Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don

<p>Abstract</p> <p>Background</p> <p>Wood is a major renewable natural resource for the timber, fibre and bioenergy industry. <it>Pinus radiata </it>D. Don is the most important commercial plantation tree species in Australia and several other countries; however, genomic resources for this species are very limited in public databases. Our primary objective was to sequence a large number of expressed sequence tags (ESTs) from genes involved in wood formation in radiata pine.</p> <p>Results</p> <p>Six developing xylem cDNA libraries were constructed from earlywood and latewood tissues sampled at juvenile (7 yrs), transition (11 yrs) and mature (30 yrs) ages, respectively. These xylem tissues represent six typical development stages in a rotation period of radiata pine. A total of 6,389 high quality ESTs were collected from 5,952 cDNA clones. Assembly of 5,952 ESTs from 5' end sequences generated 3,304 unigenes including 952 contigs and 2,352 singletons. About 97.0% of the 5,952 ESTs and 96.1% of the unigenes have matches in the UniProt and TIGR databases. Of the 3,174 unigenes with matches, 42.9% were not assigned GO (Gene Ontology) terms and their functions are unknown or unclassified. More than half (52.1%) of the 5,952 ESTs have matches in the Pfam database and represent 772 known protein families. About 18.0% of the 5,952 ESTs matched cell wall related genes in the MAIZEWALL database, representing all 18 categories, 91 of all 174 families and possibly 557 genes. Fifteen cell wall-related genes are ranked in the 30 most abundant genes, including <it>CesA</it>, <it>tubulin</it>, <it>AGP</it>, <it>SAMS</it>, <it>actin</it>, <it>laccase, CCoAMT, MetE</it>, <it>phytocyanin, pectate lyase</it>, <it>cellulase, SuSy</it>, <it>expansin</it>, <it>chitinase </it>and <it>UDP-glucose dehydrogenase</it>. Based on the PlantTFDB database 41 of the 64 transcription factor families in the poplar genome were identified as being involved in radiata pine wood formation. Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development.</p> <p>Conclusion</p> <p>The first large scale genomic resource in radiata pine was generated from six developing xylem cDNA libraries. Cell wall-related genes and transcription factors were identified. Juvenile earlywood has a distinct transcriptome, which is likely to contribute to the undesirable properties of juvenile wood in radiata pine. The publicly available resource of radiata pine will also be valuable for gene function studies and comparative genomics in forest trees.</p

Text messaging and brief phone calls for weight loss in overweight and obese English- and Spanish-speaking adults: A 1-year, parallel-group, randomized controlled trial.

BACKGROUND:Weight loss interventions based solely on text messaging (short message service [SMS]) have been shown to be modestly effective for short periods of time and in some populations, but limited evidence is available for positive longer-term outcomes and for efficacy in Hispanic populations. Also, little is known about the comparative efficacy of weight loss interventions that use SMS coupled with brief, technology-mediated contact with health coaches, an important issue when considering the scalability and cost of interventions. We examined the efficacy of a 1-year intervention designed to reduce weight among overweight and obese English- and Spanish-speaking adults via SMS alone (ConTxt) or in combination with brief, monthly health-coaching calls. ConTxt offered 2-4 SMS/day that were personalized, tailored, and interactive. Content was theory- and evidence-based and focused on reducing energy intake and increasing energy expenditure. Monthly health-coaching calls (5-10 minutes' duration) focused on goal-setting, identifying barriers to achieving goals, and self-monitoring. METHODS AND FINDINGS:English- and Spanish-speaking adults were recruited from October 2011 to March 2013. A total of 298 overweight (body mass index [BMI] 27.0 to 39.9 kg/m2) adults (aged 21-60 years; 77% female; 41% Hispanic; 21% primarily Spanish speaking; 44% college graduates or higher; 22% unemployed) were randomly assigned (1:1) to receive either ConTxt only (n = 101), ConTxt plus health-coaching calls (n = 96), or standard print materials on weight reduction (control group, n = 101). We used computer-based permuted-block randomization with block sizes of three or six, stratified by sex and Spanish-speaking status. Participants, study staff, and investigators were masked until the intervention was assigned. The primary outcome was objectively measured percent of weight loss from baseline at 12 months. Differences between groups were evaluated using linear mixed-effects regression within an intention-to-treat framework. A total of 261 (87.2%) and 253 (84.9%) participants completed 6- and 12-month visits, respectively. Loss to follow-up did not differ by study group. Mean (95% confidence intervals [CIs]) percent weight loss at 12 months was -0.61 (-1.99 to 0.77) in the control group, -1.68 (-3.08 to -0.27) in ConTxt only, and -3.63 (-5.05 to -2.81) in ConTxt plus health-coaching calls. At 12 months, mean (95% CI) percent weight loss, adjusted for baseline BMI, was significantly different between ConTxt plus health-coaching calls and the control group (-3.0 [-4.99 to -1.04], p = 0.003) but not between the ConTxt-only and the control group (-1.07 [-3.05 to 0.92], p = 0.291). Differences between ConTxt plus health-coaching calls and ConTxt only were not significant (-1.95 [-3.96 to 0.06], p = 0.057). These findings were consistent across other weight-related secondary outcomes, including changes in absolute weight, BMI, and percent body fat at 12 months. Exploratory subgroup analyses suggested that Spanish speakers responded more favorably to ConTxt plus health-coaching calls than English speakers (Spanish contrast: -7.90 [-11.94 to -3.86], p &lt; 0.001; English contrast: -1.82 [-4.03 to 0.39], p = 0.107). Limitations include the unblinded delivery of the intervention and recruitment of a predominantly female sample from a single site. CONCLUSIONS:A 1-year intervention that delivered theory- and evidence-based weight loss content via daily personalized, tailored, and interactive SMS was most effective when combined with brief, monthly phone calls. TRIAL REGISTRATION:ClinicalTrials.gov NCT01171586

Cdc42-Dependent Transfer of mir301 from Breast Cancer-Derived Extracellular Vesicles Regulates the Matrix Modulating Ability of Astrocytes at the Blood–Brain Barrier

Breast cancer brain metastasis is a major clinical challenge and is associated with a dismal prognosis. Understanding the mechanisms underlying the early stages of brain metastasis can provide opportunities to develop efficient diagnostics and therapeutics for this significant clinical challenge. We have previously reported that breast cancer-derived extracellular vesicles (EVs) breach the blood–brain barrier (BBB) via transcytosis and can promote brain metastasis. Here, we elucidate the functional consequences of EV transport across the BBB. We demonstrate that brain metastasis-promoting EVs can be internalized by astrocytes and modulate the behavior of these cells to promote extracellular matrix remodeling in vivo. We have identified protein and miRNA signatures in these EVs that can lead to the interaction of EVs with astrocytes and, as such, have the potential to serve as targets for development of diagnostics and therapeutics for early detection and therapeutic intervention in breast cancer brain metastasis

Cdc42-Dependent Transfer of mir301 from Breast Cancer-Derived Extracellular Vesicles Regulates the Matrix Modulating Ability of Astrocytes at the Blood–Brain Barrier

Breast cancer brain metastasis is a major clinical challenge and is associated with a dismal prognosis. Understanding the mechanisms underlying the early stages of brain metastasis can provide opportunities to develop efficient diagnostics and therapeutics for this significant clinical challenge. We have previously reported that breast cancer-derived extracellular vesicles (EVs) breach the blood–brain barrier (BBB) via transcytosis and can promote brain metastasis. Here, we elucidate the functional consequences of EV transport across the BBB. We demonstrate that brain metastasis-promoting EVs can be internalized by astrocytes and modulate the behavior of these cells to promote extracellular matrix remodeling in vivo. We have identified protein and miRNA signatures in these EVs that can lead to the interaction of EVs with astrocytes and, as such, have the potential to serve as targets for development of diagnostics and therapeutics for early detection and therapeutic intervention in breast cancer brain metastasis

Assessing the risks of recycling urban stormwater for potable supply via an aquifer

Urbanisation and the subsequent increase in impervious land use generate increased urban stormwater which can be recycled viamanaged aquifer recharge (MAR) to supplement more traditional surface or ground water supplies. This paper compares the quality of stormwater from two urban catchments in South Australia to assess the risks, in accordance with the Australian Guidelines for Water Recycling, of recycling stormwater via a limestone aquifer for potable water use. In the regional city of Mount Gambier, stormwater MARin a karstic aquifer has been used to supplement the city\u27s drinking water supply for over 100 years. The source water was generally high quality with some instances of turbidity, iron and lead exceeding the Australian Drinking Water Guidelines (ADWG). Effort wasmade to constrain the estimate of minimum residence time within the karstic aquifer to at least two years for evaluation of the potential for passive treatment of trace organic chemicals in this system. In the second example, a purpose built MAR site in Parafield, a northern suburb of Adelaide, has been designed and operated asa full scale trial to determine if wetland treated urban stormwater can be recovered at a standard which meets the ADWG. Based on the analysis undertaken, the source water was generally of high quality with occasional instances of levels of iron and microbial indicators in excess of the ADWG. After a mean residence time in the aquifer of 240 days, recovered water qualitymet the ADWGwith the exception of iron. However, given the uncertainty in pathogen concentrations in the treated stormwater post-recovery from the aquifer, disinfection and aeration for iron removal would be necessary to ensure that the ADWG were met if the water was to be utilised for potable water supply

Associations between reliable changes in depression and changes in BMI, total body fatness and visceral adiposity during a 12-month weight loss trial.

We investigated associations between changes in depression and body composition over a 12-month weight loss trial. Of the 298 adults (BMI &gt; 27 m/kg2), 219 with complete depression and body composition data were included. A 10-item Center for Epidemiologic Studies Depression Scale measured depression; dual-energy X-ray absorptiometry measured body composition. Multinomial logistic regression predicted reliable changes in depression by BMI, body fat (BF) and visceral adiposity (VAT). Multiplicative interaction terms tested modification by sex and ethnicity. Participants with increases in body composition were less likely to experience improvements in depression (BMI: RRR = 0.79 (0.68-0.91), p &lt; 0.01; BF: RRR = 0.97 (0.94 - 0.99), p = 0.01; VAT: RRR = 0.99 (0.98-1.00), p = 0.02), but not worsening of depression (BMI: RRR = 1.29 (0.96-1.73), p = 0.10; BF: RRR = 1.04 (0.99-1.09), p = 0.15; VAT: RRR = 1.01 (1.00-1.03), p = 0.18). Sex and ethnicity interaction terms were not significant. However, the relationship was only significant among females, among non-Latinos for BMI and BF, and among Latinos for VAT. Our study supports the association between depression and obesity and highlights the need for longitudinal studies investigating VAT and depression in diverse ethnic groups

Serum Protein Signatures Using Aptamer-Based Proteomics for Minimal Change Disease and Membranous Nephropathy

Introduction: Minimal change disease (MCD) and membranous nephropathy (MN) are glomerular diseases (glomerulonephritis [GN]) that present with the nephrotic syndrome. Although circulating PLA2R antibodies have been validated as a biomarker for MN, the diagnosis of MCD and PLA2R-negative MN still relies on the results of kidney biopsy or empirical corticosteroids in children. We aimed to identify serum protein biomarker signatures associated with MCD and MN pathogenesis using aptamer-based proteomics. Methods: Quantitative SOMAscan proteomics was applied to the serum of adult patients with MCD (n = 15) and MN(n = 37) and healthy controls (n = 20). Associations between the 1305proteins detected with SOMAscan were assessed using multiple statistical tests, expression pattern analysis, and systems biology analysis. Results: A total of 208 and 244 proteins were identified that differentiated MCD and MN, respectively, with high statistical significance from the healthy controls (Benjamin-Hochberg [BH] P \u3c 0.0001). There were 157 proteins that discriminated MN from MCD (BH P \u3c 0.05). In MCD, 65 proteins were differentially expressed as compared with MN and healthy controls. When compared with MCD and healthy controls, 44 discriminatory proteins were specifically linked to MN. Systems biology analysis of these signatures identified cell death and inflammation as key pathways differentiating MN from MCD and healthy controls. Dysregulation of fatty acid metabolism pathways was confirmed in both MN and MCD as compared with the healthy subjects. Conclusion: SOMAscan represents a promising proteomic platform for biomarker development in GN. Validation of a greater number of discovery biomarkers in larger patient cohorts is needed before these data can be translated for clinical care

Macromolecularly crowded in vitro microenvironments accelerate the production of extracellular matrix-rich supramolecular assemblies

Therapeutic strategies based on the principles of tissue engineering by self-assembly put forward the notion that functional regeneration can be achieved by utilising the inherent capacity of cells to create highly sophisticated supramolecular assemblies. However, in dilute ex-vivo microenvironments, prolonged culture time is required to develop an extracellular matrix-rich implantable device. Herein, we assessed the influence of macromolecular crowding, a biophysical phenomenon that regulates intra- and extra-cellular activities in multicellular organisms, in human corneal fibroblast culture. In the presence of macromolecules, abundant extracellular matrix deposition was evidenced as fast as 48 h in culture, even at low serum concentration. Temperature responsive copolymers allowed the detachment of dense and cohesive supramolecularly assembled living substitutes within 6 days in culture. Morphological, histological, gene and protein analysis assays demonstrated maintenance of tissue-specific function. Macromolecular crowding opens new avenues for a more rational design in engineering of clinically relevant tissue modules in vitro

Impact of suboptimal APOBEC3G neutralization on the emergence of HIV drug resistance in humanized mice

HIV diversification facilitates immune escape and complicates antiretroviral therapy. In this study, we take advantage of a humanized mouse model to probe the contribution of APOBEC3 mutagenesis to viral evolution. Humanized mice were infected with isogenic HIV molecular clones (HIV-WT, HIV-45G, HIV-ΔSLQ) that differ in their ability to counteract APOBEC3G (A3G). Infected mice remained naïve or were treated with the RT inhibitor lamivudine (3TC). Viremia, emergence of drug resistant variants and quasispecies diversification in the plasma compartment were determined throughout infection. While both HIV-WT and HIV-45G achieved robust infection, over time HIV-45G replication was significantly reduced compared to HIV-WT in the absence of 3TC treatment. In contrast, treatment response differed significantly between HIV-45G and HIV-WT infected mice. Antiretroviral treatment failed in 91% of HIV-45G infected mice while only 36% of HIV-WT infected mice displayed a similar negative outcome. Emergence of 3TC resistant variants and nucleotide diversity were determined by analyzing 155,462 single HIV reverse transcriptase (RT) and 6,985 vif sequences from 33 mice. Prior to treatment, variants with genotypic 3TC resistance (RT-M184I/V) were detected at low levels in over a third of all animals. Upon treatment, the composition of the plasma quasispecies rapidly changed leading to a majority of circulating viral variants encoding RT-184I. Interestingly, increased viral diversity prior to treatment initiation correlated with higher plasma viremia in HIV-45G but not in HIV-WT infected animals. Taken together, HIV variants with suboptimal anti-A3G activity were attenuated in the absence of selection but display a fitness advantage in the presence of antiretroviral treatment.IMPORTANCE Both viral (e.g., reverse transcriptase, RT) and host factors (e.g., APOBEC3G (A3G)) can contribute to HIV sequence diversity. This study shows that suboptimal anti-A3G activity shapes viral fitness and drives viral evolution in the plasma compartment of humanized mice