bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactisBl-04
Authors: Andersen Joakim M , Barrangou Rodolphe , Hachem Maher Abou , Lahtinen Sampo J , Goh Yong Jun , Svensson Birte , Klaenhammer Todd R
Published: May 2013

Background

Probiotic bifidobacteria in combination with prebiotic carbohydrates have documented positive effects on human health regarding gastrointestinal disorders and improved immunity, however the selective routes of uptake remain unknown for most candidate prebiotics. The differential transcriptomes of Bifidobacterium animalis subsp. lactis Bl-04, induced by 11 potential prebiotic oligosaccharides were analyzed to identify the genetic loci involved in the uptake and catabolism of α- and β-linked hexoses, and β-xylosides.

Results

The overall transcriptome was modulated dependent on the type of glycoside (galactosides, glucosides or xylosides) utilized. Carbohydrate transporters of the major facilitator superfamily (induced by gentiobiose and β-galacto-oligosaccharides (GOS)) and ATP-binding cassette (ABC) transporters (upregulated by cellobiose, GOS, isomaltose, maltotriose, melibiose, panose, raffinose, stachyose, xylobiose and β-xylo-oligosaccharides) were differentially upregulated, together with glycoside hydrolases from families 1, 2, 13, 36, 42, 43 and 77. Sequence analysis of the identified solute-binding proteins that determine the specificity of ABC transporters revealed similarities in the breadth and selectivity of prebiotic utilization by bifidobacteria.

Conclusion

This study identified the differential gene expression for utilization of potential prebiotics highlighting the extensive capabilities of Bifidobacterium lactis Bl-04 to utilize oligosaccharides. Results provide insights into the ability of this probiotic microbe to utilize indigestible carbohydrates in the human gastrointestinal tract.
Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains
Authors: Espinosa Angarica Vladimir , Ventura Salvador , Sancho Javier
Published: May 2013

Background

Prion proteins conform a special class among amyloids due to their ability to transmit aggregative folds. Prions are known to act as infectious agents in neurodegenerative diseases in animals, or as key elements in transcription and translation processes in yeast. It has been suggested that prions contain specific sequential domains with distinctive amino acid composition and physicochemical properties that allow them to control the switch between soluble and β-sheet aggregated states. Those prion-forming domains are low complexity segments enriched in glutamine/asparagine and depleted in charged residues and prolines. Different predictive methods have been developed to discover novel prions by either assessing the compositional bias of these stretches or estimating the propensity of protein sequences to form amyloid aggregates. However, the available algorithms hitherto lack a thorough statistical calibration against large sequence databases, which makes them unable to accurately predict prions without retrieving a large number of false positives.

Results

Here we present a computational strategy to predict putative prion-forming proteins in complete proteomes using probabilistic representations of prionogenic glutamine/asparagine rich regions. After benchmarking our predictive model against large sets of non-prionic sequences, we were able to filter out known prions with high precision and accuracy, generating prediction sets with few false positives. The algorithm was used to scan all the proteomes annotated in public databases for the presence of putative prion proteins. We analyzed the presence of putative prion proteins in all taxa, from viruses and archaea to plants and higher eukaryotes, and found that most organisms encode evolutionarily unrelated proteins with susceptibility to behave as prions.

Conclusions

To our knowledge, this is the first wide-ranging study aiming to predict prion domains in complete proteomes. Approaches of this kind could be of great importance to identify potential targets for further experimental testing and to try to reach a deeper understanding of prions’ functional and regulatory mechanisms.
Characterization of human plasma-derived exosomal RNAs by deep sequencing
Authors: Huang Xiaoyi , Yuan Tiezheng , Tschannen Michael , Sun Zhifu , Jacob Howard , Du Meijun , Liang Meihua , Dittmar Rachel L , Liu Yong , Liang Mingyu , Kohli Manish , Thibodeau Stephen N , Boardman Lisa , Wang Liang
Published: May 2013

Background

Exosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers. To characterize exosomal RNA profiles systemically, we performed RNA sequencing analysis using three human plasma samples and evaluated the efficacies of small RNA library preparation protocols from three manufacturers. In all we evaluated 14 libraries (7 replicates).

Results

From the 14 size-selected sequencing libraries, we obtained a total of 101.8 million raw single-end reads, an average of about 7.27 million reads per library. Sequence analysis showed that there was a diverse collection of the exosomal RNA species among which microRNAs (miRNAs) were the most abundant, making up over 42.32% of all raw reads and 76.20% of all mappable reads. At the current read depth, 593 miRNAs were detectable. The five most common miRNAs (miR-99a-5p, miR-128, miR-124-3p, miR-22-3p, and miR-99b-5p) collectively accounted for 48.99% of all mappable miRNA sequences. MiRNA target gene enrichment analysis suggested that the highly abundant miRNAs may play an important role in biological functions such as protein phosphorylation, RNA splicing, chromosomal abnormality, and angiogenesis. From the unknown RNA sequences, we predicted 185 potential miRNA candidates. Furthermore, we detected significant fractions of other RNA species including ribosomal RNA (9.16% of all mappable counts), long non-coding RNA (3.36%), piwi-interacting RNA (1.31%), transfer RNA (1.24%), small nuclear RNA (0.18%), and small nucleolar RNA (0.01%); fragments of coding sequence (1.36%), 5′ untranslated region (0.21%), and 3′ untranslated region (0.54%) were also present. In addition to the RNA composition of the libraries, we found that the three tested commercial kits generated a sufficient number of DNA fragments for sequencing but each had significant bias toward capturing specific RNAs.

Conclusions

This study demonstrated that a wide variety of RNA species are embedded in the circulating vesicles. To our knowledge, this is the first report that applied deep sequencing to discover and characterize profiles of plasma-derived exosomal RNAs. Further characterization of these extracellular RNAs in diverse human populations will provide reference profiles and open new doors for the development of blood-based biomarkers for human diseases.
Sequencing platform and library preparation choices impact viral metagenomes
Authors: Solonenko Sergei A , Ignacio-Espinoza J César , Alberti Adriana , Cruaud Corinne , Hallam Steven , Konstantinidis Kostas , Tyson Gene , Wincker Patrick , Sullivan Matthew B
Published: May 2013

Background

Microbes drive the biogeochemistry that fuels the planet. Microbial viruses modulate their hosts directly through mortality and horizontal gene transfer, and indirectly by re-programming host metabolisms during infection. However, our ability to study these virus-host interactions is limited by methods that are low-throughput and heavily reliant upon the subset of organisms that are in culture. One way forward are culture-independent metagenomic approaches, but these novel methods are rarely rigorously tested, especially for studies of environmental viruses, air microbiomes, extreme environment microbiology and other areas with constrained sample amounts. Here we perform replicated experiments to evaluate Roche 454, Illumina HiSeq, and Ion Torrent PGM sequencing and library preparation protocols on virus metagenomes generated from as little as 10pg of DNA.

Results

Using %G + C content to compare metagenomes, we find that (i) metagenomes are highly replicable, (ii) some treatment effects are minimal, e.g., sequencing technology choice has 6-fold less impact than varying input DNA amount, and (iii) when restricted to a limited DNA concentration (<1μg), changing the amount of amplification produces little variation. These trends were also observed when examining the metagenomes for gene function and assembly performance, although the latter more closely aligned to sequencing effort and read length than preparation steps tested. Among Illumina library preparation options, transposon-based libraries diverged from all others and adaptor ligation was a critical step for optimizing sequencing yields.

Conclusions

These data guide researchers in generating systematic, comparative datasets to understand complex ecosystems, and suggest that neither varied amplification nor sequencing platforms will deter such efforts.
Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction
Authors: Beneventi Magda Aparecida , da Silva Orzenil Bonfim , de Sá Maria Eugênia Lisei , Firmino Alexandre Augusto Pereira , de Amorim Regina Maria Santos , Albuquerque Érika Valéria Saliba , da Silva Maria Cristina Mattar , da Silva Joseane Padilha , Campos Magnólia de Araújo , Lopes Marcus José Conceição , Togawa Roberto Coiti , Pappas Georgios Joanis , Grossi–de–Sa Maria Fatima
Published: May 2013

Background

Root-knot nematodes (RKN– Meloidogyne genus) present extensive challenges to soybean crop. The soybean line (PI 595099) is known to be resistant against specific strains and races of nematode species, thus its differential gene expression analysis can lead to a comprehensive gene expression profiling in the incompatible soybean-RKN interaction. Even though many disease resistance genes have been studied, little has been reported about phytohormone crosstalk on modulation of ROS signaling during soybean-RKN interaction.

Results

Using 454 technology to explore the common aspects of resistance reaction during both parasitism and resistance phases it was verified that hormone, carbohydrate metabolism and stress related genes were consistently expressed at high levels in infected roots as compared to mock control. Most noteworthy genes include those encoding glycosyltransferases, peroxidases, auxin-responsive proteins and gibberellin-regulated genes. Our data analysis suggests the key role of glycosyltransferases, auxins and components of gibberellin signal transduction, biosynthesis and deactivation pathways in the resistance reaction and their participation in jasmonate signaling and redox homeostasis in mediating aspects of plant growth and responses to biotic stress.

Conclusions

Based on this study we suggest a reasonable model regarding to the complex mechanisms of crosstalk between plant hormones, mainly gibberellins and auxins, which can be crucial to modulate the levels of ROS in the resistance reaction to nematode invasion. The model also includes recent findings concerning to the participation of DELLA-like proteins and ROS signaling controlling plant immune or stress responses. Furthermore, this study provides a dataset of potential candidate genes involved in both nematode parasitism and resistance, which can be tested further for their role in this biological process using functional genomics approaches.
Comparing the effects of isoflurane and pentobarbital on the responses of cutaneous mechanoreceptive afferents
Authors: Cheng Ju-Wen , Weber Alison I , Bensmaia Sliman J
Published: May 2013

Background

While pentobarbital has been used extensively in neurophysiological experiments investigating activity in peripheral nerves, it has fallen out of favor as an anesthetic because of safety concerns and is often replaced with isoflurane. However, the effects of isoflurane on the excitability of mechanoreceptive afferents have yet to be conclusively elucidated.

Methods

To fill this gap, we collected extracellular single-unit recordings of cutaneous mechanoreceptive afferents from the sciatic nerve of 21 rats during vibratory stimulation of the hindpaw. We then compared the strength and temporal structure of the afferent response measured under pentobarbital and isoflurane anesthesia.

Results

We found that the strength and temporal structure of afferent responses were statistically equivalent whether these were evoked under isoflurane or pentobarbital.

Conclusions

We conclude that, if these two anesthetics have any effect on the responses of mechanoreceptive afferents, their effects are indistinguishable.
Novel study design to assess the utility of the copd assessment test in a primary care setting
Authors: Gruffydd-Jones Kevin , Marsden Helen , Holmes Steve , Kardos Peter , Escamilla Roger , Dal Negro Roberto , Roberts June , Nadeau Gilbert , Leather David , Jones Paul
Published: May 2013

The quality of a consultation provided by a physician can have a profound impact on the quality of care and patient engagement in treatment decisions. When the COPD Assessment Test (CAT) was developed, one of its aims was to aid the communication between physician and patient about the impact of COPD. We developed a novel study design to assess this in a primary care consultation.

Primary care physicians across five countries in Europe conducted videoed consultations with six standardised COPD patients (played by trained actors) which had patient-specific issues that the physician needed to identify through questioning. Half the physicians saw the patients with the completed CAT, and half without. Independent assessors scored the physicians on their ability to identify and address the patient-specific issues, review standard COPD aspects, their understanding of the case and their overall performance. This novel study design presented many challenges which needed to be addressed to achieve an acceptable level of robustness to assess the utility of the CAT. This paper discusses these challenges and the measures adopted to eliminate or minimise their impact on the study results.
Recruitment strategies and yields for the Pathobiology of Prediabetes in a Biracial Cohort: a prospective natural history study of incident dysglycemia
Authors: Ebenibo Sotonte , Edeoga Chimaroke , Ammons Ann , Egbuonu Nonso , Dagogo-Jack Samuel ,   the Pathobiology of Prediabetes in a Biracial Cohort (POP-ABC) Research Group
Published: May 2013

Background

The Pathobiology of Prediabetes in A Biracial Cohort study is a prospective evaluation of the transition from normal to impaired glucose regulation among African American and Caucasian adults with parental type 2 diabetes. This report describes recruitment strategies and relative yields for the 376 enrolled subjects.

Methods

Recruitment occurred over 3.4 years, with clinical and metabolic assessments during 2.1-5.5 years of quarterly follow-up. The major recruitment sources were advertisements, community outreach, and clinical facilities. Advertisements included newspaper, television, radio, Internet, distributed brochures, utility bill inserts, and direct mailing. Community outreach included screening events during religious gatherings and health fairs, and referral by friends and families. The category of clinical facilities covered all subjects referred by health workers or recruited through area clinics and hospitals.

Results

57.7% of participants were African American and 42.3% were Caucasian; the mean age (± SD) was 44.2 ± 10.6 years, and ~70% were female. Advertisements yielded 52.4% of all participants, compared to 34.8% from community outreach and 12.8% from clinical facilities (P for trend < 0.0001). More Caucasians than African Americans cited advertising as the source of study information, whereas more African Americans than Caucasians cited community outreach. The accrual from clinical facilities was similar in both groups.

Conclusions

Advertisements and community outreach were robust recruitment sources for assembling a diverse longitudinal diabetes offspring cohort, but each had differential yields in African Americans and Caucasians. Thus, a multifaceted approach comprising passive and active components is needed to recruit a multiracial clinical research population.
Protein body formation in stable transgenic tobacco expressing elastin-like polypeptide and hydrophobin fusion proteins
Authors: Gutiérrez Sonia P , Saberianfar Reza , Kohalmi Susanne E , Menassa Rima
Published: May 2013

Background

Plants are recognized as an efficient and inexpensive system to produce valuable recombinant proteins. Two different strategies have been commonly used for the expression of recombinant proteins in plants: transient expression mediated by Agrobacterium; or stable transformation of the plant genome. However, the use of plants as bioreactors still faces two main limitations: low accumulation levels of some recombinant proteins and lack of efficient purification methods. Elastin-like polypeptide (ELP), hydrophobin I (HFBI) and Zera® are three fusion partners found to increase the accumulation levels of recombinant proteins and induce the formation of protein bodies (PBs) in leaves when targeted to the endoplasmic reticulum (ER) in transient expression assays. In this study the effects of ELP and HFBI fusion tags on recombinant protein accumulation levels and PB formation was examined in stable transgenic Nicotiana tabacum.

Results

The accumulation of recombinant protein and PB formation was evaluated in two cultivars of Nicotiana tabacum transformed with green fluorescent protein (GFP) fused to ELP or HFBI, both targeted and retrieved to the ER. The ELP and HFBI tags increased the accumulation of the recombinant protein and induced the formation of PBs in leaves of stable transgenic plants from both cultivars. Furthermore, these tags induced the formation of PBs in a concentration-dependent manner, where a specific level of recombinant protein accumulation was required for PBs to appear. Moreover, agro-infiltration of plants accumulating low levels of recombinant protein with p19, a suppressor of post-transcriptional gene silencing (PTGS), increased accumulation levels in four independent transgenic lines, suggesting that PTGS might have caused the low accumulation levels in these plants.

Conclusion

The use of ELP and HFBI tags as fusion partners in stable transgenic plants of tobacco is feasible and promising. In a constitutive environment, these tags increase the accumulation levels of the recombinant protein and induce the formation of PBs regardless of the cultivar used. However, a specific level of recombinant protein accumulation needs to be reached for PBs to form.
Economic evaluation of agomelatine relative to other antidepressants for treatment of major depressive disorders in Greece
Authors: Maniadakis Nikos , Kourlaba Georgia , Mougiakos Theodoros , Chatzimanolis Ioannis , Jonsson Linus
Published: May 2013

Background

Major depressive disorder (MDD) constitutes an important public health problem, as it is highly prevalent in the industrialized world and it is associated with substantial economic consequences for patients, health care providers, insurance and social security organizations and employers. To conduct an economic evaluation comparing agomelatine with other commonly used alternatives for treating patients with major depressive disorder (MDD) in Greece.

Methods

An existing international Markov model designed to evaluate the cost-effectiveness of agomelatine was adapted to the Greek setting. It reflects six different health states, in which patients may move on a monthly basis. The analysis was undertaken from a societal perspective. Transition probabilities, utilities and costs assigned to each health state were extracted from the published literature, government sources and expert opinion. Data reflects the year 2012 and was discounted using a rate of 3.5%. Probabilistic analysis was undertaken to deal with uncertainty.

Results

Base case analyses revealed that agomelatine is a dominant therapy for MDD relative to escitalopram, fluoxetine and sertraline, and it appeared to be cost-effective compared to venlafaxine (ICER: €547/QALY). Agomelatine remained a dominant treatment against generic sertraline and fluoxetine, and it appeared to be a cost-effective alternative compared to generic venlafaxine and escitalopram (ICER: €1,446/QALY and €3,303/QALY, respectively). Excluding the indirect cost from the analysis, agomelatine remained a cost-effective alternative over all comparators. In the probabilistic sensitivity analysis agomelatine was dominant in 44.5%, 89.6%, 70.6% and 84.6% of simulated samples against branded venlafaxine, escitalopram, fluoxetine and sertraline, respectively.

Conclusion

The present evaluation indicates that agomelatine is either a dominant or a cost-effective alternative relative to branded or generic alternatives, in Greece.
A versatile, efficient strategy for assembly of multi-fragment expression vectors in Saccharomyces cerevisiae using 60 bp synthetic recombination sequences
Authors: Kuijpers Niels GA , Solis-Escalante Daniel , Bosman Lizanne , van den Broek Marcel , Pronk Jack T , Daran Jean-Marc , Daran-Lapujade Pascale
Published: May 2013

Background

In vivorecombination of overlapping DNA fragments for assembly of large DNA constructs in the yeastSaccharomyces cerevisiaeholds great potential for pathway engineering on a small laboratory scale as well as for automated high-throughput strain construction. However, the currentin vivoassembly methods are not consistent with respect to yields of correctly assembled constructs and standardization of parts required for routine laboratory implementation has not been explored. Here, we present and evaluate an optimized and robust method forin vivoassembly of plasmids from overlapping DNA fragments inS. cerevisiae.

Results

To minimize occurrence of misassembled plasmids and increase the versatility of the assembly platform, two main improvements were introduced; i) the essential elements of the vector backbone (yeast episome and selection marker) were disconnected and ii) standardized 60 bp synthetic recombination sequences non-homologous with the yeast genome were introduced at each flank of the assembly fragments. These modifications led to a 100 fold decrease in false positive transformants originating from the backbone as compared to previous methods. Implementation of the 60 bp synthetic recombination sequences enabled high flexibility in the design of complex expression constructs and allowed for fast and easy construction of all assembly fragments by PCR. The functionality of the method was demonstrated by the assembly of a 21 kb plasmid out of nine overlapping fragments carrying six glycolytic genes with a correct assembly yield of 95%. The assembled plasmid was shown to be a high fidelity replica of thein silicodesign and all glycolytic genes carried by the plasmid were proven to be functional.

Conclusion

The presented method delivers a substantial improvement for assembly of multi-fragment expression vectors inS. cerevisiae. Not only does it improve the efficiency ofin vivoassembly, but it also offers a versatile platform for easy and rapid design and assembly of synthetic constructs. The presented method is therefore ideally suited for the construction of complex pathways and for high throughput strain construction programs for metabolic engineering purposes. In addition its robustness and ease of use facilitate the construction of any plasmid carrying two or more genes.
Growth hormone response to submaximal doses of ghrelin remains unchanged during the follicular phase of the cycle
Authors: Messini Christina I , Dafopoulos Konstantinos , Malandri Maria , Georgoulias Panagiotis , Anifandis George , Messinis Ioannis E
Published: May 2013

Background

Previous data have shown that ghrelin-induced growth hormone (GH) secretion is augmented in women by exogenous but not by endogenous estrogens. The purpose of this study was to examine the response of GH to low-dose scheme of ghrelin administration in relation to physiological changes in estradiol levels during the normal menstrual cycle.

Methods

Ten normally cycling women were studied in two menstrual cycles. Two consecutive dosages of ghrelin (0.15 μg/kg and 0.30 μg/kg) were injected intravenously at 0 and 90 min in the early and late follicular phases of one cycle. Saline was injected in the preceding cycle. Blood samples were taken at −15, 0, 30, 60, 90, 120, 150 and 180 min. The GH response was assessed.

Results

Serum estradiol concentrations were significantly higher in the late than in the early follicular phase. After ghrelin, but not after saline administration, plasma ghrelin and serum GH levels increased significantly in both phases, peaking at 30 min and 120 min. The peak value at 120 min was significantly higher than at 30 min (P<0.001). There were no significant differences in ghrelin and GH levels between the two phases at all time points.

Conclusions

The present results show no difference in GH response to two consecutive submaximal doses of ghrelin between the early and the late follicular phase of the cycle. It is suggested that estradiol is not possibly involved in the physiological process that regulates ghrelin-induced GH secretion in women during the normal menstrual cycle.
Delayed brain ischemia tolerance induced by electroacupuncture pretreatment is mediated via MCP-induced protein 1
Authors: Jin Zhuqing , Liang Jian , Wang Jing , Kolattukudy Pappachan E
Published: May 2013

Background

Emerging studies have demonstrated that pretreatment with electroacupuncture (EA) induces significant tolerance to focal cerebral ischemia. The present study seeks to determine the involvement of monocyte chemotactic protein-induced protein 1 (MCPIP1), a recently identified novel modulator of inflammatory reactions, in the cerebral neuroprotection conferred by EA pretreatment in the animal model of focal cerebral ischemia and to elucidate the mechanisms of EA pretreatment-induced ischemic brain tolerance.

Methods

Twenty-four hours after the end of the last EA pretreatment, focal cerebral ischemia was induced by middle cerebral artery occlusion (MCAO) for 90 minutes in male C57BL/6 mice and MCPIP1 knockout mice. Transcription and expression of MCPIP1 gene was monitored by qRT-PCR, Western blot and immunohistochemistry. The neurobehavioral scores, infarction volumes, proinflammatory cytokines and leukocyte infiltration in brain and NF-κB signaling were evaluated after ischemia/reperfusion.

Results

MCPIP1 protein and mRNA levels significantly increased specifically in mouse brain undergoing EA pretreatment. EA pretreatment significantly attenuated the infarct volume, neurological deficits, upregulation of proinflammatory cytokines and leukocyte infiltration in the brain of wild-type mice after MCAO compared with that of the non-EA group. MCPIP1-deficient mice failed to evoke EA pretreatment-induced tolerance compared with that of the control MCPIP1 knockout group without EA treatment. Furthermore, the activation of NF-κB signaling was significantly reduced in EA-pretreated wild-type mice after MCAO compared to that of the non-EA control group and MCPIP1-deficient mice failed to confer the EA pretreatment-induced inhibition of NF-κB signaling after MCAO.

Conclusions

Our data demonstrated that MCPIP1 deficiency caused significant lack of EA pretreatment-induced cerebral protective effects after MCAO compared with the control group and that MCPIP1 is involved in EA pretreatment-induced delayed brain ischemia tolerance.
The Caenorhabditis elegans voltage-gated calcium channel subunits UNC-2 and UNC-36 and the calcium-dependent kinase UNC-43/CaMKII regulate neuromuscular junction morphology
Authors: Caylor Raymond C , Jin Yishi , Ackley Brian D
Published: May 2013

Background

The conserved Caenorhabditis elegans proteins NID-1/nidogen and PTP-3A/LAR-RPTP function to efficiently localize the presynaptic scaffold protein SYD-2/α-liprin at active zones. Loss of function in these molecules results in defects in the size, morphology and spacing of neuromuscular junctions.

Results

Here we show that the Cav2-like voltage-gated calcium channel (VGCC) proteins, UNC-2 and UNC-36, and the calmodulin kinase II (CaMKII), UNC-43, function to regulate the size and morphology of presynaptic domains in C. elegans. Loss of function in unc-2, unc-36 or unc-43 resulted in slightly larger GABAergic neuromuscular junctions (NMJs), but could suppress the synaptic morphology defects found in nid-1/ nidogen or ptp-3/ LAR mutants. A gain-of-function mutation in unc-43 caused defects similar to those found in nid-1 mutants. Mutations in egl-19, Cav1-like, or cca-1, Cav3-like, α1 subunits, or the second α2/δ subunit, tag-180, did not suppress nid-1, suggesting a specific interaction between unc-2 and the synaptic extracellular matrix (ECM) component nidogen. Using a synaptic vesicle marker in time-lapse microscopy studies, we observed GABAergic motor neurons adding NMJ-like structures during late larval development. The synaptic bouton addition appeared to form in at least two ways: (1) de novo formation, where a cluster of vesicles appeared to coalesce, or (2) when a single punctum became enlarged and then divided to form two discrete fluorescent puncta. In comparison to wild type animals, we found unc-2 mutants exhibited reduced NMJ dynamics, with fewer observed divisions during a similar stage of development.

Conclusions

We identified UNC-2/UNC-36 VGCCs and UNC-43/CaMKII as regulators of C. elegans synaptogenesis. UNC-2 has a modest role in synapse formation, but a broader role in regulating dynamic changes in the size and morphology of synapses that occur during organismal development. During the late 4th larval stage (L4), wild type animals exhibit synaptic morphologies that are similar to those found in animals lacking NID-1/PTP-3 adhesion, as well as those with constitutive activation of UNC-43. Genetic evidence indicates that the VGCCs and the NID-1/PTP-3 adhesion complex provide opposing functions in synaptic development, suggesting that modulation of synaptic adhesion may underlie synapse development in C. elegans.
A standard vector for the chromosomal integration and characterization of BioBrick™ parts in Escherichia coli
Authors: Zucca Susanna , Pasotti Lorenzo , Politi Nicolò , Cusella De Angelis Maria Gabriella , Magni Paolo
Published: May 2013

Background

The chromosomal integration of biological parts in the host genome enables the engineering of plasmid-free stable strains with single-copy insertions of the desired gene networks. Although different integrative vectors were proposed, no standard pre-assembled genetic tool is available to carry out this task. Synthetic biology concepts can contribute to the development of standardized and user friendly solutions to easily produce engineered strains and to rapidly characterize the desired genetic parts in single-copy context.

Results

In this work we report the design of a novel integrative vector that allows the genomic integration of biological parts compatible with the RFC10, RFC23 and RFC12 BioBrick™ standards in Escherichia coli. It can also be specialized by using BioBrick™ parts to target the desired integration site in the host genome. The usefulness of this vector has been demonstrated by integrating a set of BioBrick™ devices in two different loci of the E. coli chromosome and by characterizing their activity in single-copy. Construct stability has also been evaluated and compared with plasmid-borne solutions.

Conclusions

Physical modularity of biological parts has been successfully applied to construct a ready-to-engineer BioBrick™ vector, suitable for a stable chromosomal insertion of standard parts via the desired recombination method, i.e. the bacteriophage integration mechanism or homologous recombination. In contrast with previously proposed solutions, it is a pre-assembled vector containing properly-placed restriction sites for the direct transfer of various formats of BioBrick™ parts. This vector can facilitate the characterization of parts avoiding copy number artefacts and the construction of antibiotic resistance-free engineered microbes, suitable for industrial use.
In vitro evaluation of β-carboline alkaloids as potential anti-Toxoplasma agents
Authors: Alomar Maria L , Rasse-Suriani Federico AO , Ganuza Agustina , Cóceres Verónica M , Cabrerizo Franco M , Angel Sergio O
Published: May 2013

Background

Toxoplasmosis is a worldwide infection caused by the protozoan parasite Toxoplasma gondii, which causes chorioretinitis and neurological defects in congenitally infected newborns or immunodeficient patients. The efficacy of the current treatment is limited, primarily by serious host toxicity. In recent years, research has focused on the development of new drugs against T. gondii. β-Carbolines (βCs), such as harmane, norharmane and harmine, are a group of naturally occurring alkaloids that show microbicidal activity. In this work, harmane, norharmane and harmine were tested against T. gondii.

Findings

The treatment of extracellular tachyzoites with harmane, norharmane and harmine showed a 2.5 to 3.5-fold decrease in the invasion rates at doses of 40 μM (harmane and harmine) and 2.5 μM (norharmane) compared with the untreated parasites. Furthermore, an effect on the replication rate could also be observed with a decrease of 1 (harmane) and 2 (norharmane and harmine) division rounds at doses of 5 to 12.5 μM. In addition, the treated parasites presented either delayed or no monolayer lysis compared with the untreated parasites.

Conclusions

The three βC alkaloids studied (norharmane, harmane and harmine) exhibit anti-T. gondii effects as evidenced by the partial inhibition of parasite invasion and replication. A dose–response effect was observed at a relatively low drug concentration (< 40 μM), at which no cytotoxic effect was observed on the host cell line (Vero).
Accuracy of tympanic temperature measurement using an infrared tympanic membrane thermometer
Authors: Gasim Gasim I , Musa Imad R , Abdien Mohamed T , Adam Ishag
Published: May 2013

Background

During investigation and diagnosis of patients, accurate temperature measurement is of great importance. The advantages of tympanic membrane thermometry are speed (temperature reading available within seconds), safety, and ease of use. The aim of this study was to compare the accuracy of infrared tympanic thermometers in comparison to mercury thermometers in measurement of body temperature.

Methods

Axillary and tympanic temperature was measured simultaneously in consecutive patients using mercury glass and infrared tympanic thermometers at Omdurman Hospital, Sudan during October 2012.

Results

In total, temperature was measured in 174 patients, 95 of whom (54.6%) were male. The mean (SD) patient age and weight was 33.18 (25.07) years and 52.13 (69.85) kg. There was no significant difference in mean (SD) temperature measurement between mercury and infrared tympanic membrane thermometers, 37.29°C (0.91) versus 37.38°C (0.95), P = 0.373, respectively. There was a significant positive correlation between axillary and tympanic body temperature measurements (r = 0.697, P < 0.001). The mean difference between the two readings (with limits of agreements) was - 0.093 (−0.20; 0.02) °C.

Conclusion

In this study, tympanic membrane thermometry is as reliable and accurate as axillary mercury glass thermometry. Thus, tympanic thermometry can be used in clinical practice, especially in the emergency setting, where ease of use and speed of obtaining the temperature reading are important.
A randomized trial of video self-instruction in cardiopulmonary resuscitation for lay persons
Authors: Godfred Rachel , Huszti Ella , Fly Deborah , Nichol Graham
Published: May 2013

Background

Cardiopulmonary resuscitation (CPR) improves outcomes after cardiac arrest. Much of the lay public is untrained in CPR skills. We evaluated the effectiveness of a compression-only CPR video self-instruction (VSI) with a personal manikin in the lay public.

Methods

Adults without prior CPR training in the past year or responsibility to provide medical care were randomized into one of three groups: 1) Untrained before testing, 2) 10-minute VSI in compressions-only CPR (CPR Anytime, American Heart Association, Dallas, TX), or 3) 22-minute VSI in compressions and ventilations (CPR Anytime). CPR proficiency was assessed using a sensored manikin. The primary outcome was composite skill competence of 90% during five minutes of skill demonstration. Evaluated were alternative cut-points for skill competence and individual components of CPR. 488 subjects (143 in untrained group, 202 in compressions-only group and 143 in compressions and ventilation group) were required to detect 21% competency with compressions-only versus 7% with untrained and 34% with compressions and ventilations.

Results

Analyzable data were available for the untrained group (n = 135), compressions-only group (n = 185) and the compressions and ventilation group (n = 119). Four (3%) achieved competency in the untrained group (p-value = 0.57 versus compressions-only), nine (4.9%) in the compressions-only group, and 12 (10.1%) in the compressions and ventilations group (p-value 0.13 vs. compressions-only). The compressions-only group had a greater proportion of correct compressions (p-value = 0.028) and compressions with correct hand placement (p-value = 0.0004) compared to the untrained group.

Conclusions

VSI in compressions-only CPR did not achieve greater overall competency but did achieve some CPR skills better than without training.
Rapid, responsive, relevant (R3) research: a call for a rapid learning health research enterprise
Authors: Riley William T , Glasgow Russell E , Etheredge Lynn , Abernethy Amy P
Published: May 2013

Our current health research enterprise is painstakingly slow and cumbersome, and its results seldom translate into practice. The slow pace of health research contributes to findings that are less relevant and potentially even obsolete. To produce more rapid, responsive, and relevant research, we propose approaches that increase relevance via greater stakeholder involvement, speed research via innovative designs, streamline review processes, and create and/or better leverage research infrastructure. Broad stakeholder input integrated throughout the research process can both increase relevance and facilitate study procedures. More flexible and rapid research designs should be considered before defaulting to the traditional two‐arm randomized controlled trial (RCT), but even traditional RCTs can be designed for more rapid findings. Review processes for grant applications, IRB protocols, and manuscript submissions can be better streamlined to minimize delays. Research infrastructures such as rapid learning systems and other health information technologies can be leveraged to rapidly evaluate new and existing treatments, and alleviate the extensive recruitment delays common in traditional research. These and other approaches are feasible but require a culture shift among the research community to value not only methodological rigor, but also the pace and relevance of research.
Generation of gene disruptions by transcription activator-like effector nucleases (TALENs) in Xenopus tropicalis embryos
Authors: Lei Yong , Guo Xiaogang , Deng Yi , Chen Yonglong , Zhao Hui
Published: May 2013

Transcription activator-like effector nucleases (TALENs) are novel engineered DNA nucleases, and have been proven to be effective for gene specific targeting in various species. Recently we reported gene disruptions in Xenopus embryos by using TALENs. Here we summarize the protocol that is used in our studies for gene disruption. This protocol covers selection of TALEN targeting sites, TALEN assembly with a modified Golden Gate method, and injection of TALEN mRNAs into Xenopus tropicalis embryos. We also provide details for detection of somatic and germ line transmitted mutations. And finally, we briefly describe establishment of knockout Xenopus lines. This protocol will facilitate broader applications of TALENs in studies of Xenopus biology.
Tackling inequalities in obesity: a protocol for a systematic review of the effectiveness of public health interventions at reducing socioeconomic inequalities in obesity among adults
Authors: Bambra Clare L , Hillier Frances C , Moore Helen J , Cairns-Nagi Joanne-Marie , Summerbell Carolyn D
Published: May 2013

Background

Socioeconomic inequalities in obesity and associated risk factors for obesity are widening throughout developed countries worldwide. Tackling obesity is high on the public health agenda both in the United Kingdom and internationally. However, what works in terms of interventions that are able to reduce inequalities in obesity is lacking.

Methods/Design

The review will examine public health interventions at the individual, community and societal level that might reduce inequalities in obesity among adults aged 18 years and over, in any setting and in any country. The following electronic databases will be searched: MEDLINE, EMBASE, CINAHL, PsycINFO, Social Science Citation Index, ASSIA, IBSS, Sociological Abstracts, and the NHS Economic Evaluation Database. Database searches will be supplemented with website and gray literature searches. No studies will be excluded based on language, country or publication date. Randomized and non-randomized controlled trials, prospective and retrospective cohort studies (with/without control groups) and prospective repeat cross-sectional studies (with/without control groups) that have a primary outcome that is a proxy for body fatness and have examined differential effects with regard to socioeconomic status (education, income, occupation, social class, deprivation, poverty) or where the intervention has been targeted specifically at disadvantaged groups or deprived areas will be included. Study inclusion, data extraction and quality appraisal will be conducted by two reviewers. Meta-analysis and narrative synthesis will be conducted. The main analysis will examine the effects of 1) individual, 2) community and 3) societal level public health interventions on socioeconomic inequalities in adult obesity. Interventions will be characterized by their level of action and their approach to tackling inequalities. Contextual information on how such public health interventions are organized, implemented and delivered will also be examined.

Discussion

The review will provide evidence, and reveal any gaps in the evidence base, of public health strategies which reduce and prevent inequalities in the prevalence of obesity in adults and provide information on the organization, implementation and delivery of such interventions.

Systematic review registration

PROSPERO registration number:CRD42013003612
What is the influence on water quality in temperate eutrophic lakes of a reduction of planktivorous and benthivorous fish? A systematic review protocol
Authors: Bernes Claes , Carpenter Stephen R , Gårdmark Anna , Larsson Per , Persson Lennart , Skov Christian , Van Donk Ellen
Published: May 2013

Background

In lakes that have become eutrophic due to sewage discharges or nutrient runoff from land, problems such as algal blooms and oxygen deficiency often persist even when nutrient supplies have been reduced. One reason is that phosphorus stored in the sediments can exchange with the water. There are indications that the high abundance of phytoplankton, turbid water and lack of submerged vegetation seen in many eutrophic lakes may represent a semi-stable state. For that reason, a shift back to more natural clear-water conditions could be difficult to achieve.

In some cases, though, temporary mitigation of eutrophication-related problems has been accomplished through biomanipulation: stocks of zooplanktivorous fish have been reduced by intensive fishing, leading to increased populations of phytoplankton-feeding zooplankton. Moreover, reduction of benthivorous fish may result in lower phosphorus fluxes from the sediments. An alternative to reducing the dominance of planktivores and benthivores by fishing is to stock lakes with piscivorous fish. These two approaches have often been used in combination.

The implementation of the EU Water Framework Directive has recently led to more stringent demands for measures against eutrophication, and a systematic review could clarify whether biomanipulation is efficient as a measure of that kind.

Methods

The review will examine primary field studies of how large-scale biomanipulation has affected water quality and community structure in eutrophic lakes or reservoirs in temperate regions. Such studies can be based on comparison between conditions before and after manipulation, on comparison between treated and non-treated water bodies, or both. Relevant outcomes include Secchi depth, concentrations of oxygen, nutrients, suspended solids and chlorophyll, abundance and composition of phytoplankton, zooplankton and fish, and coverage of submerged macrophytes.
Generating metadata from web documents: a systematic approach
Authors: Hsueh Hsiang-Yuan , Chen Chun-Nan , Huang Kun-Fu
Published: May 2013

In this paper, a mechanism generating RDF Semantic Web schema from Web document set as the semantic metadata is proposed. Analyzing both the structural and un-structural content of Web documents, semi-structured Web documents can be conceptualized as resource objects with inter-relationships in RDF diagram. Technically, hyperlinks, basic annotations, and keywords in web documents will be properly analyzed, and corresponding RDF schema will be generated following the mechanism and rules proposed in this paper. It is expected that with the semantic metadata of document sets on the Web being systematically translated instead of manually edited, the semantic operation on the Web, such as semantic query or semantic search, will be possible in the future.
Patient centred care in diabetology: an Islamic perspective from Iran
Authors: Larijani Bagher , Zahedi Farzaneh
Published: May 2013

Patient-centred system of care is essential in managing many disorders such as diabetes mellitus. The cultural and religious context can influence the involvement of patients and their families in such a care. We intend to discuss patient-centred care in diabetology in view of Islam. For more clarification, we will take into consideration a few illustrative lines of argument in detail about situation in Iran. In conclusion, dynamic spirit of Islamic jurisprudence is reflected in its adaptability to change in medical practice. In recent decades, Iranian religious scholars have provided scientists in new fields of science and research with appropriate directions and guidelines. Decree issued by Iranian religious leaders permitting research on stem cells for therapeutic purposes in many disorders including diabetes mellitus is one example. Understanding of the nature of Islam is importance for communication with patients in Islamic countries.
Some coupled common fixed points for a pair of mappings in partially ordered G-metric spaces
Authors: Chandok Sumit , Sintunavarat Wutiphol , Kumam Poom
Published: May 2013

The purpose of this paper is to establish some coupled coincidence point theorems for a pair of mappings having a mixed g-monotone property in partially ordered G-metric spaces. Also, we present a result on the existence and uniqueness of coupled common fixed points. The results presented in the paper generalize and extend several well-known results in the literature. To illustrate our results, we give some examples.