Homology Recognition Research Articles

Atavisms and the homology of hyobranchial elements in lower vertebrates.

The homology of branchial arch segments in salamanders has been a matter of controversy since the last century. Many investigators term the most medial paired elements of salamander branchial arches "ceratobranchials" and the next distal paired elements "epibranchials." This suggests that the first two segmental elements of the salamander branchial arch are not homologous with elements occupying the same position in ray-finned fishes, Latimeria, "rhipidistians," and lungfishes, in which these bones are called hypobranchials and ceratobranchials, respectively. Three lines of evidence suggest that it is more parsimonious to interpret urodele branchial arch segments as being homologous with those of other vertebrate clades-(1) comparative osteology, (2) comparative myology, and (3) the discovery of cartilaginous structures forming a third segmental unit that we interpret as atavistic epibranchials of the branchial arch in one population of the salamander Notophthalmus viridescens. These structures possess all the defining attributes of atavisms, and illustrate the special role that atavistic features play in resolving questions of homology recognition.

Effector lymphocyte response to homologous tumor antigens in various stages of malignant disease as monitored by leukocyte adherence inhibition — cell mediated immunity (LAI-CMI)

Leukocyte adherence inhibition-cell mediated immunity (LAI-CMI) studies were performed on leukocytes obtained from patients with various stages of breast cancer, colon carcinoma and lung cancer in order to monitor cell mediated immunity during tumor progression. In the presence of autologous serum, all patients with localized tumors showed positive LAI-CMI indexes (> 20%), while significant reduction of homologous tumor antigen recognition as measured by the LAI-CMI responses was observed in nearly all patients with Stage IV breast cancer, Duke C colon cancer and Stage III lung cancer. On substituting autologous serum with normal AB serum, leukocytes from patients with large tumor burdens responded to homologous tumor antigens. These results indicate the existence of organ-specific serum factor(s) which may mask the receptor sites on effector cells for tumor recognition. Patients with such serum blocking factor(s) showed significant increase of IgG immune complexes IgM, IgA and alpha-2-macroglobulins. Application of a protein A affinity column purification resulted in a major reduction of IgG and other immune globulins but not of alpha-2-macroglobulin. The blocking effects of autologous serum, however, were not completely abrogated by fitration on the protein A column, thus suggesting that SBF may be heterogeneous in nature and may occur in other serum protein fractions beside the immune globulins.

Gene conversion, recombination nodules, and the initiation of meiotic synapsis.

AbstractThe nature of the relationship between the two types of meiotic recombination outcomes, exchange (crossing‐over) and simple gene conversion, has been debated for years. I here propose that these two types of events are not necessarily causally related and hypothesize that the primary role of events detected as simple gene conversion is in the recognition of homology during synapsis.

SC-formation in someAllium species, and a discussion of the significance of SC-associated structures and of the mechanisms for presynaptic alignment

Earlier observations on synaptonemal complex (SC) formation inAllium are supplemented by data from diploidA. sphaerocephalon, pentaploidA. oleraceum and allotetraploidA. senescens. Accumulating information about structures like lateral element thickenings and -doublings allows to draw conclusions about their nature. The occurrence of discrete intercalary and terminal homologous associations prior to synapsis is confirmed for a range ofAllium species and it is argued that they are a general phenomenon. Several hypotheses on homologous recognition and/or attraction are discussed in the light of the observations on homologous alignment inAllium.

A unique four-stranded model of a homologous recombination intermediate

This paper proposes a model of four-stranded DNA synapsis during recombination between homologous segments of two DNA duplexes. The proposed intermediate is one of only two known models having relative chain orientations about the synaptic junction that are consistent with recent topological results on the integrative recombination of bacteriophage lambda. This model has the advantage of providing a mechanism for recognition of sequence homology between duplexes through specific hydrogen-bond formation; other models are discussed in comparison. The new model is based on an alternative family of DNA structures having chain directions opposite to those of the Watson-Crick family of structures. Idealized coordinates for generating both right- and left-handed forms of these alternative structures are presented for further study.

Homologous recombination in Escherichia coli: dependence on substrate length and homology.

We studied the in vivo recombination between homologous DNA sequences cloned in phage lambda and a pBR322-derived plasmid by assaying for the formation of phage-plasmid cointegrates by a single (or an odd number of) reciprocal exchange. (1) Recombination proceeds by the RecBC pathway in wild-type cells and by low levels of a RecF-dependent pathway in recBC- cells. The RecE pathway appears not to generate phage-plasmid cointegrates. (2) Recombination is linearly dependent on the length of the homologous sequences. In both RecBC and RecF-dependent pathways there is a minimal length, called the minimal efficient processing segment (MEPS), below which recombination becomes inefficient. The length of MEPS is between 23-27 base pairs (bp) and between 44-90 bp for the RecBC- and RecF-dependent pathways, respectively. A model, based on overlapping MEPS, of the correlation of genetic length with physical length is presented. The bases for the different MEPS length of the two pathways are discussed in relationship to the enzymes specific to each pathway. (3) The RecBC and the RecF-dependent pathways are each very sensitive to substrate homology. In wild-type E. coli, reduction of homology from 100% to 90% decreases recombinant frequency over 40-fold. The homology dependence of the RecBC and RecF-dependent pathways are similar. This suggests that a component common to both, probably recA, is responsible for the recognition of homology.

Homologous recognition of a promoter domain common to the MSV LTR and the HSV tk gene

We have partially purified, from rat liver, a nuclear protein fraction with sequence-specific affinity to a promoter domain shared by the herpesvirus tk gene and the Moloney murine sarcoma virus LTR. For both promoters, the protein-binding domain occurs roughly 80 bp upstream of the mRNA cap site and harbors the pentanucleotide sequence 5′-CCAAT-3′. The MSV LTR pentanucleotide occurs on the coding strand in an orientation pointing toward the retroviral transcription unit. The HSV tk pentanucleotide occurs on the non-coding strand in an orientation pointing away from the gene. Assays in microinjected frog oocytes and transfected mouse L cells indicate that equivalent point mutations, introduced at each residue of the CAT pentanucleotide of each promoter, lead to similar changes in promoter activity. Furthermore, they similarly alter binding of the nuclear protein fraction. Surprisingly, a C to G transversion at the first residue of the CAT pentanucleotide, which severely impairs the activity of both promoters, appears to increase affinity of the CAT binding protein.

Lipopolysaccharide structures of Campylobacter fetus are related to heat-stable serogroups.

To determine whether lipopolysaccharide (LPS) structures of Campylobacter fetus are related to the three known heat-stable serogroups, proteinase K-treated whole cell lysates obtained from strains of each serogroup were electrophoresed in polyacrylamide gels. All strains had smooth-type LPS with multiple high-molecular-weight repeating units. The profiles of serogroup A from C. fetus subsp. fetus and from C. fetus subsp. venerealis were identical, but they were different from those of C. fetus subsp. fetus serogroups B and AB. When we immunoblotted the LPS of these serogroups with normal or immune rabbit serum we found homologous recognition between serogroups A from C. fetus subsp. fetus and C. fetus subsp. venerealis. Similarly, serogroups AB and B from C. fetus subsp. fetus showed homologous recognition. However, antiserum against serogroup A did not recognize serogroups B and AB and vice versa. Absorption studies confirmed the identity of LPS from all serogroup A C. fetus strains and cross-reactivity of the serogroup B and AB strains with one another. Serogroup A strains were resistant to the bactericidal activity in normal human serum, whereas serogroup B and AB strains generally were susceptible; isolates from humans predominantly belonged to serogroup A. Results of these studies suggest that the LPS composition forms the basis for the heat-stable serotyping system for C. fetus and that the structural and antigenic variants are associated with differential serum susceptibility.

Restriction endonuclease accessibility of the developmentally regulated goat gamma-, beta C-, and beta A-globin genes in chromatin. Differences in 5' regions which show unusually high sequence homology.

The chromatin structure of the developmentally regulated fetal (gamma), preadult (beta C), and adult (beta A) beta-globin genes of the goat has been investigated using a nuclear restriction enzyme accessibility assay. In fetal liver nuclei only the PvuII site immediately proximal to the gamma-globin gene is available for digestion, while the homologous recognition sequences 5' to beta A and beta C are not accessible. Conversely, that site upstream of the beta C transcription unit is exclusively digested in bone marrow nuclei prepared from animals expressing the juvenile form of the protein. In nonerythropoietic tissue none of the PvuII recognition sequences flanking the three genes are digested using identical reaction conditions. These results are particularly striking since the nucleotide sequence extending for hundreds of bases in either direction from this restriction site is remarkably homologous among the three genes. In addition, we have mapped an endogenous nuclease-hypersensitive site approximately 1150 nucleotides 5' to the gamma-globin gene which is evident only in fetal liver tissue.

Synaptonemal complex formation in pollen mother cells of Tradescantia

Seven nuclei of Tradescantia sp. (2n=12) were prepared using Gillies' modification of the Counce-Meyer whole-mount spreading technique. These nuclei were examined for the type (homologous and nonhomologous), amount, and location of synaptonemal complex (SC) formation. Estimates of the total potential number of discrete initiations of SC formation ranged from 251–299 per nucleus. The average distance between sites of initiation ranged from 7.3 to 11.2 μm in the different nuclei. Two groups of Tradescantia were used. Of the T. ohiensis var. paludosa plants, the one instance of irregularity in synapsis was associated with a pairing partner switchpoint. In the other plants derived from Mericle's Clone 02, all nuclei, even those in early zygotene, had several examples of foldback synapsis. The significance of the location of SC formation, and the occurrence of foldback synapsis is considered and a model of SC formation is proposed. In this model, a “recognition of homology” step is not considered necessary for SC formation; homologous synapsis is usually accomplished by spatial and temporal coordination of zygotene DNA synthesis.

Studies on the control of diploid-like meiosis in polyploid taxa of Chrysanthemum

Chromosome pairing during meiosis was studied in colchiploids of Ch. japonense 6X and Ch. boreale 2X. In both species chromosomes paired predominantly as bivalents, even though because of complete homology they possess the ability to pair as multivalents. Multivalent formation is prevented by restriction of pairing initiation to a single site (=zygomere) per chromosome. Multivalent suppressor systems in polyploids may evolve through gradual reduction in number of zygomeres, and differentiation in their homology recognition and regulation system.

Critical examination of postulated cladistic relationships among species of flour beetles (genus Tribolium, Tenebrionidae, Coleoptera).

Cytological considerations have led to the hypothesis that Tribolium confusum (CF) evolved from an ancestor similar to T. castaneum (CS) by translocation of an autosome to the X chromosome, and that T. destructor (DEST) was derived from CF. T. brevicornis (BREV) is regarded as the most primitive on morphological grounds. Electrophoretic analyses of 19 strains of CS, 7 of CF, and 1 each of DEST and BREV do not support this postulated evolutionary pathway. CF and CS are much more similar to BREV than they are to each other. (Comparisons of morphological mutations in CS and CF also indicate that the two species are not similar genetically.) DEST and CF are very dissimilar electrophoretically. It is likely that the species evolved independently from an ancestral stock which may be represented by BREV. Recognition of gene homology in different species is the keystone for all attempts at constructing genetically meaningful evolutionary pathways. The difficulties involved in doing so are pointed out.

The prediction of protein structure from amino acid sequence

Methods of predicting protein conformation from amino acid sequence are reviewed. Several widely used algorithms to predict local secondary structure are first discussed. Four general approaches to predict the tertiary structure are then described: (1) energy calculations from an open chain; (2) recognition of sequence homology with a known structure; (3) uses of a sequence template that dictates a particular fold; (4) docking alpha-helices and beta-strands. Throughout this review, the likely success of these methods is considered.

Sorting out of coaggregated brain cell types mediated by specific cell recognition factors in vitro: I. Experimental histogenesis and quantitative analysis

Two region-specific cell recognition factors (CRF, cerebrum specific, and OTF, optic tectum specific), which markedly increased the size of aggregates formed by dissociated cells of homologous type, have also been shown to promote selective association of homologous cells within coaggregates formed from commingled cerebrum and tectum cell suspensions. The resulting patterns of cell sorting were examined quantitatively. Nearest-neighbor analysis of cell associations within equatorial histological sections of these coaggregates evaluated the enhanced association of regionally homologous brain cell types in response to each specific brain cell recognition factor. The statistical analysis also examined a characteristic positional segregation of cerebrum and tectum cells in the sorted out coaggregates: tectum cells tended to segregate toward the periphery of the coaggregate while cerebrum cells massed in the core. These data demonstrate that the cells of each population associated preferentially with one another in direct response to their homologous cell recognition factor. The application of this quantitative nearest-neighbor analysis for making assessments of associative affinities between neural cell populations is evaluated and implications of using this analysis for studying regional and functional homology between nerve cells during development are discussed.

Studies on the control of diploid-like meiosis in polyploid taxa of Chrysanthemum. I. Hexaploid Ch. japonense Nakai.

Chromosome pairing during meiosis was studied in colchiploids of Ch. japonense 6X and Ch. boreale 2X. In both species chromosomes paired predominantly as bivalents, even though because of complete homology they possess the ability to pair as multivalents. Multivalent formation is prevented by restriction of pairing initiation to a single site (=zygomere) per chromosome. Multivalent suppressor systems in polyploids may evolve through gradual reduction in number of zygomeres, and differentiation in their homology recognition and regulation system.

Genetic studies on heterochromatin in Drosophila melanogaster and their implications for the functions of satellite DNA

In Drosophila melanogaster the centromeric heterochromatin of all chromosomes consists almost entirely of several different satellite DNA sequences. In view of this we have examined by genetic means the meiotic consequences of X chromosomes with partial deletions of their heterochromatin, and have found that the amount and position of recombination on each heterochromatically deleted X is substantially different from that of a normal X. It appears that the amount of heterochromatin is important in modifying the "centromere effect" on recombination.--In all the deleted Xs tested, chromosome segregation is not appreciably altered from that of a nondeleted control chromosome. Thus satellite DNA does not appear to be an important factor in determining the regular segregation of sex chromosomes in Drosophila. Additionally, since X chromosomes with massive satellite DNA deficiencies are able to participate in a chromocenter within salivary gland nuclei, a major role of satellite DNA in chromocenter formation in this tissue is also quite unlikely.--In order to examine the mechanisms by which the amount of satellite DNA is increased or decreased in vivo, we have measured cytologically the frequency of spontaneous sister chromatid exchanges in a ring Y chromosome which is entirely heterochromatic and consists almost exclusively of satellite DNA. In larval neuroblast cells the frequency of spontaneous SCE in this Y is approximately 0.3% per cell division. Since there is no meiotic recombination in D. melanogaster males and since meiotic recombination in the female does not occur in heterochromatin, our results provide a minimum estimate of the in vivo frequency of SCE in C-banded heterochromatin (which is predominantly simple sequence DNA), without the usual complications of substituted base analogs, incorporated radioactive label or substantial genetic content.--We emphasise that: (a) satellite DNA is not implicated in any major way in recognition processes such as meiotic homologue recognition or chromocenter formation in salivaries, (b) there is likely to be continuous variation in the amount of satellite DNA between individuals of a species; and (c) the amount of satellite DNA can have a crucial functional role in the meiotic recombination system.

Chromatographic solute identification using peak shape analysis

Solute identification by retention data alone does not yield a positive identification for two or more solutes with approximately the same retention times. In such cases, two columns with two different stationary phases are needed for solute verification. For this reason, the concentration profiles of gas chromatographic peaks have been studied using the empirically derived eight-parameter model of Chesler and Cram. A non-linear least squares fit of the data to this model has made it possible to derive parameters which allow homologous class recognition and specific solute identification. Two methods for determining the initial estimates are presented. In one method the initial estimates were calculated from the data in a purely empirical manner, while the other is based mathematically on the model. The fitted values of the parameters from the two methods are compared for the purpose of illustrating the dependence of the fit on the choice of initial estimates. Some of the parameters are believed to have physical significance. For example, an almost linear relationship between one of the fitted parameters, C 2, and the diffusion coefficient, D AB, of the solute in the carrier gas was found. Similar results were found for C 7 versus D AB, the capacity ratio k′ and C 2, and k′/(1 + k′) 2 and C 2.

Notes on Health Resorts: XIX.--South Africa as a Health Resort

Homology recognition and DNA-strand invasion ensure faithful homolog pairing and segregation during the first meiotic division¹. RAD51 and DMC1 recombinases catalyze these steps², with BRCA2 promoting their assembly into nuclear foci³. The recently identified human SWS1-SWSAP1 complex, related to the Shu complex in yeast, promotes RAD51 focus formation in cell lines^4,5. We show here that mouse SWS1-SWSAP1 is critical for meiotic homologous recombination (HR) by promoting the assembly of RAD51 and DMC1 on early recombination intermediates. Absence of the complex perturbs meiotic progression in males and females and both sexes are sterile, although a fraction of meiocytes form crossovers. Remarkably, loss of the DNA damage checkpoint kinase CHK2 rescues fertility specifically in females without rescuing crossover numbers. Unlike the Shu complex, the BRCA2 C terminus (known to be required for RAD51 stabilization^6,7) is dispensible for RAD51 and DMC1 focus formation. However, concomitant loss of the BRCA2 C terminus aggravates the meiotic defects in Shu mutant spermatocytes. These results point to a complex interplay of factors that ensure recombinase function and hence meiotic progression in the mouse.