X-ROS signaling: rapid mechano-chemo transduction in heart

A gestational vulnerability window for smoking exposure and the increased risk of preterm birth: how timing and intensity of maternal smoking matter

BACKGROUND

Reducing the incidence of preterm birth is a national priority. Maternal cigarette smoking is strongly and consistently associated with preterm birth. The objective of this study was to examine prenatal exposure based on combined measures of timing (by trimester) and intensity level (the number of cigarettes smoked per day) of maternal smoking to identify a pregnancy period with the highest risk of preterm birth.

METHODS

A sample of 2,485,743 singleton births was drawn from the 2010 National Center of Health Statistics (NCHS) linked birth/infant death file of US residents in 33 states that implemented the revised 2003 birth certificate. Nine mutually exclusive smoking status categories were created to assess prenatal exposure across pregnancy in association with preterm birth. Gestational age was based on the obstetric estimate. Multiple logistic regression analyses were conducted to compare the odds of preterm birth among women who smoked at different intensity levels in the second or third trimester with those who smoked only in the first trimester.

RESULTS

Overall, 7.95% of women had a preterm birth; 8.90% of low intensity (less than a pack/day) smokers in the first trimester only, 12.99% of low and 15.38% of high intensity (pack a day or more) smokers in the first two trimesters, and 10.56% of low and 11.35% of high intensity smokers in all three trimesters delivered preterm. First and second trimester high (aOR 1.85, 95% CI: 1.66, 2.06) and low intensity smokers (aOR 1.51, 95% CI: 1.41, 1.61) had higher odds of preterm birth compared to those who smoked less than a pack a day only in the first trimester, but the odds did not increase for all three trimester smokers relative to the first and second trimester smokers. In sensitivity analysis, adjustment for exposure misclassification error corrected data and testing for effect modification by maternal race/ethnicity found no significant interaction.

CONCLUSIONS

This study documented a biologically plausible vulnerability window for smoking exposure and the increased risk of preterm birth. For women who do not modify their smoking behavior preconception, preterm birth risk of smoking remains low until late in the first trimester.

Green sol-gel synthesis of novel nanoporous copper aluminosilicate for the eradication of pathogenic microbes in drinking water and wastewater treatment

We used a green sol-gel synthesis method to fabricate a novel nanoporous copper aluminosilicate (CAS) material. Nanoporous CAS was characterized using X-ray powder diffraction (XRD), field emission transmission and scanning electron microscopies (FE-TEM/FE-SEM), Fourier transform infrared (FTIR) spectroscopy, and optical analyses. The CAS was also evaluated for use as a promising disinfectant for the inactivation of waterborne pathogens. The antimicrobial action and minimum inhibitory concentration (MIC) of this CAS disinfectant were determined against eight microorganisms (Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, Listeria monocytogenes, Staphylococcus aureus, Enterococcus faecalis, Candida albicans, and Aspergillus niger). An antimicrobial susceptibility testing of CAS was measured. Results of disc diffusion method pointed out that the diameters of the zone using well diffusion were wider than disc diffusion methods, and the findings also showed that the MIC of the CAS disinfectant against E. coli, S. enterica, and P. aeruginosa was 100 mg/L within 20 min of contact time. Meanwhile, the MIC of the CAS disinfectant was 100 mg/L within 40 min of contact time for the other strains. The efficacy of antimicrobial action (100%) reached within 20 to 40 min against all tested microbes. Herein, the antimicrobial susceptibility testing of CAS disinfectant showed no toxicity for human and bacterial cells. It can be concluded that nanoporous CAS is a promising, economically, and worthy weapon for water disinfection.

More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics

Metaproteomics, the study of protein expression in microbial communities, is a versatile tool for environmental microbiology. Achieving sufficiently high metaproteome coverage to obtain a comprehensive picture of the activities and interactions in microbial communities is one of the current challenges in metaproteomics. An essential step to maximize the number of identified proteins is peptide separation via liquid chromatography (LC) prior to mass spectrometry (MS). Thorough optimization and comparison of LC methods for metaproteomics are, however, currently lacking. Here, we present an extensive development and test of different 1D and 2D-LC approaches for metaproteomic peptide separations. We used fully characterized mock community samples to evaluate metaproteomic approaches with very long analytical columns (50 and 75 cm) and long gradients (up to 12 h). We assessed a total of over 20 different 1D and 2D-LC approaches in terms of number of protein groups and unique peptides identified, peptide spectrum matches (PSMs) generated, the ability to detect proteins of low-abundance species, the effect of technical replicate runs on protein identifications and method reproducibility. We show here that, while 1D-LC approaches are faster and easier to set up and lead to more identifications per minute of runtime, 2D-LC approaches allow for a higher overall number of identifications with up to >10,000 protein groups identified. We also compared the 1D and 2D-LC approaches to a standard GeLC workflow, in which proteins are pre-fractionated via gel electrophoresis. This method yielded results comparable to the 2D-LC approaches, however with the drawback of a much increased sample preparation time. Based on our results, we provide recommendations on how to choose the best LC approach for metaproteomics experiments, depending on the study aims.

Genome-Wide Association Mapping of Grain Micronutrients Concentration in Aegilops tauschii

Bread wheat is an important and the most consumed cereal worldwide. However, people with predominantly cereal-based diets are increasingly affected by micronutrient deficiencies, suggesting the need for biofortified wheat varieties. The limited genetic diversity in hexaploid wheat warrants exploring the wider variation present in wheat wild relatives, among these Aegilops tauschii, the wild progenitor of the bread wheat D genome. In this study, a panel of 167 Ae. tauschii accessions was phenotyped for grain Fe, Zn, Cu, and Mn concentrations for 3 years and was found to have wide variation for these micronutrients. Comparisons between the two genetic subpopulations of Ae. tauschii revealed that lineage 2 had higher mean values for Fe and Cu concentration than lineage 1. To identify potentially new genetic sources for improving grain micronutrient concentration, we performed a genome-wide association study (GWAS) on 114 non-redundant Ae. tauschii accessions using 5,249 genotyping-by-sequencing (GBS) markers. Best linear unbiased predictor (BLUP) values were calculated for all traits across the three growing seasons. A total of 19 SNP marker trait associations (MTAs) were detected for all traits after applying Bonferroni corrected threshold of -log10(P-value) ≥ 4.68. These MTAs were found on all seven chromosomes. For grain Fe, Zn, Cu, and Mn concentrations, five, four, three, and seven significant associations were detected, respectively. The associations were linked to the genes encoding transcription factor regulators, transporters, and phytosiderophore synthesis. The results demonstrate the utility of GWAS for understanding the genetic architecture of micronutrient accumulation in Ae. tauschii, and further efforts to validate these loci will aid in using them to diversify the D-genome of hexaploid wheat.

Exploring the Intersection Between Violence Against Women and Children from the Perspective of Parents Convicted of Child Homicide

Violence against women and violence against children are distinct research fields. Quantitative studies have demonstrated their intersection, but qualitative data provides an opportunity for a comprehensive understanding of this interface. Interviews with 22 parents/caregivers convicted of child homicide provided an opportunity to explore the context of violent experiences in their lives including their use of violence and their experiences of it in their intimate and parenting relationships. Using a feminist framework, we found that patriarchal family structures, gender and power dynamics contribute to the use of violence. Revenge child homicide was common with distinct gendered differences. This study calls for closer collaboration between the two fields to assist in developing prevention interventions to address and eradicate both forms of violence.

Characterization and Mutational Analysis of a Monogalactosyldiacylglycerol Synthase Gene OsMGD2 in Rice

Monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) are the two predominant galactolipids present in the photosynthetic membrane in many photosynthetic organisms, including algae and higher plants. These galactolipids are the main constituents of thylakoid membrane and are essential for chloroplast biogenesis and photoautotrophic growth. In silico analysis revealed that rice (Oryza sativa L.) genome has three genes encoding MGDG synthase (OsMGD1, 2, and 3). Although subcellular localization analysis demonstrated that OsMGD2 is localized to chloroplast, its expression was observed mainly in anther and endosperm, suggesting that MGDG might have an important role in the development of flower and grain in rice. Knock-out mutants of OsMGD2 were generated employing the CRISPR/Cas9 system and their morphology, yield and grain quality related traits were studied. The leaf of osmgd2 mutants showed reduced MGDG (∼11.6%) and DGDG (∼9.5%) content with chlorophyll a content decreased by ∼23%, consequently affecting the photosynthesis. The mutants also exhibited poor agronomic performance with plant height and panicle length decreased by ∼12.2 and ∼7.3%, respectively. Similarly, the number of filled grains per panicle was reduced by 43.8%, while the 1000 grain weight was increased by ∼6.3% in the mutants. The milled rice of mutants also had altered pasting properties and decreased linoleic acid content (∼26.6%). Put together, the present study demonstrated that OsMGD2 is the predominantly expressed gene encoding MGDG synthase in anther and grain and plays important roles in plant growth and development, as well as in grain quality.

A Bioinformatics Approach to Explore MicroRNAs as Tools to Bridge Pathways Between Plants and Animals. Is DNA Damage Response (DDR) a Potential Target Process?

MicroRNAs, highly-conserved small RNAs, act as key regulators of many biological functions in both plants and animals by post-transcriptionally regulating gene expression through interactions with their target mRNAs. The microRNA research is a dynamic field, in which new and unconventional aspects are emerging alongside well-established roles in development and stress adaptation. A recent hypothesis states that miRNAs can be transferred from one species to another and potentially target genes across distant species. Here, we propose to look into the trans-kingdom potential of miRNAs as a tool to bridge conserved pathways between plant and human cells. To this aim, a novel multi-faceted bioinformatic analysis pipeline was developed, enabling the investigation of common biological processes and genes targeted in plant and human transcriptome by a set of publicly available Medicago truncatula miRNAs. Multiple datasets, including miRNA, gene, transcript and protein sequences, expression profiles and genetic interactions, were used. Three different strategies were employed, namely a network-based pipeline, an alignment-based pipeline, and a M. truncatula network reconstruction approach, to study functional modules and to evaluate gene/protein similarities among miRNA targets. The results were compared in order to find common features, e.g., microRNAs targeting similar processes. Biological processes like exocytosis and response to viruses were common denominators in the investigated species. Since the involvement of miRNAs in the regulation of DNA damage response (DDR)-associated pathways is barely explored, especially in the plant kingdom, a special attention is given to this aspect. Hereby, miRNAs predicted to target genes involved in DNA repair, recombination and replication, chromatin remodeling, cell cycle and cell death were identified in both plants and humans, paving the way for future interdisciplinary advancements.

Minor Effects of 11 Dof Family Genes Contribute to the Missing Heritability of Heading Date in Rice (Oryza sativa L.)

DNA binding with one finger (Dof) proteins are plant-specific transcription factors with important and diverse functions in seed germination, flowering time, and biotic and abiotic stresses. In this study, haplotype-based association analysis was conducted between heading date and 30 Dof family genes in a worldwide germplasm collection. Of these, 22 Dof genes were associated with heading date. Multiple comparisons among haplotypes revealed their diverse functions in promoting and suppressing heading date under short-day (SD) and long-day (LD) conditions. They cumulatively made a considerable contribution to the missing heritability of heading date. A set of knockout mutants of 30 Dof genes generated by CRISPR/Cas9-mediated genome editing technology showed that 11 and 9 Dof genes regulated heading date under LD and SD, respectively. Phenotype measurement of mutants showed that these 11 and 9 Dof genes slightly regulated heading with effects of 2-5 days under LD and SD, respectively. Both mutant and natural variation assays indicated functional redundancy in regulating heading date among Dof family genes. Nucleotide diversity analysis suggested that most Dof genes have been subjected to selection during domestication and improvement. Beyond heading date, this set of mutants is also a good resource for evaluating the function of Dof genes in regulating stress tolerance and seed germination.

Neuroendocrine Control of Sleep

Sleep is a phenomenon in animal behavior as enigmatic as it is ubiquitous, and one deeply tied to endocrine function. Though there are still many unanswered questions about the neurochemical basis of sleep and its functions, extensive interactions have been identified between sleep and the endocrine system, in both the endocrine system's effect on sleep and sleep's effect on the endocrine system. Unfortunately, until recent years, much research on sleep behavior largely disregarded its connections with the endocrine system. Use of both clinical studies and rodent models to investigate interactions between neuroendocrine function, including biological sex, and sleep therefore presents a promising area of further exploration. Further investigation of the neurobiological and neuroendocrine basis of sleep could have wide impact on a number of clinical and basic science fields. In this review, we summarize the state of basic sleep biology and its connections to the field of neuroendocrine biology, as well as suggest key future directions for the neuroendocrine regulation of sleep that may significantly impact new therapies for sleep disorders in women and men.

CACNA1C rs1006737, Threatening Life Events, and Gene-Environment Interaction Predict Major Depressive Disorder

INTRODUCTION

CACNA1C rs1006737 is a novel variant in discovery of replicable associations in major depressive disorder (MDD). However, there have been no specific studies considered effect of environmental pathogens to date examining its clinical significance. In this study we investigated the interaction effect between CACNA1C rs1006737 polymorphism and threatening life events (TLEs) in MDD and carried out a meta-analysis of published findings.

METHODS

A total of 1,177 consecutive participants were genotyped. Information on exposure to TLEs, socio-demographic data, and history of psychological problems among first-degree relatives was collected. MDD was diagnosed according to the Chinese version of the 24-item Hamilton Rating Scale for Depression.

RESULTS

There was a significant interaction effect between CACNA1C rs1006737 polymorphism and TLEs in MDD. A dose-response relationship was found between CACNA1C rs1006737 genotypes and TLEs in MDD. The results of the meta-analysis showed that CACNA1C rs1006737 genotypes interacted with TLEs in MDD.

CONCLUSION

CACNA1C rs1006737 genotype and previous exposure to TLEs interact to influence the risk of developing MDD. We propose that CACNA1C rs1006737 may represent a target for novel pharmacological therapies to prevent or treat MDD.

Interplay between correlations and Majorana mode in proximitized quantum dot

We study the low energy spectrum and transport properties of a correlated quantum dot coupled between normal and superconducting reservoirs and additionally hybridized with a topological superconducting nanowire, hosting the Majorana end-modes. In this setup the Majorana quasiparticle leaking into the quantum dot can be confronted simultaneously with the on-dot pairing and correlations. We study this interplay, focusing on the quantum phase transition from the spinless (BCS-type) to the spinful (singly occupied) configuration, where the subgap Kondo effect may arise. Using the selfconsistent perturbative treatment for correlations and the unbiased numerical renormalization group calculations we find that the Majorana mode has either constructive or destructive effect on the low-energy transport behavior of the quantum dot, depending on its spin. This spin-selective influence could be verified by means of the polarized STM spectroscopy.

Detection of Pesticide Residues in Selected Bee Products of Honeybees (Apis melllifera L.) Colonies in a Preliminary Study from Seychelles Archipelago

Pesticide residues in honey and pollen from Seychelles against a target of 108 pesticides using LC-MS/MS were analyzed. Fifteen pesticides were detected, at trace levels (< 15 ppb) and below the acceptable maximum residue limits (MRLs) as per EU regulations. In honey, six insecticide and three fungicide residues were detected. Eight insecticide and four fungicide residues were detected in the pollen matrix. The least contaminated honey and pollen samples had three and nine chemical residues respectively while the most contaminated honey and pollen samples had eight and eleven chemical residues respectively. Contact and oral LD₅₀ values were used to calculate Pollen Hazard Quotients (PHQ) = concentration in ppb ÷ LD₅₀ as µg/bee. The pollen hazard quotients (PHQ) obtained are way below those reported in literature. Residues were detected in low quantities, however, their high frequency and diversity and possible synergistic interactions may lead to negative impact on honeybees' health in Seychelles.

Myocardial reperfusion injury and oxidative stress: Therapeutic opportunities

Acute myocardial infarction (AMI) is the leading cause of death worldwide. Its associated mortality, morbidity and complications have significantly decreased with the development of interventional cardiology and percutaneous coronary angioplasty (PCA) treatment, which quickly and effectively restore the blood flow to the area previously subjected to ischemia. Paradoxically, the restoration of blood flow to the ischemic zone leads to a massive production of reactive oxygen species (ROS) which generate rapid and severe damage to biomolecules, generating a phenomenon called myocardial reperfusion injury (MRI). In the clinical setting, MRI is associated with multiple complications such as lethal reperfusion, no-reflow, myocardial stunning, and reperfusion arrhythmias. Despite significant advances in the understanding of the mechanisms accounting for the myocardial ischemia reperfusion injury, it remains an unsolved problem. Although promising results have been obtained in experimental studies (mainly in animal models), these benefits have not been translated into clinical settings. Thus, clinical trials have failed to find benefits from any therapy to prevent MRI. There is major evidence with respect to the contribution of oxidative stress to MRI in cardiovascular diseases. The lack of consistency between basic studies and clinical trials is not solely based on the diversity inherent in epidemiology but is also a result of the methodological weaknesses of some studies. It is quite possible that pharmacological issues, such as doses, active ingredients, bioavailability, routes of administration, co-therapies, startup time of the drug intervention, and its continuity may also have some responsibility for the lack of consistency between different studies. Furthermore, the administration of high ascorbate doses prior to reperfusion appears to be a safe and rational therapy against the development of oxidative damage associated with myocardial reperfusion. In addition, the association with N-acetylcysteine (a glutathione donor) and deferoxamine (an iron chelator) could improve the antioxidant cardioprotection by ascorbate, making it even more effective in preventing myocardial reperfusion damage associated with PCA following AMI.

Scarless genome editing: progress towards understanding genotype-phenotype relationships

The ability to predict phenotype from genotype has been an elusive goal for the biological sciences for several decades. Progress decoding genotype-phenotype relationships has been hampered by the challenge of introducing precise genetic changes to specific genomic locations. Here we provide a comparative review of the major techniques that have been historically used to make genetic changes in cells as well as the development of the CRISPR technology which enabled the ability to make marker-free disruptions in endogenous genomic locations. We also discuss how the achievement of truly scarless genome editing has required further adjustments of the original CRISPR method. We conclude by examining recently developed genome editing methods which are not reliant on the induction of a DNA double strand break and discuss the future of both genome engineering and the study of genotype-phenotype relationships.

Different Diversity and Distribution of Archaeal Community in the Aqueous and Oil Phases of Production Fluid From High-Temperature Petroleum Reservoirs

To get a better knowledge on how archaeal communities differ between the oil and aqueous phases and whether environmental factors promote substantial differences on microbial distributions among production wells, we analyzed archaeal communities in oil and aqueous phases from four high-temperature petroleum reservoirs (55–65°C) by using 16S rRNA gene based 454 pyrosequencing. Obvious dissimilarity of the archaeal composition between aqueous and oil phases in each independent production wells was observed, especially in production wells with higher water cut, and diversity in the oil phase was much higher than that in the corresponding aqueous phase. Statistical analysis further showed that archaeal communities in oil phases from different petroleum reservoirs tended to be more similar, but those in aqueous phases were the opposite. In the high-temperature ecosystems, temperature as an environmental factor could have significantly affected archaeal distribution, and archaeal diversity raised with the increase of temperature (p < 0.05). Our results suggest that to get a comprehensive understanding of petroleum reservoirs microbial information both in aqueous and oil phases should be taken into consideration. The microscopic habitats of oil phase, technically the dispersed minuscule water droplets in the oil could be a better habitat that containing the indigenous microorganisms.

Efficient Gene Transfer and Gene Editing in Sterlet (Acipenser ruthenus)

The sturgeon (Acipenseriformes) is an important farmed species because of its economical value. However, neither gene transfer nor gene editing techniques have been established in sturgeon for molecular breeding and gene functional study until now. In this study, we accomplished gene transfer and gene editing in sterlet (Acipenser ruthenus), which has the shortest sexual maturation period of sturgeons. The plasmid encoding enhanced green fluorescent protein (EGFP) was transferred into the embryos of sterlet at injection concentration of 100 ng/μL, under which condition high survival rate and gene transfer rate could be achieved. Subsequently, exogenous EGFP was efficiently disrupted by transcription activator-like effector nucleases (TALENs) or clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease/guide RNA (gRNA), with injection concentrations of 300 ng/μL TALENs, or 100 ng/μL Cas9 nuclease and 30 ng/μL gRNA, respectively, under which condition high survival rate and gene mutation rate could be achieved. Finally, the endogenous gene no tail in sterlet was successfully mutated by Cas9 nuclease/gRNA. We observed the CRISPR-induced no tail mutation, at a high efficiency with the mutant P0 embryos displaying the expected phenotype of bent spine and twisted tail.

Extracting Stage-Specific and Dynamic Modules Through Analyzing Multiple Networks Associated with Cancer Progression

Determining the dynamics of pathways associated with cancer progression is critical for understanding the etiology of diseases. Advances in biological technology have facilitated the simultaneous genomic profiling of multiple patients at different clinical stages, thus generating the dynamic genomic data for cancers. Such data provide enable investigation of the dynamics of related pathways. However, methods for integrative analysis of dynamic genomic data are inadequate. In this study, we develop a novel nonnegative matrix factorization algorithm for dynamic modules ( NMF-DM), which simultaneously analyzes multiple networks for the identification of stage-specific and dynamic modules. NMF-DM applies the temporal smoothness framework by balancing the networks at the current stage and the previous stage. Experimental results indicate that the NMF-DM algorithm is more accurate than the state-of-the-art methods in artificial dynamic networks. In breast cancer networks, NMF-DM reveals the dynamic modules that are important for cancer stage transitions. Furthermore, the stage-specific and dynamic modules have distinct topological and biochemical properties. Finally, we demonstrate that the stage-specific modules significantly improve the accuracy of cancer stage prediction. The proposed algorithm provides an effective way to explore the time-dependent cancer genomic data.

Innate Immune Mechanisms in Myocardial Infarction - An Update

Acute myocardial infarction (AMI) is a disease associated with high morbidity and mortality. Currently there are no available treatments specifically targeting the post-ischemic myocardial processes that lead to heart failure and recurrent coronary events. The innate immune system plays a central role in the two consecutive phases that follow an acute ischemic event: the inflammatory phase and the reparatory phase. The inflamatory phase involves a massive infiltration of neutrophils and inflammatory Ly6Chi monocytes into the injured myocardium. The reparatory phase is orchestrated by reparatory Ly6Clo macrophages that clear necrotic and apoptotic cells through efferocytosis, secrete anti-inflammatory mediators and stimulate fibrosis and repair. Important recent studies provided proof that Ly6Chi monocytes that enter the myocardium in the inflammatory phase upregulate the orphan nuclear receptor Nr4a1 and switch phenotype to Ly6CloNr4a1hi reparatory macrophages. Additionally, neutrophils have been shown to promote cardiac recovery by upregulating expression of the efferocytosis receptor MerTK on reparatory macrophages. A finely tuned balance between the inflammatory and the reparatory phases is thus essential for limiting myocardial damage and promoting efficient recovery. Treatment strategies targeting only the inflammatory phase have so far failed to improve prognosis in AMI patients. A detailed understanding of the interplay between the two phases of the innate immune response is paramount for designing efficient therapies able to improve post- AMI prognosis. In the current review, we summarize the state-of-the-art of the field and discuss previous therapeutic attempts and currently ongoing clinical trials targeting innate immune mechanisms in AMI patients.

Increased Frequency of Peripheral B and T Cells Expressing Granulocyte Monocyte Colony-Stimulating Factor in Rheumatoid Arthritis Patients

Objectives

Granulocyte monocyte colony-stimulating factor (GM-CSF) is currently considered a crucial inflammatory mediator and a novel therapeutic target in rheumatoid arthritis (RA), despite the fact that its precise cellular sources remain uncertain. We studied the expression of GM-CSF in peripheral lymphocytes from RA patients and its change with antirheumatic therapies.

Methods

Intracellular GM-CSF expression was assessed by flow cytometry in stimulated peripheral B (CD19+) and T (CD3+) cells from RA patients (n = 40), disease (n = 31 including osteoarthritis n = 15, psoriatic arthritis n = 10, and systemic rheumatic diseases n = 6) and healthy (n = 16) controls. The phenotype of GM-CSF+ B cells was assessed as well as longitudinal changes in GM-CSF+ lymphocytes during methotrexate (MTX, n = 10) or anti-tumor necrosis factor (anti-TNF, n = 10) therapy.

Results

Among untreated RA patients with active disease (Disease Activity Score 28-C-reactive protein = 5.6 ± 0.89) an expanded population of peripheral GM-CSF+ B (4.1 ± 2.2%) and T (3.4 ± 1.6%) cells was detected compared with both disease (1.7 ± 0.9%, p < 0.0001 and 1.7 ± 1.3%, p < 0.0001, respectively) and healthy (0.3 ± 0.2%, p < 0.0001 and 0.6 ± 0.6%, p < 0.0001) controls. RA GM-CSF+ B cells displayed more commonly a plasmablast or transitional phenotype (37.12 ± 18.34% vs. 14.26 ± 9.46%, p = 0.001 and 30.49 ± 15.04% vs. 2.45 ± 1.84%, p < 0.0001, respectively) and less a memory phenotype (21.46 ± 20.71% vs. 66.99 ± 16.63%, p < 0.0001) compared to GM-CSF- cells. GM-CSF expression in RA patients did not correlate to disease duration, activity or serological status. Anti-TNF treatment led to a statistically significant decrease in GM-CSF+ B and T cells while MTX had no significant effect.

Discussion

This is the first study showing an expanded population of GM-CSF+ B and T lymphocytes in patients with active RA which declined after anti-TNF therapy.

Genome Editing in Rice: Recent Advances, Challenges, and Future Implications

Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.

Genome Editing in Rice: Recent Advances, Challenges, and Future Implications

Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.

microRNAs and Their Targets in Apple (Malus domestica cv. "Fuji") Involved in Response to Infection of Pathogen Valsa mali

miRNAs are important regulators involving in plant-pathogen interactions. However, their roles in apple tree response to Valsa canker pathogen (Valsa mali, Vm) infection were poorly understood. In this study, we constructed two miRNA libraries using the twig bark tissues of apple tree (Malus domestica Borkh. cv. "Fuji") inoculated with Vm (IVm) and PDA medium (control, BMd). Among all detected miRNAs, 23 miRNAs were specifically isolated from BMd and 39 miRNAs were specifically isolated from IVm. Meanwhile, the expression of 294 miRNAs decreased; and another 172 miRNAs showed an increased expression trend in IVm compared with that in BMd. Furthermore, two degradome sequencing libraries were also constructed to identify the target genes of these miRNAs. In total, 353 differentially expressed miRNAs between IVm and BMd were detected to be able to target 1,077 unigenes with 2,251 cleavage sites. Based on GO and KEGG analysis, these genes were found to be mainly related to transcription regulation and signal transduction. In addition, we selected 17 miRNAs and 22 corresponding target genes to screen the expression profiles when apple twigs were infected by Vm. The expression trends of most miRNAs/target genes were consist with the results of deep sequencing. Many of them may involve in the apple twig-Vm interaction by inducing/reducing their expression. What's more, miRNAs and their target genes regulate the apple twig-Vm interaction by forming many complicated regulation networks rather than one to one model. It is worth that a conserved miRNAs mdm-miR482b, which was down regulated in IVm compared with BMd, has 14 potential target genes, most of which are disease resistance related genes. This indicates that mdm-miR482b may play important roles in apple twig response to Vm. More important, the feedback regulation of sRNA pathway in apple twig is also very complex, and play critical role in the interaction between apple twig and Vm based on the results of expression analysis. In all, the results will provide insights into the crucial functions of miRNAs in the woody plant, apple tree-Vm interaction.

The Association Between Patient-Reported and Objective Oral Anticancer Medication Adherence Measures: A Systematic Review

PROBLEM IDENTIFICATION

Oral anticancer medication (OAM) use has been steadily increasing, leading to several patient benefits. A notable challenge for nurses is accurate monitoring of patient OAM regimens because nonadherence is associated with poor health outcomes and decreased survival. Currently, no gold standard measure of OAM adherence exists. The authors conducted a systematic review of the association between objective and patient-reported measures of OAM adherence.
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LITERATURE SEARCH

A systematic electronic literature search was conducted using PubMed, EMBASE, Scopus, PsycINFO®, Cochrane Library, Web of Science, and CINAHL® databases through November 2014. 
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DATA EVALUATION

Articles were independently reviewed to determine whether they included an original characterization of the level of association between objective and patient-reported measures of OAM adherence.
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SYNTHESIS

From a total of 11,135 articles retrieved, eight studies met inclusion criteria. Objective adherence was primarily assessed using pill counts or Medication Event Monitoring System (MEMSCap™). Patient-reported adherence was most commonly assessed using study-specific questionnaires. Significant positive correlations were observed between objective and patient-reported adherence across most studies, with three studies reporting higher rates of adherence via patient reporting.
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CONCLUSIONS

Despite variation in the OAMs and measures used, patient-reported adherence rates were equal to or higher than objective adherence measures across studies. Social desirability bias may be a concern; however, given the significant concordance observed, using patient-reported methods in future studies of OAM adherence may be justified. 
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IMPLICATIONS FOR NURSING

This review provides evidence to support nursing use of patient-reported measures to accurately monitor OAM adherence and potentially improve the quality of patient-provider communication.

[Mitochondrial DNA diversity in prehispanic bone remains on the eastern Colombian Andes]

INTRODUCTION

DNA extracted from ancient human bones allows to analyze the genetic makeup of pre-Columbian populations and to determine the dynamics that gave rise to the diversity of contemporary populations.

OBJECTIVE

To determine the genetic diversity of skeletal remains associated with the Templo del Sol (Sun Temple) and their relationship with other contemporary and ancient communities of America.

MATERIALS AND METHODS

We analyzed 13 individuals belonging to the pre-Columbian Muisca Period (IX-XVI centuries AD) from the vicinities of the Templo del Sol (Sun Temple) (Sogamoso, Boyacá) in the eastern Colombian Andes. Mitochondrial DNA was amplified and RFLPs were performed in order to type the four traditional Amerindian haplogroups (A, B, C and D). In addition, autosomal markers including amelogenin and Y-chromosome STRs were amplified.

RESULTS

Among the observed mitochondrial lineages, haplogroup A was the most frequent, followed by haplogroups B and C; no evidence of haplogroup D was found. The genetic variation analysis indicated a similar diversity of pre-ColumbianMuiscas to that of contemporary populations belonging to the Chibcha linguistic family from Colombia and Central America. Molecular sexing was accomplished and it was compared to osteological data. With only one exception, anthropological and molecular data were consistent.

CONCLUSIONS

Our results contribute new genetic elements supporting the hypothesis of Central American origin of the Chibcha groups of the Cundiboyacense plateau, and allowed sex typing and kinship evaluations.

Anti-obesity effect of a traditional Chinese dietary habit-blending lard with vegetable oil while cooking

Obesity, which is associated with dietary habits, has become a global social problem and causes many metabolic diseases. In China, both percentages of adult obesity and overweight are far lower compared to western countries. It was designed to increase the two levels of daily intake in human, namely 3.8% and 6.5%, which are recommendatory intake (25 g/d) and Chinese citizens' practical intake (41.4 g/d), respectively. The mice were respectively fed with feeds added with soybean oil, lard or the oil blended by both for 12 weeks. In the mice fed with diet containing 3.8% of the three oils or 6.5% blended oil, their body weight, body fat rate, cross-sectional area of adipocytes, adipogenesis and lipogenesis in adipose were decreased, whereas hydrolysis of triglyserides in adipose was increased. This study demonstrated that the oil mixture containing lard and soybean oil had a remarkable anti-obesity effect. It suggests that the traditional Chinese dietary habits using oils blended with lard and soybean oil, might be one of the factors of lower percentages of overweight and obesity in China, and that the increasing of dietary oil intake and the changing of its component resulted in the increasing of obesity rate in China over the past decades.

Health Benefits of Fasting and Caloric Restriction

PURPOSE OF REVIEW

Obesity and obesity-related diseases, largely resulting from urbanization and behavioral changes, are now of global importance. Energy restriction, though, is associated with health improvements and increased longevity. We review some important mechanisms related to calorie limitation aimed at controlling of metabolic diseases, particularly diabetes.

RECENT FINDINGS

Calorie restriction triggers a complex series of intricate events, including activation of cellular stress response elements, improved autophagy, modification of apoptosis, and alteration in hormonal balance. Intermittent fasting is not only more acceptable to patients, but it also prevents some of the adverse effects of chronic calorie restriction, especially malnutrition. There are many somatic and potentially psychologic benefits of fasting or intermittent calorie restriction. However, some behavioral modifications related to abstinence of binge eating following a fasting period are crucial in maintaining the desired favorable outcomes.

Nerve Decompression Improves Spinal Synaptic Plasticity of Opioid Receptors for Pain Relief

Nerve decompression is an essential therapeutic strategy for pain relief clinically; however, its potential mechanism remains poorly understood. Opioid analgesics acting on opioid receptors (OR) within the various regions of the nervous system have been used widely for pain management. We therefore hypothesized that nerve decompression in a neuropathic pain model of chronic constriction injury (CCI) improves the synaptic OR plasticity in the dorsal horn, which is in response to alleviate pain hypersensitivity. After CCI, the Sprague-Dawley rats were assigned into Decompression group, in which the ligatures around the sciatic nerve were removed at post-operative week 4 (POW 4), and a CCI group, in which the ligatures remained. Pain hypersensitivity, including thermal hyperalgesia and mechanical allodynia, was entirely normalized in Decompression group within the following 4 weeks. Substantial reversal of mu- and delta-OR immunoreactive (IR) expressions in Decompression group was detected in primary afferent terminals in the dorsal horn. In Decompression group, mu-OR antagonist (CTOP, D-Phe-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH2 [Disulfide Bridge: 2-7]) and delta-OR antagonist (NTI, 17-(cyclopropylmethyl)-6,7-dehydro-4,5α-epoxy-3,14-dihydroxy-6,7-2',3'-indolomorphinan hydrochloride) re-induced pain hypersensitivity by intrathecal administration in a dose-responsive manner. Additionally, mu-OR agonist (DAMGO, [D-Ala2, NMe-Phe4, Gly-ol5]-enkephalin) and delta-OR agonist (SNC80, ((+)-4-[(αR)-α-((2S,5R)-4-allyl-2,5-dimethyl-1-piperazinyl)-3-methoxybenzyl]-N,N-diethyl-benzamide) were administrated intrathecally to attenuating CCI-induced chronic and acute pain hypersensitivity dose-dependently. Our current results strongly suggested that nerve decompression provides the opportunity for improving the synaptic OR plasticity in the dorsal horn and pharmacological blockade presents a novel insight into the therapeutic strategy for pain hypersensitivity.

Transcriptional control of microglia phenotypes in health and disease

Microglia are the main resident macrophage population of the CNS and perform numerous functions required for CNS development, homeostasis, immunity, and repair. Many lines of evidence also indicate that dysregulation of microglia contributes to the pathogenesis of neurodegenerative and behavioral diseases. These observations provide a compelling argument to more clearly define the mechanisms that control microglia identity and function in health and disease. In this Review, we present a conceptual framework for how different classes of transcription factors interact to select and activate regulatory elements that control microglia development and their responses to internal and external signals. We then describe functions of specific transcription factors in normal and pathological contexts and conclude with a consideration of open questions to be addressed in the future.

Longitudinal associations between perceived age discrimination and subjective well-being: variations by age and subjective life expectancy

OBJECTIVES

Perceived age discrimination can have negative effects on one's subjective well-being (SWB). The response to age discrimination might differ based on age, and based on perceived longevity, or subjective life expectancy (SLE). These differential effects have not yet been prospectively examined within adult life span samples.

METHOD

We examined the association between perceived age discrimination at baseline (T1) and SWB at follow-up (T2), and the moderation effect of SLE. We compared differences in these effects between middle-aged and older adults. Analyses were based on participants who took part in the 2008 (T1) and 2011 (T2) assessments of the German Ageing Survey (DEAS; listwise N = 1534), a population-based representative sample of the German adult population. Participants were categorized as middle-aged (ages 40-64; n = 919) or older adults (ages 65-93; n = 615).

RESULTS

Regression analyses indicated that T1 perceived age discrimination significantly predicts lower T2 SWB among middle-aged, but not among older adults, after adjusting for covariates and T1 SWB. There is a significant interaction between age discrimination and SLE for predicting SWB, only among middle-aged participants, suggesting that age discrimination predicts decreases in SWB for those reporting higher, but not lower levels of SLE.

CONCLUSION

People in the transition from midlife to old age, who hold higher SLE, appear to be more vulnerable to age discrimination. This may be due to the experience of age discrimination as an 'off-time', or unexpected event for those in midlife who have a higher expectation to live longer.

Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data

BACKGROUND

The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function.

RESULTS

We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic.

CONCLUSION

Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .

Host-Parasite Interactions in Human Malaria: Clinical Implications of Basic Research

The malaria parasite, Plasmodium, is one of the oldest parasites documented to infect humans and has proven particularly hard to eradicate. One of the major hurdles in designing an effective subunit vaccine against the malaria parasite is the insufficient understanding of host–parasite interactions within the human host during infections. The success of the parasite lies in its ability to evade the human immune system and recruit host responses as physiological cues to regulate its life cycle, leading to rapid acclimatization of the parasite to its immediate host environment. Hence understanding the environmental niche of the parasite is crucial in developing strategies to combat this deadly infectious disease. It has been increasingly recognized that interactions between parasite proteins and host factors are essential to establishing infection and virulence at every stage of the parasite life cycle. This review reassesses all of these interactions and discusses their clinical importance in designing therapeutic approaches such as design of novel vaccines. The interactions have been followed from the initial stages of introduction of the parasite under the human dermis until asexual and sexual blood stages which are essential for transmission of malaria. We further classify the interactions as “direct” or “indirect” depending upon their demonstrated ability to mediate direct physical interactions of the parasite with host factors or their indirect manipulation of the host immune system since both forms of interactions are known to have a crucial role during infections. We also discuss the many ways in which this understanding has been taken to the field and the success of these strategies in controlling human malaria.

Identification of an immunogenic neo-epitope encoded by mouse sarcoma using CXCR3 ligand mRNAs as sensors

The CXCR3 ligands CXCL9, 10, and 11 play critical roles in the amplification of immune responses by recruiting CXCR3⁺ immune effector cells to the tumor site. Taking advantage of this property of CXCR3 ligands, we aimed to establish a novel approach to identify immunogenic mutated-antigens. We examined the feasibility of using CXCR3 ligand mRNAs as sensors for detection of specific immune responses in human and murine systems. We further investigated whether this approach is applicable for the identification of immunogenic mutated-antigens by using murine sarcoma lines. Rapid synthesis of CXCR3 ligand mRNAs occurred shortly after specific immune responses in both human and murine immune systems. Particularly, in CMS5 tumor-bearing mice, we detected specific immune responses to mutated mitogen-activated protein kinase 2 (ERK2), which has previously been identified as an immunogenic mutated-antigen. Furthermore, by combining this approach with whole-exome and transcriptome sequencing analyses, we identified an immunogenic neo-epitope derived from mutated staphylococcal nuclease domain-containing protein 1 (Snd1) in CMS7 tumor-bearing mice. Most importantly, we successfully detected the specific immune response to this neo-epitope even without co-administration of anti-cytotoxic T-lymphocyte protein-4 (CTLA-4), anti-programmed cell death-1 (PD-1) and anti-glucocorticoid-induced TNFR-related protein (GITR) antibodies, which vigorously augmented the immune response and consequently enabled us to detect the specific immune response to this neo-epitope by conventional IFNγ intracellular staining method. Our data indicate the potential usefulness of this strategy for the identification of immunogenic mutated-antigens. We propose that this approach would be of great help for the development of personalized cancer vaccine therapies in future.

Prospects of metformin in the treatment of endometriosis

According to recent year studies, the classical biguanide metformin has antiproliferative, proapoptotic and anti-inflammatory effects in addition to the main hypoglycemic effect. There are clinical and experimental studies these effects in the therapy of oncological and benign hyperplastic diseases. There is no data about the clinical efficacy of metformin in the therapy of endometriosis in the domestic literature, and there were a few studies in foreign sources. There was a decrease in the severity of the pain syndrome and an increase of pregnancy rate in two clinical studies with small samples. However, future studies are needed to investigate the mechanisms of the target drug effect and to develop effective regimens for the treatment of endometriosis.

Dawn arrives at Ceres: Exploration of a small, volatile-rich world

On 6 March 2015, Dawn arrived at Ceres to find a dark, desiccated surface punctuated by small, bright areas. Parts of Ceres' surface are heavily cratered, but the largest expected craters are absent. Ceres appears gravitationally relaxed at only the longest wavelengths, implying a mechanically strong lithosphere with a weaker deep interior. Ceres' dry exterior displays hydroxylated silicates, including ammoniated clays of endogenous origin. The possibility of abundant volatiles at depth is supported by geomorphologic features such as flat crater floors with pits, lobate flows of materials, and a singular mountain that appears to be an extrusive cryovolcanic dome. On one occasion, Ceres temporarily interacted with the solar wind, producing a bow shock accelerating electrons to energies of tens of kilovolts.

Metaresearch for Evaluating Reproducibility in Ecology and Evolution

Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of "positive" or "significant" results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish-or-perish research culture that encourages questionable research practices. We argue that these conditions constitute sufficient reason to systematically evaluate the reproducibility of the evidence base in ecology and evolution. In some cases, the direct replication of ecological research is difficult because of strong temporal and spatial dependencies, so here, we propose metaresearch projects that will provide proxy measures of reproducibility.

CRP1 Protein: (dis)similarities between Arabidopsis thaliana and Zea mays

Biogenesis of chloroplasts in higher plants is initiated from proplastids, and involves a series of processes by which a plastid able to perform photosynthesis, to synthesize amino acids, lipids, and phytohormones is formed. All plastid protein complexes are composed of subunits encoded by the nucleus and chloroplast genomes, which require a coordinated gene expression to produce the correct concentrations of organellar proteins and to maintain organelle function. To achieve this, hundreds of nucleus-encoded factors are imported into the chloroplast to control plastid gene expression. Among these factors, members of the Pentatricopeptide Repeat (PPR) containing protein family have emerged as key regulators of the organellar post-transcriptional processing. PPR proteins represent a large family in plants, and the extent to which PPR functions are conserved between dicots and monocots deserves evaluation, in light of differences in photosynthetic metabolism (C3 vs. C4) and localization of chloroplast biogenesis (mesophyll vs. bundle sheath cells). In this work we investigated the role played in the process of chloroplast biogenesis by At5g42310, a member of the Arabidopsis PPR family which we here refer to as AtCRP1 (Chloroplast RNA Processing 1), providing a comparison with the orthologous ZmCRP1 protein from Zea mays. Loss-of-function atcrp1 mutants are characterized by yellow-albinotic cotyledons and leaves owing to defects in the accumulation of subunits of the thylakoid protein complexes. As in the case of ZmCRP1, AtCRP1 associates with the 5' UTRs of both psaC and, albeit very weakly, petA transcripts, indicating that the role of CRP1 as regulator of chloroplast protein synthesis has been conserved between maize and Arabidopsis. AtCRP1 also interacts with the petB-petD intergenic region and is required for the generation of petB and petD monocistronic RNAs. A similar role has been also attributed to ZmCRP1, although the direct interaction of ZmCRP1 with the petB-petD intergenic region has never been reported, which could indicate that AtCRP1 and ZmCRP1 differ, in part, in their plastid RNA targets.

Drosophila microRNA-34 Impairs Axon Pruning of Mushroom Body γ Neurons by Downregulating the Expression of Ecdysone Receptor

MicroRNA-34 (miR-34) is crucial for preventing chronic large-scale neurite degeneration in the aged brain of Drosophila melanogaster. Here we investigated the role of miR-34 in two other types of large-scale axon degeneration in Drosophila: axotomy-induced axon degeneration in olfactory sensory neurons (OSNs) and developmentally related axon pruning in mushroom body (MB) neurons. Ectopically overexpressed miR-34 did not inhibit axon degeneration in OSNs following axotomy, whereas ectopically overexpressed miR-34 in differentiated MB neurons impaired γ axon pruning. Intriguingly, the miR-34-induced γ axon pruning defect resulted from downregulating the expression of ecdysone receptor B1 (EcR-B1) in differentiated MB γ neurons. Notably, the separate overexpression of EcR-B1 or a transforming growth factor- β receptor Baboon, whose activation can upregulate the EcR-B1 expression, in MB neurons rescued the miR-34-induced γ axon pruning phenotype. Future investigations of miR-34 targets that regulate the expression of EcR-B1 in MB γ neurons are warranted to elucidate pathways that regulate axon pruning, and to provide insight into mechanisms that control large-scale axon degeneration in the nervous system.

Targeting Non-classical Myelin Epitopes to Treat Experimental Autoimmune Encephalomyelitis

Qa-1 epitopes, the peptides that bind to non-classical major histocompatibility complex Ib Qa-1 molecules and are recognized by Qa-1-restricted CD8+ regulatory T (Treg) cells, have been identified in pathogenic autoimmune cells that attack myelin sheath in experimental autoimmune encephalomyelitis (EAE, an animal model for multiple sclerosis [MS]). Additionally, immunization with such epitopes ameliorates the EAE. However, identification of such epitopes requires knowledge of the pathogenic autoimmune cells which are largely unknown in MS patients. Hence, we asked whether the CD8+ Treg cells could directly target the myelin sheath to ameliorate EAE. To address this question, we analyzed Qa-1 epitopes in myelin oligodendrocyte glycoprotein (MOG that is a protein in myelin sheath). Here, we report identification of a MOG-specific Qa-1 epitope. Immunization with this epitope suppressed ongoing EAE, which was abrogated by CD8+ T cell depletion. Additionally, the epitope immunization activated the epitope-specific CD8+ T cells which specifically accumulated in the CNS-draining cervical lymph nodes. Finally, CD8+ T cells primed by the epitope immunization transferred EAE suppression. Hence, this study reveals a novel regulatory mechanism mediated by the CD8+ Treg cells. We propose that immunization with myelin-specific HLA-E epitopes (human homologues of Qa-1 epitopes) is a promising therapy for MS.

[Real-time quantification to analyze historical Colombian samples detecting a short fragment of hypervariable region II of mitochondrial DNA]

INTRODUCTION

Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples. Materials and methods: The proposed method is based on the use of mini-primers for the specific amplification of short fragments of mitochondrial DNA. The subsequent purification of these amplified fragments allows a standard curve to be constructed with concentrations in accordance to the state of degradation of the samples. Results: The proposed method successfully detected DNA from ancient samples including bone remains and mummified tissue. DNA inhibitory substances were also detected. Conclusion: The proposed method represents a simpler and cost-effective way to detect low amounts of aDNA, and a tool to differentiate DNA-free samples from samples with inhibitory substances.

Supercritical Carbon Dioxide Extraction of Coronene in the Presence of Perchlorate for In Situ Chemical Analysis of Martian Regolith

The analysis of the organic compounds present in the martian regolith is essential for understanding the history and habitability of Mars, as well as studying the signs of possible extant or extinct life. To date, pyrolysis, the only technique that has been used to extract organic compounds from the martian regolith, has not enabled the detection of unaltered native martian organics. The elevated temperatures required for pyrolysis extraction can cause native martian organics to react with perchlorate salts in the regolith and possibly result in the chlorohydrocarbons that have been detected by in situ instruments. Supercritical carbon dioxide (SCCO2) extraction is an alternative to pyrolysis that may be capable of delivering unaltered native organic species to an in situ detector. In this study, we report the SCCO2 extraction of unaltered coronene, a representative polycyclic aromatic hydrocarbon (PAH), from martian regolith simulants, in the presence of 3 parts per thousand (ppth) sodium perchlorate. PAHs are a class of nonpolar molecules of astrobiological interest and are delivered to the martian surface by meteoritic infall. We also determined that the extraction efficiency of coronene was unaffected by the presence of perchlorate on the regolith simulant, and that no sodium perchlorate was extracted by SCCO2. This indicates that SCCO2 extraction can provide de-salted samples that could be directly delivered to a variety of in situ detectors. SCCO2 was also used to extract trace native fluorescent organic compounds from the martian regolith simulant JSC Mars-1, providing further evidence that SCCO2 extraction may provide an alternative to pyrolysis to enable the delivery of unaltered native organic compounds to an in situ detector on a future Mars rover.

KEY WORDS

Biomarkers-Carbon dioxide-In situ measurement-Mars-Search for Mars' organics. Astrobiology 16, 703-714.

The early events underlying genome evolution in a localized Sinorhizobium meliloti population

BACKGROUND

Population genetic analyses based on genome-wide sequencing data have been carried out for Sinorhizobium medicae and S. meliloti, two closely related bacterial species forming nitrogen-fixing symbioses with plants of the genus Medicago. However, genome coverage was low or the isolates had a broad geographic distribution, making it difficult to interpret the estimated diversity and to unravel the early events underlying population genetic variations and ecological differentiation.

RESULTS

Here, to gain insight into the early genome level variation and diversification within S. meliloti populations, we first used Illumina paired-end reads technology to sequence a new clone of S. meliloti strain GR4, a highly competitive strain for alfalfa nodulation. The Illumina data and the GR4 genome sequence previously obtained with 454 technology were used to generate a high-quality reference genome sequence. We then used Illumina technology to sequence the genomes of 13 S. meliloti isolates representative of the genomic variation within the GR4-type population, obtained from a single field site with a high degree of coverage. The genome sequences obtained were analyzed to determine nucleotide diversity, divergence times, polymorphism and genomic variation. Similar low levels of nucleotide diversity were observed for the chromosome, pSymB and pSymA replicons. The isolates displayed other types of variation, such as indels, recombination events, genomic island excision and the transposition of mobile elements.

CONCLUSIONS

Our results suggest that the GR4-type population has experienced a process of demographic expansion and behaves as a stable genotypic cluster of genome-wide similarity, with most of the genome following a clonal pattern of evolution. Although some of genetic variation detected within the GR4-type population is probably due to genetic drift, others might be important in diversification and environmental adaptation.

Dynamic role and importance of surrogate species for assessing potential adverse environmental impacts of genetically engineered insect-resistant plants on non-target organisms

Surrogate species have a long history of use in research and regulatory settings to understand the potentially harmful effects of toxic substances including pesticides. More recently, surrogate species have been used to evaluate the potential effects of proteins contained in genetically engineered insect resistant (GEIR) crops. Species commonly used in GEIR crop testing include beneficial organisms such as honeybees, arthropod predators, and parasitoids. The choice of appropriate surrogates is influenced by scientific factors such as the knowledge of the mode of action and the spectrum of activity as well as societal factors such as protection goals that assign value to certain ecosystem services such as pollination or pest control. The primary reasons for using surrogates include the inability to test all possible organisms, the restrictions on using certain organisms in testing (e.g., rare, threatened, or endangered species), and the ability to achieve greater sensitivity and statistical power by using laboratory testing of certain species. The acceptance of surrogate species data can allow results from one region to be applied or "transported" for use in another region. On the basis of over a decade of using surrogate species to evaluate potential effects of GEIR crops, it appears that the current surrogates have worked well to predict effects of GEIR crops that have been developed (Carstens et al. GM Crops Food 5:1-5, 2014), and it is expected that they should work well to predict effects of future GEIR crops based on similar technologies.