Comparative genomic analysis reveals significant enrichment of mobile genetic elements and genes encoding surface structure-proteins in hospital-associated clonal complex 2 Enterococcus faecalis

Background  

Enterococci rank among the leading causes of nosocomial infections. The failure to identify pathogen-specific genes in Enterococcus faecalis has led to a hypothesis where the virulence of different strains may be linked to strain-specific genes, and where the combined endeavor of the different gene-sets result in the ability to cause infection. Population structure studies by multilocus sequence typing have defined distinct clonal complexes (CC) of E. faecalis enriched in hospitalized patients (CC2, CC9, CC28 and CC40).     

Review and meta‐analysis of natural selection in mitochondrial complex I in metazoans

Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may provide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial‐encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high‐resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis.     

Mechanisms of metal resistance in plants: aluminum and heavy metals

Plants have evolved sophisticated mechanisms to deal with toxic levels of metals in the soil. In this paper, an overview of recent progress with regards to understanding fundamental molecular and physiological mechanisms underlying plant resistance to both aluminum (Al) and heavy metals is presented. The discussion of plant Al resistance will focus on recent advances in our understanding of a mechanism based on Al exclusion from the root apex, which is facilitated by Al-activated exudation of organic acid anions. The consideration of heavy metal resistance will focus on research into a metal hyperaccumulating plant species, the Zn/Cd hyperaccumulator, Thlaspi caerulescens, as an example for plant heavy metal research. Based on the specific cases considered in this paper, it appears that quite different strategies are used for Al and heavy metal resistance. For Al, our current understanding of a resistance mechanism based on excluding soil-borne Al from the root apex is presented. For heavy metals, a totally different strategy based on extreme tolerance and metal hyperaccumulation is described for a hyperaccumulator plant species that has evolved on naturally metalliferous soils. The reason these two strategies are the focus of this paper is that, currently, they are the best understood mechanisms of metal resistance in terrestrial plants. However, it is likely that other mechanisms of Al and/or heavy metal resistance are also operating in certain plant species, and there may be common features shared for dealing with Al and heavy resistance. Future research may uncover a number of novel metal resistance mechanisms in plants. Certainly the complex genetics of Al resistance in some crop plant species, such as rice and maize, suggests that a number of presently unidentified mechanisms are part of an overall strategy of metal resistance in crop plants.     

Cell-to-cell transfer of glial proteins to the squid giant axon: The glia- neuron protein transfer hypothesis

The hypothesis that glial cells synthesize proteins which are transferred to adjacent neurons was evaluated in the giant fiber of the squid (Loligo pealei). When giant fibers are separated from their neuron cell bodies and incubated in the presence of radioactive amino acids, labeled proteins appear in the glial cells and axoplasm. Labeled axonal proteins were detected by three methods: extrusion of the axoplasm from the giant fiber, autoradiography, and perfusion of the giant fiber. This protein synthesis is completely inhibited by puromycin but is not affected by chloramphenicol. The following evidence indicates that the labeled axonal proteins are not synthesized within the axon itself. (a) The axon does not contain a significant amount of ribosomes or ribosomal RNA. (b) Isolated axoplasm did not incorporate [(3)H]leucine into proteins. (c) Injection of Rnase into the giant axon did not reduce the appearance of newly synthesized proteins in the axoplasm of the giant fiber. These findings, coupled with other evidence, have led us to conclude that the adaxonal glial cells synthesize a class of proteins which are transferred to the giant axon. Analysis of the kinetics of this phenomenon indicates that some proteins are transferred to the axon within minutes of their synthesis in the glial cells. One or more of the steps in the transfer process appear to involve Ca++, since replacement of extracellular Ca++ by either Mg++ or Co++ significantly reduces the appearance of labeled proteins in the axon. A substantial fraction of newly synthesized glial proteins, possibly as much as 40 percent, are transferred to the giant axon. These proteins are heterogeneous and range in size from 12,000 to greater than 200,000 daltons. Comparisons of the amount of amino acid incorporation in glia cells and neuron cell bodies raise the possibility that the adaxonal glial cells may provide an important source of axonal proteins which is supplemental to that provided by axonal transport from the cell body. These findings are discussed with reference to a possible trophic effect of glia on neurons and metabolic cooperation between adaxonal glia and the axon.     

Life Cycle Greenhouse Gas Emissions of Electricity Generated from Conventionally Produced Natural Gas

This research provides a systematic review and harmonization of the life cycle assessment (LCA) literature of electricity generated from conventionally produced natural gas. We focus on estimates of greenhouse gases (GHGs) emitted in the life cycle of electricity generation from natural gas‐fired combustion turbine (NGCT) and combined‐cycle (NGCC) systems. The smaller set of LCAs of liquefied natural gas power systems and natural gas plants with carbon capture and storage were also collected, but analyzed to a lesser extent. A meta‐analytical process we term “harmonization” was employed to align several system boundaries and technical performance parameters to better allow for cross‐study comparisons, with the aim of clarifying central tendency and reducing variability in estimates of life cycle GHG emissions. Of over 250 references identified, 42 passed screens for technological relevance and study quality, providing a total of 69 estimates for NGCT and NGCC. Harmonization increased the median estimates in each category as a result of several factors not typically considered in the previous research, including the regular clearing of liquids from a well, and consolidated the interquartile range for NGCC to 420 to 480 grams of carbon dioxide equivalent per kilowatt‐hour (g CO₂‐eq/kWh) and for NGCT to 570 to 750 g CO₂‐eq/kWh, with medians of 450 and 670 CO₂‐eq/kWh, respectively. Harmonization of thermal efficiency had the largest effect in reducing variability; methane leakage rate is likely similarly influential, but was unharmonized in this assessment as a result of the significant current uncertainties in its estimation, an area that is justifiably receiving significant research attention.     

Inflammatory myofibroblastic tumor of the breast. A case report

BACKGROUND: Inflammatory myofibroblastic tumor (IMT) of the breast is a very rare tumor like lesion with only 6 previously reported cases. Very little is known about the cytology of IMT. We present the fine needle aspiration (FNA) cytology of a case of recurrent, bilateral IMT of the breast and detail the clinical course, radiologic findings, morphologic appearances and immunohistochemical profile of the lesion. CASE: A 79-year-old female was initially seen in 1991 because of a suspicious mammographic abnormality in her right breast. Ultrasound-guided FNA cytology showed an unusual "inflammatory" lesion with occasional aggregates of cellular connective tissue fragments, sheets of uniform ductal epithelial cells with myoepithelial cells, spindle cells, lymphocytes and histiocytelike cells. The lesion was excised, and histology confirmed a benign process with spindle cells, lymphocytes and histiocytes. No malignant features were noted. During follow-up many new lesions appeared in both breasts, and after several FNA procedures and local excisions, bilateral mastectomy was performed at the patient's urging. She remained disease free. CONCLUSION: Although IMT of the breast has benign cytology and histology, clinically and on imaging, it resembles carcinoma. Awareness of the condition may help prevent a false diagnosis of carcinoma.     

Enterococcal surface protein Esp is not essential for cell adhesion and intestinal colonization of Enterococcus faecium in mice

Background  

Enterococcus faecium has globally emerged as a cause of hospital-acquired infections with high colonization rates in hospitalized patients. The enterococcal surface protein Esp, identified as a potential virulence factor, is specifically linked to nosocomial clonal lineages that are genetically distinct from indigenous E. faecium strains. To investigate whether Esp facilitates bacterial adherence and intestinal colonization of E. faecium, we used human colorectal adenocarcinoma cells (Caco-2 cells) and an experimental colonization model in mice.