Immune tolerance: Are regulatory T cell subsets needed to explain suppression of autoimmunity?

The potential for self-reactive T cells to cause autoimmune disease is held in check by Foxp3(+) regulatory T cells (Tregs), essential mediators of peripheral immunological tolerance. Tregs have the capacity to suppress multiple branches of the immune system, tightly controlling the different subsets of effector T cells across multiple different tissue environments. Recent genetic experiments have found mutations that disrupt specific Treg: effector T cell relationships, leading to the possibility that subsets of Tregs are required to suppress each subset of effector T cells. Here we review the environmental factors and mechanisms that allow Tregs to suppress specific subsets of effector T cells, and find that a parsimonious explanation of the genetic data can be made without invoking Treg subsets. Instead, Tregs show a functional and chemotactic plasticity based on microenvironmental influences that allows the common pool of cells to suppress multiple distinct immune responses.     

Targeted polyubiquitylation of RASSF1C by the Mule and SCFβ-TrCP ligases in response to DNA damage

RASSF1A [Ras association (RalGDS/AF-6) domain family member 1A] and RASSF1C are two ubiquitously expressed isoforms of the RASSF1 gene. The promoter of RASSF1A is frequently hypermethylated, resulting in inactivation in various human cancers. RASSF1A is implicated in the regulation of apoptosis, microtubule stability and cell cycle arrest. However, little is known about the regulation and function of RASSF1C. In the present study we show that exogenously expressed RASSF1C is a very unstable protein that is highly polyubiquitylated and degraded via the proteasome. Furthermore, RASSF1C degradation is enhanced when cells are exposed to stress signals, such as UV irradiation. Mule, a HECT (homologous with E6-associated protein C-terminus) family E3 ligase, but not SCFβ-TrCP [where SCF is Skp1 (S-phase kinase-associated protein 1)/cullin/F-box and β-TrCP is β-bransducin repeat-containing protein] or CUL4 (cullin 4)-DDB1 (damage-specific DNA-binding protein 1), is the E3 ligase for RASSF1C under normal conditions, whereas both Mule and SCFβ-TrCP target RASSF1C degradation in response to UV irradiation. GSK3 (glycogen synthase kinase 3) phosphorylates RASSF1C to promote RASSF1C degradation subsequently, which is negatively regulated by the PI3K (phosphoinositide 3-kinase)/Akt pathway. Thus the present study reveals a novel regulation of RASSF1C and the potentially important role of RASSF1C in DNA damage responses.     

Are molecular tools solving the challenges posed by detection of plant pathogenic bacteria and viruses?

Plant pathogenic bacteria, phytoplasmas, viruses and viroids are difficult to control, and preventive measures are essential to minimize the losses they cause each year in different crops. In this context, rapid and accurate methods for detection and diagnosis of these plant pathogens are required to apply treatments, undertake agronomic measures or proceed with eradication practices, particularly for quarantine pathogens. In recent years, there has been an exponential increase in the number of protocols based on nucleic-acid tools being those based on PCR or RT-PCR now routinely applied worldwide. Nucleic acid extraction is still necessary in many cases and in practice inhibition problems are decreasing the theoretical sensitivity of molecular detection. For these reasons, integrated protocols that include the use of molecular techniques as screening methods, followed by confirmation by other techniques supported by different biological principles are advisable. Overall, molecular techniques based on different types of PCR amplification and very especially on real-time PCR are leading to high throughput, faster and more accurate detection methods for the most severe plant pathogens, with important benefits for agriculture. Other technologies, such as isothermal amplification, microarrays, etc. have great potential, but their practical development in plant pathology is still underway. Despite these advances, there are some unsolved problems concerning the detection of many plant pathogens due to their low titre in the plants, their uneven distribution, the existence of latent infections and the lack of validated sampling protocols. Research based on genomic advances and innovative detection methods as well as better knowledge of the pathogens' lifecycle, will facilitate their early and accurate detection, thus improving the sanitary status of cultivated plants in the near future.     

On the definition of the reproductive value: response to the discussion by Bacaër and Abdurahman

The note attempts to address concerns expressed by Bacaër and Abdurahman (J Math Biol, 2008) in this journal about the definition of generalized reproductive value (RV) as proposed by Ediev (Theor Popul Biol 72(4):480–484, 2007).     

Acquisition of thermotolerance induced by heat and arsenite in HeLa S3 cells: Multiple pathways to induce tolerance?

Recent data indicate that cells may acquire thermotolerance via more than one route. In this study, we observed differences in thermotolerance development in HeLa S3 cells induced by prior heating (15 minutes at 44 degrees C) or pretreatment with sodium-arsenite (1 hour at 37 degrees C, 100 microM). Inhibition of overall protein and heat shock protein (HSP) synthesis (greater than 95%) by cycloheximide (25 micrograms/ml) during tolerance development nearly completely abolished thermotolerance induced by arsenite, while significant levels of heat-induced thermotolerance were still apparent. The same dependence of protein synthesis was found for resistance against sodium-arsenite toxicity. Toxic heat, but not toxic arsenite treatments caused heat damage in the cell nucleus, measured as an increase in the protein mass of nuclei isolated from treated cells (intranuclear protein aggregation). Recovery from this intranuclear protein aggregation was observed during post-heat incubations of the cells at 37 degrees C. The rate of recovery was faster in heat-induced tolerant cells than in nontolerant cells. Arsenite-induced tolerant cells did not show an enhanced rate of recovery from the heat-induced intranuclear protein aggregation. In parallel, hyperthermic inhibition of RNA synthesis was the same in tolerant and nontolerant cells, whereas post-heat recovery was enhanced in heat-induced, but not arsenite-induced thermotolerant cells. The more rapid recovery from heat damage in the nucleus (protein aggregation and RNA synthesis) in cells made tolerant by a prior heat treatment seemed related to the ability of heat (but not arsenite) to induce HSP translocations to the nucleus.     

Rad3 and Sty1 function in Schizosaccharomyces pombe: an integrated response to DNA damage and environmental stress?

In Schizosaccharomyces pombe , the Ataxia Telangiectasia-mutated (Atm)/Atm and Rad 3 Related (Atr) homologue Rad3 is an essential regulator of the response to DNA damage and stalled replication forks. Rad3 activates the downstream kinases Chk1 and Cds1. These kinases in turn inhibit cell cycle progression by mediating Cdc2 phosphorylation. Studies in both yeast and mammalian cells suggest additional roles for Rad3 in regulating cellular responses to environmental stress. In S. pombe , cellular responses to various environmental stresses are regulated primarily through the stress-activated MAP kinase p38 homologue Sty1. An important function of Sty1 is to drive cells rapidly through mitosis by facilitating the accumulation of Cdc25. Interestingly, Sty1 is activated simultaneously with Rad3 following exposure to UV radiation or ionizing radiation (IR). Similarly, exposure to environmental stresses induces the expression of rad3 ⁺, cds1 ⁺ and other checkpoint regulator genes. It is currently unclear how the pathways regulated by Sty1 and Rad3 and their opposing effects on mitosis are integrated. Recent studies suggest that Sty1 and Rad3 function together to regulate the expression of several stress response genes following exposure to IR. In this review, we discuss current knowledge on the interaction of Rad3/Atm and Sty1/p38 in regulating cellular responses to environmental stress and DNA damage.     

Do non-ruminant wildlife pose a risk of paratuberculosis to domestic livestock and vice versa in Scotland?

Paratuberculosis (Johne's disease) was long considered only a disease of ruminants. Recently non-ruminant wildlife species have been shown to harbor Mycobacterium avium subsp. paratuberculosis, the causative organism of paratuberculosis. We review the known non-ruminant wildlife host range of M. avium subsp. paratuberculosis and consider their role in the epidemiology of paratuberculosis in domestic ruminant livestock. Mycobacterium avium subsp. paratuberculosis has been isolated from lagomorph, canid, mustelid, corvid, and murid species. In agricultural environments domestic ruminants may contact wildlife and/or their excreta when grazing or feeding on farm-stored feed contaminated with wildlife feces, opening up the possibility of inter-species transmission. Of the wildlife species known to harbor M. avium subsp. paratuberculosis in Scotland, the rabbit is likely to pose the greatest risk to grazing livestock. Paratuberculosis in domestic ruminants is a notoriously difficult disease to control; the participation of non-ruminant wildlife in the epidemiology of the disease may partially account for this difficulty.     

Biosynthesis of protein products by animal cells. Are growth and non-growth associated concepts valid or useful?

The application of simple growth and non-growth associated concepts from microbial systems describing substrate uptake and production formation is considered unlikely to assist in the understanding of antibody formation and, hence, in maximising antibody yield. Such concepts have many significant limitations — notably, their strict application only to products of catabolic pathways and their inability to include metabolisms which either have multiple catabolic pathways (eg, fermentation and respiration in yeast and animal cells) or in which the major product of interest is predominantly anabolic in nature (eg. amino acid production in bacteria and antibody formation in animal cells). In addition, products which undergo an assembly and secretion process or a secretion process which allows intracellular pools of product to exist are also not well described by such simple relationships. In this work, inadequacies in the current approach to the study of the kinetics of growth of hybridoma cells and antibody production are described and the examples of growth ofSaccharomyces cerevisiae andCandida utilis, amino acid production by bacteria and antibody production by animal cells are used to illustrate these limitations. Having identified these limitations, suggestions are made as to how studies might be undertaken to assist our future understanding of the process of antibody manufacture and, subsequently, maximizing antibody yield. The process of characterising the metabolism of anabolic products is subject to detailed computer simulation of the pathways involved. It is argued that such approaches will assist us in understanding more fully the nature of biosynthetic products and how they integrate with the major energy producing pathways of the cell and the cell cycle. This will assist in maximising the yield of such products.     

The physiology and proteomics of drought tolerance in maize: early stomatal closure as a cause of lower tolerance to short-term dehydration?

Understanding the response of a crop to drought is the first step in the breeding of tolerant genotypes. In our study, two maize (Zea mays L.) genotypes with contrasting sensitivity to dehydration were subjected to moderate drought conditions. The subsequent analysis of their physiological parameters revealed a decreased stomatal conductance accompanied by a slighter decrease in the relative water content in the sensitive genotype. In contrast, the tolerant genotype maintained open stomata and active photosynthesis, even under dehydration conditions. Drought-induced changes in the leaf proteome were analyzed by two independent approaches, 2D gel electrophoresis and iTRAQ analysis, which provided compatible but only partially overlapping results. Drought caused the up-regulation of protective and stress-related proteins (mainly chaperones and dehydrins) in both genotypes. The differences in the levels of various detoxification proteins corresponded well with the observed changes in the activities of antioxidant enzymes. The number and levels of up-regulated protective proteins were generally lower in the sensitive genotype, implying a reduced level of proteosynthesis, which was also indicated by specific changes in the components of the translation machinery. Based on these results, we propose that the hypersensitive early stomatal closure in the sensitive genotype leads to the inhibition of photosynthesis and, subsequently, to a less efficient synthesis of the protective/detoxification proteins that are associated with drought tolerance.     

Are the patterns of regeneration in the endangered Eucalyptus gunnii ssp. divaricata shifting in response to climate?

Increasing drought frequency is a major driver of changes in forest structure and has been implicated in the decline of the endangered tree species, Eucalyptus gunnii ssp. divaricata (McAulay & Brett) in the Central Plateau region of Tasmania, Australia. In this study, we examined patterns of regeneration, aspects of the water relations of E. gunnii ssp. divaricata and its replacement Eucalyptus pauciflora and, whether shifts in stand dominance have occurred where the subspecies co‐occurs with E. pauciflora could be related to recent changes in climate. Successful E. gunnii ssp. divaricata seedling regeneration was restricted to micro‐sites with relatively deep soils within slight depressions. In contrast, poor E. gunnii ssp. divaricata regeneration and declining adult cohorts of this species all occurred on steeper, concave micro‐sites with shallow soils. This apparent shift in suitable regeneration micro‐site, from sites with shallow to deeper soils, may be linked to an observed 25% reduction in summer rainfall over the last 50 years. On slopes surrounding waterlogged depressions where E. gunnii ssp. divaricata co‐occurs with E. pauciflora, E. pauciflora was in higher abundance than E. gunnii ssp. divaricata in small adult and sapling size‐classes, compared with the adult cohorts (>30 cm d.b.h.), a trend consistent with a shift in stand dominance. Despite existing paradigms related to differential drought tolerance between these two species as a driver of this shift in stand dominance, there were no differences in predawn (Ψ_pd) water potentials between species. Furthermore, pressure–volume analysis showed that E. gunnii ssp. divaricata had lower values for osmotic potential at turgor loss point (?2.33 ± 0.06 MPa) than E. pauciflora (?2.13 ± 0.03 MPa), suggesting that E. gunnii ssp. divaricata may be more drought tolerant than E. pauciflora, in contrast to the prevailing paradigm that it is more susceptible to drought than E. pauciflora.     

Comparison of in-vitro and in-vivo response to fetal hemoglobin production and γ-mRNA expression by hydroxyurea in Hemoglobinopathies

BACKGROUND:

Hydroxyurea, which induces Fetal hemoglobin (HbF) synthesis, is the only drug widely used in different hemoglobinopathies; however, the response is very variable. We compared the efficacy of hydroxyurea in-vitro in erythroid cultures and in-vivo in the same patients with different hemoglobinopathies to induce HbF production and enhance γ-messenger RNA expression.

MATERIALS AND METHODS:

A total of 24-patients with different Hemoglobinopathies were given hydroxyurea and their response was studied in-vivo and in-vitro on mononuclear cells collected from them simultaneously.

RESULTS:

A total of 57.7% of patients (responders) showed no further crisis or transfusion requirements after hydroxyurea therapy with a mean increase in fetal cells (F-cells) of 63.8 ± 59.1% and γ-mRNA expression of 205.5 ± 120.8%. In-vitro results also showed a mean increase in F-cells of 27.2 ± 24.7% and γ-mRNA expression of 119.6% ± 65.4% among the treated cells. Nearly 19.0% of the partial-responders reduced their transfusion requirements by 50% with a mean increase in F-cells of 61.2 ± 25.0% and 28.4 ± 25.3% and γ-mRNA-expression of 21.0% ± 1.4% and 80.0% ± 14.1% in-vivo and in-vitro respectively. The non-responders (15.3%) showed no change in their clinical status and there was no significant increase in F-cells levels and γ-mRNA expression in-vivo or in-vitro.

CONCLUSION:

Thus, this method may help to predict the in-vivo response to hydroxyurea therapy; however, a much larger study is required.     

Are online prediction tools a valid alternative to genomic profiling in the context of systemic treatment of ER-positive breast cancer?

Background

Clinicians use clinical and pathological parameters, such as tumour size, grade and nodal status, to make decisions on adjuvant treatments for breast cancer. However, therapeutic decisions based on these features tend to vary due to their subjectivity. Computational and mathematical algorithms were developed using clinical outcome data from breast cancer registries, such as Adjuvant! Online and NHS PREDICT. More recently, assessments of molecular profiles have been applied in the development of better prognostic tools.

Methods

Based on the available literature on online registry-based tools and genomic assays, we evaluated whether these online tools could be valid and accurate alternatives to genomic and molecular profiling of the individual breast tumour in aiding therapeutic decisions, particularly in patients with early ER-positive breast cancer.

Results and conclusions

Early breast cancer is currently considered a systemic disease and a complex ecosystem with behaviour determined by the complex genetic and molecular signatures of the tumour cells, mammary stem cells, microenvironment and host immune system. We anticipate that molecular profiling will continue to evolve, expanding beyond the primary tumour to include the tumour microenvironment, cancer stem cells and host immune system. This should further refine therapeutic decisions and optimise clinical outcome.This article was specially invited by the editors and represents work by leading researchers.

     

Role of the Polymerase ? sub-unit DPB2 in DNA replication,cell cycle regulation and DNA damage response in Arabidopsis

Faithful DNA replication maintains genome stability in dividing cells and from one generation to the next. This is particularly important in plants because the whole plant body and reproductive cells originate from meristematic cells that retain their proliferative capacity throughout the life cycle of the organism. DNA replication involves large sets of proteins whose activity is strictly regulated, and is tightly linked to the DNA damage response to detect and respond to replication errors or defects. Central to this interconnection is the replicative polymerase DNA Polymerase ϵ (Pol ϵ) which participates in DNA replication per se, as well as replication stress response in animals and in yeast. Surprisingly, its function has to date been little explored in plants, and notably its relationship with DNA Damage Response (DDR) has not been investigated. Here, we have studied the role of the largest regulatory sub-unit of Arabidopsis DNA Pol ϵ: DPB2, using an over-expression strategy. We demonstrate that excess accumulation of the protein impairs DNA replication and causes endogenous DNA stress. Furthermore, we show that Pol ϵ dysfunction has contrasting outcomes in vegetative and reproductive cells and leads to the activation of distinct DDR pathways in the two cell types.     

Variation in tolerance to hypoxia in a predator and prey species: an ecological advantage of being small?

Three physiological variables, haematocrit, haemoglobin concentration and ventilation frequency, were measured to test how fathead minnows Pimephales promelas and small and large yellow perch Perca flavescens responded to three different dissolved oxygen concentrations. All fish were monitored continuously for any indications of stress in response to these manipulations. Within and between species, smaller individuals were the most tolerant of hypoxic environments. A species effect, however, did contribute to this observation, with fathead minnows being more tolerant of hypoxic environments than similar-sized yellow perch. In aquatic ecosystems where smaller fishes are more tolerant to hypoxia than their larger predators, hypoxic environments may have the potential to act as a refuge from predators.     

The interplay of DNA polymerase λ in diverse DNA damage repair pathways in higher plant genome in response to environmental and genotoxic stress factors

DNA repair mechanisms are essential for the maintenance of genomic stability, proper cellular function and survival for all organisms. Plants, with their intrinsic immobility, are vastly exposed to a wide range of environmental agents and also endogenous processes which frequently cause damage to DNA and impose genotoxic stress. Therefore, in order to survive under frequent and extreme environmental stress conditions, plants have developed a vast array of efficient and powerful DNA damage repair mechanisms to ensure rapid and precise repair of genetic material for maintaining genome stability and faithful transfer of genetic information over generations.¹ Recently, we have defined the role of DNA polymerase λ in repair of UV-B-induced photoproducts in Arabidopsis thaliana via nucleotide excision repair pathway.² Here, we have further discussed potential function of DNA polymerase λ in various DNA repair pathways in higher plant genome in response to environmental and genotoxic stress factors.     

Global DNA methylation profile at LINE-1 repeats and promoter methylation of genes involved in DNA damage response and repair pathways in human peripheral blood mononuclear cells in response to γ-radiation

Molecular and Cellular Biochemistry - DNA methylation is an epigenetic mechanism, which plays an important role in gene regulation. The present study evaluated DNA methylation profile of LINE1...     

Is oral microbiome of children able to maintain resistance and functional stability in response to short-term interference of ingesta?

Dear Editor,A series of studies had focused on the ecological stability of human microbiome (Lozupone et al.,2012;Faith et al.,2013;Moya and Ferrer,2016).Despite the continuous perturbation and the highly personalized composition within the human microbiome (Human Microbiome Project,2012),healthy adults stably maintain their microbial communities in terms of space and time (Faith et al.,2013;Moya and Ferrer,2016;Oh et al.,2016).This stability is proved to be critical for the well-being of human body (Lozupone et al.,2012).On the contrary,major shifts in microbial community composition are often related to diseases (Lynch and Pedersen,2016).