Anti-viral Activities of <Emphasis Type="Italic">Oroxylum indicum</Emphasis> Extracts on Chikungunya Virus Infection

Chikungunya virus (CHIKV) is a re-emerging mosquito-borne alphavirus that poses a threat to human worldwide. Driven by the lack of approved medication and vaccination, research on anti-Chikungunya agents has received great attention. In an effort to determine potential inhibitor of CHIKV, this study aimed at investigating the potential anti-viral activity of Oroxylum indicum extracts towards CHIKV-infected Vero cells. The virucidal, pre- and post-treatment effects of O. indicum were evaluated, using the maximum non-toxic dose of O. indicum methanol and aqueous extracts as determined by cytotoxicity assay. The viral inhibitory effect was assessed by the morphological changes of Vero cells and further confirmed by plaque assay. Both methanol and aqueous extracts of O. indicum had similar cytotoxicity in Vero cells. Interestingly, the virucidal effect of O. indicum aqueous extract revealed a significant reduction on the viral titre (p < 0.05). The prophylactic effect of aqueous extract was demonstrated when the pre-treated cells exhibited a significant anti-CHIKV activity (p < 0.05). However, methanol extract of this plant exerted an anti-viral activity against CHIKV only to a certain extent. Therefore, the aqueous extract of this plant has a potential to inhibit the virus and acts as prophylactic agent against CHIKV. Further studies however are needed to substantiate the finding and to determine the important compound of this plant as well as the mechanism of action in treating CHIKV infection.     

Variation of cytosine methylation patterns in European beech (<Emphasis Type="Italic">Fagus sylvatica</Emphasis> L.)

The role of epigenetic phenomena in plant adaptation is becoming widely recognized and the potential of epigenetics for forestry practice has been demonstrated as well. In this study, methylation-sensitive amplification polymorphism (MSAP) markers were investigated in 20 European beech (Fagus sylvatica L.) provenances that cover most of Europe and were planted in two climatically contrasting provenance trial plots. Correlations of cytosine-methylation patterns at five loci and overall DNA methylation with climatic conditions of the sites of population origin and budburst phenology were detected, suggesting that methylation at particular loci was influenced by the weather or photoperiod during embryogenesis or even earlier. Alternation of methylation patterns may also have been caused by genetic mutation. Frequencies of methylation patterns at three loci differed between the two trial locations, indicating that a climatically induced change of methylation during the ontogeny occurs as well. The results suggest that the rules for collection, transfer, and use of forest reproductive materials should also consider epigenetic effects.     

Cellulase production from palm oil mill effluent in Malaysia: Economical and technical perspectives

The demand for cellulases has increased tremendously over the last few decades. This is due to its numerous applications in industry and also because it can be used to hydrolyze cellulosic materials into sugars that can be fermented into bioethanol and bio‐based products. This does not only open up a big and significant market for cellulases, but also provides another source of biofuel and bioenergy in the future. Nevertheless, the cost of the existing substrates for cellulase fermentation is very high if required for large‐scale production. Sustainable supplies and an economically feasible biomass are needed to reduce the cost of cellulase production. Palm oil mill effluent (POME) is rich in carbohydrates, proteins, nitrogenous compounds, lipids, minerals, cellulose, hemicelluloses and lignin. It can be used naturally as a fermentation medium, either for cellulase or other value‐added product fermentation. In Malaysia, a large and continually increasing amount of POME is produced every year because of the high global demand for palm oil. Hence, the development of cellulase production from POME is reviewed, covering the POME production, cellulase production and the major challenges together with the future prospects of these processes.     

Historical and ecological divergence among populations of Monttea chilensis (Plantaginaceae), an endemic endangered shrub bordering the Atacama Desert,Chile

The coastal deserts of northern Chile show an important latitudinal gradient of aridity with more arid areas to the north of the Atacama Desert than to the south. Several plant species have disjunct distributions that correspond with the extremes of this latitudinal gradient. In this study, using genetic (chloroplast and nuclear DNA), morphological (vegetative and floral traits of various kinds) and climatic and topographic information, we explored ecological and historical events that have putatively shaped patterns of variation among Monttea chilensis populations—a species that shows this disjunct distribution. Through phylogeographic and phylogenetic analyses, two divergent lineages were identified located at the latitudinal extremes. The lineage located northern lineage (NG) of the Atacama Desert showed more genetic diversity and better-resolved phylogeographic structure than the southern lineage (SG). Considerable morphological variation across the geographical range corresponds with these genetic groups. We observed contrasting relationships between floral and vegetative traits: populations from the most arid region NG possessed larger flowers, but smaller vegetative values, and vice versa. Niche modelling and multivariate analyses, including environmental data, revealed different environmental requirements for each lineage. NG plants occur in regions with warmer and drier climatic conditions and at higher altitudes, while SG populations inhabit colder and more humid environments and lower altitudes. The evolutionary history of M. chilensis exhibits a phylogeographical footprint consistent with past fragmentation and allopatric differentiation, where the hyper-arid zone formed by the Atacama Desert clearly acted as an important gene flow barrier. This barrier has led to considerable differentiation in morphology and ecology, resulting in two ecotypes or geographical races, suggesting incipient speciation promoted by local adaptation and geographical isolation.     

Arabinogalactan-protein epitope Gal4 is differentially regulated and localized in cell lines of hybrid fir (<Emphasis Type="Italic">Abies alba</Emphasis> × <Emphasis Type="Italic">Abies cephalonica</Emphasis>) with different embryogenic and regeneration potential

Arabinogalactan proteins (AGPs) are important proteoglycans regulating somatic embryogenesis in diverse plant species. Embryogenic cells of somatic embryos are covered by special extracellular cell wall layer called extracellular surface matrix network (ECMSN) at their early developmental stages. Here we show that highly embryogenic cell line AC78 of hybrid fir (Abies alba × Abies cephalonica) differs from very low-embryogenic cell line AC77 in the abundance, subcellular localization and deposition of subset of secreted AGPs. A specific AGP epitope containing Gal residues and reacting to Gal4 antibody is secreted and deposited into ECMSN, which covers the surface of the embryogenic cells showing high embryogenic and regeneration capacity in the cell line AC78. On the other hand, this Gal4 AGP epitope was not secreted and/or found on the surface of meristematic cells showing low embryogenic and regeneration capacity in the cell line AC77, as well as on the surface of non-embryogenic suspensor cells and callus cells in both cell lines AC77 and AC78. As a positive control, we have used another AGP epitope LM2 (containing glucuronic acid) showing no significant differences in these two Abies hybrid lines. This study defines specific AGPs containing β-(1→6)-galactotetraosyl group as a first molecular component of ECMSN covering embryogenic cells in gymnosperms. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Hypotheses and trends on how body size affects trophic interactions in a guild of South American killifishes

A chief structuring force in food webs is the hierarchy of trophic interactions, where bigger animals feed on smaller ones. The anatomic and physiological explanations of why body size determines this hierarchy are embodied within the concept of gape limitation. The relaxation of gape limitation and an increase in energetic demands due to predators' larger body size determine the size and diversity of prey species. However, these patterns may be related to further trends in trophic interactions with body size, which have been less considered. Specifically, the passive incorporation of prey should involve a nested distribution of prey among predator size classes. However, predators avoid smaller resources because of their low energy return, with a clumped distribution of prey potentially generating modular organization with qualitative changes in prey identity (e.g. zooplankton, macroinvertebrates and fishes). Finally, size‐mediated interactions (such as direct and indirect competition) may cause predators of similar body size to differentiate among prey organisms, resulting in a checkerboard distribution of prey identity. Consequently, nestedness, modularity and checkerboard distributions of prey among predators of different size classes should form emergent network structures that are directly related to clear ecological mechanisms. We analyse these predictions in a killifish guild, where trends in trophic positions, prey richness, evenness and the number of energy sources systematically scale with body size. We found significant nestedness and segregation in diet among different size classes, supporting the progressive incorporation of prey items coupled with prey differentiation among similar classes. However, we also detected an ‘anti‐modular’ trend, which contradicts theoretical expectations and previous results. We hypothesize that this anti‐modularity is determined by the high biodiversity of the system and the continuous representation of prey size classes. These results reinforce the concept of size‐mediated interactions and its connection with community biodiversity as a main structuring force of food webs.     

Identification of ncRNAs as potential therapeutic targets in multiple sclerosis through differential ncRNA – mRNA network analysis

Background

Several studies have revealed a potential role for both small nucleolar RNAs (snoRNAs) and microRNAs (miRNAs) in the physiopathology of relapsing-remitting multiple sclerosis (RRMS). This potential implication has been mainly described through differential expression studies. However, it has been suggested that, in order to extract additional information from large-scale expression experiments, differential expression studies must be complemented with differential network studies. Thus, the present work is aimed at the identification of potential therapeutic ncRNA targets for RRMS through differential network analysis of ncRNA – mRNA coexpression networks. ncRNA – mRNA coexpression networks have been constructed from both selected ncRNA (specifically miRNAs, snoRNAs and sdRNAs) and mRNA large-scale expression data obtained from 22 patients in relapse, the same 22 patients in remission and 22 healthy controls. Condition-specific (relapse, remission and healthy) networks have been built and compared to identify the parts of the system most affected by perturbation and aid the identification of potential therapeutic targets among the ncRNAs.

Results

All the coexpression networks we built present a scale-free topology and many snoRNAs are shown to have a prominent role in their architecture. The differential network analysis (relapse vs. remission vs. controls’ networks) has revealed that, although both network topology and the majority of the genes are maintained, few ncRNA – mRNA links appear in more than one network. We have selected as potential therapeutic targets the ncRNAs that appear in the disease-specific network and were found to be differentially expressed in a previous study.

Conclusions

Our results suggest that the diseased state of RRMS has a strong impact on the ncRNA – mRNA network of peripheral blood leukocytes, as a massive rewiring of the network happens between conditions. Our findings also indicate that the role snoRNAs have in targeted gene silencing is a widespread phenomenon. Finally, among the potential therapeutic target ncRNAs, SNORA40 seems to be the most promising candidate.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1396-5) contains supplementary material, which is available to authorized users.     

An in vitro testing of chemoresistance in leukaemic patients

The fact that leukaemic cells are primarily or secondarily resistant to cytostatics is a serious phenomenon, which leads to the failure of chemotherapy of malignant diseases in clinical practise. Some detoxification and transporting systems are responsible for the generation of chemoresistance on the cellular level and the decrease of effectiveness in treatment. In vitro testing of chemoresistance of leukaemic cells is presently an inseparable component of “tailoring” therapy in the developing field of predictive oncology. The aim of this work was to estimate profiles of drug resistance, based on the predictive in vitro test, and to help in choosing the most effective cytostatic. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazoline (MTT) assay was used, based on the direct effect of cytostatics on the viability of leukaemic cells in vitro. The number of living leukaemic cells was evaluated by a computer program, where LC₅₀ (concentration of cytostatics lethal to 50% of leukaemic cells) was established from the achieved dose-relation curves. Seventy-one samples of leukaemic cells isolated from the patients’ peripheral blood or bone marrow were examined. All samples were tested to 3 cytostatics minimally. It was found by the in vitro assay, that resistance to dexamethasone, prednisolone, etoposide and vincristine is increased in patients with acute myeloid leukaemia disease, compared to the acute lymphoblastic leukaemia patients. In patients with a relapsed disease population, leukaemic cells are highly heterogeneous in the MTT assay. It was concluded that the MTT assay can be used to study drug interactions in vitro in leukaemia samples. The type of interaction was highly different between patients, and depended on drug concentrations.