Phylogenetic diversification of immunoglobulin genes and the antibody repertoire

Immunoglobulins are encoded by a large multigene system that undergoes somatic rearrangement and additional genetic change during the development of immunoglobulin-producing cells. Inducible antibody and antibody-like responses are found in all vertebrates. However, immunoglobulin possessing disulfide-bonded heavy and light chains and domain-type organization has been described only in representatives of the jawed vertebrates. High degrees of nucleotide and predicted amino acid sequence identity are evident when the segmental elements that constitute the immunoglobulin gene loci in phylogenetically divergent vertebrates are compared. However, the organization of gene loci and the manner in which the independent elements recombine (and diversify) vary markedly among different taxa. One striking pattern of gene organization is the "cluster type" that appears to be restricted to the chondrichthyes (cartilaginous fishes) and limits segmental rearrangement to closely linked elements. This type of gene organization is associated with both heavy- and light-chain gene loci. In some cases, the clusters are "joined" or "partially joined" in the germ line, in effect predetermining or partially predetermining, respectively, the encoded specificities (the assumption being that these are expressed) of the individual loci. By relating the sequences of transcribed gene products to their respective germ-line genes, it is evident that, in some cases, joined-type genes are expressed. This raises a question about the existence and/or nature of allelic exclusion in these species. The extensive variation in gene organization found throughout the vertebrate species may relate directly to the role of intersegmental (V<==>D<==>J) distances in the commitment of the individual antibody-producing cell to a particular genetic specificity. Thus, the evolution of this locus, perhaps more so than that of others, may reflect the interrelationships between genetic organization and function.      

Beta 1 integrin (CD29) expression on human postnatal T cell subsets defined by selective CD45 isoform expression

The integrin beta 1 (CD29) is a marker for total very late activation Ag integrins on cells, and exhibits considerable fluctuation in cell surface density at various stages of T cell development. We have analyzed beta 1 integrin expression on subsets of human thymus, and on T cells from healthy babies and children, in comparison to healthy adults aged 26 to 75. T cells from adult peripheral blood include a CD29-, a CD29lo, and a CD29hi set. Compared with adults, PBMC T cells from children have reduced numbers of both CD29lo and CD29hi subsets but equivalent numbers of CD29- T cells. The number of CD29hi T cells increases gradually with age, achieving adult levels only at about 26 yr of age; in aged adults (69 to 75 yr), nearly all T cells have a CD29hi phenotype. Most thymocytes and cord blood T cells, in contrast, have a single peak of CD29 staining that is intermediate to the two peaks seen in adults. Multi-negative progenitor and CD45RO- thymocytes (presumptive thymic generative line-age) are 98% CD29hi. Progenitor thymocytes and adult PBMC T cells express equivalent amounts of beta 1 and alpha 4, but progenitors are alpha 5hi, whereas PBMC T cells are alpha 5lo. T cells from children have reduced beta 1hi and alpha 5lo, but nearly comparable numbers of alpha 4hi. This suggests that the major very late activation Ag integrins during childhood may be alpha 5 beta 1 and alpha 4 complexed with an alternate beta chain. In children, the majority of CD29hi cells are also CD45RAhi, in contrast to the pattern in adults, in whom the majority of CD29hi T cells are CD45RA-. This suggests that in children, the main defense against infection may reside in the CD29hi45RAhi T cells, which have not yet made the transition to CD45RO and to bona fide memory status. The proliferative response to tetanus toxoid of 4- to 6-mo-old babies correlates with the number of CD29hi45RAhi T cells, suggesting that it derives at least in part from cells that do not express a "memory" phenotype. These observations show a pattern of alternating high and low density CD29 during T cell development, which is consistent with the idea that CD29 is a marker for functionally defined T cell sets. Analysis of the CD29 expression of CD29hi thymocytes developing in vitro supports this view. We suggest that the intensity of CD29 expression on a T cell varies, dependent upon the microenvironmental interactions required by a differentiating T cell.     

Transient accumulation and subsequent rapid loss of messenger RNA encoding high molecular mass CD45 isoforms after T cell activation.

High molecular mass isoforms of CD45 protein tyrosine phosphatase, predominantly CD45RA, are expressed on naive T cells with increasing density during the first 2 days of cellular activation, and subsequently down-regulated concurrent with increasing expression of the low Mr isoform, CD45RO. We show this to be de novo synthesis of CD45RA dependent upon both RNA and protein synthesis. Using a probe shown to detect mRNA encoding the alternatively spliced abc, ab, bc, and b exon isoforms of CD45, the expression of CD45 was analyzed. Kinetic studies of the transition from high to low Mr CD45 mRNA indicate an immediate decrease in the level of high Mr CD45 mRNA after mitogen stimulation of T cells, quickly followed at 4 h by an increase to above steady state levels. This is consistent with the transitory increase in cell-surface density of CD45RA observed at 1 to 2 days poststimulation. Within 24 h of stimulation the level of high Mr CD45 mRNA declines precipitously such that little or no mRNA encoding any of the alternatively spliced exons is detectable. High levels of CD45 mRNA are detectable at later points but this does not hybridize with the Sfa N1 probe recognizing the abc exons suggesting that only the CD45RO mRNA splicing pattern is operative. We also show that CD45 mRNA have a relatively short t1/2. In mitogen-stimulated cells the t1/2 of high and low m.w. CD45 mRNA was estimated at 2.25 h and 3.5 h, respectively. In unstimulated T cells the t1/2 of high Mr CD45 mRNA was estimated at 2.8 h. CD45 mRNA is super-induced in the presence of the protein synthesis inhibitor, cycloheximide, indicating that the degradation and/or splicing of CD45 mRNA is controlled by a labile pathway, and suggesting that mechanisms may exist in vivo to prolong synthesis of CD45RA. The kinetics of accumulation for high Mr CD45 mRNA are very similar to those of the TCR beta-chain and pp56lck suggesting that these functionally linked signaling molecules are regulated in tandem. This implicates stringent molecular control mechanisms on the production of mRNA encoding either high or low m.w. isoforms, consistent with the fundamental role of CD45 in signal transduction, and the apparent need to selectively and sequentially express functionally distinct external CD45 domains.     

Factors influencing the potential mobility and bioavailability of exchangeable ammonium ion in dried lake sediments

Abstract

The effect of drying temperature and oxidation on the level of exchangeable ammonium ion found in sediments has been examined using samples collected from along a polluted creek and from shallow lake bays. The sediments were dried at temperatures between 20°C and 100°C (either in air or under a nitrogen atmosphere), and the ammonium ion content was extracted into 0.1 M KCl prior to analysis using an ion selective electrode. Exposure to air during the drying stage usually resulted in lower ammonium values, while increasing the drying temperature altered the amount of displaceable (i.e. available) ammonium ion extracted, generally in an upward direction. The amount detected (5–25 μ g^?1) varied between sites, and surface sediment values differed from the 10–50 cm core material results. The pH of the extracts varied with the drying temperature used, indicating that the heating process promoted some chemical changes in the test samples. The study has demonstrated that in nutrient level surveys, the analytical data produced can depend greatly on the sample preparation procedure selected. It also indicated the type of changes which could occur when dredged sediments are land dumped.     

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy,cultivation, single-cell PCR and amplicon sequencing

Extremophiles - Genotypic and morphological diversity of cyanobacteria in the Rupite hot spring (Bulgaria) was investigated by means of optical microscopy, cultivation, single-cell PCR, and 16S...     

Germline mutations in BMPR1A/ALK3 cause a subset of cases of juvenile polyposis syndrome and of Cowden and Bannayan-Riley-Ruvalcaba syndromes

Juvenile polyposis syndrome (JPS) is an inherited hamartomatous-polyposis syndrome with a risk for colon cancer. JPS is a clinical diagnosis by exclusion, and, before susceptibility genes were identified, JPS could easily be confused with other inherited hamartoma syndromes, such as Bannayan-Riley-Ruvalcaba syndrome (BRRS) and Cowden syndrome (CS). Germline mutations of MADH4 (SMAD4) have been described in a variable number of probands with JPS. A series of familial and isolated European probands without MADH4 mutations were analyzed for germline mutations in BMPR1A, a member of the transforming growth-factor beta-receptor superfamily, upstream from the SMAD pathway. Overall, 10 (38%) probands were found to have germline BMPR1A mutations, 8 of which resulted in truncated receptors and 2 of which resulted in missense alterations (C124R and C376Y). Almost all available component tumors from mutation-positive cases showed loss of heterozygosity (LOH) in the BMPR1A region, whereas those from mutation-negative cases did not. One proband with CS/CS-like phenotype was also found to have a germline BMPR1A missense mutation (A338D). Thus, germline BMPR1A mutations cause a significant proportion of cases of JPS and might define a small subset of cases of CS/BRRS with specific colonic phenotype.     

Singlet Oxygen and Other Reactive Oxygen Species are Involved in Regulation of Release of Iron-Binding Chelators from Scenedesmus cells

Freshly-added iron only slightly affected the growth of iron-sufficient cells of the green alga Scenedesmus incrassatulus Bohl, strain R-83, but induced accumulation of malondialdehyde (MDA) in cells and excretion of MDA in the medium. These effects were stronger in response to Fe²⁺ as compared to Fe³⁺, but Fe³⁺ induced the release of more iron-binding chelators from these cells than Fe²⁺. Fe³⁺ added either in dark or in light induced release of equal concentrations of iron-complexing agents, part of which formed strong chelates with iron in the medium. Exogenously added hydrogen peroxide inhibited iron-induced release of chelators but the effect was removed by addition of the hydroxyl radical scavenger dimethylsulfoxide (DMSO). Malondialdehyde also inhibited the release of chelators. Release of chelators was induced in the absence of iron salts by photoexcited chlorophyll (Chl). The Chl-induced release was efficiently inhibited by singlet oxygen scavengers such as dimethylfuran, -carotene, sodium azide and vitamin B₆, and stimulated in D₂O or DMSO. Exogenously added catalase inhibited the release more than added superoxide dismutase. The Fe³-induced release of chelators was also inhibited by scavengers of singlet oxygen, but was not affected by sodium azide and by ethanol. Hence both H₂O₂ and singlet oxygen were involved in induction of chelator release in the absence of iron in light. The induction of chelator release by iron in dark involved H₂O₂, but not singlet oxygen.     

RHAMM is a centrosomal protein that interacts with dynein and maintains spindle pole stability

The receptor for hyaluronan-mediated motility (RHAMM), an acidic coiled coil protein, has previously been characterized as a cell surface receptor for hyaluronan, and a microtubule-associated intracellular hyaluronan binding protein. In this study, we demonstrate that a subset of cellular RHAMM localizes to the centrosome and functions in the maintenance of spindle integrity. We confirm a previous study showing that the amino terminus of RHAMM interacts with microtubules and further demonstrate that a separate carboxy-terminal domain is required for centrosomal targeting. This motif overlaps the defined hyaluronan binding domain and bears 72% identity to the dynein interaction domain of Xklp2. RHAMM antibodies coimmunprecipitate dynein IC from Xenopus and HeLa extracts. Deregulation of RHAMM expression inhibits mitotic progression and affects spindle architecture. Structure, localization, and function, along with phylogenetic analysis, suggests that RHAMM may be a new member of the TACC family. Thus, we demonstrate a novel centrosomal localization and mitotic spindle-stabilizing function for RHAMM. Moreover, we provide a potential mechanism for this function in that RHAMM may cross-link centrosomal microtubules, through a direct interaction with microtubules and an association with dynein.     

KIAA0101 interacts with BRCA1 and regulates centrosome number

To find genes and proteins that collaborate with BRCA1 or BRCA2 in the pathogenesis of breast cancer, we used an informatics approach and found a candidate BRCA interactor, KIAA0101, to function like BRCA1 in exerting a powerful control over centrosome number. The effect of KIAA0101 on centrosomes is likely direct, as its depletion does not affect the cell cycle, KIAA0101 localizes to regions coincident with the centrosomes, and KIAA0101 binds to BRCA1. We analyzed whether KIAA0101 protein is overexpressed in breast cancer tumor samples in tissue microarrays, and we found that overexpression of KIAA0101 correlated with positive Ki67 staining, a biomarker associated with increased disease severity. Furthermore, overexpression of the KIAA0101 gene in breast tumors was found to be associated with significantly decreased survival time. This study identifies KIAA0101 as a protein important for breast tumorigenesis, and as this factor has been reported as a UV repair factor, it may link the UV damage response to centrosome control.     

Diurnal and seasonal changes in the intensity of photosynthesis in stems of lilac (Syringa vulgaris L.)

It has been demonstrated that during the whole year the stems are photosyntheticaly active and capable of assimilating atmospheric CO₂. The intensity of photosynthesis varies. During the vegetation period the registered net photosynthesis lasted up to 13 hours per day, and in the leafless period for 2–3 hours a day. Photosynthesis was registered also at temperatures below zero (−3 °C) as a reduced CO₂ evolution in light in comparison with darkness. The maximal net photosynthesis values during the vegetation period amounted to 6 up 8 μmol (CO₂)·m⁻²·s⁻¹, and in the leafless period 0.5 – 1 μmol (CO₂)·m⁻²·s⁻¹, and they were close to being up to twice as big as the values obtained of darkness respiration. An increase of the photosynthetic activity of stems preceded the spring development of the leaves.