bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein phosphatases PP2A, PP4 and PP6: mediators and regulators in development and responses to environmental cues
Authors: LILLO CATHRINE , KATAYA AMR R. A. , HEIDARI BEHZAD , CREIGHTON MARIA T. , NEMIE‐FEYISSA DUGASSA , GINBOT ZEKARIAS , JONASSEN ELSE M.
Published: May 2014

The three closely related groups of serine/threonine protein phosphatases PP2A, PP4 and PP6 are conserved throughout eukaryotes. The catalytic subunits are present in trimeric and dimeric complexes with scaffolding and regulatory subunits that control activity and confer substrate specificity to the protein phosphatases. In Arabidopsis, three scaffolding (A subunits) and 17 regulatory (B subunits) proteins form complexes with five PP2A catalytic subunits giving up to 255 possible combinations. Three SAP‐domain proteins act as regulatory subunits of PP6. Based on sequence similarities with proteins in yeast and mammals, two putative PP4 regulatory subunits are recognized in Arabidopsis. Recent breakthroughs have been made concerning the functions of some of the PP2A and PP6 regulatory subunits, for example the FASS/TON2 in regulation of the cellular skeleton, B′ subunits in brassinosteroid signalling and SAL proteins in regulation of auxin transport. Reverse genetics is starting to reveal also many more physiological functions of other subunits. A system with key regulatory proteins (TAP46, TIP41, PTPA, LCMT1, PME‐1) is present in all eukaryotes to stabilize, activate and inactivate the catalytic subunits. In this review, we present the status of knowledge concerning physiological functions of PP2A, PP4 and PP6 in Arabidopsis, and relate these to yeast and mammals.
Identification of quantitative trait loci and a candidate locus for freezing tolerance in controlled and outdoor environments in the overwintering crucifer Boechera stricta
Authors: HEO JAE‐YUN , FENG DONGSHENG , NIU XIAOMU , MITCHELL‐OLDS THOMAS , VAN TIENDEREN PETER H. , TOMES DWIGHT , SCHRANZ M. ERIC
Published: May 2014

Development of chilling and freezing tolerance is complex and can be affected by photoperiod, temperature and photosynthetic performance; however, there has been limited research on the interaction of these three factors. We evaluated 108 recombinant inbred lines of Boechera stricta, derived from a cross between lines originating from Montana and Colorado, under controlled long day (LD), short‐day (SD) and in an outdoor environment (OE). We measured maximum quantum yield of photosystem II, lethal temperature for 50% survival and electrolyte leakage of leaves. Our results revealed significant variation for chilling and freezing tolerance and photosynthetic performance in different environments. Using both single‐ and multi‐trait analyses, three main‐effect quantitative trait loci (QTL) were identified. QTL on linkage group (LG)3 were SD specific, whereas QTL on LG4 were found under both LD and SD. Under all conditions, QTL on LG7 were identified, but were particularly predictive for the outdoor experiment. The co‐localization of photosynthetic performance and freezing tolerance effects supports these traits being co‐regulated. Finally, the major QTL on LG7 is syntenic to the Arabidopsis C‐repeat binding factor locus, known regulators of chilling and freezing responses in Arabidopsis thaliana and other species.
Potato plants ectopically expressing Arabidopsis thaliana CBF3 exhibit enhanced tolerance to high‐temperature stress
Authors: DOU HAIOU , XV KUNPENG , MENG QINGWEI , LI GANG , YANG XINGHONG
Published: May 2014

CBF3, a known cold‐inducible gene that encodes a transcription factor, was isolated from Arabidopsis thaliana and introduced into the potato (Solanum tuberosum cv. ‘luyin NO.1’) under the control of the CaMV35S promoter or the rd29A promoter. Our results revealed that temperature of 40 °C or higher can significantly induce AtCBF3 expression. After heat stress, the net photosynthetic rate (Pn), the maximal photochemical efficiency of photosystem II (PSII) (Fv/Fm) and the accumulation of the D1 protein were higher in the transgenic lines than in the wild‐type (WT) line. Moreover, compared with the WT line, O2●− and H2O2 accumulation in the transgenic lines were reduced. A Q‐PCR assay of a subset of the genes involved in photosynthesis and antioxidant defence further verified the above results. Interestingly, under heat stress conditions, the accumulation of heat‐shock protein 70 (HSP70) increased in the WT line but decreased in the transgenic lines. These results suggest that potato plants ectopically expressing AtCBF3 exhibited enhanced tolerance to high temperature, which is associated with improved photosynthesis and antioxidant defence via induction of the expression of many stress‐inducible genes. However, this mechanism may not depend upon the regulatory pathways in which HSP70 is involved.
Scanning ion‐selective electrode technique and X‐ray microanalysis provide direct evidence of contrasting Na+ transport ability from root to shoot in salt‐sensitive cucumber and salt‐tolerant pumpkin under NaCl stress
Authors: Lei Bo , Huang Yuan , Sun Jingyu , Xie Junjun , Niu Mengliang , Liu Zhixiong , Fan Molin , Bie Zhilong
Published: May 2014

Grafting onto salt‐tolerant pumpkin rootstock can increase cucumber salt tolerance. Previous studies have suggested that this can be attributed to pumpkin roots with higher capacity to limit the transport of Na+ to the shoot than cucumber roots. However, the mechanism remains unclear. This study investigated the transport of Na+ in salt‐tolerant pumpkin and salt‐sensitive cucumber plants under high (200 mM) or moderate (90 mM) NaCl stress. Scanning ion‐selective electrode technique showed that pumpkin roots exhibited a higher capacity to extrude Na+, and a correspondingly increased H+ influx under 200 or 90 mM NaCl stress. The 200 mM NaCl induced Na+/H+ exchange in the root was inhibited by amiloride (a Na+/H+ antiporter inhibitor) or vanadate [a plasma membrane (PM) H+‐ATPase inhibitor], indicating that Na+ exclusion in salt stressed pumpkin and cucumber roots was the result of an active Na+/H+ antiporter across the PM, and the Na+/H+ antiporter system in salt stressed pumpkin roots was sufficient to exclude Na+. X‐ray microanalysis showed higher Na+ in the cortex, but lower Na+ in the stele of pumpkin roots than that in cucumber roots under 90 mM NaCl stress, suggesting that the highly vacuolated root cortical cells of pumpkin roots could sequester more Na+, limit the radial transport of Na+ to the stele and thus restrict the transport of Na+ to the shoot. These results provide direct evidence for pumpkin roots with higher capacity to limit the transport of Na+ to the shoot than cucumber roots.
Transcriptional profiling in dioecious plant Populus cathayana reveals potential and sex‐related molecular adaptations to solar UV‐B radiation
Authors: Jiang Hao , Zhang Sheng , Feng Lihua , Korpelainen Helena , Li Chunyang
Published: May 2014

There is increasing evidence confirming that dioecious plants have evolved a series of sex‐related physiological mechanisms allowing acclimation to environmental stresses, but few studies have attempted to thoroughly uncover the potential molecular regulation underlying these responses. Recently, we found in the dioecious plant, Populus cathayana, that males possess a greater tolerance to enhanced UV‐B radiation than do females. To continue this work further, comparative transcriptome analyses were carried out. A total of 362 and 296 differentially expressed genes (DEGs) were detected in males and females, respectively. Similarly, as shown in previous studies, these DEGs were involved in a set of conserved functions and pathways related to UV‐B stress, regardless of the sex. On the other hand, sex‐related responses via transcriptome remodeling were detected, as changes in sex‐related gene expression occurred in some pathways. For example, many DEGs involved in amino acid metabolism were mainly upregulated in males but downregulated in females. In some pathways, DEGs were expressed predominantly or exclusively in one sex. This may directly contribute to sex‐related physiological responses. Taken together, our results not only provide strong evidence that males and females have adopted sex‐related molecular strategies in response to solar UV‐B radiation but also suggest many new insights, in particular into molecular regulation, via sex‐biased gene expression. We conclude that these results can further enhance the sustainable exploitation and management of P. cathayana plants.
Multimodality systematic approach to mediastinal lymph node staging in non‐small cell lung cancer
Authors: Saettele Timothy M. , Ost David E.
Published: May 2014

Establishing an accurate diagnosis and stage for non‐small cell lung cancer has important implications for treatment and prognosis. Ideally, the process should be performed in a way that maximizes the information from each procedure while minimizing the risk to the patient. The concepts of decision analysis and Bayes' theorem form a basis to develop the strategy. In this framework, the pre‐test probability of malignancy is estimated in the lung nodule or mass, the regional lymph nodes and in distant sites. Invasive diagnostic tests are performed in sites with a pre‐test probability greater than the testing threshold, beginning with those sites that would yield the highest stage, if positive. Modalities are chosen that are able to biopsy the suspicious sites and present the least amount of risk to the patient. Following each test, the post‐test probability of malignancy is calculated to determine if it crosses the testing or test‐treatment thresholds. The process continues with further tests until a diagnosis and stage are established.
Multiscale Change Point Inference
Authors: Frick Klaus , Munk Axel , Sieling Hannes
Published: May 2014

We introduce a new estimator, the simultaneous multiscale change point estimator SMUCE, for the change point problem in exponential family regression. An unknown step function is estimated by minimizing the number of change points over the acceptance region of a multiscale test at a level α. The probability of overestimating the true number of change points K is controlled by the asymptotic null distribution of the multiscale test statistic. Further, we derive exponential bounds for the probability of underestimating K. By balancing these quantities, α will be chosen such that the probability of correctly estimating K is maximized. All results are even non-asymptotic for the normal case. On the basis of these bounds, we construct (asymptotically) honest confidence sets for the unknown step function and its change points. At the same time, we obtain exponential bounds for estimating the change point locations which for example yield the minimax rate O(n−1) up to a log-term. Finally, the simultaneous multiscale change point estimator achieves the optimal detection rate of vanishing signals as n → ∞, even for an unbounded number of change points. We illustrate how dynamic programming techniques can be employed for efficient computation of estimators and confidence regions. The performance of the multiscale approach proposed is illustrated by simulations and in two cutting edge applications from genetic engineering and photoemission spectroscopy.
Effect of Ambient Temperature on Stress Measurement Method Using Copper Foil
Authors: Ono Y. , Morito S.
Published: May 2014

The copper electroplating stress measurement method uses the grain growth in the copper on a machine element that has been subjected to repeated loads. Because this growth is also caused by thermal energy, the effect of the ambient temperature on grain growth density and grain orientation was investigated. Cyclic torsion tests were carried out at temperatures from 293 to 353 K. The relationship among the grain growth density, maximum shear stress, number of cycles, and ambient temperature was formulated to measure the maximum shear stress occurring on the machine element. Moreover, cyclic bending–torsion tests were also performed, and the orientations of grown grains were analysed by electron backscatter diffraction. The slip directions of grown grains corresponded closely with the direction of shear stress in spite of the ambient temperatures. This means that principal stresses can be measured by using the pole figure or the inverse pole figure of grown grains at temperatures up to 353 K.
Experimental Investigation of Bond Stress and Deformations in LWAC Ties Reinforced with GFRP Bars
Authors: Carmo R. N. F. , Costa H. , Bento G.
Published: May 2014

The structures' durability is an engineering concern for a long time but has been increased in the last years. Lightweight aggregate concrete (LWAC) combined with glass fibre reinforced polymer bars allows to create structures with high performance in terms of durability. The glass fibre reinforced polymer (GFRP) bars have different ribs from those of steel bars, and consequently, its bond to concrete is affected. Moreover, the Young's modulus of GFRP is much below compared with that of steel, and this influences significantly the behaviour of structural elements reinforced with this material. This paper presents an experimental study focused on bond between LWAC and reinforcing bars of GFRP. Thirty‐six pull‐out tests were carried out using steel and GFRP bars. These reinforcements were combined with three types of concrete, all with the same design density 1900 kg m−3 but with different values of compressive strength: 35, 55 and 70 MPa. Furthermore, 12 reinforced ties were tested, combining different types of bars (steel and GFRP), two different diameters (12 and 16 mm) and the three types of LWAC. Based on experimental results, several relations were established to understand the behaviour of LWAC structures reinforced with GFRP bars, mainly in the serviceability conditions. These results point out that ties deformation and crack width are very affected by the reduced Young's modulus of GFRP: deformations and crack width of ties reinforced with GFRP are significantly higher, approximately three times greater, compared with those of ties reinforced with steel. The tension stiffening effect was also analysed in detail, and it was found that it is slightly influenced by the concrete compressive strength but is highly dependent of the Young's modulus of the reinforcing material.
To conserve or not to conserve (mass in numerical models)
Authors: Hetényi György
Published: May 2014

Mass conservation is a fundamental physical law. Yet, computer models aiming to simulate Earth evolution commonly fail to respect it. Indeed, most geodynamic models implement phase transitions of rocks – such as metamorphism (solid–solid phase change) or melting (solid–liquid phase change) – following a simplifying assumption dating back to 1897 which is conserving volume rather than mass. The underlying problem is present at different scales, illustrated here by three examples: metamorphism in the continental crust, phase changes in the mantle transition zone and melt crystallization during columnar jointing. These illustrate that phase changes may become a driving force of a system's deformation and point to important differences with respect to simplified models. Developing and applying mass‐conserving approaches in future modelling tools are therefore not an option, but a necessity.
Cytomegalovirus infection after acute rejection therapy in seropositive kidney transplant recipients
Authors: Lee Y.‐M. , Kim Y.H. , Han D.J. , Park S.‐K. , Park J.S. , Sung H. , Hong H.‐L. , Kim T. , Kim S.‐H. , Choi S.‐H. , Kim Y.S. , Woo J.H. , Lee S.‐O.
Published: May 2014

Background

Acute rejection (AR) after solid organ transplantation has been known to be a risk factor for cytomegalovirus (CMV) infection. However, data regarding the risk for CMV infection during and after anti‐rejection therapy are limited. This study investigated whether the risk of CMV infection and disease within 6 months of kidney transplantation (KT) increases in CMV‐seropositive KT recipients who develop AR.

Methods

A total of 992 seropositive KT recipients, including 75 patients (8%) who developed AR within 6 months after KT and 917 patients (92%) who did not, were recruited between May 2007 and April 2012.

Results

No significant difference was found in the incidence of CMV infection between the groups (AR group, 13% [10/75] vs. non‐AR group, 10% [92/917], P = 0.37). The number of KT recipients in each group receiving preemptive therapy for CMV was similar (5% [4/75] vs. 6% [53/917], P > 0.99). While the incidence of CMV syndrome was comparable (0% [0/75] vs. 1% [12/917], P > 0.99), the incidence of tissue‐invasive CMV disease (8% [6/75] vs. 3% [27/917], P = 0.04), particularly gastrointestinal CMV disease, was significantly greater in patients who experienced AR. No CMV‐related mortality occurred in either group. AR (odds ratio, 2.81; 95% confidence interval, 1.08–7.29; P = 0.03) was an independent risk factor for tissue‐invasive CMV disease within 6 months of KT.

Conclusions

A high index of suspicion and active evaluation for tissue‐invasive CMV disease in KT recipients suffering AR may be necessary to ensure appropriate treatment.
Clinical features and outcomes of influenza infections in lung transplant recipients: a single‐season cohort study
Authors: Schuurmans M.M. , Isenring B.D. , Jungo C. , Boeni J. , Mueller N.J. , Kohler M. , Benden C.
Published: May 2014

Background

For lung transplant recipients (LTRs) influenza infections pose a considerable risk for complications. These infections have mainly been described in hospitalized patients. The aim of this study was to describe characteristics of predominantly outpatient‐treated influenza infections.

Methods

We conducted a single‐season (2010/2011) retrospective observational study using database information of our cohort. Patients with evidence for respiratory tract infection received empirical oseltamivir and an oral antibiotic, pending results from nasopharyngeal swab analysis. In laboratory‐confirmed influenza infection, treatment was continued and serial weekly swabs were performed until virologic results were negative.

Results

We identified 22 infections in 21 of 173 patients followed up; influenza A virus was diagnosed in 13 and influenza B virus in 9 infections. Leading presenting symptoms were cough and rhinorrhea. Oseltamivir was given within 48 h of symptom onset in 13 infections and within 72 h in 21 infections. Prolonged viral shedding (PVS) for ≥7 days was detected in 15 infections; median shedding duration for influenza A was 21 days. In univariable analysis, viral load (VL) at diagnosis was associated with extended duration of shedding (P = 0.006). Multivariable analysis confirmed this association. Bronchiolitis obliterans syndrome stage increased in 3 patients at 6‐month follow‐up.

Conclusion

In this study, PVS of influenza virus was detected in the majority of LTRs and high VL at diagnosis was predictive for prolonged shedding, which occurred despite extended antiviral therapy.
Whole‐genome profiling and shotgun sequencing delivers an anchored, gene‐decorated, physical map assembly of bread wheat chromosome 6A
Authors: Poursarebani Naser , Nussbaumer Thomas , Šimková Hana , Šafář Jan , Witsenboer Hanneke , van Oeveren Jan , Doležel Jaroslav , Mayer Klaus F.X. , Stein Nils , Schnurbusch Thorsten
Published: May 2014

Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence‐based physical map of wheat chromosome 6A using whole‐genome profiling (WGP™). The bacterial artificial chromosome (BAC) contig assembly tools fingerprinted contig (fpc) and linear topological contig (ltc) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that ltc created a highly robust assembly compared with those formed by fpc. The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP™ tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to the ‘decoration’ of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the sequencing of wheat chromosome 6A, and is of immediate use for map‐based isolation of agronomically important genes/quantitative trait loci located on this chromosome.
Globalisation and Industrial Policy: The Case of China
Authors: Nolan Peter
Published: May 2014

After a quarter of a century of industrial policy, China's objective of nurturing a group of globally competitive state‐owned enterprises appears to have succeeded beyond most expectations. However, China's SOEs are far from catching up with the world's leading firms. Protection through state ownership in a massive, fast‐growing economy has permitted China's SOEs to earn large profits and achieve high market capitalisations, but this is not the same thing as building globally competitive firms. The fact that China's industrial policy has been unsuccessful after a quarter of a century of intense effort demonstrates how difficult it is to construct an industrial policy in the era of capitalist globalisation, which has produced intense global industrial concentration across large parts of the global value chain. Although the detailed content of the next stage of reform of China's large state‐owned enterprises is unclear, China's determination to build a group of globally competitive large companies remains undimmed.
Molecular cloning and characterization of the cinnamate 4‐hydroxylase gene from Eupatorium adenophorum
Authors: Chen Lijuan , Guo Huiming , Lin Yi , Wu Yulun , Cheng Hongmei
Published: May 2014

Cinnamate‐4‐hydroxylase (CA4H), a cytochrome P450‐dependent monooxygenase, plays crucial roles in phenylpropanoid metabolism and plant defense. Previously, the authors showed that the expression of CA4H was induced in response to an allelopathic substance in Eupatorium adenophorum. Here, the full‐length cDNA of EaCA4H was cloned by using rapid amplification of cDNA ends. The 1518 bp open reading frame of EaCA4H was deduced to encode a protein of 505 amino acid residues. Like other CA4H proteins, the predicted EaCA4H polypeptides contained conserved domains of cytochrome P450. A Southern blot analysis indicated that at least five copies of EaCA4H exists in the genome of E. adenophorum. Subcellular localization revealed nuclear‐localized EaCA4H–green fluorescent protein fusion protein in onion epidermal cells. Heterologous silencing of endogenous CA4H in tobacco by a conserved EaCA4H fragment resulted in reduced expressions of key enzymatic genes and the production of downstream flavonoids in the phenylpropanoid pathway. Intriguingly, similar effects were observed in transgenic tobacco plants overexpressing EaCA4H. Altogether, the results indicate that the disturbed expression of CA4H in plants leads to relatively low expression levels of key enzymatic genes and the accumulation of the flavonoids that are involved in phenylpropanoid metabolism.
Quality of bone healing: Perspectives and assessment techniques
Authors: Guda Teja , Labella Carl , Chan Rodney , Hale Robert
Published: May 2014

Bone regeneration and healing is an area of extensive research providing an ever‐expanding set of not only therapeutic solutions for surgeons but also diagnostic tools. Multiple factors such as an ideal graft, the appropriate biochemical and mechanical wound environment, and viable cell populations are essential components in promoting healing. While bony tissue performs many functions, critical is mechanical strength, followed closely by structure. Many tools are available to evaluate bone quality in terms of quantity, structure, and strength; the purpose of this article is to identify the factors that can be evaluated and the advantages and disadvantages of each in assessing the quality of bone healing in both preclinical research and clinical settings.
Generalized joint laxity and multidirectional instability of the shoulder
Authors: Saccomanno Maristella , Fodale Mario , Capasso Luigi , Cazzato Giampiero , Milano Giuseppe
Published: May 2014

Generalized joint laxity and shoulder instability are common conditions that exhibit a wide spectrum of different clinical forms and may coexist in the same patient. Generalized joint laxity can be congenital or acquired. It is fundamental to distinguish laxity from instability. Laxity is a physiological condition that may predispose to the development of shoulder instability. A high prevalence of generalized joint laxity has been identified in patients with multidirectional instability of the shoulder. Multidirectional instability is defined as symptomatic instability in two or more directions. The diagnosis and treatment of this condition are still challenging because of complexities in its classification and etiology. These complexities are compounded when multidirectional instability and laxity exist in the same patient. With an improved understanding of the clinical symptoms and physical examination findings, a successful strategy for conservative and/or surgical treatments can be developed. Conservative treatment is the first-line option. If it fails, different surgical options are available. Historically, open capsular shift has been considered the gold standard in the surgical management of these patients. Nowadays, advanced arthroscopic techniques offer several advantages over traditional open approaches and have shown similar outcomes. The correct approach to the management of failed stabilization procedures has not been yet defined.
Draft Genome Sequence of the Novel Thermoacidophilic Archaeon
Acidianus copahuensis
Strain ALE1, Isolated from the Copahue Volcanic Area in Neuquén, Argentina
Authors: Urbieta M. Sofía , Rascovan Nicolás , Castro Camila , Revale Santiago , Giaveno M. Alejandra , Vazquez Martín , Donati Edgardo R.
Published: May 2014

Acidianus copahuensis
is a recently characterized thermoacidophilic archaeon isolated from the Copahue volcanic area in Argentina. Here, we present its draft genome sequence, in which we found genes involved in key metabolic pathways for developing under Copahue's extreme environmental conditions, such as sulfur and iron oxidation, carbon fixation, and metal tolerance.
Whole-Genome Sequences of 13 Endophytic Bacteria Isolated from Shrub Willow (
Salix
) Grown in Geneva, New York
Authors: Gan Huan You , Gan Han Ming , Savka Michael A. , Triassi Alexander J. , Wheatley Matthew S. , Smart Lawrence B. , Fabio Eric S. , Hudson André O.
Published: May 2014

Shrub willow,
Salix
spp. and hybrids, is an important bioenergy crop. Here we report the whole-genome sequences and annotation of 13 endophytic bacteria from stem tissues of
Salix purpurea
grown in nature and from commercial cultivars and
Salix viminalis
×
Salix miyabeana
grown in bioenergy fields in Geneva, New York.
Draft Genome Sequence of Stenotrophomonas maltophilia SeITE02, a Gammaproteobacterium Isolated from Selenite-Contaminated Mining Soil
Authors: Bertolini Cristina , van Aerle Ronny , Lampis Silvia , Moore Karen A. , Paszkiewicz Konrad , Butler Clive S. , Vallini Giovanni , van der Giezen Mark
Published: May 2014

Stenotrophomonas maltophilia
strain SeITE02 was isolated from the rhizosphere of the selenium-hyperaccumulating legume
Astragalus bisculcatus
. In this report, we provide the 4.56-Mb draft genome sequence of
S. maltophilia
SeITE02, a gammaproteobacterium that can withstand high concentrations of selenite and reduce these to elemental selenium.
Draft Genome Sequence of
Geobacillus
sp. Strain FW23, Isolated from a Formation Water Sample
Authors: Pore Soham D. , Arora Preeti , Dhakephalkar Prashant K.
Published: May 2014

The thermophilic
Geobacillus
sp. strain FW23 was isolated from the Mehsana oil wells in Gujrat, India, during a screening for oil-degrading bacteria. Here, we report the draft genome sequence of
Geobacillus
sp. FW23, which may help reveal the genomic differences between this strain and the earlier reported species of the genus
Geobacillus
.
Complete Genome Sequence of Neisseria meningitidis Serogroup A Strain NMA510612, Isolated from a Patient with Bacterial Meningitis in China
Authors: Zhang Yan , Yang Jian , Xu Li , Zhu Yafang , Liu Bo , Shao Zhujun , Zhang Xiaobing , Jin Qi
Published: May 2014

Serogroup A meningococcal strains have been involved in several pandemics and a series of epidemics worldwide in the past. Determination of the genome sequence of the prevalent genotype strain will help us understand the genetic background of the evolutionary and epidemiological properties of these bacteria. We sequenced the complete genome of
Neisseria meningitidis
NMA510612, a clinical isolate from a patient with meningococcal meningitis.
Draft Genome Sequence of Mycobacterium vulneris DSM 45247
T
Authors: Croce Olivier , Robert Catherine , Raoult Didier , Drancourt Michel
Published: May 2014

We report the draft genome sequence of
Mycobacterium vulneris
DSM 45247
T
strain, an emerging, opportunistic pathogen of the
Mycobacterium avium
complex. The genome described here is composed of 6,981,439 bp (with a G+C content of 67.14%) and has 6,653 protein-coding genes and 84 predicted RNA genes.
Draft Genome Sequence of Mycobacterium tuberculosis Clinical Strain G-12-005
Authors: Berland Jean-Luc , de Carvalho Fabíola Marques , de Almeida Luiz Gonzaga Paula , Bablishvili Nino , Gauthier Marie , Paranhos-Baccalà Glaucia , de Vasconcelos Ana Tereza Ribeiro
Published: May 2014

Infection caused by drug-resistant
Mycobacterium tuberculosis
is a growing concern, especially in eastern Europe. We report an annotated draft genome sequence of
M. tuberculosis
strain G-12-005 obtained from a patient in Georgia.
Prevalence of Unclassified Bacteria in Tropical Coastal Waters of Malaysia Revealed by Metagenomic Approach
Authors: Chan Kok-Gan , Chong Teik-Min
Published: May 2014

The metagenomes of marine prokaryotes from coastal seawaters in Malaysia are reported in this study. The investigation of the microbial communities using 16S rRNA gene amplicon metagenomic sequencing revealed that majority of the bacteria in the seawater samples remain unclassified.
Complete Genome Sequence of Pandoraea pnomenusa 3kgm, a Quorum-Sensing Strain Isolated from a Former Landfill Site
Authors: Chan Kok-Gan , Yin Wai-Fong , Goh Share-Yuan
Published: May 2014

Pandoraea pnomenusa
strain 3kgm has been identified as a quorum-sensing strain isolated from soil. Here, we report the complete genome sequence of
P. pnomenusa
strain 3kgm by using the Pacific Biosciences single-molecule real-time (PacBio RS SMRT) sequencer high-resolution technology.
Examining the Delivery Modes of Metacognitive Awareness and Active Reading Lessons in a College Nonmajors Introductory Biology Course
Authors: Hill Kendra M. , Brözel Volker S. , Heiberger Greg A.
Published: May 2014

Current research supports the role of metacognitive strategies to enhance reading comprehension. This study measured the effectiveness of online versus face-to-face metacognitive and active reading skills lessons introduced by Biology faculty to college students in a nonmajors introductory biology course. These lessons were delivered in two lectures either online (Group 1: N = 154) or face to face (Group 2: N = 152). Previously validated pre- and post- surveys were used to collect and compare data by paired and independent t-test analysis (α = 0.05). Pre- and post- survey data showed a statistically significant improvement in both groups in metacognitive awareness (p = 0.001, p = 0.003, respectively) and reading comprehension (p < 0.001 for both groups). When comparing the delivery mode of these lessons, no difference was detected between the online and face-to-face instruction for metacognitive awareness (pre- p = 0.619, post- p = 0.885). For reading comprehension, no difference in gains was demonstrated between online and face-to-face (p = 0.381); however, differences in pre- and post- test scores were measured (pre- p = 0.005, post- p = 0.038). This study suggests that biology instructors can easily introduce effective metacognitive awareness and active reading lessons into their course, either through online or face-to-face instruction.
Designing PCR Primers Painlessly
Authors: Feeney Morgan , Murphy Kevin , Lopilato Jane
Published: May 2014

Students design primers using web-based tools along with a printed sequence of a prokaryotic gene showing both DNA strands and translation of the coding strand into amino acids. The melting temperature of each primer is determined and the pair closest in temperature can be used to amplify and clone a gene into a vector for a one-semester laboratory exercise. By working through this primer design exercise, students see first hand what is involved in the process of amplifying DNA.
Evaluating Biological Claims to Enhance Critical Thinking through Position Statements
Authors: Addy Tracie M. , Stevenson Maura O.
Published: May 2014

Critical thinking is an important skill for undergraduates to learn, yet rarely is it formally taught in the classroom. Here we explain how critical thinking can be fostered within an undergraduate biology course by encouraging students to evaluate biological claims related to current topics within the course. We found that with the completion of two writing assignments within a four-week period, students demonstrated a significantly greater ability to analyze the evidence within the claims. These results support the notion that even short-term learning experiences focused upon critical thinking can enhance students’ skills beyond discipline-specific knowledge.
Creative Teaching Models for the Innovative Faint of HeartReview of:	Exemplary College Science Teaching;	YagerRobert E. (ed); (	2013).	National Science Teachers Association Press,	Arlington, VA.	243 pages.
Authors: Anderson Deborah K.
Published: May 2014

Review of:
Exemplary College Science Teaching;
Robert E. Yager (ed); (2013). National Science Teachers Association Press, Arlington, VA. 243 pages.
Journal Watch
Authors: Herzog Jennifer A.
Published: May 2014

In this section, I provide articles on recent developments and new technology used in microbiology and related fields. I also post articles that may help you bring new information or techniques into your laboratory or classroom via case studies or lab exercises. I hope you find this information useful, and I encourage you to send suggestions, questions or comments to me at
herzogja@herkimer.edu.
I look forward to hearing from you!
Letter to the Editor
Authors: Hoskins Sally G. , Kenyon Kristy L.
Published: May 2014

The authors respond to a previously published JMBE article, “The CREATE Method Does Not Result in Greater Gains in Critical Thinking than a More Traditional Method of Analyzing the Primary Literature” by M. Segura-Totten and N. Dalman (JMBE 14: 166–175, 2013).
From the Editor-in-Chief: Changes to Enhance the Author Experience
Authors: Elliott Samantha
Published: May 2014

JMBE
Editor-in-Chief, Dr. Samantha Elliott, thanks past volunteers for their efforts and discusses several new author enhancements related to the recently expanded scope, including video tutorials, a self-assessment tool, and a thematic issue.
Wet Needling of Myofascial Trigger Points in Abdominal Muscles for Treatment of Primary Dysmenorrhoea
Authors: Huang Qiang-Min , Liu Lin
Published: May 2014

Objectives

To evaluate the effect of wet needling (related to acupuncture) and home stretching exercises on myofascial trigger points (MTrPs) in abdominal muscles for the treatment of dysmenorrhoea.

Methods

The effect of wet needing of MTrPs in abdominal muscles, supplemented by home stretching exercises, was observed in 65 patients with moderate and severe primary dysmenorrhoea. The MTrPs in the abdominal region were localised and repeatedly needled with lidocaine injection. Menstrual pain was evaluated with a Visual Analogue Scale (VAS) score after every treatment, with the final evaluation made at a 1-year follow-up. Treatment was stopped when the VAS pain score reduced to ≤3. Symptoms scores were analysed with one-way analysis of variance.

Results

The mean VAS pain score before treatment was 7.49±1.16. After a single wet needling session, 41 patients had a reduction in their VAS pain score to <3 during their following menstrual cycle, with a mean of 1.63±0.49. Twenty-four patients who needed two treatments showed a reduction in menstrual pain scores to 0.58±0.50. After 1 year, the mean VAS pain score among all patients was 0.28±0.45, with a response rate of 100%.

Conclusions

Primary dysmenorrhoea was significantly reduced 1 year after wet needling to MTrPs in the abdominal region and home stretching exercises, justifying further research with controlled trials.
Rare cause of hip pain in a young girl
Authors: Raza Ali , Kailash Kailash , Malviya Ajay
Published: May 2014

Synovial chondromatosis (SC) is a rare benign disorder of unknown aetiology resulting in multiple cartilaginous loose bodies that form within a synovial joint. It is predominantly seen in men (2:1) in the third and fifth decade of life and is extremely rare in children. Hip joint is an extremely rare and unusual site of presentation thus leading to delay in diagnosis and associated morbidity. We report a successfully treated case of SC in a 12-year-old girl complaining of hip pain over a year. In addition, this is also the first case of a child with SC of the hip being treated arthroscopically.
Older females are at higher risk for medical complications during 21 km road race running: a prospective study in 39 511 race starters—SAFER study III
Authors: Schwabe Karen , Schwellnus Martin P , Derman Wayne , Swanevelder Sonja , Jordaan Esme
Published: May 2014

Background

The half-marathon (21 km) race is a very popular mass community-based distance running event. It is important to determine risk factors for medical complications during these events, so that prevention programmes can be developed.

Objective

To determine risk factors associated with medical complications during 21 km road running events.

Design

Prospective study.

Setting

Two Oceans half-marathon (21 km) races.

Participants

39 511 starters in the 21 km race.

Methods

Medical complications (defined as any runner requiring assessment by a doctor at the race medical facility or a local hospital on race day) were recorded over a 4-year study period. Medical complications were subdivided according to the system affected and by final diagnosis. A Poisson regression model was used to determine risk factors for any medical complication and more common specific complications.

Results

Independent risk factors for medical complication during 21 km running were older female runners (women >50 vs  ≤50 years; p<0.0001) and year of observation (2008 vs 2011; p=0.0201: 2009 vs 2011: p=0.0019; 2010 vs 2011: p=0.0096). Independent risk factors for specific common medical complications were: postural hypotension (women, slow running pace), musculoskeletal complications (less running experience, slower running pace) and dermatological complications (women).

Conclusions

Older female runners are at higher risk of developing medical complications during 21 km road running races. Environmental conditions in a particularly cold climate may also play a role. Less running experience and slower running pace are associated with specific medical complications. Medical staff can now plan appropriate care on race days, and interventions can be developed to reduce the risk of medical complications in 21 km races.
Associations between damage location and five main body region injuries of MAIS 3–6 injured occupants
Authors: Tang Youming , Cao Libo , Kan Steven
Published: May 2014

Objectives

To examine the damage location distribution of five main body region injuries of maximum abbreviated injury score (MAIS) 3–6 injured occupants for nearside struck vehicle in front-to-side impact crashes.

Design and setting

MAIS 3–6 injured occupants information was extracted from the US-National Automotive Sampling System/Crashworthiness Data System in the year 2007; it included the head/face/neck, chest, pelvis, upper extremity and lower extremity. Struck vehicle collision damage was classified in a three-dimensional system according to the J224 Collision Deformation Classification of SAE Surface Vehicle Standard.

Participants

Nearside occupants seated directly adjacent to the struck side of the vehicle with MAIS 3–6 injured, in light truck vehicles–passenger cars (LTV–PC) side impact crashes.

Outcome measures

Distribution of MAIS 3–6 injured occupants by body regions and specific location of damage (lateral direction, horizontal direction and vertical direction) were examined. Injury risk ratio was also assessed.

Results

The lateral crush zone contributed to MAIS 3–6 injured occupants (n=705) and 50th centile injury risks when extended into zone 3. When the crush extended to zone 4, the injury risk ratio of MAIS 3–6 injured occupants approached 81%. The horizontal crush zones contributing to the highest injury risk ratio of MAIS 3–6 occupants were zones ‘D’ and ‘Y’, and the injury risk ratios were 25.4% and 36.9%, respectively. In contrast, the lowest injury risk ratio was 5.67% caused by zone ‘B’. The vertical crush zone which contributed to the highest injury risk ratio of MAIS 3–6 occupants was zone ‘E’, whose injury risk ratio was 58%. In contrast, the lowest injury risk ratio was 0.14% caused by zone ‘G+M’.

Conclusions

The highest injury risk ratio of MAIS 3–6 injured occupants caused by crush intrusion between 40 and 60 cm in LTV–PC nearside impact collisions and the damage region of the struck vehicle was in the zones ‘E’ and ‘Y’.
A comparative assessment of the price, brands and pack characteristics of illicitly traded cigarettes in five cities and towns in South Africa
Authors: Wherry Anna E , McCray Cheyenne A , Adedeji-Fajobi Temidayo I , Sibiya Xolani , Ucko Peter , Lebina Limakatso , Golub Jonathan E , Cohen Joanna E , Martinson Neil A
Published: May 2014

Objective

The prevalence of illicitly traded cigarettes in South Africa has been reported to be 40–50%. However, these estimates do not account for the more nuanced characteristics of the illicit cigarette trade. With the goal of better understanding contraband cigarettes in South Africa, this study piloted three methods for assessing the price, brands, pack features and smoker's views about illicit cigarettes in five cities/towns. Data were collected in June and July 2012.

Setting

A convenience sample of three South African cities (Johannesburg, Durban and Nelspruit) and two smaller towns (Musina and Ficksburg) were chosen for this study.

Outcome measures

Three cross-sectional approaches were used to assess the characteristics of contraband cigarettes: (1) a dummy purchase of cigarettes from informal retailers, (2) the collection of discarded cigarette packs and (3) a survey of tobacco smokers.

Participants

For the purposes of the survey, 40 self-reported smokers were recruited at taxi ranks in each downtown site. Adults who were over the age of 18 were asked to verbally consent to participate in the study and answer a questionnaire administered by a researcher.

Results

The leading reason for labelling a pack as illicit in each city/town was the absence of an excise stamp (28.6% overall), and the least common reason was an illegal tar or nicotine level (11.1% overall). The overall proportion of informal vendors who sold illicit cigarettes was 41%. Singles and packs of 20 were consistently cheaper at informal vendors. Survey participants’ responses reflected varied perspectives on illicit cigarettes and purchasing preferences.

Conclusions

Each approach generated an interesting insight into physical aspects of illicit cigarettes. While this pilot study cannot be used to generate generalisable statistics on illicit cigarettes, more systematic surveys of this nature could inform researchers’ and practitioners’ initiatives to combat illicit and legal cigarette sales and usage.
A cautionary lesson on the use of targeted methods for EGFR mutation analysis: a case report
Authors: Walsh K , Wallace W A , Butler R , Mackean M J , Harrison D J , Stirling D , Oniscu A
Published: May 2014

Epidermal growth factor receptor (EGFR) mutation analysis is recommended for lung cancer patients prior to the prescription of first-line EGFR tyrosine kinase inhibitors in order to predict response to treatment. There are many methods available to identify mutations in theEGFRgene; a large number of clinical laboratories use thetherascreenEGFR RGQ PCR kit (Qiagen). We report a case where this kit detected an exon 19 deletion, predicting sensitivity to tyrosine kinase inhibitors (TKIs), which on further analysis was found to be a 2 bp indel (c.2239_2240delinsCC, p.(Leu747Pro)). Two of four published cases with this mutation were found to be associated with resistance to EGFR TKI. The sample was also tested using two other commercial kits, one of which indicated a deletion. This is a rare mutation making the erroneous detection of a deletion unlikely; however, it is important that clinical laboratories are aware of the potential failings of two commercial kits forEGFRmutation analysis.
Narrating the self-injured body
Authors: Chandler Amy
Published: May 2014

Illness narratives have traditionally been used as a conceptual tool for exploring experiences of chronic illness or disease. In this paper, I suggest that Frank's typology of illness narratives (chaos, restitution and quest) also offers an illuminating approach to analysing accounts of self-injury, demonstrating the diverse ways in which self-injury is practiced, experienced and narrated. Drawing on 24 narrative interviews with 12 people who had self-injured, I focus on participants’ accounts of their self-injured bodies. The approach is phenomenological, and concerned with talk about the experience of living with and in a body that has been marked by self-injury. Thus, theactof self-injury is not the sole focus, and particular attention is paid to accounts of the bodily aftermath: scars, marks and wounds. Scars left by self-injury can be seen as communicative, and the analysis developed here demonstrates some of the various ways that these marks may be read. Attending to these diverse narratives can contribute to the provision of compassionate, non-judgemental care for patients who have self-injured. Further, highlighting the existence of different ways of narrating the self-injured body may offer an optimistic resource for people who have self-injured.