Sequence homology and immunologic cross-reactivity of human cytomegalovirus with HLA-DR beta chain: a means for graft rejection and immunosuppression

A peptide (Leu-Gly-Arg-Pro-Asp-Glu-Asp-Ser-Ser-Ser-Ser-Ser-Ser-Ser-Cys) that was identical to residues 82 through 96 of a predicted protein of 208 amino acids from the immediate-early region (IE-2) nucleic acid sequence of human cytomegalovirus was chemically synthesized. By computer analysis, the first five amino acids of this peptide showed sequence homology to the beta chain of the human histocompatibility complex HLA-DR. The homologous amino acids, 53 through 57, were located in a region that is conserved between the human DR beta chain and the beta chain of the H-2 class II histocompatibility antigen for mice. The shared region between the IE-2 protein and DR beta chain were similar in both hydrophilicity and predicted beta-turn potential. The IE-2 viral peptide induced antibodies that specifically recognized the human DR beta chain. These observations describe a protein encoded by the IE-2 region of human cytomegalovirus that contains sequence homology and shows immunologic cross-reactivity with a conserved domain of HLA-DR and suggest a mechanism to explain how human cytomegalovirus infection contributes to graft rejection after transplantation.     

Duchenne muscular dystrophy and dystrophin: Sequence homology observations

Duchenne muscular dystrophy (DMD) is a genetically transmitted disease characterized by progressive muscle weakness and usually leads to death. DMD results from the absence, deficiency or dysfunction of the protein dystrophin. Analysis of protein data bases, including homology alignments and domain recognition patterns, have located highly significant correlations between dystrophin and other calcium regulating proteins. In particular, a major portion of the dystrophin sequence has been found to contain repeating units of approximately 100 amino acid residues. These repeating units were found to exhibit significant homology to troponin I. Troponin I has been found to bind to the calcium binding proteins calmodulin and troponin C. The regions of highest homology were characterized by patterns of high localization of charged amino acids and thus could represent a possible calmodulin or troponin C surface accessible binding site. Since subcellular localization studies have indicated that dystrophin is associated with the triadic junction, these findings imply that dystrophin could be involved in controlling intracellular calcium homeostasis.Special issue dedicated to Dr. Lawrence Austin.     

<Emphasis Type="Italic">Chenopodium album</Emphasis> pollen profilin (Che a 2): homology modeling and evaluation of cross-reactivity with allergenic profilins based on predicted potential IgE epitopes and IgE reactivity analysis

The inhalation of Chenopodium album (C. album) pollen has been reported as an important cause of allergic respiratory symptoms. The aim of this study was to produce the recombinant profilin of C. album (rChe a 2) pollen and to investigate its cross-reactivity with other plant-derived profilins based on potential conformational epitopes and IgE reactivity analysis. Che a 2-coding sequence was cloned, expressed, and purified using one step metal affinity chromatography to recover high-purity target protein. We assessed cross-reactivity and predicted IgE potential epitopes among rChe a 2 and other plant-derived profilins. Immunodetection and inhibition assays using sixteen individual sera from C. album allergic patients demonstrated that purified rChe a 2 could be the same as that in the crude extract. The results of inhibition assays among rChe a 2 and other plant-derived profilins were in accordance with those of the homology of predicted conserved conformational regions. In this study, amino acid sequence homology analysis showed that a high degree of IgE cross-reactivity among plant-derived profilins may depend on predicted potential IgE epitopes.     

Sequence structure relationships in metalloproteins-I. A predictive model of hemerythrin

Utilization of simple algorithmic schemes coupled with chemical data and the known conformational requirements of metal ions has resulted in the prediction of the basic tertiary structure of a metalloprotein, the hemerythrin subunit.     

Human-associated microbial signatures: examining their predictive value

Host-associated microbial communities are unique to individuals, affect host health, and correlate with disease states. Although advanced technologies capture detailed snapshots of microbial communities, high within- and between-subject variation hampers discovery of microbial signatures in diagnostic or forensic settings. We suggest turning to machine learning and discuss key directions toward harnessing human-associated microbial signatures.     

Analysis of cDNA clones for Acanthamoeba profilin-I and profilin-II shows end to end homology with vertebrate profilins and a small family of profilin genes.

We have cloned and sequenced full length cDNAs for Acanthamoeba profilin-I and profilin-II. The genes and the encoded proteins are nearly identical except for the region between bp 121 and 210 where 35% of the nucleotides and 47% of amino acids differ. Most of these substitutions are conservative, although three of them are responsible for the differences in the isoelectric points of the isoforms [Kaiser et al., Cell Biol., 102:221-226, 1986]. The DNA sequence revealed six corrections in the previously published protein sequence of profilin-I [Ampe et al., J. Biol. Chem. 260:834-840, 1985] and for the first time resolved the ambiguities at the five positions where profilin-IA and -IB differ. The DNA sequence of profilin-II also allowed us to make two corrections in the protein sequence [Ampe et al., FEBS Lett. 228:17-21, 1988a]. Probes prepared from the cDNAs revealed 1 profilin-IA gene, one strongly cross-hybridizing profilin-I gene and one strongly reacting profilin-II gene on Southern blots of Acanthamoeba DNA. Weaker reactions with other genomic DNA fragments leave open the possibility of one additional gene each for profilin-I and profilin-II. Four different profilin RNAs were resolved on Northern blots. It possible to align the sequences of the three Acanthamoeba profilins with the sequences of nine other profilins from five different phyla. There are only two invariant residues in these profilin sequences, but many pairwise identities and conservative substitutions that indicate considerable divergence of this family of proteins from its ancestral precursor.     

ANKRD33 is overexpressed in gastric adenocarcinoma and predictive for poor prognosis

ABSTRACT

The aim of the current study was to investigate and discuss the function of ANKRD33 gene in the pathogenesis of gastric adenocarcinoma. The marked up-regulated expression of ANKRD33 gene in gastric adenocarcinoma tissues compared to normal tissues was found by bioinformatics analysis. Kaplan-Meier analysis revealed that high expression of ANKRD33 is correlated with lower overall survival of gastric adenocarcinoma patients. The results of qPCR revealed that mRNA expression level of ANKRD33 was dramatically higher in AGS, SGC7901, and BGC823 cell lines than that in the GES1 cells. Knockdown of ANKRD33 remarkably inhibited the viability, invasion, and migration of AGS and BGC823 cells. Furthermore, the ratio of p-AKT/AKT and p-mTOR/mTOR was significantly decreased in AGS cells which transfected with si- ANKRD33. All the above results illustrated that ANKRD33 would act as a tumor forwarder in gastric adenocarcinoma development and have a high potential to be a marker molecule in the diagnosis and treatment of gastric tumors.     

X-ray structure determination of human profilin II: A comparative structural analysis of human profilins

Human profilins are multifunctional, single-domain proteins which directly link the actin microfilament system to a variety of signalling pathways via two spatially distinct binding sites. Profilin binds to monomeric actin in a 1:1 complex, catalyzes the exchange of the actin-bound nucleotide and regulates actin filament barbed end assembly. Like SH3 domains, profilin has a surface-exposed aromatic patch which binds to proline-rich peptides. Various multidomain proteins including members of the Ena/VASP and formin families localize profilin:actin complexes through profilin:poly-L-proline interactions to particular cytoskeletal locations (e.g. focal adhesions, cleavage furrows). Humans express a basic (I) and an acidic (II) isoform of profilin which exhibit different affinities for peptides and proteins rich in proline residues. Here, we report the crystallization and X-ray structure determination of human profilin II to 2.2 A. This structure reveals an aromatic extension of the previously defined poly-L-proline binding site for profilin I. In contrast to serine 29 of profilin I, tyrosine 29 in profilin II is capable of forming an additional stacking interaction and a hydrogen bond with poly-L-proline which may account for the increased affinity of the second isoform for proline-rich peptides. Differential isoform specificity for proline-rich proteins may be attributed to the differences in charged and hydrophobic residues in and proximal to the poly-L-proline binding site. The actin-binding face remains nearly identical with the exception of five amino acid differences. These observations are important for the understanding of the functional and structural differences between these two classes of profilin isoforms.     

Sequence homology of group A streptococcal Pep M5 protein with other coiled-coil proteins

Group A streptococcal Pep M5 protein, an antiphagocytic determinant of the bacteria, is an alpha-helical coiled-coil molecule, and exhibits significant sequence homology with tropomyosin and myosin, but to a lesser degree with other coiled-coil proteins. Moreover, Pep M5 is more homologous to myosin than to tropomyosin, and the homologies are more numerous between the C-terminal domain of the Pep M5 protein and the S2 fragment of myosin. The C-terminal domain of the Pep M5 protein exhibits extensive sequence identity with the C-terminal region of Pep M6 molecule, another M protein serotype. Thus, regions within two M protein serotypes are homologous to the S2 region of the myosin molecule. These observations are consistent with the immunological findings of other investigators and thus may explain some of the previously reported immunological cross-reactions between antigens of the group A streptococcus and mammalian heart tissue.     

A quality metric for homology modeling: the H-factor

Background  

The analysis of protein structures provides fundamental insight into most biochemical functions and consequently into the cause and possible treatment of diseases. As the structures of most known proteins cannot be solved experimentally for technical or sometimes simply for time constraints, in silico protein structure prediction is expected to step in and generate a more complete picture of the protein structure universe. Molecular modeling of protein structures is a fast growing field and tremendous works have been done since the publication of the very first model. The growth of modeling techniques and more specifically of those that rely on the existing experimental knowledge of protein structures is intimately linked to the developments of high resolution, experimental techniques such as NMR, X-ray crystallography and electron microscopy. This strong connection between experimental and in silico methods is however not devoid of criticisms and concerns among modelers as well as among experimentalists.     

A test for nucleotide sequence homology

Two macromolecular sequences which have evolved from a common ancestor sequence will tend to include a large number of elements unaffected by replacement mutations in both sequences, as long as the evolutionary rate is not too high or the divergence time is not too great. The positions of corresponding elements may have changed in either daughter sequence due to deletion/insertion mutations involving other sequence elements, but their order can be expected to be the same in both sequences. These sets of correspondences, called matches, may be computed by a recursive algorithm which incorporates constraints on the number of deletion/insertion mutations hypothesized to have occurred. A test is developed which computes the significance of each deletion/insertion hypothesized, based on Monte-Carlo sampling of random sequences with the same base composition as the experimental sequences being tested. Applying the test to 5 S RNAs confirms the relation of Escherichia coli and KB carcinoma 5 S RNAs and establishes the previously undetected homology between Pseudomonas fluorescens and KB 5 S RNAs.     

A new generation of predictive models: The added value of hybrid models for manufacturing processes of therapeutic proteins

Due to the lack of complete understanding of metabolic networks and reaction pathways, establishing a universal mechanistic model for mammalian cell culture processes remains a challenge. Contrarily, data-driven approaches for modeling these processes lack extrapolation capabilities. Hybrid modeling is a technique that exploits the synergy between the two modeling methods. Although mammalian cell cultures are among the most relevant processes in biotechnology and indeed looks ideal for hybrid modeling, their application has only been proposed but never developed in the literature. This study provides a quantitative assessment of the improvement brought by hybrid models with respect to the state-of-the-art statistical predictive models in the context of therapeutic protein production. This is illustrated using a dataset obtained from a 3.5 L fed-batch experiment. With the goal to robustly define the process design space, hybrid models reveal a superior capability to predict the time evolution of different process variables using only the initial and process conditions in comparison to the statistical models. Hybrid models not only feature more accurate prediction results but also demonstrate better robustness and extrapolation capabilities. For the future application, this study highlights the added value of hybrid modeling for model-based process optimization and design of experiments.     

Sequence of the peh gene of Erwinia carotovora: homology between Erwinia and plant enzymes

Polygalacturonase (Peh) and other pectolytic enzymes play a crucial role in the maceration of vegetables by soft rot Erwinia spp. We have sequenced the peh gene of Erwinia carotovora subsp. carotovora, and identified its product as a precursor of molecular weight 42,639, and a mature protein of molecular weight 42,200. A putative KdgR-binding site was identified in the region 5' to the peh gene. The Peh protein showed significant homology with Peh from tomato. In addition, we have found homologies between pectin methylesterase and pectate lyase from Erwinia and their counterparts in tomato. These homologies are described, and their significance discussed.     

Sequence and codon recognition of bean mitochondria and chloroplast tRNAsTrp: evidence for a high degree of homology.

Bean mitochondria and chloroplast tRNAsTrp, purified by RPC-5 chromatography and two-dimensional gel electrophoresis, have been sequenced using post-labeling techniques. The high degree of sequence homology between bean mitochondria and chloroplast tRNAsTrp shows that these two tRNAs are coded for by closely related genes which have probably evolved from a common ancestor gene. The anticodon of bean mitochondria tRNATrp is CmCA, which can recognize UGG (the codon for tryptophan in the universal code) and is complementary neither to UGA (which codes for tryptophan in mammalian and yeast mitochondria) nor to CGG (which could be a tryptophan codeword in plant mitochondria).     

Does minimizing homoplasy really maximize homology? MaHo: A method for evaluating homology among most parsimonious trees

Parsimony analysis aims at finding the tree that best fits hypotheses of homology. However, parsimony does not directly maximize homology, but minimizes homoplasy. When a parsimony analysis results in more than a single most-parsimonious tree (MPT), it is shown that the number of homologous characters may vary significantly. We propose a method called MaHo to identify, among the MPTs, the tree(s) that has (have) the highest number of characters that are homologies. We apply this approach to the phylogenetic relationships of the Dombeyoideae (Malvaceae) of the Mascarene Islands. A parsimony analysis was performed, including 31 representatives of the Dombeyoideae. The search resulted in 29,336 MPTs. MaHo was used in order to improve the resolution of the consensus and to increase the number of unambiguous homologies. The consensus of the 7592 MPTs presenting the highest number of homologies was chosen. This resulted in unravelling five additional synapomorphies and in reducing the number of MPTs.     

Deep homology: A view from systematics

Over the past decade, it has been discovered that disparate aspects of morphology – often of distantly related groups of organisms – are regulated by the same genetic regulatory mechanisms. Those discoveries provide a new perspective on morphological evolutionary change. A conceptual framework for exploring these research findings is termed ‘deep homology’. A comparative framework for morphological relations of homology is provided that distinguishes analogy, homoplasy, plesiomorphy and synapomorphy. Four examples – three from plants and one from animals – demonstrate that homologous developmental mechanisms can regulate a range of morphological relations including analogy, homoplasy and examples of uncertain homology. Deep homology is part of a much wider range of phenomena in which biological (genes, regulatory mechanisms, morphological traits) and phylogenetic levels of homology can both be disassociated. Therefore, to understand homology, precise, comparative, independent statements of both biological and phylogenetic levels of homology are necessary.     

Positive predictive value of noninvasive prenatal testing for sex chromosome abnormalities

Molecular Biology Reports - Early and intermediate serological screening cannot detect sex chromosome abnormalities. Currently, noninvasive prenatal testing (NIPT) is the only procedure available...     

A predictive study of cupressaceae pollen season onset, severity, maximum value and maximum value date

In this paper Cupressaceae pollen season onset, severity, maximum value and maximum value date, have been studied for 15 consecutive years (1982–1996). The data set was obtained using a Hirst spore-trap (Burkard Manufacturing). In order to determine the influence of the previous months’ meteorological variables on Cupressaceae season’s parameters, the sums of maximum, average and minimum temperatures, and total rainfall for the months of October, November and December were used as independent variables in predictive formulae built by multiple regression analyses. The variance explained percentage by regression analyses varied between 60 and 87%. Total rainfall in the months prior to anthesis and temperature (particularly minimum temperature) are important factors to consider in forecasting models of Cupressaceae pollen season parameters, but meteorological conditions at the time of pollen production are also important and can modify the pre-established potential of pollination.