Telomere length alterations in microsatellite stable colorectal cancer and association with the immune response

Telomeres are repetitive sequences (TTAGGG) located at the end of chromosomes. Telomeres progressively shorten with each cell replication cycle, ultimately leading to chromosomal instability and loss of cell viability. Telomere length anomaly appears to be one of the earliest and most prevalent genetic alterations in malignant transformation. Here we aim to estimate telomere length from whole-exome sequencing data in colon tumors and normal colonic mucosa, and to analyze the potential association of telomere length with clinical factors and gene expression in colon cancer.Reads containing at least five repetitions of the telomere sequence (TTAGGG) were extracted from the raw sequences of 42 adjacent normal-tumor paired samples. The number of reads from the tumor sample was normalized to build the Tumor Telomere Length Ratio (TTLR), considered an estimation of telomere length change in the tumor compared to the paired normal tissue. We evaluated the associations between TTLR and clinical factors, gene expression and copy number (CN) aberrations measured in the same tumor samples.Colon tumors showed significantly shorter telomeres than their paired normal samples. No significant association was observed between TTLR and gender, age, tumor location, prognosis, stromal infiltration or molecular subtypes. The functional gene set enrichment analysis showed pathways related to immune response significantly associated with TLLR.By extracting a relative measure of telomere length from whole-exome sequencing data, we have assessed that colon tumor cells predominantly shorten telomeres, and this alteration is associated with expression changes in genes related to immune response and inflammation in tumor cells.     

Nascent helix in the multiphosphorylated peptide alphaS2-casein(2-20).

Sequence-specific nuclear magnetic resonance (NMR) assignments have been determined for the peptide alphaS2-CN(2-20) containing the multiphosphorylated motif-8Ser(P)-Ser(P)-Ser(P)-Glu-Glu12- in the presence of molar excess Ca2+. The secondary structure of the peptide was characterized by sequential (i,i + 1), medium-range (i,i + 2/3/4) nOes and H alpha chemical shifts. Molecular modelling of the peptide based on these constraints suggests a nascent helix for residues Ser(P)9 to Glu12. The spectral data for alphaS2-CN(2-20) were compared with those of other casein phosphopeptides beta-CN(1-25) and alphaS1-CN(59-79) that also contain the multiphosphorylated motif. This comparison revealed a similar pattern of secondary amide chemical shifts in the multiphosphorylated motif. However, the patterns of medium-range nOe connectivities in the three peptides suggests they have distinctly different conformations in the presence of Ca2+ despite having a high degree of sequential similarity.     

Production of Guanine from NH4CN Polymerizations

The synthesis of adenine from the polymerization of concentrated ammonium cyanide solutions is well known. We show here that guanine is also produced by this reaction but at yields ranging from 10 to 40 times less than that of adenine. This synthesis is effective at both +80 and −20°C. Since high concentrations of NH₄CN are obtainable only by freezing, this prebiotic synthesis would be applicable to frozen regions of the primitive Earth, the Jovian satellite Europa and other icy satellites, and the parent body of the Murchison meteorite. Received: 18 September 1998 / Accepted: 31 March 1999     

From protons to OXPHOS supercomplexes and Alzheimer's disease: Structure-dynamics-function relationships of energy-transducing membranes

By the elucidation of high-resolution structures the view of the bioenergetic processes has become more precise. But in the face of these fundamental advances, many problems are still unresolved. We have examined a variety of aspects of energy-transducing membranes from large protein complexes down to the level of protons and functional relevant picosecond protein dynamics. Based on the central role of the ATP synthase for supplying the biological fuel ATP, one main emphasis was put on this protein complex from both chloroplast and mitochondria. In particular the stoichiometry of protons required for the synthesis of one ATP molecule and the supramolecular organisation of ATP synthases were examined. Since formation of supercomplexes also concerns other complexes of the respiratory chain, our work was directed to unravel this kind of organisation, e.g. of the OXPHOS supercomplex I₁III₂IV₁, in terms of structure and function. Not only the large protein complexes or supercomplexes work as key players for biological energy conversion, but also small components as quinones which facilitate the transfer of electrons and protons. Therefore, their location in the membrane profile was determined by neutron diffraction. Physico-chemical features of the path of protons from the generators of the electrochemical gradient to the ATP synthase, as well as of their interaction with the membrane surface, could be elucidated by time-resolved absorption spectroscopy in combination with optical pH indicators. Diseases such as Alzheimer's dementia (AD) are triggered by perturbation of membranes and bioenergetics as demonstrated by our neutron scattering studies.     

The genomic architecture of the PROS1 gene underlying large tandem duplication mutation that causes thrombophilia from hereditary protein S deficiency

Hereditary protein S deficiency from a mutation in the PROS1 gene causes a genetic predisposition to develop venous thromboembolic disorders in humans. Recently, the acknowledgment of the clinical significance of large copy number mutations in protein S deficiency has increased. In this study, the authors investigated the genomic architecture of PROS1 in order to understand the microscopic sequence environment leading to large intragenic copy number mutations in the gene. The study subjects were 3 unrelated male patients with hereditary protein S deficiency from a tandem duplication mutation involving exons 5–10 of PROS1. Breakpoint analyses revealed 10-bp microhomology sequences in the intervening sequence (IVS)-4 and IVS-10 at the duplication junction without additional sequence changes, suggesting a single replication-based event as the potential molecular mechanism of rearrangement and founder effect in the mutant alleles. Further analyses on nucleotide sequences flanking the microhomology sequence revealed the presence of a repeat element (LTR-ERV1) and quadruplex-forming G-rich sequences in IVS-4. The results from genotyping multi-allelic short tandem repeats supported founder effect in the identical mutations in the 3 unrelated patients. In conclusion, we identified unique genomic architectures in the intervening sequences of PROS1 that underlie a large intragenic tandem duplication mutation leading to inherited thrombophilia.     

Cholemic nephropathy – Historical notes and novel perspectives

Acute kidney injury is common in patients with liver disease and associated with significant morbidity and mortality. Besides bacterial infections, fluid loss, and use of nephrotoxic drugs AKI in liver disease may be triggered by tubular toxicity of cholephiles. Cholemic nephropathy, also known as bile cast nephropathy, supposedly represents a widely underestimated but important cause of renal dysfunction in cholestasic or advanced liver diseases with jaundice. Cholemic nephropathy describes impaired renal function along with characteristic histomorphological changes consisting of intratubular cast formation and tubular epithelial cell injury directed towards distal nephron segments. The underlying pathophysiologic mechanisms are not entirely understood and clear defined diagnostic criteria are still missing.This review aims to summarize (i) the present knowledge on clinical and morphological characteristics of cholemic nephropathy, (ii) available preclinical models, (iii) potential pathomechanisms especially the potential role of bile acids, and (iv) future diagnostic and therapeutic strategies for cholemic nephropathy. This article is part of a Special Issue entitled: Cholangiocytes in Health and Disease edited by Jesus Banales, Marco Marzioni, Nicholas LaRusso and Peter Jansen.     

甘肃黄花烟草愈伤组织抗氰呼吸的研究

根据呼吸抑制剂试验和氧肟酸滴定法测定结果表明,甘肃黄花烟草愈伤组织呼吸中有明显的抗氰交替途径运行,平均占总呼吸的31%;但仍以细胞色素途径为主,平均占总呼吸的46%;还有23%不受 KCN 加 m-CLAM 抑制的未知剩余呼吸。改变培养基的激素成分和浓度,在不引起愈伤组织发生明显分化条件下,愈伤组织的生长和呼吸速率虽有不同,但抗氰交替途径和细胞色素途径对总呼吸的相对贡献程度和二者的变化趋势基本一致。     

Carbon-nitrogen relations during batch growth ofNannochloropsis oculata (Eustigmatophyceae) under alternating light and dark

Nannochloropsis oculata (strain CCAP 849/1) was sampled at least every 12 h over a 26-d period of batch culture growth in a 12 h/12 h light/dark illumination cycle. Exponential cell-specific growth rate was 0.5 d^–1. Cell division occurred during the dark phase, while ammonium uptake, pigment synthesis and cell volume increase occurred mainly during the light. Stationary phase cells were on average larger that the largest exponentially growing cells. The lag phase prior to cell division was short with the C/N ratio returning to 6.25 (from 28) within 2 d of refeeding with ammonium. Significant Chl.a synthesis commenced after this period; net synthesis of Chl.a ceased on exhaustion of the N-source with a 40% fall in levels by the end of the stationary phase. Levels of carotenoids per cell also declined during N-deprivation although per ml of culture levels remained constant. Ammonium-refeeding of N-deprived cells resulted in a very rapid rise in glutamine (Gln) and very high ratios of glutamine/glutamate (Gln/Glu peaking at 35 within 1 h); peak Gln/Glu was lower in cells refed in the dark or after a shorter period of N-deprivation. The major intracellular amino acids during exponential phase were Glu, Gln, alanine and arginine, but on exhaustion of the N-source, levels of Gln fell rapidly (Gln/Glu falling to below 0.1 from 0.5–0.9 in the light and 0.3 in darkness during exponential growth). During N-deprivation tyrosine accumulated within the cells. Comparisons are drawn with the growth ofIsochrysis galbana, another alga used in aquaculture, under identical conditions.Author for correspondence