Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and Functional Aspects of RGD-Containing Cyclic Pentapeptides as Highly Potent and Selective Integrin αVβ3 Antagonists

The αVβ3 integrin is implicated in human tumor metastasis and in angiogenesis. The design of low-molecular-mass αVβ3 antagonists by “spatial screening” led to the highly active peptides c(RGDFV) and c(RGDFV). Here the influence of the amino acids in positions 4 and 5 flanking the RGD-sequence on the inhibition of vitronectin and fibrinogen binding to the isolated αVβ3 and αIIbβ3 receptors was investigated. The influence of the side chain and the backbone conformation on activity and selectivity was studied. The compounds were divided into conformational classes. For each class at least one representative peptide was subjected to detailed structure determination in solution. The peptides of classes 1, 2, and 3 show a βII‘/γ-turn arrangement with the d-amino acid in the i + 1 position of the βII‘-turn. By contrast, the peptides of class 4 reveal a modified βII‘/γ-turn pattern with glycine in the i + 1 position of the βII‘-turn and the d-amino acid in the i + 1 position of the γ-turn. Class 1 is divided into.
Genetic Diversity in Population of Fusarium Solani From Cumin in Iran

Nineteen isolates of Fusarium solani were recovered from crown and root rotted parts of cumin plants collected from the major cumin producing area in Iran during 1999-2000 using Nash-Snyder media. One hundred and fifty eight nit mutants of F. solani were generated using PDA amended with 3% and 5% potassium chlorate. Of the nit mutants generated, 47/7%, 26/6% and 25/9% were nit1, nit3 and nitM, respectively. Nit mutants were used to force heterokaryon formation to determine VCGs and their relation to pathogenecity and geographic origin. Fifteen VCGs were determined for F. solani isolates, that 12 were single members VCGs. There was no specific relation between VCGs and geographic origin in F. solani isolates. This is the first research on the genetic diversity of F. solani from cumin.
Analysis of Phytochemical and Antibacterial Activity of Carissa spinarum Linn Crude Extracts

Aims: To screen for the antibacterial activity of Carissa spinarum L. crude extracts against Escherichia coli and Staphylococcus aureus . The phytochemicals that are responsible for the bioactivity were also screened. Study Design: In vitro assay of antibacterial properties. Place and Duration of Study: Samples were collected from Samunge village at Loliondo in Ngorongoro district located in northern Tanzania. Extraction and phytochemical analyses were conducted at the Department of Traditional Medicine of the National Institute of Medical Research (NIMR) in Dar-es-Salaam, Tanzania. Antimicrobial bioassay was carried out at Department of Molecular Biology and Biotechnology at the University of Dar-es-Salaam between March 2013 and June 2013. Methodology: Disk diffusion test was used to determine antimicrobial activity of the plant extracts. Chemical tests were used to determine the group of phytochemicals present in
Climatic relationships of some New Zealand forest tree species

A dataset of some 10 000 plots was used to describe the climatic relationships of 33 widespread New Zealand tree species. Estimates of mean annual temperature, temperature seasonality, mean annual solar radiation, and moisture balance were derived from mathematical surfaces fitted to climate station data. Plots were also categorized into five lithological classes and three drainage classes. Generalized additive models were used to examine species/environment relationships. Mean annual temperature and mean annual solar radiation are most strongly correlated with current tree distributions, followed by moisture balance, temperature seasonality, lithology, and drainage. Most broad-leaved tree species other than Nothofagus spp. reach their greatest levels of occurrence in warm, moist environments with high solar radiation. In contrast, Nothofagus spp. generally reach their greatest levels of occurrence in cooler and/or lower insolation environments, and all have lower levels of occurrence on rhyolitic substrates which have resulted from large-scale geomorphic disturbance, mostly over the past few thousand years. Although coniferous species have widely differing climatic optima, many are biased towards lithological classes characterized either by large-scale geomorphic disturbance or harsh edaphic conditions. The relevance of these results to particular synecological questions is briefly discussed. Continuing adjustments in the range of slow-dispersing Nothofagus spp. are strongly suggested, and the climatic suitability of extensive rhyolitic basins in the central North Island, from which these species are largely absent, is confirmed.
Health and reproduction: the sex-specific clinical profile of great tits (Parus major) in relation to breeding

To describe the changes in clinical profile of individuals that occur during different stages of the reproductive cycle, 17 condition indices including leukocyte counts, plasma protein and metabolite concentrations, hematocrit, and hemoparasite prevalence were examined in prelaying and brood-rearing great tits (Parus major). The metabolic profile pointed to increased fat metabolism during the prebreeding period. Protein metabolism did not indicate nutritional limitation. Prelaying birds had elevated gamma-globulin levels, which may indicate either greater investment in humoral immune defence or, alternatively, greater exposure to immune challenge than for breeders. The sexes did not differ with respect to prevalence of hemoparasites, but females had generally lower albumin/globulin ratios than males, which might indicate a greater predisposition to infectious diseases. Breeding females had higher hematocrit values and heterophile/lymphocyte ratios than males, suggesting that brood rearing imposes a greate.
Diatom and crustacean zooplankton communities, their seasonal variability and representation in the sediments of subarctic Lake Saanajärvi

Present and past diatom and crustacean zooplankton communities of subarctic Lake Saanajarvi in Finnish Lapland were studied with special emphasis on their representation in the sediment surface. Two years monitoring of the present state of the lake revealed it to be ultraoligotrophic with a biomass peak during autumn overturn. Chrysophytes and diatoms were the most abundant phytoplankton groups, with four species forming the main bulk of the crustacean zooplankton community. The comparison of the present plankton community with the species composition in the sediment surface showed that only some plankton groups are suitable for paleolimnological studies. The value of diatoms for paleolimnological studies was supported by the observation that all of the species recorded from various habitats in the lake were detectable in the sediment. In addition, some species (e.g. Cyclotella glomerata) that limnological sampling had not detected were found in the sediment record. Similarly, the zooplankton class Chydoridae and Daphnia hyalina species were equally or better represented in the sediment than in the water column. On the other hand, the sediment trap and core evidence of the whole crustacean zooplankton community suggested many zooplankton species have little or no significance in paleolimnological studies. For example the two dominant copepod species, Eudiaptomus graciloides and Cyclops abyssorum, were not detectable in sediment trap samples. These findings indicate that only a small fraction of the living biota are preserved in the sediments, and this should be taken into account when drawing conclusions based on the detection of just one such species group.
Flashes of Photuris Fireflies: Their Value and Use in Recognizing Species

Mating flashes provide excellent clues for recognizing biological species of fireflies. Since Photuris species also flash in contexts in which species-specificity would appear to be irrelevant, mating flashes must be distinguished; since the parameters of mating flashes that do not encode species information may vary considerably, these signals must be critically analyzed. The use of mating flashes for species recognition has spatial and temporal limitations.
Constraints on the plasticity of Daphnia magna influenced by fish-kairomones

1. Daphnia magna reproduced at a smaller size (body mass) when exposed to fish-kairomone than D. magna growing up without this cue. 2. The total egg mass for first reproduction was the same in both groups, but the proportion of clutch mass to total body mass was about 11% higher in daphniids exposed to fish-kairomone. This difference was about the same for low and high food concentrations (0·5 or 1·5 mgC l−1). 3. Although egg mass was the same, triglyceride (TAG) content of the egg material was significantly lower when daphniids were exposed to fish-kairomones for both food concentrations. 4. The TAG content of the clutch was lowered to the extent that the TAG proportion in the clutch in relation to the somatic mass of the animal was the same for animals treated with fish-kairomone and controls (5% of body mass at first reproduction). 5. The lower TAG content per clutch resulted in a lower quality of the individual egg in daphniids exposed to fish-kairomone. The resulting higher susceptibility to starvation under low food conditions is a substantial cost of the plastic response to fish-kairomones. 6. This cost may set a limit on the plastic response in resource allocation of Daphnia magna exposed to fish-kairomones. However, daphniids living in a system with fish predation are more likely to be eaten by fish than to starve to death.
Comparison of dispersal and other movements in two Badger (Meles meles) populations

The dispersal and other movement patterns in two Badger populations, one in rural Gloucestershire and the other in suburban Bristol, are described and categorized into nine different types of movement. Movements were less common in the high density Badger population in Gloucestershire, but disturbance increased the likelihood of movements occurring. In the lower density Bristol population, where the social structure was more fluid, movements were more common. However, in both populations truly itinerant Badgers appeared to be rare. More male than female Badgers moved, but for each type of movement there was no difference in the distance moved by males and females. Movements were rare in animals less than a year old; most movements occurred in sexually mature animals, i.e. those more than 2 years old.
Ecologic Overlap and Interspecific Strife in Breeding Population of Anna and Allen Hummingbirds

Analyses of interspecific competition in natural populations are fundamental to modern theory in ecology and evolution. Yet, at least among higher vertebrates, few examples with supporting details are on record, and current theories require corroboration in the field (Errington 1946; Crombie 1947; Richards 1948; Lack 1949). This will come slowly, chiefly because the proper recording and interpretation of competitive incidents in the field require a long and intimate field acquaintance with a given species and because the details of such incidents are often elusive or subtle. Also, the true nature of adaptive differences between closely similar species may escape detection unless these are observed in competition (Lack 1944; Crombie 1947). The object of this paper is to examine ecological differences between two sympatric species of hummingbirds which overlap in both geographic and habitat distribution, providing an example of what, in Schmalhausen's (1949) classification of competitive situations, is termed "active intergroup competition. " The Anna hummingbird (Calypte anna) and the Allen hummingbird (Selasphorus sasin, formerly S. alleni) are almost restrictedly Californian in breeding distribution, and their breeding ranges overlap along the coast from the San Francisco Bay region to Ventura County (Grinnell and Miller 1944). The evidence to be presented here was obtained in the course of a five-year census, in the period from 1943 to 1947, of the breeding population of hummingbirds in Woolsey Canyon, which drains into Strawberry Creek on the west side of the Berkeley Hills. The study area, now a part of the University of California campus, totals about 125 acres and, until 1948, supported a complex of woodland and chaparral vegetation surrounded by open grassy slopes such as typically fills the canyons in the central Coast Ranges (see Fig. 1). Studies of territoriality in hummingbirds reported earlier (Pitelka 1942) have been continued, and while data presented in this paper concern specifically the populations of Woolsey Canyon, much original information on behavior to be reported elsewhere has been used in interpreting the data on these populations.
Plant Communities of the Coastal Plain of North Carolina and their Successional Relations

The eastern one third of North Carolina is included in the Atlantic coastal plain, a belt of recently deposited surficial sands lying unconformably on older strata. In North Carolina these sands are distributed in six sea terraces representing six successive upward diastrophic movements of the region, dating from late Pliocene time to the present. The upper three which are older, higher, and farther inland, and characterized by rolling topography, constitute the upper coastal plain, while the lower three which are younger, lower and near the ocean, and characterized by level topography with low relief, constitute the lower coastal plain. The basic key to the vegetation of both is found in these physiographic conditions. The plant communities which are universally recognized as distinctive of the coastal plain attain in all instances their best development in the lower coastal plain, hence the major part of the discussion will pertain to this easterly half of the whole sandy area.
An Annotated Checklist of the Caddisflies (Insecta: Trichoptera) of Kentucky

Abstract Distributional records for 293 caddisfly species representing 22 families and 68 genera are reported from Kentucky along with information on taxonomy, flight period, habitat, and conservation status. Sixty-nine species represent new records for the Commonwealth. Kentucky's geographic regions are compared with respect to species richness. Distributions are summarized for all species; detailed occurrence data are provided for new records, species with limited distributions, and those representing substantial range extensions. A total of 69 species (24% of the fauna) are identified as imperiled or vulnerable within Kentucky.
Morphological and molecular analysis of six aphelenchoidoids from Australian conifers and their relationship to Bursaphelenchus (Fuchs, 1937)

Six isolates of Australian Aphelenchoidoidea, viz., Laimaphelenchus preissii from native coniferous Callitris preissii trees, L. australis from the common pine plantation trees of Pinus radiata and P. pinaster and L. heidelbergi and two morphospecies of Aphelenchoides (H1 and K1) and Cryptaphelenchus sp. (K2) from diseased P. radiata trees, were studied using light microscopy, scanning electron microscopy and phylogenetic analyses of nearly full length sequences of SSU, D2/D3 expansion segments of LSU rDNA and a fragment of cytochrome oxidase subunit I (COI). Bayesian phylogenetic analyses of SSU, LSU and COI of the six nematode species revealed that none of these Australian aphelenchoidoids was inferred to be closely related to Bursaphelenchus. The selected isolates of Aphelenchoides and Laimaphelenchus used in this study were paraphyletic in all molecular analyses. Cryptaphelenchus sp. (K2) was inferred to be sister to Seinura with SSU sequences.
CYTOCHROME f LOSS IN ASTAXANTHIN‐ACCUMULATING RED CELLS OF HAEMATOCOCCUS PLUVIALIS (CHLOROPHYCEAE): COMPARISON OF PHOTOSYNTHETIC ACTIVITY, PHOTOSYNTHETIC ENZYMES, AND THYLAKOID MEMBRANE POLYPEPTIDES IN RED AND GREEN CELLS

Photosynthetic activity, chloroplast enzymes, and poly‐peptides were compared in green and red (ketocarotenoid‐containing) cultures of the microalga Haematococcus pluvialis Flotow. Green cultures, grown at 80 μmol pho‐tons.m‐2. s‐1 in an acetate‐containing medium, had a mean generation time of 27 h. Ketocarotenoid accumulation was induced by transfer of green cultures to PO4‐deficient medium and exposure to 250 μmol photons.m‐2. s‐1. Under these conditions, there was no increase in cell number, and the cultures turned red. Relative amounts of enzymes and thylakoid polypeptides in red and green cells were ascertained by immunoprobing with standardization on a chlorophyll (Chl) basis. In red cultures, the level of cytochrome f was greatly decreased (< 1% of green cell level), which is expected to greatly impair the linear electron flow from photosystem (PS) II to PS I. Also, the levels of apoproteins in red cells, namely, of CPI, D2, CP47, LHC I, and ribulose‐1, 5‐bisphosphate carboxylase were reduced to 15, 18, 29, 48, and 80%, respectively, of those in green cells. Only adenosine triphosphate syn‐thase exhibited no significant change in the two types of cultures. The respiration rate of red cultures was much higher (100 μmoles O2. mg Chl‐1.h‐1) than that of green cells (16 μmoles O2. mg Chl‐1.h‐1). Conversely, net O2 evolution (at Pmax in green cultures was 80 μmoles O2. mg Chl‐1.h‐1 but was —40 μmoles O2. mg Chl‐1.h‐1 in red cultures. PS II activity was demonstrated in broken cells of both green and red cultures, showing activity of 40 and 15 μmoles DCPIP‐mg Chl‐1.h‐1 (with DPC as electron donor), respectively. In contrast, PS I activity measured by the Mehler reaction showed that red rather than green cells had a greater activity (64 vs. 46 μmoles O2. mg Chl‐1.h‐1, respectively). Thus, in spite of the decline of O2 evolution in red cells, the photosystems were still functional. We postulate that the decline of O2, evolution in red cells is largely attributable to an increase in the respiration rate and the impairment of linear electron flow from PS II to PS I and, to some extent, to a decrease in components of the photosystems.
Soil structure and soil‐borne diseases: using epidemiological concepts to scale from fungal spread to plant epidemics

Many epidemics of root diseases involving soil fungi depend on the interplay between fungal growth and the spatial and temporal heterogeneity of the soil environment. Colonization or infection of a root occurs at fine scales with growth and movement of fungal mycelia through soil. However, epidemics are observed at coarser scales, and depend on a cascading spread through populations of roots. We briefly review conventional analyses of soil‐borne epidemics and argue that these treat soil physical conditions at scales too coarse to be meaningful for interactions between soil, plants and fungi, and fail to consider the effect of soil physical conditions on the underlying epidemiological processes. Instead, we propose a conceptual epidemiological framework that integrates spatial scales and use this to review the effect of soil structure on the dynamics of soil‐borne pathogenic fungi. Using the soil‐borne fungal plant pathogen Rhizoctonia solani as an example, we demonstrate that invasion of fungi into host populations is critically affected by environmental conditions operating at each of two scales: (i) at the microscopic scale (μm − cm) the fungus preferentially explores certain pathways in soil, and small changes in soil physical conditions make the fungus switch from small, dense colonies to large, sparse and rapidly expanding ones; (ii) at the larger scale (cm − dm) a critical density of susceptible hosts is required, in excess of which fungi switch from non‐invasive to invasive spread. Finally, we suggest that the approach will increase the applicability of research dealing with microscopic soil–plant–microbe interactions towards the solution of large‐scale epidemiological problems.
Comparison of Susceptibility to Kabatana takedai (Microspora) among Salmonid Fishes

Kabatana takedai (Microspora) is known as an enzootic pathogen of salmonids in limited water systems such as the Chitose River in Hokkaido, northern Japan. In this study, susceptibility to K. takedai was compared among masu salmon Oncorhynchus masou originating from the Chitose River, Shiribetsu River and Shari River, and rainbow trout O. mykiss from Shizuoka Prefecture, Japan. After exposure of fish to the Chitose River water, cysts of K. takedai in the heart and trunk muscle were examined by microscopy. Prevalence and intensity of infection were not considerably different among the three populations of masu salmon, whereas rainbow trout was more susceptible to K. takedai than masu salmon, particularly in the heart. A newly developed PCR test showed the higher percentage of fish with pre-cyst stage of K. takedai in the heart of rainbow trout than in masu salmon, suggesting that K. takedai established the cardiac infection at early stages more in rainbow trout than in masu salmon. A histopathological observation indicated that K. takedai infection in the heart caused granulomatous inflammation characterized by fibrinoid degeneration, but there was no difference in the progress of the inflammation between the two fish species.
Bifurcations and Dynamic Complexity in Simple Ecological Models

Many biological populations breed seasonally and have nonoverlapping generations, so that their dynamics are described by first-order difference equations, Nt+1 = F (Nt). In many cases, F(N) as a function of N will have a hump. We show, very generally, that as such a hump steepens, the dynamics goes from a stable point, to a bifurcating hierarchy of stable cycles of period 2n, into a region of chaotic behavior where the population exhibits an apparently random sequence of "outbreaks" followed by "crashes. " We give a detailed account of the underlying mathematics of this process and review other situations (in two- and higher dimensional systems, or in differential equation systems) where apparently random dynamics can arise from bifurcation processes. This complicated behavior, in simple deterministic models, can have disturbing implications for the analysis and interpretation of biological data.
The Effects of Stream Channelization and Restoration on Mammal Species and Habitat in Riparian Corridors

ABSTRACT We investigated differences in habitat characteristics, mammal richness, and mammal activity among three stream types: channelized, unchannelized, and restored. Riparian plant species richness was significantly higher at the unchannelized stream than at the other two streams. The Kentucky Macroinvertebrate Bioassessment Index was highest at the unchannelized stream and much lower at the restored stream than the other two streams. Small mammal activity did not differ among stream types. Richness of terrestrial mammals, as determined by motion-sensitive cameras, did not differ significantly among streams. Track plot surveys showed, however, that unchannelized and restored streams had significantly higher terrestrial mammal species richness than the channelized stream. Likewise, track transect surveys conducted in snow, showed that species richness at the unchannelized stream was significantly higher than the channelized stream. There was some indication that bat activity was affected by an interaction between month and stream type. Results suggested that channelization and restoration affect habitat characteristics, mammal richness, and mammal activity; however, restored streams have potential to recover many of the characteristics of an unchannelized stream.