Deciphering the neural and molecular mechanisms of C. elegans behavior

Because of its small and well-characterized nervous system and amenability to genetic manipulation, the nematode Caenorhabditis elegans offers the promise of understanding the mechanisms underlying a whole animal's behavior at the molecular and cellular levels. In fact, this goal was a primary motivation behind the development of C. elegans as an experimental organism 40 years ago. Yet it has proven surprisingly difficult to obtain a mechanistic understanding of how the C. elegans nervous system generates behavior, despite the existence of a 'wiring diagram' that contains a degree of information about neural connectivity unparalleled in any organism. This review describes three types of information--molecular data on cellular neurochemistry, temporal information about neural activity patterns, and behavioral data on the consequences of neural ablation and manipulation--that, along with genetic analysis, may ultimately lead to a complete functional map of the C. elegans nervous system.     

Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei,the hyper-cellulolytic filamentous fungus

The filamentous fungus Trichoderma reesei is a potent cellulase producer and the best-studied cellulolytic fungus. A lot of investigations not only on glycoside hydrolases produced by T. reesei, but also on the machinery controlling gene expression of these enzyme have made this fungus a model organism for cellulolytic fungi. We have investigated the T. reesei strain including mutants developed in Japan in detail to understand the molecular mechanisms that control the cellulase gene expression, the biochemical and morphological aspects that could favor this phenotype, and have attempted to generate novel strains that may be appropriate for industrial use. Subsequently, we developed recombinant strains by combination of these insights and the heterologous-efficient saccharifing enzymes. Resulting enzyme preparations were highly effective for saccharification of various biomass. In this review, we present some of the salient findings from the recent biochemical, morphological, and molecular analyses of this remarkable cellulase hyper-producing fungus.     

Physiological and molecular mechanisms of plant salt tolerance

Salt tolerance is an important economic trait for crops growing in both irrigated fields and marginal lands. The plant kingdom contains plant species that possess highly distinctive capacities for salt tolerance as a result of evolutionary adaptation to their environments. Yet, the cellular mechanisms contributing to salt tolerance seem to be conserved to some extent in plants although some highly salt-tolerant plants have unique structures that can actively excrete salts. In this review, we begin by summarizing the research in Arabidopsis with a focus on the findings of three membrane transporters that are important for salt tolerance: SOS1, AtHKT1, and AtNHX1. We then review the recent studies in salt tolerance in crops and halophytes. Molecular and physiological mechanisms of salt tolerance in plants revealed by the studies in the model plant, crops, and halophytes are emphasized. Utilization of the Na⁺ transporters to improve salt tolerance in plants is also summarized. Perspectives are provided at the end of this review.     

Deciphering the molecular basis of uterine receptivity

Uterine receptivity is defined as a limited time period during which the uterus enters into an appropriately differentiated state that is ready for the initiation of implantation by competent blastocysts. Although various cellular aspects and molecular pathways involved in uterine receptivity have been identified by gene expression studies and genetically engineered mouse models, a comprehensive understanding of the window of uterine receptivity is still missing. This review focuses on the recent progress in this area, with particular focus on the molecular basis of stromal‐epithelial dialogue and crosstalk between the blastocyst and the uterus during implantation. A better understanding of the underlying mechanisms governing the window of uterine receptivity is hoped to generate new strategies to correct implantation failure and to improve pregnancy rates in women. Mol. Reprod. Dev. 80: 8–21, 2013. © 2012 Wiley Periodicals, Inc.     

Deciphering the molecular mechanism of stop codon readthrough

Recognition of the stop codon by the translation machinery is essential to terminating translation at the right position and to synthesizing a protein of the correct size. Under certain conditions, the stop codon can be recognized as a coding codon promoting translation, which then terminates at a later stop codon. This event, called stop codon readthrough, occurs either by error, due to a dedicated regulatory environment leading to generation of different protein isoforms, or through the action of a readthrough compound. This review focuses on the mechanisms of stop codon readthrough, the nucleotide and protein environments that facilitate or inhibit it, and the therapeutic interest of stop codon readthrough in the treatment of genetic diseases caused by nonsense mutations.     

Soluble guanylate cyclase in molecular mechanisms underlying the therapeutic action of drugs

The influence of ambroxol (a mucolytic agent) on the activity of human platelet soluble guanylate cyclase and rat lung soluble guanylate cyclase and activation of both enzymes by NO-donors (sodium nitroprusside (SNP) and Sin-1) were investigated. Ambroxol in the range of concentrations from 0.1 to 10 ??M had no effect on the basal activity of both enzymes. Ambroxol inhibited in a concentration-dependent manner the SNP-induced human platelet soluble guanylate cyclase and rat lung soluble guanylate cyclase with the IC₅₀ values of 3.9 and 2.1 ??M, respectively. Ambroxol did not influence the stimulation of both enzymes by protoporphyrin IX. The influence of artemisinin (an antimalarial agent) on human platelet soluble guanylate cyclase activity and the enzyme activation by NO-donors were investigated. Artemisinin (0.1?100 ??M) had no effect on the basal activity of the enzyme. Artemisinin inhibited in a concentration-dependent manner the SNP-induced activation of human platelet guanylate cyclase with the IC₅₀ value of 5.6 ??M. Artemisinin (10 ??M) also inhibited (by 71 ± 4.0%) the activation of the enzyme by a thiol-dependent NO-donor, the derivative of furoxan, 3,4-dicyano-1,2,5-oxadiazolo-2-oxide (10 ??M), but did not influence the stimulation of soluble guanylate cyclase by protoporphyrin IX. It was concluded that the signaling system NO-soluble guanylate cyclase-cGMP is involved in the molecular mechanism of the therapeutic action of ambroxol and artemisinin.     

植物与植食性昆虫相互作用的分子机制

在长期的协同进化中,植物建立起应对昆虫取食为害的精密而又复杂的防御机制,植物转录组调控中防御应答基因的表达及防御物质的合成因不同的昆虫取食方式而异。一般来说,咀嚼式口器昆虫取食时造成大面积组织伤害,可诱导植物产生伤害反应;而刺吸式口器昆虫因其特殊的口针取食,诱导植物激活病原体相关的防御途径。不同的防御途径激活不同的识别机制和信号途径。本文从信号识别和转导上综述了不同食性的昆虫取食植物时所引发的防御反应,分析了昆虫-植物相互作用关系的分子机制。     

Deciphering the roles of acyl-CoA-binding proteins in plant cells

Lipid trafficking is vital for metabolite exchange and signal communications between organelles and endomembranes. Acyl-CoA-binding proteins (ACBPs) are involved in the intracellular transport, protection, and pool formation of acyl-CoA esters, which are important intermediates and regulators in lipid metabolism and cellular signaling. In this review, we highlight recent advances in our understanding of plant ACBP families from a cellular and developmental perspective. Plant ACBPs have been extensively studied in Arabidopsis thaliana (a dicot) and to a lesser extent in Oryza sativa (a monocot). Thus far, they have been detected in the plasma membrane, vesicles, endoplasmic reticulum, Golgi apparatus, apoplast, cytosol, nuclear periphery, and peroxisomes. In combination with biochemical and molecular genetic tools, the widespread subcellular distribution of respective ACBP members has been explicitly linked to their functions in lipid metabolism during development and in response to stresses. At the cellular level, strong expression of specific ACBP homologs in specialized cells, such as embryos, stem epidermis, guard cells, male gametophytes, and phloem sap, is of relevance to their corresponding distinct roles in organ development and stress responses. Other interesting patterns in their subcellular localization and spatial expression that prompt new directions in future investigations are discussed.     

Deciphering the molecular structure of cryptolepain in organic solvents

Solvent composition plays a major role in stabilizing/destabilizing the forces that are responsible for the native structure of a protein. Often, the solvent composition drives the protein into non-native conformations. Elucidation of such non-native structures provides valuable information about the molecular structure of the protein, which is unavailable otherwise. Inclusion of methanol (non-fluorinated alcohol) or TFE (fluorinated alcohol) in the solvent composition drove cryptolepain, a serine protease and an all-β-protein, into a non-native structure with an enhanced β-sheet or induction of α-helix. These solvents did not much affect cryptolepain under neutral conditions, even at higher concentrations, but the effects were predominant at lower pH, when the protein molecule is under stress. The organic solvent-induced state is partially unfolded with similar characteristics to the molten globule state seen with protein under a variety of conditions. Chemical- or temperature-induced unfolding of cryptolepain in the presence of organic solvent is distinctly different from that in the absence of organic solvent. Such different unfolding provided evidence of two structural variants in the molecular structure of the protein as well as the differential stabilization/destabilization of such structural variants and their sequential unfolding.     

Enhancement of hormone action by a phorbol ester and anti-tubulin alkaloids involves different mechanisms

The tumor-promoting phorbol ester 12-O-tetradecanoyl phorbol-13-acetate (TPA) enhanced 1-isoproterenol and prostaglandin E1 stimulated cyclic AMP formation in clones of mouse myeloid leukemic cells. The enhancement was found up to 3h after TPA treatment and had disappeared after 24h, indicating its reversibility. The effect of TPA was not inhibited by removal of extracellular Ca2+ or pre-treatment with the calcium ionophore A23187. This enhancement by TPA seems to involve a different pathway than enhancement of response to the same hormones after treatment with the anti-tubulin alkaloids colchicine or vinblastine, since a myeloid leukemic cell mutant clone that was non-responsive to the anti-tubulin alkaloids responded to TPA. Furthermore, combined treatment of colchicine-sensitive cells with TPA and colchicine showed an additive stimulating effect. The enhancement of cell response to hormones by TPA was found in myeloid leukemic cell clones that either were or were not induced to differentiate after treatment with TPA. This suggests that enhancement of the effect of these and possibly other hormones by TPA may be an initial step of TPA action, but that this enhancement is not sufficient to induce the wide repertoire of TPA effects including induction of differentiation.     

Computer search for molecular mechanisms of ulcerogenic action of non-steroidal anti-inflammatory drugs

Peptic ulcers are the most frequent side effect of therapy with non-steroidal anti-inflammatory drugs (NSAIDs). Good experimental evidence exists that pathogenesis of peptic ulcers cannot be attributed only to inhibition of cyclooxygenases. The knowledge about other molecular mechanisms of drug action associated with development of peptic ulcers could be useful for design of new safer NSAIDs. However, considerable time and material resources are needed for corresponding experimental studies. For simplification of the experimental search, we have developed an approach for in silico identification of putative molecular mechanisms of drug actions associated with their side effects. We have generated a data set of 85 NSAIDs, which includes information about their structures and side effects. Unknown molecular mechanisms of action of these NSAIDs were evaluated by the computer program PASS (Prediction of Activity Spectra for Substances) predicting more than 3000 molecular mechanisms of action based on structural formula of sub-stances. Statistically significant associations have been found between predicted molecular mechanisms of action and development of peptic ulcers. Twenty six molecular mechanisms of action probably associated with development of peptic ulcers have been found: two of them were known previously and 24 were quite new. Analyzing Gene Ontology data, data on signal and metabolic pathways, and available MEDLINE publication data, we proposed hypotheses on the role of 10 molecular mechanisms of action in the pathogenesis of peptic ulcer.     

Towards understanding molecular mechanisms of action of homeopathic drugs: An overview

The changes in the contents of cyclic AMP, cyclic GMP, ATP, ADP, AMP and fructose-2,6-bisphosphate that occur in the mantle tissue of the mussel Mytilus galloprovincialis Lmk were analysed with regard to the annual gametogenic cycle. Throughout 2 years, the lowest contents of AMP, ADP and ATP were detected during late winter-spring, whereas the maximum appeared in the autumn months. During the second year, fructose-2,6-bisphosphate and cAMP showed a very similar behaviour. The levels of both compounds rose throughout the year until a maximum in September. Their behaviour was also similar to that observed during the first year, but displaced in time. Both in 1998 and in 1999, the highest level of cGMP was detected during the spring-summer months. The results obtained suggest that the glycolytic pathway, with regard to the breeding cycle, might be regulated by fructose-2,6-bisphosphate and cyclic AMP through the activation of 6-phosphofructo-1-kinase, which is the main regulating enzyme of the glycolysis in mantle of M. galloprovincialis.     

Deciphering the molecular basis of memory failure in Alzheimer's disease

Acutely developing lesions of the brain have been highly instructive in elucidating the neural systems underlying memory in humans and animal models. Much less has been learned from chronic neurodegenerative disorders that insidiously impair memory. But the advent of a detailed molecular hypothesis for the development of Alzheimer's disease and the creation of compelling mouse models thereof have begun to change this situation. Experiments in rodents suggest that soluble oligomers of the amyloid beta protein (Abeta) may discretely interfere with synaptic mechanisms mediating aspects of learning and memory, including long-term potentiation. In humans, memory impairment correlates strongly with cortical levels of soluble Abeta species, which include oligomers. Local inflammatory changes, neurofibrillary degeneration, and neurotransmitter deficits all contribute to memory impairment, but available evidence suggests that these develop as a consequence of early Abeta accumulation. Accordingly, attempts to slow memory and cognitive loss by decreasing cerebral Abeta levels have entered human trials.     

Quantitation of the molecular mechanisms of biological synergism in a mixture of DNA-acting aromatic drugs

It is suggested that the widely reported biological synergism of a mixture of DNA-targeting aromatic drug molecules both in vivo and in vitro can be explained, in part, at the molecular level by competition between two basic mechanisms: the 'interceptor' (hetero-association between Drug1 and Drug2) and 'protector' mechanisms (complexation of Drug1 and Drug2 on DNA-binding sites). In the present work a complete analytical methodology has been developed to quantify these processes, providing an estimate of the relative importance of the interceptor/protector mechanisms using just a set of equilibrium association constants. The general methodology may be applied to other molecules with receptors for aromatic drugs.