DEVELOPMENT OF A REFINED DATABASE OF RELATIVE POTENCY ESTIMATES TO FACILITATE BETTER CHARACTERIZATION OF VARIABILITY AND UNCERTAINTY IN THE CURRENT MAMMALIAN TEFS FOR PCDDS, PCDFS, AND DIOXIN-LIKE PCBS

EPA Science Inventory

The toxic equivalency factor (TEF) approach has been widely accepted as the most feasible and plausible method presently available for evaluating potential health risks associated with exposure to mixtures of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofuran...

Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter

PubMed Central

Assefa, Kebebew; Cannarozzi, Gina; Girma, Dejene; Kamies, Rizqah; Chanyalew, Solomon; Plaza-Wüthrich, Sonia; Blösch, Regula; Rindisbacher, Abiel; Rafudeen, Suhail; Tadele, Zerihun

2015-01-01

Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding. PMID:25859251

Toxic equivalency factors (TEFs) for PCBs, PCDDs, PCDFs for humans and wildlife

USGS Publications Warehouse

Van Den, Berg; Birnbaum, L.; Bosveld, A.T.C.; Brunstrom, B.; Cook, P.; Feeley, M.; Giesy, J.P.; Hanberg, A.; Hasegawa, R.; Kennedy, S.W.; Kubiak, T.; Larsen, J.C.; Van Leeuwen, F. X. R.; Liem, A.K.D.; Nolt, C.; Peterson, R.E.; Poellinger, L.; Safe, S.; Schrenk, D.; Tillitt, D.; Tysklind, M.; Younes, M.; Waern, F.; Zacharewski, T.

1998-01-01

An expert meeting was organized by the World Health Organization (WHO) and held in Stockholm on 15-18 June 1997. The objective of this meeting was to derive consensus toxic equivalency factors (TEFs) for polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) and dioxinlike polychlorinated biphenyls (PCBs) for both human, fish, and wildlife risk assessment. Based on existing literature data, TEFs were (re)evaluated and either revised (mammals) or established (fish and birds). A few mammalian WHO-TEFs were revised, including 1,2,3,7,8-pentachlorinated DD, octachlorinated DD, occachlorinated DF, and PCB 77. These mammalian TEFs are also considered applicable for humans and wild mammalian species. Furthermore, it was concluded that there was insufficient in vivo evidence to continue the use of TEFs for some di-ortho PCBs, as suggested earlier by Ahlborg et al. In addition, TEFs for fish and birds were determined. The WHO working group attempted to harmonize TEFs across different taxa to the extent possible. However, total synchronization of TEFs was not feasible, as there were orders of a magnitude difference in TEFs between taxa for some compounds. In this respect, the absent or very low response of fish to mono-ortho PCBs is most noticeable compared to mammals and birds. Uncertainties that could compromise the TEF concept were also reviewed, including nonadditive interactions, differences in shape of the dose-response curve, and species responsiveness. In spite of these uncertainties, it was concluded that the TEF concept is still the most plausible and feasible approach for risk assessment of halogenated aromatic hydrocarbons with dioxinlike properties.

Clinical Study of Congenital Esophageal Stenosis: Comparison according to Association of Esophageal Atresia and Tracheoesophageal Fistula

PubMed Central

Kim, Soo-Hong; Kim, Hyun-Young; Lee, Seong-Cheol; Park, Kwi-Won

2017-01-01

Purpose Congenital esophageal atresia (CES) is a rare congenital disease. The severity of symptoms is variable; thus, diagnosis is difficult and tends to be delayed. CES is frequently accompanied by esophageal atresia (EA) with/without tracheoesophageal fistula (TEF). We investigated the characteristics of CES by reviewing our experience with CES patients and researched the differences between CES with EA-TEF and isolated CES. Methods A total of 31 patients underwent operations for CES were reviewed retrospectively. The patients were divided into two groups according to the association with EA-TEF, and compared the differences. Results Sixteen boys and 15 girls were included. The mean age at symptom onset was 8 months old, and the mean age at diagnosis was 21 months old. Nine patients with EA-TEF were included group A, whereas the other 22 patients were assigned to group B. There were no differences in sex, gestational age, associated anomalies and pathologic results between the groups. In group A, the age at diagnosis and age at surgery were younger than in group B despite the age at symptom occurrence being similar. Postoperative complications occurred only in group A. Conclusion In this study, symptoms occurred during the weaning period, and vomiting was the most frequent symptom. CES patients with EA-TEF tended to be diagnosed and treated earlier despite the age at symptom occurrence being similar. CES patients with EA-TEF had more postoperative complications; therefore, greater attention should be paid during the postoperative period. PMID:28730131

The 2005 World Health Organization Re-evaluation of Human and Mammalian Toxic Equivalency Factors for Dioxins and Dioxin-like Compounds

PubMed Central

van den Berg, Martin; Birnbaum, Linda S.; Denison, Michael; De Vito, Mike; Farland, William; Feeley, Mark; Fiedler, Heidelore; Hakansson, Helen; Hanberg, Annika; Haws, Laurie; Rose, Martin; Safe, Stephen; Schrenk, Dieter; Tohyama, Chiharu; Tritscher, Angelika; Tuomisto, Jouko; Tysklind, Mats; Walker, Nigel; Peterson, Richard E.

2007-01-01

In June 2005 a WHO-IPCS expert meeting was held in Geneva during which the toxic equivalency factors (TEFs) for dioxin like compounds, including some polychlorinated biphenyls (PCBs), were re-evaluated. For this re-evaluation process the refined TEF database recently published by Haws and coworkers (Toxicol. Sci. 2006, 89:4-30) was used as a starting point. Decisions about a TEF value were made based on a combination of unweighted relative effect potency (REP) distributions from this database, expert judgement and point estimates. Previous TEFs were assigned in increments of 0.01, 0.05, 0.1, etc., but for this re-evaluation it was decided to use half order of magnitude increments on a logarithmic scale of 0.03, 0.1, 0.3 etc. Changes were decided by the expert panel for 2,3,4,7,8-pentachlorodibenzofuran (PeCDF) (TEF=0.3), 1,2,3,7,8-pentachlorodibenzofuran (PeCDF) (TEF=0.03), octachlorodibenzo-p-dioxin (OCDD) and octachlorodibenzofuran (OCDF) (TEFs=0.0003), 3,4,4’,5-tetrachlorbiphenyl (PCB 81) (TEF=0.0003), 3,3’,4,4’,5,5’-hexachlorobiphenyl (PCB 169) (TEF=0.03) and a single TEF value (0.00003) for all relevant mono-ortho substituted PCBs. Additivity, an important prerequisite of the TEF concept was again confirmed by results from recent in vivo mixture studies. Some experimental evidence shows that nondioxin-like aryl hydrocarbon receptor (AhR) agonists/antagonists are able to impact the overall toxic potency of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds and this needs to be investigated further. Certain individual and groups of compounds were identified for possible future inclusion in the TEF concept, including 3,4,4’-TCB (PCB 37), polybrominated dibenzo-p-dioxins (PBDDs) and dibenzofurans (PBDFs), mixed polyhalogenated dibenzo-p-dioxins and dibenzofurans, polyhalogenated naphthalenes and polybrominated biphenyls (PBBs). Concern was expressed about direct application of the TEF/TEQ approach to abiotic matrices such as soil, sediment etc., for direct application in human risk assessment. This is problematic, as the present TEF scheme and TEQ methodology is primarily intended for estimating exposure and risks via oral ingestion (e.g., by dietary intake). A number of future approaches to determine alternative or additional TEFs were also identified. These included the use of a probabilistic methodology to determine TEFs that better describe the associated levels of uncertainty and ‘systemic’ TEFs for blood and adipose tissue and total toxic equivalency (TEQ) for body burden. PMID:16829543

Dynamic pushing on three frictional surfaces: maximum acceptable forces, cardiopulmonary and calf muscle metabolic responses in healthy men.

PubMed

Maikala, Rammohan V; Dempsey, Patrick G; Ciriello, Vincent M; O'Brien, Niall V

2009-06-01

Pushing is an important materials handling activity in many occupations; however, pushing-related physiological investigations are still in infancy. The purpose was to evaluate maximum acceptable forces and physiological responses while pushing on: treadmill (TREAD); plywood floor (PLY); and Teflon floor (TEF). Acceptable forces, cardiopulmonary and calf muscle oxygenation and blood volume responses were collected simultaneously while 12 men (age 39 +/- 13 years; height 178 +/- 6 cm; and body mass 91.5 +/- 16 kg) pushed for 2 h on each surface at their psychophysical workload. Participants selected higher forces on the PLY, resulting in higher pulmonary oxygen uptake compared to that of TEF (by approximately 9%) and TREAD (by approximately 18%). Pushing on the TEF demonstrated 50-56% lower blood volume changes and 1.5-1.8 times more oxygenation-force ratio than that for other surfaces. It is concluded that, to avoid a potential slip, participants were conservative in selecting acceptable forces to push on the slippery TEF. Part of this compensatory strategy on the TEF resulted in less muscle activity and, therefore, less demand for oxygen delivery to the calf muscle than for other surfaces. The present findings of significant force- and physiological-related differences in treadmill vs. high inertia pushcart clearly demonstrate that pushing experiments are essential to evaluate functional abilities of the workers.

Postoperative Complications and Functional Outcome after Esophageal Atresia Repair: Results from Longitudinal Single-Center Follow-Up.

PubMed

Friedmacher, Florian; Kroneis, Birgit; Huber-Zeyringer, Andrea; Schober, Peter; Till, Holger; Sauer, Hugo; Höllwarth, Michael E

2017-06-01

Esophageal atresia (EA) and tracheoesophageal fistula (TEF) represent major therapeutic challenges, frequently associated with serious morbidities following surgical repair. The aim of this longitudinal study was to assess temporal changes in morbidity and mortality of patients with EA/TEF treated in a tertiary-level center, focusing on postoperative complications and their impact on long-term gastroesophageal function. One hundred nine consecutive patients with EA/TEF born between 1975 and 2011 were followed for a median of 9.6 years (range, 3-27 years). Comparative statistics were used to evaluate temporal changes between an early (1975-1989) and late (1990-2011) study period. Gross types of EA were A (n = 6), B (n = 5), C (n = 89), D (n = 7), and E (n = 2). Seventy (64.2%) patients had coexisting anomalies, 13 (11.9%) of whom died before EA correction was completed. In the remaining 96 infants, surgical repair was primary (n = 66) or delayed (n = 25) anastomosis, closure of TEF in EA type E (n = 2), and esophageal replacement with colon interposition (n=2) or gastric transposition (n=1). Long-gap EA was diagnosed in 23 (24.0%) cases. Postoperative mortality was 4/96 (4.2%). Overall survival increased significantly between the two study periods (42/55 vs. 50/54; P = 0.03). Sixty-nine (71.9%) patients presented postoperatively with anastomotic strictures requiring a median of 3 (range, 1-15) dilatations. Revisional surgery was required for anastomotic leakage (n = 5), recurrent TEF with (n = 1) or without (n=9) anastomotic stricture, undetected proximal TEF (n = 4), and refractory anastomotic strictures with (n = 1) or without (n = 2) fistula. Normal dietary intake was achieved in 89 (96.7%) patients, while 3 (3.3%) remained dependent on gastrostomy feedings. Manometry showed esophageal dysmotility in 78 (84.8%) infants at 1 year of age, increasing to 100% at 10-year follow-up. Fifty-six (60.9%) patients suffered from dysphagia with need for endoscopic foreign body removal in 12 (13.0%) cases. Anti-reflux medication was required in 43 (46.7%) children and 30 (32.6%) underwent fundoplication. The rate of gastroesophageal reflux increased significantly between the two study periods (29/42 vs. 44/50; P = 0.04). Twenty-two (23.9%) cases of endoscopic esophagitis and one Barrett's esophagus were identified. Postoperative complications after EA/TEF repair are common and should be expertly managed to reduce the risk of long-term morbidity. Regular multidisciplinary surveillance with transitional care into adulthood is recommended in all patients with EA/TEF.

Structural airway abnormalities contribute to dysphagia in children with esophageal atresia and tracheoesophageal fistula.

PubMed

Baxter, Katherine J; Baxter, Lauren M; Landry, April M; Wulkan, Mark L; Bhatia, Amina M

2018-01-31

Long-term dysphagia occurs in up to 50% of repaired esophageal atresia and tracheoesophageal fistula (EA/TEF) patients. The underlying factors are unclear and may include stricture, esophageal dysmotility, or associated anomalies. Our purpose was to determine whether structural airway abnormalities (SAA) are associated with dysphagia in EA/TEF. We conducted a retrospective chart review of children who underwent EA/TEF repair in our hospital system from 2007 to 2016. Children with identified SAA (oropharyngeal abnormalities, laryngeal clefts, laryngomalacia, vocal cord paralysis, and tracheomalacia) were compared to those without airway abnormalities. Dysphagia outcomes were determined by the need for tube feeding and the modified pediatric Functional Oral Intake Scale (FOIS) at 1 year. SAA was diagnosed in 55/145 (37.9%) patients with EA/TEF. Oropharyngeal aspiration was more common in children with SAA (58.3% vs. 36.4%, p=0.028). Children with SAA were more likely to require tube feeding both at discharge (79.6% vs. 48.3%, p<0.001) and at 1 year (52.7% vs. 13.6%, p<0.001) and had lower mean FOIS (4.18 vs. 6.21, p<0.001). In the logistic regression model adjusting for gestational age, long gap EA, and esophageal stricture, the presence of SAA remained a significant risk factor for dysphagia (OR 4.17 (95% CI 1.58-11.03)). SAA are common in children with EA/TEF and are associated with dysphagia, even after accounting for gestational age, esophageal gap and stricture. This study highlights the need for a multidisciplinary approach, including early laryngoscopy and bronchoscopy, in the evaluation of the EA/TEF child with dysphagia. Level II retrospective prognostic study. Copyright © 2018. Published by Elsevier Inc.

Comparative Study of Esophageal Stent and Feeding Gastrostomy/Jejunostomy for Tracheoesophageal Fistula Caused by Esophageal Squamous Cell Carcinoma

PubMed Central

Chiu, Yi-Chun; Lu, Hung-I; Huang, Cheng-Hua; Rau, Kun-Ming; Liu, Chien-Ting

2012-01-01

Background A malignant tracheoesophageal/bronchoesophageal fistula (TEF) is a life-threatening complication of esophageal squamous cell carcinoma. A feeding gastrostomy/jejunostomy had been the most common treatment method for patients with TEF before the era of stenting. The aim of this retrospective study is to compare the prognosis of esophageal squamous cell carcinoma patients with TEF treated with an esophageal metallic stent to those treated with a feeding gastrostomy/jejunostomy. Methods We retrospectively reviewed a total of 1011 patients with esophageal squamous cell carcinoma between 1996 and 2011 at Kaohsiung Chang Gung Memorial Hospital, and 86 patients with TEF (8.5%) were identified. The overall survival and other clinical data were compared between 30 patients treated with an esophageal metallic stent and 35 patients treated with a feeding gastrostomy/jejunostomy. Results Among the 65 patients receiving either an esophageal metallic stent or a feeding gastrostomy/jejunostomy, univariate analysis showed that treatment modality with an esophageal metallic stent (P = 0.007) and radiotherapy treatment after fistula diagnosis (P = 0.04) were predictive of superior overall survival. In the multivariate comparison, treatment modality with an esophageal metallic stent (P = 0.026, odds ratio: 1.859) represented the independent predictive factor of superior overall survival. There were no significant differences between groups in mean decrease in serum albumin or mean body weight loss. Compared to the feeding gastrostomy/jejunostomy group, a significantly higher proportion of patients in the stenting group (53% versus 14%, P = 0.001) were able to receive chemotherapy within 30 days after fistula diagnosis, indicating better infection control in the stenting group. Conclusions Compared with a feeding gastrostomy/jejunostomy, an esophageal metallic stent significantly improves overall survival in patients with malignant TEF in our retrospective analysis. Esophageal metallic stent placement may be considered the first-line of treatment for patients with malignant TEF. PMID:22912737

Basic Knowledge of Tracheoesophageal Fistula and Esophageal Atresia.

PubMed

Lee, Sura

2018-02-01

Tracheoesophageal fistula (TEF) and esophageal atresia (EA) are rare anomalies in neonates. Up to 50% of neonates with TEF/EA will have Vertebral anomalies (V), Anal atresia (A), Cardiac anomalies (C), Tracheoesophageal fistula (T), Esophageal atresia (E), Renal anomalies (R), and Limb anomalies (L) (VACTERL) association, which has the potential to cause serious morbidity. Timely management of the neonate can greatly impact the infant's overall outcome. Spreading latest evidence-based knowledge and sharing practical experience with clinicians across various levels of the neonatal intensive care unit and well-baby units have the potential to decrease the rate of morbidity and mortality. PubMed, CINAHL, Cochrane Review, and Google Scholar were used to search key words- tracheoesophageal fistula, esophageal atresia, TEF/EA, VACTERL, long gap, post-operative management, NICU, pediatric surgery-for articles that were relevant and current. Advancements in both technology and medicine have helped identify and decrease postsurgical complications. More understanding and clarity are needed to manage acid suppression and its effects in a timely way. Knowing the clinical signs of potential TEF/EA, clinicians can initiate preoperative management and expedite transfer to a hospital with pediatric surgeons who are experts in TEF/EA management to prevent long-term morbidity. Various methods of perioperative management exist, and future studies should look into standardizing perioperative care. Other areas of research should include acid suppression recommendation, reducing long-term morbidity seen in patients with TEF/EA, postoperative complications, and how we can safely and effectively decrease the length of time to surgery for long-gap atresia in neonates.

[Possibilities and results of surgical treatment of benign tracheoesophageal fistula].

PubMed

Krajc, T; Janík, M; Lucenic, M; Benej, R; Harustiak, S

2010-08-01

Review of literature and a single-institution retrospective analysis of possibilities and results of various surgical techniques in treatment of benign tracheoesophageal fistula (TEF). Between 1995 and 2010, 26 patients with benign tracheoesophageal fistula of various etiology underwent surgical treatment at the Department of Thoracic Surgery of Slovak Medical University and Faculty Hospital in Bratislava. The majority of patients had a postintubation TEF (21 cases), two fistulas were of traumatic origin, one iatrogenic, one congenital with adulthood manifestation and one tracheo-neoesophageal (TNEF) following an esophagectomy for carcinoma via extended cervical approach with lymphadenectomy and sternal retraction adpoted from transcervical extended mediastinal lymphadenectomy. We review the possible means of surgical treatment of TEF, of which we most frequently used segmental tracheal resection with end-to-end anastomosis and a non-overlying suture of the esophageal defect without muscle flap interposition (16 patients), transsection of the fistula with muscular flap interposition via cervical (2 patients) or transthoracic (1 patient) approach; or a T-tube insertion with (1 patient) or without (5 patients) discision and suture of the TEF. The only tracheo-neoesophageal fistula in our experience had been treated by neoesophagectomy, covering of tracheal defect by intercostal muscle flap and cervical esophagostomy. Short- and long-term results of TEF treatment in our institution have been favourable, with perioperative mortality of 3.8% (the patient with tracheo-neoesophageal fistula). Morbidity included 1 partial tracheal anastomotic dehiscence, 3 temporary left recurrent nerve palsies, temporary deglutition disorders (15 patients), tracheal anastomosis granulations in 1 patient and 2 wound infections. Out of 26 patients 15 (58%) are being followed-up on a regular basis, all with good (12 patients) or satisfactory (3 patients) functional results. In the paper we analyze the advantages and disadvantages of various techniques and their alternatives in the treatment of TEF. As the most reliable and suitable solution for patients with postintubation TEF, breathing spontaneously and with acceptable nutritional status, we favour segmental trachea resection with end-to-end anastomosis and esophageal suture without muscle interposition, regardless of presence of concomitant tracheal stenosis. Fistulae of other etiologies require diverse approaches, especially tailored with respect to their location. Management of tracheo-neoesophageal fistula following esophagectomy for carcinoma is extremely demanding. Therefore, it is crucial to adhere to basic rules of prevention of such benign but potentially fatal entities as TEF and TNEF.

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef).

PubMed

Cannarozzi, Gina; Plaza-Wüthrich, Sonia; Esfeld, Korinna; Larti, Stéphanie; Wilson, Yi Song; Girma, Dejene; de Castro, Edouard; Chanyalew, Solomon; Blösch, Regula; Farinelli, Laurent; Lyons, Eric; Schneider, Michel; Falquet, Laurent; Kuhlemeier, Cris; Assefa, Kebebew; Tadele, Zerihun

2014-07-09

Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource. The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten. It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.

Characterization of the dinophysistoxin-2 acute oral toxicity in mice to define the Toxicity Equivalency Factor.

PubMed

Abal, Paula; Louzao, M Carmen; Cifuentes, José Manuel; Vilariño, Natalia; Rodriguez, Ines; Alfonso, Amparo; Vieytes, Mercedes R; Botana, Luis M

2017-04-01

Ingestion of shellfish with dinophysistoxin-2 (DTX2) can lead to diarrheic shellfish poisoning (DSP). The official control method of DSP toxins in seafood is the liquid chromatography-mass spectrometry analysis (LC-MS). However in order to calculate the total toxicity of shellfish, the concentration of each compound must be multiplied by individual Toxicity Equivalency Factor (TEF). Considering that TEFs caused some controversy and the scarce information about DTX2 toxicity, the aim of this study was to characterize the oral toxicity of DTX2 in mice. A 4-Level Up and Down Procedure allowed the characterization of DTX2 effects and the estimation of DTX2 oral TEF based on determination of the lethal dose 50 (LD50). DTX2 passed the gastrointestinal barrier and was detected in urine and feces. Acute toxicity symptoms include diarrhea and motionless, however anatomopathology study and ultrastructural images restricted the toxin effects to the gastrointestinal tract. Nevertheless enterocytes microvilli and tight junctions were not altered, disconnecting DTX2 diarrheic effects from paracellular epithelial permeability. This is the first report of DTX2 oral LD 50 (2262 μg/kg BW) indicating that its TEF is about 0.4. This result suggests reevaluation of the present TEFs for the DSP toxins to better determine the actual risk to seafood consumers. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metrics and Methodologies for Measuring Teaching Quality in Higher Education: Developing the Teaching Excellence Framework (TEF)

ERIC Educational Resources Information Center

Gunn, Andrew

2018-01-01

The creation of the Teaching Excellence Framework (TEF) represents a significant development concerning the teaching mission of the university in the UK. This paper considers the background to, and the development of, the TEF. It explains the context from which the TEF emerged and unpacks a series of rationales which illustrate the need for, and…

Recurrent and acquired tracheoesophageal fistulae (TEF)-Minimally invasive management.

PubMed

Nazir, Zafar; Khan, Muhammad Arif Mateen; Qamar, Javaria

2017-10-01

Recurrent and acquired fistulae are a serious complication of congenital esophageal atresia and tracheoesophageal fistula (TEF) repair and foreign body ingestion (FBI) (e.g., button battery). We report our experience with a minimally invasive approach to recurrent and acquired TEF. Medical records of patients referred for management of recurrent and acquired TEF between 2003 and 2015 were reviewed retrospectively. Patients underwent endoscopic procedures (de-epithelization of fistulous tract and fibrin tissue adhesive-Tisseel R ) under general anesthesia. Nine children (7 male, 2 female) with age range 3months to 3years (mean 1.5year) were managed. TEF closed spontaneously in four patients, whereas in 5 patients the TEF closed after combined endoscopic procedure. Three patients required repeat endoscopic procedures. Follow-up ranged between 7months to 10years (mean 4.2years). Active observation and repeat combined endoscopic procedures are safe alternatives to open surgical repair of acquired and recurrent TEF. Level IV study. Copyright © 2017 Elsevier Inc. All rights reserved.

Surgical Management of Benign Acquired Tracheoesophageal Fistulas: A Ten-Year Experience.

PubMed

Bibas, Benoit Jacques; Guerreiro Cardoso, Paulo Francisco; Minamoto, Helio; Eloy-Pereira, Leandro Picheth; Tamagno, Mauro Federico L; Terra, Ricardo Mingarini; Pêgo-Fernandes, Paulo Manoel

2016-10-01

Benign tracheoesophageal fistulas (TEFs) are rare, and surgical correction is the ideal method of treatment. The objective of this study was to evaluate the results of operative treatment of benign TEFs in patients from a tertiary referral center. Retrospective study of patients with benign TEFs who were treated between January 2005 and December 2014. Preoperative evaluation included computed tomography of the chest, bronchoscopy, and upper endoscopy. Preoperative treatment included nutritional support by gastrostomy and treatment of lung infections. Surgical repair was done with tracheal resection and reconstruction, laryngotracheal resection, or membranous tracheal repair without resection. Esophageal management consisted of two-layer closure. Twenty patients (11 men) with mean age 48 ± 17 years were included. The most frequent cause was postintubation injury (n = 16; 80%). The median TEF length was 9 mm (interquartile range [IQR], 2 to 25 mm). The most commonly used surgical approaches were cervicotomy (n = 15; 75%) and cervicosternotomy (n = 3; 15%). Eleven patients required tracheal resection; median length was 3 cm (IQR, 3 to 5.5 cm). Seven patients (35%) required intraoperative tracheostomy. Complications occurred in 55% of patients. There was one dehiscence of the tracheal anastomosis, and one procedure-related death. Ninety-five percent of patients had complete closure of the TEF occurred in 95% of cases. Two patients had tracheal stenosis recurrence, and one patient had both TEF and tracheal stenosis recurrence. Two patients have indwelling silicone tracheal stents. Surgical treatment of TEF is effective. Nonetheless, morbidity and mortality are not negligible, even when performed at a referral center and after appropriate preoperative evaluation. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

The Automation of the Transonic Experimental Facility (TEF) and the Aerodynamic Experimental Facility (AEF)

DTIC Science & Technology

2015-10-01

ARL-TR-7506 ● OCT 2015 US Army Research Laboratory The Automation of the Transonic Experimental Facility (TEF) and the...Laboratory The Automation of the Transonic Experimental Facility (TEF) and the Aerodynamic Experimental Facility (AEF) by Charith R Ranawake Weapons...To) 05/2015–08/2015 4. TITLE AND SUBTITLE The Automation of the Transonic Experimental Facility (TEF) and the Aerodynamic Experimental Facility

The effect of fast eating on the thermic effect of food in young Japanese women.

PubMed

Toyama, Kenji; Zhao, Xifan; Kuranuki, Sachi; Oguri, Yasuo; Kashiwa Kato, Eriko; Yoshitake, Yutaka; Nakamura, Teiji

2015-03-01

The relationship between eating speed and the thermic effect of food (TEF) remains unclear. We investigated the difference in the TEF when meals containing the same amount of energy were eaten in 5 min (fast eating) or 15 min (regular eating). Subjects were nine non-obese young women. Following a 350 kcal (1464 kJ) meal, energy expenditure and autonomic nervous system activity were measured. The frequency of mastication was also calculated. The TEF for the 15-min period after the start of eating with fast eating was significantly lower than with regular eating (p < 0.01). There was a significant positive correlation between the low-frequency/high-frequency ratio and TEF at 5-min intervals up to 20 min after the start of eating and between total mastication frequency and TEF during ingestion. Fast eating may reduce the TEF, potentially because a decrease in mastication frequency decreases sympathetic nervous system activity.

Somatic embryogenesis and massive shoot regeneration from immature embryo explants of tef.

PubMed

Gugsa, Likyelesh; Kumlehn, Jochen

2011-01-01

Tef (Eragrostis tef) provides a major source of human nutrition in the Horn of Africa, but biotechnology has had little impact on its improvement to date. Here, we report the elaboration of an in vitro regeneration protocol, based on the use of immature zygotic embryos as explant. Explant size was an important determinant of in vitro regeneration efficiency, as was the formulation of the culture medium. Optimal results were obtained by culturing 0.2-0.35 mm embryo explants on a medium containing KBP minerals, 9.2-13.8 μM 2,4-dichlorophenoxyacetic acid, 6 mM glutamine, and 0.5% Phytagel. Although this protocol was effective for both the improved cultivar "DZ-01-196" and the landrace "Fesho", the former produced consistently more embryogenic tissue and a higher number of regenerants. An average of more than 2,800 shoots could be obtained from each "DZ-01-196" explant after 12 weeks of in vitro culture. These shoots readily formed roots, and plantlets transferred to soil were able to develop into morphologically normal, fertile plants. This regeneration and multiplication system should allow for the application of a range of biotechnological methods to tef.

TRAQUEOESOPHAGEAL FISTULA PATIENTS FED THROUGH PERCUTANEOUS ENDOSCOPIC GASTROSTOMY/GASTROJEJUNOSTOMY: NUTRITIONAL STATUS AND CLINICAL OUTCOME.

PubMed

Santos, Carla Adriana; Pereira, Marta; Martins, Vera Santos; Fonseca, Jorge

2015-08-01

tracheoesophageal fistula (TEF) may result from cancer or mechanical ventilation. Endoscopic Gastrostomy or Gastrojejunostomy (PEG/PEG-J) is used for nutritional support. in TEF-patients, evaluating nutritional status when PEG is performed, safety of PEG/PEG-J and clinical outcome. from the files of PEG/PEG-J feed TEF-patients we collected: clinical data, Body Mass Index, albumin, transferrin and cholesterol when gastrostomy was performed, and clinical outcome globally and according with the TEF cause: Group 1: complication of mechanical ventilation, Group 2: cancer. twelve patients, 18-91 years (median: 53), 11 PEG, one PEG-J: six complications of ventilation (neurological diseases), 6 cancers. Mean period from TEF diagnosis until gastrostomy: 2 months in Group 1, 10 months in Group 2. In the day of the gastrostomy, patients presented with malnutrition parameters, most strikingly in the cancer group. Group 1: died a single patient, 3 closed the TEF, resuming oral intake, 2 are still PEG-feed. All cancer patients died (7 months after gastrostomy). One needed a jejunal extension to create a PEG-J. No more complications. PEG/PEG-J was safe in TEF-patients, but cancer patients underwent gastrostomy too late. In TEF-patients, PEG/PEG-J should be considered in a regular basis, earlier in the disease evolution, before established malnutrition. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Efficient transcription of the glycolytic gene ADH1 and three translational component genes requires the GCR1 product, which can act through TUF/GRF/RAP binding sites.

PubMed Central

Santangelo, G M; Tornow, J

1990-01-01

Glycolytic gene expression in Saccharomyces cerevisiae is thought to be activated by the GCR and TUF proteins. We tested the hypothesis that GCR function is mediated by TUF/GRF/RAP binding sites (UASRPG elements). We found that UASRPG-dependent activation of a heterologous gene and transcription of ADH1, TEF1, TEF2, and RP59 were sensitive to GCR1 disruption. GCR is not required for TUF/GRF/RAP expression or in vitro DNA-binding activity. Images PMID:2405258

MCAT elements and the TEF-1 family of transcription factors in muscle development and disease.

PubMed

Yoshida, Tadashi

2008-01-01

MCAT elements are located in the promoter-enhancer regions of cardiac, smooth, and skeletal muscle-specific genes including cardiac troponin T, beta-myosin heavy chain, smooth muscle alpha-actin, and skeletal alpha-actin, and play a key role in the regulation of these genes during muscle development and disease. The binding factors of MCAT elements are members of the transcriptional enhancer factor-1 (TEF-1) family. However, it has not been fully understood how these transcription factors confer cell-specific expression in muscle, because their expression patterns are relatively broad. Results of recent studies revealed multiple mechanisms whereby TEF-1 family members control MCAT element-dependent muscle-specific gene expression, including posttranslational modifications of TEF-1 family members, the presence of muscle-selective TEF-1 cofactors, and cell-selective control of TEF-1 accessibility to MCAT elements. In addition, of particular interest, recent studies regarding MCAT element-dependent transcription of the myocardin gene and the smooth muscle alpha-actin gene in muscle provide evidence for the transcriptional diversity among distinct cell types and subtypes. This article summarizes the role of MCAT elements and the TEF-1 family of transcription factors in muscle development and disease, and reviews recent progress in our understanding of the transcriptional regulatory mechanisms involved in MCAT element-dependent muscle-specific gene expression.

Somatic Embryogenesis and Massive Shoot Regeneration from Immature Embryo Explants of Tef

PubMed Central

Gugsa, Likyelesh; Kumlehn, Jochen

2011-01-01

Tef (Eragrostis tef) provides a major source of human nutrition in the Horn of Africa, but biotechnology has had little impact on its improvement to date. Here, we report the elaboration of an in vitro regeneration protocol, based on the use of immature zygotic embryos as explant. Explant size was an important determinant of in vitro regeneration efficiency, as was the formulation of the culture medium. Optimal results were obtained by culturing 0.2–0.35 mm embryo explants on a medium containing KBP minerals, 9.2–13.8 μM 2,4-dichlorophenoxyacetic acid, 6 mM glutamine, and 0.5% Phytagel. Although this protocol was effective for both the improved cultivar “DZ-01-196” and the landrace “Fesho”, the former produced consistently more embryogenic tissue and a higher number of regenerants. An average of more than 2,800 shoots could be obtained from each “DZ-01-196” explant after 12 weeks of in vitro culture. These shoots readily formed roots, and plantlets transferred to soil were able to develop into morphologically normal, fertile plants. This regeneration and multiplication system should allow for the application of a range of biotechnological methods to tef. PMID:22028975

Application of MPVR and TL-VR with 64-row MDCT in neonates with congenital EA and distal TEF.

PubMed

Wen, Yang; Peng, Yun; Zhai, Ren-You; Li, Ying-Zi

2011-03-28

To assess the application of multiple planar volume reconstruction (MPVR) and three-dimensional (3D) transparency lung volume rendering (TL-VR) with 64-row multidetector-row computed tomography (MDCT) in neonates with congenital esophageal atresia (EA) and distal tracheoesophageal fistula (TEF). Twenty neonates (17 boys, 3 girls) with EA and distal TEF at a mean age of 4.6 d (range 1-16 d) were enrolled in this study. A helical scan of 64-row MDCT was performed at the 64 mm × 0.625 mm collimation. EA and TEF were reconstructed with MPVR and TL-VR, respectively. Initial diagnosis of EA was made by chest radiography showing the inserted catheter in the proximal blind-ended esophageal pouch. Manifestations of MDCT images were compared with the findings at surgery. MDCT showed the proximal and distal esophageal pouches in 20 cases. No significant difference was observed in gaps between the proximal and distal esophageal pouches detected by MPVR and TL-VR. The lengths of gaps between the proximal and distal esophageal pouches detected by MPVR and TL-VR correlated well with the findings at surgery (R = 0.87, P < 0.001). The images of MPVR revealed the orifice of TEF in 13 cases, while TL-VR images showed the orifice of TEF in 4 cases. EA and distal TEF can be reconstructed using MPVR and TL-VR of 64-row MDCT, which is a noninvasive technique to demonstrate the distal esophageal pouches and inter-pouch distance in neonates with EA and distal TEF.

The structural characteristics and expression of neuropeptides in the esophagus of patients with congenital esophageal atresia and tracheoesophageal fistula.

PubMed

Li, Kai; Zheng, Shan; Xiao, Xianmin; Wang, Qihong; Zhou, Yiming; Chen, Lian

2007-08-01

The aim of this study was to investigate the structural characteristics and the expression of a group of neuropeptides in the esophagus of patients with congenital esophageal atresia and tracheoesophageal fistula (EA-TEF), as well to elucidate the roles of these neuropeptides in the pathogenesis of postoperative incoordination of esophagus after successful surgical repair of EA-TEF. Twenty-four specimens from distal tracheoesophageal fistulas of patients with EA-TEF (EA-TEF group) and 10 esophageal specimens from neonates who died of nonesophageal diseases (control group) were studied. All of the specimens were subjected to routine pathologic study, ultrastructural observation, and immunohistochemical staining for neuron-specific enolase, substance P, vasoactive intestinal polypeptide, and nitric oxide synthase. In the EA-TEF group, mitochondria were distributed along the membrane of smooth muscle cell, whereas mitochondria in the control group were distributed along the karyotheca of the smooth muscle cells. The ratio of granulated vesicles to clear vesicles in the varicosity of the intramuscular motor nerve ending of the EA-TEF group (0.520 +/- 0.137) was much higher than that in the control group (0.192 +/- 0.020, P < .05). The percentages of specimens shown to have positive expression of neuron-specific enolase and substance P in the EA-TEF group (20.8% and 12.5%, respectively) were significantly lower than those in the control group (90% and 80% respectively, P < .05). The percentages of specimens shown to have positive expression of vasoactive intestinal polypeptide and nitric oxide synthase in the EA-TEF group (83.3% and 75%, respectively) were significantly higher than that in the control group (30% and 10% respectively, P < .05). Imbalance of neurotransmitters excretion in nerve vesicle, abnormal intrinsic dysplasia of nerve plexus and increased expression of certain neuropeptides were the main characteristics of esophagus with abnormal intrinsic innervation, which may be responsible for the postoperative esophageal dysfunction of EA-TEF.

Recovery of arctic tundra from thermal erosion disturbance is constrained by nutrient accumulation: a modeling analysis.

PubMed

Pearce, A R; Rastetter, E B; Kwiatkowski, B L; Bowden, W B; Mack, M C; Jiang, Y

2015-07-01

Abstract. We calibrated the Multiple Element Limitation (MEL) model to Alaskan arctic tundra to simulate recovery of thermal erosion features (TEFs) caused by permafrost thaw and mass wasting. TEFs could significantly alter regional carbon (C) and nutrient budgets because permafrost soils contain large stocks of soil organic matter (SOM) and TEFs are expected to become more frequent as the climate warms. We simulated recovery following TEF stabilization and did not address initial, short-term losses of C and nutrients during TEF formation. To capture the variability among and within TEFs, we modeled a range of post-stabilization conditions by varying the initial size of SOM stocks and nutrient supply rates. Simulations indicate that nitrogen (N) losses after the TEF stabilizes are small, but phosphorus (P) losses continue. Vegetation biomass recovered 90% of its undisturbed C, N, and P stocks in 100 years using nutrients mineralized from SOM. Because of low litter inputs but continued decomposition, younger SOM continued to be lost for 10 years after the TEF began to recover, but recovered to about 84% of its undisturbed amount in 100 years. The older recalcitrant SOM in mineral soil continued to be lost throughout the 100-year simulation. Simulations suggest that biomass recovery depended on the amount of SOM remaining after disturbance. Recovery was initially limited by the photosynthetic capacity of vegetation but became co-limited by N and P once a plant canopy developed. Biomass and SOM recovery was enhanced by increasing nutrient supplies, but the magnitude, source, and controls on these supplies are poorly understood. Faster mineralization of nutrients from SOM (e.g., by warming) enhanced vegetation recovery but delayed recovery of SOM. Taken together, these results suggest that although vegetation and surface SOM on TEFs recovered quickly (25 and 100 years, respectively), the recovery of deep, mineral soil SOM took centuries and represented a major ecosystem C loss.

Teaching Excellence Framework (TEF): Re-Examining Its Logic and Considering Possible Systemic and Institutional Outcomes

ERIC Educational Resources Information Center

Rudd, Tim

2017-01-01

This paper offers conceptual and theoretical insights relating to the Teaching Excellence Framework (TEF), highlighting a range of potential systemic and institutional outcomes and issues. The paper is organised around three key areas of discussion that are often under-explored in debates. Firstly, after considering the TEF in the wider context of…

Recommended Toxicity Equivalence Factors (TEFs) for Human Health Risk Assessments of 2,3,7,8-Tetrachlorodibenzo-p-dioxin and Dioxin-Like Compounds

EPA Science Inventory

The Risk Assessment Forum (RAF) Human Health TEFs document describes EPA’s updated approach for evaluating the human health risks from exposures to environmental media containing dioxin-like compounds. It recommends the use of consensus TEF values for 2,3,7,8-tetrachlorodibenzo-...

Long-Term Prognosis of Patients with Esophageal Atresia and/or Tracheoesophageal Fistula.

PubMed

Bakal, Unal; Ersoz, Fikret; Eker, Irem; Sarac, Mehmet; Aydin, Mustafa; Kazez, Ahmet

2016-05-01

To investigate long-term prognosis of infants with esophageal atresia (EA) and/or tracheoesophageal fistula (TEF). The data of patients with EA were investigated from their medical files. For the neurodevelopmental evaluation, they were requested to come for a return visit to authors' polyclinic. Intellectual development was assessed by Ankara Developmental Screening Inventory (ADSI) (for 0-6 age) and Wechsler Intelligence Scale for Children-Revised (WISC-R) (for 6-16 age). Of the 57 patients, 50 had EA+ distal TEF (87.7 %), six had isolated EA (10.5 %) and one had isolated TEF (1.8 %). Of the total patients, 18 cases (31 %) died and remaining 39 cases (69 %) survived. In the surviving cases, the most common long-term complication was dysphagia (n = 37, 94.8 %). Intellectual levels of the 24 patients assessed by ADSI were normal and of the remaining 15 cases evaluated by WISC-R ranged between 95 and 110 points. The long-term complications and hospital visits are common in surviving cases of EA; however, they have normal cognitive functions and physical developmental characteristics.

High-throughput discovery of mutations in tef semi-dwarfing genes by next-generation sequencing analysis.

PubMed

Zhu, Qihui; Smith, Shavannor M; Ayele, Mulu; Yang, Lixing; Jogi, Ansuya; Chaluvadi, Srinivasa R; Bennetzen, Jeffrey L

2012-11-01

Tef (Eragrostis tef) is a major cereal crop in Ethiopia. Lodging is the primary constraint to increasing productivity in this allotetraploid species, accounting for losses of ∼15-45% in yield each year. As a first step toward identifying semi-dwarf varieties that might have improved lodging resistance, an ∼6× fosmid library was constructed and used to identify both homeologues of the dw3 semi-dwarfing gene of Sorghum bicolor. An EMS mutagenized population, consisting of ∼21,210 tef plants, was planted and leaf materials were collected into 23 superpools. Two dwarfing candidate genes, homeologues of dw3 of sorghum and rht1 of wheat, were sequenced directly from each superpool with 454 technology, and 120 candidate mutations were identified. Out of 10 candidates tested, six independent mutations were validated by Sanger sequencing, including two predicted detrimental mutations in both dw3 homeologues with a potential to improve lodging resistance in tef through further breeding. This study demonstrates that high-throughput sequencing can identify potentially valuable mutations in under-studied plant species like tef and has provided mutant lines that can now be combined and tested in breeding programs for improved lodging resistance.

Transient Stability Output Margin Estimation Based on Energy Function Method

NASA Astrophysics Data System (ADS)

Miwa, Natsuki; Tanaka, Kazuyuki

In this paper, a new method of estimating critical generation margin (CGM) in power systems is proposed from the viewpoint of transient stability diagnostic. The proposed method has the capability to directly compute the stability limit output for a given contingency based on transient energy function method (TEF). Since CGM can be directly obtained by the limit output using estimated P-θ curves and is easy to understand, it is more useful rather than conventional critical clearing time (CCT) of energy function method. The proposed method can also estimate CGM as its negative value that means unstable in present load profile, then negative CGM can be directly utilized as generator output restriction. The proposed method is verified its accuracy and fast solution ability by applying to simple 3-machine model and IEEJ EAST10-machine standard model. Furthermore the useful application to severity ranking of transient stability for a lot of contingency cases is discussed by using CGM.

Alterations in hyolaryngeal elevation after esophageal anastomosis: A possible mechanism for airway aspiration.

PubMed

Demir, Numan; Arslan, Selen Serel; Yalcin, Sule; Karaduman, Ayşe; Tanyel, Feridun Cahit; Soyer, Tutku

2017-10-01

A prospective study was performed to evaluate anatomical alterations and hyolaryngeal elevation (HE) by videofluoroscopic swallowing study (VFSS) in patients with esophageal atresia-tracheoesophageal fistula (EA-TEF). Patients operated for EA-TEF were evaluated for age, sex, type of atresia and time to esophageal anastomosis. All patients were evaluated by videofluoroscopic swallowing study (VFSS). Penetration-Aspiration scale (PAS≥7 is considered as aspiration), distance between upper esophageal sphincter and 2nd cervical vertebrae (UES-C2) and hyolaryngeal elevation (HE) were evaluated by the same deglutitionist who was blind to the study. The results of EA-TEF patients were compared with healthy children. Eighteen patients with EA-TEF and 10 healthy controls were included. The median age was 16months (12-36m) in EA-TEF and 18months (13-51m) in controls. Male-to-female ratio was 5:4 and 4:1 respectively. 12 of cases were isolated-EA, 1 of them was EA-proximal TEF and 5 of the cases were EA-distal TEF. Half of the cases had primary EAN and others underwent delayed esophageal repair. Early oral feeding was also started in 9 patients (50%) whereas others had delayed oral feeding. VFSS showed aspiration in 27.7 (n=5) of cases (PAS≥7) in EA group. The median distance between UES-C2 was 3.04cm (min: 2.17-max: 3.94) in EA and 4.17cm (min: 3.45-max: 6.24cm) in controls. Median distance for HE was 0.37cm (min: 0.18-max: 1.1cm) in EA and 1.15 (min: 0.61-max: 1.06cm) in controls. The distance between UES-C2 was significantly lower than controls (p<0.05) and HE was decreased in EA-TEF without any statistical significance. Children with EA-TEF had shortened distance between airway and upper esophagus. HE may be inefficient to protect airway during deglutition. Anatomical alterations after EAN suggest that airway problems may be related with decreased HE in children with EATEF. Level II (Development of diagnostic criteria in a consecutive series of patients and a universally applied "gold standard"). Copyright © 2017 Elsevier Inc. All rights reserved.

Long-Term Outcomes of Patients with Tracheoesophageal Fistula/Esophageal Atresia: Survey Results from Tracheoesophageal Fistula/Esophageal Atresia Online Communities.

PubMed

Acher, Charles Wynn; Ostlie, Daniel J; Leys, Charles M; Struckmeyer, Shannon; Parker, Matthew; Nichol, Peter F

2016-12-01

Introduction  Outcome studies of tracheoesophageal fistula (TEF) and/or esophageal atresia (EA) are limited to retrospective chart reviews. This study surveyed TEF/EA patients/parents engaged in social media communities to determine long-term outcomes. Materials and Methods  A 50-point survey was designed to study presentation, interventions, and ongoing symptoms after repair in patients with TEF/EA. It was validated using a test population and made available on TEF/EA online communities. Results  In this study, 445 subjects completed the survey during a 2-month period. Mean age of patients when surveyed was 8.7 years (0-61 years) and 56% were male. Eighty-nine percent of surveys were completed by the parent of the patient. Sixty-two percent of patients underwent repair in the first 7 days of life. Standard open repair was most common (56%), followed by primary esophageal replacement (13%) and thoracoscopic repair (13%). Out of 405, 106 (26%) patients had postoperative leak. Postoperative leak was least likely in primary esophageal replacement (18%) and standard open repair (19%). Leak occurred in 32% of patients who had thoracoscopic repair; 31% (128/413) reported long-gap atresia, which was significantly associated with increased risk of postoperative leak (54/128, 42%) when compared with standard short-gap atresia (odds ratio, 3.5; p  = 0.001). Out of 409, 221 (54%) patients reported dysphagia after repair, with only 77/221 (34.8%) reporting resolution by age 5. Out of 381, 290 (76%) patients reported symptoms of gastroesophageal reflux disease (GERD). There was no difference in dysphagia rates or GERD symptoms based on type of initial repair. Antireflux surgery was required in 63/290, 22% of patients with GERD (15% of all patients) and 27% of these patients who had surgery required more than one procedure antireflux procedure. The most common was Nissen fundoplication (73%), followed by partial wrap (14%). Reflux recurred in 32% of patients after antireflux surgery. Conclusion  TEF/EA patients have long-term dysphagia and GERD that may be under reported. Retrospective studies of outcomes after TEF/EA repair may underestimate long-term esophageal dysmotility, dysphagia, GERD, and strictures that occur regardless of the type of repair and adversely affect quality of life. Fifteen percent of all TEF/EA patients surveyed required an antireflux procedure during childhood, and more than one-quarter of those required repeat surgery. These data demonstrate the need for long-term follow-up as pediatric patients transition to adult care. Georg Thieme Verlag KG Stuttgart · New York.

Effect of sourdough addition and storage time on in vitro starch digestibility and estimated glycemic index of tef bread.

PubMed

Shumoy, Habtu; Van Bockstaele, Filip; Devecioglu, Dilara; Raes, Katleen

2018-10-30

The effect of sourdough amount and storage time on starch digestibility and estimated glycemic index (eGI) of tef bread was investigated. The rapidly digestible starch (RDS), slowly digestible starch (SDS) and resistant starch (RS) of 0-30% sourdough fresh tef breads ranged from 49 to 58, 16 to 29 and 20 to 26 g/100 g starch, respectively. Storage of tef breads up to 5 days decreased the RDS by more than 2-fold while SDS and RS increased by 2 and 3 fold, respectively. The eGI for fresh and stored breads ranged from 39 to 89. Addition of sourdough increased the eGI of fresh breads while no uniform pattern was seen in the stored breads. As the storage time increased, all the breads showed a decrease in eGI. In vivo study is necessary to further investigate the effect of sourdough on GI of tef bread. Copyright © 2018 Elsevier Ltd. All rights reserved.

Gibberellin Deficiency Confers Both Lodging and Drought Tolerance in Small Cereals

PubMed Central

Plaza-Wüthrich, Sonia; Blösch, Regula; Rindisbacher, Abiel; Cannarozzi, Gina; Tadele, Zerihun

2016-01-01

Tef [Eragrostis tef (Zucc.) Trotter] and finger millet [Eleusine coracana Gaertn] are staple cereal crops in Africa and Asia with several desirable agronomic and nutritional properties. Tef is becoming a life-style crop as it is gluten-free while finger millet has a low glycemic index which makes it an ideal food for diabetic patients. However, both tef and finger millet have extremely low grain yields mainly due to moisture scarcity and susceptibility of the plants to lodging. In this study, the effects of gibberellic acid (GA) inhibitors particularly paclobutrazol (PBZ) on diverse physiological and yield-related parameters were investigated and compared to GA mutants in rice (Oryza sativa L.). The application of PBZ to tef and finger millet significantly reduced the plant height and increased lodging tolerance. Remarkably, PBZ also enhanced the tolerance of both tef and finger millet to moisture deficit. Under moisture scarcity, tef plants treated with PBZ did not exhibit drought-related symptoms and their stomatal conductance was unaltered, leading to higher shoot biomass and grain yield. Semi-dwarf rice mutants altered in GA biosynthesis, were also shown to have improved tolerance to dehydration. The combination of traits (drought tolerance, lodging tolerance and increased yield) that we found in plants with altered GA pathway is of importance to breeders who would otherwise rely on extensive crossing to introgress each trait individually. The key role played by PBZ in the tolerance to both lodging and drought calls for further studies using mutants in the GA biosynthesis pathway in order to obtain candidate lines which can be incorporated into crop-breeding programs to create lodging tolerant and climate-smart crops. PMID:27242844

Stable carbon and nitrogen isotope trophic enrichment factors for Steller sea lion vibrissae relative to milk and fish/invertebrate diets

USGS Publications Warehouse

Stricker, Craig A.; Christ, Aaron M.; Wunder, Michael B.; Doll, Andrew C.; Farley, Sean D.; Rea, Lorrie D.; Rosen, David A. S.; Scherer, R. D.; Tollit, Dominic J.

2015-01-01

Nutritional constraints have been proposed as a contributor to population declines in the endangered Steller sea lion Eumetopias jubatus in some regions of the North Pacific. Isotopic analysis of vibrissae (whiskers) is a potentially useful approach to resolving the nutritional ecology of this species because long-term (up to 8 yr) dietary information is sequentially recorded and metabolically inert once formed. Additionally, vibrissae are grown in utero, potentially offering indirect inference on maternal diet. However, diet reconstruction using isotopic techniques requires a priori knowledge of trophic enrichment factors (TEFs), which can vary relative to diet quality and among animal species. In this study, we provide new TEF estimates for (1) maternal relative to pup vibrissae during both gestation and nursing and (2) adult vibrissae relative to a complex diet. Further, we refine vibrissa-milk TEFs based on an additional 76 animals with an age distribution ranging from 1 to 20 mo. Mother-pup vibrissae TEF values during gestation and nursing were near zero for δ13C and averaged 0.8 and 1.6‰, respectively, for δ15N. In contrast, vibrissa-fish/invertebrate TEFs averaged 3.3 (± 0.3 SD) and 3.7‰ (±0.3) for lipid-free δ13C and δ15N, respectively. Average lipid-free δ13C and δ15N vibrissa-milk TEFs were 2.5 (±0.9) and 1.8‰ (±0.8), respectively, and did not differ among metapopulations. Empirically determined TEFs are critical for accurate retrospective diet modeling, particularly for evaluating the hypothesis of nutritional deficiency contributing to the lack of Steller sea lion population recovery in some regions of Alaska.

Thermic responses to vegetarian meals and yoga exercise.

PubMed

Agte, V; Chiplonkar, S

1992-01-01

The thermic effect (TEF) of vegetarian meals was measured for breakfast and lunch in 6 lean healthy men (18-25 years) during normal feeding (NF) and with 20% overfeeding (OF) on 28 successive days. The energy contents of breakfast were 223 +/- 10 and 330 +/- 48 kcal, and those of lunch were 1,033 +/- 220 and 1,247 +/- 222 kcal in NF and OF, respectively. In NF, the TEF per 180 min was 32.7 +/- 8.6 and 54.8 +/- 6.3 kcal for breakfast and lunch, respectively. In OF, the TEF was 38.3 +/- 8.3 kcal for breakfast and 57.2 +/- 5.4 kcal for lunch. The increase in total TEF due to OF was nonsignificant (p greater than 0.2). In response to 20% OF, adaptive thermogenesis was manifested mainly through an increase in the resting metabolic rate of 4.9% (p less than 0.001). In both feeding, regimes, the percent TEF was higher for breakfast than for lunch (p less than 0.05). Regression analysis of TEF versus calorie load indicated a stable component of 42 kcal with a 2% rate of increase. Yoga exercises were performed from 16.00 to 17.00 daily. The thermic effect of yoga exercises observed from 17.10 to 18.30 was 21 kcal and persisted beyond 90 min, indicating the role of yoga in energy metabolism.

Cross-sectional Associations between Exposure to Persistent Organic Pollutants and Leukocyte Telomere Length among U.S. Adults in NHANES, 2001–2002

PubMed Central

Mitro, Susanna D.; Birnbaum, Linda S.; Needham, Belinda L.; Zota, Ami R.

2015-01-01

Background: Exposure to persistent organic pollutants (POPs) such as dioxins, furans, and polychlorinated biphenyls (PCBs) may influence leukocyte telomere length (LTL), a biomarker associated with chronic disease. In vitro research suggests dioxins may bind to the aryl hydrocarbon receptor (AhR) and induce telomerase activity, which elongates LTL. However, few epidemiologic studies have investigated associations between POPs and LTL. Objectives: We examined the association between 18 PCBs, 7 dioxins, and 9 furans and LTL among 1,330 U.S. adults from NHANES 2001–2002. Methods: We created three summed POP metrics based on toxic equivalency factor (TEF), a potency measure including affinity for the AhR: a) non–dioxin-like PCBs (composed of 10 non–dioxin-like PCBs; no AhR affinity and no TEF); b) non-ortho PCBs (composed of 2 non–ortho-substituted PCBs with high TEFs); and c) toxic equivalency (TEQ) (composed of 7 dioxins, 9 furans, 2 non–ortho-substituted PCBs, and 6 mono–ortho-substituted PCBs; weighted by TEF). We tested the association between each metric and LTL using linear regression, adjusting for demographics, blood cell count and distribution, and another metric with a different TEF (i.e., non-ortho PCBs and TEQ adjusted for non–dioxin-like PCBs; non–dioxin-like PCBs adjusted for non-ortho PCBs). Results: In adjusted models, each doubling of serum concentrations of non-ortho PCBs and TEQ was associated with 3.74% (95% CI: 2.10, 5.40) and 5.29% (95% CI: 1.66, 9.05) longer LTLs, respectively. Compared with the lowest quartile, the highest quartile of exposure was associated with 9.16% (95% CI: 2.96, 15.73) and 7.84% (95% CI: –0.53, 16.92) longer LTLs, respectively. Non–dioxin-like PCBs were not associated with LTL. Conclusions: POPs with high TEFs and AhR affinity were associated with longer LTL. Because many dioxin-associated cancers are also associated with longer LTL, these results may provide insight into the mechanisms underlying PCB- and dioxin-related carcinogenesis. Citation: Mitro SD, Birnbaum LS, Needham BL, Zota AR. 2016. Cross-sectional associations between exposure to persistent organic pollutants and leukocyte telomere length among U.S. adults in NHANES, 2001–2002. Environ Health Perspect 124:651–658; http://dx.doi.org/10.1289/ehp.1510187 PMID:26452299

Etiology of Esophageal Atresia and Tracheoesophageal Fistula: “Mind the Gap”

PubMed Central

de Jong, Elisabeth M.; Felix, Janine F.; de Klein, Annelies

2010-01-01

Esophageal atresia and tracheoesophageal fistula (EA/TEF) are major congenital malformations affecting 1:3500 live births. Current research efforts are focused on understanding the etiology of these defects. We describe well-known animal models, human syndromes, and associations involving EA/TEF, indicating its etiologically heterogeneous nature. Recent advances in genotyping technology and in knowledge of human genetic variation will improve clinical counseling on etiologic factors. This review provides a clinical summary of environmental and genetic factors involved in EA/TEF. PMID:20425471

Surgical treatment of benign tracheo-oesophageal fistulas with tracheal resection and oesophageal primary closure: is the muscle flap really necessary?

PubMed

Camargo, José Jesus; Machuca, Tiago Noguchi; Camargo, Spencer Marcantônio; Lobato, Vivalde F; Medina, Carlos Remolina

2010-03-01

Nowadays, despite the advances of the low-pressure high-volume cuffs, post-intubation tracheo-oesophageal fistula (TEF) still poses a major challenge to thoracic surgeons. The original technique includes interposition of muscle flaps between suture lines to avoid recurrence. It is not clear if this manoeuvre is indispensable and, in fact, we and others have faced problems with it. Our aim is to present our experience with TEF management in a consecutive group with no muscle interposition. From June 1992 to November 2007, we evaluated 14 patients presenting with TEF, with a mean age of 44 years (from 18 to 79 years). Thirteen patients had a prolonged intubation history. The remaining case was a 40-year-old male with congenital TEF. Three patients had been previously submitted to failed repairs in other institutions. Ten patients had associated tracheal stenosis, which was subglottic in three of them. Regarding surgical technique, in all cases, we performed a single-staged procedure, which consisted of tracheal resection and anastomosis with double-layer oesophageal closure. In none of our cases was a muscle flap interposed between suture lines. All operations were performed through a cervical incision; however, in one case, an extension with partial sternotomy was required. There was no operative mortality. Thirteen patients were extubated in the first 24h after the procedure, while one patient required 48 h of mechanical ventilation. Four complications were recorded: one each of pneumonia and left vocal cord paralysis and two small tracheal dehiscences managed with a T-tube and a tracheostomy tube. After discharge, three patients returned to their native cities and were lost to follow-up. The remaining 11 patients have been followed up by a mean of 32 months (from three to 108 months), with 10 presenting excellent and one good anatomic and functional results. The single-staged repair with tracheal resection and anastomosis with oesophageal closure provides good short- and mid-term results for TEF management. The interposition of a muscle flap between suture lines may not be crucial to prevent recurrence. Copyright (c) 2009 European Association for Cardio-Thoracic Surgery. Published by Elsevier B.V. All rights reserved.

GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain.

PubMed Central

Tornow, J; Zeng, X; Gao, W; Santangelo, G M

1993-01-01

In Saccharomyces cerevisiae, efficient expression of glycolytic and translational component genes requires two DNA binding proteins, RAP1 (which binds to UASRPG) and GCR1 (which binds to the CT box). We generated deletions in GCR1 to test the validity of several different models for GCR1 function. We report here that the C-terminal half of GCR1, which includes the domain required for DNA binding to the CT box in vitro, can be removed without affecting GCR1-dependent transcription of either the glycolytic gene ADH1 or the translational component genes TEF1 and TEF2. We have also identified an activation domain within a segment of the GCR1 protein (the N-terminal third) that is essential for in vivo function. RAP1 and GCR1 can be co-immunoprecipitated from whole cell extracts, suggesting that they form a complex in vivo. The data are most consistent with a model in which GCR1 is attracted to DNA through contact with RAP1. Images PMID:8508768

Tip-enhanced fluorescence with radially polarized illumination for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA

NASA Astrophysics Data System (ADS)

Wei, Shih-Chung; Chuang, Tsung-Liang; Wang, Da-Shin; Lu, Hui-Hsin; Gu, Frank X.; Sung, Kung-Bin; Lin, Chii-Wann

2015-02-01

A tip nanobiosensor for monitoring DNA replication was presented. The effects of excitation power and polarization on tip-enhanced fluorescence (TEF) were assessed with the tip immersed in fluorescein isothiocyanate solution first. The photon count rose on average fivefold with radially polarized illumination at 50 mW. We then used polymerase-functionalized tips for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA. The amplicon-SYBR Green I complex was detected and compared to real-time loop-mediated isothermal amplification. The signals of the reaction using 4 and 0.004 ng/μl templates were detected 10 and 30 min earlier, respectively. The results showed the potential of TEF in developing a nanobiosensor for real-time DNA amplification.

Clinical Study of Congenital Esophageal Stenosis: Comparison according to Association of Esophageal Atresia and Tracheoesophageal Fistula.

PubMed

Kim, Soo-Hong; Kim, Hyun-Young; Jung, Sung-Eun; Lee, Seong-Cheol; Park, Kwi-Won

2017-06-01

Congenital esophageal atresia (CES) is a rare congenital disease. The severity of symptoms is variable; thus, diagnosis is difficult and tends to be delayed. CES is frequently accompanied by esophageal atresia (EA) with/without tracheoesophageal fistula (TEF). We investigated the characteristics of CES by reviewing our experience with CES patients and researched the differences between CES with EA-TEF and isolated CES. A total of 31 patients underwent operations for CES were reviewed retrospectively. The patients were divided into two groups according to the association with EA-TEF, and compared the differences. Sixteen boys and 15 girls were included. The mean age at symptom onset was 8 months old, and the mean age at diagnosis was 21 months old. Nine patients with EA-TEF were included group A, whereas the other 22 patients were assigned to group B. There were no differences in sex, gestational age, associated anomalies and pathologic results between the groups. In group A, the age at diagnosis and age at surgery were younger than in group B despite the age at symptom occurrence being similar. Postoperative complications occurred only in group A. In this study, symptoms occurred during the weaning period, and vomiting was the most frequent symptom. CES patients with EA-TEF tended to be diagnosed and treated earlier despite the age at symptom occurrence being similar. CES patients with EA-TEF had more postoperative complications; therefore, greater attention should be paid during the postoperative period.

Thermic effect of a meal and appetite in adults: an individual participant data meta-analysis of meal-test trials

PubMed Central

Ravn, Anne-Marie; Gregersen, Nikolaj Ture; Christensen, Robin; Rasmussen, Lone Graasbøl; Hels, Ole; Belza, Anita; Raben, Anne; Larsen, Thomas Meinert; Toubro, Søren; Astrup, Arne

2013-01-01

Background Thermic effect of a meal (TEF) has previously been suggested to influence appetite. Objective The aim of this study was to assess whether there is an association between appetite and TEF. Second, to examine whether protein intake is associated with TEF or appetite. Design Individual participant data (IPD) meta-analysis on studies were performed at the Department of Nutrition, Exercise and Sports, University of Copenhagen, Denmark. Five randomized meal-test studies, with 111 participants, were included. The included studies measured energy expenditure (EE) in respiration chambers and pre- and postprandial appetite sensations using Visual Analog Scales (VAS). The primary meta-analysis was based on a generic-inverse variance random-effects model, pooling individual study Spearman's correlation coefficients, resulting in a combined r-value with 95% confidence interval (95% CI). The I 2 value quantifies the proportion (%) of the variation in point estimates due to among-study differences. Results The IPD meta-analysis found no association between satiety and TEF expressed as the incremental area under the curve (TEFiAUC) (r=0.06 [95% CI −0.16 to 0.28], P=0.58; I 2=15.8%). Similarly, Composite Appetite Score (CAS) was not associated with TEFiAUC (r=0.08 [95% CI −0.12 to 0.28], P=0.45; I 2=0%). Posthoc analyses showed no association between satiety or CAS and TEF expressed as a percentage of energy intake (EI) (P>0.49) or TEF expressed as a percentage of baseline EE (P>0.17). When adjusting for covariates, TEFiAUC was associated with protein intake (P=0.0085). Conclusions This IPD meta-analysis found no evidence supporting an association between satiety or CAS and TEF at protein intakes ∼15 E% (range 11–30 E%). PMID:24376394

Chromosomal localization and cDNA cloning of the human DBP and TEF genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khatib, Z.A.; Inaba, T.; Valentine, M.

1994-09-15

The authors have isolated cDNA and genomic clones and determined the human chromosome positions of two genes encoding transcription factors expressed in the liver and the pituitary gland: albumin D-site-binding protein (DBP) and thyrotroph embryonic factor (TEF). Both proteins have been identified as members of the PAR (proline and acidic amino acid-rich) subfamily of bZIP transcription factors in the rat, but human homologues have not been characterized. Using a fluorescence in situ hybridization technique, the DBP locus was assigned to chromosome 19q13, and TEF to chromosome 22q13. Each assignment was confirmed by means of human chromosome segregation in somatic cellmore » hybrids. Coding sequences of DBP and TEF, extending beyond the bZIP domain to the PAR region, were highly conserved in both human-human and interspecies comparisons. Conservation of the exon-intron boundaries of each bZIP domain-encoding exon suggested derivation from a common ancestral gene. DBP and TEF mRNAs were expressed in all tissues and cell lines examined, including brain, lung, liver, spleen, and kidney. Knowledge of the human chromosome locations of these PAR proteins will facilitate studies to assess their involvement in carcinogenesis and other fundamental biological processes. 37 refs., 5 figs., 1 tab.« less

Isolation and characterisation of nanoparticles from tef and maize starch modified with stearic acid.

PubMed

Cuthbert, Wokadala O; Ray, Suprakas S; Emmambux, Naushad M

2017-07-15

Nanoparticles were isolated from tef and maize starch modified with added stearic acid after pasting at 90°C for 130min. This was followed by thermo-stable alpha-amylase hydrolysis of the paste. The resultant residues were then characterized using X-ray diffraction (XRD), differential scanning calorimetry (DSC), dynamic laser scattering particle size distribution (DLPSD), atomic force microscopy (AFM) and high-resolution transmission electron microscopy (HRTEM). XRD and DSC showed that the isolated residues consisted of amylose-lipid complexes. These complexes were type II with melting temperature above 104°C. DLPSD, AFM and HRTEM showed that the isolated tef and maize starch residues consisted of nanoparticles which became more distinct with increased hydrolysis time. The isolated tef and maize nanoparticles had distinct particles of about 3-10nm and 2.4-6.7nm, respectively and the yield was about 24-30%. The results demonstrated that distinct (physically separate) nanoparticles of less than 10nm can be isolated after formation during pasting of tef and maize starch with stearic acid. The production and isolation of the nanoparticles uses green chemistry principles and these nanoparticles can be used in food and non-food systems as nanofillers. Copyright © 2017 Elsevier Ltd. All rights reserved.

The vagus and recurrent laryngeal nerves in the rodent experimental model of esophageal atresia.

PubMed

Qi, B Q; Merei, J; Farmer, P; Hasthorpe, S; Myers, N A; Beasley, S W; Hutson, J M

1997-11-01

After surgical correction of their esophageal atresia and tracheoesophageal fistula (EA-TEF), many patients exhibit evidence of esophageal dysmotility. Controversy exists as to whether the esophageal motility disorders result from denervation caused by surgery or from an inherent abnormal innervation of the esophagus. The present study used an Adriamycin-induced EA-TEF fetal rat model to trace the course and branching of both the vagus and recurrent laryngeal nerves. Abnormalities observed in EA-TEF rat fetuses include: (1) fewer branches from both recurrent laryngeal nerves; (2) deviation of the left vagus from its normal course below the aorta, passing behind the fistula to approach and join with the right vagus to form a single nerve trunk on the right side of the esophagus; (3) relatively few branches from the single vagal nerve trunk (composed of fibers of the left and the right vagus) on the surface of the lower esophagus. Fetuses affected by EA-TEF have inherent abnormalities in the course and branching pattern of the vagus nerves as they descend through the thorax, culminating in a deficient extrinsic nerve fiber plexus in the lower esophagus. These observations may account for the esophageal motility disorders seen in patients who have EA-TEF even before surgical intervention.

DEVELOPMENT OF WEIGHTED DISTRIBUTIONS OF REPS FOR DIOXIN-LIKE COMPOUNDS

EPA Science Inventory

Potential health risks associated with exposure to mixtures of dioxin-like compounds are currently assessed using a toxic equivalency factor (TEF) approach. Recently, both the WH0 and NAS reviewed the TEF methodology and acknowledged the importance of better characterizing varia...

Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies.

PubMed

Carlson, Alexis; Justo, Alfredo; Hibbett, David S

2014-01-01

Trametes is a cosmopolitan genus of white rot polypores, including the "turkey tail" fungus, T. versicolor. Although Trametes is one of the most familiar genera of polypores, its species-level taxonomy is unsettled. The ITS region is the most commonly used molecular marker for species delimitation in fungi, but it has been shown to have a low molecular variation in Trametes resulting in poorly resolved phylogenies and unclear species boundaries, especially in the T. versicolor species complex (T. versicolor sensu stricto, T. ochracea, T. pubescens, T. ectypa). Here we evaluate the performance of three protein-coding genes (TEF1, RPB1, RPB2) for species delimitation and phylogenetic reconstruction in Trametes. We obtained 59 TEF1, 34 RPB1 and 55 RPB2 sequences from 69 individuals, focusing on the T. versicolor complex and performed phylogenetic analyses with maximum likelihood and parsimony methods. All three protein-coding genes outperformed ITS for separating species in the T. versicolor complex. The multigene phylogenetic analysis shows the highest amount of resolution and supported nodes separating T. ectypa, T. ochracea, T. pubescens and T. versicolor with strong support. In addition three slineages are resolved in the species complex of T. elegans. The T. elegans complex includes three species: T. elegans (based on material from Puerto Rico, Belize, the Philippines), T. aesculi (from North America) and T. repanda (from Papua New Guinea, the Philippines, Venezuela). The utility of gene markers varies, with TEF1 having the highest PCR and sequencing success rate and RPB1 offering the best backbone resolution for the genus. © 2014 by The Mycological Society of America.

Identification of rare heterozygous missense mutations in FANCA in esophageal atresia patients using next-generation sequencing.

PubMed

Feng, Yu; Chen, Runsen; Da, Min; Qian, Bo; Mo, Xuming

2018-06-30

Esophageal atresia and tracheoesophageal fistula (EA/TEF) are relatively common malformations in newborns, but the etiology of EA/TEF remains unknown. Fanconi anemia (FA) complementation group A (FANCA) is a key component of the FA core complex and is essential for the activation of the DNA repair pathway. The middle region (amino acids 674-1208) of FANCA is required for its interaction with FAAP20. We performed targeted sequencing of this binding region of FANCA (exons 23-36) in 40 EA/TEF patients. We also investigated the effect of the p.A958V mutation on the protein-protein interaction between FANCA and FAAP20 using an in vitro binding assay and co-immunoprecipitation. Immunolocalization analysis was performed to investigate the subcellular localization of FANCA, and tissue sections and immunohistochemistry were used to explore the expression of FANCA. We identified four rare missense variants in the FANCA binding region. FANCA mutations were significantly overrepresented in EA/TEF patients compared with 4300 control subjects from the NHLBI-ESP project (Fisher's exact p = 2.17 × 10 -5 , odds ratio = 31.75). p.A958V, a novel de novo mutation in the FANCA gene, was identified in one patient with EA/TEF. We provide further evidence that the p.A958V mutation reduces the binding affinity of FANCA for FAAP20. Interestingly, the p.A958V mutation impaired the nuclear localization of the FANCA protein expressed in HeLa cells. We found that FANCA was more highly expressed in stratified squamous epithelium than in smooth muscle. In conclusion, mutations in the FANCA gene are associated with EA/TEF in humans. Copyright © 2018. Published by Elsevier B.V.

Swallowing Dysfunction and Quality of Life in Adults With Surgically Corrected Esophageal Atresia/Tracheoesophageal Fistula as Infants: Forty Years of Follow-up.

PubMed

Gibreel, Waleed; Zendejas, Benjamin; Antiel, Ryan M; Fasen, Geoffrey; Moir, Christopher R; Zarroug, Abdalla E

2017-08-01

The aim of the study was to evaluate and study the full spectrum of swallowing dysfunction and long-term disease-specific outcomes in adults with surgically corrected esophageal atresia/tracheaesophageal fistula (EA/TEF). Long-term outcomes for adults who underwent EA/TEF repair because infants are lacking. We developed a disease-specific swallowing dysfunction questionnaire (SDQ) to assess swallowing dysfunction and quality of life (QOL) of adult patients with surgically corrected EA/TEF. Patients were surveyed with the newly developed SDQ and with a generic QOL tool (36-Item Short Form Health Survey). Ninety-seven patients underwent EA/TEF repair at our institution from 1950 to 1997. Forty-six (61%) patients completed the survey. Median follow-up was 40 years (range 18-63). Results suggest that some degree of swallowing dysfunction is common (82%), worse with hard consistencies (70%), and is associated with frequently needing sips of liquids to facilitate swallowing (75%). The presence of swallowing dysfunction was, however, often mild and did not seem to affect patients' food choices, or their day-to-day activities. QOL did not differ from that of the general population, regardless of the presence or absence of swallowing dysfunction. The presence of gastroesophageal reflux disease (26%), esophageal stricture (39%), or both (15%) does not account for all situations of swallowing dysfunction, nor does it significantly impact QOL. Swallowing dysfunction is common in adults who underwent EA/TEF repair as infants; however, patients reported minimal effect on QOL or day-to-day activities. The SDQ is a valid and reliable tool to measure the full spectrum of swallowing dysfunction in the EA/TEF repair population.

Environmental factors in the etiology of esophageal atresia and congenital diaphragmatic hernia: results of a case-control study.

PubMed

Felix, Janine F; van Dooren, Marieke F; Klaassens, Merel; Hop, Wim C J; Torfs, Claudine P; Tibboel, Dick

2008-02-01

Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) and congenital diaphragmatic hernia (CDH) are severe congenital anomalies. Their etiologies are mostly unknown and are thought to be multifactorial. No specific environmental factors have consistently been described as risk factors. In a study conducted during the years 2000 to 2004 in a pediatric surgical referral center in the Netherlands, parents of children with EA/TEF or with CDH of the Bochdalek type and parents of a group of children without major birth defects filled out a questionnaire about possible exposure to environmental risk factors during the period from 1 month before conception to the end of the first trimester of pregnancy. Children with chromosomal anomalies were excluded. Questionnaires were returned for 47 out of 64 cases (73%) with EA/TEF, for 63 out of 77 cases (82%) with CDH, and for 202 out of 243 controls (83%). In EA/TEF, maternal age was borderline significantly higher than in controls (32.2 vs. 30.6 years, p = .05). Contact with herbicides or insecticides was associated with EA/TEF in univariate analysis (OR 2.0; 95% CI: 1.0-4.1) and in multivariate analysis, although of borderline significance. In univariate analysis, CDH was significantly associated with maternal use of alcohol (OR 2.9; 95% CI: 1.6-5.2). We found a significant association between maternal alcohol use around the time of conception and CDH. A possible explanation might be the effect of alcohol on the retinoic acid pathway. An association was found between contact with herbicides or insecticides and EA/TEF. (c) 2008 Wiley-Liss, Inc.

Acute Toxicities of the Saxitoxin Congeners Gonyautoxin 5, Gonyautoxin 6, Decarbamoyl Gonyautoxin 2&3, Decarbamoyl Neosaxitoxin, C-1&2 and C-3&4 to Mice by Various Routes of Administration

PubMed Central

Selwood, Andrew I.; Waugh, Craig; Harwood, David T.; Rhodes, Lesley L.; Reeve, John; Sim, Jim; Munday, Rex

2017-01-01

Paralytic shellfish poisoning results from consumption of seafood naturally contaminated by saxitoxin and its congeners, the paralytic shellfish toxins (PSTs). The levels of such toxins are regulated internationally, and maximum permitted concentrations in seafood have been established in many countries. A mouse bioassay is an approved method for estimating the levels of PSTs in seafood, but this is now being superseded in many countries by instrumental methods of analysis. Such analyses provide data on the levels of many PSTs in seafood, but for risk assessment, knowledge of the relative toxicities of the congeners is required. These are expressed as “Toxicity Equivalence Factors” (TEFs). At present, TEFs are largely based on relative specific activities following intraperitoneal injection in a mouse bioassay rather than on acute toxicity determinations. A more relevant parameter for comparison would be median lethal doses via oral administration, since this is the route through which humans are exposed to PSTs. In the present study, the median lethal doses of gonyautoxin 5, gonyautoxin 6, decarbamoyl neosaxitoxin and of equilibrium mixtures of decarbamoyl gonyautoxins 2&3, C1&2 and C3&4 by oral administration to mice have been determined and compared with toxicities via intraperitoneal injection. The results indicate that the TEFs of several of these substances require revision in order to more accurately reflect the risk these toxins present to human health. PMID:28230783

Comparison of environmental risk factors for esophageal atresia, anorectal malformations, and the combined phenotype in 263 German families.

PubMed

Zwink, N; Choinitzki, V; Baudisch, F; Hölscher, A; Boemers, T M; Turial, S; Kurz, R; Heydweiller, A; Keppler, K; Müller, A; Bagci, S; Pauly, M; Brokmeier, U; Leutner, A; Degenhardt, P; Schmiedeke, E; Märzheuser, S; Grasshoff-Derr, S; Holland-Cunz, S; Palta, M; Schäfer, M; Ure, B M; Lacher, M; Nöthen, M M; Schumacher, J; Jenetzky, E; Reutter, H

2016-11-01

Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) and anorectal malformations (ARM) represent the severe ends of the fore- and hindgut malformation spectra. Previous research suggests that environmental factors are implicated in their etiology. These risk factors might indicate the influence of specific etiological mechanisms on distinct developmental processes (e.g. fore- vs. hindgut malformation). The present study compared environmental factors in patients with isolated EA/TEF, isolated ARM, and the combined phenotype during the periconceptional period and the first trimester of pregnancy in order to investigate the hypothesis that fore- and hindgut malformations involve differing environmental factors. Patients with isolated EA/TEF (n = 98), isolated ARM (n = 123), and the combined phenotype (n = 42) were included. Families were recruited within the context of two German multicenter studies of the genetic and environmental causes of EA/TEF (great consortium) and ARM (CURE-Net). Exposures of interest were ascertained using an epidemiological questionnaire. Chi-square, Fisher's exact, and Mann-Whitney U-tests were used to assess differences between the three phenotypes. Newborns with isolated EA/TEF and the combined phenotype had significantly lower birth weights than newborns with isolated ARM (P = 0.001 and P < 0.0001, respectively). Mothers of isolated EA/TEF consumed more alcohol periconceptional (80%) than mothers of isolated ARM or the combined phenotype (each 67%). Parental smoking (P = 0.003) and artificial reproductive techniques (P = 0.03) were associated with isolated ARM. Unexpectedly, maternal periconceptional multivitamin supplementation was most frequent among patients with the most severe form of disorder, i.e. the combined phenotype (19%). Significant differences in birth weight were apparent between the three phenotype groups. This might be attributable to the limited ability of EA/TEF fetuses to swallow amniotic fluid, thus depriving them of its nutritive properties. Furthermore, the present data suggest that fore- and hindgut malformations involve differing environmental factors. Maternal periconceptional multivitamin supplementation was highest among patients with the combined phenotype. This latter finding is contrary to expectation, and warrants further analysis in large prospective epidemiological studies. © 2015 International Society for Diseases of the Esophagus.

In vivo biochemical analyses reveal distinct roles of β-importins and eEF1A in tRNA subcellular traffic

PubMed Central

Huang, Hsiao-Yun

2015-01-01

Bidirectional tRNA movement between the nucleus and the cytoplasm serves multiple biological functions. To gain a biochemical understanding of the mechanisms for tRNA subcellular dynamics, we developed in vivo β-importin complex coimmunoprecipitation (co-IP) assays using budding yeast. Our studies provide the first in vivo biochemical evidence that two β-importin family members, Los1 (exportin-t) and Msn5 (exportin-5), serve overlapping but distinct roles in tRNA nuclear export. Los1 assembles complexes with RanGTP and tRNA. Both intron-containing pre-tRNAs and spliced tRNAs, regardless of whether they are aminoacylated, assemble into Los1–RanGTP complexes, documenting that Los1 participates in both primary nuclear export and re-export of tRNAs to the cytoplasm. In contrast, β-importin Msn5 preferentially assembles with RanGTP and spliced, aminoacylated tRNAs, documenting its role in tRNA nuclear re-export. Tef1/2 (the yeast form of translation elongation factor 1α [eEF1A]) aids the specificity of Msn5 for aminoacylated tRNAs to form a quaternary complex consisting of Msn5, RanGTP, aminoacylated tRNA, and Tef1/2. Assembly and/or stability of this quaternary complex requires Tef1/2, thereby facilitating efficient re-export of aminoacylated tRNAs to the cytoplasm. PMID:25838545

A Proteomic Approach to Investigate the Drought Response in the Orphan Crop Eragrostis tef.

PubMed

Kamies, Rizqah; Farrant, Jill M; Tadele, Zerihun; Cannarozzi, Gina; Rafudeen, Mohammed Suhail

2017-11-15

The orphan crop, Eragrostis tef , was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions. Validation of the iTRAQ dataset was done with selected stress-related proteins, fructose-bisphosphate aldolase (FBA) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX). Western blot analyses confirmed protein presence and showed increased protein abundance levels during water deficit while enzymatic activity for FBA, MDHAR and POX increased at selected RWC points. Gene ontology (GO)-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in tef upregulated proteins, while terms linked to reactive oxygen species (ROS)-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in tef downregulated proteins.

Morphological and molecular characterization of Fusarium spp pathogenic to pecan tree in Brazil.

PubMed

Lazarotto, M; Milanesi, P M; Muniz, M F B; Reiniger, L R S; Beltrame, R; Harakava, R; Blume, E

2014-11-11

The occurrence of Fusarium spp associated with pecan tree (Carya illinoinensis) diseases in Brazil has been observed in recent laboratory analyses in Rio Grande do Sul State. Thus, in this study, we i) obtained Fusarium isolates from plants with disease symptoms; ii) tested the pathogenicity of these Fusarium isolates to pecan; iii) characterized and grouped Fusarium isolates that were pathogenic to the pecan tree based on morphological characteristics; iv) identified Fusarium spp to the species complex level through TEF-1α sequencing; and v) compared the identification methods used in the study. Fifteen isolates collected from the inflorescences, roots, and seeds of symptomatic plants (leaf necrosis or root rot) were used for pathogenicity tests. Morphological characterization was conducted using only pathogenic isolates, for a total of 11 isolates, based on the mycelial growth rate, sporulation, colony pigmentation, and conidial length and width variables. Pathogenic isolates were grouped based on morphological characteristics, and molecular characterization was performed by sequencing TEF-1α genes. Pathogenic isolates belonging to the Fusarium chlamydosporum species complex, Fusarium graminearum species complex, Fusarium proliferatum, and Fusarium oxysporum were identified based on the TEF-1α region. Morphological characteristics were used to effectively differentiate isolates and group the isolates according to genetic similarity, particularly conidial width, which emerged as a key morphological descriptor in this study.

Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium.

PubMed

Al-Hatmi, Abdullah M S; Van Den Ende, A H G Gerrits; Stielow, J Benjamin; Van Diepeningen, Anne D; Seifert, Keith A; McCormick, Wayne; Assabgui, Rafik; Gräfenhan, Tom; De Hoog, G Sybren; Levesque, C André

2016-02-01

The genus Fusarium includes more than 200 species of which 73 have been isolated from human infections. Fusarium species are opportunistic human pathogens with variable aetiology. Species determination is best made with the combined phylogeny of protein-coding genes such as elongation factor (TEF1), RNA polymerase (RPB2) and the partial β-tubulin (BT2) gene. The internal transcribed spacers 1, 2 and 5.8S rRNA gene (ITS) have also been used, however, ITS cannot discriminate several closely related species and has nonorthologous copies in Fusarium. Currently, morphological approaches and tree-building methods are in use to define species and to discover hitherto undescribed species. Aftter a species is defined, DNA barcoding approaches can be used to identify species by the presence or absence of discrete nucleotide characters. We demonstrate the potential of two recently discovered DNA barcode loci, topoisomerase I (TOP1) and phosphoglycerate kinase (PGK), in combination with other routinely used markers such as TEF1, in an analysis of 144 Fusarium strains belonging to 52 species. Our barcoding study using TOP1 and PKG provided concordance of molecular data with TEF1. The currently accepted Fusarium species sampled were well supported in phylogenetic trees of both new markers. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

TOXIC EQUIVALENCY FACTORS (TEFS) FOR PCBS, PCDDS, PCDFS FOR HUMANS AND WILDLIFE

EPA Science Inventory

An expert meeting was organized by the World Health Organization (WHO) and held ih Stockholm on 15-18 June 1997. The objective of this meeting was to derive cohsensus toxic equivalency factors (TEFs) for polychlorinated didbenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) and dio...

Why International Students Have Been "TEF-ed Out"?

ERIC Educational Resources Information Center

Hayes, Aneta

2017-01-01

The article offers a critical review of the developments in the proposals for the Teaching Excellence Framework (TEF) in the UK, focusing particularly on international students. The analysis points to the absence of views and discussions regarding the group of international learners, which warrants the claim that international students have been…

Development of Weighted Distributions of REPs for Dioxin-Like Compounds: Implications for Risk Assessment

EPA Science Inventory

In their recent reevaluation of the TEF methodology, the WHO expert panel indicated that consideration should be given to developing weighted distributions of REP values to establish TEFs for each dioxin-like compound (DLC). As such, we developed a consensus-based weighting frame...

Diagnosis and surgical management of recurrent tracheoesophageal fistulas.

PubMed

Coran, A G

2013-01-01

Recurrent tracheoesophageal fistula (TEF) is difficult to diagnose and even more difficult to repair. The key to the diagnosis is an adequate contrast study and bronchoscopy. The key to the repair is complete separation of the esophagus from the trachea, with the placement of viable tissue between the two suture lines. I have presented a personal experience with 38 consecutive repairs of recurrent TEFs. The original series of 26 patients had three recurrences, all of which were re-repaired successfully. My more recent experience with the last 12 patients, who were far more complex, was also successful in ultimately repairing the recurrent TEFs. © 2013 Wiley Periodicals, Inc. and the International Society for Diseases of the Esophagus.

A PRELIMINARY APPROACH TO CHARACTERIZING VARIABILITY AND UNCERTAINTY IN THE MAMMALIAN PCDD/F AND PCB TEFS

EPA Science Inventory

The current toxic equivalency factors (TEFs) for PCDD/Fs and "dioxin-like" PCBs represent consensus-based values that were recommended by an international panel of experts convened by the World Health Organization (WHO) in June of 19971. As a part of the development of the mamma...

THE 2005 WORLD HEALTH ORGANIZATION RE-EVALUATION OF HUMAN AND MAMMALIAN TOXIC EQUIVALENCY FACTORS FOR DIOXINS AND DIOXIN-LIKE COMPOUNDS

EPA Science Inventory

In June 2005 a WHO-IPCS expert meeting was held in Geneva during which the toxic equivalency factors (TEFs) for dioxin like compounds, including some polychlorinated biphenyls (PCBs), were re-evaluated. For this re-evaluation process the refined TEF database recently published by...

Integrative modules for efficient genome engineering in yeast

PubMed Central

Amen, Triana; Kaganovich, Daniel

2017-01-01

We present a set of vectors containing integrative modules for efficient genome integration into the commonly used selection marker loci of the yeast Saccharomyces cerevisiae. A fragment for genome integration is generated via PCR with a unique set of short primers and integrated into HIS3, URA3, ADE2, and TRP1 loci. The desired level of expression can be achieved by using constitutive (TEF1p, GPD1p), inducible (CUP1p, GAL1/10p), and daughter-specific (DSE4p) promoters available in the modules. The reduced size of the integrative module compared to conventional integrative plasmids allows efficient integration of multiple fragments. We demonstrate the efficiency of this tool by simultaneously tagging markers of the nucleus, vacuole, actin, and peroxisomes with genomically integrated fluorophores. Improved integration of our new pDK plasmid series allows stable introduction of several genes and can be used for multi-color imaging. New bidirectional promoters (TEF1p-GPD1p, TEF1p-CUP1p, and TEF1p-DSE4p) allow tractable metabolic engineering. PMID:28660202

Polybrominated Dibenzo-p-Dioxins, Dibenzofurans, and Biphenyls: Inclusion in the Toxicity Equivalency Factor Concept for Dioxin-Like Compounds

PubMed Central

van den Berg, Martin

2013-01-01

In 2011, a joint World Health Organization (WHO) and United Nations Environment Programme (UNEP) expert consultation took place, during which the possible inclusion of brominated analogues of the dioxin-like compounds in the WHO Toxicity Equivalency Factor (TEF) scheme was evaluated. The expert panel concluded that polybrominated dibenzo-p-dioxins (PBDDs), dibenzofurans (PBDFs), and some dioxin-like biphenyls (dl-PBBs) may contribute significantly in daily human background exposure to the total dioxin toxic equivalencies (TEQs). These compounds are also commonly found in the aquatic environment. Available data for fish toxicity were evaluated for possible inclusion in the WHO-UNEP TEF scheme (van den Berg et al., 1998). Because of the limited database, it was decided not to derive specific WHO-UNEP TEFs for fish, but for ecotoxicological risk assessment, the use of specific relative effect potencies (REPs) from fish embryo assays is recommended. Based on the limited mammalian REP database for these brominated compounds, it was concluded that sufficient differentiation from the present TEF values of the chlorinated analogues (van den Berg et al., 2006) was not possible. However, the REPs for PBDDs, PBDFs, and non-ortho dl-PBBs in mammals closely follow those of the chlorinated analogues, at least within one order of magnitude. Therefore, the use of similar interim TEF values for brominated and chlorinated congeners for human risk assessment is recommended, pending more detailed information in the future. PMID:23492812

Polybrominated dibenzo-p-dioxins, dibenzofurans, and biphenyls: inclusion in the toxicity equivalency factor concept for dioxin-like compounds.

PubMed

van den Berg, Martin; Denison, Michael S; Birnbaum, Linda S; Devito, Michael J; Fiedler, Heidelore; Falandysz, Jerzy; Rose, Martin; Schrenk, Dieter; Safe, Stephen; Tohyama, Chiharu; Tritscher, Angelika; Tysklind, Mats; Peterson, Richard E

2013-06-01

In 2011, a joint World Health Organization (WHO) and United Nations Environment Programme (UNEP) expert consultation took place, during which the possible inclusion of brominated analogues of the dioxin-like compounds in the WHO Toxicity Equivalency Factor (TEF) scheme was evaluated. The expert panel concluded that polybrominated dibenzo-p-dioxins (PBDDs), dibenzofurans (PBDFs), and some dioxin-like biphenyls (dl-PBBs) may contribute significantly in daily human background exposure to the total dioxin toxic equivalencies (TEQs). These compounds are also commonly found in the aquatic environment. Available data for fish toxicity were evaluated for possible inclusion in the WHO-UNEP TEF scheme (van den Berg et al., 1998). Because of the limited database, it was decided not to derive specific WHO-UNEP TEFs for fish, but for ecotoxicological risk assessment, the use of specific relative effect potencies (REPs) from fish embryo assays is recommended. Based on the limited mammalian REP database for these brominated compounds, it was concluded that sufficient differentiation from the present TEF values of the chlorinated analogues (van den Berg et al., 2006) was not possible. However, the REPs for PBDDs, PBDFs, and non-ortho dl-PBBs in mammals closely follow those of the chlorinated analogues, at least within one order of magnitude. Therefore, the use of similar interim TEF values for brominated and chlorinated congeners for human risk assessment is recommended, pending more detailed information in the future.

USING DOSE ADDITION TO ESTIMATE CUMULATIVE RISKS FROM EXPOSURES TO MULTIPLE CHEMICALS

EPA Science Inventory

The Food Quality Protection Act (FQPA) of 1996 requires the EPA to consider the cumulative risk from exposure to multiple chemicals that have a common mechanism of toxicity. Three methods, hazard index (HI), point-of-departure index (PODI), and toxicity equivalence factor (TEF), ...

In vivo biochemical analyses reveal distinct roles of β-importins and eEF1A in tRNA subcellular traffic.

PubMed

Huang, Hsiao-Yun; Hopper, Anita K

2015-04-01

Bidirectional tRNA movement between the nucleus and the cytoplasm serves multiple biological functions. To gain a biochemical understanding of the mechanisms for tRNA subcellular dynamics, we developed in vivo β-importin complex coimmunoprecipitation (co-IP) assays using budding yeast. Our studies provide the first in vivo biochemical evidence that two β-importin family members, Los1 (exportin-t) and Msn5 (exportin-5), serve overlapping but distinct roles in tRNA nuclear export. Los1 assembles complexes with RanGTP and tRNA. Both intron-containing pre-tRNAs and spliced tRNAs, regardless of whether they are aminoacylated, assemble into Los1-RanGTP complexes, documenting that Los1 participates in both primary nuclear export and re-export of tRNAs to the cytoplasm. In contrast, β-importin Msn5 preferentially assembles with RanGTP and spliced, aminoacylated tRNAs, documenting its role in tRNA nuclear re-export. Tef1/2 (the yeast form of translation elongation factor 1α [eEF1A]) aids the specificity of Msn5 for aminoacylated tRNAs to form a quaternary complex consisting of Msn5, RanGTP, aminoacylated tRNA, and Tef1/2. Assembly and/or stability of this quaternary complex requires Tef1/2, thereby facilitating efficient re-export of aminoacylated tRNAs to the cytoplasm. © 2015 Huang and Hopper; Published by Cold Spring Harbor Laboratory Press.

AN ALTERNATIVE METHOD FOR ESTABLISHING TEFS FOR DIXON-LIKE COMPOUNDS. PART 2. DEVELOPMENT OF AN APPROACH TO QUANTITATIVELY WEIGHT THE UNDERLYING POTENCY DATA

EPA Science Inventory

The current approach for evaluating potential health risks associated with exposure to mixtures of polychlorinated dibenzo-p-dixoins (PCDDs), polychlorinated dibenzofurans (PCDFs) and dioxin-like polychlorinated biphenyls (PCBs) [hereafter referred to as "dioxin-like compoun...

Postprandial thermogenesis and substrate oxidation are unaffected by sleep restriction

PubMed Central

Shechter, Ari; Rising, Russell; Wolfe, Scott; Albu, Jeanine B.; St-Onge, Marie-Pierre

2014-01-01

Background/Objectives The extent to which alterations in energy expenditure (EE) in response to sleep restriction contribute to the short sleep-obesity relationship is not clearly defined. Short sleep may induce changes in resting metabolic rate (RMR), thermic effect of food (TEF), and postprandial substrate oxidation. Subjects/Methods Ten females (age and BMI: 22-43 y and 23.4-28 kg/m2) completed a randomized, crossover study assessing the effects of short (4 h/night) and habitual (8 h/night) sleep duration on fasting and postprandial RMR and respiratory quotient (RQ). Measurements were taken after 3 nights using whole-room indirect calorimetry. The TEF was assessed over a 6-h period following consumption of a high-fat liquid meal. Results Short vs. habitual sleep did not affect RMR (1.01 ± 0.05 and 0.97 ± 0.04 kcal/min; p=0.23). Fasting RQ was significantly lower after short vs. habitual sleep (0.84 ± 0.01 and 0.88 ± 0.01; p=0.028). Postprandial EE (short: 1.13 ± 0.04 and habitual: 1.10 ± 0.04, p=0.09) and RQ (short: 0.88 ± 0.01 and habitual: 0.88 ± 0.01, p=0.50) after the high-fat meal were not different between conditions. TEF was similar between conditions (0.24 ± 0.02 kcal/min in both; p=0.98), as was the ~6-h incremental area under the curve (1.16 ± 0.10 and 1.17 ± 0.09 kcal/min x 356 min after short and habitual sleep, respectively; p=0.92). Conclusions Current findings observed in non-obese healthy premenopausal women do not support the hypothesis that alterations in TEF and postprandial substrate oxidation are major contributors to the higher rate of obesity observed in short sleepers. In exploring a role of sleep duration on EE, research should focus on potential alterations in physical activity to explain the increased obesity risk in short sleepers. PMID:24352294

The Teaching Excellence Framework in the United Kingdom: An Opportunity to Include International Students as "Equals"?

ERIC Educational Resources Information Center

Hayes, Aneta

2017-01-01

Research on international students in British higher education points to marginalization of their unique perspectives in university classrooms. The aim of the article is to consider how the most recent policy changes, particularly the teaching excellence framework (TEF), continue to do so. The article also argues that the TEF, being a major higher…

The effect of resistance exercise on the thermic effect of food.

PubMed

Denzer, Charlene M; Young, John C

2003-09-01

The thermic effect of food (TEF) is the increment in energy expenditure above resting metabolic rate associated with the cost of absorption and processing of food for storage. Previous studies have shown that TEF is enhanced by aerobic endurance exercise of sufficient duration and intensity. The purpose of this study was to determine if a similar effect occurs with a single bout of resistance exercise (weightlifting). VO2 was measured in 9 healthy volunteers (3 males and 6 females) for 2 hours after ingestion of a 2760 kJ (660 kcal) carbohydrate meal with and without prior completion of a resistance training regimen (2 sets of 10 repetitions of 10 different exercises). The meal caused an immediate and persistent thermic effect in both the control and the exercise trial. Mean oxygen consumption over baseline increased 20% in the control trial and 34% in the exercise trial. TEF calculated from VO2 and RER (total area under the response curve above baseline) was 73% greater in the exercise trial compared with the control trial (159 +/- 18 vs. 92 +/- 14 KJ/2 hrs, p < .02). These results indicate that TEF in response to a carbohydrate meal is enhanced following a single bout of resistance exercise.

Use of a Palmaz stent for tracheomalacia: case report of an infant with esophageal atresia.

PubMed

Tazuke, Y; Kawahara, H; Yagi, M; Yoneda, A; Soh, H; Maeda, K; Yamamoto, T; Imura, K

1999-08-01

A male infant with congenital cardiac anomalies and esophageal atresia with tracheoesophageal fistula (EA-TEF) showed intractable respiratory symptoms after delayed primary repair of EA-TEF. Computed tomography demonstrated that the trachea was compressed by the enlarged aorta. Artificial ventilation was necessary even after aortopexy performed at 2 months of age. At 140 days of age, an expandable metallic stent (Palmaz stent) was inserted through a rigid bronchoscope into the trachea underfluoroscopic control. His respiratory status improved dramatically, and he was extubated in 18 hours. Although the follow-up period has been 9 months, the short-term result is satisfactory. The expandable metallic stent placement should be considered in patients with EA-TEF who show intractable respiratory symptoms caused by tracheomalacia.

In vitro and in silico derived relative effect potencies of ah-receptor-mediated effects by PCDD/Fs and PCBs in rat, mouse, and guinea pig CALUX cell lines.

PubMed

Ghorbanzadeh, Mehdi; van Ede, Karin I; Larsson, Malin; van Duursen, Majorie B M; Poellinger, Lorenz; Lücke-Johansson, Sandra; Machala, Miroslav; Pěnčíková, Kateřina; Vondráček, Jan; van den Berg, Martin; Denison, Michael S; Ringsted, Tine; Andersson, Patrik L

2014-07-21

For a better understanding of species-specific relative effect potencies (REPs), responses of dioxin-like compounds (DLCs) were assessed. REPs were calculated using chemical-activated luciferase gene expression assays (CALUX) derived from guinea pig, rat, and mouse cell lines. Almost all 20 congeners tested in the rodent cell lines were partial agonists and less efficacious than 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). For this reason, REPs were calculated for each congener using concentrations at which 20% of the maximal TCDD response was reached (REP20TCDD). REP20TCDD values obtained for PCDD/Fs were comparable with their toxic equivalency factors assigned by the World Health Organization (WHO-TEF), while those for PCBs were in general lower than the WHO-TEF values. Moreover, the guinea pig cell line was the most sensitive as indicated by the 20% effect concentrations of TCDD of 1.5, 5.6, and 11.0 pM for guinea pig, rat, and mouse cells, respectively. A similar response pattern was observed using multivariate statistical analysis between the three CALUX assays and the WHO-TEFs. The mouse assay showed minor deviation due to higher relative induction potential for 2,3,7,8-tetrachlorodibenzofuran and 2,3,4,6,7,8-hexachlorodibenzofuran and lower for 1,2,3,4,6,7,8-heptachlorodibenzofuran and 3,3',4,4',5-pentachlorobiphenyl (PCB126). 2,3,7,8-Tetrachlorodibenzofuran was more than two times more potent in the mouse assay as compared with that of rat and guinea pig cells, while measured REP20TCDD for PCB126 was lower in mouse cells (0.05) as compared with that of the guinea pig (0.2) and rat (0.07). In order to provide REP20TCDD values for all WHO-TEF assigned compounds, quantitative structure-activity relationship (QSAR) models were developed. The QSAR models showed that specific electronic properties and molecular surface characteristics play important roles in the AhR-mediated response. In silico derived REP20TCDD values were generally consistent with the WHO-TEFs with a few exceptions. The QSAR models indicated that, e.g., 1,2,3,7,8-pentachlorodibenzofuran and 1,2,3,7,8,9-hexachlorodibenzofuran were more potent than given by their assigned WHO-TEF values, and the non-ortho PCB 81 was predicted, based on the guinea-pig model, to be 1 order of magnitude above its WHO-TEF value. By combining in vitro and in silico approaches, REPs were established for all WHO-TEF assigned compounds (except OCDD), which will provide future guidance in testing AhR-mediated responses of DLCs and to increase our understanding of species variation in AhR-mediated effects.

Characterization of the translation elongation factor 1-α gene in a wide range of pathogenic Aspergillus species.

PubMed

Nouripour-Sisakht, Sadegh; Ahmadi, Bahram; Makimura, Koichi; Hoog, Sybren de; Umeda, Yoshiko; Alshahni, Mohamed Mahdi; Mirhendi, Hossein

2017-04-01

We aimed to evaluate the resolving power of the translation elongation factor (TEF)-1α gene for phylogenetic analysis of Aspergillus species. Sequences of 526 bp representing the coding region of the TEF-1α gene were used for the assessment of levels of intra- and inter-specific nucleotide polymorphism in 33 species of Aspergillus, including 57 reference, clinical and environmental strains. Analysis of TEF-1α sequences indicated a mean similarity of 92.6 % between the species, with inter-species diversity ranging from 0 to 70 nucleotides. The species with the closest resemblance were A. candidus/A. carneus, and A. flavus/A. oryzae/A. ochraceus, with 100 and 99.8 % identification, respectively. These species are phylogenetically very close and the TEF-1α gene appears not to have sufficient discriminatory power to differentiate them. Meanwhile, intra-species differences were found within strains of A. clavatus, A. clavatonanicus, A. candidus, A. fumigatus, A. terreus, A. alliaceus, A. flavus, Eurotium amstelodami and E. chevalieri. The tree topology with strongly supported clades (≥70 % bootstrap values) was almost compatible with the phylogeny inferred from analysis of the DNA sequences of the beta tubulin gene (BT2). However, the backbone of the tree exhibited low bootstrap values, and inter-species correlations were not obvious in some clades; for example, tree topologies based on BT2 and TEF-1α genes were incompatible for some species, such as A. deflectus, A. janus and A. penicillioides. The gene was not phylogenetically more informative than other known molecular markers. It will be necessary to test other genes or larger genomic regions to better understand the taxonomy of this important group of fungi.

Congenital esophageal stenosis associated with esophageal atresia/tracheoesophageal fistula: clinical and radiologic features.

PubMed

Yoo, Hye Jin; Kim, Woo Sun; Cheon, Jung-Eun; Yoo, So-Young; Park, Kwi-Won; Jung, Sung-Eun; Shin, Su-Mi; Kim, In-One; Yeon, Kyung Mo

2010-08-01

Congenital esophageal stenosis (CES) can be associated with esophageal atresia/tracheoesophageal fistula (EA/TEF). Because there are a variety of degrees of obstruction and symptoms of CES, it is frequently difficult to make a pre- and post-operative diagnosis of the distal CES associated with EA/TEF. To evaluate the clinical and radiologic features of congenital esophageal stenosis associated with esophageal atresia/tracheoesophageal fistula. We retrospectively reviewed postoperative esophagograms and medical records of 187 children (107 boys, 80 girls) who had primary repair of EA/TEF from 1992 to 2009 at our institution. We evaluated the incidence of CES, clinical findings, radiologic features and management of CES in these children. CES was diagnosed in 22 of 187 EA/TEF children (12%); one child had double CES lesions, for a total of 23 lesions. Ten of those 22 children (45%) had presented with significant symptoms of esophageal obstruction. The diagnosis of CES was delayed in 10 children (45%) until 1-10 years of age. On esophagogram, CES (n = 23) was located in the distal esophagus (n = 20, 87%) or mid-esophagus (n = 3, 13%). The degree of stenosis was severe (n = 6, 26%), moderate (n = 10, 43%), or mild (n = 7, 30%). Eight children, including two with unsuccessful esophageal balloon dilatation of CES, were treated surgically. Histologic examination revealed tracheobronchial remnant (n = 7) or fibromuscular hyperplasia (n = 1). One child with surgically treated CES developed achalasia at the age of 3 years 9 months. Esophagography after EA/TEF repair should be performed with a high index of suspicion for the presence of distal CES, because the diagnosis and adequate management of CES can often be delayed.

The TEF modeling and analysis approach to advance thermionic space power technology

NASA Astrophysics Data System (ADS)

Marshall, Albert C.

1997-01-01

Thermionics space power systems have been proposed as advanced power sources for future space missions that require electrical power levels significantly above the capabilities of current space power systems. The Defense Special Weapons Agency's (DSWA) Thermionic Evaluation Facility (TEF) is carrying out both experimental and analytical research to advance thermionic space power technology to meet this expected need. A Modeling and Analysis (M&A) project has been created at the TEF to develop analysis tools, evaluate concepts, and guide research. M&A activities are closely linked to the TEF experimental program, providing experiment support and using experimental data to validate models. A planning exercise has been completed for the M&A project, and a strategy for implementation was developed. All M&A activities will build on a framework provided by a system performance model for a baseline Thermionic Fuel Element (TFE) concept. The system model is composed of sub-models for each of the system components and sub-systems. Additional thermionic component options and model improvements will continue to be incorporated in the basic system model during the course of the program. All tasks are organized into four focus areas: 1) system models, 2) thermionic research, 3) alternative concepts, and 4) documentation and integration. The M&A project will provide a solid framework for future thermionic system development.

Predictors of post-treatment stenosis in cervical esophageal cancer undergoing high-dose radiotherapy

PubMed Central

Kim, Jun Won; Kim, Tae Hyung; Kim, Jie-Hyun; Lee, Ik Jae

2018-01-01

AIM To evaluate toxicity and treatment outcome of high-dose radiotherapy (RT) for cervical esophageal cancer (CEC). METHODS We reviewed a total of 62 consecutive patients who received definitive RT for stage I to III cervical esophageal cancer between 2001 and 2015. Patients who received < 45 Gy, treated for lesions below sternal notch, treated with palliative aim, treated with subsequent surgical resection, or diagnosed with synchronous hypopharyngeal cancer were excluded. Treatment failures were divided into local (occurring within the RT field), outfield-esophageal, and regional [occurring in regional lymph node(s)] failures. Factors predictive of esophageal stenosis requiring endoscopic dilation were analyzed. RESULTS Grade 1, 2, and 3 esophagitis occurred in 19 (30.6%), 39 (62.9%), and 4 patients (6.5%), respectively, without grade ≥ 4 toxicities. Sixteen patients (25.8%) developed post-RT stenosis, of which 7 cases (43.8%) were malignant. Four patients (6.5%) developed tracheoesophageal fistula (TEF), of which 3 (75%) cases were malignant. Factors significantly correlated with post-RT stenosis were stage T3/4 (P = 0.001), complete circumference involvement (P < 0.0001), stenosis at diagnosis (P = 0.024), and endoscopic complete response (P = 0.017) in univariate analysis, while complete circumference involvement was significant in multivariate analysis (P = 0.003). A higher dose (≥ 60 Gy) was not associated with occurrence of post-RT stenosis or TEF. With a median follow-up of 24.3 (range, 3.4-152) mo, the 2 y local control, outfield esophageal control, progression-free survival, and overall survival (OS) rates were 78.9%, 90.2%, 49.6%, and 57.3%, respectively. Factors significantly correlated with OS were complete circumference involvement (P = 0.023), stenosis at diagnosis (P < 0.0001), and occurrence of post-RT stenosis or TEF (P < 0.001) in univariate analysis, while stenosis at diagnosis (P = 0.004) and occurrence of post-RT stenosis or TEF (P = 0.023) were significant in multivariate analysis. CONCLUSION Chemoradiation for CEC was well tolerated, and a higher dose was not associated with stenosis. Patients with complete circumferential involvement require close follow-up. PMID:29467556

Stephen L. Gans Distinguished Overseas Lecture. The neural crest in pediatric surgery.

PubMed

Tovar, Juan A

2007-06-01

This review highlights the relevance of the neural crest (NC) as a developmental control mechanism involved in several pediatric surgical conditions and the investigative interest of following some of its known signaling pathways. The participation of the NC in facial clefts, ear defects, branchial fistulae and cysts, heart outflow tract and aortic arch anomalies, pigmentary disorders, abnormal enteric innervation, neural tumors, hemangiomas, and vascular anomalies is briefly reviewed. Then, the literature on clinical and experimental esophageal atresia-tracheoesophageal fistula (EA-TEF) and congenital diaphragmatic hernia (CDH) is reviewed for the presence of associated NC defects. Finally, some of the molecular signaling pathways involved in both conditions (sonic hedgehog, Hox genes, and retinoids) are summarized. The association of facial, cardiovascular, thymic, parathyroid, and C-cell defects together with anomalies of extrinsic and intrinsic esophageal innervation in babies and/or animals with both EA-TEF and CDH strongly supports the hypothesis that NC is involved in the pathogenesis of these malformative clusters. On the other hand, both EA-TEF and CDH are observed in mice mutant for genes involved in the previously mentioned signaling pathways. The investigation of NC-related molecular pathogenic pathways involved in malformative associations like EA-TEF and CDH that are induced by chromosomal anomalies, chemical teratogens, and engineered mutations is a promising way of clarifying why and how some pediatric surgical conditions occur. Pediatric surgeons should be actively involved in these investigations.

Polychlorinated naphthalenes and polychlorinated biphenyls in fishes from Michigan waters including the Great Lakes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kannan, K.; Yamashita, N.; Imagawa, Takashi

2000-02-15

Polychlorinated naphthalene (PCN) and polychlorinated biphenyl (PCB) congeners were measured in while body and fillet of fishes collected from Michigan waters, including the Great Lakes, during 1996--1997. PCNs were found in all the fishes analyzed including those from Siskiwit Lake, a remote lake located near the southern shoreline of Isle Royale National park in Lake Superior. Concentration of total PCNs in fishes ranged from 19 to 31 400 pg/g, wet wt, and varied depending on sampling location and species. Fishes from the Detroit River contained the greatest concentrations of both PCNs and PCBs. Concentrations of total PCNs in fishes frommore » Michigan waters were significantly correlated with the concentrations of PCBs. As with total PCN concentrations, the profiles of PCN isomer/congener distribution in fishes varied among sampling locations and species. Fishes from the Detroit River contained PCN profile similar to that of Halowax 1014, whereas those from Siskiwit Lake and lake Superior contained greater proportions of congeners which have great bioaccumulative potential. Estimated concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin equivalents (TEQs) of PCNs ranged from 0.007 to 11 pg/g, wet wt. PCN congeners 66/67 and 69 accounted for greater than 80% of the TEQs contributed by PCNs. TEQs contributed by PCBs, estimated based on H411E bioassay-derived TEFs, were in the range of 0.06--11 pg/g, wet wt, which were similar to those contributed by PCNs. When international TEFs (1-TEFs) for coplanar PCBs were applied, estimated PCB-TEQs ranged from 0.46 to 79 pg/g, wet wt, which were 5--10 times greater than those that were estimated from H411E TEFs. PCB congener 126 contributed greater than 50% of the TEQs contributed by PCBs in all the fishes. Overall, when similarly derived TEFs were used. PCNs contributed 2--57% of the sum of TEQs of PCNs and PCBs.« less

Comparison of mathematically-predicted toxic equivalents (TEQs) and bioassay-derived dioxin-equivalents (TCDD-EQs) in heron embryos

USGS Publications Warehouse

Rattner, B.; Hatfield, J.; Melancon, M.; Custer, T.; Tillitt, D.

1995-01-01

Pipping black-crowned night-heron (Nycticorax nycticorax) embryos were collected from an uncontaminated site (Chincoteague National Wildlife Refuge,VA) and three polluted sites (Cat Island, Green Bay, WI; Bair and West Marin Islands, San Francisco Bay, CA). Hepatic microsomal monooxygenases were induced up to 85-fold relative to the reference site, and was associated with concentrations of total PCBs and 11 PCB congeners that are presumed to concern.to express toxicity through the Ah receptor. TEQs [mathematically predicted; summed product of PCB congener concentrations using 5 different sets of toxic equivalency factors (TEFs)] were compared to TCDD-EQs [derived by bioassay; ethoxyresorufin-O-dealkylase activity of treated H411E rat hepatoma cells]. Although TEQs were up to 15-fold greater than TCDD-EQs, the pattern among sites was consistent and TEQs were highly correlated with TCDD-EQs. TEFs based on single congener mammalian studies yielded TEQs that greatly exceeded values from the H411E bioassay of field sample. TEFs generated from avian egg injection studies yielded TEQs that most closely approximated bioassay-derived TCDD-EQs. Cytochrome P450 parameters were related to TEQs and TCDD-EQs; adjusted r2 often exceeded 0.5 for the relation among mathematically predicted TEQs and cytochrome P450 measurements. These data document the general predictive value of TEQs and TCDD-EQs for P450 induction in field collected samples, but also indicate the need for development of TEFs for the species and biological end point of concern.

BMP antagonism by Noggin is required in presumptive notochord cells for mammalian foregut morphogenesis.

PubMed

Fausett, Sarah R; Brunet, Lisa J; Klingensmith, John

2014-07-01

Esophageal atresia with tracheoesophageal fistula (EA/TEF) is a serious human birth defect, in which the esophagus ends before reaching the stomach, and is aberrantly connected with the trachea. Several mouse models of EA/TEF have recently demonstrated that proper dorsal/ventral (D/V) patterning of the primitive anterior foregut endoderm is essential for correct compartmentalization of the trachea and esophagus. Here we elucidate the pathogenic mechanisms underlying the EA/TEF that occurs in mice lacking the BMP antagonist Noggin, which display correct dorsal/ventral patterning. To clarify the mechanism of this malformation, we use spatiotemporal manipulation of Noggin and BMP receptor 1A conditional alleles during foregut development. Surprisingly, we find that the expression of Noggin in the compartmentalizing endoderm is not required to generate distinct tracheal and esophageal tubes. Instead, we show that Noggin and BMP signaling attenuation are required in the early notochord to correctly resolve notochord cells from the dorsal foregut endoderm, which in turn, appears to be a prerequisite for foregut compartmentalization. Collectively, our findings support an emerging model for a mechanism underlying EA/TEF in which impaired notochord resolution from the early endoderm causes the foregut to be hypo-cellular just prior to the critical period of compartmentalization. Our further characterizations suggest that Noggin may regulate a cell rearrangement process that involves reciprocal E-cadherin and Zeb1 expression in the resolving notochord cells. Copyright © 2014. Published by Elsevier Inc.

Human Orthobunyavirus Infections, Tefé, Amazonas, Brazil

PubMed Central

Naveca, Felipe Gomes; Nascimento, Valdinete Alves; Souza, Victor Costa; de Figueiredo, Regina M.P.

2018-01-01

Introduction: Several orthobunyaviruses are important arthropod-borne pathogens, responsible for a variety of diseases in humans, from acute febrile illness to encephalitis. Methods: We collected serum samples from a series of dengue suspected cases in Tefé, a mid-size city located in the interior of the Amazonas state, Brazil. Viral RNA extraction was performed, and specimens were tested for dengue virus using RT-PCR. Thirty dengue negative samples were further tested for Mayaro virus (MAYV) and Oropouche virus (OROV) using an RT-qPCR protocol previously described. Positive samples were characterized by MegaBLAST analysis over the entire nucleotide collection of the main public databases, and also by maximum likelihood phylogenetic reconstruction of the S genome segment. Results: We detected nine OROV or OROV-like positive cases among 30 patients reporting fever and headache, as the most common symptoms. The closest nucleotide sequence returned from the MegaBLAST analysis belongs to an OROV isolated in Peru 2008. Moreover, all Tefé samples grouped in the same clade with the OROV reference sequence and other closely-related OROV-like viruses. Discussion: Dengue viruses are still the most important arbovirus worldwide, causing hundreds of millions of infections every year. Nonetheless, other arboviruses like chikungunya virus, Zika virus, and yellow fever virus have emerged in the last few years and are now a public health concern in several countries. OROV is believed to have caused more than 500,000 febrile infections in Brazil over recent decades. Therefore, the results described in this study strengthen that this arbovirus, and its closely-related recombinants, should be under continuous surveillance, at least in the endemic countries of Latin America. PMID:29623245

Boltzmann Transport Equation Algorithms for Infinite-Slab Buildup and Albedo Factors

DTIC Science & Technology

1990-09-30

DATA FOR LEAD, G EO M ETR Y A ................................................................................................. 40 17 MODEL FITS TO...NEUTRON BUILDUP FACTOR MODEL CONSTANTS AND LEAST- SQUARES FUNCTION VALUES FOR IRON, GEOMETRY A ................ 47 17 NEUTRON BUILDUP FACTOR MODEL...hs 4- * Co ) 4y-hs N’I -96sin 5) g-po) ( E-E0) (8a) and ’ 4ph ,+TEf2(-gA)] =0 (8b) for 4[0,1] and OE[0,2n]. Here p specifies lateral position in

Development of a yeast heterologous expression cassette based on the promoter and terminator elements of the Eremothecium cymbalariae translational elongation factor 1α (EcTEF1) gene.

PubMed

Linder, Tomas

2018-04-01

A new expression cassette ( EC0 ) consisting of the fused 5' and 3' intergenic regions (IGRs) of the Eremothecium cymbalariae translational elongation factor 1α ( EcTEF1 ) gene was evaluated through expression of the bacterial hygromycin B phosphotransferase ( hph ) resistance gene in the common baker's yeast Saccharomyces cerevisiae . Progressively shorter versions of the hph -containing EC cassette ( hphEC1 though hphEC6 ) with trimmed 5' and 3' EcTEF1 IGRs were tested for their ability to confer resistance to hygromycin B in S. cerevisiae . Hygromycin B resistance was retained in all six generated hphEC variants up to a concentration of 400 mg/L. The hphEC6 cassette was the shortest cassette to be assayed in this study with 366 and 155 bp of the EcTEF1 5' and 3' IGRs, respectively. When tested for deletion of the S. cerevisiae proline oxidase gene PUT1 , the hphEC6 cassette was shown to successfully act as a selection marker on hygromycin B-containing medium. The hphEC6 cassette could be placed immediately adjacent to a kanMX4 G418 disulfate resistance marker without any discernable effect on the ability of the yeast to grow in the presence of both hygromycin B and G418 disulfate. Co-cultivation experiments under non-selective conditions demonstrated that a PUT1 deletion strain carrying the hphEC6 cassette displayed equivalent fitness to an otherwise isogenic PUT1 deletion strain carrying the kanMX4 cassette.

Rejection triggers liver transplant tolerance: Involvement of mesenchyme-mediated immune control mechanisms in mice.

PubMed

Morita, Miwa; Joyce, Daniel; Miller, Charles; Fung, John J; Lu, Lina; Qian, Shiguang

2015-09-01

Liver tolerance was initially recognized by the spontaneous acceptance of liver allografts in many species. The underlying mechanisms are not completely understood. However, liver transplant (LT) tolerance absolutely requires interferon (IFN)-γ, a rejection-associated inflammatory cytokine. In this study, we investigated the rejection of liver allografts deficient in the IFN-γ receptor and reveal that the liver graft is equipped with machineries capable of counterattacking the host immune response through a mesenchyme-mediated immune control (MMIC) mechanism. MMIC is triggered by T effector (Tef) cell-derived IFN-γ that drives expression of B7-H1 on graft mesenchymal cells leading to Tef cell apoptosis. We describe the negative feedback loop between graft mesenchymal and Tef cells that ultimately results in LT tolerance. Comparable elevations of T-regulatory cells and myeloid-derived suppressor cells were observed in both rejection and tolerance groups and were not dependent on IFN-γ stimulation, suggesting a critical role of Tef cell elimination in tolerance induction. We identify potent MMIC activity in hepatic stellate cells and liver sinusoidal endothelial cells. MMIC is unlikely exclusive to the liver, given that spontaneous acceptance of kidney allografts has been reported, although less commonly, probably reflecting variance in MMIC activity. MMIC may represent an important homeostatic mechanism that supports peripheral tolerance and could be a target for the prevention and treatment of transplant rejection. This study highlights that the graft is an active participant in the equipoise between tolerance and rejection and warrants more attention in the search for tolerance biomarkers. © 2015 by the American Association for the Study of Liver Diseases.

Rejection Triggers Liver Transplant Tolerance: Involvements of Mesenchyme-Mediated Immune Control Mechanisms

PubMed Central

Morita, Miwa; Joyce, Daniel; Miller, Charles; Fung, John J.; Lu, Lina; Qian, Shiguang

2015-01-01

Liver tolerance was initially recognized by the spontaneous acceptance of liver allograft in many species. The underlying mechanisms are not completely understood. We have been inspired by an unexpected phenomenon that the liver transplant tolerance absolutely requires interferon (IFN)-γ, a rejection-associated inflammatory cytokine. In this study, we investigate the rejection of liver allografts deficient in IFN-γ receptor and reveal that the liver graft is equipped with machineries capable of counterattacking the host immune response through a mesenchyme-mediated immune control (MMIC) mechanism. MMIC is triggered by T effectors (Tef) cell-derived IFN-γ to drive the expression of B7-H1 on graft mesenchymal cells leading to Tef cell apoptosis. We describe the negative feedback loop between graft mesenchymal and Tef cells that ultimately results in liver transplant tolerance. Comparable elevations of T regulatory cells and myeloid-derived suppressor cells are seen in both rejection and tolerance groups, and are not dependent on IFN-γ stimulation, suggesting a critical role of Tef cell elimination in tolerance induction. We identify potent MMIC activity in hepatic stellate cells and liver sinusoidal endothelial cells. MMIC is unlikely exclusive to the liver, as spontaneous acceptance of kidney allografts has been reported, although less commonly, probably reflecting variance in MMIC activity. MMCI may represent an important homeostatic mechanism that supports peripheral tolerance, and could be a target for the prevention and treatment of transplant rejection. This study highlights that the graft is actively participant in the equipoise between tolerance and rejection and warrants more attention in the search for tolerance biomarkers. PMID:25998530

Respiratory problems in children with esophageal atresia and tracheoesophageal fistula.

PubMed

Porcaro, Federica; Valfré, Laura; Aufiero, Lelia Rotondi; Dall'Oglio, Luigi; De Angelis, Paola; Villani, Alberto; Bagolan, Pietro; Bottero, Sergio; Cutrera, Renato

2017-09-05

Children with congenital esophageal atresia (EA) and tracheoesophageal fistula (TEF) have chronic respiratory symptoms including recurrent pneumonia, wheezing and persistent cough. The aim of this study is to describe the clinical findings of a large group of children with EA and TEF surgically corrected and the instrumental investigation to which they have undergone in order to better understand the patient's needs and harmonize the care. A retrospective data collection was performed on 105 children with EA and TEF followed at Department of Pediatric Medicine of Bambino Gesù Children's Hospital (Rome, Italy) between 2010 and 2015. 69/105 (66%) children reported lower respiratory symptoms with a mean age onset of 2.2 ± 2.5 years and only 63/69 (91%) performed specialist assessment at Respiratory Unit. Recurrent pneumonia (33%) and wheezing (31%) were the most reported symptoms. The first respiratory evaluation was performed after surgically correction of gastroesophageal reflux (GER) at mean age of 3.9 ± 4.2 years. Twenty nine patients have undergone to chest CT with contrast enhancement detecting localized atelectasis (41%), residual tracheal diverticulum (34%), bronchiectasis (31%), tracheal vascular compression (21%), tracheomalacia (17%) and esophageal diverticulum (14%). Fifty three patients have undergone to airways endoscopy detecting tracheomalacia (66%), residual tracheal diverticulum (26%), recurrent tracheoesophageal fistula (19%) and vocal cord paralysis (11%). Our study confirms that respiratory symptoms often complicate EA and TEF; their persistence despite medical and surgical treatment of GER means that other etiological hypothesis must be examined and that a complete respiratory diagnostic work up must be considered.

Effect of theanine and polyphenols enriched fractions from decaffeinated tea dust on the formation of Maillard reaction products and sensory attributes of breads.

PubMed

Culetu, Alina; Fernandez-Gomez, Beatriz; Ullate, Monica; del Castillo, Maria Dolores; Andlauer, Wilfried

2016-04-15

The antiglycoxidative properties of theanine (TEF) and polyphenols enriched fractions (PEF) prepared from tea dust were tested in a model system composed of bovine serum albumin (BSA) and methylglyoxal (MGO). PEF caused a decrease in available free amino groups of BSA in presence and absence of MGO, suggesting the simultaneous occurrence of glycoxidation reaction and phenols-protein interaction. The presence of PEF and TEF inhibited formation of fluorescent advanced glycation end-products (AGEs). Moreover, theanine (TB) and polyphenol-enriched bread (PB) were formulated. A significant increase in free amino groups was observed in TBs with a dose-response effect, while addition of PEF in bread produced a significant decrease (p<0.05). PEF efficiently reduced fluorescent AGE formation in breads compared with TEF. The results are in line with the simplified model systems. PEF used as food ingredient allows obtaining a tasty food possessing health promoting properties and lower content of potential harmful compounds (AGEs). Copyright © 2015 Elsevier Ltd. All rights reserved.

Mutations in Elongation Factor Ef-1α Affect the Frequency of Frameshifting and Amino Acid Misincorporation in Saccharomyces Cerevisiae

PubMed Central

Sandbaken, M. G.; Culbertson, M. R.

1988-01-01

A mutational analysis of the eukaryotic elongation factor EF-1α indicates that this protein functions to limit the frequency of errors during genetic code translation. We found that both amino acid misincorporation and reading frame errors are controlled by EF-1α. In order to examine the function of this protein, the TEF2 gene, which encodes EF-1α in Saccharomyces cerevisiae, was mutagenized in vitro with hydroxylamine. Sixteen independent TEF2 alleles were isolated by their ability to suppress frameshift mutations. DNA sequence analysis identified eight different sites in the EF-1α protein that elevate the frequency of mistranslation when mutated. These sites are located in two different regions of the protein. Amino acid substitutions located in or near the GTP-binding and hydrolysis domain of the protein cause suppression of frameshift and nonsense mutations. These mutations may effect mistranslation by altering the binding or hydrolysis of GTP. Amino acid substitutions located adjacent to a putative aminoacyl-tRNA binding region also suppress frameshift and nonsense mutations. These mutations may alter the binding of aminoacyl-tRNA by EF-1α. The identification of frameshift and nonsense suppressor mutations in EF-1α indicates a role for this protein in limiting amino acid misincorporation and reading frame errors. We suggest that these types of errors are controlled by a common mechanism or closely related mechanisms. PMID:3066688

Using support vector machine to predict eco-environment burden: a case study of Wuhan, Hubei Province, China.

PubMed

Li, Xiang-Mei; Zhou, Jing-Xuan; Yuan, Song-Hu; Zhou, Xin-Ping; Fu, Qiang

2008-02-01

The human socio-economic development depends on the planet's natural capital. Humans have had a considerable impact on the earth, such as resources depression and environment deterioration. The objective of this study was to assess the impact of socio-economic development on the ecological environment of Wuhan, Hubei Province, China, during the general planning period 2006-2020. Support vector machine (SVM) model was constructed to simulate the process of eco-economic system of Wuhan. Socio-economic factors of urban total ecological footprint (TEF) were selected by partial least squares (PLS) and leave-one-out cross validation (LOOCV). Historical data of socio-economic factors as inputs, and corresponding historical data of TEF as target outputs, were presented to identify and validate the SVM model. When predicted input data after 2005 were presented to trained model as generalization sets, TEFs of 2005, 2006,..., till 2020 were simulated as output in succession. Up to 2020, the district would have suffered an accumulative TEF of 28.374 million gha, which was over 1.5 times that of 2004 and nearly 3 times that of 1988. The per capita EF would be up to 3.019 gha in 2020. The simulation indicated that although the increase rate of GDP would be restricted in a lower level during the general planning period, urban ecological environment burden could not respond to the socio-economic circumstances promptly. SVM provides tools for dynamic assessment of regional eco-environment. However, there still exist limitations and disadvantages in the model. We believe that the next logical step in deriving better dynamic models of ecosystem is to integrate SVM and other algorithms or technologies.

Relative effect potency estimates of dioxin-like activity for dioxins, furans, and dioxin-like PCBs in adults based on two thyroid outcomes.

PubMed

Trnovec, Tomáš; Jusko, Todd A; Šovčíková, Eva; Lancz, Kinga; Chovancová, Jana; Patayová, Henrieta; Palkovičová, L'ubica; Drobná, Beata; Langer, Pavel; Van den Berg, Martin; Dedik, Ladislav; Wimmerová, Soňa

2013-08-01

Toxic equivalency factors (TEFs) are an important component in the risk assessment of dioxin-like human exposures. At present, this concept is based mainly on in vivo animal experiments using oral dosage. Consequently, the current human TEFs derived from mammalian experiments are applicable only for exposure situations in which oral ingestion occurs. Nevertheless, these "intake" TEFs are commonly-but incorrectly-used by regulatory authorities to calculate "systemic" toxic equivalents (TEQs) based on human blood and tissue concentrations, which are used as biomarkers for either exposure or effect. We sought to determine relative effect potencies (REPs) for systemic human concentrations of dioxin-like mixture components using thyroid volume or serum free thyroxine (FT4) concentration as the outcomes of interest. We used a benchmark concentration and a regression-based approach to compare the strength of association between each dioxin-like compound and the thyroid end points in 320 adults residing in an organochlorine-polluted area of eastern Slovakia. REPs calculated from thyroid volume and FT4 were similar. The regression coefficient (β)-derived REP data from thyroid volume and FT4 level were correlated with the World Health Organization (WHO) TEF values (Spearman r = 0.69, p = 0.01 and r = 0.62, p = 0.03, respectively). The calculated REPs were mostly within the minimum and maximum values for in vivo REPs derived by other investigators. Our REPs calculated from thyroid end points realistically reflect human exposure scenarios because they are based on chronic, low-dose human exposures and on biomarkers reflecting body burden. Compared with previous results, our REPs suggest higher sensitivity to the effects of dioxin-like compounds.

Complexes of monocationic Group 13 elements with pentaphospha- and pentaarsaferrocene.

PubMed

Fleischmann, Martin; Welsch, Stefan; Krauss, Hannes; Schmidt, Monika; Bodensteiner, Michael; Peresypkina, Eugenia V; Sierka, Marek; Gröger, Christian; Scheer, Manfred

2014-03-24

Reactions of the sandwich complexes [Cp*Fe(η(5)-E5)] (Cp*=η(5)-C5Me5; E=P (1), As (2)) with the monovalent Group 13 metals Tl(+), In(+), and Ga(+) containing the weakly coordinating anion [TEF] ([TEF]=[Al{OC(CF3)3}4](-)) are described. Here, the one-dimensional coordination polymers [M(μ,η(5):η(1 -E5 FeCp*)3]n [TEF]n (E=P, M=Tl (3 a), In (3 b), Ga (3 c); E=As, M=Tl (4 a), In (4 b)) are obtained as sole products in good yields. All products were analyzed by single-crystal X-ray diffraction, revealing a similar assembly of the products with η(5)-bound E5 ligands and very weak σ-interactions between one P or As atom of the ring to the neighbored Group 13 metal cation. By exchanging the [TEF] anion of 4 a for the larger [FAl] anion ([FAl]=[FAl{OC6F10(C6F5)}3](-)), the coordination compound [Tl{(η(5)-As5)FeCp*}3][FAl] (5) without any σ-interactions of the As5-ring is obtained. All products are readily soluble in CH2 Cl2 and exhibit a dynamic coordination behavior in solution, which is supported by NMR spectroscopy and ESI-MS spectrometry as well as by osmometric molecular-weight determination. For a better understanding of the proceeding equilibrium DFT calculations of the cationic complexes were performed for the gas phase and in solution. Furthermore, the (31)P{(1)H} magic-angle spinning (MAS) NMR spectra of 3 a-c are presented and the first crystal structure of the starting material 2 was determined. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The disposal of a lime water treatment residue on soil and spoil material from a coalmine: a glasshouse investigation.

PubMed

Titshall, L W; Hughes, J C; Morris, C D; Zacharias, P J K

2007-01-01

Eragrostis tef (Zucc.), Cenchrus ciliaris L., and Digitaria eriantha Steud. were grown in a soil (Psammentic Haplustalf) and spoil material from a coalmine both treated with a lime water treatment residue (WTR) at rates of 0, 50, 100, 200, and 400 g kg(-1). The yield of the grasses, from the sum of the three harvests, and concentrations of B, Ca, Cu, K, Fe, Mg, Mn, N, Na, P, and Zn in foliage from the second harvest were determined. The yield of grasses grown in the soil decreased exponentially as WTR application increased. The yields of C. ciliaris, D. eriantha, and E. tef (in the 400 g kg(-1) WTR treated soil) decreased by 74.4, 78.7, and 59.8%, respectively, when compared with the control treatments. In the spoil, the yield of E. tef and D. eriantha decreased by 13.6% and and D. eriantha by 23.9%, while an increase was observed for C. ciliaris (45.4%), at the highest WTR application rate. No relationship existed between yield of E. tef and WTR application rate when grown in the spoil, while a weak negative linear relationship (p < 0.05) was found for D. eriantha and a positive linear relationship existed for C. ciliaris. Magnesium concentrations of the grasses were positively correlated to WTR application rate. Grasses grown in the soil had higher Na concentrations, while those grown in the spoil typically had higher B, N, and Zn concentrations. The decreases in yield were attributed to nutrient deficiencies (notably Zn), induced by high WTR application rates that led to high substrate pH. Disposal of high rates of WTR on the mine materials was not recommended.

Maternal hyperthyroidism increases the prevalence of foregut atresias in fetal rats exposed to adriamycin.

PubMed

Fragoso, Ana Catarina; Martinez, Leopoldo; Estevão-Costa, José; Tovar, Juan A

2014-02-01

Gastrointestinal malformations such as esophageal atresia with tracheoesophageal fistula (EA/TEF) and duodenal atresia (DA) have been reported in infants born to hyperthyroid mothers or with congenital hypothyroidism. The present study aimed to test whether maternal thyroid status during embryonic foregut division has any influence on the prevalence of EA/TEF and DA in an accepted rat model of these malformations. Pregnant rats received either vehicle or 1.75 mg/kg i.p. adriamycin on gestational days 7, 8 and 9. Transient maternal hyper or hypothyroidism was induced by oral administration of levothyroxine (LT4, 50 μg/kg/day) or propylthiouracil (PTU, 2 mg/kg/day), respectively, on days 7 to 12 of gestation. Plasma cholesterol, total T3, free T4 and TSH were measured at gestational days 7, 12, and 21. At the end of gestation, the mothers were sacrificed and embryo-fetal mortality was recorded. Fetuses were dissected to determine the prevalence of esophageal and intestinal atresias. At gestational day 12, mothers treated with LT4 or PTU had hyper or hypothyroid status, respectively; plasma cholesterol levels were similar. In the adriamycin-exposed fetuses from hyperthyroid mothers, the embryonal resorption rate and the prevalence of both EA/TEF and DA were significantly higher than in the other groups; maternal hypothyroidism during the same period did not have significant effect on the prevalence of atresias. Maternal hyperthyroidism during the embryonic window corresponding to foregut cleavage increased the prevalence of both EA/TEF and duodenal atresia in fetal rats exposed to adriamycin. This suggests that maternal thyroid hormone status might be involved in the pathogenesis of foregut atresias and invites further research on this likely clinically relevant issue in humans.

Genus-Specific Primers for Study of Fusarium Communities in Field Samples

PubMed Central

Edel-Hermann, Véronique; Gautheron, Nadine; Durling, Mikael Brandström; Kolseth, Anna-Karin; Steinberg, Christian; Persson, Paula; Friberg, Hanna

2015-01-01

Fusarium is a large and diverse genus of fungi of great agricultural and economic importance, containing many plant pathogens and mycotoxin producers. To date, high-throughput sequencing of Fusarium communities has been limited by the lack of genus-specific primers targeting regions with high discriminatory power at the species level. In the present study, we evaluated two Fusarium-specific primer pairs targeting translation elongation factor 1 (TEF1). We also present the new primer pair Fa+7/Ra+6. Mock Fusarium communities reflecting phylogenetic diversity were used to evaluate the accuracy of the primers in reflecting the relative abundance of the species. TEF1 amplicons were subjected to 454 high-throughput sequencing to characterize Fusarium communities. Field samples from soil and wheat kernels were included to test the method on more-complex material. For kernel samples, a single PCR was sufficient, while for soil samples, nested PCR was necessary. The newly developed primer pairs Fa+7/Ra+6 and Fa/Ra accurately reflected Fusarium species composition in mock DNA communities. In field samples, 47 Fusarium operational taxonomic units were identified, with the highest Fusarium diversity in soil. The Fusarium community in soil was dominated by members of the Fusarium incarnatum-Fusarium equiseti species complex, contradicting findings in previous studies. The method was successfully applied to analyze Fusarium communities in soil and plant material and can facilitate further studies of Fusarium ecology. PMID:26519387

Dynamical theory of responsivity and response time of a high temperature superconductor photo-thermoelectrical bolometer

NASA Astrophysics Data System (ADS)

Kaila, M. M.

2002-11-01

Dynamical theory of responsivity and response time for an high temperature superconductor (HTSC) photo-thermoelectrical bolometer is analysed in this paper. There is a thermoelectric feedback (TEF) due to the heat transfer from the sensitive area (HTSC-BiSb thermojunction) towards the cold junction of the thermocouple. This is in addition to the normal electrothermal feedback (ETF) between the detector and the substrate, in a photoelectrical bolometer. The two legs of the thermocouple are connected in a parallel geometry configuration. It is seen that TEF can be used in combination with the ETF to enhance responsivity and response time of the detector.

Blue pigment in Hypocrea caerulescens sp. nov. and two additional new species in sect. Trichoderma

PubMed Central

Jaklitsch, Walter M.; Stadler, Marc; Voglmayr, Hermann

2012-01-01

Three new species of Hypocrea/Trichoderma sect. Trichoderma (Hypocreaceae, Hypocreales, Ascomycota, Fungi) are described from recent collections in southern Europe and the Canary Islands. They have been characterized by morphological and molecular methods, including microscopic examination of the teleomorph in thin sections, the anamorph, growth rate experiments and phylogenetic analyses based on a part of the translation elongation factor 1-alpha encoding gene (tef1) containing the two last introns and a part of the rpb2 gene, encoding the second largest RNA polymerase subunit. Analyses involving tef1 did not unequivocally resolve the sister clade relationship of Hypocrea caerulescens relative to the Koningii and Viride clades, while analyses based on rpb2 clearly suggest a close relationship with the former, although the phenotype of H. caerulescens is similar to H. viridescens, particularly by its warted conidia and a coconut-like odor in CMD culture. Hypocrea hispanica and T. samuelsii however are clearly related to the Viride clade by both phylogenetic markers, despite their morphological similarity to H. koningii and its relatives. An apparently specific blue pigment is formed in CMD cultures by Hypocrea caerulescens but could not be obtained by extraction with organic solvents. PMID:22453122

Clinical porcine islet xenotransplantation under comprehensive regulation.

PubMed

Matsumoto, S; Tan, P; Baker, J; Durbin, K; Tomiya, M; Azuma, K; Doi, M; Elliott, R B

2014-01-01

Xenotransplantation with porcine islets is a promising approach to overcome the shortage of human donors. This is the first report of phase 1/2a xenotransplantation study of encapsulated neonatal porcine islets under the current framework of regulations for xenotransplantation in New Zealand. Newborn piglets were anesthetized and bled, and the pancreata were removed with the use of sterile technique and processed. Encapsulated neonatal porcine islets were implanted with the use of laparoscopy into the peritoneal cavity of 14 patients with unstable type 1 diabetes without any immunosuppressive drugs. The patients received encapsulated islets of 5,000 (n = 4; group 1), 10,000 (n = 4; group 2), 15,000 (n = 4; group 3), or 20,000 (n = 2; group 4) islet equivalents per kg body weight. Outcome was determined from adverse event reports, HbA1c, total daily insulin dose, and frequency of unaware hypoglycemic events. To assess graft function, transplant estimated function (TEF) scores were calculated. Sufficient or marginal numbers of encapsulated neonatal porcine islets were transplanted into streptozotocin-induced diabetic B6 mice as an in vivo functional assay. There were 4 serious adverse events, of which 3 were considered to be possibly related to the procedure. Tests for porcine endogenous retrovirus DNA and RNA were all negative. The numbers of unaware hypoglycemia events were reduced after transplantation in all groups. Four of 14 patients attained HbA1c <7% compared with 1 at baseline. The average TEF scores were 0.17, 0.02, -0.01, and 0.08 in groups 1, 2, 3, and 4 respectively. The in vivo study demonstrated that a sufficient number of the transplanted group reversed diabetes with positive porcine C-peptide. Transplantation of encapsulated neonatal porcine islets was safe and was followed by a reduction in unaware hypoglycemia events in unstable type 1 diabetic patients. The mouse in vivo assessment data demonstrated certain graft function. Copyright © 2014 Elsevier Inc. All rights reserved.

Strategies for the Construction of Supramolecular Dimers versus Homoleptic 1D Coordination Polymers Starting from the Diphosphorus [Cp2Mo2(CO)4(η2‐P2)] Complex and Silver(I) Salts

PubMed Central

Elsayed Moussa, Mehdi; Fleischmann, Martin; Peresypkina, Eugenia V.; Dütsch, Luis; Seidl, Michael; Balázs, Gabor

2017-01-01

The reactions of the tetrahedral diphosphorus [Cp2Mo2(CO)4(η2‐P2)] (1; Cp = C5H5) complex with Ag[Al{OC(CF3)3}4] (AgTEF) (A) and Ag[FAl{OC(C6F5)(C6F10)}3] (AgFAl) (B) were studied. The first reaction led to the formation of the [Ag2(η2‐1)2(η1:η1‐1)2][TEF]2 (2) dimer and the [Ag2(η1:η1‐1)3]n[TEF]2n (3) coordination polymer, whereas the second reaction afforded the [Ag2(η1:η1‐1)2(η1‐CH2Cl2)2(η2‐C7H8)2][FAl]2 (4) or the [Ag2(η2‐1)2(η1:η1‐1)2][FAl]2 (5) dimer and the [Ag2(η1:η1‐1)4]n[FAl]2n (6) coordination polymer. In each case, the products obtained depended on the ratio of the reactants and/or the synthetic procedure. PMID:28943780

Review of esophageal injuries and stenosis: Lessons learn and current concepts of management.

PubMed

Ramareddy, Raghu Sampalli; Alladi, Anand

2016-01-01

To review the patients with esophageal injuries and stenosis with respect to their etiology, clinical course, management, and the lessons learnt from these. Retrospective descriptive observation review of children with esophageal injuries and stenosis admitted between January 2009 and April 2015. Eighteen children with esophageal injuries of varied etiology were managed and included, seven with corrosive injury, five with perforation due to various causes, three with mucosal erosion, two with trachea esophageal fistula (TEF), and one wall erosion. The five children who had perforation were due to poststricture dilatation in a child with esophageal atresia and secondary to foreign body impaction or its attempted retrieval in four. Alkaline button cell had caused TEF in two. Three congenital esophageal stenosis (CES) had presented with dysphagia and respiratory tract infection. Six corrosive stricture and two CES responded to dilatation alone and one each of them required surgery. Four of the children with esophageal perforation were detected early and required drainage procedure (1), diversion (1), and medical management (2). Pseudo diverticulum was managed expectantly. Among TEF, one had spontaneous closure and other one was lost to follow-up. All the remaining nineteen children have recovered well except one CES had mortality. Esophageal injuries though rare can be potentially devastating and life-threatening.

Comparative chronic toxicity of imidacloprid, clothianidin, and thiamethoxam to Chironomus dilutus and estimation of toxic equivalency factors.

PubMed

Cavallaro, Michael C; Morrissey, Christy A; Headley, John V; Peru, Kerry M; Liber, Karsten

2017-02-01

Nontarget aquatic insects are susceptible to chronic neonicotinoid insecticide exposure during the early stages of development from repeated runoff events and prolonged persistence of these chemicals. Investigations on the chronic toxicity of neonicotinoids to aquatic invertebrates have been limited to a few species and under different laboratory conditions that often preclude direct comparisons of the relative toxicity of different compounds. In the present study, full life-cycle toxicity tests using Chironomus dilutus were performed to compare the toxicity of 3 commonly used neonicotinoids: imidacloprid, clothianidin, and thiamethoxam. Test conditions followed a static-renewal exposure protocol in which lethal and sublethal endpoints were assessed on days 14 and 40. Reduced emergence success, advanced emergence timing, and male-biased sex ratios were sensitive responses to low-level neonicotinoid exposure. The 14-d median lethal concentrations for imidacloprid, clothianidin, and thiamethoxam were 1.52 μg/L, 2.41 μg/L, and 23.60 μg/L, respectively. The 40-d median effect concentrations (emergence) for imidacloprid, clothianidin, and thiamethoxam were 0.39 μg/L, 0.28 μg/L, and 4.13 μg/L, respectively. Toxic equivalence relative to imidacloprid was estimated through a 3-point response average of equivalencies calculated at 20%, 50%, and 90% lethal and effect concentrations. Relative to imidacloprid (toxic equivalency factor [TEF] = 1.0), chronic (lethality) 14-d TEFs for clothianidin and thiamethoxam were 1.05 and 0.14, respectively, and chronic (emergence inhibition) 40-d TEFs were 1.62 and 0.11, respectively. These population-relevant endpoints and TEFs suggest that imidacloprid and clothianidin exert comparable chronic toxicity to C. dilutus, whereas thiamethoxam induced comparable effects only at concentrations an order of magnitude higher. However, the authors caution that under field conditions, thiamethoxam readily degrades to clothianidin, thereby likely enhancing toxicity. Environ Toxicol Chem 2017;36:372-382. © 2016 SETAC. © 2016 SETAC.

One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes.

PubMed

Stielow, J B; Lévesque, C A; Seifert, K A; Meyer, W; Iriny, L; Smits, D; Renfurm, R; Verkley, G J M; Groenewald, M; Chaduli, D; Lomascolo, A; Welti, S; Lesage-Meessen, L; Favel, A; Al-Hatmi, A M S; Damm, U; Yilmaz, N; Houbraken, J; Lombard, L; Quaedvlieg, W; Binder, M; Vaas, L A I; Vu, D; Yurkov, A; Begerow, D; Roehl, O; Guerreiro, M; Fonseca, A; Samerpitak, K; van Diepeningen, A D; Dolatabadi, S; Moreno, L F; Casaregola, S; Mallet, S; Jacques, N; Roscini, L; Egidi, E; Bizet, C; Garcia-Hermoso, D; Martín, M P; Deng, S; Groenewald, J Z; Boekhout, T; de Beer, Z W; Barnes, I; Duong, T A; Wingfield, M J; de Hoog, G S; Crous, P W; Lewis, C T; Hambleton, S; Moussa, T A A; Al-Zahrani, H S; Almaghrabi, O A; Louis-Seize, G; Assabgui, R; McCormick, W; Omer, G; Dukik, K; Cardinali, G; Eberhardt, U; de Vries, M; Robert, V

2015-12-01

The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β -tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.

Evaluation of reference genes for gene expression studies in radish (Raphanus sativus L.) using quantitative real-time PCR.

PubMed

Xu, Yuanyuan; Zhu, Xianwen; Gong, Yiqin; Xu, Liang; Wang, Yan; Liu, Liwang

2012-08-03

Real-time quantitative reverse transcription PCR (RT-qPCR) is a rapid and reliable method for gene expression studies. Normalization based on reference genes can increase the reliability of this technique; however, recent studies have shown that almost no single reference gene is universal for all possible experimental conditions. In this study, eight frequently used reference genes were investigated, including Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Actin2/7 (ACT), Tubulin alpha-5 (TUA), Tubulin beta-1 (TUB), 18S ribosomal RNA (18SrRNA), RNA polymerase-II transcription factor (RPII), Elongation factor 1-b (EF-1b) and Translation elongation factor 2 (TEF2). Expression stability of candidate reference genes was examined across 27 radish samples, representing a range of tissue types, cultivars, photoperiodic and vernalization treatments, and developmental stages. The eight genes in these sample pools displayed a wide range of Ct values and were variably expressed. Two statistical software packages, geNorm and NormFinder showed that TEF2, RPII and ACT appeared to be relatively stable and therefore the most suitable for use as reference genes. These results facilitate selection of desirable reference genes for accurate gene expression studies in radish. Copyright © 2012 Elsevier Inc. All rights reserved.

Electrochemical monitoring-on-chip (E-MoC) of HIV-infection in presence of cocaine and therapeutics.

PubMed

Kaushik, Ajeet; Vabbina, Phani Kiran; Atluri, Venkata; Shah, Pratikkumar; Vashist, Arti; Jayant, Rahul Dev; Yandart, Adriana; Nair, Madhavan

2016-12-15

Electrochemical monitoring-on-chip (E-MoC)-based approach for rapid assessment of human immunodeficiency virus (HIV)-infection in the presence of cocaine (Coc) and specific drugs namely i.e., tenofovir (Tef), rimcazole (RA) is demonstrated here, for the first time, using electrochemical impedance spectroscopy (EIS). An in-vitro primary human astrocytes (HA) model was developed using a cultureware chip (CC, used for E-MoC) for HIV-infection, Coc exposure and treatment with anti-HIV drug i.e., Tef, and Coc antagonist i.e., RA. The charge transfer resistance (Rct) value of each CC well varies with respect to infection and treatment demonstrated highly responsive sensitivity of developed chip. The results of E-MoC, a proof-of-the concept, suggested that HIV-infection progression due to Coc ingestion and therapeutic effects of highly specific drugs are measurable on the basis of cell electrophysiology. Though, this work needs various molecular biology-based optimizations to promote this technology as an analytical tool for the rapid assessment of HIV-infection in a patient to manage HIV diseases for timely diagnosis. The presented study is based on using CNS cells and efforts are being made to perform this method using peripheral cells such as monocytes derived dendritic cells. Copyright © 2016 Elsevier B.V. All rights reserved.

Assays of dioxins and dioxin-like compounds in actually contaminated soils using transgenic tobacco plants carrying a recombinant mouse aryl hydrocarbon receptor-mediated β-glucuronidase reporter gene expression system

PubMed Central

Inui, Hideyuki; Gion, Keiko; Utani, Yasushi; Wakai, Taketo; Kodama, Susumu; Eun, Heesoo; Kim, Yun-Seok; Ohkawa, Hideo

2012-01-01

The transgenic tobacco plant XD4V-26 carrying the recombinant mouse aryl hydrocarbon receptor XD4V-mediated β-glucuronidase (GUS) reporter gene expression system was used for assay of dioxins and dioxin-like compounds consisting of polychlorodibenzo-p-dioxins, polychlorinated dibenzofurans, and coplanar polychlorinated biphenyls (Co-PCBs) in actually contaminated soils. The transgenic tobacco plant XD4V-26 showed a significant dose-dependent induced GUS activity when cultured on MS medium containing PCB126 [toxic equivalency factor (TEF) = 0.1]. In contrast, PCB169 and PCB180, which have 0.03 of TEF and unassigned TEF values, respectively, did not significantly induce GUS activity under the same conditions as with PCB126. When the tobacco plants were cultivated for up to 5 weeks on actually contaminated soils with dioxins and dioxin-like compounds collected from the periphery of an incinerator used for disposal of life and industrial wastes, GUS activity in the leaves was dose-dependently increased. The plants clearly detected 360 pg-TEQ g−1 of dioxins and dioxin-like compounds in this assay. There was a positive correlation between GUS activity and TEQ value of dioxins and dioxin-like compounds in the plants. This assay does not require any extraction and purification processes for the actually contaminated soil samples. PMID:22428884

Assays of dioxins and dioxin-like compounds in actually contaminated soils using transgenic tobacco plants carrying a recombinant mouse aryl hydrocarbon receptor-mediated β-glucuronidase reporter gene expression system.

PubMed

Inui, Hideyuki; Gion, Keiko; Utani, Yasushi; Wakai, Taketo; Kodama, Susumu; Eun, Heesoo; Kim, Yun-Seok; Ohkawa, Hideo

2012-01-01

The transgenic tobacco plant XD4V-26 carrying the recombinant mouse aryl hydrocarbon receptor XD4V-mediated β-glucuronidase (GUS) reporter gene expression system was used for assay of dioxins and dioxin-like compounds consisting of polychlorinated dibenzeno-p-dioxins, polychlorinated dibenzofurans, and coplanar polychlorinated biphenyls (Co-PCBs) in actually contaminated soils. The transgenic tobacco plant XD4V-26 showed a significant dose-dependent induced GUS activity when cultured on MS medium containing PCB126 [toxic equivalency factor (TEF) = 0.1]. In contrast, PCB169 and PCB180, which have 0.03 of TEF and unassigned TEF values, respectively, did not significantly induce GUS activity under the same conditions as with PCB126. When the tobacco plants were cultivated for up to 5 weeks on actually contaminated soils with dioxins and dioxin-like compounds collected from the periphery of an incinerator used for disposal of residential and industrial wastes, GUS activity in the leaves was dose-dependently increased. The plants clearly detected 360 pg-TEQ g(-1) of dioxins and dioxin-like compounds in this assay. There was a positive correlation between GUS activity and TEQ value of dioxins and dioxin-like compounds in the plants. This assay does not require any extraction and purification processes for the actually contaminated soil samples.

Assays of dioxins and dioxin-like compounds in actually contaminated soils using transgenic tobacco plants carrying a recombinant mouse aryl hydrocarbon receptor-mediated β-glucuronidase reporter gene expression system.

PubMed

Inui, Hideyuki; Gion, Keiko; Utani, Yasushi; Wakai, Taketo; Kodama, Susumu; Eun, Heesoo; Kim, Yun-Seok; Ohkawa, Hideo

2012-01-01

The transgenic tobacco plant XD4V-26 carrying the recombinant mouse aryl hydrocarbon receptor XD4V-mediated β-glucuronidase (GUS) reporter gene expression system was used for assay of dioxins and dioxin-like compounds consisting of polychlorodibenzo-p-dioxins, polychlorinated dibenzofurans, and coplanar polychlorinated biphenyls (Co-PCBs) in actually contaminated soils. The transgenic tobacco plant XD4V-26 showed a significant dose-dependent induced GUS activity when cultured on MS medium containing PCB126 [toxic equivalency factor (TEF) = 0.1]. In contrast, PCB169 and PCB180, which have 0.03 of TEF and unassigned TEF values, respectively, did not significantly induce GUS activity under the same conditions as with PCB126. When the tobacco plants were cultivated for up to 5 weeks on actually contaminated soils with dioxins and dioxin-like compounds collected from the periphery of an incinerator used for disposal of life and industrial wastes, GUS activity in the leaves was dose-dependently increased. The plants clearly detected 360 pg-TEQ g(-1) of dioxins and dioxin-like compounds in this assay. There was a positive correlation between GUS activity and TEQ value of dioxins and dioxin-like compounds in the plants. This assay does not require any extraction and purification processes for the actually contaminated soil samples.

Integration of different data gap filling techniques to facilitate ...

EPA Pesticide Factsheets

Data gap filling techniques are commonly used to predict hazard in the absence of empirical data. The most established techniques are read-across, trend analysis and quantitative structure-activity relationships (QSARs). Toxic equivalency factors (TEFs) are less frequently used data gap filling techniques which are applied to estimate relative potencies for mixtures of chemicals that contribute to an adverse outcome through a common biological target. For example, The TEF approach has been used for dioxin-like effects comparing individual chemical activity to that of the most toxic dioxin: 2,3,7,8-tetrachlorodibenzo-p-dioxin. The aim of this case study was to determine whether integration of two data gap filling techniques: QSARs and TEFs improved the predictive outcome for the assessment of a set of polychlorinated biphenyl (PCB) congeners and their mixtures. PCBs are associated with many different adverse effects, including their potential for neurotoxicity, which is the endpoint of interest in this study. The dataset comprised 209 PCB congeners, out of which 87 altered in vitro Ca(2+) homeostasis from which neurotoxic equivalency values (NEQs) were derived. The preliminary objective of this case study was to develop a QSAR model to predict NEQ values for the 122 untested PCB congeners. A decision tree model was developed using the number of position specific chlorine substitutions on the biphenyl scaffold as a fingerprint descriptor. Three different positiona

Effects of Dietary Protein Source and Quantity during Weight Loss on Appetite, Energy Expenditure, and Cardio-Metabolic Responses.

PubMed

Li, Jia; Armstrong, Cheryl L H; Campbell, Wayne W

2016-01-26

Higher protein meals increase satiety and the thermic effect of feeding (TEF) in acute settings, but it is unclear whether these effects remain after a person becomes acclimated to energy restriction or a given protein intake. This study assessed the effects of predominant protein source (omnivorous, beef/pork vs. lacto-ovo vegetarian, soy/legume) and quantity (10%, 20%, or 30% of energy from protein) on appetite, energy expenditure, and cardio-metabolic indices during energy restriction (ER) in overweight and obese adults. Subjects were randomly assigned to one protein source and then consumed diets with different quantities of protein (4 weeks each) in a randomized crossover manner. Perceived appetite ratings (free-living and in-lab), TEF, and fasting cardio-metabolic indices were assessed at the end of each 4-week period. Protein source and quantity did not affect TEF, hunger, or desire to eat, other than a modestly higher daily composite fullness rating with 30% vs. 10% protein diet (p = 0.03). While the 20% and 30% protein diets reduced cholesterol, triacylglycerol, and APO-B vs. 10% protein (p < 0.05), protein source did not affect cardio-metabolic indices. In conclusion, diets varying in protein quantity with either beef/pork or soy/legume as the predominant source have minimal effects on appetite control, energy expenditure and cardio-metabolic risk factors during ER-induced weight loss.

Toxicology Education Foundation

MedlinePlus

... public understanding of toxicology through access to objective, science-based information on the safety of chemicals and other agents encountered in daily life. TEF is celebrating our 15th year as an ...

Nanostar probes for tip-enhanced spectroscopy

NASA Astrophysics Data System (ADS)

Kim, Woong; Kim, Nara; Park, Joon Won; Kim, Zee Hwan

2015-12-01

To overcome the current limit of tip-enhanced spectroscopy that is based on metallic nano-probes, we developed a new scanning probe with a metallic nanostar, a nanoparticle with sharp spikes. A Au nanoparticle of 5 nm was first attached to the end of a tip through DNA-DNA hybridization and mechanical pick-up. The nanoparticle was converted to a nanostar with a core diameter of ~70 nm and spike lengths between 50 nm and 80 nm through the reduction of Au3+ with ascorbic acid in the presence of Ag+. Fabrication yields of such tips exceeded 60%, and more than 80% of such tips showed a mechanical durability sufficient for use in scanning microscopy. Effectiveness of the new probes for tip-enhanced Raman scattering (TERS) and tip-enhanced fluorescence (TEF) was confirmed. The probes exhibited the necessary enhancement for TEF, and the tip-on and tip-off ratios varied between 5 and 100. This large tip-to-tip variability may arise from the uncontrolled orientation of the apexes of the spike with respect to the sample surface, which calls for further fabrication improvement. The result overall supports a new fabrication approach for the probe that is effective for tip-enhanced spectroscopy.To overcome the current limit of tip-enhanced spectroscopy that is based on metallic nano-probes, we developed a new scanning probe with a metallic nanostar, a nanoparticle with sharp spikes. A Au nanoparticle of 5 nm was first attached to the end of a tip through DNA-DNA hybridization and mechanical pick-up. The nanoparticle was converted to a nanostar with a core diameter of ~70 nm and spike lengths between 50 nm and 80 nm through the reduction of Au3+ with ascorbic acid in the presence of Ag+. Fabrication yields of such tips exceeded 60%, and more than 80% of such tips showed a mechanical durability sufficient for use in scanning microscopy. Effectiveness of the new probes for tip-enhanced Raman scattering (TERS) and tip-enhanced fluorescence (TEF) was confirmed. The probes exhibited the necessary enhancement for TEF, and the tip-on and tip-off ratios varied between 5 and 100. This large tip-to-tip variability may arise from the uncontrolled orientation of the apexes of the spike with respect to the sample surface, which calls for further fabrication improvement. The result overall supports a new fabrication approach for the probe that is effective for tip-enhanced spectroscopy. Electronic supplementary information (ESI) available: Illustrations of TERS and TEF experiments, information about the TEM images, scheme of surface preparation and peak assignments of TERS spectra. See DOI: 10.1039/c5nr06657c

Challenging surgical dogma in the management of proximal esophageal atresia with distal tracheoesophageal fistula: Outcomes from the Midwest Pediatric Surgery Consortium.

PubMed

Lal, Dave R; Gadepalli, Samir K; Downard, Cynthia D; Ostlie, Daniel J; Minneci, Peter C; Swedler, Ruth M; Chelius, Thomas H; Cassidy, Laura; Rapp, Cooper T; Billmire, Deborah; Bruch, Steven; Burns, R Carland; Deans, Katherine J; Fallat, Mary E; Fraser, Jason D; Grabowski, Julia; Hebel, Ferdynand; Helmrath, Michael A; Hirschl, Ronald B; Kabre, Rashmi; Kohler, Jonathan; Landman, Matthew P; Leys, Charles M; Mak, Grace Z; Raque, Jessica; Rymeski, Beth; Saito, Jacqueline M; St Peter, Shawn D; von Allmen, Daniel; Warner, Brad W; Sato, Thomas T

2017-06-01

Perioperative management of infants with esophageal atresia and tracheoesophageal fistula (EA/TEF) is frequently based on surgeon experience and dogma rather than evidence-based guidelines. This study examines whether commonly perceived important aspects of practice affect outcome in a contemporary multi-institutional cohort of patients undergoing primary repair for the most common type of esophageal atresia anomaly, proximal EA with distal TEF. The Midwest Pediatric Surgery Consortium conducted a multicenter, retrospective study examining selected outcomes on infants diagnosed with proximal EA with distal TEF who underwent primary repair over a 5-year period (2009-2014), with a minimum 1-year follow up, across 11 centers. 292 patients with proximal EA and distal TEF who underwent primary repair were reviewed. The overall mortality was 6% and was significantly associated with the presence of congenital heart disease (OR 4.82, p=0.005). Postoperative complications occurred in 181 (62%) infants, including: anastomotic stricture requiring intervention (n=127; 43%); anastomotic leak (n=54; 18%); recurrent fistula (n=15; 5%); vocal cord paralysis/paresis (n=14; 5%); and esophageal dehiscence (n=5; 2%). Placement of a transanastomotic tube was associated with an increase in esophageal stricture formation (OR 2.2, p=0.01). Acid suppression was not associated with altered rates of stricture, leak or pneumonia (all p>0.1). Placement of interposing prosthetic material between the esophageal and tracheal suture lines was associated with an increased leak rate (OR 4.7, p<0.001), but no difference in the incidence of recurrent fistula (p=0.3). Empiric postoperative antibiotics for >24h were used in 193 patients (66%) with no difference in rates of infection, shock or death when compared to antibiotic use ≤24h (all p>0.3). Hospital volume was not associated with postoperative complication rates (p>0.08). Routine postoperative esophagram obtained on day 5 resulted in no delayed/missed anastomotic leaks or a difference in anastomotic leak rate as compared to esophagrams obtained on day 7. Morbidity after primary repair of proximal EA and distal TEF patients is substantial, and many common practices do not appear to reduce complications. Specifically, this large retrospective series does not support the use of prophylactic antibiotics beyond 24h and empiric acid suppression may not prevent complications. Use of a transanastomotic tube was associated with higher rates of stricture, and interposition of prosthetic material was associated with higher leak rates. Routine postoperative esophagram can be safely obtained on day 5 resulting in earlier initiation of oral feeds. Treatment study. III. Copyright © 2017 Elsevier Inc. All rights reserved.

Relative effect potency estimates of dioxin-like activity for dioxins, furans, and dioxin-like PCBs in adults based on cytochrome P450 1A1 and 1B1 gene expression in blood.

PubMed

Wimmerová, Soňa; van den Berg, Martin; Chovancová, Jana; Patayová, Henrieta; Jusko, Todd A; van Duursen, Majorie B M; Palkovičová Murínová, Ľubica; Canton, Rocio F; van Ede, Karin I; Trnovec, Tomáš

2016-11-01

In the risk assessment of PCDDs, PCDFs, and dioxin-like (DL) PCBs, regulatory authorities support the use of the toxic equivalency factor (TEF)-scheme derived from a heterogeneous data set of the relative effect potency (REPs) estimates. We sought to determine REPs for dioxin-like compounds (DLCs) using expression of cytochrome P450 (CYP) 1A1 and 1B1 mRNA in human peripheral blood mononuclear cells representing two different pathways. We used a sex and age adjusted regression-based approach comparing the strength of association between each DLC and the cytochrome P450 (CYP) 1A1 and 1B1 mRNA expression in 320 adults residing in an organochlorine-polluted area of eastern Slovakia. We calculated REPs based on CYP1A1 expression for 4 PCDDs, 8 PCDFs, and 1 PCB congener, and based on CYP1B1 expression for 5 PCDFs and 11 PCB congeners. REPs from CYP1A1 correlated with REPs previously derived from thyroid volume (ρ=0.85; p<0.001) and serum FT4 (ρ=0.77; p=0.009). The 13 log REPs from CYP1A1 correlated with log WHO-TEFs (r=0.63; p=0.015) and 11 log PCB REPs with PCB consensus toxicity factors (CTFs) for compounds with WHO-TEFs (r=0.80; p=0.003). The complete set of derived 56 log REPs correlated with the log CTFs (r=0.77; p=0.001) and log WHO-TEFs (r=0.81; p<0.001). REPs calculated from thyroid and cytochrome P450 endpoints realistically reflect human exposure scenarios because they are based on human chronic and low-dose exposures. While the CYP 1A1 seems more suitable for toxicity evaluation of PCDD/Fs, the CYP 1B1 is more apt for PCDFs and PCBs and reflects different pathways. Copyright © 2016 Elsevier Ltd. All rights reserved.

Insights into the phylogeny of Northern Hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1-α gene sequences.

PubMed

Klopfenstein, Ned B; Stewart, Jane E; Ota, Yuko; Hanna, John W; Richardson, Bryce A; Ross-Davis, Amy L; Elías-Román, Rubén D; Korhonen, Kari; Keča, Nenad; Iturritxa, Eugenia; Alvarado-Rosales, Dionicio; Solheim, Halvor; Brazee, Nicholas J; Łakomy, Piotr; Cleary, Michelle R; Hasegawa, Eri; Kikuchi, Taisei; Garza-Ocañas, Fortunato; Tsopelas, Panaghiotis; Rigling, Daniel; Prospero, Simone; Tsykun, Tetyana; Bérubé, Jean A; Stefani, Franck O P; Jafarpour, Saeideh; Antonín, Vladimír; Tomšovský, Michal; McDonald, Geral I; Woodward, Stephen; Kim, Mee-Sook

2017-01-01

Armillaria possesses several intriguing characteristics that have inspired wide interest in understanding phylogenetic relationships within and among species of this genus. Nuclear ribosomal DNA sequence-based analyses of Armillaria provide only limited information for phylogenetic studies among widely divergent taxa. More recent studies have shown that translation elongation factor 1-α (tef1) sequences are highly informative for phylogenetic analysis of Armillaria species within diverse global regions. This study used Neighbor-net and coalescence-based Bayesian analyses to examine phylogenetic relationships of newly determined and existing tef1 sequences derived from diverse Armillaria species from across the Northern Hemisphere, with Southern Hemisphere Armillaria species included for reference. Based on the Bayesian analysis of tef1 sequences, Armillaria species from the Northern Hemisphere are generally contained within the following four superclades, which are named according to the specific epithet of the most frequently cited species within the superclade: (i) Socialis/Tabescens (exannulate) superclade including Eurasian A. ectypa, North American A. socialis (A. tabescens), and Eurasian A. socialis (A. tabescens) clades; (ii) Mellea superclade including undescribed annulate North American Armillaria sp. (Mexico) and four separate clades of A. mellea (Europe and Iran, eastern Asia, and two groups from North America); (iii) Gallica superclade including Armillaria Nag E (Japan), multiple clades of A. gallica (Asia and Europe), A. calvescens (eastern North America), A. cepistipes (North America), A. altimontana (western USA), A. nabsnona (North America and Japan), and at least two A. gallica clades (North America); and (iv) Solidipes/Ostoyae superclade including two A. solidipes/ostoyae clades (North America), A. gemina (eastern USA), A. solidipes/ostoyae (Eurasia), A. cepistipes (Europe and Japan), A. sinapina (North America and Japan), and A. borealis (Eurasia) clade 2. Of note is that A. borealis (Eurasia) clade 1 appears basal to the Solidipes/Ostoyae and Gallica superclades. The Neighbor-net analysis showed similar phylogenetic relationships. This study further demonstrates the utility of tef1 for global phylogenetic studies of Armillaria species and provides critical insights into multiple taxonomic issues that warrant further study.

Predictors of post-treatment stenosis in cervical esophageal cancer undergoing high-dose radiotherapy.

PubMed

Kim, Jun Won; Kim, Tae Hyung; Kim, Jie-Hyun; Lee, Ik Jae

2018-02-21

To evaluate toxicity and treatment outcome of high-dose radiotherapy (RT) for cervical esophageal cancer (CEC). We reviewed a total of 62 consecutive patients who received definitive RT for stage I to III cervical esophageal cancer between 2001 and 2015. Patients who received < 45 Gy, treated for lesions below sternal notch, treated with palliative aim, treated with subsequent surgical resection, or diagnosed with synchronous hypopharyngeal cancer were excluded. Treatment failures were divided into local (occurring within the RT field), outfield-esophageal, and regional [occurring in regional lymph node(s)] failures. Factors predictive of esophageal stenosis requiring endoscopic dilation were analyzed. Grade 1, 2, and 3 esophagitis occurred in 19 (30.6%), 39 (62.9%), and 4 patients (6.5%), respectively, without grade ≥ 4 toxicities. Sixteen patients (25.8%) developed post-RT stenosis, of which 7 cases (43.8%) were malignant. Four patients (6.5%) developed tracheoesophageal fistula (TEF), of which 3 (75%) cases were malignant. Factors significantly correlated with post-RT stenosis were stage T3/4 ( P = 0.001), complete circumference involvement ( P < 0.0001), stenosis at diagnosis ( P = 0.024), and endoscopic complete response ( P = 0.017) in univariate analysis, while complete circumference involvement was significant in multivariate analysis ( P = 0.003). A higher dose (≥ 60 Gy) was not associated with occurrence of post-RT stenosis or TEF. With a median follow-up of 24.3 (range, 3.4-152) mo, the 2 y local control, outfield esophageal control, progression-free survival, and overall survival (OS) rates were 78.9%, 90.2%, 49.6%, and 57.3%, respectively. Factors significantly correlated with OS were complete circumference involvement ( P = 0.023), stenosis at diagnosis ( P < 0.0001), and occurrence of post-RT stenosis or TEF ( P < 0.001) in univariate analysis, while stenosis at diagnosis ( P = 0.004) and occurrence of post-RT stenosis or TEF ( P = 0.023) were significant in multivariate analysis. Chemoradiation for CEC was well tolerated, and a higher dose was not associated with stenosis. Patients with complete circumferential involvement require close follow-up.

Molecular Diversity of Seed-borne Fusarium Species Associated with Maize in India

PubMed Central

Aiyaz, Mohammed; Divakara, Shetty Thimmappa; Mudili, Venkataramana; Moore, Geromy George; Gupta, Vijai Kumar; Yli-Mattila, Tapani; Nayaka, Siddaiah Chandra; Niranjana, Siddapura Ramachandrappa

2016-01-01

A total of 106 maize seed samples were collected from different agro-climatic regions of India. Sixty-two Fusarium isolates were recovered, 90% of which were identified as Fusarium verticillioides based on morphological and molecular characters. Use of the tef-1α gene corrected/refined the morphological species identifications of 11 isolates, and confirmed those of the remaining isolates. Genetic diversity among the Fusarium isolates involved multilocus fingerprinting profiles by Inter Simple Sequence Repeats (ISSR) UPGMA and tef-1α gene phenetic analyses; for which, we observed no significant differences among the isolates based on geographic origin or fumonisin production; most of the subdivision related to species. Genotyping was performed on the F. verticillioides isolates, using 12 primer sets from the fumonisin pathway, to elucidate the molec-ular basis of fumonisin production or non-production. One fumonisin-negative isolate, UOMMF-16, was unable to amplify nine of the 12 fumonisin cluster genes tested. We also used the CD-ELISA method to confirm fumonisin production for our 62 Fusarium isolates. Only 15 isolates were found to be fumonisin-negative. Interestingly, genotypic characterization re-vealed six isolates with various gene deletion patterns that also tested positive for the production of fumonisins via CD-ELISA. Our findings confirm the importance of molecular studies for species delimitation, and for observing genetic and phenotypic diversity, among the Fusaria. PMID:27226769

Systematics of Hypocrea citrina and related taxa

PubMed Central

Overton, Barrie E.; Stewart, Elwin L.; Geiser, David M.; Jaklitsch, Walter M.

2006-01-01

Morphological studies and phylogenetic analyses of DNA sequences from three genomic regions – the internal transcribed spacer (ITS) regions of the nuclear ribosomal gene repeat, a partial sequence of RNA polymerase II subunit (rpb2), and a partial sequence of translation elongation factor (tef1) – were used to investigate the systematics of Hypocrea citrina and related species. A neotype specimen is designated for H. citrina that conforms to Persoon's description of a yellow effuse fungus occurring on leaf litter. Historical information and results obtained in this study provide the foundation for selection of a lectotype specimen from Fries's herbarium for H. lactea. The results indicate that (1) Hypocrea citrina and H. pulvinata are distinct species; (2) H. lactea sensu Fries is a synonym of the older name H. citrina; (3) H. pulvinata, H. protopulvinata, and H. americana are phylogenetically distinct species that form a well-supported polyporicolous clade; (4) H. citrina is situated in a clade closely related to H. pulvinata; and (5) H. microcitrina and H. pseudostraminea reside in a highly supported clade phylogenetically distinct from H. citrina. Hypocrea protopulvinata, H. microcitrina, H. megalocitrina, H. pseudostraminea, and a new species, H. aurantiistroma, are reported and described from North America. Variation in rpb2 and tef1 gene sequences suggests geographical subgroupings between European and North American isolates of H. pulvinata. The phylogenies inferred from ITS, rpb2, and tef1 gene sequences are concordant. Hypocrea citrina var. americana is elevated to species status, Hypocrea americana. PMID:18490988

Genetics Home Reference: esophageal atresia/tracheoesophageal fistula

MedlinePlus

... are some genetic conditions more common in particular ethnic groups? Genetic Changes Isolated EA/TEF is considered to be a multifactorial condition, which means that multiple gene variations and environmental factors likely contribute to its occurrence. ...

Variation in PAH patterns in road runoff.

PubMed

Aryal, Rupak; Furumai, Hiroaki; Nakajima, Fumiyuki; Beecham, Simon

2013-01-01

Twelve particle-bound polycyclic aromatic hydrocarbons (PAHs) were measured in the first flush regime of road runoff during nine events in Winterthur in Switzerland. The total PAH contents ranged from 17 to 62 μg/g. The PAH patterns measured at different time intervals during the first flush periods were very similar within each event irrespective of variation in suspended solids (SS) concentration within the first flush regime. However, the PAH patterns were different from event to event. This indicates that the environment plays an important role in PAH accumulation in SS. A toxicity identification evaluation approach using a toxicity equivalency factor (TEF) was applied to compare toxicities in the different events. The TEFs were found to be between 8 and 33 μg TEQ g(-1) (TEQ: toxic equivalent concentration). In some cases, two events having similar total PAH contents showed two fold toxicity differences.

Molecular phylogeny and a new Iranian species of Caudospora (Sydowiellaceae, Diaporthales).

PubMed

Voglmayr, Hermann; Mehrabi, Mehdi

2018-05-02

For the first time, molecular phylogenetic data on the peculiar diaporthalean genus Caudospora are available. Macro- and microscopic morphology and phylogenetic multilocus analyses of partial nuc SSU-ITS-LSU rDNA, cal , ms204 , rpb1 , rpb2 , tef1 and tub2 sequences revealed two distinct species of Caudospora , which are described and illustrated by light and scanning electron microscopy. Caudospora iranica is described as a new species from corticated dead twigs of Quercus sp. collected in Iran. It differs from the generic type, C. taleola , mainly by coarsely verrucose ascospores. The asexual morph of C. taleola on natural substrate is described and illustrated. Caudospora taleola is neotypified, and it is recorded from Iran for the first time. Phylogenetic analyses of a multigene matrix containing a representative selection of Diaporthales from four loci (ITS, LSU rDNA, rpb2 and tef1 ) revealed a placement of Caudospora within Sydowiellaceae.

Predictive factors for complications in children with esophageal atresia and tracheoesophageal fistula.

PubMed

Shah, R; Varjavandi, V; Krishnan, U

2015-04-01

The objective of this study was to describe the incidence of complications in children with esophageal atresia (EA) with or without tracheoesophageal fistula (TEF) at a tertiary pediatric hospital and to identify predictive factors for their occurrence. A retrospective chart review of 110 patients born in or transferred to Sydney Children's Hospital with EA/TEF between January 1999 and December 2010 was done. Univariate and multivariate regression analyses were performed to identify predictive factors for the occurrence of complications in these children. From univariate analysis, early esophageal stricture formation was more likely in children with 'long-gap' EA (odds ratio [OR] = 16.32). Patients with early strictures were more likely to develop chest infections (OR = 3.33). Patients with severe tracheomalacia were more likely to experience 'cyanotic/dying' (OR = 180) and undergo aortopexy (OR = 549). Patients who had gastroesophageal reflux disease were significantly more likely to require fundoplication (OR = 10.83) and undergo aortopexy (OR = 6.417). From multivariate analysis, 'long-gap' EA was a significant predictive factor for late esophageal stricture formation (P = 0.007) and for gastrostomy insertion (P = 0.001). Reflux was a significant predictive factor for requiring fundoplication (P = 0.007) and gastrostomy (P = 0.002). Gastrostomy insertion (P = 0.000) was a significant predictive factor for undergoing fundoplication. Having a prior fundoplication (P = 0.001) was a significant predictive factor for undergoing a subsequent aortopexy. Predictive factors for the occurrence of complications post EA/TEF repair were identified in this large single centre pediatric study. © 2014 International Society for Diseases of the Esophagus.

Selection and Validation of Reference Genes for Quantitative Real-Time Polymerase Chain Reaction Studies in Mossy Maze Polypore, Cerrena unicolor (Higher Basidiomycetes).

PubMed

Yang, Jie; Lin, Qi; Lin, Juan; Ye, Xiuyun

2016-01-01

With its ability to produce ligninolytic enzymes such as laccases, white-rot basidiomycete Cerrena unicolor, a medicinal mushroom, has great potential in biotechnology. Elucidation of the expression profiles of genes encoding ligninolytic enzymes are important for increasing their production. Quantitative real-time polymerase chain reaction (qPCR) is a powerful tool to study transcriptional regulation of genes of interest. To ensure accuracy and reliability of qPCR analysis of C. unicolor, expression levels of seven candidate reference genes were studied at different growth phases, under various induction conditions, and with a range of carbon/nitrogen ratios and carbon and nitrogen sources. The stability of the genes were analyzed with five statistical approaches, namely geNorm, NormFinder, BestKeeper, the ΔCt method, and RefFinder. Our results indicated that the selection of reference genes varied with sample sets. A combination of four reference genes (Cyt-c, ATP6, TEF1, and β-tubulin) were recommended for normalizing gene expression at different growth phases. GAPDH and Cyt-c were the appropriate reference genes under different induction conditions. ATP6 and TEF1 were most stable in fermentation media with various carbon/nitrogen ratios. In the fermentation media with various carbon or nitrogen sources, 18S rRNA and GAPDH were the references of choice. The present study represents the first validation analysis of reference genes in C. unicolor and serves as a foundation for its qPCR analysis.

TEF Bibliography

Science.gov Websites

] Cervero, Robert; Kockelman, Kara. (1997). "Travel demand and the 3Ds: Density, diversity, and design efficient design of sustainable goods and services." The International Journal of Life Cycle Assessment . Upper Saddle River, NJ: FT Press. [202] Das, Sujit. (2004). "A Comparative Assessment of

Extent and Determinants of Thermogenic Responses to 24 Hours of Fasting, Energy Balance, and Five Different Overfeeding Diets in Humans

PubMed Central

Pannacciulli, Nicola; Bonfiglio, Susan; Pacak, Karel; Krakoff, Jonathan

2013-01-01

Context: Individual variation in the ability to convert excess calories to heat and the effects of dietary macronutrient composition are unclear. Objective: Stability and determinants of the energy expenditure (EE) response to overconsumption were assessed. Design, Setting, and Participants: Twenty subjects (75% male) with normal glucose regulation were evaluated during 24 hours each of energy balance, fasting, and 5 different diets with 200% energy requirements in a clinical research unit. Interventions: Five 1-day overfeeding diets were given in random order: high carbohydrate (75%) and low protein (3%); high carbohydrate and normal protein (20%); high fat (46%) and low protein; high fat (60%) and normal protein; and balanced (50% carbohydrates, 20% protein). Main Outcome Measures: The 24-hour EE, sleeping EE, and thermic effect of food (TEF) during each diet were measured with a metabolic chamber. Appetitive hormones were measured before and after the diets. Results: The EE response to overfeeding exhibited good intraindividual reproducibility. Similar increases above eucaloric feeding in 24-hour EE (mean 10.7 ± 5.7%, P < .001; range 2.9–18.8%) and sleeping EE (14.4 ± 11.3%, P < .001; range 1.0–45.1%) occurred when overfeeding diets containing 20% protein, despite differences in fat and carbohydrate content, but the EE response during overfeeding diets containing 3% protein was attenuated. The percent body fat negatively correlated with TEF during normal protein overfeeding (r = −0.53, P < .01). Fasting peptide YY negatively correlated with TEF (r = −0.56, P < .01) and the increase in sleeping EE (r = −0.54, P < .01) during overfeeding. Conclusions: There is an intrinsic EE response to overfeeding that negatively associates with adiposity, although it represents a small percentage of consumed calories. PMID:23666976

Do 16 Polycyclic Aromatic Hydrocarbons Represent PAH Air Toxicity?

PubMed Central

Samburova, Vera; Zielinska, Barbara; Khlystov, Andrey

2017-01-01

Estimation of carcinogenic potency based on analysis of 16 polycyclic aromatic hydrocarbons (PAHs) ranked by U.S. Environmental Protection Agency (EPA) is the most popular approach within scientific and environmental air quality management communities. The majority of PAH monitoring projects have been focused on particle-bound PAHs, ignoring the contribution of gas-phase PAHs to the toxicity of PAH mixtures in air samples. In this study, we analyzed the results of 13 projects in which 88 PAHs in both gas and particle phases were collected from different sources (biomass burning, mining operation, and vehicle emissions), as well as in urban air. The aim was to investigate whether 16 particle-bound U.S. EPA priority PAHs adequately represented health risks of inhalation exposure to atmospheric PAH mixtures. PAH concentrations were converted to benzo(a)pyrene-equivalent (BaPeq) toxicity using the toxic equivalency factor (TEF) approach. TEFs of PAH compounds for which such data is not available were estimated using TEFs of close isomers. Total BaPeq toxicities (∑88BaPeq) of gas- and particle-phase PAHs were compared with BaPeq toxicities calculated for the 16 particle-phase EPA PAH (∑16EPABaPeq). The results showed that 16 EPA particle-bound PAHs underrepresented the carcinogenic potency on average by 85.6% relative to the total (gas and particle) BaPeq toxicity of 88 PAHs. Gas-phase PAHs, like methylnaphthalenes, may contribute up to 30% of ∑88BaPeq. Accounting for other individual non-EPA PAHs (i.e., benzo(e)pyrene) and gas-phase PAHs (i.e., naphthalene, 1- and 2-methylnaphthalene) will make the risk assessment of PAH-containing air samples significantly more accurate. PMID:29051449

Dynamics and control of sister kinetochore behavior during the meiotic divisions in Drosophila spermatocytes

PubMed Central

2018-01-01

Sister kinetochores are connected to the same spindle pole during meiosis I and to opposite poles during meiosis II. The molecular mechanisms controlling the distinct behavior of sister kinetochores during the two meiotic divisions are poorly understood. To study kinetochore behavior during meiosis, we have optimized time lapse imaging with Drosophila spermatocytes, enabling kinetochore tracking with high temporal and spatial resolution through both meiotic divisions. The correct bipolar orientation of chromosomes within the spindle proceeds rapidly during both divisions. Stable bi-orientation of the last chromosome is achieved within ten minutes after the onset of kinetochore-microtubule interactions. Our analyses of mnm and tef mutants, where univalents instead of bivalents are present during meiosis I, indicate that the high efficiency of normal bi-orientation depends on pronounced stabilization of kinetochore attachments to spindle microtubules by the mechanical tension generated by spindle forces upon bi-orientation. Except for occasional brief separation episodes, sister kinetochores are so closely associated that they cannot be resolved individually by light microscopy during meiosis I, interkinesis and at the start of meiosis II. Permanent evident separation of sister kinetochores during M II depends on spindle forces resulting from bi-orientation. In mnm and tef mutants, sister kinetochore separation can be observed already during meiosis I in bi-oriented univalents. Interestingly, however, this sister kinetochore separation is delayed until the metaphase to anaphase transition and depends on the Fzy/Cdc20 activator of the anaphase-promoting complex/cyclosome. We propose that univalent bi-orientation in mnm and tef mutants exposes a release of sister kinetochore conjunction that occurs also during normal meiosis I in preparation for bi-orientation of dyads during meiosis II. PMID:29734336

Low-protein diet induces, whereas high-protein diet reduces hepatic FGF21 production in mice, but glucose and not amino acids up-regulate FGF21 in cultured hepatocytes.

PubMed

Chalvon-Demersay, Tristan; Even, Patrick C; Tomé, Daniel; Chaumontet, Catherine; Piedcoq, Julien; Gaudichon, Claire; Azzout-Marniche, Dalila

2016-10-01

Fibroblast growth factor 21 (FGF21) is a polypeptide secreted by the liver and involved in several metabolic processes such as thermogenesis and lipid oxidation. The nutritional mechanisms controlling FGF21 production are poorly understood. This study aimed to investigate how dietary carbohydrates and proteins impact FGF21 production and how in turn, FGF21 is involved in the metabolic adaptation to changes in the carbohydrate and protein contents of the diet. For that purpose, we fed 25 male C57BL/6 mice diets composed of different protein and carbohydrate contents (normal-protein and carbohydrate diet (N=9, NPNC), low-protein high-carbohydrate diet (N=8, LPHC), high-protein low-carbohydrate diet (N=8, HPLC) for 3 weeks. We measured liver Fgf21 gene expression, synthesis and secretion as well as different parameters related to energy and glucose metabolism. We also investigated the direct role of amino acids and glucose in the control of Fgf21 gene expression in hepatocyte primary cultures (n=6). In vivo, FGF21 responds acutely to LPHC intake whereas under an HPLC diet, plasma FGF21 circulating levels are low in the fasted and refed states. In hepatocytes, Fgf21 expression was controlled by glucose but not amino acids. Both diets increased the thermic effect of feeding (TEF) and ketogenesis was increased in fasted HPLC mice. The results presented suggest that dietary glucose, rather than amino acids, directly controls FGF21 secretion, and that FGF21 may be involved in the increased TEF response to LPHC. The effects of the HPLC diet on ketogenesis and TEF are probably controlled by other metabolic pathways. Copyright © 2016 Elsevier Inc. All rights reserved.

Do 16 Polycyclic Aromatic Hydrocarbons Represent PAH Air Toxicity?

PubMed

Samburova, Vera; Zielinska, Barbara; Khlystov, Andrey

2017-08-15

Estimation of carcinogenic potency based on analysis of 16 polycyclic aromatic hydrocarbons (PAHs) ranked by U.S. Environmental Protection Agency (EPA) is the most popular approach within scientific and environmental air quality management communities. The majority of PAH monitoring projects have been focused on particle-bound PAHs, ignoring the contribution of gas-phase PAHs to the toxicity of PAH mixtures in air samples. In this study, we analyzed the results of 13 projects in which 88 PAHs in both gas and particle phases were collected from different sources (biomass burning, mining operation, and vehicle emissions), as well as in urban air. The aim was to investigate whether 16 particle-bound U.S. EPA priority PAHs adequately represented health risks of inhalation exposure to atmospheric PAH mixtures. PAH concentrations were converted to benzo(a)pyrene-equivalent (BaPeq) toxicity using the toxic equivalency factor (TEF) approach. TEFs of PAH compounds for which such data is not available were estimated using TEFs of close isomers. Total BaPeq toxicities (∑ 88 BaPeq) of gas- and particle-phase PAHs were compared with BaPeq toxicities calculated for the 16 particle-phase EPA PAH (∑ 16EPA BaPeq). The results showed that 16 EPA particle-bound PAHs underrepresented the carcinogenic potency on average by 85.6% relative to the total (gas and particle) BaPeq toxicity of 88 PAHs. Gas-phase PAHs, like methylnaphthalenes, may contribute up to 30% of ∑ 88 BaPeq. Accounting for other individual non-EPA PAHs (i.e., benzo(e)pyrene) and gas-phase PAHs (i.e., naphthalene, 1- and 2-methylnaphthalene) will make the risk assessment of PAH-containing air samples significantly more accurate.

Transportation Energy Futures (TEF) Data and Sources

Science.gov Websites

|agency|4-d|gis|geographic information systems?|municipal|neighborhood|urban density|municipal |carsharing|marketing|real-time|traffic information|eco-driving|idle)$ ^(vmt|vehicle miles traveled|reduction drive|eco-driving|congestion|commute|telework|alternative work|parking|real-time|traffic information

Biodiversity of Trichoderma (Hypocreaceae) in Southern Europe and Macaronesia

PubMed Central

Jaklitsch, W.M.; Voglmayr, H.

2015-01-01

The first large-scale survey of sexual and asexual Trichoderma morphs collected from plant and fungal materials conducted in Southern Europe and Macaronesia including a few collections from French islands east of Africa yielded more than 650 specimens identified to the species level. Routine sequencing of tef1 revealed a genetic variation among these isolates that exceeds previous experience and ca. 90 species were recognized, of which 74 are named and 17 species newly described. Aphysiostroma stercorarium is combined in Trichoderma. For the first time a sexual morph is described for T. hamatum. The hitherto most complete phylogenetic tree is presented for the entire genus Trichoderma, based on rpb2 sequences. For the first time also a genus-wide phylogenetic tree based on acl1 sequences is shown. Detailed phylogenetic analyses using tef1 sequences are presented in four separate trees representing major clades of Trichoderma. Discussions involve species composition of clades and ecological and biogeographic considerations including distribution of species. PMID:26955191

Morphological and molecular characterization of Cladosporium cladosporioides species complex causing pecan tree leaf spot.

PubMed

Walker, C; Muniz, M F B; Rolim, J M; Martins, R R O; Rosenthal, V C; Maciel, C G; Mezzomo, R; Reiniger, L R S

2016-09-16

The objective of this study was to characterize species of the Cladosporium cladosporioides complex isolated from pecan trees (Carya illinoinensis) with symptoms of leaf spot, based on morphological and molecular approaches. Morphological attributes were assessed using monosporic cultures on potato dextrose agar medium, which were examined for mycelial growth, sporulation, color, and conidia and ramoconidia size. Molecular characterization comprised isolation of DNA and subsequent amplification of the translation elongation factor 1α (TEF-1α) region. Three species of the C. cladosporioides complex were identified: C. cladosporioides, Cladosporium pseudocladosporioides, and Cladosporium subuliforme. Sporulation was the most important characteristic differentiating species of this genus. However, morphological features must be considered together with molecular analysis, as certain characters are indistinguishable between species. TEF-1αcan be effectively used to identify and group isolates belonging to the C. cladosporioides complex. The present study provides an important example of a methodology to ascertain similarity between isolates of this complex causing leaf spot in pecan trees, which should facilitate future pathogenicity studies.

Cantharellus violaceovinosus, a new species from tropical Quercus forests in eastern Mexico

PubMed Central

Herrera, Mariana; Bandala, Victor M.; Montoya, Leticia

2018-01-01

Abstract During explorations of tropical oak forests in central Veracruz (eastern Mexico), the authors discovered a Cantharellus species that produces basidiomes with strikingly violet pileus and a hymenium with yellow, raised gill-like folds. It is harvested locally and valued as a prized edible wild mushroom. Systematic multiyear sampling of basidiomes allowed the recording of the morphological variation exhibited by fresh fruit bodies in different growth stages, which supports the recognition of this Cantharellus species from others in the genus. Two molecular phylogenetic analyses based on a set of sequences of species of all major clades in Cantharellus, one including sequences of the transcription elongation factor 1-alpha (tef-1α) and a combined tef-1α and nLSU region (the large subunit of the ribosome), confirm the isolated position of the new species in a clade close to C. lewisii from USA, in the subgenus Cantharellus. Detailed macroscopic and microscopic descriptions, accompanied by illustrations and a taxonomic discussion are presented. PMID:29681739

Cantharellus violaceovinosus, a new species from tropical Quercus forests in eastern Mexico.

PubMed

Herrera, Mariana; Bandala, Victor M; Montoya, Leticia

2018-01-01

During explorations of tropical oak forests in central Veracruz (eastern Mexico), the authors discovered a Cantharellus species that produces basidiomes with strikingly violet pileus and a hymenium with yellow, raised gill-like folds. It is harvested locally and valued as a prized edible wild mushroom. Systematic multiyear sampling of basidiomes allowed the recording of the morphological variation exhibited by fresh fruit bodies in different growth stages, which supports the recognition of this Cantharellus species from others in the genus. Two molecular phylogenetic analyses based on a set of sequences of species of all major clades in Cantharellus , one including sequences of the transcription elongation factor 1-alpha (tef-1α) and a combined tef-1α and nLSU region (the large subunit of the ribosome), confirm the isolated position of the new species in a clade close to C. lewisii from USA, in the subgenus Cantharellus. Detailed macroscopic and microscopic descriptions, accompanied by illustrations and a taxonomic discussion are presented.

Transportation Energy Futures: Combining Strategies for Deep Reductions in Energy Consumption and GHG Emissions (Brochure)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2013-03-01

This fact sheet summarizes actions in the areas of light-duty vehicle, non-light-duty vehicle, fuel, and transportation demand that show promise for deep reductions in energy use. Energy efficient transportation strategies have the potential to simultaneously reduce oil consumption and greenhouse gas (GHG) emissions. The Transportation Energy Futures (TEF) project examined how the combination of multiple strategies could achieve deep reductions in GHG emissions and petroleum use on the order of 80%. Led by NREL, in collaboration with Argonne National Laboratory, the project's primary goal was to help inform domestic decisions about transportation energy strategies, priorities, and investments, with an emphasismore » on underexplored opportunities. TEF findings reveal three strategies with the potential to displace most transportation-related petroleum use and GHG emissions: 1) Stabilizing energy use in the transportation sector through efficiency and demand-side approaches. 2) Using additional advanced biofuels. 3) Expanding electric drivetrain technologies.« less

A taxonomic and phylogenetic re-appraisal of the genus Curvularia

USDA-ARS?s Scientific Manuscript database

Species of Curvularia are important plant and human pathogens worldwide. In this study, the genus Curvularia is re-assessed based on molecular phylogenetic analysis and morphological observations of available isolates and specimens. A multi-gene phylogenetic tree inferred from ITS, TEF and GPDH gene...

Trichoderma asperellum reconsidered: two cryptic species

USDA-ARS?s Scientific Manuscript database

Analysis of a world-wide collection of strains of Trichoderma asperellum using multilocus genealogies of four genomic regions (tef1, rbp2, act, ITS1, 2, 5.8s), sequence polymorphism-derived (SPD) markers, matrix-assisted laser desorption/ionisation–time of flight mass spectrometry (MALDI-TOF MS) of ...

Occultocarpon, a new monotypic genus of Gnomoniaceae on Alnus nepalensis from China

USDA-ARS?s Scientific Manuscript database

A new monotypic genus Occultocarpon and its species, O. ailaoshanense, was discovered on the bark of branches of Alnus nepalensis (Betulaceae) in Yunnan, China. A phylogeny based on three genes (LSU, rpb2, tef1-a) reveals that O. ailaoshanense belongs to the Gnomoniaceae (Diaporthales, Ascomycetes) ...

Insecticide seed treatments for sugarbeet

USDA-ARS?s Scientific Manuscript database

Pest feeding and vectoring of viruses cause serious problems in sugarbeet production worldwide. In order to ameliorate pest and disease problems on sugarbeet, two seed treatments, Poncho Beta (60 g a.i. clothianidin + 8 g a.i. beta-cyfluthrin/100,000 seed) and Cruiser Tef (60 g a.i. thiamethoxam + 8...

Yorkie and Scalloped: partners in growth activation.

PubMed

Bandura, Jennifer L; Edgar, Bruce A

2008-03-01

The Hippo (Hpo) signaling pathway limits organ growth in organisms from Drosophila to mammals by suppressing the activity of the transcriptional coactivator Yorkie (Yki)/YAP. The TEAD/TEF factor Scalloped (Sd) has been identified as the first known transcription factor to partner with Yki as a downstream target of Hpo signaling.

Where Do We Go from Here?

ERIC Educational Resources Information Center

Raban, Colin; Cairns, David

2015-01-01

In June 2015, the Higher Education Funding Council for England (HEFCE) proposed a lighter touch quality assessment regime that would place greater reliance on institutions' own governance arrangements. In July 2015 the Minister for Higher Education announced a Teaching Excellence Framework (TEF) parts of which appear inconsistent with HEFCE's…

A class-wide phylogenetic assessment of Dothideomycetes

USDA-ARS?s Scientific Manuscript database

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 355 isolates and 41 families (6 newly described in this volume) in Dothideomycetes. All currently accepted orders in the class is represented for the first time. Subclass Pleosporomycetidae is ex...

Taxonomy and phylogeny of Pluteus glaucotinctus sensu lato (Agaricales, Basidiomycota), a multicontinental species complex

Treesearch

Nelson Menolli; Alfredo Justo; Pedro Arrillaga; C.K. Pradeep; Andrew M. Minnis; Marina Capelari

2014-01-01

In order to better understand species delimitation in the Pluteus glaucotinctus species complex, we present a detailed study based on morphological and DNA sequence (nrITS + tef1) data. Pluteus glaucotinctus sensu stricto is known only from the type collection (Democratic Republic of the Congo), which is re-...

Molecular diversity of seed-borne Fusarium species associated with maize in India

USDA-ARS?s Scientific Manuscript database

A total of 62 Fusarium isolates were recovered from 106 maize seeds sampled across 13 states in India, 90% of which were identified as F. verticillioides. Our study included (1) species confirmation through PCR assay using the tef-1a gene, (2) a fumonisin cluster genotype assay using developed multi...

Seed treatments for the control of insects and diseases in sugarbeet

USDA-ARS?s Scientific Manuscript database

Insect feeding and vectoring of viruses cause serious problems in sugarbeet production worldwide. In order to ameliorate insect and disease problems on sugarbeet, two seed treatments, Poncho Beta (60 g a.i. clothianidin + 8 g a.i. beta-cyfluthrin/100,000 seed) and Cruiser Tef (60 g a.i. thiamethoxa...

Integration of different data gap filling techniques to facilitate assessment of polychlorinated biphenyls: A proof of principle case study (ASCCT meeting)

EPA Science Inventory

Data gap filling techniques are commonly used to predict hazard in the absence of empirical data. The most established techniques are read-across, trend analysis and quantitative structure-activity relationships (QSARs). Toxic equivalency factors (TEFs) are less frequently used d...

The Teaching Excellence Framework: Would You Tell Me, Please, Which Way I Ought to Go from Here

ERIC Educational Resources Information Center

Berger, Dan; Wild, Charles

2016-01-01

The UK government's Green Paper, "Fulfilling Our Potential: Teaching Excellence, Social Mobility and Student Choice", presents both significant challenges and opportunities for universities. Whilst the quantitative element of the proposed Teaching Excellence Framework (TEF), underpinned by Big Data, offers the tantalizing opportunity to…

76 FR 787 - Notice of Availability of the Recommended Toxicity Equivalence Factors (TEFs) for Human Health...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-06

... manufacturing, combustion, and metal processing. There is global contamination of air, soil and water with trace... food chain, and accumulate in the tissues of animals. Human exposures to these compounds occur primarily through eating contaminated foods. The health effects from exposures to dioxins and DLCs have been...

Emissions of EC, OC, and PAHs from cottonseed oil biodiesel in a heavy-duty diesel engine.

PubMed

Song, Wei W; He, Ke B; Wang, Jian X; Wang, Xin T; Shi, Xiao Y; Yu, Chao; Chen, Wen M; Zheng, Liang

2011-08-01

Biodiesel fuels, made from renewable resources, have emerged as viable alternatives to conventional diesel fuel, but their impact on emissions is not fully understood. This study examines elemental carbon (EC), organic carbon (OC), and polycyclic aromatic hydrocarbons (PAHs) emissions from cottonseed oil biodiesel (CSO-B100). Relative to normal diesel fuel, CSO-B100 reduced EC emissions by 64% (±16%). The bulk of EC emitted from CSO-B100 was in the fine particle mode (<1.4 μm), which is similar to normal diesel. OC was found in all size ranges, whereas emissions of OC(1.4-2.5) were proportionately higher in OC(2.5) from CSO-B100 than from diesel. The CSO-B100 emission factors derived from this study are significantly lower, even without aftertreatment, than the China-4 emission standards established in Beijing and Euro-IV diesel engine standards. The toxic equivalency factors (TEFs) for CSO-B100 was half the TEFs of diesel, which suggests that PAHs emitted from CSO-B100 may be less toxic.

A coconut oil-rich meal does not enhance thermogenesis compared to corn oil in a randomized trial in obese adolescents

PubMed Central

LaBarrie, Janna; St-Onge, Marie-Pierre

2017-01-01

Background Consumption of medium chain triglycerides (MCT) in overweight adults increases thermogenesis and improves weight management. Coconut oil is a rich natural source of MCT, but its thermogenic effect is unknown. Our study evaluated the effects of a test oil enriched in coconut oil, on energy expenditure, satiety, and metabolic markers in a randomized, double blind, cross-over study. Methods and findings Fifteen children, age 13-18 years, body mass index >85th percentile for age and sex, were enrolled. Two test meals, containing 20 g of fat from either corn oil or a coconut oil-enriched baking fat (1.1 g of fatty acids with chain lengths ≤ 10C), were administered. A fasting blood sample was taken before breakfast and at 30, 45, 60, 120, and 180 min post-meal for measurement of metabolites. Thermic effect of food (TEF) was assessed over 6 h using indirect calorimetry. Satiety was measured using visual analog scales (VAS). There was no significant effect of fat type, time, or fat type × time interaction on TEF, appetite/satiety, glucose, and insulin area under the curve. There was a significant effect of fat type on leptin (P=0.027), triglycerides (P=0.020) and peptide YY (P=0.0085); leptin and triglyceride concentrations were lower and peptide YY concentrations were higher with corn oil consumption. Conclusion A coconut oil-enriched baking fat does not enhance thermogenesis and satiety in children. Given that this is the only current study of its kind, more research is needed into the use of coconut oil as a tool in weight management in overweight and obese children. PMID:28758166

Effects of Gene Orientation and Use of Multiple Promoters on the Expression of XYL1 and XYL2 in Saccharomyces cerevisiae

NASA Astrophysics Data System (ADS)

Bae, Ju Yun; Laplaza, José; Jeffries, Thomas W.

Orientation of adjacent genes has been reported to affect their expression in eukaryotic systems, and metabolic engineering also often makes repeated use of a few promoters to obtain high expression. To improve transcriptional control in heterologous expression, we examined how these factors affect gene expression and enzymatic activity in Saccharomyces cerevisiae. We assembled d-xylose reductase (XYL1) and d-xylitol dehydrogenase (XYL2) in four ways. Each pair of genes was placed in two different tandem (l→2→ or √1√2), convergent (1→√2), and divergent (√1 2→) orientations in autonomous plasmids. The TEF1 promoter was used to drive XYL1 and the TDH3 promoter to drive XYL2 in each of the constructs. The effects of gene orientation on growth, transcription, and enzyme activity were analyzed. The transcription level as measured by quantitative PCR (q-PCR) correlated with enzyme activities, but our data did not show a significant effect of gene orientation. To test the possible dilution of promoter strength due to multiple use of the same promoter, we examined the level of expression of XYL1 driven by either the TEF1 or TDH3 promoter when carried on a single copy plasmid. We then coexpressed XYL2 from either a single or multicopy plasmid, which was also driven by the same promoter. XYL2 transcript and enzyme expression increased with plasmid copy number, while the expression of XYLl was constant regardless of the number of other TEF1 or TDH3 promoters present in the cell. According to our data, there is no significant effect of gene orientation or multiple promoter use on gene transcription and translation when genes are expressed from plasmids; however, other factors could affect expression of adjacent genes in chromosomes.

Colletotrichum gloeosporioides s.l. associated with Theobroma cacao and other plants in Panama: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes.

PubMed

Rojas, Enith I; Rehner, Stephen A; Samuels, Gary J; Van Bael, Sunshine A; Herre, Edward A; Cannon, Paul; Chen, Rui; Pang, Junfeng; Wang, Ruiwu; Zhang, Yaping; Peng, Yan-Qiong; Sha, Tao

2010-01-01

Colletotrichum interacts with numerous plant species overtly as symptomatic pathogens and cryptically as asymptomatic endophytes. It is not known whether these contrasting ecological modes are optional strategies expressed by individual Colletotrichum species or whether a species' ecology is explicitly pathogenic or endophytic. We explored this question by inferring relationships among 77 C. gloeosporioides s.l. strains isolated from asymptomatic leaves and from anthracnose lesions on leaves and fruits of Theobroma cacao (cacao) and other plants from Panamá. ITS and 5'-tef1 were used to assess diversity and to delineate operational taxonomic units for multilocus phylogenetic analysis. The ITS and 5'-tef1 screens concordantly resolved four strongly supported lineages, clades A-D: Clade A includes the ex type of C. gloeosporioides, clade B includes the ex type ITS sequence of C. boninense, and clades C and D are unidentified. The ITS yielded limited resolution and support within all clades, in particular the C. gloeosporioides clade (A), the focal lineage dealt with in this study. In contrast the 5'-tef1 screen differentiated nine distinctive haplotype subgroups within the C. gloeosporioides clade that were concordant with phylogenetic terminals resolved in a five-locus nuclear phylogeny. Among these were two phylogenetic species associated with symptomatic infections specific to either cacao or mango and five phylogenetic species isolated principally as asymptomatic infections from cacao and other plant hosts. We formally describe two new species, C. tropicale and C. ignotum, that are frequent asymptomatic associates of cacao and other Neotropical plant species, and epitypify C. theobromicola, which is associated with foliar and fruit anthracnose lesions of cacao. Asymptomatic Colletotrichum strains isolated from cacao plants grown in China included six distinct C. gloeosporioides clade taxa, only one of which is known to occur in the Neotropics.

Enhanced thermic effect of food, postprandial NEFA suppression and raised adiponectin in obese women who eat slowly.

PubMed

Reddy, Narendra L; Peng, Chenjing; Carreira, Marcos C; Halder, Louise; Hattersley, John; Piya, Milan K; Tripathi, Gyanendra; Randeva, Harpal S; Casanueva, Felipe F; McTernan, Philip G; Kumar, Sudhesh; Barber, Thomas M

2015-06-01

Meal duration may influence cardiometabolic health. The aim of this study was to explore postprandial effects of meal duration on human metabolism and appetite. Postprandial comparisons following a standard meal eaten slowly over 40 min ('D40') and the same meal eaten quickly over 10 min ('D10') on a different day. Each participant therefore acted as their own control, thereby limiting confounding factors. Obese premenopausal Caucasian women (n = 10) with confirmed normoglycaemia were recruited from an obesity clinic at UHCW, Coventry UK. Subjects underwent whole-body calorimetry (8-h) on two separate days. Following standard lunch (D40 vs D10), 4-h postprandial analysis included thermic effect of food (TEF) and bloods taken at predefined times (including baseline fasting). Analytes included lipid profile, adiponectin, insulin, glucose, ghrelin, leptin, endotoxin, gut and pancreatic hormones. Appetite was measured using visual-analogue scales and ad libitum food intake at subsequent meal. Paired sample t-tests [including area under the curve (AUC)] were used to compare D40 and D10 trials. Postprandial TEF (over 240-min) was significantly greater for D40 than D10 [mean (SEM): 80·9 kcal (3·8) vs 29·9 kcal (3·4); 10·6% vs 3·9%, respectively, P = 0·006; AUC 71·7 kcal.h vs 22·4 kcal.h, respectively, P = 0·02]. Postprandial plasma NEFA was significantly lower, and adiponectin levels were significantly higher for D40 than D10 [AUC (SEM): NEFA 627 μmol.h/l (56) vs 769 μmol.h/l (60), respectively, P = 0·02; adiponectin 33·4 μg.h/ml (3·9) vs 27·3 μg.h/ml (3·8), respectively, P = 0·04]. Other postprandial analytes and appetite measures were equivalent. In obese women, eating slowly associates with enhanced TEF, elevated serum adiponectin and suppressed NEFA. © 2015 John Wiley & Sons Ltd.

What Makes an Excellent Lecturer? Academics' Perspectives on the Discourse of "Teaching Excellence" in Higher Education

ERIC Educational Resources Information Center

Wood, Margaret; Su, Feng

2017-01-01

In the context of the Teaching Excellence Framework (TEF), we examine academics' perspectives on the discourse of "teaching excellence" based on an empirical study with 16 participants from five post-1992 universities. The article reports the findings on academics' views of the term and concept of "teaching excellence",…

Re-Evaluating Student Evaluation of Teaching: The Teaching Evaluation Form.

ERIC Educational Resources Information Center

Wolfer, Terry A.; Johnson, Miriam McNown

2003-01-01

Reports on the aggregate analysis of scores generated by a standardized instrument, the Teaching Evaluation Form (TEF; Hudson, 1982), at the College of Social Work, University of South Carolina. Data included more than 11,000 completions of the instrument in 508 class sections offered during a 4-year period. Analysis revealed a severely negatively…

Designing a Teaching Excellence Framework: Lessons from Other Sectors. Occasional Paper 13

ERIC Educational Resources Information Center

Darian, Louisa

2016-01-01

The Government is committed to introducing a Teaching Excellence Framework (TEF) to assess the quality of teaching and learning in higher education. Designing the right solution is challenging. There is no off-the-shelf solution from other countries that we can lift. But we can learn lessons from other sectors. This pamphlet explores rating…

Initial characterization of unidentified Armillaria isolate from Serbia using LSU-IGS1 and TEF-1a genes

Treesearch

N. Keca; N. B. Klopfenstein; M.-S. Kim; H. Solheim; S. Woodward

2014-01-01

Armillaria species have a global distribution and play variable ecological roles, including causing root disease of diverse forest, ornamental and horticultural trees. Accurate identification of Armillaria species is critical to understand their distribution and ecological roles. This work focused on characterizing an unidentified Armillaria isolate from a Serbian...

Inspirational Teaching in Higher Education: What Does It Look, Sound and Feel Like?

ERIC Educational Resources Information Center

Derounian, James G.

2017-01-01

This article discusses the qualities of inspirational teaching in higher education (HE). It starts by arguing how topical this subject is, given emphasis world-wide on quality assurance measures, such as the UK Government's 2016 "Teaching Excellence Framework" TEF. The paper then moves to review the academic and practice literature in…

Employability and Higher Education: The Follies of the "Productivity Challenge" in the Teaching Excellence Framework

ERIC Educational Resources Information Center

Frankham, Jo

2017-01-01

This article considers questions of "employability," a notion foregrounded in the Green and White Papers on the Teaching Excellence Framework (TEF). The paper first questions government imperatives concerning employability and suggests a series of mismatches that are evident in the rhetorics in this area. This summary opens up elements…

Light directs zebrafish period2 expression via conserved D and E boxes.

PubMed

Vatine, Gad; Vallone, Daniela; Appelbaum, Lior; Mracek, Philipp; Ben-Moshe, Zohar; Lahiri, Kajori; Gothilf, Yoav; Foulkes, Nicholas S

2009-10-01

For most species, light represents the principal environmental signal for entraining the endogenous circadian clock. The zebrafish is a fascinating vertebrate model for studying this process since unlike mammals, direct exposure of most of its tissues to light leads to local clock entrainment. Importantly, light induces the expression of a set of genes including certain clock genes in most zebrafish cell types in vivo and in vitro. However, the mechanism linking light to gene expression remains poorly understood. To elucidate this key mechanism, here we focus on how light regulates transcription of the zebrafish period2 (per2) gene. Using transgenic fish and stably transfected cell line-based assays, we define a Light Responsive Module (LRM) within the per2 promoter. The LRM lies proximal to the transcription start site and is both necessary and sufficient for light-driven gene expression and also for a light-dependent circadian clock regulation. Curiously, the LRM sequence is strongly conserved in other vertebrate per2 genes, even in species lacking directly light-sensitive peripheral clocks. Furthermore, we reveal that the human LRM can substitute for the zebrafish LRM to confer light-regulated transcription in zebrafish cells. The LRM contains E- and D-box elements that are critical for its function. While the E-box directs circadian clock regulation by mediating BMAL/CLOCK activity, the D-box confers light-driven expression. The zebrafish homolog of the thyrotroph embryonic factor binds efficiently to the LRM D-box and transactivates expression. We demonstrate that tef mRNA levels are light inducible and that knock-down of tef expression attenuates light-driven transcription from the per2 promoter in vivo. Together, our results support a model where a light-dependent crosstalk between E- and D-box binding factors is a central determinant of per2 expression. These findings extend the general understanding of the mechanism whereby the clock is entrained by light and how the regulation of clock gene expression by light has evolved in vertebrates.

Selection of yeast Saccharomyces cerevisiae promoters available for xylose cultivation and fermentation.

PubMed

Nambu-Nishida, Yumiko; Sakihama, Yuri; Ishii, Jun; Hasunuma, Tomohisa; Kondo, Akihiko

2018-01-01

To efficiently utilize xylose, a major sugar component of hemicelluloses, in Saccharomyces cerevisiae requires the proper expression of varied exogenous and endogenous genes. To expand the repertoire of promoters in engineered xylose-utilizing yeast strains, we selected promoters in S. cerevisiae during cultivation and fermentation using xylose as a carbon source. To select candidate promoters that function in the presence of xylose, we performed comprehensive gene expression analyses using xylose-utilizing yeast strains both during xylose and glucose fermentation. Based on microarray data, we chose 29 genes that showed strong, moderate, and weak expression in xylose rather than glucose fermentation. The activities of these promoters in a xylose-utilizing yeast strain were measured by lacZ reporter gene assays over time during aerobic cultivation and microaerobic fermentation, both in xylose and glucose media. In xylose media, P TDH3 , P FBA1 , and P TDH1 were favorable for high expression, and P SED1 , P HXT7 , P PDC1 , P TEF1 , P TPI1 , and P PGK1 were acceptable for medium-high expression in aerobic cultivation, and moderate expression in microaerobic fermentation. P TEF2 allowed moderate expression in aerobic culture and weak expression in microaerobic fermentation, although it showed medium-high expression in glucose media. P ZWF1 and P SOL4 allowed moderate expression in aerobic cultivation, while showing weak but clear expression in microaerobic fermentation. P ALD3 and P TKL2 showed moderate promoter activity in aerobic cultivation, but showed almost no activity in microaerobic fermentation. The knowledge of promoter activities in xylose cultivation obtained in this study will permit the control of gene expression in engineered xylose-utilizing yeast strains that are used for hemicellulose fermentation. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Armillaria phylogeny based on tef-1α sequences suggests ongoing divergent speciation within the boreal floristic kingdom

Treesearch

Ned B. Klopfenstein; John W. Hanna; Amy L. Ross-Davis; Jane E. Stewart; Yuko Ota; Rosario Medel-Ortiz; Miguel Armando Lopez-Ramirez; Ruben Damian Elias-Roman; Dionicio Alvarado-Rosales; Mee-Sook Kim

2013-01-01

Armillaria plays diverse ecological roles in forests worldwide, which has inspired interest in understanding phylogenetic relationships within and among species of this genus. Previous rDNA sequence-based phylogenetic analyses of Armillaria have shown general relationships among widely divergent taxa, but rDNA sequences were not reliable for separating closely related...

TeX4 (X = F, Cl, Br) as Lewis acids--complexes with soft thio- and seleno-ether ligands.

PubMed

Hector, Andrew L; Jolleys, Andrew; Levason, William; Reid, Gillian

2012-08-28

TeF(4) reacts with OPR(3) (R = Me or Ph) in anhydrous CH(2)Cl(2) to give the colourless, square based pyramidal 1 : 1 complexes [TeF(4)(OPR(3))] only, in which the OPR(3) is coordinated basally in the solid state, (R = Me: d(Te-O) = 2.122(2) Å; R = Ph: d(Te-O) = 2.1849(14) Å). Variable temperature (19)F{(1)H}, (31)P{(1)H} and (125)Te{(1)H} NMR spectroscopic studies strongly suggest this is the low temperature structure in solution, although the systems are dynamic. The much softer donor ligands SMe(2) and SeMe(2) show a lower affinity for TeF(4), although unstable, yellow products with spectroscopic features consistent with [TeF(4)(EMe(2))] are obtained by the reaction of TeF(4) in neat SMe(2) or via reaction in CH(2)Cl(2) with SeMe(2). TeX(4) (X = F, Cl or Br) causes oxidation and halogenation of TeMe(2) to form X(2)TeMe(2). The Br(2)TeMe(2) hydrolyses in trace moisture to form [BrMe(2)Te-O-TeMe(2)Br], the crystal structure of which has been determined. TeX(4) (X = Cl or Br) react with the selenoethers SeMe(2), MeSe(CH(2))(3)SeMe or o-C(6)H(4)(SeMe)(2) (X = Cl) in anhydrous CH(2)Cl(2) to give the distorted octahedral monomers trans-[TeX(4)(SeMe(2))(2)], cis-[TeX(4){MeSe(CH(2))(3)SeMe}] and cis-[TeCl(4){o-C(6)H(4)(SeMe)(2)}], which have been characterised by IR, Raman and multinuclear NMR ((1)H, (77)Se{(1)H} and (125)Te{(1)H}) spectroscopy, and via X-ray structure determinations of representative examples. Tetrahydrothiophene (tht) can form both 1 : 1 and 1 : 2 Te : L complexes. For X = Br, the former has been shown to be a Br-bridged dimer, [Br(3)(tht)Te(μ-Br)(2)TeBr(3)(tht)], by crystallography with the tht ligands anti, whereas the latter are trans-octahedral monomers. Like its selenoether analogue, MeS(CH(2))(3)SMe forms distorted octahedral cis-chelates, [TeX(4){MeS(CH(2))(3)SMe}], whereas the more rigid o-C(6)H(4)(SMe)(2) unexpectedly forms a zig-zag chain polymer in the solid state, [TeCl(4){o-C(6)H(4)(SMe)(2)}](n), in which the dithioether adopts an extremely unusual bridging mode. This is in contrast to the chelating monomer, cis-[TeCl(4){o-C(6)H(4)(SeMe)(2)}], formed with the analogous selenoether and may be attributed to small differences in the ligand chelate bite angles. The wider bite angle xylyl-linked bidentates, o-C(6)H(4)(CH(2)EMe(2))(2) behave differently; the thioether forms cis-chelated [TeX(4){o-C(6)H(4)(CH(2)SMe)(2)}] confirmed crystallographically, whereas the selenoether undergoes C-Se cleavage and rearrangement on treatment with TeX(4), forming the cyclic selenonium salts, [C(9)H(11)Se](2)[TeX(6)]. The tetrathiamacrocycle, [14]aneS(4) (1,4,8,11-tetrathiacyclotetradecane), does not react cleanly with TeCl(4), but forms the very poorly soluble [TeCl(4)([14]aneS(4))](n), shown by crystallography to be a zig-zag polymer with exo-coordinated [14]aneS(4) units linked via alternate S atoms to a cis-TeCl(4) unit. Trends in the (125)Te{(1)H} NMR shifts for this series of Te(IV) halides chalcogenoether complexes are discussed.

Comparison of Effectiveness of Supervised Exercise Program and Cyriax Physiotherapy in Patients with Tennis Elbow (Lateral Epicondylitis): A Randomized Clinical Trial

PubMed Central

Viswas, Rajadurai; Ramachandran, Rejeeshkumar; Korde Anantkumar, Payal

2012-01-01

Objective. To compare the effectiveness of supervised exercise program and Cyriax physiotherapy in the treatment of tennis elbow (lateral epicondylitis). Design. Randomized clinical trial. Setting. Physiotherapy and rehabilitation centre. Subjects. This study was carried out with 20 patients, who had tennis elbow (lateral epicondylitis). Intervention. Group A (n = 10) had received supervised exercise program. Group B (n = 10) was treated with Cyriax physiotherapy. All patients received three treatment sessions per week for four weeks (12 treatment sessions). Outcome measures. Pain was evaluated using a visual analogue scale (VAS), and functional status was evaluated by completion of the Tennis Elbow Function Scale (TEFS) which were recorded at base line and at the end of fourth week. Results. Both the supervised exercise program and Cyriax physiotherapy were found to be significantly effective in reduction of pain and in the improvement of functional status. The supervised exercise programme resulted in greater improvement in comparison to those who received Cyriax physiotherapy. Conclusion. The results of this clinical trial demonstrate that the supervised exercise program may be the first treatment choice for therapist in managing tennis elbow. PMID:22629225

Environmental Impact Statement. Small Intercontinental Ballistic Missile Program Malmstrom Air Force Base, Montana. Appendix E

DTIC Science & Technology

1987-12-01

c-oup nustemnera. It the -"ociltng fr-o the increased coads aaacntated ,ith the n bcei aseline inremtental poern comtes fe-s BaRsin, the coat. lei...for 0111 thdis pr~oject W tEF: 540 21. Authorization. Section 6.0 of the DEIS contains a -;t of only federal "Authorizing Agust 21. 1987 Actions

Ingested Metallic Spool: A Rare Cause of Acquired Tracheoesophageal Fistula.

PubMed

Hashim, Imran; Talat, Nabila

2017-01-01

Foreign body (FB) ingestion is a common problem in children. Prolonged impaction of FB in esophagus may result in tracheoesophageal fistula (TEF). A 6-year-old girl presented with progressive dysphagia and recurrent chest infections. No history of FB ingestion was given by parents. Further investigations revealed FB (spool) in cervical esophagus. Patient was successfully managed by surgery through trans-cervical approach.

Ingested Metallic Spool: A Rare Cause of Acquired Tracheoesophageal Fistula

PubMed Central

Talat, Nabila

2017-01-01

Foreign body (FB) ingestion is a common problem in children. Prolonged impaction of FB in esophagus may result in tracheoesophageal fistula (TEF). A 6-year-old girl presented with progressive dysphagia and recurrent chest infections. No history of FB ingestion was given by parents. Further investigations revealed FB (spool) in cervical esophagus. Patient was successfully managed by surgery through trans-cervical approach. PMID:28164003

RAMI modeling of plant systems for proposed tritium production and extraction facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blanchard, A.

2000-04-05

The control of life-cycle cost is a primary concern during the development, construction, operation, and decommissioning of DOE systems and facilities. An effective tool that can be used to control these costs, beginning with the design stage, is called a reliability, availability, maintainability, and inspectability analysis or, simply, RAMI for short. In 1997, RAMI technology was introduced to the Savannah River Site with applications at the conceptual design stage beginning with the Accelerator Production of Tritium (APT) Project and later extended to the Commercial Light Water Reactor (CLWR) Tritium Extraction Facility (TEF) Project. More recently it has been applied tomore » the as-build Water Treatment Facilities designed for ground water environmental restoration. This new technology and database was applied to the assessment of balance-of-plant systems for the APT Conceptual Design Report. Initial results from the Heat Removal System Assessment revealed that the system conceptual design would cause the APT to fall short of its annual production goal. Using RAM technology to immediately assess this situation, it was demonstrated that the product loss could be gained back by upgrading the system's chiller unit capacity at a cost of less than $1.3 million. The reclaimed production is worth approximately $100 million. The RAM technology has now been extended to assess the conceptual design for the CLWR-TEF Project. More specifically, this technology and database is being used to translate high level availability goals into lower level system design requirements that will ensure the TEF meets its production goal. Results, from the limited number of system assessments performed to date, have already been used to modify the conceptual design for a remote handling system, improving its availability to the point that a redundant system, with its associated costs of installation and operation may no longer be required. RAMI results were also used to justify the elimination of a metal uranium bed in the design of a water cracker system, producing a significant reduction in the estimated construction and operating costs.« less

Esophageal atresia in newborns: a wide spectrum from the isolated forms to a full VACTERL phenotype?

PubMed

La Placa, Simona; Giuffrè, Mario; Gangemi, Antonella; Di Noto, Stefania; Matina, Federico; Nociforo, Federica; Antona, Vincenzo; Di Pace, Maria Rita; Piccione, Maria; Corsello, Giovanni

2013-07-10

VATER association was first described in 1972 by Quan and Smith as an acronym which identifies a non-random co-occurrence of Vertebral anomalies, Anal atresia, Tracheoesophageal fistula and/or Esophageal atresia, Radial dysplasia. It is even possible to find out Cardiovascular, Renal and Limb anomalies and the acronym VACTERL was adopted, also, embodying Vascular, as single umbilical artery, and external genitalia anomalies. Data on patients with esophageal atresia (EA) with or without tracheoesophageal fistula (TEF) admitted in the Neonatal Intensive Care Unit (NICU) between January 2003 and January 2013 were evaluated for the contingent occurrence of typical VACTERL anomalies (VACTERL-type) and non tipical VACTERL anomalies (non-VACTERL-type). The inclusion criterion was the presence of EA with or without TEF plus two or more of the following additional malformations: vertebral defects, anal atresia, cardiovascular defects, renal anomalies and lower limb deformities, like radial dysplasia. Among 52 patients with EA/TEF, 20 (38,4%) had isolated EA and 7 (21,8%) had a recognized etiology such a syndrome and therefore were excluded. Among 32 infants with EA and associated malformations, 15 (46,8%) had VACTERL association. The most common anomalies were congenital heart defects (73,3%), followed by vertebral anomalies (66,6%). Many patients also had additional non-VACTERL-type defects. Single umbilical artery was the most common one followed by nervous system abnormalities and anomalies of toes. Between the groups of infants with VACTERL type and non-VACTERL-type anomalies, there are several overlapping data regarding both the tipically described spectrum and the most frequently reported non-VACTERL-type malformations. Thus, it is possible to differentiate infants with a full phenotype (VACTERL full phenotype) and patients that do not meet all the criteria mentioned above, but with some homologies with the first group (VACTERL partial phenotype). The high frequency of non-VACTERL-type anomalies encountered in full and partial phenotype patients would suggest the need for an extension of the clinical criteria for the diagnosis of VACTERL association and also for pre- and post-operative management and follow-up in the short and long term.

Skin temperature response to a liquid meal intake is different in men than in women.

PubMed

Martinez-Tellez, Borja; Ortiz-Alvarez, Lourdes; Sanchez-Delgado, Guillermo; Xu, Huiwen; Acosta, Francisco M; Merchan-Ramirez, Elisa; Muñoz-Hernandez, Victoria; Martinez-Avila, Wendy D; Contreras-Gomez, Miguel A; Gil, Angel; Labayen, Idoia; Ruiz, Jonatan R

2018-06-02

The thermic effect of food (TEF) refers to the increase of the metabolic rate and body temperature in response to a single meal. To date, most of the studies have focused to determine the TEF in terms of energy expenditure, but little is known about which is the response in terms of skin temperature. The aim of this study was to analyze whether the thermic effect of food (TEF) on the skin temperature with a standardized and individualized liquid meal test is different in young adult men than in young adult women. A total of 104 young adults (36 men and 68 women, age: 18-25 years old) consumed a standardized and individualized liquid meal (energy intake: 50% of measured basal metabolic rate, 50% carbohydrates, 35% fat, 15% protein). The skin temperature was measured by means of 17 iButtons during 3 h and 20 min. The mean, proximal, distal, and supraclavicular skin temperature, as well as the peripheral gradient, were determined as a proxy of a peripheral vasoconstriction. The participants reported the thermal sensation of the whole body, clavicular, feet, and hands zones. The body composition was measured by dual X-ray absorptiometry. The overall, mean, proximal, and supraclavicular skin temperature significantly increased after the meal intake (all P < 0.05 vs. the baseline temperature). There was a postprandial peripheral vasoconstriction right after the meal intake and over the first hour and a peripheral vasodilatation during the second and third hour. Women had a higher increase in all skin temperature parameters in comparison to men (all, P < 0.05), whereas there were no sex differences in the proximal skin temperature (P = 0.279). The pattern of thermal sensation was similar between sexes, but women always felt colder than men. All of the results persisted after adjusting the analyses for body composition or menstrual cycle. A standardized and individualized liquid meal test increases the skin temperature in young adults, being the thermic effect higher in women than in men. Copyright © 2018 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Unsteady Aerodynamics for Micro Air Vehicles (Aerodynamique instable pour micro-vehicules aeriens)

DTIC Science & Technology

2010-09-01

SLOVAQUIE ESPAGNE Akadémia ozbrojených síl gen. SDG TECEN / DGAM PAYS-BAS M.R. Štefánika, Distribučné a C/ Arturo Soria 289 Royal Netherlands Military...1000 Ljubljana PO Box 18 Academy Library 197 21 Praha 9 P.O. Box 90.002 SPAIN 4800 PA Breda SDG TECEN / DGAM DENMARK C/ Arturo Soria 289 Danish

Foraging habits in a generalist predator: sex and age influence habitat selection and resource use among bottlenose dolphins (Tursiops truncatus)

USGS Publications Warehouse

Sam Rossman,; McCabe, Elizabeth Berens; Nelio B. Barros,; Hasand Gandhi,; Peggy H. Ostrom,; Stricker, Craig A.; Randall S. Wells,

2015-01-01

This study examines resource use (diet, habitat use, and trophic level) within and among demographic groups (males, females, and juveniles) of bottlenose dolphins (Tursiops truncatus). We analyzed the δ13C and δ15N values of 15 prey species constituting 84% of the species found in stomach contents. We used these data to establish a trophic enrichment factor (TEF) to inform dietary analysis using a Bayesian isotope mixing model. We document a TEF of 0‰ and 2.0‰ for δ13C and δ15N, respectively. The dietary results showed that all demographic groups relied heavily on low trophic level seagrass-associated prey. Bayesian standard ellipse areas (SEAb) were calculated to assess diversity in resource use. The SEAb of females was nearly four times larger than that of males indicating varied resource use, likely a consequence of small home ranges and habitat specialization. Juveniles possessed an intermediate SEAb, generally feeding at a lower trophic level compared to females, potentially an effect of natal philopatry and immature foraging skills. The small SEAb of males reflects a high degree of specialization on seagrass associated prey. Patterns in resource use by the demographic groups are likely linked to differences in the relative importance of social and ecological factors.

Saprophytic and Potentially Pathogenic Fusarium Species from Peat Soil in Perak and Pahang

PubMed Central

Karim, Nurul Farah Abdul; Mohd, Masratulhawa; Nor, Nik Mohd Izham Mohd; Zakaria, Latiffah

2016-01-01

Isolates of Fusarium were discovered in peat soil samples collected from peat swamp forest, waterlogged peat soil, and peat soil from oil palm plantations. Morphological characteristics were used to tentatively identify the isolates, and species confirmation was based on the sequence of translation elongation factor-1α (TEF-1α) and phylogenetic analysis. Based on the closest match of Basic Local Alignment Search Tool (BLAST) searches against the GenBank and Fusarium-ID databases, five Fusarium species were identified, namely F. oxysporum (60%), F. solani (23%), F. proliferatum (14%), F. semitectum (1%), and F. verticillioides (1%). From a neighbour-joining tree of combined TEF-1α and β-tubulin sequences, isolates from the same species were clustered in the same clade, though intraspecies variations were observed from the phylogenetic analysis. The Fusarium species isolated in the present study are soil inhabitants and are widely distributed worldwide. These species can act as saprophytes and decomposers as well as plant pathogens. The presence of Fusarium species in peat soils suggested that peat soils could be a reservoir of plant pathogens, as well-known plant pathogenic species such F. oxysporum, F. solani, F. proliferatum, and F. verticillioides were identified. The results of the present study provide knowledge on the survival and distribution of Fusarium species. PMID:27019679

Regulation of tRNA Bidirectional Nuclear-Cytoplasmic Trafficking in Saccharomyces cerevisiae

PubMed Central

Murthi, Athulaprabha; Shaheen, Hussam H.; Huang, Hsiao-Yun; Preston, Melanie A.; Lai, Tsung-Po; Phizicky, Eric M.

2010-01-01

tRNAs in yeast and vertebrate cells move bidirectionally and reversibly between the nucleus and the cytoplasm. We investigated roles of members of the β-importin family in tRNA subcellular dynamics. Retrograde import of tRNA into the nucleus is dependent, directly or indirectly, upon Mtr10. tRNA nuclear export utilizes at least two members of the β-importin family. The β-importins involved in nuclear export have shared and exclusive functions. Los1 functions in both the tRNA primary export and the tRNA reexport processes. Msn5 is unable to export tRNAs in the primary round of export if the tRNAs are encoded by intron-containing genes, and for these tRNAs Msn5 functions primarily in their reexport to the cytoplasm. The data support a model in which tRNA retrograde import to the nucleus is a constitutive process; in contrast, reexport of the imported tRNAs back to the cytoplasm is regulated by the availability of nutrients to cells and by tRNA aminoacylation in the nucleus. Finally, we implicate Tef1, the yeast orthologue of translation elongation factor eEF1A, in the tRNA reexport process and show that its subcellular distribution between the nucleus and cytoplasm is dependent upon Mtr10 and Msn5. PMID:20032305

Regulation of tRNA bidirectional nuclear-cytoplasmic trafficking in Saccharomyces cerevisiae.

PubMed

Murthi, Athulaprabha; Shaheen, Hussam H; Huang, Hsiao-Yun; Preston, Melanie A; Lai, Tsung-Po; Phizicky, Eric M; Hopper, Anita K

2010-02-15

tRNAs in yeast and vertebrate cells move bidirectionally and reversibly between the nucleus and the cytoplasm. We investigated roles of members of the beta-importin family in tRNA subcellular dynamics. Retrograde import of tRNA into the nucleus is dependent, directly or indirectly, upon Mtr10. tRNA nuclear export utilizes at least two members of the beta-importin family. The beta-importins involved in nuclear export have shared and exclusive functions. Los1 functions in both the tRNA primary export and the tRNA reexport processes. Msn5 is unable to export tRNAs in the primary round of export if the tRNAs are encoded by intron-containing genes, and for these tRNAs Msn5 functions primarily in their reexport to the cytoplasm. The data support a model in which tRNA retrograde import to the nucleus is a constitutive process; in contrast, reexport of the imported tRNAs back to the cytoplasm is regulated by the availability of nutrients to cells and by tRNA aminoacylation in the nucleus. Finally, we implicate Tef1, the yeast orthologue of translation elongation factor eEF1A, in the tRNA reexport process and show that its subcellular distribution between the nucleus and cytoplasm is dependent upon Mtr10 and Msn5.

New species and new behavioral data of Phlugiola Karny, 1907 (Orthoptera: Tettigoniidae: Meconematinae) from the Brazilian Amazonian Rainforest.

PubMed

Mendes, Diego Matheus DE Mello; Oliveira, Jomara Cavalcante DE; Alves-Oliveira, João Rafael; Rafael, José Albertino

2017-03-16

Phlugiola Karny, 1907 is a genus of small predatory katydids with six included species distributed in Brazil, Bolivia, Colombia, Peru and Suriname. In this paper two new Brazilian species are described, Phlugiola longipedes sp. nov. (type locality: Amazonas, Tefé) and Phlugiola igarape sp. nov., (type locality: Acre, Bujari) both from tropical rainforests. Behavioral data and natural history notes are provided.

First report of the Armillaria root disease pathogen, Armillaria sinapina, on subalpine fir (Abies lasiocarpa) and quaking aspen (Populus tremuloides) in Colorado

Treesearch

K. S. Burns; J. W. Hanna; Ned Klopfenstein; M.-S. Kim

2016-01-01

In July 2014, mycelial fans (isolates CO104F, CO106F, and CO108F) of Armillaria sp. were collected from forest trees in Colorado. These isolates were all identified as A. sinapina based on a somatic pairing test against 18 tester isolates representing six North American Armillaria spp. and nucleotide sequences of the translation elongation factor 1alpha (tef-...

Species clarification of the culinary Bachu mushroom in western China.

PubMed

Zhao, Qi; Sulayman, Mamtimin; Zhu, Xue-Tai; Zhao, Yong-Chang; Yang, Zhu-Liang; Hyde, Kevin D

2016-01-01

The Bachu mushroom, previously identified as Helvella leucopus, is characterized by a saddle-shaped, to irregularly lobed pileus, with a gray, brown to blackish hymenium and a whitish to pale receptacle surface and white, terete stipe with enlarged basal grooves. It has high economic value, mostly as a dietary supplement in western China, and its medicinal functions have raised broad interest. In the present paper species of the Bachu mushroom in Xinjiang Autonomous Region, western China were investigated with morphology and DNA sequence data. Phylogenetic analyses inferred from ITS, 28S and TEF1 sequence data strongly supported lineages corresponding to morphological features. The Bachu mushroom, which differs from the European Helvella leucopus, comprises two distinct new species, namely Helvella bachu and Helvella subspadicea. In this paper we introduce the new species with descriptions and figures and compare them with similar taxa. The European Helvella spadicea is also re-examined, described and illustrated. © 2016 by The Mycological Society of America.

Irregular meal-pattern effects on energy expenditure, metabolism, and appetite regulation: a randomized controlled trial in healthy normal-weight women.

PubMed

Alhussain, Maha H; Macdonald, Ian A; Taylor, Moira A

2016-07-01

Obesity is increasing in parallel with greater all-day food availability. The latter may promote meal irregularity, dysregulation of the energy balance, and poor metabolic health. We investigated the effect of meal irregularity on the thermic effect of food (TEF), lipid concentrations, carbohydrate metabolism, subjective appetite, and gut hormones in healthy women. Eleven normal-weight women (18-40 y of age) were recruited in a randomized crossover trial with two 14-d isoenergetic diet periods (identical foods provided and free living) that were separated by a 14-d habitual diet washout period. In period 1, participants followed a regular meal pattern (6 meals/d) or an irregular meal pattern (3-9 meals/d), and in period 2, the alternative meal pattern was followed. Before and after each period, when participants were fasting and for 3 h after intake of a test drink, measurements were taken of energy expenditure, circulating glucose, lipids (fasting only), insulin, glucagon-like peptide 1 (GLP-1), peptide YY (PYY), and ghrelin. An ad libitum test meal was offered. Subjective appetite ratings were assessed while fasting, after the test drink, after the ad libitum meal, and during the intervention. Continuous interstitial glucose monitoring was undertaken for 3 consecutive days during each intervention, and the ambulatory activity pattern was recorded (ambulatory energy expenditure estimation). Regularity was associated with a greater TEF (P < 0.05) and a lower incremental area under the curve (iAUC) for glucose after intake of the test drink (over 3 h) and, for some identical meals, during the 2 interventions (over 90 min) (day 7: after breakfast; day 9: after lunch and dinner). There was no difference between treatments for the test-drink gut hormone response. A time effect was noted for fasting GLP-1, fasting PYY, PYY responses, and hunger-rating responses to the test drink (P < 0.05). Lower hunger and higher fullness ratings were seen premeal and postmeal during the regular period while subjects were free living. Meal regularity appears to be associated with greater TEF and lower glucose responses, which may favor weight management and metabolic health. This trial was registered at clinicaltrials.gov as NCT02052076. © 2016 American Society for Nutrition.

The role of energy expenditure in the differential weight loss in obese women on low-fat and low-carbohydrate diets.

PubMed

Brehm, Bonnie J; Spang, Suzanne E; Lattin, Barbara L; Seeley, Randy J; Daniels, Stephen R; D'Alessio, David A

2005-03-01

We have recently reported that obese women randomized to a low-carbohydrate diet lost more than twice as much weight as those following a low-fat diet over 6 months. The difference in weight loss was not explained by differences in energy intake because women on the two diets reported similar daily energy consumption. We hypothesized that chronic ingestion of a low-carbohydrate diet increases energy expenditure relative to a low-fat diet and that this accounts for the differential weight loss. To study this question, 50 healthy, moderately obese (body mass index, 33.2 +/- 0.28 kg/m(2)) women were randomized to 4 months of an ad libitum low-carbohydrate diet or an energy-restricted, low-fat diet. Resting energy expenditure (REE) was measured by indirect calorimetry at baseline, 2 months, and 4 months. Physical activity was estimated by pedometers. The thermic effect of food (TEF) in response to low-fat and low-carbohydrate breakfasts was assessed over 5 h in a subset of subjects. Forty women completed the trial. The low-carbohydrate group lost more weight (9.79 +/- 0.71 vs. 6.14 +/- 0.91 kg; P < 0.05) and more body fat (6.20 +/- 0.67 vs. 3.23 +/- 0.67 kg; P < 0.05) than the low-fat group. There were no differences in energy intake between the diet groups as reported on 3-d food records at the conclusion of the study (1422 +/- 73 vs. 1530 +/- 102 kcal; 5954 +/- 306 vs. 6406 +/- 427 kJ). Mean REE in the two groups was comparable at baseline, decreased with weight loss, and did not differ at 2 or 4 months. The low-fat meal caused a greater 5-h increase in TEF than did the low-carbohydrate meal (53 +/- 9 vs. 31 +/- 5 kcal; 222 +/- 38 vs. 130 +/- 21 kJ; P = 0.017). Estimates of physical activity were stable in the dieters during the study and did not differ between groups. These results confirm that short-term weight loss is greater in obese women on a low-carbohydrate diet than in those on a low-fat diet even when reported food intake is similar. The differential weight loss is not explained by differences in REE, TEF, or physical activity and likely reflects underreporting of food consumption by the low-fat dieters.

Track-average LET of secondary electrons generated in LiF:Mg,Ti and liquid water by 20-300 kV x-ray, 137Cs and 60Co beams.

PubMed

Cabrera-Santiago, A; Massillon-Jl, G

2016-11-21

Electrons generated in matter by photons could be a fundamental basis for an adequate analysis of radiation effects and damage. We have studied separately the 'primary electrons' generated directly by photons from the 'secondary electrons' (SE) produced by electron-electron interactions. In this work, track-average linear energy transfer, [Formula: see text], of SE in LiF:Mg,Ti and liquid water produced by twelve photon energy beams from 20 kV x-ray to 60 Co gamma rays have been investigated using the EGSnrc Monte Carlo Code. The exposure of LiF:Mg,Ti in different phantom materials has been considered. Depending on the photon energy, SE represent 40%-90% of the total electron fluence (TEF) between 1 keV and 10 keV, being higher when the photon energy increases. Independent of the medium, [Formula: see text] versus mean photon energy displays a local minimum at around 40 keV, followed by a local maximum at ~80 keV-100 keV. The [Formula: see text] of SE generated by the x-ray beams are of order of 11 keV µm -1 to 19 keV µm -1 in LiF:Mg,Ti and 5 keV µm -1 to 9 keV µm -1 in liquid water which represent 3-5 times those produced by 60 Co gamma rays in both media. These values were considerably greater than those of TEF, by factors of 3-8. Furthermore, [Formula: see text] of SE generated in liquid water by 20 kV-200 kV x-rays are similar to those of 76 MeV-120 MeV 3 He ions. Contrary to the TEF, where [Formula: see text] were independent of the phantom material, at low photon energies [Formula: see text] of SE was found to be sensitive to the surrounding medium showing higher values within the phantom than in air. This result, which agrees with published experimental results, implies the importance of the SE ionization density for an understanding of dosimeter response induced by photon beams.

A field trial of a PCR-based Mansonella ozzardi diagnosis assay detects high-levels of submicroscopic M. ozzardi infections in both venous blood samples and FTA card dried blood spots.

PubMed

Medeiros, Jansen Fernandes; Almeida, Tatiana Amaral Pires; Silva, Lucyane Bastos Tavares; Rubio, Jose Miguel; Crainey, James Lee; Pessoa, Felipe Arley Costa; Luz, Sergio Luiz Bessa

2015-05-20

Mansonella ozzardi is a poorly understood human filarial parasite with a broad distribution throughout Latin America. Most of what is known about its parasitism has come from epidemiological studies that have estimated parasite incidence using light microscopy. Light microscopy can, however, miss lighter, submicroscopic, infections. In this study we have compared M. ozzardi incidence estimates made using light microscopy, with estimates made using PCR. 214 DNA extracts made from Large Volume Venous Blood Samples (LVVBS) were taken from volunteers from two study sites in the Rio Solimões region: Codajás [n = 109] and Tefé [n = 105] and were subsequently assayed for M. ozzardi parasitism using a diagnostic PCR (Mo-dPCR). Peripheral finger-prick blood samples were taken from the same individuals and used for microscopic examination. Finger-prick blood, taken from individuals from Tefé, was also used for the creation of FTAcard dried blood spots (DBS) that were subsequently subjected to Mo-dPCR. Overall M. ozzardi incidence estimates made with LVVBS PCRs were 1.8 times higher than those made using microscopy (44.9% [96/214] compared with 24.3% [52/214]) and 1.5 times higher than the PCR estimates made from FTAcard DBS (48/105 versus 31/105). PCR-based detection of FTAcard DBS proved 1.3 times more sensitive at diagnosing infections from peripheral blood samples than light microscopy did: detecting 24/105 compared with 31/105. PCR of LVVBS reported the fewest number of false negatives, detecting: 44 of 52 (84.6%) individuals diagnosed by microscopy; 27 of 31 (87.1%) of those diagnosed positive from DBSs and 17 out of 18 (94.4%) of those diagnosed as positive by both alternative methodologies. In this study, Mo-dPCR of LVVBS was by far the most sensitive method of detecting M. ozzardi infections and detected submicroscopic infections. Mo-dPCR FTAcard DBS also provided a more sensitive test for M. ozzardi diagnosis than light microscopy based diagnosis did and thus in settings where only finger-prick assays can be carried-out, it may be a more reliable method of detection. Most existing M. ozzardi incidence estimates, which are often based on light microscope diagnosis, are likely to dramatically underestimate true M. ozzardi parasitism incidence levels.

I-S/A AMPE (Inter-Service/Agency Automated Message Processing Exchange) Database Update User’s Manual.

DTIC Science & Technology

1987-03-31

I E.EF-C.-J I So-SUSSCR I SEP -RJLITI 4 1 So"-.LESC F Il BEP -TEF-r, I I So4-SIJSCR I EEP- POLUT 1 001---- 5 ISk-SUESEC PI E: I Si -SUE:-CP I EP-TEPtl...wartime) E-𔃾 r 3 Table 1;-l (cont) U Code Agency - Department of Defense DQ Central Security Service 3 DR Defense Contract Audit Agency DS Defense

A vertically aligned carbon nanotube-based impedance sensing biosensor for rapid and high sensitive detection of cancer cells.

PubMed

Abdolahad, Mohammad; Taghinejad, Mohammad; Taghinejad, Hossein; Janmaleki, Mohsen; Mohajerzadeh, Shams

2012-03-21

A novel vertically aligned carbon nanotube based electrical cell impedance sensing biosensor (CNT-ECIS) was demonstrated for the first time as a more rapid, sensitive and specific device for the detection of cancer cells. This biosensor is based on the fast entrapment of cancer cells on vertically aligned carbon nanotube arrays and leads to mechanical and electrical interactions between CNT tips and entrapped cell membranes, changing the impedance of the biosensor. CNT-ECIS was fabricated through a photolithography process on Ni/SiO(2)/Si layers. Carbon nanotube arrays have been grown on 9 nm thick patterned Ni microelectrodes by DC-PECVD. SW48 colon cancer cells were passed over the surface of CNT covered electrodes to be specifically entrapped on elastic nanotube beams. CNT arrays act as both adhesive and conductive agents and impedance changes occurred as fast as 30 s (for whole entrapment and signaling processes). CNT-ECIS detected the cancer cells with the concentration as low as 4000 cells cm(-2) on its surface and a sensitivity of 1.7 × 10(-3)Ω cm(2). Time and cell efficiency factor (TEF and CEF) parameters were defined which describe the sensor's rapidness and resolution, respectively. TEF and CEF of CNT-ECIS were much higher than other cell based electrical biosensors which are compared in this paper.

Dietary Intakes of Minerals, Essential and Toxic Trace Elements for Adults from Eragrostis tef L.: A Nutritional Assessment.

PubMed

Koubová, Eva; Sumczynski, Daniela; Šenkárová, Lenka; Orsavová, Jana; Fišera, Miroslav

2018-04-12

This study analysed the contents of thirty-six mineral and trace elements in teff ( Eragrostis tef L.) grains. What is more, dietary intakes were calculated. Inductively coupled plasma mass spectrometry (ICP-MS) was used to assess mineral and trace element contents. Consequently, the appropriate Recommended Dietary Allowance (RDA) or adequate intake (AI), and provisional tolerable weekly intake (PTWI) or provisional tolerable monthly intake (PTMI) values for adults were determined according to the Food and Agriculture Organization/World Health Organization (FAO/WHO) and Institute of Medicine (IOM) regulations. Teff is a significant contributor to RDAs and AIs for females in the following order: Mn > Cu > Zn ≥ Mg > Fe ≥ P and Ca. For males, teff contributes in the order, Mn > Cu > Fe > Zn ≥ P ≥ Mg > and Ca. The concentration of arsenic (65.9 µg/kg) in brown teff originating in Bolivia exceeded the average acceptable value set by Reg. No. 1881 of 6-50 µg/kg in cereals consumed in the EU. The PTWIs or PTMIs for Al, Cd, Sn and Hg were all under 7%, which is below the limits of toxic element intake related to the body weight of 65 kg for adult females and 80 kg for males, set by the FAO/WHO. Teff grains can be recommended as a valuable and safe source of minerals and trace elements.

Origin, divergence, and phylogeny of asexual Epichloë endophyte in Elymus species from western China.

PubMed

Song, Hui; Nan, Zhibiao

2015-01-01

Asexual Epichloë species are likely derived directly from sexual Epichloë species that then lost their capacity for sexual reproduction or lost sexual reproduction because of interspecific hybridization between distinct lineages of sexual Epichloë and/or asexual Epichloë species. In this study we isolated asexual Epichloë endophytes from Elymus species in western China and sequenced intron-rich regions in the genes encoding β-tubulin (tubB) and translation elongation factor 1-α (tefA). Our results showed that there are no gene copies of tubB and tefA in any of the isolates. Phylogenetic analysis showed that sequences in this study formed a single clade with asexual Epichloë bromicola from Hordeum brevisubulatum, which implies asexual Epichloë endophytes that are symbionts in a western Chinese Elymus species likely share a common ancestor with asexual E. bromicola from European H. brevisubulatum. In addition, our results revealed that asexual E. bromicola isolates that are symbionts in a western Chinese Elymus species and sexual Epichloë species that are symbionts in a North American Elymus species have a different origin. Further analysis found that Epichloë species likely originated in Eurasia. In addition, the results support the hypothesis that migratory birds or humans might have aided the dispersal of these fungal endophytes to other continents.

In-Flight and Post-Flight Impact Data Analysis from DEBIE2 (Debris In-Orbit Evaluator) on Board of ISS

NASA Astrophysics Data System (ADS)

Menicucci, Alessandra; Drolshagen, Gerhard; Kuitunen, Juha; Butenko, Yuriy; Mooney, Cathal

2013-08-01

DEBIE2 (Debris-in-orbit-evaluator) was launched in February 2008 as part of the European Technology Exposure Facility (EuTEF) and installed on the exterior of Columbus on ISS. DEBIE2 is an active detector, composed by 3 sensor units able to monitor the sub-micron micro-meteoroid and debris population in space. Each DEBIE sensor consists of a thin aluminium foil coupled with 2 wire grids sensitive to the plasma generated by particles impacting on the foil where also 2 piezoelectric sensors are glued. If the particle penetrates the foil, this can be detected by a third electron plasma detector located just behind the foil. The combination of these information allows to estimate the micro-particles and debris fluxes. EuTEF and DEBIE2 were retrieved after 18 months in flight and returned to Earth with the Space Shuttle Mission STS-128. In this paper, the results of the analysis of in-flight impact data are presented as well as the comparison with the models. The DEBIE2 sensor pointing the Zenith direction, was found to have one wire of the upper grid cut in two pieces by an impact. The postflight analysis focused on this sensor and included optical and SEM/EDX scanning. The results from this inspection will be also presented in this paper.

Dietary Intakes of Minerals, Essential and Toxic Trace Elements for Adults from Eragrostis tef L.: A Nutritional Assessment

PubMed Central

Koubová, Eva; Šenkárová, Lenka

2018-01-01

This study analysed the contents of thirty-six mineral and trace elements in teff (Eragrostis tef L.) grains. What is more, dietary intakes were calculated. Inductively coupled plasma mass spectrometry (ICP-MS) was used to assess mineral and trace element contents. Consequently, the appropriate Recommended Dietary Allowance (RDA) or adequate intake (AI), and provisional tolerable weekly intake (PTWI) or provisional tolerable monthly intake (PTMI) values for adults were determined according to the Food and Agriculture Organization/World Health Organization (FAO/WHO) and Institute of Medicine (IOM) regulations. Teff is a significant contributor to RDAs and AIs for females in the following order: Mn > Cu > Zn ≥ Mg > Fe ≥ P and Ca. For males, teff contributes in the order, Mn > Cu > Fe > Zn ≥ P ≥ Mg > and Ca. The concentration of arsenic (65.9 µg/kg) in brown teff originating in Bolivia exceeded the average acceptable value set by Reg. No. 1881 of 6–50 µg/kg in cereals consumed in the EU. The PTWIs or PTMIs for Al, Cd, Sn and Hg were all under 7%, which is below the limits of toxic element intake related to the body weight of 65 kg for adult females and 80 kg for males, set by the FAO/WHO. Teff grains can be recommended as a valuable and safe source of minerals and trace elements. PMID:29649158

Origin, Divergence, and Phylogeny of Asexual Epichloë Endophyte in Elymus Species from Western China

PubMed Central

Song, Hui; Nan, Zhibiao

2015-01-01

Asexual Epichloë species are likely derived directly from sexual Epichloë species that then lost their capacity for sexual reproduction or lost sexual reproduction because of interspecific hybridization between distinct lineages of sexual Epichloë and/or asexual Epichloë species. In this study we isolated asexual Epichloë endophytes from Elymus species in western China and sequenced intron-rich regions in the genes encoding β-tubulin (tubB) and translation elongation factor 1-α (tefA). Our results showed that there are no gene copies of tubB and tefA in any of the isolates. Phylogenetic analysis showed that sequences in this study formed a single clade with asexual Epichloë bromicola from Hordeum brevisubulatum, which implies asexual Epichloë endophytes that are symbionts in a western Chinese Elymus species likely share a common ancestor with asexual E. bromicola from European H. brevisubulatum. In addition, our results revealed that asexual E. bromicola isolates that are symbionts in a western Chinese Elymus species and sexual Epichloë species that are symbionts in a North American Elymus species have a different origin. Further analysis found that Epichloë species likely originated in Eurasia. In addition, the results support the hypothesis that migratory birds or humans might have aided the dispersal of these fungal endophytes to other continents. PMID:25970178

Global diversity of the Ganoderma lucidum complex (Ganodermataceae, Polyporales) inferred from morphology and multilocus phylogeny.

PubMed

Zhou, Li-Wei; Cao, Yun; Wu, Sheng-Hua; Vlasák, Josef; Li, De-Wei; Li, Meng-Jie; Dai, Yu-Cheng

2015-06-01

Species of the Ganoderma lucidum complex are used in many types of health products. However, the taxonomy of this complex has long been chaotic, thus limiting its uses. In the present study, 32 collections of the complex from Asia, Europe and North America were analyzed from both morphological and molecular phylogenetic perspectives. The combined dataset, including an outgroup, comprised 33 ITS, 24 tef1α, 24 rpb1 and 21 rpb2 sequences, of which 19 ITS, 20 tef1α, 20 rpb1 and 17 rpb2 sequences were newly generated. A total of 13 species of the complex were recovered in the multilocus phylogeny. These 13 species were not strongly supported as a single monophyletic lineage, and were further grouped into three lineages that cannot be defined by their geographic distributions. Clade A comprised Ganoderma curtisii, Ganoderma flexipes, Ganoderma lingzhi, Ganoderma multipileum, Ganoderma resinaceum, Ganoderma sessile, Ganoderma sichuanense and Ganoderma tropicum, Clade B comprised G. lucidum, Ganoderma oregonense and Ganoderma tsugae, and Clade C comprised Ganoderma boninense and Ganoderma zonatum. A dichotomous key to the 13 species is provided, and their key morphological characters from context, pores, cuticle cells and basidiospores are presented in a table. The taxonomic positions of these species are briefly discussed. Noteworthy, the epitypification of G. sichuanense is rejected. Copyright © 2014 Elsevier Ltd. All rights reserved.

Attenuating the Biologic Drive for Weight Regain Following Weight Loss: Must What Goes Down Always Go Back Up?

PubMed Central

Melby, Christopher L.; Paris, Hunter L.; Foright, Rebecca M.; Peth, James

2017-01-01

Metabolic adaptations occur with weight loss that result in increased hunger with discordant simultaneous reductions in energy requirements—producing the so-called energy gap in which more energy is desired than is required. The increased hunger is associated with elevation of the orexigenic hormone ghrelin and decrements in anorexigenic hormones. The lower total daily energy expenditure with diet-induced weight loss results from (1) a disproportionately greater decrease in circulating leptin and resting metabolic rate (RMR) than would be predicted based on the decline in body mass, (2) decreased thermic effect of food (TEF), and (3) increased energy efficiency at work intensities characteristic of activities of daily living. These metabolic adaptations can readily promote weight regain. While more experimental research is needed to identify effective strategies to narrow the energy gap and attenuate weight regain, some factors contributing to long-term weight loss maintenance have been identified. Less hunger and greater satiation have been associated with higher intakes of protein and dietary fiber, and lower glycemic load diets. High levels of physical activity are characteristic of most successful weight maintainers. A high energy flux state characterized by high daily energy expenditure and matching energy intake may attenuate the declines in RMR and TEF, and may also result in more accurate regulation of energy intake to match daily energy expenditure. PMID:28481261

Tactile Sensory Supplementation of Gravitational References to Optimize Sensorimotor Recovery

NASA Technical Reports Server (NTRS)

Black, F. O.; Paloski, W. H.; Bloomberg, J. J.; Wood, S. J.

2007-01-01

Integration of multi-sensory inputs to detect tilts relative to gravity is critical for sensorimotor control of upright orientation. Displaying body orientation using electrotactile feedback to the tongue has been developed by Bach-y- Rita and colleagues as a sensory aid to maintain upright stance with impaired vestibular feedback. This investigation has explored the effects of Tongue Elecrotactile Feedback (TEF) for control of posture and movement as a sensorimotor countermeasure, specifically addressing the optimal location of movement sensors.

Motility, digestive and nutritional problems in Esophageal Atresia.

PubMed

Gottrand, Madeleine; Michaud, Laurent; Sfeir, Rony; Gottrand, Frédéric

2016-06-01

Esophageal atresia (EA) with or without tracheoesophageal fistula (TEF) is a rare congenital malformation. Digestive and nutritional problems remain frequent in children with EA both in early infancy and at long-term follow-up. These patients are at major risk of presenting with gastroesophageal reflux and its complications, such as anastomotic strictures. Esophageal dysmotility is constant, and can have important consequences on feeding and nutritional status. Patients with EA need a systematic follow-up with a multidisciplinary team. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synthetic muscle promoters: activities exceeding naturally occurring regulatory sequences

NASA Technical Reports Server (NTRS)

Li, X.; Eastman, E. M.; Schwartz, R. J.; Draghia-Akli, R.

1999-01-01

Relatively low levels of expression from naturally occurring promoters have limited the use of muscle as a gene therapy target. Myogenic restricted gene promoters display complex organization usually involving combinations of several myogenic regulatory elements. By random assembly of E-box, MEF-2, TEF-1, and SRE sites into synthetic promoter recombinant libraries, and screening of hundreds of individual clones for transcriptional activity in vitro and in vivo, several artificial promoters were isolated whose transcriptional potencies greatly exceed those of natural myogenic and viral gene promoters.

In vitro digestibility, free and bound phenolic profiles and antioxidant activity of thermally treated Eragrostis tef L.

PubMed

Koubová, Eva; Mrázková, Martina; Sumczynski, Daniela; Orsavová, Jana

2018-06-01

Total phenolic content, phenolic profile and antioxidant activity were determined in free and bound phenolic fractions of thermally treated brown and white teff grains. Phenolic content in raw brown and white teff (1540 and 992 mg gallic acid equivalent kg -1 ) as well as antioxidant activity (6.3 and 5.5 mmol trolox equivalent kg -1 ) were higher in free phenolic fractions. The most significant decrease in total phenolics was observed after application of the sous-vide method (35% for brown teff and 11% for white teff). Main free phenolics of heat-treated teff were ferulic, protocatechuic, p-coumaric and ellagic acids, rutin and epigallocatechin. Main bound phenolics were ferulic, gallic, sinapic and ellagic acids, catechin and epigallocatechin. The detrimental effect on free and bound quercetin and bound cinnamic acid concentrations was also examined during heat treatment. Thermally treated brown teff showed a high level of in vitro organic matter digestibility if water cooking and rice cooker (both 99.5%) and sous-vide (96.5%) methods were applied. The sous-vide method may be recommended as the most suitable hydrothermal treatment for grains of teff when compared with water cooking and rice cooker methods. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Dioxins, Furans and PCBs in Recycled Water for Indirect Potable Reuse

PubMed Central

Rodriguez, Clemencia; Cook, Angus; Devine, Brian; Van Buynder, Paul; Lugg, Richard; Linge, Kathryn; Weinstein, Philip

2008-01-01

An assessment of potential health impacts of dioxin and dioxin-like compounds in recycled water for indirect potable reuse was conducted. Toxic equivalency factors (TEFs) for 2,3,7,8-substituted polychlorinated dibenzo-p-dioxins (PCDD) and dibenzofurans (PCDFs) and dioxin-like polychlorinated biphenyls (PCBs) congeners have been developed by the World Health Organization to simplify the risk assessment of complex mixtures. Samples of secondary treated wastewater in Perth, Australia were examined pre-and post-tertiary treatment in one full-scale and one pilot water reclamation plant. Risk quotients (RQs) were estimated by expressing the middle-bound toxic equivalent (TEQ) and the upper-bound TEQ concentration in each sampling point as a function of the estimated health target value. The results indicate that reverse osmosis (RO) is able to reduce the concentration of PCDD, PCDF and dioxin-like PCBs and produce water of high quality (RQ after RO=0.15). No increased human health risk from dioxin and dioxin-like compounds is anticipated if highly treated recycled water is used to augment drinking water supplies in Perth. Recommendations for a verification monitoring program are offered. PMID:19151430

Genetic and Cellular Mechanisms Regulating Anterior Foregut and Esophageal Development

PubMed Central

Jacobs, Ian J.; Ku, Wei-Yao; Que, Jianwen

2012-01-01

Separation of the single anterior foregut tube into the esophagus and trachea involves cell proliferation and differentiation, as well as dynamic changes in cell-cell adhesion and migration. These biological processes are regulated and coordinated at multiple levels through the interplay of the epithelium and mesenchyme. Genetic studies and in vitro modeling have shed light on relevant regulatory networks that include a number of transcription factors and signaling pathways. These signaling molecules exhibit unique expression patterns and play specific functions in their respective territories before the separation process occurs. Disruption of regulatory networks inevitably leads to defective separation and malformation of the trachea and esophagus and results in the formation of a relatively common birth defect, esophageal atresia with or without tracheoesophageal fistula (EA/TEF). Significantly, some of the signaling pathways and transcription factors involved in anterior foregut separation continue to play important roles in the morphogenesis of the individual organs. In this review, we will focus on new findings related to these different developmental processes and discuss them in the context of developmental disorders (or birth defects) commonly seen in clinics. PMID:22750256

FTIR spectroscopy supported by statistical techniques for the structural characterization of plastic debris in the marine environment: Application to monitoring studies.

PubMed

Mecozzi, Mauro; Pietroletti, Marco; Monakhova, Yulia B

2016-05-15

We inserted 190 FTIR spectra of plastic samples in a digital database and submitted it to Independent Component Analysis (ICA) to extract the "pure" plastic polymers present. These identified plastics were polypropylene (PP), high density polyethylene (HDPE), low density polyethylene (LDPE), high density polyethylene terephthalate (HDPET), low density polyethylene terephthalate (LDPET), polystyrene (PS), Nylon (NL), polyethylene oxide (OPE), and Teflon (TEF) and they were used to establish the similarity with unknown plastics using the correlation coefficient (r), and the crosscorrelation function (CC). For samples with r<0.8 we determined the Mahalanobis Distance (MD) as additional tool of identification. For instance, for the four plastic fragments found in the Carretta carretta, one plastic sample was assigned to OPE due to its r=0.87; for all the other three plastic samples, due to the r values ranging between 0.83 and0.70, the support of MD suggested LDPET and OPE as co-polymer constituents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Translations on Eastern Europe, Political, Sociological and Military Affairs, Number 1603

DTIC Science & Technology

1978-11-01

earlycniia hood with equal fluency while their hearts beat in unison and they share the same patriotic feelings. ThP noble idea of unity in the...moral judgment? If he as ’Wit"ChlreTef I" are inV°ked t0 the Credit °f the dividual while he as profit calculated on his own, brings a cement ...repaired with the mortar of words; it must be tracked down to its foundation and must be analyzed with lull attention and responsibility/without

Development of a PCR-RFLP method based on the transcription elongation factor 1-α gene to differentiate Fusarium graminearum from other species within the Fusarium graminearum species complex.

PubMed

Garmendia, Gabriela; Umpierrez-Failache, Mariana; Ward, Todd J; Vero, Silvana

2018-04-01

Fusarium head blight (FHB) is a destructive disease of cereals crops worldwide and a major food safety concern due to grain contamination with trichothecenes and other mycotoxins. Fusarium graminearum, a member of the Fusarium graminearum species complex (FGSC) is the dominant FHB pathogen in many parts of the world. However, a number of other Fusarium species, including other members of the FGSC, may also be present for example in Argentina, New Zealand, Ethiopia, Nepal, Unites States in cereals such as wheat and barley. Proper species identification is critical to research aimed at improving disease and mycotoxin control programs. Identification of Fusarium species is are often unreliable by traditional, as many species are morphologically cryptic. DNA sequence-based methods offer a reliable means of species identification, but can be expensive when applied to the analyses of population samples. To facilitate identification of the major causative agent of FHB, this work describes an easy and inexpensive method to differentiate F. graminearum from the remaining species within the FGSC and from the other common Fusarium species causing FHB in cereals. The developed method is based on a PCR-RFLP of the transcription elongation factor (TEF 1-α) gene using the restriction enzyme BsaHI. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Cylindrocladium scoparium on Eucalyptus.

PubMed

Qiao, Tian-Min; Zhang, Jing; Li, Shu-Jiang; Han, Shan; Zhu, Tian-Hui

2016-10-01

Eucalyptus dieback disease, caused by Cylindrocladium scoparium , has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP) were developed for detection of C. scoparium based on factor 1-alpha (tef1) and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium . The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products.

Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Cylindrocladium scoparium on Eucalyptus

PubMed Central

Qiao, Tian-Min; Zhang, Jing; Li, Shu-Jiang; Han, Shan; Zhu, Tian-Hui

2016-01-01

Eucalyptus dieback disease, caused by Cylindrocladium scoparium, has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP) were developed for detection of C. scoparium based on factor 1-alpha (tef1) and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium. The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products. PMID:27721691

Numerical investigations on aerodynamic forces of deformable foils in hovering motions

NASA Astrophysics Data System (ADS)

Su, Xiaohui; Yin, Zhen; Cao, Yuanwei; Zhao, Yong

2017-04-01

In this paper, the aerodynamic forces of deformable foils for hovering flight are numerically investigated by a two-dimensional finite-volume arbitrary Lagrangian Eulerian Navier-Stokes solver. The effects of deformation on the lift force generation mechanisms of deformable wings in hovering flight are studied by comparison and analysis of deformable and rigid wing results. The prescribed deformation of the wings changes their morphing during hovering motion in both camber and angle of incidence. The effects of deflection amplitude, deflection phase, and rotation location on the aerodynamic performances of the foils, as well as the associated flow structures, are investigated in details, respectively. Results obtained show that foil morphing changes both Leading Edge Vortex (LEV) and Trailing Edge Vortex (TEV) generation and development processes. Consequently, the lift force generation mechanisms of deformable wings differ from those of rigid foil models. For the full deformation foil model studied, the effect of foil deformation enhances its lift force during both wake capture and delayed stall. There is an optimized camber amplitude, which was found to be 0.1*chord among those cases simulated. Partial deformation in the foil does not enhance its lift force due to unfavorable foil camber. TEV is significantly changed by the local angle of attack due to the foil deformation. On the other hand, Trailing Edge Flap (TEF) deflection in the hinge connected two-rigid-plate model directly affects the strength of both the LEV and TEV, thus influencing the entire vortex shedding process. It was found that lift enhancement can reach up to 33.5% just by the TEF deflection alone.

Cloning of an SNF2/SWI2-related protein that binds specifically to the SPH motifs of the SV40 enhancer and to the HIV-1 promoter.

PubMed

Sheridan, P L; Schorpp, M; Voz, M L; Jones, K A

1995-03-03

We have isolated a human cDNA clone encoding HIP116, a protein that binds to the SPH repeats of the SV40 enhancer and to the TATA/inhibitor region of the human immunodeficiency virus (HIV)-1 promoter. The predicted HIP116 protein is related to the yeast SNF2/SWI2 transcription factor and to other members of this extended family and contains seven domains similar to those found in the vaccinia NTP1 ATPase. Interestingly, HIP116 also contains a C3HC4 zinc-binding motif (RING finger) interspersed between the ATPase motifs in an arrangement similar to that found in the yeast RAD5 and RAD16 proteins. The HIP116 amino terminus is unique among the members of this family, and houses a specific DNA-binding domain. Antiserum raised against HIP116 recognizes a 116-kDa nuclear protein in Western blots and specifically supershifts SV40 and HIV-1 protein-DNA complexes in gel shift experiments. The binding site for HIP116 on the SV40 enhancer directly overlaps the site for TEF-1, and like TEF-1, binding of HIP116 to the SV40 enhancer is destroyed by mutations that inhibit SPH enhancer activity in vivo. Purified fractions of HIP116 display strong ATPase activity that is preferentially stimulated by SPH DNA and can be inhibited specifically by antibodies to HIP116. These findings suggest that HIP116 might affect transcription, directly or indirectly, by acting as a DNA binding site-specific ATPase.

Review of oesophageal atresia and tracheoesophageal fistula in hospital sultanah bahiyah, alor star. Malaysia from january 2000 to december 2009.

PubMed

Narasimman, S; Nallusamy, M; Hassan, S

2013-01-01

Oesophageal atresia (EA) and tracheoesophageal fistula (TEF) is one of the congenital anomaly occurring in the newborns with the incidence of 1 in 2500 births seen worldwide. A retrospective review of newborns admitted to Hospital Sultanah Bahiyah (HSB) from 1st January 2000 to 31st December 2009 was done. The objective was to look at the influence of birth weight, time of surgical intervention, presence of other congenital anomaly and presence of preoperative pneumonia to the immediate outcome (mortality) of the surgery. There were 47 patients with oesophageal atresia, out of which 26 (55%) were males and 21 (45%) females. The distribution of patients by race were 34 Malays (72%), 9 Chinese (19%) and 4 Indians (9%). The birth weight of the babies range from 0.8 kg to 4.0 kg and there was a significant association with the outcome of the surgery (p< 0.05). Most of the babies (20) were operated within 24 hours of presentation but there was no significant association to the outcome. 23 (49%) of them were born with congenital malformation and there was a significant association with the outcome of the surgery (p<0.05). Based on the chest roentgenogram, 20 (43%) of them had pneumonia with significant association with the outcome (p<0.05). The mortality rate is 23% and the causes of death were pneumonia (36%), renal failure (18%), cardiac malformation (18%) and multiple congenital malformations (28%). The outcome of EA and TEF is determined mainly by birth weight, congenital malformations and presence of preoperative pneumonia in HSB.

Dioxin-like activity of brominated dioxins as individual compounds or mixtures in in vitro reporter gene assays with rat and mouse hepatoma cell lines.

PubMed

Suzuki, G; Nakamura, M; Michinaka, C; Tue, N M; Handa, H; Takigami, H

2017-10-01

In vitro reporter gene assays detecting dioxin-like compounds have been developed and validated since the middle 1990's, and applied to the determination of dioxin-like activities in various samples for their risk management. Data on characterizing the potency of individual brominated dioxins and their activity in mixture with chlorinated dioxins are still limited on the cell-based assay. This study characterized the dioxin-like activities of the 32 brominated dioxins, such as polybrominated dibenzo-p-dioxins, polybrominated dibenzofurans (PBDFs), coplanar polybrominated biphenyls, mixed halogenated dibenzo-p-dioxins and dibenzofurans (PXDFs), as a sole component or in a mixture by DR-CALUX (dioxin-responsive chemically activated luciferase expression) using the rat hepatoma H4IIE cell line and XDS-CALUX (xenobiotic detection systems-chemically activated luciferase expression) assays using the mouse hepatoma H1L6.1 cell line. The 2,3,7,8-TCDD-relative potencies (REPs) of most of the brominated dioxins were within a factor of 10 of the WHO toxicity equivalency factor (WHO-TEF) for the chlorinated analogues. The REPs of a few PXDFs were an order of magnitude higher than the corresponding WHO-TEFs, indicating their toxicological importance. Results with reconstituted mixtures suggest that the activity of brominated and chlorinated dioxins in both CALUX assays was dose-additive. Thus, obtained results indicated the applicability of the CALUX assays as screening tools of brominated dioxins together with their chlorinated analogues. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Case for Simulation-Based Mastery Learning Education Courses for Practicing Surgeons.

PubMed

Baumann, Lauren M; Barsness, Katherine A

2018-03-12

Pediatric surgeons rely on simulation courses to develop skills for safe minimally invasive repair of complex congenital anomalies. The majority of minimally invasive surgery (MIS) training courses occur during short "exposure courses" at annual conferences. Little data are available to support the benefit of these courses relative to the safe implementation of new skills. The purpose of this article is to determine the impact of an exposure course for advanced neonatal MIS on self-perceived comfort levels with independent performance of advanced MISs. Participants of a 4-hour hands-on course for neonatal MIS were surveyed regarding clinical practices and pre- and post-training perceived "comfort levels" of MIS skills for thoracoscopic esophageal atresia with tracheoesophageal fistula (tTEF) repair, thoracoscopic left upper lobe pulmonary lobectomy (tLobe), and laparoscopic duodenal atresia (lapDA) repair. Descriptive analyses were performed. Seventeen participants completed pre- and postcourse surveys. The majority of participants had no prior experience with tLobe (59%) or lapDA (53%), and 35% had no experience with tTEF repair. Similarly, the majority were "not comfortable" with these procedures. After the short course, the majority of surgeons reported that they were "likely to perform" these operations within 6 months, despite low levels of baseline experience and comfort levels. An exposure training course led to immediate perception of increased skills and confidence. However, these courses typically do not provide basic tenets of expert performance that demands deliberate practice. Future course design should transition to a mastery learning framework wherein regular skill assessments, milestones, and unlimited education time are prioritized before implementation of the new skills.

Interrelationship and path coefficient analysis of yield components in F4 progenies of tef (Eragrostis tef).

PubMed

Debebe, Abel; Singh, Harijat; Tefera, Hailu

2014-01-01

This experiment was conducted at Debre Zeit and Akaki during 2004-2005 cropping season on F2-derived F4 bulk families of three crosses, viz, DZ-01-974 x DZ-01-2786, DZ-01-974 x DZ-Cr-37 and Alba x Kaye Murri. To estimate the correlations and path coefficients between yield and yield components, 63 F4 families were taken randomly from each of the three crosses. The 189 F4 families, five parents and two checks were space planted following in 14 x 14 simple lattice design. Study of associations among traits indicated that yield was positively associated with shoot biomass, harvest index, lodging index and panicle kernel weight at phenotypic level at Debre Zeit. At Akaki, yield had significant positive correlation with shoot biomass, harvest index, plant height, panicle length and panicle weight. At genotypic level, grain yield per plot exhibited positive association with harvest index, shoot biomass, lodging index and panicle kernel weight at Debre Zeit. By contrast, days to heading, days to maturity, plant height and panicle length showed negative association with yield. At Akaki, kernel yield per plot was positively correlated at genotypic level with all the traits considered where lodging index had the highest correlation followed by shoot biomass, panicle kernel weight and harvest index. Path coefficient analysis at both phenotypic and genotypic levels for both the locations suggested those shoot biomass and harvest indexes are the two important yield determining traits. These two traits might be useful in indirect selection for yield improvement in the material generated from the three crosses under consideration.

Polyflex expandable stents in the treatment of esophageal disease: initial experience.

PubMed

Pennathur, Arjun; Chang, Andrew C; McGrath, Kevin M; Steiner, Gregory; Alvelo-Rivera, Miguel; Awais, Omar; Gooding, William E; Christie, Neil A; Gilbert, Sebastien; Landreneau, Rodney J; Luketich, James D

2008-06-01

The new generation of expandable plastic esophageal stents (Polyflex; Boston Scientific, Natick, MA), combine the features of plastic and self-expanding metallic stents. The main objective of this study is to evaluate our initial experience with Polyflex expandable stents in the treatment of esophageal disease from two institutions. A total of 58 Polyflex stents were placed in 38 patients over a two-year period. There were 24 men and 14 women, with a median age of 63 years (range, 25 to 83). The most common indication for placement was an esophageal stricture in 25 patients (66%); other causes included leak in 8 (21%) and tracheoesophageal fistula (TEF) in 5 (13%). We evaluated the hospital course, complications, and outcomes. The median postoperative stay was one day. Complications included migration in 38 stents (63%) (28 patients; 73%), retrosternal chest discomfort in nine, reflux in four, airway obstruction in one, and food impaction in three. Continued leak or a persistent TEF occurred in five patients (38%). Reintervention was required predominantly due to migration of the stent at a mean interval of 46 days (range, 1 to 353). Patients with dysphagia improved significantly with dysphagia scores (1 = no dysphagia; 5 = unable to swallow saliva) improving from 3.44 to 2.15 (p < 0.0001). Polyflex stents were effective in the relief of dysphagia due to strictures. They were less effective in esophageal perforations or leaks. Their primary disadvantage is a high migration rate and further improvements in design are required to decrease this high incidence of migration.

Xenobiotic metabolism in the fourth dimension: PARtners in time.

PubMed

Green, Carla B; Takahashi, Joseph S

2006-07-01

A significant portion of the transcriptome in mammals, including the PAR bZIP transcription factors DBP, HLF, and TEF, is under circadian clock control. In this issue of Cell Metabolism, Gachon and colleagues (Gachon et al., 2006) show that disruption of these three genes in mice alters gene expression patterns of many proteins involved in drug metabolism and in liver and kidney responses to xenobiotic agents. Triple mutant mice have severe physiological deficits, including increased hypersensitivity to xenobiotic agents and premature aging, highlighting the profound effect the circadian clock has on this important response system.

Circumscription and Taxonomic Arrangement of Nigroboletus roseonigrescens Gen. Et Sp. Nov., a New Member of Boletaceae from Tropical South–Eastern China

PubMed Central

Gelardi, Matteo; Vizzini, Alfredo; Ercole, Enrico; Horak, Egon; Ming, Zhang; Li, Tai–Hui

2015-01-01

Nigroboletus is proposed as a novel genus in family Boletaceae, subfamily Boletoideae, to include N. roseonigrescens, a new boletoid species from tropical environment in south–eastern China. Detailed morphological description, color pictures of both fresh basidiomes in habitat and dried material along with photomicrographs and line drawings of the main anatomical features are provided, supported by a comprehensive phylogeny based on multigene molecular analysis (nrITS, nrLSU, rpb1, rpb2 and tef1-α datasets). Taxonomic placement and evolutionary relationships of Nigroboletus are investigated. PMID:26263180

The Acoustic Model Evaluation Committee (AMEC) Reports. Volume 3. Evaluation of the RAYMODE X Propagation Loss Model. Book 2. Appendices A-D

DTIC Science & Technology

1982-09-01

2 of 3 The Acasstic Model Evaluation Committee (AMEC) Reports Vodlme III, Appendices A-i) Elakiaie of Me RAYAODE X f*W#ton Loss Model (U) Prepared by...Richard B. Laer, NORDP Numerical Modefa Division 11N Pylos of RAYNONE X (g) ’T evy •u v ,ap,.,,.,.nDTiC hpWor 1984;& AELE TEfTE Aft 12 W~ LAJ...Activity NSTL Station, Mississippi 39529 84 04 06 511 CONFIDENTIAL .%.. CONFIDENTIAL Appendix IliA. Accuracy Assessment of RAYMODE X Compared to SUDS

2,3,7,8-Tetrachlorodibenzo-p-dioxin equivalents in tissues of birds at Green Bay, Wisconsin, USA

USGS Publications Warehouse

Jones, Paul D.; Giesy, John P.; Newsted, John L.; Verbrugge, David A.; Beaver, Donald L.; Ankley, Gerald T.; Tillitt, Donald E.; Lodge, Keith B.; Niemi, Gerald J.

1993-01-01

The environment has become contaminated with complex mixtures of planar, chlorinated hydrocarbons (PCHs) such as polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and structurally similar compounds. Because the potencies of individual congeners to cause the same adverse effects vary greatly and the relative as well as absolute concentrations of individual PCH vary among samples from different locations, it is difficult to assess the toxic effects of these mixtures on wildlife. These compounds can cause a number of adverse effects, however, because the toxic effects which occur at ecologically-relevant concentrations such as embryo-lethality and birth defects appear to be mediated through the same mechanism, the potency of individual congeners can be reported relative to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) which is the most toxic congener in the PCH class. The concentations of 2,3,7,8-TCDD Equivalents (TCDD-EQ) were determined in the tissues of aquatic and terrestrial birds of Green Bay, Wisconsin by the H4IIE bioassay system and compared toxic equivalency factors (TEFs) with the concentration predicted by the use of toxic equivalency factors applied to concentrations of PCH, which were determined by instrumental analyses. Concentrations of TCDD-EQ ranged from 0.52 to 440 ng/kg, wet weight. The greatest concentrations occurred in the fish-eating birds. Concentrations of TCDD-EQ, which were determined by the two methods were significantly correlated, but the additive model which used the TEFs with concentrations of measured PCB, PCDD and PCDF congeners underestimated the concentrations of TCDD-EQ measured by the H4IIE bioassay by an average of 57%. This is thought to be due to contributions from un-quantified PCH, which are known to occur in the environment. Of the quantified PCH congeners, PCDD and PCDF contributed a small portion of the TCDD-EQ in the aquatic birds, while most of the TCDD-EQ were due to non-ortho-substituted PCBs. In the terrestrial birds, the proportion of the TCDD-EQ contributed by the PCDD and PCDF was greater.This paper has been reviewed in accord with U.S. Environmental Protection Agency policy. Mention of specific products or trade names does not imply endorsement by the U.S. Government.

Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.).

PubMed

Huis, Rudy; Hawkins, Simon; Neutelings, Godfrey

2010-04-19

Quantitative real-time PCR (qRT-PCR) is currently the most accurate method for detecting differential gene expression. Such an approach depends on the identification of uniformly expressed 'housekeeping genes' (HKGs). Extensive transcriptomic data mining and experimental validation in different model plants have shown that the reliability of these endogenous controls can be influenced by the plant species, growth conditions and organs/tissues examined. It is therefore important to identify the best reference genes to use in each biological system before using qRT-PCR to investigate differential gene expression. In this paper we evaluate different candidate HKGs for developmental transcriptomic studies in the economically-important flax fiber- and oil-crop (Linum usitatissimum L). Specific primers were designed in order to quantify the expression levels of 20 different potential housekeeping genes in flax roots, internal- and external-stem tissues, leaves and flowers at different developmental stages. After calculations of PCR efficiencies, 13 HKGs were retained and their expression stabilities evaluated by the computer algorithms geNorm and NormFinder. According to geNorm, 2 Transcriptional Elongation Factors (TEFs) and 1 Ubiquitin gene are necessary for normalizing gene expression when all studied samples are considered. However, only 2 TEFs are required for normalizing expression in stem tissues. In contrast, NormFinder identified glyceraldehyde-3-phosphate dehydrogenase (GADPH) as the most stably expressed gene when all samples were grouped together, as well as when samples were classed into different sub-groups.qRT-PCR was then used to investigate the relative expression levels of two splice variants of the flax LuMYB1 gene (homologue of AtMYB59). LuMYB1-1 and LuMYB1-2 were highly expressed in the internal stem tissues as compared to outer stem tissues and other samples. This result was confirmed with both geNorm-designated- and NormFinder-designated-reference genes. The use of 2 different statistical algorithms results in the identification of different combinations of flax HKGs for expression data normalization. Despite such differences, the use of geNorm-designated- and NormFinder-designated-reference genes enabled us to accurately compare the expression levels of a flax MYB gene in different organs and tissues. Our identification and validation of suitable flax HKGs will facilitate future developmental transcriptomic studies in this economically-important plant.

Rapid identification of the genus Dekkera/Brettanomyces, the Dekkera subgroup and all individual species.

PubMed

Hulin, M; Harrison, E; Stratford, M; Wheals, A E

2014-09-18

The genus Dekkera/Brettanomyces comprises five described species: Dekkera bruxellensis, D. anomala, Brettanomyces custersianus, B. naardenensis and B. nanus. Some of them, especially D. bruxellensis, are important spoilage organisms, particularly in the wine and beverage industries. Because of their economic importance many different methods have been developed to identify members of the genus in general and D. bruxellensis in particular. These methods vary in their rapidity, complexity and cost but, partly because of confidentiality issues, it is unclear which methods are used, or how widely, in the relevant industries. Building on previous work with the genera Saccharomyces and Zygosaccharomyces, a suite of eight PCR primer pairs has been designed either on the D1-D2 region of the 26S rRNA gene or translation elongation factor TEF1-α. These primers can specifically identify the genus as a whole, only Dekkera species, each one of the five recognised species as well as a significant subgroup of D. bruxellensis represented by NCYC 3426. Multiplexing has also been tried and it has been shown to be possible with some combinations of genus or Dekkera-level and species-specific primers. Using direct colony PCR amplification followed by gel electrophoresis, a clear positive result can be obtained in less than 3h, thus providing a quick, reliable and inexpensive way to identify target species. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural organization and chromosomal assignment of the mouse embryonic TEA domain-containing factor (ETF) gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suzuki, Kazuo; Yasunami, Michio; Matsuda, Yoichi

1996-09-01

Embryonic TEA domain-containing factor (ETF) belongs to the family of proteins structurally related to transcriptional enhancer factor-1 (TEF-1) and is implicated in neural development. Isolation and characterization of the cosmid clones encoding the mouse ETF gene (Etdf) revealed that Etdf spans approximately 17.9 kb and consists of 12 exons. The exon-intron structure of Etdf closely resembles that of the Drosophila scalloped gene, indicating that these genes may have evolved from a common ancestor. Then multiple transcription initiation sites revealed by S1 protection and primer extension analyses are consistent with the absence of the canonical TATA and CAAT boxes in themore » 5{prime}-flanking region, which contains many potential regulatory sequences, such as the E-box, N-box, Sp1 element, GATA-1 element, TAATGARAT element, and B2 short interspersed element (SINE) as well as several direct and inverted repeat sequences. The Etdf locus was assigned to the proximal region of mouse chromosome 7 using fluorescence in situ hybridization and linkage mapping analyses. These results provide the molecular basis for studying the regulation, in vivo function, and evolution of Etdf. 29 refs., 5 figs., 1 tab.« less

Structural organization and chromosomal assignment of the mouse embryonic TEA domain-containing factor (ETF) gene.

PubMed

Suzuki, K; Yasunami, M; Matsuda, Y; Maeda, T; Kobayashi, H; Terasaki, H; Ohkubo, H

1996-09-01

Embryonic TEA domain-containing factor (ETF) belongs to the family of proteins structurally related to transcriptional enhancer factor-1 (TEF-1) and is implicated in neural development. Isolation and characterization of the cosmid clones encoding the mouse ETF gene (Etdf) revealed that Etdf spans approximately 17.9 kb and consists of 12 exons. The exon-intron structure of Etdf closely resembles that of the Drosophila scalloped gene, indicating that these genes may have evolved from a common ancestor. The multiple transcription initiation sites revealed by S1 protection and primer extension analyses are consistent with the absence of the canonical TATA and CAAT boxes in the 5'-flanking region, which contains many potential regulatory sequences, such as the E-box, N-box, Sp1 element, GATA-1 element, TAATGARAT element, and B2 short interspersed element (SINE) as well as several direct and inverted repeat sequences. The Etdf locus was assigned to the proximal region of mouse chromosome 7 using fluorescence in situ hybridization and linkage mapping analyses. These results provide the molecular basis for studying the regulation, in vivo function, and evolution of Etdf.

Fate and hazard of the electrochemical oxidation of triclosan. Evaluation of polychlorodibenzo‑p‑dioxins and polychlorodibenzofurans (PCDD/Fs) formation.

PubMed

Solá-Gutiérrez, Claudia; San Román, M Fresnedo; Ortiz, Inmaculada

2018-06-01

Triclosan (TCS) is widely used as antiseptic or preservative in many personal care products (PCPs), such as cosmetics, hand wash, toothpaste and deodorant soaps, among others. It is characterized by acute toxicity, resistance to biodegradation, environmental persistence and relatively high lipophilicity. In order to protect the environment and natural resources from the negative effects of the discharge of polluted wastewater with TCS, the application of efficient remediation technologies able to degrade the pollutant to harmless levels becomes crucial. Electrochemical oxidation, among all advanced oxidation processes (AOPs), has been reported as very effective in the complete degradation of a number of persistent pollutants; therefore, its performance using boron-doped diamond (BDD) anodes, and response to operation variables, has been studied in this work. As expected, complete degradation of TCS was achieved in all the studied conditions; however, going a step further and knowing that TCS is a precursor of polychlorinated dibenzo‑p‑dioxins and dibenzofurans (PCDD/Fs), their quantitative presence in the oxidation media has been assessed. Results showed the dominance of dichlorinated (DCDD) and trichlorinated (TrCDD/Fs) in the homologue profile of total PCDD/Fs, reaching values up to 1.48 × 10 5  pg L -1 in samples with initial concentration of TCS of 100 mg L -1 and NaCl as electrolyte. Under these conditions, the International Toxicity Equivalency Factor (I-TEF) achieved values up to 2.76 × 10 2  pg L -1 . Nevertheless, the presence of copper in the oxidation medium tends to reduce I-TEF values. Finally, considering the information reported in literature, a mechanism describing the formation of low chlorinated PCDD/Fs from TCS oxidation reactions is proposed. Copyright © 2018. Published by Elsevier B.V.

Molecular phylogenetic and scanning electron microscopical analyses places the Choanephoraceae and the Gilbertellaceae in a monophyletic group within the Mucorales (Zygomycetes, Fungi).

PubMed

Voigt, Kerstin; Olsson, L

2008-09-01

A multi-gene genealogy based on maximum parsimony and distance analyses of the exonic genes for actin (act) and translation elongation factor 1 alpha (tef), the nuclear genes for the small (18S) and large (28S) subunit ribosomal RNA (comprising 807, 1092, 1863, 389 characters, respectively) of all 50 genera of the Mucorales (Zygomycetes) suggests that the Choanephoraceae is a monophyletic group. The monotypic Gilbertellaceae appears in close phylogenetic relatedness to the Choanephoraceae. The monophyly of the Choanephoraceae has moderate to strong support (bootstrap proportions 67% and 96% in distance and maximum parsimony analyses, respectively), whereas the monophyly of the Choanephoraceae-Gilbertellaceae clade is supported by high bootstrap values (100% and 98%). This suggests that the two families can be joined into one family, which leads to the elimination of the Gilbertellaceae as a separate family. In order to test this hypothesis single-locus neighbor-joining analyses were performed on nuclear genes of the 18S, 5.8S, 28S and internal transcribed spacer (ITS) 1 ribosomal RNA and the translation elongation factor 1 alpha (tef) and beta tubulin (betatub) nucleotide sequences. The common monophyletic origin of the Choanephoraceae-Gilbertellaceae clade could be confirmed in all gene trees and by investigation of their ultrastructure. Sporangia with persistent, sutured walls splitting in half at maturity and ellipsoidal sporangiospores with striated ornamentations and polar ciliate appendages arising from spores in persistent sporangia and dehiscent sporangiola represent synapomorphic characters of this group. We discuss our data in the context of the historical development of their taxonomy and physiology and propose a reduction of the two families to one family, the Choanephoraceae sensu lato comprising species which are facultative plant pathogens and parasites, especially in subtropical to tropical regions.

Cosmic radiation exposure of biological test systems during the EXPOSE-E mission.

PubMed

Berger, Thomas; Hajek, Michael; Bilski, Pawel; Körner, Christine; Vanhavere, Filip; Reitz, Günther

2012-05-01

In the frame of the EXPOSE-E mission on the Columbus external payload facility EuTEF on board the International Space Station, passive thermoluminescence dosimeters were applied to measure the radiation exposure of biological samples. The detectors were located either as stacks next to biological specimens to determine the depth dose distribution or beneath the sample carriers to determine the dose levels for maximum shielding. The maximum mission dose measured in the upper layer of the depth dose part of the experiment amounted to 238±10 mGy, which relates to an average dose rate of 408±16 μGy/d. In these stacks of about 8 mm height, the dose decreased by 5-12% with depth. The maximum dose measured beneath the sample carriers was 215±16 mGy, which amounts to an average dose rate of 368±27 μGy/d. These values are close to those assessed for the interior of the Columbus module and demonstrate the high shielding of the biological experiments within the EXPOSE-E facility. Besides the shielding by the EXPOSE-E hardware itself, additional shielding was experienced by the external structures adjacent to EXPOSE-E, such as EuTEF and Columbus. This led to a dose gradient over the entire exposure area, from 215±16 mGy for the lowest to 121±6 mGy for maximum shielding. Hence, the doses perceived by the biological samples inside EXPOSE-E varied by 70% (from lowest to highest dose). As a consequence of the high shielding, the biological samples were predominantly exposed to galactic cosmic heavy ions, while electrons and a significant fraction of protons of the radiation belts and solar wind did not reach the samples.

A coconut oil-rich meal does not enhance thermogenesis compared to corn oil in a randomized trial in obese adolescents.

PubMed

LaBarrie, Janna; St-Onge, Marie-Pierre

2017-01-01

Consumption of medium chain triglycerides (MCT) in overweight adults increases thermogenesis and improves weight management. Coconut oil is a rich natural source of MCT, but its thermogenic effect is unknown. Our study evaluated the effects of a test oil enriched in coconut oil, on energy expenditure, satiety, and metabolic markers in a randomized, double blind, cross-over study. Fifteen children, age 13-18 years, body mass index >85th percentile for age and sex, were enrolled. Two test meals, containing 20 g of fat from either corn oil or a coconut oil-enriched baking fat (1.1 g of fatty acids with chain lengths ≤ 10C), were administered. A fasting blood sample was taken before breakfast and at 30, 45, 60, 120, and 180 min post-meal for measurement of metabolites. Thermic effect of food (TEF) was assessed over 6 h using indirect calorimetry. Satiety was measured using visual analog scales (VAS). There was no significant effect of fat type, time, or fat type × time interaction on TEF, appetite/satiety, glucose, and insulin area under the curve. There was a significant effect of fat type on leptin (P=0.027), triglycerides (P=0.020) and peptide YY (P=0.0085); leptin and triglyceride concentrations were lower and peptide YY concentrations were higher with corn oil consumption. A coconut oil-enriched baking fat does not enhance thermogenesis and satiety in children. Given that this is the only current study of its kind, more research is needed into the use of coconut oil as a tool in weight management in overweight and obese children.

Morphological and molecular analysis of Fusarium lateritium, the cause of gray necrosis of hazelnut fruit in Italy.

PubMed

Vitale, S; Santori, A; Wajnberg, E; Castagnone-Sereno, P; Luongo, L; Belisario, A

2011-06-01

Fusarium lateritium is a globally distributed plant pathogen. It was recently reported as the causal agent of nut gray necrosis (NGN) on hazelnut. Isolate characterization within F. lateritium was undertaken to investigate how morphological and molecular diversity was associated with host and geographic origin. Morphological studies combined with inter-simple-sequence repeat (ISSR) analysis, and phylogenetic analyses using translation elongation factor 1α (TEF-1α), β-tubulin genes, and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were conducted to resolve relationships among 32 F. lateritium isolates from NGN-affected hazelnut fruit, and 14 from other substrates or 8 from other hosts than hazelnut. Colonies of F. lateritium from hazelnut showed dark grayish-olive differing from the orange-yellow color of all other isolates from other hosts. Generally, isolates from NGN-affected fruit failed to produce sporodochia on carnation leaf agar. The influence of host and substrate on the genetic structure of F. lateritium was supported by ISSR and analyzed with principal coordinates analysis. A relationship between hazelnut and genetic variation was inferred. Phylogenetic analysis of ITS provided limited resolution while TEF-1α and β-tubulin analyses allowed a clear separation between the European and non-European F. lateritium isolates retrieved from GenBank, regardless of host. Though morphological traits of F. lateritium isolates from hazelnut were generally uniform in defining a typical morphogroup, they were not yet phylogenetically defined. In contrast, the typology related to slimy deep orange cultures, due to spore mass, grouped clearly separated from the other F. lateritium isolates and revealed a congruence between morphology and phylogeny.

Polycyclic aromatic hydrocarbon emission profiles and removal efficiency by electrostatic precipitator and wetfine scrubber in an iron ore sintering plant

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ettore Guerriero; Antonina Lutri; Rosanna Mabilia

2008-11-15

A monitoring campaign of polychlorinated dibenzo-p-dioxins and dibenzofurans, polyaromatic hydrocarbons (PAHs), and polychlorinated biphenyl was carried out in an Italian iron ore sintering plant by sampling the combustion gases at the electrostatic precipitator (ESP) outlet, at the Wetfine scrubber (WS) outlet, and by collecting the ESP dust. Few data are available on these micropollutants produced in iron ore sintering plants, particularly from Italian plants. This study investigates the PAH emission profiles and the removal efficiency of ESPs and WS. PAHs were determined at the stack, ESP outlet flue gases, and in ESP dust to characterize the emission profiles and themore » performance of the ESP and the WS for reducing PAH emission. The 11 PAHs monitored are listed in the Italian legislative decree 152/2006. The mean total PAH sum concentration in the stack flue gases is 3.96 {mu}g/N m{sup 3}, in ESP outlet flue gases is 9.73 {mu}g/N m{sup 3}, and in ESP dust is 0.53 {mu}g/g. Regarding the emission profiles, the most abundant compound is benzo(b)fluoranthene, which has a relative low BaP toxic equivalency factors (TEF) value, followed by dibenzo(a,l)pyrene, which has a very high BaP(TEF) value. The emission profiles in ESP dust and in the flue gases after the ESP show some changes, whereas the fingerprint in ESP and stack flue gases is very similar. The removal efficiency of the ESP and of WS on the total PAH concentration is 5.2 and 59.5%, respectively. 2 figs., 5 tabs.« less

STS-128 EVA 1 MISSE 6 Relocation OPS

NASA Image and Video Library

2009-09-02

S128-E-007230 (1 Sept. 2009) --- Astronaut Nicole Stott, Expedition 20 flight engineer, participates in the STS-128 mission's first session of extravehicular activity (EVA) as construction and maintenance continue on the International Space Station. During the six-hour, 35-minute spacewalk, Stott and astronaut John “Danny” Olivas (out of frame), mission specialist, removed an empty ammonia tank from the station’s truss and temporarily stowed it on the station’s robotic arm. Olivas and Stott also retrieved the European Technology Exposure Facility (EuTEF) and Materials International Space Station Experiment (MISSE) from the Columbus laboratory module and installed them on Discovery’s payload bay for return.

STS-128 EVA 1 MISSE 6 Relocation OPS

NASA Image and Video Library

2009-09-02

S128-E-007229 (1 Sept. 2009) --- Astronaut Nicole Stott, Expedition 20 flight engineer, participates in the STS-128 mission's first session of extravehicular activity (EVA) as construction and maintenance continue on the International Space Station. During the six-hour, 35-minute spacewalk, Stott and astronaut John “Danny” Olivas (out of frame), mission specialist, removed an empty ammonia tank from the station’s truss and temporarily stowed it on the station’s robotic arm. Olivas and Stott also retrieved the European Technology Exposure Facility (EuTEF) and Materials International Space Station Experiment (MISSE) from the Columbus laboratory module and installed them on Discovery’s payload bay for return.

STS-128 EVA 1 MISSE 6 Relocation OPS

NASA Image and Video Library

2009-09-02

S128-E-007225 (1 Sept. 2009) --- Astronaut John “Danny” Olivas, STS-128 mission specialist, participates in the mission's first session of extravehicular activity (EVA) as construction and maintenance continue on the International Space Station. During the six-hour, 35-minute spacewalk, Olivas and astronaut Nicole Stott (out of frame), mission specialist, removed an empty ammonia tank from the station’s truss and temporarily stowed it on the station’s robotic arm. Olivas and Stott also retrieved the European Technology Exposure Facility (EuTEF) and Materials International Space Station Experiment (MISSE) from the Columbus laboratory module and installed them on Discovery’s payload bay for return.

STS-128 EVA 1 MISSE 6 Relocation OPS

NASA Image and Video Library

2009-09-02

S128-E-007242 (1 Sept. 2009) --- Astronaut Nicole Stott, Expedition 20 flight engineer, participates in the STS-128 mission's first session of extravehicular activity (EVA) as construction and maintenance continue on the International Space Station. During the six-hour, 35-minute spacewalk, Stott and astronaut John “Danny” Olivas (out of frame), mission specialist, removed an empty ammonia tank from the station’s truss and temporarily stowed it on the station’s robotic arm. Olivas and Stott also retrieved the European Technology Exposure Facility (EuTEF) and Materials International Space Station Experiment (MISSE) from the Columbus laboratory module and installed them on Discovery’s payload bay for return.

STS-128 EVA 1 MISSE 6 Relocation OPS

NASA Image and Video Library

2009-09-02

S128-E-007239 (1 Sept. 2009) --- Astronaut Nicole Stott, Expedition 20 flight engineer, participates in the STS-128 mission's first session of extravehicular activity (EVA) as construction and maintenance continue on the International Space Station. During the six-hour, 35-minute spacewalk, Stott and astronaut John “Danny” Olivas (out of frame), mission specialist, removed an empty ammonia tank from the station’s truss and temporarily stowed it on the station’s robotic arm. Olivas and Stott also retrieved the European Technology Exposure Facility (EuTEF) and Materials International Space Station Experiment (MISSE) from the Columbus laboratory module and installed them on Discovery’s payload bay for return.

Curvularia microspora sp. nov. associated with leaf diseases of Hippeastrum striatum in China.

PubMed

Liang, Yin; Ran, Shuang-Fei; Bhat, Jayarama; Hyde, Kevin D; Wang, Yong; Zhao, De-Gang

2018-01-01

An undescribed Curvularia sp. was isolated from the leaf spot disease of Barbados Lily ( Hippeastrum striatum (Lam.) Moore). Phylogenetic analyses of combined ITS, 28S, GPD1 and TEF1 sequence data place nine strains of this species in the trifolii -clade, but they clustered together as an independent lineage with strong support. This species was morphologically compared with related species in the trifolii -clade. Based on differences in morphology and phylogeny, it is concluded that this species is a new taxon, introduced as Curvularia microspora sp. nov. Pathogenicity testing determined the new species to be pathogenic on H. striatum .

Engineering Yarrowia lipolytica to express secretory invertase with strong FBA1IN promoter.

PubMed

Hong, Seung-Pyo; Seip, John; Walters-Pollak, Dana; Rupert, Ross; Jackson, Raymond; Xue, Zhixiong; Zhu, Quinn

2012-02-01

Oleaginous yeast Yarrowia lipolytica is an important host for the production of lipid-derived compounds or heterologous proteins. Selection of strong promoters and effective expression systems is critical for heterologous protein secretion. To search for a strong promoter in Y. lipolytica, activities of FBA1, TDH1 and GPM1 promoters were compared to that of TEF1 promoter by constructing GUS reporter fusions. The FBA1 promoter activity was 2.2 and 5.5 times stronger than the TDH1 and GPM1 promoters, respectively. The FBA1IN promoter (FBA1 sequence of -826 to +169) containing an intron (+64 to +165) showed five-fold higher expression than the FBA1 promoter (-831 to -1). The transcriptional enhancement by the 5'-region within the FBA1 gene was confirmed by GPM1::FBA1 chimeric promoter construction. Using the strong FBA1IN promoter, four different S. cerevisiae SUC2 expression cassettes were tested for the SUC+ phenotype in Y. lipolytica. Functional invertase secretion was facilitated by the Xpr2 prepro-region with an additional 13 amino acids of mature Xpr2, or by the native Suc2 signal sequence. However, these two secretory signals in tandem, or the mature Suc2 with no secretory signal, did not direct secretion of functional invertase. Unlike previously reported Y. lipolytica SUC+ strains, our engineered stains secreted most of invertase into the medium. Copyright © 2011 John Wiley & Sons, Ltd.

Phytotoxicity of sorgoleone found in grain Sorghum root exudates.

PubMed

Einhellig, F A; Souza, I F

1992-01-01

Root exudates ofSorghum bicolor consist primarily of a dihydroquinone that is quickly oxidized to ap-benzoquinone named sorgoleone. The aim of this investigation was to determine the potential activity of sorgoleone as an inhibitor of weed growth. Bioassays showed 125μM sorgoleone reduced radicle elongation ofEragrostis tef. In liquid culture, 50-μM sorgoleone treatments stunted the growth ofLemna minor. Over a 10-day treatment period, 10μM sorgoleone in the nutrient medium reduced the growth of all weed seedlings tested:Abutilon theophrasti, Datura stramonium, Amaranthus retroflexus, Setaria viridis, Digitaria sanguinalis, andEchinochloa crusgalli. These data show sorgoleone has biological activity at extremely low concentrations, suggesting a strong contribution toSorghum allelopathy.

Three new Graphium species from baobab trees in South Africa and Madagascar.

PubMed

Cruywagen, E M; de Beer, Z W; Roux, J; Wingfield, M J

2010-12-01

Baobabs (Adansonia spp.) are iconic trees, known for their immense size, strange forms, sources of food and as the subjects of myths and mysteries. It is thus surprising that little is known regarding the fungi that infect these trees. During a survey to determine which wound infecting fungi occur on baobabs, synnematous structures were observed and Graphium-like isolates were obtained. Culture characteristics and micro-morphology, together with DNA sequence comparisons for the SSU rRNA, rRNA-ITS and TEF-1α gene regions were used to characterise these fungi. These data revealed three novel Graphium spp. and these are described as G. adansoniae, G. madagascariense and G. fabiforme.

Eight new Arthrinium species from China

PubMed Central

Wang, Mei; Tan, Xiao-Ming; Liu, Fang; Cai, Lei

2018-01-01

Abstract The genus Arthrinium includes important plant pathogens, endophytes and saprobes with a wide host range and geographic distribution. In this paper, 74 Arthrinium strains isolated from various substrates such as bamboo leaves, tea plants, soil and air from karst caves in China were examined using a multi-locus phylogeny based on a combined dataset of ITS rDNA, TEF1 and TUB2, in conjunction with morphological characters, host association and ecological distribution. Eight new species were described based on their distinct phylogenetic relationships and morphological characters. Our results indicated a high species diversity of Arthrinium with wide host ranges, amongst which, Poaceae and Cyperaceae were the major host plant families of Arthrinium species. PMID:29755262

Eight new Arthrinium species from China.

PubMed

Wang, Mei; Tan, Xiao-Ming; Liu, Fang; Cai, Lei

2018-01-01

The genus Arthrinium includes important plant pathogens, endophytes and saprobes with a wide host range and geographic distribution. In this paper, 74 Arthrinium strains isolated from various substrates such as bamboo leaves, tea plants, soil and air from karst caves in China were examined using a multi-locus phylogeny based on a combined dataset of ITS rDNA, TEF1 and TUB2, in conjunction with morphological characters, host association and ecological distribution. Eight new species were described based on their distinct phylogenetic relationships and morphological characters. Our results indicated a high species diversity of Arthrinium with wide host ranges, amongst which, Poaceae and Cyperaceae were the major host plant families of Arthrinium species.

Exposure Assessment of Polycyclic Aromatic Hydrocarbon (PAHs) in Childcare Centers of Muang, Nakhon Ratchasima

NASA Astrophysics Data System (ADS)

Jitlada, C.; Pentamwa, P.

2018-03-01

This study aims to characterize airborne polycyclic aromatic hydrocarbons (PAHs) as of particulate and vapor phases variation. The samples were collected from the childcare centers where divided into urban and rural areas in Nakhon Ratchasima Province of Thailand. The airborne samples were collected from five childcare centers during the dry season in the year 2017. The PAHs species were determined by the gas chromatography and mass spectroscopy (GS/MS) method. Results show that the total concentrations of PAHs were higher than vapor phase that both similar in urban area and rural area. The dominant PAHs compounds of both urban and rural areas were benzo(a)pyrene, benzo(a,h)anthracene and indeno(1,2,3-cd)pyrene, respectively. Furthermore, the concentrations of PAHs in municipality (urban) childcare centers were higher than rural childcare centers area of Nakhon Ratchasima province. The risks associated with exposure to PAHs were evaluated using the TEF approach. The estimated value of lifetime lung cancer risks children in urban were significantly (p < 0.05) 2 times of children in rural, thus demonstrating that exposure to PAHs at levels found at urban site may be cause potential health risks.

In vitro susceptibility and multilocus sequence typing of Fusarium isolates causing keratitis.

PubMed

Dallé da Rosa, P; Nunes, A; Borges, R; Batista, B; Meneghello Fuentefria, A; Goldani, L Z

2018-05-17

Fungal keratitis is recognized as a significant cause of ocular morbidity and blindness especially in developing countries. In this study, we aimed to present the molecular identification and susceptibility of Fusarium isolates causing fungal keratitis in a university hospital in southern Brazil. The samples were identified using the second largest subunit of the RNA polymerase gene (RPB2) and the translation elongation factor 1-alpha (TEF1), while the antifungal susceptibility was tested by the broth microdilution method according to the Clinical and Laboratory Standards Institute (CLSI) methodology. The majority of the isolates belonged to the Fusarium solani species complex (F. solani, F. keratoplasticum and F. falciforme) and Fusarium oxysporum species complex. Antifungal susceptibility has shown that amphotericin B and natamycin were the most effective antifungals across all isolates, followed by voriconazole. Variation among Fusarium complexes in their antifungal sensitivities was observed in our study. The identification of Fusarium species from human samples is important not only from an epidemiological viewpoint, but also for choosing the appropriate antifungal agent for difficult-to-treat Fusarium infections such as keratitis. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Extracellular expression of YlLip11 with a native signal peptide from Yarrowia lipolytica MSR80 in three different yeast hosts.

PubMed

Kumari, Arti; Baronian, Keith; Kunze, Gotthard; Gupta, Rani

2015-06-01

Lipase YlLip11 from Yarrowia lipolytica was expressed with a signal peptide encoding sequence in Arxula adeninivorans, Saccharomyces cerevisiae and Hansenula polymorpha using the Xplor®2 transformation/expression platform and an expression module with the constitutive Arxula-derived TEF1 promoter. The YlLip11 signal peptide was functional in all of the yeast hosts with 97% of the recombinant enzyme being secreted into the culture medium. However, recombinant YlLip11 with His Tag fused at C-terminal was not active. The best recombinant YlLip11 producing A. adeninivorans G1212/YRC102-YlLip11 transformant cultivated in shake flasks produced 2654 U/L lipase, followed by S. cerevisiae SEY6210/YRC103-YlLip11 (1632U/L) and H. polymorpha RB11/YRC103-YlLip11 (1144U/L). Although the biochemical parameters of YlLip11 synthesized in different hosts were similar, their glycosylation level and thermo stability differed. The protein synthesized by the H. polymorpha transformant had the highest degree of glycosylation and with a t1/2 of 60min at 70°C, exhibited the highest thermostability. Copyright © 2015 Elsevier Inc. All rights reserved.

Cosmic Radiation Exposure of Biological Test Systems During the EXPOSE-E Mission

PubMed Central

Hajek, Michael; Bilski, Pawel; Körner, Christine; Vanhavere, Filip; Reitz, Günther

2012-01-01

Abstract In the frame of the EXPOSE-E mission on the Columbus external payload facility EuTEF on board the International Space Station, passive thermoluminescence dosimeters were applied to measure the radiation exposure of biological samples. The detectors were located either as stacks next to biological specimens to determine the depth dose distribution or beneath the sample carriers to determine the dose levels for maximum shielding. The maximum mission dose measured in the upper layer of the depth dose part of the experiment amounted to 238±10 mGy, which relates to an average dose rate of 408±16 μGy/d. In these stacks of about 8 mm height, the dose decreased by 5–12% with depth. The maximum dose measured beneath the sample carriers was 215±16 mGy, which amounts to an average dose rate of 368±27 μGy/d. These values are close to those assessed for the interior of the Columbus module and demonstrate the high shielding of the biological experiments within the EXPOSE-E facility. Besides the shielding by the EXPOSE-E hardware itself, additional shielding was experienced by the external structures adjacent to EXPOSE-E, such as EuTEF and Columbus. This led to a dose gradient over the entire exposure area, from 215±16 mGy for the lowest to 121±6 mGy for maximum shielding. Hence, the doses perceived by the biological samples inside EXPOSE-E varied by 70% (from lowest to highest dose). As a consequence of the high shielding, the biological samples were predominantly exposed to galactic cosmic heavy ions, while electrons and a significant fraction of protons of the radiation belts and solar wind did not reach the samples. Key Words: Space radiation—Dosimetry—Passive radiation detectors—Thermoluminescence—EXPOSE-E. Astrobiology 12, 387–392. PMID:22680685

Survival of Bacillus pumilus spores for a prolonged period of time in real space conditions.

PubMed

Vaishampayan, Parag A; Rabbow, Elke; Horneck, Gerda; Venkateswaran, Kasthuri J

2012-05-01

To prevent forward contamination and maintain the scientific integrity of future life-detection missions, it is important to characterize and attempt to eliminate terrestrial microorganisms associated with exploratory spacecraft and landing vehicles. Among the organisms isolated from spacecraft-associated surfaces, spores of Bacillus pumilus SAFR-032 exhibited unusually high resistance to decontamination techniques such as UV radiation and peroxide treatment. Subsequently, B. pumilus SAFR-032 was flown to the International Space Station (ISS) and exposed to a variety of space conditions via the European Technology Exposure Facility (EuTEF). After 18 months of exposure in the EXPOSE facility of the European Space Agency (ESA) on EuTEF under dark space conditions, SAFR-032 spores showed 10-40% survivability, whereas a survival rate of 85-100% was observed when these spores were kept aboard the ISS under dark simulated martian atmospheric conditions. In contrast, when UV (>110 nm) was applied on SAFR-032 spores for the same time period and under the same conditions used in EXPOSE, a ∼7-log reduction in viability was observed. A parallel experiment was conducted on Earth with identical samples under simulated space conditions. Spores exposed to ground simulations showed less of a reduction in viability when compared with the "real space" exposed spores (∼3-log reduction in viability for "UV-Mars," and ∼4-log reduction in viability for "UV-Space"). A comparative proteomics analysis indicated that proteins conferring resistant traits (superoxide dismutase) were present in higher concentration in space-exposed spores when compared to controls. Also, the first-generation cells and spores derived from space-exposed samples exhibited elevated UVC resistance when compared with their ground control counterparts. The data generated are important for calculating the probability and mechanisms of microbial survival in space conditions and assessing microbial contaminants as risks for forward contamination and in situ life detection.

Communities of practice in life sciences and the need for brokering

PubMed Central

Tierney, Anne

2016-01-01

Etienne Wenger’s work on communities of practice is influential in teaching and learning in higher education. A core work of many postgraduate certificate in teaching and learning (PGCert) courses for new lecturers, it is studied, in the main, as a means to understand how to support and encourage students to achieve more effective learning. Communities of practice can also be applied to academics. In the context of the Research Excellence Framework (REF) and its predecessors, the gulf between research-focused and teaching-Focused academics in life sciences has widened, so that in many institutions, these two groups have evolved into two distinct communities of practice; one whose priority is disciplinary research, the other’s learning and teaching. However, in 2015, the UK government announced that a Teaching Excellence Framework (TEF) would be introduced into higher education in England, as early as 2017. While the exact details of TEF remain unclear, it is certain that “excellence” and “student satisfaction” will be high on the agenda. It is vital, therefore, that the two communities of practice, research-focused and teaching-focused, find ways to come together in order to ensure high quality teaching and learning. Wenger proposes that this can be done through the process of “brokering”, which allows expertise from both communities of practice to cross from one to the other, strengthening both. This should be encouraged at departmental and institutional level, but another vital origin of brokering can be forged at a(n) (inter)national level at meetings such as the SEB Annual Conference, where teaching-focused academics have the opportunity to mix with research-active colleagues. While this paper is informed by recent and current events in the UK Higher Education sector, it is of interest to academics who work in an environment where research and teaching have become separate to any extent. PMID:26998239

Tidal breathing parameters measured using structured light plethysmography in healthy children and those with asthma before and after bronchodilator.

PubMed

Hmeidi, Hamzah; Motamedi-Fakhr, Shayan; Chadwick, Edward; Gilchrist, Francis J; Lenney, Warren; Iles, Richard; Wilson, Rachel C; Alexander, John

2017-03-01

Structured light plethysmography (SLP) is a light-based, noncontact technique that measures tidal breathing by monitoring displacements of the thoracoabdominal (TA) wall. We used SLP to measure tidal breathing parameters and their within-subject variability (v) in 30 children aged 7-16 years with asthma and abnormal spirometry (forced expiratory volume in 1 sec [FEV1] <80% predicted) during a routine clinic appointment. As part of standard care, the reversibility of airway obstruction was assessed by repeating spirometry after administration of an inhaled bronchodilator. In this study, SLP was performed before and after bronchodilator administration, and also once in 41 age-matched controls. In the asthma group, there was a significant increase in spirometry-assessed mean FEV1 after administration of bronchodilator. Of all measured tidal breathing parameters, the most informative was the inspiratory to expiratory TA displacement ratio (IE50 SLP , calculated as TIF50 SLP /TEF50 SLP , where TIF50 SLP is tidal inspiratory TA displacement rate at 50% of inspiratory displacement and TEF50 SLP is tidal expiratory TA displacement rate at 50% of expiratory displacement). Median (m) IE50 SLP and its variability (vIE50 SLP ) were both higher in children with asthma (prebronchodilator) compared with healthy children (mIE50 SLP : 1.53 vs. 1.22, P  <   0.001; vIE50 SLP : 0.63 vs. 0.47, P  <   0.001). After administration of bronchodilators to the asthma group, mIE50 SLP decreased from 1.53 to 1.45 ( P  =   0.01) and vIE50 SLP decreased from 0.63 to 0.60 ( P  =   0.04). SLP-measured tidal breathing parameters could differentiate between children with and without asthma and indicate a response to bronchodilator. © 2017 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

Final Report - DuraMelter 100 Tests to Support LAW Glass Formulation Correlation Development, VSL-06R6480-1, Rev. 0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kruger, Albert A.; Muller, I. S.; Gong, W.

2013-12-03

This report describes the results of work and testing specified by Test Specifications 24590-LAW-TSP-RT-04-004, Rev. 0, Test Plans VSL-05T5480-1, Rev. 0 and Text Exceptions 24590-LAW-TEF-RT-05-00002. The work and any associated testing followed established quality assurance requirements and was conducted as authorized. The descriptions provided in this test report are an accurate account of both the conduct of the work and the data collected. Results required by the Test Plan are reported. Also reported are any unusual or anomalous occurences that are different from the starting hypotheses. The test results and this report have been reviewed and verified.

A class-wide phylogenetic assessment of Dothideomycetes

PubMed Central

Schoch, C.L.; Crous, P.W.; Groenewald, J.Z.; Boehm, E.W.A.; Burgess, T.I.; de Gruyter, J.; de Hoog, G.S.; Dixon, L.J.; Grube, M.; Gueidan, C.; Harada, Y.; Hatakeyama, S.; Hirayama, K.; Hosoya, T.; Huhndorf, S.M.; Hyde, K.D.; Jones, E.B.G.; Kohlmeyer, J.; Kruys, Å.; Li, Y.M.; Lücking, R.; Lumbsch, H.T.; Marvanová, L.; Mbatchou, J.S.; McVay, A.H.; Miller, A.N.; Mugambi, G.K.; Muggia, L.; Nelsen, M.P.; Nelson, P.; Owensby, C A.; Phillips, A.J.L.; Phongpaichit, S.; Pointing, S.B.; Pujade-Renaud, V.; Raja, H.A.; Plata, E. Rivas; Robbertse, B.; Ruibal, C.; Sakayaroj, J.; Sano, T.; Selbmann, L.; Shearer, C.A.; Shirouzu, T.; Slippers, B.; Suetrong, S.; Tanaka, K.; Volkmann-Kohlmeyer, B.; Wingfield, M.J.; Wood, A.R.; Woudenberg, J.H.C.; Yonezawa, H.; Zhang, Y.; Spatafora, J.W.

2009-01-01

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon. PMID:20169021

Trichoderma martiale sp. nov., a new endophyte from sapwood of Theobroma cacao with a potential for biological control.

PubMed

Hanada, Rogério E; de Jorge Souza, T; Pomella, Alan W V; Hebbar, K Prakash; Pereira, José O; Ismaiel, Adnan; Samuels, Gary J

2008-11-01

The new species Trichoderma martiale was isolated as an endophyte from sapwood in trunks of Theobroma cacao (cacao, Malvaceae) in Brazil. Based on sequences of translation-elongation factor 1-alpha (tef1) and RNA polymerase II subunit (rpb2) T. martiale is a close relative of, and morphologically similar to, T. viride, but differs in the production of discrete pustules on corn meal-dextrose agar (CMD) and SNA, in having a faster rate of growth, and in being a tropical endophyte. This new species was shown, in small-scale, in situ field assays, to limit black pod rot of cacao caused by Phytophthora palmivora, the cause of black pod disease.

Biochemical characteristics of a free cyanide and total nitrogen assimilating Fusarium oxysporum EKT01/02 isolate from cyanide contaminated soil.

PubMed

Akinpelu, Enoch A; Adetunji, Adewole T; Ntwampe, Seteno K O; Nchu, Felix; Mekuto, Lukhanyo

2017-10-01

Sustainability of nutrient requirements for microbial proliferation on a large scale is a challenge in bioremediation processes. This article presents data on biochemical properties of a free cyanide resistant and total nitrogen assimilating fungal isolate from the rhizosphere of Zea mays (maize) growing in soil contaminated with a cyanide-based pesticide. DNA extracted from this isolate were PCR amplified using universal primers; TEF1-α and ITS. The raw sequence files are available on the NCBI database. Characterisation using biochemical data was obtained using colorimetric reagents analysed with VITEK ® 2 software version 7.01. The data will be informative in selection of biocatalyst for environmental engineering application.

Presence of organophosphorus pesticide oxygen analogs in air samples

NASA Astrophysics Data System (ADS)

Armstrong, Jenna L.; Fenske, Richard A.; Yost, Michael G.; Galvin, Kit; Tchong-French, Maria; Yu, Jianbo

2013-02-01

A number of recent toxicity studies have highlighted the increased potency of oxygen analogs (oxons) of several organophosphorus (OP) pesticides. These findings were a major concern after environmental oxons were identified in environmental samples from air and surfaces following agricultural spray applications in California and Washington State. This paper reports on the validity of oxygen analog measurements in air samples for the OP pesticide, chlorpyrifos. Controlled environmental and laboratory experiments were used to examine artificial formation of chlorpyrifos-oxon using OSHA Versatile Sampling (OVS) tubes as recommended by NIOSH method 5600. Additionally, we compared expected chlorpyrifos-oxon attributable to artificial transformation to observed chlorpyrifos-oxon in field samples from a 2008 Washington State Department of Health air monitoring study using non-parametric statistical methods. The amount of artificially transformed oxon was then modeled to determine the amount of oxon present in the environment. Toxicity equivalency factors (TEFs) for chlorpyrifos-oxon were used to calculate chlorpyrifos-equivalent air concentrations. The results demonstrate that the NIOSH-recommended sampling matrix (OVS tubes with XAD-2 resin) was found to artificially transform up to 30% of chlorpyrifos to chlorpyrifos-oxon, with higher percentages at lower concentrations (<30 ng m-3) typical of ambient or residential levels. Overall, the 2008 study data had significantly greater oxon than expected by artificial transformation, but the exact amount of environmental oxon in air remains difficult to quantify with the current sampling method. Failure to conduct laboratory analysis for chlorpyrifos-oxon may result in underestimation of total pesticide concentration when using XAD-2 resin matrices for occupational or residential sampling. Alternative methods that can accurately measure both OP pesticides and their oxygen analogs should be used for air sampling, and a toxicity equivalent factor approach should be used to determine potential health risks from exposures.

Assessment of a Pan-Dermatophyte Nested-PCR Compared with Conventional Methods for Direct Detection and Identification of Dermatophytosis Agents in Animals.

PubMed

Piri, Fahimeh; Zarei Mahmoudabadi, Ali; Ronagh, Ali; Ahmadi, Bahram; Makimura, Koichi; Rezaei-Matehkolaei, Ali

2018-06-26

Conventional direct microscopy with potassium hydroxide (KOH) and culture were found to lack the ability to establish a fast and specific diagnosis of dermatophytosis. A pan-dermatophyte nested-PCR assay was developed using a novel primer pair targeting the translation elongation factor 1-α (Tef-1α) sequences for direct detection and identification of most veterinary relevant dermatophytes in animal samples suspected to dermatophytosis. A total of 140 animal skin and hair samples were subjected to direct microscopy, culture, and ITS-RFLP/ITS-sequencing of culture isolates for the detection and identification of dermatophytosis agents. Nested-PCR sequencing was performed on all the extracted DNAs using a commercial kit after dissolving the specimens by mechanical beating. Nested-PCR was positive in 90% of samples, followed by direct microscopy (85.7%) and culture (75%). The degree of agreement between nested-PCR and direct microscopy (94.4%) was higher than with culture (83.3%). In 105 culture positive cases, the measures of agreement for the identification of dermatophytosis agents were as follows: 100% between nested-PCR sequencing and ITS-RFLP/ITS-sequencing and 63.8% between nested-PCR sequencing and culture. The developed nested-PCR was faster as well as more sensitive and specific than conventional methods for detection and identification of dermatophytes in clinical samples, which was particularly suitable for epidemiological studies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Distribution, sources and ecological risk assessment of PAHs in historically contaminated surface sediments at Bhavnagar coast, Gujarat, India.

PubMed

Dudhagara, Dushyant R; Rajpara, Rahul K; Bhatt, Jwalant K; Gosai, Haren B; Sachaniya, Bhumi K; Dave, Bharti P

2016-06-01

The concentration, distribution and ecological risk of polycyclic aromatic hydrocarbons (PAHs) have been investigated in surface sediments near Bhavnagar coast. The concentration of ∑PAHs ranged from 5.02 to 981.18 μg g(-1) dry weight, indicating heavy pollution compared to other historically polluted study sites. It was found to be introduced via mixed origins such as burning of gas, oil, coal, production of petrochemicals, cement, and rubber tires. Domestic fuel burning and motor vehicles are also culprits for air pollution. Industrial effluents and accidental oil spillage can also be considered. PAHs can be exposed through air, water, soil and food sources including ingestion, inhalation, and dermal content in both occupational and non-occupational levels by single or sometimes multiple exposures routes concomitantly. Furthermore, diagnostic ratios, statistical principal component analysis (PCA) and hierarchical cluster analysis (HCA) models have confirmed that the sources of PAHs were both - petrogenic and pyrogenic. For both the sites, assessment of ecological risk of the elevated levels of these pollutants has been exercised based on toxic equivalency factors (TEFs) and risk quotient (RQ) methods. The composite results indicated accurately that both the sites, bears potentially acute and chronic health hazards such as decreased immune functionality, genotoxicity, malignancy and developmental malfunctions in humans. The sites studied here and the workers have been exposed to hazardous pollutants for a longer period of time. Evidences indicate that mixtures of PAHs are carcinogenic to humans, based on occupational studies on workers, exposed to these pollutants. Hence, the present study and statistical approaches applied herein clearly indicate the historic mix routes of PAHs that resulted in magnified concentrations leading to high ecosystem risk. Thus, the scientific communities are urged to develop strategies to minimize the concentrations of PAHs from the historically impacted coastlines, thereby concerning for the future investigations and restoration of these sites. Copyright © 2016 Elsevier Ltd. All rights reserved.

Transportation Energy Futures Series: Vehicle Technology Deployment Pathways: An Examination of Timing and Investment Constraints

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plotkin, S.; Stephens, T.; McManus, W.

2013-03-01

Scenarios of new vehicle technology deployment serve various purposes; some will seek to establish plausibility. This report proposes two reality checks for scenarios: (1) implications of manufacturing constraints on timing of vehicle deployment and (2) investment decisions required to bring new vehicle technologies to market. An estimated timeline of 12 to more than 22 years from initial market introduction to saturation is supported by historical examples and based on the product development process. Researchers also consider the series of investment decisions to develop and build the vehicles and their associated fueling infrastructure. A proposed decision tree analysis structure could bemore » used to systematically examine investors' decisions and the potential outcomes, including consideration of cash flow and return on investment. This method requires data or assumptions about capital cost, variable cost, revenue, timing, and probability of success/failure, and would result in a detailed consideration of the value proposition of large investments and long lead times. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency effort to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Transportation Energy Futures Series. Vehicle Technology Deployment Pathways. An Examination of Timing and Investment Constraints

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plotkin, Steve; Stephens, Thomas; McManus, Walter

2013-03-01

Scenarios of new vehicle technology deployment serve various purposes; some will seek to establish plausibility. This report proposes two reality checks for scenarios: (1) implications of manufacturing constraints on timing of vehicle deployment and (2) investment decisions required to bring new vehicle technologies to market. An estimated timeline of 12 to more than 22 years from initial market introduction to saturation is supported by historical examples and based on the product development process. Researchers also consider the series of investment decisions to develop and build the vehicles and their associated fueling infrastructure. A proposed decision tree analysis structure could bemore » used to systematically examine investors' decisions and the potential outcomes, including consideration of cash flow and return on investment. This method requires data or assumptions about capital cost, variable cost, revenue, timing, and probability of success/failure, and would result in a detailed consideration of the value proposition of large investments and long lead times. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency effort to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Isolation of Neofusicoccum parvum from withered grapes: strain characterization, pathogenicity and its detrimental effects on passito wine aroma.

PubMed

Lorenzini, M; Cappello, M S; Zapparoli, G

2015-11-01

There is scarce information on the occurrence of several fungi that infect withered grapes to produce passito wine. Isolation and characterization of Neofusicoccum parvum strains and evaluation of their effects on withered grape and wine were carried out. Nine isolates were phenotypically characterized by colony morphology and genetically discriminated by molecular methods. Two representative strains were identified as N. parvum according to the phylogenetic analysis of internal transcribed spacer (ITS), and a part of translation elongation factor 1-alfa (TEF) and β-tubulin DNA sequences. The pathogenicity of both strains on grape berries varied according to the inoculation and incubation conditions. Under withering conditions, infected berries showed browning and shrivelling and some berries showed pycnidial development on the surface. The infection affected laccase, esterase, β-glucosidase and tannase on grape juice as well as the content of several aroma molecules on resulting wines. Strain-specific effects on wine composition were also observed. Neofusicoccum parvum occurred in withered grapes and was able to infect grapes under withering condition changing the aroma wine. This study reports for the first time the N. parvum isolation in fruit-drying rooms and indicates its important role on postharvest grape infection. © 2015 The Society for Applied Microbiology.

Modular Ligation Extension of Guide RNA Operons (LEGO) for Multiplexed dCas9 Regulation of Metabolic Pathways in Saccharomyces cerevisiae.

PubMed

Deaner, Matthew; Holzman, Allison; Alper, Hal S

2018-04-16

Metabolic engineering typically utilizes a suboptimal step-wise gene target optimization approach to parse a highly connected and regulated cellular metabolism. While the endonuclease-null CRISPR/Cas system has enabled gene expression perturbations without genetic modification, it has been mostly limited to small sets of gene targets in eukaryotes due to inefficient methods to assemble and express large sgRNA operons. In this work, we develop a TEF1p-tRNA expression system and demonstrate that the use of tRNAs as splicing elements flanking sgRNAs provides higher efficiency than both Pol III and ribozyme-based expression across a variety of single sgRNA and multiplexed contexts. Next, we devise and validate a scheme to allow modular construction of tRNA-sgRNA (TST) operons using an iterative Type IIs digestion/ligation extension approach, termed CRISPR-Ligation Extension of sgRNA Operons (LEGO). This approach enables facile construction of large TST operons. We demonstrate this utility by constructing a metabolic rewiring prototype for 2,3-butanediol production in 2 distinct yeast strain backgrounds. These results demonstrate that our approach can act as a surrogate for traditional genetic modification on a much shorter design-cycle timescale. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhanced leavening properties of baker's yeast by reducing sucrase activity in sweet dough.

PubMed

Zhang, Cui-Ying; Lin, Xue; Feng, Bing; Liu, Xiao-Er; Bai, Xiao-Wen; Xu, Jia; Pi, Li; Xiao, Dong-Guang

2016-07-01

Leavening ability in sweet dough is required for the commercial applications of baker's yeast. This property depends on many factors, such as glycolytic activity, sucrase activity, and osmotolerance. This study explored the importance of sucrase level on the leavening ability of baker's yeast in sweet dough. Furthermore, the baker's yeast strains with varying sucrase activities were constructed by deleting SUC2, which encodes sucrase or replacing the SUC2 promoter with the VPS8/TEF1 promoter. The results verify that the sucrase activity negatively affects the leavening ability of baker's yeast strains under high-sucrose conditions. Based on a certain level of osmotolerance, sucrase level plays a significant role in the fermentation performance of baker's yeast, and appropriate sucrase activity is an important determinant for the leavening property of baker's yeast in sweet dough. Therefore, modification on sucrase activity is an effective method for improving the leavening properties of baker's yeast in sweet dough. This finding provides guidance for the breeding of industrial baker's yeast strains for sweet dough leavening. The transformants BS1 with deleted SUC2 genetic background provided decreased sucrase activity (a decrease of 39.3 %) and exhibited enhanced leavening property (an increase of 12.4 %). Such a strain could be useful for industrial applications.

Characterization and pathogenicity of Fusarium species associated with leaf spot of mango (Mangifera indica L.).

PubMed

Omar, Nurul Husna; Mohd, Masratulhawa; Mohamed Nor, Nik Mohd Izham; Zakaria, Latiffah

2018-01-01

Leaf spot diseases are mainly caused by fungi including Fusarium. In the present study several species of Fusarium were isolated from the leaf spot lesion of mango (Mangifera indica L.) Based on morphological characteristics, TEF-1α sequences and phylogenetic analysis, five species were identified as F. proliferatum, F. semitectum, F. mangiferae, F. solani and F. chlamydosporum. Pathogenicity test indicated that representative isolates of F. proliferatum, F. semitectum and F. chlamydosporum were pathogenic on mango leaves causing leaf spot with low to moderate virulence. Nevertheless, abundance of spots on the leaf can disrupt photosynthesis which in turn reduced growth, and lead to susceptibility to infection by opportunistic pathogens due to weakening of the plant. Fusarium solani and F. mangiferae were non-pathogenic and it is possible that both species are saprophyte which associated with nutrient availability on the surface of the leaf through decaying leave tissues. The occurrence of Fusarium spp. on the leaf spot lesion and the effect from the disease needs to be considered when developing disease management method of mango cultivation as numerous spot on the leaves could effect the photosynthesis process and finally giving low yield and less quality of mango. Copyright © 2017. Published by Elsevier Ltd.

TNF-alpha suppresses the expression of clock genes by interfering with E-box-mediated transcription.

PubMed

Cavadini, Gionata; Petrzilka, Saskia; Kohler, Philipp; Jud, Corinne; Tobler, Irene; Birchler, Thomas; Fontana, Adriano

2007-07-31

Production of TNF-alpha and IL-1 in infectious and autoimmune diseases is associated with fever, fatigue, and sleep disturbances, which are collectively referred to as sickness behavior syndrome. In mice TNF-alpha and IL-1 increase nonrapid eye movement sleep. Because clock genes regulate the circadian rhythm and thereby locomotor activity and may alter sleep architecture we assessed the influence of TNF-alpha on the circadian timing system. TNF-alpha is shown here to suppress the expression of the PAR bZip clock-controlled genes Dbp, Tef, and Hlf and of the period genes Per1, Per2, and Per3 in fibroblasts in vitro and in vivo in the liver of mice infused with the cytokine. The effect of TNF-alpha on clock genes is shared by IL-1beta, but not by IFN-alpha, and IL-6. Furthermore, TNF-alpha interferes with the expression of Dbp in the suprachiasmatic nucleus and causes prolonged rest periods in the dark when mice show spontaneous locomotor activity. Using clock reporter genes TNF-alpha is found here to inhibit CLOCK-BMAL1-induced activation of E-box regulatory elements-dependent clock gene promoters. We suggest that the increase of TNF-alpha and IL-1beta, as seen in infectious and autoimmune diseases, impairs clock gene functions and causes fatigue.

Pestalotiopsis and allied genera from Camellia, with description of 11 new species from China.

PubMed

Liu, Fang; Hou, Lingwei; Raza, Mubashar; Cai, Lei

2017-04-13

A total of 124 Pestalotiopsis-like isolates associated with symptomatic and asymptomatic tissues of Camellia sinensis and other Camellia spp. from eight provinces in China were investigated. Based on single- and multi-locus (ITS, TEF, TUB2) phylogenies, as well as morphological characters, host associations and geographical distributions, they were classified into at least 19 species in three genera, i.e. Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis. Eight novel species in Pestalotiopsis and three novel species in Pseudopestalotiopsis were described. Our data suggested that the currently widely used loci in Pestalotiopsis-like genera do not consistently provide stable and sufficient resolution tree topologies, especially for Neopestalotiopsis. Moreover, the number, branch pattern and length of the conidial basal appendages were revealed to be phylogenetically informative characters in Pestalotiopsis.

Binding properties and colour of Bologna sausage made with varying fat levels, protein levels and cooking temperatures.

PubMed

Carballo, J; Mota, N; Barreto, G; Colmenero, F J

1995-01-01

A little-studied procedure for adjusting the properties of low-fat products is to use the influence that both composition and certain processing factors exert on these properties. The object of the present work was to assess the effects of protein level (P, ranging from 10% to 16%), fat level (F, ranging from 10.1% to 22%) and cooking temperature (HT, ranging from 77 °C to 105 °C) on the binding properties and colour of meat emulsions. Protein content was the variable that most influenced total expressible fluid (TEF) and purge loss. Heating rate had scarcely any effect on the binding properties of Bologna sausages. Analysis of variance indicated that the regression models for parameters L, a and b were not significant.

A new species of Trichoderma hypoxylon harbours abundant secondary metabolites.

PubMed

Sun, Jingzu; Pei, Yunfei; Li, Erwei; Li, Wei; Hyde, Kevin D; Yin, Wen-Bing; Liu, Xingzhong

2016-11-21

Some species of Trichoderma are fungicolous on fungi and have been extensively studied and commercialized as biocontrol agents. Multigene analyses coupled with morphology, resulted in the discovery of T. hypoxylon sp. nov., which was isolated from surface of the stroma of Hypoxylon anthochroum. The new taxon produces Trichoderma- to Verticillium-like conidiophores and hyaline conidia. Phylogenetic analyses based on combined ITS, TEF1-α and RPB2 sequence data indicated that T. hypoxylon is a well-distinguished species with strong bootstrap support in the polysporum group. Chemical assessment of this species reveals a richness of secondary metabolites with trichothecenes and epipolythiodiketopiperazines as the major compounds. The fungicolous life style of T. hypoxylon and the production of abundant metabolites are indicative of the important ecological roles of this species in nature.

Genetic and cellular mechanisms of the formation of Esophageal Atresia and Tracheoesophageal Fistula

PubMed Central

Jacobs, Ian J.; Que, Jianwen

2015-01-01

Foregut separation involves dynamic changes in the activities of signaling pathways and transcription factors. Recent mouse genetic studies demonstrate that some of these pathways interact with each other to form a complex network, leading to a unique dorsal-ventral patterning in the early foregut. In this review we will discuss how this unique dorsal-ventral patterning is set prior to the foregut separation and how disruption of this patterning affects the separation process. We will further discuss the roles of downstream targets of these pathways in regulating separation at cellular and molecular levels. Understanding the mechanism of normal separation process will provide us insights into the pathobiology of a relatively common birth defect Esophageal Atresia (EA) with/without Tracheo-esophageal Fistula (TEF). PMID:23679023

First Report of Leaf Spot Caused by Alternaria tenuissima on Black Chokeberry (Aronia melanocarpa) in Korea.

PubMed

Wee, Jung-In; Park, Jong-Han; Back, Chang-Gi; You, Young-Hyun; Chang, Taehyun

2016-09-01

In July 2015, diseased leaves of black chokeberry ( Aronia melanocarpa ) were observed in Danyang and Gochang, Korea. The symptoms appeared as circular or irregular brown leaf spots, from which Alternaria tenuissima was isolated. The isolates were cultured on potato dextrose agar, and their morphological characteristics were observed under a light microscope. The colonies were whitish to ash colored. The pathogenicity test on healthy black chokeberry leaves produced circular brown spots, in line with the original symptoms. Molecular analyses of the ITS, GPD, RPB2, and TEF genes were conducted to confirm the identity of the pathogen. The phylogeny of the multi-gene sequences indicated that the causal agent was A. tenuissima . This study is the first report of A. tenuissima leaf spot on black chokeberry ( A. melanocarpa ).

Predicting signatures of anisotropic resonance energy transfer in dye-functionalized nanoparticles† †Electronic supplementary information (ESI) available: Molecular structure and TDM of Cy3B. Table of dielectric constants. Dielectric mismatch at the surface of the NP: excitonic states and TEF of the NP. Additional data in RET rates calculation. Experimental absorption and PL spectra of the dye and the NP. Master equations and time-dependent populations. Steady-state rates and spectra. Blocking and back-transfer effects. Octahedral tessellation. Average RET rates. Details on Fig. 5 inset of the main text. Poisson distribution of the number of dyes per NP. See DOI: 10.1039/c6ra22433d Click here for additional data file.

PubMed Central

Corni, Stefano; Delgado, Alain; Bertoni, Andrea; Goldoni, Guido

2016-01-01

Resonance energy transfer (RET) is an inherently anisotropic process. Even the simplest, well-known Förster theory, based on the transition dipole–dipole coupling, implicitly incorporates the anisotropic character of RET. In this theoretical work, we study possible signatures of the fundamental anisotropic character of RET in hybrid nanomaterials composed of a semiconductor nanoparticle (NP) decorated with molecular dyes. In particular, by means of a realistic kinetic model, we show that the analysis of the dye photoluminescence difference for orthogonal input polarizations reveals the anisotropic character of the dye–NP RET which arises from the intrinsic anisotropy of the NP lattice. In a prototypical core/shell wurtzite CdSe/ZnS NP functionalized with cyanine dyes (Cy3B), this difference is predicted to be as large as 75% and it is strongly dependent in amplitude and sign on the dye–NP distance. We account for all the possible RET processes within the system, together with competing decay pathways in the separate segments. In addition, we show that the anisotropic signature of RET is persistent up to a large number of dyes per NP. PMID:28066545

Occurrence of nitro- and oxy-PAHs in agricultural soils in eastern China and excess lifetime cancer risks from human exposure through soil ingestion.

PubMed

Sun, Zhe; Zhu, Ying; Zhuo, Shaojie; Liu, Weiping; Zeng, Eddy Y; Wang, Xilong; Xing, Baoshan; Tao, Shu

2017-11-01

The quality of agricultural soil is vital to human health, however soil contamination is a severe problem in China. Polycyclic aromatic hydrocarbons (PAHs) have been found to be among the major soil contaminants in China. PAH derivatives could be more toxic but their measurements in soils are extremely limited. This study reports levels, spatial distributions and compositions of 11 nitrated (nPAHs) and 4 oxygenated PAHs (oPAHs) in agricultural soils covering 26 provinces in eastern China to fill the data gap. The excess lifetime cancer risk (ELCR) from the exposure to them in addition to 21 parent PAHs (pPAHs) via soil ingestion has been estimated. The mean concentration of ∑nPAHs and ∑oPAHs in agricultural soils is 50±45μg/kg and 9±8μg/kg respectively. Both ∑nPAHs and ∑oPAHs follow a similar spatial distribution pattern with elevated concentrations found in Liaoning, Shanxi, Henan and Guizhou. However if taking account of pPAHs, the high ELCR by soil ingestion is estimated for Shanxi, Zhejiang, Liaoning, Jiangsu and Hubei. The maximum ELCR is estimated at ca.10 -5 by both deterministic and probabilistic studies with moderate toxic equivalent factors (TEFs). If maximum TEFs available are applied, there is a 0.2% probability that the ELCR will exceed 10 -4 in the areas covered. There is a great chance to underestimate the ELCR via soil ingestion for some regions if only the 16 priority PAHs in agricultural soils are considered. The early life exposure and burden are considered extremely important to ELCR. Emission sources are qualitatively predicted and for areas with higher ELCR such as Shanxi and Liaoning, new loadings of PAHs and derivatives are identified. This is the first large scale study on nPAHs and oPAHs contamination levels in agricultural soils in China. The risk assessment based on this underpins the policy making and is valuable for both scientists and policy makers. Copyright © 2017 Elsevier Ltd. All rights reserved.

Resequencing three candidate genes discovers seven potentially deleterious variants susceptibility to major depressive disorder and suicide attempts in Chinese.

PubMed

Rao, Shitao; Leung, Cherry She Ting; Lam, Macro Hb; Wing, Yun Kwok; Waye, Mary Miu Yee; Tsui, Stephen Kwok Wing

2017-03-01

To date almost 200 genes were found to be associated with major depressive disorder (MDD) or suicide attempts (SA), but very few genes were reported for their molecular mechanisms. This study aimed to find out whether there were common or rare variants in three candidate genes altering the risk for MDD and SA in Chinese. Three candidate genes (HOMER1, SLC6A4 and TEF) were chosen for resequencing analysis and association studies as they were reported to be involved in the etiology of MDD and SA. Following that, bioinformatics analyses were applied on those variants of interest. After resequencing analysis and alignment for the amplicons, a total of 34 common or rare variants were found in the randomly selected 36 Hong Kong Chinese patients with both MDD and SA. Among those, seven variants show potentially deleterious features. Rs60029191 and a rare variant located in regulatory region of the HOMER1 gene may affect the promoter activities through interacting with predicted transcription factors. Two missense mutations existed in the SLC6A4 coding regions were firstly reported in Hong Kong Chinese MDD and SA patients, and both of them could affect the transport efficiency of SLC6A4 to serotonin. Moreover, a common variant rs6354 located in the untranslated region of this gene may affect the expression level or exonic splicing of serotonin transporter. In addition, both of a most studied polymorphism rs738499 and a low-frequency variant in the promoter region of the TEF gene were found to be located in potential transcription factor binding sites, which may let the two variants be able to influence the promoter activities of the gene. This study elucidated the potentially molecular mechanisms of the three candidate genes altering the risk for MDD and SA. These findings implied that not only common variants but rare variants could make contributions to the genetic susceptibility to MDD and SA in Chinese. Copyright © 2016 Elsevier B.V. All rights reserved.

Developing tools for risk assessment in protected species: relative potencies inferred from competitive binding of halogenated aromatic hydrocarbons to aryl hydrocarbon receptors from beluga (Delphinapterus leucas) and mouse

PubMed Central

Jensen, Brenda A.; Reddy, Christopher M.; Nelson, Robert K.; Hahn, Mark E.

2011-01-01

Persistent organic pollutants such as halogenated aromatic hydrocarbons (HAHs) biomagnify in food webs and accumulate to high concentrations in top predators like odontocete cetaceans (toothed whales). The most toxic HAHs are the 2,3,7,8-substituted halogenated dibenzo-p-dioxins and furans, and non-ortho-substituted polychlorinated biphenyls (PCBs), which exert their effects via the aryl hydrocarbon receptor (AHR). Understanding the impact of HAHs in wildlife is limited by the lack of taxon-specific information about the relative potencies of toxicologically important congeners. To assess whether Toxic Equivalency Factors (TEFs) determined in rodents are predictive of HAH relative potencies in a cetacean, we used beluga and mouse AHRs expressed in vitro from cloned cDNAs to measure the relative AHR-binding affinities of ten HAHs from five different structural classes. The rank order of mean IC50s for competitive binding to beluga AHR was: TCDD

Developing tools for risk assessment in protected species: Relative potencies inferred from competitive binding of halogenated aromatic hydrocarbons to aryl hydrocarbon receptors from beluga (Delphinapterus leucas) and mouse.

PubMed

Jensen, Brenda A; Reddy, Christopher M; Nelson, Robert K; Hahn, Mark E

2010-11-01

Persistent organic pollutants such as halogenated aromatic hydrocarbons (HAHs) biomagnify in food webs and accumulate to high concentrations in top predators like odontocete cetaceans (toothed whales). The most toxic HAHs are the 2,3,7,8-substituted halogenated dibenzo-p-dioxins and furans, and non-ortho-substituted polychlorinated biphenyls (PCBs), which exert their effects via the aryl hydrocarbon receptor (AHR). Understanding the impact of HAHs in wildlife is limited by the lack of taxon-specific information about the relative potencies of toxicologically important congeners. To assess whether Toxic Equivalency Factors (TEFs) determined in rodents are predictive of HAH relative potencies in a cetacean, we used beluga and mouse AHRs expressed in vitro from cloned cDNAs to measure the relative AHR-binding affinities of ten HAHs from five different structural classes. The rank order of mean IC(50)s for competitive binding to beluga AHR was: TCDD

Levels of non-ortho-substituted (coplanar), mono- and di-ortho-substituted polychlorinated biphenyls, dibenzo-p-dioxins, and dibenzofurans in human serum and adipose tissue.

PubMed Central

Patterson, D G; Todd, G D; Turner, W E; Maggio, V; Alexander, L R; Needham, L L

1994-01-01

We have measured non-ortho-substituted (coplanar) polychlorinated biphenyl (PCB) levels as well as polychlorinated dibenzo-p-dioxin (PCDD) and polychlorinated dibenzofuran (PCDF) levels in human adipose tissue and serum collected in Atlanta, Georgia. The results show that the concentrations of the coplanar PCBs can be more than an order of magnitude higher than the concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin. Our measurements in pooled serum collected in 1982, 1988, and 1989 show a decrease in coplanar PCB levels from 1982 to 1989. We found that the pattern of relative amounts of coplanar PCBs in adipose tissue varied greatly from person to person unlike the PCDD and PCDF patterns, which were more nearly the same. Age was significantly correlated with the concentrations of 2,3,7,8-TCDD,3,3'4,4'-PCB, 3,3',4,4',5-PCB, and 3,3'4,4',5,5'-PCB in adipose tissue. We also measured levels of the mono- and di-ortho chlorine-substituted PCBs in human serum. The levels for some of these PCB congeners were three orders of magnitude higher than the coplanar PCBs, PCDDs, and PCDFs. We used the international toxicity equivalency factors (TEFs) for PCDDs and PCDFs and the TEFs proposed by Safe for PCBs to calculate the 2,3,7,8-TCDD equivalents. Four PCBs (3,3',4,4',5-; 2,3',4,4',5-;2,3,3',4,4'-;2,3,3',4,4',5-) make a larger contribution than 2,3,7,8-TCDD, while four other PCBs (3,3',4,4'5,5'-; 2,2',3,4,4',5'-;2,2',4,4',5,5'-;2,2',3,4,4',5,5'-) make nearly the same contribution as 2,3,7,8-TCDD. The mono-ortho-chlorine-substituted 2,3',4,4',5-PCB, however, is the major contributor to the total 2,3,7,8-TCDD equivalents in general population samples from the United States, Sweden, and Japan.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8187709

Risk assessment of great horned owls (Bubo virginianus) exposed to polychlorinated biphenyls and DDT along the Kalamazoo River, Michigan, USA.

PubMed

Strause, Karl D; Zwiernik, Matthew J; Im, Sook Hyeon; Bradley, Patrick W; Moseley, Pamela P; Kay, Denise P; Park, Cyrus S; Jones, Paul D; Blankenship, Alan L; Newsted, John L; Giesy, John P

2007-07-01

The great horned owl (GHO; Bubo virginianus) was used in a multiple lines of evidence study of polychlorinated biphenyls (PCBs) and p,p'-dichlorodiphenyltrichloroethane (DDT) exposures at the Kalamazoo River Superfund Site (KRSS), Kalamazoo, Michigan, USA. The study examined risks from total PCBs, including 2,3,7,8-tetrachlorodibenzo-p-dioxin equivalents (TEQWorld Health Organization [WHO]-Avian Toxicity Equivalency Factor [TEF]), and total DDTs (sum of DDT, dichlorodiphenyldichloroethylene [DDE], and dichlorodiphenyldichloroethane [DDD]; sigmaDDT) by measuring concentrations in eggs and nestling blood plasma in two regions of the KRSS (upper, lower) and an upstream reference area (RA). An ecological risk assessment compared concentrations of the contaminants of concern (COCs) in eggs or plasma to toxicity reference values. Productivity and relative abundance measures for KRSS GHOs were compared with other GHO populations. Egg shell thickness was measured to assess effects of p,p'-DDE. The concentrations of PCBs in eggs were as great as 4.7 x 10(2) and 4.0 x 10(4) ng PCB/g, wet weight at the RA and combined KRSS sites, respectively. Egg TEQ(WHO-Avian) calculated from aryl hydrocarbon receptor-active PCB congeners and WHO TEFs ranged to 8.0 and 1.9 x 10(2) pg TEQ(WHO-Avian)/g, (wet wt) at the RA and combined KRSS, respectively. Egg sigmaDDT concentrations were as great as 4.2 x 10(2) and 5.0 x 10(3) ng sigmaDDT/g (wet wt) at the RA and combined KRSS, respectively. Hazard quotients (HQs) for the upper 95% confidence interval (UCI) (geometric mean) and least observable adverse effect concentration (LOAEC) for COCs in eggs were < or = 1.0 for all sites. Hazard quotient values based on the no observable adverse effect concentration (NOAEC) 95% UCI in eggs were < or = 1.0, except at the LKRSS (PCB HQ = 3.1; TEQ(WHO-Avian) HQ = 1.3). Productivity and relative abundance measures indicated no population level effects in the UKRSS.

Identification and characterization of Pestalotiopsis-like fungi related to grapevine diseases in China.

PubMed

Jayawardena, Ruvishika S; Zhang, Wei; Liu, Mei; Maharachchikumbura, Sajeewa S N; Zhou, Ying; Huang, JinBao; Nilthong, Somrudee; Wang, ZhongYue; Li, XingHong; Yan, JiYe; Hyde, Kevin D

2015-05-01

Pestalotiopsis-like fungi are an important plant pathogenic genus causing postharvest fruit rot and trunk diseases in grapevine in many countries. Pestalotiopsis-like fungi diseases were studied in vineyards in nine provinces across China. Multi-gene (ITS, β-tubulin and tef1) analysis coupled with morphology showed that a Neopestalotiopsis sp. and Pestalotiopsis trachicarpicola are associated in causing grapevine fruit rot and trunk diseases in China. Pestalotiopsis trachicarpicola is reported as the causative agent of grapevine diseases in the world for the first time. Neopestalotiopsis sp. caused significantly longer lesions than the other taxon present. This study represents the first attempt to identify and characterize the Pestalotiopsis-like fungi causing grapevine diseases in China using both morphological and molecular approaches. Copyright © 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Final Report - ILAW PCT, VHT, Viscosity, and Electrical Conductivity Model Development, VSL-07R1230-1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kruger, Albert A.; Cooley, S. K.; Joseph, I.

This report describes the results of work and testing specified by the Test Specifications (24590-LAW-TSP-RT-01-013 Rev.1 and 24590-WTP-TSP-RT-02-001 Rev.0), Test Plans (VSL-02T4800-1 Rev.1 & TP-RPP-WTP-179 Rev.1), and Text Exception (24590-WTP-TEF-RT-03-040). The work and any associated testing followed established quality assurance requirements and conducted as authorized. The descriptions provided in this test report are an accurate account of both the conduct of the work and the data collected. Results required by the Test Plans are reported. Also reported are any unusual or anomalous occurrences that are different from the starting hypotheses. The test results and this report have been reviewed andmore » verified.« less

Dolabra nepheliae on rambutan and lychee represents a novel lineage of phytopathogenic Eurotiomycetes

PubMed Central

Schoch, Conrad L.; Farr, David F.; Nishijima, Kate; Keith, Lisa; Goenaga, Ricardo

2010-01-01

Rambutan (Nephelium lappaceum) and lychee (Litchi chinensis) are tropical trees in the Sapindaceae that produce delicious edible fruits and are increasingly cultivated in tropical regions. These trees are afflicted with a stem canker disease associated with the ascomycete Dolabra nepheliae. Previously known from Asia and Australia, this fungus was recently reported from Hawaii and Puerto Rico. The sexual and asexual states of Dolabra nepheliae are redescribed and illustrated. In addition, the ITS and large subunit of the nuclear ribosomal DNA plus fragments from the genes RPB2, TEF1, and the mitochondrial small ribosomal subunit were sequenced for three isolates of D. nepheliae and compared with other sequences of ascomycetes. It was determined that D. nepheliae represents a new lineage within the Eurotiomycetes allied with Phaeomoniella chlamydospora, the causal agent of Petri grapevine decline. PMID:20802819

Dolabra nepheliae on rambutan and lychee represents a novel lineage of phytopathogenic Eurotiomycetes.

PubMed

Rossman, Amy Y; Schoch, Conrad L; Farr, David F; Nishijima, Kate; Keith, Lisa; Goenaga, Ricardo

2010-07-01

Rambutan (Nephelium lappaceum) and lychee (Litchi chinensis) are tropical trees in the Sapindaceae that produce delicious edible fruits and are increasingly cultivated in tropical regions. These trees are afflicted with a stem canker disease associated with the ascomycete Dolabra nepheliae. Previously known from Asia and Australia, this fungus was recently reported from Hawaii and Puerto Rico. The sexual and asexual states of Dolabra nepheliae are redescribed and illustrated. In addition, the ITS and large subunit of the nuclear ribosomal DNA plus fragments from the genes RPB2, TEF1, and the mitochondrial small ribosomal subunit were sequenced for three isolates of D. nepheliae and compared with other sequences of ascomycetes. It was determined that D. nepheliae represents a new lineage within the Eurotiomycetes allied with Phaeomoniella chlamydospora, the causal agent of Petri grapevine decline.

A multi-gene phylogeny of Chlorophyllum (Agaricaceae, Basidiomycota): new species, new combination and infrageneric classification

PubMed Central

Ge, Zai-Wei; Jacobs, Adriaana; Vellinga, Else C.; Sysouphanthong, Phongeun; van der Walt, Retha; Lavorato, Carmine; An, Yi-Feng; Yang, Zhu L.

2018-01-01

Abstract Taxonomic and phylogenetic studies of Chlorophyllum were carried out on the basis of morphological differences and molecular phylogenetic analyses. Based on the phylogeny inferred from the internal transcribed spacer (ITS), the partial large subunit nuclear ribosomal DNA (nrLSU), the second largest subunit of RNA polymerase II (rpb2) and translation elongation factor 1-α (tef1) sequences, six well-supported clades and 17 phylogenetic species are recognised. Within this phylogenetic framework and considering the diagnostic morphological characters, two new species, C. africanum and C. palaeotropicum, are described. In addition, a new infrageneric classification of Chlorophyllum is proposed, in which the genus is divided into six sections. One new combination is also made. This study provides a robust basis for a more detailed investigation of diversity and biogeography of Chlorophyllum. PMID:29681738

First Report of Leaf Spot Caused by Alternaria tenuissima on Black Chokeberry (Aronia melanocarpa) in Korea

PubMed Central

Wee, Jung-In; Park, Jong-Han; Back, Chang-Gi; You, Young-Hyun

2016-01-01

In July 2015, diseased leaves of black chokeberry (Aronia melanocarpa) were observed in Danyang and Gochang, Korea. The symptoms appeared as circular or irregular brown leaf spots, from which Alternaria tenuissima was isolated. The isolates were cultured on potato dextrose agar, and their morphological characteristics were observed under a light microscope. The colonies were whitish to ash colored. The pathogenicity test on healthy black chokeberry leaves produced circular brown spots, in line with the original symptoms. Molecular analyses of the ITS, GPD, RPB2, and TEF genes were conducted to confirm the identity of the pathogen. The phylogeny of the multi-gene sequences indicated that the causal agent was A. tenuissima. This study is the first report of A. tenuissima leaf spot on black chokeberry (A. melanocarpa). PMID:27790070

Multidrug-resistant Fusarium in keratitis: a clinico-mycological study of keratitis infections in Chennai, India.

PubMed

Tupaki-Sreepurna, Ananya; Al-Hatmi, Abdullah M S; Kindo, Anupma J; Sundaram, Murugan; de Hoog, G Sybren

2017-04-01

In this study, we aimed to present the first molecular epidemiological data from Chennai, India, analyse keratitis cases that have been monitored in a university hospital during 2 years, identify the responsible Fusarium species and determine antifungal susceptibilities. A total of 10 cases of keratitis were included in the study. Fusarium isolates were identified using the second largest subunit of the RNA polymerase gene (RPB2) and the translation elongation factor 1 alpha (TEF1). Antifungal susceptibility was tested by the broth microdilution method according to the Clinical and Laboratory Standards Institute (CLSI) methodology. The aetiological agents belonged to Fusarium solani species complex (FSSC) (n = 9) and Fusarium sambucinum species complex (FSAMSC) (n = 1), and the identified species were Fusarium keratoplasticum (n = 7), Fusarium falciforme (n = 2) and Fusarium sporotrichioides (n = 1). All strains showed multidrug resistance to azoles and caspofungin but exhibited lower minimum inhibitory concentration (MIC) to natamycin and amphotericin B. Fusarium keratoplasticum and Fusarium falciforme belonging to the Fusarium solani species complex were the major aetiological agents of Fusarium keratitis in this study. Early presentation and 5% topical natamycin was associated with better patient outcome. Preventative measures and monitoring of local epidemiological data play an important role in clinical practice. © 2016 Blackwell Verlag GmbH.

Molecular and physiological characteristics of a grape yeast strain containing atypical genetic material.

PubMed

Cappello, M S; Poltronieri, P; Blaiotta, G; Zacheo, G

2010-11-15

The knowledge about wine yeasts remains largely dominated by the extensive studies on Saccharomyces (S.) cerevisiae. Molecular methods, allowing discrimination of both species and strains in winemaking, can profitably be applied for characterization of the microflora occurring in winemaking and for monitoring the fermentation process. Recently, some novel yeast isolates have been described as hybrid between S. cerevisiae and Saccharomyces species, leaving the Saccharomyces strains containing non-Saccharomyces hybrids essentially unexplored. In this study, we have analyzed a yeast strain isolated from "Primitivo" grape (http://www.ispa.cnr.it/index.php?page=collezioni&lang=en accession number 12998) and we found that, in addition to the S. cerevisiae genome, it has acquired genetic material from a non-Saccharomyces species. The study was focused on the analysis of chromosomal and mitochondrial gene sequences (ITS and 26S rRNA, SSU and COXII, ACTIN-1 and TEF), 2D-PAGE mitochondrial proteins, and spore viability. The results allowed us to formulate the hypothesis that in the MSH199 isolate a DNA containing an rDNA sequence from Hanseniaspora vineae, a non-Saccharomyces yeast, was incorporated through homologous recombination in the grape environment where yeast species are propagated. Moreover, physiological characterization showed that the MSH199 isolate possesses high technological quality traits (fermentation performance) and glycerol production, resistance to ethanol, SO₂ and temperature) useful for industrial application. Copyright © 2010 Elsevier B.V. All rights reserved.

Description and phylogenetic placement of Beauveria hoplocheli sp. nov. used in the biological control of the sugarcane white grub, Hoplochelus marginalis, on Reunion Island.

PubMed

Robène-Soustrade, Isabelle; Jouen, Emmanuel; Pastou, Didier; Payet-Hoarau, Magali; Goble, Tarryn; Linderme, Daphné; Lefeuvre, Pierre; Calmès, Cédric; Reynaud, Bernard; Nibouche, Samuel; Costet, Laurent

2015-01-01

On Reunion Island successful biological control of the sugarcane white grub Hoplochelus marginalis Fairmaire (Coleoptera: Melolonthidae) has been conducted for decades with strains from the entomopathogenic fungal genus Beauveria (Ascomycota: Hypocreales). A study based on morphological characters combined with a multisequence phylogenetic analysis of genes that encode the translation elongation factor 1-alpha (TEF1), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2) and the Bloc nuc intergenic region was carried out on Beauveria strains isolated on Reunion and Madagascar from H. marginalis. This study revealed that these strains, previously identified as Beauveria brongniartii, did not match that species and are closely related to but still distinct from B. malawiensis strains. Therefore we describe the Reunion Island fungus as the new species B. hoplocheli. © 2015 by The Mycological Society of America.

Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation

PubMed Central

Zhang, Y.; Schoch, C.L.; Fournier, J.; Crous, P.W.; de Gruyter, J.; Woudenberg, J.H.C.; Hirayama, K.; Tanaka, K.; Pointing, S.B.; Spatafora, J.W.; Hyde, K.D.

2009-01-01

Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str., Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic. PMID:20169024

An overview of the genus Glyphium and its phylogenetic placement in Patellariales

PubMed Central

Boehm, Eric W.A.; Marson, Guy; Mathiassen, Geir H.; Gardiennet, Alain; Schoch, Conrad L.

2015-01-01

Glyphium encompasses species with erect, carbonaceous ligulate to dolabrate ascomata that are strongly laterally compressed and dehisce along a longitudinal slit. The five currently recognized members of the genus are separated primarily by whether the ascospores disassociate into part-spores within the ascus. Glyphium has traditionally been placed in Mytilinidiaceae (Mytilinidiales, Pleosporomycetidae, Dothideomycetes). The present study, based on freshly collected material of G. elatum and G. grisonense, was initiated to determine the phylogenetic placement of Glyphium. Phylogenies inferred from the analysis of sequences of six gene regions (nuLSU, nuSSU, mtSSU, TEF1, RPB1, RPB2) derived from six accessions indicate that Glyphium belongs to Patellariales (Pleosporomycetidae, Dothideomycetes) . Our phylogenies also support the phylogenetic relationship of Patellaria and Hysteropatella within this order. The nomenclatural history of Glyphium is summarized and a key to species is provided. PMID:25661715

Three former taxa of Cucurbitaria and considerations on Petrakia in the Melanommataceae

PubMed Central

Jaklitsch, Walter M.; Voglmayr, Hermann

2017-01-01

Based on phylogenetic analyses of an ITS-LSU-SSU-rpb2-tef1 sequence data matrix three taxa once classified in Cucurbitaria are referred to the Melanommataceae. Cucurbitaria rhododendri, also known as Melanomma rhododendri, is not congeneric with the generic type of Melanomma, M. pulvis-pyrius and thus classified in the new genus Alpinaria. Cucurbitaria piceae, known as Gemmamyces piceae, the cause of the Gemmamyces bud blight of Picea spp., belongs also to the Melanommataceae. The name Gemmamyces is conserved. For Cucurbitaria obducens, also known as Teichospora obducens, the new genus Praetumpfia is described, as it cannot be accommodated in any known genus. All species are redescribed and epitypified. Based on sequence data and morphology, Blastostroma, Mycodidymella and Xenostigmina are synonyms of Petrakia. The genus Petrakia is emended. We also provide sequences of additional markers for Beverwykella pulmonaria, Melanomma pulvis-pyrius, Petrakia echinata and Pseudotrichia mutabilis. PMID:29104325

Diplodia quercivora sp. nov.: a new species of Diplodia found on declining Quercus canariensis trees in Tunisia.

PubMed

Linaldeddu, Benedetto T; Franceschini, Antonio; Alves, Artur; Phillips, Alan J L

2013-01-01

During a study of the species of Botryosphaeriaceae associated with oak decline in Tunisia, a large collection of Diplodia strains were isolated from Quercus afares, Q. canariensis and Q. suber trees showing a progressive dieback of shoots and branches, trunk canker and exudates and collar rot. Most of the isolates were identified as Diplodia corticola, while two isolates from Q. canariensis were morphologically and phylogenetically (ITS and tef1-α sequences data) distinct from all other known species of Diplodia. They are described here as Diplodia quercivora sp. nov. In addition, phylogenetic analyses showed for the first time the existence of two distinct lineages within D. corticola. In artificial inoculation experiments, D. quercivora caused necrotic lesions on bark and wood of three Mediterranean oak species, Q. ilex, Q. pubescens and Q. suber. In particular, among the oak species tested, Q. pubescens was the most susceptible.

Influence of Selected Organic Micropollutants on Organisms

NASA Astrophysics Data System (ADS)

Włodarczyk-Makuła, Maria

2017-03-01

This article describes the toxicity of organic micropollutants on tested microorganisms. Itis a current issue because organic micropollutants are identified in all elements of environmental (surface water, ground water, soils) and in food products. The organic micropollutants include: polychlorinated dibenzodioxyns PCDD, polychlorinated dibenzofurans PCDF, polychlorinated biphenyls PCB, polycyclic aromatic hydrocarbons PAH, halogenated compounds and by-products of water treatment. Some organic compounds cause hazard for health and human life due to their estrogenic biological activity, carcinogenic, mutagenic or teratogenic activity. The influence on organisms indicators of these compounds based on literature data were presented. The level of TEQ (toxic equivalency) in response to organic chlorine derivatives (PCDDs, PCDF, PCBs) is usually determined by toxic equivalency factor (TEF). The International Agency for Research on Cancer classifies organic micropollutants as carcinogenic to humans (Group 1), possibly carcinogenic (Group 2A) or probably carcinogenic to humans (Group 2B).

Transportation Energy Futures Series. Potential for Energy Efficiency Improvement Beyond the Light-Duty-Vehicle Sector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vyas, A. D.; Patel, D. M.; Bertram, K. M.

2013-02-01

Considerable research has focused on energy efficiency and fuel substitution options for light-duty vehicles, while much less attention has been given to medium- and heavy-duty trucks, buses, aircraft, marine vessels, trains, pipeline, and off-road equipment. This report brings together the salient findings from an extensive review of literature on future energy efficiency options for these non-light-duty modes. Projected activity increases to 2050 are combined with forecasts of overall fuel efficiency improvement potential to estimate the future total petroleum and greenhouse gas (GHG) emissions relative to current levels. This is one of a series of reports produced as a result ofmore » the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Transportation Energy Futures Series: Potential for Energy Efficiency Improvement Beyond the Light-Duty-Vehicle Sector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vyas, A. D.; Patel, D. M.; Bertram, K. M.

2013-03-01

Considerable research has focused on energy efficiency and fuel substitution options for light-duty vehicles, while much less attention has been given to medium- and heavy-duty trucks, buses, aircraft, marine vessels, trains, pipeline, and off-road equipment. This report brings together the salient findings from an extensive review of literature on future energy efficiency options for these non-light-duty modes. Projected activity increases to 2050 are combined with forecasts of overall fuel efficiency improvement potential to estimate the future total petroleum and greenhouse gas (GHG) emissions relative to current levels. This is one of a series of reports produced as a result ofmore » the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Production of Lycopene in the Non-Carotenoid-Producing Yeast Yarrowia lipolytica

PubMed Central

Ketelhot, Markus; Gatter, Michael; Barth, Gerold

2014-01-01

The codon-optimized genes crtB and crtI of Pantoea ananatis were expressed in Yarrowia lipolytica under the control of the TEF1 promoter of Y. lipolytica. Additionally, the rate-limiting genes for isoprenoid biosynthesis in Y. lipolytica, GGS1 and HMG1, were overexpressed to increase the production of lycopene. All of the genes were also expressed in a Y. lipolytica strain with POX1 to POX6 and GUT2 deleted, which led to an increase in the size of lipid bodies and a further increase in lycopene production. Lycopene is located mainly within lipid bodies, and increased lipid body formation leads to an increase in the lycopene storage capacity of Y. lipolytica. Growth-limiting conditions increase the specific lycopene content. Finally, a yield of 16 mg g−1 (dry cell weight) was reached in fed-batch cultures, which is the highest value reported so far for a eukaryotic host. PMID:24375130

Phylogenetic relationship and species delimitation of matsutake and allied species based on multilocus phylogeny and haplotype analyses.

PubMed

Ota, Yuko; Yamanaka, Takashi; Murata, Hitoshi; Neda, Hitoshi; Ohta, Akira; Kawai, Masataka; Yamada, Akiyoshi; Konno, Miki; Tanaka, Chihiro

2012-01-01

Tricholoma matsutake (S. Ito & S. Imai) Singer and its allied species are referred to as matsutake worldwide and are the most economically important edible mushrooms in Japan. They are widely distributed in the northern hemisphere and established an ectomycorrhizal relationship with conifer and broadleaf trees. To clarify relationships among T. matsutake and its allies, and to delimit phylogenetic species, we analyzed multilocus datasets (ITS, megB1, tef, gpd) with samples that were correctly identified based on morphological characteristics. Phylogenetic analyses clearly identified four major groups: matsutake, T. bakamatsutake, T. fulvocastaneum and T. caligatum; the latter three species were outside the matsutake group. The haplotype analyses and median-joining haplotype network analyses showed that the matsutake group included four closely related but clearly distinct taxa (T. matsutake, T. anatolicum, Tricholoma sp. from Mexico and T. magnivelare) from different geographical regions; these were considered to be distinct phylogenetic species.

Observed and Potential Responses of Upland Tundra Ecosystems to a Changing Climate: Results from the Arctic Long-Term Ecological Research Project, North Slope, Alaska, USA

NASA Astrophysics Data System (ADS)

Bowden, W. B.

2014-12-01

The Arctic is one of the most rapidly changing biomes on earth. Research at the Toolik Field Station by the Arctic Long-Term Ecological Research project provides a perspective on changes that are impacting the upland tussock tundra region of the North Slope of Alaska, a region that is typical of ~15% of the arctic region. The arctic is responding to a combination of long-term, gradual changes (presses) and short-term, event-driven changes (pulses). The most important press, of course, is the persistent rise in average annual air temperature observed in most places (though not at Toolik). Associated with this increase in SAT is a well-documented increase in shallow permafrost temperature (which is observed around Toolik). Our long-term research shows that this trend will favor taller and more productive shrub and grass vegetation. Higher SAT translates to earlier spring breakup and later onset of winter. This change in seasonality is affecting interactions between shrub leaf-out, insect emergence, and bird nesting. Persistent and more frequent droughts are having important impacts on the ability of Arctic grayling - the top consumer is most upland tundra streams - to survive and has the potential to block their ability to migrate to essential overwintering lakes. The interaction between temperature (which is changing) and light (which is not) creates a "seasonal asynchrony" that may be increasing the loading of nutrients - notably nitrate - to upland tundra streams late in the season, with impacts that we do not fully understand yet. The upland tundra environment is also responding to an increasing frequency of pulses, most notably wildfires and the development of thermo-erosional failures (TEFs). Wildfires transfer large quantities of carbon and nitrogen directly to the atmosphere. TEFs may deliver large quantities of sediment and nutrients to streams and lakes. Currently these pulse disturbances seem to be having only limited, local impacts. However, as shallow permafrost in the arctic region approaches the 0ºC tipping point, the combination of presses and pulses may radically and rapidly alter upland tundra terrestrial and aquatic ecosystems. These changes will almost certainly occur more rapidly than would be the case if the region were influenced by the press of warming temperature alone.

Resolving the Lophiostoma bipolare complex: Generic delimitations within Lophiostomataceae.

PubMed

Hashimoto, A; Hirayama, K; Takahashi, H; Matsumura, M; Okada, G; Chen, C Y; Huang, J W; Kakishima, M; Ono, T; Tanaka, K

2018-06-01

Lophiostoma bipolare was taxonomically revised based on the morphological observations and phylogenetic analyses of molecular data from nuclear rDNA SSU-ITS-LSU, TUB , tef1 , and rpb2 genes. Twenty-nine strains were morphologically similar to Lo . bipolare . A total of 174 sequences were generated from the Lo . bipolare complex. Phylogenetic analyses based on TUB sequence revealed 11 distinct species within the Lo. bipolare complex. Morphological features of the ascospores and the anatomical structure of the ascomata from both field collections as well as axenic culture, which have been reported previously as variable features at intraspecific levels, were compared to evaluate the taxonomic reliability of these features. To clarify the generic position of the 11 species, phylogenetic analyses were done on SSU-ITS-LSU- tef1 - rpb2 gene sequences. The Lo . bipolare complex shared phylogenetic relationships with Pseudolophiostoma and Vaginatispora , and formed an additional five distinct clades from other members of Lophiostomataceae . According to its phylogenetic position, Lo. bipolare sensu stricto was distantly related to Lophiostoma s. str., and formed an independent clade within Lophiostomataceae. Lophiostoma bipolare s. str. could be distinguished from the other lophiostomataceous genera by the clypeus around the ostiolar neck and by the thin and uniformly thick peridium. A novel genus described as Lentistoma was established to accommodate this species, and the epitypification of Lentistoma bipolare (basionym: Massarina bipolaris ) was proposed. Other lineages of the Lo. bipolare complex could not be separated on the basis of the ascospore size and sheath variations, but were distinguished based on ascomatal features, such as the existence of the clypeus, brown hyphae surrounding the peridium, and the contexture of the peridium, which were stable indicators of generic boundaries in Lophiostomataceae . Four additional new genera with five new species were recognised based on these morphological differences: Crassiclypeus ( C . aquaticus ), Flabellascoma ( F . cycadicola and F . minimum ), Leptoparies ( Lep . palmarum ), and Pseudopaucispora ( Pseudop . brunneospora ). Three new species were added to Pseudolophiostoma ( Pseudol . cornisporum , Pseudol . obtusisporum , and Pseudol . tropicum ) and two new species were added to Vaginatispora ( V . amygdali and V . scabrispora ). The re-evaluation of the validity of several previously recognised genera resulted in the introduction of two new genera with new combinations for Lophiostoma pseudoarmatisporum as Parapaucispora pseudoarmatispora and Vaginatispora fuckelii as Neovaginatispora fuckelii .

Cytochrome P4501A induction in avian hepatocyte cultures exposed to polychlorinated biphenyls: Comparisons with AHR1-mediated reporter gene activity and in ovo toxicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manning, Gillian E., E-mail: gmann017@uottawa.ca; Environment Canada, National Wildlife Research Centre, Ottawa, ON, Canada K1A 0H3; Mundy, Lukas J., E-mail: lukas.mundy@ec.gc.ca

2013-01-01

Avian-specific toxic equivalency factors (TEFs) were developed by the World Health Organization to simplify environmental risk assessments of dioxin-like compounds (DLCs), but TEFs do not account for differences in the toxic and biochemical potencies of DLCs among species of birds. Such variability may be due to differences in species sensitivity to individual DLCs. The sensitivity of avian species to DLCs was recently associated with the identity of amino acids 324 and 380 in the aryl hydrocarbon receptor 1 (AHR1) ligand binding domain. A luciferase reporter gene (LRG) assay, measuring AHR1-mediated induction of a cytochrome P450 1A5 (CYP1A5) reporter gene, inmore » combination with a species' AHR1 ligand binding domain sequence, were also shown to predict avian species sensitivity to polychlorinated biphenyls (PCBs) and PCB relative potency in a given species. The goals of the present study were to (1) characterize the concentration-dependent effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin and PCBs 126, 77, 105 and 118 on induction of ethoxyresorufin O-deethylase (EROD) activity and CYP1A4/5 mRNA in chicken, ring-necked pheasant and Japanese quail embryo hepatocytes and (2) compare these in vitro results to those previously generated by the LRG assay and in ovo toxicity studies. EROD activity and CYP1A4/5 mRNA expression data support and complement the findings of the LRG assay. CYP1A enzyme activity and mRNA expression were significantly correlated both with luciferase activity and in ovo toxicity induced by PCBs. Relative potency values were generally similar between the LRG and EROD assays and indicate that the relative potency of some PCBs may differ among species. -- Highlights: ► The chicken isn't the most sensitive species to CYP1A induction by PCB 105 and 118. ► The relative potency of PCBs differs between avian species. ► EROD activity was correlated with luciferase activity from the LRG assay. ► EROD activity was a better predictor of toxicity than CYP1A4/5 mRNA expression.« less

Prevalence of Depression and Depression Care for Populations Registered in Primary Care in Two Remote Cities in the Brazilian Amazon.

PubMed

Ribeiro Dos Santos, Edinilza; Huang, Hsiang; Menezes, Paulo Rossi; Scazufca, Marcia

2016-01-01

The prevalence of depression has been widely studied in high-income countries and in large cities of low-income countries; however, little is known about the prevalence and treatment gap of depression in remote areas of the Amazonian region in Brazil. The objectives of this study are to estimate the prevalence of depression in adults registered with the Family Health Strategy in two remote cities in the Brazilian Amazon and to investigate the proportion of individuals with depression that received mental health care. This is a cross-sectional study of an adult population registered with primary care clinics in the cities of Coari and Tefé, State of Amazon, Brazil. Depression was defined as a score of ≥10 on the Patient Health Questionnaire-9. Depression care was evaluated by asking participants with depression if they received antidepressants and/or had been seen by a health professional at a community mental health center in the three months prior to the interview. Poisson regression was used to examine the unadjusted and adjusted associations between depression and exposure variables. The overall prevalence of depression was 19.1% (95% CI: 17.2-21.1), with 22.2% (95% CI: 19.3-25.0) among women and 16.0% (95% CI: 13.4-18.5) among men. The prevalence of depression in Coari and Tefé were 18.3% (CI 95% 15.7-21.0) and 19.9% (95% CI:17.2-22.7), respectively. Being a woman, lacking social support, increasing exposure to stressful life events and having a higher number medical comorbidities were consistently associated with depression. Lower educational attainment and income, tobacco use, and risky alcohol use were also associated with depression in the unadjusted analyses. Only 11.5% of those with depression were receiving antidepressants and/or visited the mental health care facility during the three months prior to the interview. Approximately one in five adults in our sample had depression. A high proportion of participants presented indicators of social disadvantage and other risk factors previously associated with depression worldwide. There was a large treatment gap for depression in the Amazonian region, which demonstrates the need for innovative models of depression care in primary care settings in Brazil.

GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research

PubMed Central

Zhang, Hao; van Diepeningen, Anne D.; van der Lee, Theo A. J.; Waalwijk, Cees; de Hoog, G. Sybren

2016-01-01

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/). PMID:27308864

GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.

PubMed

Brankovics, Balázs; Zhang, Hao; van Diepeningen, Anne D; van der Lee, Theo A J; Waalwijk, Cees; de Hoog, G Sybren

2016-06-01

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).

Practical aspects of estimating energy components in rodents

PubMed Central

van Klinken, Jan B.; van den Berg, Sjoerd A. A.; van Dijk, Ko Willems

2013-01-01

Recently there has been an increasing interest in exploiting computational and statistical techniques for the purpose of component analysis of indirect calorimetry data. Using these methods it becomes possible to dissect daily energy expenditure into its components and to assess the dynamic response of the resting metabolic rate (RMR) to nutritional and pharmacological manipulations. To perform robust component analysis, however, is not straightforward and typically requires the tuning of parameters and the preprocessing of data. Moreover the degree of accuracy that can be attained by these methods depends on the configuration of the system, which must be properly taken into account when setting up experimental studies. Here, we review the methods of Kalman filtering, linear, and penalized spline regression, and minimal energy expenditure estimation in the context of component analysis and discuss their results on high resolution datasets from mice and rats. In addition, we investigate the effect of the sample time, the accuracy of the activity sensor, and the washout time of the chamber on the estimation accuracy. We found that on the high resolution data there was a strong correlation between the results of Kalman filtering and penalized spline (P-spline) regression, except for the activity respiratory quotient (RQ). For low resolution data the basal metabolic rate (BMR) and resting RQ could still be estimated accurately with P-spline regression, having a strong correlation with the high resolution estimate (R2 > 0.997; sample time of 9 min). In contrast, the thermic effect of food (TEF) and activity related energy expenditure (AEE) were more sensitive to a reduction in the sample rate (R2 > 0.97). In conclusion, for component analysis on data generated by single channel systems with continuous data acquisition both Kalman filtering and P-spline regression can be used, while for low resolution data from multichannel systems P-spline regression gives more robust results. PMID:23641217

Pestalotiopsis revisited.

PubMed

Maharachchikumbura, S S N; Hyde, K D; Groenewald, J Z; Xu, J; Crous, P W

2014-09-01

Species of Pestalotiopsis occur commonly as plant pathogens, and represent a fungal group known to produce a wide range of chemically novel, diverse metabolites. In the present study, we investigated 91 Pestalotiopsis isolates from the CBS-KNAW Fungal Biodiversity Centre (CBS) culture collection. The phylogeny of the Amphisphaeriaceae was constructed based on analysis of 28S nrRNA gene (LSU) sequence data, and taxonomic changes are proposed to reflect more natural groupings. We combined morphological and DNA data, and segregated two novel genera from Pestalotiopsis, namely Neopestalotiopsis and Pseudopestalotiopsis. The three genera are easily distinguishable on the basis of their conidiogenous cells and colour of their median conidial cells. We coupled morphological and combined sequence data of internal transcribed spacer (ITS), partial β-tubulin (TUB) and partial translation elongation factor 1-alpha (TEF) gene regions, which revealed 30 clades in Neopestalotiopsis and 43 clades in Pestalotiopsis. Based on these data, 11 new species are introduced in Neopestalotiopsis, 24 in Pestalotiopsis, and two in Pseudopestalotiopsis. Several new combinations are proposed to emend monophyly of Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis.

Valsaria and the Valsariales

PubMed Central

Fournier, J.; Dai, D. Q.; Hyde, K. D.; Voglmayr, H.

2016-01-01

More than 100 recent collections of Valsaria sensu lato mostly from Europe were used to elucidate the species composition within the genus. Multigene phylogeny based on SSU, LSU, ITS, rpb2 and tef1 sequences revealed a monophyletic group of ten species within the Dothideomycetes, belonging to three morphologically similar genera. This group could not be accommodated in any known family and are thus classified in the new family Valsariaceae and the new order Valsariales. The genus Valsaria sensu stricto comprises V. insitiva, V. robiniae, V. rudis, V. spartii, V. lopadostomoides sp. nov. and V. neotropica sp. nov., which are phylogenetically well-defined, but morphologically nearly indistinguishable species. The new monotypic genus Bambusaria is introduced to accommodate Valsaria bambusae. Munkovalsaria rubra and Valsaria fulvopruinata are combined in Myrmaecium, a genus traditionally treated as a synonym of Valsaria, which comprises three species, with M. rubricosum as its generic type. This work is presented as a basis for additional species to be detected in future. PMID:27274717

In vivo topography of Rap1p-DNA complex at Saccharomyces cerevisiae TEF2 UAS(RPG) during transcriptional regulation.

PubMed

De Sanctis, Veronica; La Terra, Sabrina; Bianchi, Alessandro; Shore, David; Burderi, Luciano; Di Mauro, Ernesto; Negri, Rodolfo

2002-04-26

We have analyzed in detail the structure of RAP1-UAS(RPG) complexes in Saccharomyces cerevisiae cells using multi-hit KMnO(4), UV and micrococcal nuclease high-resolution footprinting. Three copies of the Rap1 protein are bound to the promoter simultaneously in exponentially growing cells, as shown by KMnO(4) multi-hit footprinting analysis, causing extended and diagnostic changes in the DNA structure of the region containing the UAS(RPG). Amino acid starvation does not cause loss of Rap1p from the complex; however, in vivo UV-footprinting reveals the occurrence of structural modifications of the complex. Moreover, low-resolution micrococcal nuclease digestion shows that the chromatin of the entire region is devoid of positioned nucleosomes but is susceptible to changes in accessibility to the nuclease upon amino acid starvation. The implications of these results for the mechanism of Rap1p action are discussed. (c) 2002 Elsevier Science Ltd.

Efficient Gate-tunable light-emitting device made of defective boron nitride nanotubes: from ultraviolet to the visible

PubMed Central

Attaccalite, Claudio; Wirtz, Ludger; Marini, Andrea; Rubio, Angel

2013-01-01

Boron nitride is a promising material for nanotechnology applications due to its two-dimensional graphene-like, insulating, and highly-resistant structure. Recently it has received a lot of attention as a substrate to grow and isolate graphene as well as for its intrinsic UV lasing response. Similar to carbon, one-dimensional boron nitride nanotubes (BNNTs) have been theoretically predicted and later synthesised. Here we use first principles simulations to unambiguously demonstrate that i) BN nanotubes inherit the highly efficient UV luminescence of hexagonal BN; ii) the application of an external perpendicular field closes the electronic gap keeping the UV lasing with lower yield; iii) defects in BNNTS are responsible for tunable light emission from the UV to the visible controlled by a transverse electric field (TEF). Our present findings pave the road towards optoelectronic applications of BN-nanotube-based devices that are simple to implement because they do not require any special doping or complex growth. PMID:24060843

Biomethane production and physicochemical characterization of anaerobically digested teff (Eragrostis tef) straw pretreated by sodium hydroxide.

PubMed

Chufo, Akiber; Yuan, Hairong; Zou, Dexun; Pang, Yunzhi; Li, Xiujin

2015-04-01

The biogas production potential and biomethane content of teff straw through pretreatment by NaOH was investigated. Different NaOH concentrations (1%, 2%, 4% and 6%) were used for each four solid loadings (50, 65, 80 and 95 g/L). The effects of NaOH as pretreatment factor on the biodegradability of teff straw, changes in main compositions and enhancement of anaerobic digestion were analyzed. The result showed that, using 4% NaOH for pretreatment in 80 g/L solid loading produced 40.0% higher total biogas production and 48.1% higher biomethane content than the untreated sample of teff straw. Investigation of changes in chemical compositions and physical microstructure indicated that there was 4.3-22.1% total lignocellulosic compositions removal after three days pretreatment with NaOH. The results further revealed that NaOH pretreatment changed the structural compositions and lignin network, and improved biogas production from teff straw. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phylogeny of the Clinically Relevant Species of the Emerging Fungus Trichoderma and Their Antifungal Susceptibilities

PubMed Central

Sandoval-Denis, Marcelo; Sutton, Deanna A.; Cano-Lira, José F.; Fothergill, Annette W.; Wiederhold, Nathan P.; Guarro, Josep

2014-01-01

A set of 73 isolates of the emerging fungus Trichoderma isolated from human and animal clinical specimens were characterized morphologically and molecularly using a multilocus sequence analysis that included the internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA and fragments of the translation elongation factor 1 alpha (Tef1), endochitinase CHI18-5 (Chi18-5), and actin 1 (Act1) genes. The most frequent species was Trichoderma longibrachiatum (26%), followed by Trichoderma citrinoviride (18%), the Hypocrea lixii/Trichoderma harzianum species complex (15%), the newly described species Trichoderma bissettii (12%), and Trichoderma orientale (11%). The most common anatomical sites of isolation in human clinical specimens were the respiratory tract (40%), followed by deep tissue (30%) and superficial tissues (26%), while all the animal-associated isolates were obtained from superficial tissue samples. Susceptibilities of the isolates to eight antifungal drugs in vitro showed mostly high MICs, except for voriconazole and the echinocandins. PMID:24719448

Optimized invertase expression and secretion cassette for improving Yarrowia lipolytica growth on sucrose for industrial applications.

PubMed

Lazar, Zbigniew; Rossignol, Tristan; Verbeke, Jonathan; Crutz-Le Coq, Anne-Marie; Nicaud, Jean-Marc; Robak, Małgorzata

2013-11-01

Yarrowia lipolytica requires the expression of a heterologous invertase to grow on a sucrose-based substrate. This work reports the construction of an optimized invertase expression cassette composed of Saccharomyces cerevisiae Suc2p secretion signal sequence followed by the SUC2 sequence and under the control of the strong Y. lipolytica pTEF promoter. This new construction allows a fast and optimal cleavage of sucrose into glucose and fructose and allows cells to reach the maximum growth rate. Contrary to pre-existing constructions, the expression of SUC2 is not sensitive to medium composition in this context. The strain JMY2593, expressing this new cassette with an optimized secretion signal sequence and a strong promoter, produces 4,519 U/l of extracellular invertase in bioreactor experiments compared to 597 U/l in a strain expressing the former invertase construction. The expression of this cassette strongly improved production of invertase and is suitable for simultaneously high production level of citric acid from sucrose-based media.

Level of Alkenylbenzenes in Parsley and Dill Based Teas and Associated Risk Assessment Using the Margin of Exposure Approach.

PubMed

Alajlouni, Abdalmajeed M; Al-Malahmeh, Amer J; Isnaeni, Farida Nur; Wesseling, Sebastiaan; Vervoort, Jacques; Rietjens, Ivonne M C M

2016-11-16

Risk assessment of parsley and dill based teas that contain alkenylbenzenes was performed. To this end the estimated daily intake (EDI) of alkenylbenzenes resulting from use of the teas was quantified. Since most teas appeared to contain more than one alkenylbenzene, a combined risk assessment was performed based on equal potency of all alkenylbenzenes or using a so-called toxic equivalency (TEQ) approach through defining toxic equivalency factors (TEFs) for the different alkenylbenzenes. The EDI values resulting from consuming one cup of tea a day were 0.2-10.1 μg/kg bw for the individual alkenylbenzenes, 0.6-13.1 μg/kg bw for the sum of the alkenylbenzenes, and 0.3-10.7 μg safrole equiv/kg bw for the sum of alkenylbenzenes when expressed in safrole equivalents. The margin of exposure (MOE) values obtained were generally <10000, indicating a concern if the teas would be consumed on a daily basis over longer periods of time.

Disentangling the Trichoderma viridescens complex.

PubMed

Jaklitsch, W M; Samuels, G J; Ismaiel, A; Voglmayr, H

2013-12-01

Trichoderma viridescens is recognised as a species complex. Multigene analyses based on the translation elongation factor 1-alpha encoding gene (tef1), a part of the rpb2 gene, encoding the second largest RNA polymerase subunit and the larger subunit of ATP citrate lyase (acl1) reveals 13 phylogenetic species with little or no phenotypic differentiation. This is the first use of acl1 in Trichoderma phylogenetics. The typification of T. viridescens s.str. is clarified and Hypocrea viridescens is replaced by the new name T. paraviridescens. Besides these two species, eleven are phylogenetically recognised and T. olivascens, T. viridarium, T. virilente, T. trixiae, T. viridialbum, T. appalachiense, T. neosinense, T. composticola, T. nothescens and T. sempervirentis are formally described and illustrated. Several species produce yellow diffusing pigment on cornmeal dextrose agar, particularly after storage at 15 °C, while T. olivascens is characterised by the formation of an olivaceous pigment. The results are compared with earlier publications on this group of species.

Pestalotiopsis revisited

PubMed Central

Maharachchikumbura, S.S.N.; Hyde, K.D.; Groenewald, J.Z.; Xu, J.; Crous, P.W.

2014-01-01

Species of Pestalotiopsis occur commonly as plant pathogens, and represent a fungal group known to produce a wide range of chemically novel, diverse metabolites. In the present study, we investigated 91 Pestalotiopsis isolates from the CBS-KNAW Fungal Biodiversity Centre (CBS) culture collection. The phylogeny of the Amphisphaeriaceae was constructed based on analysis of 28S nrRNA gene (LSU) sequence data, and taxonomic changes are proposed to reflect more natural groupings. We combined morphological and DNA data, and segregated two novel genera from Pestalotiopsis, namely Neopestalotiopsis and Pseudopestalotiopsis. The three genera are easily distinguishable on the basis of their conidiogenous cells and colour of their median conidial cells. We coupled morphological and combined sequence data of internal transcribed spacer (ITS), partial β-tubulin (TUB) and partial translation elongation factor 1-alpha (TEF) gene regions, which revealed 30 clades in Neopestalotiopsis and 43 clades in Pestalotiopsis. Based on these data, 11 new species are introduced in Neopestalotiopsis, 24 in Pestalotiopsis, and two in Pseudopestalotiopsis. Several new combinations are proposed to emend monophyly of Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis. PMID:25492988

Effects of prenatal exposure to cigarettes on anthropometrics, energy intake, energy expenditure, and screen time in children.

PubMed

Cameron, Jameason D; Doucet, Éric; Adamo, Kristi B; Walker, Mark; Tirelli, Alessandro; Barnes, Joel D; Hafizi, Kaamel; Murray, Marisa; Goldfield, Gary S

2018-06-15

Maternal prenatal smoking is associated with downstream childhood obesity. Although animal research suggests reduced resting energy expenditure (REE), decreased physical activity (PA), and increased energy intake as mechanisms, these relationships are unclear in humans. The objectives were to examine the association of prenatal maternal smoking with non-volitional energy expenditure (REE and the thermic effect of feeding [TEF]), child adiposity, energy intake, free-living PA (daily light PA (LPA), daily moderate-to-vigorous PA (MVPA), daily sedentary behavior (SB)), and screen time (television and computer/video game) in children. As part of a longitudinal study, 46 children (n = 27 controls and n = 19 smoking exposed) with mean age 7.6 ± 2 years were recruited. Body weight and composition (Bioelectrical Impedance), height (Stadiometer), waist circumference (cm; tape), BMI (kg/m 2 ), REE (kcal/day; indirect calorimetry), PA (minutes; Accelerometry), screen time (hours; self-report) and ad libitum energy intake (lunch buffet; 7-day food log) were measured. Effects sizes were evaluated using Cohen's d. Relative to controls, after controlling for age and family income, children who were exposed to cigarette smoke in utero exhibited greater waist circumference (p = 0.04, Cohen's d = 1.03), percent body fat (%BF; p = 0.02, Cohen's d = 0.97), and a trend for BMI (p = 0.05, Cohen's d = 0.86). Exposed children did not differ in REE (trend for lower: p = 0.1, Cohen's d = 0.42) or TEF but were shown to have significantly higher ad libitum energy intake (p = 0.02, Cohen's D = 0.70) from the palatable lunch buffet, but not from the out of laboratory 7-day energy intake (p = 0.8). Examining screen time behaviors, exposed children spent more time watching television during the week (p = 0.03, Cohen's D = 0.82), and overall television watching (p = 0.02, Cohen's D = 0.80); there were no group differences in any other screen time behaviors. Children exposed to cigarette smoke in utero exhibit greater adiposity, and this exposure may have as contributing factors higher screen time, ad libitum energy intake, and a trend for reduced REE. The data suggest that lifestyle factors such as diet and screen time represent targets for obesity prevention in a high-risk population of young children exposed to prenatal cigarette smoke. Findings also highlight the need for smoking cessation programs to reduce downstream obesity in offspring. Copyright © 2018. Published by Elsevier Inc.

Production of biodegradable plastic by polyhydroxybutyrate (PHB) accumulating bacteria using low cost agricultural waste material.

PubMed

Getachew, Anteneh; Woldesenbet, Fantahun

2016-12-12

Polyhydroxybutyrates (PHBs) are macromolecules synthesized by bacteria. They are inclusion bodies accumulated as reserve materials when the bacteria grow under different stress conditions. Because of their fast degradability under natural environmental conditions, PHBs are selected as alternatives for production of biodegradable plastics. The aim of this work was to isolate potential PHB producing bacteria, evaluate PHB production using agro-residues as carbon sources. Among fifty bacterial strains isolated from different localities, ten PHB accumulating strains were selected and compared for their ability to accumulate PHB granules inside their cells. Isolate Arba Minch Waste Water (AWW) identified as Bacillus spp was found to be the best producer. The optimum pH, temperature, and incubation period for best PHB production by the isolate were 7, 37 °C, and 48 h respectively at 150 rpm. PHB production was best with glucose as carbon source and peptone as nitrogen source. The strain was able to accumulate 55.6, 51.6, 37.4 and 25% PHB when pretreated sugar cane bagasse, corn cob, teff straw (Eragrostis tef) and banana peel were used as carbon sources respectively. Fourier transform-infrared authentication results of the extracted and purified PHB identified its functional units as C-H, CH 2 , C=O and C-O groups. UV-Vis spectrophotometric analysis and biodegradability test confirmed the similarity of the extract with standard PHB and its suitability for bioplastic production. The isolated Bacillus sp can be used for feasible production of PHB using agro-residues especially sugarcane bagasse which can reduce the production cost in addition to reducing the disposal problem of these substrates. The yield of PHB can further be boosted by optimization of production parameters as substrates.

Clinical evaluation of disc battery ingestion in children.

PubMed

Mirshemirani, AliReza; Khaleghnejad-Tabari, Ahmad; Kouranloo, Jaefar; Sadeghian, Naser; Rouzrokh, Mohsen; Roshanzamir, Fatolah; Razavi, Sajad; Sayary, Ali Akbar; Imanzadeh, Farid

2012-04-01

BACKGROUND The purpose of this study was to evaluate the characteristics, management, and outcomes of disc battery ingestion in children. METHODS We reviewed the medical records of children admitted to Mofid Children's Hospital due to disc battery ingestion from January 2006 to January 2010. Clear history, clinical symptoms and results of imaging studies revealed diagnosis of disc battery ingestion in suspected patients. The clinical data reviewed included age, gender, clinical manifestation, radiologic findings, location of disc battery, duration of ingestion, endoscopic results and surgical treatment. RESULTS We found 22 cases (11 males and 11 females) of disc battery ingestion with a mean age of 4.3 years (range: 9 months to 12 years). Common symptoms were vomiting, cough, dysphagia, and dyspnea. The mean duration of ingestion was 2.7 days (4 hours to 1.5 months). A total of 19 patients had histories of disc battery ingestion, but three cases referred with the above symptoms, and the batteries were accidentally found by x-ray. Only three cases had batteries impacted in the esophagus. Twelve batteries were removed endoscopically, 6 batteries spontaneously passed through the gastrointestinal (GI) tract within 5 to 7 days, and 4 patients underwent surgery due to complications: 3 due to tracheo-esophageal fistula (TEF) and 1 due to intestinal perforation. There was no mortality in our study. CONCLUSION Most cases of disc battery ingestion run uneventful courses, but some may be complicated. If the battery lodges in the esophagus, emergency endoscopic management is necessary. However, once in the stomach, it will usually pass through the GI tract.

Blood levels of dioxins, furans, dioxin-like PCBs, and TEQs in general populations: a review, 1989-2010.

PubMed

Consonni, Dario; Sindaco, Raffaella; Bertazzi, Pier Alberto

2012-09-01

A comprehensive worldwide literature review of blood levels of dioxins and dioxin-like compounds in non-exposed adult general populations was performed. The studies published in 1989-2010 reporting information on polychlorinated dibenzo-para-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), non-ortho-PCBs (nPCBs), mono-ortho-PCBs (mPCBs) levels and Toxic Equivalencies (TEQs, a summary weighted measure of their combined toxicity) were reviewed. TEQs were calculated using as standard the most recent WHO 2005 reevaluation of Toxic Equivalency Factors (TEFs). Weighted multiple regression analyses adjusted for year, subject's age, type of sample analyzed, method used for values below detection limit, and central tendency measure used were performed for each congener and standardized TEQs (log-transformed). We identified 187 studies regarding 29,687 subjects of 26 countries. Year of blood collection ranged from 1985 to 2008. The studies reporting congener levels 161. In adjusted analyses, European countries showed higher levels of most dioxin-like congeners and TEQs. A strong positive association of subjects' age with most congeners and with TEQ values was found, confirming previous findings. Significant decreases over time (1985-2008) were documented for PCCDs, PCDFs, and TEQs including their contributions. No significant decrease was found for non-ortho-PCBs, notably PCB 126. Only some mono-ortho-PCBs showed clear significant declines. Accordingly, TEQs including only PCB contribution did not decrease over time. In interpreting these findings, it should be considered that for dioxin-like PCBs the analysis period was shorter (17 years), since these compounds were first measured in 1992. Copyright © 2012 Elsevier Ltd. All rights reserved.

Genotyping and In Vitro Antifungal Susceptibility Testing of Fusarium Isolates from Onychomycosis in India.

PubMed

Gupta, Chhavi; Jongman, Marit; Das, Shukla; Snehaa, K; Bhattacharya, S N; Seyedmousavi, S; van Diepeningen, Anne D

2016-08-01

Onychomycosis refers to fungal infection of the nail and is commonly caused by dermatophytes, while yeasts and non-dermatophytic molds (NDM) are increasingly recognized as pathogens in nail infections. The present study was done to delineate molecular epidemiology of Fusarium onychomycosis in India. Five hundred nail samples of Indian patients clinically suspected of onychomycosis were subjected to direct microscopy and fungal culture. Representative Fusarium isolates were further identified to species level by multi-locus sequencing for internal transcribed spacer, translation elongation factor 1 alpha (tef1-α) and RNA polymerase II subunit (rpb2) regions (primer pairs: ITS1/ITS4, EF1/EF2, 5f2/7cr, respectively). These representative strains were also tested for in vitro antifungal susceptibility by the broth microdilution method. Members of the genus Fusarium proved to be the most common NDM responsible for onychomycosis. The Fusarium spp. responsible for onychomycosis belonged to the Fusarium solani species complex (F. keratoplasticum and F. falciforme) and Fusarium fujikuroi species complex (F. proliferatum, F. acutatum and F. sacchari). Antifungal susceptibility results indicated that amphotericin B was the most effective antifungal across all isolates (MIC ranging 0.5-2 mg/L), followed by voriconazole (MIC ranging 1-8 µg/ml). However, a large variation was shown in susceptibility to posaconazole (MIC ranging 0.5 to >16 µg/ml). To conclude, we identified different Fusarium spp. responsible for onychomycosis in India with variation within species in susceptibility to antifungal agents, showing that fusariosis requires correct and prompt diagnosis as well as antifungal susceptibility testing.

Determination and risk assessment of naturally occurring genotoxic and carcinogenic alkenylbenzenes in nutmeg-based plant food supplements.

PubMed

Al-Malahmeh, Amer J; Alajlouni, Abdalmajeed M; Ning, Jia; Wesseling, Sebastiaan; Vervoort, Jacques; Rietjens, Ivonne M C M

2017-10-01

A risk assessment of nutmeg-based plant food supplements (PFS) containing different alkenylbenzenes was performed based on the alkenylbenzene levels quantified in a series of PFS collected via the online market. The estimated daily intake (EDI) of the alkenylbenzenes amounted to 0.3 to 312 μg kg -1 body weight (bw) for individual alkenylbenzenes, to 1.5 to 631 μg kg -1 bw when adding up the alkenylbenzene levels assuming equal potency, and to 0.4 to 295 μg kg -1 bw when expressed in safrole equivalents using toxic equivalency factors (TEFs). The margin of exposure approach (MOE) was used to evaluate the potential risks. Independent of the method used for the intake estimate, the MOE values obtained were generally lower than 10000 indicating a priority for risk management. When taking into account that PFS may be used for shorter periods of time and using Haber's rule to correct for shorter than lifetime exposure it was shown that limiting exposure to only 1 or 2 weeks would result in MOE values that would be, with the presently determined levels of alkenylbenzenes and proposed uses of the PFS, of low priority for risk management (MOE > 10000). It is concluded that the results of the present paper reveal that nutmeg-based PFS consumption following recommendations for daily intake especially for longer periods of time raise a concern. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Loss of the Drosophila cell polarity regulator Scribbled promotes epithelial tissue overgrowth and cooperation with oncogenic Ras-Raf through impaired Hippo pathway signaling

PubMed Central

2011-01-01

Background Epithelial neoplasias are associated with alterations in cell polarity and excessive cell proliferation, yet how these neoplastic properties are related to one another is still poorly understood. The study of Drosophila genes that function as neoplastic tumor suppressors by regulating both of these properties has significant potential to clarify this relationship. Results Here we show in Drosophila that loss of Scribbled (Scrib), a cell polarity regulator and neoplastic tumor suppressor, results in impaired Hippo pathway signaling in the epithelial tissues of both the eye and wing imaginal disc. scrib mutant tissue overgrowth, but not the loss of cell polarity, is dependent upon defective Hippo signaling and can be rescued by knockdown of either the TEAD/TEF family transcription factor Scalloped or the transcriptional coactivator Yorkie in the eye disc, or reducing levels of Yorkie in the wing disc. Furthermore, loss of Scrib sensitizes tissue to transformation by oncogenic Ras-Raf signaling, and Yorkie-Scalloped activity is required to promote this cooperative tumor overgrowth. The inhibition of Hippo signaling in scrib mutant eye disc clones is not dependent upon JNK activity, but can be significantly rescued by reducing aPKC kinase activity, and ectopic aPKC activity is sufficient to impair Hippo signaling in the eye disc, even when JNK signaling is blocked. In contrast, warts mutant overgrowth does not require aPKC activity. Moreover, reducing endogenous levels of aPKC or increasing Scrib or Lethal giant larvae levels does not promote increased Hippo signaling, suggesting that aPKC activity is not normally rate limiting for Hippo pathway activity. Epistasis experiments suggest that Hippo pathway inhibition in scrib mutants occurs, at least in part, downstream or in parallel to both the Expanded and Fat arms of Hippo pathway regulation. Conclusions Loss of Scrib promotes Yorkie/Scalloped-dependent epithelial tissue overgrowth, and this is also important for driving cooperative tumor overgrowth with oncogenic Ras-Raf signaling. Whether this is also the case in human cancers now warrants investigation since the cell polarity function of Scrib and its capacity to restrain oncogene-mediated transformation, as well as the tissue growth control function of the Hippo pathway, are conserved in mammals. PMID:21955824

One shall become two: Separation of the esophagus and trachea from the common foregut tube

PubMed Central

Billmyre, Katherine Kretovich; Hutson, Mary; Klingensmith, John

2016-01-01

The alimentary and respiratory organ systems arise from a common endodermal origin, the anterior foregut tube. Formation of the esophagus from the dorsal region and the trachea from the ventral region of the foregut primordium occurs via a poorly understood compartmentalization process. Disruption of this process can result in severe birth defects, such as esophageal atresia and tracheoesphageal fistula (EA/TEF), in which the lumina of the trachea and esophagus remain connected. Here we summarize the signaling networks known to be necessary for regulating dorso-ventral patterning within the common foregut tube and cellular behaviors that may occur during normal foregut compartmentalization. We propose that dorso-ventral patterning serves to establish a lateral region of the foregut tube that is capable of undergoing specialized cellular rearrangements, culminating in compartmentalization. We review established as well as new rodent models that may be useful in addressing this hypothesis. Finally, we discuss new experimental models that could help elucidate the mechanism behind foregut compartmentalization. An integrated approach to future foregut morphogenesis research will allow for a better understanding of this complex process. PMID:25329576

Transportation Energy Futures Series: Effects of Travel Reduction and Efficient Driving on Transportation: Energy Use and Greenhouse Gas Emissions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Porter, C. D.; Brown, A.; DeFlorio, J.

2013-03-01

Since the 1970s, numerous transportation strategies have been formulated to change the behavior of drivers or travelers by reducing trips, shifting travel to more efficient modes, or improving the efficiency of existing modes. This report summarizes findings documented in existing literature to identify strategies with the greatest potential impact. The estimated effects of implementing the most significant and aggressive individual driver behavior modification strategies range from less than 1% to a few percent reduction in transportation energy use and GHG emissions. Combined strategies result in reductions of 7% to 15% by 2030. Pricing, ridesharing, eco-driving, and speed limit reduction/enforcement strategiesmore » are widely judged to have the greatest estimated potential effect, but lack the widespread public acceptance needed to accomplish maximum results. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Transportation Energy Futures Series. Effects of Travel Reduction and Efficient Driving on Transportation. Energy Use and Greenhouse Gas Emissions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Porter, C. D.; Brown, A.; DeFlorio, J.

2013-03-01

Since the 1970s, numerous transportation strategies have been formulated to change the behavior of drivers or travelers by reducing trips, shifting travel to more efficient modes, or improving the efficiency of existing modes. This report summarizes findings documented in existing literature to identify strategies with the greatest potential impact. The estimated effects of implementing the most significant and aggressive individual driver behavior modification strategies range from less than 1% to a few percent reduction in transportation energy use and GHG emissions. Combined strategies result in reductions of 7% to 15% by 2030. Pricing, ridesharing, eco-driving, and speed limit reduction/enforcement strategiesmore » are widely judged to have the greatest estimated potential effect, but lack the widespread public acceptance needed to accomplish maximum results. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Three new species of Trichoderma with hyaline ascospores from China.

PubMed

Zhu, Z X; Zhuang, W Y

2015-01-01

Collections of Trichoderma having hyaline ascospores from different areas of China were examined. Using combined analyses of morphological data, culture characters and phylogenetic information based on rDNA sequences of partial nuc translation elongation factor 1-α encoding gene (TEF1-α) and the gene encoding the second largest nuc RNA polymerase subunit (RPB2), three new species, Trichoderma applanatum, T. oligosporum and T. sinoluteum, were discovered and are described. Trichoderma applanatum produces continuous flat to pulvinate, white to cream stromata with dense orange or pale brown ostioles, and simple acremonium-like to verticillium-like conidiophores, belongs to the Hypocreanum clade and is closely related to T. decipiens. Trichoderma oligosporum forms reddish brown stromata with a downy surface, hyaline conidia and gliocladium-like conidiophores, and is closely related to but distinct from T. crystalligenum in the Psychrophila clade. Trichoderma sinoluteum, as a member of the Polysporum clade, is characterized by pale yellow stromata, white pustulate conidiomata, pachybasium-like conidiophores, and hyaline conidia. Differences between the new species and their close relatives are discussed. © 2015 by The Mycological Society of America.

Diversity and effect of Trichoderma spp. associated with green mold disease on Lentinula edodes in China.

PubMed

Wang, Gangzheng; Cao, Xiantao; Ma, Xiaolong; Guo, Mengpei; Liu, Changhao; Yan, Lianlian; Bian, Yinbing

2016-08-01

Lentinula edodes, one of the most important edible mushrooms in China, is affected heavily by the infection of green mold that overgrows mushroom mycelia. We collected the diseased samples from main L. edodes cultivation regions in China to characterize the pathogen and to study the effect of Trichoderma spp. on L. edodes species. We identified six Trichoderma species, that is, T. harzianum, T. atroviride, T. viride, T. pleuroticola, T. longibrachiatum, and T. oblongisporum based on the internal transcribed spacer or tef1-α sequences and morphology characteristics. In confrontation cultures on Petri plates or in tubes, and in L. edodes cultures in a medium containing Trichoderma metabolites, L. edodes mycelia were not only distorted and swollen, but also inhibited by Trichoderma isolates. It is not possible that adjusting pH value or temperature is used for controlling L. edodes green disease, because the growth of most of Trichoderma isolates and L. edodes shared similar pH and temperature conditions. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Independent origins and incipient speciation among host-associated populations of Thielaviopsis ethacetica in Cameroon.

PubMed

Mbenoun, Michael; Wingfield, Michael J; Letsoalo, Teboho; Bihon, Wubetu; Wingfield, Brenda D; Roux, Jolanda

2015-11-01

Thielaviopsis ethacetica was recently reinstated as a distinct taxon using DNA phylogenies. It is widespread affecting several crop plants of global economic importance. In this study, microsatellite markers were developed and used in conjunction with sequence data to investigate the genetic diversity and structure of Th. ethacetica in Cameroon. A collection of 71 isolates from cacao, oil palm, and pineapple, supplemented with nine isolates from other countries were analysed. Four genetic groups were identified. Two of these were associated with oil palm in Cameroon and showed high genetic diversity, suggesting that they might represent an indigenous population of the pathogen. In contrast, the remaining two groups, associated with cacao and pineapple, had low genetic diversity and, most likely, represent introduced populations. There was no evidence of gene flow between these groups. Phylogenetic analyses based on sequences of the tef1-α as well as the combined flanking regions of six microsatellite loci were consistent with population genetic analyses and suggested that Th. ethacetica is comprised of two divergent genetic lineages. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Glycerol positive promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae.

PubMed

Ho, Ping-Wei; Klein, Mathias; Futschik, Matthias; Nevoigt, Elke

2018-05-01

Glycerol offers several advantages as a substrate for biotechnological applications. An important step toward using the popular production host Saccharomyces cerevisiae for glycerol-based bioprocesses has been the fact that in recent studies commonly used S. cerevisiae strains were engineered to grow in synthetic medium containing glycerol as the sole carbon source. For metabolic engineering projects of S. cerevisiae growing on glycerol, characterized promoters are missing. In the current study, we used transcriptome analysis and a yECitrine-based fluorescence reporter assay to select and characterize 25 useful promoters. The promoters of the genes ALD4 and ADH2 showed 4.2-fold and 3-fold higher activities compared to the well-known strong TEF1 promoter. Moreover, the collection contains promoters with graded activities in synthetic glycerol medium and different degrees of glucose repression. To demonstrate the general applicability of the promoter collection, we successfully used a subset of the characterized promoters with graded activities in order to optimize growth on glycerol in an engineered derivative of CEN.PK, in which glycerol catabolism exclusively occurs via a non-native DHA pathway.

Large-scale production of tannase using the yeast Arxula adeninivorans.

PubMed

Böer, Erik; Breuer, Friederike Sophie; Weniger, Michael; Denter, Sylvia; Piontek, Michael; Kunze, Gotthard

2011-10-01

Tannase (tannin acyl hydrolase, EC 3.1.1.20) hydrolyses the ester and depside bonds of gallotannins and gallic acid esters and is an important industrial enzyme. In the present study, transgenic Arxula adeninivorans strains were optimised for tannase production. Various plasmids carrying one or two expression modules for constitutive expression of tannase were constructed. Transformant strains that overexpress the ATAN1 gene from the strong A. adeninivorans TEF1 promoter produce levels of up to 1,642 U L(-1) when grown in glucose medium in shake flasks. The effect of fed-batch fermentation on tannase productivity was then investigated in detail. Under these conditions, a transgenic strain containing one ATAN1 expression module produced 51,900 U of tannase activity per litre after 142 h of fermentation at a dry cell weight of 162 g L(-1). The highest yield obtained from a transgenic strain with two ATAN1 expression modules was 31,300 U after 232 h at a dry cell weight of 104 g L(-1). Interestingly, the maximum achieved yield coefficients [Y(P/X)] for the two strains were essentially identical.

SRC activates TAZ for intestinal tumorigenesis and regeneration.

PubMed

Byun, Mi Ran; Hwang, Jun-Ha; Kim, A Rum; Kim, Kyung Min; Park, Jung Il; Oh, Ho Taek; Hwang, Eun Sook; Hong, Jeong-Ho

2017-12-01

Proto-oncogene tyrosine-protein kinase Src (cSRC) is involved in colorectal cancer (CRC) development and damage-induced intestinal regeneration, although the cellular mechanisms involved are poorly understood. Here, we report that transcriptional coactivator with PDZ binding domain (TAZ) is activated by cSRC, regulating CRC cell proliferation and tumor formation, where cSRC overexpression increases TAZ expression in CRC cells. In contrast, knockdown of cSRC decreases TAZ expression. Additionally, direct phosphorylation of TAZ at Tyr316 by cSRC stimulates nuclear localization and facilitates transcriptional enhancer factor TEF-3 (TEAD4)-mediated transcription. However, a TAZ phosphorylation mutant significantly decreased cell proliferation, wound healing, colony forming, and tumor formation. In a CRC mouse model, Apc Min/+ , activated SRC expression was associated with increased TAZ expression in polyps and TAZ depletion decreased polyp formation. Moreover, intestinal TAZ knockout mice had intestinal regeneration defects following γ-irradiation. Finally, significant correspondence between SRC activation and TAZ overexpression was observed in CRC patients. These results suggest that TAZ is a critical factor for SRC-mediated intestinal tumor formation and regeneration. Copyright © 2017 Elsevier B.V. All rights reserved.

Gluten-Free Sources of Fermentable Extract: Effect of Temperature and Germination Time on Quality Attributes of Teff [Eragrostis tef (zucc.) Trotter] Malt and Wort.

PubMed

Di Ghionno, Lidia; Marconi, Ombretta; Lee, Eung Gwan; Rice, Christopher J; Sileoni, Valeria; Perretti, Giuseppe

2017-06-14

This study was conducted to evaluate the behavior of a white teff variety called Witkop during malting by using different parameters (germination temperature and duration) and to identify the best malting program. Samples were evaluated for standard quality malt and wort attributes, pasting characteristics, β-glucan and arabinoxylan content, and sugar profile. It was concluded that malting teff at 24 °C for 6 days produced acceptable malt in terms of quality attributes and sugar profile for brewing. The main attributes were 80.4% extract, 80.9% fermentability, 1.53 mPa s viscosity, 7.4 EBC-U color, 129 mg/L FAN, and 72.1 g/L of total fermentable sugars. Statistical analysis showed that pasting characteristics of teff malt were negatively correlated with some malt quality attributes, such as extract and fermentability. Witkop teff appeared to be a promising raw material for malting and brewing. However, the small grain size may lead to difficulties in handling malting process, and a bespoke brewhouse plant should be developed for the production at industrial scale.

Molecular Characterisation of Endophytic Fungi from Roots of Wild Banana (Musa acuminata)

PubMed Central

Zakaria, Latiffah; Jamil, Muhamad Izham Muhamad; Anuar, Intan Sakinah Mohd

2016-01-01

Endophytic fungi inhabit apparently healthy plant tissues and are prevalent in terrestrial plants, especially root tissues, which harbour a wide assemblage of fungal endophytes. Therefore, this study focused on the isolation and characterisation of endophytic fungi from the roots of wild banana (Musa acuminata). A total of 31 isolates of endophytic fungi were isolated from 80 root fragments. The endophytic fungi were initially sorted according to morphological characteristics and identified using the sequences of the translation elongation factor-1α (TEF-1α) gene of Fusarium spp. and the Internal Transcribed Spacer (ITS) regions of other fungi. The most common fungal isolates were species of the genus Fusarium, which were identified as F. proliferatum, Fusarium sp., F. solani species complex, and F. oxysporum. Other isolated endophytic fungi included Curvularia lunata, Trichoderma atroviride, Calonectria gracilis, Rhizoctonia solani, Bionectria ochroleuca, and Stromatoneurospora phoenix (Xylariceae). Several of the fungal genera, such as Fusarium, Trichoderma, Rhizoctonia, and Xylariceae, are among the common fungal endophytes reported in plants. This study showed that the roots of wild banana harbour a diverse group of endophytic fungi. PMID:27019688

Five new species of entomopathogenic fungi from the Amazon and evolution of neotropical Ophiocordyceps.

PubMed

Sanjuan, Tatiana I; Franco-Molano, Ana E; Kepler, Ryan M; Spatafora, Joseph W; Tabima, Javier; Vasco-Palacios, Aída M; Restrepo, Silvia

2015-10-01

The neotropical biogeographic zone is a 'hot spot' of global biodiversity, especially for insects. Fungal pathogens of insects appear to track this diversity. However, the integration of this unique component of fungal diversity into molecular phylogenetic analyses remains sparse. The entomopathogenic fungal genus Ophiocordyceps is species rich in this region with the first descriptions dating to the early nineteenth century. In this study, material from various ecosystems throughout Colombia and Ecuador was examined. Molecular phylogenetic analyses of five nuclear loci including SSU, LSU, TEF, RPB1, and RPB2 were conducted alongside a morphological evaluation. Thirty-five specimens were examined representing fifteen different species of Ophiocordyceps, and five new species, Ophiocordyceps blattarioides, Ophiocordyceps tiputini, Ophiocordyceps araracuarensis, Ophiocordyceps fulgoromorphila, and Ophiocordyceps evansii, were described. An accurate identification of the host allowed us to conclude that host identity and host habitat are positively correlated with phylogenetic species of Ophiocordyceps and are probably strong drivers for speciation of neotropical entomopathogenic fungi. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Defining the phylogenetic position of Amanita species from Andean Colombia.

PubMed

Vargas, Natalia; Pardo-de La Hoz, Carlos José; Danies, Giovanna; Franco-Molano, Ana Esperanza; Jiménez, Pedro; Restrepo, Silvia; Grajales, Alejandro

2017-01-01

Amanita is a worldwide-distributed fungal genus, with approximately 600 known species. Most species within the genus are ectomycorrhizal (ECM), with some saprotrophic representatives. In this study, we constructed the first comprehensive phylogeny including ECM species from Colombia collected in native Quercus humboldtii forests and in introduced Pinus patula plantations. We included 8 species (A. brunneolocularis, A. colombiana, A. flavoconia, A. fuligineodisca, A. muscaria, A. rubescens, A. sororcula, and A. xylinivolva) out of 16 species reported for the country, two new reports: A. citrina and A. virosa, and a new variety A. brunneolocularis var. pallida. Morphological taxonomic keys together with a phylogenetic approach using three nuclear gene regions: partial nuc rDNA 28S nuc rDNA internal transcribed spacers ITS1 and ITS2 and partial translation elongation factor 1-α gene (TEF1), were used to classify the specimens. Several highly supported clades were obtained from the phylogenetic hypotheses obtained by Bayesian inference and maximum likelihood approaches, allowing us to position the Colombian collections in a coherent infrageneric level and to contribute to the knowledge of local Amanita diversity.

Transforming growth factor-beta inhibits the expression of clock genes.

PubMed

Gast, Heidemarie; Gordic, Sonja; Petrzilka, Saskia; Lopez, Martin; Müller, Andreas; Gietl, Anton; Hock, Christoph; Birchler, Thomas; Fontana, Adriano

2012-07-01

Disturbances of sleep-wake rhythms are an important problem in Alzheimer's disease (AD). Circadian rhythms are regulated by clock genes. Transforming growth factor-beta (TGF-β) is overexpressed in neurons in AD and is the only cytokine that is increased in cerebrospinal fluid (CSF). Our data show that TGF-β2 inhibits the expression of the clock genes Period (Per)1, Per2, and Rev-erbα, and of the clock-controlled genes D-site albumin promoter binding protein (Dbp) and thyrotroph embryonic factor (Tef). However, our results showed that TGF-β2 did not alter the expression of brain and muscle Arnt-like protein-1 (Bmal1). The concentrations of TGF-β2 in the CSF of 2 of 16 AD patients and of 1 of 7 patients with mild cognitive impairment were in the dose range required to suppress the expression of clock genes. TGF-β2-induced dysregulation of clock genes may alter neuronal pathways, which may be causally related to abnormal sleep-wake rhythms in AD patients. © 2012 New York Academy of Sciences.

DNA barcoding survey of Trichoderma diversity in soil and litter of the Colombian lowland Amazonian rainforest reveals Trichoderma strigosellum sp. nov. and other species.

PubMed

López-Quintero, Carlos A; Atanasova, Lea; Franco-Molano, A Esperanza; Gams, Walter; Komon-Zelazowska, Monika; Theelen, Bart; Müller, Wally H; Boekhout, Teun; Druzhinina, Irina

2013-11-01

The diversity of Trichoderma (Hypocreales, Ascomycota) colonizing leaf litter as well as the rhizosphere of Garcinia macrophylla (Clusiaceae) was investigated in primary and secondary rain forests in Colombian Amazonia. DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %). Four ITS 1 and 2 phylotypes (13 strains) could not be identified with certainty. Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov. Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.

Antioxidant capacity, total phenolics and nutritional content in selected ethiopian staple food ingredients.

PubMed

Forsido, Sirawdink Fikreyesus; Rupasinghe, H P Vasantha; Astatkie, Tess

2013-12-01

The total antioxidant capacity, total phenolics content (TPC) and nutritional content of five types of enset (Enset ventricosum) flour in comparison with four staples (teff [Eragrostis tef], wheat, corn and tapioca) were evaluated. Teff, corn and "amicho" (corm of enset) had the highest ferric reducing antioxidant power (FRAP). The FRAP and TPC of teff (1.8 mmol Trolox equivalence/100 g dry matter (DM) and 123.6 mg gallic acid equivalent/100 g DM, respectively) were over 4-fold larger than the lowest obtained from "bulla" (dehydrated juice of pseudostem of enset). Corn had the lowest IC(50) value of 1,1-diphenyl-2-picrylhydrazyl radical scavenging (10.27 mg DM mL(-1)). Teff had the highest crude fat content (3.71%) and some mineral profile (P, Mg, Mn and Cu). Enset products had higher fiber, Ca, K, Mg and Mn content as compared to wheat and corn. Ethiopian staple teff has a potential for developing value-added food products with nutritional and health benefits.

Morphological reassessment and molecular phylogenetic analyses of Amauroderma s.lat. raised new perspectives in the generic classification of the Ganodermataceae family.

PubMed

Costa-Rezende, D H; Robledo, G L; Góes-Neto, A; Reck, M A; Crespo, E; Drechsler-Santos, E R

2017-12-01

Ganodermataceae is a remarkable group of polypore fungi, mainly characterized by particular double-walled basidiospores with a coloured endosporium ornamented with columns or crests, and a hyaline smooth exosporium. In order to establish an integrative morphological and molecular phylogenetic approach to clarify relationship of Neotropical Amauroderma s.lat. within the Ganodermataceae family, morphological analyses, including scanning electron microscopy, as well as a molecular phylogenetic approach based on one (ITS) and four loci (ITS-5.8S, LSU, TEF-1α and RPB1 ), were carried out. Ultrastructural analyses raised up a new character for Ganodermataceae systematics, i.e . , the presence of perforation in the exosporium with holes that are connected with hollow columns of the endosporium. This character is considered as a synapomorphy in Foraminispora , a new genus proposed here to accommodate Porothelium rugosum (≡ Amauroderma sprucei ). Furtadoa is proposed to accommodate species with monomitic context: F. biseptata, F. brasiliensis and F. corneri . Molecular phylogenetic analyses confirm that both genera grouped as strongly supported distinct lineages out of the Amauroderma s.str. clade.

Polycyclic aromatic hydrocarbons (PAHs) in water from three estuaries of China: Distribution, seasonal variations and ecological risk assessment.

PubMed

Yan, Jinxia; Liu, Jingling; Shi, Xuan; You, Xiaoguang; Cao, Zhiguo

2016-08-15

The distribution, seasonal variations and ecological risk assessment of polycyclic aromatic hydrocarbons (PAHs) in water from three estuaries in Hai River Basin of China, which has been suffering from different anthropogenic pressures, were investigated. In three estuaries, the average concentration of ΣPAHs was the lowest in Luan River estuary, followed by Hai River estuary, and the highest in Zhangweixin River estuary. There were significant seasonal variations in ΣPAHs, the concentrations of ΣPAHs were higher in November than in May and August. The composition profiles of PAHs in different sites were significantly different, and illustrated seasonal variations. Generally, 2-ring (Nap) and 3-ring PAHs (Acp, Fl and Phe) were the most abundant components at most sampling sites in three estuaries. The PAHs in three estuaries were mainly originated from pyrogenic sources. A method based on toxic equivalency factors (TEFs) and risk quotient (RQ) was proposed to assess the ecological risk of ΣPAHs, with the ecological risk of individual PAHs being considered separately. The results showed that the ecological risks caused by ΣPAHs were high in Hai River estuary and Zhangweixin River estuary, and moderate in Luan River estuary. The mean values of ecological risk in August were lower than those in November. The contributions of individual PAHs to ecological risk were different in May, August and November. 3-ring and 4-ring PAHs accounted for much more ecological risk than 2-ring, 5-ring and 6-ring, although the contributions of 5-ring and 6-ring to ecological risk were higher than these to PAHs concentrations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of maturity at harvest on the nutritive value and ruminal digestion of Eragrostis tef (cv. Moxie) when fed to beef cattle.

PubMed

Vinyard, J R; Hall, J B; Sprinkle, J E; Chibisa, G E

2018-05-18

Teff (Eragrostis tef cv. Moxie), a warm-season annual grass, could be an excellent forage for beef cattle. However, there is limited information on its nutritive value to cattle when harvested at different stages of maturity. Thus, the objective of this research was to determine the effect of feeding teff hay harvested at the boot (BT), early-heading (EH), or late-heading (LH) stages of maturity on nutrient intake, ruminal fermentation characteristics, omasal nutrient flow, and N utilization in beef cattle. Six ruminally cannulated beef heifers (mean initial BW ± SD, 476 ± 32.6) were used in a replicated 3 × 3 Latin square design with 28-d periods (18 d for adaptation and 10 d for measurements). Dry matter intake was measured daily. Indwelling pH loggers were used to measure ruminal pH from d 21 to 28. Ruminal fluid and omasal digesta were collected from d 26 to 28 to determine fermentation characteristics and omasal nutrient flow. Fecal and urine samples to quantify N excretion were also collected (d 26 to 28). Blood samples for plasma urea-N (PUN) determination were collected 3 h post-feeding on d 28. There were no changes (P > 0.28) in the ADF or NDF content of teff with advancing maturity, but iNDF increased (P < 0.01) with increasing maturity. Maturity had no effect (P ≥ 0.14) on DMI, and ruminal total short-chain fatty acid (SCFA) concentration, pH, digestibility and outflow of DM, OM, NDF, ADF, and CP. However, the CP content of BT hay was greater (P < 0.01) than for EH and LH hay (18.1, 14.1, and 11.5%, respectively, DM basis), and this resulted in the higher CP intake (P < 0.01) for heifers fed the BT than the EH and LH hay. Consequently, ruminal ammonia-N (NH3-N) concentration was greater (P < 0.01) for heifers fed BT than EH and LH hay, thereby possibly explaining the tendency for a decrease (P = 0.08) in PUN concentration, and a decrease (P < 0.01) in the excretion of total N, urine N and urea-N (UUN) with advancing maturity. However, fecal N excretion (g/d) did not differ (P = 0.76). In conclusion, despite a decrease in CP intake and ruminal NH3-N concentration, feeding beef heifers EH and LH compared to BT teff hay did not compromise ruminal digestion and outflow of DM, OM, NDF, ADF, and CP, and microbial protein synthesis. Advancing maturity in teff hay also resulted in a decrease in the excretion of total N and urine N and UUN when fed to cattle.

No effect of the Trp64Arg beta(3)-adrenoceptor gene variant on weight loss, body composition, or energy expenditure in obese, caucasian postmenopausal women.

PubMed

Rawson, Eric S; Nolan, Amy; Silver, Kristi; Shuldiner, Alan R; Poehlman, Eric T

2002-06-01

The Trp64Arg polymorphism in the beta(3)-adrenoceptor gene has been associated with increased prevalence of obesity, type 2 diabetes, and low rates of energy expenditure, although these findings are not unanimous. It is currently unknown if the presence of the Trp64Arg gene variant impedes the loss of body weight in obese, postmenopausal women via a reducing effect on energy expenditure. The objective of this study was to compare body composition and energy expenditure in carriers and noncarriers of the Trp64Arg variant in the beta(3)-adrenoceptor before and after weight loss. We measured body composition, total daily energy expenditure (TEE), resting metabolic rate (RMR), physical activity energy expenditure (PAEE), thermic effect of feeding (TEF), and respiratory quotient (RQ) in 34 obese, postmenopausal women (19 carriers and 15 noncarriers for the Trp64Arg variant) before and after a weight loss intervention. There were no differences in body composition or daily energy expenditure and its components between the 2 groups at baseline. There were significant reductions in body mass, body mass index (BMI), percent body fat, fat-free mass, and fat mass (main effect, all P <.0001) when analyzed with the 2 genotypes combined, but no significant differences between carriers and noncarriers with respect to change in these variables (group x time interaction term, all P >.05). Total energy expenditure tended to be reduced (490 kJ x d(-1), P =.13) in both groups following weight loss, but there was no significant group x time interaction term (P =.78), indicating no difference in the response of the 2 genotypes. There was a 9% reduction in RMR (611 kJ x d(-1), P <.001) when both groups were considered together, but no significant group x time interaction term (P =.84), suggesting that both groups responded in a similar manner to the weight loss intervention. PAEE and the TEF were not different following weight loss (both P >.60). There was a trend for RQ to be reduced after weight loss (P =.07), but there was no difference between carriers or noncarriers of the Trp64Arg variant (P =.58). In summary, we found that obese postmenopausal women who carry the Trp64Arg variant in the beta(3)-adrenoceptor had similar changes in body composition and energy expenditure to noncarriers of the variant in response to prolonged caloric restriction. These results suggest that the presence of the Trp64Arg variant in the beta(3)-adrenoceptor should not be a hindrance to weight reduction. Copyright 2002, Elsevier Science (USA). All rights reserved.

Effect of feed intake on heat production and protein and fat deposition in milk-fed veal calves.

PubMed

Labussiere, E; Maxin, G; Dubois, S; van Milgen, J; Bertrand, G; Noblet, J

2009-04-01

Energy requirements for veal calves have not been updated recently despite the increased age at slaughter and the predominance of the Prim'Holstein breed in Europe. The objectives of this study were to determine the effects of four feeding levels (FLs) on protein and fat deposition and heat production in milk-fed calves at three stages of fattening and to determine energy requirements of calves. At each stage, 16 Prim'Holstein male calves (mean body weight (BW): 73.4, 151.6 and 237.4 kg) were fed a milk replacer at 79%, 87%, 95% or 103% of a reference FL. Measurements for one stage were conducted over 4 successive weeks in two open-circuit respiration chambers and consisted of a 6-day nitrogen and energy balance followed by a fasting day for estimating fasting heat production (FHP) of the calves. Heat production (HP) measurements were analyzed using a modeling approach to partition it between HP due to physical activity (AHP), feed intake (thermic effect of feeding (TEF)) and FHP. There was no effect of FL and stage on apparent digestibility coefficients, except for a tendency for increased digestibility coefficient of fat as animals got older. The metabolizable energy (ME)/digestible energy (DE) ratio did not depend on FL but decreased (P < 0.01) as animals got older in connection with marked increases in urinary glucose and urea excretion. The AHP and TEF components of HP were not affected by stage or FL and averaged 8.4% and 7.8% of ME intake, respectively. The FHP, expressed per kg BW0.85, increased with increasing FL, suggesting that also ME requirement for maintenance (MEm) may depend on FL. For an average intake of 625 kJ ME/kg BW0.85 per day (95% of the reference FL), FHP was 298 kJ/kg BW0.85 per day. Energy retention as protein and fat increased with increasing FL resulted in higher BW gain. But the rate of increase depended on stage of growth. The slope relating protein deposition to FL was lower in the finishing phase than in the growing phase, while the slope for lipid deposition was greater. Protein and fat contents of BW gain were not affected by FL but increased as animals got older. From these results, the energy requirements of veal calves are proposed according to a new approach, which considers that MEm (expressed per kg BW0.85) depends on ME intake (kJ/kg BW0.85) according to the following relationship: MEm = 197 + 0.25 × ME intake. The corresponding marginal efficiencies of ME utilization for protein and fat deposition are then 82% and 87%, respectively.

Stereopsidales - A New Order of Mushroom-Forming Fungi

PubMed Central

Sjökvist, Elisabet; Pfeil, Bernard E.; Larsson, Ellen; Larsson, Karl-Henrik

2014-01-01

One new order, one new family, and one new combination are presented, as the result of molecular phylogenetic analyses. The new order Stereopsidales and the new family Stereopsidaceae are described incorporating Stereopsis radicans and S. globosa, formerly Clavulicium globosum. We show that not only do these species represent an old overlooked lineage, but both species harbor cryptic diversity. In addition, a third species, C. macounii, appears as a plausible sister to the new lineage, but there is conflict in the data. All specimens of S. radicans and S. globosa analysed here are from the South and Central Americas; several records of S. radicans have been made also from tropical Asia. We expect the true diversity in this group to be a lot higher than presented in this paper. Stereopsis radicans was formerly included in Polyporales, but a placement within that order is rejected by our data through SH tests. The dataset consisted of four nuclear markers: rpb2, tef1, LSU and SSU, each of which was analysed separately using maximum likelihood and Bayesian inference. Recombination detection tests indicate no plausible recombinations. The potential of S. radicans, S. globosa and C. macounii being amphitallic is briefly discussed. PMID:24777067

Malassezia arunalokei sp. nov., a Novel Yeast Species Isolated from Seborrheic Dermatitis Patients and Healthy Individuals from India

PubMed Central

Honnavar, Prasanna; Prasad, Gandham S.; Ghosh, Anup; Dogra, Sunil; Handa, Sanjeev

2016-01-01

The majority of species within the genus Malassezia are lipophilic yeasts that colonize the skin of warm-blooded animals. Two species, Malassezia globosa and Malassezia restricta, are implicated in the causation of seborrheic dermatitis/dandruff (SD/D). During our survey of SD/D cases, we isolated several species of Malassezia and noticed vast variations within a few lipid-dependent species. Variations observed in the phenotypic characteristics (colony morphology, absence of catalase activity, growth at 37°C, and precipitation surrounding wells containing Tween 20 or Cremophor EL) suggested the possible presence of a novel species. Sequence divergence observed in the internal transcribed spacer (ITS) region, the D1/D2 domain, and the intergenic spacer 1 (IGS1) region of rDNA and the TEF1 gene, PCR-restriction fragment length polymorphism (RFLP) analysis of the ITS2 region, and fluorescent amplified fragment length polymorphism analysis support the existence of a novel species. Based on phenotypic and molecular characterization of these strains, we propose a new species, namely, M. arunalokei sp. nov., and we designate NCCPF 127130 (= MTCC 12054 = CBS 13387) as the type strain. PMID:27147721

Malassezia arunalokei sp. nov., a Novel Yeast Species Isolated from Seborrheic Dermatitis Patients and Healthy Individuals from India.

PubMed

Honnavar, Prasanna; Prasad, Gandham S; Ghosh, Anup; Dogra, Sunil; Handa, Sanjeev; Rudramurthy, Shivaprakash M

2016-07-01

The majority of species within the genus Malassezia are lipophilic yeasts that colonize the skin of warm-blooded animals. Two species, Malassezia globosa and Malassezia restricta, are implicated in the causation of seborrheic dermatitis/dandruff (SD/D). During our survey of SD/D cases, we isolated several species of Malassezia and noticed vast variations within a few lipid-dependent species. Variations observed in the phenotypic characteristics (colony morphology, absence of catalase activity, growth at 37°C, and precipitation surrounding wells containing Tween 20 or Cremophor EL) suggested the possible presence of a novel species. Sequence divergence observed in the internal transcribed spacer (ITS) region, the D1/D2 domain, and the intergenic spacer 1 (IGS1) region of rDNA and the TEF1 gene, PCR-restriction fragment length polymorphism (RFLP) analysis of the ITS2 region, and fluorescent amplified fragment length polymorphism analysis support the existence of a novel species. Based on phenotypic and molecular characterization of these strains, we propose a new species, namely, M. arunalokei sp. nov., and we designate NCCPF 127130 (= MTCC 12054 = CBS 13387) as the type strain. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Molecular Diagnostics of Arthroconidial Yeasts, Frequent Pulmonary Opportunists.

PubMed

Kaplan, Engin; Al-Hatmi, Abdullah M S; Ilkit, Macit; Gerrits van den Ende, A H G; Hagen, Ferry; Meis, Jacques F; de Hoog, G Sybren

2018-01-01

Magnusiomyces capitatus and Saprochaete clavata are members of the clade of arthroconidial yeasts that represent emerging opportunistic pulmonary pathogens in immunocompromised patients. Given that standard ribosomal DNA (rDNA) identification often provides confusing results, in this study, we analyzed 34 isolates with the goal of finding new genetic markers for classification using multilocus sequencing and amplified fragment length polymorphism (AFLP). The interspecific similarity obtained using rDNA markers (the internal transcribed spacer [ITS] and large subunit regions) was in the range of 96 to 99%, whereas that obtained using protein-coding loci ( Rbp2 , Act , and Tef1α ) was lower at 89.4 to 95.2%. Ultimately, Rbp2 was selected as the best marker for species distinction. On the basis of cloned ITS data, some strains proved to be misidentified in comparison with the identities obtained with phenotypic characters, protein sequences, and AFLP profiles, indicating that different copies of the ribosomal operon were present in a single species. Antifungal susceptibility testing revealed that voriconazole had the lowest MIC against M. capitatus , while amphotericin B had the lowest MIC against S. clavata Both species exhibited in vitro resistance to fluconazole and micafungin. Copyright © 2017 American Society for Microbiology.

Transportation Energy Futures Series. Effects of the Built Environment on Transportation. Energy Use, Greenhouse Gas Emissions, and Other Factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Porter, C. D.; Brown, A.; Dunphy, R. T.

2013-03-15

Planning initiatives in many regions and communities aim to reduce transportation energy use, decrease emissions, and achieve related environmental benefits by changing land use. This report reviews and summarizes findings from existing literature on the relationship between the built environment and transportation energy use and greenhouse gas emissions, identifying results trends as well as potential future actions. The indirect influence of federal transportation and housing policies, as well as the direct impact of municipal regulation on land use are examined for their effect on transportation patterns and energy use. Special attention is given to the 'four D' factors of density,more » diversity, design and accessibility. The report concludes that policy-driven changes to the built environment could reduce transportation energy and GHG emissions from less than 1% to as much as 10% by 2050, the equivalent of 16%-18% of present-day urban light-duty-vehicle travel. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Transportation Energy Futures Series: Effects of the Built Environment on Transportation: Energy Use, Greenhouse Gas Emissions, and Other Factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Porter, C. D.; Brown, A.; Dunphy, R. T.

2013-03-01

Planning initiatives in many regions and communities aim to reduce transportation energy use, decrease emissions, and achieve related environmental benefits by changing land use. This report reviews and summarizes findings from existing literature on the relationship between the built environment and transportation energy use and greenhouse gas emissions, identifying results trends as well as potential future actions. The indirect influence of federal transportation and housing policies, as well as the direct impact of municipal regulation on land use are examined for their effect on transportation patterns and energy use. Special attention is given to the 'four D' factors of density,more » diversity, design and accessibility. The report concludes that policy-driven changes to the built environment could reduce transportation energy and GHG emissions from less than 1% to as much as 10% by 2050, the equivalent of 16%-18% of present-day urban light-duty-vehicle travel. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Extracellular ice phase transitions in insects.

PubMed

Hawes, T C

2014-01-01

At temperatures below their temperature of crystallization (Tc), the extracellular body fluids of insects undergo a phase transition from liquid to solid. Insects that survive the transition to equilibrium (complete freezing of the body fluids) are designated as freeze tolerant. Although this phenomenon has been reported and described in many Insecta, current nomenclature and theory does not clearly delineate between the process of transition (freezing) and the final solid phase itself (the frozen state). Thus freeze tolerant insects are currently, by convention, described in terms of the temperature at which the crystallization of their body fluids is initiated, Tc. In fact, the correct descriptor for insects that tolerate freezing is the temperature of equilibrium freezing, Tef. The process of freezing is itself a separate physical event with unique physiological stresses that are associated with ice growth. Correspondingly there are a number of insects whose physiological cryo-limits are very specifically delineated by this transitional envelope. The distinction also has considerable significance for our understanding of insect cryobiology: firstly, because the ability to manage endogenous ice growth is a fundamental segregator of cryotype; and secondly, because our understanding of internal ice management is still largely nascent.

Molecular and Morphological Analysis Reveals Five New Species of Zygophiala Associated with Flyspeck Signs on Plant Hosts from China

PubMed Central

Gao, Liu; Zhang, Mian; Zhao, Wanyu; Hao, Lu; Chen, Hongcai; Zhang, Rong; Batzer, Jean C.; Gleason, Mark L.; Sun, Guangyu

2014-01-01

Species in the genus Zygophiala are associated with sooty blotch and flyspeck disease on a wide range of hosts. In this study, 63 Zygophiala isolates collected from flyspeck colonies on a range of plants from several regions of China were used for phylogeny, host range and geographic distribution analysis. Phylogenetic trees were constructed on four genes - internal transcribed spacer (ITS), partial translation elongation factor 1-alpha (TEF), β-tubulin (TUB2), and actin (ACT) – both individually and in combination. Isolates were grouped into 11 clades among which five new species, Z. emperorae, Z. trispora, Z. musae, Z. inaequalis and Z. longispora, were described. Species of Zygophiala differed in observed host range and geographic distribution. Z. wisconsinensis and Z. emperorae were the most prevalent throughout the sampled regions of China, whereas Z. trispora, Z. musae, Z. inaequalis and Z. longispora were collected only in southern China. The hosts of Z. wisconsinensis and Z. emperorae were mainly in the family Rosaceae whereas Z. trispora, Z. musae, Z. inaequalis and Z. longispora were found mainly on banana (Musa spp.). Cross inoculation tests provided evidence of host specificity among SBFS species. PMID:25329930

Space Shuttle drops down the SAA doses on ISS

NASA Astrophysics Data System (ADS)

Dachev, T. P.; Semkova, J.; Tomov, B.; Matviichuk, Yu.; Dimitrov, Pl.; Koleva, R.; Malchev, St.; Reitz, G.; Horneck, G.; De Angelis, G.; Häder, D.-P.; Petrov, V.; Shurshakov, V.; Benghin, V.; Chernykh, I.; Drobyshev, S.; Bankov, N. G.

2011-06-01

Long-term analysis of data from two radiation detection instruments on the International Space Station (ISS) shows that the docking of the Space Shuttle drops down the measured dose rates in the region of the South Atlantic Anomaly (SAA) by a factor of 1.5-3. Measurements either by the R3DE detector, which is outside the ISS at the EuTEF facility on the Columbus module behind a shielding of less than 0.45 g cm -2, and by the three detectors of the Liulin-5 particle telescope, which is inside the Russian PEARS module in the spherical tissue equivalent phantom behind much heavier shielding demonstrate that effect. Simultaneously the estimated averaged incident energies of the incoming protons rise up from about 30 to 45 MeV. The effect is explained by the additional shielding against the SAA 30-150 MeV protons, provided by the 78 tons Shuttle to the instruments inside and outside of the ISS. An additional reason is the ISS attitude change (performed for the Shuttle docking) leading to decreasing of dose rates in two of Liulin-5 detectors because of the East-West proton fluxes asymmetry in SAA. The Galactic Cosmic Rays dose rates are practically not affected.

Global molecular epidemiology and genetic diversity of Fusarium, a significant emerging group of human opportunists from 1958 to 2015.

PubMed

Al-Hatmi, Abdullah Ms; Hagen, Ferry; Menken, Steph Bj; Meis, Jacques F; de Hoog, G Sybren

2016-12-07

Fusarium is a rapidly emerging, multidrug-resistant genus of fungal opportunists that was first identified in 1958 and is presently recognized in numerous cases of fusariosis each year. The authors examined trends in global Fusarium distribution, clinical presentation and prevalence since 1958 with the assumption that their distributions in each region had remained unaltered. The phylogeny and epidemiology of 127 geographically diverse isolates, representing 26 Fusarium species, were evaluated using partial sequences of the RPB2 and TEF1 genes, and compared with AFLP fingerprinting data. The molecular data of the Fusarium species were compared with archived data, which enabled the interpretation of hundreds of cases published in the literature. Our findings indicate that fusariosis is globally distributed with a focus in (sub)tropical areas. Considerable species diversity has been observed; genotypic features did not reveal any clustering with either the clinical data or environmental origins. This study suggests that infections with Fusarium species might be truly opportunistic. The three most common species are F. falciforme and F. keratoplasticum (members of F. solani species complex), followed by F. oxysporum (F. oxysporum species complex).

Reconsidering species boundaries in the Ceratocystis paradoxa complex, including a new species from oil palm and cacao in Cameroon.

PubMed

Mbenoun, Michael; Wilhelm de Beer, Z; Wingfield, Michael J; Wingfield, Brenda D; Roux, Jolanda

2014-01-01

The Ceratocystis paradoxa complex accommodates a group of fungal pathogens that have become specialized to infect mostly monocotyledonous plants. Four species currently are recognized in this group, including C. paradoxa, which has a widespread distribution and broad host range. In this study, multigene phylogenetic analyses involving sequences of the ITS, β-tubulin and TEF-1α gene loci, in combination with phenotypic and mating studies, were used to characterize purported C. paradoxa isolates from Cameroon and to compare them with isolates from elsewhere, including protologs and type specimens of known species. We show that the C. paradoxa complex comprises substantially greater species diversity than previously recognized. One new species in this group is described from Cameroon as Ceratocystis cerberus, while C. paradoxa sensu stricto (s. str.) and four other species are redefined. Lectotypes are designated for C. ethacetica and Endoconidium fragrans (synonym of C. ethacetica), while epitypes are designated for C. paradoxa s. str., C. ethacetica and C. musarum. A neotype is designated for Catenularia echinata (synonym of C. ethacetica) and two species, previously treated in Thielaviopsis, are transferred to Ceratocystis. © 2014 by The Mycological Society of America.

Cupreoboletus (Boletaceae, Boletineae), a new monotypic genus segregated from Boletus sect. Luridi to reassign the Mediterranean species B. poikilochromus.

PubMed

Gelardi, Matteo; Simonini, Giampaolo; Ercole, Enrico; Davoli, Paolo; Vizzini, Alfredo

2015-01-01

Cupreoboletus is erected as a new monospecific genus of Boletaceae to accommodate the thermophilic southern European species Boletus poikilochromus, characterized by discoloration toward copper-red tints overall, hymenophore forming tiny crystals on drying, a pervasive and long lasting sweet odor and presence of pseudocystidia. Macro- and microscopic descriptions of the species based on re-examination of the type material and recent Italian collections including additional topotypical samples are provided and accompanied by photos and line drawings of the main anatomical structures. In addition, an epitype specimen is selected. Phylogenetic relationships were inferred from multigene molecular analysis based on partial sequences of the nuc rDNA 28S D1/D2 (28S) and internal transcribed spacer (ITS) regions and genes for ribosomal RNA polymerase II subunits 1 (rpb1) and 2 (rpb2) and translation-elongation factor 1-α (tef1α). Ecological context, geographical range and delimitation from closely allied taxa also were elucidated. B. martaluciae is treated as a synonym of C. poikilochromus according to the morphological and molecular comparative study. © 2015 by The Mycological Society of America.

Waterborne Exophiala species causing disease in cold-blooded animals.

PubMed

de Hoog, G S; Vicente, V A; Najafzadeh, M J; Harrak, M J; Badali, H; Seyedmousavi, S

2011-12-01

The majority of mesophilic waterborne species of the black yeast genus Exophiala (Chaetothyriales) belong to a single clade judging from SSU rDNA data. Most taxa are also found to cause cutaneous or disseminated infections in cold-blooded, water animals, occasionally reaching epidemic proportions. Hosts are mainly fish, frogs, toads, turtles or crabs, all sharing smooth, moist or mucous skins and waterborne or amphibian lifestyles; occasionally superficial infections in humans are noted. Cold-blooded animals with strictly terrestrial life styles, such as reptiles and birds are missing. It is concluded that animals with moist skins, i.e. those being waterborne and those possessing sweat glands, are more susceptible to black yeast infection. Melanin and the ability to assimilate alkylbenzenes are purported general virulence factors. Thermotolerance influences the choice of host. Exophiala species in ocean water mostly have maximum growth temperatures below 30 °C, whereas those able to grow until 33(-36) °C are found in shallow waters and occasionally on humans. Tissue responses vary with the phylogenetic position of the host, the lower animals showing poor granulome formation. Species circumscriptions have been determined by multilocus analyses involving partial ITS, TEF1, BT2 and ACT1.

Global molecular epidemiology and genetic diversity of Fusarium, a significant emerging group of human opportunists from 1958 to 2015

PubMed Central

Al-Hatmi, Abdullah MS; Hagen, Ferry; Menken, Steph BJ; Meis, Jacques F; de Hoog, G Sybren

2016-01-01

Fusarium is a rapidly emerging, multidrug-resistant genus of fungal opportunists that was first identified in 1958 and is presently recognized in numerous cases of fusariosis each year. The authors examined trends in global Fusarium distribution, clinical presentation and prevalence since 1958 with the assumption that their distributions in each region had remained unaltered. The phylogeny and epidemiology of 127 geographically diverse isolates, representing 26 Fusarium species, were evaluated using partial sequences of the RPB2 and TEF1 genes, and compared with AFLP fingerprinting data. The molecular data of the Fusarium species were compared with archived data, which enabled the interpretation of hundreds of cases published in the literature. Our findings indicate that fusariosis is globally distributed with a focus in (sub)tropical areas. Considerable species diversity has been observed; genotypic features did not reveal any clustering with either the clinical data or environmental origins. This study suggests that infections with Fusarium species might be truly opportunistic. The three most common species are F. falciforme and F. keratoplasticum (members of F. solani species complex), followed by F. oxysporum (F. oxysporum species complex). PMID:27924809

EXPOSE-E: an ESA astrobiology mission 1.5 years in space.

PubMed

Rabbow, Elke; Rettberg, Petra; Barczyk, Simon; Bohmeier, Maria; Parpart, André; Panitz, Corinna; Horneck, Gerda; von Heise-Rotenburg, Ralf; Hoppenbrouwers, Tom; Willnecker, Rainer; Baglioni, Pietro; Demets, René; Dettmann, Jan; Reitz, Guenther

2012-05-01

The multi-user facility EXPOSE-E was designed by the European Space Agency to enable astrobiology research in space (low-Earth orbit). On 7 February 2008, EXPOSE-E was carried to the International Space Station (ISS) on the European Technology Exposure Facility (EuTEF) platform in the cargo bay of Space Shuttle STS-122 Atlantis. The facility was installed at the starboard cone of the Columbus module by extravehicular activity, where it remained in space for 1.5 years. EXPOSE-E was returned to Earth with STS-128 Discovery on 12 September 2009 for subsequent sample analysis. EXPOSE-E provided accommodation in three exposure trays for a variety of astrobiological test samples that were exposed to selected space conditions: either to space vacuum, solar electromagnetic radiation at >110 nm and cosmic radiation (trays 1 and 3) or to simulated martian surface conditions (tray 2). Data on UV radiation, cosmic radiation, and temperature were measured every 10 s and downlinked by telemetry. A parallel mission ground reference (MGR) experiment was performed on ground with a parallel set of hardware and samples under simulated space conditions. EXPOSE-E performed a successful 1.5-year mission in space.

Origin and distribution of Sporothrix globosa causing sapronoses in Asia.

PubMed

Moussa, Tarek A A; Kadasa, Naif M S; Al Zahrani, Hassan S; Ahmed, Sarah Abdallah; Feng, Peiying; Gerrits van den Ende, Albertus H G; Zhang, Yu; Kano, Rui; Li, Fuqiu; Li, Shanshan; Song, Yang; Dong, Bilin; Rossato, Luana; Dolatabadi, Somayeh; Hoog, Sybren de

2017-05-01

The aim of the study was to evaluate the main sources and epidemiological patterns and speculate on the evolutionary origin of Sporothrix globosa in Asia. Case and case series literature on sporotrichosis in Asia from January 2007 onwards were reviewed using meta-analysis. Phylogenetic analysis of relevant S. globosa was carried out on the basis of concatenated sequences of ITS, TEF3 and CAL. A haplotype network of CAL sequences of 281 Sporothrix isolates was analysed to determine the population structure of S. globosa. Nearly all cases of sporotrichosis caused by S. globosa in Asia were human. In contrast to the remaining pathogenic Sporothrix species, feline transmission was exceptional; nearly all regional cat-associated cases were caused by Sporothrix schenckii. While the latter species was highly variable and showed recombination, S. globosa seemed to be a clonal offshoot, as was Sporothrix brasiliensis. The origin of the segregants was located in an area of high variability in S. schenckii with a relatively high frequency of Asian strains. In Asia, S. globosa was the prevalent species. The low diversity of S. globosa suggested a recent divergence with a founder effect of low variability from the variable ancestral species, S. schenckii.

Barcoding and species recognition of opportunistic pathogens in Ochroconis and Verruconis.

PubMed

Samerpitak, Kittipan; Gerrits van den Ende, Bert H G; Stielow, J Benjamin; Menken, Steph B J; de Hoog, G Sybren

2016-02-01

The genera Ochroconis and Verruconis (Sympoventuriaceae, Venturiales) have remarkably high molecular diversity despite relatively high degrees of phenotypic similarity. Tree topologies, inter-specific and intra-specific heterogeneities, barcoding gaps and reciprocal monophyly of all currently known species were analyzed. It was concluded that all currently used genes viz. SSU, ITS, LSU, ACT1, BT2, and TEF1 were unable to reach all 'gold standard' criteria of barcoding markers. They could nevertheless be used for reasonably reliable identification of species, because the markers, although variable, were associated with large inter-specific heterogeneity. Of the coding protein-genes, ACT1 revealed highest potentiality as barcoding marker in mostly all parts of the investigated sequence. SSU, LSU, ITS, and ACT1 yielded consistent monophyly in all investigated species, but only SSU and LSU generated clear barcoding gaps. For phylogeny, LSU was an informative marker, suitable to reconstruct gene-trees showing correct phylogenetic relationships. Cryptic species were revealed especially in complexes with very high intra-specific variability. When all these complexes will be taxonomically resolved, ACT1 will probably appear to be the most reliable barcoding gene for Ochroconis and Verruconis. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Analysis and toxicity of 59 PAH in petrogenic and pyrogenic environmental samples including dibenzopyrenes, 7H-benzo[c]fluorene, 5-methylchrysene and 1-methylpyrene.

PubMed

Richter-Brockmann, Sigrid; Achten, Christine

2018-06-01

In this study 59 PAH were analyzed in samples of petrogenic and pyrogenic sources as well as mixed environmental matrices. Among the analytes, PAH of molecular weights from 128 Da to 302 Da in alkylated and in native form were included. Results show that non-EPA PAH make up 69.3–95.1% of the overall toxic equivalents (TEQ) as based on the toxic equivalent factors (TEF) of 24 PAH. Particularly 7H-benzo[c]fluorene, dibenzopyrene isomers and alkylated PAH (in particular 5-methylchrysene and 1-methylpyrene) turned out to have a huge impact on the toxicity and must not be neglected in future risk assessment. In detail, dibenzopyrenes have a high impact on toxicity predominantly in pyrogenic materials (21% to 84%; mean: 59%) whereas 7H-benzo[c]fluorene dominates toxicity of petrogenic materials (up to 80%; mean: 26%). However, in the studied mixed environmental samples the toxic impact of both groups together is as high as about 80%. Many non-EPA PAH are not considered in risk assessment and amongst them there are some very toxic ones. This needs to be carefully evaluated in future studies.

Increased Production of Fatty Acids and Triglycerides in Aspergillus oryzae by Enhancing Expressions of Fatty Acid Synthesis-Related Genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamano, Koichi; Bruno, Kenneth S.; Karagiosis, Sue A.

2013-01-01

Microbial production of fats and oils is being developedas a means of converting biomass to biofuels. Here we investigate enhancing expression of enzymes involved in the production of fatty acids and triglycerides as a means to increase production of these compounds in Aspergillusoryzae. Examination of the A.oryzaegenome demonstrates that it contains twofatty acid synthases and several other genes that are predicted to be part of this biosynthetic pathway. We enhancedthe expressionof fatty acid synthesis-related genes by replacing their promoters with thepromoter fromthe constitutively highly expressedgene tef1. We demonstrate that by simply increasing the expression of the fatty acid synthasegenes wemore » successfullyincreasedtheproduction of fatty acids and triglyceridesby more than two fold. Enhancement of expression of the fatty acid pathway genes ATP-citrate lyase and palmitoyl-ACP thioesteraseincreasedproductivity to a lesser extent.Increasing expression ofacetyl-CoA carboxylase caused no detectable change in fatty acid levels. Increases in message level for each gene were monitored usingquantitative real-time RT-PCR. Our data demonstrates that a simple increase in the abundance of fatty acid synthase genes can increase the detectable amount of fatty acids.« less

Uranium isotopes in groundwater occurring at Amazonas State, Brazil.

PubMed

da Silva, Márcio Luiz; Bonotto, Daniel Marcos

2015-03-01

This paper reports the behavior of the dissolved U-isotopes (238)U and (234)U in groundwater providing from 15 cities in Amazonas State, Brazil. The isotope dilution technique accompanied by alpha spectrometry were utilized for acquiring the U content and (234)U/(238)U activity ratio (AR) data, 0.01-1.4µgL(-1) and 1.0-3.5, respectively. These results suggest that the water is circulating in a reducing environment and leaching strata containing minerals with low uranium concentration. A tendency to increasing ARs values following the groundwater flow direction is identified in Manaus city. The AR also increases according to the SW-NE directions: Uarini→Tefé; Manacapuru→Manaus; Presidente Figueiredo→São Sebastião do Uatumã; and Boa Vista do Ramos→Parintins. Such trends are possibly related to several factors, among them the increasing acid character of the waters. The waters analyzed are used for human consumption and the highest dissolved U content is much lower than the maximum established by the World Health Organization. Therefore, in view of this radiological parameter they can be used for drinking purposes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Dioxin risk assessment: mechanisms of action and possible toxicity in human health.

PubMed

Tavakoly Sany, Seyedeh Belin; Hashim, Rosli; Salleh, Aishah; Rezayi, Majid; Karlen, David J; Razavizadeh, Bi Bi Marzieh; Abouzari-Lotf, Ebrahim

2015-12-01

Dioxin-like compounds (DLCs) have been classified by the World Health Organization (WHO) as one of the most persistent toxic chemical substances in the environment, and they are associated with several occupational activities and industrial accidents around the world. Since the end of the 1970s, these toxic chemicals have been banned because of their human toxicity potential, long half-life, wide dispersion, and they bioaccumulate in the food web. This review serves as a primer for environmental health professionals to provide guidance on short-term risk assessment of dioxin and to identify key findings for health and exposure assessment based on policies of different agencies. It also presents possible health effects of dioxins, mechanisms of action, toxic equivalency factors (TEFs), and dose-response characterization. Key studies related to toxicity values of dioxin-like compounds and their possible human health risk were identified through PubMed and supplemented with relevant studies characterized by reviewing the reference lists in the review articles and primary literature. Existing data decreases the scope of analyses and models in relevant studies to a manageable size by focusing on the set of important studies related to the perspective of developing toxicity values of DLCs.

Engineering of synthetic, stress-responsive yeast promoters

PubMed Central

Rajkumar, Arun S.; Liu, Guodong; Bergenholm, David; Arsovska, Dushica; Kristensen, Mette; Nielsen, Jens; Jensen, Michael K.; Keasling, Jay D.

2016-01-01

Advances in synthetic biology and our understanding of the rules of promoter architecture have led to the development of diverse synthetic constitutive and inducible promoters in eukaryotes and prokaryotes. However, the design of promoters inducible by specific endogenous or environmental conditions is still rarely undertaken. In this study, we engineered and characterized a set of strong, synthetic promoters for budding yeast Saccharomyces cerevisiae that are inducible under acidic conditions (pH ≤ 3). Using available expression and transcription factor binding data, literature on transcriptional regulation, and known rules of promoter architecture we improved the low-pH performance of the YGP1 promoter by modifying transcription factor binding sites in its upstream activation sequence. The engineering strategy outlined for the YGP1 promoter was subsequently applied to create a response to low pH in the unrelated CCW14 promoter. We applied our best promoter variants to low-pH fermentations, enabling ten-fold increased production of lactic acid compared to titres obtained with the commonly used, native TEF1 promoter. Our findings outline and validate a general strategy to iteratively design and engineer synthetic yeast promoters inducible to environmental conditions or stresses of interest. PMID:27325743

Electrochemical Membrane for Carbon Dioxide Capture and Power Generation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghezel-Ayagh, Hossein

FuelCell Energy, Inc. (FCE), in collaboration with AECOM Corporation (formerly URS Corporation) and Pacific Northwest National Laboratory, has been developing a novel Combined Electric Power and Carbon-dioxide Separation (CEPACS) system. The CEPACS system is based on electrochemical membrane (ECM) technology derived from FCE’s carbonate fuel cell products featuring internal (methane steam) reforming and carrying the trade name of Direct FuelCell®. The unique chemistry of carbonate fuel cells offers an innovative approach for separation of CO 2 from existing fossil-fuel power plant exhaust streams (flue gases). The ECM-based CEPACS system has the potential to become a transformational CO 2-separation technology bymore » working as two devices in one: it separates the CO 2 from the exhaust of other plants such as an existing coal-fired plant and simultaneously produces clean electric power at high efficiency using a supplementary fuel. The development effort was carried out under the U.S. Department of Energy (DOE) cooperative agreement DE-FE0007634. The overall objective of this project was to successfully demonstrate the ability of FCE’s ECM-based CEPACS system technology to separate ≥90% of the CO 2 from a simulated Pulverized Coal (PC) power plant flue gas stream and to compress the captured CO2 to a state that can be easily transported for sequestration or beneficial use. In addition, a key objective was to show, through the technical and economic feasibility study and bench scale testing, that the ECM-based CEPACS system is an economical alternative for CO 2 capture in PC power plants, and that it meets DOE’s objective related to the incremental cost of electricity (COE) for post-combustion CO 2 capture (no more than 35% increase in COE). The project was performed in three budget periods (BP). The specific objective for BP1 was to complete the Preliminary Technical and Economic Feasibility Study. The T&EF study was based on the carbon capture system size suitable for a reference 550 MW PC power plant. The specific objectives for BP2 were to perform (flue gas) contaminant effect evaluation tests, small area membrane tests using clean simulated flue gas, design a flue gas pretreatment system for processing of the gas feed to ECM, update the Technical & Economic Feasibility Study (T&EFS) incorporating results of contaminant effect tests and small area membrane tests, and to prepare a test facility for bench scale testing. The specific objectives for BP3 were to perform bench scale testing (parametric and long-duration testing) of a 11.7 m 2 ECM-based CO 2 capture, purification and compression system, and update (as final) the Technical and Economic Feasibility Study. In addition, an Environmental Health and Safety evaluation (assessment) of the ECM technology was included. This final technical report presents the progress made under the project.« less

Determination of PCDD/Fs, PBDD/Fs and dioxin-like PCBs in human milk from mothers residing in the rural areas in Flanders, using the CALUX bioassay and GC-HRMS.

PubMed

Croes, K; Colles, A; Koppen, G; De Galan, S; Vandermarken, T; Govarts, E; Bruckers, L; Nelen, V; Schoeters, G; Van Larebeke, N; Denison, M S; Mampaey, M; Baeyens, W

2013-09-15

Since the CALUX (Chemically Activated LUciferase gene eXpression) bioassay is a fast and inexpensive tool for the determination of dioxin-like compounds in a large number of samples and requires only small sample volumes, the use of this technique in human biomonitoring programs provides a good alternative to GC-HRMS. In this study, a new CALUX method for the separate analysis of PCDD/Fs and dioxin-like PCBs (dl-PCBs) in small amounts of human milk samples with the new sensitive H1L7.5c1 cell line was used to analyze 84 human milk samples, collected from mothers residing in the Flemish rural communities. The geometric mean CALUX-Bioanalytical Equivalent (CALUX-BEQ) values, reported for the 84 mothers from the study area were 10.4 (95% CI: 9.4-11.4) pg CALUX-BEQ per gram lipid or 0.41 (95% CI: 0.37-0.45) pg CALUX-BEQ per gram milk for the PCDD/Fs and 1.73 (1.57-1.91) pg CALUX-BEQ per gram lipid or 0.07 (95% CI: 0.06-0.08) pg CALUX-BEQ per gram milk for the dioxin-like PCBs. Multiple regression analysis showed significant associations between PCDD/Fs and weight change after pregnancy, smoking and consumption of local eggs. One pooled human milk sample was analyzed with both CALUX and GC-HRMS. The ratio of CALUX and GC-HRMS results for this sample were respectively 1.60, 0.58 and 1.23 for the PCDD/Fs, the dl-PCBs and the sum of both fractions, when using the 2005-TEF values. Additionally, also low levels of certain brominated dioxins and furans were detected in the pooled sample with GC-HRMS. Copyright © 2013 Elsevier B.V. All rights reserved.

The predictive power of the elimination of dioxin-like pollutants from pigs: an in vivo study.

PubMed

Shen, Heqing; Henkelmann, Bernhard; Rambeck, Walter Albert; Mayer, Richard; Wehr, Ulrich; Schramm, Karl-Werner

2012-01-01

Pigs accidentally given feed contaminated by dioxin-like pollutants are a serious public health issue. We have examined whether pigs with limited exposure during early periods of fattening would be categorized as non-compliant with the EU limit at slaughtering when growth-dilution, excretion and metabolism effects are considered. Sixteen female and sixteen castrated male weaned pigs were divided into four groups (e.g. DG0, DG1, DG2 and DG3) in week 2 after birth. From weeks 3 to 13, groups DG1, DG2, and DG3 pigs were fed with a polychlorinated dibenzo-p-dioxin/dibenzofuran (PCDD/F) and polychlorinated biphenyl (PCB) mixture at dosages of 1, 10 and 100ng-toxic equivalent (TEQ) per kg dry mass feed in capsules, respectively. From weeks 13 to 23, the animals were nourished with clear feed. Control group DG0 was always fed with clear feed. Subcutaneous fat samples were collected at weeks 13, 18 and 23 by biopsies. The pollutant residues were analyzed by high resolution gas chromatography-high resolution mass spectrometry and quantified by a (13)C-isotope dilution method. The results showed the following: (1) when slaughtered at week 23, the TEQ for DG1 pigs (0.66±0.21pg/g fat) was under the EU limit of 1pg PCDD/F-TEQ/g fat; (2) PCDD/F congener-specific first-order elimination rates were linearly correlated with their toxicity equivalency factors (TEFs), and the rates were significantly dose-dependent for the more toxic congeners (TEF≥0.1). Therefore, the pigs' exposure above the EU limit during the early fattening stage did not necessarily lead to their categorization as non-compliant pork; and the residual TEQ for pork can be predicted from early exposure concentrations based on the models established here. Copyright © 2011 Elsevier Ltd. All rights reserved.

Transportation Energy Futures Series. Projected Biomass Utilization for Fuels and Power in a Mature Market

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruth, M.; Mai, T.; Newes, E.

2013-03-01

The viability of biomass as transportation fuel depends upon the allocation of limited resources for fuel, power, and products. By focusing on mature markets, this report identifies how biomass is projected to be most economically used in the long term and the implications for greenhouse gas (GHG) emissions and petroleum use. In order to better understand competition for biomass between these markets and the potential for biofuel as a market-scale alternative to petroleum-based fuels, this report presents results of a micro-economic analysis conducted using the Biomass Allocation and Supply Equilibrium (BASE) modeling tool. The findings indicate that biofuels can outcompetemore » biopower for feedstocks in mature markets if research and development targets are met. The BASE tool was developed for this project to analyze the impact of multiple biomass demand areas on mature energy markets. The model includes domestic supply curves for lignocellulosic biomass resources, corn for ethanol and butanol production, soybeans for biodiesel, and algae for diesel. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Transportation Energy Futures Series: Projected Biomass Utilization for Fuels and Power in a Mature Market

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruth, M.; Mai, T.; Newes, E.

2013-03-01

The viability of biomass as transportation fuel depends upon the allocation of limited resources for fuel, power, and products. By focusing on mature markets, this report identifies how biomass is projected to be most economically used in the long term and the implications for greenhouse gas (GHG) emissions and petroleum use. In order to better understand competition for biomass between these markets and the potential for biofuel as a market-scale alternative to petroleum-based fuels, this report presents results of a micro-economic analysis conducted using the Biomass Allocation and Supply Equilibrium (BASE) modeling tool. The findings indicate that biofuels can outcompetemore » biopower for feedstocks in mature markets if research and development targets are met. The BASE tool was developed for this project to analyze the impact of multiple biomass demand areas on mature energy markets. The model includes domestic supply curves for lignocellulosic biomass resources, corn for ethanol and butanol production, soybeans for biodiesel, and algae for diesel. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.« less

Novel species of Botryosphaeriaceae associated with shoot blight of pistachio.

PubMed

Chen, ShuaiFei; Li, GuoQing; Liu, FeiFei; Michailides, Themis J

2015-01-01

Various species of phytopathogenic Botryosphaeriaceae were identified previously from pistachio trees worldwide. Disease symptoms caused by pathogens in Botryosphaeriaceae on pistachio include panicle and shoot blight, leaf defoliation, fruit discoloration and decay. In this study species of Botryosphaeriaceae were collected from blighted pistachio shoots in Arizona, USA, and Greece. The aims of this study were to identify these Botryosphaeriaceae isolates and to test their pathogenicity to pistachio. The fungi were identified based on comparisons of DNA sequence data of the nuclear rDNA internal transcribed spacer region (ITS), a partial translation elongation factor 1-alpha gene (TEF1), a partial β-tubulin gene (TUB2) and morphological characteristics. Results indicated that some isolates collected from pistachio represent two previously undescribed species, which we described here as Lasiodiplodia americana sp. nov. from the United States and Neofusicoccum hellenicum sp. nov. from Greece. Field inoculations of L. americana and N. hellenicum on branches of four pistachio cultivars showed that both L. americana and N. hellenicum are pathogenic on pistachio. The four pistachio cultivars differed in their susceptibility to the Botryosphaeriaceae species. Results of this study suggested that the two new species of Botryosphaeriaceae need to be monitored carefully to determine the distribution of these pathogens and the possible spread to other areas. © 2015 by The Mycological Society of America.

Use of phylogenetical analysis to predict susceptibility of pathogenic Candida spp. to antifungal drugs.

PubMed

Maheux, Andrée F; Sellam, Adnane; Piché, Yves; Boissinot, Maurice; Pelletier, René; Boudreau, Dominique K; Picard, François J; Trépanier, Hélène; Boily, Marie-Josée; Ouellette, Marc; Roy, Paul H; Bergeron, Michel G

2016-12-01

Successful treatment of a Candida infection relies on 1) an accurate identification of the pathogenic fungus and 2) on its susceptibility to antifungal drugs. In the present study we investigated the level of correlation between phylogenetical evolution and susceptibility of pathogenic Candida spp. to antifungal drugs. For this, we compared a phylogenetic tree, assembled with the concatenated sequences (2475-bp) of the ATP2, TEF1, and TUF1 genes from 20 representative Candida species, with published minimal inhibitory concentrations (MIC) of the four principal antifungal drug classes commonly used in the treatment of candidiasis: polyenes, triazoles, nucleoside analogues, and echinocandins. The phylogenetic tree revealed three distinct phylogenetic clusters among Candida species. Species within a given phylogenetic cluster have generally similar susceptibility profiles to antifungal drugs and species within Clusters II and III were less sensitive to antifungal drugs than Cluster I species. These results showed that phylogenetical relationship between clusters and susceptibility to several antifungal drugs could be used to guide therapy when only species identification is available prior to information pertaining to its resistance profile. An extended study comprising a large panel of clinical samples should be conducted to confirm the efficiency of this approach in the treatment of candidiasis. Copyright © 2016. Published by Elsevier B.V.

Molecular phylogeny of Rigidoporus microporus isolates associated with white rot disease of rubber trees (Hevea brasiliensis).

PubMed

Oghenekaro, Abbot O; Miettinen, Otto; Omorusi, Victor I; Evueh, Grace A; Farid, Mohd A; Gazis, Romina; Asiegbu, Fred O

2014-01-01

Rigidoporus microporus (Polyporales, Basidiomycota) syn. Rigidoporus lignosus is the most destructive root pathogen of rubber plantations distributed in tropical and sub-tropical regions. Our primary objective was to characterize Nigerian isolates from rubber tree and compare them with other West African, Southeast Asian and American isolates. To characterize the 20 isolates from Nigeria, we used sequence data of the nuclear ribosomal DNA ITS and LSU, β-tubulin and translation elongation factor 1-α (tef1) gene sequences. Altogether, 40 isolates of R. microporus were included in the analyses. Isolates from Africa, Asia and South/Central America formed three distinctive clades corresponding to at least three species. No phylogeographic pattern was detected among R. microporus collected from West and Central African rubber plantations suggesting continuous gene flow among these populations. Our molecular phylogenetic analysis suggests the presence of two distinctive species associated with the white rot disease. Phylogenetic analyses placed R. microporus in the Hymenochaetales in the vicinity of Oxyporus. This is the first study to characterize R. microporus isolates from Nigeria through molecular phylogenetic techniques, and also the first to compare isolates from rubber plantations in Africa and Asia. Copyright © 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Fusarium species causing eumycetoma: Report of two cases and comprehensive review of the literature.

PubMed

Al-Hatmi, Abdullah M S; Bonifaz, Alexandro; Tirado-Sánchez, Andrés; Meis, Jacques F; de Hoog, G Sybren; Ahmed, Sarah A

2017-03-01

Recently, mycetoma was added to the World Health Organization's list of neglected tropical disease priorities. Fusarium as a genus has been reported to cause eumycetoma, but little is known about the species involved in this infection and their identification. In this study, molecular tools were applied to identify Fusarium agents from human eumycetoma cases. The partial translation elongation factor 1-alpha (TEF-1α) gene was used as diagnostic parameter. Two additional cases of eumycetoma, due to F. keratoplasticum and F. pseudensiforme, respectively, are presented. A systematic literature review was performed to assess general features, identification, treatment and outcome of eumycetoma infections due to Fusarium species. Of the 20 reviewed patients, the majority (75%) were male. Most agents belonged to the F. solani species complex, ie F. keratoplasticum, F. pseudensiforme, and an undescribed lineage of F. solani. In addition, F. thapsinum, a member of Fusarium fujikuroi species complex was encountered. The main antifungal drugs used were itraconazole, ketoconazole and amphotericin B, but cure rates were low (15%). Partial response or relapse was observed in some cases, and a case ended in amputation. Clinical management of eumycetoma due to Fusarium is complex and combination therapy might be required to increase cure rates. © 2016 Blackwell Verlag GmbH.

Curvularia malina sp. nov. incites a new disease of warm-season turfgrasses in the southeastern United States.

PubMed

Tomaso-Peterson, Maria; Jo, Young-Ki; Vines, Phillip L; Hoffmann, Federico G

2016-09-01

A novel species of Curvularia was identified as a foliar pathogen of Cynodon dactylon (bermudagrass) and Zoysia matrella (zoysiagrass), two important warm-season turfgrasses in the southeastern United States. Field symptoms were conspicuous chocolate brown to black spots in turf of both species on golf course putting greens and fairways. Leaves of plants within these spots exhibited prominent, black eyespot lesions from which a darkly pigmented fungus was consistently isolated. The fungus produced gray- to black-olivaceous mycelium within 10 d on potato dextrose agar at 25 C but never produced conidia despite numerous attempts to induce them. Field symptoms were reproduced in inoculated plants of both grasses, and re-isolation of the pathogen from symptomatic tissues confirmed its pathogenicity in fulfillment of Koch's postulates. A phylogenetic analysis was performed using sequence markers of internal nuclear ribosomal transcribed spacer region (ITS), glyceralde-hyde-3-phosphate dehydrogenase (GPD1) and translation elongation factor 1-α (TEF 1). The concatenated phylogenetic tree showed strong support for a new species within Curvularia that is distinctly divergent from other Curvularia spp. Therefore, the darkly pigmented pathogen of warm-season turfgrasses is described and illustrated as a new species, Curvularia malina. © 2016 by The Mycological Society of America.

Beauveria medogensis sp. nov., a new fungus of the entomopathogenic genus from China.

PubMed

Imoulan, Abdessamad; Wu, Hai-Jun; Lu, Wei-Lai; Li, Yi; Li, Bin-Bin; Yang, Rei-Heng; Wang, Wen-Jing; Wang, Xiao-Liang; Kirk, Paul M; Yao, Yi-Jian

2016-09-01

Beauveria is among the most ubiquitous genera of entomopathogenic fungi throughout the world. A previously unknown species of the genus was recently discovered from a soil sample collected from Tibetan Plateau, China and is here described as new to science, B. medogensis sp. nov. The new species is distinguished from its closest relatives based on both morphological characterization and molecular phylogenetic analyses. Beauveria medogensis is characterized by globose to subglobose conidia, morphologically similar to some other species of in the genus, but was conclusively separated from those species in the phylogenetic analyses including sequences of four nuclear genes (RPB1, RPB2, TEF1 and Bloc). The new species was clustered in the analyses in a single terminal lineage which was grouped with B. australis sequences together as a sister clade to the B. brongniartii terminal clade. Although molecularly closely related, the new species is distinct morphologically from its closest sisters, B. australis and B. brongniartii, in producing globose to subglobose conidia rather than subglobose, broadly ellipsoid to ellipsoid conidia or ellipsoidal to cylindrical conidia. As isolated from a soil sample, the entomopathogenicity of the new species has been confirmed using Helicoverpa armigera and Tenebrio molitor larvae. Copyright © 2016 Elsevier Inc. All rights reserved.

Risk assessment of combined exposure to alkenylbenzenes through consumption of plant food supplements containing parsley and dill.

PubMed

Alajlouni, Abdalmajeed M; Al-Malahmeh, Amer J; Wesseling, Sebastiaan; Kalli, Marina; Vervoort, Jacques; Rietjens, Ivonne M C M

2017-12-01

A risk assessment was performed of parsley- and dill-based plant food supplements (PFS) containing apiol and related alkenylbenzenes. First, the levels of the alkenylbenzenes in the PFS and the resulting estimated daily intake (EDI) resulting from use of the PFS were quantified. Since most PFS appeared to contain more than one alkenylbenzene, a combined risk assessment was performed based on equal potency or using a so-called toxic equivalency (TEQ) approach based on toxic equivalency factors (TEFs) for the different alkenylbenzenes. The EDIs resulting from daily PFS consumption amount to 0.74-125 µg kg -1 bw for the individual alkenylbenzenes, 0.74-160 µg kg -1 bw for the sum of the alkenylbenzenes, and 0.47-64 µg kg -1 bw for the sum of alkenylbenzenes when expressed in safrole equivalents. The margins of exposure (MOEs) obtained were generally below 10,000, indicating a priority for risk management if the PFS were to be consumed on a daily basis. Considering short-term use of the PFS, MOEs would increase above 10,000, indicating low priority for risk management. It is concluded that alkenylbenzene intake through consumption of parsley- and dill-based PFS is only of concern when these PFS are used for long periods of time.

Associations between dioxins/furans and dioxin-like PCBs in estuarine sediment and blue crab

USGS Publications Warehouse

Liebens, J.; Mohrherr, C.J.; Karouna-Renier, N. K.; Snyder, R.A.; Rao, K.R.

2011-01-01

The objective of the present study was to evaluate the relationships between the quantity, toxicity, and compositional profile of dioxin/furan compounds (PCDD/Fs) and dioxin-like polychlorinated biphenyls (DL-PCBs) in estuarine sediment and in the blue crab (Callinectes sapidus). Sediment and blue crab samples were collected in three small urban estuaries that are in relatively close proximity to each other. Results show that differences between PCDD/F and DL-PCB mass concentrations and total toxic equivalents (TEQ) toxicity in sediments of the three estuaries are reflected in those of the blue crab. TEQs are higher in the hepatopancreas of the crabs than in the sediment, but the concentration factor is inversely proportional to the TEQ in the sediments. Congener profiles in the crabs are systematically different from those in the sediments, and the difference is more pronounced for PCDD/Fs than for DL-PCBs, possibly due to differences in metabolization rates. Compared with sediment profiles, more lesser-chlorinated PCDD/Fs that have higher TEFs accumulate in crab hepatopancreas. This selective bioaccumulation of PCDD/Fs results in a TEQ augmentation in crab hepatopancreas compared with sediments. The bioaccumulation in the blue crab is also selective for PCDD/Fs over DL-PCBs. ?? 2011 Springer Science+Business Media B.V.

High genetic diversity and connectivity in Colossoma macropomum in the Amazon basin revealed by microsatellite markers.

PubMed

Fazzi-Gomes, Paola; Guerreiro, Sávio; Palheta, Glauber David Almeida; Melo, Nuno Filipe Alves Correa de; Santos, Sidney; Hamoy, Igor

2017-01-01

Colossoma macropomum is the second largest scaled fish of the Amazon. It is economically important for commercial fisheries and for aquaculture, but few studies have examined the diversity and genetic structure of natural populations of this species. The aim of this study was to investigate the levels of genetic variability and connectivity that exist between three natural populations of C. macropomum from the Amazon basin. In total, 247 samples were collected from the municipalities of Tefé, Manaus, and Santarém. The populations were genotyped using a panel of 12 multiplex microsatellite markers. The genetic diversity found in these populations was high and similar to other populations described in the literature. These populations showed a pattern of high gene flow associated with the lack of a genetic structure pattern, indicating that the number of migrants per generation and recent migration rates are high. The values of the FST, RST, and exact test of differentiation were not significant for pairwise comparisons between populations. The Bayesian population clustering analysis indicated a single population. Thus, the data provide evidence for high genetic diversity and high gene flow among C. macropomum populations in the investigated region of the Amazon basin. This information is important for programs aiming at the conservation of natural populations.

High genetic diversity and connectivity in Colossoma macropomum in the Amazon basin revealed by microsatellite markers

PubMed Central

Fazzi-Gomes, Paola; Guerreiro, Sávio; Palheta, Glauber David Almeida; de Melo, Nuno Filipe Alves Correa; Santos, Sidney; Hamoy, Igor

2017-01-01

Abstract Colossoma macropomum is the second largest scaled fish of the Amazon. It is economically important for commercial fisheries and for aquaculture, but few studies have examined the diversity and genetic structure of natural populations of this species. The aim of this study was to investigate the levels of genetic variability and connectivity that exist between three natural populations of C. macropomum from the Amazon basin. In total, 247 samples were collected from the municipalities of Tefé, Manaus, and Santarém. The populations were genotyped using a panel of 12 multiplex microsatellite markers. The genetic diversity found in these populations was high and similar to other populations described in the literature. These populations showed a pattern of high gene flow associated with the lack of a genetic structure pattern, indicating that the number of migrants per generation and recent migration rates are high. The values of the FST, RST, and exact test of differentiation were not significant for pairwise comparisons between populations. The Bayesian population clustering analysis indicated a single population. Thus, the data provide evidence for high genetic diversity and high gene flow among C. macropomum populations in the investigated region of the Amazon basin. This information is important for programs aiming at the conservation of natural populations. PMID:28170026

New Ceratocystis species from Eucalyptus and Cunninghamia in South China.

PubMed

Liu, FeiFei; Mbenoun, Michael; Barnes, Irene; Roux, Jolanda; Wingfield, Michael J; Li, GuoQing; Li, JieQiong; Chen, ShuaiFei

2015-06-01

During routine surveys for possible fungal pathogens in the rapidly expanding plantations of Eucalyptus and Cunninghamia lanceolata in China, numerous isolates of unknown species in the genus Ceratocystis (Microascales) were obtained from tree wounds. In this study we identified the Ceratocystis isolates from Eucalyptus and Cunninghamia in the GuangDong, GuangXi, FuJian and HaiNan Provinces of South China based on morphology and through comparisons of DNA sequence data for the ITS, partial β-tubulin and TEF-1α gene regions. Morphological and DNA sequence comparisons revealed two previously unknown species residing in the Indo-Pacific Clade. These are described here as Ceratocystis cercfabiensis sp. nov. and Ceratocystis collisensis sp. nov. Isolates of Ceratocystis cercfabiensis showed intragenomic variation in their ITS sequences and four strains were selected for cloning of the ITS gene region. Twelve ITS haplotypes were obtained from 17 clones selected for sequencing, differing in up to seven base positions and representing two separate phylogenetic groups. This is the first evidence of multiple ITS types in isolates of Ceratocystis residing in the Indo-Pacific Clade. Caution should thus be exercised when using the ITS gene region as a barcoding marker for Ceratocystis species in this clade. This study also represents the first record of a species of Ceratocystis from Cunninghamia.

Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells

PubMed Central

Huang, Lei; Owen, Jonas K.; Xie, Anna; Navarro, Antonia; Monsivais, Diana; Coon V, John S.; Kim, J. Julie; Dai, Yang; Bulun, Serdar E.

2012-01-01

Background Progesterone, via its nuclear receptor (PR), exerts an overall tumorigenic effect on both uterine fibroid (leiomyoma) and breast cancer tissues, whereas the antiprogestin RU486 inhibits growth of these tissues through an unknown mechanism. Here, we determined the interaction between common or cell-specific genome-wide binding sites of PR and mRNA expression in RU486-treated uterine leiomyoma and breast cancer cells. Principal Findings ChIP-sequencing revealed 31,457 and 7,034 PR-binding sites in breast cancer and uterine leiomyoma cells, respectively; 1,035 sites overlapped in both cell types. Based on the chromatin-PR interaction in both cell types, we statistically refined the consensus progesterone response element to G•ACA• • •TGT•C. We identified two striking differences between uterine leiomyoma and breast cancer cells. First, the cis-regulatory elements for HSF, TEF-1, and C/EBPα and β were statistically enriched at genomic RU486/PR-targets in uterine leiomyoma, whereas E2F, FOXO1, FOXA1, and FOXF sites were preferentially enriched in breast cancer cells. Second, 51.5% of RU486-regulated genes in breast cancer cells but only 6.6% of RU486-regulated genes in uterine leiomyoma cells contained a PR-binding site within 5 kb from their transcription start sites (TSSs), whereas 75.4% of RU486-regulated genes contained a PR-binding site farther than 50 kb from their TSSs in uterine leiomyoma cells. RU486 regulated only seven mRNAs in both cell types. Among these, adipophilin (PLIN2), a pro-differentiation gene, was induced via RU486 and PR via the same regulatory region in both cell types. Conclusions Our studies have identified molecular components in a RU486/PR-controlled gene network involved in the regulation of cell growth, cell migration, and extracellular matrix function. Tissue-specific and common patterns of genome-wide PR binding and gene regulation may determine the therapeutic effects of antiprogestins in uterine fibroids and breast cancer. PMID:22272226

Genomic deletion of GIT2 induces a premature age-related thymic dysfunction and systemic immune system disruption

PubMed Central

Siddiqui, Sana; Lustig, Ana; Carter, Arnell; Sankar, Mathavi; Daimon, Caitlin M.; Premont, Richard T.; Etienne, Harmonie; van Gastel, Jaana; Azmi, Abdelkrim; Janssens, Jonathan; Becker, Kevin G.; Zhang, Yongqing; Wood, William; Lehrmann, Elin; Martin, James G.; Martin, Bronwen; Taub, Dennis D.; Maudsley, Stuart

2017-01-01

Recent research has proposed that GIT2 (G protein-coupled receptor kinase interacting protein 2) acts as an integrator of the aging process through regulation of ‘neurometabolic’ integrity. One of the commonly accepted hallmarks of the aging process is thymic involution. At a relatively young age, 12 months old, GIT2−/− mice present a prematurely distorted thymic structure and dysfunction compared to age-matched 12 month-old wild-type control (C57BL/6) mice. Disruption of thymic structure in GIT2−/− (GIT2KO) mice was associated with a significant reduction in the expression of the cortical thymic marker, Troma-I (cytokeratin 8). Double positive (CD4+CD8+) and single positive CD4+ T cells were also markedly reduced in 12 month-old GIT2KO mice compared to age-matched control wild-type mice. Coincident with this premature thymic disruption in GIT2KO mice was the unique generation of a novel cervical ‘organ’, i.e. ‘parathymic lobes’. These novel organs did not exhibit classical peripheral lymph node-like characteristics but expressed high levels of T cell progenitors that were reflexively reduced in GIT2KO thymi. Using signaling pathway analysis of GIT2KO thymus and parathymic lobe transcriptomic data we found that the molecular signaling functions lost in the dysfunctional GIT2KO thymus were selectively reinstated in the novel parathymic lobe – suggestive of a compensatory effect for the premature thymic disruption. Broader inspection of high-dimensionality transcriptomic data from GIT2KO lymph nodes, spleen, thymus and parathymic lobes revealed a systemic alteration of multiple proteins (Dbp, Tef, Per1, Per2, Fbxl3, Ddit4, Sin3a) involved in the multidimensional control of cell cycle clock regulation, cell senescence, cellular metabolism and DNA damage. Altered cell clock regulation across both immune and non-immune tissues therefore may be responsible for the premature ‘aging’ phenotype of GIT2KO mice. PMID:28260693

A proposed procedure for derivation of regulatory values for carcinogenic airborne polycyclic aromatic hydrocarbons (PAHs) based on coal tar pitch (CTP) volatiles.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foureman, G.L.; Smith, R.L.

A procedure for estimating upper bound lifetime human cancer risk from air levels of six common carcinogenic polycyclic aromatic hydrocarbons (PAHs), termed APAHs of concern, is proposed. These PAHs are benzo(a)pyrene, benz(a)anthracene, benzo(b)fluoranthene, benzo(k)fluoranthene, indeno(1,2,3-c,d)pyrene, and chrysene. In application, this proposed procedure would regard any given air level obtained for a APAH of concern to originate from a standard mixture of coal tar pitch (CTP). The given air level for the APAHs of concern is then related to a corresponding air level of CTP and thence, to an inhalation unit cancer risk calculated for CTP. Reference values for the proceduremore » are the relative and absolute PAH composition of a CTP standard (SRM-1597) and the inhalation unit cancer risk. Qualitative characterization of the results are a vital part of the procedure especially when more than one APAH of concern{at} is being considered. Toxic equivalency factors (TEFs) may be used as an evaluative tool in characterization of the procedure and outcome. Limitations of this proposed procedure include the uneven database for the reference values and the inability to consider air samples inclusive of another common carcinogenic PAH, dibenz(a,h)anthracene, due to its lack of documentation in CTP and high TEF« less

Isolation, Culture and Characterization of Hirsutella sinensis Mycelium from Caterpillar Fungus Fruiting Body

PubMed Central

Ko, Yun-Fei; Liau, Jian-Ching; Lee, Chien-Sheng; Chiu, Chen-Yaw; Martel, Jan; Lin, Chuan-Sheng; Tseng, Shun-Fu; Ojcius, David M.; Lu, Chia-Chen; Lai, Hsin-Chih; Young, John D.

2017-01-01

The caterpillar fungus Ophiocordyceps sinensis (previously called Cordyceps sinensis) has been used for centuries in Asia as a tonic to improve health and longevity. Recent studies show that O. sinensis produces a wide range of biological effects on cells, laboratory animals and humans, including anti-fatigue, anti-infection, anti-inflammatory, antioxidant, and anti-tumor activities. In view of the rarity of O. sinensis fruiting bodies in nature, cultivation of its anamorph mycelium represents a useful alternative for large-scale production. However, O. sinensis fruiting bodies harvested in nature harbor several fungal contaminants, a phenomenon that led to the isolation and characterization of a large number of incorrect mycelium strains. We report here the isolation of a mycelium from a fruiting body of O. sinensis and we identify the isolate as O. sinensis’ anamorph (also called Hirsutella sinensis) based on multi-locus sequence typing of several fungal genes (ITS, nrSSU, nrLSU, RPB1, RPB2, MCM7, β-tubulin, TEF-1α, and ATP6). The main characteristics of the isolated mycelium, including its optimal growth at low temperature (16°C) and its biochemical composition, are similar to that of O. sinensis fruiting bodies, indicating that the mycelium strain characterized here may be used as a substitute for the rare and expensive O. sinensis fruiting bodies found in nature. PMID:28046129

Phylogeny and pathogenicity of Lasiodiplodia species associated with dieback of mango in Peru.

PubMed

Rodríguez-Gálvez, Edgar; Guerrero, Pakita; Barradas, Carla; Crous, Pedro W; Alves, Artur

2017-04-01

Mango, which is an important tropical fruit crop in the region of Piura (Peru), is known to be prone to a range of diseases caused by Lasiodiplodia spp. The aim of this study was to evaluate the incidence and prevalence of mango dieback in the region of Piura, and to identify the species of Lasiodiplodia associated with the disease and evaluate their pathogenicity towards mango. Mango dieback was present in all orchards surveyed but incidence varied with location. Identification of fungal isolates was based on morphological and cultural characteristics as well as sequence data of the rDNA internal transcribed spacer region (ITS) and translation elongation factor 1-alpha gene (tef1-α). The following Lasiodiplodia species were identified: Lasiodiplodia brasiliense, Lasiodiplodia egyptiacae (for which the new combination Lasiodiplodia laeliocattleyae is introduced), Lasiodiplodia iraniensis, Lasiodiplodia pseudotheobromae, Lasiodiplodia theobromae, and a Lasiodiplodia sp. Individual and combined gene genealogies suggest that this Lasiodiplodia sp. is possibly a hybrid of Lasiodiplodia citricola and Lasiodiplodia parva. Apart from Lasiodiplodia theobromae, which was the most prevalent species, all other species are newly reported from Peru. Moreover, L. iraniensis is reported for the first time on mango. Inoculation trials of mango plants confirmed Koch's postulates, and revealed differences in aggressiveness among species and isolates. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Transportation Energy Futures Series: Alternative Fuel Infrastructure Expansion: Costs, Resources, Production Capacity, and Retail Availability for Low-Carbon Scenarios

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melaina, M. W.; Heath, G.; Sandor, D.

2013-04-01

Achieving the Department of Energy target of an 80% reduction in greenhouse gas emissions by 2050 depends on transportation-related strategies combining technology innovation, market adoption, and changes in consumer behavior. This study examines expanding low-carbon transportation fuel infrastructure to achieve deep GHG emissions reductions, with an emphasis on fuel production facilities and retail components serving light-duty vehicles. Three distinct low-carbon fuel supply scenarios are examined: Portfolio: Successful deployment of a range of advanced vehicle and fuel technologies; Combustion: Market dominance by hybridized internal combustion engine vehicles fueled by advanced biofuels and natural gas; Electrification: Market dominance by electric drive vehiclesmore » in the LDV sector, including battery electric, plug-in hybrid, and fuel cell vehicles, that are fueled by low-carbon electricity and hydrogen. A range of possible low-carbon fuel demand outcomes are explored in terms of the scale and scope of infrastructure expansion requirements and evaluated based on fuel costs, energy resource utilization, fuel production infrastructure expansion, and retail infrastructure expansion for LDVs. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored transportation-related strategies for abating GHGs and reducing petroleum dependence.« less

Transportation Energy Futures Series. Non-Cost Barriers to Consumer Adoption of New Light-Duty Vehicle Technologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stephens, Thomas

2013-03-01

Consumer preferences are key to the adoption of new vehicle technologies. Barriers to consumer adoption include price and other obstacles, such as limited driving range and charging infrastructure; unfamiliarity with the technology and uncertainty about direct benefits; limited makes and models with the technology; reputation or perception of the technology; standardization issues; and regulations. For each of these non-cost barriers, this report estimates an effective cost and summarizes underlying influences on consumer preferences, approximate magnitude and relative severity, and assesses potential actions, based on a comprehensive literature review. While the report concludes that non-cost barriers are significant, effective cost andmore » potential market share are very uncertain. Policies and programs including opportunities for drivers to test drive advanced vehicles, general public outreach and information programs, incentives for providing charging and fueling infrastructure, and development of technology standards were examined for their ability to address barriers, but little quantitative data exists on the effectiveness of these measures. This is one in a series of reports produced as a result of the Transportation Energy Futures project, a Department of Energy-sponsored multi-agency effort to pinpoint underexplored strategies for reducing GHGs and petroleum dependence related to transportation. View all reports on the TEF Web page, http://www.eere.energy.gov/analysis/transportationenergyfutures/index.html.« less

The 'species complex' issue in clinically relevant fungi: A case study in Scedosporium apiospermum.

PubMed

Chen, Min; Zeng, Jingsi; De Hoog, G Sybren; Stielow, Benjamin; Gerrits Van Den Ende, A H G; Liao, Wanqing; Lackner, Michaela

2016-02-01

The genus Scedosporium currently comprises six species, Scedosporium apiospermum, Scedosporium boydii, Pseudallescheria angusta, Scedosporium minutisporum, Scedosporium dehoogii, and Scedosporium aurantiacum, most of which can be distinguished with the primary fungal DNA barcode, the ITS1/2 region of the rDNA gene cluster. In the present study, four additional genetic loci were explored from a phylogenetic point of view enabling a barcoding approach based on K2P pairwise distances to resolve the taxa Scedosporium. We included partial γ-actin (ACT), β-tubulin (BT2), elongation factor 1α (TEF1), and the small ribosomal protein 60S L10 (L1) (RP60S). Phylogenetic inference of each marker individually showed that four out of six species within Scedosporium can be distinguished unambiguously, while strains of S. apiospermum, S. boydii, and P. angusta showed occasional recombination, and accordingly, no genealogical concordance between markers was obtainable. We defined S. apiospermum, S. boydii, and P. angusta as the 'S. apiospermum species complex' since observed differences were not consistent between lineages, and no clinical differences are known between entities within the complex. While BT2 revealed the best performance among the genetic loci tested at the lineage level, barcoding of the ITS region is sufficient for distinction of all entities in Scedosporium at the species or 'complex' level. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

A monograph of the entomopathogenic genera Hypocrella, Moelleriella, and Samuelsia gen. nov. (Ascomycota, Hypocreales, Clavicipitaceae), and their aschersonia-like anamorphs in the Neotropics

PubMed Central

Chaverri, P.; Liu, M.; Hodge, K.T.

2008-01-01

The present taxonomic revision deals with Neotropical species of three entomopathogenic genera that were once included in Hypocrella s. l.: Hypocrella s. str. (anamorph Aschersonia), Moelleriella (anamorph aschersonia-like), and Samuelsia gen. nov (anamorph aschersonia-like). Species of Hypocrella, Moelleriella, and Samuelsia are pathogens of scale insects (Coccidae and Lecaniidae, Homoptera) and whiteflies (Aleyrodidae, Homoptera) and are common in tropical regions. Phylogenetic analyses of DNA sequences from nuclear ribosomal large subunit (28S), translation elongation factor 1-α (TEF 1-α), and RNA polymerase II subunit 1 (RPB1) and analyses of multiple morphological characters demonstrate that the three segregated genera can be distinguished by the disarticulation of the ascospores and shape and size of conidia. Moelleriella has filiform multi-septate ascospores that disarticulate at the septa within the ascus and aschersonia-like anamorphs with fusoid conidia. Hypocrella s. str. has filiform to long-fusiform ascospores that do not disarticulate and Aschersonia s. str. anamorphs with fusoid conidia. The new genus proposed here, Samuelsia, has filiform to long-fusiform ascospores that do not disarticulate and aschersonia-like anamorphs with small allantoid conidia. In addition, the present study presents and discusses the evolution of species, morphology, and ecology in Hypocrella, Moelleriella, and Samuelsia based on multigene phylogenetic analyses. PMID:18490956

Aspergillus niger contains the cryptic phylogenetic species A. awamori.

PubMed

Perrone, Giancarlo; Stea, Gaetano; Epifani, Filomena; Varga, János; Frisvad, Jens C; Samson, Robert A

2011-11-01

Aspergillus section Nigri is an important group of species for food and medical mycology, and biotechnology. The Aspergillus niger 'aggregate' represents its most complicated taxonomic subgroup containing eight morphologically indistinguishable taxa: A. niger, Aspergillus tubingensis, Aspergillus acidus, Aspergillus brasiliensis, Aspergillus costaricaensis, Aspergillus lacticoffeatus, Aspergillus piperis, and Aspergillus vadensis. Aspergillus awamori, first described by Nakazawa, has been compared taxonomically with other black aspergilli and recently it has been treated as a synonym of A. niger. Phylogenetic analyses of sequences generated from portions of three genes coding for the proteins β-tubulin (benA), calmodulin (CaM), and the translation elongation factor-1 alpha (TEF-1α) of a population of A. niger strains isolated from grapes in Europe revealed the presence of a cryptic phylogenetic species within this population, A. awamori. Morphological, physiological, ecological and chemical data overlap occurred between A. niger and the cryptic A. awamori, however the splitting of these two species was also supported by AFLP analysis of the full genome. Isolates in both phylospecies can produce the mycotoxins ochratoxin A and fumonisin B₂, and they also share the production of pyranonigrin A, tensidol B, funalenone, malformins, and naphtho-γ-pyrones. In addition, sequence analysis of four putative A. awamori strains from Japan, used in the koji industrial fermentation, revealed that none of these strains belong to the A. awamori phylospecies. Copyright © 2011 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Identification of Pathogenic Fusarium spp. Causing Maize Ear Rot and Potential Mycotoxin Production in China

PubMed Central

Duan, Canxing; Qin, Zihui; Yang, Zhihuan; Li, Weixi; Sun, Suli; Zhu, Zhendong; Wang, Xiaoming

2016-01-01

Ear rot is a serious disease that affects maize yield and grain quality worldwide. The mycotoxins are often hazardous to humans and livestock. In samples collected in China between 2009 and 2014, Fusarium verticillioides and F. graminearum species complex were the dominant fungi causing ear rot. According to the TEF-1α gene sequence, F. graminearum species complex in China included three independent species: F. graminearum, F. meridionale, and F. boothii. The key gene FUM1 responsible for the biosynthesis of fumonisin was detected in all 82 F. verticillioides isolates. Among these, 57 isolates mainly produced fumonisin B1, ranging from 2.52 to 18,416.44 µg/g for each gram of dry hyphal weight, in vitro. Three different toxigenic chemotypes were detected among 78 F. graminearum species complex: 15-ADON, NIV and 15-ADON+NIV. Sixty and 16 isolates represented the 15-ADON and NIV chemotypes, respectively; two isolates carried both 15-ADON and NIV-producing segments. All the isolates carrying NIV-specific segment were F. meridionale. The in vitro production of 15-ADON, 3-ADON, DON, and ZEN varied from 5.43 to 81,539.49; 6.04 to 19,590.61; 13.35 to 19,795.33; and 1.77 to 430.24 µg/g of dry hyphal weight, respectively. Altogether, our present data demonstrate potential main mycotoxin production of dominant pathogenic Fusarium in China. PMID:27338476

Phylogenetic diversity of human pathogenic Fusarium and emergence of uncommon virulent species.

PubMed

Salah, Husam; Al-Hatmi, Abdullah M S; Theelen, Bart; Abukamar, Mohammed; Hashim, Samar; van Diepeningen, Anne D; Lass-Florl, Cornelia; Boekhout, Teun; Almaslamani, Muna; Taj-Aldeen, Saad J

2015-12-01

Fusarium species cause a broad spectrum of infections. However, little is known about the etiological agents to the species level. We identified Fusarium species isolated from clinical specimens including those of high risk patients to better understand the species involved in the pathogenesis. A set of 44 Fusarium isolates were identified by two-locus sequence typing using partial sequences of the second largest subunit of RNA polymerase (RPB2) and translation elongation factor 1 alpha (TEF-1α). The identified species belonged to four species complexes (SC); the most common SC was Fusarium solani (FSSC) (75%), followed by Fusarium oxysporum (FOSC) (4.5%), Fusarium fujikuroi (FFSC) (13.6%), and Fusarium dimerum (FDSC) (6.8%). Sites of infections were nails (n = 19, 43.2%), skin (n = 7, 15.9%), cornea (n = 6, 13.6%), blood (n = 3, 9%), wound (n = 4, 6.8%), burn (n = 2, 4.5%), tissue (n = 2, 4.5%), and urine (n = 1, 2.27%). Fusarium acutatum was rare and seem restricted to the Middle East. Comorbidities associated with invasive infections were hematological malignancy and autoimmune disorders. Members of the FSSC predominantly caused cornea, nail and bloodstream infections. Less frequently encountered were the FOSC, FFSC and FDSC. More accurate molecular identification of Fusarium species is important to predict therapeutic outcome and the emergence of these species. Copyright © 2015 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Effects of Grain Size on Ultrasonic Attenuation in Type 316L Stainless Steel

PubMed Central

Wan, Tao; Wakui, Takashi; Futakawa, Masatoshi; Obayashi, Hironari

2017-01-01

A lead bismuth eutectic (LBE) spallation target will be installed in the Target Test Facility (TEF-T) in the Japan Proton Accelerator Research Complex (J-PARC). The spallation target vessel filled with LBE is made of type 316L stainless steel. However, various damages, such as erosion/corrosion damage and liquid metal embrittlement caused by contact with flowing LBE at high temperature, and irradiation hardening caused by protons and neutrons, may be inflicted on the target vessel, which will deteriorate the steel and might break the vessel. To monitor the target vessel for prevention of an accident, an ultrasonic technique has been proposed to establish off-line evaluation for estimating vessel material status during the target maintenance period. Basic R&D must be carried out to clarify the dependency of ultrasonic wave propagation behavior on material microstructures and obtain fundamental knowledge. As a first step, ultrasonic waves scattered by the grains of type 316L stainless steel are investigated using new experimental and numerical approaches in the present study. The results show that the grain size can be evaluated exactly and quantitatively by calculating the attenuation coefficient of the ultrasonic waves scattered by the grains. The results also show that the scattering regimes of ultrasonic waves depend heavily on the ratio of wavelength to average grain size, and are dominated by grains of extraordinarily large size along the wave propagation path. PMID:28773115

Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains

PubMed Central

Jaklitsch, Walter; Gazis, Romina; Degenkolb, Thomas; Samuels, Gary J.

2016-01-01

Trichoderma harzianum is known as a cosmopolitan, ubiquitous species associated with a wide variety of substrates. It is possibly the most commonly used name in agricultural applications involving Trichoderma, including biological control of plant diseases. While various studies have suggested that T. harzianum is a species complex, only a few cryptic species are named. In the present study the taxonomy of the T. harzianum species complex is revised to include at least 14 species. Previously named species included in the complex are T. guizhouense, T. harzianum, and T. inhamatum. Two new combinations are proposed, T. lentiforme and T. lixii. Nine species are described as new, T. afarasin, T. afroharzianum, T. atrobrunneum, T. camerunense, T. endophyticum, T. neotropicale, T. pyramidale, T. rifaii and T. simmonsii. We isolated Trichoderma cultures from four commercial biocontrol products reported to contain T. harzianum. None of the biocontrol strains were identified as T. harzianum s. str. In addition, the widely applied culture ‘T. harzianum T22’ was determined to be T. afroharzianum. Some species in the T. harzianum complex appear to be exclusively endophytic, while others were only isolated from soil. Sexual states are rare. Descriptions and illustrations are provided. A secondary barcode, nuc translation elongation factor 1-α (TEF1) is needed to identify species in this complex. PMID:25661720

Leaf-inhabiting genera of the Gnomoniaceae, Diaporthales

PubMed Central

Sogonov, M.V.; Castlebury, L.A.; Rossman, A.Y.; Mejía, L.C.; White, J.F.

2008-01-01

The Gnomoniaceae are characterised by ascomata that are generally immersed, solitary, without a stroma, or aggregated with a rudimentary stroma, in herbaceous plant material especially in leaves, twigs or stems, but also in bark or wood. The ascomata are black, soft-textured, thin-walled, and pseudoparenchymatous with one or more central or eccentric necks. The asci usually have a distinct apical ring. The Gnomoniaceae includes species having ascospores that are small, mostly less than 25 μm long, although some are longer, and range in septation from non-septate to one-septate, rarely multi-septate. Molecular studies of the Gnomoniaceae suggest that the traditional classification of genera based on characteristics of the ascomata such as position of the neck and ascospores such as septation have resulted in genera that are not monophyletic. In this paper the concepts of the leaf-inhabiting genera in the Gnomoniaceae are reevaluated using multiple genes, specifically nrLSU, translation elongation factor 1-alpha (tef1-α), and RNA polymerase II second largest subunit (rpb2) for 64 isolates. ITS sequences were generated for 322 isolates. Six genera of leaf-inhabiting Gnomoniaceae are defined based on placement of their type species within the multigene phylogeny. The new monotypic genus Ambarignomonia is established for an unusual species, A. petiolorum. A key to 59 species of leaf-inhabiting Gnomoniaceae is presented and 22 species of Gnomoniaceae are described and illustrated. PMID:19287541

Estimation of PAHs dry deposition and BaP toxic equivalency factors (TEFs) study at Urban, Industry Park and rural sampling sites in central Taiwan, Taichung.

PubMed

Fang, Guor-Cheng; Chang, Kuan-Foo; Lu, Chungsying; Bai, Hsunling

2004-05-01

The concentrations of polycyclic aromatic hydrocarbons (PAHs) in gas phase and particle bound were measured simultaneously at industrial (INDUSTRY), urban (URBAN), and rural areas (RURAL) in Taichung, Taiwan. And the PAH concentrations, size distributions, estimated PAHs dry deposition fluxes and health risk study of PAHs in the ambient air of central Taiwan were discussed in this study. Total PAH concentrations at INDUSTRY, URBAN, and RURAL sampling sites were found to be 1650 +/- 1240, 1220 +/- 520, and 831 +/- 427 ng/m3, respectively. The results indicated that PAH concentrations were higher at INDUSTRY and URBAN sampling sites than the RURAL sampling sites because of the more industrial processes, traffic exhausts and human activities. The estimation dry deposition and size distribution of PAHs were also studied. The results indicated that the estimated dry deposition fluxes of total PAHs were 58.5, 48.8, and 38.6 microg/m2/day at INDUSTRY, URBAN, and RURAL, respectively. The BaP equivalency results indicated that the health risk of gas phase PAHs were higher than the particle phase at three sampling sites of central Taiwan. However, compared with the BaP equivalency results to other studies conducted in factory, this study indicated the health risk of PAHs was acceptable in the ambient air of central Taiwan.

Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains.

PubMed

Chaverri, Priscila; Branco-Rocha, Fabiano; Jaklitsch, Walter; Gazis, Romina; Degenkolb, Thomas; Samuels, Gary J

2015-01-01

Trichoderma harzianum is known as a cosmopolitan, ubiquitous species associated with a wide variety of substrates. It is possibly the most commonly used name in agricultural applications involving Trichoderma, including biological control of plant diseases. While various studies have suggested that T. harzianum is a species complex, only a few cryptic species are named. In the present study the taxonomy of the T. harzianum species complex is revised to include at least 14 species. Previously named species included in the complex are T. guizhouense, T. harzianum, and T. inhamatum. Two new combinations are proposed, T. lentiforme and T. lixii. Nine species are described as new, T. afarasin, T. afroharzianum, T. atrobrunneum, T. camerunense, T. endophyticum, T. neotropicale, T. pyramidale, T. rifaii and T. simmonsii. We isolated Trichoderma cultures from four commercial biocontrol products reported to contain T. harzianum. None of the biocontrol strains were identified as T. harzianum s. str. In addition, the widely applied culture 'T. harzianum T22' was determined to be T. afroharzianum. Some species in the T. harzianum complex appear to be exclusively endophytic, while others were only isolated from soil. Sexual states are rare. Descriptions and illustrations are provided. A secondary barcode, nuc translation elongation factor 1-α (TEF1) is needed to identify species in this complex. © 2015 by The Mycological Society of America.

Species or Genotypes? Reassessment of Four Recently Described Species of the Ceratocystis Wilt Pathogen, Ceratocystis fimbriata, on Mangifera indica.

PubMed

Oliveira, Leonardo S S; Harrington, Thomas C; Ferreira, Maria A; Damacena, Michelle B; Al-Sadi, Abdullah M; Al-Mahmooli, Issa H S; Alfenas, Acelino C

2015-09-01

Ceratocystis wilt is among the most important diseases on mango (Mangifera indica) in Brazil, Oman, and Pakistan. The causal agent was originally identified in Brazil as Ceratocystis fimbriata, which is considered by some as a complex of many cryptic species, and four new species on mango trees were distinguished from C. fimbriata based on variation in internal transcribed spacer sequences. In the present study, phylogenetic analyses using DNA sequences of mating type genes, TEF-1α, and β-tubulin failed to identify lineages corresponding to the four new species names. Further, mating experiments found that the mango isolates representing the new species were interfertile with each other and a tester strain from sweet potato (Ipomoea batatas), on which the name C. fimbriata is based, and there was little morphological variation among the mango isolates. Microsatellite markers found substantial differentiation among mango isolates at the regional and population levels, but certain microsatellite genotypes were commonly found in multiple populations, suggesting that these genotypes had been disseminated in infected nursery stock. The most common microsatellite genotypes corresponded to the four recently named species (C. manginecans, C. acaciivora, C. mangicola, and C. mangivora), which are considered synonyms of C. fimbriata. This study points to the potential problems of naming new species based on introduced genotypes of a pathogen, the value of an understanding of natural variation within and among populations, and the importance of phenotype in delimiting species.

Distribution and Genetic Variability of Fusarium oxysporum Associated with Tomato Diseases in Algeria and a Biocontrol Strategy with Indigenous Trichoderma spp.

PubMed

Debbi, Ali; Boureghda, Houda; Monte, Enrique; Hermosa, Rosa

2018-01-01

Fifty fungal isolates were sampled from diseased tomato plants as result of a survey conducted in seven tomato crop areas in Algeria from 2012 to 2015. Morphological criteria and PCR-based identification, using the primers PF02 and PF03, assigned 29 out of 50 isolates to Fusarium oxysporum ( Fo ). The banding patterns amplified for genes SIX1, SIX3 and SIX4 served to identify races 2 and 3 of Fo f. sp. lycopersici (FOL), and Fo f. sp. radicis lycopersici (FORL) among the Algerian isolates. All FOL isolates showed pathogenicity on the susceptible tomato cv. "Super Marmande," while nine of out 10 Algerian FORL isolates were pathogenic on tomato cv. "Rio Grande." Inter simple sequence repeat (ISSR) fingerprints showed high genetic diversity among Algerian Fo isolates. Seventeen Algerian Trichoderma isolates were also obtained and assigned to the species T. asperellum (12 isolates), T. harzianum (four isolates) and T. ghanense (one isolate) based on ITS and tef1 α gene sequences. Different in vitro tests identified the antagonistic potential of native Trichoderma isolates against FORL and FOL. Greenhouse biocontrol assays performed on "SM" tomato plants with T. ghanense T8 and T. asperellum T9 and T17, and three Fo isolates showed that isolate T8 performed well against FORL and FOL. This finding was based on an incidence reduction of crown and root rot and Fusarium wilt diseases by 53.1 and 48.3%, respectively.

Cryptic MCAT enhancer regulation in fibroblasts and smooth muscle cells. Suppression of TEF-1 mediated activation by the single-stranded DNA-binding proteins, Pur alpha, Pur beta, and MSY1.

PubMed

Carlini, Leslie E; Getz, Michael J; Strauch, Arthur R; Kelm, Robert J

2002-03-08

An asymmetric polypurine-polypyrimidine cis-element located in the 5' region of the mouse vascular smooth muscle alpha-actin gene serves as a binding site for multiple proteins with specific affinity for either single- or double-stranded DNA. Here, we test the hypothesis that single-stranded DNA-binding proteins are responsible for preventing a cryptic MCAT enhancer centered within this element from cooperating with a nearby serum response factor-interacting CArG motif to trans-activate the minimal promoter in fibroblasts and smooth muscle cells. DNA binding studies revealed that the core MCAT sequence mediates binding of transcription enhancer factor-1 to the double-stranded polypurine-polypyrimidine element while flanking nucleotides account for interaction of Pur alpha and Pur beta with the purine-rich strand and MSY1 with the complementary pyrimidine-rich strand. Mutations that selectively impaired high affinity single-stranded DNA binding by fibroblast or smooth muscle cell-derived Pur alpha, Pur beta, and MSY1 in vitro, released the cryptic MCAT enhancer from repression in transfected cells. Additional experiments indicated that Pur alpha, Pur beta, and MSY1 also interact specifically, albeit weakly, with double-stranded DNA and with transcription enhancer factor-1. These results are consistent with two plausible models of cryptic MCAT enhancer regulation by Pur alpha, Pur beta, and MSY1 involving either competitive single-stranded DNA binding or masking of MCAT-bound transcription enhancer factor-1.

Two new species of the Fusarium solani species complex isolated from compost and hibiscus (Hibiscus sp.).

PubMed

Šišić, Adnan; Al-Hatmi, Abdullah M S; Baćanović-Šišić, Jelena; Ahmed, Sarah A; Dennenmoser, Dominic; de Hoog, G Sybren; Finckh, Maria R

2018-03-22

Two new species in the Fusarium solani species complex (FSSC) are described and introduced. The new taxa are represented by German isolates CBS 142481 and CBS 142480 collected from commercial yard waste compost and vascular tissue of a wilting branch of hibiscus, respectively. The phylogenetic relationships of the collected strains to one another and within the FSSC were evaluated based on DNA sequences of 6 gene loci. Due to the limited sequence data available for reference strains in GenBank, however, a multi-gene phylogenetic analysis included partial sequences for the internal transcribed spacer region and intervening 5.8S nrRNA gene (ITS), translation elongation factor 1-alpha (tef1) and the RNA polymerase II second largest subunit (rpb2). Morphological and molecular phylogenetic data independently showed that these strains are distinct populations of the FSSC, nested within Clade 3. Thus, we introduce Fusarium stercicola and Fusarium witzenhausenense as novel species in the complex. In addition, 19 plant species of 7 legume genera were evaluated for their potential to host the newly described taxa. Eighteen plant species were successfully colonized, with 6 and 9 of these being symptomatic hosts for F. stercicola and F. witzenhausenense, respectively. As plants of the family Fabaceae are very distant to the originally sourced material from which the new taxa were recovered, our results suggest that F. stercicola and F. witzenhausenense are not host-specific and are ecologically fit to sustain stable populations in variety of habitats.

Fusarium proliferatum - Causal agent of garlic bulb rot in Spain: Genetic variability and mycotoxin production.

PubMed

Gálvez, Laura; Urbaniak, Monika; Waśkiewicz, Agnieszka; Stępień, Łukasz; Palmero, Daniel

2017-10-01

Fusarium proliferatum is a world-wide occurring fungal pathogen affecting several crops included garlic bulbs. In Spain, this is the most frequent pathogenic fungus associated with garlic rot during storage. Moreover, F. proliferatum is an important mycotoxigenic species, producing a broad range of toxins, which may pose a risk for food safety. The aim of this study is to assess the intraspecific variability of the garlic pathogen in Spain implied by analyses of translation elongation factor (tef-1α) and FUM1 gene sequences as well as the differences in growth rates. Phylogenetic characterization has been complemented with the characterization of mating type alleles as well as the species potential as a toxin producer. Phylogenetic trees based on the sequence of the translation elongation factor and FUM1 genes from seventy nine isolates from garlic revealed a considerable intraspecific variability as well as high level of diversity in growth speed. Based on the MAT alleles amplified by PCR, F. proliferatum isolates were separated into different groups on both trees. All isolates collected from garlic in Spain proved to be fumonisin B 1 , B 2 , and B 3 producers. Quantitative analyses of fumonisins, beauvericin and moniliformin (common secondary metabolites of F. proliferatum) showed no correlation with phylogenetic analysis neither mycelial growth. This pathogen presents a high intraspecific variability within the same geographical region and host, which is necessary to be considered in the management of the disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

Anatomizing one of the largest saltwater inflows into the Baltic Sea in December 2014

NASA Astrophysics Data System (ADS)

Gräwe, Ulf; Naumann, Michael; Mohrholz, Volker; Burchard, Hans

2015-11-01

In December 2014, an exceptional inflow event into the Baltic Sea was observed, a so-called Major Baltic Inflow (MBI). Such inflow events are important for the deep water ventilation in the Baltic Sea and typically occur every 3-10 years. Based on first observational data sets, this inflow had been ranked as the third largest since 100 years. With the help of a multinested modeling system, reaching from the North Atlantic (8 km resolution) to the Western Baltic Sea (600 m resolution, which is baroclinic eddy resolving), this event is reproduced in detail. The model gave a slightly lower salt transport of 3.8 Gt, compared to the observational estimate of four Gt. Moreover, by using passive tracers to mark the different inflowing water masses, including an age tracer, the inflowing water masses could be tracked and their paths and timing through the different basins could be reproduced and investigated. The analysis is supported by the recently developed Total Exchange Flow (TEF) to quantify the volume transport in different salinity classes. To account for uncertainties in the modeled velocity and tracer fields, a Monte Carlo Analysis (MCA) is applied to correct possible biases and errors. With the help of the MCA, 95% confidence intervals are computed for the transport estimates. Based on the MCA, the "best guess" of the volume transport is 291.0 ± 13.65 km3 and 3.89 ± 0.18 Gt for the total salt transport.

Unraveling Trichoderma species in the attine ant environment: description of three new taxa.

PubMed

Montoya, Quimi Vidaurre; Meirelles, Lucas Andrade; Chaverri, Priscila; Rodrigues, Andre

2016-05-01

Fungus-growing "attine" ants forage diverse substrates to grow fungi for food. In addition to the mutualistic fungal partner, the colonies of these insects harbor a rich microbiome composed of bacteria, filamentous fungi and yeasts. Previous work reported some Trichoderma species in the fungus gardens of leafcutter ants. However, no studies systematically addressed the putative association of Trichoderma with attine ants, especially in non-leafcutter ants. Here, a total of 62 strains of Trichoderma were analyzed using three molecular markers (ITS, tef1 and rpb2). In addition, 30 out of 62 strains were also morphologically examined. The strains studied correspond to the largest sampling carried out so far for Trichoderma in the attine ant environment. Our results revealed the richness of Trichoderma in this environment, since we found 20 Trichoderma species, including three new taxa described in the present work (Trichoderma attinorum, Trichoderma texanum and Trichoderma longifialidicum spp. nov.) as well as a new phylogenetic taxon (LESF 545). Moreover, we show that all 62 strains grouped within different clades across the Trichoderma phylogeny, which are identical or closely related to strains derived from several other environments. This evidence supports the transient nature of the genus Trichoderma in the attine ant colonies. The discovery of three new species suggests that the dynamic foraging behavior of these insects might be responsible for accumulation of transient fungi into their colonies, which might hold additional fungal taxa still unknown to science.

Generic concepts in Nectriaceae

PubMed Central

Lombard, L.; van der Merwe, N.A.; Groenewald, J.Z.; Crous, P.W.

2015-01-01

The ascomycete family Nectriaceae (Hypocreales) includes numerous important plant and human pathogens, as well as several species used extensively in industrial and commercial applications as biodegraders and biocontrol agents. Members of the family are unified by phenotypic characters such as uniloculate ascomata that are yellow, orange-red to purple, and with phialidic asexual morphs. The generic concepts in Nectriaceae are poorly defined, since DNA sequence data have not been available for many of these genera. To address this issue we performed a multi-gene phylogenetic analysis using partial sequences for the 28S large subunit (LSU) nrDNA, the internal transcribed spacer region and intervening 5.8S nrRNA gene (ITS), the large subunit of the ATP citrate lyase (acl1), the RNA polymerase II largest subunit (rpb1), RNA polymerase II second largest subunit (rpb2), α-actin (act), β-tubulin (tub2), calmodulin (cmdA), histone H3 (his3), and translation elongation factor 1-alpha (tef1) gene regions for available type and authentic strains representing known genera in Nectriaceae, including several genera for which no sequence data were previously available. Supported by morphological observations, the data resolved 47 genera in the Nectriaceae. We re-evaluated the status of several genera, which resulted in the introduction of six new genera to accommodate species that were initially classified based solely on morphological characters. Several generic names are proposed for synonymy based on the abolishment of dual nomenclature. Additionally, a new family is introduced for two genera that were previously accommodated in the Nectriaceae. PMID:26955195

Two novel Fusarium species that cause canker disease of prickly ash (Zanthoxylum bungeanum) in northern China form a novel clade with Fusarium torreyae.

PubMed

Zhou, Xue; O'Donnell, Kerry; Aoki, Takayuki; Smith, Jason A; Kasson, Matthew T; Cao, Zhi-Min

2016-01-01

Canker disease of prickly ash (Zanthoxylum bungeanum) has caused a decline in the production of this economically important spice in northern China in the past 25 y. To identify the etiological agent, 38 fungal isolates were recovered from symptomatic tissues from trees in five provinces in China. These isolates were identified by conducting BLASTN queries of NCBI GenBank and phylogenetic analyses of DNA sequence data from the nuclear ribosomal internal transcribed spacer region (ITS rDNA), a portion of the translation elongation factor 1-α (TEF1) gene, and genes encoding RNA polymerase II largest (RPB1) and second largest (RPB2) subunits. Results of these analyses suggested that 30/38 isolates belonged to two novel fusaria most closely related to the Florida torreya (Torreya taxifolia Arn.) pathogen, Fusarium torreyae in Florida and Georgia. These three canker-inducing tree pathogens form a novel clade within Fusarium here designated the F. torreyae species complex (FTOSC). BLASTN queries of GenBank also revealed that 5/38 isolates recovered from cankers represented an undescribed phylogenetic species within the F. solani species complex (FSSC) designated FSSC 6. Stem inoculations of three fusaria on Z. bungeanum resulted in consistent canker symptoms from which these three fusaria were recovered. The two novel fusaria, however, induced significantly larger lesions than FSSC 6. Herein, the two novel prickly ash pathogens are formally described as F. zanthoxyli and F. continuum. © 2016 by The Mycological Society of America.

Detection of human pathogenic Fusarium species in hospital and communal sink biofilms by using a highly specific monoclonal antibody.

PubMed

Al-Maqtoofi, Marwan; Thornton, Christopher R

2016-11-01

The fungus Fusarium is well known as a plant pathogen, but has recently emerged as an opportunistic pathogen of humans. Habitats providing direct human exposure to infectious propagules are largely unknown, but there is growing evidence that plumbing systems are sources of human pathogenic strains in the Fusarium solani species complex (FSSC) and Fusarium oxysporum species complex (FOSC), the most common groups infecting humans. Here, a newly developed Fusarium-specific monoclonal antibody (mAb ED7) was used to track FSSC and FOSC strains in sink drain biofilms by detecting its target antigen, an extracellular 200 kDa carbohydrate, in saline swabs. The antigen was detectable in 52% of swab samples collected from sinks across a University campus and a tertiary care hospital. The mAb was 100% accurate in detecting FSSC, FOSC, and F. dimerum species complex (FDSC) strains that were present, as mixed fungal communities, in 83% of sink drain biofilms. Specificity of the ELISA was confirmed by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2 rRNA-encoding regions of culturable yeasts and molds that were recovered using mycological culture, while translation elongation factor (TEF)-1α analysis of Fusarium isolates included FSSC 1-a, FOSC 33, and FDSC ET-gr, the most common clinical pathotypes in each group. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

The genus Bipolaris

PubMed Central

Manamgoda, D.S.; Rossman, A.Y.; Castlebury, L.A.; Crous, P.W.; Madrid, H.; Chukeatirote, E.; Hyde, K.D.

2014-01-01

The genus Bipolaris includes important plant pathogens with worldwide distribution. Species recognition in the genus has been uncertain due to the lack of molecular data from ex-type cultures as well as overlapping morphological characteristics. In this study, we revise the genus Bipolaris based on DNA sequence data derived from living cultures of fresh isolates, available ex-type cultures from worldwide collections and observation of type and additional specimens. Combined analyses of ITS, GPDH and TEF gene sequences were used to reconstruct the molecular phylogeny of the genus Bipolaris for species with living cultures. The GPDH gene is determined to be the best single marker for species of Bipolaris. Generic boundaries between Bipolaris and Curvularia are revised and presented in an updated combined ITS and GPDH phylogenetic tree. We accept 47 species in the genus Bipolaris and clarify the taxonomy, host associations, geographic distributions and species’ synonymies. Modern descriptions and illustrations are provided for 38 species in the genus with notes provided for the other taxa when recent descriptions are available. Bipolaris cynodontis, B. oryzae, B. victoriae, B. yamadae and B. zeicola are epi- or neotypified and a lectotype is designated for B. stenospila. Excluded and doubtful species are listed with notes on taxonomy and phylogeny. Seven new combinations are introduced in the genus Curvularia to accomodate the species of Bipolaris transferred based on the phylogenetic analysis. A taxonomic key is provided for the morphological identification of species within the genus. PMID:25492990

Teff (Eragrostis tef) as a raw material for malting, brewing and manufacturing of gluten-free foods and beverages: a review.

PubMed

Gebremariam, Mekonnen Melaku; Zarnkow, Martin; Becker, Thomas

2014-11-01

The demand for gluten-free foods is certainly increasing. Interest in teff has increased noticeably due to its very attractive nutritional profile and gluten-free nature of the grain, making it a suitable substitute for wheat and other cereals in their food applications as well as foods for people with celiac disease. The main objective of this article is to review researches on teff, evaluate its suitability for different food applications, and give direction for further research on its applications for health food market. Teff is a tropical low risk cereal that grows in a wider ecology and can tolerate harsh environmental conditions where most other cereals are less viable. It has an excellent balance of amino acid composition (including all 8 essential amino acids for humans) making it an excellent material for malting and brewing. Because of its small size, teff is made into whole-grain flour (bran and germ included), resulting in a very high fiber content and high nutrient content in general. Teff is useful to improve the haemoglobin level in human body and helps to prevent malaria, incidence of anaemia and diabetes. The nutrient composition of teff grain indicates that it has a good potential to be used in foods and beverages worldwide. The high levels of simple sugars and α-amino acids as a result of breakdown of starch and protein, respectively, are essential for fermentation and beer making.

Performance improvement in a tubular heat exchanger by punched delta-winglet vortex generators

NASA Astrophysics Data System (ADS)

Khanoknaiyakarn, C.; Promvonge, P.; Thianpong, C.; Skullong, S.

2018-01-01

A novel tubular heat exchanger incorporated with punched delta-winglet vortex generators (called perforated delta-winglet vortex generator, P-DWVG) is proposed for improving its thermal performance and energy saving. The P-DWVG elements are punched out from a straight tape having its width nearly equal to the tube diameter before insertion. The main aim at employing the P-DWVG insert is to produce counter-rotating vortices along the tube to promote turbulence intensity inside as well as to transport the cold fluid at the central core to the near-wall regions. The experiment was performed to study thermal behaviors in a uniform heat-fluxed tube inserted with P-DWVGs. The P-DWVGs with the attack angle of 45° were mounted periodically with three different blockage ratios (BR = 0.1, 0.2 and 0.3) and two pitch ratios (PR = 2 and 3). Air as the test fluid was varied to obtain turbulent airflow for Reynolds number (Re) in a range of 4,150-25,500. The experimental results show that the P-DWVG provides a considerable increase in the rate of heat transfer around 3.1-4.01 times whereas friction factor increases around 11.44- 34.23 times higher than the plain tube. To assess the real benefits of P-DWVGs, thermal performance factor (TEF) is examined and in the range of 1.39-1.48 where its maximum is at BR = 0.1 and PR = 2.

Entomopathogens of Amazonian stick insects and locusts are members of the Beauveria species complex (Cordyceps sensu stricto).

PubMed

Sanjuan, Tatiana; Tabima, Javier; Restrepo, Silvia; Læssøe, Thomas; Spatafora, Joseph W; Franco-Molano, Ana Esperanza

2014-01-01

In the Amazon the only described species of Cordyceps sensu stricto (Hypocreales, Cordycipitaceae) that parasitize insects of Orthopterida (orders Orthoptera and Phasmida) are Cordyceps locustiphila and C. uleana. However, the type specimens for both taxa have been lost and the concepts of these species are uncertain. To achieve a more comprehensive understanding of the systematics of these species, collections of Cordyceps from the Amazon regions of Colombia, Ecuador and Guyana were subjected to morphological, ecological and molecular phylogenetic studies. Phylogenetic analyses were conducted on partial sequences of SSU, LSU, TEF, RPB1 and RPB2 nuclear loci. Two new species are proposed including C. diapheromeriphila, a parasite of Phasmida, and C. acridophila, a parasite of the superfamily Acridomorpha (Orthoptera), which is broadly distributed across the Amazon. For C. locustiphila a lectotypification and an epitypification are made. Cordyceps locustiphila is host specific with Colpolopha (Acridomorpha: Romaleidae), and its distribution coincides with that of its host. The phylogenetic placement of these three species was resolved with strong support in the Beauveria clade of Cordyceps s. str. (Cordycipitaceae). This relationship and the morphological similarity of their yellow stromata with known teleomorphs of the clade, suggest that the holomorphs of these species may include Beauveria or Beauveria-like anamorphs. The varying host specificity of the beauverioid Cordyceps species suggest the potential importance of identifying the natural host taxon before future consideration of strains for use in biological control of pest locusts.

Major contribution of the Ehrlich pathway for 2-phenylethanol/rose flavor production in Ashbya gossypii.

PubMed

Ravasio, Davide; Wendland, Jürgen; Walther, Andrea

2014-09-01

Aroma alcohols of fermented food and beverages are derived from fungal amino acids catabolism via the Ehrlich pathway. This linear pathway consists of three enzymatic reactions to form fusel alcohols. Regulation of some of the enzymes occurs on the transcriptional level via Aro80. The riboflavin overproducer Ashbya gossypii produces strong fruity flavours in contrast to its much less aromatic relative Eremothecium cymbalariae. Genome comparisons indicated that A. gossypii harbors genes for aromatic amino acid catabolism (ARO8a, ARO8b, ARO10, and ARO80) while E. cymbalariae only encodes ARO8a and thus lacks major components of aromatic amino acid catabolism. Volatile compound (VOC) analysis showed that both Eremothecium species produce large amounts of isoamyl alcohol while A. gossypii also produces high levels of 2-phenylethanol. Deletion of the A. gossypii ARO-genes did not confer any growth deficiencies. However, A. gossypii ARO-mutants (except Agaro8a) were strongly impaired in aroma production, particularly in the production of the rose flavour 2-phenylethanol. Conversely, overexpression of ARO80 via the AgTEF1 promoter resulted in 50% increase in VOC production. Together these data indicate that A. gossypii is a very potent flavour producer and that amongst the non-Saccharomyces biodiversity strains can be identified that could provide positive sensory properties to fermented beverages. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Population genetic structure and mycotoxin potential of the wheat crown rot and head blight pathogen Fusarium culmorum in Algeria.

PubMed

Laraba, Imane; Boureghda, Houda; Abdallah, Nora; Bouaicha, Oussama; Obanor, Friday; Moretti, Antonio; Geiser, David M; Kim, Hye-Seon; McCormick, Susan P; Proctor, Robert H; Kelly, Amy C; Ward, Todd J; O'Donnell, Kerry

2017-06-01

Surveys for crown rot (FCR) and head blight (FHB) of Algerian wheat conducted during 2014 and 2015 revealed that Fusarium culmorum strains producing 3-acetyl-deoxynivalenol (3ADON) or nivalenol (NIV) were the causal agents of these important diseases. Morphological identification of the isolates (n FCR=110, n FHB=30) was confirmed by sequencing a portion of TEF1. To assess mating type idiomorph, trichothecene chemotype potential and global population structure, the Algerian strains were compared with preliminary sample of F. culmorum from Italy (n=27), Australia (n=30) and the United States (n=28). A PCR assay for MAT idiomorph revealed that MAT1-1 and MAT1-2 strains were segregating in nearly equal proportions, except within Algeria where two-thirds of the strains were MAT1-2. An allele-specific PCR assay indicated that the 3ADON trichothecene genotype was predominant globally (83.8% 3ADON) and in each of the four countries sampled. In vitro toxin analyses confirmed trichothecene genotype PCR data and demonstrated that most of the strains tested (77%) produced culmorin. Global population genetic structure of 191 strains was assessed using nine microsatellite markers (SSRs). AMOVA of the clone corrected data indicated that 89% of the variation was within populations. Bayesian analysis of the SSR data identified two globally distributed, sympatric populations within which both trichothecene chemotypes and mating types were represented. Copyright © 2017. Published by Elsevier Inc.

Automated prediction of protein function and detection of functional sites from structure.

PubMed

Pazos, Florencio; Sternberg, Michael J E

2004-10-12

Current structural genomics projects are yielding structures for proteins whose functions are unknown. Accordingly, there is a pressing requirement for computational methods for function prediction. Here we present PHUNCTIONER, an automatic method for structure-based function prediction using automatically extracted functional sites (residues associated to functions). The method relates proteins with the same function through structural alignments and extracts 3D profiles of conserved residues. Functional features to train the method are extracted from the Gene Ontology (GO) database. The method extracts these features from the entire GO hierarchy and hence is applicable across the whole range of function specificity. 3D profiles associated with 121 GO annotations were extracted. We tested the power of the method both for the prediction of function and for the extraction of functional sites. The success of function prediction by our method was compared with the standard homology-based method. In the zone of low sequence similarity (approximately 15%), our method assigns the correct GO annotation in 90% of the protein structures considered, approximately 20% higher than inheritance of function from the closest homologue.

Simple Test Functions in Meshless Local Petrov-Galerkin Methods

NASA Technical Reports Server (NTRS)

Raju, Ivatury S.

2016-01-01

Two meshless local Petrov-Galerkin (MLPG) methods based on two different trial functions but that use a simple linear test function were developed for beam and column problems. These methods used generalized moving least squares (GMLS) and radial basis (RB) interpolation functions as trial functions. These two methods were tested on various patch test problems. Both methods passed the patch tests successfully. Then the methods were applied to various beam vibration problems and problems involving Euler and Beck's columns. Both methods yielded accurate solutions for all problems studied. The simple linear test function offers considerable savings in computing efforts as the domain integrals involved in the weak form are avoided. The two methods based on this simple linear test function method produced accurate results for frequencies and buckling loads. Of the two methods studied, the method with radial basis trial functions is very attractive as the method is simple, accurate, and robust.

CFD analysis to study effect of circular vortex generator placed in inlet section to investigate heat transfer aspects of solar air heater.

PubMed

Gawande, Vipin B; Dhoble, A S; Zodpe, D B

2014-01-01

CFD analysis of 2-dimensional artificially roughened solar air heater duct with additional circular vortex generator, inserted in inlet section is carried out. Circular transverse ribs on the absorber plate are placed as usual. The analysis is done to investigate the effect of inserting additional vortex generator on the heat transfer and flow friction characteristics inside the solar air heater duct. This investigation covers relative roughness pitch in the range of 10 ≤ P/e ≤ 25 and relevant Reynolds numbers in the range of 3800 ≤ Re ≤ 18000. Relative roughness height (e/D) is kept constant as 0.03 for analysis. The turbulence created due to additional circular vortex generator increases the heat transfer rate and at the same time there is also increase in friction factor values. For combined arrangement of ribs and vortex generator, maximum Nusselt number is found to be 2.05 times that of the smooth duct. The enhancement in Nusselt number with ribs and additional vortex generator is found to be 1.06 times that of duct using ribs alone. The maximum increase in friction factor with ribs and circular vortex generator is found to be 2.91 times that of the smooth duct. Friction factor in a combined arrangement is 1.114 times that in a duct with ribs alone on the absorber plate. The augmentation in Thermal Enhancement Factor (TEF) with vortex generator in inlet section is found to be 1.06 times more than with circular ribs alone on the absorber plate.

Phylogeny and origin of 82 zygomycetes from all 54 genera of the Mucorales and Mortierellales based on combined analysis of actin and translation elongation factor EF-1alpha genes.

PubMed

Voigt, K; Wöstemeyer, J

2001-05-30

True fungi (Eumycota) are heterotrophic eukaryotic microorganisms encompassing ascomycetes, basidiomycetes, chytridiomycetes and zygomycetes. The natural systematics of the latter group, Zygomycota, are very poorly understood due to the lack of distinguishing morphological characters. We have determined sequences for the nuclear-encoded genes actin (act) from 82 zygomycetes representing all 54 currently recognized genera from the two zygomycetous orders Mucorales and Mortierellales. We also determined sequences for translation elongation factor EF-1alpha (tef) from 16 zygomycetes (total of 96,837 bp). Phylogenetic analysis in the context of available sequence data (total 2,062 nucleotide positions per species) revealed that current classification schemes for the mucoralean fungi are highly unnatural at the family and, to a large extent, at the genus level. The data clearly indicate a deep, ancient and distinct dichotomy of the orders Mucorales and Mortierellales, which are recognized only in some zygomycete systems. Yet at the same time the data show that two genera - Umbelopsis and Micromucor - previously placed within the Mortierellales on the basis of their weakly developed columella (a morphological structure of the sporangiophore well-developed within all Mucorales) are in fact members of the Mucorales. Phylogenetic analyses of the encoded amino acid sequences in the context of homologues from eukaryotes and archaebacterial outgroups indicate that the Eumycota studied here are a natural group but provide little or no support for the monophyly of either zygomycetes, ascomycetes or basidiomycetes. The data clearly indicate that a complete revision of zygomycete natural systematics is necessary.

Effects of urbanization on gaseous and particulate polycyclic aromatic hydrocarbons and polychlorinated biphenyls in a coastal city, China: levels, sources, and health risks.

PubMed

Hong, Youwei; Chen, Jinsheng; Zhang, Fuwang; Zhang, Han; Xu, Lingling; Yin, Liqian; Chen, Yanting

2015-10-01

Gas/particle distributions of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) were measured in Xiamen from May 2009 to March 2010 to evaluate the impacts of urbanization on the fate of persistent organic pollutants (POPs) in the atmospheric environment. In a newly developing area (NDA), the concentrations of 16 PAHs (gas + particle) were significantly higher than that a historically urbanized area (HUA) (p value <0.05), while the trend of 28 PCBs was reversed. Diagnostic ratios and principle component analysis (PCA) implied that atmospheric PAHs in the NDA were mainly derived from petrogenic combustion, including mixed sources of vehicle emissions, biomass burning and oil combustion, while pyrogenic combustion (e.g., traffic and coal combustion) was considered the major source of PAHs in the HUA. Atmospheric PCBs in both HUA and NDA were dominated by TriCBs and PeCBs related to the use of commercial mixtures (Aroclors 1242 and 1254). Based on the toxicological equivalent factor (TEF) approach, total benzo[a]pyrene equivalent values in the HUA and NDA were 1.12 and 2.02 ng m(-3), respectively, exceeding the standard threshold values (1.0 ng m(-3)) of China and WHO. Average daily intake of dioxin-like compounds was 0.2 pg kg(-1) day(-1) in the HUA, which are below the WHO tolerable daily intake level. The results showed that the contribution to the toxic equivalency (TEQ) was dominated by PCB169, PCB105, and PCB81.

Distribution and Genetic Variability of Fusarium oxysporum Associated with Tomato Diseases in Algeria and a Biocontrol Strategy with Indigenous Trichoderma spp.

PubMed Central

Debbi, Ali; Boureghda, Houda; Monte, Enrique; Hermosa, Rosa

2018-01-01

Fifty fungal isolates were sampled from diseased tomato plants as result of a survey conducted in seven tomato crop areas in Algeria from 2012 to 2015. Morphological criteria and PCR-based identification, using the primers PF02 and PF03, assigned 29 out of 50 isolates to Fusarium oxysporum (Fo). The banding patterns amplified for genes SIX1, SIX3 and SIX4 served to identify races 2 and 3 of Fo f. sp. lycopersici (FOL), and Fo f. sp. radicis lycopersici (FORL) among the Algerian isolates. All FOL isolates showed pathogenicity on the susceptible tomato cv. “Super Marmande,” while nine of out 10 Algerian FORL isolates were pathogenic on tomato cv. “Rio Grande.” Inter simple sequence repeat (ISSR) fingerprints showed high genetic diversity among Algerian Fo isolates. Seventeen Algerian Trichoderma isolates were also obtained and assigned to the species T. asperellum (12 isolates), T. harzianum (four isolates) and T. ghanense (one isolate) based on ITS and tef1α gene sequences. Different in vitro tests identified the antagonistic potential of native Trichoderma isolates against FORL and FOL. Greenhouse biocontrol assays performed on “SM” tomato plants with T. ghanense T8 and T. asperellum T9 and T17, and three Fo isolates showed that isolate T8 performed well against FORL and FOL. This finding was based on an incidence reduction of crown and root rot and Fusarium wilt diseases by 53.1 and 48.3%, respectively. PMID:29515557

Rainforest understory beetles of the Neotropics, Mizotrechus Bates 1872, a generic synopsis with descriptions of new species from Central America and northern South America (Coleoptera, Carabidae, Perigonini).

PubMed

Erwin, Terry L

2011-01-01

Information on the single previously described species, Mizotrechus novemstriatus Bates 1872 (type locality: Brazil - Amazonas, Tefé), is updated and 17 new species for the genus from Nicaragua, Costa Rica, Panamá, Colombia, Venezuela, and Guyane are described. The species records in the literature and on determined specimens in some collections of Mizotrechus novemstriatus Bates from Central America are not that species; currently, Mizotrechus novemstriatus is known only from its type locality in Amazonian Brazil. For the new species described, their known general distributions are as follows: Mizotrechus batesisp. n. (Guyane), Mizotrechus bellorumsp. n. (Guyane), Mizotrechus bruleisp. n. (Guyane), Mizotrechus belevederesp. n. (Guyane), Mizotrechus costaricensissp. n. (Costa Rica), Mizotrechus dalensisp. n. (Guyane), Mizotrechus edithpiafaesp. n. (provenance unknown), Mizotrechus fortunensissp. n. (Panamá), Mizotrechus gorgona. sp. n. (Colombia), Mizotrechus grossussp. n. (Guyane), Mizotrechus jefesp. n. (Panamá), Mizotrechus marielaforetaesp. n. (Guyane), Mizotrechus minutussp. n. (Guyane), Mizotrechus neblinensissp. n. (Guyane, Venezuela), Mizotrechus poirierisp. n. (Guyane), and Mizotrechus woldaisp. n. (Panamá). Long-term use of flight intercept traps in Guyane provided so many new species that apparently the use of FITs is the way to collect adults of this taxon, previously known from very few specimens. Many more species of this genus can be expected to be discovered throughout the Neotropics; the present contribution is a preliminary synopsis with identification key and adult images of all known species. Likely numerous species are yet to be discovered throughout tropical climes.

Revision of the Massarineae (Pleosporales, Dothideomycetes)

PubMed Central

Tanaka, K.; Hirayama, K.; Yonezawa, H.; Sato, G.; Toriyabe, A.; Kudo, H.; Hashimoto, A.; Matsumura, M.; Harada, Y.; Kurihara, Y.; Shirouzu, T.; Hosoya, T.

2015-01-01

We here taxonomically revise the suborder Massarineae (Pleosporales, Dothideomycetes, Ascomycota). Sequences of SSU and LSU nrDNA and the translation elongation factor 1-alpha gene (tef1) are newly obtained from 106 Massarineae taxa that are phylogenetically analysed along with published sequences of 131 taxa in this suborder retrieved from GenBank. We recognise 12 families and five unknown lineages in the Massarineae. Among the nine families previously known, the monophyletic status of the Dictyosporiaceae, Didymosphaeriaceae, Latoruaceae, Macrodiplodiopsidaceae, Massarinaceae, Morosphaeriaceae, and Trematosphaeriaceae was strongly supported with bootstrap support values above 96 %, while the clades of the Bambusicolaceae and the Lentitheciaceae are moderately supported. Two new families, Parabambusicolaceae and Sulcatisporaceae, are proposed. The Parabambusicolaceae is erected to accommodate Aquastroma and Parabambusicola genera nova, as well as two unnamed Monodictys species. The Parabambusicolaceae is characterised by depressed globose to hemispherical ascomata with or without surrounding stromatic tissue, and multi-septate, clavate to fusiform, hyaline ascospores. The Sulcatisporaceae is established for Magnicamarosporium and Sulcatispora genera nova and Neobambusicola. The Sulcatisporaceae is characterised by subglobose ascomata with a short ostiolar neck, trabeculate pseudoparaphyses, clavate asci, broadly fusiform ascospores, and ellipsoid to subglobose conidia with or without striate ornamentation. The genus Periconia and its relatives are segregated from the Massarinaceae and placed in a resurrected family, the Periconiaceae. We have summarised the morphological and ecological features, and clarified the accepted members of each family. Ten new genera, 22 new species, and seven new combinations are described and illustrated. The complete ITS sequences of nrDNA are also provided for all new taxa for use as barcode markers. PMID:26955201

Endoscopic management of complications of self-expandable metal stents for treatment of malignant esophageal stenosis and tracheoesophageal fistulas.

PubMed

Bor, Renáta; Fábián, Anna; Bálint, Anita; Farkas, Klaudia; Szűcs, Mónika; Milassin, Ágnes; Czakó, László; Rutka, Mariann; Molnár, Tamás; Szepes, Zoltán

2017-08-01

Self-expandable metal stent (SEMS) implantation may rapidly improve the symptoms of malignant esophageal stenosis and tracheoesophageal fistulas (TEF). However, dysphagia often returns subsequently and repeated endoscopic intervention may be necessary. The aims of the study were to identify the risk factors of complications, and the frequency and efficacy of repeated endoscopic interventions; and to provide technical recommendations on appropriate stent selection. We analyzed retrospectively the clinical data of 212 patients with locally advanced esophageal cancer who underwent SEMS implantation. A total of 238 SEMS implantations were performed with 99.06% technical success and 1.26% procedure-related deaths in the enrolled 212 cases. Complications occurred in 84 patients (39.62%) and in 55 cases (25.94%) repeated endoscopic procedures were required. Early reintervention 24-48 h after the stent implantations was necessary due to stent migration (12 cases), arrhythmia (2 cases), intolerable retrosternal pain (1 case) and dyspnea (1 case). An average of 1.98 repeated gastroscopies (range 1-6; median 2), 13.58 weeks (range 1.5-48; median 11) after the stent implantation were performed during the follow-up period: 37 stent repositions, 23 restent implantations, 15 endoscopic esophageal dilations and 7 stent removals. In 48 cases (87.3%) oral feeding of patients was made possible by endoscopic interventions. In a quarter of SEMS implantations, complications occur that can be successfully managed by endoscopic interventions. Our experiences have shown that individualized stent choice may substantially reduce the complications rate and make repeated endoscopic interventions easier.

CFD Analysis to Study Effect of Circular Vortex Generator Placed in Inlet Section to Investigate Heat Transfer Aspects of Solar Air Heater

PubMed Central

Gawande, Vipin B.; Dhoble, A. S.; Zodpe, D. B.

2014-01-01

CFD analysis of 2-dimensional artificially roughened solar air heater duct with additional circular vortex generator, inserted in inlet section is carried out. Circular transverse ribs on the absorber plate are placed as usual. The analysis is done to investigate the effect of inserting additional vortex generator on the heat transfer and flow friction characteristics inside the solar air heater duct. This investigation covers relative roughness pitch in the range of 10 ≤ P/e ≤ 25 and relevant Reynolds numbers in the range of 3800 ≤ Re ≤ 18000. Relative roughness height (e/D) is kept constant as 0.03 for analysis. The turbulence created due to additional circular vortex generator increases the heat transfer rate and at the same time there is also increase in friction factor values. For combined arrangement of ribs and vortex generator, maximum Nusselt number is found to be 2.05 times that of the smooth duct. The enhancement in Nusselt number with ribs and additional vortex generator is found to be 1.06 times that of duct using ribs alone. The maximum increase in friction factor with ribs and circular vortex generator is found to be 2.91 times that of the smooth duct. Friction factor in a combined arrangement is 1.114 times that in a duct with ribs alone on the absorber plate. The augmentation in Thermal Enhancement Factor (TEF) with vortex generator in inlet section is found to be 1.06 times more than with circular ribs alone on the absorber plate. PMID:25254251

Structure-Activity Relationship Studies Using Natural and Synthetic Okadaic Acid/Dinophysistoxin Toxins.

PubMed

Twiner, Michael J; Doucette, Gregory J; Pang, Yucheng; Fang, Chao; Forsyth, Craig J; Miles, Christopher O

2016-11-04

Okadaic acid (OA) and the closely related dinophysistoxins (DTXs) are algal toxins that accumulate in shellfish and are known serine/threonine protein phosphatase (ser/thr PP) inhibitors. Phosphatases are important modulators of enzyme activity and cell signaling pathways. However, the interactions between the OA/DTX toxins and phosphatases are not fully understood. This study sought to identify phosphatase targets and characterize their structure-activity relationships (SAR) with these algal toxins using a combination of phosphatase activity and cytotoxicity assays. Preliminary screening of 21 human and yeast phosphatases indicated that only three ser/thr PPs (PP2a, PP1, PP5) were inhibited by physiologically saturating concentrations of DTX2 (200 nM). SAR studies employed naturally-isolated OA, DTX1, and DTX2, which vary in degree and/or position of methylation, in addition to synthetic 2- epi -DTX2. OA/DTX analogs induced cytotoxicity and inhibited PP activity with a relatively conserved order of potency: OA = DTX1 ≥ DTX2 > 2- epi -DTX. The PPs were also differentially inhibited with sensitivities of PP2a > PP5 > PP1. These findings demonstrate that small variations in OA/DTX toxin structures, particularly at the head region (i.e., C1/C2), result in significant changes in toxicological potency, whereas changes in methylation at C31 and C35 (tail region) only mildly affect potency. In addition to this being the first study to extensively test OA/DTX analogs' activities towards PP5, these data will be helpful for accurately determining toxic equivalence factors (TEFs), facilitating molecular modeling efforts, and developing highly selective phosphatase inhibitors.

Large-spored Alternaria pathogens in section Porri disentangled

PubMed Central

Woudenberg, J.H.C.; Truter, M.; Groenewald, J.Z.; Crous, P.W.

2014-01-01

The omnipresent fungal genus Alternaria was recently divided into 24 sections based on molecular and morphological data. Alternaria sect. Porri is the largest section, containing almost all Alternaria species with medium to large conidia and long beaks, some of which are important plant pathogens (e.g. Alternaria porri, A. solani and A. tomatophila). We constructed a multi-gene phylogeny on parts of the ITS, GAPDH, RPB2, TEF1 and Alt a 1 gene regions, which, supplemented with morphological and cultural studies, forms the basis for species recognition in sect. Porri. Our data reveal 63 species, of which 10 are newly described in sect. Porri, and 27 species names are synonymised. The three known Alternaria pathogens causing early blight on tomato all cluster in one clade, and are synonymised under the older name, A. linariae. Alternaria protenta, a species formerly only known as pathogen on Helianthus annuus, is also reported to cause early blight of potato, together with A. solani and A. grandis. Two clades with isolates causing purple blotch of onion are confirmed as A. allii and A. porri, but the two species cannot adequately be distinguished based on the number of beaks and branches as suggested previously. This is also found among the pathogens of Passifloraceae, which are reduced from four to three species. In addition to the known pathogen of sweet potato, A. bataticola, three more species are delineated of which two are newly described. A new Alternaria section is also described, comprising two large-spored Alternaria species with concatenate conidia. PMID:25492985

Large-spored Alternaria pathogens in section Porri disentangled.

PubMed

Woudenberg, J H C; Truter, M; Groenewald, J Z; Crous, P W

2014-09-01

The omnipresent fungal genus Alternaria was recently divided into 24 sections based on molecular and morphological data. Alternaria sect. Porri is the largest section, containing almost all Alternaria species with medium to large conidia and long beaks, some of which are important plant pathogens (e.g. Alternaria porri, A. solani and A. tomatophila). We constructed a multi-gene phylogeny on parts of the ITS, GAPDH, RPB2, TEF1 and Alt a 1 gene regions, which, supplemented with morphological and cultural studies, forms the basis for species recognition in sect. Porri. Our data reveal 63 species, of which 10 are newly described in sect. Porri, and 27 species names are synonymised. The three known Alternaria pathogens causing early blight on tomato all cluster in one clade, and are synonymised under the older name, A. linariae. Alternaria protenta, a species formerly only known as pathogen on Helianthus annuus, is also reported to cause early blight of potato, together with A. solani and A. grandis. Two clades with isolates causing purple blotch of onion are confirmed as A. allii and A. porri, but the two species cannot adequately be distinguished based on the number of beaks and branches as suggested previously. This is also found among the pathogens of Passifloraceae, which are reduced from four to three species. In addition to the known pathogen of sweet potato, A. bataticola, three more species are delineated of which two are newly described. A new Alternaria section is also described, comprising two large-spored Alternaria species with concatenate conidia.

Methods of Constructing a Blended Performance Function Suitable for Formation Flight

NASA Technical Reports Server (NTRS)

Ryan, John J.

2017-01-01

This paper presents two methods for constructing an approximate performance function of a desired parameter using correlated parameters. The methods are useful when real-time measurements of a desired performance function are not available to applications such as extremum-seeking control systems. The first method approximates an a priori measured or estimated desired performance function by combining real-time measurements of readily available correlated parameters. The parameters are combined using a weighting vector determined from a minimum-squares optimization to form a blended performance function. The blended performance function better matches the desired performance function mini- mum than single-measurement performance functions. The second method expands upon the first by replacing the a priori data with near-real-time measurements of the desired performance function. The resulting blended performance function weighting vector is up- dated when measurements of the desired performance function are available. Both methods are applied to data collected during formation- flight-for-drag-reduction flight experiments.

Comparison of genetic algorithms with conjugate gradient methods

NASA Technical Reports Server (NTRS)

Bosworth, J. L.; Foo, N. Y.; Zeigler, B. P.

1972-01-01

Genetic algorithms for mathematical function optimization are modeled on search strategies employed in natural adaptation. Comparisons of genetic algorithms with conjugate gradient methods, which were made on an IBM 1800 digital computer, show that genetic algorithms display superior performance over gradient methods for functions which are poorly behaved mathematically, for multimodal functions, and for functions obscured by additive random noise. Genetic methods offer performance comparable to gradient methods for many of the standard functions.

On computing closed forms for summations. [polynomials and rational functions

NASA Technical Reports Server (NTRS)

Moenck, R.

1977-01-01

The problem of finding closed forms for a summation involving polynomials and rational functions is considered. A method closely related to Hermite's method for integration of rational functions derived. The method expresses the sum of a rational function as a rational function part and a transcendental part involving derivatives of the gamma function.

Alzheimer Classification Using a Minimum Spanning Tree of High-Order Functional Network on fMRI Dataset

PubMed Central

Guo, Hao; Liu, Lei; Chen, Junjie; Xu, Yong; Jie, Xiang

2017-01-01

Functional magnetic resonance imaging (fMRI) is one of the most useful methods to generate functional connectivity networks of the brain. However, conventional network generation methods ignore dynamic changes of functional connectivity between brain regions. Previous studies proposed constructing high-order functional connectivity networks that consider the time-varying characteristics of functional connectivity, and a clustering method was performed to decrease computational cost. However, random selection of the initial clustering centers and the number of clusters negatively affected classification accuracy, and the network lost neurological interpretability. Here we propose a novel method that introduces the minimum spanning tree method to high-order functional connectivity networks. As an unbiased method, the minimum spanning tree simplifies high-order network structure while preserving its core framework. The dynamic characteristics of time series are not lost with this approach, and the neurological interpretation of the network is guaranteed. Simultaneously, we propose a multi-parameter optimization framework that involves extracting discriminative features from the minimum spanning tree high-order functional connectivity networks. Compared with the conventional methods, our resting-state fMRI classification method based on minimum spanning tree high-order functional connectivity networks greatly improved the diagnostic accuracy for Alzheimer's disease. PMID:29249926

Functional Parallel Factor Analysis for Functions of One- and Two-dimensional Arguments.

PubMed

Choi, Ji Yeh; Hwang, Heungsun; Timmerman, Marieke E

2018-03-01

Parallel factor analysis (PARAFAC) is a useful multivariate method for decomposing three-way data that consist of three different types of entities simultaneously. This method estimates trilinear components, each of which is a low-dimensional representation of a set of entities, often called a mode, to explain the maximum variance of the data. Functional PARAFAC permits the entities in different modes to be smooth functions or curves, varying over a continuum, rather than a collection of unconnected responses. The existing functional PARAFAC methods handle functions of a one-dimensional argument (e.g., time) only. In this paper, we propose a new extension of functional PARAFAC for handling three-way data whose responses are sequenced along both a two-dimensional domain (e.g., a plane with x- and y-axis coordinates) and a one-dimensional argument. Technically, the proposed method combines PARAFAC with basis function expansion approximations, using a set of piecewise quadratic finite element basis functions for estimating two-dimensional smooth functions and a set of one-dimensional basis functions for estimating one-dimensional smooth functions. In a simulation study, the proposed method appeared to outperform the conventional PARAFAC. We apply the method to EEG data to demonstrate its empirical usefulness.

Meshless Local Petrov-Galerkin Euler-Bernoulli Beam Problems: A Radial Basis Function Approach

NASA Technical Reports Server (NTRS)

Raju, I. S.; Phillips, D. R.; Krishnamurthy, T.

2003-01-01

A radial basis function implementation of the meshless local Petrov-Galerkin (MLPG) method is presented to study Euler-Bernoulli beam problems. Radial basis functions, rather than generalized moving least squares (GMLS) interpolations, are used to develop the trial functions. This choice yields a computationally simpler method as fewer matrix inversions and multiplications are required than when GMLS interpolations are used. Test functions are chosen as simple weight functions as in the conventional MLPG method. Compactly and noncompactly supported radial basis functions are considered. The non-compactly supported cubic radial basis function is found to perform very well. Results obtained from the radial basis MLPG method are comparable to those obtained using the conventional MLPG method for mixed boundary value problems and problems with discontinuous loading conditions.

Development of recombinant Yarrowia lipolytica producing virus-like particles of a fish nervous necrosis virus.

PubMed

Luu, Van-Trinh; Moon, Hye Yun; Hwang, Jee Youn; Kang, Bo-Kyu; Kang, Hyun Ah

2017-08-01

Nervous necrosis virus (NNV) causes viral encephalopathy and retinopathy, a devastating disease of many species of cultured marine fish worldwide. In this study, we used the dimorphic non-pathogenic yeast Yarrowia lipolytica as a host to express the capsid protein of red-spotted grouper nervous necrosis virus (RGNNV-CP) and evaluated its potential as a platform for vaccine production. An initial attempt was made to express the codon-optimized synthetic genes encoding intact and N-terminal truncated forms of RGNNV-CP under the strong constitutive TEF1 promoter using autonomously replicating sequence (ARS)-based vectors. The full-length recombinant capsid proteins expressed in Y. lipolytica were detected not only as monomers and but also as trimers, which is a basic unit for formation of NNV virus-like particles (VLPs). Oral immunization of mice with whole recombinant Y. lipolytica harboring the ARS-based plasmids was shown to efficiently induce the formation of IgG against RGNNV-CP. To increase the number of integrated copies of the RGNNV-CP expression cassette, a set of 26S ribosomal DNA-based multiple integrative vectors was constructed in combination with a series of defective Ylura3 with truncated promoters as selection markers, resulting in integrants harboring up to eight copies of the RGNNV-CP cassette. Sucrose gradient centrifugation and transmission electron microscopy of this high-copy integrant were carried out to confirm the expression of RGNNV-CPs as VLPs. This is the first report on efficient expression of viral capsid proteins as VLPs in Y. lipolytica, demonstrating high potential for the Y. lipolytica expression system as a platform for recombinant vaccine production based on VLPs.

Gpd1 and Gpd2 Fine-Tuning for Sustainable Reduction of Glycerol Formation in Saccharomyces cerevisiae▿

PubMed Central

Hubmann, Georg; Guillouet, Stephane; Nevoigt, Elke

2011-01-01

Gpd1 and Gpd2 are the two isoforms of glycerol 3-phosphate dehydrogenase (GPDH), which is the rate-controlling enzyme of glycerol formation in Saccharomyces cerevisiae. The two isoenzymes play crucial roles in osmoregulation and redox balancing. Past approaches to increase ethanol yield at the cost of reduced glycerol yield have most often been based on deletion of either one or two isogenes (GPD1 and GPD2). While single deletions of GPD1 or GPD2 reduced glycerol formation only slightly, the gpd1Δ gpd2Δ double deletion strain produced zero glycerol but showed an osmosensitive phenotype and abolished anaerobic growth. Our current approach has sought to generate “intermediate” phenotypes by reducing both isoenzyme activities without abolishing them. To this end, the GPD1 promoter was replaced in a gpd2Δ background by two lower-strength TEF1 promoter mutants. In the same manner, the activity of the GPD2 promoter was reduced in a gpd1Δ background. The resulting strains were crossed to obtain different combinations of residual GPD1 and GPD2 expression levels. Among our engineered strains we identified four candidates showing improved ethanol yields compared to the wild type. In contrast to a gpd1Δ gpd2Δ double-deletion strain, these strains were able to completely ferment the sugars under quasi-anaerobic conditions in both minimal medium and during simultaneous saccharification and fermentation (SSF) of liquefied wheat mash (wheat liquefact). This result implies that our strains can tolerate the ethanol concentration at the end of the wheat liquefact SSF (up to 90 g liter−1). Moreover, a few of these strains showed no significant reduction in osmotic stress tolerance compared to the wild type. PMID:21724879

Structure–Activity Relationship Studies Using Natural and Synthetic Okadaic Acid/Dinophysistoxin Toxins

PubMed Central

Twiner, Michael J.; Doucette, Gregory J.; Pang, Yucheng; Fang, Chao; Forsyth, Craig J.; Miles, Christopher O.

2016-01-01

Okadaic acid (OA) and the closely related dinophysistoxins (DTXs) are algal toxins that accumulate in shellfish and are known serine/threonine protein phosphatase (ser/thr PP) inhibitors. Phosphatases are important modulators of enzyme activity and cell signaling pathways. However, the interactions between the OA/DTX toxins and phosphatases are not fully understood. This study sought to identify phosphatase targets and characterize their structure–activity relationships (SAR) with these algal toxins using a combination of phosphatase activity and cytotoxicity assays. Preliminary screening of 21 human and yeast phosphatases indicated that only three ser/thr PPs (PP2a, PP1, PP5) were inhibited by physiologically saturating concentrations of DTX2 (200 nM). SAR studies employed naturally-isolated OA, DTX1, and DTX2, which vary in degree and/or position of methylation, in addition to synthetic 2-epi-DTX2. OA/DTX analogs induced cytotoxicity and inhibited PP activity with a relatively conserved order of potency: OA = DTX1 ≥ DTX2 >> 2-epi-DTX. The PPs were also differentially inhibited with sensitivities of PP2a > PP5 > PP1. These findings demonstrate that small variations in OA/DTX toxin structures, particularly at the head region (i.e., C1/C2), result in significant changes in toxicological potency, whereas changes in methylation at C31 and C35 (tail region) only mildly affect potency. In addition to this being the first study to extensively test OA/DTX analogs’ activities towards PP5, these data will be helpful for accurately determining toxic equivalence factors (TEFs), facilitating molecular modeling efforts, and developing highly selective phosphatase inhibitors. PMID:27827901

The genus Parasola in Pakistan with the description of two new species

PubMed Central

Hussain, Shah; Ahmad, Habib; Ullah, Sadiq; Afshan, Najam-Ul-Sehar; Pfister, Donald H.; Sher, Hassan; Ali, Haidar; Khalid, Abdul N.

2018-01-01

Abstract Parasola is a genus of small, veil-less coprinoid mushrooms in the family Psathyrellaceae (Agaricales). The genus is not well documented in Asia, specifically in Pakistan. In this study we describe two new species Parasola glabra and P. pseudolactea from Pakistan, based on morphological and molecular data. Phylogeny based on three DNA regions: nuc rDNA region encompassing the internal transcribed spacers 1 and 2 along with the 5.8S rDNA (ITS), nuc 28S rDNA D1-D2 domains (28S) and translation elongation factor 1α gene (TEF1α) show that the new taxa are clustered in a clade formed by the members of section Parasola of genus Parasola. Parasola glabra with grayish pileus, slightly depressed pileal disc, lamellae separated from the stipe by pseudocollarium, basidiospores 14.5–16.5 × 9.5–11.5 × 8.0–10.5 µm, in front view broadly ovoid to oblong, some with rhomboidal outline, in side view ellipsoid, with eccentric germ-pore of 1.5 µm diameter. Parasola pseudolactea with yellowish brown to dull brown pileus, disc indistinctly umbonate, lamellae free, pseudocollarium absent, basidiospores 13.5–14.5 × 10.5–12.0 × 9.5–10.5 µm, in face view rounded triangular to heart shaped, rarely ovoid to subglobose, in side view ellipsoid to oblong, with eccentric germ-pore of 1.5 µm diam. In addition to these new species, P. auricoma and P. lilatincta were also studied. Morphological descriptions for the new species and comparison with known Parasola species are provided. Our observations highlight the diversity of Parasola in northern Pakistan and further document the need for additional systematic focus on the region’s fungi. PMID:29681732

Effects of 3,3′,4,4′,5-pentachlorobiphenyl (PCB 126) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) injected into the yolks of chicken (Gallus domesticus) eggs prior to incubation

USGS Publications Warehouse

Powell, D.C.; Aulerich, R.J.; Meadows, J.C.; Tillitt, D.E.; Giesy, J.P.; Stromborg, K.L.; Bursian, S.J.

1996-01-01

The yolks of White Leghorn chicken (Gallus domesticus) eggs were injected prior to incubation with either 3,3′,4,4′,5- pentachlorobiphenyl (PCB 126) at doses ranging from 0.1 to 12.8 μg/kg egg or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses ranging from 0.04 to 0.64 μg/kg egg. Chicks were subjected to necropsy within 24 h of hatching. The brain, bursa, heart, liver, and spleen were removed and weighed. Assessment of the rate of hatching indicated an LD50±S.E. of 2.3±0.19 μg/kg egg (7.1±0.58 nmol/kg egg) for PCB 126 and 0.15±0.012 μg/kg egg (0.47±0.037 nmol/kg egg) for TCDD. No significant differences in the incidence of developmental abnormalities (structural defects and edema) were observed in TCDD-exposed embryos, while PCB 126 caused significantly more developmental abnormalities at 3.2, 6.4, and 12.8 μg/kg egg than the vehicle control. PCB 126 caused lower hatchling weights and greater relative brain, heart, and liver weights when compared to the vehicle control group at a dose of 3.2 μg/kg egg which is greater than the LD50. TCDD at 0.08 μg/kg egg caused relative bursa weights to be less than those of the vehicle control. A toxic equivalency factor (TEF) of 0.07 was determined for PCB 126 in relation to TCDD based on overt lethality.

Polychlorinated dibenzo-p-dioxins, dibenzofurans, biphenyls and 2,3,7,8-tetrachlorodibenzo-p-dioxin equivalents in fishes from Saginaw Bay, Michigan

USGS Publications Warehouse

Giesy, John P.; Jude, David J.; Tillitt, Donald E.; Gale, Robert W.; Meadows, John C.; Zajieck, James L.; Peterman, Paul H.; Verbrugge, David A.; Sanderson, J. Thomas; Schwartz, Ted R.; Tuchman, Marc L.

1997-01-01

Concentrations of polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), polychlorinated naphthalenes (PCNs), polychlorinated dibenzothiophenes (PCDTs), and 2,3,7,8-tetrachlo-rodibenzo-p-dioxin (2,3,7,8-TCDD) equivalents were measured in composite samples of forage fishes and several sizes of walleyes (Stizostedion vitreum) and common carp (Cyprinus carpio) collected from Saginaw Bay, Michigan, USA. The concentrations of 2,3,7,8-TCDD equivalents determined from the use of TCDD equivalency factors (TEFs) and instrumentally determined concentrations of individual congeners were designated TEq. The 2,3,7,8-TCDD equivalents determined on the same extracts with the H4IIE bioassay were defined as TCDD-EQ. Concentrations of TCDD-EQ and TEq were significantly, but poorly correlated (R2 = 0.44). Concentrations of TCDD-EQ and TEq ranged from 10.6 to 348 and 13.5 to 69.5 ng/kg, wet weight, respectively. The ratio of TCDD-EQ to TEq ranged from 0.5 to 5.0, with the greatest ratio observed in common carp but the average ratio between TEq and TCDD-EQ was approximately 1.0. In common carp, larger walleye, and medium-sized alewife (Alosa pseudoharengus) there were significant concentrations of TCDD-EQ that could not be accounted for by TEq calculated from an additive model of PCBs, PCDDs, or PCDFs. As much as 75% of the TCDD-EQ in some samples could not be accounted for by TEqs. It is unlikely that PCNs, PCDTs, or polychlorinated diphenyl ethers (PCDEs) occurred at concentrations that were, based on their relative potencies, great enough to contribute significant quantities of TCDD-EQ. The discrepency between TCDD-EQs and TEqs was not due to antagonisms among congeners or extraction efficiencies.

Cloning and characterization of the mouse alpha1C/A-adrenergic receptor gene and analysis of an alpha1C promoter in cardiac myocytes: role of an MCAT element that binds transcriptional enhancer factor-1 (TEF-1).

PubMed

O'Connell, T D; Rokosh, D G; Simpson, P C

2001-05-01

alpha1-Adrenergic receptor (AR) subtypes in the heart are expressed by myocytes but not by fibroblasts, a feature that distinguishes alpha1-ARs from beta-ARs. Here we studied myocyte-specific expression of alpha1-ARs, focusing on the subtype alpha1C (also called alpha1A), a subtype implicated in cardiac hypertrophic signaling in rat models. We first cloned the mouse alpha1C-AR gene, which consisted of two exons with an 18 kb intron, similar to the alpha1B-AR gene. The receptor coding sequence was >90% homologous to that of rat and human. alpha1C-AR transcription in mouse heart was initiated from a single Inr consensus sequence at -588 from the ATG; this and a putative polyadenylation sequence 8.5 kb 3' could account for the predominant 11 kb alpha1C mRNA in mouse heart. A 5'-nontranscribed fragment of 4.4 kb was active as a promoter in cardiac myocytes but not in fibroblasts. Promoter activity in myocytes required a single muscle CAT (MCAT) element, and this MCAT bound in vitro to recombinant and endogenous transcriptional enhancer factor-1. Thus, alpha1C-AR transcription in cardiac myocytes shares MCAT dependence with other cardiac-specific genes, including the alpha- and beta-myosin heavy chains, skeletal alpha-actin, and brain natriuretic peptide. However, the mouse alpha1C gene was not transcribed in the neonatal heart and was not activated by alpha1-AR and other hypertrophic agonists in rat myocytes, and thus differed from other MCAT-dependent genes and the rat alpha1C gene.

Source identification and seasonal variation of polycyclic aromatic hydrocarbons associated with atmospheric fine and coarse particles in the Metropolitan Area of Porto Alegre, RS, Brazil

NASA Astrophysics Data System (ADS)

Teixeira, Elba Calesso; Agudelo-Castañeda, Dayana M.; Fachel, Jandyra Maria Guimarães; Leal, Karen Alam; Garcia, Karine de Oliveira; Wiegand, Flavio

2012-11-01

The purpose of the present study was to evaluate the polycyclic aromatic hydrocarbons (PAHs) in fine (PM2.5) and coarse particles (PM2.5-10) in an urban and industrial area in the Metropolitan Area of Porto Alegre (MAPA), Brazil. Sixteen U.S. Environmental Protection Agency (EPA) priority polycyclic aromatic hydrocarbons (PAHs) were measured. Filters containing ambient air particulate were extracted with dichloromethane using Soxhlet. Extracts were later analyzed, for determining PAH concentrations, using a gaseous chromatograph coupled with a mass spectrometer (GC-MS). The polycyclic aromatic hydrocarbons (PAHs) were more concentrated in PM2.5 with an average of 70% of total PAHs in the MAPA. The target PAH apportionment among the main emission sources was carried out by diagnostic PAH concentration ratios, and principal component analysis (PCA). PAHs with higher molecular weight showed higher percentages in the fine particles in the MAPA. Based on the diagnostic ratios and PCA analysis, it may be concluded that the major contribution of PAHs was from vehicular sources (diesel and gasoline), especially in the PM2.5 fraction, as well as coal and wood burning. The winter/summer ratio in the PM2.5 and PM2.5-10 fractions in the MAPA was 3.1 and 1.8, respectively, revealing the seasonal variation of PAHs in the two fractions. The estimated toxicity equivalent factor (TEF), used to assess the contribution of the carcinogenic potency, confirms a significant presence of the moderately active carcinogenic PAHs BaP and DahA in the samples collected in the MAPA.

Short-term temperature-dependent air-surface exchange and atmospheric concentrations of polychlorinated naphthalenes and organochlorine pesticides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, R.G.M.; Burnett, V.; Harner, T.

2000-02-01

Atmospheric concentrations of five organochlorine (OC) pesticides, some of which have been banned for a number of years, and polychlorinated naphthalenes (PCNs) were measured at a U.K. site over periods of 6 h for 7 days resulting in 28 samples. Mean concentrations of the pesticides were {alpha}-HCH 90 pg m{sup {minus}3}, {gamma}-HCH 500, {rho},{rho}{prime}-DDE 8, dieldrin 63, endrin 22, and HCB 39. PCN mean homologue concentrations were {sub 3}CNs 67 pg m{sup {minus}3}, {sub 4}CNs 78, {sub 5}CNs 5, {sub 6}CNs 0.6, {sub 7}CNs 0.6, and {Sigma}PCNs 152. TEQ concentrations for those PCNs ascribed TEF values ranged between 0.36 andmore » 3.6 fg m{sup {minus}3} which corresponds to {approximately}3.0--30% of the TEQ concentrations of PCDD/Fs at the same site. All the compounds measured, except HCB, exhibited a strong temperature-dependent diurnal cycling. Results from Clausius-Clapeyron plots show that pesticide concentrations were controlled by temperature-driven air-surface recycling throughout the first 5 days when stable atmospheric conditions were dominant, while during the last 2 days advection became more influential as more unstable and cooler weather started to influence the site. PCN concentrations were controlled primarily by a mixture of recycling and advection throughout the first 5 days and then by advection in the final 2 days, suggesting that there are ongoing emissions from diffuse point sources of PCNs into the U.K. atmosphere. This study provides further evidence of the rapid air-surface exchange of semivolatile organic compounds (SOCs) and shows how different factors alone or in combination can produce rapid changes in the atmospheric concentrations of past and present SOCs.« less

Rainforest understory beetles of the Neotropics, Mizotrechus Bates 1872, a generic synopsis with descriptions of new species from Central America and northern South America (Coleoptera, Carabidae, Perigonini)

PubMed Central

Erwin, Terry L.

2011-01-01

Abstract Information on the single previously described species, Mizotrechus novemstriatus Bates 1872 (type locality: Brazil – Amazonas, Tefé), is updated and 17 new species for the genus from Nicaragua, Costa Rica, Panamá, Colombia, Venezuela, and Guyane are described. The species records in the literature and on determined specimens in some collections of Mizotrechus novemstriatus Bates from Central America are not that species; currently, Mizotrechus novemstriatus is known only from its type locality in Amazonian Brazil. For the new species described, their known general distributions are as follows: Mizotrechus batesi sp. n. (Guyane), Mizotrechus bellorum sp. n. (Guyane), Mizotrechus brulei sp. n. (Guyane), Mizotrechus belevedere sp. n. (Guyane), Mizotrechus costaricensis sp. n. (Costa Rica), Mizotrechus dalensi sp. n. (Guyane), Mizotrechus edithpiafae sp. n. (provenance unknown), Mizotrechus fortunensis sp. n. (Panamá), Mizotrechus gorgona. sp. n. (Colombia), Mizotrechus grossus sp. n. (Guyane), Mizotrechus jefe sp. n. (Panamá), Mizotrechus marielaforetae sp. n. (Guyane), Mizotrechus minutus sp. n. (Guyane), Mizotrechus neblinensis sp. n. (Guyane, Venezuela), Mizotrechus poirieri sp. n. (Guyane), and Mizotrechus woldai sp. n. (Panamá). Long-term use of flight intercept traps in Guyane provided so many new species that apparently the use of FITs is the way to collect adults of this taxon, previously known from very few specimens. Many more species of this genus can be expected to be discovered throughout the Neotropics; the present contribution is a preliminary synopsis with identification key and adult images of all known species. Likely numerous species are yet to be discovered throughout tropical climes. PMID:22287885

Teff, an Orphan Cereal in the Chloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses.

PubMed

Zhang, Wei; Xu, Jianhong; Bennetzen, Jeffrey L; Messing, Joachim

2016-06-13

Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae, where the genome of teff (Eragrostis tef) has been sequenced. We find gene duplications, deletions, and rapid mutations in protein-coding sequences. The main SSPs in teff, like other grasses, are prolamins, here called eragrostins. Teff has γ- and δ-prolamins, but has no β-prolamins. One δ-type prolamin (δ1) in teff has higher methionine (33%) levels than in maize (23-25%). The other δ-type prolamin (δ2) has reduced methionine residues (<10%) and is phylogenetically closer to α prolamins. Prolamin δ2 in teff represents an intermediate between δ and α types that appears to have been lost in maize and other Panicoideae, and was replaced by the expansion of α-prolamins. Teff also has considerably larger numbers of α-prolamin genes, which we further divide into five sub-groups, where α2 and α5 represent the most abundant α-prolamins both in number and in expression. In addition, indolines that determine kernel softness are present in teff and the panicoid cereal called foxtail millet (Setaria italica) but not in sorghum or maize, indicating that these genes were only recently lost in some members of the Panicoideae Moreover, this study provides not only information on the evolution of SSPs in the grass family but also the importance of α-globulins in protein aggregation and germplasm divergence. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Atan1p-an extracellular tannase from the dimorphic yeast Arxula adeninivorans: molecular cloning of the ATAN1 gene and characterization of the recombinant enzyme.

PubMed

Böer, Erik; Bode, Rüdiger; Mock, Hans-Peter; Piontek, Michael; Kunze, Gotthard

2009-06-01

The tannase-encoding Arxula adeninivorans gene ATAN1 was isolated from genomic DNA by PCR, using as primers oligonucleotide sequences derived from peptides obtained after tryptic digestion of the purified tannase protein. The gene harbours an ORF of 1764 bp, encoding a 587-amino acid protein, preceded by an N-terminal secretion sequence comprising 28 residues. The deduced amino acid sequence was similar to those of tannases from Aspergillus oryzae (50% identity), A. niger (48%) and putative tannases from A. fumigatus (52%) and A. nidulans (50%). The sequence contains the consensus pentapeptide motif (-Gly-X-Ser-X-Gly-) which forms part of the catalytic centre of serine hydrolases. Expression of ATAN1 is regulated by the carbon source. Supplementation with tannic acid or gallic acid leads to induction of ATAN1, and accumulation of the native tannase enzyme in the medium. The enzymes recovered from both wild-type and recombinant strains were essentially indistinguishable. A molecular mass of approximately 320 kDa was determined, indicating that the native, glycosylated tannase consists of four identical subunits. The enzyme has a temperature optimum at 35-40 degrees C and a pH optimum at approximately 6.0. The enzyme is able to remove gallic acid from both condensed and hydrolysable tannins. The wild-type strain LS3 secreted amounts of tannase equivalent to 100 U/l under inducing conditions, while the transformant strain, which overexpresses the ATAN1 gene from the strong, constitutively active A. adeninivorans TEF1 promoter, produced levels of up to 400 U/l when grown in glucose medium in shake flasks. Copyright (c) 2009 John Wiley & Sons, Ltd.

Diversifying crops for food and nutrition security - a case of teff.

PubMed

Cheng, Acga; Mayes, Sean; Dalle, Gemedo; Demissew, Sebsebe; Massawe, Festo

2017-02-01

There are more than 50000 known edible plants in the world, yet two-thirds of global plant-derived food is provided by only three major cereals - maize (Zea mays), wheat (Triticum aestivum) and rice (Oryza sativa). The dominance of this triad, now considered truly global food commodities, has led to a decline in the number of crop species contributing to global food supplies. Our dependence on only a few crop species limits our capability to deal with challenges posed by the adverse effects of climate change and the consequences of dietary imbalance. Emerging evidence suggests that climate change will cause shifts in crop production and yield loss due to more unpredictable and hostile weather patterns. One solution to this problem is through the wider use of underutilised (also called orphan or minor) crops to diversify agricultural systems and food sources. In addition to being highly nutritious, underutilised crops are resilient in natural and agricultural conditions, making them a suitable surrogate to the major crops. One such crop is teff [Eragrostis tef (Zucc.) Trotter], a warm-season annual cereal with the tiniest grain in the world. Native to Ethiopia and often the sustenance for local small farmers, teff thrives in both moisture-stressed and waterlogged soil conditions, making it a dependable staple within and beyond its current centre of origin. Today, teff is deemed a healthy wheat alternative in the West and is sought-after by health aficionados and those with coeliac disease or gluten sensitivity. The blooming market for healthy food is breathing new life into this underutilised crop, which has received relatively limited attention from mainstream research perhaps due to its 'orphan crop' status. This review presents the past, present and future of an ancient grain with a potential beyond its size. © 2015 Cambridge Philosophical Society.

Benchmark dose and the three Rs. Part I. Getting more information from the same number of animals.

PubMed

Slob, Wout

2014-08-01

Evaluating dose-response data using the Benchmark dose (BMD) approach rather than by the no observed adverse effect (NOAEL) approach implies a considerable step forward from the perspective of the Reduction, Replacement, and Refinement, three Rs, in particular the R of reduction: more information is obtained from the same number of animals, or, vice versa, similar information may be obtained from fewer animals. The first part of this twin paper focusses on the former, the second on the latter aspect. Regarding the former, the BMD approach provides more information from any given dose-response dataset in various ways. First, the BMDL (= BMD lower confidence bound) provides more information by its more explicit definition. Further, as compared to the NOAEL approach the BMD approach results in more statistical precision in the value of the point of departure (PoD), for deriving exposure limits. While part of the animals in the study do not directly contribute to the numerical value of a NOAEL, all animals are effectively used and do contribute to a BMDL. In addition, the BMD approach allows for combining similar datasets for the same chemical (e.g., both sexes) in a single analysis, which further increases precision. By combining a dose-response dataset with similar historical data for other chemicals, the precision can even be substantially increased. Further, the BMD approach results in more precise estimates for relative potency factors (RPFs, or TEFs). And finally, the BMD approach is not only more precise, it also allows for quantification of the precision in the BMD estimate, which is not possible in the NOAEL approach.

Mink biomagnification factors for dioxin-like compounds fed Saginaw Bay carp

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kubiak, T.J.; Tillitt, D.E.; Heaton, S.N.

1994-12-31

Diets containing 0, 10, 20 and 40% Saginaw Bay carp were fed to ranch mink to assess reproductive effects. All carp diets adversely affected reproduction. The diets and livers of the adult mink at the end of the study were chemically analyzed for planar halogenated hydrocarbons (PHHS) that induce aryl hydrocarbon hydroxylase (AHH)/ethoxyresorufin o-deethylase (EROD). Biomagnification factors (BMFS) from diets to mink livers were calculated. AHH and EROD-active PCB congeners uniformly magnified across diets except for PCB 126, which had higher magnification at lowest carp and control diets. PCB and PCDF congener magnification ranged from incalculable to 60-fold higher andmore » individual PCDDs ranged from incalculable to 165 times the diet. As expected from previous mammalian studies, 2378-TCDD magnified over an order of magnitude more than 2378-TCDF but by 4 to 5-fold less than 23478-PCDF. Based on dioxin equivalents theory and TEFS, PCB 126 ranked first in the liver residues of 2378-TCDD equivalents followed by PCB 105, 23478-PCDF and 2378-TCDD. Magnification factors allow for interpretation of relative exposure risks from certain wild forage species if wild mink liver concentrations are known. Conversely, knowledge of wild mink forage item concentrations allows for calculation of an estimated wild mink liver residue, when the concentration and dietary forage percentage are multiplied by the BMF. Therefore, BMFs can assist in the elucidation of relative risk of a population to these contaminants without necessarily having large numbers of mink samples, especially in habitats such as the Saginaw Bay area where mink and otter populations are presumed to be affected by high PHH contamination.« less

Tocotrienols promote apoptosis in human breast cancer cells by inducing poly(ADP-ribose) polymerase cleavage and inhibiting nuclear factor kappa-B activity.

PubMed

Loganathan, R; Selvaduray, K R; Nesaretnam, K; Radhakrishnan, A K

2013-04-01

Tocotrienols and tocopherols are members of the vitamin E family, with similar structures; however, only tocotrienols have been reported to achieve potent anti-cancer effects. The study described here has evaluated anti-cancer activity of vitamin E to elucidate mechanisms of cell death, using human breast cancer cells. Anti-cancer activity of a tocotrienol-rich fraction (TRF) and a tocotrienol-enriched fraction (TEF) isolated from palm oil, as well as pure vitamin E analogues (α-tocopherol, α-, δ- and γ-tocotrienols) were studied using highly aggressive triple negative MDA-MB-231 cells and oestrogen-dependent MCF-7 cells, both of human breast cancer cell lines. Cell population growth was evaluated using a Coulter particle counter. Cell death mechanism, poly(ADP-ribose) polymerase cleavage and levels of NF-κB were determined using commercial ELISA kits. Tocotrienols exerted potent anti-proliferative effects on both types of cell by inducing apoptosis, the underlying mechanism of cell death being ascertained using respective IC50 concentrations of all test compounds. There was marked induction of apoptosis in both cell lines by tocotrienols compared to treatment with Paclitaxel, which was used as positive control. This activity was found to be associated with cleavage of poly(ADP-ribose) polymerase (a DNA repair protein), demonstrating involvement of the apoptotic cell death signalling pathway. Tocotrienols also inhibited expression of nuclear factor kappa-B (NF-κB), which in turn can increase sensitivity of cancer cells to apoptosis. Tocotrienols induced anti-proliferative and apoptotic effects in association with DNA fragmentation, poly(ADP-ribose) polymerase cleavage and NF-κB inhibition in the two human breast cancer cell lines. © 2013 Blackwell Publishing Ltd.

Assessing the inhalation cancer risk of particulate matter bound polycyclic aromatic hydrocarbons (PAHs) for the elderly in a retirement community of a mega city in North China.

PubMed

Han, Bin; Liu, Yating; You, Yan; Xu, Jia; Zhou, Jian; Zhang, Jiefeng; Niu, Can; Zhang, Nan; He, Fei; Ding, Xiao; Bai, Zhipeng

2016-10-01

Assessment of the health risks resulting from exposure to ambient polycyclic aromatic hydrocarbons (PAHs) is limited by the lack of environmental exposure data among different subpopulations. To assess the exposure cancer risk of particulate carcinogenic polycyclic aromatic hydrocarbon pollution for the elderly, this study conducted a personal exposure measurement campaign for particulate PAHs in a community of Tianjin, a city in northern China. Personal exposure samples were collected from the elderly in non-heating (August-September, 2009) and heating periods (November-December, 2009), and 12 PAHs individuals were analyzed for risk estimation. Questionnaire and time-activity log were also recorded for each person. The probabilistic risk assessment model was integrated with Toxic Equivalent Factors (TEFs). Considering that the estimation of the applied dose for a given air pollutant is dependent on the inhalation rate, the inhalation rate from both EPA exposure factor book was applied to calculate the carcinogenic risk in this study. Monte Carlo simulation was used as a probabilistic risk assessment model, and risk simulation results indicated that the inhalation-ILCR values for both male and female subjects followed a lognormal distribution with a mean of 4.81 × 10 -6 and 4.57 × 10 -6 , respectively. Furthermore, the 95 % probability lung cancer risks were greater than the USEPA acceptable level of 10 -6 for both men and women through the inhalation route, revealing that exposure to PAHs posed an unacceptable potential cancer risk for the elderly in this study. As a result, some measures should be taken to reduce PAHs pollution and the exposure level to decrease the cancer risk for the general population, especially for the elderly.

Outbreak of Fusarium oxysporum infections in children with cancer: an experience with 7 episodes of catheter-related fungemia.

PubMed

Carlesse, Fabianne; Amaral, Anna-Paula C; Gonçalves, Sarah S; Xafranski, Hemilio; Lee, Maria-Lucia M; Zecchin, Victor; Petrilli, Antonio S; Al-Hatmi, Abdullah M; Hagen, Ferry; Meis, Jacques F; Colombo, Arnaldo L

2017-01-01

Fusarium species are widely spread in nature as plant pathogens but are also able to cause opportunistic fungal infections in humans. We report a cluster of Fusarium oxysporum bloodstream infections in a single pediatric cancer center. All clinical and epidemiological data related to an outbreak involving seven cases of fungemia by Fusarium oxysporum during October 2013 and February 2014 were analysed. All cultured isolates ( n  = 14) were identified to species level by sequencing of the TEF1 and RPB2 genes. Genotyping of the outbreak isolates was performed by amplified fragment length polymorphism fingerprinting. In a 5-month period 7 febrile pediatric cancer patients were diagnosed with catheter-related Fusarium oxysporum bloodstream infections. In a time span of 11 years, only 6 other infections due to Fusarium were documented and all were caused by a different species, Fusarium solani . None of the pediatric cancer patients had neutropenia at the time of diagnosis and all became febrile within two days after catheter manipulation in a specially designed room. Extensive environmental sampling in this room and the hospital did not gave a clue to the source. The outbreak was terminated after implementation of a multidisciplinary central line insertion care bundle. All Fusarium strains from blood and catheter tips were genetically related by amplified fragment length polymorphism fingerprinting. All patients survived the infection after prompt catheter removal and antifungal therapy. A cluster with, genotypical identical, Fusarium oxysporum strains infecting 7 children with cancer, was most probably catheter-related. The environmental source was not discovered but strict infection control measures and catheter care terminated the outbreak.

Evaluation of the release of dioxins and PCBs during kiln-firing of ball clay.

PubMed

Broadwater, Kendra; Meeker, John D; Luksemburg, William; Maier, Martha; Garabrant, David; Demond, Avery; Franzblau, Alfred

2014-01-01

Ball clay is known to be naturally contaminated with high levels of polychlorinated di-benzo-p-dioxins (PCDDs). This study evaluated the potential for PCDD, polychlorinated dibenzofuran (PCDF) and polychlorinated biphenyl (PCB) release during the kiln firing of ball clay in an art studio. Toxic equivalence (TEQ) were calculated using World Health Organization (WHO) 2005 toxic equivalence factors (TEF) and congener concentrations. Ten bags of commercial ball clay were found to have an average TEQ of 1,370 nanograms/kilogram (ng kg(-1)) dry weight (dw), almost exclusively due to PCDDs (99.98% of TEQ). After firing, none of the 29 dioxin-like analytes was measured above the limits of detection (LOD) in the clay samples. Air samples were taken during firings using both low-flow and high-flow air samplers. Few low-flow air samples contained measurable levels of dioxin congeners above the LOD. The mean TEQ in the high volume air samples ranged from 0.07 pg m(-3) to 0.21 pg m(-3) when firing ball clay, and was 0.11 pg m(-3) when no clay was fired. These concentrations are within the range measured in typical residences and well-controlled industrial settings. The congener profiles in the high-flow air samples differed from the unfired clay; the air samples had a considerable contribution to the TEQ from PCDFs and PCBs. Given that the TEQs of all air samples were very low and the profiles differed from the unfired clay, it is likely that the PCDDs in dry ball clay were destroyed during kiln firing. These results suggest that inhalation of volatilized dioxins during kiln firing of dry ball clay is an unlikely source of exposure for vocational and art ceramicists. Copyright © 2013 Elsevier Ltd. All rights reserved.

Estimating parameter of Rayleigh distribution by using Maximum Likelihood method and Bayes method

NASA Astrophysics Data System (ADS)

Ardianti, Fitri; Sutarman

2018-01-01

In this paper, we use Maximum Likelihood estimation and Bayes method under some risk function to estimate parameter of Rayleigh distribution to know the best method. The prior knowledge which used in Bayes method is Jeffrey’s non-informative prior. Maximum likelihood estimation and Bayes method under precautionary loss function, entropy loss function, loss function-L 1 will be compared. We compare these methods by bias and MSE value using R program. After that, the result will be displayed in tables to facilitate the comparisons.

[Methodological aspects related to the determination of the relative renal function using 99mTC MAG3].

PubMed

Ladrón De Guevara Hernández, D; Ham, H; Franken, P; Piepsz, A; Lobo Sotomayor, G

2002-01-01

The aim of the study was to evaluate three different methods for calculating the split renal function in patients with only one functioning kidney, keeping in mind that the split function should be zero on the side of the non-functioning kidney. We retrospectively selected 28 99mTc MAG3 renograms performed in children, 12 with unilateral nephrectomy, 4 with unilateral agenesis and 12 with a non-functioning kidney. A renal and perirenal region of interest (ROI) were delineated around the functioning kidney. The ROIs around the empty kidney were drawn symmetrically to the contralateral side. The split renal function was calculated using three different methods, the integral method, the slope method and the Patlak-Rutland algorithm. For the whole group of 28 kidneys as well as for the three categories of patients, the three methods provided a split function on the side of the non-functioning kidney close to the zero value, regardless of whether the empty kidney was the left or the right one. We recommend the use of the integral method for the whole range of split renal function with 99mTc MAG3. No significant improvement was obtained by means of the more sophisticated Patlak-Rutland method.

Hip joint center localisation: A biomechanical application to hip arthroplasty population

PubMed Central

Bouffard, Vicky; Begon, Mickael; Champagne, Annick; Farhadnia, Payam; Vendittoli, Pascal-André; Lavigne, Martin; Prince, François

2012-01-01

AIM: To determine hip joint center (HJC) location on hip arthroplasty population comparing predictive and functional approaches with radiographic measurements. METHODS: The distance between the HJC and the mid-pelvis was calculated and compared between the three approaches. The localisation error between the predictive and functional approach was compared using the radiographic measurements as the reference. The operated leg was compared to the non-operated leg. RESULTS: A significant difference was found for the distance between the HJC and the mid-pelvis when comparing the predictive and functional method. The functional method leads to fewer errors. A statistical difference was found for the localization error between the predictive and functional method. The functional method is twice more precise. CONCLUSION: Although being more individualized, the functional method improves HJC localization and should be used in three-dimensional gait analysis. PMID:22919569

Quantum phase space with a basis of Wannier functions

NASA Astrophysics Data System (ADS)

Fang, Yuan; Wu, Fan; Wu, Biao

2018-02-01

A quantum phase space with Wannier basis is constructed: (i) classical phase space is divided into Planck cells; (ii) a complete set of Wannier functions are constructed with the combination of Kohn’s method and Löwdin method such that each Wannier function is localized at a Planck cell. With these Wannier functions one can map a wave function unitarily onto phase space. Various examples are used to illustrate our method and compare it to Wigner function. The advantage of our method is that it can smooth out the oscillations in wave functions without losing any information and is potentially a better tool in studying quantum-classical correspondence. In addition, we point out that our method can be used for time-frequency analysis of signals.

Relationships between the decoupled and coupled transfer functions: Theoretical studies and experimental validation

NASA Astrophysics Data System (ADS)

Wang, Zengwei; Zhu, Ping; Liu, Zhao

2018-01-01

A generalized method for predicting the decoupled transfer functions based on in-situ transfer functions is proposed. The method allows predicting the decoupled transfer functions using coupled transfer functions, without disassembling the system. Two ways to derive relationships between the decoupled and coupled transfer functions are presented. Issues related to immeasurability of coupled transfer functions are also discussed. The proposed method is validated by numerical and experimental case studies.

A review of contemporary methods for the presentation of scientific uncertainty.

PubMed

Makinson, K A; Hamby, D M; Edwards, J A

2012-12-01

Graphic methods for displaying uncertainty are often the most concise and informative way to communicate abstract concepts. Presentation methods currently in use for the display and interpretation of scientific uncertainty are reviewed. Numerous subjective and objective uncertainty display methods are presented, including qualitative assessments, node and arrow diagrams, standard statistical methods, box-and-whisker plots,robustness and opportunity functions, contribution indexes, probability density functions, cumulative distribution functions, and graphical likelihood functions.

Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data.

PubMed

Taugourdeau, Simon; Villerd, Jean; Plantureux, Sylvain; Huguenin-Elie, Olivier; Amiaud, Bernard

2014-04-01

Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete-case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete-case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices.

Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data

PubMed Central

Taugourdeau, Simon; Villerd, Jean; Plantureux, Sylvain; Huguenin-Elie, Olivier; Amiaud, Bernard

2014-01-01

Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete-case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete-case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices. PMID:24772273

Yager’s ranking method for solving the trapezoidal fuzzy number linear programming

NASA Astrophysics Data System (ADS)

Karyati; Wutsqa, D. U.; Insani, N.

2018-03-01

In the previous research, the authors have studied the fuzzy simplex method for trapezoidal fuzzy number linear programming based on the Maleki’s ranking function. We have found some theories related to the term conditions for the optimum solution of fuzzy simplex method, the fuzzy Big-M method, the fuzzy two-phase method, and the sensitivity analysis. In this research, we study about the fuzzy simplex method based on the other ranking function. It is called Yager's ranking function. In this case, we investigate the optimum term conditions. Based on the result of research, it is found that Yager’s ranking function is not like Maleki’s ranking function. Using the Yager’s function, the simplex method cannot work as well as when using the Maleki’s function. By using the Yager’s function, the value of the subtraction of two equal fuzzy numbers is not equal to zero. This condition makes the optimum table of the fuzzy simplex table is undetected. As a result, the simplified fuzzy simplex table becomes stopped and does not reach the optimum solution.

Measuring Spatial Accessibility of Health Care Providers – Introduction of a Variable Distance Decay Function within the Floating Catchment Area (FCA) Method

PubMed Central

Groneberg, David A.

2016-01-01

We integrated recent improvements within the floating catchment area (FCA) method family into an integrated ‘iFCA`method. Within this method we focused on the distance decay function and its parameter. So far only distance decay functions with constant parameters have been applied. Therefore, we developed a variable distance decay function to be used within the FCA method. We were able to replace the impedance coefficient β by readily available distribution parameter (i.e. median and standard deviation (SD)) within a logistic based distance decay function. Hence, the function is shaped individually for every single population location by the median and SD of all population-to-provider distances within a global catchment size. Theoretical application of the variable distance decay function showed conceptually sound results. Furthermore, the existence of effective variable catchment sizes defined by the asymptotic approach to zero of the distance decay function was revealed, satisfying the need for variable catchment sizes. The application of the iFCA method within an urban case study in Berlin (Germany) confirmed the theoretical fit of the suggested method. In summary, we introduced for the first time, a variable distance decay function within an integrated FCA method. This function accounts for individual travel behaviors determined by the distribution of providers. Additionally, the function inherits effective variable catchment sizes and therefore obviates the need for determining variable catchment sizes separately. PMID:27391649

The Relation of Finite Element and Finite Difference Methods

NASA Technical Reports Server (NTRS)

Vinokur, M.

1976-01-01

Finite element and finite difference methods are examined in order to bring out their relationship. It is shown that both methods use two types of discrete representations of continuous functions. They differ in that finite difference methods emphasize the discretization of independent variable, while finite element methods emphasize the discretization of dependent variable (referred to as functional approximations). An important point is that finite element methods use global piecewise functional approximations, while finite difference methods normally use local functional approximations. A general conclusion is that finite element methods are best designed to handle complex boundaries, while finite difference methods are superior for complex equations. It is also shown that finite volume difference methods possess many of the advantages attributed to finite element methods.

The solitary wave solution of coupled Klein-Gordon-Zakharov equations via two different numerical methods

NASA Astrophysics Data System (ADS)

Dehghan, Mehdi; Nikpour, Ahmad

2013-09-01

In this research, we propose two different methods to solve the coupled Klein-Gordon-Zakharov (KGZ) equations: the Differential Quadrature (DQ) and Globally Radial Basis Functions (GRBFs) methods. In the DQ method, the derivative value of a function with respect to a point is directly approximated by a linear combination of all functional values in the global domain. The principal work in this method is the determination of weight coefficients. We use two ways for obtaining these coefficients: cosine expansion (CDQ) and radial basis functions (RBFs-DQ), the former is a mesh-based method and the latter categorizes in the set of meshless methods. Unlike the DQ method, the GRBF method directly substitutes the expression of the function approximation by RBFs into the partial differential equation. The main problem in the GRBFs method is ill-conditioning of the interpolation matrix. Avoiding this problem, we study the bases introduced in Pazouki and Schaback (2011) [44]. Some examples are presented to compare the accuracy and easy implementation of the proposed methods. In numerical examples, we concentrate on Inverse Multiquadric (IMQ) and second-order Thin Plate Spline (TPS) radial basis functions. The variable shape parameter (exponentially and random) strategies are applied in the IMQ function and the results are compared with the constant shape parameter.

A survey of functional behavior assessment methods used by behavior analysts in practice.

PubMed

Oliver, Anthony C; Pratt, Leigh A; Normand, Matthew P

2015-12-01

To gather information about the functional behavior assessment (FBA) methods behavior analysts use in practice, we sent a web-based survey to 12,431 behavior analysts certified by the Behavior Analyst Certification Board. Ultimately, 724 surveys were returned, with the results suggesting that most respondents regularly use FBA methods, especially descriptive assessments. Moreover, the data suggest that the majority of students are being formally taught about the various FBA methods and that educators are emphasizing the range of FBA methods in their teaching. However, less than half of the respondents reported using functional analyses in practice, although many considered descriptive assessments and functional analyses to be the most useful FBA methods. Most respondents reported using informant and descriptive assessments more frequently than functional analyses, and a majority of respondents indicated that they "never" or "almost never" used functional analyses to identify the function of behavior. © Society for the Experimental Analysis of Behavior.

Efficient Bayesian hierarchical functional data analysis with basis function approximations using Gaussian-Wishart processes.

PubMed

Yang, Jingjing; Cox, Dennis D; Lee, Jong Soo; Ren, Peng; Choi, Taeryon

2017-12-01

Functional data are defined as realizations of random functions (mostly smooth functions) varying over a continuum, which are usually collected on discretized grids with measurement errors. In order to accurately smooth noisy functional observations and deal with the issue of high-dimensional observation grids, we propose a novel Bayesian method based on the Bayesian hierarchical model with a Gaussian-Wishart process prior and basis function representations. We first derive an induced model for the basis-function coefficients of the functional data, and then use this model to conduct posterior inference through Markov chain Monte Carlo methods. Compared to the standard Bayesian inference that suffers serious computational burden and instability in analyzing high-dimensional functional data, our method greatly improves the computational scalability and stability, while inheriting the advantage of simultaneously smoothing raw observations and estimating the mean-covariance functions in a nonparametric way. In addition, our method can naturally handle functional data observed on random or uncommon grids. Simulation and real studies demonstrate that our method produces similar results to those obtainable by the standard Bayesian inference with low-dimensional common grids, while efficiently smoothing and estimating functional data with random and high-dimensional observation grids when the standard Bayesian inference fails. In conclusion, our method can efficiently smooth and estimate high-dimensional functional data, providing one way to resolve the curse of dimensionality for Bayesian functional data analysis with Gaussian-Wishart processes. © 2017, The International Biometric Society.

Performance of wave function and density functional methods for water hydrogen bond spin-spin coupling constants.

PubMed

García de la Vega, J M; Omar, S; San Fabián, J

2017-04-01

Spin-spin coupling constants in water monomer and dimer have been calculated using several wave function and density functional-based methods. CCSD, MCSCF, and SOPPA wave functions methods yield similar results, specially when an additive approach is used with the MCSCF. Several functionals have been used to analyze their performance with the Jacob's ladder and a set of functionals with different HF exchange were tested. Functionals with large HF exchange appropriately predict 1 J O H , 2 J H H and 2h J O O couplings, while 1h J O H is better calculated with functionals that include a reduced fraction of HF exchange. Accurate functionals for 1 J O H and 2 J H H have been tested in a tetramer water model. The hydrogen bond effects on these intramolecular couplings are additive when they are calculated by SOPPA(CCSD) wave function and DFT methods. Graphical Abstract Evaluation of the additive effect of the hydrogen bond on spin-spin coupling constants of water using WF and DFT methods.

Improvements to the kernel function method of steady, subsonic lifting surface theory

NASA Technical Reports Server (NTRS)

Medan, R. T.

1974-01-01

The application of a kernel function lifting surface method to three dimensional, thin wing theory is discussed. A technique for determining the influence functions is presented. The technique is shown to require fewer quadrature points, while still calculating the influence functions accurately enough to guarantee convergence with an increasing number of spanwise quadrature points. The method also treats control points on the wing leading and trailing edges. The report introduces and employs an aspect of the kernel function method which apparently has never been used before and which significantly enhances the efficiency of the kernel function approach.

On the Convergence Analysis of the Optimized Gradient Method.

PubMed

Kim, Donghwan; Fessler, Jeffrey A

2017-01-01

This paper considers the problem of unconstrained minimization of smooth convex functions having Lipschitz continuous gradients with known Lipschitz constant. We recently proposed the optimized gradient method for this problem and showed that it has a worst-case convergence bound for the cost function decrease that is twice as small as that of Nesterov's fast gradient method, yet has a similarly efficient practical implementation. Drori showed recently that the optimized gradient method has optimal complexity for the cost function decrease over the general class of first-order methods. This optimality makes it important to study fully the convergence properties of the optimized gradient method. The previous worst-case convergence bound for the optimized gradient method was derived for only the last iterate of a secondary sequence. This paper provides an analytic convergence bound for the primary sequence generated by the optimized gradient method. We then discuss additional convergence properties of the optimized gradient method, including the interesting fact that the optimized gradient method has two types of worstcase functions: a piecewise affine-quadratic function and a quadratic function. These results help complete the theory of an optimal first-order method for smooth convex minimization.

On the Convergence Analysis of the Optimized Gradient Method

PubMed Central

Kim, Donghwan; Fessler, Jeffrey A.

2016-01-01

This paper considers the problem of unconstrained minimization of smooth convex functions having Lipschitz continuous gradients with known Lipschitz constant. We recently proposed the optimized gradient method for this problem and showed that it has a worst-case convergence bound for the cost function decrease that is twice as small as that of Nesterov’s fast gradient method, yet has a similarly efficient practical implementation. Drori showed recently that the optimized gradient method has optimal complexity for the cost function decrease over the general class of first-order methods. This optimality makes it important to study fully the convergence properties of the optimized gradient method. The previous worst-case convergence bound for the optimized gradient method was derived for only the last iterate of a secondary sequence. This paper provides an analytic convergence bound for the primary sequence generated by the optimized gradient method. We then discuss additional convergence properties of the optimized gradient method, including the interesting fact that the optimized gradient method has two types of worstcase functions: a piecewise affine-quadratic function and a quadratic function. These results help complete the theory of an optimal first-order method for smooth convex minimization. PMID:28461707

A Meshless Method Using Radial Basis Functions for Beam Bending Problems

NASA Technical Reports Server (NTRS)

Raju, I. S.; Phillips, D. R.; Krishnamurthy, T.

2004-01-01

A meshless local Petrov-Galerkin (MLPG) method that uses radial basis functions (RBFs) as trial functions in the study of Euler-Bernoulli beam problems is presented. RBFs, rather than generalized moving least squares (GMLS) interpolations, are used to develop the trial functions. This choice yields a computationally simpler method as fewer matrix inversions and multiplications are required than when GMLS interpolations are used. Test functions are chosen as simple weight functions as they are in the conventional MLPG method. Compactly and noncompactly supported RBFs are considered. Noncompactly supported cubic RBFs are found to be preferable. Patch tests, mixed boundary value problems, and problems with complex loading conditions are considered. Results obtained from the radial basis MLPG method are either of comparable or better accuracy than those obtained when using the conventional MLPG method.

Solutions to Kuessner's integral equation in unsteady flow using local basis functions

NASA Technical Reports Server (NTRS)

Fromme, J. A.; Halstead, D. W.

1975-01-01

The computational procedure and numerical results are presented for a new method to solve Kuessner's integral equation in the case of subsonic compressible flow about harmonically oscillating planar surfaces with controls. Kuessner's equation is a linear transformation from pressure to normalwash. The unknown pressure is expanded in terms of prescribed basis functions and the unknown basis function coefficients are determined in the usual manner by satisfying the given normalwash distribution either collocationally or in the complex least squares sense. The present method of solution differs from previous ones in that the basis functions are defined in a continuous fashion over a relatively small portion of the aerodynamic surface and are zero elsewhere. This method, termed the local basis function method, combines the smoothness and accuracy of distribution methods with the simplicity and versatility of panel methods. Predictions by the local basis function method for unsteady flow are shown to be in excellent agreement with other methods. Also, potential improvements to the present method and extensions to more general classes of solutions are discussed.

Computer program for calculating and fitting thermodynamic functions

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Gordon, Sanford

1992-01-01

A computer program is described which (1) calculates thermodynamic functions (heat capacity, enthalpy, entropy, and free energy) for several optional forms of the partition function, (2) fits these functions to empirical equations by means of a least-squares fit, and (3) calculates, as a function of temperture, heats of formation and equilibrium constants. The program provides several methods for calculating ideal gas properties. For monatomic gases, three methods are given which differ in the technique used for truncating the partition function. For diatomic and polyatomic molecules, five methods are given which differ in the corrections to the rigid-rotator harmonic-oscillator approximation. A method for estimating thermodynamic functions for some species is also given.

Revealing protein functions based on relationships of interacting proteins and GO terms.

PubMed

Teng, Zhixia; Guo, Maozu; Liu, Xiaoyan; Tian, Zhen; Che, Kai

2017-09-20

In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. These methods supposed that two proteins share the same function if they interact with each other. However, it is reported by recent studies that the functions of two interacting proteins may be just related. It will mislead the prediction of protein function. Therefore, there is a need for investigating the functional relationship between interacting proteins. In this paper, the functional relationship between interacting proteins is studied and a novel method, called as GoDIN, is advanced to annotate functions of interacting proteins in Gene Ontology (GO) context. It is assumed that the functional difference between interacting proteins can be expressed by semantic difference between GO term and its relatives. Thus, the method uses GO term and its relatives to annotate the interacting proteins separately according to their functional roles in the PPI network. The method is validated by a series of experiments and compared with the concerned method. The experimental results confirm the assumption and suggest that GoDIN is effective on predicting functions of protein. This study demonstrates that: (1) interacting proteins are not equal in the PPI network, and their function may be same or similar, or just related; (2) functional difference between interacting proteins can be measured by their degrees in the PPI network; (3) functional relationship between interacting proteins can be expressed by relationship between GO term and its relatives.

Prediction of EST functional relationships via literature mining with user-specified parameters.

PubMed

Wang, Hei-Chia; Huang, Tian-Hsiang

2009-04-01

The massive amount of expressed sequence tags (ESTs) gathered over recent years has triggered great interest in efficient applications for genomic research. In particular, EST functional relationships can be used to determine a possible gene network for biological processes of interest. In recent years, many researchers have tried to determine EST functional relationships by analyzing the biological literature. However, it has been challenging to find efficient prediction methods. Moreover, an annotated EST is usually associated with many functions, so successful methods must be able to distinguish between relevant and irrelevant functions based on user specifications. This paper proposes a method to discover functional relationships between ESTs of interest by analyzing literature from the Medical Literature Analysis and Retrieval System Online, with user-specified parameters for selecting keywords. This method performs better than the multiple kernel documents method in setting up a specific threshold for gathering materials. The method is also able to uncover known functional relationships, as shown by a comparison with the Kyoto Encyclopedia of Genes and Genomes database. The reliable EST relationships predicted by the proposed method can help to construct gene networks for specific biological functions of interest.

Dual number algebra method for Green's function derivatives in 3D magneto-electro-elasticity

NASA Astrophysics Data System (ADS)

Dziatkiewicz, Grzegorz

2018-01-01

The Green functions are the basic elements of the boundary element method. To obtain the boundary integral formulation the Green function and its derivative should be known for the considered differential operator. Today the interesting group of materials are electronic composites. The special case of the electronic composite is the magnetoelectroelastic continuum. The mentioned continuum is a model of the piezoelectric-piezomagnetic composites. The anisotropy of their physical properties makes the problem of Green's function determination very difficult. For that reason Green's functions for the magnetoelectroelastic continuum are not known in the closed form and numerical methods should be applied to determine such Green's functions. These means that the problem of the accurate and simply determination of Green's function derivatives is even harder. Therefore in the present work the dual number algebra method is applied to calculate numerically the derivatives of 3D Green's functions for the magnetoelectroelastic materials. The introduced method is independent on the step size and it can be treated as a special case of the automatic differentiation method. Therefore, the dual number algebra method can be applied as a tool for checking the accuracy of the well-known finite difference schemes.

Relationships between the generalized functional method and other methods of nonimaging optical design.

PubMed

Bortz, John; Shatz, Narkis

2011-04-01

The recently developed generalized functional method provides a means of designing nonimaging concentrators and luminaires for use with extended sources and receivers. We explore the mathematical relationships between optical designs produced using the generalized functional method and edge-ray, aplanatic, and simultaneous multiple surface (SMS) designs. Edge-ray and dual-surface aplanatic designs are shown to be special cases of generalized functional designs. In addition, it is shown that dual-surface SMS designs are closely related to generalized functional designs and that certain computational advantages accrue when the two design methods are combined. A number of examples are provided. © 2011 Optical Society of America

An exploration of function analysis and function allocation in the commercial flight domain

NASA Technical Reports Server (NTRS)

Mcguire, James C.; Zich, John A.; Goins, Richard T.; Erickson, Jeffery B.; Dwyer, John P.; Cody, William J.; Rouse, William B.

1991-01-01

The applicability is explored of functional analysis methods to support cockpit design. Specifically, alternative techniques are studied for ensuring an effective division of responsibility between the flight crew and automation. A functional decomposition is performed of the commercial flight domain to provide the information necessary to support allocation decisions and demonstrate methodology for allocating functions to flight crew or to automation. The function analysis employed 'bottom up' and 'top down' analyses and demonstrated the comparability of identified functions, using the 'lift off' segment of the 'take off' phase as a test case. The normal flight mission and selected contingencies were addressed. Two alternative methods for using the functional description in the allocation of functions between man and machine were investigated. The two methods were compared in order to ascertain their relative strengths and weaknesses. Finally, conclusions were drawn regarding the practical utility of function analysis methods.

Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lutsker, V.; Niehaus, T. A., E-mail: thomas.niehaus@physik.uni-regensburg.de; Aradi, B.

2015-11-14

Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply themore » method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.« less

A computational method for solving stochastic Itô–Volterra integral equations based on stochastic operational matrix for generalized hat basis functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heydari, M.H., E-mail: heydari@stu.yazd.ac.ir; The Laboratory of Quantum Information Processing, Yazd University, Yazd; Hooshmandasl, M.R., E-mail: hooshmandasl@yazd.ac.ir

2014-08-01

In this paper, a new computational method based on the generalized hat basis functions is proposed for solving stochastic Itô–Volterra integral equations. In this way, a new stochastic operational matrix for generalized hat functions on the finite interval [0,T] is obtained. By using these basis functions and their stochastic operational matrix, such problems can be transformed into linear lower triangular systems of algebraic equations which can be directly solved by forward substitution. Also, the rate of convergence of the proposed method is considered and it has been shown that it is O(1/(n{sup 2}) ). Further, in order to show themore » accuracy and reliability of the proposed method, the new approach is compared with the block pulse functions method by some examples. The obtained results reveal that the proposed method is more accurate and efficient in comparison with the block pule functions method.« less

Transfer Function Identification Using Orthogonal Fourier Transform Modeling Functions

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

2013-01-01

A method for transfer function identification, including both model structure determination and parameter estimation, was developed and demonstrated. The approach uses orthogonal modeling functions generated from frequency domain data obtained by Fourier transformation of time series data. The method was applied to simulation data to identify continuous-time transfer function models and unsteady aerodynamic models. Model fit error, estimated model parameters, and the associated uncertainties were used to show the effectiveness of the method for identifying accurate transfer function models from noisy data.

A threshold selection method based on edge preserving

NASA Astrophysics Data System (ADS)

Lou, Liantang; Dan, Wei; Chen, Jiaqi

2015-12-01

A method of automatic threshold selection for image segmentation is presented. An optimal threshold is selected in order to preserve edge of image perfectly in image segmentation. The shortcoming of Otsu's method based on gray-level histograms is analyzed. The edge energy function of bivariate continuous function is expressed as the line integral while the edge energy function of image is simulated by discretizing the integral. An optimal threshold method by maximizing the edge energy function is given. Several experimental results are also presented to compare with the Otsu's method.

Compositions and methods for hydrocarbon functionalization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunnoe, Thomas Brent; Fortman, George; Boaz, Nicholas C.

Embodiments of the present disclosure provide for methods of hydrocarbon functionalization, methods and systems for converting a hydrocarbon into a compound including at least one group ((e.g., hydroxyl group) (e.g., methane to methanol)), functionalized hydrocarbons, and the like.

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

PubMed

Du, Yushen; Wu, Nicholas C; Jiang, Lin; Zhang, Tianhao; Gong, Danyang; Shu, Sara; Wu, Ting-Ting; Sun, Ren

2016-11-01

Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available. To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available. Copyright © 2016 Du et al.

An indirect method for numerical optimization using the Kreisselmeir-Steinhauser function

NASA Technical Reports Server (NTRS)

Wrenn, Gregory A.

1989-01-01

A technique is described for converting a constrained optimization problem into an unconstrained problem. The technique transforms one of more objective functions into reduced objective functions, which are analogous to goal constraints used in the goal programming method. These reduced objective functions are appended to the set of constraints and an envelope of the entire function set is computed using the Kreisselmeir-Steinhauser function. This envelope function is then searched for an unconstrained minimum. The technique may be categorized as a SUMT algorithm. Advantages of this approach are the use of unconstrained optimization methods to find a constrained minimum without the draw down factor typical of penalty function methods, and that the technique may be started from the feasible or infeasible design space. In multiobjective applications, the approach has the advantage of locating a compromise minimum design without the need to optimize for each individual objective function separately.

Functional comparison of microarray data across multiple platforms using the method of percentage of overlapping functions.

PubMed

Li, Zhiguang; Kwekel, Joshua C; Chen, Tao

2012-01-01

Functional comparison across microarray platforms is used to assess the comparability or similarity of the biological relevance associated with the gene expression data generated by multiple microarray platforms. Comparisons at the functional level are very important considering that the ultimate purpose of microarray technology is to determine the biological meaning behind the gene expression changes under a specific condition, not just to generate a list of genes. Herein, we present a method named percentage of overlapping functions (POF) and illustrate how it is used to perform the functional comparison of microarray data generated across multiple platforms. This method facilitates the determination of functional differences or similarities in microarray data generated from multiple array platforms across all the functions that are presented on these platforms. This method can also be used to compare the functional differences or similarities between experiments, projects, or laboratories.

Three-dimensional computed tomographic volumetry precisely predicts the postoperative pulmonary function.

PubMed

Kobayashi, Keisuke; Saeki, Yusuke; Kitazawa, Shinsuke; Kobayashi, Naohiro; Kikuchi, Shinji; Goto, Yukinobu; Sakai, Mitsuaki; Sato, Yukio

2017-11-01

It is important to accurately predict the patient's postoperative pulmonary function. The aim of this study was to compare the accuracy of predictions of the postoperative residual pulmonary function obtained with three-dimensional computed tomographic (3D-CT) volumetry with that of predictions obtained with the conventional segment-counting method. Fifty-three patients scheduled to undergo lung cancer resection, pulmonary function tests, and computed tomography were enrolled in this study. The postoperative residual pulmonary function was predicted based on the segment-counting and 3D-CT volumetry methods. The predicted postoperative values were compared with the results of postoperative pulmonary function tests. Regarding the linear correlation coefficients between the predicted postoperative values and the measured values, those obtained using the 3D-CT volumetry method tended to be higher than those acquired using the segment-counting method. In addition, the variations between the predicted and measured values were smaller with the 3D-CT volumetry method than with the segment-counting method. These results were more obvious in COPD patients than in non-COPD patients. Our findings suggested that the 3D-CT volumetry was able to predict the residual pulmonary function more accurately than the segment-counting method, especially in patients with COPD. This method might lead to the selection of appropriate candidates for surgery among patients with a marginal pulmonary function.

Biologically plausible particulate air pollution mortality concentration-response functions.

PubMed Central

Roberts, Steven

2004-01-01

In this article I introduce an alternative method for estimating particulate air pollution mortality concentration-response functions. This method constrains the particulate air pollution mortality concentration-response function to be biologically plausible--that is, a non-decreasing function of the particulate air pollution concentration. Using time-series data from Cook County, Illinois, the proposed method yields more meaningful particulate air pollution mortality concentration-response function estimates with an increase in statistical accuracy. PMID:14998745

Functional connectivity change as shared signal dynamics

PubMed Central

Cole, Michael W.; Yang, Genevieve J.; Murray, John D.; Repovš, Grega; Anticevic, Alan

2015-01-01

Background An increasing number of neuroscientific studies gain insights by focusing on differences in functional connectivity – between groups, individuals, temporal windows, or task conditions. We found using simulations that additional insights into such differences can be gained by forgoing variance normalization, a procedure used by most functional connectivity measures. Simulations indicated that these functional connectivity measures are sensitive to increases in independent fluctuations (unshared signal) in time series, consistently reducing functional connectivity estimates (e.g., correlations) even though such changes are unrelated to corresponding fluctuations (shared signal) between those time series. This is inconsistent with the common notion of functional connectivity as the amount of inter-region interaction. New Method Simulations revealed that a version of correlation without variance normalization – covariance – was able to isolate differences in shared signal, increasing interpretability of observed functional connectivity change. Simulations also revealed cases problematic for non-normalized methods, leading to a “covariance conjunction” method combining the benefits of both normalized and non-normalized approaches. Results We found that covariance and covariance conjunction methods can detect functional connectivity changes across a variety of tasks and rest in both clinical and non-clinical functional MRI datasets. Comparison with Existing Method(s) We verified using a variety of tasks and rest in both clinical and non-clinical functional MRI datasets that it matters in practice whether correlation, covariance, or covariance conjunction methods are used. Conclusions These results demonstrate the practical and theoretical utility of isolating changes in shared signal, improving the ability to interpret observed functional connectivity change. PMID:26642966

Reliability of functional and predictive methods to estimate the hip joint centre in human motion analysis in healthy adults.

PubMed

Kainz, Hans; Hajek, Martin; Modenese, Luca; Saxby, David J; Lloyd, David G; Carty, Christopher P

2017-03-01

In human motion analysis predictive or functional methods are used to estimate the location of the hip joint centre (HJC). It has been shown that the Harrington regression equations (HRE) and geometric sphere fit (GSF) method are the most accurate predictive and functional methods, respectively. To date, the comparative reliability of both approaches has not been assessed. The aims of this study were to (1) compare the reliability of the HRE and the GSF methods, (2) analyse the impact of the number of thigh markers used in the GSF method on the reliability, (3) evaluate how alterations to the movements that comprise the functional trials impact HJC estimations using the GSF method, and (4) assess the influence of the initial guess in the GSF method on the HJC estimation. Fourteen healthy adults were tested on two occasions using a three-dimensional motion capturing system. Skin surface marker positions were acquired while participants performed quite stance, perturbed and non-perturbed functional trials, and walking trials. Results showed that the HRE were more reliable in locating the HJC than the GSF method. However, comparison of inter-session hip kinematics during gait did not show any significant difference between the approaches. Different initial guesses in the GSF method did not result in significant differences in the final HJC location. The GSF method was sensitive to the functional trial performance and therefore it is important to standardize the functional trial performance to ensure a repeatable estimate of the HJC when using the GSF method. Copyright © 2017 Elsevier B.V. All rights reserved.

On a method for generating inequalities for the zeros of certain functions

NASA Astrophysics Data System (ADS)

Gatteschi, Luigi; Giordano, Carla

2007-10-01

In this paper we describe a general procedure which yields inequalities satisfied by the zeros of a given function. The method requires the knowledge of a two-term approximation of the function with bound for the error term. The method was successfully applied many years ago [L. Gatteschi, On the zeros of certain functions with application to Bessel functions, Nederl. Akad. Wetensch. Proc. Ser. 55(3)(1952), Indag. Math. 14(1952) 224-229] and more recently too [L. Gatteschi and C. Giordano, Error bounds for McMahon's asymptotic approximations of the zeros of the Bessel functions, Integral Transform Special Functions, 10(2000) 41-56], to the zeros of the Bessel functions of the first kind. Here, we present the results of the application of the method to get inequalities satisfied by the zeros of the derivative of the function . This function plays an important role in the asymptotic study of the stationary points of the solutions of certain differential equations.

Protein-protein interaction network-based detection of functionally similar proteins within species.

PubMed

Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

2012-07-01

Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.