118,459 research outputs found
AGenDA: gene prediction by cross-species sequence comparison
No full textTaher L, Rinner O, Garg S, Sczyrba A, Morgenstern B. AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research. 2004;32(Web Server):W305-W308.Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprinting: they exploit the fact that functionally important regions in genomic sequences are usually more conserved than non-functional regions. We created a WWW-based software program for homology-based gene prediction at BiBiServ (Bielefeld Bioinformatics Server). Our tool takes pairs of evolutionary related genomic sequences as input data, e.g. from human and mouse. The server runs CHAOS and DIALIGN to create an alignment of the input sequences and subsequently searches for conserved splicing signals and start/stop codons near regions of local sequence conservation. Genes are predicted based on local homology information and splice signals. The server returns predicted genes together with a graphical representation of the underlying alignment. The program is available at http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/
Covert brain ischaemia in splenectomised adults with thalassemia intermedia: An emerging entity
No full text[No abstract available]Chen SQ, 1996, AM J PHYSIOL-HEART C, V270, pH1951; Goldschmidt N, 2008, THROMB HAEMOSTASIS, V100, P864, DOI 10.1160-TH08-03-0157; Karimi M, 2010, THROMB HAEMOSTASIS, V103, P989, DOI 10.1160-TH09-09-0661; LONGSTRETH WT JR, 2005, STROKE, V36, P56; Pantoni L, 2007, CURR OPIN NEUROL, V20, P390, DOI 10.1097-WCO.0b013e328172d661; Taher A, 2006, THROMB HAEMOSTASIS, V96, P488, DOI 10.1160-TH06-05-0267; Taher AT, 2008, BLOOD REV, V22, P283, DOI 10.1016-j.blre.2008.04.001; Taher AT, 2010, J THROMB HAEMOST, V8, P54, DOI 10.1111-j.1538-7836.2009.03651.x21
AGenDA: homology-based gene prediction
No full textTaher L, Rinner O, Garg S, et al. AGenDA: homology-based gene prediction. BIOINFORMATICS. 2003;19(12):1575-1577.We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment
Thrombosis in thalassemia: Why are we so concerned?
No full textAlthough life expectancy of thalassemia patients has markedly improved over the last few decades, patients still suffer from many complications of this congenital disease. The presence of a high incidence of thromboembolic events (TEE), mainly in β-thalassemia intermedia (β-TI), has led to the identification of a hypercoagulable state in these patients. In this review, the molecular and cellular mechanisms leading to hypercoagulability in thalassemia are highlighted, with a special focus on thalassemia intermedia being the group with the highest incidence of thrombotic events as compared to other types of thalassemia. Clinical experience and available clues on optimal management are also discussed. © 2011 Informa Healthcare USA, Inc.Atichartakarn V, 2002, BRIT J HAEMATOL, V118, P893, DOI 10.1046-j.1365-2141.2002.03711.x; Atichartakarn V, 2003, INT J HEMATOL, V77, P299, DOI 10.1007-BF02983790; Yashar Vered Borenstain-Ben, 1993, American Journal of Hematology, V44, P63, DOI 10.1002-ajh.2830440114; Pignatti CB, 1998, ACTA HAEMATOL-BASEL, V99, P76; Borgna-Pignatti C, 2004, HAEMATOLOGICA, V89, P1187; BUTTHEP P, 1995, THROMB HAEMOSTASIS, V74, P1045; Butthep P, 1997, SE ASIAN J TROP M S3, V28, P141; Cadili A, 2008, AM J MED, V121, P371, DOI 10.1016-j.amjmed.2008.02.014; Cappellini MD, 2010, ANN N Y ACAD SCI, V1202, P231; Cappellini MD, 2000, BRIT J HAEMATOL, V111, P467, DOI 10.1046-j.1365-2141.2000.02376.x; Cappellini MD, 2005, ANN N Y ACAD SCI, V1054, P317; Crary SE, 2009, BLOOD, V114, P2861, DOI 10.1182-blood-2009-04-210112; DELPRINCIPE D, 1993, BRIT J HAEMATOL, V84, P111; ELDOR A, 1991, BLOOD, V77, P1749; ELDOR A, 1989, AM J HEMATOL, V32, P94, DOI 10.1002-ajh.2830320204; Habib A, 2008, HAEMATOL-HEMATOL J, V93, P941, DOI 10.3324-haematol.12460; Helley D, 1996, THROMB HAEMOSTASIS, V76, P322; HERSHKO C, 1978, BRIT J HAEMATOL, V40, P255, DOI 10.1111-j.1365-2141.1978.tb03662.x; Hovav T, 1999, BRIT J HAEMATOL, V106, P178; Iolascon A, 2001, HAEMATOLOGICA, V86, P1112; Karimi M, 2010, THROMB HAEMOSTASIS, V103, P989, DOI 10.1160-TH09-09-0661; Kuypers FA, 2004, CELL MOL BIOL, V50, P147; Manfre L, 1999, AM J ROENTGENOL, V173, P1477; Ruf A, 1997, BRIT J HAEMATOL, V98, P51, DOI 10.1046-j.1365-2141.1997.1502965.x; Rund D, 2005, NEW ENGL J MED, V353, P1135, DOI 10.1056-NEJMra050436; Steinberg MH, 2009, DISORDERS OF HEMOGLOBIN: GENETICS, PATHOPHYSIOLOGY, AND CLINICAL MANAGEMENT, 2ND EDITION, P1, DOI 10.1017-CBO9780511596582; Sumiyoshi A, 1992, SE ASIAN J TROP M S2, V23, P29; Taher A, 2006, THROMB HAEMOSTASIS, V96, P488, DOI 10.1160-TH06-05-0267; Taher A, 2009, BRIT J HAEMATOL, V147, P634, DOI 10.1111-j.1365-2141.2009.07848.x; Taher AT, 2008, BLOOD REV, V22, P283, DOI 10.1016-j.blre.2008.04.001; Taher AT, 2010, BRIT J HAEMATOL, V150, P486, DOI 10.1111-j.1365-2141.2010.08220.x; Taher AT, 2011, BRIT J HAEMATOL, V152, P512, DOI 10.1111-j.1365-2141.2010.08486.x; Taher AT, 2010, J THROMB HAEMOST, V8, P2152, DOI 10.1111-j.1538-7836.2010.03940.x; Taher AT, 2010, J THROMB HAEMOST, V8, P54, DOI 10.1111-j.1538-7836.2009.03651.x; Taher AT, 2010, BLOOD, V115, P1886, DOI 10.1182-blood-2009-09-243154; Tavazzi D, 2001, BRIT J HAEMATOL, V112, P48, DOI 10.1046-j.1365-2141.2001.02482.x; Tripodi A, 2009, HAEMATOL-HEMATOL J, V94, P1520, DOI 10.3324-haematol.2009.010546; WINICHAGOON P, 1981, Southeast Asian Journal of Tropical Medicine and Public Health, V12, P556; Zalloua PA, 2003, THROMB HAEMOSTASIS, V89, P767; ZURLO MG, 1989, LANCET, V2, P2716191
Management of Non-Transfusion-Dependent Thalassemia: A Practical Guide
No full textDespite their transfusion-independence, non-transfusion-dependent thalassemia (NTDT) patients experience a variety of serious clinical complications that require prompt and comprehensive management. Transfusion therapy may still be an important part of management of this disease, in cases of acute stress, to support growth and development in childhood, or to prevent clinical morbidities stemming from ineffective erythropoiesis or hemolytic anemia. Although splenectomy is associated with improvements in hemoglobin levels, it leads to several short- and long-term adverse events, warranting caution in application of this intervention. Fetal hemoglobin induction therapy has been evaluated in non-randomized studies, with benefits extending beyond hematologic improvements to lowering morbidity risk. Effective and safe iron chelation therapy is now available for NTDT patients in whom iron overload develops, irrespective of transfusions, due to increased intestinal absorption, ultimately leading to clinically high iron burden levels and subsequent morbidity. 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Iron overload in non-transfusion-dependent thalassemia: A clinical perspective
No full textIron overload due to increased intestinal iron absorption represents an important clinical problem in patients with non-transfusion-dependent thalassemia (NTDT), particularly as they advance in age. Current models for iron metabolism in patients with beta (β)-thalassemia intermedia (TI) suggest that suppression of serum hepcidin results in increased iron absorption and release of iron from the reticuloendothelial system, leading to depletion of macrophage iron, relatively low levels of serum ferritin, and liver iron loading. The clinical consequences of iron overload in patients with NTDT are multifactorial and include endocrinopathy, bone disease, thromboembolism, pulmonary hypertension, cerebrovascular and neuronal damage, liver fibrosis or cirrhosis, and increased risk of hepatocellular carcinoma. Although serum ferritin levels correlate with liver iron concentration (LIC), they underestimate iron load in these patients compared with transfusion-dependent patients with equivalent LIC. Therefore, direct measurement of LIC is recommended with chelation therapy as indicated. © 2012 Elsevier Ltd.Au WY, 2009, ANN HEMATOL, V88, P947, DOI 10.1007-s00277-009-0701-2; Borgna-Pignatti C, 2004, BRIT J HAEMATOL, V124, P114, DOI 10.1046-j.1365-2141.2003.04732.x; Chui DHK, 2003, BLOOD, V101, P791, DOI 10.1182-blood-2002-07-1975; Gardenghi S, 2010, HEMATOL ONCOL CLIN N, V24, P1089, DOI 10.1016-j.hoc.2010.08.003; Lal A, 2011, NEW ENGL J MED, V364, P710, DOI 10.1056-NEJMoa1010174; LOMBARDO T, 1995, ANN HEMATOL, V71, P135, DOI 10.1007-BF01702649; Mancuso Andrea, 2010, World J Hepatol, V2, P171, DOI 10.4254-wjh.v2.i5.171; Mavrogeni S, 2008, INT J CARDIOVAS IMAG, V24, P849, DOI 10.1007-s10554-008-9332-2; Melchiori L, 2010, ADV HEMATOL, V2010; Musallam KM, 2012, ANN HEMATOL, V91, P235, DOI 10.1007-s00277-011-1291-3; Musallam KM, 2011, HAEMATOL-HEMATOL J, V96, P1605, DOI 10.3324-haematol.2011.047852; Musallam KM, 2011, EUR J HAEMATOL, V87, P539, DOI 10.1111-j.1600-0609.2011.01706.x; Origa R, 2008, HAEMATOL-HEMATOL J, V93, P1095, DOI 10.3324-haematol.12484; Origa R, 2007, HAEMATOL-HEMATOL J, V92, P583, DOI 10.3324-haematol.10842; Pakbaz Z, 2007, PEDIATR BLOOD CANCER, V49, P329, DOI 10.1002-pbc.21275; Pietrangelo A, 2004, NEW ENGL J MED, V350, P2383, DOI 10.1056-NEJMra031573; Pantalone GR, 2010, BRIT J HAEMATOL, V150, P245, DOI 10.1111-j.1365-2141.2010.08180.x; Roghi A, 2010, ANN HEMATOL, V89, P585, DOI 10.1007-s00277-009-0879-3; St Pierre TG, 2005, BLOOD, V105, P855, DOI 10.1182-blood-2004-01-0177; Taher A, 2008, HAEMATOL-HEMATOL J, V93, P1584, DOI 10.3324-haematol.13098; Taher A, 2009, BRIT J HAEMATOL, V146, P569, DOI 10.1111-j.1365-2141.2009.07810.x; Taher A, 2009, BRIT J HAEMATOL, V147, P634, DOI 10.1111-j.1365-2141.2009.07848.x; Taher AT, 2010, AM J HEMATOL, V85, P288, DOI 10.1002-ajh.21626; Taher AT, 2010, BRIT J HAEMATOL, V150, P486, DOI 10.1111-j.1365-2141.2010.08220.x; Taher AT, 2011, BRIT J HAEMATOL, V152, P512, DOI 10.1111-j.1365-2141.2010.08486.x; Taher AT, 2010, J THROMB HAEMOST, V8, P54, DOI 10.1111-j.1538-7836.2009.03651.x; Tanno T, 2009, BLOOD, V114, P181, DOI 10.1182-blood-2008-12-195503; Tanno T, 2007, NAT MED, V13, P1096, DOI 10.1038-nm1629; Tanno T, 2010, ADV HEMATOL, V2010; Voskaridou E, 2004, BRIT J HAEMATOL, V126, P736, DOI 10.1111-j.1365-2141.2004.05104.x; Wood JC, 2005, BLOOD, V106, P1460, DOI 10.1182-blood-2004-10-398222252
New Trends in Iron Chelation: Impacting Outcomes
No full textThe availability of the effective, well-tolerated, and convenient, once-daily oral iron chelation therapy, deferasirox, has the potential to change clinical practice in a number of ways. It is possible that the outcome of patients who are currently receiving chelation therapy could be improved by freeing them from the burden of frequent, intravenous infusions of deferoxamine (DFO) and thereby improving long-term compliance. In addition, the ease of treatment may make treatment accessible to patients who currently do not receive iron chelation therapy. The potential of deferasirox therapy is illustrated in two typical clinical cases. One outlines a patient with β-thalassemia who is struggling to comply with DFO or DFO-deferiprone combination therapy and is consequently failing therapy and susceptible to the serious clinical sequelae of iron overload. The other is a patient with myelodysplastic syndrome who is transfusion-dependent and chelation-naïve, initiating therapy for the first time. © 2007 Elsevier Inc. All rights reserved.Alessandrino EP, 2002, HAEMATOLOGICA, V87, P1286; BRITTENHAM GM, 1994, NEW ENGL J MED, V331, P567, DOI 10.1056-NEJM199409013310902; Cappellini MD, 2005, BLOOD, V106; Cappellini MD, 2006, BLOOD, V107, P3455, DOI 10.1182-blood-2005-08-3430; Davis BA, 2000, BLOOD, V95, P1229; Gattermann N., 2005, HEMATOL ONCOL CLI S1, V19, P13; Gattermann N, 2005, HEMATOL ONCOL CLI S1, V19, P18; Greenberg Peter L, 2006, J Natl Compr Canc Netw, V4, P58; Kattamis C, 2005, BLOOD, V106; Malcovati L, 2005, J CLIN ONCOL, V23, P7594, DOI 10.1200-JCO.2005.01.7038; Piga A, 2006, HAEMATOL-HEMATOL J, V91, P873; TAHER A, 2005, BLOOD, V106; VICHINSKY E, 2005, BLOOD, V10622
Effects of moderate water stress and shading on survival, growth and resource allocation of two cork oak (Quercus suber L.) provenances
No full textSixty-four plants of Cork oak (Quercus suber L.) originating from Spain and Tunisia provenances were grown under a combination of two light levels (15 % (moderate shade) versus 5 % (deep shade) of full-light) and two water regimes (well-watered versus moderate water stress) in a nursery in Spain. Ten response variables including seedling survival, height, diameter, height-to-diameter ratio, above-and below-ground biomass, total biomass, shoot-to-root ratio, number and length of growth unit were measured for each provenance. In average, seedling survival was 89 % and was independent of the studied factors (provenance, light, water regime). Seedling height was similar in both provenances, while diameter was significantly larger in the Spanish provenance. Water stress adversely affected the balance between height and diameter for the Spanish provenance, but not for the Tunisian provenance, while light, and independently of seedlings’ provenance, affected 80 % (8/10) of traits studied. Thus, the Tunisian provenance seemed to be more tolerant to water stress while none of both provenances seemed to be more tolerant to shade. However, when considering both factors the Spanish provenance showed a better seedlings’ acclimation to water stress under deep shade and may constitute accordingly a better material for afforestation as in Mediterranean conditions, as our results show, light and water stress may act in a coordinate manner. This variability would be mainly genetically controlled, as both provenances were cultivated under the same environmental conditions. Our results may be helpful in regeneration, cultivation and afforestation of cork oak.Effets d’un stress hydrique modéré et de l’ombrage sur la survie, la croissance et l’allocation des ressources de deux provenances de Chêne-liège (Quercus suber L.).
Deux provenances (64 plants) de Chêne-liège (Quercus suber L.) originaires de l’Espagne et de la Tunisie ont été élevées sous deux niveaux d’intensité lumineuse (15 % (ombre modérée) et 5 % (ombre profonde) de pleine lumière) et deux régimes hydriques (plants irrigués à 100 % de la capacité au champ et plants soumis à un stress hydrique modéré) dans une pépinière en Espagne. Dix variables comprenant la survie des plants, la hauteur, le diamètre, le rapport hauteur/ diamètre, les biomasses aérienne, souterraine et totale, le rapport biomasse tige/racine, le nombre et la longueur des unités de croissance ont été mesurées pour chaque provenance. Le taux de survie des plants a été de 89 % indépendamment des facteurs étudiés (provenance, lumière, régime hydrique). La hauteur des plants a été similaire pour les deux provenances, alors que leur diamètre a été significativement plus grand pour la provenance Espagnole. Le stress hydrique a affecté l’équilibre de croissance entre la hauteur et le diamètre des plants mais seulement pour la provenance Espagnole, alors que la lumière, et indépendamment de la provenance des plants, a affecté 80 % (8/10) des traits étudiés. Ainsi, la provenance Tunisienne a semblé plus tolérante au stress hydrique, alors qu’aucune des deux provenances n’a semblé plus tolérante que l’autre à l’ombrage. Cependant, lorsqu’on considère les deux facteurs, la provenance Espagnole a montré une plus grande capacité à s’acclimater au stress hydrique sous de faibles conditions lumineuses, ce qui lui confère ainsi un intérêt potentiel pour le reboisement puisqu’en conditions méditerranéennes, comme nos résultats le montrent, la lumière et le stress hydrique peuvent agir d’une façon conjuguée. Cette variabilité serait essentiellement de nature génétique, puisque les deux provenances ont été cultivées dans les mêmes conditions pédoclimatiques.Mechergui Taher, Pardos Marta. Effects of moderate water stress and shading on survival, growth and resource allocation of two cork oak (Quercus suber L.) provenances . In: Revue d'Écologie (La Terre et La Vie), tome 73, n°2, 2018. pp. 180-190
Optimal management of β thalassaemia intermedia
No full textOur understanding of the molecular and pathophysiological mechanisms underlying the disease process in patients with β thalassaemia intermedia (TI) has substantially increased over the past decade. The hallmark of disease process in patients with TI includes ineffective erythropoiesis, chronic haemolytic anaemia, and iron overload. There are a number of options currently available for managing patients with TI including splenectomy, transfusion therapy, iron chelation therapy, modulation of fetal haemoglobin production, and several other agents targeting specific clinical complications. Limited studies assessed the efficacy and safety of these modalities; hence, there are currently no clear guidelines for managing patients with TI. 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Computational methods for splice site prediction
No full textTaher L. Computational methods for splice site prediction. Bielefeld (Germany): Bielefeld University; 2006.Completing the genome sequence of a given organism is just the beginning of a series of subsequent tasks, namely, the discovery of the corresponding sequence complexities. For eukaryotic organisms, this refers especially to the documentation of the coding exons of each gene, as well as non-coding and regulatory sequences. In spite of the extensive research done in the area, the production of genomic data remains far ahead of the ability to reliably predict such features computationally.
Eukaryotic genes consist predominantly of exons and introns; while the introns are non-coding regions that are removed from the primary transcript during RNA splicing, the exons are the coding regions that are spliced together during the mRNA maturation process. The borders between exons and introns present conserved dinucleotides, and are called splice sites; the intron-exon boundary is referred to as acceptor splice site and the exon-intron boundary as donor splice site.
Accurate eukaryotic gene prediction clearly requires exact splice site prediction methods. There are different pattern recognition techniques available to assess the quality of candidate splice sites; most of them proceed by computing a score derived from models about the distribution of the nucleotides in the neighbourhood of a splice site consensus sequence. Using Support Vector Machines (SVM) and a kernel particularly designed for the study of biological sequences, we investigate which pattern occurrences in which positions are relevant for splice site prediction. In addition, we propose a splice site prediction method that improves traditional position-specific weight matrices. Finally, we contribute with an intron model that relies on secondary structure information and demonstrates the ability to distinguish intron sequences from random data
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