Signs of trauma in an adult parietal bone exhumed from a Portuguese prehistoric collective burial

A fragment of parietal bone from an adult individual of unknown sex exhumed from the collective burial of Praia da Samarra (Sintra, Portugal), dated to the end of the Neolithic, presents signs of different types of trauma. These include thinning of the skull vault and incisions marks. Differential diagnoses for these alterations are discussed: for the first one, depressed skull factures is the most likely cause. For the incisions, trepanation (more probable) and trauma due to a sharp force are proposed. These hypotheses are also discussed in terms of other similar findings from coeval Portuguese collective burials.     

Neotropical C3/C4 grass distributions – present,past and future

Changes in C₄ grass distribution and abundance are frequently observed in Quaternary, Holocene and future environmental‐change scenarios. However, the factors driving these dynamics are not fully understood, and conflicting theories have been reported. In this paper, we present a very large dataset of modern altitudinal distribution profiles of C₃ and C₄ grasses covering the entire Neotropical Andes, which was compared with actual climate data. The results of multivariate analysis demonstrate that, in the Neotropical Andes, mean annual temperature is the main factor governing the modern altitudinal distribution of C₃ and C₄ grass species. The C₃ and C₄ grass distributions were compared with simulations based on the Lund‐Potsdam‐Jena dynamic global vegetation model (LPJ‐DGVM), which allowed the present grass distribution to be estimated. Finally, the DGVM was employed to simulate past and future scenarios, using the IPCC's climate projections for 2100 and PMIP2 models for the Holocene Optimum (HO, 6000 years bp ) and the Last Glacial Maximum (LGM, 21 000 years bp ). The results were found to be significantly different from those obtained using a simple photosynthetic model. According to LPJ forced with the PMIP2 models for the LGM, during the LGM, the C₄ grasses would not have reached higher altitudes than found in the present day.     

π–π Stacking mediated drug–drug interactions in human CYP2E1

Because of having many low molecular mass substrates, CYP2E1 is of particular interests to the pharmaceutical industry. Many evidences showed that this enzyme can adopt multiple substrates to significantly reduce the oxidation rate of the substrates. The detailed mechanism for this observation is still unclear. In the current study, we employed GPU‐accelerated molecular dynamics simulations to study the multiple‐binding mode of human CYP2E1, with an aim of offering a mechanistic explanation for the unexplained multiple‐substrate binding. Our results showed that Thr303 and Phe478 were key factors for the substrate recognition and multiple‐substrate binding. The former can form a significant hydrogen bond to recognize and position the substrate in the productive binding orientation in the active site. The latter acted as a mediator for the substrate communications via π–π stacking interactions. In the multiple‐binding mode, the aforementioned π–π stacking interactions formed by the aromatic rings of both substrates and Phe478 drove the first substrate far away from the catalytic center, orienting in an additional binding position and going against the substrate metabolism. All these findings could give atomic insights into the detailed mechanism for the multiple‐substrate binding in human CYP2E1, providing useful information for the drug metabolism mechanism and personalized use of clinical drugs. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

Algae Permeability to Me2SO from −3 to 23°C

Biphasic transport of water and dimethyl sulfoxide (Me₂SO), a common cryoprotective agent (CPA), in algal cells was induced and measured on a cryoperfusion stage. A two-step experimental protocol provided data for the volumetric response of Chlorococcum (C.) texanum to impermeable and permeable solutes. First, the cells were exposed to a 500-mOsm sucrose solution, causing immediate shrinkage of the cell to a minimum equilibrium volume. Then an isoosmotic 200-mOsm/300-mOsm CPA/sucrose solution was introduced to the cells, resulting in increased cell volume to a new equilibrium state. Experiments were conducted at temperatures between −3 and 23°C. Cell volumes were measured off-line by computer analysis of video images. A network thermodynamic model was fit to the transient volume data to determine permeabilities of C. texanum to water and Me₂SO over the full temperature range, and results were calculated with two numeric methods. Biphasic transport was found to be slower at colder temperatures, with water entering the cell faster than Me₂SO. Experimental results were also compared with data from similar experiments using methanol (MeOH) as the CPA. MeOH influx was calculated to be a magnitude larger than that of water. Additionally, MeOH permeability was at least three orders of magnitude greater than Me₂SO permeability, and the difference in these solute permeabilities increased as temperature decreased.     

Glacial–interglacial deep-water changes in the NW Pacific inferred from single foraminiferal δO and δC

Oxygen and carbon isotope values of single benthic foraminiferal tests in a core from the Shatsky Rise, NW Pacific Ocean, show greater intra-horizon variance during the Holocene than during the Last Glacial Maximum (LGM). This greater variance is caused by the introduction of glacial specimens some 20 cm upward from their original deposition layer due to bioturbation. In contrast, foraminiferal populations belonging to glacial layers do not include Holocene specimens. The difference in direction of bioturbation greatly modifies climate information in horizons formed during and after deglacial events. After omitting glacial specimens from Holocene sediments, the glacial–interglacial difference in δ¹⁸O suggests that Pacific deep-water temperature changed by 2.4–3.8°C at the most. The δ¹³C values suggest that nutrient concentration was higher during the LGM than the Holocene. The glacial deep North Pacific Ocean apparently was influenced by cold deep waters of southern origin.     

Brain‐derived neurotrophic factor induces migration of endothelial cells through a TrkB–ERK–integrin αVβ3–FAK cascade

Brain‐derived neurotrophic factor (BDNF) promotes the regeneration of periodontal tissue. Since angiogenesis is important for tissue regeneration, investigating effect of BDNF on endothelial cell function may help to reveal its mechanism, whereby, BDNF promotes periodontal tissue regeneration. In this study, we examined the influence of BDNF on migration in human microvascular endothelial cells (HMVECs), focusing on the effects on extracellular signal‐regulated kinase (ERK), integrin α_Vβ₃, and focal adhesion kinase (FAK). The migration of endothelial cells was assessed with a modified Boyden chamber and a wound healing assay. The expression of integrin α_Vβ₃ and the phosphorylation of ERK and FAK were analyzed by immunoblotting and immunofluorescence microscopy. BDNF (25 ng/ml) induced cell migration. PD98059, an ERK inhibitor, K252a, a specific inhibitor for TrkB, a high affinity receptor of BDNF, and an anti‐integrin α_Vβ₃ antibody suppressed the BDNF‐induced migration. BDNF increased the levels of integrin α_Vβ₃ and phosphorylated ERK1/2 and FAK. The ERK inhibitor and TrkB inhibitor also reduced levels of integrin α_Vβ₃ and phosphorylated FAK. We propose that BDNF stimulates endothelial cell migration by a process involving TrkB/ERK/integrin α_Vβ₃/FAK, and this may help to enhance the regeneration of periodontal tissue. J. Cell. Physiol. 227: 2123–2129, 2012. © 2011 Wiley Periodicals, Inc.     

Molecular determinants of desensitization and assembly of the chimeric GABAA receptor subunits (α1/γ2) and (γ2/α1) in combinations with β2 and γ2

Two γ-aminobutyric acid_A (GABA_A) receptor chimeras were designed in order to elucidate the structural requirements for GABA_A receptor desensitization and assembly. The (α1/γ2) and (γ2/α1) chimeric subunits representing the extracellular N-terminal domain of α1 or γ2 and the remainder of the γ2 or α1 subunits, respectively, were expressed with β2 and β2γ2 in Spodoptera frugiperda (Sf-9) cells using the baculovirus expression system. The (α1/γ2)β2 and (α1/γ2)β2γ2 but not the (γ2/α1)β2 and (γ2/α1)β2γ2 subunit combinations formed functional receptor complexes as shown by whole-cell patch–clamp recordings and [³H]muscimol and [³H]flunitrazepam binding. Moreover, the surface immunofluorescence staining of Sf-9 cells expressing the (α1/γ2)-containing receptors was pronounced, as opposed to the staining of the (γ2/α1)-containing receptors, which was only slightly higher than background. To explain this, the (α1/γ2) and (γ2/α1) chimeras may act like α1 and γ2 subunits, respectively, indicating that the extracellular N-terminal segment is important for assembly. However, the (α1/γ2) chimeric subunit had characteristics different from the α1 subunit, since the (α1/γ2) chimera gave rise to no desensitization after GABA stimulation in whole-cell patch–clamp recordings, which was independent of whether the chimera was expressed in combination with β2 or β2γ2. Surprisingly, the (α1/γ2)(γ2/α1)β2 subunit combination did desensitize, indicating that the C-terminal segment of the α1 subunit may be important for desensitization. Moreover, desensitization was observed for the (α1/γ2)β2γ2 receptor with respect to the direct activation by pentobarbital. This suggests differences in the mechanism of channel activation for pentobarbital and GABA.     

Optimization of some culture parameters and properties of β-glucosidase and β-xylosidase from Penicillium funiculosum NRRL – 13033

Penicillium funiculosum NRRL 13033 produced β-glucosidase and β-xylosidase activities when grown on wheat straw. The addition of some inducers (individually or in combination) to the fermentation medium were tested for the production of both enzymes. The relation of mycelial bound enzyme to cell free enzyme was studied during incubation period of fermentation. The optimum activity of β-glucosidase and β-xylosidase were found to be in the pH 4.5 using phosphate-citrate buffer at 50°C for 60 min and at 55°C for 40 min respectively. β-Glucosidase lost about 40% of its original activity by heating to 65°C for 60 min, while, β-xylosidase activity was found to be nearly stable with the same treatment. Both enzyme activities were greatly inhibited when 1.0% (w/v) of xylose and glucose were added to the assay mixture.     

Phospholipase C β2 in vascular smooth muscle

Receptor-mediated inositol 1,4,5-trisphosphate formation in most tissues is dependent on a variety of phospholipase C isoforms. To determine which phospholipase C isoforms were present in vascular smooth muscle compared to brain, liver, and spleen, we extracted proteins from these tissues and separated and identified the phospholipase C isoforms by immunoblotting. Aliquots of rat tail artery were examined by this procedure, together with aliquots of rat liver, spleen, cerebral cortex, hippocampus, cerebellum, aorta, and mesenteric artery. Phospholipase C γ1 was shown to be present in all of these tissues, while phospholipase C β1 was shown to be limited to fractions from brain. Phospholipase C Δ1 was detected in rat tail artery, mesenteric artery, aorta, and brain. Phospholipase C β2 was found in rat tail artery, liver, and brain. This is the first report of phospholipase C β2 in tissues other than HL60 cells. Since G proteins activate IP₃ production via stimulation of phospholipase Cβ isoforms in many tissues, and agonist-stimulated IP₃ production in smooth muscle requires G protein activation, phospholipase C β2 may be required for agonist-stimulated force production in vascular smooth muscle. © 1996 Wiley-Liss, Inc.     

Evolutionary implications of C3–C4 intermediates in the grass Alloteropsis semialata

C₄ photosynthesis is a complex trait resulting from a series of anatomical and biochemical modifications to the ancestral C₃ pathway. It is thought to evolve in a stepwise manner, creating intermediates with different combinations of C₄‐like components. Determining the adaptive value of these components is key to understanding how C₄ photosynthesis can gradually assemble through natural selection. Here, we decompose the photosynthetic phenotypes of numerous individuals of the grass Alloteropsis semialata, the only species known to include both C₃ and C₄ genotypes. Analyses of δ¹³C, physiology and leaf anatomy demonstrate for the first time the existence of physiological C₃–C₄ intermediate individuals in the species. Based on previous phylogenetic analyses, the C₃–C₄ individuals are not hybrids between the C₃ and C₄ genotypes analysed, but instead belong to a distinct genetic lineage, and might have given rise to C₄ descendants. C₃ A. semialata, present in colder climates, likely represents a reversal from a C₃–C₄ intermediate state, indicating that, unlike C₄ photosynthesis, evolution of the C₃–C₄ phenotype is not irreversible.     

Poly(L–lysine)–DNA interactions in NaCl solutions: B → C and B → ψ Transitions

Thermal denaturation and circular dichroism (CD) properties of poly(L -lysine)–DNA complexes vary greatly when these complexes are prepared differently, that is, whether by NaCl-gradient dialysis starting from 2.0 M NaCl or by direct mixing at low salt. These differing properties were investigated in more detail by examining complexes, made by direct mixing in the presence of various concentrations of NaCl, both before and after the NaCl was dialyzed out of the complex solution. The precipitation curves of DNA due to polylysine binding indicate that such binding is noncooperative at zero salt; from 0.1 up to 1.0 M NaCl they exhibit varying degrees of cooperatively. Starting from zero salt, as the NaCl concentration used for complex formation is increased, both the CD and the melting properties of the complexes are shifted from those of directly mixed at zero salt to those of reconstitution: in the CD spectra there is a gradual shift from a B → C transition to a B → ψ transition; thermal denaturation results show a gradual increase in the melting temperatures of both free DNA (t_m) and polylysine-bound DNA (t′_m). The progressive shift from B → C to B → ψ suggests a close relationship between these two transitions. Large aggregates of the complexes do not warrant the appearance of ψ-type CD spectra: ψ-spectra have been obtained in the supernatants of polylysine–DNA complexes made and measured at 1.0 M NaCl while slightly perturbed CD spectra in B → C transition have been observed in turbid solutions of fully covered complexes made at very low salt. If the complexes are made at intermediate salts and dialyzed to a very low salt, although up to 60% of the DNA is still bound by polylysine, the CD spectra of the complexes are shifted back to the B-type CD characteristic of pure DNA.     

Reduced C/EBPβ‐LIP translation improves metabolic health

Inactivation of target of rapamycin complex 1 (TORC1) signaling is considered important for the beneficial effects of caloric restriction (CR) on metabolism and health span. It is however not fully elucidated which cellular processes downstream of TORC1 are the main regulators of metabolic health. In this issue of EMBO Reports, Zidek et al 1 describe that inhibition of mammalian TORC1 (mTORC1) leads to decreased translation of CCAAT/enhancer‐binding protein β (C/EBPβ)‐liver inhibitory protein (LIP). Moreover, loss of C/EBPβ‐LIP in mice improves metabolic health, similar to the effects of CR. Zidek et al 1 thus report that reduced C/EBPβ‐LIP translation is a novel mTORC1‐regulated process that could play a major role in mediating the beneficial metabolic effects of caloric restriction.     

Role of JAK2–STAT3 in TLR2‐mediated tissue factor expression

Tissue factor (TF) is a core protein with an essential function in the coagulation cascade that maintains the homeostasis of the blood vessels. TF not only participates in neointima formation, but also causes the development of atherosclerosis. This study investigated the mechanism regulating TF expression in macrophages using Pam₃CSK₄, a TLR2 ligand. Pam₃CSK₄ induced TF expression in two types of macrophages (Raw264.7 and BMDM), but not in TLR2 KO mice derived BMDM. Pam₃CSK₄ induced TF expression was inhibited by pretreatment with pan‐JAK inhibitor or JAK2 inhibitor AG490. JAK2 knock‐down by siRNA inhibited Pam₃CSK₄ induced TF expression. Pam₃CSK₄ stimulated STAT3 phosphorylation (S727), while STAT3 knock‐down by siRNA reduced Pam₃CSK₄ induced TF expression. These results suggest that Pam₃CSK₄ induced TF expression is regulated by the JAK2–STAT3 signaling pathway. Pam₃CSK₄, unlike increased TF expression, significantly decreased RGS2 expression, while RGS2 overexpression decreased Pam₃CSK₄ induced TF expression. Inhibition of TF by RGS2 WT did not occur in mutants with flawed RGS domains. We also investigated the correlation between RGS2 and STAT3 phosphorylation. RGS2 knock‐down elevated Pam₃CSK₄ induced STAT3 phosphorylation, but RGS2 overexpression had the opposite effect on STAT3 phosphorylation. These results suggest that, while Pam₃CSK₄ induced TF expression is regulated by JAK2–STAT3 signaling, RGS2 is a negative regulator targeted to STAT3. J. Cell. Biochem. 114: 1315–1321, 2013. © 2012 Wiley Periodicals, Inc.     

Modeling of α(1–4) chain arrangements in α(1–4)(1–6) glucans: The action and outcome of β-amylase and Pseudomonas stutzeri amylase on an α(1–4)(1–6) glucan model

Simulated enzymic debranching of a β-limit dextrin model, prepared from a computed construct made by random extension and branching, and given the CCL value of w-maize amylopectin (and equal amounts of external chains with ECL values of 2 and 3) has been related to experimental chromatograms of the debranched β-limit dextrin of the amylopectin. The profile was similar to those from gel chromatograms and IEC-PAD chromatography.The equivalent lengths in glucosyl units of grid-links (g-links) of internal and external chains in constructs were calculated from the ICL and ECL values of amylopectin and models produced from the constructs with the appropriate lengths for internal and external chains. These derived models were subjected to simulated hydrolysis by Pseudomonas stutzeri amylase and the products compared with those of the experimental distribution from w-maize amylopectin. With the model the amounts of maltotetraose and maltodextrins released were similar to the experimental values but the distribution of branched maltodextrins was quite different. Unlike w-maize amylopectin – a polymer with the cluster structure – which has given a profile of molecular sizes of maltodextrins with low amounts of single and small numbers of internal chains and with a peak at a M_W of about 14,000 (13 chains), in the model the proportion of maltodextrin with one internal chain was high and as d.p. increased the amounts decreased exponentially. This would be expected if the distribution of internal chains in the core was random. It is suggested that in the core of a model prepared from a construct made with alternating probabilities of extension – one in which this probability is high relative to branching, and a second in which it is low – may give clusters of branched maltodextrins with short internal chains which are joined by longer chains; more closely approximating the distribution of internal chains of different lengths in amylopectin.An arrangement for amylopectin molecules in the starch granule has been proposed. In this, they have a wafer-like, discoidal shape, composed of the amorphous zone overlain with the double helical, crystalline region. The flat macromolecules are concentrically layered with the former on the inside and the latter oriented to the outside of the granule.