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The T-cell receptor mediating restrictive recognition of antigen.

Four facts characterize restrictive recognition of antigen. First, in large measure, allele-specific determinants on R are recognized when R is functioning either as a restricting element (RL) or as an allo-target (or even xeno-target) (RF). Second, there is a high frequency of virgin antigen-responsive t cells with alloreactivity, i.e. anti-RF. Third, there is a strict relationship between the class of effector function and the class of RL recognized (restrictive recognition of antigen, XF) but a relaxed relationship between class of effector function and class of RF recognized (alloreactivity). Fourth, the effector T cell functions anti-RL-dependently when XF is the target (restrictive recognition of antigen) and anti-RL-independently when RF is the target (alloreactivity). From these facts are derived the following conclusions. The T cell uses a dual recognitive, single receptor (Model I, Figure 1). A single germ-line VT locus specifying anti-allele-specific recognition of species R encodes both the anti-R and the anti-X combining sites. A "learning" process (occurring in the thymus) is required to establish the restriction specificity (anti-RL) as well as the effector function/class of RL relationship. The repertoire is derived by somatic mutation of all germ-line VT genes specifying anti-RF (Model IA, Table 3 and Figure 9). Given Model IA (Table 3 and Figure 9), we can account further for the existence of an extensive polymorphism of R and minimal polygeneism, for the high frequency of crossreactivity between anti-XF and RF, and for the physiology and genetics of cell-cell communication in immune responsiveness.

Animals↗

Characterization and comparative genomic analysis of intronless Adams with testicular gene expression.

ADAM (a disintegrin and metalloprotease) family members with testis-specific or -predominant gene expression are divided phylogenically into two groups: ADAMs 2, 3, 5, 27, and 32 (the first group) and ADAMs 4, 6, 20, 21, 24, 25, 26, 29, 30, and 34 (the second group). We cloned and sequenced cDNAs for previously unidentified mouse Adams that belong to the second group. We found that all the Adam genes in the second phylogenic group are transcribed by both somatic and germ cells in mouse testis, representing a unique expression pattern different from that of the first-group Adams. Genomic analyses revealed that all the second-group Adam genes lack introns interrupting protein-coding sequences and many of them are present as multicopy genes, resulting in total of 14 functional mouse genes in this phylogenic group. Comparing the mouse and human ADAM genes, we found that a number of these mouse Adam genes do not have human orthologues and, even if they exist, some orthologues are pseudogenes in human. These results suggest the differential expansion of the second-group Adam genes in the mouse genome during evolution and a relationship between these Adams and male reproduction unique to mouse.

Amino Acid Sequence↗

Evolutionary relationships of vertebrate lactate dehydrogenase isozymes A4 (muscle), B4 (heart), and C4 (testis).

The amino acid sequence variation among seven lactate dehydrogenase isozymes from dogfish muscle, chicken muscle and heart, pig muscle and heart, and mouse and rat testes were compared with respect to the whole lactate dehydrogenase polypeptide chain as well as their four functional domains. The coenzyme-binding domain is more conserved than the substrate-binding domain. The sequence of the loop and helix alpha D region of testicular LDH-C4 isozymes is very different from those of somatic LDH-A4 and LDH-B4 isozymes, while the NH2-terminal arm is extremely variable. The most parsimonious phylogenetic tree among these seven vertebrate lactate dehydrogenase sequences clearly indicates that the LDH-A4 and LDH-B4 isozymes are more closely related to each other than either to the LDH-C4 isozymes.

Amino Acid Sequence↗

Expression of individual immunoglobulin genes occurs in an unusual system consisting of multiple independent loci.

Humoral immunity is effected through the rearrangement of immunoglobulin (Ig) genes in individual somatic cells committed to the B lymphocyte lineage. Haplotype or allelic exclusion restricts B lymphocytes to the expression of a single Ig receptor that can sustain further somatic modification. In most species, a specific Ig chain is encoded at a single genetic locus. However, in cartilaginous fish, hundreds of independent Ig heavy- (IgH) and Ig light-chain (IgL) gene loci are present, many of which are joined in the germ line. Ig gene transcripts have been amplified from single peripheral blood lymphocytes isolated from the clearnose skate (Raja eglanteria) using reverse-transcription PCR, and a single productive IgH transcript was detected in the majority of cells analyzed. Similarly, only a single IgL transcript was detected in over half of the individual cells. Taken together, these findings suggest that a mechanism for haplotype exclusion arose early in the evolution of antibody diversity and is independent of a single genetic locus.

Amino Acid Sequence↗

Morphogenesis of the eggshell in Drosophila.

The Drosophila eggshell is a specialized extracellular matrix that forms between the oocyte and overlaying somatic follicle cells during the latter stages of oogenesis. Largely proteinaceous, the eggshell is a highly organized multilayered structure with regional specializations designed to perform a variety of functions. Production of a functional eggshell features: (1) the differentiation of subsets of follicle cells in response to ovarian signals, (2) directed migrations of the follicle cells within the developing egg chamber, (3) expression of eggshell structural genes by the follicle cells in a defined temporal and spatial order, (4) postdepositional modifications of the eggshell proteins including several temporally regulated proteolytic cleavage events, and (5) regulated trafficking of several eggshell proteins in the assembling structure. By exploiting the genetic advantages of Drosophila and using evolution as a guide, the eggshell provides an excellent experimental system to study, in vivo, molecular mechanisms used to regulate protein-protein interactions throughout the assembly of a complex extracellular architecture in a developing organism.

Amino Acid Sequence↗

[Genetic factors and colorectal cancers development: therapeutic impact].

Colorectal tumorigenesis is associated with the progressive increase of epithelium dysplasia and wall invasion. These criteria are evaluated through histological staging, that enables a reliable estimation of patient prognosis, and is the best tool for therapeutic decision. Adjuvant chemotherapy is systematically proposed in case of lymph nodes and/or distant metastases (stages III and IV respectively). Its benefit in stage II tumors however remains unclear. Independently of the nature of the treatment, one third of all stage II-III tumors will metastasize. One important element to improve our tools for therapeutic decision is the identification of prognostic parameters, independent of the histological and morphological classifications. In a preliminary study, we allelotyped a series of 401 colon tumors and have shown that 5q and 8p allelic status were significantly predictive of the patients evolution. As a first approach, analysis of 47 tumors using microarray expression measures has allowed to validate the strong correlation between RNA levels and genomic status (i.e. mutation and allelic status) of known genes (APC, SMAD4, TP53, MLH1). We are now planning to characterize a series of 185 stage II-III colon tumors at both genomic and transcriptomic levels, in combination with the clinicopathological findings. Disease-free patients were followed at least 3 years after surgical resection. A tight collaboration of 5 departments of digestive oncology allowed to collect all clinical and biological resources for this project. Depending on our findings, correlations will be made between gene expression levels and somatic mutations of the coreesponding genes. Real time RT-PCR and immunohistochemical analyses will be performed on selected genes. Finally, biological mechanisms will be investigated to look for new therapeutic targets.

Colorectal Neoplasms↗

Reproductive ageing and sexual selection on male body size in a wild population of antler flies (Protopiophila litigata).

Little is known about the importance of trade-offs between ageing and other life history traits, or the effects of ageing on sexual selection, particularly in wild populations suffering high extrinsic mortality rates. Life history theory suggests that trade-offs between reproduction and somatic maintenance may constrain individuals with higher initial reproductive rates to deteriorate more rapidly, resulting in reduced sexual selection strength. However, this trade-off may be masked by increased condition dependence of reproductive effort in older individuals. We tested for this trade-off in males in a wild population of antler flies (Protopiophila litigata). High mating rate was associated with reduced longevity, as a result of increased short-term mortality risk or accelerated ageing in traits affecting viability. In contrast, large body size was associated with accelerated ageing in traits affecting mating success, resulting in reduced sexual selection for large body size. Thus, ageing can affect sexual selection and evolution in wild populations.

Aging↗

Karyological analysis of an interspecific hybrid between the dioecious Silene latifolia and the hermaphroditic Silene viscosa.

The genus Silene is a good model for studying evolution of the sex chromosomes, since it includes species that are hermaphroditic and dioecious, while maintain a basic chromosome number of 2n = 24. For some combinations of Silene species it is possible to construct interspecific hybrids. Here, we present a detailed karyological analysis of a hybrid between the dioecious Silene latifolia as the maternal plant and a related species, hermaphroditic Silene viscosa, used as a pollen partner. Using genomic probes (the genomic in situ hybridization (GISH) technique), we were able to clearly discriminate parental genomes and to show that they are largely separated in distinct nuclear domains. Molecular GISH and fluorescence in situ hybridization (FISH) markers document that the hybrid genome of somatic cells was strictly additive and stable, and that it had 12 chromosomes originating from each parent, including the only X chromosome of S. latifolia. Meiotic analysis revealed that, although related, respective parental chromosomes did not pair or paired only partially, which resulted in frequent chromosome abnormalities such as bridges and irregular non-disjunctions. GISH and FISH markers clearly document that the larger genome of S. latifolia and its largest chromosome component, the X chromosome, were mostly employed in chromosome lagging and misdivision.

Chimera↗

Assignment of the beta-subunit of rod photoreceptor cGMP phosphodiesterase gene PDEB (homolog of the mouse rd gene) to human chromosome 4p16.

The gene encoding the beta-subunit of rod photoreceptor cGMP phosphodiesterase (gene symbol PDEB, homolog of the mouse rd gene) is mapped to human chromosome 4 using somatic cell hybrids and further localized to the chromosome band 4p16 using in situ hybridization. A mutation in the mouse gene underlies the recessive trait of retinal degeneration in the rd mouse. Thus, the human homolog is a candidate for lesions causing retinal degeneration.

3',5'-Cyclic-GMP Phosphodiesterases↗

Sequence and phylogeny of HERV-W pol fragments.

A new human endogenous retroviral family (HERV-W) has been described that is related to multiple sclerosis-associated retrovirus (MSRV) sequences that have been identified in particles recovered from monocyte cultures from patients with multiple sclerosis. Using the PCR approach with a human monochromosomal somatic cell hybrid DNA panel, 24 pol fragments of the HERV-W family from chromsomes 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 20, 21, X, and Y were identified and analyzed. They showed a high degree of nucleotide sequence similarity (89.3-91.3%) with that of the HERV-W. Translation of the pol fragments showed no frameshift and termination codon by deletion/insertion or point mutation in some clones: HWP4-1, HWP4-2 from chromosome 4, and HWPX-1 from chromosome X. Phylogenetic analysis of the HERV-W family indicates that the pol fragments have evolved independently among chromosomes or represent separate integration events during primate evolution.

Amino Acid Sequence↗

Oocyte and somatic 5S ribosomal RNA and 5S RNA encoding genes in Xenopus tropicalis.

We have investigated the structure of oocyte and somatic 5S ribosomal RNA and of 5S RNA encoding genes in Xenopus tropicalis. The sequences of the two 5S RNA families differ in four positions, but only one of these substitutions, a C to U transition in position 79 within the internal control region of the corresponding 5S RNA encoding genes, is a distinguishing characteristic of all Xenopus somatic and oocyte 5S RNAs characterized to date, including those from Xenopus laevis and Xenopus borealis. 5S RNA genes in Xenopus tropicalis are organized in clusters of multiple repeats of a 264 base pair unit; the structural and functional organization of the Xenopus tropicalis oocyte 5S gene is similar to the somatic but distinct from the oocyte 5S DNA in Xenopus laevis and Xenopus borealis. A comparative sequence analysis reveals the presence of a strictly conserved pentamer motif AAAGT in the 5'-flanking region of Xenopus 5S genes which we demonstrate in a separate communication to serve as a binding signal for an upstream stimulatory factor.

Animals↗

A homologous subfamily of satellite III DNA on human chromosomes 14 and 22.

We describe a new subfamily of human satellite III DNA that is represented on two different acrocentric chromosomes. This DNA is composed of a tandemly repeated array of diverged 5-base-pair monomer units of the sequence GGAAT or GGAGT. These monomers are organised into a 1.37-kilobase higher-order structure that is itself tandemly reiterated. Using a panel of somatic cell hybrids containing specific human chromosomes, this higher-order structure is demonstrated on chromosomes 14 and 22, but not on the remaining acrocentric chromosomes. In situ hybridisation studies have localised the sequence to the proximal p-arm region of these chromosomes. Analysis by pulsed-field gel electrophoresis (PFGE) reveals that 70-110 copies of the higher-order structure are tandemly organised on a chromosome into a major domain which appears to be flanked on both sides by non-tandemly repeated genomic DNA. In addition, some of the satellite III sequences are interspersed over a number of other PFGE fragments. This study provides fundamental knowledge on the structure and evolution of the acrocentric chromosomes, and should extend our understanding of the complex process of interchromosomal interaction which may be responsible for Robertsonian translocation and meiotic nondisjunction involving these chromosomes.

Animals↗

Regional assignments of NP and MPI on chromosome 7 in pig, Sus scrofa.

Fibroblasts from a pig with a spontaneous reciprocal translocation involving chromosome 7, were used to prepare a set of pig-mouse somatic cell hybrids. The isozyme analysis strongly indicated that in pigs, the NP (nucleoside phosphorylase) gene is located on the distal part of the long arm of chromosome 7, (q21----qter), while the MPI (mannose phosphate isomerase) gene is in the region q21----pter. This confirmed previously reported chromosomal assignment of these genes in pigs and that this synteny has been evolutionarily conserved in several different animal species.

Animals↗

Julie's museum: the evolution of thinking, dreaming and historicization in the treatment of traumatized patients.

The author contends that, following Freud, trauma may be viewed as a disruption of the ego's 'protective shield' and that a central factor of this shield is an internalized relationship to a thinking-containing mother. Severe trauma destroy this inner connection, resulting in the reversal of a-function and the establishment of a rigid traumatic organization (ss-screen) that brings coherence to the shattered psyche. However, this is an 'organized chaos' in which concrete forms of thinking predominate. The patient's ability to think, dream and imagine is significantly curtailed and she is consequently locked in a traumatic world from which she is unable to evolve. He offers a detailed case history to illustrate these points and the vital role the analyst's imaginative capacities play in the analysis of such individuals. Finally, he addresses the development of the capacity to represent the trauma, starting with primitive, often somatically encoded experiences, and evolving toward the capacity for historicization.

Child↗

Psychologic evolution of patients with Menière's disease in relation to therapy.

The state of anxiety experienced by menieric patients indicates the importance of the psychologic component in this disease. Uncertainties as to the type of treatment that is actually curative for this disease have put doubts on the favorable outcome for patients referred for endolymphatic shunt procedures; some clinicians claim that in such cases surgery simply had a psychologic support function. To evaluate the effectiveness of such a statement, the authors have studied three groups of patients: patients who underwent surgery; patients who underwent medical treatment; and nonmenieric, otosclerotic subjects prior to surgery as a control group. The first group was further divided into subjects with and without improvement after surgery. The following personality tests were used: Minnesota Multiphase Personality Inventory, reduced version; Adjective Check List; State-Trait Anxiety Inventory; and Symptom Check List. The results relative to the whole menieric group show a tendency toward a state of dysphoria and more striking somatizations than in the otosclerotic group. In regard to the distinction between operated and nonoperated patients, the former group showed a personality with a strong neurotic trait associated with dysphoria and a state of free anxiety tending toward hypochondria. The outcome of the operation (improvement of the vertigo) does not seem to influence the personality of the subjects, even though there are signs of higher anxiety levels than in subjects without improvement.

Adult↗

The survival of slow reproducers.

Multicellularity, and the attendant segregation of the germ line, entails the loss of reproductive capacity by the soma: in Volvox carteri, less than 1 cell in 100 contributes to the next generation. However, compensatory advantages are unlikely to be very large (Koufopanou & Bell, 1993. Proc. R. Soc. Lond. (B) 254,107-113). Somewhat similarly, sex implies the generation of males, hence a dramatic reproductive slowdown (Barton & Charlesworth, 1998. Science281, 1986-1990); yet, a compensating (two-fold) advantage of sex has not been found. Here, I try to evaluate the actual cost of maintaining slow reproductive cycles, namely cycles that necessitate the production of "dead end" units such as somatic cells or males. In a quantitative model for the competition of individuals with different, heritable reproductive rates, this cost turns out to be unexpectedly small, and may even sometimes become irrelevant. The bases for this are made fairly clear: thus, when all enjoy high fecundity (e.g. a long reproductive life) the handicap of a slower reproduction vanishes; alternatively, a slight separation of ecological niches may be sufficient for survival of slower but otherwise unchanged reproducers; and finally, inherent to slow reproduction is a low rate of destabilizing genetic change. These facts are largely independent of the formal model details, and are supported by direct computer simulations. They give a quantitative basis for analysing the evolution and prevalence of slow life cycles. The implications of these findings for the evolution of multicellularity are briefly discussed.

Animals↗

Origin and diversification of the clonogenic cell in multiple myeloma: lessons from the immunoglobulin repertoire.

The study of immunoglobulin genes in multiple myeloma over the last decade has provided important information regarding biology, ontogenetic assignment, disease evolution, pathogenic consequences and tumor-specific therapeutic intervention. Detailed analysis of VH genes has revealed the clonal relationship between switch variants expressed by the bone marrow plasma cell and myeloma progenitors in the marrow and peripheral blood. Regarding VH usage, a bias was found against the V4-34 gene encoding antibodies with cold agglutinin specificity (anti-I/i), thus explaining in part the absence of autoimmune phenomena in myeloma compared to other B cell lymphoproliferative disorders. However, in some studies a substantial number of cases analyzed were carrying the rearranged Humkappav325 Vkapppa gene, known to be over utilized by B cell chronic lymphocytic leukemia clones and possessing autoantibody binding activity. VH genes accumulate somatic hypermutations following a distribution compatible with antigen selection, but with no intraclonal heterogeneity. The analysis of Vkappa genes indicates a bias in usage of Vkappa family members; somatic hypermutation, in line with antigen selection, of the expressed Vkappa genes is higher than any other B cell lymphoid disorder. Similar conclusions were reached for Vlambda genes; in this case, the analysis raises the controversial issue of N nucleotide insertion at Vlambda-Jlambda junctions, apparently as a result of TdT activity. A complementary imprint of antigen selection as evidenced by somatic hypermutation of either the VH or VL clonogenic genes has been observed. The absence of ongoing somatic mutations in either VH or VL genes gives rise to the notion that the cell of origin in myeloma is a post-germinal center memory B cell.

Antigens, Neoplasm↗

Processes of copy-number change in human DNA: the dynamics of {alpha}-globin gene deletion.

Ectopic recombination between locally repeated DNA sequences is of fundamental importance in the evolution of gene families, generating copy-number variation in human DNA and often leading to pathological rearrangements. Despite its importance, little is known about the dynamics and processes of these unequal crossovers and the degree to which meiotic recombination plays a role in instability. We address this issue by using as a highly informative system the duplicated alpha-globin genes in which ectopic recombination can lead to gene deletions, often very prevalent in populations affected by malaria, as well as reduplications. Here we show that spontaneous deletions can be accessed directly in genomic DNA by using single-DNA-molecule methods. These deletions proved to be remarkably common in both blood and sperm. Somatic deletions arise by a strictly intrachromosomal pathway of homologous exchange that also operates in the germ line and can generate mutational mosaicism, whereas sperm deletions frequently involve recombinational interactions between homologous chromosomes that most likely occur at meiosis. Ectopic recombination frequencies show surprisingly little requirement for long, identical homology blocks shared by paralogous sequences, and exchanges can occur even between short regions of sequence identity. Finally, direct knowledge of germ-line deletion rates can give insights into the fitness of individuals with these alpha-globin gene deletions, providing a new approach to investigating historical levels of selection operating in human populations.

DNA↗