A simple, quantitative approach to the coupling of photophosphorylation to electron flow in terms of proton fluxes.

A simple relationship between observed phosphorylation efficiencies (P/e ratios) and internal proton concentration in spinach chloroplast thylakoids has been derived. P/e ratios, varked by either changing the light intensity or by adding the energy transfer inhibitor, 4'-deoxyphlorizin, were found to change with internal proton concentration in accordance with this relationship. A quantitative prediction of the effect of uncouplers on the P/e ratio can probably also be made. By extrapolation of plots of observed P/e ratios against internal proton concentration divided by the overall rate of electron flow, a maximum intrinsic P/e of about 0.66 is obtained. Assuming that two protons appear inside thylakoids per electron transferred, a P/e ratio of 0.66 suggests that three internal protons are consumed for each ATP formed. Internal protons may be considered to be substrates for the phosphorylation reaction. Hill plots of phosphorylation rate vs. internal proton concentration also indicate that three protons are consumed for each ATP synthesized. Thus, the H+ concentration gradient behaves quantitatively, as well as qualitatively, as if it is the connecting link between electron flow and phosphorylation in illuminated thylakoids.     

A mixed-model approach to mapping quantitative trait loci in barley on the basis of multiple environment data

In this article, I propose a mixed-model method to detect QTL with significant mean effect across environments and to characterize the stability of effects across multiple environments. I demonstrate the method using the barley dataset by the North American Barley Genome Mapping Project. The analysis raises the need for mixed modeling in two different ways. First, it is reasonable to regard environments as a random sample from a population of target environments. Thus, environmental main effects and QTL-by-environment interaction effects are regarded as random. Second, I expect a genetic correlation among pairs of environments caused by undetected QTL. I show how random QTL-by-environment effects as well as genetic correlations are straightforwardly handled in a mixed-model framework. The main advantage of this method is the ability to assess the stability of QTL effects. Moreover, the method allows valid statistical inferences regarding average QTL effects.     

The structure of Ca(2+) release units in arthropod body muscle indicates an indirect mechanism for excitation-contraction coupling

The relative disposition of ryanodine receptors (RyRs) and L-type Ca(2+) channels was examined in body muscles from three arthropods. In all muscles the disposition of ryanodine receptors in the junctional gap between apposed SR and T tubule elements is highly ordered. By contrast, the junctional membrane of the T tubule is occupied by distinctive large particles that are clustered within the small junctional domain, but show no order in their arrangement. We propose that the large particles of the junctional T tubules represent L-type Ca(2+) channels involved in excitation-contraction (e-c) coupling, based on their similarity in size and location with the L-type Ca(2+) channels or dihydropyridine receptors (DHPRs) of skeletal and cardiac muscle. The random arrangement of DHPRs in arthropod body muscles indicates that there is no close link between them and RyRs. This matches the architecture of vertebrate cardiac muscle and is in keeping with the similarity in e-c coupling mechanisms in cardiac and invertebrate striated muscles.     

A multi-scale approach to understand the mechanobiology of intermediate filaments

The animal cell cytoskeleton consists of three interconnected filament systems: actin microfilaments, microtubules and the lesser known intermediate filaments (IFs). All mature IF proteins share a common tripartite domain structure and the ability to assemble into 8–12 nm wide filaments. At the time of their discovery in the 1980s, IFs were only considered as passive elements of the cytoskeleton mainly involved in maintaining the mechanical integrity of tissues. Since then, our knowledge of IFs structure, assembly plan and functions has improved dramatically. Especially, single IFs show a unique combination of extensibility, flexibility and toughness that is a direct consequence of their unique assembly plan. In this review we will first discuss the mechanical design of IFs by combining the experimental data with recent multi-scale modeling results. Then we will discuss how mechanical forces may interact with IFs in vivo both directly and through the activation of other proteins such as kinases.     

The effects of isoproterenol, UDCG 115, and caffeine on the heart related to excitation-contraction coupling in heart muscle

A myothermal technique was used to measure initial heat and tension independent heat from isometrically contracting papillary muscles taken from the right ventricle of rabbits. Tension independent heat produced by the muscle at Lo was isolated with a 2,3-butanedione monoxime (diacetyl monoxime)--hyperosmotic Krebs solution. The effects of the inotropic drugs isoproterenol (1 X 10(-7) M), UDCG 115 (2 X 10(-4) M), and caffeine (2 X 10(-3) M) on heat and mechanical output were measured. We tested the hypothesis that these drugs alter peak twitch tension by increasing the total amount of Ca2+ cycled during the twitch, assuming that net tension independent heat is proportional to total Ca2+ cycled. The hypothesis was rejected for each drug as the positive inotropic effects of isoproterenol and UDCG 115 on twitch tension were not accompanied by increases in net tension independent heat. Net tension independent heat was actually depressed by UDCG 115. The negative inotropic effect of caffeine on twitch tension was accompanied by an increase in tension independent heat at times between the end of mechanical relaxation and the next stimulus. Possible mechanisms to account for these results are discussed.     

A small sequence in the third intracellular loop of the VPAC(1) receptor is responsible for its efficient coupling to the calcium effector

The stimulatory effect of VIP on intracellular calcium concentration ([Ca(2+)](i)) has been investigated in Chinese hamster ovary cells stably transfected with the reporter gene aequorin, and expressing human VPAC(1), VPAC(2), chimeric VPAC(1)/VPAC(2), or mutated receptors. The VIP-induced [Ca(2+)](i) increase was linearly correlated with receptor density and was higher in cells expressing VPAC(1) receptors than in cells expressing a similar VPAC(2) receptor density. The study was performed to establish the receptor sequence responsible for that difference. VPAC(1)/VPAC(2) chimeric receptors were first used for a broad positioning: those having the third intracellular loop (IC(3)) of the VPAC(1) or of the VPAC(2) receptor behaved, in that respect, phenotypically like VPAC(1) and VPAC(2) receptor, respectively. Replacement in the VPAC(2) receptor of the sequence 315-318 (VGGN) within the IC(3) by its VPAC(1) receptor counterpart 328-331 (IRKS) and the introduction of VGGN in state of IRKS in VPAC(1) was sufficient to mimic the VPAC(1) and VPAC(2) receptor characteristics, respectively. Thus, a small sequence in the IC(3) of the VPAC(1) receptor, probably through interaction with G(alphai) and G(alphaq) proteins, is responsible for the efficient agonist-stimulated [Ca(2+)](i) increase.     

A small sequence in the third intracellular loop of the VPAC(1) receptor is responsible for its efficient coupling to the calcium effector

The stimulatory effect of vasoactive intestinal peptide (VIP) on the intracellular calcium concentration ([Ca(2+)](i)) has been investigated in Chinese hamster ovary cells stably transfected with the reporter gene aequorin, and expressing human VPAC(1), VPAC(2), chimaeric VPAC(1)/VPAC(2) or mutated receptors. The VIP-induced increase in [Ca(2+)](i) was linearly correlated with receptor density, and was higher in cells expressing VPAC(1) receptors than in cells expressing a similar density of VPAC(2) receptors. The study was performed to establish the receptor sequence responsible for this difference. VPAC(1)/VPAC(2) chimaeric receptors were first used for broad positioning: those receptors having the third intracellular loop (IC3) of the VPAC(1) or the VPAC(2) receptor behaved, in this respect, phenotypically like VPAC(1) and VPAC(2) receptors respectively. Replacement in the VPAC(2) receptor of the sequence comprising residues 315-318 (VGGN) within IC3 by its VPAC(1) receptor counterpart (residues 328-331; IRKS) and the introduction of VGGN instead of IRKS into VPAC(1) was sufficient to mimic VPAC(1) and VPAC(2) receptor characteristics respectively. Thus a small sequence in the IC3 domain of the VPAC(1) receptor is responsible for the efficient agonist-stimulated increase in [Ca(2+)](i).     

A cytochemical approach to the wound repair mechanism inUdotea petiolata (Siphonales)

Summary When injured, the thalli of the coenocytic algaUdotea petiolata undergo a rapid sealing process mainly due to the extrusion of two successive plugs. In the first, external and transitory plug, sulphated polysaccharides are the predominant components. In the second, permanent and internal plug, roundish bodies having a complex polysaccharidic composition are embedded in a fibrillar matrix of still unknown nature. The sulphated sugars were identified and located by means of Alcian Blue staining and X-ray microanalysis. A periodic acid-thiocarbohydrazide-silver proteinate technique proved useful especially in the study of the roundish bodies and in the compositional and structural comparison of the siphon wall with the wound wall. Phosphotungstic acid at low pH was used to evidentiate an extensive plasma membrane activity in the repairing cytoplasm.Supported by a grant of C.N.R.     

A metadynamic approach to understand the recognition mechanism of the histone H3 tail with the ATRXADD domain

The binding affinity between the histone 3 (H3) tail and the ADD domain of ATRX (ATRX_ADD) increases with the subsequent addition of methyl groups on lysine 9 on H3. To improve our understanding of how the difference in methylation state affects binding between H3 and the ATRX_ADD, we adopted a metadynamic approach to explore the recognition mechanism between the two proteins and identify the key intermolecular interactions that mediate this protein-peptide interaction (PPI). The non-methylated H3 peptide is recognized only by the PHD finger of ATRX_ADD while mono-, di-, and trimethylated H3 is recognized by both the PHD and GATA-like zinc finger of the domain. Furthermore, water molecules play an important role in orienting the lysine 9 anchor towards the GATA-like zinc finger, which results in stabilizing the lysine 9 binding pocket on ATRX_ADD. We compared our computational results against experimentally determined NMR and X-ray structures by demonstrating the RMSD, order parameter S² and hydration number of the complex. The metadynamics data provide new insight into roles of water-bridges and the mechanisms through which K9 hydration stabilizes the H3K9me3:ATRX_ADD PPI, providing context for the high affinity demonstrated between this protein and peptide.     

A MaxEnt modelling approach to understand the climate change effects on the distributional range of White-bellied Sholakili Sholicola albiventris (Blanford, 1868) in the Western Ghats,India

Each species is uniquely influenced by anthropogenic climate change. Change in temperature and precipitation due to climate change may lead to species adaptation or extinction, or in some cases, a range shift. To know the influence of climate change on a restricted and endemic bird species of the Western Ghats (WG), White-bellied Sholakili (WBS) Sholicola albiventris (Blanford, 1868), we conducted a study by using species distribution modelling. We considered 73 spatial bias-corrected occurrence points of WBS along with environmental variables like the mean temperature of coldest quarter (Bio 11), precipitation of driest month (Bio 14) and mean precipitation of warmest quarter (Bio 18). We used the MaxEnt application with ENM evaluate tool in R statistical package for developing a climate model for WBS. Bio 11 was observed to be the most crucial climate variable shaping the habitat of WBS. The current study predicts that only 2823km² in WG is suitable for WBS. One-third of this area falls under the protected area network, of which 52% is becoming unsuitable to this narrow endemic due to climate warming. The model also predicts 26% to 45% habitat loss under different climate change scenarios by the 2050s.     

A quantitative approach to the experimental transmission success of Echinostoma friedi (Trematoda: Echinostomatidae) in rats

Using a range of parameters, the ability of rats (Rattus norvegicus) to successfully transmit Echinostoma friedi to the next host was examined under experimental conditions. The concept of Experimental Transmission Success (TM), defined as the number of hosts that become successfully infected after exposure to a number of infective stages produced by a previous host per unit of inoculation at which this latter host was exposed, was introduced. Using data for the egg output and miracidium hatching and infectivity, the TM permits us to estimate the ability of a particular definitive host species to successfully transmit a parasite species. This concept may be also useful to compare the transmission fitness of a parasite in different definitive host species. Moreover, variations of the Experimental Transmission Success over the course of the infection were calculated by the use of the Weekly Experimental Transmission Success (TMW). Overall, considering the complete duration of the experiment, the TM of E. friedi using rats as definitive hosts was 0.68 infected snails/metacercaria. However, positive values of the TMW were only obtained from 2 to 4 wk post-infection, with a maximum during the third wk post-infection. When comparing the TM values of E. friedi in rats with those calculated in hamsters on the basis of previously published data, E. friedi appears to be more appropriate to move through this portion of its life cycle when using hamsters (Mesocricetus auratus) as the final host than rats.     

A mechanism for coupling exit from mitosis to partitioning of the nucleus

Exit from mitosis must not occur prior to partitioning of chromosomes between daughter cells. We find that the GTP binding protein Tem1, a regulator of mitotic exit, is present on the spindle pole body that migrates into the bud during S phase and mitosis. Tem1's exchange factor, Lte1, localizes to the bud. Thus, Tem1 and Lte1 are present in the same cellular compartment (the bud) only after the nucleus enters the bud during nuclear division. We also find that the presence of Tem1 and Lte1 in the bud is required for mitotic exit. Our results suggest that the spatial segregation of Tem1 and Lte1 ensures that exit from mitosis only occurs after the genetic material is partitioned between mother and daughter cell.     

Structural modeling of SoxF protein from Chlorobium tepidum: an approach to understand the molecular basis of thiosulfate oxidation

Microbial redox reactions of inorganic sulfur compounds play a vital role in balancing the turnover of this element in the environment. These vital reactions are carried out by the enzyme system encoded by the sox operon. The central player of the sulfur oxidation biochemistry is the SoxY–Z protein complex. Another protein called SoxF having sulfide dehydrogenase activity has the ability to reactivate the inactivated SoxY–Z protein complex. This SoxF protein is obtained from the sox operon of Chlorobium tepidium. In the present work an attempt has been made to understand the structural details of the activity of SoxF protein. A plausible biochemical mechanism has been predicted regarding the involvement of the SoxF protein in biological sulfur anion oxidation process. Since this is the first report regarding the structural biology of SoxF protein this study may shed light in the hitherto unknown molecular biochemistry of sulfur anion oxidation by sox operon.