bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of insulin therapy in patients with Type 2 diabetes mellitus: beyond basal insulin
Authors: Blak B. T. , Smith H. T. , Hards M. , Curtis B. H. , Ivanyi T.
Published: January 2012

Diabet. Med. 29, e13–e20 (2012)

Aims  To describe patients with Type 2 diabetes mellitus treated with basal insulin, with or without oral antidiabetics in UK primary care, and evaluate insulin treatment patterns and factors explaining changes in therapy.

Methods  Retrospective analysis of patients with Type 2 diabetes within The Health Improvement Network UK primary care database. Patients receiving basal insulin between January and June 2006 were followed until July 2009.

Results  Analysis included 3185 patients, mean age 65.6 years [standard deviation (SD) 12.4], 50.9% men, median diabetes duration 9.6 years, median basal insulin use 1.3 years, 86.5% had received oral antidiabetics in the previous 12 months. Mean follow‐up was 2.9 years (SD 1.0), 59.8% patients maintained basal insulin throughout follow‐up with a mean HbA1C of 69 mmol/mol (SD 19; 8.4%, SD 1.7) at baseline and 65 mmol/mol (SD 17; 8.1%, SD 1.6) during follow‐up. During follow‐up, 6.9% of patients discontinued, 19.3% intensified with and 14.1% switched to prandial or premixed insulin. Patients who intensified (prandial) had a mean HbA1c of 77 mmol/mol (SD 18; 9.2%, SD 1.6) before change and a mean HbA1c of 71 mmol/mol (SD 21; 8.6%, SD 2.0) at the end of the study. Those switching to premixed insulin had a mean HbA1c of 80 mmol/mol (SD 18; 9.5%, SD 1.7) before change and a mean HbA1c of 69 mmol/mol (SD 17; 8.5%, SD 1.5) at the end of the study. Increasing HbA1c and longer diabetes duration explained intensification and switch.

Conclusions  The majority of patients had HbA1c above the 53 mmol/mol (< 7%) target at baseline and post‐intensification/switch. The HbA1c levels were reduced by intensification/switch suggesting that insulin changes did have some impact. Most patients did not change insulin treatment despite having higher than recommended HbA1c levels. Reasons for not changing treatment in face of unsatisfactory clinical outcomes are unclear. Further research is warranted to explore barriers towards therapy change.
Temporal changes in the diagnosis of type 1 diabetes by diabetic ketoacidosis in Brazil: A nationwide survey
Authors: Negrato C. A. , Cobas R. A. , Gomes M. B. ,   on behalf of the Brazilian Type 1 Diabetes Study Group (BrazDiab1SG)
Published: January 2012

Diabet. Med. 29, 1142–1147 (2012)

Aims  To examine the temporal trends in the frequency of diabetic ketoacidosis at onset compared to other modalities of diagnosis of Type 1 diabetes in Brazil.

Methods  This was a retrospective, cross‐sectional and multicenter study conducted between December 2008 and December 2010 in 28 public clinics at secondary and tertiary levels of care, located in 20 cities in four geographic regions of Brazil. Each clinic provided data extracted from at least 50 outpatients with Type 1 diabetes diagnosed between 1960 and 2010, using standardized chart review forms. Data were obtained from 3591 patients (56.0% females, 57.1% Caucasians). Median values (range) for age, age at diagnosis and duration of diabetes were, respectively, 19 years (1–66 years), 10 years (< 1–44 years) and 7 years (< 1–50 years). Logistic regression was performed with diabetic ketoacidosis (Yes/No) as the dependent variable and other clinical features as independent variables.

Results  Type 1 diabetes diagnosis was made by diabetic ketoacidosis in 1,520 (42.3%), by fasting plasma glucose in 1413 (39.4%), by random blood glucose in 516 (14.4%), by oral glucose tolerance test in 66 (1.8%) and by other methods in 76 (2.1%) cases, respectively. Diagnosis made before the year 2000 had a greater odds to occur by diabetic ketoacidosis (Odds ratio 1.26, 95% confidence intervals (CI) 1.09–1.48). Since then, a decrease has occurred. Economic status, geographic region and age were significantly related to diabetic ketoacidosis at diagnosis.

Conclusions  Although high prevalence of diabetic ketoacidosis at diagnosis of Type 1 diabetes in Brazil is observed, recently, more patients have been diagnosed by other methods.
Comparison of renal resistive index among patients with Type 2 diabetes with different levels of creatinine clearance and urinary albumin excretion
Authors: Afsar B. , Elsurer R.
Published: January 2012

Diabet. Med. 29, 1043–1046 (2012)

Aim  To evaluate the prevalence of increased renal resistive index and related factors among patients with Type 2 diabetes with different levels of creatinine clearance and urinary albumin excretion.

Methods  Laboratory analyses, including calculation of 24‐h urinary albumin excretion and 24‐h creatinine clearance, and renal doppler ultrasonography to measure renal resistive index, were carried out for patients newly diagnosed with Type 2 diabetes mellitus.

Results  Participants were classified into four groups according to 24‐h creatinine clearance and 24‐h urinary albumin excretion levels. Group 1 was composed of 73 patients (54.1%) with normal 24‐h creatinine clearance and 24‐h urinary albumin excretion. Group 2 was composed of 34 (25.2%) patients with normal 24‐h creatinine clearance and increased 24‐h urinary albumin excretion. Group 3 was composed of 14 (10.4%) patients with decreased 24‐h creatinine clearance and normal 24‐h urinary albumin excretion. Group 4 was composed of 14 (10.4%) patients with both decreased 24‐h creatinine clearance and increased 24‐h urinary albumin excretion . In total, 41 patients (30.4%) had increased renal resistive index levels. Comparison of the four groups with respect to increased renal resistive index revealed: among group 1 patients, 10 (13.7%) had increased renal resistive index levels; among group 2 patients, 14 (41.2%) had increased renal resistive index levels; among group 3 patients, eight (57.1%) had increased renal resistive index levels; among group 4 patients, nine (64.3%) had increased renal resistive index levels (P < 0.0001 for trend). In multivariate regression, 24‐h creatinine clearance (P < 0.0001), but not 24‐h urinary albumin excretion, was related to increased renal resistive index levels.

Conclusion  Renal resistive index levels were highest in patients with Type 2 diabetes with both decreased 24‐h creatinine clearance and increased 24‐h urinary albumin excretion, whereas they were lowest in patients with normal creatinine clearance and normal urinary albumin excretion.
Pancreatic exocrine function in patients with diabetes
Authors: Larger E. , Philippe M. F. , Barbot‐Trystram L. , Radu A. , Rotariu M. , Nobécourt E. , Boitard C.
Published: January 2012

Diabet. Med. 29, 1047–1054 (2012)

Background  Decreased function of the exocrine pancreas is frequent in patients with diabetes. Our aim was to investigate clinical correlates of pancreatic exocrine failure in patients with diabetes.

Patients and methods  We investigated exocrine function by assaying both elastase‐1 concentration and chymotrypsin activity in 667 patients. We conducted separate analysis on patients with Type 1 diabetes and patients with Type 2 diabetes. Patients were separated into three groups according to whether both elastase‐1 concentration and chymotrypsin activity were normal, or one or both were altered.

Results  A total of 667 consecutive patients were analysed, including 195 with Type 1 and 472 with Type 2 diabetes. Elastase‐1 concentration was < 200 μg/g in 23% of the patients. Chymotrypsin activity was < 6 U/g in 26% of the patients. In 66% of the patients elastase‐1 concentration was > 200 μg/g and chymotrypsin activity > 6U/g. One test was below threshold in 19%, both in 15%. In patients with Type 1 diabetes, the three groups defined by results of elastase‐1 concentration and chymotrypsin activity differed with regard to duration of diabetes and prevalence of glutamic acid decarboxylase antibodies, but not BMI or HbA1c, or prevalence of retinopathy, neuropathy, nephropathy or vascular disease. In patients with Type 2 diabetes, the three groups differed with regard to BMI, use of insulin and vascular disease, but not known duration.

Conclusion  Factors associated with pancreatic exocrine failure differ in patients with Type 1 diabetes compared with patients with type 2 diabetes. In patients with Type 2 diabetes, association of decreased pancreatic exocrine function with BMI and vascular disease suggests a role of pancreatic arteriopathy.
Body mass estimation in Early Miocene native South American ungulates: a predictive equation based on 3D landmarks
Authors: Cassini G. H. , Vizcaíno S. F. , Bargo M. S.
Published: January 2012

South American native ungulates include extinct taxa that evolved within the geographical context given by the isolation of South America during most of the Cenozoic. The ungulates (orders Notoungulata, Litopterna and Astrapotheria) of the Santa Cruz Formation (late Early Miocene) are particularly interesting for paleobiological studies due to their diversity, richness and quality of preservation of the specimens. The body mass estimation of extinct species is one of the basic biological attributes for paleobiological reconstructions. The most common way to estimate body mass from fossils is using linear regression. Here, we used geometric morphometric techniques in order to estimate their body mass. We used regressions based on centroid size of 3D craniomandibular landmark configurations, including extant ungulates (their size and ecological relatives). Cases were weighted to maximize the taxonomic evenness. A broad body size range was recorded. The highest predictive power is obtained with those functions derived from the highest taxonomic and ecological diversity. The highest taxonomic richness corresponds to masses below 100 kg. Among Notoungulata, typotheres (Hegetotheriidae + Interatheriidae) vary from 1 to less than 10 kg, while the smaller toxodontid reached 100 kg and the larger 500 kg. Litoptern proterotheriid body masses vary from 10 to 50 kg, and macraucheniids surpass 100 kg. The astrapotheres (Astrapotheria) reached (or even surpassed) 1000 kg, being the only megamammal in the Santacrucian ungulate assemblage.
Introduction: Why People Do Not Accept Evolution: Using Protistan Diversity to Promote Evolution Literacy
Authors: Paz‐y‐Miño‐C. Guillermo , Espinosa Avelina
Published: January 2012

The controversy evolution vs. creationism is inherent to the incompatibility between scientific rationalism/empiricism and the belief in supernatural causation. To test this hypothesis, we conceptualized a Cartesian landscape where the dependent variable acceptance of evolution was plotted as function of three factors, each represented by an index (value range 0 to 3): Religiosity Index (RI), Science Index (SI), and Evolution Index (EI). The indexes summarized an individual's personal religious convictions, familiarity with the processes and forces of change in organisms (= concept of evolution), and understanding the essence of science (= method to explore reality). We compared and contrasted acceptance of evolution among four populations of variable educational attainment: 244 professors of New England, United States (93% Ph.D./doctorate holders), 50 protistologists from 25 countries (70% Ph.D./doctorate holders), 62 educators of prospective teachers (83% Ph.D./doctorate holders), and 827 college students. The New England faculty held the highest acceptance of evolution position (RI = 0.49; SI = 2.49; EI = 2.49), followed by the protistologists (RI = 0.46; SI = 2.30; EI = 2.48), the educators of prospective teachers (RI = 0.83; SI = 1.96; EI = 1.96), and the students (RI = 0.89; SI = 1.80; EI = 1.60); therefore, the data supported our hypothesis. Proper science education, public outreach and robust debate over the controversy “evolution versus creationism” should suffice to improve society's evolution literacy, and qualified scholars ought to lead this mission.
Reversible Cytotoxic Edema in TPN‐Related Hepatic Encephalopathy
Authors: Zuccoli Giulio , Sreedher Gayathri
Published: January 2012

Hepatic encephalopathy (HE) is an uncommon complication of total parenteral nutrition (TPN). Cytotoxic edema has not been reported in children with TPN‐related HE. We describe a case of TPN‐related HE presenting with diffuse cytotoxic edema which reversed after liver transplantation.
Effect of intercrops on thrips species composition and population abundance on French beans in Kenya
Authors: Nyasani J. O. , Meyhöfer R. , Subramanian S. , Poehling H.‐M.
Published: January 2012

The study aimed at determining thrips species composition and thrips population density on French bean planted as a sole crop and as an intercrop with either sunflower, Irish potato, or baby corn, in various combinations. Field experiments were conducted in two seasons to examine: (1) thrips population development and thrips species composition over time, (2) effect of intercrops on thrips population density and natural enemies, and (3) effect of intercrops on French bean yield. The experiments were conducted at the Kenya Agricultural Research Institute, Embu, Kenya in a randomized complete block design with four replicates. The thrips population on French beans increased with time. It showed a peak at the flowering stage then started declining when the crops were nearing senescence. French beans hosted four thrips species, Megalurothrips sjostedti (Trybom), Frankliniella schultzei (Trybom), Frankliniella occidentalis (Pergande), and Hydatothrips aldolfifriderici (Karny) (all Thysanoptera: Thripidae) in order of decreasing abundance. The main thrips species on Irish potato and sunflower was F. schultzei. Baby corn hosted only Frankliniella williamsi (Hood) and Thrips pusillus (Bagnall). A monocrop of French bean hosted more thrips than a French bean intercrop mix. Thrips natural enemies such as Orius spp. and Ceranisus spp. were recorded in all crop plants but in especially high numbers on French bean and baby corn, respectively. Plots with French bean alone had about 1.4 times higher yields compared to intercropped plots of French bean with sunflower and French bean with baby corn. However, the percentage of pods that could get rejected on the market due to thrips damage was highest on plots with French bean alone (68 and 63%) and lowest on plots with French bean and baby corn (35 and 37%) in the first and second seasons, respectively. This study showed that a complex of thrips is found in the field and its composition varies with crop stage and species. Intercropping French bean with other crops compromises on French bean yield but reduces damage to the French bean pods, thereby enhancing marketable yield.
Population genetic structure of a specialist leafhopper on Zea: likely anthropogenic and ecological determinants of gene flow
Authors: Medina Raul F. , Reyna Steven M. , Bernal Julio S.
Published: January 2012

Corn leafhopper, Dalbulus maidis DeLong & Wolcott (Hemiptera: Cicadellidae), is a specialist herbivore on the genus Zea (Poaceae). The genera Dalbulus and Zea evolved in central Mexico. We sought to determine whether population genetic structuring is prevalent in corn leafhoppers inhabiting three of its host plants: (1) the highland species perennial teosinte (Zea diploperennis Iltis, Doebley & Guzman), (2) the mid‐ to lowland‐species Balsas teosinte (Zea mays ssp. parviglumis Iltis & Doebley), and (3) the ubiquitous domesticated maize (Zea mays ssp. mays L.). We used amplified fragment length polymorphisms to detect population structuring and genetic differentiation among corn leafhoppers on the three host plants in western‐central and ‐northern Mexico. Our results showed that corn leafhopper in Mexico is composed of at least two genetically discrete populations: an ‘Itinerant’ population associated with the annual hosts maize and Balsas teosinte, which appears to be widely distributed in Mexico, and a ‘Las Joyas’ population restricted to perennial teosinte and confined to a small mountain range (Sierra de Manantlán) in western‐central Mexico. Our results further suggested that population structuring is not due to isolation by distance or landscape features: Las Joyas and Itinerant corn leafhopper populations are genetically distinct despite their geographic proximity (ca. 4 km), whereas Itinerant corn leafhoppers separated by hundreds of kilometers (>800 km), mountain ranges, and a maritime corridor (Sea of Cortez) are not genetically distinct. Based on our results and on published ethnohistorical and archaeological data, we propose pre‐Columbian and modern scenarios, including likely ecological and anthropogenic influences, in which the observed genetic population structuring of corn leafhopper could have originated and could be maintained. Also, we hypothesize that after evolving on the lowland Balsas teosinte, corn leafhopper expanded its host range to include maize and then the highland perennial teosinte, following the domestication and spread of maize within the last 9 000 years.
Continuous low‐dose oral contraceptive in the treatment of colorectal endometriosis evaluated by rectal endoscopic ultrasonography
Authors: FERRARI STEFANO , PERSICO PAOLA , DI PUPPO FRANCESCA , VIGANO PAOLA , TANDOI IACOPO , GARAVAGLIA ELISABETTA , GIARDINA PAOLO , MEZZI GIANNI , CANDIANI MASSIMO
Published: January 2012

Objective. Limited attention has been focused on the medical treatment of bowel endometriosis. This study evaluates the efficacy of administration of a continuous low‐dose oral contraceptive in treating pain and other symptoms associated with colorectal endometriotic nodules, as evaluated by rectal endoscopic ultrasonography. Design. Prospective observational study. Setting. Academic Department of San Raffaele Scientific Institute, Obstetrics and Gynecology Unit. Population. Symptomatic women of reproductive age (n=26) with colorectal nodules infiltrating at least the bowel muscularis propria and without a stenosis >50%. In 31% of the patients, endoscopic ultrasonography permitted diagnosis of nodules located more than 10 cm from the anal rim. Methods. Patients received a continuous low‐dose oral contraceptive containing 15 μg ethinylestradiol and 60 μg gestodene for 12 months. Subjective symptoms were prospectively evaluated, and nodule volumes were monitored using endoscopic ultrasonography. Main outcome measures. Nodule measurements were performed at baseline and after 12 months of treatment. Symptoms at the start and after 12 months were evaluated. Results. A significant improvement in the intensity of all the considered symptoms (dysmenorrhea, non‐menstrual pelvic pain, deep dyspareunia and painful defecation) was seen when evaluated by a visual analog scale. A reduction in terms of both diameter (mean reduction 26%) and volume of the nodules (mean reduction 62%) was observed after a 12 month period. Conclusions. A continuous low‐dose oral contraceptive therapy may reduce bowel endometriosis‐associated symptoms. In addition, this therapy induces a significant volumetric reduction of colorectal plaques when evaluated by endoscopic ultrasonography.
Annular hypopigmented mycosis fungoides: a novel ringed variant
Authors: Uhlenhake Elizabeth E. , Mehregan Darius M.
Published: January 2012

Hypopigmented mycosis fungoides (MF) is a relatively uncommon variant of cutaneous lymphoma that is mostly seen in darker skin types. We present a novel and unique clinical presentation in an African‐American female patient, consisting of regular hypopigmented annular rings in areas of normal skin and in more typical hypopigmented patches of MF. The lesions appeared diffusely on all extremities, anterior chest and back. Histopathologic examination showed an atypical lymphocytic infiltrate at the dermal–epidermal junction with epidermotropism and few Pautrier's collections. The patient was otherwise healthy and improved with narrowband ultraviolet (UV)‐B. This case represents a presentation of a most unusual variant of hypopigmented MF, for which we propose the name ‘annular hypopigmented MF’.

Uhlenhake EE, Mehregan DM. Annular hypopigmented mycosis fungoides: a novel ringed variant.
Within‐Visit Variability of Blood Pressure and All‐Cause and Cardiovascular Mortality Among US Adults
Authors: Muntner Paul , Levitan Emily B. , Reynolds Kristi , Mann Devin M. , Tonelli Marcello , Oparil Suzanne , Shimbo Daichi
Published: January 2012

J Clin Hypertens (Greenwich). 2012;14:165–171. ©2012 Wiley Periodicals, Inc.

The association between within‐visit variability of systolic blood pressure (SBP) and diastolic blood pressure (DBP) and all‐cause and cardiovascular (CVD) mortality was examined using the Third National Health and Nutrition Survey (n=15,317). Three SBP and DBP readings were taken by physicians during a single medical evaluation. Within‐visit variability for each participant was defined using the standard deviation of SBP and DBP across these measurements. Mortality was assessed over 14 years (n=3848 and n=1684 deaths from all causes and CVD, respectively). After age, sex, and race‐ethnicity adjustment, the hazard ratios (95% confidence intervals) for all‐cause mortality associated with the 4 highest quintiles of within‐visit standard deviation of SBP (2.00–2.99 mm Hg, 3.00–3.99 mm Hg, 4.00–5.29 mm Hg, and ≥5.30 mm Hg) compared with participants in the lowest quintile of within‐visit standard deviation of SBP (<2.0 mm Hg) were 1.04 (0.87–1.26), 1.09 (0.92–1.29), 1.06 (0.88–1.28), and 1.13 (0.95–1.33), respectively (P=.136). The analogous hazard ratios for CVD mortality were 0.95 (0.69–1.32), 0.96 (0.67–1.36), 0.95 (0.74–1.23), and 1.04 (0.80–1.35), respectively (P=.566). No association with mortality was present after further adjustment and when modeling within‐visit standard deviation of SBP as a continuous variable. Standard deviation of DBP was not associated with mortality.
Urinary Leukotriene E4 Concentrations as a Potential Marker of Inflammation in Dogs with Inflammatory Bowel Disease
Authors: Im Hof M. , Schnyder M. , Hartnack S. , Stanke‐Labesque F. , Luckschander N. , Burgener I.A.
Published: January 2012

Background

Inflammatory bowel disease (IBD) and food‐responsive diarrhea (FRD) are chronic enteropathies of dogs (CCE) that currently can only be differentiated by their response to treatment after exclusion of other diseases. In humans, increased urinary concentrations of leukotriene E4 (LTE4) have been associated with activeIBD.

Objectives

To evaluate urinaryLTE4 concentrations in dogs withIBD,FRD, and healthy controls, and to assess correlation of urinaryLTE4 concentrations with the canineIBDactivity index (CIBDAI) scores.

Animals

Eighteen dogs withIBD, 19 dogs withFRD, and 23 healthy control dogs.

Methods

In this prospective study, urine was collected andCIBDAIscores were calculated in client‐owned dogs withIBDand those withFRD. Quantification ofLTE4 in urine was performed by liquid chromatography‐tandem mass spectrometry and corrected to creatinine.

Results

UrinaryLTE4 concentrations were highest in dogs withIBD(median 85.2 pg/mg creatinine [10th–90th percentiles 10.9–372.6]) followed by those withFRD(median 31.2 pg/mg creatinine [10th–90th percentiles 6.2–114.5]) and control dogs (median 21.1 pg/mg creatinine [10th–90th percentiles 9.1–86.5]). UrinaryLTE4 concentrations were higher in dogs withIBDthan in control dogs (P = .011), but no significant difference betweenIBDandFRDwas found. No correlation was found between urinaryLTE4 concentrations andCIBDAI.

Conclusions and Clinical Importance

The higher urinaryLTE4 concentrations in dogs withIBDsuggest that cysteinyl leukotriene pathway activation might be a component of the inflammatory process in canineIBD. Furthermore, urinaryLTE4 concentrations are of potential use as a marker of inflammation in dogs withCCE.
Reproductive Effects of Prolonged Experimentally Induced Hypothyroidism in Bitches
Authors: Panciera D.L. , Purswell B.J. , Kolster K.A. , Werre S.R. , Trout S.W.
Published: January 2012

Background

Hypothyroidism has detrimental effects on reproduction in females of many species. Studies of hypothyroidism in bitches are limited and results conflicting.

Hypothesis

Hypothyroidism interferes with reproductive function and health of offspring in bitches.

Animals

A total of 9 healthy mixed‐breed bitches (control) and 9 mixed breed bitches with hypothyroidism induced by radioactive iodine administration.

Methods

Dogs in both groups were bred 20.9 ± 4.0 and 56 ± 7.6 weeks after radioiodine administration in the hypothyroid group and again after levothyroxine was administered for 37 ± 14 weeks to hypothyroid dogs. Measures of the estrus cycle, fertility, gestation, whelping, and pup health were evaluated at each breeding. Comparisons were made between hypothyroid and control dogs as well as within groups between times.

Results

Pregnancy was documented in all dogs in both groups at the 1st breeding, 4/8 and 6/6 untreated hypothyroid and control dogs, respectively, at the 2nd breeding, and 6/6 and 5/6 treated hypothyroid and control dogs, respectively, at the 3rd breeding. Periparturient mortality was higher and birth weight was lower in pups born to untreated hypothyroid dogs compared with control dogs or treated hypothyroid dogs. There was no difference in interestrus interval, gestation duration, breeding behavior, interval between birth of pups, or serum progesterone concentrations at any breeding between or within groups. Resolution of hypothyroidism reversed the detrimental effects of thyroid hormone deficiency on reproduction.

Conclusions and Clinical Importance

Hypothyroidism causes reversible periparturient mortality and low birth weight in offspring. Further investigation is necessary to determine if fertility is affected.
Braiding via geometric Lie algebra actions
Authors: Cautis Sabin , Kamnitzer Joel
Published: January 2012

We introduce the idea of a geometric categorical Lie algebra action on derived categories of coherent sheaves. The main result is that such an action induces an action of the braid group associated to the Lie algebra. The same proof shows that strong categorical actions in the sense of Khovanov–Lauda and Rouquier also lead to braid group actions. As an example, we construct an action of Artin’s braid group on derived categories of coherent sheaves on cotangent bundles to partial flag varieties.
Low resistance and thermally stable Ti/Al-based Ohmic contacts to N-face n-GaN for vertical light-emitting diodes by using Ti(Ga) solid solution and TiN layers
Authors: Jeon Joon-Woo , Yum Woong-Sun , Seong Tae-Yeon , Youl Lee Sang , Song June-O
Published: January 2012

The authors report on the formation of highly reliable Ti/Al-based ohmic contacts to N-face n-GaN for high-performance vertical light-emitting diodes by using Ti(Ga) solid solution and TiN layers. The Ti(Ga) solid solution layer is used to minimize the outdiffusion of Ga atoms from the n-GaN surface region. Unlike the Ti/Al contacts, the Ti(Ga)/Ti/Al and Ti(Ga)/TiN/Al samples exhibit ohmic behavior with contact resistivities of 3.9 – 4.8 × 10−4 Ωcm2 after annealing at 250 °C. It was further shown that unlike the Ti(Ga)/TiN/Al samples, the Ti/Al and the Ti(Ga)/Ti/Al samples are largely electrically degraded when annealed at 300 °C in an oven. Based on x-ray photoemission spectroscopy and secondary ion mass spectrometry results, ohmic formation and degradation mechanisms are briefly described and discussed.
A Phosphorylated Pseudokinase Complex Controls Cell Wall Synthesis in Mycobacteria
Authors: Gee Christine L. , Papavinasasundaram Kadamba G. , Blair Sloane R. , Baer Christina E. , Falick Arnold M. , King David S. , Griffin Jennifer E. , Venghatakrishnan Harene , Zukauskas Andrew , Wei Jun-Rong , Dhiman Rakesh K. , Crick Dean C. , Rubin Eric J. , Sassetti Christopher M. , Alber Tom
Published: January 2012

Structure-function studies in mycobacteria reveal how a Ser-Thr protein kinase and pseudokinase work together to regulate the synthesis of the bacterial cell wall.
Depletion of Extracellular Ca
2+
Prompts Astroglia to Moderate Synaptic Network Activity
Authors: Rusakov Dmitri A.
Published: January 2012

Reduced extracellular calcium stimulates astrocytes to release adenosine triphosphate, which activates inhibitory neurons and may limit excitability.
Stochastic or Asymmetric Fate Determination?
Authors: Mueller Kristen L.
Published: January 2012

Cell-fate decisions in activated B lymphocytes are determined by stochastic competition.
Multiple cis-acting targeting sequences are required for orb mRNA localization during Drosophila oogenesis.
Authors: Lantz V , Schedl P
Published: January 2012

The targeting of positional information to specific regions of the oocyte or early embryo is one of the key processes in establishing anterior-posterior and dorsal-ventral polarity. In many developmental systems, this is accomplished by localization of mRNAs. The germ line-specific Drosophila orb gene plays a critical role in defining both axes of the developing oocyte, and its mRNA is localized in a complex pattern during oogenesis. We have identified a 280-bp sequence from the orb 3' untranslated region capable of reproducing this complex localization pattern. Furthermore, we have found that multiple cis-acting elements appear to be required for proper targeting of orb mRNA.
Continued functioning of the secretory pathway is essential for ribosome synthesis.
Authors: Mizuta K , Warner J R
Published: January 2012

To explore the regulatory elements that maintain the balanced synthesis of the components of the ribosome, we isolated a temperature-sensitive (ts) mutant of Saccharomyces cerevisiae in which transcription both of rRNA and of ribosomal protein genes is defective at the nonpermissive temperature. Temperature sensitivity for growth is recessive and segregates 2:2. A gene that complements the ts phenotype was cloned from a genomic DNA library. Sequence analysis revealed that this gene is SLY1, encoding a protein essential for protein and vesicle transport between the endoplasmic reticulum and the Golgi apparatus. In the strain carrying our ts allele of SLY1, accumulation of the carboxypeptidase Y precursor was detected at the nonpermissive temperature, indicating that the secretory pathway is defective. To ask whether the effect of the ts allele on ribosome synthesis was specific for sly1 or was a general result of the inactivation of the secretion pathway, we assayed the levels of mRNA for several ribosomal proteins in cells carrying ts alleles of sec1, sec7, sec11, sec14, sec18, sec53, or sec63, representing all stages of secretion. In each case, the mRNA levels were severely depressed, suggesting that this is a common feature in mutants of protein secretion. For the mutants tested, transcription of rRNA was also substantially reduced. Furthermore, treatment of a sensitive strain with brefeldin A at a concentration sufficient to block the secretion pathway also led to a decrease of the level of ribosomal protein mRNA, with kinetics suggesting that the effect of a secretion defect is manifest within 15 to 30 min. We conclude that the continued function of the entire secretion pathway is essential for the maintenance of ribosome synthesis. The apparent coupling of membrane synthesis and ribosome synthesis suggest the existence of a regulatory network that connects the production of the various structural elements of the cell.
The Aspergillus nidulans abaA gene encodes a transcriptional activator that acts as a genetic switch to control development.
Authors: Andrianopoulos A , Timberlake W E
Published: January 2012

The Aspergillus nidulans abaA gene encodes a protein containing an ATTS DNA-binding motif and is required for the terminal stages of conidiophore development. Results from gel mobility shift and protection, missing-contact, and interference footprint assays showed that AbaA binds to the sequence 5'-CATTCY-3', where Y is a pyrimidine, making both major- and minor-groove contacts. Multiple AbaA binding sites are present in the cis-acting regulatory regions of several developmentally controlled structural genes as well as those of the upstream regulatory gene brlA, the downstream regulatory gene wetA, and abaA itself. These cis-acting regulatory regions confer AbaA-dependent transcriptional activation in a heterologous Saccharomyces cerevisiae gene expression system. From these observations, we propose that the AbaA transcription factor establishes a novel set of feedback regulatory loops responsible for determination of conidiophore development.
Characterization of cis-acting elements in light regulation of the nuclear gene encoding the A subunit of chloroplast isozymes of glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana.
Authors: Conley T R , Park S C , Kwon H B , Peng H P , Shih M C
Published: January 2012

We have characterized cis-acting elements involved in light regulation of the nuclear gene (GapA) encoding the A subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in Arabidopsis thaliana. Our results show that a 1.1-kb promoter fragment of the GapA gene is sufficient to confer light inducibility and organ specificity in transgenic Nicotiana tabacum (tobacco) plants, using the beta-glucuronidase gene of Escherichia coli as the reporter gene. Deletion analysis indicates that the -359 to -110 bp region of the GapA gene is necessary for light responsiveness. Within this region there are three copies of a decamer repeat (termed the Gap box) having the consensus sequence 5'-CAAATGAA(A/G)A-3', which has not been characterized in the promoter regions of other light-regulated genes. A deletion (to -247) producing loss of one copy of these elements from the GapA promoter reduces light induction by two- to threefold compared with a promoter deletion (to -359) with all three Gap boxes present, while deletion of all three Gap boxes (to -110) abolishes light induction completely. Gel mobility shift experiments using tobacco nuclei as the source of nuclear proteins show that GapA promoter fragments that contain these repeats bind strongly to a factor in the nuclear extract and that binding can be abolished by synthetic competitors consisting only of a monomer or dimer of the Gap box. Furthermore, a trimer, dimer, and monomer of the Gap box show binding activity and, like the authentic GapA promoter-derived probes, show binding activities that are correlated with Gap box copy number. These results strongly suggest that these repeats play important roles in light regulation of the GapA gene of A. thaliana.
Requirements for intercistronic distance and level of eukaryotic initiation factor 2 activity in reinitiation on GCN4 mRNA vary with the downstream cistron.
Authors: Grant C M , Miller P F , Hinnebusch A G
Published: January 2012

Translational control of the GCN4 gene in response to amino acid availability is mediated by four short open reading frames in the GCN4 mRNA leader (uORFs) and by phosphorylation of eukaryotic initiation factor 2 (eIF-2). We have proposed that reducing eIF-2 activity by phosphorylation of its alpha subunit or by a mutation in the eIF-2 recycling factor eIF-2B allows ribosomes which have translated the 5'-proximal uORF1 to bypass uORF2 to uORF4 and reinitiate at GCN4 instead. In this report, we present two lines of evidence that all ribosomes which synthesize GCN4 have previously translated uORF1, resumed scanning, and reinitiated at the GCN4 start site. First, GCN4 expression was abolished when uORF1 was elongated to make it overlap the beginning of the GCN4 coding region. Second, GCN4 expression was reduced as uORF1 was moved progressively closer to GCN4, decreasing to only 5% of the level seen in the absence of all uORFs when only 32 nucleotides separated uORF1 from GCN4. We additionally found that inserting small synthetic uORFs between uORF4 and GCN4 inhibited GCN4 expression under derepressing conditions, confirming the idea that reinitiation at GCN4 under conditions of diminished eIF-2 activity is proportional to the distance of the reinitiation site downstream from uORF1. While uORF4 and GCN4 appear to be equally effective at capturing ribosomes scanning downstream from the 5' cap of mRNA, these two ORFs differ greatly in their ability to capture reinitiating ribosomes scanning from uORF1. When the active form of eIF-2 is present at high levels, reinitiation appears to be much more efficient at uORF4 than at GCN4 when each is located very close to uORF1. Under conditions of reduced recycling of eIF-2, reinitiation at uORF4 is substantially suppressed, which allows ribosomes to reach the GCN4 start site; in contrast, reinitiation at GCN4 in constructs lacking uORF4 is unaffected by decreasing the level of eIF-2 activity. This last finding raises the possibility that time-dependent binding to ribosomes of a second factor besides the eIF-2-GTP-Met-tRNA(iMet) ternary complex is rate limiting for reinitiation at GCN4. Moreover, our results show that the efficiency of translational reinitiation can be strongly influenced by the nature of the downstream cistron as well as the intercistronic distance.
His-154 is involved in the linkage of the Saccharomyces cerevisiae L-A double-stranded RNA virus Gag protein to the cap structure of mRNAs and is essential for M1 satellite virus expression.
Authors: Blanc A , Ribas J C , Wickner R B , Sonenberg N
Published: January 2012

The coat protein (Gag) of the double-stranded RNA virus L-A was previously shown to form a covalent bond with the cap structure of eukaryotic mRNAs. Here, we identify the linkage as a phosphoroimidazole bond between the alpha phosphate of the cap structure and a nitrogen in the Gag protein His-154 imidazole side chain. Mutations of His-154 abrogate the ability of Gag to bind to the cap structure, without affecting cap recognition, in vivo virus particle formation from an L-A cDNA clone, or in vitro specific binding and replication of plus-stranded single-stranded RNA. However, genetic analyses demonstrate that His-154 is essential for M1 satellite virus expression.
Complementation of mutant and wild-type human mitochondrial DNAs coexisting since the mutation event and lack of complementation of DNAs introduced separately into a cell within distinct organelles.
Authors: Yoneda M , Miyatake T , Attardi G
Published: January 2012

The rules that govern complementation of mutant and wild-type mitochondrial genomes in human cells were investigated under different experimental conditions. Among mitochondrial transformants derived from an individual affected by the MERRF (myoclonus epilepsy associated with ragged red fibers) encephalomyopathy and carrying in heteroplasmic form the mitochondrial tRNA(Lys) mutation associated with that syndrome, normal protein synthesis and respiration was observed when the wild-type mitochondrial DNA exceeded 10% of the total complement. In these transformants, the protective effect of wild-type mitochondrial DNA was shown to involve interactions of the mutant and wild-type gene products. Very different results were obtained in experiments in which two mitochondrial DNAs carrying nonallelic disease-causing mutations were sequentially introduced within distinct organelles into the same human mitochondrial DNA-less (rho 0) cell. In transformants exhibiting different ratios of the two genomes, no evidence of cooperation between their products was observed, even 3 months after the introduction of the second mutation. These results pointed to the phenotypic independence of the two genomes. A similar conclusion was reached in experiments in which mitochondria carrying a chloramphenicol resistance-inducing mitochondrial DNA mutation were introduced into chloramphenicol-sensitive cells. A plausible interpretation of the different results obtained in the latter two sets of experiments, compared with the complementation behavior observed in the heteroplasmic MERRF transformants, is that in the latter, the mutant and wild-type genomes coexisted in the same organelles from the time of the mutation. This would imply that the way in which mitochondrial DNA is sorted among different organelles plays a fundamental role in determining the oxidative-phosphorylation phenotype in mammalian cells. These results have significant implications for mitochondrial genetics and for studies on the transmission and therapy of mitochondrial DNA-linked diseases.
Modulating the potency of an activator in a yeast in vitro transcription system.
Authors: Ohashi Y , Brickman J M , Furman E , Middleton B , Carey M
Published: January 2012

The intrinsic stimulatory potential or potency of a eukaryotic gene activator is controlled by the interaction between the activation domain and the transcriptional machinery. To further understand this interaction, we undertook a biochemical study to identify parameters that could be used to modulate activator potency. We considered how varying the number of activation domains, their flexibility, and the number of promoter sites affects potency in a yeast nuclear extract. The effects of GAL4 derivatives bearing either one, two, or four herpes simplex virus VP16 activation domains (amino acids 413 to 454) were measured on DNA templates containing one or two GAL4 sites in a Saccharomyces cerevisiae nuclear extract. We found that multimerized VP16 activation domains acted synergistically to increase the potency of the activators. The spacing between the activation domains was critical, such that the increased flexibility imparted by a protein linker contributed to increased activator potency. With highly potent activators, the levels of transcription stimulated on a single site were saturating, whereas the stimulatory effect of weaker activators increased with the number of sites. We discuss how these biochemical studies relate to the mechanism of gene activation and synergy in a yeast in vitro system.
The lung-specific surfactant protein B gene promoter is a target for thyroid transcription factor 1 and hepatocyte nuclear factor 3, indicating common factors for organ-specific gene expression along the foregut axis.
Authors: Bohinski R J , Di Lauro R , Whitsett J A
Published: January 2012

We used the lung epithelial cell-specific surfactant protein B (SPB) gene promoter as a model with which to investigate mechanisms involved in transcriptional control of lung-specific genes. In a previous study, we showed that the SPB promoter specifically activated expression of a linked reporter gene in the continuous H441 lung cell line and that H441 nuclear proteins specifically protected a region of this promoter from bp -111 to -73. In this study, we further show that this region is a complex binding site for thyroid transcription factor 1 (TTF-1) and hepatocyte nuclear factor 3 (HNF-3). Whereas TTF-1 bound two highly degenerate and closely spaced sites, HNF-3 proteins bound a TGT3 motif (TGTTTGT) that is also found in several liver-specific gene regulatory regions, where it appears to be a weak affinity site for HNF-3. Point mutations of these binding sites eliminated factor binding and resulted in significant decreases in transfected SPB promoter activity. In addition, we developed a cotransfection assay and showed that a family of lung-specific gene promoters that included the SPB, SPC, SPA, and Clara cell secretory protein (CCSP) gene promoters were specifically activated by cotransfected TTF-1. We conclude that TTF-1 and HNF-3 are major activators of lung-specific genes and propose that these factors are involved in a general mechanism of lung-specific gene transcription. Importantly, these data also show that common factors are involved in organ-specific gene expression along the mammalian foregut axis.
Interaction of several related GC-box- and GT-box-binding proteins with the intronic enhancer is required for differential expression of the gb110 gene in embryonal carcinoma cells.
Authors: Hamann L , Bayer K U , Jensen K , Harbers K
Published: January 2012

The molecular mechanisms by which expression of a gene is down-regulated after differentiation of F9 embryonal carcinoma cells into parietal endoderm-like cells was studied by characterizing the cis- and trans-regulatory elements of the gb110 gene. This gene encodes a putative RNA helicase, and its expression is down-regulated when F9 cells are differentiated with retinoic acid and cyclic AMP. The 5'-flanking region of the gene has all of the features of a GC-rich island promoter and seems to play only a minor role, if any, in the regulated expression. A 133-bp enhancer in the first intron was identified by transient chloramphenicol acetyltransferase assays that activated expression in undifferentiated F9 cells about 50- to 100-fold. As this enhancer was not active in differentiated F9 cells, it seems to be the prime mediator of the differentiation-specific down-regulation of the gb110 gene. Four different protein-binding sites, three of which contain GC- and GT-box motifs, were identified in the enhancer element. The fourth site, interacting with previously described transcription factor FTZ-F1/ELP, seems to be of minor importance for the activity of the enhancer. Mutational analysis showed that the cooperative interaction of several most likely related proteins with the three GC- and GT-box motifs was required for full enhancer activity. On the basis of their binding properties, at least two of these proteins seem to be identical or closely related to ubiquitous transcription factor Sp1. One of the GT-box-binding proteins was present in undifferentiated F9 cells but not, however, in its differentiated derivatives. The cell specificity of this transcription factor explains why the gb110 gene is not expressed or expressed only at low levels in parietal endoderm-like cells.
DNA methylation represses the murine alpha 1(I) collagen promoter by an indirect mechanism.
Authors: Rhodes K , Rippe R A , Umezawa A , Nehls M , Brenner D A , Breindl M
Published: January 2012

Several lines of evidence indicate that DNA methylation plays a role in the transcriptional regulation of the murine alpha 1(I) collagen gene. To study the molecular mechanisms involved, a reporter gene construct containing the alpha 1(I) promoter and part of the first exon linked to the luciferase gene (Col3luc) was methylated in vitro and transfected into murine fibroblasts and embryonal carcinoma cells. Methylation resulted in repression of the alpha 1(I) promoter in both cell types, although it was less pronounced in embryonal carcinoma cells than in fibroblasts. The extent of repression depended on the density of methylation. DNase footprint and mobility shift assays indicated that the trans-acting factors binding to the alpha 1(I) promoter and first exon are ubiquitous factors and that their DNA binding is not inhibited by methylation. Transfection of Col3luc into Drosophila SL2 cells together with expression vectors for the transcription factors Sp1 and NF-1 showed that DNA methylation also inhibits the alpha 1(I) promoter in nonvertebrate cells, although to a much lesser extent than in murine cells. However, Sp1 and NF-1 transactivated the unmethylated and methylated reporter gene in SL2 cells equally well, confirming that these factors can bind and transactivate methylated DNA and indicating that DNA methylation represses the alpha 1(I) promoter by an indirect mechanism. This was further confirmed by cotransfection experiments with unspecific methylated competitor DNA which partially restored the activity of the methylated alpha 1(I) promoter. Our results suggest that DNA methylation can inhibit promoter activity by an indirect mechanism independent of methyl-C-binding proteins and that in vertebrate cells, chromatin structure and methyl-C-binding proteins cooperatively mediate the transcriptional inhibitory effect of DNA methylation.