An aerotaxis receptor influences invasion of Agrobacterium tumefaciens into its host

Agrobacterium tumefaciens is a soil-borne pathogenic bacterium that causes crown gall disease in many plants. Chemotaxis offers A. tumefaciens the ability to find its host and establish infection. Being an aerobic bacterium, A. tumefaciens possesses one chemotaxis system with multiple potential chemoreceptors. Chemoreceptors play an important role in perceiving and responding to environmental signals. However, the studies of chemoreceptors in A. tumefaciens remain relatively restricted. Here, we characterized a cytoplasmic chemoreceptor of A. tumefaciens C58 that contains an N-terminal globin domain. The chemoreceptor was designated as Atu1027. The deletion of Atu1027 not only eliminated the aerotactic response of A. tumefaciens to atmospheric air but also resulted in a weakened chemotactic response to multiple carbon sources. Subsequent site-directed mutagenesis and phenotypic analysis showed that the conserved residue His100 in Atu1027 is essential for the globin domain's function in both chemotaxis and aerotaxis. Furthermore, deleting Atu1027 impaired the biofilm formation and pathogenicity of A. tumefaciens. Collectively, our findings demonstrated that Atu1027 functions as an aerotaxis receptor that affects agrobacterial chemotaxis and the invasion of A. tumefaciens into its host.

Screening for Antibody Deficiencies in Adults by Serum Electrophoresis and Calculated Globin

PURPOSE

This study aimed to investigate the correlation between calculated globulin (CG, total protein level minus albumin level) and the gamma globulin fraction (Gamma), obtained from serum protein electrophoresis with serum IgG levels in adults (≥ 18 years).

METHODS

Using linear regression models, analyses of CG and Gamma levels correlation with IgG levels in adults were performed. Receiver-operator curves were created to determine cutoff values and the respective sensitivity and specificity measures.

RESULTS

A total of 886 samples were analyzed. CG and Gamma were positively and statistically correlated with IgG levels (r2 = 0.4628 for CG, and = 0.7941 for Gamma, p < 0.0001 for both analyses). For the detection of hypogammaglobulinemia, i.e., IgG level below the reference value (6 g/L), a CG cutoff value of 24 g/L showed a sensitivity of 86.2% (95% CI 69.4-94.5) and a specificity of 92% (90.0-93.6). A Gamma cutoff value of 7.15 g/L yielded a sensitivity of 100% (88.3-100) and a specificity of 96.8 (95.3-97.8).

CONCLUSION

Both CG and Gamma levels determined by protein electrophoresis analysis may be used to screen for antibody deficiencies in adults, enabling earlier diagnosis of antibody deficiencies in a routine clinical setting.

The effect of pH and nitrite on the haem pocket of GLB-33, a globin-coupled neuronal transmembrane receptor of Caenorhabditis elegans

Out of the 34 globins in Caenorhabditis elegans, GLB-33 is a putative globin-coupled transmembrane receptor with a yet unknown function. The globin domain (GD) contains a particularly hydrophobic haem pocket, that rapidly oxidizes to a low-spin hydroxide-ligated haem state at physiological pH. Moreover, the GD has one of the fastest nitrite reductase activity ever reported for globins. Here, we use a combination of electronic circular dichroism, resonance Raman and electron paramagnetic resonance (EPR) spectroscopy with mass spectrometry to study the pH dependence of the ferric form of the recombinantly over-expressed GD in the presence and absence of nitrite. The competitive binding of nitrite and hydroxide is examined as well as nitrite-induced haem modifications at acidic pH. Comparison of the spectroscopic results with data from other haem proteins allows to deduce the important effect of Arg at position E10 in stabilization of exogenous ligands. Furthermore, continuous-wave and pulsed EPR indicate that ligation of nitrite occurs in a nitrito mode at pH 5.0 and above. At pH 4.0, an additional formation of a nitro-bound haem form is observed along with fast formation of a nitri-globin.

Nitric Oxide Derived from Cytoglobin-Deficient Hepatic Stellate Cells Causes Suppression of Cytochrome c Oxidase Activity in Hepatocytes

Aims: Cell-cell interactions between hepatocytes (Hep) and other liver cells are key to maintaining liver homeostasis. Cytoglobin (CYGB), expressed exclusively by hepatic stellate cells (HSC), is essential in mitigating mitochondrial oxidative stress. CYGB absence causes Hep dysfunction and evokes hepatocarcinogenesis through an elusive mechanism. CYGB deficiency is speculated to hinder nitric oxide dioxygenase (NOD) activity, resulting in the elevated formation and release of nitric oxide (NO). Hence, we hypothesized that NO accumulation induced by the loss of NOD activity in CYGB-deficient HSC could adversely affect mitochondrial function in Hep, leading to disease progression. Results: NO, a membrane-permeable gas metabolite overproduced by CYGB-deficient HSC, diffuses into the neighboring Hep to reversibly inhibit cytochrome c oxidase (CcO), resulting in the suppression of respiratory function in an electron transport chain (ETC). The binding of NO to CcO is proved using purified CcO fractions from Cygb knockout (Cygb^-/-) mouse liver mitochondria. Its inhibitory action toward CcO-specific activity is fully reversed by the external administration of oxyhemoglobin chasing away the bound NO. Thus, these findings indicate that the attenuation of respiratory function in ETC causes liver damage through the formation of excessive reactive oxygen species. Treating Cygb^-/- mice with an NO synthase inhibitor successfully relieved NO-induced inhibition of CcO activity in vivo. Innovation and Conclusion: Our findings provide a biochemical link between CYGB-absence in HSC and neighboring Hep dysfunction; mechanistically the absence of CYGB in HSC causes mitochondrial dysfunction of Hep via the inhibition of CcO activity by HSC-derived NO. Antioxid. Redox Signal. 38, 463-479.

Comparison of age-related vascular changes in the optic disc of patients with diabetes, with glaucomatous and non-glaucomatous features

Objective

To identify age-related vascular changes in the optic discs of patients with diabetes with and without signs of glaucoma.

Methods and analysis

A total of 2153 eyes of 1797 patients with diabetes without significant retinopathy were monitored with 10 Topcon-NW400 images obtained over 10.27±1.58 years. 571 non-diabetics eyes were selected as controls. Laguna ONhE uses convolutional neural networks to identify optic disc edges, vessels, cup and rim, and provides a glaucoma assessment index—Globin Distribution Function (GDF).

Results

In the first image, vessel pixels accounted for 33.88% of the disc area (SD=3.72) in non-glaucoma (DN) and 31.35% (SD=4.05; p<0.0001) in glaucoma cases (DG). This number of pixels was reduced by −0.55% each year (SD=0.77) in the DN and −0.76% (SD=0.86; p=0.0014) in the DG. In the first image, 76.55% of the disc pixels (SD=11.13) belonged to the rim in the DN and 62.05% (SD=11.00; p=0.0014) in the DG, decreasing annually by −0.33% (SD=0.99) in the DN and −0.68% (SD=1.08; p<0.00001) in the DG groups. All rim sectors were reduced over time in the DG group, particularly superotemporal (41°–80°) and inferotemporal (271°–310°). The reduction was smaller in DN, presenting as progressive thickening of the temporal sector (311°–40°). No changes in age were observed in healthy controls.

Conclusion

Patients with diabetes show progressive reduction of vessels and neuroretinal rim at the optic disc, which is more intense in association with glaucoma. In the absence of glaucoma, the temporal sector of the diabetic rim was not reduced but thickened, displacing the cup nasally.

Thalassaemia

Thalassaemia is a diverse group of genetic disorders with a worldwide distribution affecting globin chain synthesis. The pathogenesis of thalassaemia lies in the unbalanced globin chain production, leading to ineffective erythropoiesis, increased haemolysis, and deranged iron homoeostasis. The clinical phenotype shows heterogeneity, ranging from close to normal without complications to severe requiring lifelong transfusion support. Conservative treatment with transfusion and iron chelation has transformed the natural history of thalassaemia major into a chronic disease with a prolonged life expectancy, albeit with co-morbidities and substantial disease burden. Curative therapy with allogeneic haematopoietic stem cell transplantation is advocated for suitable patients. The understanding of the pathogenesis of the disease is guiding therapeutic advances. Novel agents have shown efficacy in improving anaemia and transfusion burden, and initial results from gene therapy approaches are promising. Despite scientific developments, worldwide inequality in the access of health resources is a major concern, because most patients live in underserved areas.

Neuroglobin: A Novel Player in the Oxidative Stress Response of Cancer Cells

Reactive oxygen species (ROS) result from intracellular aerobic metabolism and/or extracellular stimuli. Although endogenous antioxidant systems exquisitely balance ROS production, an excess of ROS production, commonly found in diverse human degenerative pathologies including cancer, gives rise to the oxidative stress. Increased oxidative stress in cancer is related to the sustained proliferation and metabolism of cancer cells. However, cancer cells show an intrinsic higher antioxidant capacity with respect to the normal counterpart as well as an ability to cope with oxidative stress-induced cell death by establishing mechanisms of adaptation, which define a selective advantage against the adverse oxidative stress environment. The identification of survival factors and adaptive pathways, set up by cancer cells against oxidative stress, provides multiple targets for the therapeutic intervention against cancer. Neuroglobin (NGB), a globin primarily described in neurons as an oxidative stress sensor and cytoprotective factor against redox imbalance, has been recently recognized as a novel tumor-associated protein. In this review, the involvement of NGB in the cancer cell adaptation and resistance to oxidative stress will be discussed highlighting the globin role in the regulation of both the stress-induced apoptotic pathway and antioxidant systems activated by cancer cells.

[Influences of DNA methylation upon neuroglobin sustained expression in oxygen- glucose deprivation model]

Objective: To investigate the influences of genomic DNA methylation upon neuroglobin sustained expression in oxygen- glucose deprivation model. Methods: With A549 cell strain as the research object, the control group were cultivated in the complete medium containing 10 μmol/L of 5-azacytidine for 4 days, and the control group was cultivated in the complete medium for 4 days.Then carried out oxygen glucose deprivation treatment for 4 h.Detecting neuroglobin expression, DNA methyltransferase expression, cell inhibition ratio and DNA methylation level at different time points. Results: DNA methylation level of the experimental group declined apparently[6 h : (1.0±0.0) vs (2.1±0.3); 12 h: ( 0.9±0.0) vs (1.4±0.0); 24 h: (0.9±0.0) vs (2.6±0.2); 36 h: (0.9±0.0) vs (2.9±0.1)], neuroglobin expression of the experimental group continued and was obviously higher than that of the control group at the same time point[NGB-PCR: 6 h: (3.3±1.1) vs (0.4±0.1); 12 h: (3.2±0.8) vs (0.1±0.1); 24 h: (4.6±0.6) vs (0.2±0.0); 36 h : (5.1±0.3) vs (0.1±0.1)], while the Cell inhibition ratio of the experimental group was obviously lower than that of the control group at the same time point[(6 h: (10.4±0.5) vs (14.1±0.7); 12 h: (22.0±1.3) vs (35.1±0.5); 24 h: (25.7±1.0) vs (40.6±1.3); 36 h: (30.0±0.8) vs (44.4±0.7)], differences had statistical significance (P<0.05).mRNA expression of three methyltransferases of the experimental group was higher than that of the control group at different time points, where, DNMT1 and DNMT3B showed great differences (P<0.05), while differences in DNMT3A of two groups had no statistical significance (P>0.05). Conclusions: In the OGD/R model of A549 cell strain, genomic DNA methylation resulted in unsustained expression of neuroglobin, but neuroglobin expression increased after demethylation inhibitor was used.

[Effects of hypoxia preconditioning on serum NGB and S-100B in patients with intracranial aneurysm surgery]

OBJECTIVE

To study the clinical effects of hypoxia preconditioning (HPC) and its effects on serum neuroglobin (NGB) and S-100B level in the patients undergoing intracranial aneurysm surgery.

METHODS

Forty patients scheduled to intracranial aneurysm surgery were randomly.divided into 2 groups: HPC group (n= 20) and control group (n= 20). The patients in HPC group were treated with 3 cycles of deoxidation-reoxygenation after intubation. The time of deoxidation in each HPC cycle was recorded, while vital signs were also recorded in each corresponding time point. Blood samples were obtained from exsanguinate radial artery and jugular bulb section at the end of each HPC cycle and corresponding time points during operation to measure serum level of NGB and S100B protein and to analysis blood gas.

RESULTS

During HPC process, the patients in group HPC experienced mild hypoxia and CO2 retention. With the times of HPC increasing, CO2 retention degree became heavier (P<0. 05) while hypoxia improved, the patients need more time to make SpO2 from 100% to 90% (P<0. 05). From T2 to T4 (the end of the third reoxygenation, during skull opened and aneurysm dipped, skull closed), NGB in group HPC was higher than that in control (P<0. 05), but S-100B level was not different between HPC and control group (P>0. 05).

CONCLUSION

HPC could induce compensatory ability of the body to hypoxia, which might be related to the up-regulation of NGB expression.

[Recent advances in study of neuroglobin expression in retinal diseases]

Neuroglobin (NGB) is widely exists in the retina and predominantly expressed in the plexiform layers and the inner segments. The physiological roles of NGB may include transportation of oxygen, protection against ischemia/hypoxia injury and oxidative stress, function as a redox-coupled sensor regulating the G-protein coupled transduction pathway, protection against neuronal apoptosis, and working as a terminal oxidase. Based on the function and distribution of NGB and the etiology and pathogenesis of retinal degeneration; it is possible that NGB may play a role in the development of retinal degeneration.

The Preparation and Testing of the Provisional British Standard for Globin Zinc Insulin

From The British Insulin Manufacturers' Biological Sub-Committee and The Department of Biological Standards, National Institute for Medical Research

Attmepts to analyse the biochemical basis of regional differences in animal eggs

The microinjection of cell material or macromolecules into living cells is potentially useful for identifying cell components responsible for positional information. Experiments with purified globin mRNA injected into frog oocytes and eggs show that macromolecules can retain their activity when injected into living cells. Experiments with histones show that injected macromolecules can take up their normal intracellular location in living cells. Attempts have been made to identify the molecules involved in regulating DNA synthesis, ribosomal RNA synthesis, and early developmental events by fractionating egg cytoplasm, and by rescuing maternal effect mutants. The present state, and theoretical basis, of such experiments is discussed.

Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription

A relationship exists between nuclear architecture and gene activity and it has been proposed that the activity of ongoing RNA polymerase II transcription determines genome organization in the mammalian cell nucleus. Recently developed 3C and 4C technology allowed us to test the importance of transcription for nuclear architecture. We demonstrate that upon transcription inhibition binding of RNA polymerase II to gene regulatory elements is severely reduced. However, contacts between regulatory DNA elements and genes in the β-globin locus are unaffected and the locus still interacts with the same genomic regions elsewhere on the chromosome. This is a general phenomenon since the great majority of intra- and interchromosomal interactions with the ubiquitously expressed Rad23a gene are also not affected. Our data demonstrate that without transcription the organization and modification of nucleosomes at active loci and the local binding of specific trans-acting factors is unaltered. We propose that these parameters, more than transcription or RNA polymerase II binding, determine the maintenance of long-range DNA interactions.

Specific real-time PCR vs. fluorescent dyes for serum free DNA quantification

BACKGROUND

Detecting and quantifying circulating free DNA in patient serum has become a major challenge. New methods using conventional or automated DNA amplification have been developed. As quantitative real-time PCR (QPCR) remains expensive and requires dedicated automated instrumentation, we questioned whether simple quantification using fluorescent dyes is efficient for determination of free DNA levels in serum.

METHODS

Serum samples from 180 cancer patients and 58 healthy volunteers were used for DNA quantification according to three methods: (i) using an exonic part of the beta-globin gene as the amplifying target; (ii) amplifying a 105-bp intron 1 part of the housekeeping cyclophilin A gene, both referring to specific standard curves; and (iii) using a PicoGreen DNA quantification kit without amplification.

RESULTS

The 58 samples from healthy controls showed a reference limit of (95th percentile) <160 cyclophilin gene copies/mL. The 180 cancer samples displayed values ranging between 300 and 215,000 copies/mL. The cyclophilin method showed a high level of correlation with both the beta-globin (r=0.911, p<0.0001) and PicoGreen (r=0.915, p<0.0001) methods.

CONCLUSIONS

Aside from the disadvantage that the QPCR assays can only be used in clinical biochemistry laboratories that possess QPCR apparatus, the use of direct PicoGreen quantification displays major advantages in a routine context: it is less time-consuming and is quite inexpensive, but is still correlated with QPCR.

The interaction between cap-binding complex and RNA export factor is required for intronless mRNA export

RNA export factor (REF) is a component of the exon junction complex (EJC) that is deposited on mRNA in a splicing-dependent manner, and targets spliced mRNA for export. In this study, analysis of the RNA-binding protein complexes revealed that REF associates with beta-globin mRNA at the region other than the EJC deposition site. Comparison between RNA polymerase II and T7 transcription and further analysis showed that the deposition of REF apart from the EJC is dependent on the 5' cap structure, but not splicing. Excess amounts of m(7)GpppG cap analog reduced REF binding to intronless mRNA, and a co-immunoprecipitation experiment revealed that REF interacts with the cap-binding protein CBP20. The export of Cy3-labeled intronless beta-globin mRNA from nuclei of HeLa cells was enhanced by co-injection of CBP20 and REF. Thus, REF recruited by CBP20 may play a stimulatory role to export the capped intronless mRNAs.

A versatile denaturing HPLC approach for human beta-globin gene mutation screening

Hemoglobinopathies represent the most common genetic disorder worldwide, with a higher prevalence among populations with a history of malaria endemicity. More than 690 mutations in the human beta-globin gene are usually the cause of beta-type hemoglobinopathies. Here, we report a rapid and highly sensitive beta-globin gene mutation screening approach based on denaturing high-performance liquid chromatography (DHPLC), which contrary to the previously described ones can be used in every HPLC apparatus. The sensitivity and specificity of the method were tested in 120 healthy Greek subjects and 25 beta-thalassemia heterozygotes and homozygotes, in which 11 different beta-globin sequence variations had been previously characterized by denaturing gradient gel electrophoresis. Using this method, we were able to rapidly identify the commonest beta-globin gene mutations, accounting for more than 90% of the mutant beta-globin alleles reported for the Hellenic population. Compared to classical mutation screening approaches, our DHPLC approach provides the means for rapid, highly sensitive, cost-effective, and semi-automated simultaneous mutational scanning of a large number of samples.

Promoter methylation of P16, RARbeta, E-cadherin, cyclin A1 and cytoglobin in oral cancer: quantitative evaluation using pyrosequencing

Methylation profiling of cancer tissues has identified this mechanism as an important component of carcinogenesis. Epigenetic silencing of tumour suppressor genes through promoter methylation has been investigated by a variety of means, the most recent of which is pyrosequencing. We have investigated quantitative methylation status in oral squamous cell carcinoma patients. Fresh tumour tissue and normal control tissue from resection margin was obtained from 79 consecutive patients undergoing resection of oral squamous cell carcinoma. DNA was extracted and bisulphite treated. PCR primers were designed to amplify 75-200 bp regions of the CpG rich gene promoters of p16, RARbeta, E-cadherin, cytoglobin and cyclinA1. Methylation status of 4-5 CpG sites per gene was determined by pyrosequencing. Significant CpG methylation of gene promoters within tumour specimens was found in 28% for p16, 73% for RARbeta, 42% for E-cadherin, 65% for cytoglobin and 53% for cyclinA1. Promoter methylation was significantly elevated in tumours compared to normal tissue for p16 (P = 0.048), cytoglobin (P = 0.002) and cyclin A1 (P = 0.001) but not in RARbeta (P = 0.088) or E-cadherin (P = 0.347). Concordant methylation was demonstrated in this tumour series (P = 0.03). Significant differences in degree of methylation of individual CpG sites were noted for all genes except RARbeta and these differences were in a characteristic pattern that was reproduced between tumour samples. Cyclin A1 promoter methylation showed an inverse trend with histological grade. Promoter methylation analysis using pyrosequencing reveals valuable quantitative data from several CpG sites. In contrast to qualitative data generated from methylation specific PCR, our data demonstrated p16 promoter methylation in a highly tumour specific pattern. Significant tumour specific methylation of cyclin A1 promoter was also seen. Cytoglobin is a novel candidate tumour suppressor gene highly methylated in upper aero-digestive tract squamous cancer.

Increased neuroglobin levels in the cerebral cortex and serum after ischemia–reperfusion insults

Neuroglobin (NGB) is a newly discovered protein localized in neurons of the central and peripheral nervous systems in vertebrates. It functions to bind, store, and facilitate the utilization of oxygen in neuronal cells. Recent studies suggest that it may modulate hypoxic and ischemic injury. The major goal of the present study is to characterize the dynamic changes of NGB protein in the brain and serum in a global forebrain ischemia-reperfusion model using gerbils. The sensitivity and validity of serum NGB as a potential biomarker for brain injury were further evaluated. Global cerebral ischemia-reperfusion models were induced by bilateral carotid occlusion for 20 min followed with 2-, 8-, 16-, 24-, 48-, or 72-h reperfusion in forty-six Mongolian gerbils. Sham-operated and operated animals were sacrificed at the designated time after reperfusion. Brains were fixed for immunocytochemical study to evaluate the time-dependent expression of NGB, and the concentration of NGB in serum was measured by enzyme-linked immunosorbent assay. Our results showed that the expression of NGB was upregulated in the cerebral cortex but significantly downregulated in the hippocampus from 2 to 72 h of reperfusion after 20 min of bilateral common carotid arteries occlusion. The concentration of NGB in serum was significantly increased at 8 h and reached a peak at 48 h of reperfusion. There is a significant correlation between NGB levels in the serum and severity of neuronal damage in the gerbil brain. In summary, the upregulation of NGB in cerebral cortex and downregulation in hippocampus after reperfusion insults in the gerbil brain are consistent with the fact that cerebral cortex is more tolerant to hypoxic or ischemic injury than the hippocampus. Moreover, the changes of NGB levels in serum may be used to monitor the extent of brain damage in ischemic brain diseases.

Outcome after portoenterostomy in biliary atresia: pivotal role of degree of liver fibrosis and intensity of stellate cell activation

OBJECTIVES

Biliary atresia (BA), a congenital idiopathic obliterative cholangiopathy, rapidly leads to liver cirrhosis and liver failure if untreated. A timely Kasai portoenterostomy (KP) variably alters this natural history. We evaluated liver fibrogenesis by the intensity of alpha-smooth-muscle actin (SMA) expression, which is a marker for hepatic stellate cell activation. We hypothesized that liver fibrogenesis as determined by intensity of alpha-SMA is already progressing at the time of KP, is related to age and degree of fibrosis at KP, and predicts outcome after KP.

METHODS

BA patients at KP (n = 22, age 22-84 days, median 59) had wedge liver biopsies assessed by quantitative morphometry of immunohistochemistry for alpha-SMA expression. Fibrosis was scored by blinded pathologists. Outcome, reflected by conjugated bilirubin concentration 3 months after KP (CBili3m), survival of the native liver, need for liver transplant, or death, were assessed for 2 to 10 years after KP.

RESULTS

At KP, age, fibrosis score, and alpha-SMA expression were significantly correlated. Moderate-severe fibrosis and intense alpha-SMA expression was observed in 15 of 22 (68%) patients. Severe fibrosis and high alpha-SMA expression were significantly associated with CBili3m greater than 2 g/dL and unfavorable liver survival (>90% of these ultimately underwent liver transplantation or died). Conversely, those with mild fibrosis and low alpha-SMA expression had normal CBili3m and favorable liver survival.

CONCLUSION

Intense liver fibrogenesis is already established in many cases of BA at the time of KP. Fibrosis scores and intensity of alpha-SMA expression may be predictors of outcome after KP and may indicate those patients who might benefit from trials of potential antifibrotic agents early in the course of BA.

Internal cavities and ligand passageways in human hemoglobin characterized by molecular dynamics simulations

Molecular dynamics simulations of the unliganded T state of human hemoglobin showed the existence of a spontaneous, very wide cavity on the distal side of the alpha subunit. This cavity consists of three tunnels spreading from the vicinity of the iron atom (the ligand binding site) to the surface of the subunit, constituting possible passageways for the entrance of the ligand. A fourth passageway was characterized due to the trajectory of water molecules entering or leaving the heme pocket. Analogous passages were observed in the beta subunits. They all appear and disappear dynamically, although some parts of them are more persistent along the trajectories. The most persistent regions within these tunnels correspond to all the xenon docking sites of human cytoglobin and to some of those of sperm whale and horse heart myoglobins and group I truncated hemoglobins.

An investigation of the tylosis with oesophageal cancer (TOC) locus in Iranian patients with oesophageal squamous cell carcinoma

Oesophageal cancer is one of the ten leading causes of cancer mortality worldwide. Earlier loss of heterozygosity (or allelic imbalance) studies have implicated regions on chromosomes 3p, 5q, 9p, 13q, 17p, 17q, and 18q in the development of sporadic oesophageal cancer and recent data have linked the familial tylosis with oesophageal cancer (TOC) gene-containing region on chromosome 17q25 with this cancer. We have studied allelic imbalance (AI) at microsatellite markers both closely linked to and distant from the TOC gene locus in 60 sporadic squamous cell oesophageal cancers from Iran and have investigated the most likely candidate gene by mutation analysis in these tumours. Forty-four out of these 60 samples (73%) show allelic imbalance at one or more loci within or adjacent to the TOC minimal region, while the highest incidence of AI was observed at the D17S2244 and D17S2246 loci (almost 70% AI in informative cases), correlating with the TOC minimal region. Analysis of the coding regions of a candidate gene in these tumours failed to show an equivalently high incidence of mutation, although two mutations and one polymorphism were observed. These data support and extend previous observations that the TOC region of chromosome 17q25 may be involved in the aetiology of the sporadic form of oesophageal cancer from a number of different geographical populations and suggest that the causative gene may be epigenetically silenced rather than mutated.

DNAase I hypersensitive site 3' to the beta-globin gene cluster containing two TAA insertions and a G-->A polymorphism is predominantly associated with the beta+-thalassemia IVS-I-6 (T-->C) mutation

Analysis of DNA polymorphic sites is an important tool for the detection of gene flow in human evolutionary studies and to study the genetic background for gene mutations. The beta-globin locus contains several single-base restriction fragment length polymorphism (RFLP) sites throughout chromosome 11. In addition to these polymorphic sequence repeats, others are being studied in order to expand our knowledge concerning the role between haplotype-genotype and phenotype associations. Far downstream of the expressed beta-globin genes, there is a hypersensitive site (HS) whose function remains obscure. We sequenced this region in 27 thalassemia patients and found a new pattern in the micro-satellite-like AT-rich region of this site: a new TAA insertion in addition to the one previously described in sickle cell patients with a concomitant polymorphism (G-->A). This new variation was found to be linked to the IVS-I-6 (T-->C) mutation. This polymorphism may be useful for studies concerning genotype and phenotype associations.

Mapping protein matrix cavities in human cytoglobin through Xe atom binding

Cytoglobin is the fourth recognized globin type, almost ubiquitously distributed in human tissues; its function is still poorly understood. Cytoglobin displays a core region of about 150 residues, structurally related to hemoglobin and myoglobin, and two extra segments, about 20 residues each, at the N- and C-termini. The core region hosts a large apolar cavity, held to provide a ligand diffusion pathway to/from the heme, and/or ligand temporary docking sites. Here we report the crystal structure (2.4A resolution, R-factor 19.1%) of a human cytoglobin mutant bearing the CysB2(38) --> Ser and CysE9(83) --> Ser substitutions (CYGB*), treated under pressurized xenon. Three Xe atoms bind to the heme distal site region of CYGB* mapping the protein matrix apolar cavity. Despite the conserved globin fold, the cavity found in CYGB* is structured differently from those recognized to play a functional role in myoglobin, neuroglobin, truncated hemoglobins, and Cerebratulus lacteus mini-hemoglobin.

[Contemporary opinions on liver fibrosis pathogenesis]

The author presents the selected aspects of liver fibrosis pathogenesis with special regards to the mechanism of hepatic stellate cells activation.

[Hemoglobin, from microorganisms to man: a single structural motif, multiple functions]

Haemoglobins from unicellular organisms, plants or animals, share a common structure, which results from the folding, around the heme group, of a polypeptide chain made from 6-8 helices. Nowadays, deciphering the genome of several species allows one to draw the evolutionary tree of this protein going back to 1800 millions of years, at a time when oxygen began to accumulate in the atmosphere. This permits to follow the evolution of the ancestral gene and of its product. It is likely that, only in complex multicellular species, transport and storage of oxygen became the main physiological function of this molecule. In addition, in unicellular organisms and small invertebrates, it is likely that the main function of this protein was to protect the organism from the toxic effect of O2, CO and NO*. The very high oxygen affinity of these molecules, leading them to act rather as a scavenger as an oxygen carrier, supports this hypothesis. Haemoglobins from microorganisms, which may probably be the closest vestiges to the ancestral molecules, are divided into three families. The first one is made from flavohaemoglobins, a group of chimerical proteins carrying a globin domain and an oxido-reduction FAD-dependant domain. The second corresponds to truncated haemoglobins, which are hexacoordinated with very high oxygen-affinity molecules, 20-40 residues shorter than classical haemoglobins. The third group is made from bacterial haemoglobins such as that of Vitreoscilla. Some specific structural arrangements in the region surrounding the heme are cause of their high oxygen affinity. In plants, two types of haemoglobins are present (non-symbiotic and symbiotic), that arose from duplication of an ancestral vegetal gene. Non-symbiotic haemoglobins, which are probably the oldest, are scarcely distributed within tissues having high energetic consumption. Conversely, symbiotic haemoglobins (also named leghaemoglobins) are present at a high concentration (mM) mostly in the rhizomes of legumes, where they are involved in nitrogen metabolism. In some species, haemoglobin was proposed to be an oxygen sensor bringing to the organism information to adjust metabolism or biosynthesis to the oxygen requirement. Elsewhere haemoglobin may act as final electron acceptors in oxido-reduction pathways. Evolution of haemoglobin in invertebrates followed a large variety of scenarios. Some surprising functions as sulphide acquisition in invertebrates living near hydrothermal vents, or a role in the phototrophism of worm need to be mentioned. In invertebrates, the size of haemoglobin varies from monomers to giant molecules associating up to 144 subunits, while in vertebrates it is always a tetramer. In some species, several haemoglobins, with completely different structure and function, may coexist. This demonstrates how hazardous may be to extrapolate the function of a protein from only structural data.

Characterization of human stellate cell activation-associated protein and its expression in human liver

This study cloned cDNA of human homologue (hSTAP) of rat stellate cell activation-associated protein (rSTAP). hSTAP gene is on chromosome 17q and is composed of four exons. Various types of cells including hepatic stellate cells expressed hSTAP mRNA. Recombinant hSTAP was a heme protein with the activity of peroxidase. hSTAP can be used as a marker of quiescent stellate cells in human liver.

The complexity of immune and alloimmune response

Alloimmune response induced by foreign histoincompatible alloantigens is a complex phenomenon possessing mechanisms, characteristics to innate and adoptive immune response. It is also modified by various immunregulating exocrine and autocrine factors. Starting the new time period of functional genomics the knowledge of human genes' structure needs a more clear insight not only about the function and contribution of genes but their historical background, origin and importance in the phylogenesis. Comparative immunology comes into focus of interest helping to understand the complexity of immune and alloimmune response. It is almost unbelievable that immune functions as phagocytosis and cytokine production like IL-1 and TNF have already emerged 700 million years ago in starfishes and sponges. Functions--including recruitment of coelomocytes, killing of micro-organisms by lysosome-like enzyme activity, opsonization by complement analogous proteins and oxidative burst function--remained unchanged during phylogenesis and could be found not only in insects but in mammals as well as representatives of innate immunity. The importance of these molecules is reflected in homology of conservative regions. One of the biggest evolutionary steps happened 500 million years ago when fish developed a jaw in the Placoderms species. This fact led to the development of gut associated immune system. The system was the basis to create the genetic material for recombination and mutation to establish variability and diversity of proteins, as immunoglobulins. It is interesting to lean how diversity of immunglobulins in sharks is insured by joining of blocks of V, D, J and C genes, in contrast to humans, where those genes are located on different chromosome regions. These differences are associated with an immediate production of specific immunglobulin or a slower one combined with immunologic memory. Similar development could be found in T cell antigen specific receptors, too. Concerning the establishment of adoptive immunity by emergence of genetic recombination, which allowed the production of a huge diversity of specific antigen binding proteins, another structure developed parallel from the histoglobin molecule. This protein was created to catch peptide particles which split from the proteins originating from microorganisms, viruses or foreign cell compartments. The cave-like groove capturing the different peptides represented a huge variability. These histocompatibility molecules emerged from this ancient structure for more than 300 million years ago. The genetic family responsible for their synthesis became the most complex gene family including many other genes involved in the immune response. The polymorphic character of the histocompatibility protein is responsible for the capture of the relevant peptides fitting best to the allotype-determined groove. In certain species the same function could be filled by different ancient molecules with the same success. Dendritic cells and their importance in differentiation and antigen presentation became in the focus of interest in the last decade. They have lymphoid and myeloid origin, mature and less differentiated subtypes with characteristic CD markers and cytokine profile. Their function and origin from the stem cell subpopulation is an important example how nature influences the development of immunity to the accommodation and survival to the always changing environment. The new molecular techniques will help to get closer to understand the function of genes regulating immune response and modify them.

A ubiquitously expressed human hexacoordinate hemoglobin

We have identified a new human hemoglobin that we call histoglobin because it is expressed in a wide array of tissues. Histoglobin shares less than 30% identity with the other human hemoglobins, and the gene contains an intron in an unprecedented location. Spectroscopic and kinetic experiments with recombinant human histoglobin indicate that it is a hexacoordinate hemoglobin with significantly different ligand binding characteristics than the other human hexacoordinate hemoglobin, neuroglobin. In contrast to the very high oxygen affinities displayed by most hexacoordinate hemoglobins, the biophysical characteristics of histoglobin indicate that it could facilitate oxygen transport. The discovery of histoglobin demonstrates that humans, like plants, differentially express multiple hexacoordinate hemoglobins.

Lacryglobin in human tears, a potential marker for cancer

Lacrygobin has been identified in human tears. This protein has high sequence homology to the mammaglobins, proteins upregulated in breast cancer and in breast cancer metastasis. In order to investigate the utility of tear screening for cancer tear samples were collected from patients with different types of cancer and compared to controls. Tear samples were taken from five controls and eight breast, six lung, five colon, one prostate and three ovary cancer patients. Tears were analysed using 2-D gel electrophoresis (n = 25) and 1-D electrophoresis (n = 3). Lacryglobin was present in the following percentage of patients: breast cancer (88%), lung (83%), colon (100%), ovary (33%), prostate (100%) and controls (60%). Two control patients with lacryglobin had a family history of breast and prostate cancer. Lacryglobin was detected in some but not all tear samples and further studies are warranted to investigate its potential as a marker for cancer.

Intra-laboratory reproducibility of human papillomavirus identification in cervical specimens by a polymerase chain reaction-based assay

BACKGROUND

polymerase chain reaction (PCR)-based assays for human papillomavirus (HPV) sequences are in wide use in clinical and epidemiological studies. The reproducibility of these assays is not extensively studied.

OBJECTIVES

to estimate the intra-laboratory reproducibility of generic and type-specific HPV diagnoses by the MY09/MY11/HMB01 consensus L1 primer-based PCR assay.

STUDY DESIGN

systematically collected specimens (n=207) were masked and retested.

RESULTS

when specimens negative in both initial and repeat assays were excluded from analysis, the diagnostic reproducibility was 98. 6% for beta-globin, 90.7% for generic HPV (any HPV type), and 76.9% for type-specific HPVs. The reproducibility of type-specific diagnosis increased with increase in signal strength in the hybridization reaction of the initial assay. When a specimen contained five or more HPV types in the initial assay, it was rare to identify all of the HPV types in the repeat assay.

CONCLUSIONS

the degree of reproducibility of the PCR diagnosis should be taken into account in the interpretation of HPV data in clinical and epidemiological studies.