Identification of the Molecular Partners of Lymphocyte Phosphatase-Associated Phosphoprotein (LPAP) That Are Involved in Human Lymphocyte Activation

Molecular Biology - Lymphocyte phosphatase-associated phosphoprotein (LPAP) is a small transmembrane protein that is found in lymphocytes and is tightly associated with the phosphatase CD45. The...     

Colocalization of the herpes simplex virus 1 UL4 protein with infected cell protein 22 in small, dense nuclear structures formed prior to onset of DNA synthesis

Herpes simplex virus 1 infected cell protein 22 (ICP22) localizes in small, dense nuclear bodies of primate cells early in infection and in the more diffuse replicative complexes after the onset of DNA synthesis. UL4, a gamma2 protein, localizes in cytoplasm and in the small nuclear structures containing ICP22 but not in replicative complexes. In rabbit skin cells, both ICP22 and UL4 localize in the dense nuclear bodies late in infection. The results suggest that the small nuclear structures perform a function involving both proteins late in infection.     

A gradient of silent substitution rate in the human pseudoautosomal region

It has been demonstrated that recombination in the human p-arm pseudoautosomal region (p-PAR) is at least twenty times more frequent than the genomic average of approximately 1 cM/Mb, which may affect substitution patterns and rates in this region. Here I report the analysis of substitution patterns and rates in 10 human, chimpanzee, gorilla, and orangutan genes across the p-PAR. Between species silent divergence in the p-PAR forms a gradient, increasing toward the telomere. The correlation of silent divergence with distance from the p-PAR boundary is highly significant (rho = 0.911, P < 0.001). After exclusion of the CpG dinucleotides this correlation is still significant (rho = 0.89, P < 0.01), thus the substitution rate gradient cannot be explained solely by the differences in the extent of methylation across the p-PAR. Frequent recombination in the PAR may result in a relatively strong effect of biased gene conversion (BGC), which, because of the increased probability of fixation of the G or C nucleotides at (A or T)/(G or C) segregating sites, may affect substitution rates. BGC, however, does not seem to be the factor creating the substitution rate gradient in the p-PAR, because the only gradient is still detactable if only A<-->T and G<-->C substitutions are taken into account (rho = 0.82, P < 0.01). I hypothesize that the substitution rate gradient in the p-PAR is due to the mutagenic effect of recombination, which is very frequent in the distal human p-PAR and might be lower near the p-PAR boundary.     

Orthologous gene-expression profiling in multi-species models: search for candidate genes

Microarray-driven gene-expression profiles are generally produced and analyzed for a single specific experimental model. We have assessed an analytical approach that simultaneously evaluates multi-species experimental models within a particular biological condition using orthologous genes as linkers for the various Affymetrix microarray platforms on multi-species models of ventilator-associated lung injury. The results suggest that this approach may be a useful tool in the evaluation of biological processes of interest and selection of process-related candidate genes.     

Type-specific antibodies to hepatitis C virus in sera from patients with various hematologic diseases

The reactivity of 100 sera taken from patients with different blood diseases and donors with respect to synthesized peptides in the variable area of protein NS4 of hepatitis C virus was studied. The presence of type-specific antibodies in the blood sera of patients with hepatitis C was shown. Two antigenic determinant corresponding to 1683-1705 and 1711-1732 amino acid residues in the protein area under study were detected. In hematological patients undergoing frequent blood transfusions mixed infection with different types of hepatitis C virus was registered; these types could be reliably determined with the use of synthetic peptides. The serotype determined with the use of peptides corresponded to the type of the circulating virus.     

DNA diversity in sex-linked and autosomal genes of the plant species Silene latifolia and Silene dioica

The relatively recent origin of sex chromosomes in the plant genus Silene provides an opportunity to study the early stages of sex chromosome evolution and, potentially, to test between the different population genetic processes likely to operate in nonrecombining chromosomes such as Y chromosomes. We previously reported much lower nucleotide polymorphism in a Y-linked gene (SlY1) of the plant Silene latifolia than in the homologous X-linked gene (SlX1). Here, we report a more extensive study of nucleotide diversity in these sex-linked genes, including a larger S. latifolia sample and a sample from the closely related species Silene dioica, and we also study the diversity of an autosomal gene, CCLS37.1. We demonstrate that nucleotide diversity in the Y-linked genes of both S. latifolia and S. dioica is very low compared with that of the X-linked gene. However, the autosomal gene also has low DNA polymorphism, which may be due to a selective sweep. We use a single individual of the related hermaphrodite species Silene conica, as an outgroup to show that the low SlY1 diversity is not due to a lower mutation rate than that for the X-linked gene. We also investigate several other possibilities for the low SlY1 diversity, including differential gene flow between the two species for Y-linked, X-linked, and autosomal genes. The frequency spectrum of nucleotide polymorphism on the Y chromosome deviates significantly from that expected under a selective-sweep model. However, we detect population subdivision in both S. latifolia and S. dioica, so it is not simple to test for selective sweeps. We also discuss the possibility that Y-linked diversity is reduced due to highly variable male reproductive success, and we conclude that this explanation is unlikely.     

High mutation rates in human and ape pseudoautosomal genes

It has been suggested that recombination may be mutagenic, which, if true, would inflate intraspecies diversity and interspecies silent divergence in regions of high recombination. Here, we test this hypothesis comparing human/orangutan genome-wide non-coding divergence (K) to that in the pseudoautosomal genes which were reported to recombine much more frequently than the rest of the genome. We demonstrate that, compared to the average human/orangutan non-coding divergence (K=3%), the substitution rate is significantly elevated in the introns of SHOX (K=5.7%), PPP2R3L (K=8.7%) and ASMT (K=6.5%) genes located in the human and orangutan Xp/Yp pseudoautosomal region (p-PAR), where recombination is over 20-fold higher than the genomic average. On the other hand, human/orangutan non-coding divergence at the Xp/Yp pseudoautosomal boundary (K=3.5%) and in the SYBL1 gene (K=2.7%), located in the human Xq/Yq pseudoautosomal region (q-PAR), where recombination is known to be less frequent than in p-PAR, was not significantly higher than the genome average. The data are consistent with the hypothesis that recombination may be mutagenic.     

Acetylcholine Receptor Gating is Influenced by the Polarity of Amino Acids at Position 9′ in the M2 Domain

Ligand-gated ion channels contain a conserved leucine at position 9′ (L9′) in the M2 transmembrane domain. We used multiple substitutions at this position in the γ subunit of the mouse acetylcholine receptor (AChR) (γL9′) to examine the role of residue polarity at this position in the gating process at both the macroscopic and single-channel levels. The midpoint of the macroscopic dose-response relationship (EC₅₀) and the channel closing rate constant, α, decreased as the polarity of the residue at that position increased, suggesting a stabilization of the open state of the channel. Both parameters showed similar dependencies on the polarity of the substituted residue. These data support the notion that during AChR gating, the amino acid at the 9′ position moves into a polar environment, and that interactions between this residue and the polar environment determine the stability of the open state. Since this residue is conserved in all other members of the ligand-gated ion channel family, we suggest that a similar mechanism applies to the other members of the family. Received: 17 September 1999/Revised: 15 December 1999