Optimization of integrated alkaline–extrusion pretreatment of barley straw for sugar production by enzymatic hydrolysis

In this work, an integrated one-step alkaline–extrusion process was tested as pretreatment for sugar production from barley straw (BS) biomass. The influence of extrusion temperature (T) and the ratio NaOH/BS dry matter (w/w) (R) into the extruder on pretreatment effectiveness was investigated in a twin-screw extruder at bench scale. A 2³ factorial design of experiments was used to analyze the effect of process conditions [T: 50–100 °C; R: 2.5–7.5% (w/w)] on composition and enzymatic digestibility of pretreated substrate (extrudate). The optimum conditions for a maximum glucan to glucose conversion were determined to be R = 6% and T = 68 °C. At these conditions, glucan yield reached close to 90% of theoretical, while xylan conversion was 71% of theoretical. These values are 5 and 9 times higher than that of the untreated material, which supports the great potential of this one-step combined pre-treatment technology for sugar production from lignocellulosic substrates. The absence of sugar degradation products is a relevant advantage over other traditional methods for a biomass to ethanol production process since inhibitory effect of such product on sugar fermentation would be prevented.     

From intestine transport to enzymatic regulation: The works of the Spanish biochemist Alberto Sols (1917–1989)

In this paper the scientific trajectory of Spanish influential biochemist Alberto Sols (1917–1989) is presented in comparative perspective. His social and academic environment, his research training under the Cori's in the US in the early 1950s and his works when coming back to Spain to develop his own scientific career are described in order to present the central argument of this paper on his path from physiological research to research on enzymatic regulation. Sols' main contributions were both scientific and academic. He and his collaborators not only contributed to biological knowledge on the biochemistry of metabolic regulation but to the active reception of biochemistry in the Spanish academia and to update of Spanish medical education.     

The role of stratifin in fibroblast–keratinocyte interaction

Stratifin is a member of 14-3-3 protein family, a highly conserved group of proteins constituted by seven isoforms. They are involved in numerous crucial intracellular functions such as cell cycle and apoptosis, regulation of signal transduction pathways, cellular trafficking, cell proliferation and differentiation, cell survival, and protein folding and processing, among others. At epidermal level, stratifin (also called 14-3-3 sigma) has been described as molecule with relevant functions. For instance, this isoform is a marker associated with keratinocyte differentiation. In this maturation process, the presence of dominant negative molecules of p53 induces a “stemness condition” of keratinocyte precursor cells and suppression of stratifin expression. In addition, the recently described keratinocyte-releasable form of stratifin is involved in dermal fibroblast MMP-1 over-expression through c-Fos and c-Jun activity. This effect is mediated, at least in part, by p38 mitogen-activated protein kinase (MAPK). Other MMP family members such as stromelysin-1 (MMP-3), stromelysin-2 (MMP-10), neutrophil collagenase (MMP-8), and membrane-type MMP-24 (MT5-MMP) are also up-regulated by stratifin. Within fibroproliferative disorder of skin, hypertrophic scar and keloids exhibit a high content of collagen, proteoglycans, and fibronectin. Thus, the MMP profile induced by stratifin is an interesting starting point to establish new therapeutic tools to control the process of wound healing. In this review, we will focus on site of synthesis and mode of action of stratifin in skin and wound healing.     

SPR and ITC determination of the kinetics and the thermodynamics of bivalent versus monovalent sugar ligand–lectin interactions

A kinetic study of the interaction of bivalent and monovalent sugar ligands with a lectin was undertaken with the aid of surface plasmon resonance (SPR) method. The study involved a series of bivalent α-d-mannopyranoside containing sugar ligands, with systematic variation in the distance between the sugar ligands. The detailed kinetic studies showed that bivalent ligands underwent a faster association (k _on) and a slower dissociation (k _off) of the ligand–lectin complexes, in comparison to the monovalent ligand–lectin complexes. The kinetic constants were complemented further by assessing the thermodynamic parameters with the aid of isothermal titration calorimetry (ITC). The initiation of cross-linking of ligand–lectin interactions emerge from the early stages of the complexation. The dynamic light scattering (DLS) and the transmission electron microscopy (TEM) techniques allowed judging the sizes and morphologies of the complex in the solution and solid states, respectively.     

Interpretation of variety × sowing date × sowing depth interaction for bean–Fusarium–Rhizoctonia pathosystem

Through this study, the sowing date?×?sowing depth?×?variety interaction for Rhizoctonia root rot (RRR) development was investigated in field trials over two growing seasons. Four-way Wald tests indicated that there was a lower RRR incidence in var. Red compared to var. White in the majority of experimental plots. At a 5?cm seeding depth, RRR incidence for plantings on 22 May and 5 June was often lower than that for 5 May date. A hierarchical cluster analysis grouped experimental plots using averages of RRR incidence, Fusarium root rot (FRR) index and the number of seeds per plant. Sowing depth influenced FRR, RRR and productivity more than variety and date factors. Comparison of clusters recognised lower disease and greater production levels for sowing on 22 May and 5 June at 5?cm depth. Thus, shallow seeding of bean varieties in late spring should be incorporated into FRR–RRR-control programmes.     

The interaction of (1–4)-fragment of thymosin β4 with calmodulin-sensitive cAMP phosphodiesterase from hypothalamus

Evidence was accumulated indicating that cyclic nucleotides are involved in regulation of growth, differentiation and function of lymphoid cells. It was previously shown that the N-fragment (1–4) of thymosin 4 (Ac-Ser-Asp-Lys-Pro-OH) inhibits in vivo the entry of cell populations into S-phase. In the course of the study of the interrelationship between the immune and neuroendocrine systems we have found that the tetrapeptide caused incomplete competitive inhibition of hypothalamic calmodulin (CaM)-dependent phosphodiesterase (PDE) stimulated by CaM. In the presence of the peptide, the 20-fold increase of the constant for PDE activation by CaM was accompanied by an insignificant rise in the maximum rate of cAMP hydrolysis. The value of the inhibition constant (K_i) amounted to 600nM. In the absence of CaM, the peptide at saturating concentrations reduced the basal activity of PDE nearly 2- to 3-fold. The effect of the peptide on PDE was noncompetitive with respect to cAMP. The results support our suggestion that the tetrapeptide realizes its effects in the immuno-neuroendocrine system by the mechanism of cyclic nucleotide metabolism.     

The helminth holobiont: a multidimensional host–parasite–microbiota interaction

Gastrointestinal helminths have developed multiple mechanisms by which they manipulate the host microbiome to make a favorable environment for their long-term survival. While the impact of helminth infections on vertebrate host immunity and its gut microbiota is relatively well studied, little is known about the structure and functioning of microbial populations supported by metazoan parasites. Here we argue that an integrated understanding of the helminth-associated microbiome and its role in the host disease pathogenesis may facilitate the discovery of specific microbial and/or genetic patterns critical for parasite biology and subsequently pave the way for the development of alternative control strategies against parasites and parasitic disease.     

Effect of α(2–6)-linked sialic acid and α(1–3)-linked fucose on the interaction ofN-linked glycopeptides and related oligosaccharides with immobilizedPhaseolus vulgaris leukoagglutinating lectin (L-PHA)

The effects of branching and substitution of branches by sialic acid and fucose on the interaction ofN-linked glycopeptides and related oligosaccharides with immobilizedPhaseolus vulgaris leukoagglutinating lectin (L-PHA) were examined. Asialo bi-, tri-and tetra-antennary glycans were all retarded but to different extents on a long column of L-PHA-agarose. Asialo tri- and tetra-antennary glycans containing the pentasaccharide unit Gal1-4GlcNAc1-2[Gal1-4GlcNAc1-6]Man were strongly retarded, whereas asialo bi- and tri-antennary glycans lacking the Gal1-4GlcNAc1-6 branch were only weakly retarded. In all instances the interaction with the lectin was completely abolished when either (2–6)-linkedN-acetylneuraminic acid or (1–3)-linked fucose was present at the galactose orN-acetylglucosamine residue of the Gal1-4GlcNAc1-6Man1-6 branch, respectively. The same substitutions on the Gal1-4GlcNAc1-6Man1-6 branch decreased but did not abolish the affinity of the lectin for the glycans. The presence of NeuAc2-6 and Fuc1-3 on the other two branches did not interfere with the binding of the glycans to L-PHA. Furthermore, it appeared that the presence of the Man1-4GlcNAc unit is requried for interaction with the lectin. In order to obtain reliable information on the relative occurrence of tri- and tetra-antennary glycopeptides, this study shows that it is essential to desialylate and to defucosylate the glycans prior to application to L-PHA-agarose.Abbreviations L-PHA leukoagglutinating phytohemagglutinin - CMP-NeuAc cytidine-5-monophospho-N-acetylneuraminic acid - GP glycopeptide - OS oligosaccharide - HPLC high-performance liquid chromatography - FNR fraction not retarded - FR fraction retarded suffixes MS, BS and TS indicate mono-, bi- and trisialyl derivatives respectively; suffix MF indicates monofucosyl derivatives.structures of the substratesOS2, OS3, OS3, OS4, GP2, GP3, GP4, GP4-MF, OS2(3) andOS2(-) are presented in Fig. 2     

The protein–protein interaction network of the human Sirtuin family

Protein–protein interaction networks are useful for studying human diseases and to look for possible health care through a holistic approach. Networks are playing an increasing and important role in the understanding of physiological processes such as homeostasis, signaling, spatial and temporal organizations, and pathological conditions. In this article we show the complex system of interactions determined by human Sirtuins (Sirt) largely involved in many metabolic processes as well as in different diseases. The Sirtuin family consists of seven homologous Sirt-s having structurally similar cores but different terminal segments, being rather variable in length and/or intrinsically disordered. Many studies have determined their cellular location as well as biological functions although molecular mechanisms through which they act are actually little known therefore, the aim of this work was to define, explore and understand the Sirtuin-related human interactome. As a first step, we have integrated the experimentally determined protein–protein interactions of the Sirtuin-family as well as their first and second neighbors to a Sirtuin-related sub-interactome. Our data showed that the second-neighbor network of Sirtuins encompasses 25% of the entire human interactome, and exhibits a scale-free degree distribution and interconnectedness among top degree nodes. Moreover, the Sirtuin sub interactome showed a modular structure around the core comprising mixed functions. Finally, we extracted from the Sirtuin sub-interactome subnets related to cancer, aging and post-translational modifications for information on key nodes and topological space of the subnets in the Sirt family network.     

The binding of mycolic acids to galectin-3: a novel interaction between a host soluble lectin and trafficking mycobacterial lipids?

Understanding the molecular mechanism of host-pathogen interactions is the basis for drug design and vaccine development. The fine composition of mycolic acids (MA), the major constituents of Mycobacterium tuberculosis (Mtb) cell envelope, as well as other cell wall-associated lipids, contribute to determine the virulence of a given strain. However, endogenous receptors for mycolic acids on susceptible cells exposed to mycobacterial infections have not been fully identified. Here, we show that galectin-3, a multifunctional beta-galactoside binding lectin present mainly in the cytoplasm of inflammatory cells and also present on the cell surface, can recognize mycobacterial mycolic acids. MA can inhibit the lectin self-association but not its carbohydrate-binding abilities and can selectively interfere in the interaction of the lectin with its receptors on temperature-sensitive dendritic cell line, suggesting that galectin-3 could be involved in the recognition of trafficking mycolic acids and participate in their interaction with host cells.     

Root characteristics of selected field crops: Data from the Wageningen Rhizolab (1990–2002)

Since being built in 1990, the rhizotron facility in Wageningen, the Wageningen Rhizolab, has been used for experiments on crops (e.g. Alfalfa, Brussels sprouts, common velvet grass, field bean, fodder radish, leeks, lupins, maize, potato, beetroot, ryegrass, spinach, spring wheat, winter rye and winter wheat). In the experiments, horizontal glass minirhizotron tubes combined with auger sampling were used to assess rooting characteristics. For this paper we took the root data from these experiments and looked for a general relationship between thermal time/time after planting and rooting depth, the velocity of the root front and root proliferation. For certain depths (fixed by the depth at which the horizontal minirhizotrons were installed) a simple linear regression was established between the average root number per cm² minirhizotron surface area and thermal time after planting. The compartments selected for each crop were those in which there had been a control treatment and/or in which conditions for rooting were considered to be optimal. We performed regression analyses per compartment and per depth, but only for the period after planting in which a linear increase of root numbers vs. thermal time was observed. After averaging the results, the regression procedure yielded two parameters of rooting for each crop: (a) the actual or thermal time at which the first root appeared at a certain depth and (b) the root proliferation rate after the first root had appeared. In this way, inherent crop differences in rooting behaviour (rooting depth and root proliferation) became apparent. For each crop, the velocity of the root front after planting could be established (calculated in cm(°C day)^–1). This parameter differed greatly between crops. Some crops (such as leeks and common velvet grass) explored the soil profile slowly: the root front moved at a velocity of only 0.07cm(°C day)^–1. Among the crops whose roots grew down much faster (0.18–0.26cm (°C day)^–1) were cereals and fodder radish. For a day with an average temperature of 15°C these rates would have corresponded with the root front travelling approximately 1–4cm per day. In the crops studied the root front velocity did not correlate with the root proliferation rate.     

Gustav Senn(1875–1945): The pioneer of chloroplast movement research

Gustav Senn analyzed for the first time light-induced movement and arrangement of chloroplasts. Using many plant species he performed physiological analyses of chloroplast migration in response to exte...     

The two-step interaction between α-dimethylaminonaphthalene-1-sulfonyl-pepsinogen-(1–12) and pepsin

The binding between α-dimethylaminonaphthalenesulfonyl-(1–12) and porcine pepsin can be detected by the large changes that occur in the fluorescence spectra of the dimethylaminonaphthalenesulfonyl chromophore due to energy transfer from tryptophan residues of the protein. The interaction was previously shown to consist of two steps: a fast step leading to a greatly enhanced fluorescence followed by a slower rearrangement step which reduces the fluorescence but leads to tighter binding and inhibition of the catalytic activity of pepsin (1). The two steps have been studied over a wide range of values of pH, temperature, and ionic strength to gain additional insights into the physical events occurring during the interaction. Based on the pH and ionic strength dependence, the initial step most likely involves electrostatic interaction of the basic peptide inhibitor with the acidic surface of pepsin in a rapid collision process. The use of this fluorescent reporter group has also suggested that the equilibrium binding after the slower rearrangement may also be pH dependent with most effective binding at higher pH. The kinetics of the slow step were measured by monitoring the continuous fluorescence decay. The resulting rates are compared to the rates observed by others for binding of pepstatin to pepsin. From the pH dependence of fluorescence, pK_app values are obtained for the dansylated peptide (3.25), for the pH dependence of the initial binding step (4.87), and for the equilibrium position (4.75).