Habitat ecology and food and feeding of the herring bow crab Varuna litterata (Fabricius, 1798) of Cochin backwaters, Kerala, India

Habitat ecology and food and feeding of the herring bow crab, Varuna litterata of Cochin Backwaters, Kerala, India were investigated for a period of one year (April 2011-March 2012). Among the 15 stations surveyed, the crabs were found to occur only in 4 stations, which had a close proximity to the sea. Sediment analysis of the stations revealed that the substratum of these stations is sandy in nature and is rich in organic carbon content (0.79% to 1.07%). These estuarine crabs is euryhaline and are found to be distributed in areas with a sandy substratum, higher organic carbon content and more tidal influx. The stomach contents analysis of crabs examined showed that their diet included crustacean remains, plants, sand and debris, fishes, miscellaneous group and unidentified matter. In adults and sub-adults, crustaceans formed the dominant food group, while in juveniles, sand and debris formed the dominant group. From the present study, V. litterata was found to be a predatory omnivore capable of ingesting both animal and plant tissues

The empirical study of the price mechanism in the Chinese housing market

In China, the history of the establishment of the private housing market is pretty short. Actually in less then two decades, the market has grown from almost the scratch to playing an important role in the economy. A great achievement! But many problems also exist. They need to be properly addressed and solved. Price problem---simply put, housing price is too high--- is one of them, and this paper is focused on it. Three basic questions are posed, i.e. (1) how to judge the housing affordability? (2) why the housing price is so high? (3) how to solve the housing price problem. The paper pays particular attention to answering the second question. Except the numerous news reports and surveys show that most of the ordinary city dwellers complained about the high housing price, the mathematical means, the four ratios, are applied to judge the housing affordability in Shanghai and Shenzhen. The results are very clear that the price problem is severe. So why? Something is wrong with the price mechanism. This research shows that mainly these five factors contribute to the price problem: the housing reform, the housing development model, the unbalanced housing market, the housing project financing and the poor governmental management. Finally the paper puts forward five suggestions to solve the housing price problem in first-hand private Chinese housing market. They include: the establishment of real estate information system, the creation of specific price management department, the government price regulation, the property tax and the legalization of "cushion money".

Effects of Different Feeding Regimes on the Digestibility and Faecal Excretion of Nitrogen, Soluble Carbohydrates and Fibre Fractions in Water Buffaloes kept under Subtropical Conditions

In the course of the ‘Livestock Revolution’, extension and intensification of, among others, ruminant livestock production systems are current phenomena, with all their positive and negative side effects. Manure, one of the inevitable secondary products of livestock rearing, is a valuable source of plant nutrients and its skillful recycling to the soil-plant interface is essential for soil fertility, nutrient - and especially phosphorus - uses efficiency and the preservation or re-establishment of environmentally sustainable farming systems, for which organic farming systems are exemplarily. Against this background, the PhD research project presented here, which was embedded in the DFG-funded Research Training Group 1397 ‘Regulation of soil organic matter and nutrient turnover in organic agriculture ’ investigated possibilities to manipulate the diets of water buffalo (Bubalus bubalis L.) so as to produce manure of desired quality for organic vegetable production, without affecting the productivity of the animals used. Consisting of two major parts, the first study (chapter 2) tested the effects of diets differing in their ratios of carbon (C) to nitrogen (N) and of structural to non-structural carbohydrates on the quality of buffalo manure under subtropical conditions in Sohar, Sultanate of Oman. To this end, two trials were conducted with twelve water buffalo heifers each, using a full Latin Square design. One control and four tests diets were examined during three subsequent 7 day experimental periods preceded each by 21 days adaptation. Diets consisted of varying proportions of Rhodes grass hay, soybean meal, wheat bran, maize, dates, and a commercial concentrate to achieve a (1) high C/N and high NDF (neutral detergent fibre)/SC (soluble carbohydrate) ratio (HH), (2) low C/N and low NDF/SC ratio (LL); (3) high C/N and low NDF/SC ratio (HL) and (4) low C/N and high NDF/SC (LH) ratio. Effects of these diets, which were offered at 1.45 times maintenance requirements of metabolizable energy, and of individual diet characteristics, respectively, on the amount and quality of faeces excreted were determined and statistically analysed. The faeces produced from diets HH and LL were further tested in a companion PhD study (Mr. K. Siegfried) concerning their nutrient release in field experiments with radish and cabbage. The second study (chapter 3) focused on the effects of the above-described experimental diets on the rate of passage of feed particles through the gastrointestinal tract of four randomly chosen animals per treatment. To this end, an oral pulse dose of 683 mg fibre particles per kg live weight marked with Ytterbium (Yb; 14.5 mg Yb g-1 organic matter) was dosed at the start of the 7 day experimental period which followed 21 days of adaptation. During the first two days a sample for Yb determination was kept from each faecal excretion, during days 3 – 7 faecal samples were kept from the first morning and the first evening defecation only. Particle passage was modelled using a one-compartment age-dependent Gamma-2 model. In both studies individual feed intake and faecal excretion were quantified throughout the experimental periods and representative samples of feeds and faeces were subjected to proximate analysis following standard protocols. In the first study the organic matter (OM) intake and excretion of LL and LH buffaloes were significantly lower than of HH and HL animals, respectively. Digestibility of N was highest in LH (88%) and lowest in HH (74%). While NDF digestibility was also highest in LH (85%) it was lowest in LL (78%). Faecal N concentration was positively correlated (P≤0.001) with N intake, and was significantly higher in faeces excreted by LL than by HH animals. Concentrations of fibre and starch in faecal OM were positively affected by the respective dietary concentrations, with NDF being highest in HH (77%) and lowest in LL (63%). The faecal C/N ratio was positively related (P≤0.001) to NDF intake; C/N ratios were 12 and 7 for HH and LL (P≤0.001), while values for HL and LH were 11.5 and 10.6 (P>0.05). The results from the second study showed that dietary N concentration was positively affecting faecal N concentration (P≤0.001), while there was a negative correlation with the faecal concentration of NDF (P≤0.05) and the faecal ratios of NDF/N and C/N (P≤0.001). Particle passage through the mixing compartment was lower (P≤0.05) for HL (0.033 h-1) than for LL (0.043 h-1) animals, while values of 0.034 h-1 and 0.038 h-1 were obtained for groups LH and HH. At 55.4 h, total tract mean retention time was significantly (P≤0.05) lower in group LL that in all other groups where these values varied between 71 h (HH) and 79 h (HL); this was probably due to the high dietary N concentration of diet LL which was negatively correlated with time of first marker appearance in faeces (r= 0.84, P≤0.001), while the dietary C concentration was negatively correlated with particle passage through the mixing compartment (r= 0.57, P≤0.05). The results suggest that manure quality of river buffalo heifers can be considerably influenced by diet composition. Despite the reportedly high fibre digestion capacity of buffalo, digestive processes did not suppress the expression of diet characteristics in the faeces. This is important when aiming at producing a specific manure quality for fertilization purposes in (organic) crop cultivation. Although there was a strong correlation between the ingestion and the faecal excretion of nitrogen, the correlation between diet and faecal C/N ratio was weak. To impact on manure mineralization, the dietary NDF and N concentrations seem to be the key control points, but modulating effects are achieved by the inclusion of starch into the diet. Within the boundaries defined by the animals’ metabolic and (re)productive requirements for energy and nutrients, diet formulation may thus take into account the abiotically and biotically determined manure turnover processes in the soil and the nutrient requirements of the crops to which the manure is applied, so as to increase nutrient use efficiency along the continuum of the feed, the animal, the soil and the crop in (organic) farming systems.

India’s Carbon Governance: The Clean Development Mechanism

Carbon Governance systems – institutional arrangements in place for mitigating greenhouse gas emissions – are different in emerging countries. Indeed, carbon is the same everywhere but Carbon Governance isn’t: in Brazil, the financial community is actively interested in carbon trading, but Chinese banks have hardly any interest in it; and while the Chinese government takes an active interest in providing capacity to project developers, the Brazilian authorities see their role uniquely as guarantors of environmental integrity of emissions reductions projects. In the case of India, carbon governance offers specific features of patterns and interactions mostly because India strongly developed the Clean Development Mechanism and its market. This article proposes a study to the research and understanding of how exactly carbon governance works in the Indian case, knowing that India is the second largest host of CDM projects.

Water for Food: Feeding what?

Key Findings: “Water for food” is not necessarily synonymous with “water for food security. Countries with similar geological conditions face very different geopolitical realities; national water policies and agricultural motivations reflect this. Water policies and research should seek to understand “water for food” and its connections with economics, the environment, and securities more broadly

Structural insights into the allosteric activation mechanism of cGMP-dependent protein kinase I

Cyclic GMP-dependent protein kinase (PKG) is a key transducer in the NO-cGMP signaling pathway. In this line, PKG has been considered an important drug target for treating hypertensive cardiovascular and pulmonary diseases. However, the investigation of PKG’s allosteric activation mechanism has been hampered by a lack of structural information. One of the fundamental questions on the cGMP-dependent activation of PKG is how the enzyme can distinguish cGMP over cAMP and selectively respond to cGMP. To ensure proper signaling, PKG must have developed unique features to ensure its activation upon the right activation signal. In this thesis, the cGMP-selective activation mechanism of PKG was studied through determining crystal structures of three truncated constructs of the regulatory domain [CNB-A (92-227), CNB-B (271-369), and CNB-A/B (92-351)] of PKG Iβ in the absence or presence of cyclic nucleotides. Herein, two individual CNB domain structures with biochemical data revealed that the C-terminal CNB domain (CNB-B) is responsible for cGMP selectivity, while the N-terminal CNB-domain (CNB-A) has a higher binding affinity for both cGMP and cAMP without showing any selectivity. Based on these crystal structures, mutagenesis studies were performed in which the critical residues for cyclic nucleotide selectivity and activation were identified. Furthermore, we discovered that the conformational changes of the C-terminal helix of the CNB-B that bridges between the regulatory and catalytic domains including the hydrophobic capping interaction are crucial for PKG activation. In addition, to observe the global conformation of the activated R-domain, I solved a co-crystal structure of the CNB-A/B with cGMP. Although a monomeric construct was crystallized, the structure displays a dimer. Strikingly, the CNB-A domain and its bound cGMP provide a key interface for this dimeric interaction. Using small angle X-ray scattering (SAXS), the existence of the cGMP-mediated dimeric interface within the CNB domains was confirmed. Furthermore, measuring cGMP-binding affinities (EC50) of the dimeric interface mutants as well as determining activation constants (Ka) revealed that the interface formation is important for PKG activation. To conclude, this thesis study provides a new mechanistic insight in PKG activation along with a newly found interface that can be targeted for designing PKG-specific activity modulators.

The NAFTA investment dispute settlement mechanism and the admissibility of amicus curiae briefs by NGOs

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Molecular mechanism involved in the mutagenicity induced by Aflatoxin B1

The aflatoxin B1 (AFB1) is a mycotoxin that has been identified as the most potent hepatocarcinogen. The metabolite resulting from detoxification process of AFB1 in liver, has the ability to react with the genomic DNA, generating AFB1-DNA adducts; during DNA replication process, this adduct induced the G:C→T:A transversion. Polymorphism in genes encoding for enzymes involved in the activation and detoxification of AFB1 and DNA repair enzymes has been associated with the risk of hepatocellular carcinoma (HCC) development. Additionally, in populations of high exposure to aflatoxin and high prevalence of hepatitis B virus (HBV) infection, has been demonstrated a synergism between these two risk factors for the development of HCC.

The use of insect cells to identify potent and selective inhibitors of the replication of the Dengue and Chikungunya viruses and unravel their molecular mechanism of action

Dengue and Chikungunya viruses cause the most important arthropod-borne viral infections for humans. These viruses are predominant in tropical and subtropical regions. In addition, these viruses are predominant in tropical and subtropical regions. Dengue mortality rate is around 1.2 to 3.5% and deaths due to chikungunya fever are around 1 in 1000; however, half of chikungunya-infected patients evolve into a chronic state that can persist for months up to years. There are no antiviral drugs available for DENV and CHIKV treatment and prevention. Moreover, vector control strategies have failed so far. Thus, the development of potent inhibitors for a broad spectrum of RNA viruses is urgently needed. We established and characterized a new embryonic insect cell line from Culex quinquefasciatus mosquito. Also we established the flaviviruses and alphavirus replication, both in C6/36 and Lulo insect cell lines, as well as in Vero cell line. In addition we carried out a reference compound library and reference panel of assays and data for DENV, which provides a benchmark for further studies. During this study, a panel of 9 antiviral molecules, with proven in vitro anti-dengue virus activity and that act at different stages of the DENV life cycle, was selected. Finally, Favipiravir or T-705, was identified as inhibitor in vitro and in vivo of alphaviruses and the mutation K291R in nsP4, which is responsible of the polymerase activity, was found as the mode of action in CHIKV. Interestingly, lysine in motif F1 is also highly conserved in positive-stranded RNA viruses and this might explain the broad spectrum of T-705 antiviral activity.

Self-deception as a mechanism for the maintenance of drug addiction

Resumen tomado de la publicaci??n

Destabilizing Mutations Alter the Hydrogen Exchange Mechanism in Ribonuclease A

The effect of strongly destabilizing mutations, I106A and V108G of Ribonuclease A (RNase A), on its structure and stability has been determined by NMR. The solution structures of these variants are essentially equivalent to RNase A. The exchange rates of the most protected amide protons in RNase A (35ºC), the I106A variant (35ºC), and the V108G variant (10ºC) yield stability values of 9.9, 6.0, and 6.8 kcal/mol, respectively, when analyzed assuming an EX2 exchange mechanism. Thus, the destabilization induced by these mutations is propagated throughout the protein. Simulation of RNase A hydrogen exchange indicates that the most protected protons in RNase A and the V108G variant exchange via the EX2 regime, whereas those of I106A exchange through a mixed EX1 1 EX2 process. It is striking that a single point mutation can alter the overall exchange mechanism. Thus, destabilizing mutations joins high temperatures, high pH and the presence of denaturating agents as a factor that induces EX1 exchange in proteins. The calculations also indicate a shift from the EX2 to the EX1 mechanism for less protected groups within the same protein. This should be borne in mind when interpreting exchange data as a measure of local stability in less protected regions

Pressure-jump-induced kinetics reveals a hydration dependent folding/unfolding mechanism of ribonuclease A

Pressure-jump (p-jump)-induced relaxation kinetics was used to explore the energy landscape of protein folding/unfolding of Y115W, a fluorescent variant of ribonuclease A. Pressure-jumps of 40MPa amplitude (5ms dead-time) were conducted both to higher (unfolding) and to lower (folding) pressure, in the range from 100 to 500MPa, between 30 and 50°C. Significant deviations from the expected symmetrical protein relaxation kinetics were observed. Whereas downward p-jumps resulted always in single exponential kinetics, the kinetics induced by upward p-jumps were biphasic in the low pressure range and monophasic at higher pressures. The relative amplitude of the slow phase decreased as a function of both pressure and temperature. At 50°C, only the fast phase remained. These results can be interpreted within the framework of a two-dimensional energy surface containing a pressure- and temperature-dependent barrier between two unfolded states differing in the isomeric state of the Asn-113–Pro-114 bond. Analysis of the activation volume of the fast kinetic phase revealed a temperature-dependent shift of the unfolding transition state to a larger volume. The observed compensation of this effect by glycerol offers an explanation for its protein stabilizing effect

Characterization and mechanism of action of the biological control agent Pantoea agglomerans EPS125

La soca EPS125 ha mostrat ser un efectiu agent de control biològic de diferents patògens fúngics de postcollita en diferents fruits. Degut a la seva elevada eficàcia, es va plantejar desenvolupar aquesta soca comercialment i per aquest motiu en el present treball es plantejà complementar la informació necessària pel seu registre. D'acord amb els resultats obtinguts mitjançant proves fenotípiques i genotípiques, la soca EPS125 queda inclosa dins l'espècie Pantoea agglomerans (Enterobacter agglomerans-Erwinia herbicola). En relació a la utilització de fonts de carboni, en el perfil i contingut d'àcids grassos cel·lulars i en el polimorfisme en la longitud dels fragments de macrorestricció genòmica (MRFLP), la soca EPS125 mostrà trets característics que la diferencien d'altres soques. Els dos marcadors moleculars (125.2 i 125.3) específics per la soca EPS125 dissenyats en el present treball mostraren ser semiespecífics per la seva detecció mitjançant la tècnica PCR i Real Time PCR. Quedant pendent l'anàlisi d'especificitat de l'ús combinat dels dos marcadors moleculars en una reacció PCR multiplex. P. agglomerans EPS125 ha mostrat ser molt efectiva en el control de Penicillium expansum en poma amb una dosi efectiva mitjana de 2.7x105 a 7x105 ufc/ml, i una ratio de 25-101 cèl·lules de la soca EPS125 per inactivar una espora del patogen segons el model de saturació hiperbòlica. Segons les aproximacions fenotípiques i estudis genotípics realitzats, sembla que els mecanismes de biocontrol utilitzats per la soca EPS125 contra P. expansum en poma estan directament relacionats amb la capacitat de formació de biofilm per aquesta soca.

Response of the benthic macroinvertebrate community to a point source in La Tordera stream (Catalonia, NE Spain)

Vam monitoritzar paràmetres físics i químics, macroinvertebrats bentònics, clorofil·la a, productors primaris i matèria orgànica durant un any (2001-2002) per examinar els efectes d'una font puntual sobre la composició taxonòmica, la estructura de la comunitat, l'organització funcional, la utilització de l'habitat i la estoquiometria al riu la Tordera (Catalunya). Aigües avall de la font puntual, concentració de nutrients, cabal i conductivitat eren majors que al tram d'aigües amunt, mentre que oxigen dissolt era menor. La densitat de macroinvertebrats era més elevada al tram d'aigües avall però la biomassa era similar als dos trams. La riquesa taxonòmica al tram de dalt era un 20% més alt que al tram de baix. Els anàlisis d'ordenació separen clarament els dos trams en el primer eix, mentre que els dos trams presentaven una pauta temporal similar en el segon eix. La similaritat entre els dos trams en composició taxonòmica, densitats i biomasses després de les crescudes d'abril i maig de 2002, indiquen que les pertorbacions del cabal poden actuar com a un mecanisme de reinici de la comunitat bentònica i jugar un paper important per a la restauració d'ecosistemes fluvials. Els dos trams presentaven una biomassa de perifiton, plantes vasculars, CPOM i FPOM similars, mentre que clorofil·la a, algues filamentoses, molses i SPOM eren majors al tram d'aigües avall. La densitat relativa de trituradors era menor sota la font puntual mentre que col·lectors i filtradors van ser afavorits. La biomassa relativa de trituradors també era menor sota la font puntual, però la biomassa de col·lectors i depredadors va augmentar. Les relacions entre densitat de grups tròfics i els seus recursos eren rarament significatives. La relació s'explicava millor amb la biomassa de macroinvertebrats. Els dos trams compartien la mateixa relació per raspadors, col·lectors i filtradors però no per trituradors i depredadors. La densitat i la biomassa de macroinvertebrats es trobaven positivament correlacionades amb la quantitat de recursos tròfics i la complexitat d'habitat, mentre que la riquesa taxonòmica es trobava negativament relacionada amb paràmetres hidràulics. La influència dels substrats inorgànics prenia menor rellevància per a la distribució dels macroinvertebrats. Els anàlisis d'ordenació mostren com les variables del microhabitat de major rellevància eren CPOM, clorofil·la a, algues filamentoses i velocitat. La cobertura de sorra només era significativa per al tram d'aigües amunt i les molses, al d'aigües avall. El número de correlacions significatives entre macroinvertebrats i les variables del microhabitat era més elevat per al tram de dalt que per al de baix, bàsicament per diferències en composició taxonòmica. La biomassa de macroinvertebrats va aportar una informació semblant a la obtinguda per la densitat. Perifiton i molses tenien uns continguts de nutrients similars en els dos trams. Els %C i %N d'algues filamentoses també eren similars en els dos trams però el %P sota la font puntual era el doble que al tram de dalt. Les relacions estoquiomètriques en CPOM, FPOM i SPOM eren considerablement menors sota la font puntual. Els continguts elementals i relacions van ser molt variables entre taxons de macroinvertebrats però no van resultar significativament diferents entre els dos trams. Dípters, tricòpters i efemeròpters presentaven una estoquiometria similar, mentre que el C i el N eren inferiors en moluscs i el P en coleòpters. Els depredadors presentaven un contingut en C i N més elevat que la resta de grups tròfics, mentre que el P era major en els filtradors. Els desequilibris elementals entre consumidors i recursos eren menors en el tram d'aigües avall. A la tardor i l'hivern la major font de nutrients va ser la BOM mentre que a la primavera i a l'estiu va ser el perifiton.

Mechanism of action of cyclic antimicrobial peptides

This PhD thesis is the result of the combination of experimental and computational techniques with the aim of understanding the mechanism of action of de novo cyclic decapeptides with high antimicrobial activity. By experimental techniques the influence of the replacement of the phenylalanine for tryptophan residue in their antimicrobial activity was tested and the stability in human serum was also analyzed, in order to evaluate their potential therapeutic application as antitumor agents. On the other hand, the interaction amongst the peptide BPC194 c(KKLKKFKKLQ), the best candidate from the whole library of cyclic peptides, and a model anionic membrane was simulated. The results showed a structure-function relationship derived from the stable conformation of the peptides involved in the membrane permeabilization. As a result, a rational design was performed being BPC490 the peptide with best antimicrobial activity compared with the best active peptide from the original library.