Miracle-dz/UniFAR-FTUs huggingface dataset:
Conformationally constrained α‐helical peptide models for protein ion channels

Recently we described the design, synthesis, and characterization of some simple amphiphilic α‐helical models for protein ion channels. These peptides, composed of only Leu and Ser residues, are hypothesized to form helical bundles capable of passing ions across phospholipid bilayers. In an effort to demonstrate that the peptides are, in fact, helical in their active ion‐conducting state, the conformationally constrained amino acid, Cα, Cα‐dimethylglycine (α‐aminoisobutyric acid, Aib), was introduced simulataneously at three positions into one of the model peptides, H2N‐(Leu‐Ser‐Leu‐Leu‐Leu‐Ser‐Leu)3‐CONH2, giving H2N‐(Leu‐Ser‐Leu‐Aib‐Leu‐Ser‐Leu)3‐CONH2. Examination of a tetrameric model for the channel suggested that this substitution should have a minimal effect on conductance. CD spectroscopy of the Aib‐modified and original peptide in phospholipid vesicles indicated that both were highly α‐helical. Furthermore, the Aib‐containing peptide formed proton channels nearly identical in conductance to the original peptide.
Increase of Liposome Stability by Incorporation of Bovine Serum Albumin

AbstractThe incorporation of the bovine serum albumin in the liposomal membrane to prevent leakage of the entrapped contents was studied. Adsorption of bovine serum albumin was found on the liposomes. After the adsorption of bovine serum albumin, by the addition of glutaraldehyde, the serum albumin molecules cross-linked to themselves and stiffened the membrane structure of the liposomes. It was found that the particle size of the liposomes increased after the treatment of glutaraldehyde. However, there was no significant change in particle size for the liposomes with the stirring effect. Adriamycin, methotrexate, carboxyfluorescein and mitoxantrone were entrapped into this liposome system. The loading efficiency demonstrated a similar value for the liposomes with and without the treatment of glutaraldehyde. However, for the entrapment of adriamycin, there showed an increase in loading efficiency with the effect of glutaraldehyde. For the leakage examination, a decrease of the release rate of the adriamyc.
The PRINTS protein fingerprint database: functional and evolutionary applications

The PRINTS database is a compendium of protein fingerprints used to assign uncharacterized sequences to known families and hence to infer tentative functions. Fingerprints are groups of conserved sequence motifs that together provide diagnostic family signatures – the diagnostic potency of fingerprints derives both from the mutual context afforded by matching motif neighbours (a feature that cannot be exploited by single-motif approaches), and from the hierarchical nature of the family analysis, which highlights the often-subtle differences that constitute the functional determinants between closely-related families and their subfamilies. In addition to its use as a signature resource, and the development of an automatic supplement, prePRINTS, we describe here other features that distinguish PRINTS from, and render it complementary to, related protein family databases; we also outline its application to investigations of evolutionary relationships and functional site predictions in complex gene families, such as ion channels, G protein-coupled receptors and phosphatases. Keywords: multiple motifs; hierarchical sequence analysis; signature database; protein family characterisation; G protein-coupled receptors; phosphatases; functional annotation; ligand binding; allosteric sites
Larval food source promotes cyclic seasonal variation in polyandry in the moth Lobesia botrana

In Mediterranean vineyards the European grapevine moth, Lobesia botrana, usually completes three non-overlapping larval generations per year. Larvae feed on inflorescences and unripe or ripe grapes. Previous work has shown that the larval food source has a huge effect on adult size and fitness. We investigated if larval food also affects the propensity of females to mate polyandrously. Levels of polyandry were monitored with baited traps in a vineyard for two years and then compared with data from laboratory trials using vine-reared individuals. In the field, polyandry levels followed a cyclic annual pattern associated with the larval food source. Large females that fed on ripe grapes exhibited significantly higher levels of polyandry than smaller females that fed on inflorescences. Females that fed on unripe grapes showed intermediate levels of remating. Polyandry also tended to increase later in each flight. Laboratory trials confirmed a direct effect of larval feeding on levels of polyandry. Overall, these results showed that the seasonal variation in polyandry exhibited by L. botrana in the field occurs, at least in part, because of food-derived changes regulating female size. Results also suggested that larval feeding could shape sexual size dimorphism and polyandry levels. Larval nutrition should therefore be considered as an important ecological factor by those studying the evolutionary significance of polyandry and sperm competition in the Lepidoptera. Copyright 2005.
Neural Networks and Related Methods for Classification

SUMMARY Feed-forward neural networks are now widely used in classification problems, whereas non linear methods of discrimination developed in the statistical field are much lesswidely known. A general framework for classification is set up within which methods from statistics, neural networks, pattern recognition and machine learning can be compared. Neural networks emerge as one of a class of flexible non-linear regression methods which can be used to classify via regression. Many interesting issues remain, including parameter estimation, the assessment of the classifiers and in algorithm development.
Biological indications of contaminant exposure in Atlantic cod (Gadus morhua) in the Baltic Sea

The Baltic Sea is exposed to severe human impacts. Besides eutrophication and overfishing, a variety of chemi- cal contaminants threaten the health of fish. During a cruise in December 2001, Atlantic cod (Gadus morhua) were col- lected in the western and southern Baltic Sea, somatic condition factors were estimated, and different biomarkers of contaminant exposure were analysed. Additionally, various polychlorinated biphenyl congeners and organochlorine pesti- cides were measured in cod liver as more general indicators of pollution, not necessarily as the causative agents for bio- marker signals. In most specimens, hepatic ethoxyresorufin-O-deethylase activity and bile 1-OH pyrene, a common polycyclic aromatic hydrocarbon metabolite, were detectable. Both features indicate an induction of the CYP1A biotrans- formation system in response to toxic substances. The increased occurrence of DNA adducts in some of the specimens also indicates the presence of genotoxic substances. Acetylcholinesterase was inhibited, an indication of exposure to orga- nophosphates, carbamates, or certain heavy metals, particularly in specimens taken at Wismar Bay and off the Lithuanian coast. In general, spatial differences in the biomarker responses as well as in contaminant loads were found, suggesting differences in physiologically active concentrations and mixtures of organic contaminants in this ecosystem.
A method for determining exoproteolytic activity in natural waters

—A very sensitive method allowing d étermination of exoproteolytic activity in nat­ ural water is based on the use of aminoacyl­ /3­naphthylamide, which gives rise to a flu­ orescent product upon hydrolysis of its pep­ tidelike bond by fîltered or unfiltered water samples. Specificity of the method to exopro­ teases is demonstrated by a strong compétitive inhibition effect of added proteins. A good corrélation is found between exo­ proteolytic activity and the rate of amino acid utilization by microheterotrophs in various aquatic environments.
Nitric oxide signaling through soluble guanylate cyclase

Soluble guanylyl/guanylate cyclase (sGC), the primary receptor for nitric oxide (NO), is a heme containing heterodimeric enzyme involved in numerous physiological events in animals. The small molecule YC-1 is known to stimulate sGC, but the mechanism behind this and the location of binding are unknown. I have developed a prokaryotic expression system for insect (Manduca sexta) sGC. The recombinant holoenzyme, like its mammalian counterpart, is responsive to NO, CO and YC-1, displaying a 175-fold increase in activity on binding. Truncated constructs of the enzyme that contain the Nterminal two-thirds of both subunits were designed to facilitate expression. With the highly pure material obtained, referred to as msGC-NT, we investigated NO and CO binding, reaction kinetics and regulation. Binding of NO to msGC-NT heme forms a sixcoordinate intermediate followed by release of the proximal histidine to yield a fivecoordinate nitrosyl complex (k6-5 = 12.8 s), as revealed by stopped-flow spectroscopy. The conversion rate is insensitive to nucleotides, YC-1 and changes in NO concentration up to ~30 micromolar. In contrast, NO release from msGC-NT is biphasic in the absence of YC-1 (koff1 = 0.10 s and koff2 = 0.0015 s), while binding of YC-1 eliminates the fast phase but has little effect on the slower phase. CO binding to msGC-NT is also regulated by YC-1. The CO release rate is reduced by YC-1 while the on rate remains unchanged, which leads to an ~50-fold increase in binding affinity. CO photolysis experiments indicate YC-1 binding leads to a substantial geminate recombination phase that is absent in the YC-1-free protein. Our data are consistent with a model for allosteric activation in which (1) YC-1 binds away from the catalytic site and (2) sGC undergoes a simple
In vitro Growth and Development of Encapsulated Shoot Tips of Different Banana and Plantain Cultivars

ABSTRACT Shoot apices isolated from in vitro cultures of eight banana and plantain (Musa sp.) cultivars were hydrogel encapsulated using 5% sodium alginate and 0.1 M calcium chloride. Both re-growth and survival were investigated at 90 days following encapsulation and subsequent development was observed on agar and cotton substrates supplied with MS nutrient medium. Cultivars (AAB, ABB and AB) displayed differences in their regrowth after encapsulation and cultivars with the B genomes exhibited better response.
A Fusion Visualization Method for Disaster Information Based on Self-Explanatory Symbols and Photorealistic Scene Cooperation

Scientific and appropriate visualizations increase the effectiveness and readability of disaster information. However, existing fusion visualization methods for disaster scenes have some deficiencies, such as the low efficiency of scene visualization and difficulties with disaster information recognition and sharing. In this paper, a fusion visualization method for disaster information, based on self-explanatory symbols and photorealistic scene cooperation, was proposed. The self-explanatory symbol and photorealistic scene cooperation method, the construction of spatial semantic rules, and fusion visualization with spatial semantic constraints were discussed in detail. Finally, a debris flow disaster was selected for experimental analysis. The experimental results show that the proposed method can effectively realize the fusion visualization of disaster information, effectively express disaster information, maintain high-efficiency visualization, and provide decision-making information support to users involved in the disaster process.
Secure Hybrid Mode-Based Cryptosystem

Problem statement: A cryptosystem provides two parties; a sender and a receiver to communicate interactively via an insecure channel in which, the sender is able to send any confidential message, document or data in a disguised form to the intended receiver. Upon receiving the disguised message, the receiver converts it to the intelligible message using his secret key. The security of the existing cryptosystems was based on a single hard problem such as factorization, discrete logarithm, quadratic residue, or elliptic curve discrete logarithm. Although these schemes appear secure, one day in a near future they may be broken if one finds a solution of a single hard problem. Approach: To overcome the disadvantage of using a single hard problem, we developed a secure hybrid mode-based cryptosystem based on the two well-known hard problems; factoring and discrete logarithm. We inject the element of the hard problems into our encrypting and decrypting equations respectively in such a way that the former equation depends on two public keys whereas the latter depends on two corresponding secret keys. Results: The new cryptosystem is shown heuristically secure against various algebraic attacks. The efficiency analysis confirms that our scheme only needs 3Texp+Thash time complexity for encryption and 2Texp time complexity for decryption and this magnitude of complexity is considered minimal for multiple hard problems-like cryptosystems. Conclusion: The newly developed hybrid mode based-cryptosystem provides greater security level than that schemes based on a single hard problem. The enemy or adversary has to solve the two problems simultaneously which is unlikely to happen in order to read any secret message.
Immunohistochemical detection of neuromodulators in the intestine of Salmo trutta L. naturally infected with Cyathocephalus truncatus Pallas (Cestoda)

Pathological and immunohistochemical investigations were carried out on the middle intestine of uninfected and parasitized brown trout, Salmo trutta L. , from the Ceresone Channel in North Italy. Eighty-six brown trout were sampled by electrofishing, and 32 (37.2%) were infected with Cyathocephalus truncatus Pallas, 1781 (Cestoda). The intensity of infection ranged from 1 to 82 parasites per host and the most infected segments were the anterior (near the pyloric caeca region) and the central part of the middle intestine. Immunohistochemical tests were applied on sections of intestinal tissue of healthy and infected fish, and the presence of substance P (SP), calcitonin gene related peptide (CGRP), met-enkephalin, vasoactive intestinal peptide (VIP), neuropeptide Y (NPY) and serotonin (5-HT) was documented. Endocrine epithelial cells of the tunica mucosa were positive to SP-, CGRP-, met-enkephalin-, and NPY-like peptides and 5-HT antisera; moreover, a higher number of these cells were recorded in the intestine of infected trout in comparison to uninfected fish. In addition, in parasitized S. trutta, SP-like and 5-HT immunoreactivities were found in likely immuno-related cells of the tunica propria-submucosa. Nerve cell bodies and terminals in the myenteric plexus were immunoreactive to almost all the tested peptides and 5-HT antisera. These data provide evidence for the role of the neuroendocrine system of S. trutta in the modulation of inflammatory responses to C. truncatus. Results are discussed with respect to a peptidergic involvement and host immune response to an intestinal tapeworm.
Synchronization of estrus and Ovulation in cattle

Summary Estrus detection has been cited as one of the most important factors affecting the reproduetive success of artificial insemination programs. Various estrus synchronization protocols have been developed to bring a large percentage of groups of females into estrus at a predetermined time. Earlier protocols have involved Controlling estrous cycle length in cattle either by extending the life span ofthe corpus luteum by the use of progestogens or shortening the life span of the corpus luteum by the use of Prostaglandin s. The reduced fertility following the earlier synchronization protocols made it necessary to understand ovarian follicular and corpus luteum dynamics in cattle. An increase in this basic understanding as well as the development of treatment regimes to manipulate ovarian follicular and corpus luteum dynamics over the last decade have resulted in development of better estrus synchronization protocols based on a) elimination of the dominant follicle and initiation of new follicular wave, b) initiation of new follicular wave, synchronization of Ovulation and timed artificial insemination. These protocols are very promising and have the potential to enhance pregnancy rates and the success of artificial insemination programs.
Age and the timing of breeding in a long‐lived bird: a role for stress hormones?

Summary 1. Young birds often reproduce later in the season than older ones, with poorer breeding success, but the proximate mechanisms involved in such a pattern remain poorly studied, especially in long-lived species. One possible mechanism is the endocrine stress response which is accompanied by the release of corticosterone. Elevated corticosterone levels can trigger physiological and behavioural responses that may delay or even suppress reproduction. 2. We tested the hypothesis that the delayed timing of breeding of young birds may be related to a greater susceptibility to stress compared with older ones during the pre-laying period of the breeding season. For this purpose, known-age (7–44 years old) pre-laying snow petrels, Pagodroma nivea, were monitored for baseline and acute stress-induced corticosterone levels. We examined whether baseline and stress-induced corticosterone levels were related to age, and whether they could influence the decision to breed and egg-laying date. 3. Young snow petrels were more likely to skip the breeding season and to breed later than middle-aged birds. In addition, the oldest birds bred later than middle-aged ones, suggesting a possible senescence on laying dates. Baseline corticosterone levels were independent of age but young and very old birds were more sensitive to stress than middle-aged ones. However, there was no effect of stress-induced corticosterone levels on breeding decision and egg-laying date. Elevated baseline corticosterone levels during the pre-laying period were associated with a higher probability of skipping breeding in females and a delayed timing of egg-laying in both sexes. 4. These results suggest that the greater susceptibility of young breeders to stress was not the functional mechanism explaining their delayed timing of breeding. Baseline corticosterone levels, although independent of age, appear to be a more likely mediator of breeding decision and egg-laying date. In long-lived birds, the relationship between age and timing of breeding may be rather indirect, as other age-related factors such as breeding experience or foraging skills may have a deeper impact on baseline corticosterone than age per se.
A review of the genus Pseudocalotes (Squamata: Agamidae), with description of a new species from West Malaysia

A new species of the genus Pseudocalotes ( P. dringi n. sp.) from the mountain forest of Western Malaysia is described. The holotype of the new species was formerly regarded as a syntype of P. floweri . A review of all species of the genus is given including a differential diagnosis and a key to the species. Diagnostic characters for the genera Bronchocela , Calotes , Dendragama were established. Paracalotes poilani and Pseudocophotis sumatrana , showing all diagnostic characters of the genus Pseudocalotes , are included in that genus. Members of Pseudocalotes of the Indochinese region can be differentiated from members inhabiting the Sunda region by the shape of the scales under the third toe.
Do Ponds on Golf Courses Provide Suitable Habitat for Wetland-Dependent Animals in Suburban Areas? An Assessment of Turtle Abundances

Abstract Golf courses represent a common type of anthropogenically modified habitat in suburban environments. Golf courses may provide suitable habitat for semi-aquatic animals in suburban areas, yet studies comparing animal abundances in golf course ponds with other pond types in suburban environments are somewhat limited. In this study, we compared turtle abundances in golf course ponds with ponds found in residential areas and ponds found in rural (farm) areas and examined the relationship between turtle abundance and residential land-cover within individual golf courses. We captured turtles in 10 golf course ponds, 5 ponds surrounded by residential development, and 5 ponds located on farms. We estimated abundance and the effects of pond area, pond type (i.e., residential, golf, farm) and percentage of residential development within golf course boundaries. Using binomial mixture models and Bayesian inference, we found that ponds surrounded by residential development had lower abundances of Painted Turtles (Chrysemys picta) and Sliders (Trachemys scripta) than ponds located on golf courses and farms. Additionally, golf courses that have a greater amount of residential development within course boundaries had fewer turtles than courses that contained minimal residential development. Our results suggest that golf courses can offer suitable habitat for semi-aquatic turtles in suburban areas. However, residential development within golf course boundaries appears to have a negative effect on local abundances. Thus, if golf courses are to be seen as reserves for wetland-dependent animals, golf courses with low housing density should be considered as a more preferable option than courses associated with extensive residential development.
Focal adhesion kinase in cancer

Focal adhesion kinase (FAK) has received much attention as a transducer of integrin-mediated signals. FAK becomes autophosphorylated on tyrosine 397 (Y397) in response to cell adhesion to the extracellular matrix (ECM) and in response to certain growth factors. Src-family kinases bind to FAK Y397 and mediate the phosphorylation of several additional tyrosine residues located within FAK. This leads to an enhancement of FAK activity and the recruitment of Grb2-SOS to the FAK signalling complex with subsequent activation of the Ras/ERK growth pathway in some cell types. Other signalling molecules such as Crk-associated substrate, Crk and paxillin can physically associate with FAK in response to adhesion to the ECM. FAK also seems to mediate cell migration and cell survival. Evidence obtained from several laboratories demonstrates that FAK is overexpressed in a variety of human cancers. FAK is not a classical oncogene and its overexpression appears to be a relatively late change in tumour progression. Because FAK can positively regulate the growth, migration and survival of cultured cells, it is likely that overexpression of FAK can contribute to the invasive/metastatic phenotype seen in late stage cancers. Therefore, FAK has received much attention as a point of therapeutic intervention in human cancers. The purpose of this article is to review the biology of FAK to date and to determine whether FAK inhibition might provide the much needed ‘magic bullet’ in cancer therapeutics.
Influence of food shortage during the summer on body composition and reproductive hormones in the red fox, Vulpes vulpes

Some mammalian carnivores compensate for prey shortage during the summer by increasing their consumption of wild berries. We tested whether such prey shortage affected all body components (e.g., fat, protein, water) equally, and whether it could affect reproduction. Two groups of wild red foxes (Vulpes vulpes) were kept in captivity: the first group was fed a control diet of dog food, and the second group was fed a diet of dog food and fresh apples for 8 weeks during midsummer. The experimental diet contained 95% of the energy content of the control diet but only 55% of the protein and 46% of the fat content. Foxes fed the experimental diet simultaneously lost body fat and protein on the apple diet, but body reserves were quickly restored upon return to the control diet. We found no evidence that protein and energy deficiency during summer impaired reproduction the following spring.