Exploiting the co-evolution of interacting proteins to discover interaction specificity

Protein interactions are fundamental to the functioning of cells, and high throughput experimental and computational strategies are sought to map interactions. Predicting interaction specificity, such as matching members of a ligand family to specific members of a receptor family, is largely an unsolved problem. Here we show that by using evolutionary relationships within such families, it is possible to predict their physical interaction specificities. We introduce the computational method of matrix alignment for finding the optimal alignment between protein family similarity matrices. A second method, 3D embedding, allows visualization of interacting partners via spatial representation of the protein families. These methods essentially align phylogenetic trees of interacting protein families to define specific interaction partners. Prediction accuracy depends strongly on phylogenetic tree complexity, as measured with information theoretic methods. These results, along with simulations of protein evolution, suggest a model for the evolution of interacting protein families in which interaction partners are duplicated in coupled processes. Using these methods, it is possible to successfully find protein interaction specificities, as demonstrated for >18 protein families.     

MAK,a computational tool kit for automated MITE analysis

Miniature inverted repeat transposable elements (MITEs) are ubiquitous and numerous in higher eukaryotic genomes. Analysis of MITE families is laborious and time consuming, especially when multiple MITE families are involved in the study. Based on the structural characteristics of MITEs and genetic principles for transposable elements (TEs), we have developed a computational tool kit named MITE analysis kit (MAK) to automate the processes (http://perl.idmb.tamu.edu/mak.htm). In addition to its ability to routinely retrieve family member sequences and to report the positions of these elements relative to the closest neighboring genes, MAK is a powerful tool for revealing anchor elements that link MITE families to known transposable element families. Implementation of the MAK is described, as are genetic principles and algorithms used in its derivation. Test runs of the programs for several MITE families yielded anchor sequences that retain TIRs and coding regions reminiscent of transposases. These anchor sequences are consistent with previously reported putative autonomous elements for these MITE families. Furthermore, analysis of two MITE families with no known links to any transposon family revealed two novel transposon families, namely Math and Kid, belonging to the IS5/Harbinger/PIF superfamily.     

Medium-chain dehydrogenases/reductases (MDR). Family characterizations including genome comparisons and active site modeling.

Completed eukaryotic genomes were screened for medium-chain dehydrogenases/reductases (MDR). In the human genome, 23 MDR forms were found, a number that probably will increase, because the genome is not yet fully interpreted. Partial sequences already indicate that at least three further members exist. Within the MDR superfamily, at least eight families were distinguished. Three families are formed by dimeric alcohol dehydrogenases (ADH; originally detected in animals/plants), cinnamyl alcohol dehydrogenases (originally detected in plants) and tetrameric alcohol dehydrogenases (originally detected in yeast). Three further families are centred around forms initially detected as mitochondrial respiratory function proteins, acetyl-CoA reductases of fatty acid synthases, and leukotriene B4 dehydrogenases. The two remaining families with polyol dehydrogenases (originally detected as sorbitol dehydrogenase) and quinone reductases (originally detected as zeta-crystallin) are also distinct but with variable sequences. The most abundant families in the human genome are the dimeric ADH forms and the quinone oxidoreductases. The eukaryotic patterns are different from those of Escherichia coli. The different families were further evaluated by molecular modelling of their active sites as to geometry, hydrophobicity and volume of substrate-binding pockets. Finally, sequence patterns were derived that are diagnostic for the different families and can be used in genome annotations.     

Family configuration and family size

In a sample of 61,829 US families, the probability of having an additional child is higher in those families with all the children the same sex as compared to those families with children of both sexes. Data are from families of American high school students who took the National Merit Scholarship Qualifying test in 1965. All families with 3 or 4 children were selected. Families with only boys were more likely to have an additional child than families with all girls. Less than 1% of the variance in family size is explained by family configuration. Although the sample size makes these results unequivocal for the population involved, the population is clearly biased in favor of white middle class families.     

On the evolution of multigene families

Multigene families are classified into three groups: small families as exemplified by hemoglobin genes of mammals; middlesize multigene families, by genes of mammalian histocompatibility antigens; and large multigene families, by variable region genes of immunoglobulins. Facts and theories on these evolving multigene families are reviewed, with special reference to the population genetics of their concerted evolution. It is shown that multigene families are evolving under continued occurrence of unequal (but homologous) crossing-over and gene conversion, and that mechanisms for maintaining genetic variability are totally different from the conventional models of population genetics. Thus, in view of widespread occurrence of multigene families in genomes of higher organisms, the evolutionary theory based mainly on change of gene frequency at each locus would appear to need considerable revision.     

One third of Japanese patients with multiple osteochondromas may have mutations in genes other than EXT1 or EXT2

Multiple osteochondromas (MO; also referred to as hereditary multiple exostoses [HME] in the literature) is an autosomal dominant disorder characterized by benign, cartilage-capped bone tumors that grow from the metaphyses of long bones. Two genes are associated with this disease: EXT1 on 8q24.11-q24.13 and EXT2 on 11p12-p11. Mutations in EXT1 and EXT2 are found in 54-96% of patients with MO and are generally more frequent in EXT1 than in EXT2. We previously studied 43 Japanese families with MO using single-strand conformation polymorphism analysis for EXT1 and EXT2, and reported 23 families (54%) with mutations and 20 families (46%) with no mutations in these genes. Among the families with mutations, 17 families (40%) had mutations in EXT1, and 6 families (14%) had mutations in EXT2. Here we examined the same 43 Japanese families using denaturing high-performance liquid chromatography as an alternative technique. We detected five mutations, three of which are novel, in seven families in addition to the previously described mutations. In summary, we detected mutations in EXT1 or EXT2 in 30 (70%) out of 43 families. Our result suggests the presence of other gene(s) responsible for MO, at least in Japanese patients.     

Role of gene duplication in evolution

It is now known that many multigene and supergene families exist in eukaryote genomes: multigene families with uniform copy members like genes for ribosomal RNA, those with variable members like immunoglobulin genes, and supergene families such as those for various growth factor and hormone receptors. Many such examples indicate that gene duplication and subsequent differentiation are extremely important for organismal evolution. In particular, gene duplication could well have been the primary mechanism for the evolution of complexity in higher organisms. Population genetic models for the origin of gene families with diverse functions are presented, in which natural selection favors those genomes with more useful mutants in duplicated genes. Since any gene has a certain probability of degenerating by mutation, success versus failure in acquiring a new gene by duplication may be expressed as the ratio of probabilities of spreading of useful versus detrimental mutations in redundant gene copies. Also examined are the effects of gene duplication on evolution by compensatory advantageous mutations. Results of the analyses show that both natural selection and random drift are important for the origin of gene families. In addition, interaction between molecular mechanisms such as unequal crossing-over and gene conversion, and selection or drift is found to have a large effect on evolution by gene duplication.     

Linkage of familial breast cancer to chromosome 17q21 may not be restricted to early-onset disease.

Lod scores for linkage between familial breast and ovarian cancer and markers on chromosome 17q21 are more frequently positive among families with disease diagnosed at younger ages than they are among older-onset families, suggesting that linkage is restricted to early-onset disease. However, for late-onset cases, the relative probability of sporadic rather than inherited disease is higher than previously suggested. If this correction is made, then later-onset families are much less informative; linkage heterogeneity based on age at onset is no longer significant; and for the sample of families as a whole, linkage is significant at a recombination fraction since demonstrated to be close to the correct local. There is probably more than one gene for inherited breast cancer, but heterogeneity may not be due to age at disease onset.     

Theory and application of open-pollination and polycross in forage grass breeding

Summary Progeny testing and selection of forage grasses by means of growing half-sib (HS) families from openpollination and polycross have been considered from theoretical and practical points of view. Special attention has been paid to the genetic variation within half-sib families, which is expected to be large as compared to the genetic variation between families. Based on observations of individual plants within plots, the environmental component of the variation is expected to be large and nonestimatable. The results of an experiment in meadow fescue (Festuca pratensis Huds.) are presented. In this experiment, randomly selected individual plants within HS families were cloned and laid out in randomized blocks. For the characters observed (earliness and raw matter yield) no significant variance component for dominance was found. The highly significant additive component estimated for earliness, as well as for yield, after each of three cuts and in total were about three times as large within as between families, as expected from the theoretical considerations. The estimated response to selection was much higher for a combination of between- and within-family selection as compared to free clone or family mean selection alone. It is suggested that a program for progeny testing and selection in a base population of perennial forage grasses should start with an experiment in which a large number of randomly selected parental clones and a fixed number of clones from each of the half-sib families derived from the mother genotypes are grown simultaneously. The selected clones within superior families could later on be further cloned, placed in a polycross field, and the new HS-families could be sown in ordinary field trials at various locations for further selection.     

beta-fructosidase superfamily: homology with some alpha-L-arabinases and beta-D-xylosidases

Comparison of the amino acid sequences of four families of glycosyl hydrolases reveals that they are homologous and have several common conserved regions. Two of these families contain beta-fructosidases (glycosyl hydrolase families GH32 and GH68) and the other two include alpha-L-arabinases and beta-xylosidases (families GH43 and GH62). The latter two families are proposed to be grouped together with the former two into the beta-fructosidase (furanosidase) superfamily. Several ORFs can be considered as a fifth family of the superfamily on the basis of sequence similarity. It is shown for the first time that a glycosyl hydrolase superfamily can include enzymes with both inversion and retention mechanism of action. Composition of the active center for enzymes of the superfamily is discussed.     

Plant noncoding RNA gene discovery by "single-genome comparative genomics"

Plant genomes have undergone multiple rounds of duplications that contributed massively to the growth of gene families. The structure of resulting families has been studied in depth for protein-coding genes. However, little is known about the impact of duplications on noncoding RNA (ncRNA) genes. Here we perform a systematic analysis of duplicated regions in the rice genome in search of such ncRNA repeats. We observe that, just like their protein counterparts, most ncRNA genes have undergone multiple duplications that left visible sequence conservation footprints. The extent of ncRNA gene duplication in plants is such that these sequence footprints can be exploited for the discovery of novel ncRNA gene families on a large scale. We developed an SVM model that is able to retrieve likely ncRNA candidates among the 100,000+ repeat families in the rice genome, with a reasonably low false-positive discovery rate. Among the nearly 4000 ncRNA families predicted by this means, only 90 correspond to putative snoRNA or miRNA families. About half of the remaining families are classified as structured RNAs. New candidate ncRNAs are particularly enriched in UTR and intronic regions. Interestingly, 89% of the putative ncRNA families do not produce a detectable signal when their sequences are compared to another grass genome such as maize. Our results show that a large fraction of rice ncRNA genes are present in multiple copies and are species-specific or of recent origin. Intragenome comparison is a unique and potent source for the computational annotation of this major class of ncRNA.     

Heavy chain variable region gene families evolved early in phylogeny. Ig complexity in fish

The V regions of channel catfish H chain cDNA clones have been analyzed. Based upon sequence relationships and hybridization analyses, five different groups of VH genes are identified whose definition is consistent with that of five different VH families. Genomic Southern blots indicate that as many as 100 different germ-line VH genes are likely represented by these families. The sequence diversity between identified members of these different families is similar in magnitude to the divergence represented between members of different human or mouse VH families. The FR regions are the most conserved regions when members of different catfish VH families are compared; specific amino acid positions appear to be highly conserved in phylogeny. Equally important is that diversity is represented in complementarity-determining regions CDR1 and CDR2 in members of the different families as well as in members of the same VH family. These results suggest that an extensive repertoire of VH genes can contribute to antibody diversity in this lower vertebrate. Sequence comparisons indicate that one of the catfish VH families shares considerable structural similarity to several higher vertebrate VH gene families--a relationship which suggests that this VH family may be ancestral to some VH gene families of higher vertebrates. Characteristic of the genomic organization of higher vertebrate H chains, catfish appear to have different VH families wherein a VH gene likely undergoes functional recombination with putative DH gene segments and one of apparently several different JH segments. The recombined V region is expressed with the same C region gene. These combined results suggest that bony fishes are the earliest known phylogenetic representatives to have evolved extensive V region gene families.     

Si Dios Quiere: Hispanic families' experiences of caring for a seriously mentally ill family member

Among Hispanics, the family is viewed as the primary care giver for seriously mentally ill family members. This paper reports on a study of minority families' conceptions of serious mental illness, of their interaction with mental health resources, and on the burdens experienced by families in caring for a seriously mentally ill family member. The focus of this paper is on Hispanic families in New Jersey, with some comparative data from other ethnic group families. Families' conceptions of serious mental illness are explored and analyzed to demonstrate the importance of concepts of nervios and fallo mental in shaping families' responses to their ill family member. Social support systems for families are also explored with particular attention to the role of religious institutions and religious healing as a major source of solace.     

Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families

The representation of protein structures as small-world networks facilitates the search for topological determinants, which may relate to functionally important residues. Here, we aimed to investigate the performance of residue centrality, viewed as a family fold characteristic, in identifying functionally important residues in protein families. Our study is based on 46 families, including 29 enzyme and 17 non-enzyme families. A total of 80% of these central positions corresponded to active site residues or residues in direct contact with these sites. For enzyme families, this percentage increased to 91%, while for non-enzyme families the percentage decreased substantially to 48%. A total of 70% of these central positions are located in catalytic sites in the enzyme families, 64% are in hetero-atom binding sites in those families binding hetero-atoms, and only 16% belong to protein-protein interfaces in families with protein-protein interaction data. These differences reflect the active site shape: enzyme active sites locate in surface clefts, hetero-atom binding residues are in deep cavities, while protein-protein interactions involve a more planar configuration. On the other hand, not all surface cavities or clefts are comprised of central residues. Thus, closeness centrality identifies functionally important residues in enzymes. While here we focus on binding sites, we expect to identify key residues for the integration and transmission of the information to the rest of the protein, reflecting the relationship between fold and function. Residue centrality is more conserved than the protein sequence, emphasizing the robustness of protein structures.     

Domain combinations in archaeal, eubacterial and eukaryotic proteomes.

There is a limited repertoire of domain families that are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products, and at the level of genes, duplication, recombination, fusion and fission are the processes that produce new genes. We attempt to gain an overview of these processes by studying the evolutionary units in proteins, domains, in the protein sequences of 40 genomes. The domain and superfamily definitions in the Structural Classification of Proteins Database are used, so that we can view all pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 783 out of the 859 superfamilies in SCOP in these genomes, and the 783 families occur in 1307 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour; 209 families do not make combinations with other families. This type of pattern can be described as a scale-free network. We also study the N to C-terminal orientation of domain pairs and domain repeats. The phylogenetic distribution of domain combinations is surveyed, to establish the extent of common and kingdom-specific combinations. Of the kingdom-specific combinations, significantly more combinations consist of families present in all three kingdoms than of families present in one or two kingdoms. Hence, we are led to conclude that recombination between common families, as compared to the invention of new families and recombination among these, has also been a major contribution to the evolution of kingdom-specific and species-specific functions in organisms in all three kingdoms. Finally, we compare the set of the domain combinations in the genomes to those in the RCSB Protein Data Bank, and discuss the implications for structural genomics.     

江苏野生藤本植物多样性初探

通过野外调查和文献资料查阅,初步统计出江苏野生藤本植物共有35科74属153种,其中蕨类植物有1科1属1种,单子叶植物有3科4属12种,双子叶植物有31科69属140种。该区藤本植物以寡种科(属)、单种科(属)为主;地理成分复杂,具有明显的热带亲缘性,并受温带成分的影响。生长型以木质藤本为主(56.58%),草质藤本次之,其中,共有17科全为木质藤本,如木通科(Lardizabalaceae)以及防己科(Menispermaceae);共有13科全为草质藤本,如百部科(Stemonaceae)以及萝藦科(Asclepiadaceae)等;共有4科含木质与草质藤本植物,如百合科(Liliaceae)以及葡萄科(Vitaceae)等。高位芽植物最多(56.58%),地面芽植物(20.39%)、一年生植物(11.19%)、地下芽植物(8.55%)及地上芽植物(3.29%)的数量依次减少。该区藤本植物攀援类型可以分为4大类,以缠绕类居多(40.13%),其他依次是卷曲类(30.26%)、搭靠类(22.37%)以及吸固类(7.24%)。有性繁育系统以两性花最多(76.97%),单性花次之(19.74%),杂性花最少(3.29%);花序组成丰富,以无限花序占有绝对优势(71.05%)。     

Detection of parent-of-origin effects based on complete and incomplete nuclear families with multiple affected children

Parent-of-origin effects are important in studying genetic traits. More than 1% of all mammalian genes are believed to show parent-of-origin effects. Some statistical methods may be ineffective or fail to detect linkage or association for a gene with parent-of-origin effects. Based on case-parents trios, the parental-asymmetry test (PAT) is simple and powerful in detecting parent-of-origin effects. However, it is common in practice to collect nuclear families with both parents as well as nuclear families with only one parent. In this paper, when only one parent is available for each family with an arbitrary number of affected children, we firstly develop a new test statistic 1-PAT to test for parent-of-origin effects in the presence of association between an allele at the marker locus under study and a disease gene. Then we extend the PAT to accommodate complete nuclear families each with one or more affected children. Combining families with both parents and families with only one parent, the C-PAT is proposed to detect parent-of-origin effects. The validity of the test statistics is verified by simulation in various scenarios of parameter values. A power study shows that using the additional information from incomplete nuclear families in the analysis greatly improves the power of the tests, compared to that based on only complete nuclear families. Also, utilizing all affected children in each family, the proposed tests have a higher power than when only one affected child from each family is selected. Additional power comparison also demonstrates that the C-PAT is more powerful than a number of other tests for detecting parent-of-origin effects.     

Review of paleontological data on the evolution of aquatic beetles (Coleoptera)

Paleontological data on the evolution of aquatic beetles are reviewed. A total of 37 beetle families are regarded as aquatic; five of them are extinct; three other extinct families could have had aquatic larvae; seven families are not known from the fossil record. The earliest records of fossil representatives of Recent families of aquatic beetles are given. The geological distribution of extinct families is reviewed, and the data on the modes of life of their representatives and on their evolution are provided. The new name Coleocatiniidae nom. nov. is proposed for Catiniidae Ponomarenko, 1968, a junior homonym of Catiniidae Embelton, 1901 (Crustacaea, Copepoda).     

Host Plants of Brevipalpus californicus, B. obovatus, and B. phoenicis (Acari: Tenuipalpidae) and their Potential Involvement in the Spread of Viral Diseases Vectored by these Mites

The family Tenuipalpidae has over 622 species in 30 genera described worldwide. A total of 928 plant species in 513 genera within 139 families are recorded hosts of one or more of the following species: Brevipalpus californicus (Banks), B. obovatus Donnadieu, and B. phoenicis (Geijskes). B. californicus has 316 plant species reported as hosts compared with 451 and 486 host plants for B. obovatus and B. phoenicis, respectively. There are 67 genera of plants within 33 families that are reported hosts of only B. californicus, 119 genera within 55 plant families that are hosts of only B. obovatus, and 118 genera of plants within 64 families that are hosts of only B. phoenicis. There are 14 genera of plants within 12 families that are hosts to both B. californicus and B. obovatus, while there are 40 genera of host plants within 26 families that are hosts for both B. californicus and B. phoenicis. A total of 70 genera of host plants within 39 families have been reported as hosts of both B. obovatus and B. phoenicis, while 77 genera of plants within 44 families have been reported as hosts of all three Brevipalpus species. Geographical differences in the three species of Brevipalpus identified on different plant species within the same genus are common.     

阴山山脉乌拉山段种子植物区系组成及特征研究

通过对阴山山脉乌拉山段种子植物区系进行调查、统计、排序,从科、属、种3个分类等级上对植物的地理分布类型、生活型、水分生态类型分别进行统计分析,并与内蒙古种子植物区系进行对比分析。结果表明:(1)乌拉山有野生种子植物67科,227属,426种,其中,裸子植物3科,5属,7种;双子叶植物58科,187属,345种;单子叶植物6科,35属,74种;(2)从地理成分来看,温带成分占绝对优势;生活型以草本植物占绝对优势;从水分生态类型看,中生植物是该区的主要成分,旱生植物在本区系也占有相当比重,说明该地区水分条件较差,在气候区上属于半干旱地区;(3)与毗邻山地植物区系的相似性分析表明,乌拉山植物区系与九峰山、大青山种子植物区系具有很近的亲缘关系,与狼山亲缘关系较远。