Structural approach of the mechanism of inhibition of alpha-chymotrypsin by coumarins

A pharmacophore associated to the inhibiton of alpha-chymotrypsin has been built based on the structural and electronic characterization of a series of coumarin derivatives.     

Structural effects of hypermodified nucleosides in the Escherichia coli and human tRNALys anticodon loop: the effect of nucleosides s2U, mcm5U, mcm5s2U, mnm5s2U, t6A, and ms2t6A

Previous nuclear magnetic resonance (NMR) studies of unmodified and pseudouridine39-modified tRNA(Lys) anticodon stem loops (ASLs) show that significant structural rearrangements must occur to attain a canonical anticodon loop conformation. The Escherichia coli tRNA(Lys) modifications mnm(5)s(2)U34 and t(6)A37 have indeed been shown to remodel the anticodon loop, although significant dynamic flexibility remains within the weakly stacked U35 and U36 anticodon residues. The present study examines the individual effects of mnm(5)s(2)U34, s(2)U34, t(6)A37, and Mg(2+) on tRNA(Lys) ASLs to decipher how the E. coli modifications accomplish the noncanonical to canonical structural transition. We also investigated the effects of the corresponding human tRNA(Lys,3) versions of the E. coli modifications, using NMR to analyze tRNA ASLs containing the nucleosides mcm(5)U34, mcm(5)s(2)U34, and ms(2)t(6)A37. The human wobble modification has a less dramatic loop remodeling effect, presumably because of the absence of a positive charge on the mcm(5) side chain. Nonspecific magnesium effects appear to play an important role in promoting anticodon stacking. Paradoxically, both t(6)A37 and ms(2)t(6)A37 actually decrease anticodon stacking compared to A37 by promoting U36 bulging. Rather than stack with U36, the t(6)A37 nucleotide in the free tRNAs is prepositioned to form a cross-strand stack with the first codon nucleotide as seen in the recent crystal structures of tRNA(Lys) ASLs bound to the 30S ribosomal subunit. Wobble modifications, t(6)A37, and magnesium each make unique contributions toward promoting canonical tRNA structure in the fundamentally dynamic tRNA(Lys)(UUU) anticodon.     

Context‐dependent interplays between truncated demographies and climate variation shape the population growth rate of a harvested species

Fisheries ecologists traditionally aimed at disentangling climate and fishing effects from the population dynamics of exploited marine fish stocks. However, recent studies have shown that internal characteristics and external forcing (climate and exploitation) have interactive rather than additive effects. Thought most of these studies explored how demographic truncation induced by exploitation affected the response of recruitment to climate, identifying a general pattern revealed to be difficult as interactions are often case‐specific. Here we compared five exploited stocks of European hake Merluccius merluccius from the Atlantic Ocean and Mediterranean Sea to investigate how the interaction between internal characteristics and external forces affect the variability of the population growth rate and their consequences on recruitment. Our results show that demographic truncation induces a novel population scenario in which the growth rate is maximized when the reproductive stock is younger and less diverse. This scenario is shaped by the climate variability and the fishing pattern. The population growth rate becomes more dependent on the maturation schedule and less on the survival rates. The consequences for the recruitment dynamics are twofold; the effect of density‐dependent regulatory processes decreases while the effect of the density‐independent drivers increases. Our study shows that the interaction between internal characteristics and external forces changes across geographic locations according to 1) the importance of demographic truncation, 2) the influence of the climate on the regional hydrography and 3) the spatiotemporal heterogeneity of the physical environment to which fish life history is adapted.     

Ticket to spawn: Combining economic and genetic data to evaluate the effect of climate and demographic structure on spawning distribution in Atlantic cod

Climate warming and harvesting affect the dynamics of species across the globe through a multitude of mechanisms, including distribution changes. In fish, migrations to and distribution on spawning grounds are likely influenced by both climate warming and harvesting. The Northeast Arctic (NEA) cod (Gadus morhua) performs seasonal migrations from its feeding grounds in the Barents Sea to spawning grounds along the Norwegian coast. The distribution of cod between the spawning grounds has historically changed at decadal scales, mainly due to variable use of the northern and southern margins of the spawning area. Based on historical landing records, two major hypotheses have been put forward to explain these changes: climate and harvesting. Climate could affect the distribution through, for example, spatial habitat shifts. Harvesting could affect the distribution through impacting the demographic structure. If demographic structure is important, theory predicts increasing spawner size with migration distance. Here, we evaluate these hypotheses with modern data from a period (2000–2016) of increasing temperature and recovering stock structure. We first analyze economic data from the Norwegian fisheries to investigate geographical differences in size of spawning fish among spawning grounds, as well as interannual differences in mean latitude of spawning in relation to changes in temperature and demographic parameters. Second, we analyze genetically determined fish sampled at the spawning grounds to unambiguously separate between migratory NEA cod and potentially smaller sized coastal cod of local origin. Our results indicate smaller spawners farther away from the feeding grounds, hence not supporting the hypothesis that harvesting is a main driver for the contemporary spawning ground distribution. We find a positive correlation between annual mean spawning latitude and temperature. In conclusion, based on contemporary data, there is more support for climate compared to harvesting in shaping spawning ground distribution in this major fish stock in the North Atlantic Ocean.     

Genotype, soil type, and locale effects on reciprocal transplant vigor, endophyte growth, and microbial functional diversity of a narrow sagebrush hybrid zone in Salt Creek Canyon, Utah

When addressing the nature of ecological adaptation and environmental factors limiting population ranges and contributing to speciation, it is important to consider not only the plant's genotype and its response to the environment, but also any close interactions that it has with other organisms, specifically, symbiotic microorganisms. To investigate this, soils and seedlings were reciprocally transplanted into common gardens of the big sagebrush hybrid zone in Salt Creek Canyon, Utah, to determine location and edaphic effects on the fitness of parental and hybrid plants. Endophytic symbionts and functional microbial diversity of indigenous and transplanted soils and sagebrush plants were also examined. Strong selection occurred against the parental genotypes in the middle hybrid zone garden in middle hybrid zone soil; F(1) hybrids had the highest fitness under these conditions. Neither of the parental genotypes had superior fitness in their indigenous soils and habitats; rather F(1) hybrids with the nonindigenous maternal parent were superiorly fit. Significant garden-by-soil type interactions indicate adaptation of both plant and soil microorganisms to their indigenous soils and habitats, most notably in the middle hybrid zone garden in middle hybrid zone soil. Contrasting performances of F(1) hybrids suggest asymmetrical gene flow with mountain, rather than basin, big sagebrush acting as the maternal parent. We showed that the microbial community impacted the performance of parental and hybrid plants in different soils, likely limiting the ranges of the different genotypes.     

Effects of bioaugmentation on enhanced reductive dechlorination of 1,1,1-trichloroethane in groundwater: a comparison of three sites

Microcosm studies investigated the effects of bioaugmentation with a mixed Dehalococcoides (Dhc)/Dehalobacter (Dhb) culture on biological enhanced reductive dechlorination for treatment of 1,1,1-trichloroethane (TCA) and chloroethenes in groundwater at three Danish sites. Microcosms were amended with lactate as electron donor and monitored over 600 days. Experimental variables included bioaugmentation, TCA concentration, and presence/absence of chloroethenes. Bioaugmented microcosms received a mixture of the Dhc culture KB-1 and Dhb culture ACT-3. To investigate effects of substrate concentration, microcosms were amended with various concentrations of chloroethanes (TCA or monochloroethane [CA]) and/or chloroethenes (tetrachloroethene [PCE], trichloroethene [TCE], or 1,1-dichloroethene [1,1-DCE]). Results showed that combined electron donor addition and bioaugmentation stimulated dechlorination of TCA and 1,1-dichloroethane (1,1-DCA) to CA, and dechlorination of PCE, TCE, 1,1-DCE and cDCE to ethane. Dechlorination of CA was not observed. Bioaugmentation improved the rate and extent of TCA and 1,1-DCA dechlorination at two sites, but did not accelerate dechlorination at a third site where geochemical conditions were reducing and Dhc and Dhb were indigenous. TCA at initial concentrations of 5 mg/L inhibited (i.e., slowed the rate of) TCA dechlorination, TCE dechlorination, donor fermentation, and methanogenesis. 1 mg/L TCA did not inhibit dechlorination of TCA, TCE or cDCE. Moreover, complete dechlorination of PCE to ethene was observed in the presence of 3.2 mg/L TCA. In contrast to some prior reports, these studies indicate that low part-per million levels of TCA (<3 mg/L) in aquifer systems do not inhibit dechlorination of PCE or TCE to ethene. In addition, the results show that co-bioaugmentation with Dhc and Dhb cultures can be an effective strategy for accelerating treatment of chloroethane/chloroethene mixtures in groundwater, with the exception that all currently known Dhc and Dhb cultures cannot treat CA.     

Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes

Background  

Chaperonin proteins are well known for the critical role they play in protein folding and in disease. However, the recent identification of three diverged chaperonin paralogs associated with the human Bardet-Biedl and McKusick-Kaufman Syndromes (BBS and MKKS, respectively) indicates that the eukaryotic chaperonin-gene family is larger and more differentiated than previously thought. The availability of complete genome sequences makes possible a definitive characterization of the complete set of chaperonin sequences in human and other species.     

Size-related consumption of Scirpus maritimus tubers by greylag geese Anser anser explained by their functional response

To explain the preference of wintering greylag geese Anser anser for small Scirpus maritimus tubers (<10mm) over larger ones, our hypothesis was that the former would provide higher intake rates. This 'consumption rate hypothesis' was tested experimentally by deriving the functional responses of geese feeding on tubers of three contrasting sizes. Goose consumption rates were measured as: (i) feeding rate (tubers/min) and (ii) instantaneous intake rate (g fresh weight/min) on various tuber densities (5-200 tubers/tray). Geese had linear functional responses over the range of tuber densities offered, and tuber size affected their consumption rate. The results were then used to re-examine intake rates according to relative biomass of tubers found in the wild. In support of our hypothesis, the larger tubers allowed the lower intake rates. Foraging mechanisms that possibly control the tuber ingestion rate of geese were explored. After controlling (through chemical analyses) that nutritional components of tubers do not differ between sizes, it was concluded that geese preference is mainly due to size-related constraints (i.e. handling time) on their ingestion rates. Additional limiting factors (tuber extraction, digestion capacity) which are likely to constrain food intake of wild geese are also discussed.