bluuebunny/crossref_metadata_2025 huggingface dataset:
Fishery Management Complexes: An Impediment or Aid to Sustainable Harvest? A Discussion Based on the Northeast Skate Complex
Authors: Hogan Fiona , Cadrin Steve , Haygood Alyssa
Published: March 2013

There are seven species of skates (family Rajidae) found along the East Coast of the USA. All seven species are currently managed by the New England Fisheries Management Council as a single management complex extending from the Gulf of Maine to Cape Hatteras. The objective of the management plan is to ensure the long-term sustainability of fishing for each species via a trip limit approach. Two species are harvested in two distinct commercial fisheries. Northeast Fisheries Science Center trawl survey data and published literature were examined to investigate differences between the individual species in the skate complex. Each species exhibited a unique thermal and geographic range in addition to vital life history traits (e.g., age at maturity, longevity, and maximum size). Thorny Skate Amblyraja radiata and Smooth Skate Malacoraja senta have narrow thermal ranges and maintain a more northern distribution. Barndoor Skate Dipturus laevis have a moderate thermal habitat. Little Skate Leucoraja erinacea and Winter Skate L. ocellata have broad thermal ranges and are distributed throughout the management area. Limited inferences can be made about the thermal preferences of Clearnose Skate Raja eglanteria without data from south of Cape Hatteras, but they appear to have a broad thermal range within the management area. Rosette Skate L. garmani have a narrow thermal range and tend to be found in the deep offshore mid-Atlantic region. The validity of managing multiple distinct species in a complex is questioned. This example shows that a mixed-stock management strategy may be inadequate to meet the sustainability needs of each species and the associated fisheries. A management strategy focused on individual species may lead to a more efficient harvest of targeted species while allowing for the rebuilding of overfished species.

Received November 8, 2011; accepted December 27, 2012
Ghost Fishing in the Southeast Alaska Commercial Dungeness Crab Fishery
Authors: Maselko Jacek , Bishop Gretchen , Murphy Peter
Published: March 2013

Entrapment of crabs by derelict crab pots (also known as ghost fishing) can be a significant consequence of commercial fishing. The prevalence of lost commercial pots and ghost-fishing entrapments was estimated for the commercial Dungeness crab Cancer magister fishery in southeastern Alaska during the 2009 and 2010 summer closures of the commercial season (16 August through 30 September). Teams of divers retrieved a random subsample of the derelict crab pots located using side-scan sonar. Altogether, we retrieved 123 derelict crab pots containing 215 entrapped Dungeness crabs. The densities of derelict crab pots varied from 1.5 to 10.1/km2, while the densities of entrapped Dungeness crabs ranged from 0 to 54.5/km2, depending on the area surveyed. Derelict crab pots were discovered to effectively ghost-fish for at least 7 years, indicating that there are long-term cumulative impacts on Dungeness crab populations. The number of derelict crab pots and entrapped Dungeness crabs at each of the surveyed areas was highly correlated with the number of fishermen, the number of pot lifts, and annual harvest in numbers, allowing for extrapolation to a regionwide estimate of crab entrapment and derelict crab pot abundance. Overall, our findings show instantaneous entrapment of less than 1% of the commercial crab harvest with a cumulative annual loss of less than 3% of the regional commercial crab harvest. We challenge the efficacy of the biodegradable escape mechanism currently employed in commercial Dungeness crab pots in southeastern Alaska and present alternatives which may require further in situ or laboratory verification of their effectiveness.

Received February 23, 2012; accepted December 27, 2012
Differences between Livestock and Crop Producers' Participation in Nutrient Trading
Authors: Sneeringer Stacy
Published: March 2013

Descriptions of agricultural producers' participation in nutrient trading schemes generally refer to crop producers reducing nutrient run‐off from fields to generate credits. However, livestock producers may participate differently than crop producers because some are regulated as Concentrated Animal Feeding Operations (CAFOs), and because agricultural producers generating manure face different costs of reducing nutrient application (and therefore generating credits) from those only using fertilizer. These differences may affect nutrient reduction credit prices and the supply of agriculturally supplied credits, thereby raising the costs to non‐agricultural operations of meeting water quality goals. We examine how CAFO laws interact with nutrient trading requirements. We model trading participation by farm type and then simulate trading participation by applying the model to 2007 Census of Agriculture data.
The Estimation of Threshold Models in Price Transmission Analysis
Authors: Greb Friederike , von Cramon-Taubadel Stephan , Krivobokova Tatyana , Munk Axel
Published: March 2013

The threshold vector error correction model is a popular tool for the analysis of spatial price transmission. In the literature, the profile likelihood estimator is the preferred choice for estimating this model. Yet, in many settings this estimator performs poorly. In particular, if the true thresholds are such that one or more regimes contain only a small number of observations, if unknown model parameters are numerous, or if parameters differ little between regimes, the profile likelihood estimator displays large bias and variance. Such settings are likely when studying price transmission. We analyze the weaknesses of the profile likelihood approach and propose an alternative regularized Bayesian estimator, which was developed for simpler but related threshold models. Simulation results show that the regularized Bayesian estimator outperforms profile likelihood in the estimation of threshold vector error correction models. Two empirical applications demonstrate the relevance of this new estimator for spatial price transmission analysis.
Enabling interspecies epigenomic comparison with CEpBrowser
Authors: Cao Xiaoyi , Zhong Sheng
Published: March 2013

Summary: We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons.

Availability: CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: http://www.cepbrowser.org/.

Contact:  szhong@ucsd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Protective Mechanical Ventilation during General Anesthesia for Open Abdominal Surgery Improves Postoperative Pulmonary Function
Authors: Severgnini Paolo , Selmo Gabriele , Lanza Christian , Chiesa Alessandro , Frigerio Alice , Bacuzzi Alessandro , Dionigi Gianlorenzo , Novario Raffaele , Gregoretti Cesare , de Abreu Marcelo Gama , Schultz Marcus J. , Jaber Samir , Futier Emmanuel , Chiaranda Maurizio , Pelosi Paolo
Published: March 2013

Background:

The impact of intraoperative ventilation on postoperative pulmonary complications is not defined. The authors aimed at determining the effectiveness of protective mechanical ventilation during open abdominal surgery on a modified Clinical Pulmonary Infection Score as primary outcome and postoperative pulmonary function.

Methods:

Prospective randomized, open-label, clinical trial performed in 56 patients scheduled to undergo elective open abdominal surgery lasting more than 2 h. Patients were assigned by envelopes to mechanical ventilation with tidal volume of 9 ml/kg ideal body weight and zero-positive end-expiratory pressure (standard ventilation strategy) or tidal volumes of 7 ml/kg ideal body weight, 10 cm H2O positive end-expiratory pressure, and recruitment maneuvers (protective ventilation strategy). Modified Clinical Pulmonary Infection Score, gas exchange, and pulmonary functional tests were measured preoperatively, as well as at days 1, 3, and 5 after surgery.

Results:

Patients ventilated protectively showed better pulmonary functional tests up to day 5, fewer alterations on chest x-ray up to day 3 and higher arterial oxygenation in air at days 1, 3, and 5 (mmHg; mean ± SD): 77.1 ± 13.0 versus 64.9 ± 11.3 (P = 0.0006), 80.5 ± 10.1 versus 69.7 ± 9.3 (P = 0.0002), and 82.1 ± 10.7 versus 78.5 ± 21.7 (P = 0.44) respectively. The modified Clinical Pulmonary Infection Score was lower in the protective ventilation strategy at days 1 and 3. The percentage of patients in hospital at day 28 after surgery was not different between groups (7 vs. 15% respectively, P = 0.42).

Conclusion:

A protective ventilation strategy during abdominal surgery lasting more than 2 h improved respiratory function and reduced the modified Clinical Pulmonary Infection Score without affecting length of hospital stay.
Coadministration of the AMPAKINE CX717 with Propofol Reduces Respiratory Depression and Fatal Apneas
Authors: Ren Jun , Lenal Floriane , Yang Michael , Ding Xiuqing , Greer John J.
Published: March 2013

Background:

Propofol (2,6-diisopropylphenol) is used for the induction and maintenance of anesthesia in human and veterinary medicine. Propofol’s disadvantages include the induction of respiratory depression and apnea. Here, the authors report a clinically feasible pharmacological solution for reducing propofol-induced respiratory depression via a mechanism that does not interfere with anesthesia. Specifically, they test the hypothesis that the AMPAKINE CX717, which has been proven metabolically stable and safe for human use, can prevent and rescue from propofol-induced severe apnea.

Methods:

The actions of propofol and the AMPAKINE CX717 were measured via (1) ventral root recordings from newborn rat brainstem–spinal cord preparations, (2) phrenic nerve recordings from an adult mouse in situ working heart–brainstem preparation, and (3) plethysmographic recordings from unrestrained newborn and adult rats.

Results:

In vitro, respiratory depression caused by propofol (2 μm, n = 11, mean ± SEM, 41±5% of control frequency, 63±5% of control duration) was alleviated by CX717 (n = 4, 50–150 μm). In situ, a decrease in respiratory frequency (44±9% of control), phrenic burst duration (66±7% of control), and amplitude (78±5% of control) caused by propofol (2 μm, n = 5) was alleviated by coadministration of CX717 (50 μm, n = 5). In vivo, pre- or coadministration of CX717 (20–25mg/kg) with propofol markedly reduced propofol-induced respiratory depression (n = 7; 20mg/kg) and propofol-induced lethal apnea (n = 6; 30mg/kg).

Conclusions:

Administration of CX717 before or in conjunction with propofol provides an increased safety margin against profound apnea and death.
Young Children with Behçet Disease Have More Intestinal Involvement
Authors: Hung Chien‐Hui , Lee Jyh‐Hong , Chen Szu‐Ta , Yang Yao‐Hsu , Lin Yu‐Tsan , Wang Li‐Chieh , Yu Hsin‐Hui , Chiang Bor‐Luen
Published: March 2013

Objective:

Gastrointestinal (GI) involvement in childhood Behçet disease (BD) is not well understood. We aimed to clarify the intestinal presentation in children with BD.

Methods:

Medical records of 85 children with recurrent oral ulcers between 1990 and 2010 at the National Taiwan University Hospital were reviewed retrospectively. Twenty of them who fulfilled the Mason and Barnes criteria for the diagnosis of childhood BD were enrolled. The clinical and laboratory characteristics were analyzed.

Results:

Among 20 patients, the median age at diagnosis was 13.2 years. The common presentations included oral ulcers (100%), genital ulcers (70%), skin lesions (65%), and GI symptoms (50%). Five of 10 patients with GI symptoms received endoscopic examinations and all had ulcers. Divided by the age of 10, patients younger than 10 years tended to have higher rates of GI symptoms initially and intestinal ulcers (P = 0.002 and 0.015, respectively). Platelet count was significantly lower in young patients (P = 0.0151). Patients without GI symptoms had higher rates of skin involvement than patients with GI symptoms (P = 0.019).

Conclusions:

Young children with BD tended to have more GI presentations. For children with BD younger than 10 years having GI symptoms, endoscopic examinations may be considered.
Use of the Noninvasive Entero‐test in the Detection of Helicobacter pylori in Children in an Endemic Area in Colombia
Authors: Arboleda Richard N. , Schneider Barbara G. , Bravo Luis E. , Romero‐Gallo Judith , Peek Richard M. , Mera Robertino M. , Yepez Maria Clara , Campo Cristina , Correa Pelayo
Published: March 2013

Background and Objective:

Gastric infection with Helicobacter pylori (H pylori), a strong risk factor for gastric cancer, is highly prevalent in children residing in the Colombian Andes. We aimed to validate the use of the Entero‐test to culture and genotype H pylori strains from asymptomatic Colombian children.

Methods:

Children (ages 10–15 years, n = 110, 80 of which were H pylori positive by the urea breath test [UBT]) were subjected to the Entero‐test, and strings were cultured and/or used for DNA extraction for polymerase chain reaction (PCR). These children had been treated for H pylori in 2007. A second population of children (ages 10–15 years, n = 95),which had not been previously treated, was also subjected to the Entero‐test.

Results:

Of UBT‐positive children in the treated group, 29 of 80 (36%) Entero‐test samples were H pylori culture positive; 29 additional string extracts were tested by PCR for the H pylori virulence factors cagA and vacA. PCR from cultures and extracts yielded a sensitivity of 74% and specificity of 87%. In the untreated group, 16 of 94 UBT‐positive children (17%) produced Entero‐tests that were culture positive. Fifty‐eight of 94 (62%) string extracts were PCR positive for cagA and/or vacA. In previously treated children, H pylori strains were more often the less virulent vacA s2 (P = 0.001), m2 (P = 0.006), and i2 genotypes (P = 0.039).

Conclusions:

The Entero‐test may be used as a noninvasive test to detect H pylori in asymptomatic children residing in high‐risk areas for gastric cancer. Treatment of H pylori in children was associated with less virulent genotypes.
Liver Disease After Intensive Care of Premature Baboons
Authors: Kerecman Jay , Mehrotra Anupamjit , Goodman Zachary
Published: March 2013

Background and Objectives:

Cholestasis affects 50% of extremely low‐birth‐weight infants. Its etiology remains poorly understood and the extent of liver injury in these infants is unclear. The premature baboon model provides an opportunity to study neonatal liver disease. We characterize hepatic histopathologic changes in this model.

Methods:

Archival tissue and data were obtained from the Southwest Foundation for Biomedical Research Primate Center, San Antonio, TX. Animals were selected based on history of antenatal steroid therapy and absence of sepsis or necrotizing enterocolitis with a protocol duration of at least 21 days and no early death (n = 45). Baboons had been treated per protocol in the neonatal intensive care unit (NICU). At necropsy, liver tissue was harvested and stored. Tissues from fetal gestational controls at similar ages were used for comparison (n = 28). Histologic changes were scored by consensus of 2 pathologists blinded to treatment group. Descriptive and comparative statistics were performed.

Results:

Control fetal livers had extramedullary hematopoiesis (EMH) that decreased across the gestational range. There was evidence of hepatocyte iron storage and ongoing portal tract development. Livers of NICU‐treated baboons had increased Kupffer cell hypertrophy and hemosiderosis. There was a shift away from erythroid EMH toward increased myeloid EMH. There was increased cholestasis, ductular proliferation, portal tract fibrosis, and steatosis in treated animals.

Conclusions:

We found pathologic changes in NICU‐treated baboons comparable with findings reported in human infants. The baboon model of prematurity may be a useful tool to explore cholestasis and liver dysfunction in extremely low‐birth‐weight infants.
Muricauda antarctica sp. nov., a marine member of the Flavobacteriaceae isolated from Antarctic seawater
Authors: Wu Yue-Hong , Yu Pei-Song , Zhou Ya-Dong , Xu Lin , Wang Chun-Sheng , Wu Min , Oren Aharon , Xu Xue-Wei
Published: March 2013

A Gram-stain-negative, rod-shaped bacterium with appendages, designated Ar-22T, was isolated from a seawater sample collected from the western part of Prydz Bay, near Cape Darnley, Antarctica. Strain Ar-22Tgrew optimally at 35 °C, at pH 7.5 and in the presence of 1–3 % (w/v) NaCl. The isolate was positive for casein, gelatin and Tween 20 decomposition and negative for H2S production and indole formation. Chemotaxonomic analysis showed that MK-6 was the major isoprenoid quinone and phosphatidylethanolamine was the major polar lipid. The major fatty acids were iso-C17 : 03-OH, iso-C15 : 1G, iso-C15 : 0and C16 : 1ω7c/iso-C15 : 02OH. The genomic DNA G+C content was 44.8 mol%. Comparative 16S rRNA gene sequence analysis revealed that strain Ar-22Tis closely related to members of the genusMuricauda, sharing 94.2–97.3 % sequence similarity with the type strains of species of the genusMuricaudaand being most closely related to theMuricauda aquimarina. Phylogenetic analysis based on the 16S rRNA gene sequence comparison confirmed that strain Ar-22Tformed a deep lineage withMuricauda flavescens.Sequence similarity between strain Ar-22TandMuricauda ruestringensisDSM 13258T, the type species of the genusMuricauda, was 96.9 %. Strain Ar-22Texhibited mean DNA–DNA relatedness values of 40.1 %, 49.4 % and 25.7 % toM. aquimarinaJCM 11811T,M. flavescensJCM 11812TandMuricauda lutimarisKCTC 22173T, respectively. On the basis of phenotypic and genotypic data, strain Ar-22Trepresents a novel species of the genusMuricauda,for which the nameMuricaudaantarcticasp. nov. (type strain Ar-22T = CGMCC 1.12174T = JCM 18450T) is proposed.
Brevibacterium

jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood
Authors: Choi Eun Jin , Lee Se Hee , Jung Ji Young , Jeon Che Ok
Published: March 2013

A Gram-staining-positive, aerobic, non-motile bacterium, designated strain SJ5-8T, was isolated from seau-jeot (shrimp jeotgal), a traditional fermented seafood in South Korea. Cells were non-spore-forming rods showing catalase- and oxidase-positive reactions. Growth of strain SJ5-8T was observed at 10–37 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.5–8.5) and in the presence of 0–14 % (w/v) NaCl (optimum, 5 %). Phylogenetic inference based on 16S rRNA gene sequences showed that the strain formed a tight phyletic lineage with members of the genus

Brevibacterium

. Strain SJ5-8T was most closely related to

Brevibacterium yomogidense

MN-6-aT,

Brevibacterium daeguense

2C6-41T and

Brevibacterium salitolerans

TRM 415T with similarities of 98.9, 97.5 and 97.4 %, respectively. The DNA–DNA relatedness values between strain SJ5-8T and the type strains of

B. yomogidense

,

B. daeguense

and

B. salitolerans

were 51.7±1.9 %, 22.2±4.0 % and 52.4±3.8 %, respectively. Chemotaxonomic data (major sole isoprenoid quinone, MK-8(H2); major diagnostic diamino acid, meso-diaminopimelic acid; major polyamines, putrescine and cadaverine; major cellular fatty acids, anteiso-C15:0, iso-C15:0 and anteiso-C17:0; major polar lipids, phosphatidylglycerol and diphosphatidylglycerol; DNA G+C content, 69.3 mol%) also supported the affiliation of strain SJ5-8T to the genus

Brevibacterium

. Therefore, strain SJ5-8T represents a novel species of the genus

Brevibacterium

, for which the name

Brevibacterium

jeotgali sp. nov. is proposed. The type strain is SJ5-8T ( = KACC 16911T = JCM 18571T).
Mongoliicoccus

alkaliphilus sp. nov. and

Litoribacter

alkaliphilus sp. nov., isolated from salt pans
Authors: Subhash Y. , Tushar L. , Sasikala Ch. , Ramana Ch. V.
Published: March 2013

Four bacterial strains (JC165T, JC166T, JC169 and JC170) were isolated from salt pan soils from a coastal region of Tamilnadu, India. They were obligately aerobic, pink- to red-pigmented, mesophilic, haloalkaliphiles having chemoorganoheterotrophic growth on various carbon sources and were catalase- and oxidase-positive. Phototrophic growth and bacteriochlorophyll a were absent in all four strains. Major carotenoids present were β-carotene and rhodoxanthin. The main fatty acid in all strains was iso-C15 : 0. The main polar lipids were phosphatidylethanolamine (PE) and phosphatidylcholine (PC) as well as a few unidentified lipids. Bacterial hopane derivatives and diplopterol (DPL) were detected in all four strains. Based on the 16S rRNA gene sequences, all four strains belong to the family

Cyclobacteriaceae

in the phylum

Bacteroidetes

. Strains JC165T and JC169 had a sequence similarity of 97.2 % with

Mongoliicoccus roseus

MIM28T, while strains JC166T and JC170 had a sequence similarity of 99.5 % with

Litoribacter ruber

YIM CH208T. Strains JC165T/JC169 and JC166T/JC170 had genomic DNA reassociation values (based on DNA–DNA hybridization) of 21±2 % and 23±1 % with

M. roseus

KCTC 19808T ( = MIM28T) and

L. ruber

KCTC 22899T ( = YIM CH208T), respectively, suggesting that they represented novel species. The reassociation values of >85 % between strains JC165T and JC169, and JC166T and JC170 suggested they were strains of the same species. The genomic information was supported by phenotypic observations leading to the proposal of two novel species,

Mongoliicoccus

alkaliphilus sp. nov. (type strain, JC165T = KCTC 32210T = LMG 27255T) and

Litoribacter

alkaliphilus sp. nov. (type strain, JC166T = KCTC 32217T = LMG 27256T).
Flavobacterium

aquaticum sp. nov., isolated from a water sample of a rice field
Authors: Subhash Y. , Sasikala Ch. , Ramana Ch. V.
Published: March 2013

Strain JC164T was isolated from a water sample from a rice field at Jamdih, Mau, Uttar Pradesh, India. Colonies of strain JC164T were brown–yellow and cells were Gram-stain-negative. Catalase, oxidase and amylase were present. iso-C15 : 0, iso-C16 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C14 : 0 were the predominant fatty acids with minor amounts of iso-C16 : 0 3-OH, anteiso-C15 : 0, C16 : 0, iso-C16 : 1 H, iso-C14 : 0 3-OH and iso-C13 : 0. Strain JC164T contained phosphatidylethanolamine and a few unidentified lipids (L1, L3 and L6) as major polar lipids. Bacteriohopane derivative 1 (BHD1) and diplopterol (DPL) were the major hopanoids. β-Carotene was one among the several spirilloxanthin series carotenoids present in strain JC164T. Genomic DNA G+C content was 39.6 mol%. 16S rRNA gene sequence comparisons indicated that strain JC164T represents a member of the genus

Flavobacterium

(family

Flavobacteriaceae

, class

Flavobacteriia

). The most closely related taxa to strain JC164T were

Flavobacterium sasangense

YC6274T (98.5 %),

Flavobacterium cucumis

R2A45-3T (98.1 %),

Flavobacterium cheniae

NJ-26T (97.2 %) and the novel strain possessed <95.1 % sequence similarity with other members of the genus

Flavobacterium

. However, strain JC164T showed 12.5±2, 13.6±1 and 17.4±2 % genomic DNA association (based on DNA–DNA hybridization) with

Flavobacterium sasangense

KCTC 22246T,

Flavobacterium cucumis

DSM 18830T and

Flavobacterium cheniae

CGMCC 1.6844T, respectively. The distinct genomic difference and morphological, physiological and chemotaxonomic differences from the previously described taxa support the classification of strain JC164T as a representative of a novel species of the genus

Flavobacterium

, for which the name

Flavobacterium

aquaticum sp. nov. is proposed. The type strain is JC164T ( = KCTC 32196T = CGMCC 1.12398 = LMG 27251T).
Tenacibaculum

xiamenense sp. nov., an algicidal bacterium isolated from coastal seawater
Authors: Li Yi , Wei Jun , Yang Caiyun , Lai Qiliang , Chen Zhangran , Li Dong , Zhang Huajun , Tian Yun , Zheng Wei , Zheng Tianling
Published: March 2013

A Gram-stain-negative, elongated rod-shaped, yellow-pigmented, aerobic bacterial strain, designated WJ-1T, was isolated from coastal seawater in Xiamen, Fujian province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WJ-1T fell within the genus

Tenacibaculum

and was most closely associated with

Tenacibaculum aestuarii

SMK-4T (96.7 % 16S rRNA gene sequence similarity); lower similarities were shown to other members of the genus

Tenacibaculum

(<96.2 %). The strain formed a distinct lineage with

Tenacibaculum litopenaei

B-IT (96.0 %),

Tenacibaculum geojense

YCS-6T (94.5 %) and

Tenacibaculum jejuense

CNURIC 013T (95.4 %). Growth was observed at temperatures from 16 to 38 °C, at salinities from 2 to 4 % and at pH 6–9. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 0 3-OH. The DNA G+C content of strain WJ-1T was 33.2 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Differential phenotypic properties and phylogenetic distinctiveness in this study distinguished strain WJ-1T from all other members of the genus

Tenacibaculum

. According to the morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain WJ-1T represents a novel species of the genus

Tenacibaculum

, for which the name

Tenacibaculum

xiamenense sp. nov. is proposed. The type strain is WJ-1T ( = CGMCC 1.12378T = LMG 27422T).
Niabella hirudinis and Niabella drilacis sp. nov., isolated from the medicinal leech Hirudo verbana
Authors: Glaeser Stefanie P. , Galatis Harald , Martin Karin , Kämpfer Peter
Published: March 2013

Two Gram-negative, rod-shaped bacteria, strains E96Tand E90T, were isolated from medicinal leeches (Hirudo verbana) and characterized by a polyphasic taxonomic approach. Phylogenetic analysis based on the nearly full-length 16S rRNA gene sequence showed that the two strains shared 98.1 % sequence similarity and were affiliated with the genusNiabellawithin the phylumBacteroidetes, with 94.4–97.6 % sequence similarity to type strains of species of the genusNiabellaand highest sequence similarity to the type strain ofNiabella aurantiaca(97.3 and 97.6 %, respectively).Niabella-related 16S rRNA gene sequences were recently detected in the bladders ofHirudo verbana; however, no cultured representatives were so far available. Genomic fingerprint analysis using repetitive element primed (rep)- and randomly amplified polymorphic DNA (RAPD)-PCRs and DNA–DNA hybridization experiments clearly showed that the strains were different from each other (DNA–DNA relatedness values of 39.1 %, reciprocal 28.0 %) and from the type strains ofN. aurantiaca(<19.7 %) andNiabella tibetensis(<41.1 %). Chemotaxonomic analyses confirmed the affiliation to the genusNiabella. Both strains contained MK-7 as the predominant menaquinone. The major fatty acids of both strains were iso-C15 : 0, iso-C15 : 1G, iso-C17 : 03-OH and summed feature 3 (C16 : 1ω7cand/or iso-C15 : 02-OH), which is characteristic for the genusNiabella. Based on genotypic, chemotaxonomic and physiological characterization, we propose two novel species of the genusNiabella,Niabellahirudinissp. nov., with strain E96T( = DSM 25812T = CCM 8411T = LMG 26956T) as the type strain, andNiabelladrilacissp. nov., with strain E90T( = DSM 25811T = CCM 8410T = LMG 26954T) as the type strain.
Geodermatophilus

normandii sp. nov., isolated from Saharan desert sand
Authors: Montero-Calasanz Maria del Carmen , Göker Markus , Pötter Gabriele , Rohde Manfred , Spröer Cathrin , Schumann Peter , Gorbushina Anna A. , Klenk Hans-Peter
Published: March 2013

A novel Gram-reaction-positive actinobacterial strain, designated CF5/3T, was isolated from a sand sample obtained in the Sahara Desert, Chad. The greenish-black-pigmented isolate was aerobic and exhibited optimal growth from 25–40 °C at pH 6.0–10.0 with 0–1 % (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus

Geodermatophilus

. The DNA G+C content of the genome of the novel strain was 75.5 mol%. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and a minor fraction of phosphatidylglycerol. MK-9(H4) was the dominant menaquinone, and galactose was detected as a diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids: iso-C15 : 0 and iso-C16 : 0. Analysis of 16S rRNA gene sequences showed 95.6–98.8 % pairwise sequence identity with the members of the genus

Geodermatophilus

. Based on phenotypic and chemotaxonomic properties, as well as phylogenetic distinctiveness, the isolate represents a novel species,

Geodermatophilus

normandii, with the type strain CF5/3T ( = DSM 45417T = CCUG 62814T = MTCC 11412T).
Sphingobium

sufflavum sp. nov., isolated from a freshwater lake
Authors: Sheu Shih-Yi , Shiau Yu-Wen , Chen Wen-Ming
Published: March 2013

A Gram-stain negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated HL-25T, was isolated and characterized in a taxonomic study using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences showed that the isolate constituted a distinct branch within the genus

Sphingobium

, showing the highest level of 16S rRNA gene sequence similarity to

Sphingobium vulgare

HU1-GD12T (96.6 %). The major fatty acids (>10 %) of strain HL-25T were C18 : 1ω7c, C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 0. The major cellular hydroxy fatty acid was C14 : 0 2-OH. The major isoprenoid quinone was Q-10 and the DNA G+C content was 63.8 mol%. The polar lipid profile consisted of a mixture of sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, an uncharacterized glycolipid, an uncharacterized aminophospholipid and four uncharacterized phospholipids. The polyamine pattern of strain HL-25T contained spermidine and putrescine. On the basis of these genotypic, chemotaxonomic and phenotypic data, strain HL-25T represents a novel species in the genus

Sphingobium

, for which the name

Sphingobium

sufflavum sp. nov. is proposed. The type strain is HL-25T ( = BCRC 80413T = KCTC 23953T).
Unraveling Root Developmental Programs Initiated by BeneficialPseudomonasspp. Bacteria
Authors: Zamioudis Christos , Mastranesti Parthena , Dhonukshe Pankaj , Blilou Ikram , Pieterse Corné M.J.
Published: March 2013

Plant roots are colonized by an immense number of microbes, referred to as the root microbiome. Selected strains of beneficial soil-borne bacteria can protect against abiotic stress and prime the plant immune system against a broad range of pathogens. Pseudomonas spp. rhizobacteria represent one of the most abundant genera of the root microbiome. Here, by employing a germ-free experimental system, we demonstrate the ability of selected Pseudomonas spp. strains to promote plant growth and drive developmental plasticity in the roots of Arabidopsis (Arabidopsis thaliana) by inhibiting primary root elongation and promoting lateral root and root hair formation. By studying cell type-specific developmental markers and employing genetic and pharmacological approaches, we demonstrate the crucial role of auxin signaling and transport in rhizobacteria-stimulated changes in the root system architecture of Arabidopsis. We further show that Pseudomonas spp.-elicited alterations in root morphology and rhizobacteria-mediated systemic immunity are mediated by distinct signaling pathways. This study sheds new light on the ability of soil-borne beneficial bacteria to interfere with postembryonic root developmental programs.
The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs
Authors: Nuthikattu Saivageethi , McCue Andrea D. , Panda Kaushik , Fultz Dalen , DeFraia Christopher , Thomas Erica N. , Slotkin R. Keith
Published: March 2013

Transposable elements (TEs) are mobile fragments of DNA that are repressed in both plant and animal genomes through the epigenetic inheritance of repressed chromatin and expression states. The epigenetic silencing of TEs in plants is mediated by a process of RNA-directed DNA methylation (RdDM). Two pathways of RdDM have been identified: RNA Polymerase IV (Pol IV)-RdDM, which has been shown to be responsible for the de novo initiation, corrective reestablishment, and epigenetic maintenance of TE and/or transgene silencing; and RNA-dependent RNA Polymerase6 (RDR6)-RdDM, which was recently identified as necessary for maintaining repression for a few TEs. We have further characterized RDR6-RdDM using a genome-wide search to identify TEs that generate RDR6-dependent small interfering RNAs. We have determined that TEs only produce RDR6-dependent small interfering RNAs when transcriptionally active, and we have experimentally identified two TE subfamilies as direct targets of RDR6-RdDM. We used these TEs to test the function of RDR6-RdDM in assays for the de novo initiation, corrective reestablishment, and maintenance of TE silencing. We found that RDR6-RdDM plays no role in maintaining TE silencing. Rather, we found that RDR6 and Pol IV are two independent entry points into RdDM and epigenetic silencing that perform distinct functions in the silencing of TEs: Pol IV-RdDM functions to maintain TE silencing and to initiate silencing in an RNA Polymerase II expression-independent manner, while RDR6-RdDM functions to recognize active Polymerase II-derived TE mRNA transcripts to both trigger and correctively reestablish TE methylation and epigenetic silencing.
Patatin-Related Phospholipase pPLAIIIδ Increases Seed Oil Content with Long-Chain Fatty Acids in Arabidopsis
Authors: Li Maoyin , Bahn Sung Chul , Fan Chuchuan , Li Jia , Phan Tien , Ortiz Michael , Roth Mary R. , Welti Ruth , Jaworski Jan , Wang Xuemin
Published: March 2013

The release of fatty acids from membrane lipids has been implicated in various metabolic and physiological processes, but in many cases, the enzymes involved and their functions in plants remain unclear. Patatin-related phospholipase As (pPLAs) constitute a major family of acyl-hydrolyzing enzymes in plants. Here, we show that pPLAIIIδ promotes the production of triacylglycerols with 20- and 22-carbon fatty acids in Arabidopsis (Arabidopsis thaliana). Of the four pPLAIIIs (α, β, γ, δ), only pPLAIIIδ gene knockout results in a decrease in seed oil content, and pPLAIIIδ is most highly expressed in developing embryos. The overexpression of pPLAIIIδ increases the content of triacylglycerol and 20- and 22-carbon fatty acids in seeds with a corresponding decrease in 18-carbon fatty acids. Several genes in the glycerolipid biosynthetic pathways are up-regulated in pPLAIIIδ-overexpressing siliques. pPLAIIIδ hydrolyzes phosphatidylcholine and also acyl-coenzyme A to release fatty acids. pPLAIIIδ-overexpressing plants have a lower level, whereas pPLAIIIδ knockout plants have a higher level, of acyl-coenzyme A than the wild type. Whereas seed yield decreases in transgenic plants that ubiquitously overexpress pPLAIIIδ, seed-specific overexpression of pPLAIIIδ increases seed oil content without any detrimental effect on overall seed yield. These results indicate that pPLAIIIδ-mediated phospholipid turnover plays a role in fatty acid remodeling and glycerolipid production.
Roles of N-Terminal Fatty Acid Acylations in Membrane Compartment Partitioning:Arabidopsis h-Type Thioredoxins as a Case Study
Authors: Traverso José A. , Micalella Chiara , Martinez Aude , Brown Spencer C. , Satiat-Jeunemaître Béatrice , Meinnel Thierry , Giglione Carmela
Published: March 2013

N-terminal fatty acylations (N-myristoylation [MYR] and S-palmitoylation [PAL]) are crucial modifications affecting 2 to 4% of eukaryotic proteins. The role of these modifications is to target proteins to membranes. Predictive tools have revealed unexpected targets of these acylations in Arabidopsis thaliana and other plants. However, little is known about how N-terminal lipidation governs membrane compartmentalization of proteins in plants. We show here that h-type thioredoxins (h-TRXs) cluster in four evolutionary subgroups displaying strictly conserved N-terminal modifications. It was predicted that one subgroup undergoes only MYR and another undergoes both MYR and PAL. We used plant TRXs as a model protein family to explore the effect of MYR alone or MYR and PAL in the same family of proteins. We used a high-throughput biochemical strategy to assess MYR of specific TRXs. Moreover, various TRX–green fluorescent protein fusions revealed that MYR localized protein to the endomembrane system and that partitioning between this membrane compartment and the cytosol correlated with the catalytic efficiency of the N-myristoyltransferase acting at the N terminus of the TRXs. Generalization of these results was obtained using several randomly selected Arabidopsis proteins displaying a MYR site only. Finally, we demonstrated that a palmitoylatable Cys residue flanking the MYR site is crucial to localize proteins to micropatching zones of the plasma membrane.
Role of the cytoskeleton in communication between L‐type Ca2+ channels and mitochondria
Authors: Viola Helena M , Hool Livia C
Published: March 2013

The L‐type Ca2+ channel is the main route for Ca2+ entry into cardiac myocytes, which is essential for the maintenance of cardiac excitation and contraction. Alterations in L‐type Ca2+ channel activity and Ca2+ homeostasis have been implicated in the development of cardiomyopathies.

Cardiac excitation and contraction is fuelled by ATP, synthesized predominantly by the mitochondria via the Ca2+‐dependent process oxidative phosphorylation. Mitochondrial reactive oxygen species (ROS) are by‐products of oxidative phosphorylation and are associated with the development of cardiac pathology.

The cytoskeleton plays a role in the communication of signals from the plasma membrane to intracellular organelles. There is good evidence that both L‐type Ca2+ channel activity and mitochondrial function can be modulated by changes in the cytoskeletal network.

Activation of the L‐type Ca2+ channel can regulate mitochondrial function through cytoskeletal proteins as a result of transmission of movement from the β2‐subunit of the channel that occurs during activation and inactivation of the channel. An association between cytoskeletal proteins and the mitochondrial voltage‐dependent anion channel (VDAC) may play a role in this response.

The L‐type Ca2+ channel is the initiator of contraction in cardiac muscle and the VDAC is responsible for regulating mitochondrial ATP/ADP trafficking. This article presents evidence that a functional coupling between L‐type Ca2+ channels and mitochondria may assist in meeting myocardial energy demand on a beat‐to‐beat basis.
Should we use one‐sided or two‐sided P values in tests of significance?
Authors: Ludbrook John
Published: March 2013

‘P’ stands for the probability, ranging in value from 0 to 1, that results from a test of significance. It can also be regarded as the strength of evidence against the statistical null hypothesis (H0).

When H0 is evaluated by statistical tests based on distributions such as t, normal or Chi‐squared, P can be derived from one tail of the distribution (one‐sided or one‐tailed P), or it can be derived from both tails (two‐sided or two‐tailed P).

Distinguished statisticians, the authors of statistical texts, the authors of guidelines for human and animal experimentation and the editors of biomedical journals give confusing advice, or none at all, about the choice between one‐ and two‐sided P values. Such a choice is available only when there are no more than two groups to be compared.

I argue that the choice between one‐ and two‐sided P values depends on the alternative hypothesis (H1), which corresponds to the scientific hypothesis. If H1 is non‐specific and merely states that the means or proportions in the two groups are unequal, then a two‐sided P is appropriate. However, if H1 is specific and, for example, states than the mean or proportion of Group A is greater than that of Group B, then a one‐sided P maybe used.

The form that H1 will take if H0 is rejected must be stipulated a priori, before the experiment is conducted.

It is essential that authors state whether the P values resulting from their tests of significance are one‐ or two‐sided.
Modifying muscular dystrophy through transforming growth factor‐β
Authors: Ceco Ermelinda , McNally Elizabeth M.
Published: March 2013

Muscular dystrophy arises from ongoing muscle degeneration and insufficient regeneration. This imbalance leads to loss of muscle, with replacement by scar or fibrotic tissue, resulting in muscle weakness and, eventually, loss of muscle function. Human muscular dystrophy is characterized by a wide range of disease severity, even when the same genetic mutation is present. This variability implies that other factors, both genetic and environmental, modify the disease outcome. There has been an ongoing effort to define the genetic and molecular bases that influence muscular dystrophy onset and progression. Modifier genes for muscle disease have been identified through both candidate gene approaches and genome‐wide surveys. Multiple lines of experimental evidence have now converged on the transforming growth factor‐β (TGF‐β) pathway as a modifier for muscular dystrophy. TGF‐β signaling is upregulated in dystrophic muscle as a result of a destabilized plasma membrane and/or an altered extracellular matrix. Given the important biological role of the TGF‐β pathway, and its role beyond muscle homeostasis, we review modifier genes that alter the TGF‐β pathway and approaches to modulate TGF‐β activity to ameliorate muscle disease.
N‐terminal domain of Pyrococcus furiosus l‐asparaginase functions as a non‐specific, stable, molecular chaperone
Authors: Tomar Rachana , Garg Dushyant K. , Mishra Rahul , Thakur Ashwani K. , Kundu Bishwajit
Published: March 2013

The enzyme l‐asparaginase of Pyrococcus furiosus (PfA) functions as a dimer with each monomer consisting of distinct N‐ and C‐terminal domains (NPfA and CPfA, respectively), connected by a linker. Here we present data to show that NPfA functions as a non‐specific molecular chaperone. Independently expressed NPfA refolded spontaneously whereas CPfA formed insoluble aggregates. However, when mixed and refolded together, NPfA augmented CPfA to fold with ~90% recovery. NPfA also protected a variety of substrate proteins from thermal and refolding‐mediated aggregation as monitored by a reduction in light scattering. The co‐appearance of substrate protein with NPfA in antibody pull‐down assays as well as in eluted gel filtration peaks indicated direct protein–protein interaction. These interactions were hydrophobic in nature as determined by 8‐anilino‐1‐naphthalene sulfonic acid fluorescence. NPfA inhibited polyglutamine‐mediated amyloid formation and also facilitated disintegration of preformed amyloid fibrils of amyloid‐β (1–42) as determined by reverse‐phase HPLC‐based sedimentation assay and thioflavin T binding assays, respectively. Dynamic light scattering experiments suggested that NPfA readily assembled into polydispersed oligomeric species. With no sequence similarity to α‐crystallin or any known molecular chaperone, we present here NPfA as a novel molecular chaperone.

Structured digital abstract

Aβ amyloid 1-42 and Aβ amyloid 1-42 bind by fluorescence technology (View interaction)

alpha-amylase and alpha-amylase bind by light scattering (View interaction)

Aβ amyloid 1-42 and Aβ amyloid 1-42 bind by transmission electron microscopy (View interaction)

NPfa binds to BCA II by anti tag coimmunoprecipitation (View interaction)

MSG and MSG bind by light scattering (View interaction)

BCA II and BCA II bind by light scattering (View interaction)
The Minimum Wage Affects Them All: Evidence on Employment Spillovers in the Roofing Sector
Authors: Aretz Bodo , Gregory Terry , Arntz Melanie
Published: March 2013

This study contributes to the sparse literature on employment spillovers of minimum wages. We exploit the minimum wage introduction and subsequent increases in the German roofing sector that gave rise to an internationally unprecedented hard bite of a minimum wage. We look at the chances of remaining employed in the roofing sector for workers with and without a binding minimum wage and use the plumbing sector that is not subject to a minimum wage as a suitable benchmark sector. By estimating the counterfactual wage that plumbers would receive in the roofing sector given their characteristics, we are able to identify employment effects along the entire wage distribution. The results indicate that the chances for roofers to remain employed in the sector in eastern Germany deteriorated along the entire wage distribution. Such employment spillovers to workers without a binding minimum wage may result from scale effects and/or capital-labour substitution.
Whole‐mount evaluation of penectomies for penile cancer: feasibility, cost and comparison to routine sectioning
Authors: Ebel Joshua J , Shabsigh Ahmad , Sharp David S , Zynger Debra L
Published: March 2013

Aims

Pathological staging in penectomies may be difficult due to the anatomical complexity of penile anatomy, and may be additionally challenging due to the low volume at most institutions. Our study aimed to assess the feasibility of whole‐mount processing for penectomy specimens.

Methods and results

A 7‐year retrospective search for partial or radical penectomies identified 55 specimens, which were processed routinely (n = 31) from 2006 to 2009 and whole‐mounted (n = 24) from 2010 to 2012. Routine cases used more slides per case compared to whole mounts (mean 10.4 versus 7.2). Recuts occurred more often in routine cases (12.9% versus 0%). More routine cases had additional blocks grossed (19.4% versus 4.2%). Upon review, five discrepancies that impacted pT staging were identified in the routine group, with none in the whole‐mount group. The average estimated additional cost for each whole‐mount case compared to routine processing was $40.74, with an increased turnaround time of 1 day.

Conclusions

Whole‐mounting is a feasible technique for penectomy that can be utilized with minimal increased cost and turnaround time, and may improve staging. Institutions in which whole‐mounting is already established for other organs, such as prostate, may wish to consider utilizing this format for penectomy specimens.