Genome-wide analysis of poly(A) site selection in schizosaccharomyces pombe,

Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3′ UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3′RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A)

General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4

Eukaryotes respond to amino acid starvation by enhancing the translation of mRNAs encoding b-ZIP family transcription factors (GCN4 in Saccharomyces cerevisiae and ATF4 in mammals), which launch transcriptional programs to counter this stress. This pathway involves phosphorylation of the eIF2 translation factor by Gcn2-protein kinases and is regulated by upstream ORFs (uORFs) in the GCN4/ATF4 5′ leaders. Here, we present evidence that the transcription factors that mediate this response are not evolutionarily conserved. Although cells of the fission yeast Schizosaccharomyces pombe respond transcriptionally to amino acid starvation, they lack clear Gcn4 and Atf4 orthologs. We used ribosome profiling to identify mediators of this response in S. pombe, looking for transcription factors that behave like GCN4. We discovered a transcription factor (Fil1) translationally induced by amino acid starvation in a 5′ leader and Gcn2-dependent manner. Like Gcn4, Fil1 is required for the transcriptional response to amino acid starvation, and Gcn4 and Fil1 regulate similar genes. Despite their similarities in regulation, function, and targets, Fil1 and Gcn4 belong to different transcription factor families (GATA and b-ZIP, respectively). Thus, the same functions are performed by nonorthologous proteins under similar regulation. These results highlight the plasticity of transcriptional networks, which maintain conserved principles with nonconserved regulators

Contribuciones para el aprendizaje de las Ciencias de la Tierra, desde un espacio de educación no formal

El presente trabajo da a conocer una serie de actividades planificadas y realizadas desde un espacio de Educación no formal como es el Museo de Ciencias Naturales y Antropológicas "Prof. Antonio Serrano", en la Ciudad de Paraná Entre Ríos, con el objetivo de promover el conocimiento de las Ciencias de la Tierra. Las mismas son proyectadas con el fin de contribuir a acortar la distancia existente entre el conocimiento geológico producido por los científicos y el conocimiento de la sociedad. Se clasifican en cuatro ejes interrelacionados entre sí; el eje Investigación y sus productos, agrupa acciones destinadas a la producción del conocimiento geológico provincial y su sociabilización, publicadas en revistas, libros, jornadas y congresos; el eje didáctico presenta actividades relacionadas con la enseñanza de las Ciencias de la Tierra, efectuando trabajos interdisciplinarios entre el Museo y las instituciones educativas; el eje académico y de extensión concentra tareas de capacitación y extensión con entidades culturales y educativas; por último el eje infraestructura destinado a fomentar la creación de espacios dinámicos, dentro y fuera ámbito del Museo. Evaluadores externos e internos, nos motivan a generar acciones de mejora continua, dirigidas a mantener la calidad en los distintos ejes, como también a proyectar nuevas propuestas. La creciente demanda de las actividades didácticas, reflejan que los objetivos planteados están siendo alcanzados y en algunos casos superados; respondiendo así el Museo Serrano a las necesidades de la comunidad.Trabajos del área Ciencias NaturalesDepartamento de Ciencias Exactas y Naturale

A novel preoperative model to predict 90-day surgical mortality in patients considered for renal cell carcinoma surgery

Introduction Surgical benefits for renal cell carcinoma must be weighed against competing causes of mortality, especially in the elderly patient population. We used a large cancer registry to evaluate the impact of patient and cancer-specific factors on 90-day mortality (90DM). A nomogram to predict the odds of short-term mortality was created. Materials and Methods The National Cancer Database was queried to identify all patients with clinically localized, nonmetastatic disease treated with partial or radical nephrectomy. Using a random sample of 60%, multiple logistic regression with 90DM outcomes were performed to identify preoperative variables associated with mortality. Variables included age, sex, race, co-morbidity score, tumor size, and presence of a thrombus. A nomogram was created and tested on the remaining 40% of patients to predict 90DM. Results 183,407 patients met inclusion criteria. Overall 90DM for the cohort was 1.9%. All preoperative variables significantly influenced the risk of 90DM. Patient age was by far the strongest predictor. Nomogram scores ranged from 0 to 12. Compared to patients with 0 to 1 points, those with 2 to 3 (odds ratio [OR] 2.89, 2.42–3.46; P 6 (OR 12.86, 10.83–15.27; P 80 years of age alone placed patients into the highest risk of surgical mortality. Conclusions Management of localized kidney cancer must consider competing causes of mortality, especially in elderly patients with multiple co-morbidities. We present a preoperative tool to calculate risk of surgical short-term mortality to aid surgeon–patient counseling

Management of Pain in Autosomal Dominant Polycystic Kidney Disease and Anatomy of Renal Innervation

Purpose Chronic pain is a prominent feature of autosomal dominant polycystic kidney disease that is difficult to treat and manage, often resulting in a decrease in quality of life. Understanding the underlying anatomy of renal innervation and the various etiologies of pain that occur in autosomal dominant polycystic kidney disease can help guide proper treatments to manage pain. Reviewing previously studied treatments for pain in autosomal dominant polycystic kidney disease can help characterize treatment in a stepwise fashion. Materials and Methods We performed a literature search of the etiology and management of pain in autosomal dominant polycystic kidney disease and the anatomy of renal innervation using PubMed® and Embase® from January 1985 to April 2014 with limitations to human studies and English language. Results Pain occurs in the majority of patients with autosomal dominant polycystic kidney disease due to renal, hepatic and mechanical origins. Patients may experience different types of pain which can make it difficult to clinically confirm its etiology. An anatomical and histological evaluation of the complex renal innervation helps in understanding the mechanisms that can lead to renal pain. Understanding the complex nature of renal innervation is essential for surgeons to perform renal denervation. The management of pain in autosomal dominant polycystic kidney disease should be approached in a stepwise fashion. Acute causes of renal pain must first be ruled out due to the high incidence in autosomal dominant polycystic kidney disease. For chronic pain, nonopioid analgesics and conservative interventions can be used first, before opioid analgesics are considered. If pain continues there are surgical interventions such as renal cyst decortication, renal denervation and nephrectomy that can target pain produced by renal or hepatic cysts. Conclusions Chronic pain in patients with autosomal dominant polycystic kidney disease is often refractory to conservative, medical and other noninvasive treatments. There are effective surgical procedures that can be performed when more conservative treatments fail. Laparoscopic cyst decortication has been well studied and results in the relief of chronic renal pain in the majority of patients. In addition, renal denervation has been used successfully and could be performed concurrently with cyst decortication. Nephrectomy should be reserved for patients with intractable pain and renal failure when other modalities have failed

Native Nephrectomy with Renal Transplantation Decreases Hypertension Medication Requirements in Autosomal Dominant Polycystic Kidney Disease

Purpose We assessed hypertensive control after native nephrectomy and renal transplantation in patients with autosomal dominant polycystic kidney disease. Materials and Methods Blood pressure control was studied retrospectively in 118 patients with autosomal dominant polycystic kidney disease who underwent renal transplantation between 2003 and 2013. Overall 54 patients underwent transplantation alone (group 1) and 64 underwent transplantation with concurrent ipsilateral nephrectomy (group 2). Of these 64 patients 32 underwent ipsilateral nephrectomy only (group 2a) and 32 underwent eventual delayed contralateral native nephrectomy (group 2b). The number of antihypertensive drugs and defined daily dose of each antihypertensive was recorded at transplantation and up to 36-month followup. Results Comparing preoperative to postoperative medications at 12, 24 and 36-month followup, transplantation with concurrent ipsilateral nephrectomy had a greater decrease in quantity (−1.2 vs −0.5 medications, p=0.008; −1.1 vs −0.3, p=0.007 and −1.2 vs −0.4, p=0.03, respectively) and defined daily dose of antihypertensive drug (−3.3 vs −1.0, p=0.0008; −2.9 vs −1.0, p=0.006 and −2.7 vs −0.6, p=0.007, respectively) than transplantation alone at each point. Native nephrectomy continued to be a predictor of hypertensive requirements on multivariable analysis (p <0.0001). The mean decrease in number of medications in group 2b from after ipsilateral nephrectomy to 12 months after contralateral nephrectomy was −0.6 (p=0.0005) and the mean decrease in defined daily dose was −0.6 (p=0.009). Conclusions In patients with autosomal dominant polycystic kidney disease undergoing renal transplantation, concurrent ipsilateral native nephrectomy is associated with a significant decrease in the quantity and defined daily dose of antihypertensive drugs needed for hypertension control. Delayed contralateral native nephrectomy is associated with improved control of blood pressure to an even greater degree

Reducing Operating Room Costs through Real Time Cost Information Feedback: A Pilot Study

Purpose: To create a protocol for providing real-time operating room (OR) cost feedback to surgeons. We hypothesize that this protocol will reduce costs in a responsible way without sacrificing quality of care. Methods: All OR costs were obtained and recorded for robot-assisted partial nephrectomy and laparoscopic donor nephrectomy. Before the beginning of this project, costs pertaining to the 20 most recent cases were analyzed. Items were identified from previous cases as modifiable for replacement or omission. Timely feedback of total OR costs and cost of each item used was provided to the surgeon after each case, and costs were analyzed. Results: A cost analysis of the robot-assisted partial nephrectomy before the washout period indicates expenditures of $5243.04 per case. Ten recommended modifiable items were found to have an average per case cost of$1229.33 representing 23.4% of the total cost. A postwashout period cost analysis found the total OR cost decreased by $899.67 (17.2$3530.05 with $457.54 attributed to modifiable items. After the washout period, modifiable items costs were reduced by$289.73 (8.0%). No complications occurred in the donor nephrectomy cases while one postoperative complication occurred in the partial nephrectomy group. Conclusion: Providing surgeons with feedback related to OR costs may lead to a change in surgeon behavior and decreased overall costs. Further studies are needed to show equivalence in patient outcomes

<i>Schizosaccharomyces pombe</i> Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex

ELL family transcription factors activate the overall rate of RNA polymerase II (Pol II) transcription elongation by binding directly to Pol II and suppressing its tendency to pause. In metazoa, ELL regulates Pol II transcription elongation as part of a large multisubunit complex referred to as the Super Elongation Complex (SEC), which includes P-TEFb and EAF, AF9 or ENL, and an AFF family protein. Although orthologs of ELL and EAF have been identified in lower eukaryotes including Schizosaccharomyces pombe, it has been unclear whether SEClike complexes function in lower eukaryotes. In this report, we describe isolation from S. pombe of an ELL-containing complex with features of a rudimentary SEC. This complex includes S. pombe Ell1, Eaf1, and a previously uncharacterized protein we designate Ell1 binding protein 1 (Ebp1), which is distantly related to metazoan AFF family members. Like the metazoan SEC, this S. pombe ELL complex appears to function broadly in Pol II transcription. Interestingly, it appears to have a particularly important role in regulating genes involved in cell separation

A Parallel Randomized Clinical Trial Examining the Return of Urinary Continence After Robot- Assisted Radical Prostatectomy with or without a Small Intestinal Submucosa Bladder Neck Sling

Purpose Urinary continence is a driver of quality of life after radical prostatectomy. In this study we evaluated the impact of a biological bladder neck sling on the return of urinary continence after robot-assisted radical prostatectomy. Materials and Methods This study compared early continence in patients undergoing robot-assisted radical prostatectomy with a sling and without a sling in a 2-group, 1:1, parallel, randomized controlled trial. Patients were blinded to group assignment. The primary outcome was defined as urinary continence (0 to 1 pad per day) at 1 month postoperatively. Inclusion criteria were organ confined prostate cancer and a prostate specific antigen less than 15 ng/ml. Exclusion criteria were any prior surgery on the prostate, a history of neurogenic bladder and history of pelvic radiation. A chi-squared test was used for the primary outcome. Results A total of 147 patients were randomized (control 74, sling 73) and 92% were available for primary end point analysis at 1 month. There were no significant differences in baseline or perioperative data except that operating room time was 20.1 minutes longer for the sling group (p=0.04). The continence rate was similar between the control and sling groups at 1 month (47.1% vs 55.2%, p=0.34) and 12 months (86.7% vs 94.5%, p=0.15), respectively. Adverse events were similar between the control and sling groups (10.8% vs 13.7%, p=0.59). Conclusions The application of an absorbable urethral sling at robot-assisted radical prostatectomy was well tolerated with no increase in obstructive symptoms in this randomized trial. However, the sling failed to show a significant improvement in continence

Correcting the Shrinkage Effects of Formalin Fixation and Tissue Processing for Renal Tumors: toward Standardization of Pathological Reporting of Tumor Size

Given the importance of correctly staging renal cell carcinomas, specific guidelines should be in place for tumor size measurement. While a standard means of renal tumor measurement has not been established, intuitively, tumor size should be based on fresh measurements. We sought to assess the accuracy of postfixation and microscopic measurements of renal tumor size, as compared to fresh measurements and radiographic size. Thirty-four nephrectomy cases performed by a single surgeon were prospectively measured at different time points. The study cases included 23 clear cell renal cell carcinomas, 6 papillary renal cell carcinomas, and 5 other renal tumors. Radiologic tumors were 12.1% larger in diameter than fresh tumors (P<0.01). Furthermore, fresh specimens were 4.6% larger than formalin-fixed specimens (P<0.01), and postfixation measurements were 7.1% greater than microscopic measurements (P<0.01). The overall mean percentage of shrinkage between fresh and histological specimens was 11.4% (P<0.01). Histological processing would cause a tumor stage shift from pT1b to pT1a for two tumors in this study. The shrinkage effects of formalin fixation and histological processing may result in understaging of renal cell carcinomas. The shrinkage factor should be considered when reporting tumor size