IFI35, mir-99a and HCV Genotype to Predict Sustained Virological Response to Pegylated-Interferon Plus Ribavirin in Chronic Hepatitis C

Although, the treatment of chronic hepatitis C (CHC) greatly improved with the use of direct antiviral agents, pegylated-interferon (PEG-IFN) plus ribavirin remains an option for many patients, worldwide. The intra-hepatic level of expression of interferon stimulated genes (ISGs) and the rs12979860 CC genotype located within IFNL3 have been associated with sustained virological response (SVR), in patients with CHC. The aim of the study was to identify micro-RNAs associated with SVR and to build an accurate signature to predict SVR. Pre-treatment liver biopsies from 111 patients, treated with PEG-IFN plus ribavirin, were studied. Fifty-seven patients had SVR, 36 non-response (NR) and 18 relapse (RR). The expression of 851 human miRNAs and 30 selected mRNAs, including ISGs, was assessed by RT-qPCR. In the first group of patients (screen), 20 miRNAs out of the 851 studied were deregulated between NRs and SVRs. From the 4 miRNAs validated (mir-23a, mir-181a*, mir-217 and mir-99a), in the second group of patients (validation), 3 (mir-23a, mir-181a* and mir-99a) were down-regulated in NRs as compared to SVRs. The ISGs, studied, were accumulated in SVRs and IFNL3 rs12979860 CT/TT carriers compared respectively to NRs and CC carriers. Combining, clinical data together with the expression of selected genes and micro-RNAs, we identified a signature (IFI35, mir-99a and HCV genotype) to predict SVR (AUC:0.876) with a positive predictive value of 86.54% with high sensibility (80%) and specificity (80.4%). This signature may help to characterize patients with low chance to respond to PEG-IFN/ribavirin and to elucidate mechanisms of NR.     

Propagation of Norway spruce via somatic embryogenesis

Somatic embryogenesis combined with cryopreservation is an attractive method to propagate Norway spruce (Picea abies) vegetatively both as a tool in the breeding programme and for large-scale clonal propagation of elite material. Somatic embryos are also a valuable tool for studying regulation of embryo development. Embryogenic cell lines of Norway spruce are established from zygotic embryos. The cell lines proliferate as proembryogenic masses (PEMs). Somatic embryos develop from PEMs. PEM-to-somatic embryo transition is a key developmental switch that determines the yield and quality of mature somatic embryos. Withdrawal of plant growth regulators (PGRs) stimulates PEM-to-somatic embryo transition accompanied by programmed cell death (PCD) in PEMs. This PCD is mediated by a marked decrease in extracellular pH. If the acidification is abolished by buffering the culture medium, PEM-to-somatic embryo transition together with PCD is inhibited. Cell death, induced by withdrawal of PGRs, can be suppressed by extra supply of lipo-chitooligosaccharides (LCOs). Extracellular chitinases are probably involved in production and degradation of LCOs. During early embryogeny, the embryos form an embryonal mass surrounded by a surface layer. The formation of a surface layer is accompanied by a switch in the expression pattern of an Ltp-like gene (Pa18) and a homeobox gene (PaHB1), from ubiquitous expression in PEMs to surface layer-specific in somatic embryos. Ectopic expression of Pa18 and PaHB1 leads to an early developmental block. Transgenic embryos and plants of Norway spruce are routinely produced by using a biolistic approach. The transgenic material is used for studying the importance of specific genes for regulating plant development, but transgenic plants can also be used for identification of candidate genes for use in the breeding programme.     

Diversity of lepidopteran stem borers on monocotyledonous plants in eastern Africa and the islands of Madagascar and Zanzibar revisited

Surveys were completed in Eritrea, Ethiopia, Kenya, Madagascar, Mozambique, Tanzania, Uganda and Zanzibar to assess the lepidopteran stem borer species diversity on wild host plants. A total of 24,674 larvae belonging to 135 species were collected from 75 species of wild host plants belonging to the Poaceae, Cyperaceae and Typhaceae. Amongst them were 44 noctuid species belonging to at least nine genera, 33 crambids, 15 pyralids, 16 Pyraloidea species not yet identified, 25 tortricids and three cossids. The noctuid larvae represented 73.6% of the total number of larvae collected, with 66.3, 3.5 and 3.8% found on Poaceae, Cyperaceae and Typhaceae, respectively. The Crambidae, Pyralidae, Tortricidae and Cossidae represented 19.8, 1.9, 2.5 and 0.1% of the total larvae collected, respectively, with 90.4% of the Crambidae and Pyralidae collected from Poaceae, and 99.7% of the Tortricidae collected from Cyperaceae. The lepidopteran stem borer species diversity in the wild host plants was far more diverse than previously reported.     

Coexistence of hepatitis B surface antigen (HBs Ag) and anti-HBs antibodies in chronic hepatitis B virus carriers: influence of "a" determinant variants

In chronic hepatitis B (CHB), the persistence of hepatitis B surface antigen (HBs Ag) is sometimes associated with antibodies (Ab) to HBs (anti-HBs). To assess the hypothesis of the selection of HBs Ag immune escape variants in CHB patients, the variability of the HBV S gene was determined for patients persistently carrying both HBs Ag and anti-HBs antibodies and patients solely positive for HBs Ag. We selected 14 patients who presented both markers (group I) in several consecutive samples and 12 patients positive for HBs Ag only (group II). The HBs Ag-encoding gene was amplified and cloned, and at least 15 clones per patient were sequenced and analyzed. The number of residue changes within the S protein was 2.7 times more frequent for group I than for group II patients and occurred mostly in the "a" determinant of the major hydrophilic region (MHR), with 9.52 versus 2.43 changes per 100 residues (P = 0.009), respectively. Ten patients (71%) from group I, but only three (25%) from group II, presented at least two residue changes in the MHR. The most frequent changes in group I patients were located at positions s145, s129, s126, s144, and s123, as described for immune escape variants. In CHB patients, the coexistence of HBs Ag and anti-HBs Ab is associated with an increase of "a" determinant variability, suggesting a selection of HBV immune escape mutants during chronic carriage. The consequences of this selection process with regard to vaccine efficacy, diagnosis, and clinical evolution remain partially unknown.     

A new minimum fluorescence parameter,as generated using pulse frequency modulation,compared with pulse amplitude modulation:<Emphasis Type="Italic"> F</Emphasis><Subscript>α</Subscript> versus<Emphasis Type="Italic"> F</Emphasis><Subscript>o</Subscript>

The minimum fluorescence parameter (F (alpha)), generated using the new pulse frequency modulation (PFM) technology, was compared with the minimum fluorescence parameter (F (o)), generated by pulse amplitude modulation (PAM), in response to a reversible low-oxygen stress in 'Honeycrisp'trade mark (HC) apples (Malus domestica) and an irreversible osmotic stress induced by water loss in two grape (Vitis spp.) cultivars ('L'Acadie' (LAc) and 'Thompson Seedless' (TS)). The minimum fluorescence values produced by both fluorometer types in response to a reversible low-oxygen stress in apples were indistinguishable: both F (o) and F (alpha) increased when O(2) levels were lowered below the anaerobic compensation point (ACP); when gas levels returned to normoxia both parameters dipped below, then returned to, the original fluorescence baseline. The two parameters also responded similarly to the irreversible osmotic stress in grapes: in both cultivars, F (alpha) and F (o) first decreased before reaching an inflection point at approximately 20% mass loss and then increased towards a second inflection point. However, the two parameters were not analogous under the irreversible osmotic stress; most notably, the relative F (alpha) values appeared to be lower than F (o) during the later stages of dehydration. This was likely due to the influence of the F (m) parameter and an overestimation of F (alpha) when measuring the fluorescence from healthy and responsive chloroplasts as found in grapes experiencing minimal water loss, but not in grapes undergoing moderate to severe dehydration. An examination of the data during a typical PFM scan reveals this fluorometer system may yield new fluorescence information with interesting biological applications.     

The stoichiometry and energetics of oxygenic phototrophic growth

The values of gross metabolic flows in cells are essentially interconnected due to conservation laws of chemical elements and interrelations of biochemical coupling. Therefore, the overall stoichiometry of cellular metabolism, such as the biomass quantum yield, the ratio between linear and circular flows via the electron transport chain, etc., can be calculated using balances of metabolic flows in the network branching points and coupling ratios related to ATP formation and expenditures. This work has studied the energetic stoichiometry of photosynthetic cells by considering the transfer of reductivity in the course of biochemical reactions. This approach yielded rigorous mathematical expressions for biomass quantum yield and other integral bioenergetic indices of cellular growth as functions of ATP balance parameters. The effect of cellular substance turnover has been taken into account. The obtained theoretical estimation of biomass quantum yield is rather close to experimental data which confirms the predictive capacity of this approach.     

Synthetic xylan-binding modules for mapping of pulp fibres and wood sections

Background  

The complex carbohydrate composition of natural and refined plant material is not known in detail but a matter that is of both basic and applied importance. Qualitative assessment of complex samples like plant and wood tissues requires the availability of a range of specific probes. Monoclonal antibodies and naturally existing carbohydrate binding modules (CBMs) have been used in the past to assess the presence of certain carbohydrates in plant tissues. However, the number of natural CBMs is limited and development of carbohydrate-specific antibodies is not always straightforward. We envisage the use of sets of very similar proteins specific for defined targets, like those developed by molecular evolution of a single CBM scaffold, as a suitable strategy to assess carbohydrate composition. An advantage of using synthetic CBMs lies in the possibility to study fine details of carbohydrate composition within non-uniform substrates like plant cell walls as made possible through minor differences in CBM specificity of the variety of binders that can be developed by genetic engineering.     

Influence of climate on individual tree growth and carbon sequestration in native‐tree plantings

Native ecosystems face challenges of past and ongoing human actions, including vegetation clearance and climate change arising from greenhouse gas emissions. Reforestation is an important tool for sequestering carbon, so we sought to determine how replanted native trees responded to weather, soil conditions and planting characteristics. We measured girth growth of 13 tree species in 19 native mixed‐species plantings and one remnant in south‐eastern Australia, bimonthly from 2011 to 2016; replantings ranged between 6 and 46 years at the commencement of measurements. Band dendrometers (flexible bands that record changes in girth) were used to measure growth, with 34 measurements per tree taken over 5 years. We used outcomes from models with several plausible weather future scenarios (Dry, Wet, Wet‐to‐Dry and Average) for 25 and 50 years for tree girth, and 25 years for carbon accumulation, into the future. Woody species richness enhanced girth growth of all tree species. Higher maximum temperatures and reduced rainfall, which generally are predicted for the region over coming decades, retarded growth of nine tree species. Planting tree density had no discernible association with growth for the range of planting densities used. The most and least carbon were sequestered in Wet and Dry projections, respectively. Three Acacia spp. (N‐fixers) grew slowest and would sequester least carbon, while four species of Eucalyptus grew fastest. These measurements of growth provide critical information for land managers to guide choice in replanting strategies for carbon storage.     

CCC and Prohexadione-Ca Enhance Rhizome Growth and Lateral Bud Production in Rhubarb (<Emphasis Type="Italic">Rheum rhabarbarum</Emphasis> L.)

Accelerating rhizome growth is crucial to enhancing propagule production in rhubarb (Rheum rhabarbarum L.) because the crop is propagated through rhizome divisions. This can be achieved through manipulating source-sink activity. This study tested the hypothesis that synthetic plant growth retardants Prohexadione-Ca and CCC enhance rhizome growth in rhubarb. Two different concentrations of these plant growth retardants and GA₃ (positive control) were foliarly applied on the cultivar German Wine at three stages of shoot growth under greenhouse conditions. Both Prohexadione-Ca and CCC favorably enhanced rhizome growth through suppressing shoot growth. CCC at 3000 mg L⁻¹ produced the best results and the effect was apparent when applied at 12 weeks after shoot emergence. The rhizome diameter, fresh weight, and the number of viable buds were enhanced significantly in plants sprayed with CCC 3000 mg L⁻¹. Both Prohexadione-Ca and CCC were equally effective in enhancing dry mass and starch allocation preferentially toward the rhizome. Prohexadione-Ca- and CCC-induced rhizome growth enhancement could possibly be due to their known role as GA biosynthesis inhibitors or through increasing photosynthetic efficiency and preferentially reallocating carbohydrates to the rhizome.