Homologous Counterparts Research Articles

Interhemispheric Inhibition in Distal and Proximal Arm Representations in the Primary Motor Cortex

Interhemispheric inhibitory interactions (IHI) operate between homologous distal hand representations in primary motor cortex (M1). It is not known whether proximal arm representations exhibit comparable effects on their homologous counterparts. We studied IHI in different arm representations, targeting triceps brachii (TB, n = 13), first dorsal interosseous (FDI, n = 13), and biceps brachii (BB, n = 7) muscles in healthy volunteers. Transcranial magnetic stimulation test stimuli (TS) were delivered to M1 contralateral to the target muscle preceded 10 ms by a conditioning stimulus (CS) to the opposite M1 at 110-150% resting motor threshold (RMT). IHI was calculated as the ratio between motor-evoked potential (MEP) amplitudes in conditioned relative to unconditioned trials. Mean RMTs were 38.9, 46.9, and 46.0% of stimulator output in FDI, TB, and BB muscles, respectively. IHI was 0.45 +/- 0.41 (FDI), 0.78 +/- 0.38 (TB), and 0.52 +/- 0.32 (BB, P < 0.01) when test MEP amplitudes were matched and 0.28 +/- 0.17 (FDI) and 0.85 +/- 0.31 (TB, P < 0.05) when TS intensities expressed as percentage RMT were matched. Significant IHI (P < 0.05) was identified with minimal CS intensities (expressed as percentage stimulator output) in the 30 s for FDI, 60 s for TB, and 40 s for BB. Additionally, a CS of roughly 120% RMT suppressed the test MEP but not a test H-reflex in BB, suggesting IHI observed in BB is likely mediated by a supraspinal mechanism. We conclude that IHI differs between different arm muscle representations, comparable between BB and FDI but lesser for TB. This finding suggests the amount of IHI between different arm representations does not strictly follow a proximal-to-distal gradient, but may be related to the role of each muscle in functional movement synergies.

Genetic Composition of theBacillus subtilisSOS System

The SOS response in bacteria includes a global transcriptional response to DNA damage. DNA damage is sensed by the highly conserved recombination protein RecA, which facilitates inactivation of the transcriptional repressor LexA. Inactivation of LexA causes induction (derepression) of genes of the LexA regulon, many of which are involved in DNA repair and survival after DNA damage. To identify potential RecA-LexA-regulated genes in Bacillus subtilis, we searched the genome for putative LexA binding sites within 300 bp upstream of the start codons of all annotated open reading frames. We found 62 genes that could be regulated by putative LexA binding sites. Using mobility shift assays, we found that LexA binds specifically to DNA in the regulatory regions of 54 of these genes, which are organized in 34 putative operons. Using DNA microarray analyses, we found that 33 of the genes with LexA binding sites exhibit RecA-dependent induction by both mitomycin C and UV radiation. Among these 33 SOS genes, there are 22 distinct LexA binding sites preceding 18 putative operons. Alignment of the distinct LexA binding sites reveals an expanded consensus sequence for the B. subtilis operator: 5'-CGAACATATGTTCG-3'. Although the number of genes controlled by RecA and LexA in B. subtilis is similar to that of Escherichia coli, only eight B. subtilis RecA-dependent SOS genes have homologous counterparts in E. coli.

Immunohistochemical localization of neurotransmitters in the nervous system of larval Limulus polyphemus (Chelicerata, Xiphosura): evidence for a conserved protocerebral architecture in Euarthropoda

The phylogenetic relationships within the Arthropoda have remained controversial for more than a century. Comparative studies on structure and development of the nervous system have contributed important arguments to this discussion. Earlier studies revealed only few similarities between the brain morphology in representatives of the Chelicerata and the Mandibulata. In the present report, we analysed the brain architecture in larvae of the horseshoe crab Limulus polyphemus Linnaeus, 1758 (Chelicerata, Xiphosura) by localizing serotonin-, histamine-, and FMRFamide-like immunoreactivity with special reference to the organization of the protocerebral neuropils. These data are discussed with regard to the brain anatomy in Crustacea, Hexapoda and ‘Myriapoda’ revealing that several protocerebral and other brain structures of horseshoe crab larvae (and other Chelicerata) have homologous counterparts in the brain of these three groups. This suggests an evolutionarily conserved brain design within the different major euarthropod taxa (retained plesiomorphically from the euarthropodan ground pattern). These conserved features most likely include (a) a corresponding pattern of brain segmentation with a preoral protocerebrum (associated with the lateral eyes), a deutocerebrum (associated with the first antennae/the chelicerae) with pre- and postoral commissural fibres and a postoral tritocerebrum (associated with the second antennae/the pedipalp); (b) bilateral symmetrically arranged median eyes with histaminergic photoreceptors; (c) the median eye center, which is targeted by the axons of these photoreceptors; (d) interneurons (including serotonergic cells) with somata in an anteriorly located medial cell cluster, that innervate the median eye center; (e) a transverse median unpaired neuropil, the central body, enwrapped by layers of neuronal somata and also innervated by columnar neurons with somata in the anteriorly located median cell cluster; (f) lateral eyes which are composed of subunits comprising several hundreds of cells and histaminergic photoreceptors; (g) these lateral eyes are associated with two optic fibres linked by straight fibers.

Human–mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation

The formation of base-pairing between the branch-site (BS) sequence and the U2 snRNP is an important step in mRNA splicing. We developed a new algorithm to identify both the BS sequence and the polypyrimidine tract (PPT) and validated its predictions experimentally. To assess BS conservation between human and mouse, we assembled and analyzed 46 812 and 242 constitutively and alternatively spliced orthologs of human-mouse intron pairs, respectively. Combinations of BSs and PPTs can be found in most of the constitutive and alternative introns. The average distance between the BS and the 3' splice site (3'ss) is 33-34 nt. Acceptor-like AG dinucleotides that resided between the predicted BS and the 3'ss were found to appear mostly within 5 nt, but not more than 19 nt, downstream of the BS. However, although 32% of homologous alternatively spliced BS sequences were fully conserved between human and mouse, only a small fraction (3%) of homologous constitutive counterparts was fully conserved. This indicates that the full sequence of the BS is under weak purifying selection in constitutively spliced introns and further strengthens the view that the BS sequence is just one of several factors determining the ability of the splicing machinery to identify the BS location. Mutations in the putative BS revealed a shift from constitutive to alternative splicing, and it also controls the inclusion/skipping ratio in alternative splicing. This suggests a role for BS sequences in regulated splicing.

Structural basis for iron binding and release by a novel class of periplasmic iron-binding proteins found in gram-negative pathogens.

We have determined the 1.35- and 1.45-A structures, respectively, of closed and open iron-loaded forms of Mannheimia haemolytica ferric ion-binding protein A. M. haemolytica is the causative agent in the economically important and fatal disease of cattle termed shipping fever. The periplasmic iron-binding protein of this gram-negative bacterium, which has homologous counterparts in many other pathogenic species, performs a key role in iron acquisition from mammalian host serum iron transport proteins and is essential for the survival of the pathogen within the host. The ferric (Fe(3+)) ion in the closed structure is bound by a novel asymmetric constellation of four ligands, including a synergistic carbonate anion. The open structure is ligated by three tyrosyl residues and a dynamically disordered solvent-exposed anion. Our results clearly implicate the synergistic anion as the primary mediator of global protein conformation and provide detailed insights into the molecular mechanisms of iron binding and release in the periplasm.

Ultrastructural analysis of chromatin in meiosis I + II of rye (Secale cereale L.)

Scanning electron microscopy (SEM) proves to be an appropriate technique for imaging chromatin organization in meiosis I and II of rye (Secale cereale) down to a resolution of a few nanometers. It could be shown for the first time that organization of basic structural elements (coiled and parallel fibers, chromomeres) changes dramatically during the progression to metaphase I and II. Controlled loosening with proteinase K (after fixation with glutaraldehyde) provides an enhanced insight into chromosome architecture even of highly condensed stages of meiosis. By selective staining with platinum blue, DNA content and distribution can be visualized within compact chromosomes as well as in a complex arrangement of fibers. Chromatin interconnecting threads, which are typically observed in prophase I between homologous and non-homologous chromosomes, stain clearly for DNA. In zygotene transversion of chromatid strands to their homologous counterparts becomes evident. In pachytene segments of synapsed and non-synapsed homologs alternate. At synapsed regions pairing is so intimate that homologous chromosomes form one filament of structural entity. Chiasmata are characterized by chromatid strands which traverse from one homolog to its counterpart. Bivalents are characteristically fused at their telomeric regions. In metaphase I and II there is no structural evidence for primary and secondary constrictions.

Cloning and expression of human GTDC1 gene (glycosyltransferase-like domain containing 1) from human fetal library.

The glycosyltransferases (GTs) catalyze the synthesis of the carbohydrate portions of glycoproteins, glycolipids, and proteoglycans. Here we report the cloning and characterization of a novel human GTDC1 (glycosyltransferase-like domain containing 1) gene, which locates on human chromosome 2q22. The GTDC1 cDNA is 2954 bp in length, encoding a putative protein of 458 amino acids. At protein level human GTDC1 has 75 and 37% identity with its homologous counterparts in the mouse and fruitfly, respectively. RT-PCR analysis revealed its relatively high expression level in the adult lung, spleen, testis, and peripheral blood leukocyte.

Glycoprotein gpTRL10 of human cytomegalovirus is dispensable for virus replication in human fibroblasts.

Human cytomegalovirus (HCMV) has a coding capacity for glycoproteins which by far exceeds that of other herpesviruses. Few of these proteins have been characterized. Glycoprotein gpTRL10 represents a structural component of HCMV. The protein has no homologous counterparts in other herpesviruses. We have isolated bacterial artificial chromosomes (BACs) harboring the genome from the low passage clinical isolate PAN and constructed a deletion mutant in reading frame TRL10. Our results show that deletion of gpTRL10 has only minimal effects on viral replication in human fibroblasts.

The Fourth Blade within the β-Propeller Is Involved Specifically in C3bi Recognition by Integrin αMβ2

Interactions between the complement degradation product C3bi and leukocyte integrin alpha M beta 2 are critical to phagocytosis of opsonized particles in host defense against foreign pathogens and certain malignant cells. Previous studies have mapped critical residues for C3bi binding to the I-domains of the alpha M and the beta2 subunits. However, the role of the alpha M beta-propeller in ligand binding remains less well defined, and the functional residues are still unknown. In the present study, we studied the function of the alpha M beta-propeller in specific ligand recognition by alpha M beta 2 using a number of different approaches, and we report four major findings. 1) Substitution of five individual segments (Asp398-Ala402, Leu412-Leu419, Tyr426-Met434, Phe435-Glu443, and Ser444-Thr451) within the W4 blade of the beta-propeller with their homologous counterparts in integrin alpha2 abrogated C3bi binding, whereas substitution of eight other segments outside this blade had no effect. 2) These five mutants defective in C3bi binding supported strong alpha M beta 2-mediated and cation-dependent cell adhesion to fibrinogen, suggesting that the conformations of these five defective mutants were intact. 3) Polyclonal antibodies recognizing sequences within the W4 blade significantly blocked C3bi binding by wild-type alpha M beta 2. 4) A synthetic peptide corresponding to Gln424-Gly440 within W4 interacted directly with C3bi. In conclusion, our data demonstrate that the W4 blade (residues Asp398 to Thr451) is involved specifically in C3bi but not fibrinogen binding to alpha M beta 2. Altogether, our study supports a model in which three separate domains of alpha M beta 2 (the alpha MI-domain, the alpha M beta-propeller, and the beta 2I-domain) function together and contribute to the formation of the C3bi-binding site.

THE FIRST BASIC PROBLEM: A REVIEW OF MOLT AND PLUMAGE HOMOLOGIES

Abstract All birds have fundamentally similar patterns of plumage succession. Thus Humphrey and Parkes (1959) proposed a system of nomenclature (the H-P system), based on homologies, that has become standard for molt studies in North America. However, presumably analogous similarities in pattern between first basic and definitive basic plumages have obscured homologies. Many plumages conventionally known as “first basic” are better considered as novel first-cycle plumages that lack homologous counterparts in subsequent cycles. Consequently, current nomenclature does not consistently reflect between-species homologies. Howell and Corben (2000b) proposed that traditional juvenal plumage can be considered an unambiguous starting point for a terminology that better reflects presumed homologies in basic plumages; alternate and other nonbasic plumages may not necessarily be homologous between species. Four underlying strategies of increasing complexity incorporate all known patterns of plumage succession: the S...

Molecular Mimicry in Type 1 Diabetes

Type 1 diabetes is caused by a T cell-mediated autoimmune destruction of the pancreatic beta cells. Molecular mimicry between viral pathogens and beta cell protein has been a popular theory to explain loss of tolerance in type 1 diabetes. However, functional data in support of this hypothesis have been lacking, presumably because the homologies were defined on the basis of linear similarities in peptide sequences, which ignores the criteria of HLA versus T cell receptor contact residues in peptide epitopes required for T cell recognition. We applied a HLA-binding dedicated peptide microarray analysis using autoreactive T cell clones specific for the autoantigen GAD65 to determine the algorithm of T cell recognition by this given T cell clone. The subsequent database search identified a 100% fit with cytomegalovirus peptide, which was subsequently shown to be recognized by these clonal T cells. However, T cell clones reactive with linear homologies previously described as putative candidates for T cell cross-reactivity between GAD65 and Coxsackie virus peptide were unable to recognize the homologous counterparts.

Comparative toxinological and immunological studies on the nematocyst venoms of the Red Sea fire corals Millepora dichotoma and M. platyphylla

A method appropriate for isolating of fire coral nematocysts of Millepora dichotoma (Md) and Millepora platyphylla (Mp) was described and compared with techniques that had been used before. Isolated nematocyst venoms of Md (Md-TX) and Mp (Mp-TX) were lethal to mice (had LD 50 values of 0.51 and 0.21 μg/g mouse body, respectively) and displayed variable hemolytic, vasopermeable and dermonecrotic properties. The potent hemolysins of Md-TX and Mp-TX, which purified by gel filtration chromatography, possessed prominent proteins of molecular weights 35 and 31 kDa and had LD 50 values 0.35 and 0.25 μg/g mouse, respectively. Hemolytic activities of crude venoms and their fraction could be inactivated using known anti-hemolytic agents. Both Md-TX and Mp-TX had distinguishable antigenic properties and their antisera raised in immunized mice and stung human were cross-reactive. ELISA assays showed an antigenic similarity among the studied fire coral homologous cytolytic counterparts.

Synthesis and properties of aromatic polyamides based on a benzonorbornane bis(ether carboxylic acid)

AbstractA set of new aromatic polyamides containing ether and benzonorbornane units were synthesized by the direct phosphorylation polycondensation of 3,6‐bis(4‐carboxyphenoxy)benzonorbornane with various aromatic diamines. The polymers were produced in high yields and moderate to high inherent viscosities (0.64–1.70 dL/g). The polyamides derived from rigid diamines such as p‐phenylenediamine and benzidine were semicrystalline and insoluble in organic solvents. The other polyamides were amorphous and organosoluble and afforded flexible and tough films via solution casting. These films exhibited good mechanical properties, with tensile strengths of 95–101 MPa, elongations at break of 13–25%, and initial moduli of 1.97–2.33 GPa. The amorphous polyamides showed glass‐transition temperatures between 176 and 212 °C (by differential scanning calorimetry) and softening temperatures between 194 and 213 °C (by thermomechanical analysis). Most of the polymers did not show significant weight loss before 450 °C in nitrogen or in air. Some properties of these polyamides were also compared with those of homologous counterparts without the pendent norbornane groups. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 947–957, 2002

Structure and expression of a hybrid proline-rich protein gene in the solanaceous species, Solanum brevidens, Solanum tuberosum, and Lycopersicum esculentum

Summary The full-length cDNA of a previously identified Solanum brevidens gene was isolated and characterised. DNA sequence analysis revealed an open reading frame that encodes a hybrid proline-rich cell wall protein of 407 amino acids. The putative protein was designated SbrPRP. The SbrPRP harbours three parts, an N-terminal signal peptide followed by a repetitive proline-rich domain and a cysteine-rich C-terminus resembling non-specific lipid-transfer proteins. The repetitive proline-rich domain contains two repeated motifs, PPHVKPPSTPK and PTPPIVSPP extended with TPKYP and TPKPPS motifs, respectively, at their N- or C-terminal. The SbrPRP gene of the non-tuberising Solanum species, Solanum brevidens , possesses highly homologous counterparts in the tuberising species, Solanum tuberosum ( StPRP ) and in the related species, Lycopersicum esculentum ( TFM7 ). All three genes are present in single- or low copy number in the corresponding genome. Organ-specific expression of the genes, however, is different in the three solanaceous species.

A short N-proximal region in the large envelope protein harbors a determinant that contributes to the species specificity of human hepatitis B virus.

Infection by hepatitis B virus (HBV) is mainly restricted to humans. This species specificity is likely determined at the early phase of the viral life cycle. Since the envelope proteins are the first viral factors to interact with the cell, they represent attractive candidates for controlling the HBV host range. To investigate this assumption, we took advantage of the recent discovery of a second virus belonging to the primate Orthohepadnavirus genus, the woolly monkey HBV (WMHBV). A recombinant plasmid was constructed for the expression of all WMHBV envelope proteins. In additional constructs, N-terminal sequences of the WMHBV large envelope protein were substituted for their homologous HBV counterparts. All wild-type and chimeric WMHBV surface proteins were properly synthesized by transfected human hepatoma cells, and they were competent to replace the original HBV proteins for the production of complete viral particles. The resulting pseudotyped virions were evaluated for their infectious capacity on human hepatocytes in primary culture. Virions pseudotyped with wild-type WMHBV envelope proteins showed a significant loss of infectivity. By contrast, infectivity was completely restored when the first 30 residues of the large protein originated from HBV. Analysis of smaller substitutions within this domain limited the most important region to a stretch of only nine amino acids. Reciprocally, replacement of this motif by WMHBV residues in the context of the HBV L protein significantly reduced infectivity of HBV. Hence this short region of the L protein contributes to the host range of HBV.

The KEX2 gene of Candida glabrata is required for cell surface integrity.

Candida glabrata has emerged as one of the most common causes of candidosis. In order to identify factors that are necessary for viability and pathogenicity of this fungal pathogen, we analysed the role of the KEX2 gene, which codes for a regulatory endoproteinase that is known to process certain virulence factors in Candida albicans. The KEX2 gene from C. glabrata was cloned and found to have 51% and 62% identity and high structural similarities to the homologous counterparts in C. albicans and Saccharomyces cerevisiae. KEX2 was expressed at all time points investigated during growth in complex medium. In order to investigate the role of this putative regulatory proteinase, Kex2-deficient mutants were produced. In addition to known kex2 phenotypes, such as pH and calcium hypersensitivity, the mutants grew in cellular aggregates and were found to be hypersensitive to several antifungal drugs that target the cell membrane, including azoles, amorolfine and amphotericin B. Ultrastructural investigation after exposure to low doses of itraconazole showed azole-specific alterations such as enlarged vacuoles and proliferation of the cytoplasmatic membrane in the kex2 mutants, but not in the control strains. In contrast, antifungals such as 5-flucytosine and hydroxypyridones inhibited growth of the kex2 mutants and the control strains to the same extent. In an in vitro model of oral candidosis, kex2 mutants showed reduced tissue damage in the presence of itraconazole compared with the control infections. These data suggest that Kex2 is involved in the processing of proteins that are essential for cell surface integrity of C. glabrata.

Structure-Function of the Putative I-domain within the Integrin β2 Subunit

The central region (residues 125-385) of the integrin beta(2) subunit is postulated to adopt an I-domain-like fold (the beta(2)I-domain) and to play a critical role in ligand binding and heterodimer formation. To understand structure-function relationships of this region of beta(2), a homolog-scanning mutagenesis approach, which entails substitution of nonconserved hydrophilic sequences within the beta(2)I-domain with their homologous counterparts of the beta(1)I-domain, has been deployed. This approach is based on the premise that beta(1) and beta(2) are highly homologous, yet recognize different ligands. Altogether, 16 segments were switched to cover the predicted outer surface of the beta(2)I-domain. When these mutant beta(2) subunits were transfected together with wild-type alpha(M) in human 293 cells, all 16 beta(2) mutants were expressed on the cell surface as heterodimers, suggesting that these 16 sequences within the beta(2)I-domain are not critically involved in heterodimer formation between the alpha(M) and beta(2) subunits. Using these mutant alpha(M)beta(2) receptors, we have mapped the epitopes of nine beta(2)I-domain specific mAbs, and found that they all recognized at least two noncontiguous segments within this domain. The requisite spatial proximity among these non-linear sequences to form the mAb epitopes supports a model of an I-domain-like fold for this region. In addition, none of the mutations that abolish the epitopes of the nine function-blocking mAbs, including segment Pro(192)-Glu(197), destroyed ligand binding of the alpha(M)beta(2) receptor, suggesting that these function-blocking mAbs inhibit alpha(M)beta(2) function allosterically. Given the recent reports implicating the segment equivalent to Pro(192)-Glu(197) in ligand binding by beta(3) integrins, these data suggest that ligand binding by the beta(2) integrins occurs via a different mechanism than beta(3). Finally, both the conformation of the beta(2)I-domain and C3bi binding activity of alpha(M)beta(2) were dependent on a high affinity Ca(2+) binding site (K(d) = 105 microm), which is most likely located within this region of beta(2).

Crystal structure of trbp111: a structure-specific tRNA-binding protein.

Trbp111 is a 111 amino acid Aquifex aeolicus structure-specific tRNA-binding protein that has homologous counterparts distributed throughout evolution. A dimer is the functional unit for binding a single tRNA. Here we report the 3D structures of the A.aeolicus protein and its Escherichia coli homolog at resolutions of 2.50 and 1.87 A, respectively. The structure shows a symmetrical dimer of two core domains and a central dimerization domain where the N- and C-terminal regions of Trbp111 form an extensive dimer interface. The core of the monomer is a classical oligonucleotide/oligosaccharide-binding (OB) fold with a five-stranded ss-barrel and a small capping helix. This structure is similar to that seen in the anticodon-binding domain of three class II tRNA synthetases and several other proteins. Mutational analysis identified sites important for interactions with tRNA. These residues line the inner surfaces of two clefts formed between the ss-barrel of each monomer and the dimer interface. The results are consistent with a proposed model for asymmetrical docking of the convex side of tRNA to the dimer.

Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches

Among the total of 274 orfs within bacteriophage T4, only half have been reasonably well characterized, and the functions of the rest have remained obscure. In order to predict the molecular functions of the orfs, a position-specific iterated (PSI)-BLAST search of bacteriophage T4 against the sequence database of known 3D structures was carried out. PSI-BLAST is one of the most powerful iterative sequence search methods using multiple sequence alignment, with the ability to detect many more proteins with distant homology than standard pairwise methods. The 3D structures of proteins are considered to be better preserved than the sequences, and the detected distantly homologous proteins are likely to possess highly similar 3D structures. Thirteen orfs of phage T4, whose homologues were not detected by standard pairwise methods, were found to have significantly homologous counterparts by this method. The plausibility of the results was confirmed by checking whether important residues at substrate/ligand-binding sites were conserved. Among them, two orfs, vs.1 and e.1, which are similar to Escherichia coli lytic enzyme and MutT protein, respectively, had not been studied previously. Also, gp rIIA, a rapid lysis protein, whose gene structure had been intensively studied during the development of molecular biology in the 1950s and yet whose molecular function remains unknown, has an N-terminal domain that is significantly similar to the N-terminal region of the heat shock protein Hsp90.

Immunochemical evaluation of bovine beta-casein and its 1-28 phosphopeptide in cheese during ripening.

Polyclonal antibodies raised against the plasmin-released 1-28 phosphopeptide from bovine beta-casein [i.e., beta-CN(f1-28)4P] specifically recognized the tryptic beta-casein 1-25 and 2-25 peptides, whatever the degree of phosphorylation, but were unresponsive to the shortened beta-casein 16-22 phosphopeptide. These antibodies were able to recognize the parent bovine beta-casein as well as the homologous water buffalo protein, but they could not detect the homologous counterparts from ovine and caprine milks. Such antibodies were used in competitive enzyme-linked immunosorbent assays to monitor the plasmin-mediated release of the 1-28 phosphopeptide from beta-casein and to evaluate the residual native beta-casein in bovine cheese sampled during ripening. Applications of these polyclonal antibodies are suggested mainly for estimating the age of hard cheeses and, possibly, for tracing the presence of bovine casein in fresh ovine and caprine cheeses.