Structural and functional diversity of transient heme binding to bacterial proteins

BackgroundHeme is an important nutritional iron source for almost all bacteria. Elevated heme concentrations, in contrast, are toxic e.g. due to the generation of reactive oxygen species. The cellular heme concentration thus requires tight regulation. The observation of heme acting as an effector molecule in heme-uptake and -utilization processes is rather new and many of these processes are unknown or rarely understood on the molecular level.Scope of reviewWe describe processes involving transient heme-protein interaction in bacteria and highlight the regulatory function of heme at key steps during heme uptake and utilization. We furthermore focus on essential structural aspects of heme binding to respective proteins.Major conclusionsThe structural and functional basis for heme-regulated processes in bacteria is diverse and ranges from increased degradation to extended half-life and from inhibition to activation of the respective heme-regulated protein. The large variety of effects is attributed to the versatile ability of heme to interact with proteins in different ways.General significanceKnowledge of the molecular mechanism of transient heme-protein interaction is central to understand the heme-regulated processes in bacteria. The heme-binding proteins involved in these processes represent potential targets for the development of novel antibacterial drugs. New antibacterial strategies are urgently needed to combat antibiotic resistance.     

An iterative deconvolution algorithm for image recovery in clinical CT: A phantom study

PurposeTo study the feasibility of using an iterative reconstruction algorithm to improve previously reconstructed CT images which are judged to be non-diagnostic on clinical review. A novel rapidly converging, iterative algorithm (RSEMD) to reduce noise as compared with standard filtered back-projection algorithm has been developed.Materials and methodsThe RSEMD method was tested on in-silico, Catphan^®500, and anthropomorphic 4D XCAT phantoms. The method was applied to noisy CT images previously reconstructed with FBP to determine improvements in SNR and CNR. To test the potential improvement in clinically relevant CT images, 4D XCAT phantom images were used to simulate a small, low contrast lesion placed in the liver.ResultsIn all of the phantom studies the images proved to have higher resolution and lower noise as compared with images reconstructed by conventional FBP. In general, the values of SNR and CNR reached a plateau at around 20 iterations with an improvement factor of about 1.5 for in noisy CT images. Improvements in lesion conspicuity after the application of RSEMD have also been demonstrated. The results obtained with the RSEMD method are in agreement with other iterative algorithms employed either in image space or with hybrid reconstruction algorithms.ConclusionsIn this proof of concept work, a rapidly converging, iterative deconvolution algorithm with a novel resolution subsets-based approach that operates on DICOM CT images has been demonstrated. The RSEMD method can be applied to sub-optimal routine-dose clinical CT images to improve image quality to potentially diagnostically acceptable levels.     

Unusual glycosylation of proteins: Beyond the universal sequon and other amino acids

BackgroundGlycosylation of proteins is the most common, multifaceted co- and post-translational modification responsible for many biological processes and cellular functions. Significant alterations and aberrations of these processes are related to various pathological conditions, and often turn out to be disease biomarkers. Conventional N-glycosylation occurs through the recognition of the consensus sequon, asparagine (Asn)-X-serine (Ser)/threonine (Thr), where X is any amino acid except for proline, with N-acetylglucosamine (GlcNAc) as the first glycosidic linkage. Usually, O-glycosylation adds a glycan to the hydroxyl group of Ser or Thr beginning with N-acetylgalactosamine (GalNAc).Scope of reviewProtein glycosylation is further governed by additional diversifications in sequon and structure, which are yet to be fully explored. This review mainly focuses on the occurrence of N-glycosylation in non-consensus motifs, where Ser/Thr at the + 2 position is substituted by other amino acids. Additionally, N-glycosylation is also observed in other amide/amine group-containing amino acids. Similarly, O-glycosylation occurs at hydroxyl group-containing amino acids other than serine/threonine. The neighbouring amino acids and local structural features around the potential glycosylation site also play a significant role in determining the extent of glycosylation. All of these phenomena that yield glycosylation at the atypical sites are reported in a variety of biological systems, including different pathological conditions.Conclusion and SignificanceTherefore, the discovery of more novel sequence patterns for N- and O-glycosylation may help in understanding the functions of complex biological processes and cellular functions. Taken together, all these information provided in this review would be helpful for the biological readers.     

The Impact of Non-cultivated Biodiversity on Enzyme Discovery and Evolution

The search for novel enzymes with biotechnological potential in the fine chemical, food and feed, detergent and cosmetics industries is driven by the need to improve existing processes and applications, to design novel processes for innovative products or intermediates or to avoid intellectual property related operative restrictions. Strategies for obtaining novel biocatalysts will be based on screening natural biodiversity or a combination of nature derived scaffolds and optimization by directed evolution technology. Considering the enormous potential of in vitro mutational and recombinatorial strategies to alter genes and improve enzyme properties, we propose that it might be advantageous to select improved molecular starting points before embarking on the arduous walk through sequence space towards optimized performance.     

Loss of DUSP3 activity radiosensitizes human tumor cell lines via attenuation of DNA repair pathways

BackgroundRadiotherapy causes the regression of many human tumors by increasing DNA damage, and the novel molecular mechanisms underlying the genomic instability leading to cancer progression and metastasis must be elucidated. Atypical dual-specificity phosphatase 3 (DUSP3) has been shown to down-regulate mitogen-activated protein kinases (MAPKs) to control the proliferation and apoptosis of human cancer cells. We have recently identified novel molecular targets of DUSP3 that function in DNA damage response and repair; however, whether DUSP3 affects these processes remains unknown.MethodsTumor cell lines in which DUSP3 activity was suppressed by pharmacological inhibitors or a targeted siRNA were exposed to gamma radiation, and proliferation, survival, DNA strand breaks and recombination repair pathways were sequentially analyzed.ResultsThe combination of reduced DUSP3 activity and gamma irradiation resulted in decreased cellular proliferation and survival and increased cellular senescence compared with the effects of radiation exposure alone. Gamma radiation-induced DNA damage was increased by the loss of DUSP3 activity and correlated with increased levels of phospho-H2AX protein and numbers of ionizing radiation-induced γ-H2AX foci, which were reflected in diminished efficiencies of homologous recombination (HR) and non-homologous end-joining (NHEJ) repair. Similar results were obtained in ATM-deficient cells, in which reduced DUSP3 activity increased radiosensitivity, independent of increased MAPK phosphorylation.ConclusionThe loss of DUSP3 activity markedly increases gamma radiation-induced DNA strand breaks, suggesting a potential novel role for DUSP3 in DNA repair.General significanceThe radioresistance of tumor cells is effectively reduced by a combination of approaches through the inhibition of DUSPs.     

Proteomics and metabolomics in biomarker discovery for cardiovascular diseases: progress and potential

Introduction: The process of discovering novel biomarkers and potential therapeutic targets may be shortened using proteomic and metabolomic approaches.

Areas covered: Several complementary strategies, each one presenting different advantages and limitations, may be used with these novel approaches. In vitro studies show how cells involved in cardiovascular disease react, although the phenotype of cultured cells differs to that occurring in vivo. Tissue analysis either in human specimens or animal models may show the proteins that are expressed in the pathological process, although the presence of structural proteins may be confounding. To identify circulating biomarkers, analyzing the secretome of cultured atherosclerotic tissue, analysis of blood cells and/or plasma may be more straightforward. However, in the latter approach, high-abundant proteins may mask small molecules that could be potential biomarkers. The study of sub-proteomes such as high-density lipoproteins may be useful to circumvent this limitation. Regarding metabolomics, most studies have been performed in small populations, and we need to perform studies in large populations in order to discover robust biomarkers.

Expert commentary: It is necessary to involve the clinicians in these areas to improve the design of clinical studies, including larger populations, in order to obtain consistent novel biomarkers.     

Metabolic utilization and remodeling of glycan biosynthesis using fucose analogs

BackgroundFucose (Fuc), a monosaccharide present at the core or the termini of glycans, critically regulates various biological phenomena and is associated with various diseases. Specifically detecting Fuc residues or inhibiting the fucosylation pathway is pivotal in understanding the mechanisms of how fucosylated glycans are related to biological processes and diseases and in developing novel therapeutic agents.Scope of reviewThis review focuses on chemical biology approaches using Fuc analogs developed for metabolically labeling fucosylated glycans or inhibiting the biosynthesis of fucosylated glycans.Major conclusionsDeveloped Fuc analogs have different potency, specificity and effects on protein and cellular functions. Developing highly enzyme-specific probes and inhibitors is desirable for future investigations.General significanceChemical glycobiology approaches using sugar analogs are useful for revealing novel mechanisms of inter-relationships among sugar metabolism pathways and manipulating glycan expression to develop new glycan-targeted therapies.     

Histo-blood group glycans in the context of personalized medicine

BackgroundA subset of histo-blood group antigens including ABO and Lewis are oligosaccharide structures which may be conjugated to lipids or proteins. They are known to be important recognition motifs not only in the context of blood transfusions, but also in infection and cancer development.Scope of reviewCurrent knowledge on the molecular background and the implication of histo-blood group glycans in the prevention and therapy of infectious and non-communicable diseases, such as cancer and cardiovascular disease, is presented.Major conclusionsGlycan-based histo-blood groups are associated with intestinal microbiota composition, the risk of various diseases as well as therapeutic success of, e.g., vaccination. Their potential as prebiotic or anti-microbial agents, as disease biomarkers and vaccine targets should be further investigated in future studies. For this, recent and future technological advancements will be of particular importance, especially with regard to the unambiguous structural characterization of the glycan portion in combination with information on the protein and lipid carriers of histo-blood group-active glycans in large cohorts.General significanceHisto-blood group glycans have a unique linking position in the complex network of genes, oncodevelopmental biological processes, and disease mechanisms. Thus, they are highly promising targets for novel approaches in the field of personalized medicine. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.     

An extraction free modified o-phthalaldehyde assay for quantifying residual protein and microbial biofilms on surfaces

Abstract

Biological contamination of surfaces in industry and healthcare is an important vector of disease transmission. Current assays for detecting surface-adherent contamination require extraction of biological soil. However, physical inaccessibility or poor solubility may limit recovery. Here, how the o-phthalaldehyde (OPA) protein assay can be modified to measure residual protein (modeled with bovine serum albumin) or biofilm on a surface without extraction is described. The assay limit of detection (LOD) for protein was 1.6 µg cm^?2. The detection threshold for Staphylococcus epidermis biofilm was 117 µg cm^?2. The clinical utility of the method was demonstrated for measurements taken from clinically used endoscopes. Since this method is more sensitive than extraction-based testing, clinical results should not be compared with conventional benchmarks. By enabling direct detection and quantification of soils in complex or hard-to-reach areas, this method has potential to improve the margin of safety in medical and industrial cleaning processes.     

Pharmacokinetic synergy from the taxane extract of Taxus chinensis improves the bioavailability of paclitaxel

BackgroundTaxus chinensis (Pilger) Rehd is widely distributed in China and the northern hemisphere, and the most popular medicinal component isolated from Taxus chinensis is paclitaxel (PTX), which has now become the first-line chemotherapeutic drug for breast cancer and ovarian cancer. Oral administration of pure PTX as a potential anti-cancer agent is compromised by low bioavailability.Hypothesis/purposeIn the clinical practice of traditional Chinese medicine, drug co-administration in the form of mixtures or formula could achieve pharmacokinetic/pharmacodynamic synergies. In this study, we aimed to investigate whether there exist any ‘inherent’ phytochemical synergy from Taxus chinensis extract that could improve PTX bioavailability.Study designPharmacokinetic study of PTX after oral administration of Taxus chinensis extracts or single PTX was performed. In addition, comparative cytotoxic studies were carried out on the MCF-7 breast cancer cell lines.MethodsThe plasma concentrations of PTX were determined using a validated high performance chromatography tandem mass spectrometry method. The cytotoxicity was compared using the MTT assay.ResultsOral administration of taxane fractions isolated from Taxus chinensis (containing 17.2% PTX) could achieve remarkably higher blood concentration and systemic exposure of PTX in rats, while the retention of PTX was significantly improved. Further tissue distribution analysis revealed that the penetration of PTX into major tissues was drastically increased compared with that of single PTX. In addition, in MCF-7 cells, the co-existing components in taxane mixtures could strengthen the inhibitory effects of PTX on tumor cell proliferation.ConclusionTogether, these results support that administration of PTX in the form of taxane mixtures may become a novel approach to improve the poor bioavailability of PTX. Moreover, the inherent synergy from Taxus chinensis taxane extracts promises a novel strategy to strengthen PTX efficacy.     

Homogentisic acid induces aggregation and fibrillation of amyloidogenic proteins

BackgroundAlkaptonuria (AKU) is an ultra-rare inborn error of metabolism characterized by homogentisic acid (HGA) accumulation due to a deficient activity of the homogentisate 1.2-dioxygenase (HGD) enzyme. This leads to the production of dark pigments that are deposited onto connective tissues, a condition named ‘ochronosis’ and whose mechanisms are not completely clear. Recently, the potential role of hitherto unidentified proteins in the ochronotic process was hypothesized, and the presence of Serum Amyloid A (SAA) in alkaptonuric tissues was reported, allowing the classification of AKU as a novel secondary amyloidosis.MethodsGel electrophoresis, Western Blot, Congo Red-based assays and electron microscopy were used to investigate the effects of HGA on the aggregation and fibrillation propensity of amyloidogenic proteins and peptides [Aβ(1–42), transthyretin, atrial natriuretic peptide, α-synuclein and SAA]. LC/MS and in silico analyses were undertaken to identify possible binding sites for HGA (or its oxidative metabolite, a benzoquinone acetate or BQA) in SAA.ResultsWe found that HGA might act as an amyloid aggregation enhancer in vitro for all the tested proteins and peptides in a time- and dose- dependent fashion, and identified a small crevice at the interface between two HGD subunits as a candidate binding site for HGA/BQA.ConclusionsHGA might be an important amyloid co- component playing significant roles in AKU amyloidosis.General significanceOur results provide a possible explanation for the clinically verified onset of amyloidotic processes in AKU and might lay the basis to setup proper pharmacological approaches to alkaptonuric ochronosis, which are still lacking.     

宫颈癌差异表达基因筛选及功能分析

目的:筛选参与宫颈癌发生、发展的关键基因,为临床诊疗提供新的靶点。方法:在NCBI-GEO数据库中筛选多组宫颈癌基因表达检测数据集,利用GEO2R分析工具筛选各组数据集的差异表达基因;应用R分析筛选不同数据集之间共有的差异表达基因;利用DAVID在线分析对差异表达基因进行功能聚类和通路分析;利用STRING分析差异表达基因编码蛋白之间的相互作用关系。结果:共选择6组表达数据集,筛选得到59个差异表达基因(宫颈癌组织vs正常组织),表达差异至少达2倍,其中包含50个表达上调基因及9个表达下调基因。这些差异表达基因参与细胞周期、DNA复制、细胞分裂等生物进程。蛋白互作分析表明,这些差异表达基因多数存在相互作用。结论:利用生物信息学方法对不同来源的基因检测数据进行整合分析,有助于更准确的筛选对宫颈癌发生、发展过程具有重要作用的关键基因,本文筛选的宫颈癌差异基因为进一步研究宫颈癌发生、发展的分子机制及临床诊疗提供思路。     

Barriers to Social Participation among Lonely Older Adults: The Influence of Social Fears and Identity

IntroductionLoneliness among older adults is a major public health problem that may be associated with processes of social participation and identity. This study therefore sought to examine the relationship between social participation and identity in a sample of lonely older adults living independently in London, England.MethodAn inductive qualitative approach, based on semi-structured interviews and thematic analysis, was employed.ResultsParticipants commonly spoke of barriers to social participation that have been reported elsewhere, including illness/disability, loss of contact with friends/relatives, lack of a supportive community, and lack of acceptable social opportunities. However, novel findings were also derived. In particular, participants commonly minimised the difficulties they faced alone, and described attempts to avoid social opportunities. These behaviours were linked to fears about engaging in social participation opportunities, including fears of social rejection and/or exploitation, and fears of losing valued aspects of identity.DiscussionIt is concluded that social participation amongst lonely older people will not improve through the removal of previously reported barriers alone; instead, older peoples’ beliefs, fears and identities must be addressed. Suggestions for implementing these findings within community organisations are provided.     

Microbial CO Conversions with Applications in Synthesis Gas Purification and Bio-Desulfurization

ABSTRACT

Recent advances in the field of microbial physiology demonstrate that carbon monoxide is a readily used substrate by a wide variety of anaerobic micro-organisms, and may be employed in novel biotechnological processes for production of bulk and fine chemicals or in biological treatment of waste streams. Synthesis gas produced from fossil fuels or biomass is rich in hydrogen and carbon monoxide. Conversion of carbon monoxide to hydrogen allows use of synthesis gas in existing hydrogen utilizing processes and is interesting in view of a transition from hydrogen production from fossil fuels to sustainable (CO₂-neutral) biomass. The conversion of CO with H₂O to CO₂ and H₂ is catalyzed by a rapidly increasing group of micro-organisms. Hydrogen is a preferred electron donor in biotechnological desulfurization of wastewaters and flue gases. Additionally, CO is a good alternative electron donor considering the recent isolation of a CO oxidizing, sulfate reducing bacterium. Here we review CO utilization by various anaerobic micro-organisms and their possible role in biotechnological processes, with a focus on hydrogen production and bio-desulfurization.     

Modulation of host HIF-1α activity and the tryptophan pathway contributes to the anti-Toxoplasma gondii potential of nanoparticles

BackgroundToxoplasmosis constitutes a large global burden that is further exacerbated by the shortcomings of available therapeutic options, thus underscoring the urgent need for better anti-Toxoplasma gondii therapy or strategies. Recently, we showed that the anti-parasitic action of inorganic nanoparticles (NPs) could, in part, be due to changes in redox status as well as in the parasite mitochondrial membrane potential.MethodsIn the present study, we explored the in vitro mode of action of the anti-T. gondii effect of NPs by evaluating the contributions of host cellular processes, including the tryptophan pathway and hypoxia-inducing factor activity. NPs, at concentrations ranging from 0.01 to 200 µg/ml were screened for anti-parasitic activity. Sulfadiazine and/or pyrimethamine served as positive controls.ResultsWe found that interplay among multiple host cellular processes, including HIF-1α activity, indoleamine 2,3-dioxygenase activity, and to a larger extent the tryptophan pathway, contribute to the anti-parasitic action of NPs.ConclusionTo our knowledge, this is the first study to demonstrate an effect of NPs on the tryptophan and/or kynurenine pathway.General significanceOur findings deepen our understanding of the mechanism of action of NPs and suggest that modulation of the host nutrient pool may represent a viable approach to the development of new and effective anti-parasitic agents.     

The biotechnological use and potential of plant pathogenic smut fungi

Plant pathogens of the family Ustilaginaceae parasitise mainly on grasses and cause smut disease. Among the best characterised members of this family are the covered smut fungus Ustilago hordei colonising barley and oat as well as the head smut Sporisorium reilianum and the corn smut Ustilago maydis, both infecting maize. Over the past years, U. maydis in particular has matured into a model system for diverse topics like plant–pathogen interaction, cellular transport processes or DNA repair. Consequently, a broad set of genetic, molecular and system biological methods has been established. This set currently serves as a strong foundation to improve existing and establish novel biotechnological applications. Here, we review four promising aspects covering different fields of applied science: (1) synthesis of secondary metabolites produced at fermenter level. (2) Lipases and other hydrolytic enzymes with potential roles in biocatalytic processes. (3) Degradation of ligno-cellulosic plant materials for biomass conversion. (4) Protein expression based on unconventional secretion, a novel approach inspired by basic research on mRNA transport. Thus, plant pathogenic Ustilaginaceae offer a great potential for future biotechnological applications by combining basic research and applied science.     

Critical analysis of life cycle inventory datasets for organic crop production systems

Purpose

Organic agriculture (OA) has gained widespread popularity due to its view as a more sustainable method of farming. Yet OA and conventional agriculture (CA) can be found to have similar or varying environmental performance using tools such as life cycle assessment (LCA). However, the current state of LCA does not accurately reflect the effects of OA; thus the aim of the present study was to identify gaps in the inventory stage and suggest improvements.

Methods

This article presents for the first time a critical analysis of the life cycle inventory (LCI) of state-of-the-art organic crop LCIs from current and recommended LCA databases ecoinvent and AGRIBALYSE®. The effects of these limitations on LCA results were analyzed and detailed ways to improve upon them were proposed.

Results and discussion

Through this analysis, unrepresentative plant protection product (PPP) manufacturing and organic fertilizer treatment inventories were found to be the main limitations in background processes, due to either the lack of available usage statistics, exclusion from the study, or use of unrepresentative proxies. Many organic crop LCIs used synthetic pesticide or mineral fertilizer proxies, which may indirectly contain OA prohibited chemicals. The effect of using these proxies can contribute between 4–78% to resource and energy-related impact categories. In a foreground analysis, the fertilizer and PPP emission models utilized by ecoinvent and AGRIBALYSE® were not well adapted to organic-authorized inputs and used simplified modeling assumptions. These critical aspects can be transferred to respective LCAs that use this data, potentially yielding unrepresentative results for relevant categories. To improve accuracy and to contribute novel data to the scientific community, new manufacturing LCIs were created for a few of the missing PPPs, as well as recommendations for fertilizer treatment LCIs and more precise emission models for PPPs and fertilizers.

Conclusions

The findings in the present article add much needed transparency regarding the limitations of available OA LCIs, offers guidance on how to make OA LCIs more representative, allow for more accurate comparisons between conventional and OA, and help practitioners to better adapt LCA methodology to OA systems.

     

Knowledge-based analysis of genetic associations of rheumatoid arthritis to inform studies searching for pleiotropic genes: a literature review and network analysis

IntroductionPleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. Gene variants directly affect the normal processes of a series of physiological and biochemical reactions, and therefore cause a variety of diseases traits to be changed accordingly. Moreover, a shared genetic susceptibility mechanism may exist between different diseases. Therefore, shared genes, with pleiotropic effects, are important to understand the sharing pathogenesis and hence the mechanisms underlying comorbidity.MethodsIn this study, we proposed combining genome-wide association studies (GWAS) and public knowledge databases to search for potential pleiotropic genes associated with rheumatoid arthritis (RA) and eight other related diseases. Here, a GWAS-based network analysis is used to recognize risk genes significantly associated with RA. These RA risk genes are re-extracted as potential pleiotropic genes if they have been proved to be susceptible genes for at least one of eight other diseases in the OMIM or PubMed databases.ResultsIn total, we extracted 116 potential functional pleiotropic genes for RA and eight other diseases, including five hub pleiotropic genes, BTNL2, HLA-DRA, NOTCH4, TNXB, and C6orf10, where BTNL2, NOTCH4, and C6orf10 are novel pleiotropic genes identified by our analysis.ConclusionsThis study demonstrates that pleiotropy is a common property of genes associated with disease traits. Our results ascertained the shared genetic risk profiles that predisposed individuals to RA and other diseases, which could have implications for identification of molecular targets for drug development, and classification of diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0715-1) contains supplementary material, which is available to authorized users.