Proteomic changes in response to crystal formation in Drosophila Malpighian tubules

Kidney stone disease is a major health burden with a complex and poorly understood pathophysiology. Drosophila Malpighian tubules have been shown to resemble human renal tubules in their physiological function. Herein, we have used Drosophila as a model to study the proteomic response to crystal formation induced by dietary manipulation in Malpighian tubules. Wild-type male flies were reared in parallel groups on standard medium supplemented with lithogenic agents: control, Sodium Oxalate (NaOx) and Ethylene Glycol (EG). Malpighian tubules were dissected after 2 weeks to visualize crystals with polarized light microscopy. The parallel group was dissected for protein extraction. A new method of Gel Assisted Sample Preparation (GASP) was used for protein extraction. Differentially abundant proteins (p<0.05) were identified by label-free quantitative proteomic analysis in flies fed with NaOx and EG diet compared with control. Their molecular functions were further screened for transmembrane ion transporter, calcium or zinc ion binder. Among these, 11 candidate proteins were shortlisted in NaOx diet and 16 proteins in EG diet. We concluded that GASP is a proteomic sample preparation method that can be applied to individual Drosophila Malpighian tubules. Our results may further increase the understanding of the pathophysiology of human kidney stone disease.     

Proteomic studies of the thylakoid membrane of Synechocystis sp. PCC 6803

Purified thylakoid membranes from the cyanobacterium Synechocystis sp. PCC 6803 were used for the first time in proteomic studies. The membranes were prepared by a combination of sucrose density centrifugation and aqueous polymer two-phase partitioning. In total, 76 different proteins were identified from 2- and 1-D gels by MALDI-TOF MS analysis. Twelve of the identified proteins have a predicted Sec/Tat signal peptide. Fourteen of the proteins were known, or predicted to be, integral membrane proteins. Among the proteins identified were subunits of the well-characterized thylakoid membrane constituents Photosystem I and II, ATP synthase, cytochrome b6f-complex, NADH dehydrogenase, and phycobilisome complex. In addition, novel thylakoid membrane proteins, both integral and peripheral were found, including enzymes involved in protein folding and pigment biosynthesis. The latter were the chlorophyll biosynthesis enzymes, light-dependent protochlorophyllide reductase and geranylgeranyl reductase as well as phytoene desaturase involved in carotenoid biosynthesis and a water-soluble carotenoid-binding protein. Interestingly, in view of the protein sorting mechanism in cyanobacteria, one of the two signal peptidases type I of Synechocystis was found in the thylakoid membrane, whereas the second one has been identified previously in the plasma membrane. Sixteen proteins are hypothetical proteins with unknown function.     

Comparative quantitative proteomics to investigate the remodeling of bioenergetic pathways under iron deficiency in Chlamydomonas reinhardtii

The basic question addressed in this study is how energy metabolism is adjusted to cope with iron deficiency in Chlamydomonas reinhardtii. To investigate the impact of iron deficiency on bioenergetic pathways, comparative proteomics was combined with spectroscopic as well as voltametric oxygen measurements to assess protein dynamics linked to functional properties of respiratory and photosynthetic machineries. Although photosynthetic electron transfer is largely compromised under iron deficiency, our quantitative and spectroscopic data revealed that the functional antenna size of photosystem II (PSII) significantly increased. Concomitantly, stress-related chloroplast polypeptides, like 2-cys peroxiredoxin and a stress-inducible light-harvesting protein, LhcSR3, as well as a novel light-harvesting protein and several proteins of unknown function were induced under iron-deprivation. Respiratory oxygen consumption did not decrease and accordingly, polypeptides of respiratory complexes, harboring numerous iron-sulfur clusters, were only slightly diminished or even increased under low iron. Consequently, iron-deprivation induces a transition from photoheterotrophic to primarily heterotrophic metabolism, indicating that a hierarchy for iron allocations within organelles of a single cell exists that is closely linked with the metabolic state of the cell.     

Plasma selenium status in children with iron deficiency anemia

Iron and selenium are trace elements necessary for the maintenance of life and health. Iron deficiency is the most common nutritional deficiency among children in the world. The purpose of this study was to evaluate plasma selenium concentrations in children with iron deficiency anemia (IDA). Plasma selenium levels were investigated in 56 children with IDA and in 48 control subjects aged 1-8 years. A spectrofluorometric method was used for the determination. Plasma selenium concentrations in children with IDA (33.6+/-8.2 microg/l) were significantly lower than in the control group (56.0+/-17.0 microg/l) (p<0.001). However, there was no relation between plasma selenium, iron and hemoglobin concentrations.     

Proteomic detection of changes in protein synthesis induced by NGX6 transfected in human nasopharyngeal carcinoma cells

In the previous study, we cloned a new gene, named NGX6, related to nasopharyngeal carcinoma (NPC) at 9p. To study its function in the pathogenesis of NPC, we have investigated changes in protein synthesis between NPC cell line HNE1 and that transfected with the gene. Using high-resolution two-dimensional electrophoresis, we found that 22 protein spots showed variations that were significant and reproducible. Analysis of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and database searches identified seven proteins that were upregulated and seven proteins that were downregulated. These proteins included Fas, zinc-finger protein (ZNF), RAB, and Ah receptor-interacting protein (AIP). The functional implications of the identified proteins are discussed.     

Association of genetic variants with response to iron supplements in pregnancy

The incidence of iron deficiency anemia in pregnancy is high in India where iron supplementation is a regular practice. The response to oral iron is influenced by several factors such as age, body mass index, gravida, socioeconomic status, food, vitamin deficiency and compliance to supplements. The major challenge is to understand the various modulators of iron status in this high-risk group so that we can improve the diagnosis and the management of these patients. The current study was designed to evaluate the iron status during pregnancy and to identify factors which might be influencing their response to oral iron. We investigated a total of 181 pregnant women with anemia (Hb < 11 g/dl) and evaluated the impact of probable factors on anemia and their iron status. Assessment of the response was based on hemoglobin and serum ferritin or transferrin saturation level after 8 and 20 weeks of iron supplementation. Socioeconomic, clinical, hematological, biochemical and genetic factors were all evaluated. Molecular analysis revealed that HFE variant allele (G) (rs1799945) was significantly associated with an adequate response to iron supplementation. We identified five subjects with a sustained poor response, and targeted re-sequencing of eleven iron-related genes was performed in them. We have identified seven novel variants in them, and in silico analysis suggested that these variants may have an iron regulatory effect. Taken together, our findings underscore the association of genetic variants with response to supplements in pregnancy, and they can be extended to other diseases where anemia and iron deficiency coexist.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-015-0474-2) contains supplementary material, which is available to authorized users.     

Diffusion of molecules and macromolecules in thylakoid membranes

The survival and fitness of photosynthetic organisms is critically dependent on the flexible response of the photosynthetic machinery, harbored in thylakoid membranes, to environmental changes. A central element of this flexibility is the lateral diffusion of membrane components along the membrane plane. As demonstrated, almost all functions of photosynthetic energy conversion are dependent on lateral diffusion. The mobility of both small molecules (plastoquinone, xanthophylls) as well as large protein supercomplexes is very sensitive to changes in structural boundary conditions. Knowledge about the design principles that govern the mobility of photosynthetic membrane components is essential to understand the dynamic response of the photosynthetic machinery. This review summarizes our knowledge about the factors that control diffusion in thylakoid membranes and bridges structural membrane alterations to changes in mobility and function. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components.     

Herbicide-binding to thylakoid membranes of a DCMU-resistant mutant of Chlamydomonas reinhardii

The specific binding of DCMU and atrazine to the thylakoid membranes of a uniparentally inherited DCMU-resistant mutant dr-416 of Chlamydomonas reinhardii was measured. Whole cells of the mutant can tolerate a 15-fold concentration of DCMU as compared to the parent strain. The same tolerance is found for the photosystem II activity of isolated thylakoid membranes. The mutant is not resistant against atrazine. In equilibrium-binding studies with [¹⁴C]atrazine and unlabelled DCMU, the specific binding for atrazine was found to be identical in the mutant and in the parent strain. The competitive binding of DCMU is significantly weaker for membranes of the mutant than of the parent strain, the equilibrium dissociation constants being 2.0 × 10^?7 M and 3.8 × 10^?8 M, respectively.     

Concurrent Proteomic Fingerprinting and Molecular Analysis of Cyathostomins

Rapid, cost‐effective, efficient, and reliable helminth species identification is of considerable importance to understand host–parasite interactions, clinical disease, and drug resistance. Cyathostomins (Nematoda: Strongylidae) are considered to be the most important equine parasites, yet research on this group is hampered by the large number of 50 morphologically differentiated species, their occurrence in mixed infections with often more than 10 species and the difficulties associated with conventional identification methods. Here, MALDI‐TOF MS, previously successfully applied to identify numerous organisms, is evaluated and compared with conventional and molecular genetic approaches. A simple and robust protocol for protein extraction and subsequent DNA isolation allowing molecular confirmation of proteomic findings is developed, showing that MALDI‐TOF MS can discriminate adult stages of the two closely related cyathostomin species Cylicostephanus longibursatus and Cylicostephanus minutus. Intraspecific variability of proteomic profiles within morphospecies demonstrated an identification of morphospecies with an accuracy of close to 100%. In contrast, three genospecies within C. minutus and sex‐specific profiles within both morphospecies could not be reliably discriminated using MALDI‐TOF MS. In conclusion, MALDI‐TOF MS complemented by the molecular protocol is a reliable and efficient approach for cyathostomin species identification.     

Towards functional proteomics of membrane protein complexes: analysis of thylakoid membranes from Chlamydomonas reinhardtii

Functional proteomics of membrane proteins is an important tool for the understanding of protein networks in biological membranes but structural studies on this part of the proteome are limited. In this study we undertook such an approach to analyse photosynthetic thylakoid membranes isolated from wild-type and mutant strains of Chlamydomonas reinhardtii. Thylakoid membrane proteins were separated by high-resolution two-dimensional gel electrophoresis (2-DE) and analysed by immuno-blotting and mass spectrometry for the presence of membrane-spanning proteins. Our data show that light-harvesting complex proteins (LHCP), that cross the membrane with three transmembrane domains, can be separated using this method. We have identified more than 30 different LHCP spots on our gels. Mass spectrometric analysis of 2-DE separated Lhcb1 indicates that this major LHCII protein can associate with the thylakoid membrane with part of its putative transit sequence. Separation of isolated photosystem I (PSI) complexes by 2-DE revealed the presence of 18 LHCI protein spots. The use of two peptide-specific antibodies directed against LHCI subunits supports the interpretation that some of these spots represent products arising from differential processing and post-translational modifications. In addition our data indicate that the reaction centre subunit of PSI, PsaA, that possesses 11 transmembrane domains, can be separated by 2-DE. Comparison between 2-DE maps from thylakoid membrane proteins isolated from a PSI-deficient (Deltaycf4) and a crd1 mutant, which is conditionally reduced in PSI and LHCI under copper-deficiency, showed the presence of most of the LHCI spots in the former but their absence in the latter. Our data demonstrate that (i) hydrophobic membrane proteins like the LHCPs can be faithfully separated by 2-DE, and (ii) that high-resolution 2-DE facilitates the comparative analysis of membrane protein complexes in wild-type and mutants cells.     

大鼠海马的表达蛋白质组学实验研究

目的：用蛋白质组学方法初步分析大鼠海马蛋白质的表达。方法：提取大鼠海马蛋白质样品后,用双向凝胶电泳对其分离,经考马斯亮蓝染色后,产生大鼠海马蛋白质双向凝胶电泳图谱。从凝胶上切割分离的蛋白质,经胰蛋白酶胶内酶解,通过基质辅助激光解吸／电离飞行时间质谱（MALDI-TOF-MS）对酶解后的肽段进行分析。根据肽段质谱数据,经数据库（NCBI）检索,对蛋白质进行鉴定。结果：鉴定了37种具有明确功能的蛋白质,它们分别属于代谢酶、细胞骨架蛋白、热休克蛋白、抗氧化蛋白、信号传导蛋白、蛋白酶体相关蛋白、神经元特异蛋白及神经胶质蛋白。另外,鉴定了3种未知功能蛋白。结论：为建立大鼠海马蛋白质组数据库提供必要的资料,为在大鼠模型上研究神经疾病发病机理奠定基础。     

Increased serum copper and decreased serum zinc levels in children with iron deficiency anemia

In order to evaluate serum copper and zinc status in children with iron deficiency anemia (IDA), 60 children with IDA aged 1–14 yr and 64 healthy children as controls aged 1–14 yr were included the study. Serum copper levels were higher in children with IDA (189 ± 49 (Μg/dL) than those of controls (163 ± 37 Μg/dL) (p = 0.001). Serum zinc levels were lower in the patient group (109 ± 59 Μg/dL) than those of control subjects (135 ± 56 Μg/dL) (p = 0.017). In addition, there were statistically significant negative correlations between hematological parameters and serum copper levels in the patient group, but not in controls. No correlation between hematological parameters and serum zinc levels were found in both patient and control groups, except positive correlation between mean corpuscular volume (MCV) and serum zinc level in patients. It was concluded that at the time of managing children with IDA, zinc deficiency must be borne in mind and if necessary treatment should be initiated with zinc.     

蛋白质组学技术及其在生物医学上的应用

蛋白质组学部分承用了创立于二十多年前的二维电泳技术。基于其高分辩能力 ,二维电泳主要用于分离和检测复杂混合物中的蛋白质。虽然没有获得更多的改进 ,但是二维电泳结合了通过质谱测定蛋白质的最新进展而成为蛋白质组学中的一项重要技术。随着人类基因组计划项目的完成及由此而产生的大量基因数据库和使用这些数据的生物信息技术 ,科学家们的下一个目标是解析生物体的完整蛋白质组 ,把蛋白质组学数据与基因组学数据关联起来并有机地结合而成为一项有力的工具以阐明病理学中的蛋白质功能、衰老的过程及发现新药目标蛋白质和疾病标识物等。文章综述了蛋白质组学技术的最新知识及其在生物医学研究中的潜在应用     

Salt-induced pH changes in spinach chloroplast suspension. Changes in surface potential and surface pH of thylakoid membranes

A pH decrease in chloroplast suspension in media of low salt concentration was observed when a salt was added at pH values higher than 4.4, while at lower pH values a pH increase was observed. The salt-induced pH changes depended on the valence and concentration of cations of added salts at neutral pH values (higher than 4.4) and on those of anions at acidic pH values (lower than 4.4). The order of effectiveness was trivalent > divalent > monovalent. The pH value change by salt addition was affected by the presence of ionic detergents depending on the sign of their charges. These characteristics agreed with those expected from the Gouy-Chapman theory on diffuse electrical double layers. The results were interpreted in terms of the changes in surface potential, surface pH and the ionization of surface groups which result in the release (or binding) of H⁺ to (or from) the outer medium.The analysis of the data of KCl-induced pH change suggests that the change in the surface charge density of thylakoid membranes depends mainly on the ionization of carboxyl groups, which is determined by the surface pH. When the carboxyl groups are fully dissociated, the surface charge density reaches ?1.0 ± 0.1 · 10^?3 elementary charge/square Å.Dependence of the estimated surface potential on the bulk pH was similar to that of electrophoretic mobility of thylakoid membrane vesicles.     

Iron deficiency and its epigenetic effects on iron homeostasis

Iron deficiency is a common micronutrient deficiency associated with metabolic changes in the levels of iron regulatory proteins, hepcidin and ferroportin. Studies have associated dysregulation of iron homeostasis to other secondary and life-threatening diseases including anaemia, neurodegeneration and metabolic diseases. Iron deficiency plays a critical role in epigenetic regulation by affecting the Fe²⁺/α-ketoglutarate-dependent demethylating enzymes, Ten Eleven Translocase 1–3 (TET 1–3) and Jumonji-C (JmjC) histone demethylase, which are involved in epigenetic erasure of the methylation marks on both DNA and histone tails, respectively. In this review, studies involving epigenetic effects of iron deficiency associated with dysregulation of TET 1–3 and JmjC histone demethylase enzyme activities on hepcidin/ferroportin axis are discussed.     

Effect of iron deficiency anaemia over glycated hemoglobin in non-diabetic women

Background: Glycated hemoglobin (HbA1c) is a form of hemoglobin bound to glucose and used as an index of glycaemic control reflecting glucose levels of the previous three months. Iron deficiency anemia (IDA) is the commonest form of anemia that affects HbA1c. Reports on the effects of IDA on HbA1c levels are inconsistent in India. Therefore, the study correlated the HbA1c and IDA in non-diabetic female patients. Methods: A correlative study between HbA1c and IDA was carried out at the Department of Biochemistry, A. J. Institute of Medical Sciences, Mangaluru, India. A total of 50 non-diabetic female patients, aged between 20-50 years, with decreased levels of Hb, MCV and MCHC were selected. Their ferritin levels were determined by ELISA method to confirm IDA. Forty confirmed iron-deficient samples whose serum ferritin levels were <90 pg/dL, were tested for HbA1c levels by nephelometry method. Results: HbA1c correlated positively with serum ferritin, Hb, MCV, MCH and MCHC (P<0.05). There was a significant decrease in mean value of HbA1c in those with severe anemia (4.50±0.34) compared to those with moderate anemia (5.18±0.35) (P<0.001). Conclusion: Results showed positive correlation of HbA1c with ferritin and hemoglobin. Therefore, iron status should be considered during the interpretation of the HbA1c concentrations in diabetes mellitus.     

Effect of dicyclohexylcarbodiimide on the proton conductance of thylakoid membranes in intact chloroplast

The effects of dicyclohexylcarbodiimide, a potent inhibitor of chloroplast ATPase, on the light-induced electric potential changes in intact chloroplasts of Peperomia metallica and of a hornwort Anthoceros sp. were investigated by means of glass microcapillary electrodes. The characteristics of potential changes induced by flashes or continuous light in chloroplasts of both species are similar except for the phase of potential rise in continuous light, which is clearly biphasic in Anthoceros chloroplasts. Dicyclohexylcarbodiimide at concentration 5 · 10⁻⁵ M completely abolishes the transient potential undershoot in the light-off reaction but has little effect on the peak value of the photoelectric response. The membrane conductance in the light and in the dark was tested by measuring the decay kinetics of flash-generated potential in dark-adapted and preilluminated chloroplasts. In the absence of dicyclohexylcarbodiimide, preillumination causes a significant acceleration of the potential decay. The light-induced changes in the decay kinetics of flash-induced responses were abolished in the presence of dicyclohexylcarbodiimide, whereas the rate of potential decay in dark-adapted chloroplasts was not altered by dicyclohexylcarbodiimide. The results are consistent with the notion that dicyclohexylcarbodiimide diminishes H⁺ conductance of energized thylakoid membranes by interacting with the H⁺ channel of ATPase. The occurrence of a lag (approx. 300 ms) on the plot of potential undershoot (diffusion potential) versus illumination time might suggest the increase in H⁺ permeability coefficient of thylakoid membrane during illumination.     

Role of iron metabolism in heart failure: From iron deficiency to iron overload

Iron metabolism is a balancing act, and biological systems have evolved exquisite regulatory mechanisms to maintain iron homeostasis. Iron metabolism disorders are widespread health problems on a global scale and range from iron deficiency to iron-overload. Both types of iron disorders are linked to heart failure. Iron play a fundamental role in mitochondrial function and various enzyme functions and iron deficiency has a particular negative impact on mitochondria function. Given the high-energy demand of the heart, iron deficiency has a particularly negative impact on heart function and exacerbates heart failure. Iron-overload can result from excessive gut absorption of iron or frequent use of blood transfusions and is typically seen in patients with congenital anemias, sickle cell anemia and beta-thalassemia major, or in patients with primary hemochromatosis. This review provides an overview of normal iron metabolism, mechanisms underlying development of iron disorders in relation to heart failure, including iron-overload cardiomyopathy, and clinical perspective on the treatment options for iron metabolism disorders.     

Serum lipid profiles of young Japanese women with iron deficiency without anemia

PurposeWe aimed to evaluate the association between iron deficiency without anemia (IDNA) and serum lipid profiles in young women of around 20 years of age.MethodsThis study included non-anemic (hemoglobin ≥ 12 g/dL) female volunteers aged 18 to 22 years who were not taking mineral/vitamin supplements and living in the metropolitan area of Tokyo, Japan. These volunteers were classified into two groups based on their sFer (serum ferritin) levels: normal group (sFer ≥ 20 ng/mL, n = 36) and IDNA group (sFer < 20 ng/mL, n = 29). Venous blood samples were obtained from the antecubital veins of these volunteers after 10–12-h fasting to measure the hematological and biochemical parameters, including lipid levels and iron status. The results of each group were compared using Student’s t-test or the Mann–Whitney U test (for inhomogeneous variance).ResultsThe serum cholesterol levels varied depending on the iron status in the women. Serum high-density lipoprotein cholesterol (HDL-C) levels in the IDNA group were significantly higher (P = 0.006) than that in the normal group. However, the levels of total cholesterol (T-CHO), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C) were not significantly different between the groups. Serum LDL-C levels were positively and significantly correlated with sFer levels in the IDNA group (Kendall’s rank correlation 0.264, P = 0.044), but not in the normal group. The sFer level was not correlated with serum HDL-C in both groups. The reason for the high serum HDL-C levels in young women with IDNA is not yet clear. Compared to the normal group, the frequency of eating bread containing bran was significantly higher (P = 0.031) and that for yogurt was significantly lower (P = 0.040) in the IDNA group. The proportion of the women who were susceptible to infection, which was measured using the Cornell Medical Index, was significantly higher in the IDNA group than in the normal group. Among those susceptible to infection, the serum HDL-C level of the volunteers in the IDNA group was significantly higher than that of the volunteers in the normal group (P = 0.024).ConclusionsOur findings suggest that lipid parameters may be associated with IDNA and susceptibility to infection. Further research is needed to elucidate the mechanisms underlying the changes in the serum cholesterol levels in individuals with IDNA and the clinical significance of these findings.