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.     

The Arcoidea (Mollusca: Bivalvia): a review of the current phenetic-based systematics

The diversity and adaptive radiations of modern Arcoidea, here considered to contain the families Arcidae, Noetiidae, Cucullaeidae, and Glycymerididae, are reviewed. Most fall into either epibyssate or endobyssate life habits with only the Glycymerididae living as free burrowers. The phenetic characters of the families within the Arcoida are reviewed and the families are shown to be supported by very few synapomorphic characters. Homoplasy is shown to be widespread and is illustrated in a series of discussions on the ligament, epibyssate–endobyssate radiations, and possible parallelism within genera, and in a review of arcoid anatomical characters. Previously published molecular data are reviewed and these support the inclusion of the Glycymerididae in the Arcoidea. They also indicate, however, that polyphyly is probably widespread at the subfamily level.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 237–251.     

A model explaining the size distribution of gene and protein families

This article deals with the theoretical size distribution of gene and protein families in complete genomes. A simple evolutionary model for the development of such families in which genes in a family are formed or selected against independently and at random, and in which new families are formed by the random splitting of existing families, is used to derive the resulting size distribution. Mathematically this turns out to be the distribution of the state of a homogeneous birth-and-death process after an exponentially distributed time, which it is shown will under certain conditions exhibit the power-law behaviour observed for gene and protein family sizes.     

Scaling law in sizes of protein sequence families: from super-families to orphan genes

It has been observed that the size of protein sequence families is unevenly distributed, with few super families with a large number of members and many "orphan" proteins that do not belong to any family. Here it is shown that the distribution of sizes of protein families in different databases and classifications (Protomap, Prodom, Cog) follows a power-law behavior with similar scaling exponents, which is characteristic of self-organizing systems. Since large databases are used in this study, a more detailed analysis of the data than in previous studies was possible. Hence, it is shown that the size distribution is governed by two exponents, different for the super families and the orphan proteins. A simple model of protein evolution is proposed, in which proteins are dynamically generated and clustered into families. The model yields a scaling behavior very similar to the distribution observed in the actual sequence databases, including the two distinct regimes for the large and small families, and thus suggests that the existence of "super families" of proteins and "orphan" proteins are two manifestations of the same evolutionary process.     

Segmental amplification in a satellite DNA: Restriction enzyme analysis of the major satellite ofMacropus rufogriseus

The 1.708 g/cc satellite DNA of the red necked wallaby is shown to consist of a number of related families of sequences arranged in tandem arrays. Particular families are subpopulations of other families; their distribution supports a model of successive amplification events during the generation of the satellite. In each amplification episode one 2,500 bp unit is multiplied into a tandemly repeated array of that unit (segmental amplification). The 1.708 g/cc sequences can be detected in related kangaroo species in much reduced amount, and with changes to the long order periodicity of the repeat units.     

Electron spin resonance dating of human bones from Brazilian shell-mounds (Sambaquís)

From the fingertip pattern analysis of 125 families with 376 children from Velanadu Brahmin and 100 families with 286 children from Telaganya Brahmin caste sects of Andhra Pradesh, India, the occurrence of an arch on at least one of the ten finger tips is shown to be aggregated in families. The mode of aggregation is in conformity with a major dominant gene with 0.28 chance of penetrance. This is to some extent contradictory to the result published from the analysis of a single Habbanite Jewish pedigree. Some implications of this discordant result are also discussed.     

On the genetics of the Pi serum proteins

Summary The authors report family studies (51 families with 134 children) on the inheritance of the Pi phenotypes. Combining these data with a Norwegian family material (77 families with 323 children) published by Fagerhol and Gedde-Dahl (1969) a total of 128 families with 457 children is now available, which allows the following conclusion: The Pi phenotypes are inherited by a simple codominant mode of heredity and they are determined by a set of (at least nine) alleles. As up to now no exception to the role of inheritance has been observed, the application of the Pi system in cases of disputed paternity seems to be discussible. Some methodological problems in connection with this are shown.Supported by the Deutsche Forschungsgemeinschaft.     

GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains

GeMMA (Genome Modelling and Model Annotation) is a new approach to automatic functional subfamily classification within families and superfamilies of protein sequences. A major advantage of GeMMA is its ability to subclassify very large and diverse superfamilies with tens of thousands of members, without the need for an initial multiple sequence alignment. Its performance is shown to be comparable to the established high-performance method SCI-PHY. GeMMA follows an agglomerative clustering protocol that uses existing software for sensitive and accurate multiple sequence alignment and profile–profile comparison. The produced subfamilies are shown to be equivalent in quality whether whole protein sequences are used or just the sequences of component predicted structural domains. A faster, heuristic version of GeMMA that also uses distributed computing is shown to maintain the performance levels of the original implementation. The use of GeMMA to increase the functional annotation coverage of functionally diverse Pfam families is demonstrated. It is further shown how GeMMA clusters can help to predict the impact of experimentally determining a protein domain structure on comparative protein modelling coverage, in the context of structural genomics.     

Molecular characterization of the MT-family of dispersed middle-repetitive DNA in rodent genomes.

We report the consensus sequence of members of a new dispersed middle-repetitive DNA family, MT, which is present in mouse and rat genomes. This family is shown to be as abundant as the described rodent B1 and B2 families. Hybridization experiments with radioactive single-stranded cDNAs from different tissues indicate that MT sequences are more abundantly cotranscribed in parts of the brain than other repetitive families.     

A simple method for detection of imprinting effects based on case-parents trios

Using data from families in which marker genotypes are known for the father, the mother and the affected offspring, a simple statistic for testing for imprinting effects is developed. The statistic considers whether the expected number of families in which the father carries more copies of a particular marker allele than the mother is equal to the expected number of families in which the mother carries more copies of the allele than the father. The proposed parent-of-origin effects test statistic (POET) is shown to be normally distributed and can be employed to test for imprinting in situations where the marker locus need not be a disease susceptibility locus and where the female and male recombination fractions are sex-specific. A simulation study is conducted to characterize the power of the POET and other properties, and its results show that it is appropriate to employ the POET.     

The Old Kinship Studies Confronts Gay Kinship: A Critique of Kath Weston

Kath Weston's highly-acclaimed analysis of gay kinship is examined in the light of the old kinship studies, especially the notion of focality. The verdict is quite contrary to Weston's, viz. that gay kinship and the idea of gay families are structural derivatives of heterosexual kinship and heterosexual families. Weston's work is shown to be part of a larger collectivist project in kinship theory in which key concerns in semantic theory are ignored.     

Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases.

Using a combination of several methods for protein sequence comparison and motif analysis, it is shown that the four recently described pseudouridine syntheses with different specificities belong to four distinct families. Three of these families share two conserved motifs that are likely to be directly involved in catalysis. One of these motifs is detected also in two other families of enzymes that specifically bind uridine, namely deoxycitidine triphosphate deaminases and deoxyuridine triphosphatases. It is proposed that this motif is an essential part of the uridine-binding site. Two of the pseudouridine syntheses, one of which modifies the anticodon arm of tRNAs and the other is predicted to modify a portion of the large ribosomal subunit RNA belonging to the peptidyltransferase center, are encoded in all extensively sequenced genomes, including the 'minimal' genome of Mycoplasma genitalium. These particular RNA modifications and the respective enzymes are likely to be essential for the functioning of any cell.     

The middle ear of the skull of birds: the Pelecaniformes and Ciconiiformes

The anatomy of the middle ear region of the skull is described for the families of the Avian orders Pelecaniformes and Ciconiiformes. Emphasis is placed on the foramina and paths of the nerves and blood vessels. The morphology of the basicranium and quadrate is also discussed. Comparative analyses of the characters are used to assess taxonomic conclusions.
Extant Pelecaniformes consist of six families, four of which are monogenic: Phaethontidae, Pelecanidae, Anhingidae and Fregatidae; one is composed of two genera: Sulidae; and the last has three genera: Phalacrocoracidae. Several years ago a relationship was suggested which would ally the Phaethontidae and the Fregatidae. While these families share several non middle ear characters the anatomy of the middle ear is not compatible with any particular relationship. Indeed, several obvious differences are described. The data presented here are consistent with the idea that the Phaethontidae and the Fregatidae each form a separate group of Pelecaniform birds, with the rest of the families forming a third group. Several differences in the middle ear region of the species of Anhingidae suggest that the family may be composed of two genera.
While sharing many Ciconiiform characters the Ciconiidae have been shown not to be as closely related to the Ardeidae as they are to other families of Ciconiiformes. In addition, evidence is presented to support the recent idea that the three species of ibis (I. ibis, I. cinereus and I. leucocephalus ) be united within the genus Mycteria. Also supported is the notion that Balaeniceps is Pelecaniform in character, and not Ciconiiform.     

Microbial genome analyses: comparative transport capabilities in eighteen prokaryotes

Here, we present a comprehensive analysis of solute transport systems encoded within the completely sequenced genomes of 18 prokaryotic organisms. These organisms include four Gram-positive bacteria, seven Gram-negative bacteria, two spirochetes, one cyanobacterium and four archaea. Membrane proteins are analyzed in terms of putative membrane topology, and the recognized transport systems are classified into 76 families, including four families of channel proteins, four families of primary carriers, 54 families of secondary carriers, six families of group translocators, and eight unclassified families. These families are analyzed in terms of the paralogous and orthologous relationships of their protein members, the substrate specificities of their constituent transporters and their distributions in each of the 18 organisms studied. The families vary from large superfamilies with hundreds of represented members, to small families with only one or a few members. The mode of transport generally correlates with the primary mechanism of energy generation, and the numbers of secondary transporters relative to primary transporters are roughly proportional to the total numbers of primary H(+) and Na(+) pumps in the cell. The phosphotransferase system is less prevalent in the analyzed bacteria than previously thought (only six of 14 bacteria transport sugars via this system) and is completely lacking in archaea and eukaryotes. Escherichia coli is shown to be exceptionally broad in its transport capabilities and therefore, at a membrane transport level, does not appear representative of the bacteria thus far sequenced. Archaea and spirochetes exhibit fewer proteins with multiple transmembrane segments and fewer net transporters than most bacteria. These results provide insight into the relevance of transport to the overall physiology of prokaryotes.     

Sperm structure of Trichoptera. IV. Rhyacophilidae and Glossosomatidae

The families Rhyacophilidae and Glossosomatidae (Trichoptera) are considered to be the most primitive ones within the order. We examined the spermatozoa of members of these families to see whether their ultrastructure is consistent with an ancestral position. Axonemal structures, after fixation with a tannic acid-containing fixative, have been shown to be particularly useful as taxonomical indicators. It was found that 4 members of Rhyacophilidae, representing 3 subgenera (Rhyacophila, Pararhyacophila, and Hyporhyacophila) all have motile spermatozoa, with a 9 + 9 + 2 axoneme in which inner (but no outer) dynein arms are present. The accessory tubules have a wall consisting of 17 protofilaments, decreasing to 16 near the distal end, whereas the examined member of Glossosomatidae, Catagapetus nigrans, has accessory tubules with 18 protofilaments and a 9 + 9 + 2 axoneme with inner dynein arms and with motility similar to the Rhyacophilidae. Sperm motility is consistent with the inclusion of these 2 families within the suborder Integripalpia, and the axonemal pattern 9 + 9 + 2 indicates that the families indeed occupy a primitive position within Trichoptera.     

Refinement by linkage analysis in two large families of the candidate region of the third locus (SCA3) for autosomal dominant cerebellar ataxia type I

The autosomal dominant cerebellar ataxias (ADCA) are clinically and genetically heterogeneous. To date, several loci (SCAI-V) have been identified for ADCA type I. We have studied two large families from the northern part of The Netherlands with ADCA type I with a broad intra-familial variation of symptoms. In both families significant linkage is shown of the disease to the markers of the SCA3 locus on chromosome 14. Through recombinations, the candidate region for SCA3 could be refined to a 13-cM range between D14S256 and D14S81. No recombinations were detected with the markers D14S291 and D14S280, which suggests that the SCA3 gene lies close to these loci. This finding will benefit the individuals at risk in these two families who are seeking predictive testing or prenatal diagnosis.