to randomise 30 patients with upper limb complex regional pain syndrome to either a variant of transcutaneous electrical nerve stimulation or placebo transcutaneous electrical nerve stimulation for three weeks. Stimulation comprised 20 pulses over 1 s with a non-stimulation interval of 5 s, a so-called repetitive electrical stimulation protocol following the timing of long-term potentiation. Pain, function and body image were measured at baseline, post-treatment and at three months follow-up. At three months, participants were invited to one-to-one interviews, which were analysed thematically. Results A transcutaneous electrical nerve stimulation protocol with electrodes applied proximal to the area of allodynia in the region of the upper arm was developed. Participant concordance with the protocol was high. Recruitment was below target (transcutaneous electrical nerve stimulation (n = 6), placebo (n = 2)). Mean (SD) pain intensity for the transcutaneous electrical nerve stimulation group on a 0 to 10 scale was 7.2 (2.4), 6.6 (2.8) and 7.8 (1.9), at baseline, post-treatment and at three-month follow-up, respectively. Qualitative data suggested that some patients found transcutaneous electrical nerve stimulation beneficial, easy to use and were still using it at three months. Conclusion Patients tolerated transcutaneous electrical nerve stimulation well, and important methodological information to facilitate the design of a large-scale trial was obtained (ISRCTN48768534). </jats:sec

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

peer-reviewedBackground Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood. Results In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms. Conclusions Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2–165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T).This research was conducted with the financial support of Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273, a Science Foundation Ireland’s Spokes Programme which is co-funded under the European Regional Development Fund under Grant Number SFI/14/SP APC/B3032, and a research grant from Janssen Biotech, Inc