Identification of potential ‘lifestyle-responsive’ epigenomic biomarkers in healthy women aged 18–40

Context: Human health is complex and multifaceted; there is a need for biomarkers that reflect the multidimensional nature of health.

Objective: To identify potential epigenomic biomarkers of health in women aged 18–40 participating in a six-month lifestyle intervention, next level health.

Materials and methods: Methylation data were obtained by reduced representation bisulphite sequencing of 21 female intervention participants as well as three non-participants. The Differential Methylation Analysis Package (DMAP) was used to investigate inter- and intra-individual variability and to identify potential targets of transient epigenetic control in the population studied.

Results: Eleven genes were identified as significantly differentially methylated post- intervention in all 21 participants. 1884 genomic locations were found to be differentially methylated amongst the total female population studied representing potential epigenomic biomarkers.

Conclusions: The ability to demonstrate epigenetic changes arising from a lifestyle intervention can provide key information on the relationship between gene regulation, human behaviour and health.     

Multiple biomarker approach in the fiddler crab to assess anthropogenic pollution in tropical coastal environments

Context: Fiddler crabs are important to the ecology of estuarine systems around the world, however, few studies have incorporated them as bioindicators. Urias estuary represents one of the most urbanized lagoons in the Gulf of California region and received discharges from different sources: shrimp farm, thermoelectric plant, fish processing plants, and untreated domestic and sewage wastes.

Objective: Assess the effects on anthropogenic contamination on female fiddler crabs reproduction, survival and genetic stability.

Methods: Exposition of wild crabs from a less impacted (reference) site to naturally contaminated sediments on under controlled laboratory conditions. Reproductive parameters, levels of DNA damage and mortality rates were measured, together with chemical analyses of sediments.

Results: The most contaminated sediments corresponded to the site where fish processing plants were located and the integrated biomarker response analysis revealed that the most adverse effects were produced by exposure to sediments from this site; these crabs showed higher mortality (67%) and poorer ovarian development than those crabs exposed to sediments from other sites.

Conclusions: Female crabs under pollution stress are able to trade-off reproduction for survival, and surviving animals were able to restore genetic stability possibly by activating DNA repair mechanisms. Multiple biomarker approach discriminates different coastal contamination scenarios.     

Mutation in the beta3 subunit of Guanine nucleotide-binding protein (GNB3) gene is not associated with Type II diabetes mellitus risk: a case–control study of a North Indian population

Context: Genetics play a major role in development and pathophysiology of Type 2 diabetes mellitus (T2DM).

Objective: To asses the association of Guanine nucleotide-binding protein (GNB3) (C825T) gene's polymorphism with T2DM.

Materials and methods: A case–control study including 400 North Indians was performed using Polymerase Chain Reaction–Restriction Fragment Length Polymorphism (PCR-RFLP) approach to analyze genetic polymorphism.

Results: No significant difference was observed in genotype and allele frequencies of GNB3 gene on comparing cases with controls.

Discussion: Our study is in agreement with studies on Polish, Japanese, Hispanic-American and Danish populations who observed no significant association between GNB3 (C825T) polymorphism and T2DM.

Conclusion: GNB3 (C825T) polymorphism is not associated with T2DM.     

Associations of rs1883832 and rs4810485 polymorphisms of CD40 gene with myocardial infarction in the Tunisian population

Context: Cluster of differentiation 40 (CD40), and its ligand CD40L, are major co-stimulatory molecules whose interactions are important in both cellular and humoral immunity, and has been suggested to play a role in the pathogenesis of acute coronary syndrome.

Objective: The aim of this study was to examine the association of CD40 polymorphisms (-1?C>T (rs1883832) and 945G>T (rs4810485)) and myocardial infarction (MI), and to test the association of CD40 gene haplotypes with MI in Tunisians.

Materials and methods: Three hundred and fifty MI patients and 301 apparently healthy controls were included in the study. The polymorphisms of CD40 were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).

Results: There were significant differences in the genotype and allele frequencies of CD40 gene -1?C>T (rs1883832) polymorphism between cases and controls. Stratifying according to gender, the association between the TT genotype and MI was statistically significant in males, only. Haplotype analysis revealed that the C-T and T-G haplotypes were associated with an increased risk of MI (p?=?0.012 and p?<?0.001, respectively).

Conclusions: Our work showed a significant association between the -1?C>T (rs1883832) polymorphism of the CD40 gene and MI in the Tunisians.     

The metabolomics and lipidomics window into thyroid cancer research

Context: Thyroid carcinoma is the most common endocrine system malignancy with a fast rising incidence in the last decade for unknown reasons. Fine needle aspiration (FNA) biopsy, the gold standard in thyroid cancer (TC) screening has still its own challenges and in some cases needs a proceeding surgery.

Objective: This review highlights the role of the two most recent “omics” approaches, “metabolomics” and “lipidomics”, in the field of TC research.

Methods: All the previous studies have been extracted from the literature and major concepts were detailed in the field of TC metabolomics and lipidomics.

Results: Metabolomics and lipidomics, have potential in finding biomarkers related to thyroid carcinoma. Among the previous studies, the most important introduced altered tissue metabolites and lipids included glucose and galactose, lactate, Scyllo- and Myo inositol, hypoxanthine, citrate, cholesterol and choline.

Conclusion: Metabolomics methods have been widely used in the field of biomarker discovery in TC and attempts are still in progress to use these methods to find a reliable biomarker panel besides current diagnostic tools.     

Habitat preference of female Corncrakes Crex crex: implications for the conservation of breeding sites in a secretive species

Capsule: Forb-rich and diverse, annually mown vegetation is the preferred Corncrake Crex crex breeding habitat in floodplains.

Aims: To identify habitat preferences of female Corncrakes and characteristics of breeding sites in floodplain habitats and derive recommendations for management.

Methods: We tracked six female Corncrakes and compared vegetation characteristics at 78 male calling sites with regard to breeding records and diurnal call activity of males, because we expect the latter to indicate female occurrence. Additionally, we analysed how practice and timing of land use in the preceding year affected vegetation structure.

Results: Females preferred areas with high cover of forbs and a distinct relief heterogeneity, which was associated with overall vegetation diversity. All calling sites with breeding records and diurnal call incidence of males showed high forb and low sedge cover, low litter heights and a close location to ditches. Favourable conditions were best provided by mowing in the preceding year.

Conclusion: In eutrophic habitats, female Corncrakes preferred a vegetation structure created by annual mowing. Because nests and unfledged chicks are threatened by mowing operations, we recommend an alternating management regime based on the identification of breeding sites using male diurnal calling activity.     

Populations evolving towards failure: costs of adaptation under competition at the range edge of an invasive perennial plant

Background: Species undergoing range expansion adapt to novel and stressful environments at range fronts. These adaptations of the edge populations may incur fitness costs. These costs may play a crucial role in stopping range expansion before absolute physiological and evolutionary limits were reached. Costs however have proven to be elusive. These may be specifically expressed under competition.

Aims: Here, we assessed the costs of adaptation in range-edge populations of an invasive plant by evaluating plant responses under competition.

Methods: We grew plants from range-centre and edge populations under competition treatments in a glasshouse. We predicted that plants from the range-edge would express lower reproductive efficiency under competition compared with centre population plants, and this would indicate a potentially maladaptive response.

Results: Under high competition, plants from the range-edge expressed lower reproductive efficiency relative to range-centre plants which supported our prediction. In addition, they were more heavily affected by competition.

Conclusions: Adaptation to novel environments at the range-edge has incurred a cost as a potentially maladaptive response under competition, which may contribute to the formation of the range-edge. This finding suggests that these costs likely form part of the classic trade-offs involved with stress-tolerance and may have effects on range evolution.     

Beta-2-glycoprotein-1 and alpha-1-antitrypsin as urinary markers of renal cancer in von Hippel–Lindau patients

Context: Von Hippel–Lindau disease (VHLD) is a rare inherited neoplastic syndrome. Among all the VHLD-associated tumors, clear cell renal cell carcinoma (ccRCC) is the major cause of death.

Objective: The aim of this paper is the discovery of new non-invasive biomarker for the monitoring of VHLD patients.

Materials and methods: We compared the urinary proteome of VHLD patients, ccRCC patients and healthy volunteers.

Results: Among all differentially expressed proteins, alpha-1-antitrypsin (A1AT) and APOH (beta-2-glycoprotein-1) are strongly over-abundant only in the urine of VHLD patients with a history of ccRCC.

Discussion and conclusion: A1AT and APOH could be promising non-invasive biomarkers.     

Ecotoxicity evaluation of PFBSK for the whole environmental compartments and comprehensive comparison of hazard and risk to PFOS

A series of perfluorobutane sulfonate (PFBS)-related substances are produced as the alternatives to corresponding perfluorooctane sulfonate (PFOS). However, there is little reliable information about PFBS available for the whole ecotoxicology compartments. At present, its ecotoxicity of perfluorobutane sulfonate potassium (PFBSK) was selected as a typical PFBS chemical to investigate and evaluate its aquatic, terrestrial, microorganism and sediment toxicity according to the Organization for Economic Cooperation and Development (OECD) guideline under the framework of the REACH regulation. Meanwhile, the ecotoxicology hazard and risk for PFBSK and PFOS were compared comprehensively.

PFBSK did not show acute and chronic aquatic, microorganisms and terrestrial animal toxicity, while exhibited some terrestrial plants toxicity. The ecotoxicology of PFBSK decreased sharply except for terrestrial plants compared with PFOS. Especially, for acute and chronic aquatic ecotoxicity, PFBSK is lower than 100 times those of PFOS.

Although the similar terrestrial plants toxicity level was observed for PFBSK and PFOS, the lower risk of PFBSK was deduced for the reason that there was far less chances to be exposed and retained in the soil and sediment for its high water solubility and low adsorption.

In conclusion, PFBSK showed lower ecotoxicity hazard and risk than those of PFOS. PFBSK could be an environmental friendly alternative to PFOS.     

Novel ortho ester-based,pH-sensitive cationic lipid for gene delivery in vitro and in vivo

Context: Cationic lipoplexes are less toxic than viral gene vectors and more convenient to prepare but their efficiencies of gene delivery are generally lower.

Objective: To develop ortho ester-based, pH-sensitive lipoplexes for efficient gene delivery both in cultured cells and in vivo.

Materials and methods: A novel cationic and acid-labile lipid (DOC) containing a cationic headgroup and a cholesterol-derived lipid tail joined together by an acid-labile ortho ester linker was designed and synthesized. DOC was formulated into liposomes with the conical helper lipid DOPE, and then into lipoplexes with plasmid DNA encoding a luciferase reporter gene. The physicochemical properties of the lipoplexes (size, surface charge and pH-sensitivity) were characterized. Gene delivery by DOC/DOPE/DNA lipoplexes was also evaluated in CV-1 cells and in CD-1 mice following intratracheal injection. Lipoplexes consisting of the acid-stable cationic lipid DC-Chol were characterized as a control.

Results: DOC formed cationic lipoplexes with DOPE and DNA. After incubation at acidic pH 4.6, DOC/DOPE/DNA lipoplexes lost their positive charges and aggregated with one another as a result of DOC hydrolysis. Both in CV-1 cell culture and in CD-1 mice, DOC/DOPE/DNA lipoplexes increased the luciferase gene expression by 5- to 10-fold compared with the analogous but acid-stable DC-Chol/DOPE/DNA lipoplexes.

Discussion and conclusion: Incorporation of an acid-labile ortho ester linker into a cationic lipid is a viable approach to enhance gene delivery by the corresponding lipoplexes both in cultured cells and in vivo.     

Spatial patterns of species diversity in sand dune plant communities in Yucatan,Mexico: importance of invasive species for species dominance patterns

Background: Coastal ecosystems in Mexico remain understudied in spite of their ecological, economic and conservation value and are being impacted by human activities along the coast. Knowledge on spatial patterns of plant species distribution that helps preserve these fragile ecosystems is crucial.

Aims: We evaluated differences in species richness, species diversity and species dominance patterns in 16 plant communities as well as the degree to which differences were driven by climatic conditions in sandy dunes in Yucatán. We evaluated the importance of invasive species in mediating patterns of species diversity and species dominance patterns.

Results: We found wide variation in plant species richness, species diversity and species dominance patterns among communities that stems from broad climatic differences along dune systems. Invasive plants represent almost one-third of total species richness and seem to be drastically changing the species dominance patterns in these communities.

Conclusions: Regional climatic differences along the Yucatán north coast seems to be a major driver of plant diversity and species composition. Our findings suggest that invasive plants have successfully colonised and spread along the coast over the past 30 years. Even though invasive species do not alter spatial patterns of species diversity, they are becoming more dominant with potential detrimental consequences for native plants.     

Silencing of RB1 and RB2/P130 during adipogenesis of bone marrow stromal cells results in dysregulated differentiation

Bone marrow adipose tissue (BMAT) is different from fat found elsewhere in the body, and only recently have some of its functions been investigated. BMAT may regulate bone marrow stem cell niche and plays a role in energy storage and thermogenesis. BMAT may be involved also in obesity and osteoporosis onset. Given the paramount functions of BMAT, we decided to better clarify the human bone marrow adipogenesis by analyzing the role of the retinoblastoma gene family, which are key players in cell cycle regulation.

Our data provide evidence that the inactivation of RB1 or RB2/P130 in uncommitted bone marrow stromal cells (BMSC) facilitates the first steps of adipogenesis. In cultures with silenced RB1 or RB2/P130, we observed an increase of clones with adipogenic potential and a higher percentage of cells accumulating lipid droplets.

Nevertheless, the absence of RB1 or RB2/P130 impaired the terminal adipocyte differentiation and gave rise to dysregulated adipose cells, with alteration in lipid uptake and release. For the first time, we evidenced that RB2/P130 plays a role in bone marrow adipogenesis.

Our data suggest that while the inactivation of retinoblastoma proteins may delay the onset of last cell division and allow more BMSC to be committed to adipocyte, it did not allow a permanent cell cycle exit, which is a prerequisite for adipocyte terminal maturation.     

Predation on artificial and natural nests in the lowland rainforest of Papua New Guinea

Capsule: Although survival of nests was similar between forest fragments and continuous forest, the range of predators differed. Artificial nests provide an under-estimate of nest predation by snakes.

Aims: To estimate the natural nest predation rate in continuous primary forest, compare it with predation rates in forest fragments. To assess the reliability of nest survival rates determined by the use of artificial nests with clay eggs and identify the main nest predators.

Methods: We observed survival of natural nests during the incubation period in continuous primary forest in Papua New Guinea. Some nests were monitored with infrared cameras. We also used artificial nests deployed with clay eggs to identify predators.

Results: There was a predation rate of 50% for natural nests and snakes were major predators of nest contents. Clutch daily survival rates (DSRs) differed among nest types. The DSR of artificial nests (0.977) was not significantly different to that of natural cup nests (0.969). Survival rates of artificial nests were similar in forest fragments and continuous forest. Forest fragments had, however, a higher proportion of avian predators than continuous forest.

Conclusion: Although, we observed similar survival rates in artificial and natural nests, the composition of nest predators was different between natural and artificial nests. Artificial nests were not suitable for estimating the real predation caused by reptiles. Nevertheless, we find that participation of avian nest predators can be estimated correctly with the use of artificial nests.     

Assessment of genotoxicity in female agricultural workers exposed to pesticides

Objective: This study was designed to determine the genotoxic effect of exposure to a mixture of pesticides in 106 female agricultural workers employed in cotton fields from India.

Methods: Comet, micronucleus and chromosomal aberrations tests were carried out in peripheral blood lymphocytes. Micronucleus test was also performed in buccal epithelial cells. Levels of antioxidant enzymes, RBC acetylcholinesterase and hematological parameters were analyzed in the blood samples of the study subjects.

Results: The results indicated significant DNA damage, increased frequency of micronuclei and chromosomal aberrations in the exposed subjects (p?<?0.05). The levels of antioxidant enzymes were significantly lowered and the rate of lipid peroxidation was elevated in the exposed subjects.

Conclusion: The outcome of the study revealed an increased risk of genotoxicity and health implications in female agricultural workers.     

Evaluation of genetic diversity and population structure of Macqueen’s Bustard Chlamydotis macqueenii in Iran

Capsule: There is low genetic diversity in the Macqueen’s Bustard Chlamydotis macqueenii in Iran.

Aims: To investigate the genetic diversity and population structure of Macqueen’s Bustard in Iran, using two mitochondrial DNA loci.

Methods: Molecular diversity of the mitochondrial cytochrome oxidase c subunit I (COI) gene and part of the mitochondrial control region D-loop (in total 1183 base pairs) were analysed from 26 individual Macqueen’s Bustards from three regions of Iran.

Results: There was little variation in nucleotides and haplotypes in the populations for genes of both CR and COI. The population had free breeding and gene flow between the three study regions in Iran: Petregan, Ferdows and Yazd.

Conclusion: The use of molecular and genetic studies is essential to strengthen the protection of genetic diversity of the Macqueen’s Bustard.     

Nurses who work rotating shifts consume more energy,macronutrients and calcium when they work the night shift versus day shift

Background: Shift work has been associated with increased body mass index (BMI), metabolic disruption and increased chronic disease risk. Typically, these reports compare individuals who work the day shift to those who work the night shift. Because shift assignment is not random, differences may reflect other, unmeasured characteristics that account for outcome differences.

Objective: To compare dietary intake on days on which the participant worked the night shift to days on which she worked the day shift in a population of female nurses who work rotating shifts at a hospital.

Methods: This cross-sectional study recruited 132 female registered nurses who work rotating shifts in surgical or internal medicine departments. Dietary intake was ascertained using food diaries and analyzed on Tzameret Nutrition Analysis Software (Israel Ministry of Health). Demographic and anthropometric variables were also recorded.

Results: Compared to dietary intake on a day the nurse worked the day shift, intake of the following nutrients increased significantly on the day she worked the night shift: energy; protein; carbohydrates; total fat; saturated fat; and calcium.

Discussion: A significant increase in calorie, macronutrient and calcium intake on days the night shift was worked compared to days the day shift was worked among female nurses who work rotating shifts was demonstrated. These findings could be extended to other professionals who work rotating shifts, including physicians and allied healthcare personnel. It appears that the difference detected may be influenced by the food supplied by the hospital as well as by increased food intake in general.     

Limited dispersal and geographic barriers cause population differentiation and structuring in Begonia maxwelliana at both large and small scales

Background: Genetic divergence is one of the key processes in speciation. In the Begoniaceae, genetic divergence caused by limited gene flow may explain its high species diversity and endemicity. This hypothesis has been supported by past genetic work but there is a lack of empirical studies on the causes of limited gene flow.

Aim: To identify the causes of limited gene flow in Begonia.

Methods: We examined the genetic structure among the populations of Begonia maxwelliana at the macro- and micro-spatial scales using microsatellites, measured seed dispersal range and observed flowering phenology.

Results: Population differentiation and structuring were detected at both the macro- and micro-scales. Dispersal range was short, and all populations showed similar reproductive behaviour.

Conclusions: The strong population differentiation and structuring among the populations studied imply that they are evolutionarily significant units and possible candidates for speciation. Geographical barriers and limited seed dispersal restrict gene flow in the populations, and these factors may be responsible for the rapid speciation and large diversity in the family.     

Progress and prospects for the discovery of biomarkers for gastric cancer: a focus on proteomics

Introduction: Patient outcomes from gastric cancer vary due to the complexity of stomach carcinogenesis. Recent research using proteomic technologies has targeted components of all of these systems in order to develop biomarkers to aid the early diagnosis of gastric cancer and to assist in prognostic stratification.

Areas covered: This review is comprised of evidence obtained from literature searches from PubMed. It covers the evidence of diagnostic, prognostic, and predictive biomarkers for gastric cancer using proteomic technologies, and provides up-to-date references.

Expert commentary: The proteomic technologies have not only enabled the screening of a large number of samples, but also enabled the identification of diagnostic, prognostic and predictive biomarkers for gastric cancer. While major challenges still remain, to date, proteomic studies in gastric cancer have provided a wealth of information in revealing proteome alterations associated with the disease.     

Comparison of transient and asymptotic perturbation analyses of three epiphytic orchid species growing in coffee plantations in Mexico: effect on conservation decisions

Background: Epiphyte removal forms part of routine management in shade coffee plantations.

Aims: Assess the current status of three population orchids growing in Mexican shaded coffee plantations and evaluate the effect of perturbing the transient behaviour of different life stages.

Methods: We modelled the short-term response of eliminating I) non-reproductive juveniles, or II) reproductive adult plants from coffee bushes, on populations of Oncidium poikilostalix, Lepanthes acuminata and Telipogon helleri (Orchidaceae). First, we calculated the transient dynamics per se and second, we made a perturbation analysis on population inertia. Finally, we made a comparison with a traditional sensitivity analysis.

Results: All three species showed different positive asymptotic growth rate: O. poikilostalix (λmax = 1.106), L. acuminata (λmax = 1.209), and T. helleri (λmax = 1.012). The effect of eliminating the major part of the juvenile or adult orchids gave population inertia in relation to steady state, respectively, (+19%, -24%) for O. poikilostalix, (+17%, -28%) for T. helleri and (+57%, -35%) for L. acuminata.

Conclusions: Eliminating juveniles or adults affects in different ways the short-term dynamics due to differential impact on size stages that have the non-linear effects associated with important disturbances that currently affect orchids growing in coffee plantations.