Impedance spectroscopy for monosaccharides detection using responsive hydrogel modified paper-based electrodes

Novel paper-based impedance sensor for saccharide sensing in the sub-mM range.

[From retroperitoneal fibrosis to gastric linitis]

Retroperitoneal fibrosis may reveal many diseases, including neoplasias. An 83-year-old man presented with an acute renal failure due to compressive retroperitoneal fibrosis. Clinically the only abnormal feature was a cutaneous subclavicular infiltrated lesion and laboratory features included hypereosinophilia, anemia and elevated acute phase reactants. A thoracic CT-scan showed pleuritis and para-esophageal lymph node and the 18FDG-PET-scan an hypermetabolism lesion of the oesophagus. Gastroscopy and colonoscopy found a gastric linitis, already multi-metastatic at diagnosis. The gastric linitis can present with many decepting clinical forms, increasing the risk of delayed diagnosis.

[From retroperitoneal fibrosis to gastric linitis]

Retroperitoneal fibrosis may reveal many diseases, including neoplasias. An 83-year-old man presented with an acute renal failure due to compressive retroperitoneal fibrosis. Clinically the only abnormal feature was a cutaneous subclavicular infiltrated lesion and laboratory features included hypereosinophilia, anemia and elevated acute phase reactants. A thoracic CT-scan showed pleuritis and para-esophageal lymph node and the 18FDG-PET-scan an hypermetabolism lesion of the oesophagus. Gastroscopy and colonoscopy found a gastric linitis, already multi-metastatic at diagnosis. The gastric linitis can present with many decepting clinical forms, increasing the risk of delayed diagnosis.

Novel splice variants of sFlt1 are upregulated in preeclampsia

Soluble fms-like tyrosine kinase-1 (sFlt1) is a truncated splice variant of Flt1, which is upregulated in preeclampsia. In this study we sought to characterize the unique C-terminus of sFlt. Through bioinformatic analyses, we identified two novel sFlt1 splice variants and two previously described sFlt1 splice variants. The novel variants are identical to the previously described sFlt1_v1 through exon 13, but then diverge to unique 3' termini consisting of a novel exon 15 (sFlt1_v2 and sFlt1_v3) or an extension of exon 14 (sFlt1_v4). Quantitative PCR showed that three out of four sFlt variants were upregulated in placenta of women with preeclampsia. Mass spectrometry analysis of sFlt1 purified from placental serum confirmed the presence of sFlt1_v1 protein, and an additional variant which includes sequence derived from exon 14. siRNA experiments targeting each variant confirmed that three of the four variants contribute significantly to total sFlt1 expression by cytotrophoblasts in vitro. These findings provide evidence that human placenta expresses a family of sFlt1 splice variants, at least three of which are expressed as proteins, and which appear to be globally upregulated in preeclampsia.

Differences in gene content between Salmonella enterica serovar Enteritidis isolates and comparison to closely related serovars Gallinarum and Dublin

Salmonella enterica serovar Enteritidis is often transmitted into the human food supply through eggs of hens that appear healthy. This pathogen became far more prevalent in poultry following eradication of the fowl pathogen S. enterica serovar Gallinarum in the mid-20th century. To investigate whether changes in serovar Enteritidis gene content contributed to this increased prevalence, and to evaluate genetic heterogeneity within the serovar, comparative genomic hybridization was performed on eight 60-year-old and nineteen 10- to 20-year-old serovar Enteritidis strains from various hosts, using a Salmonella-specific microarray. Overall, almost all the serovar Enteritidis genomes were very similar to each other. Excluding two rare strains classified as serovar Enteritidis in the Salmonella reference collection B, only eleven regions of the serovar Enteritidis phage type 4 (PT4) chromosome (sequenced at the Sanger Center) were absent or divergent in any of the other serovar Enteritidis strains tested. The more recent isolates did not have consistent differences from 60-year-old field isolates, suggesting that no large genomic additions on a whole-gene scale were needed for serovar Enteritidis to become more prevalent in domestic fowl. Cross-hybridization of phage genes on the array with related genes in the examined genomes grouped the serovar Enteritidis isolates into two major lineages. Microarray comparisons of the sequenced serovar Enteritidis PT4 to isolates of the closely related serovars Dublin and Gallinarum (biovars Gallinarum and Pullorum) revealed several genomic areas that distinguished them from serovar Enteritidis and from each other. These differences in gene content could be useful in DNA-based typing and in understanding the different phenotypes of these related serovars.

Characterization of Salmonella enterica subspecies I genovars by use of microarrays

Subspecies 1 of Salmonella enterica is responsible for almost all Salmonella infections of warm-blooded animals. Within subspecies 1 there are over 2,300 known serovars that differ in their prevalence and the diseases that they cause in different hosts. Only a few of these serovars are responsible for most Salmonella infections in humans and domestic animals. The gene contents of 79 strains from the most prevalent serovars were profiled by microarray analysis. Strains within the same serovar often differed by the presence and absence of hundreds of genes. Gene contents sometimes differed more within a serovar than between serovars. Groups of strains that share a distinct profile of gene content can be referred to as "genovars" to distinguish them from serovars. Several misassignments within the Salmonella reference B collection were detected by genovar typing and were subsequently confirmed serologically. Just as serology has proved useful for understanding the host range and pathogenic manifestations of Salmonella, genovars are likely to further define previously unrecognized specific features of Salmonella infections.

Complete genome sequence of Salmonella enterica serovar Typhimurium LT2

Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of non-typhoid salmonellosis is increasing worldwide, causing millions of infections and many deaths in the human population each year. Here we sequenced the 4,857-kilobase (kb) chromosome and 94-kb virulence plasmid of S. typhimurium strain LT2. The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria, sample sequencing of both S. enterica serovar Paratyphi A (S. paratyphi A) and Klebsiella pneumoniae, and hybridization of three unsequenced genomes to a microarray of S. typhimurium LT2 genes. Lateral transfer of genes is frequent, with 11% of the S. typhimurium LT2 genes missing from S. enterica serovar Typhi (S. typhi), and 29% missing from Escherichia coli K12. The 352 gene homologues of S. typhimurium LT2 confined to subspecies I of S. enterica-containing most mammalian and bird pathogens-are useful for studies of epidemiology, host specificity and pathogenesis. Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets.

The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi

The Escherichia coli K-12 genome (ECO) was compared with the sampled genomes of the sibling species Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A (collectively referred to as SAL) and the genome of the close outgroup Klebsiella pneumoniae (KPN). There are at least 160 locations where sequences of >400 bp are absent from ECO but present in the genomes of all three SAL and 394 locations where sequences are present in ECO but close homologs are absent in all SAL genomes. The 394 sequences in ECO that do not occur in SAL contain 1350 (30.6%) of the 4405 ECO genes. Of these, 1165 are missing from both SAL and KPN. Most of the 1165 genes are concentrated within 28 regions of 10-40 kb, which consist almost exclusively of such genes. Among these regions were six that included previously identified cryptic phage. A hypothetical ancestral state of genomic regions that differ between ECO and SAL can be inferred in some cases by reference to the genome structure in KPN and the more distant relative Yersinia pestis. However, many changes between ECO and SAL are concentrated in regions where all four genera have a different structure. The rate of gene insertion and deletion is sufficiently high in these regions that the ancestral state of the ECO/SAL lineage cannot be inferred from the present data. The sequencing of other closely related genomes, such as S.bongori or Citrobacter, may help in this regard.

[Renal osteodystrophy(II)]

Renal bone disease represents one of the major complications of end-stage renal disease, accounting for the numerous and various changes at bone level, determined by abnormal calcium and phosphorus homeostasis and by changes in calcitriol and PTH synthesis. PTH represents as well a major uraemic toxin, exerting profound systemic effects, particularly at the cardiovascular level. PTH synthesis is mainly controlled by changes in calcium-phosphorus balance and calcitriol production by the kidneys. Several others factors are important in the development of secondary hyperparathyroidism: acidosis, autonomisation of PTH secretion and peripheral (target-organ) resistance to PTH actions. Although bone biopsy represents the definitive diagnostic test to differentiate between osteitis fibrosa, low-turnover bone disease and bone involvement unrelated to disturbed calcium metabolism (i.e. beta 2-microglobulin-related amyloidosis), plasma intact PTH generally exhibits a reasonably good relation with bone histology parameters. Moreover serum bone-specific alkaline phosphatase isoenzyme, serum pyridinoline and the novel serum markers for bone turnover are highly specific and correlate with bone histomorphometry parameters, so that, preventive and therapeutic strategies should be re-evaluated based solely on biochemical parameters.

Web-based visualization tools for bacterial genome alignments

With the increase in the flow of sequence data, both in contigs and whole genomes, visual aids for comparison and analysis studies are becoming imperative. We describe three web-based tools for visualizing alignments of bacterial genomes. The first, called Enteric, produces a graphical, hypertext view of pairwise alignments between a reference genome and sequences from each of several related organisms, covering 20 kb around a user-specified position. Insertions, deletions and rearrangements relative to the reference genome are color-coded, which reveals many intriguing differences among genomes. The second, Menteric, computes and displays nucleotide-level multiple alignments of the same sequences, together with annotations of ORFs and regulatory sites, in a 1 kb region surrounding a given address. The third, a Java-based viewer called Maj, combines some features of the previous tools, and adds a zoom-in mechanism. We compare the Escherichia coli K-12 genome with the partially sequenced genomes of Klebsiella pneumoniae, Yersinia pestis, Vibrio cholerae, and the Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A. Examination of the pairwise and multiple alignments in a region allows one to draw inferences about regulatory patterns and functional assignments. For example, these tools revealed that rffH, a gene involved in enterobacterial common antigen (ECA) biosynthesis, is partly deleted in one of the genomes. We used PCR to show that this deletion occurs sporadically in some strains of some serovars of S.enterica subspecies I but not in any strains tested from six other subspecies. The resulting cell surface diversity may be associated with selection by the host immune response.

[Renal osteodystrophy (I)]

Renal bone disease represents one of the major complications of end-stage renal disease, accounting for the numerous and various changes at bone level, determined by abnormal calcium and phosphorus homeostasis and by changes in calcitriol and PTH synthesis. PTH represents as well a major uraemic toxin, exerting profound systemic effects, particularly at the cardiovascular level. PTH synthesis is mainly controlled by changes in calcium-phosphorus balance and calcitriol production by the kidneys. Several others factors are important in the development of secondary hyperparathyroidism: acidosis, autonomisation of PTH secretion and peripheral (target-organ) resistance to PTH actions. Although bone biopsy represents the definitive diagnostic test to differentiate between osteitis fibrosa, low-turnover bone disease and bone involvement unrelated to disturbed calcium metabolism (i.e. beta 2-microglobulin-related amyloidosis), plasma intact PTH generally exhibits a reasonably good relation with bone histology parameters. Moreover serum bone-specific alkaline phosphatase isoenzyme, serum pyridinoline and the novel serum markers for bone turnover are highly specific and correlate with bone histomorphometry parameters, so that, preventive and therapeutic strategies should be re-evaluated based solely on biochemical parameters.

[Prognosis and treatment of membranous glomerulonephritis-a 5-year prospective study]

The aims of the study were to describe the clinical, pathological and biological features of membranous GN and to prospectively evaluate the relationships between individual negative prognostic factors--type of therapy and outcome. Between 1993-1998, 13/150 (8.7%) consecutive patients with renal biopsy had membranous GN (M = 62%, age = 42.5 +/- 14.5 years). Main (major) findings in these patients were: asymptomatic proteinuria--23.1%, heavy proteinuria (> 10 g/day)--33.3%, microscopic hematuria--53.8%, increased plasma creatinine levels--33.3%, hypertension--23.1% cases. 60% of the patients with nephrotic proteinuria had an underlying cause (infection, malignancy, immune-mediated systemic diseases). 40% of the patients with nephrotic proteinuria had 0 or less than 2 negative prognostic factors (without any of the recognized severe morphological changes). The following differentiated treatment protocols were applied: no treatment for asymptomatic proteinuria (group A), i.v. methyl-prednisolone boluses + prednisone 1 mg/kgc/day 3 months for those patients with few negative prognostic factors (group B), and steroids (as above) + cyclophosphamide (2 mg/kgc/day 3 months) or the Ponticelli regime in patients with important risk factors (group C). Outcome after a median follow-up period of 24 months was: complete remission in all cases from groups A + B (with only one exception were the underlying cause was breast malignancy); in group C in 75% of the subjects a complete or partial remission (proteinuria < 1 g/day) was obtained. Only one case progressed to chronic renal failure. There were no secondary effects from corticoids or immunosuppressive therapy.

CONCLUSIONS

In membranous GN treatment should be tailored to the presence and type of negative prognostic factors. Even in high-risk patients combined steroids and immunosuppressive therapy determines a favorable outcome in 75% of the cases, without severe adverse effects.

Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions

Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily for DNA sequences. Two of the methods are already in common use; these are based on good column agreement and high information content. Three additional methods find blocks with minimal evolutionary change, blocks that differ in at most k positions per row from a known center sequence and blocks that differ in at most k positions per row from a center sequence that is unknown a priori. The center sequence in the latter two methods is a way to model potential binding sites for known or unknown proteins in DNA sequences. The efficacy of each method was evaluated by analysis of three extensively analyzed regulatory regions in mammalian beta-globin gene clusters and the control region of bacterial arabinose operons. Although all five methods have quite different theoretical underpinnings, they produce rather similar results on these data sets when their parameters are adjusted to best approximate the experimental data. The optimal parameters for the method based on information content varied little for different regulatory regions of the beta-globin gene cluster and hence may be extrapolated to many other regulatory regions. The programs based on maximum allowed mismatches per row have simple parameters whose values can be chosen a priori and thus they may be more useful than the other methods when calibration against known functional sites is not available.

A computer program for aligning a cDNA sequence with a genomic DNA sequence

We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small number of sequencing errors. A freely available computer program, described herein, solves the problem for a 100-kb genomic sequence in a few seconds on a workstation.

[The relationships of rapidly progressive glomerulonephritis (RPGN), crescentic glomerulonephritis and vasculitis: the clinical, histopathological and therapeutic considerations]

Rapidly progressive glomerulonephritis (RPGN) is a rare but severe condition, with a particular poor outcome in the absence of aggressive therapy. Our study describes all RPGN consecutive cases treated during the 1994-1995 period, with special interest in revealing negative prognostic features at presentation and the optimum therapeutic strategy. 14 (20% of all ARF for the same period) cases were classified as RPGN. Although rare (30%), extrarenal symptoms were related with a more unfavourable course. Creatinine clearance at presentation was not a reliable prognostic factor in our study. ANCA was found in 86% of our patients (p-ANCA/c-ANCA = 2/1), and therapeutic success was associated with ANCA disappearance. Crescentic glomerulonephritis was seen in 93% of all cases 77% of which were type III, pauciimune, ANCA positive. Vasculitic lesions and fibrous crescents, but not % of glomerular circumference or % of affected glomeruli were also related with a poor prognosis. Only 43% of our RPGN cases survived with a normal renal function. i.v. metil-prednisolone (at presentation, as soon as possible) followed by i.v. cyclophosphamide up to six months was the best therapeutic regimen, with no important side-effects.