Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families

International audienceBackground: Disulphide bridges are well known to play key roles in stability, folding and functions of proteins. Introduction or deletion of disulphides by site-directed mutagenesis have produced varying effects on stability and folding depending upon the protein and location of disulphide in the 3-D structure. Given the lack of complete understanding it is worthwhile to learn from an analysis of extent of conservation of disulphides in homologous proteins. We have also addressed the question of what structural interactions replaces a disulphide in a homologue in another homologue.Results: Using a dataset involving 34,752 pairwise comparisons of homologous protein domains corresponding to 300 protein domain families of known 3-D structures, we provide a comprehensive analysis of extent of conservation of disulphide bridges and their structural features. We report that only 54% of all the disulphide bonds compared between the homologous pairs are conserved, even if, a small fraction of the non-conserved disulphides do include cytoplasmic proteins. Also, only about one fourth of the distinct disulphides are conserved in all the members in protein families. We note that while conservation of disulphide is common in many families, disulphide bond mutations are quite prevalent. Interestingly, we note that there is no clear relationship between sequence identity between two homologous proteins and disulphide bond conservation. Our analysis on structural features at the sites where cysteines forming disulphide in one homologue are replaced by non-Cys residues show that the elimination of a disulphide in a homologue need not always result in stabilizing interactions between equivalent residues.Conclusion: We observe that in the homologous proteins, disulphide bonds are conserved only to a modest extent. Very interestingly, we note that extent of conservation of disulphide in homologous proteins is unrelated to the overall sequence identity between homologues. The non-conserved disulphides are often associated with variable structural features that were recruited to be associated with differentiation or specialisation of protein function

Diagnostic utility of p63/P501S double sequential immunohistochemical staining in differentiating urothelial carcinoma from prostate carcinoma

<p>Abstract</p> <p>Background</p> <p>Distinguishing urothelial carcinoma (UC) from prostate carcinoma (PC) is important due to potential therapeutic and prognostic implications. However, this can be a diagnostic challenge when there is limited tissue and in poorly differentiated tumors. We evaluated the diagnostic utility of a dual immunohistochemical stain comprising p63 and P501S (prostein), applied sequentially on a single slide and visualized by double chromogen reaction, in differentiating these two cancers. Thus far, there have been no previous studies assessing the diagnostic utility of p63 and P501S combined together as a dual immunostain in distinguishing between these two cancers.</p> <p>Methods</p> <p>p63/P501S dual-color sequential immunohistochemical staining was performed on archival material from 132 patients with high-grade UC and 23 patients with PC, and evaluated for p63 (brown nuclear) and P501S (red cytoplasmic) expression. Both the staining intensity and percentage of positive tumor cells were assessed.</p> <p>Results</p> <p>p63 was positive in 119/132 of UC and negative in PC. P501S was positive in 22/23 of PC and negative in UC. The p63+/P501S- immunoprofile had 90% sensitivity and 100% specificity for UC. The p63-/P501S+ immunoprofile had 96% sensitivity and 100% specificity for PC.</p> <p>Conclusion</p> <p>Our results indicate that double sequential immunohistochemical staining with p63 and P501S is highly specific and can be a useful tool in distinguishing UC from PC especially when there is limited diagnostic tissue as it can be performed on a single slide.</p

Pathology Case Study: Left Internal Carotid Artery Thrombosis

This âTransfusion Medicineâ case study provided by the University of Pittsburgh Department of Pathology is an excellent resource for students and instructors in the health science fields. This particular case involves the diagnosis of a 36-year-old male admitted to the hospitalâs emergency room âin an altered state of consciousness.â Laboratory results including drug/alcohol screens, an MRI, CT scan and EEG were used to diagnose the patient in this case. The official diagnosis of this patient is provided in the âFinal Diagnosisâ section, and is accompanied by a discussion of the case and a short list of references. This is an excellent resource for students in the health sciences to familiarize themselves with using patient history and laboratory results to diagnose patientâs conditions

Emergence of Maruca vitrata as a major pest of food legumes and evolution of management practices in Asia and Africa

Legume pod borer, Maruca vitrata, has emerged as a major pest on food legumes in Asia and Africa. It is an oligophagous pest, feeding on over 70 species in Fabaceae. We examine the species complex in Asia, Africa, Oceania, and the Americas, with an emphasis on molecular taxonomy. Studies on pheromone production and perception suggest the existence of pheromone polymorphism, especially in Asia and Africa. No Maruca-resistant varieties are available in the major food legumes including cowpea, pigeonpea, mungbean, and yard-long bean. Legume growers use chemical pesticides indiscriminately, leading to the development of pesticide resistance. However recent developments in habitat management, classical biocontrol with more efficient parasitoids, biopesticides, and judicious use of insecticides pave the way for sustainable management of M. vitrata, which can reduce the pesticide misuse. Active engagement of the private sector and policy makers can increase the adoption of integrated pest management approaches in food legumes

Impact toughness of copper, zinc, tin, a-brass and phosphor bronze at different temperatures

Metals and alloys should have adequate toughness apart fiom other properties like tensile strength, corrosion resistance, creep resistance, fatigue strength etc. This will enable them to withstand impact loading. Toughness depends on temperature, crystal structure etc. An attempt has been made to determine toughness of copper, zinc and tin and their alloys over a range of temperatures fiom 263K to recrystallization temperature (0.4 Tm) Toughness increases as temperature increases, remains constant and then decreases near about the recrystallization temperature for allmetals and alloys tested. The initial increase is due to an increase in dislocation mobility and the final decrease is due to coarsening of grains

Phylogeographical Structure in Mitochondrial DNA of Legume Pod Borer (Maruca vitrata) Population in Tropical Asia and Sub-Saharan Africa.

This study was undertaken to assess the genetic diversity and host plant races of M. vitrata population in South and Southeast Asia and sub-Saharan Africa. The cytochrome c oxidase subunit 1 (cox1) gene was used to understand the phylogenetic relationship of geographically different M. vitrata population, but previous studies did not include population from Southeast Asia, the probable center of origin for Maruca, and from east Africa. Extensive sampling was done from different host plant species in target countries. Reference populations from Oceania and Latin America were used. An amplicon of 658 bp was produced by polymerase chain reaction, and 64 haplotypes were identified in 686 M. vitrata individuals. Phylogenetic analysis showed no difference among the M. vitrata population from different host plants. However, the results suggested that M. vitrata has formed two putative subspecies (which cannot be differentiated based on morphological characters) in Asia and sub-Saharan Africa, as indicated by the high pairwise FST values (0.44-0.85). The extremely high FST values (≥ 0.93) of Maruca population in Latin America and Oceania compared to Asian and African population seem to indicate a different species. On the continental or larger geographical region basis, the genetic differentiation is significantly correlated with the geographical distance. In addition, two putative species of Maruca, including M. vitrata occur in Australia, Indonesia and Papua New Guinea. The negative Tajima's D and Fu's FS values showed the recent demographic expansion of Maruca population. The haplotype network and Automatic Barcode Gap Discovery analyses confirmed the results of phylogenetic analysis. Thus, this study confirmed the presence of three putative Maruca species, including one in Latin America, one in Oceania (including Indonesia) and M. vitrata in Asia, Africa and Oceania. Hence, the genetic differences in Maruca population should be carefully considered while designing the pest management strategies in different regions

Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates

Ser/Thr and Tyr protein kinases orchestrate many signalling pathways and hence loss in this balance leads to many disease phenotypes. Due to their high abundance, diversity and importance, efforts have been made in the past to classify kinases and annotate their functions at both gross and fine levels. These kinases are conventionally classified into subfamilies based on the sequences of catalytic domains. Usually the domain architecture of a full-length kinase is consistent with the subfamily classification made based on the sequence of kinase domain. Important contributions of modular domains to the overall function of the kinase are well known. Recently occurrence of two kinds of outlier kinases-''Hybrid'' and ``Rogue'' has been reported. These show considerable deviations in their domain architectures from the typical domain architecture known for the classical kinase subfamilies. This article provides an overview of the different subfamilies of human kinases and the role of non-kinase domains in functions and diseases. Importantly this article provides analysis of hybrid and rogue kinases encoded in the human genome and highlights their conservation in closely related primate species. These kinases are examples of elegant rewiring to bring about subtle functional differences compared to canonical variants

Unity and diversity among viral kinases

Viral kinases are known to undergo autophosphorylation and also phosphorylate viral and host substrates. Viral kinases have been implicated in various diseases and are also known to acquire host kinases for mimicking cellular functions and exhibit virulence. Although substantial analyses have been reported in the literature on diversity of viral kinases, there is a gap in the understanding of sequence and structural similarity among kinases from different classes of viruses. In this study, we performed a comprehensive analysis of protein kinases encoded in viral genomes. Homology search methods have been used to identify kinases from 104,282 viral genomic datasets. Serine/threonine and tyrosine kinases are identified only in 390 viral genomes. Out of seven viral classes that are based on nature of genetic material, only viruses having double-stranded DNA and single-stranded RNA retroviruses are found to encode kinases. The 716 identified protein kinases are classified into 63 subfamilies based on their sequence similarity within each cluster, and sequence signatures have been identified for each subfamily. 11 clusters are well represented with at least 10 members in each of these clusters. Kinases from dsDNA viruses, Phycodnaviridae which infect green algae and Herpesvirales that infect vertebrates including human, form a major group. From our analysis, it has been observed that the protein kinases in viruses belonging to same taxonomic lineages form discrete clusters and the kinases encoded in alphaherpesvirus form host-specific clusters. A comprehensive sequence and structure-based analysis enabled us to identify the conserved residues or motifs in kinase catalytic domain regions across all viral kinases. Conserved sequence regions that are specific to a particular viral kinase cluster and the kinases that show close similarity to eukaryotic kinases were identified by using sequence and three-dimensional structural regions of eukaryotic kinases as reference. The regions specific to each viral kinase cluster can be used as signatures in the future in classifying uncharacterized viral kinases. We note that kinases from giant viruses Marseilleviridae have close similarity to viral oncogenes in the functional regions and in putative substrate binding regions indicating their possible role in cancer

Wpływ wyciągu alkoholowego z Graptophyllum pictum (L.) na działanie cisplatyny wywołującej nerfotoksyczność u szczurów

The purpose of the present study is to investigate whether the alcoholic extract of Graptophyllum pictum (L.) Griff. could decrease the intensity of nephrotoxicity in albino rats. Cisplatin at a single dose of 12 mg/kg body weight was administered intraperitonially to albino male Wistar rats. Nephrotoxicity was assessed by determining the serum creatinine and urea levels as well as renal antioxidant status in rats after cisplatin administration. Ethanolic extract of G. pictum at 150 and 300 mg/kg body weight was administered orally after cisplatin injection for 15 days. The extracts could significantly reduce the elevated serum creatinine and urea levels. Renal antioxidant defence systems, such as superoxide dismutase, catalase, glutathione peroxidase activities and reduced glutathione level, depleted by cisplatin therapy were restored to normal by treatment with the extract. Cisplatin induced lipid peroxidation was also found markedly reduced by treatment with the extract. This result indicated that ethanolic extract of G. pictum rendered significant preventive effect against cisplatin induced nephrotoxicity.Celem niniejszej pracy było zbadanie właściwości wyciągu alkoholowego z Graptophyllum pictum (L.) zmniejszającej nefrotoksyczność indukowaną cisplatyną u szczurów. Cisplatynę podawano szczurom dootrzewnowo w pojedynczej dawce w ilości 12 mg/kg masy ciała. Nefrotoksyczność oceniono na podstawie określenia stężenia kreatyniny w surowicy, poziomu mocznika, a także aktywności przeciwutleniającej nerek u szczurów. Wyciąg alkoholowy z G. pictum podawano dożołądkowo w dawkach od 150 do 300 mg/kg masy ciała przez 15 dni po uprzednim podaniu cisplatyny. Wykazano, że podawanie ekstrakty mogą istotnie obniżyć stężenie mocznika i kreatyniny podwyższone przez cisplatynę. Ponadto podawanie cisplatyny wywołało zaburzenia w działaniu dysmutazy ponadtlenkowej, kata65 Effect of ethanol extract of Graptophyllum pictum (L.) Griff. on cisplatin induced nephrotoxicity in rats lazy, peroksydazy glutationowej, powodując zaburzenia mechanizmów obronnych nerek oraz obniżenie poziomu glutationu, natomiast ich prawidłowe funkcjonowanie zostało przywrócone po podaniu ekstraktu. Badanie również wykazało, że wzrost poziomu peroksydacji tłuszczów wywołany za pomocą cisplatyny zostaje znacznie zmniejszony w wyniku podawania ekstraktu. Przedstawione wyniki badań wskazują na prewencyjne działanie wyciągu alkoholowego otrzymanego z G. pictum przeciwko nefrotoksyczności indukowanej cisplatyną