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.