Miracle-dz/UniFAR-FTUs huggingface dataset:
Kinetic evidence for a constricted ammonia tunnel

Cytidine 5¢-triphosphate (CTP) synthase catalyses the ATPdependent formation of CTP from uridine 5¢-triphosphate using either NH3 or L-glutamine as the nitrogen source. The hydrolysis of glutamine is catalysed in the C-terminal glutamine amide transfer domain and the nascent NH3 that is generated is transferred via an NH3 tunnel [Endrizzi, J.A. , Kim, H. , Anderson, P.M. & Baldwin, E.P. (2004) Biochemistry 43, 6447–6463] to the active site of the N-terminal synthase domain where the amination reaction occurs. Replacement of Leu109 by alanine inEscherichia coli CTP synthase causes an uncoupling of glutamine hydrolysis and glutamine-dependent CTP formation [Iyengar, A. & Bearne, S.L. (2003) Biochem. J. 369, 497–507]. To test our hypothesis that L109A CTP synthase has a constricted or a leaky NH3 tunnel, we examined the ability of wild-type and L109A CTP synthases to utilize NH3 ,N H 2OH, and NH2NH2 as exogenous substrates, and as nascent substrates generated via the hydrolysis of glutamine, c-glutamyl hydroxamate, and c-glutamyl hydrazide, respectively. We show that the uncoupling of the hydrolysis ofc-glutamyl hydroxamate and nascent NH2OH production from N 4 -hydroxy-CTP formation is more pronounced with the L109A enzyme, relative to the wild-type CTP synthase. These results suggest that the NH3 tunnel of L109A, in the presence of bound allosteric effector guanosine 5¢-triphosphate, is not leaky but contains a constriction that discriminates between NH3 and NH2OH on the basis of size.
β-carotene ameliorates CUS-induced circadian alternations of locomotor activity and melatonin patterns in rats

Abstract Circadian and stress systems have a crucial role in adaptation of organisms to environmental challenges. This study investigates the ability of Oscillatoria brevis (O. brevis) β-carotene extract (βC) in modulating the circadian alternations of locomotor activity (LA) and serum melatonin (M) rhythms under chronic unpredictable stress (CUS) in rats. Twenty rats (5 rats/group) were used in monitoring LA using running wheels. Eighty rats (20 rats/group) were used in observing circadian serum M profile. Rats were randomly divided into four groups, viz. control, βC-treated, CUS-exposed, and “βC-treated&CUS-exposed” groups. CUS-exposure was applied for 21 days. One hour before exposure, βC was daily administered (10 mg/kg), intraperitoneally (IP). Blood was sampled at 6-h intervals for 5 rats/time point at Zeitgeber (ZT) 3, 9, 15, and 21. Results demonstrated that unstressed rats exhibited circadian M pattern and nocturnal LA rhythm with acrophase around ZT 21 and ZT 15, respectively. CUS-exposure revealed a disturbance in these patterns. Phase shifting of M and LA profiles was recorded. A decrease M acrophase and a significant decrease in LA (p < 0.05) were recorded at ZT 9. Daily βC administration in stressed rats modulates the CRs alternation induced by CUS. It may be concluded that βC ameliorated the induced alternations in circadian rhythms.
Nocturnal parasitism of moth eggs by Trichogramma wasps

ABSTRACT Parasitoid wasps of the genus Trichogramma are used worldwide as biological control agents against lepidopteran pests. Trichogramma wasps develop inside eggs of a wide range of host species, most of them moths. They are generally considered as diurnal insects. Here, we investigated whether Trichogramma wasps can also successfully parasitise host eggs at night under controlled laboratory conditions. Eggs of the moth Ephestia kuehniella were offered under dark conditions (scotophase) to females of Trichogramma brassicae and Trichogramma evanescens either from 9:00 PM to 9:00 AM or from 11:00 AM to 5:00 PM at four different temperatures (5°C, 10°C, 15°C and 20°C). Both species are known to parasitise E. kuehniella eggs in the photophase during daytime. The results show that T. brassicae did not parasitise eggs in the scotophase at night and only very few in the artificially induced scotophase during daytime from 10°C to 20°C. In contrast, T. evanescens parasitised more eggs in the dark both at night and artificially induced scotophase during daytime. Parasitism in the scotophase already started at 5°C, with more eggs being parasitised and more offspring being produced at higher temperatures. T. evanescens displayed higher parasitism activity in the induced scotophase during daytime than in the scotophase at night. The present study suggests that Trichogramma are capable of successfully parasitising host eggs at night, even at low temperatures, but that nocturnal activity with respect to parasitism varies between wasp species.
Identification of Efficacious Adjuvants for Sethoxydim and Bentazon

Experimental adjuvants were tested to maximize herbicidal activity of sethoxydim on quackgrass and of bentazon on common lambsquarters. Efficacious adjuvants were identified by measuring the 14C-herbicide droplet spread and absorption, as influenced by various adjuvants, on the target weed. The absorption and droplet spreadability of sethoxydim and bentazon on quackgrass and common lambsquarters leaves were increased or were decreased depending on the type of adjuvant used. No correlation was found between sethoxydim droplet spread and absorption on quackgrass. With bentazon, the relationship between these two factors was greater. Thus, measurement of droplet spread, as affected by adjuvants, was useful only as a screening technique for bentazon. Blending surfactants with paraffinic oil or soybean oil to form a crop oil concentrate changed the efficacy of the surfactant compared to the surfactant by itself. Surfactants most effective as components of paraffinic-oil based crop oil concentrate were different from surfactants ideal for inclusion with soybean oil-based crop oil concentrate. Thus, the effectiveness of a crop oil concentrate depends on herbicide, surfactant, and oil types. In the field, several of the superior adjuvants identified in the laboratory enhanced sethoxydim and bentazon activity on grass and broadleaf weeds.
Spring phenological adaptation of blue honeysuckle (Lonicera caerulea L.) foundation germplasm in a temperate climate1

Abstract: Blue honeysuckle (Lonicera caerulea L.) is a novel fruit crop that stands out for its northern climatic adaptation. Understanding spring phenological adaptation to temperate climate is central to development of a broader range of production and greater mainstream crop potential. In 2012 and 2013 across three sites in the Fraser Valley, British Columbia, spring phenophases from bud break to fruit harvest were determined across three foundation groups. Genetic variability is characterized for Russian, Japanese, and Kuril blue honeysuckle foundation groups used in breeding at the University of Saskatchewan, Saskatoon, SK. Germplasm group membership is the principal feature of phenological adaptation. Although temperate climate adaptation is limited in the Russian germplasm, the intermediate Japanese and later Kuril spring phenology provide an adequate degree of temperate climate adaptation to facilitate commercial production. These findings demonstrate that blue honeysuckle has phenological adaptation to a temperate climate. Diversity between and within genetic groups presents opportunities for crop enhancement, especially through breeding for later bloom periods.
Cell Division Studies of Escherichia Coli: Expression and Protein Localization of Cell Septation Gene, FtsA.

FtsA is a gene essential for cell septation. It has been postulated to have both regulatory and structural functions. To study the structural involvement of the FtsA protein in septum formation, four FtsA-LacZ protein fusions were constructed using a mini-Mu transposon (MudII1734). When maxicells containing either ftsA-lacZ or ftsA specifying plasmids were radioactively labelled and fractionated, FtsA-LacZ fusion protein and FtsA were located in both the membrane and cytoplasmic fractions. The FtsA-LacZ fusion proteins were also located in dividing wild type dividing cells by measuring fJgalactosidase activity. Cell envelope fractions from a sucrose equilibrium gradient had P-galactosidase activity in outer membraneheavy(OM„) and outer membrane-1ight(0ML) fractions. To verify the cellular location of native FtsA protein in membrane fractions, an expression plasmid was constructed by placing a ftsA-lacZ gene fusion downstream from a X PL promoter. The FtsA-LacZ fusion protein was overproduced and purified by 0-galactosidase affinity column chromatography. Polyclonal antibodies to this protein were isolated and demonstrated to be specific for the FtsA-LacZ fusion, FtsA protein and B-galactosidase. Cross reactivity to FtsA protein was found in outer membrane fractions, 0M„ and 0ML, and inner membrane fraction of wild type cells. These data suggest that the FtsA protein may be functioning as an inner-outer membrane protein in septation.
Spatial variation in herbivory, climate and isolation predicts plant height and fruit phenotype in Plectritis congesta populations on islands

Climate and herbivory can each drive natural selection on plant traits but may interact to give rise to different patterns in trait distributions when surveyed across island populations. These different patterns may arise because the occurrence of ungulate herbivores often varies across archipelagos, potentially leading to strong and abrupt spatial heterogeneity in the direction or intensity of natural selection. In contrast, climate tends to vary gradually and thus is more likely to lead to gradual clines in trait values. Population isolation may also affect trait values, given that random genetic drift may fix alleles or traits in the absence of gene flow or because gene flow between populations with similar or opposing selection pressures may augment or swamp the effects of selection. Here, we estimate the independent and interactive effects of deer, climate and isolation on fruit phenotype and plant height in 285 Plectritis congesta populations at 77 island and 44 mainland sites in western North America. Plectritis congesta is a palatable winter annual with two fruit phenotypes based on a simple Mendelian locus with clear dominance and heritable variation in height as a polygenic trait. Fruit phenotype and plant height were well predicted by deer occurrence; plants in populations with resident deer were short (15.0 ± 1.1 cm) and mainly expressed wingless fruits (73.0 ± 4.0%), whereas plants in populations without deer were 2.6 times taller (38.9 ± 5.3 cm) and only 9.0 ± 1.6% expressed wingless fruits. Wingless fruits were less common in populations experiencing wetter conditions with more seasonal variability in temperatures, particularly in the absence of deer. In contrast, population isolation was unrelated to fruit phenotype, except in populations rarely exposed to deer, where plants expressed phenotypes more like those in populations without deer as isolation increased. Our results are consistent with the hypothesis that spatial variation in browsing by deer or other factors correlated with it contributes to population‐level variation in fruit phenotype and plant height in P. congesta and that climate leads to a modest spatial gradient in plant height. Synthesis. The occurrence of deer at 285 island and mainland populations of Plectritis congesta predicted plant height and fruit phenotype, supporting the hypothesis that spatial variation in herbivory is a key factor affecting population‐level variation in the distribution of these heritable traits.
Evolutionary and biogeographic relationships of related Ranunculus taxa: dispersal, vicariance and pseudovicariance as mechanisms of change

Background: The disjunct distribution patterns of a taxon may arise when previously continuous distribution ranges are fragmented. The phenomena of vicariance and dispersal, together with hybridisation as an important source of genetic variation in natural populations, can play an important role for structuring the distribution of taxa. Aims: We investigated the biogeographical relationships of the Iberian endemic plant Ranunculus angustifolius s.l. by reconstructing ancestral geographical distributions, using a combination of phylogenetic and distributional information. Methods: Phylogenetic and network analyses of nuclear internal transcribed spacers and plastid sequence data (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM) were used to infer vicariance and dispersal events. Results: Phylogenetic and biogeographical analyses suggested that both dispersal and vicariance were important in creating the current disjunct distribution pattern. Some other factors, such as hybridisation, introgression and vicariance (or pseudovicariance), were important in the evolutionary history of the taxa R. angustifolius s.l. Conclusions: Our results demonstrate the importance for analysing biogeographical patterns with the use of both nuclear and chloroplast DNA to infer the evolutionary history of plant species with a disjunct distribution. Our results show that phenomena such as dispersal, vicariance and pseudovicariance are not mutually exclusive.
Heritability: the link between development and the microevolution of molar tooth form

Abstract The developmental gene expression, morphogenesis, and population variation in mammalian molar teeth has become increasingly well understood, providing a model system for synthesizing evolution and developmental genetics. In this study, we estimated additive genetic covariances in molar shape (G) using parent-offspring regression in Cryptotis parva, the Least Shrew. We found that crown shape had an overall h2 value of 0.34 (±0.08), with higher heritabilities in molar cusps than notches. We compared the genetic covariances to phenotypic (P) and environmental (E) covariances, and to the covariances in crown features expected from the enamel knot developmental cascade (D). We found that G and D were not strongly correlated and that major axes of G (evolutionary lines of least resistance) are better predictors of evolutionary divergences in soricines than is D. We conclude that the enamel knot cascade does impose constraints on the evolution of molar shape, but that it is so permissive that the divergences among soricines (whose last common ancestor lived about 14 million years ago) do not fully explore its confines. Over tens of millions of years, G will be a better predictor of the major axes of evolution in molar shape than D.
Water-Deficit Stress Tolerance Differs between Two Locoweed Genera (Astragalus and Oxytropis) with Fungal Endophytes

Locoweeds are plants of the genera Astragalus and Oxytropis (Fabaceae family) and are toxic to cattle, sheep, and horses. The toxic property of locoweeds is due to the alkaloid swainsonine (SWA), which is synthesized by an endophytic fungus Alternaria spp. section Undifilum. Although the endophyte–locoweed complex is often considered mutualistic, empirical evidence for benefits to host plants is lacking. This study: 1) compared the growth, photosynthesis, and leaf pigment and antioxidant concentrations between endophyte-infected and endophyte-free plants under well-watered and water-deficit conditions; and 2) measured SWA to determine whether SWA concentrations are attenuated by water deficit and leaf age. Locoweed species in this study were woolly loco and silky crazyweed. Endophyte-infected and endophyte-free (by removal of seed coat) seedlings, as confirmed by DNA analyses, were grown under greenhouse conditions for 6 mo, after which plants were subjected to three 12- to 15-d water-deficit periods that created sublethal drought conditions. Results suggest that the endophyte did not influence photosynthetic gas exchange and leaf pigment concentrations. Under well-watered conditions only, endophyte-infected woolly loco plants had lower shoot and root biomass and higher concentrations of α-tocopherol than endophyte-free plants. SWA analyses revealed taxon-specific effects of water deficit, with water deficit increasing SWA concentrations in young leaves of woolly loco but not affecting SWA concentration in silky crazyweed. These results suggest that the endophyte behaves as a parasite in woolly loco plants grown under optimal but not under water-limited conditions. Further, results indicate that drought conditions elevate the toxicity of woolly loco plants. Improved understanding of endophyte-locoweed interactions and factors influencing SWA levels will contribute to the development of livestock management strategies to predict toxicity in particular locoweed populations. Nomenclature: Silky crazyweed, Oxytropis sericea Nutt. ; woolly loco, Astragalus mollissimus Torr.
Produção e distribuição temporal de néctar em área de regeneração de cerrado: implicações na polinização e estrutura de comunidade de abelhas

8 1. Introdução. 9 2. Material e Métodos. 10 2.1. Área de estudo.10 2.1. 1. Caracterização do bioma Cerrado.10 2.1. 2. Local de estudo.11 2.2. Coleta de dados.12 2.2.1. Avaliação das espécies nectaríferas em floração. 12 2.2.2. Avaliação da produção de néctar segundo a forma e o tamanho das flores.13 2.2.3. Avaliação da distribuição temporal do néctar. 13 2.3 Análises estatísticas. 13 3. Resultados.14 3.1. Espécies nectaríferas em floração na EEJ.14 3.2. Avaliação da produção de néctar segundo a forma e o tamanho das flores.16 3.3. Avaliação da distribuição temporal do néctar. 20 4. Discussão. 23 5. Referências bibliográficas. 27 Capítulo II A produção do néctar está associada à diversidade de visitantes florais e interação intraespecífica pólen/estigma em espécies de plantas nectaríferas? 32 Resumo.33 Abstract.34. 34 1. Introdução. 35 2. Material e Métodos. 36
Variability in DNA COI sequences reveals new haplotypes in freshwater turtles from northern region of India

Abstract The chelonian represents a diverse order of turtles. Little is known about this group from India at molecular level. Cytochrome c oxidase I (COI) sequences of 125 individuals from nine species of freshwater turtles were generated and analyzed. A total of 118 nucleotide positions in COI gene as character-based DNA barcodes for each species were identified. Neighbour-joining (NJ) analyses tree well differentiated freshwater hard shell and softshell turtle. Overall species divergence (K2P) was 13.3%. Analysis of COI sequences from present study, combined with sequences downloaded from NCBI GenBank, revealed new COI haplotypes from Northern region of India.
Characterizing change points and continuous transitions in movement behaviours using wavelet decomposition

Individual behaviour, that is, the reaction of an organism to internal state, conspecifics and individuals of other species as well as the environment, is a crucial building block of their ecology. Modern tracking techniques produce high‐frequency observations of spatial positions of animals and accompanying speed and tortuosity measurements. However, inferring behavioural modes from movement trajectories remains a challenge. Changes in behavioural modes occur at different temporal and spatial scales and may take two forms: abrupt, representing distinct change points; or continuous, representing smooth transitions between movement modes. The multi‐scale nature of these behavioural changes necessitates development of methods that can pinpoint behavioural states across spatial and temporal scales. We propose a novel segmentation method based on the discrete wavelet transform (DWT), where the movement signal is decomposed into low‐frequency approximation and high‐frequency detail sub‐bands to screen for behavioural changes at multiple scales. Approximation sub‐bands characterizes broad changes by taking the continuous variations between behavioural modes into account, whereas detail sub‐bands are employed to detect abrupt, finer scale change points. We tested the ability of our method to identify behavioural modes in simulated trajectories by comparing it to three state‐of‐the‐art methods from the literature. We further validated the method using an annotated dataset of turkey vultures (Cathartes aura) relating extracted segments to the expert knowledge of migratory vs. non‐migratory patterns. Our results show that the proposed DWT segmentation is more versatile than other segmentation methods, as it can be applied to different movement parameters, performs better or equally well on the simulated data, and correctly identifies behavioural modes identified by the experts. It is hence a valuable addition to the toolbox of land managers and conservation practitioners to understand the behavioural patterns expressed by animals in natural and human‐dominated landscapes.
COMPUTATIONAL STUDIES ON THE COGNATE AND NON-COGNATE AMINOACYL-tRNAs

Although kinetic proofreading plays a major role in the fidelity of protein synthesis, it only includes the codon-anticodon interaction without considering the amino acid side chain. It is not known whether the ribosome has a specific interaction with the amino acid side chain or if the correctly charged tRNA behaves in such a way that brings this fidelity to protein synthesis process. To answer this question, we performed some preliminary calculations using numerical analysis on the misacylated tRNAs and compared the results with that of the cognate aminoacyltRNAs. Due to the large size of the molecule, we used 2-layered ONIOM (QM/MM) calculations. Interestingly, it was observed that only the initiator tRNAi met has a specific interaction with the amino acid side chain. (Keywords: Protein synthesis, aminoacyl-tRNA, ribosome.)
Landscape‐level tree cover predicts species richness of large‐bodied frugivorous birds in forest fragments

Large‐bodied frugivorous birds play an important role in dispersing large‐sized seeds in Neotropical rain forests, thereby maintaining tree species richness and diversity. Conversion of contiguous forest land to forest fragments is thought to be driving population declines in large‐bodied frugivores, but the mechanistic drivers of this decline remain poorly understood. To assess the importance of fragment‐level versus local landscape attributes in influencing the species richness of large‐bodied (>100 g) frugivorous birds, we surveyed 15 focal species in 22 forest fragments (2.7 to 33.6 ha, avg. = 16.0 ha) in northwest Ecuador in 2014. Fragment habitat variables included density of large trees, canopy openness and height, and fragment size; landscape variables included elevation and the proportion of tree cover within a 1 km radius of each fragment. At both the individual species level, and across the community of 12 species of avian frugivore we detected, there was higher richness and probability of presence in fragments with more tree cover on surrounding land. This tendency was particularly pronounced among some endangered species. These findings corroborate the idea that partially forested land surrounding fragments may effectively increase the suitable habitat for forest‐dwelling frugivorous birds in fragmented landscapes. These results can help guide conservation priorities within fragmented landscapes, with particular reference to retaining trees and reforesting to attain high levels of tree cover in areas between forest patches.