A synaptobrevin-like gene in the Xq28 pseudoautosomal region undergoes X inactivation.

The X and Y chromosomes that maintain human dimorphism are thought to have descended from a single progenitor, with the Y chromosome becoming largely depleted of genes. A number of genes, however, retain copies on both X and Y chromosomes and escape the inactivation that affects most X-linked genes in somatic cells. Many of those genes are present in two pseudoautosomal regions (PARs) at the termini of the short (p) and long (q) arms of the sex chromosomes. For both PARs, pairing facilitates the exchange of information, ensuring the homogenisation of X and Y chromosomal material in these regions. We report here a strikingly different regulation of expression of a gene in Xq PAR. Unlike all Xp PAR genes studied so far, a synaptobrevin-like gene, tentatively named SYBL1, undergoes X inactivation. In addition, it is also inactive on the Y chromosome, thereby maintaining dosage compensation in an unprecedented way.

Reduction of Corky Root Infections on Greenhouse Tomato Crops by Soil Solarization in South Italy.

Five greenhouse experiments were conducted in southeastern Sicily (Italy) from 2000 to 2009 to evaluate the effectiveness of soil solarization in reducing natural infections of tomato corky root caused by Pyrenochaeta lycopersici. Tests were performed with clear, traditional, and innovative plastic films and fumigant applications. In all the trials, soil solarization was effective in controlling corky root disease relative to an untreated control. Although inducing different thermal regimes in the soil, the use of different greenhouse covering and mulching films for solarization proved effective in reducing corky root severity relative to the untreated control. Solarization reduced infections caused by P. lycopersici comparable with methyl bromide fumigation and greater than metham sodium and metham potassium. Among the tested films, green coextruded film may be most attractive because it can be left on after solarization as mulch.

Duplication and distribution of repetitive elements and non-unique regions in the human genome.

Genome mapping efforts and the initial sequencing of large segments of human DNA permit ongoing assessment of the patterns and extent of sequence duplication and divergence in the human genome. Initial sequence data indicate that the most highly repetitive sequences show isochore-related enrichment and clustering produced by successive insertional recombination and local duplication of particular repetitive elements. Regional duplication is also observed for a number of otherwise unique genomic sequences and thereby makes these segments become repetitive. The consequences of these duplication events are: (1) clustering of related genes, along with a variety of coregulatory mechanisms; and (2) recombinations between the nearby homologous sequences, which can delete genes in individuals and account for a significant fraction of human genetic disease.

Recombination trapping: an in-vivo approach to recover cDNAs encoded in YACs.

We have developed an approach to identify and localize cDNAs encoded by YACs. In this scheme, a YAC truncation vector containing a cDNA library is used to interrupt the YAC by homologous recombination in yeast. This approach generates YACs truncated at the site of recombination between the cDNA and the cognate YAC sequence and thus localizes the gene in the YAC. This method results in the production of a large percentage of true recombinants identifying gene encoding regions of the genome. This approach is shown to identify an unique EST sequence from a YAC in Xp22, the recently described transketolase-like gene in a YAC from Xq28 and a putative kinesin-like gene in Xq13. This system should also be useful in the mapping of YACs by targeted integration. We have constructed a new telomere truncation vector, pGR8, which incorporates two selectable markers, HIS5 and LYS2. This vector overcomes problems of previous vectors including: incompatibility with most YAC libraries, vector homology with the YAC arms and high backgrounds resulting from the use of a single selectible marker. A third counterselection with 5-fluoroorotic acid (5FOA) against yeast clones retaining the URA3 gene was also employed to reduce background further. Therefore, this vector and approach should be useful to the transcriptional analysis of YAC maps of any genome.

Determination of the sequence of an expressible cDNA clone encoding ERp60/calregulin by the use of a novel nested set method.

An analysis of the N-terminal sequence of the luminal endoplasmic reticulum protein, ERp60, showed that it was identical to the well-characterized Ca2+-binding protein, calregulin. A full-length, expressible cDNA clone encoding this protein was isolated from a mouse fibroblast cDNA library. A novel nested set strategy for the production of overlapping fragments for DNA sequencing was used to determine the complete nucleotide (nt) sequence of both strands of the ERp60 clone. This method utilizes a series of nonspecific deletion primers in conjunction with a specific site primer to generate the nested set fragments. This procedure possesses several advantages over other nested set techniques, since it does not require (i) the re-cloning of the DNA insert into other vectors, (ii) any prior knowledge of the restriction sites of the nt sequence, or (iii) the transformation and analysis of bacterial subclones. ERp60 has a 17-amino acid (aa) signal sequence and the mature protein contains 399 aa with a calculated M(r) of 46,347.

Cloning of a cDNA encoding a novel heat-shock protein from Dictyostelium discoideum.

We have cloned, from Dictyostelium discoideum, a cDNA encoding a new heat-shock (HS) protein (Hsp) with a predicted molecular mass of 31,447 Da. Outside of its low molecular mass, this Hsp does not share any similarity with the small Hsp currently identified or with alpha-crystallins. Northern blot analysis indicates that this HS-inducible gene is also developmentally regulated

Glypican 3 and glypican 4 are juxtaposed in Xq26.1.

Recently, we have shown that mutations in the X-linked glypican 3 (GPC3) gene cause the Simpson-Golabi-Behmel overgrowth syndrome (SGBS; ). The next centromeric gene detected is another glypican, glypican 4 (GPC4), with its 5' end 120763bp downstream of the 3' terminus of GPC3. One recovered GPC4 cDNA with an open reading frame of 1668nt encodes a putative protein containing three heparan sulfate glycosylation signals and the 14 signature cysteines of the glypican family. This protein is 94.3% identical to mouse GPC4 and 26% identical to human GPC3. In contrast to GPC3, which produces a single transcript of 2.3kb and is stringently restricted in expression to predominantly mesoderm-derived tissues, Northern analyses show that GPC4 produces two transcripts, 3.4 and 4.6kb, which are very widely expressed (though at a much higher level in fetal lung and kidney). Interestingly, of 20 SGBS patients who showed deletions in GPC3, one was also deleted for part of GPC4. Thus, GPC4 is not required for human viability, even in the absence of GPC3. This patient shows a complex phenotype, including the unusual feature of hydrocephalus; but because an uncle with SGBS is less affected, it remains unclear whether the GPC4 deletion itself contributes to the phenotype.

Expressed STSs and transcription of human Xq28.

STSs, which have been used to build and format clone contigs, have been used here to assemble a transcriptional map across a cytogenetic band. Of fifty one STSs in Xq28, 20 were positive by RT-PCR. Thus, an additional 20 possible ESTs were detected among the STSs, and seven of these also identified cDNAs in at least one library. The transcripts confirm the high expression level of this region, correlated with its GC compositional map and CpG island content.

Analysis of the structure and synthesis of GRP94, an abundant stress protein of the endoplasmic reticulum.

The synthesis and cotranslational modification of GRP94, an abundant, resident protein of the endoplasmic reticulum belonging to the hsp90 family of stress proteins, has been studied in transient expression studies in COS cells. A fraction of the expressed murine GRP94 was more highly glycosylated than normal, having a greater number of endoglycosidase H (Endo H)-sensitive oligosaccharide moieties than authentic GRP94. To understand better the basis for the appearance of the hyperglycosylated form and determine the acceptor sites that were used for this extra glycosylation, we have used in vitro mutagenesis techniques to construct a set of point mutants and deletion mutants of GRP94. Analysis of the expression of wild-type GRP94 and the mutant proteins has revealed that Asn-196 is the acceptor site used in normal glycosylation of GRP94 and that hyperglycosylation is dependent upon the level of expression of the GRP94 and is occurring at acceptor sites in the carboxy-terminal region of the protein. We have shown, in addition, that Cys-117 is involved in the formation of a disulfide-bonded homodimer of GRP94. Finally, analysis of deletions made from the amino terminus of the mature protein has demonstrated that these alterations change the pattern of usage of the remaining N-glycosylation sites in the mutants.

Thyroid function in healthy centenarians.

Seven thyroid function parameters (total T3, TT3; total T4, TT4; free T3, FT3; free T4, FT4; TSH; anti-thyroglobulin antibodies, TGAb; and anti-microsomal antibodies, TMAb) were studied in a series of 20 healthy centenarians in order to evaluate their thyroid function status. Our results showed that all the parameters were within normal range, with the exception of TT4 values which were reduced in 60% of centenarians examined. Therefore, the authors believe that the production of thyroid hormones seems to decrease in advanced years, but that this may not solely depend on thyroid parenchyma involution, but also on a lower demand by the hormone sensitive tissues. Centenarians seem to be adapted euthyroid subjects who present low, nonetheless adequate, levels of circulating thyroid hormone (T4).

Use of disphosphonates in the treatment of osteoporosis in thyroidectomized patients on levothyroxin replacement therapy.

Bone mineral density at medio distal (MD-BMD) and ultra distal (UD-BMD) sites of non dominant radius were studied, using a DEXA Mineralometer (TURBOSCAN-NIM) on a series of 20 patients, over 60 years old, all thyroidectomized for thyroid carcinoma and treated with levothyroxin replacement therapy. T3 and T4 (RIA method), TSH (IRMA method) and two cardiac parameters as TPER (time peak ejection rate) and TPFR (time peak filling rate) by angiocardioscintigraphy were also determined. Results showed that 19 patients considering MD-BMD values and ten considering UD-BMD values were at risk of fractures. Circulating T3 levels were within normal range in 17 patients, elevated in two cases and reduced in one case. Circulating T4 levels were within normal range in 15 patients, increased in four cases and reduced in one case. Circulating TSH levels were within normal range in 17 patients, reduced in two cases and elevated in one case. TPER were reduced in 18 patients and normal in two cases. TPFR were reduced in six patients and normal in fourteen cases. The authors administered alendronate (10 mg/day) which seems to prevent bone loss, especially at the level of the trabecular bone. Bone loss reverted at 6 and 12 months, confirming that disphosphonates slow down this phenomenon in a situation of increased bone turnover (e.g. patients on long-term L-T4 therapy).

Sequence and gene content in 52 kb including and centromeric to the G6PD gene in Xq28.

A cosmid containing 36.4 kb of high GC human DNA centromeric to the G6PD gene has been analyzed. The sequence was 99.9% precise, based on the comparison of 4.3 kb that overlaps an earlier analysis of 20.1 kb containing G6PD. Properties of the entire 52 kb region that may be characteristic of high GC portions of the genome include a very high density of sixty-two half or full Alu sequences, or 1.2/kb, and an absence of L1 sequences. Other highly repetitive sequences include 11 MER sequences, one of them interrupted at two positions by groups of 3 Alu elements. In segments of unique sequence, computer-aided analysis predicted three possible genes, one of which has thus far been confirmed by the recovery of a corresponding cDNA, both by a direct hybridization method and by a PCR-based method based on a primer pair inferred from the genomic sequence. The cDNA has been sequenced, and is completely concordant with counterpart genomic sequence; it has no resemblance to any previously described gene.

Pathological consequences of sequence duplications in the human genome.

As large-scale sequencing accumulates momentum, an increasing number of instances are being revealed in which genes or other relatively rare sequences are duplicated, either in tandem or at nearby locations. Such duplications are a source of considerable polymorphism in populations, and also increase the evolutionary possibilities for the coregulation of juxtaposed sequences. As a further consequence, they promote inversions and deletions that are responsible for significant inherited pathology. Here we review known examples of genomic duplications present on the human X chromosome and autosomes.

ERp99, an abundant, conserved glycoprotein of the endoplasmic reticulum, is homologous to the 90-kDa heat shock protein (hsp90) and the 94-kDa glucose regulated protein (GRP94).

We have isolated an expressible full-length cDNA clone encoding murine ERp99, an abundant, conserved transmembrane glycoprotein of the endoplasmic reticulum membrane. ERp99 is synthesized as a 92,475-kDa precursor containing 802 amino acids. It possesses a signal peptide of 21 amino acids which is cleaved cotranslationally. Analysis of the amino acid sequence deduced from the nucleotide sequence of the cDNA clone led us to propose a model for the orientation of ERp99 in the endoplasmic reticulum membrane. In this model, ERp99 possesses one membrane-spanning, stop transfer segment in the N-terminal region. The protein chain passes through the membrane only once, and approximately 75% of the protein remains on the cytoplasmic side of the ER membrane. Comparison of the ERp99 sequence to the sequence of other proteins revealed that ERp99 has extensive homology with the 90-kDa heat shock protein of Saccharomyces cerevisiae (hsp90) and the 83-kDa heat shock protein of Drosophila melanogaster. In addition, the N terminus of mature ERp99 is identical to that of the 94-kDa glucose regulated protein (GRP94) of mammalian cells.

Physical linkage of expressed sequence tags (ESTs) to polymorphic markers on the X chromosome.

Expressed sequence tags (ESTs) can in principle serve as specialized sequence tagged sites (STSs) to assemble a functional map of the human genome. The strategy of physically linking ESTs to the nearest genetic linkage markers should provide specific candidate genes for the X-linked diseases associated with these markers or loci. Therefore, 19 ESTs assigned to the X chromosome in the Genome Database (GDB) were analyzed. Eighteen were confirmed to be X-specific and were localized to regions of the X chromosome using a panel of somatic cell hybrids. Localization was then refined by positioning them on yeast artificial chromosome (YAC)-based maps. Seventeen ESTs identified cognate YACs by PCR screening and 12 of the ESTs have been assembled in YAC contigs containing polymorphic and other X chromosomal markers. Two of them also produced syntenically equivalent products in mouse. Thus localizing ESTs relative to polymorphic markers will help to assemble an integrated physical and transcriptional map of the chromosome and provide candidates for disease-gene searches.

Structure and assembly of the endoplasmic reticulum. The synthesis of three major endoplasmic reticulum proteins during lipopolysaccharide-induced differentiation of murine lymphocytes.

Monospecific rabbit antibodies have been prepared against ERp72, ERp99, and ERp60, major protein components of a detergent-solubilized extract of endoplasmic reticulum purified from mineral oil-induced plasmacytoma 315 tissue. When subcellular fractions of mineral oil-induced plasmacytoma 315 tissue were assayed by an immunoprecipitation procedure, all three endoplasmic reticulum proteins (ERps) were found to be enriched in the rough endoplasmic reticulum. In murine lymphoid cells, the three ERps represent two major structural classes of protein. Both ERp72 and ERp60 contain no endoglycosidase H-sensitive, N-linked oligosaccharides. On the other hand, ERp99 is glycoprotein containing, in all likelihood, one endoglycosidase H-sensitive oligosaccharide. Immunologically cross-reacting proteins of similar molecular weight have also been detected in other eukaryotic cell lines. The anti-ERp antibodies were used to quantitate the synthesis and accumulation of the three ERps in splenic lymphocytes cultured in the presence and absence of bacterial lipopolysaccharide (Escherichia coli serotype B5:055) (LPS). In the presence of LPS, lymphocytes differentiate from resting cells into actively secreting cells. The synthesis of ERp72 and ERp99 increased 3- and 10-fold, respectively, in response to LPS. The synthesis of ERp60 does not change significantly. The turnover rates for these three proteins are similar in both control and LPS-treated lymphocytes. As a result, membranes isolated from LPS-treated cells are enriched in ERp72 and ERp99.

An enzyme-linked immunoassay for the detection of antibodies to endoplasmic reticulum.

A simple, sensitive solid-phase assay for the detection of antibodies to endoplasmic reticulum is described. The assay is dependent upon the amount of antigen bound to the solid support and upon the amount of antibody bound to the support via the relevant antigen. The assay can be used to measure both polyclonal and monoclonal antibody to endoplasmic reticulum. It has been used to isolate several monoclonal antibodies which can recognize and precipitate specific proteins of the endoplasmic reticulum. In addition, it has been used to probe the membrane orientation of endoplasmic reticulum antigens.

Structure and assembly of the endoplasmic reticulum: biosynthesis and intracellular sorting of ERp61, ERp59, and ERp49, three protein components of murine endoplasmic reticulum.

Rabbit antibodies have been prepared against ERp61, ERp59, and ERp49, three protein components of rough endoplasmic reticulum (RER) purified from mineral oil-induced plasmacytoma 315 (MOPC-315) tissue. Analysis of subcellular fractions of MOPC-315 tissue by an immunoprecipitation procedure demonstrated that all three endoplasmic reticulum proteins (ERps) were most enriched in the RER. Immunologically cross-reacting proteins of similar molecular weight have been detected in other eucaryotic cell lines. We have used these antibodies to study the post-translational processing and biosynthetic sorting of the three ERps in pulse-labeled MOPC-315 cells. No larger precursor forms of the ERps were detected and none of the ERps were found to possess asparagine-linked oligosaccharide moieties. We have used a sucrose gradient analysis of pulse-labeled MOPC-315 cells to study the biosynthetic sorting of ERp61, ERp59 and ERp49 and have found no evidence to suggest that these proteins ever leave the endoplasmic reticulum. In addition, all three ERps appeared to have luminally exposed domains. ERp61 and ERp59 were entirely protected by the ER membrane in the absence of detergent, while ERp49 was a transmembrane protein that also possesses a cytoplasmically exposed domain. We have used the anti-ERp antibodies to quantitate the synthesis and accumulation of the three ERps during lipopolysaccharide (LPS)-induced lymphocyte differentiation. After 48 h of culture in the presence of LPS, the synthesis of ERp49 increased sixfold relative to that in control cells. The synthesis and membrane accumulation of ERp61 and ERp59 were less affected by the LPS treatment. Thus, membranes isolated from LPS-treated cells were enriched in ERp49 relative to those isolated from control cells.

ERp72, an abundant luminal endoplasmic reticulum protein, contains three copies of the active site sequences of protein disulfide isomerase.

We have cloned, sequenced, and expressed full length cDNA clones encoding two abundant, luminal endoplasmic reticulum proteins (ERp), ERp59/PDI and ERp72. ERp59/PDI has been identified as the microsomal enzyme protein disulfide isomerase (PDI). An analysis of the amino acid sequence of ERp72 showed that it shared sequence identity with ERp59/PDI at three discrete regions, having three copies of the sequences that are thought to be the CGHC-containing active sites of ERp59/PDI. Thus, ERp72 appears to be a newly described member of the family of CGHC-containing proteins. ERp59/PDI has the sequence KDEL at its COOH terminus while ERp72 has the related sequence KEEL. Removal of the KDEL of ERp59/PDI or the KEEL of ERp72 by in vitro mutagenesis techniques and subsequent analysis of the mutants in transient expression assays, showed that both sequences are endoplasmic reticulum retention signals for their respective proteins. The most dramatic difference in secretion between the wild type and the mutant forms of the protein was seen in the case of ERp72.

Sequence analysis of 139 kb in Xp22.1 containing spermine synthase and the 5' region of PEX.

Human Xp22.1 contains genes involved in mineral balance that are implicated in X-linked hypophosphatemia (XLH) in humans, its murine homologue (Hyp), and another distinct murine hypophosphatemic disorder (Gy). In XLH, a gene, PEX, has been found to be mutated in up to 83% of patients but the sequences of the promoter and 5' end have not been characterized. To further the understanding of this genomic region, 139,454 bp in Xp22.1 have been sequenced. Our analysis confirms the three most 5' published exons of PEX and extends through a putative PEX promoter region. The 5' untranslated sequence of PEX and the mouse and rat equivalents are very highly homologous, implying a conserved functional significance. In addition, we mapped and analyzed another gene 5' of PEX, spermine synthase (SpS), which encodes a ubiquitous enzyme of polyamine metabolism that may contribute to the pathophysiology of Gy. SpS consists of 11 exons spread over 54 kb. The definition of the locations of SpS and the putative promoter region of PEX will facilitate functional analysis of these genes.