bluuebunny/crossref_metadata_2025 huggingface dataset:
Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system
Authors: Voelker Gary , Bowie Rauri C. K. , Klicka John
Published: May 2013

The evolution of migration in birds has fascinated biologists for centuries. In this study, we performed phylogenetic‐based analyses of Catharus thrushes, a model genus in the study of avian migration, and their close relatives. For these analyses, we used both mitochondrial and nuclear genes, and the resulting phylogenies were used to trace migratory traits and biogeographic patterns. Our results provide the first robust assessment of relationships within Catharus and relatives and indicate that both mitochondrial and autosomal genes contribute to overall support of the phylogeny. Measures of phylogenetic informativeness indicated that mitochondrial genes provided more signal within Catharus than did nuclear genes, whereas nuclear loci provided more signal for relationships between Catharus and close relatives than did mitochondrial genes. Insertion and deletion events also contributed important support across the phylogeny. Across all taxa included in the study, and for Catharus, possession of long‐distance migration is reconstructed as the ancestral condition, and a North American (north of Mexico) ancestral area is inferred. Within Catharus, sedentary behaviour evolved after the first speciation event in the genus and is geographically and temporally correlated with Central American distributions and the final closure of the Central American Seaway. Migratory behaviour subsequently evolved twice in Catharus and is geographically and temporally correlated with a recolonization of North America in the late Pleistocene. By temporally linking speciation events with changes in migratory condition and events in Earth history, we are able to show support for several competing hypotheses relating to the geographic origin of migration.
Tracking climate change in a dispersal‐limited species: reduced spatial and genetic connectivity in a montane salamander
Authors: Velo‐Antón G. , Parra J. L. , Parra‐Olea G. , Zamudio K. R.
Published: May 2013

Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane‐adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans‐Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico.
Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex
Authors: Roda Federico , Ambrose Luke , Walter Gregory M. , Liu Huanle L. , Schaul Andrea , Lowe Andrew , Pelser Pieter B. , Prentis Peter , Rieseberg Loren H. , Ortiz‐Barrientos Daniel
Published: May 2013

Instances of parallel ecotypic divergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel divergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection of Senecio species showed that members of the S. lautus complex form a distinct lineage that has diversified recently in Australasia. An inspection of thousands of polymorphisms in the genome of 27 natural populations from the S. lautus complex in Australia revealed a signal of strong genetic structure independent of habitat and phenotype. Additionally, genetic differentiation between populations was correlated with the geographical distance separating them, and the genetic diversity of populations strongly depended on geographical location. Importantly, coastal forms appeared in several independent phylogenetic clades, a pattern that is consistent with the parallel evolution of these forms. Analyses of the patterns of genomic differentiation between populations further revealed that adjacent populations displayed greater genomic heterogeneity than allopatric populations and are differentiated according to variation in soil composition. These results are consistent with a process of parallel ecotypic divergence in face of gene flow.
Melanins and melanogenesis: methods, standards, protocols
Authors: d'Ischia Marco , Wakamatsu Kazumasa , Napolitano Alessandra , Briganti Stefania , Garcia‐Borron José‐Carlos , Kovacs Daniela , Meredith Paul , Pezzella Alessandro , Picardo Mauro , Sarna Tadeusz , Simon John D. , Ito Shosuke
Published: May 2013

Despite considerable advances in the past decade, melanin research still suffers from the lack of universally accepted and shared nomenclature, methodologies, and structural models. This paper stems from the joint efforts of chemists, biochemists, physicists, biologists, and physicians with recognized and consolidated expertise in the field of melanins and melanogenesis, who critically reviewed and experimentally revisited methods, standards, and protocols to provide for the first time a consensus set of recommended procedures to be adopted and shared by researchers involved in pigment cell research. The aim of the paper was to define an unprecedented frame of reference built on cutting‐edge knowledge and state‐of‐the‐art methodology, to enable reliable comparison of results among laboratories and new progress in the field based on standardized methods and shared information.
Modulation of the Photophysical Properties of Pyrene by the Microstructures of Five Poly(alkyl methacrylate)s Over a Broad Temperature Range
Authors: Atvars Teresa D. Z. , Abraham Shibu , Hill Anita J. , Pas Steven J. , Chesta Carlos , Weiss Richard G.
Published: May 2013

Pyrene fluorescence spectra have been recorded in five poly(alkyl methacrylate)s (where alkyl is ethyl butyl, isobutyl, cyclohexyl and hexadecyl) over a 20–400 K temperature range. The changes in the position and the full width at half maximum (FWHM) of the 0–0 emission band (peak I) have been correlated with the structural characteristics of the alkyl groups in the different relaxation regimes of the polymers to assess the degree of coupling of the excited singlet states with the polymer cybotactic regions. Data treatment of the peak I positions using an electron–phonon model indicates that longitudinal optical modes are involved, and that the magnitude of coupling depends on the polymer structure and follows the same trend as the glass transition temperatures. The same spectral parameters have been correlated also with “hole” free volumes from positron annihilation spectroscopy over temperature ranges which span the glass or melting transitions of the polymers. Reasons why free volume and FWHM measurements follow the same trends, and other aspects of the systems, are discussed.
Erythema dose ‐ a novel global objective index for facial erythema by computer‐aided image analysis
Authors: Choi Jae Woo , Kwon Soon Hyo , Jo Seong Moon , Youn Sang Woong
Published: May 2013

Background

Facial erythema is a common but morbid condition caused by several inflammatory disorders. Since most of the current severity indexes lack objectivity and global assessment, the computer‐aided image analysis (CAIA) has been suggested.

Objective

The purpose of this study is to compare the validity and efficacy of novel CAIA erythema index – erythema dose (ED) with two other CAIA indexes.

Methods

For mild, moderated and severe erytherotelangiectatic rosacea patients, their photographs of right cheek were assessed with red‐blue difference index in image (RBI), a*, and ED. For each index, the differences between severity groups were analyzed. The correlations between the three indexes were evaluated. To evaluate the capability of differentiating the pathologic erythema from the red component of the normal skin, each index was calculated at both the erythema and normal area.

Results

The a* and ED significantly changed according to the severity, while the RBI did not. The ED was different between both mild‐moderate and moderate‐severe, while the a* only between mild‐moderate. There was a strong positive correlation between a* and ED. The difference between erythema and normal skin was more prominent in ED than in a*.

Conclusion

We confirmed that the ED is well correlated with both subjective assessment, as well as the other CAIA index a*. The ED has the advantage of specifically visualizing and analyzing the pathologic erythema.
Extraplastidial cytidinediphosphate diacylglycerol synthase activity is required for vegetative development in Arabidopsis thaliana
Authors: Zhou Yonghong , Peisker Helga , Weth Agnes , Baumgartner Werner , Dörmann Peter , Frentzen Margrit
Published: May 2013

Cytidinediphosphate diacylglycerol synthase (CDS) catalyzes the activation of phosphatidic acid to cytidinediphosphate (CDP)‐diacylglycerol, a central intermediate in glycerolipid biosynthesis in prokaryotic and eukaryotic organisms. Cytidinediphosphate‐diacylglycerol is the precursor to phosphatidylinositol, phosphatidylglycerol (PG) and cardiolipin of eukaryotic phospholipids that are essential for various cellular functions. Isoforms of CDS are located in plastids, mitochondria and the endomembrane system of plants and are encoded by five genes in Arabidopsis. Two genes have previously been shown to code for the plastidial isoforms which are indispensable for the biosynthesis of plastidial PG, and thus biogenesis and function of thylakoid membranes. Here we have focused on the extraplastidial CDS isoforms, encoded by CDS1 and CDS2 which are constitutively expressed contrary to CDS3. We provide evidence that these closely related CDS genes code for membrane proteins located in the endoplasmic reticulum and possess very similar enzymatic properties. Development and analysis of Arabidopsis mutants lacking either one or both CDS1 and CDS2 genes clearly shows that these two genes have redundant functions. As reflected in the seedling lethal phenotype of the cds1cds2 double mutant, plant cells require at least one catalytically active microsomal CDS isoform for cell division and expansion. According to the altered glycerolipid composition of the double mutant in comparison with wild‐type seedlings, it is likely that the drastic decrease in the level of phosphatidylinositol and the increase in phosphatidic acid cause defects in cell division and expansion.
Structural characterizations of the chloroplast translocon protein Tic110
Authors: Tsai Jia‐Yin , Chu Chiung‐Chih , Yeh Yi‐Hung , Chen Lih‐Jen , Li Hsou‐min , Hsiao Chwan‐Deng
Published: May 2013

Tic110 is a major component of the chloroplast protein import translocon. Two functions with mutually exclusive structures have been proposed for Tic110: a protein‐conducting channel with six transmembrane domains and a scaffold with two N‐terminal transmembrane domains followed by a large soluble domain for binding transit peptides and other stromal translocon components. To investigate the structure of Tic110, Tic110 from Cyanidioschyzon merolae (CmTic110) was characterized. We constructed three fragments, CmTic110A, CmTic110B and CmTic110C, with increasing N‐terminal truncations, to perform small‐angle X‐ray scattering (SAXS) and X‐ray crystallography analyses and Dali structural comparison. Here we report the molecular envelope of CmTic110B and CmTic110C determined by SAXS, and the crystal structure of CmTic110C at 4.2 Å. Our data indicate that the C‐terminal half of CmTic110 possesses a rod‐shaped helix‐repeat structure that is too flattened and elongated to be a channel. The structure is most similar to the HEAT‐repeat motif that functions as scaffolds for protein–protein interactions.
Hsc70‐induced Changes in Clathrin‐Auxilin Cage Structure Suggest a Role for Clathrin Light Chains in Cage Disassembly
Authors: Young Anna , Stoilova‐McPhie Svetla , Rothnie Alice , Vallis Yvonne , Harvey‐Smith Phillip , Ranson Neil , Kent Helen , Brodsky Frances M. , Pearse Barbara M. F. , Roseman Alan , Smith Corinne J.
Published: May 2013

The molecular chaperone, Hsc70, together with its co‐factor, auxilin, facilitates the ATP‐dependent removal of clathrin during clathrin‐mediated endocytosis in cells. We have used cryo‐electron microscopy to determine the 3D structure of a complex of clathrin, auxilin401‐910 and Hsc70 at pH 6 in the presence of ATP, frozen within 20 seconds of adding Hsc70 in order to visualize events that follow the binding of Hsc70 to clathrin and auxilin before clathrin disassembly. In this map, we observe density beneath the vertex of the cage that we attribute to bound Hsc70. This density emerges asymmetrically from the clathrin vertex, suggesting preferential binding by Hsc70 for one of the three possible sites at the vertex. Statistical comparison with a map of whole auxilin and clathrin previously published by us reveals the location of statistically significant differences which implicate involvement of clathrin light chains in structural rearrangements which occur after Hsc70 is recruited. Clathrin disassembly assays using light scattering suggest that loss of clathrin light chains reduces the efficiency with which auxilin facilitates this reaction. These data support a regulatory role for clathrin light chains in clathrin disassembly in addition to their established role in regulating clathrin assembly.
pH‐Dependent Recycling of Galectin‐3 at the Apical Membrane of Epithelial Cells
Authors: Straube Tamara , von Mach Tobias , Hönig Ellena , Greb Christoph , Schneider Dominik , Jacob Ralf
Published: May 2013

The β‐galactoside binding protein galectin‐3 is highly expressed in a variety of epithelial cell lines. Polarized MDCK cells secrete this lectin predominantly into the apical medium by non‐classical secretion. Once within the apical extracellular milieu, galectin‐3 can re‐enter the cell followed by passage through endosomal organelles and modulate apical protein sorting. Here, we could show that galectin‐3 is internalized by non‐clathrin mediated endocytosis. Within endosomal organelles this pool associates with newly synthesized neurotrophin receptor in the biosynthetic pathway and assists in its membrane targeting. This recycling process is accompanied by transient interaction of galectin‐3 with detergent insoluble membrane microdomains in a lactose‐ and pH‐dependent manner. Moreover, in the presence of lactose, apical sorting of the neurotrophin receptor is affected following endosomal deacidification. Taken together, our results suggest that internalized galectin‐3 directs the subcellular targeting of apical glycoproteins by membrane recycling.
Serial haemostatic monitoring of dogs with multicentric lymphoma
Authors: Kol A. , Marks S. L. , Skorupski K. A. , Kass P. H. , Guerrero T. , Gosselin R. C. , Borjesson D. L.
Published: May 2013

Lymphoma is the most common haematopoietic malignancy in dogs and it has been associated with hypercoagulability and subsequent thromboembolism. The objectives of this study were to serially characterize the haemostatic status of dogs with multicentric lymphoma. Thromboelastography, thrombin–antithrombin complex concentration and routine haematology and coagulation panels were measured. Twenty‐seven dogs were included in the study and 15 completed the study in remission. At presentation, 81% (22/27) of dogs with multicentric lymphoma had altered haemostatic profiles consistent with hypercoagulability. Laboratory evidence of hypercoagulability did not resolve during treatment or for up to 1 month following attainment of clinical remission. Accelerated rate of clot formation at the time of chemotherapeutic protocol completion was associated with decreased survival time. We concluded that dogs with multicentric lymphoma were frequently hypercoagulable from presentation through 4 weeks after the completion of chemotherapy. Increased angle and shortenedKin dogs that have successfully completed their chemotherapeutic protocol may be associated with shorter survival times.
Collection, processing and testing of bone, corneas, umbilical cord blood and haematopoietic stem cells by European Blood Alliance members
Authors: Närhi M. , Natri O. , Desbois I. , Kinggaard Holm D. , Galea G. , Aranko K. , Korhonen M. , Nordstrom K.
Published: May 2013

Background and Objectives

A questionnaire study was carried out in collaboration with the European Blood Alliance (EBA) Tissues and Cells (T&C) working group. The aim was to assess the level of involvement and commonality of processes on the procurement, testing and storage of bone, corneas, umbilical cord blood (UCB) and haematopoietic stem cells (HSC) in order to identify different practices and to explore whether recommendations can be made for harmonization.

Materials and Methods

An online questionnaire was used for data collection in 2011, and 43 replies were received covering 71 product answers from 13 countries.

Results and conclusions

Estimated percentages of tissue and cell banking covered by EBA member blood banks as a proportion of all collections of each individual country varied markedly. There were also major differences in the amounts of products collected and discarded and in proportions tissues provided for grafting. However, discarding of certain collections also reflects the practice of increasing the likelihood of the very best units being used for transplantation. Harmonization of possible practices should focus on matching supply with demand and on identifying the most efficient operators. This could allow for the development of practices for minimizing unnecessary collections.
Q Fever in Alberta, Canada: 1998–2011
Authors: Snedeker K. G. , Sikora C.
Published: May 2013

Establishing the diagnosis of Q fever (Coxiella burnetii) is important in directing the application of therapy to prevent severe manifestations of the infection. In Alberta, Canada, the presence of high livestock density creates a significant risk of infection, but to date, there has been no comprehensive analysis of local Q fever epidemiological trends and exposure patterns. Between 1998 and 2011, there were 39 cases and an overall adjusted case rate of 0.087 per 100 000 person‐years. Cases were identified most commonly during the May–June season (Figure 2). The median age at date of diagnosis was 49.0 (range: 8.7–71.5) with slightly higher percentage of cases in men (56.4%) than in women (43.6%). There was an apparent geographical clustering of cases. The majority of these cases, with exposure data (n = 31), reported contact with farms and/or livestock, predominantly cattle (6), sheep (5) and goats (5). Cases tended to occur in census divisions with higher density of sheep, goats and cattle. Our findings suggest the need for an increase in targeted messages about Q fever to those in the livestock industry, as more targeted case finding among patients with a high index of suspicion for Q fever. In addition, widespread implementation of a standard questionnaire for cases would enhance surveillance of Q fever in Alberta.
Impairment of pancreatic β‐cell function by chronic intermittent hypoxia
Authors: Wang Ning , Khan Shakil A. , Prabhakar Nanduri R. , Nanduri Jayasri
Published: May 2013

New Findings

What is the central question of this study?

Periodic decreases in arterial blood O2 or chronic intermittent hypoxia (CIH) is a hallmark feature of sleep apnoea patients. Despite a large body of clinical evidence linking sleep‐disordered breathing with apnoeas to diabetes, the causal relationships between CIH and β‐cell function and the underlying molecular mechanisms have not been established.

What is the main finding and its importance?

In a rodent model, we show that mitochondrial oxidative stress generated by CIH leads to pancreatic β‐cell dysfunction manifested by augmented basal insulin secretion, insulin resistance, defective proinsulin processing and impaired glucose‐stimulated insulin secretion. The results of the present study provide evidence for direct effects of CIH on β‐cell function, which may be an underlying molecular mechanism contributing to the development of type 2 diabetes among sleep apnoea patients.

Breathing disorders with recurrent apnoea produce periodic decreases in arterial blood O2, i.e. chronic intermittent hypoxia (CIH). Recurrent apnoea patients and CIH‐exposed rodents exhibit several co‐morbidities, including diabetes. However, the effects of CIH on pancreatic β‐cell function are not known. In the present study, we investigated pancreatic β‐cell function in C57BL6 mice exposed to 30 days of CIH. Compared with control animals, the CIH‐exposed mice exhibited elevated levels of fasting plasma insulin but comparable glucose levels and higher homeostasis model assessment, indicating insulin resistance. Pancreatic β‐cell morphology was unaltered in CIH‐exposed mice. Insulin content was decreased in CIH‐exposed β‐cells, and this effect was associated with increased proinsulin levels. The mRNA and protein levels of the enzyme prohormone convertase 1, which converts proinsulin to insulin, were downregulated in CIH‐treated islets. More importantly, glucose‐stimulated insulin secretion was impaired in CIH‐exposed mice and in isolated islets. Mitochondrial levels of reactive oxygen species (ROS) were elevated in CIH‐exposed pancreatic islets. Treatment of mice with mito‐tempol, a scavenger of mitochondrial ROS, during exposure to CIH prevented the augmented insulin secretion and restored the proinsulin and homeostasis model assessment values to control levels. These results demonstrate that CIH leads to pancreatic β‐cell dysfunction, manifested by augmented basal insulin secretion, insulin resistance, defective proinsulin processing, impaired glucose‐stimulated insulin secretion and increased mitochondrial ROS, which mediate the effects of CIH on pancreatic β‐cell function.
Sternohyoid and diaphragm muscle form and function during postnatal development in the rat
Authors: O’Connell R. A. , Carberry J. , O’Halloran K. D.
Published: May 2013

New Findings

What is the central question of this study?

Co‐ordinated activity of the thoracic pump and pharyngeal dilator muscles is critical for maintaining airway calibre and respiratory homeostasis. Whilst postnatal maturation of the diaphragm has been well characterized, surprisingly little is known about the developmental programme in the airway dilator muscles.

What is the main finding and its importance?

Developmental increases in force‐generating capacity and fatigue in the sternohyoid and diaphragm muscles are attributed to a maturational shift in muscle myosin heavy chain phenotype. This maturation is accelerated in the sternohyoid muscle relative to the diaphragm and may have implications for the control of airway calibre in vivo.

The striated muscles of breathing, including the thoracic pump and pharyngeal dilator muscles, play a critical role in maintaining respiratory homeostasis. Whilst postnatal maturation of the diaphragm has been well characterized, surprisingly little is known about the developmental programme in airway dilator muscles given that co‐ordinated activity of both sets of muscles is needed for the maintenance of airway calibre and effective pulmonary ventilation. The form and function of sternohyoid and diaphragm muscles from Wistar rat pups [postnatal day (PD) 10, 20 and 30] was determined. Isometric contractile and endurance properties were examined in tissue baths containing Krebs solution at 35°C. Myosin heavy chain (MHC) isoform composition was determined using immunofluorescence. Muscle oxidative and glycolytic capacity was assessed by measuring the activities of succinate dehydrogenase and glycerol‐3‐phosphate dehydrogenase using semi‐quantitative histochemistry. Sternohyoid and diaphragm peak isometric force and fatigue increased significantly with postnatal maturation. Developmental myosin disappeared by PD20, whereas MHC2B areal density increased significantly from PD10 to PD30, emerging earlier and to a much greater extent in the sternohyoid muscle. The numerical density of fibres expressing MHC2X and MHC2B increased significantly during development in the sternohyoid. Diaphragm succinate dehydrogenase activity and sternohyoid glycerol‐3‐phosphate dehydrogenase activity increased significantly with age. Developmental increases in force‐generating capacity and fatigue in the sternohyoid and diaphragm muscles are attributed to a postnatal shift in muscle MHC phenotype. The accelerated maturation of the sternohyoid muscle relative to the diaphragm may have implications for the control of airway calibre in vivo.
Impact of Component Sizing in Plug-In Hybrid Electric Vehicles for Energy Resource and Greenhouse Emissions Reduction1
Authors: Malikopoulos Andreas A.
Published: May 2013

Widespread use of alternative hybrid powertrains currently appears inevitable and many opportunities for substantial progress remain. The necessity for environmentally friendly vehicles, in conjunction with increasing concerns regarding U.S. dependency on foreign oil and climate change, has led to significant investment in enhancing the propulsion portfolio with new technologies. Recently, plug-in hybrid electric vehicles (PHEVs) have attracted considerable attention due to their potential to reduce petroleum consumption and greenhouse gas (GHG) emissions in the transportation sector. PHEVs are especially appealing for short daily commutes with excessive stop-and-go driving. However, the high costs associated with their components, and in particular, with their energy storage systems have been significant barriers to extensive market penetration of PHEVs. In the research reported here, we investigated the implications of motor/generator and battery size on fuel economy and GHG emissions in a medium duty PHEV. An optimization framework is proposed and applied to two different parallel powertrain configurations, pretransmission and post transmission, to derive the Pareto frontier with respect to motor/generator and battery size. The optimization and modeling approach adopted here facilitates better understanding of the potential benefits from proper selection of motor/generator and battery size on fuel economy and GHG emissions. This understanding can help us identify the appropriate sizing of these components and thus reducing the PHEV cost. Addressing optimal sizing of PHEV components could aim at an extensive market penetration of PHEVs.
Analytical Model to Estimate the Downhole Casing Wear Using the Total Wellbore Energy
Authors: Kumar Aniket , Nwachukwu Joseph , Samuel Robello
Published: May 2013

The increasing complexities of wellbore geometry imply an increasing potential of damage resulting from the casing-wear downhole. Much work has been done to quantify and estimate wear in casing; however, the results of such predictions have been mixed. While the locations of critical-wear areas along the casing string have been predicted fairly accurately, quantifying the actual amount of casing wear has been a magnitude off. A mathematical model that describes this casing wear in terms of the total wellbore energy has been developed and used to estimate the depth of the wear groove and the wear volume downhole. The wellbore energy provides a mathematical criterion to quantify the borehole quality and incorporates the parameters, borehole curvature, and the wellbore torsion. The casing wear observed downhole is also an integral function of these two parameters. Hence, a combined “wear-energy” model has been proposed to estimate the casing wear in curved sections of the wellbore that have the drill string lying on its low side. The fundamental assumption of this model is that the volume worn away from the casing wall is proportional to the work done by friction on its inner wall by the tool joints only. It also assumes that the primary mechanism for casing wear is the rotation of the drill string, and the wear caused during tripping is insignificant. The borehole torsion models of wellbore trajectory, namely spatial-arc, natural-curve, cylindrical-helix, and constant-tool face, have been incorporated separately to enhance the accuracy of estimating the wear volume downhole. The wear-energy model for a detailed analysis of a practical example using real-time well survey data will be presented. Wear zones along the wellbore have been identified using a mathematical criterion of the “contact zone parameter.” The wear-groove depths for each contact zone along with an equivalent average wear for the curved section of the wellbore have been estimated. The wear volumes predicted by the various curvature and torsion models of wellbore energy have been graphically studied. The wellbore torsion has been found to significantly impact the casing-wear downhole.
Enterococcus faecalis Grows on Ascorbic Acid
Authors: Mehmeti Ibrahim , Solheim Margrete , Nes Ingolf F. , Holo Helge
Published: May 2013

We show that
Enterococcus faecalis
can utilize ascorbate for fermentative growth. In chemically defined media, growth yield was limited by the supply of amino acids, and the cells showed a much higher demand for amino acids than when they were grown on glucose.
Evaluation of Aerated Steam Treatment of Alfalfa and Mung Bean Seeds To Eliminate High Levels of Escherichia coli O157:H7 and O178:H12, Salmonella enterica, and Listeria monocytogenes
Authors: Studer Patrick , Heller Werner E. , Hummerjohann Jörg , Drissner David
Published: May 2013

Sprouts contaminated with human pathogens are able to cause food-borne diseases due to the favorable growth conditions for bacteria during germination and because of minimal processing steps prior to consumption. We have investigated the potential of hot humid air, i.e., aerated steam, to treat alfalfa and mung bean seeds which have been artificially contaminated with
Escherichia coli
O157:H7,
Salmonella enterica
subsp.
enterica
serovar Weltevreden, and
Listeria monocytogenes
Scott A. In addition, a recently collected
E. coli
O178:H12 isolate, characterized by a reduced heat sensitivity, was exposed to the treatment described. Populations of
E. coli
O157:H7 and
S. enterica
on alfalfa and mung bean seeds could be completely eliminated by a 300-s treatment with steam at 70 ± 1°C as revealed by enrichment studies.
L. monocytogenes
and
E. coli
O178:H12 could not be completely eliminated from artificially inoculated seeds. However, bacterial populations were reduced by more than 5 log CFU/g on alfalfa and by more than 4 log CFU/g on mung bean seeds. The germination rate of mung beans was not affected by the 300-s treatment compared to the germination rate of untreated seeds whereas that of alfalfa seeds was significantly lower by 11.9%. This chemical-free method is an effective alternative to the 20,000-ppm hypochlorite treatment presently recommended by the U.S. Food and Drug Administration (FDA).
The Microbiome of the Red Sea Coral Stylophora pistillata Is Dominated by Tissue-Associated Endozoicomonas Bacteria
Authors: Bayer Till , Neave Matthew J. , Alsheikh-Hussain Areej , Aranda Manuel , Yum Lauren K. , Mincer Tracy , Hughen Konrad , Apprill Amy , Voolstra Christian R.
Published: May 2013

Endozoicomonas
bacteria were found highly associated with the coral
Stylophora pistillata
, and these bacteria are also ubiquitously associated with diverse corals worldwide. Novel
Endozoicomonas
-specific probes revealed that
Endozoicomonas
bacteria were abundant in the endodermal tissues of
S. pistillata
and appear to have an intimate relationship with the coral.
Development of a Propionibacterium-Escherichia coli Shuttle Vector for Metabolic Engineering of Propionibacterium jensenii, an Efficient Producer of Propionic Acid
Authors: Zhuge Xin , Liu Long , Shin Hyun-dong , Chen Rachel R. , Li Jianghua , Du Guocheng , Chen Jian
Published: May 2013

Propionic acid (PA) is an important chemical building block and is widely applied for organic synthesis, food, feedstuff, and pharmaceuticals. To date, the strains that can efficiently produce PA have includedPropionibacterium thoenii,P. freudenreichii, andP. acidipropionici. In this report, we show thatP. jenseniiATCC 4868 is also able to produce PA in much higher yields than the previously reported strains. To further improve the production capacity, aP. jensenii-Escherichia colishuttle vector was developed for the metabolic engineering ofP. jensenii. Specifically, a 6.9-kb endogenous plasmid, pZGX01, was isolated fromP. acidipropioniciATCC 4875 and sequenced. Since the sequencing analysis indicated that pZGX01 could encode 11 proteins, the transcriptional levels of the corresponding genes were also investigated. Then, aP. jensenii-Escherichia colishuttle vector was constructed using the pZGX01 plasmid, theE. colipUC18 plasmid, and a chloramphenicol resistance gene. Interestingly, not only could the developed shuttle vector be transformed intoP. jenseniiATCC 4868 and 4870, but it also could be transformed intofreudenreichiiATCC 6207 subspecies ofP. freudenreichii. Finally, the glycerol dehydrogenase gene (gldA) fromKlebsiella pneumoniaewas expressed inP. jenseniiATCC 4868 with the constructed shuttle vector. In a 3-liter batch culture, the PA production by the engineeredP. jenseniiATCC 4868 strain reached 28.23 ± 1.0 g/liter, which was 26.07% higher than that produced by the wild-type strain (22.06 ± 1.2 g/liter). This result indicated that the constructed vector can be used a useful tool for metabolic engineering ofP. jensenii.
Involvement of the Novel Two-Component NsrRS and LcrRS Systems in Distinct Resistance Pathways against Nisin A and Nukacin ISK-1 in Streptococcus mutans
Authors: Kawada-Matsuo Miki , Oogai Yuichi , Zendo Takeshi , Nagao Junichi , Shibata Yukie , Yamashita Yoshihisa , Ogura Yoshitoshi , Hayashi Tetsuya , Sonomoto Kenji , Komatsuzawa Hitoshi
Published: May 2013

The novel two-component systems NsrRS and LcrRS are individually associated with resistance against the distinct lantibiotics nisin A and nukacin ISK-1 in
Streptococcus mutans
. NsrRS regulates the expression of NsrX, which is associated with nisin A binding, and LcrRS regulates the expression of the ABC transporter LctFEG.
Development of Biotin-Prototrophic and -Hyperauxotrophic Corynebacterium glutamicum Strains
Authors: Ikeda Masato , Miyamoto Aya , Mutoh Sumire , Kitano Yuko , Tajima Mei , Shirakura Daisuke , Takasaki Manami , Mitsuhashi Satoshi , Takeno Seiki
Published: May 2013

To develop the infrastructure for biotin production through naturally biotin-auxotrophicCorynebacterium glutamicum, we attempted to engineer the organism into a biotin prototroph and a biotin hyperauxotroph. To confer biotin prototrophy on the organism, the cotranscribedbioBFgenes ofEscherichia coliwere introduced into theC. glutamicumgenome, which originally lacked thebioFgene. The resulting strain still required biotin for growth, but it could be replaced by exogenous pimelic acid, a source of the biotin precursor pimelate thioester linked to either coenzyme A (CoA) or acyl carrier protein (ACP). To bridge the gap between the pimelate thioester and its dedicated precursor acyl-CoA (or -ACP), thebioIgene ofBacillus subtilis, which encoded a P450 protein that cleaves a carbon-carbon bond of an acyl-ACP to generate pimeloyl-ACP, was further expressed in the engineered strain by using a plasmid system. This resulted in a biotin prototroph that is capable of thede novosynthesis of biotin. On the other hand, thebioYgene responsible for biotin uptake was disrupted in wild-typeC. glutamicum. Whereas the wild-type strain required approximately 1 μg of biotin per liter for normal growth, thebioYdisruptant (ΔbioY) required approximately 1 mg of biotin per liter, almost 3 orders of magnitude higher than the wild-type level. The ΔbioYstrain showed a similar high requirement for the precursor dethiobiotin, a substrate forbioB-encoded biotin synthase. To eliminate the dependency on dethiobiotin, thebioBgene was further disrupted in both the wild-type strain and the ΔbioYstrain. By selectively using the resulting two strains (ΔbioBand ΔbioBY) as indicator strains, we developed a practical biotin bioassay system that can quantify biotin in the seven-digit range, from approximately 0.1 μg to 1 g per liter. This bioassay proved that the engineered biotin prototroph ofC. glutamicumproduced biotin directly from glucose, albeit at a marginally detectable level (approximately 0.3 μg per liter).
The Highly Autoaggregative and Adhesive Phenotype of the Vaginal Lactobacillus plantarum Strain CMPG5300 Is Sortase Dependent
Authors: Malik Shweta , Petrova Mariya I. , Claes Ingmar J. J. , Verhoeven Tine L. A. , Busschaert Pieter , Vaneechoutte Mario , Lievens Bart , Lambrichts Ivo , Siezen Roland J. , Balzarini Jan , Vanderleyden Jos , Lebeer Sarah
Published: May 2013

Lactobacilli are important for the maintenance of a healthy ecosystem in the human vagina. Various mechanisms are postulated but so far are poorly substantiated by molecular studies, such as mutant analysis. Bacterial autoaggregation is an interesting phenomenon that can promote adhesion to host cells and displacement of pathogens. In this study, we report on the identification of a human vaginal isolate,
Lactobacillus plantarum
strain CMPG5300, which shows high autoaggregative and adhesive capacity. To investigate the importance of sortase-dependent proteins (SDPs) in these phenotypes, a gene deletion mutant was constructed for
srtA
, the gene encoding the housekeeping sortase that covalently anchors these SDPs to the cell surface. This mutant lost the capacity to autoaggregate, showed a decrease in adhesion to vaginal epithelial cells, and lost biofilm-forming capacity under the conditions tested. These results indicate that the housekeeping sortase SrtA of CMPG5300 is a key determinant of the peculiar surface properties of this vaginal
Lactobacillus
strain.
Precipitation of Iron on the Surface of Leptospira interrogans Is Associated with Mutation of the Stress Response Metalloprotease HtpX
Authors: Henry Rebekah , Lo Miranda , Khoo Chenai , Zhang Hailong , Boysen Reinhard I. , Picardeau Mathieu , Murray Gerald L. , Bulach Dieter M. , Adler Ben
Published: May 2013

High concentrations of free metal ions in the environment can be detrimental to bacterial survival. However, bacteria utilize strategies, including the activation of stress response pathways and immobilizing chemical elements on their surface, to limit this toxicity. In this study, we characterized LA4131, the HtpX-like M48 metalloprotease from
Leptospira interrogans
, with a putative role in bacterial stress response and membrane homeostasis. Growth of the
la4131
transposon mutant strain (L522) in 360 μM FeSO
4
(10-fold the normal
in vitro
concentration) resulted in the production of an amorphous iron precipitate. Atomic force microscopy and transmission electron microscopy analysis of the strain demonstrated that precipitate production was associated with the generation and release of outer membrane vesicles (OMVs) from the leptospiral surface. Transcriptional studies indicated that inactivation of
la4131
resulted in altered expression of a subset of metal toxicity and stress response genes. Combining these findings, this report describes OMV production in response to environmental stressors and associates OMV production with the
in vitro
activity of an HtpX-like metalloprotease.
A Stable Hybrid Containing Haploid Genomes of Two Obligate Diploid Candida Species
Authors: Chakraborty Uttara , Mohamed Aiyaz , Kakade Pallavi , Mugasimangalam Raja C. , Sadhale Parag P. , Sanyal Kaustuv
Published: May 2013

Candida albicans
and
Candida dubliniensis
are diploid, predominantly asexual human-pathogenic yeasts. In this study, we constructed tetraploid (4
n
) strains of
C. albicans
of the same or different lineages by spheroplast fusion. Induction of chromosome loss in the tetraploid
C. albicans
generated diploid or near-diploid progeny strains but did not produce any haploid progeny. We also constructed stable heterotetraploid somatic hybrid strains (2
n
+ 2
n
) of
C. albicans
and
C. dubliniensis
by spheroplast fusion. Heterodiploid (
n
+
n
) progeny hybrids were obtained after inducing chromosome loss in a stable heterotetraploid hybrid. To identify a subset of hybrid heterodiploid progeny strains carrying at least one copy of all chromosomes of both species, unique centromere sequences of various chromosomes of each species were used as markers in PCR analysis. The reduction of chromosome content was confirmed by a comparative genome hybridization (CGH) assay. The hybrid strains were found to be stably propagated. Chromatin immunoprecipitation (ChIP) assays with antibodies against centromere-specific histones (
C. albicans
Cse4/
C. dubliniensis
Cse4) revealed that the centromere identity of chromosomes of each species is maintained in the hybrid genomes of the heterotetraploid and heterodiploid strains. Thus, our results suggest that the diploid genome content is not obligatory for the survival of either
C. albicans
or
C. dubliniensis
. In keeping with the recent discovery of the existence of haploid
C. albicans
strains, the heterodiploid strains of our study can be excellent tools for further species-specific genome elimination, yielding true haploid progeny of
C. albicans
or
C. dubliniensis
in future.
Frequency and Genetic Diversity of the
MAT1
Locus of Histoplasma capsulatum Isolates in Mexico and Brazil
Authors: Rodríguez-Arellanes Gabriela , Nascimento de Sousa Carolina , de Medeiros-Muniz Mauro , Ramírez José A. , Pizzini Cláudia V. , de Abreu-Almeida Marcos , Evangelista de Oliveira Manoel M. , Fusco-Almeida Ana-Marisa , Vite-Garín Tania , Pitangui Nayla S. , Estrada-Bárcenas Daniel A. , González-González Antonio E. , Mendes-Giannini María José Soares , Zancopé-Oliveira Rosely M. , Taylor Maria-Lucia
Published: May 2013

The
MAT1-1
and
MAT1-2
idiomorphs associated with the
MAT1
locus of
Histoplasma capsulatum
were identified by PCR. A total of 28 fungal isolates, 6 isolates from human clinical samples and 22 isolates from environmental (infected bat and contaminated soil) samples, were studied. Among the 14 isolates from Mexico, 71.4% (95% confidence interval [95% CI], 48.3% to 94.5%) were of the
MAT1-2
genotype, whereas 100% of the isolates from Brazil were of the
MAT1-1
genotype. Each
MAT1
idiomorphic region was sequenced and aligned, using the sequences of the G-217B (+ mating type) and G-186AR (− mating type) strains as references. BLASTn analyses of the
MAT1-1
and
MAT1-2
sequences studied correlated with their respective + and − mating type genotypes. Trees were generated by the maximum likelihood (ML) method to search for similarity among isolates of each
MAT1
idiomorph. All
MAT1-1
isolates originated from Brazilian bats formed a well-defined group; three isolates from Mexico, the G-217B strain, and a subgroup encompassing all soil-derived isolates and two clinical isolates from Brazil formed a second group; last, one isolate (EH-696P) from a migratory bat captured in Mexico formed a third group of the
MAT1-1
genotype. The
MAT1-2
idiomorph formed two groups, one of which included two
H. capsulatum
isolates from infected bats that were closely related to the G-186AR strain. The other group was formed by two human isolates and six isolates from infected bats. Concatenated ML trees, with internal transcribed spacer 1 (ITS1) -5.8S-ITS2 and
MAT1-1
or
MAT1-2
sequences, support the relatedness of
MAT1-1
or
MAT1-2
isolates.
H. capsulatum
mating types were associated with the geographical origin of the isolates, and all isolates from Brazil correlated with their environmental sources.
The Fission Yeast Synaptobrevin Ortholog Syb1 Plays an Important Role in Forespore Membrane Formation and Spore Maturation
Authors: Yamaoka Tomomi , Imada Kazuki , Fukunishi Kana , Yamasaki Yuriko , Shimoda Chikashi , Nakamura Taro
Published: May 2013

Synaptobrevin, also called vesicle-associated membrane protein (VAMP), is a component of the plasma membrane N-methylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, which plays a key role in intracellular membrane fusion. Previous studies have revealed that, similar to synaptobrevin in other organisms, the fission yeast synaptobrevin ortholog Syb1 associates with post-Golgi secretory vesicles and is essential for cytokinesis and cell elongation. Here, we report that Syb1 has a role in sporulation. After nitrogen starvation, green fluorescent protein (GFP)-Syb1 is found in intracellular dots. As meiosis proceeds, GFP-Syb1 accumulates around the nucleus and then localizes at the forespore membrane (FSM). We isolated a
syb-S1
mutant, which exhibits a defect in sporulation. In
syb1-S1
mutants, the FSM begins to form but fails to develop a normal morphology. Electron microscopy shows that an abnormal spore wall is often formed in
syb1-S1
mutant spores. Although most
syb1-S1
mutant spores are germinated, they are less tolerant to ethanol than wild-type spores. The
syb1-S1
allele carries a missense mutation, resulting in replacement of a conserved cysteine residue adjacent to the transmembrane domain, which reduces the stability and abundance of the Syb1 protein. Taken together, these results indicate that Syb1 plays an important role in both FSM assembly and spore wall formation.
Environmentally Regulated Glycosome Protein Composition in the African Trypanosome
Authors: Bauer Sarah , Morris James C. , Morris Meredith T.
Published: May 2013

Trypanosomes compartmentalize many metabolic enzymes in glycosomes, peroxisome-related microbodies that are essential to parasite survival. While it is understood that these dynamic organelles undergo profound changes in protein composition throughout life cycle differentiation, the adaptations that occur in response to changes in environmental conditions are less appreciated. We have adopted a fluorescent-organelle reporter system in procyclic
Trypanosoma brucei
by expressing a fluorescent protein (FP) fused to a glycosomal targeting sequence (peroxisome-targeting sequence 2 [PTS2]). In these cell lines, PTS2-FP is localized within import-competent glycosomes, and organelle composition can be analyzed by microscopy and flow cytometry. Using this reporter system, we have characterized parasite populations that differ in their glycosome composition. In glucose-rich medium, two parasite populations are observed; one population harbors glycosomes bearing the full repertoire of glycosome proteins, while the other parasite population contains glycosomes that lack the usual glycosome-resident proteins but do contain the glycosome membrane protein TbPEX11. Interestingly, these cells lack TbPEX13, a protein essential for the import of proteins into the glycosome. This bimodal distribution is lost in low-glucose medium. Furthermore, we have demonstrated that changes in environmental conditions trigger changes in glycosome protein composition. These findings demonstrate a level of procyclic glycosome diversity heretofore unappreciated and offer a system by which glycosome dynamics can be studied in live cells. This work adds to our growing understanding of how the regulation of glycosome composition relates to environmental sensing.