Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of roads and adjacent areas on diversity of terrestrial isopods of Hungarian highway verges

Abstract Transportation infrastructure may be the most important driver of social and economic development, but it is a major cause of environmental change in landscapes. The main objective of this paper is to report road edge effects on isopods of Hungarian highway verges. We examined the isopod diversity along five highways (M0, M1, M3, M5, M7) while accounting for road edge proximity and the adjacent areas. Double-glass pitfall traps were set in a total of 15 sites and at three distances from the edge of the roads next to different types of adjacent areas. We found differences between ecological parameters of isopod communities in relation to adjacent areas as well as to road edge proximity. The highest diversity was observed near urban areas, while the lowest was near the arable fields. Isopod diversity increased with decreasing distance from a road. Species diversity of different types of verges based on adjacent areas varied strongly in relation to road edge proximity. A medium distance (40 m) from roads had a positive effect on species richness, while verges next to arable fields were the most species-rich habitats. The general conclusion of this study is that highway verges provided suitable environment conditions for generalist isopod species but may be a limiting factor for specialist isopods. Moreover, highway verges function as corridors for isopods. The proximity of roads and urban areas positively affected isopods, and verges close to roads and urban areas are considered as an attractive environment for isopods in heterogeneous roadside verges.
Sexual dimorphism and sex determination in Black-necked Grebes Podiceps nigricollis: on the need to account for geographical variation in morphology and sex ratio

ABSTRACT Capsule: The sex of Black-necked Grebes Podiceps nigricollis in Spain can be determined successfully using a locally derived discriminant function analysis (DFA) but a function derived from a North American population was not successful. Aims: To determine the extent of sexual size dimorphism in the Black-necked Grebe and develop discriminant functions based on morphometric data. We also assessed the accuracy of visual sexing by fieldworkers with different levels of experience and compared the discriminant function for European birds with one for North American birds, in order to determine the geographical specificity of the function. Methods: We used a data set of 370 Black-necked Grebes from a European population throughout the non-breeding seasons of 2008–11 in the Odiel saltmarshes (Spain), as well as published data from North America, to compare the accuracy of DFAs developed for European and North American populations when applied to the same population. Results: Males were significantly larger than females for all body measurements. The DFA with the highest success rate included one single linear dimension (head-bill length), showing an efficiency of 88.5% in the same sample used to build the function and up to 91.5% in independent samples of birds. The more experienced ringer showed higher accuracy in visual sexing than the less experienced one (84 vs. 70%), although self-consistency in sex assignment of a given individual was similar. The function developed for European birds performed poorly for American birds (79.1% sexed correctly) and vice versa (18.4% sexed correctly). Conclusion: Morphological and sex ratio differences between European and American subspecies both contribute to the discrepancy in the success rate. This illustrates the need for caution when applying discriminant functions developed in one bird population to individuals elsewhere.
Direct Evidence of Effect of Glycerol on Hydration and Helix-to-Sheet Transition of Myoglobin

By using wide-angle X-ray scattering (WAXS), small-angle neutron scattering, and theoretical scattering function simulation, we have clarified the effect of glycerol on both the thermal structure transition and the hydration-shell of myoglobin. At the glycerol concentration, ≤ ∼40 % v/v, the decreasing tendency in the maximum dimension and the radius of gyration was observed by X-ray scattering. The neutron scattering result using the inverse contrast variation method directly shows the preservation of the hydration-shell density at the concentration ≤ ∼40 % v/v. This phenomenon is reasonably explained by the preferential exclusion of glycerol from the protein surface to preserve the hydration shell, as suggested by the previous studies. While, at the concentration, ≥ 50 % v/v, the opposite tendency was observed. It suggests the preferential solvation (partial preferential penetration or replacement of glycerol into or with hydration-shell water surrounding the protein surface) occurs at the higher concentration. The observed WAXS scattering data covers the distinct hierarchical structural levels of myoglobin structure ranging from the tertiary structure to the secondary one. Therefore, we have clarified the effect of glycerol on the thermal structural stability myoglobin at different hierarchical structural levels separately. Against the temperature rise, the structural transition temperatures for all hierarchical structural levels were elevated. Especially, the tertiary structure of myoglobin was more stabilized compared with the internal-structure and the helix-to-cross transition. It suggests that the protective action of glycerol on protein structures essentially results from the preservation of the preferential hydration-shell of proteins.
SELF-PRUNING affects auxin responses synergistically with the cyclophilin A DIAGEOTROPICA in tomato

Summary The antiflorigenic signal SELF-PRUNING, which controls growth habit, exerts its effects through auxin transport, signaling and metabolism in tomato. Abstract The SELF PRUNING (SP) gene is a key regulator of growth habit in tomato (Solanum lycopersicum). It is an ortholog of TERMINAL FLOWER 1, a phosphatidyl-ethanolamine binding protein with anti-florigenic activity in Arabidopsis thaliana. A spontaneous loss-of-function sp mutation has been bred into a large number of industrial tomato cultivars, as it produces a suite of pleiotropic effects that are favorable for mechanical harvesting, including determinate growth habit, short plant stature and simultaneous fruit ripening. However, the physiological basis for these phenotypic differences has not been thoroughly explained. Here, we show that the sp mutation alters polar auxin transport as well as auxin responses such gravitropic curvature and elongation of excised hypocotyl segments. We further demonstrate that free auxin levels and auxin-regulated gene expression patterns are altered in sp, with epistatic effects of diageotropica, a mutation in a cyclophilin A protein-encoding gene. Our results indicate that SP impacts growth habit in tomato, at least in part, via changes in auxin transport and responsiveness. These findings hint at novel targets that could be manipulated in the control of growth habit and productivity.
LEAF PETIOLES BLANCHING INFLUENCE ON THE YIELD AND CHEMICAL COMPOSITION OF CARDOON (Cynara cardunculus L.)

The influence of leaf blanching with black polyethyl ene non-woven (PP) or white and black polypropylene foil (PE) used as soil mulching and blanching of le av s on yield, usefulness and biological value of c ardoon leaf petioles were evaluated in the presented work. T he effect of blanching duration of petioles (30, 25 and 10 days before leaves’ harvest) on the content of b ioactive compounds was also estimated. The aim of th e research was to evaluate the total yield of leaves, yi ld structure, dry weight, content of crude fibre, total sugars, L-ascorbic acid, chlorophyll, phenolic acid s n conversion to caffeic acid, total flavonoides and DPPH activity in leaf petioles depending on the metho d and duration of leaves blanching. The content of apigenin, chlorogenic acid and cynarin in leaf peti ol s were marked with HPLC. Petioles of non blanched plants showed more dry weight and contained more L-as corbic acid, chlorphyll, total phenolic acids and flavonoides than the uncovered ones. As a tendency i t was observed that together with lengthening the blanching time from 10 to 30 days before harvest, t he level of dry weight, crude fibre, total sugars, L-ascorbic acid and chlorophyll decreased. A reverse relationship was observed related to the blanching duration, as extending the time from 10 to 30 days be fore harvest, the content of total phenolic acids i ncreased from 0.144 to 0.155% of fresh weight, while the conte nt of flavonoides decreased from 0.662 to 0.352% of fresh weight. Lengthening blanching from 10 to 30 da ys before harvest of leaves decreased the content o f apigenin and cynarin in petioles while increased the content of chlorogenic acid. The antioxidant activ ity DPPH did not depend on the method and duration of bla nching. Unusual nutritional and medicinal benefits of cardoon petioles come from its rich and valuable ch mical composition.
The Organizational Principles of Membranes Below 100 nm: Experimental Breakthroughs Occasion a “Modeling Manifesto”

New experimental techniques reveal the plasma membrane to be heterogeneous and "scale-rich," from nanometers to microns, and from microseconds to seconds. This is critical information, as heterogeneous, scale-dependent transport governs the molecular encounters that underlie cellular signaling. The data are rich, and reaffirm the importance of the cortical cytoskeleton, protein aggregates, and lipidomic complexity to the statistics of molecular encounters. Moreover, the data demand simulation approaches with a particular set of features, hence the “manifesto”. Together with the experimental data, simulations which satisfy these requirements hold the promise of a deeper understanding of membrane spatiotemporal organization. Several experimental breakthroughs are reviewed, the constraints that they place on simulations are discussed, and the status of simulation approaches which aim to meet them are detailed.
DETECTION OF VIRULENCE FACTORS IN CANDIDA ISOLATED FROM DIFFERENT CLINICAL SPECIMENS

Candida species are emerged as successful pathogens in both invasive and mucosal infections. Various virulence factors have contributed to their pathogenicity. The purpose of this prospective study was to isolate, speciate, and determine virulence factors of Candida species isolated from various clinical specimens. Total of 136Candida were isolated from various clinical specimens, identified up to species level by standard mycological techniques. All isolates were tested in vitro for biofilm formation (BF), proteinase (SAPs), phospholipase (PL), and haemolysin (HF) activity. One thirty six Candida, were isolated from different clinical samples. 71(52%) were C.albicans and 65(47%) non-albicans Candida (NAC) species. Biofilm formation was detected in 86(63%), proteinases activity (SAPs) in 90(66.2%), phospholipases (PL) activity in, 94((69.11%)and haemolysins (HF) activity was demonstrated in 123(90%). From the present study it can be established, that both C.albicans and NAC species are causing candidiasis and form biofilm, produce extracellular phospholipases, proteinases and haemolysins.
Capturing diverse microbial sequence with comprehensive and scalable probe design

Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. We developed CATCH (Compact Aggregation of Targets for Comprehensive Hybridization), a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs compact probe sets that achieve full coverage of known sequence diversity and that scale well with this diversity. To illustrate applications of CATCH, we focused on capturing viral genomes. We designed, synthesized, and validated multiple probe sets, including one that targets whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriched unique viral content on average 18× and allowed us to assemble genomes that we could not otherwise recover, while accurately preserving within-sample diversity. We used this approach to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of viral infections in samples with unknown content. Together, this work demonstrates a path toward more sensitive, cost-effective metagenomic sequencing.
The identification and characterization of microbial FK506-binding proteins

FK506-binding proteins (FKBPs) represent a diverse family of enzymes which typically exhibit peptidyl-prolyl cis-trans isomerase (PPIase) activity, catalysing a rate limiting step of protein folding. Prior studies have identified FKBP members BPSL0918 and the macrophage infectivity potentiator (MIP) as virulence determinants of the tropical pathogen Burkholderia pseudomallei. Due to the strong association with virulence, a range of small molecule inhibitors have been developed to interact with the PPIase domain of B. pseudomallei MIP. Targeting the shared PPIase domain of FKBPs may allow for the inhibition of multiple FKBPs, potentially enhancing drug efficacy. However, the biological roles of the remaining B. pseudomallei FKBPs remains unknown. This study aimed to identify and experimentally validate FKBPs as potential anti-virulence targets for the purpose of investigating the potential for multi-target inhibition using MIP inhibitors from previous studies. Through phylogenetic analysis 58 putative FKBPs were identified within the 16 bacterial taxa studied. BPSL2254, a putative SlyD-like FKBP closely related to the virulence associated BPSL0918, was recombinantly expressed and purified from E. coli. To investigate PPIase activity for the subsequent assessment of inhibitors, purified BPSL2254 was used in protease-coupled assays in which no PPIase activity was detected. The closely-related environmental saprophyte B. thailandensis encodes BTH_I1911 gene product, which was determined to share 98% amino acid sequence identity with BPSL2254. B. thailandensis was used as a surrogate model featuring an in-frame deletion of the BTH_I1911 gene. The contribution of BTH_I1911 to virulence was assessed through a range of in vitro assays to evaluate potential as an anti-virulence target. The role of BTH_I1911 in the capacity of B. thailandensis to invade J774A.1 macrophages and form biofilm remains inconclusive. However, the BTH_I1911 null strain appeared to exhibit filamentation after incubation in M9 minimal media. Further study is required to conclusively determine the enzymatic activities of BPSL2254, which in turn may facilitate assessment of inhibitors. Investigation of putative FKBPs identified here may lead to the identification of novel virulence determinants. Further study including the use of in vitro assays and the infection of animal models are required to elucidate the role of BTH_I1911 as a virulence determinant.
Automatic Assessment of Crown Projection Area on Single Trees and Stand-Level, Based on Three-Dimensional Point Clouds Derived from Terrestrial Laser-Scanning

Crown projection area (CPA) is a critical parameter in assessing inter-tree competition and estimating biomass volume. A multi-layer seeded region growing-based approach to the fully automated assessment of CPA based on 3D-point-clouds derived from terrestrial laser scanning (TLS) is presented. Independently repeated manual CPA-measurements in a subset of the stand serve as the reference and enable quantification of the inter-observer bias. Allometric models are used to predict CPA for the whole stand and are compared to the TLS-based estimates on the single tree- and stand-level. It is shown that for single trees, the deviation between CPA measurements derived from TLS data and manual measurements is on par with the deviations between manual measurements by different observers. The inter-observer bias propagates into the allometric models, resulting in a high uncertainty of the derived estimates at tree-level. Comparing the allometric models to the TLS measurements at stand-level reveals the high influence of crown morphology, which only can be taken into account by the TLS measurements and not by the allometric models.
A revision of Homalium sect. Odontolobus (Salicaceae) endemic to Madagascar

Abstract Applequist, W.L. (2018). A revision of Homalium sect. Odontolobus (Salicaceae) endemic to Madagascar. Candollea 73: 27–48. In English, English and French abstracts. DOI: http://dx.doi. org/10.15553/c2018v731a4 Homalium sect. Odontolobus Warb. (Salicaceae) is endemic to Madagascar and formerly included three species. In this revision, nine species are recognized, three of them newly described (Homalium densispicatum Appleq., Homalium masoalense Appleq., Homalium ovatifolium Appleq.) and three transferred from Homalium sect. Blackwellia Benth. Homalium densispicatum has highly reduced flowers like those of Homalium moniliforme H. Perrier, but the leaves are larger and the inflorescences thicker, with flowers in elongated many-flowered glomerules. Homalium masoalense and Homalium ovatifolium are northern species that have frequently ovate leaves and long styles and filaments; the flowers of Homalium masoalense are larger, with longer sepals, while Homalium ovatifolium has often canescent inflorescences. Two new subspecies are described: Homalium moniliforme subsp. littorale Appleq. and Homalium planiflorum subsp. roseiflorum Appleq. A key for identification of the species of Homalium sect. Odontolobus is provided.
Assessment of genetic structure among different pear species (Pyrus spp.) using apple-derived SSR and evidence of duplications in the pear genome

ABSTRACT Simple sequence repeat (SSRs) markers derived from Malus were used to assess their transferability in the analysis of the genetic diversity and relationship of some Pyrus species. All studied microsatellite loci produced fragments and were polymorphic among the studied samples. Fifty-one allelic variants were detected at eight SSR loci, ranging from five (MS14h03, CH02b10 and CH03g06) to nine (CH02h11a), with a mean of 6.37 alleles per locus. A relatively high level of diversity was recorded among the studied accessions. The average of Shannon's index (I) was 1.04. The Dice genetic similarity coefficient ranged greatly and ‘Khoj 1’ (a member of P. communis) and ‘Shinko’ (a cultivar belonging to P. pyrifolia) had the lowest (0.21) values, while ‘Chojuro’ and ‘Nijisseiki’, two cultivars belonging to P. pyrifolia, had the highest genetic similarity (0.97) among the studied samples. Bayesian cluster analysis and principal coordinates analysis plot separated the P. pyrifolia samples from other species, and formed three distinct groups, indicating high genetic differences between P. pyrifolia and other studied pear species. Several private alleles were observed in some of the studied species that would be of great importance for species identification. Furthermore, in 23 samples, more than two alleles were observed in the CH04e03 locus, indicating presence of locus duplication in these samples. Our observations suggest that, for this locus, at least two homologous chromosomes or genomic regions may be presented in the genome of some pear samples.
Investigation of prey ingestion and digestion in the ciliate predator Tetrahymena pyriformis and the impact on growth

This study evaluated the effect of four prey states on ingestion, digestive vacuole (DV) formation, digestion and growth in the ciliate Tetrahymena pyriformis. The prey included several strains of live RFP-expressing heterotrophic bacteria (Live), heat-killed-DTAF-stained heterotrophic bacteria (Dead), live autotrophic Synechococcus species (Pico) together with fluorescently-labelled microspheres (FLMs). Prey biovolume did not affect ingestion rates over the 5 minute period tested, therefore the effect of the different prey states could be directly compared. Live heterotrophic bacteria were able to quickly upregulate DV formation rate; something not demonstrated by any other prey. All prey, except FLMs, showed controlled vacuole filling over a 20 minute period whereby new DVs contained an equivalent number of prey to those in older vacuoles. Live heterotrophic and autotrophic prey yielded a significantly lower maximum number of prey/vacuole compared to Dead cells, and whereas significant differences in prey/vacuole between bacterial species were discerned for Dead species, no such differences were evident for Live species. It was hypothesised that ingestion of prey is receptor-mediated and that the predominant pathway into the ciliate for Live prey is the lectin-receptor-based route, and that for inert prey is the non-specific-receptor-mediated route, with a yet unidentified route for Dead prey. Using pulse-chase experiments, the digestion of Live and Dead heterotrophic bacteria were found to be equivalent, i.e. ca. 50% of ingested cells within a DV were digested. There was however a very strong relationship (for both prey states) between biovolume of prey in the vacuole and the total biovolume of prey digested in that vacuole implying that larger prey cells might lead to higher ciliate specific growth rates. This was not found to be the case. No relationship between ciliate specific growth rate was discerned with prey biovolume, or even digestion rates, as % prey/vacuole/min over the digestion period (where there is a linear decline in prey due to digestion). The digestion period (DP) was considerably shorted with Dead cells and it was hypothesised that, due to an incomplete suite of ligands, DVs did not go through the complete sequence of fusion events with lysosomes. Digestion of prey had little effect on ciliate growth rates. However there was no obvious relationship between growth rate and any parameter tested. This suggests that digestion and growth are too far removed with regards to cellular processes. In conclusion, the findings suggest that there are two prey recognition systems in T. pyriformis, one which recognised prey particles and leads to ingestion, and a second, present in the DV, which recognises the type of prey enclosed within it and leads to digestion behavioural changes.
Eigenvector index for two female fertility traits based in random regression coefficients matrix in Holstein cows

A total of 71,518 days open (DO) and number of services per conception (NSC) records of 28,523 Iranian Holstein cows were analysed by random regression model. Akaike’s information criterion and likelihood ratio test suggested that a model with quadratic Legendre polynomials for additive genetic and permanent environmental was best. Heritability in different parities ranged from 0.103 to 0.045 in first parity and 0.054 to 0.030 in sixth parity for DO and NSC, respectively. Estimated genetic correlations between parities decreased continuously with increasing distance between parities for both DO and NSC. The first eigenfunction explained 89.99% and 97.22 % of the total genetic variance of DO and NSC, while the second eigenfunction accounted 6.24% and 3.18%, respectively. Different selection indices were constructed for DO and NSC. Genetic response to improve overall fertility was greater when the index included the first eigenvector than the response obtained from indices excluding it. Similar genetic gains were obtained from the first eigenvector, which had a nearly flat associated eigenfunction along lactations and from selection by the intercept of the random regression. The first eigenvector indices were responsible of changes in the level of DO and NSC in a similar manner for all parities, without altering the shape of the response curve across parities. The second and third eigenvector indices modified the shape of this curve but the improvement in genetic gains by including them in the selection index were small (DO) or negligible (NSC) due to the small amount of variability associated with these components.