bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates
Authors: van Staalduinen Laura M. , McSorley Fern R. , Schiessl Katharina , Séguin Jacqueline , Wyatt Peter B. , Hammerschmidt Friedrich , Zechel David L. , Jia Zongchao
Published: March 2014

Significance

Inorganic phosphate (Pi) is an essential component of many biological molecules and thus is required by all life forms. However, soluble Pi is typically at low abundance in the environment. To compensate, microbes have evolved unique carbon–phosphorus-bond cleaving reactions to use organophosphonates as an alternative source of Pi. The marine-derived enzyme PhnZ utilizes a new oxidative mechanism for CP bond cleavage involving iron and molecular oxygen. The three-dimensional structure of PhnZ reveals unique active site features that contribute to catalysis of CP bond cleavage and substrate specificity, as well as an evolutionary link between phosphodiester bond hydrolysis and oxidative bond cleavage. This evolutionary link likely reflects the ancient origins of organophosphonates in the environment.
High frequency of cultivable human subgroup F adenoviruses in stool samples from a paediatric population admitted to hospital with acute gastroenteritis
Authors: Arcangeletti Maria-Cristina , Germini Diego , Martorana Davide , Rodighiero Isabella , De Conto Flora , Medici Maria-Cristina , Chezzi Carlo , Calderaro Adriana
Published: March 2014

The family Adenoviridae consists of five genera of which the genus Mastadenovirus includes human viruses classified into 57 serotypes clustered into seven subgroups (A–G). Serotypes 40 and 41 (subgroup F) are specifically associated with childhood gastroenteritis and are the most common cause of acute gastroenteritis in young children after rotaviruses and noroviruses. Standard methods for laboratory diagnosis of adenovirus infection include electron microscopy (EM) and conventional cell culture (CCC), although it is widely considered that adenoviruses 40 and 41 are difficult to cultivate, such that their circulation is most likely underestimated. One hundred and ten faecal specimens from paediatric patients with gastroenteritis were confirmed positive for adenovirus by EM and/or CCC at the Virology Unit of the University Hospital of Parma, Italy, during the period January 2010–December 2012. They were analysed to determine the actual prevalence of adenovirus 40 and 41 in these patients using PCR and restriction endonuclease analysis, and to evaluate their ability to be cultivated in standard cell lines. The results showed a high prevalence of subgroup F (62.7 %), with serotype 41 (89.8 %) predominating over serotype 40 (10.2 %). Surprisingly, among the 75 adenoviruses isolated by CCC, 37 (49 %) belonged to subgroup F, suggesting a higher capacity of adenovirus 40 and 41 to replicate in cell culture than previously thought. PCR and restriction enzyme techniques provide an efficient means of diagnosing enteric adenoviruses correctly, including subgroup F adenovirus strains in young children with gastroenteritis.
Identification of five patterns of nucleosome positioning that globally describe transcription factor function
Authors: Maehara Kazumitsu , Ohkawa Yasuyuki
Published: March 2014

Following the binding of transcription factors (TF) to specific regions, chromatin remodeling including alterations in nucleosome positioning (NP) occurs. These changes in NP cause selective gene expression to determine cell function. However whether specific NP patterns upon TF binding determine the transcriptional regulation such as gene activation or suppression is unclear. Here we identified five patterns of NP around TF binding sites (TFBSs) using fixed MNase-Seq analysis. The most frequently observed NP pattern described the transcription state. The five patterns explained approximately 80% of the whole NP pattern on the genome in mouse C2C12 cells. We further performed ChIP-Seq using the input obtained from the fixed MNase-Seq. The result showed that a single trial of ChIP-Seq could visualize the NP patterns around the TFBS and predict the function of the transcriptional regulation at the same time. These findings indicate that NP can directly predict the function of TFs.
Inhibition of the Arabidopsis Salt Overly Sensitive Pathway by 14-3-3 Proteins
Authors: Zhou Huapeng , Lin Huixin , Chen She , Becker Katia , Yang Yongqing , Zhao Jinfeng , Kudla Jörg , Schumaker Karen S. , Guo Yan
Published: March 2014

The Salt Overly Sensitive (SOS) pathway regulates intracellular sodium ion (Na+) homeostasis and salt tolerance in plants. Until recently, little was known about the mechanisms that inhibit the SOS pathway when plants are grown in the absence of salt stress. In this study, we report that the Arabidopsis thaliana 14-3-3 proteins λ and κ interact with SOS2 and repress its kinase activity. Growth in the presence of salt decreases the interaction between SOS2 and the 14-3-3 proteins, leading to kinase activation in planta. 14-3-3 λ interacts with the SOS2 junction domain, which is important for its kinase activity. A phosphorylation site (Ser-294) is identified within this domain by mass spectrometry. Mutation of Ser-294 to Ala or Asp does not affect SOS2 kinase activity in the absence of the 14-3-3 proteins. However, in the presence of 14-3-3 proteins, the inhibition of SOS2 activity is decreased by the Ser-to-Ala mutation and enhanced by the Ser-to-Asp exchange. These results identify 14-3-3 λ and κ as important regulators of salt tolerance. The inhibition of SOS2 mediated by the binding of 14-3-3 proteins represents a novel mechanism that confers basal repression of the SOS pathway in the absence of salt stress.
Arabidopsis DELLA and JAZ Proteins Bind the WD-Repeat/bHLH/MYB Complex to Modulate Gibberellin and Jasmonate Signaling Synergy
Authors: Qi Tiancong , Huang Huang , Wu Dewei , Yan Jianbin , Qi Yijun , Song Susheng , Xie Daoxin
Published: March 2014

Integration of diverse environmental and endogenous signals to coordinately regulate growth, development, and defense is essential for plants to survive in their natural habitat. The hormonal signals gibberellin (GA) and jasmonate (JA) antagonistically and synergistically regulate diverse aspects of plant growth, development, and defense. GA and JA synergistically induce initiation of trichomes, which assist seed dispersal and act as barriers to protect plants against insect attack, pathogen infection, excessive water loss, and UV irradiation. However, the molecular mechanism underlying such synergism between GA and JA signaling remains unclear. In this study, we revealed a mechanism for GA and JA signaling synergy and identified a signaling complex of the GA pathway in regulation of trichome initiation. Molecular, biochemical, and genetic evidence showed that the WD-repeat/bHLH/MYB complex acts as a direct target of DELLAs in the GA pathway and that both DELLAs and JAZs interacted with the WD-repeat/bHLH/MYB complex to mediate synergism between GA and JA signaling in regulating trichome development. GA and JA induce degradation of DELLAs and JASMONATE ZIM-domain proteins to coordinately activate the WD-repeat/bHLH/MYB complex and synergistically and mutually dependently induce trichome initiation. This study provides deep insights into the molecular mechanisms for integration of different hormonal signals to synergistically regulate plant development.
Weekly administration of rapamycin improves survival and biomarkers in obese male mice on high‐fat diet
Authors: Leontieva Olga V. , Paszkiewicz Geraldine M. , Blagosklonny Mikhail V.
Published: March 2014

Recent discoveries have revealed the key role of mTOR (target of rapamycin) in aging. Furthermore, rapamycin extends lifespan in mice, especially in female mice. Here, we treated obese male mice on high‐fat diet with rapamycin given intermittently: either weekly (once a week) or alternating bi‐weekly (three injections every other week). While only marginally reducing obesity, intermittent administration of rapamycin significantly extended lifespan. Significance was achieved for weekly treated group and for the three rapamycin‐received groups combined. In weekly treatment group, 100% mice were alive by the age of 2 years, whereas 60% of mice died in untreated group by this age. The effect of weekly treatment on survival was highly significant and cannot be fully explained by partial reduction in obesity. Alternating bi‐weekly treatments seem to be less effective than weekly treatment, although effects of additional factors (see ) may not be excluded. After one year of treatment, all survived mice were sacrificed 8 days after the last administration of rapamycin to avoid its direct interference with parameters examined. Fasting levels of cardiac and hepatic p‐S6, a marker of mTORC1 activity, were lower in weekly treatment group compared with control mice. In contrast, levels of p‐Akt (S473), glucose, triglycerides and insulin were unchanged, whereas leptin and IGF‐1 tended to be lower. Thus, weekly treatment with rapamycin may slow down aging in obese male mice on high‐fat diet.
The diversity of young adult wheeze: a cluster analysis in a longitudinal birth cohort
Authors: Kurukulaaratchy R. J. , Zhang H. , Raza A. , Patil V. , Karmaus W. , Ewart S. , Arshad S. H.
Published: March 2014

Background

Cluster analyses have enhanced understanding of the heterogeneity of both paediatric and adult wheezing. However, while adolescence represents an important transitional phase, the nature of young adult wheeze has yet to be clearly characterised.

Objectives

To use cluster analysis to define, for the first time, clinically relevant young adult wheeze clusters in a longitudinal birth cohort.

Methods

K‐means cluster analysis was undertaken among 309 currently wheezing subjects at 18 years in the Isle of Wight birth cohort (N = 1456). Thirteen disease‐characterising clustering variables at 18 years were used. Resulting clusters were then further characterised by severity indices plus potential risk factors for wheeze development throughout the 1st 18 years of life.

Results

Six wheeze clusters were identified. Cluster 1 (12.3%) male‐early‐childhood‐onset‐atopic‐wheeze‐with‐normal‐lung‐function had male predominance, normal spirometry, low bronchodilator reversibility (BDR), intermediate bronchial hyper‐responsiveness (BHR), high atopy prevalence and more admissions. Cluster 2 (24.2%) early‐childhood‐onset‐wheeze‐with‐intermediate‐lung‐function had no specific sex association, intermediate spirometry, BDR, BHR, more significant BTS step therapy and admissions. Cluster 3 (9.7%) female‐early‐childhood‐onset‐atopic‐wheeze‐with‐impaired‐lung‐function showed female predominance, high allergic disease comorbidity, more severe BDR and BHR, greatest airflow obstruction, high smoking prevalence, higher symptom severity and admissions. Cluster 4 (19.4%) female‐undiagnosed‐wheezers had adolescent‐onset non‐atopic wheeze, low BDR and BHR, impaired but non‐obstructed spirometry, high symptom frequency and highest smoking prevalence. Cluster 5 (24.6%) female‐late‐childhood‐onset‐wheeze‐with‐normal‐lung‐function showed no specific atopy association, normal spirometry, low BDR, BHR and symptom severity. Cluster 6 (9.7%) male‐late‐childhood‐onset‐atopic‐wheeze‐with‐impaired‐lung‐function had high atopy and rhinitis prevalence, increased BDR and BHR, moderately impaired spirometry, high symptom severity and higher BTS step therapy.

Conclusions and Clinical Relevance

Young adult wheeze is diverse and can be classified into distinct clusters. More severe clusters merit attention and are associated with childhood onset, atopy, impaired lung function and in some, smoking. Smoking‐associated undiagnosed wheezers also merit recognition. Better understanding of young adult wheeze could facilitate better later adult respiratory health.
Procollagen type I N‐terminal peptide in preterm infants is associated with growth during the first six months post‐term
Authors: van de Lagemaat Monique , van der Veer Eveline , van Weissenbruch Mirjam M. , Lafeber Harrie N. , Rotteveel Joost
Published: March 2014

Objective

To identify growth‐related collagen and bone parameters in small‐for‐gestational‐age (SGA) and appropriate‐for‐gestational‐age (AGA) preterm infants during the first six months post‐term. In SGA preterm infants, increased growth and decreased bone acquisition, which we demonstrated previously, may be reflected by these markers.

Design

Observational study within a randomized controlled trial.

Patients

Thirty‐three SGA (weight, length or both at birth <‐2 SDS) and 98 AGA preterm infants (gestational age [median (IQR)]: 31·1 (1·6) vs 30·3 (2·0) weeks; 72·7% vs 42·9% boys).

Measurements

Weight (g), length (cm), procollagen type I N‐terminal peptide (PINP; μg/l), urinary helical peptide (UHP; μg/mmol creatinine) and alkaline phosphatase (ALP; U/l) expressed as standard deviation scores (SDS) at term age, three and six months post‐term.

Results

Weight and length gain during the first six months post‐term and PINP SDS at term age, three months and six months post‐term were higher in SGA compared with AGA infants. UHP SDS and ALP SDS were similar in SGA and AGA infants. PINP SDS and UHP SDS at term age and PINP SDS at three months were associated with subsequent weight and length gain until six months post‐term.

Conclusions

Increased growth in SGA compared with AGA preterm infants is reflected by increased collagen type I synthesis during the first six months post‐term, suggesting that PINP and UHP correspond with growth in preterm infants. An explanation for decreased bone acquisition of SGA preterm infants may be that increased collagen type I synthesis is not directly followed by increased bone mineralization.
The incidence, management, and evolution of rapamycin‐related side effects in kidney transplant recipients
Authors: Verhave Jacobien , Boucher Anne , Dandavino Raymond , Collette Suzon , Senécal Lynne , Hebert Marie‐Josée , Girardin Catherine , Cardinal Héloïse
Published: March 2014

Conversion from a calcineurin‐inhibitor‐based immunosuppression to a rapamycin‐based immunosuppression may preserve kidney graft function. The side effects of rapamycin can limit its usefulness, but their management and evolution are rarely reported in clinical trials. We performed a retrospective cohort study in patients transplanted before December 31, 2008 and who received rapamycin to replace calcineurin inhibitors. In 219 patients studied, 98% presented ≥1 side effects after starting rapamycin. Side effects occurring in ≥10% of patients were dyslipidemia (52%, 95% confidence interval (CI): 45–59%), peripheral edema (37%, 95%CI: 31–43%), cytopenia (36%, 95% CI: 30–42%), acne (29%, 95% CI: 23–35%), proteinuria (23%, 95% CI: 17–29%), and oral ulcers 14% (95% CI: 10–18%). Proteinuria, ulcers, and edema were difficult to manage and were more likely to cause cessation of rapamycin. Rapamycin was discontinued in 46% of patients (95% CI: 40–52%). Age (odds ratio [OR] per 10‐yr increase: 1.29, 95% CI: 1.05–1.59) and obesity (OR: 2.57, 95% CI: 1.10–6.01) were independently associated with cessation of rapamycin. We conclude that successful control of dyslipidemia and cytopenia can be achieved without discontinuing rapamycin. Most other side effects are harder to manage. Leaner and younger patients are less likely to discontinue rapamycin due to side effects.
Renal retransplantation after kidney and pancreas transplantation using the renal vessels of the failed allograft: pitfalls and pearls
Authors: Chedid Marcio F. , Moreno Gonzales Manuel , Raghavaiah Suresh , Chauhan Ashutosh , Taner Timucin , Nedredal Geir I. , Park Walter D. , Stegall Mark D.
Published: March 2014

Renal retransplantation after a failed prior kidney and pancreas transplant is being increasingly performed. In these complex cases, both iliac fossae have been used for prior transplants, and the placement of the new allograft can be problematic. We describe our experience with an alternative technique for renal retransplantation (RRTx) in the setting of severe bilateral aortoiliac atherosclerosis or scarring and fibrosis on the iliac vessels. Nephrectomy of the failed allograft is performed, and the renal vessels of the failed allograft (RVFA) are preserved. The new kidney is implanted on RVFA at the same operative time. This technique was attempted and successfully accomplished in a total of six patients (mean operative time = 240 ± 63 min). One postoperative complication occurred: poor arterial inflow to the allograft, being corrected reoperatively. Hospitalizations ranged from five to eight d. Five of the six patients were alive with a functioning allograft at last follow‐up (a single graft failure occurred 21 months postoperatively in the setting of post‐transplant lymphoproliferative disease that also led to patient death). Renal vessels of the failed allograft seem to be suitable alternative vascular conduits for renal retransplantation after prior kidney and pancreas transplants.
Improved survival outcomes in patients with non‐alcoholic steatohepatitis and alcoholic liver disease following liver transplantation: an analysis of 2002–2012 United Network for Organ Sharing data
Authors: Wong Robert J. , Chou Christina , Bonham Clark A. , Concepcion Waldo , Esquivel Carlos O. , Ahmed Aijaz
Published: March 2014

There is an increasing trend of patients with hepatocellular carcinoma (HCC) and non‐alcoholic fatty liver disease undergoing liver transplantation in the US. Our study utilized data from the 2002 to 2012 United Network for Organ Sharing registry to evaluate model for end‐stage liver disease era trends in US liver transplantations focused on patients with non‐alcoholic steatohepatitis (NASH), hepatitis C (HCV), alcoholic liver disease (ALD), and HCC. Survival outcomes were stratified by liver disease etiology and compared across time periods using Kaplan–Meier and Cox proportional hazards models. Patients with NASH were more likely to be women, had higher body mass index (BMI), and had higher prevalence of diabetes and cardiac disease. However, overall long‐term survival was significantly higher in patients with NASH and ALD (p < 0.001). Compared to HCV, patients with NASH had significantly higher post‐transplantation survival (HR 0.69, 95% CI 0.63–0.77), and lower risk of graft failure (HR 0.76, 95% CI 0.69–0.83). Despite having higher BMI and higher prevalence of diabetes and cardiac disease, patients with NASH had better post‐liver transplantation survival compared to patients with HCV or HCC. Patients with ALD also had superior survival outcomes. However, these survival differences were limited to patients without HCC that underwent liver transplantation.
Correlation between CT‐based measured renal volumes and nuclear‐renography‐based split renal function in living kidney donors. Clinical diagnostic utility and practice patterns
Authors: Diez Alejandro , Powelson John , Sundaram Chandru P. , Taber Tim E. , Mujtaba Muhammad A. , Yaqub Muhammad S. , Mishler Dennis P. , Goggins William C. , Sharfuddin Asif A.
Published: March 2014

Introduction

Living donor evaluation involves imaging to determine the choice of kidney for nephrectomy. Our aim was to study the diagnostic accuracy and correlation between CT‐based volume measurements and split renal function (SRF) as measured by nuclear renography in potential living donors and its impact on kidney selection decision.

Methods

We analyzed 190 CT‐based volume measurements in healthy donors, of which 65 donors had a radionuclide study performed to determine SRF.

Results

There were no differences in demographics, anthropometric measurements, total volumes, eGFR, creatinine clearances between those who required a nuclear scan and those who did not. There was a significant correlation between CT‐volume‐measurement‐based SRF and nuclear‐scan‐based SRF (Pearson coefficient r 0.59; p < 0.001). Furthermore, selective nuclear‐based SRF allowed careful selection of donor nephrectomy, leaving the donor with the higher functioning kidney in most cases. There was also a significantly higher number of right‐sided nephrectomies selected after nuclear‐based SRF studies.

Conclusion

CT‐based volume measurements in living donor imaging have sufficient correlation with nuclear‐based SRF. Selective use of nuclear‐scan‐based SRF allows careful selection for donor nephrectomy.
SPAK mediates KCC3‐enhanced cervical cancer tumorigenesis
Authors: Chiu Min‐Hsi , Liu Hsiao‐Sheng , Wu Yi‐Hui , Shen Meng‐Ru , Chou Cheng‐Yang
Published: March 2014

Ste20‐related proline/alanine‐rich kinase (SPAK) plays a role in regulating many biological activities, and interacts with K‐Cl co‐transporter 3 (KCC3); however, the importance of SPAK for KCC3 function has not been demonstrated. Here, we investigated the role of SPAK in KCC3‐regulated cell invasiveness and tumor formation. We show that induction of KCC3 expression triggers activation of the NF‐κB and SPAK signaling cascades, leading to activation of p38 mitogen‐activated protein kinase (MAPK) and matrix metalloproteinase‐2 (MMP2). A small interference RNA‐mediated reduction in SPAK protein levels suppressed the invasive ability and oncogenic potential of cervical cancer cells, and decreased tumor formation in mouse xenografts. A combination of experimental approaches, including RT‐PCR and real‐time RT‐PCR, gelatin zymography, NF‐κB luciferase activity and chromatin immunoprecipitation assays, showed that the induction of KCC3 over‐expression increased MMP2 expression and augmented binding of NF‐κB to its putative SPAK promoter binding site, suggesting that the SPAK/MMP2 axis is up‐regulated by NF‐κB. Pharmacological inhibition of NF‐κB or MMP2 abrogated KCC3‐triggered, SPAK‐dependent cell invasiveness. Furthermore, p38 MAPK was identified as the upstream regulator of KCC3‐dependent MMP2 activation. We conclude that SPAK may promote KCC3‐mediated tumor aggressiveness via the NF‐κB/p38 MAPK/MMP2 axis.

Structured digital abstract

KCC3 physically interacts with SPAK by anti-bait co-immunoprecipitation (view interaction)
Structure of a novel farnesylated bilin from an insect – formation by α‐cleavage of heme A of mitochondrial cytochrome c oxidases?
Authors: Kayser Hartmut , Wray Victor , Nimtz Manfred
Published: March 2014

Biliproteins are present in almost all forms of life, and many of them play vital roles in photobiology. The bilin ligand of a recently characterized 500‐kDa biliprotein from an insect has been isolated and its structure elucidated with chemical and spectroscopic techniques (UV–visible, IR, MS, NMR, and CD). This blue pigment, named CV‐bilin, represents a unique high molecular mass derivative of biliverdin IXα, with an unusual 10E‐configuration and a molecular mass of 852 Da, corresponding to C48H60N4O10. The high mass of this open‐chain tetrapyrrole results from the presence of an epoxi‐dihydroxyethylfarnesyl substituent at C‐18 and a hydroxymethyl substituent at C‐13. This substitution pattern exactly reflects that of heme A of mitochondrial cytochrome c oxidases with a hydroxyethylfarnesyl chain and a formyl group at corresponding positions of the cyclic tetrapyrrole. As no other natural product is known to show these structural features (heme O, the precursor of heme A, has a methyl group at C‐13), this bilin is presumed to be derived from heme A by cleavage of the α‐methine bridge and oxidative modifications at C‐13 and the hydroxyethylfarnesyl chain. Possibly, a bilin structurally related to this insect bilin is also produced in other organisms as a result of mitochondrial turnover or degradation. As CV‐bilin in complex with a specific protein is accumulated at the end of larval life, stored in the pupa, and finally transferred to the oocytes, a possible role of the free or protein‐bound pigment in egg or embryonic development is discussed.
Social cognition and underlying cognitive mechanisms in children with an extra X chromosome: a comparison with autism spectrum disorder
Authors: van Rijn S. , Stockmann L. , van Buggenhout G. , van Ravenswaaij‐Arts C. , Swaab H.
Published: March 2014

Individuals with an extra X chromosome are at increased risk for autism symptoms. This study is the first to assess theory of mind and facial affect labeling in children with an extra X chromosome. Forty‐six children with an extra X chromosome (29 boys with Klinefelter syndrome and 17 girls with Trisomy X), 56 children with autism spectrum disorder (ASD) and 88 non‐clinical controls, aged 9–18 years, were included. Similar to children with ASD, children with an extra X chromosome showed significant impairments in social cognition. Regression analyses showed that different cognitive functions predicted social cognitive skills in the extra X and ASD groups. The social cognitive deficits were similar for boys and girls with an extra X chromosome, and not specific for a subgroup with high Autism Diagnostic Interview Revised autism scores. Thus, children with an extra X chromosome show social cognitive deficits, which may contribute to social dysfunction, not only in children showing a developmental pattern that is ‘typical’ for autism but also in those showing mild or late presenting autism symptoms. Our findings may also help explain variance in type of social deficit: children may show similar social difficulties, but these may arise as a consequence of different underlying information processing deficits.
Basaltic diversity at the Apollo 12 landing site: Inferences from petrologic examinations of the soil sample 12003
Authors: Snape Joshua F. , Joy Katherine H. , Crawford Ian A. , Alexander Louise
Published: March 2014

A detailed petrologic survey has been made of 17 basaltic chips (sized between 1 and 10 mm) from the 12003 soil sample as part of an ongoing study of basaltic diversity at the Apollo 12 landing site. An attempt has been made to classify these samples according to the well‐established grouping of olivine, pigeonite, ilmenite, and feldspathic basalts. Particular attention has been paid to variations in major, minor, and trace element mineral chemistry (determined by electron microprobe analysis and laser ablation ICP‐MS), which may be indicative of particular basaltic suites and less susceptible to sampling bias than bulk sample characteristics. Examples of all three main (olivine, pigeonite, and ilmenite) basaltic suites have been identified within the 12003 soil. One sample is identified as a possible new addition to the feldspathic suite, which currently consists of only one other confirmed sample. Identification of additional feldspathic basalts strengthens the argument that they represent a poorly sampled basaltic flow local to the Apollo 12 site, rather than exotic material introduced to the site by impact mixing processes. Three samples are identified as representing members of one or two previously unrecognized basaltic suites.
VEGF‐C Induces Lymphangiogenesis and Angiogenesis in the Rat Mesentery Culture Model
Authors: Sweat Richard S. , Sloas David C. , Murfee Walter L.
Published: March 2014

Objective

Lymphatic and blood microvascular systems are critical for tissue function. Insights into the coordination of both systems can be gained by investigating the relationships between lymphangiogenesis and angiogenesis. Recently, our laboratory established the rat mesentery culture model as a novel tool to investigate multicellular interactions during angiogenesis in an intact microvascular network scenario. The objective of this study was to determine whether the rat mesentery culture model can be used to study lymphangiogenesis.

Methods

Mesenteric tissue windows were harvested from adult male Wistar rats and cultured for three or five days in either serum‐free MEM or MEM supplemented with VEGF‐C. Tissues were immunolabeled for PECAM and LYVE‐1 to identify blood and lymphatic endothelial cells, respectively. Tissues selected randomly from those containing vascular networks were quantified for angiogenesis and lymphangiogenesis.

Results

VEGF‐C treatment resulted in an increase in the density of blood vessel sprouting compared to controls by day 3. By day 5, lymphatic sprouting was increased compared to controls.

Conclusions

These results are consistent with in vivo findings that lymphangiogenesis lags angiogenesis after chronic stimulation and establish a tool for investigating the interrelationships between lymphangiogenesis and angiogenesis in a multisystem microvascular environment.
The fine tuning role of microRNA–RNA interaction in odontoblast differentiation and disease
Authors: Sun Q , Liu H , Chen Z
Published: March 2014

Dentinogenesis imperfecta and dentin dysplasia are two common types of genetic oral diseases resulted from the aberrant differentiation of odontoblast. Understanding the mechanisms of odontoblast differentiation is crucial for finding the diagnosis candidate genes and treatment targets for such kinds of diseases. Previous work has identified a battery of transcription factors and growth factors regulating odontoblast differentiation; however, the post‐transcriptional regulating mechanisms of them are poorly studied. MicroRNAs (miRNA) are a group of non‐coding RNAs widely studied in organ development, inflammation, and tumorigenesis because of its inhibitory effects on the target mRNAs. Also, miRNAs along with their binding targets form a complex competing endogenous RNA (ceRNA) network where miRNAs serve as the fine tuning balancers between their targets. Recent reports demonstrated the essential role of the miRNA pathway in dentinogenesis and the regulatory role of several specific miRNAs in the in vitro model of odontoblast differentiation. Herein, we will discuss the general roles of miRNA in diseases, the function of miRNAs during odontoblast differentiation, and finally the potential pathological mechanisms through which miRNAs cause the odontoblast‐related diseases.
Growth, reproductive phenology and yield responses of a potential biofuel plant, Jatropha curcas grown under projected 2050 levels of elevated CO2
Authors: Kumar Sumit , Chaitanya Bharatula S.K. , Ghatty Sreenivas , Reddy Attipalli R.
Published: March 2014

Jatropha (Jatropha curcas) is a non‐edible oil producing plant which is being advocated as an alternative biofuel energy resource. Its ability to grow in diverse soil conditions and minimal requirements of essential agronomical inputs compared with other oilseed crops makes it viable for cost‐effective advanced biofuel production. We designed a study to investigate the effects of elevated carbon dioxide concentration ([CO2]) (550 ppm) on the growth, reproductive development, source‐sink relationships, fruit and seed yield of J. curcas. We report, for the first time that elevated CO2 significantly influences reproductive characteristics of Jatropha and improve its fruit and seed yields. Net photosynthetic rate of Jatropha was 50% higher in plants grown in elevated CO2 compared with field and ambient CO2‐grown plants. The study also revealed that elevated CO2 atmosphere significantly increased female to male flower ratio, above ground biomass and carbon sequestration potential in Jatropha (24 kg carbon per tree) after 1 year. Our data demonstrate that J. curcas was able to sustain enhanced rate of photosynthesis in elevated CO2 conditions as it had sufficient sink strength to balance the increased biomass yields. Our study also elucidates that the economically important traits including fruit and seed yield in elevated CO2 conditions were significantly high in J. curcas that holds great promise as a potential biofuel tree species for the future high CO2 world.
Identification and suppression of the p‐coumaroyl CoA:hydroxycinnamyl alcohol transferase in Zea mays L.
Authors: Marita Jane M. , Hatfield Ronald D. , Rancour David M. , Frost Kenneth E.
Published: March 2014

Grasses, such as Zea mays L. (maize), contain relatively high levels of p‐coumarates (pCA) within their cell walls. Incorporation of pCA into cell walls is believed to be due to a hydroxycinnamyl transferase that couples pCA to monolignols. To understand the role of pCA in maize development, the p‐coumaroyl CoA:hydroxycinnamyl alcohol transferase (pCAT) was isolated and purified from maize stems. Purified pCAT was subjected to partial trypsin digestion, and peptides were sequenced by tandem mass spectrometry. TBLASTN analysis of the acquired peptide sequences identified a single full‐length maize cDNA clone encoding all the peptide sequences obtained from the purified enzyme. The cDNA clone was obtained and used to generate an RNAi construct for suppressing pCAT expression in maize. Here we describe the effects of suppression of pCAT in maize. Primary screening of transgenic maize seedling leaves using a new rapid analytical platform was used to identify plants with decreased amounts of pCA. Using this screening method, mature leaves from fully developed plants were analyzed, confirming reduced pCA levels throughout plant development. Complete analysis of isolated cell walls from mature transgenic stems and leaves revealed that lignin levels did not change, but pCA levels decreased and the lignin composition was altered. Transgenic plants with the lowest levels of pCA had decreased levels of syringyl units in the lignin. Thus, altering the levels of pCAT expression in maize leads to altered lignin composition, but does not appear to alter the total amount of lignin present in the cell walls.
OsNIP3;1, a rice boric acid channel, regulates boron distribution and is essential for growth under boron‐deficient conditions
Authors: Hanaoka Hideki , Uraguchi Shimpei , Takano Junpei , Tanaka Mayuki , Fujiwara Toru
Published: March 2014

Boron is an essential micronutrient for higher plants. Boron deficiency is an important agricultural issue because it results in loss of yield quality and/or quantity in cereals and other crops. To understand boron transport mechanisms in cereals, we characterized OsNIP3;1, a member of the major intrinsic protein family in rice (Oryza sativa L.), because OsNIP3;1 is the most similar rice gene to the Arabidopsis thaliana boric acid channel genes AtNIP5;1 and AtNIP6;1. Yeast cells expressing OsNIP3;1 imported more boric acid than control cells. GFP‐tagged OsNIP3;1 expressed in tobacco BY2 cells was localized to the plasma membrane. The accumulation of OsNIP3;1 transcript increased fivefold in roots within 6 h of the onset of boron starvation, but not in shoots. Promoter–GUS analysis suggested that OsNIP3;1 is expressed mainly in exodermal cells and steles in roots, as well as in cells around the vascular bundles in leaf sheaths and pericycle cells around the xylem in leaf blades. The growth of OsNIP3;1 RNAi plants was impaired under boron limitation. These results indicate that OsNIP3;1 functions as a boric acid channel, and is required for acclimation to boron limitation. Boron distribution among shoot tissues was altered in OsNIP3;1 knockdown plants, especially under boron‐deficient conditions. This result demonstrates that OsNIP3;1 regulates boron distribution among shoot tissues, and that the correct boron distribution is crucial for plant growth.
Silencing the vacuolar invertase gene GhVIN1 blocks cotton fiber initiation from the ovule epidermis, probably by suppressing a cohort of regulatory genes via sugar signaling
Authors: Wang Lu , Cook Akiko , Patrick John W. , Chen Xiao‐Ya , Ruan Yong‐Ling
Published: March 2014

Cotton fibers, the most important source of cellulose for the global textile industry, are single‐celled trichomes derived from the ovule epidermis at or just prior to anthesis. Despite progress in understanding cotton fiber elongation and cell‐wall biosynthesis, knowledge regarding the molecular basis of fiber cell initiation, the first step of fiber development determining the fiber yield potential, remains elusive. Here, we provide evidence that expression of a vacuolar invertase (VIN) is an early event that is essential for cotton fiber initiation. RNAi‐mediated suppression of GhVIN1, a major VIN gene that is highly expressed in wild‐type fiber initials, resulted in significant reduction of VIN activity and consequently a fiberless seed phenotype in a dosage dependent manner. The absence of a negative effect on seed development in these fiberless seeds indicates that the phenotype is unlikely to be due to lack of carbon nutrient. Gene expression analyses coupled with in vitro ovule culture experiments revealed that GhVIN1‐derived hexose signaling may play an indispensable role in cotton fiber initiation, probably by regulating the transcription of several MYB transcription factors and auxin signaling components that were previously identified as required for fiber initiation. Together, the data represent a significant advance in understanding the mechanisms of cotton fiber initiation, and provide the first indication that VIN‐mediated hexose signaling may act as an early event modulating the expression of regulatory genes and hence cell differentiation from the ovule epidermis.
RNA‐Seq transcriptome analysis to identify genes involved in metabolism‐based diclofop resistance in Lolium rigidum
Authors: Gaines Todd A. , Lorentz Lothar , Figge Andrea , Herrmann Johannes , Maiwald Frank , Ott Mark‐Christoph , Han Heping , Busi Roberto , Yu Qin , Powles Stephen B. , Beffa Roland
Published: March 2014

Weed control failures due to herbicide resistance are an increasing and worldwide problem that significantly affect crop yields. Metabolism‐based herbicide resistance (referred to as metabolic resistance) in weeds is not well characterized at the genetic level. An RNA‐Seq transcriptome analysis was used to find candidate genes that conferred metabolic resistance to the herbicide diclofop in a diclofop‐resistant population (R) of the major global weed Lolium rigidum. A reference cDNA transcriptome (19 623 contigs) was assembled and assigned putative annotations. Global gene expression was measured using Illumina reads from untreated control, adjuvant‐only control, and diclofop treatment of R and susceptible (S). Contigs that showed constitutive expression differences between untreated R and untreated S were selected for further validation analysis, including 11 contigs putatively annotated as cytochrome P450 (CytP450), glutathione transferase (GST), or glucosyltransferase (GT), and 17 additional contigs with annotations related to metabolism or signal transduction. In a forward genetics validation experiment, nine contigs had constitutive up‐regulation in R individuals from a segregating F2 population, including three CytP450, one nitronate monooxygenase (NMO), three GST, and one GT. Principal component analysis using these nine contigs differentiated F2‐R from F2‐S individuals. In a physiological validation experiment in which 2,4‐D pre‐treatment induced diclofop protection in S individuals due to increased metabolism, seven of the nine genetically validated contigs were induced significantly. Four contigs (two CytP450, NMO, and GT) were consistently highly expressed in nine field‐evolved metabolic resistant L. rigidum populations. These four contigs were strongly associated with the resistance phenotype and are major candidates for contributing to metabolic diclofop resistance.
Arabidopsis guard cell integrity involves the epigenetic stabilization of the FLP and FAMA transcription factor genes
Authors: Lee EunKyoung , Lucas Jessica Regan , Goodrich Justin , Sack Fred David
Published: March 2014

Arabidopsis guard cell (GC) fate is conferred via a transient pulse of expression of FAMA that encodes a bHLH transcription factor. Stomata often function for years, suggesting that the FAMA expression window stabilizes long‐term GC identity or that additional factors operate. Transgenic lines harboring a copy of a FAMA transgene were found to induce the fate resetting of mature GCs to that of lineage‐specific stem cells causing new stomata to arise within shells of the old, a Stoma‐in‐Stoma (SIS) phenotype. These lines disrupt the normal trimethylation on lysine 27 of histone3 (H3K27me3) on stomatal stem cell genes, a phenotype rescued by constitutive expression of the Polycomb Group (PcG) gene CURLY LEAF. Thus the stability of stomatal fate is enforced by a PcG‐mediated reduction in the transcriptional accessibility of stem cell genes and by the endogenous FAMA gene itself. Moreover, a transgenic FOUR LIPS gene, which encodes a MYB protein that is not required for GC fate, also induces a SIS phenotype and disrupts H3K27 trimethylation. Thus FLP might indirectly enforce GC fate as well.
The rice FISH BONE gene encodes a tryptophan aminotransferase, which affects pleiotropic auxin‐related processes
Authors: Yoshikawa Takanori , Ito Momoyo , Sumikura Tsuyoshi , Nakayama Akira , Nishimura Takeshi , Kitano Hidemi , Yamaguchi Isomaro , Koshiba Tomokazu , Hibara Ken‐Ichiro , Nagato Yasuo , Itoh Jun‐Ichi
Published: March 2014

Auxin is a fundamental plant hormone and its localization within organs plays pivotal roles in plant growth and development. Analysis of many Arabidopsis mutants that were defective in auxin biosynthesis revealed that the indole‐3‐pyruvic acid (IPA) pathway, catalyzed by the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) and YUCCA (YUC) families, is the major biosynthetic pathway of indole‐3‐acetic acid (IAA). In contrast, little information is known about the molecular mechanisms of auxin biosynthesis in rice. In this study, we identified a auxin‐related rice mutant, fish bone (fib). FIB encodes an orthologue of TAA genes and loss of FIB function resulted in pleiotropic abnormal phenotypes, such as small leaves with large lamina joint angles, abnormal vascular development, small panicles, abnormal organ identity and defects in root development, together with a reduction in internal IAA levels. Moreover, we found that auxin sensitivity and polar transport activity were altered in the fib mutant. From these results, we suggest that FIB plays a pivotal role in IAA biosynthesis in rice and that auxin biosynthesis, transport and sensitivity are closely interrelated.
Engineering Solutions to the Greenhouse Gases Generated by Hydroelectric Plants
Authors: Vincent Wong Kaufui
Published: March 2014

There is a controversy brewing for about 10 years that hydroelectric power plants are not a clean, renewable source of electricity. The current review indicates that the source of methane is not in the mechanics or mechanical design of the equipment used. The source of the methane is from nature, and man's failure to do the right thing. This methane may be reduced or completely eliminated. If this cannot be accomplished or if it is too expensive to retrofit the hydroelectric plant, then the deep water may be preprocessed (and the methane collected) before being used in the water turbine. Several methods have been introduced and discussed. Details have been omitted so that practicing engineers and other professionals can obtain funds to research and develop or invent the practical solutions suited to conditions local to the problem.
Fluidized Bed Technology for Concentrating Solar Power With Thermal Energy Storage
Authors: Ma Zhiwen , Glatzmaier Greg , Mehos Mark
Published: March 2014

A generalized modeling method is introduced and used to evaluate thermal energy storage (TES) performance. The method describes TES performance metrics in terms of three efficiencies: first-law efficiency, second-law efficiency, and storage effectiveness. By capturing all efficiencies in a systematic way, various TES technologies can be compared on an equal footing before more detailed simulations of the components and concentrating solar power (CSP) system are performed. The generalized performance metrics are applied to the particle-TES concept in a novel CSP thermal system design. The CSP thermal system has an integrated particle receiver and fluidized-bed heat exchanger, which uses gas/solid two-phase flow as the heat-transfer fluid, and solid particles as the heat carrier and storage medium. The TES method can potentially achieve high temperatures (>800 °C) and high thermal efficiency economically.
Coupled Experimental Study and Thermodynamic Modeling of Melting Point and Thermal Stability of Li2CO3-Na2CO3-K2CO3 Based Salts
Authors: Chen Chunlin , Tran Ty , Olivares Rene , Wright Steven , Sun Shouyi
Published: March 2014

Nitrate based salts have application as a heat transfer fluid and thermal energy storage media in solar field installations and are normally used from 200 °C up to maximum temperatures of ∼550 °C. Molten K2CO3-Na2CO3-Li2CO3 could potentially be used as heat transfer fluid and thermal energy storage media to replace nitrate salts due to its wider temperature operating window (400–900 °C), which improves the heat transfer efficiency. There will be improved operability and the process will be more economical viable if the lower temperature at which carbonate salts can operate could be decreased. This paper explores the melting point and high temperature stability of K2CO3-Na2CO3-Li2CO3 based salt mixtures, the effect of atmosphere and the effect of additives to the melt using experimental investigation and thermodynamic modeling.
The Application of Novel Platinum-Reinforced Tin-Silver-Copper Solder to Bifacial Photovoltaic Module for Improvement of Yield and Reliability
Authors: Lo Chin Kim , Lim Yun Seng , Wong Mee Chu , Tian Yee Kai
Published: March 2014

The characteristics of solder joints between the busbars of solar cells and copper ribbons can affect the performance of a photovoltaic (PV) module significantly. The resistivity of the joints and the intermetallic compound structures within the joints are the two main characteristics that impose a substantial impact on the yield and the reliability of the PV module. In this paper, we aim to present and analyze a novel platinum-reinforced tin-silver-copper (Sn-3.8Ag-0.7Cu-0.2Pt) as the lead-free solder material to connect copper ribbons to the metallization of bifacial solar cells. The performance of the PV module using platinum-reinforced solder is investigated by constructing two bifacial PV modules using the popular lead-free Sn-3.8Ag-0.7Cu solder and Sn-3.8Ag-0.7Cu-0.2Pt solder, respectively. Micrographs of the joints are obtained to show that the platinum-reinforced solder joint has fewer voids and a more evenly distributed and thinner intermetallic layer than that of a conventional SnAgCu solder joint. As a result, the physical attachment between the busbars and the ribbon using SnAgCuPt solder is stronger than that using SnAgCu solder. The power outputs of both PV modules are measured together with two commercial PV modules under the sun using an IV plotter. The results show that the total energy yield of the bifacial PV module with the new solder is about 6–10% higher than that with the conventional SnAgCu solder. The energy yield of the bifacial PV module using SnAgCuPt solder is 35.8% and 0.2% higher than that of the commercially available monofacial polycrystalline and monocrystalline PV modules, respectively.
Reduction of Voltage Harmonics in Solar Photovoltaic fed Inverter of Single Phase Stand Alone Power System
Authors: Albert Alexander S. , Thathan Manigandan
Published: March 2014

In this paper, an optimal harmonic stepped waveform (OHSW) method is proposed to reduce the voltage harmonics available at the output of solar photovoltaic (SPV) fed fifteen level cascaded multilevel inverter (CMLI). This technique is used to solve the harmonic elimination equations based on stepped waveform analysis in order to obtain the optimal switching angles. The OHSW method considers the output voltage waveform as four equal symmetries in each half cycle and the magnitude of six numbers of harmonic orders is reduced. Simulations are carried out in Matlab/Simulink and a 3 kWp solar plant is implemented in hardware to show the effectiveness of the proposed system.