Miracle-dz/UniFAR-FTUs huggingface dataset:
Thermodynamics of molecular recognitions between antineoplastic drug taxol and phosphatidylcholine

The aim of this study was to study the basic features of Taxol recognition with phospholipids by applying the thermodynamic and spectroscopic measurements. The obtained information could be used further for deductions on its precise cellular and pharmacological mechanisms of action, on improvements of its solubility properties by phospholipids, as well as for designing the novel lipidic carriers for drug delivery.
Using Mechanistic Models to Scale Ecological Processes across Space and Time

Abstract Human activities affect the natural environment at local to global scales. To understand these effects, knowledge derived from short-term studies on small plots needs to be projected to much broader spatial and temporal scales. One way to project short-term, plot-scale knowledge to broader scales is to embed that knowledge in a mechanistic model of the ecosystem. The National Science Foundation's Long Term Ecological Research (LTER) Network makes two vital contributions to this type of modeling effort: (1) a commitment to multidisciplinary research at individual sites, which results in a broad range of mutually consistent data, and (2) long-term data sets essential for estimating rate constants for slow ecosystem processes that dominate long-term ecosystem dynamics. In this article, we present four examples of how a mechanistic approach to modeling ecological processes can be used to make projections to broader scales. The models are all applied to sites in the LTER Network.
Trophic ecomorphology of Potamotrygon falkneri and Potamotrygon motoro (Chondrichthyes - Potamotrygonidae) on the upper Paraná river floodplain, Brazil

In this paper the the null hypothesis of absence of ecomorphological diversification was tested between Potamotrygon falkneri and Potamotrygon motoro (Chondrichthyes, Potamotrygonidae) on the upper Parana river floodplain, Brazil. In the Principal Components Analysis, the five ecomorphological indices were positively correlated with axis 1. Their most relevant contributions were relative width of the mouth and relative opening of the spiracle. The Discriminant Canonical Analysis indicated that the width of the spiracles, followed by the width of the mouth, are the linear measurements that contributed the most to the morphological segregation between the two species. The Mantel test revealed that there is a significant correlation (Z = 0.27; p = 0.0002) between the ecomorphological distance matrix and the feeding habit model matrix, indicating dependence of the feeding habitats of species in relation the body shape of stingrays. P. falkneri presented comparatively larger spiracles, mouth, and pelvic and pectoral fins than P. motoro, which may influence in the capture of mobile prey (fishes), while P. motoro can use of the suction mechanism, favoring the consumption of prey with little evasive capacity. Ecomorphological diversification culminated in the exploitation of different food resources and provided the coexistence of P. falkneri and P. motoro in Parana river.
Connect-and-Slice: An Hybrid Approach for Reconstructing 3D Objects

Converting point clouds generated by Laser scanning, multiview stereo imagery or depth cameras into compact polygon meshes is a challenging problem in vision. Existing methods are either robust to imperfect data or scalable, but rarely both. In this paper, we address this issue with an hybrid method that successively connects and slices planes detected from 3D data. The core idea consists in constructing an efficient and compact partitioning data structure. The later is i) spatially-adaptive in the sense that a plane slices a restricted number of relevant planes only, and ii) composed of components with different structural meaning resulting from a preliminary analysis of the plane connectivity. Our experiments on a variety of objects and sensors show the versatility of our approach as well as its competitiveness with respect to existing methods.
Land snails as indicators of soil humidity in Danubian woodland (SW Slovakia).

ABSTRAC T: Moisture along with available calcium content are the major environmental factors controlling species richness and composition of the terrestrial molluscan fauna. In the present study, we focused on snails in a floodplain forest and their response on humidity. We described the model of response and calculate the humidity optima of particular species if possible. Generalised linear model (GLM) combined with Poisson distribution was used to ch aracterise the change of species abundance along a humidity gradient. From 31 species tested, 21 have shown significant response to humidity. The majority of specie s tested had unimodal response, four species showed monotonic regression type. Based on their humidity optima, species distributed along a moisture gradient belonged to three main ecological groups: (i) mesohygrophilous woodland species living mostly in non-inundated areas with humidity optima below 4, (ii) hygrophilous, forest hygrophilous and euryhygric species with optima between 4 and 6 and (iii) strongly hygrophilous (polyhygrophilous) species with mois ture optima above 6. Estimated moisture preferences for Danubian floodplain woodland land snail fauna would be a useful tool in a longterm biological monitoring of changing moisture regime.
An integrated genetic/RFLP map of the Arabidopsis thaliana genome.

Summary We have assembled an integrated genetic/restriction fragment length polymorphism (RFLP) linkage map of the nuclear genome of the flowering plant Arabidopsis thaliana. The map is based on two independent sets of RFLP data, RFLP data for 123 new markers, and pair-wise segregation data of 125 classical genetic markers. Mathematical integration of the independent data sets was performed using the join map computer package. Sixty-two markers common to two or more data sets were exploited to facilitate integration of the individual maps. The current map, which encompasses a total genetic distance of 520 cM, contains 125 classical genetic markers and 306 RFLP markers. Comparison of the integrated consensus map with the individual maps demonstrates that the overall linear order of the integrated map is in good agreement with the component maps. It must be emphasized, however, that the integrated map represents the ‘best fit’ which is clearly subject to the statistical limitations of the available data. We present several examples where local differences in map order are observed between the integrated and component maps. It is likely, given the problems associated with statistical integration of mapping data from different populations, that the integrated map will contain additional local inconsistencies and problematic regions. None the less, the unified map provides a framework for building an increasingly accurate and useful map. Subsequent refinements of the map will be available electronically and researchers are invited to submit revised map data to the corresponding author for inclusion in future updates (see Appendix 1).
Can the stomatal changes caused by acute ozone exposure be predicted by changes occurring in the mesophyll? A simplification for models of vegetation response to the global increase in tropospheric elevated ozone episodes

The prediction of complex interactive effects of rising concentrations of ozone and CO2on vegetation will require robust models based on mechanistic understanding of how these two gases affect photosynthesis. This paper describes the development of a model of acute ozone exposure effects on wheat leaf photosynthesis, based on the mechanism of reactive oxygen scavenging processes. Based on experimental data, the dose of ozone to the leaf above a threshold flux, here termed the effective ozone dose, was found to be linearly related to the decline in the in vivo maximum rate of carboxylation. The proposed mechanism is that ozone damage to the photosynthetic ap paratus will only occur above a critical rate of ozone delivery. By combining the model of the response of ribulose-1,5-bisphosphate-saturated and limited photosynthesis to ozone exposure with both a mechanistic biochemical model of leaf photosynthesis and a phenomenological model of stomatal conductance, it was possible to investigate the degree of dependency of ozone-induced stomatal closure on changes in the mesophyll. The stomatal conductance of the model simulation compared well with the magnitude of measured stomatal closure. The results indicate that the stomatal changes caused by acute ozone exposure can be predicted from changes in the mesophyll rather than directly on the stomata. The findings that the effects of ozone on photosynthesis can be predicted by an effective ozone dose to the leaf, and that the resulting reduction in CO2 assimilation rate can, in turn, predict stomatal closure, greatly simplifies modelling the effects of elevated concentrations of ozone and CO2 on wheat photosynthesis. Future work should determine whether the model can be adapted to predict chronic ozone exposure effects on photosynthesis, and whether it can be applied to other species by adjusting the values of threshold flux, related to the maximum scavenging capacity within the leaf, and the ozone slope coefficient, representing the inherent sensitivity of the photosynthetic apparatus to ozone.
Cephalopod bacterial associations: characterization and isolation of the symbiotic complex in the Accessory Nidamental Glands

Accessory nidamental glands (ANGs) in the reproductive system of female Myopsidae and Sepioidae (Cephalopoda) host a dense bacterial community in their tubules. Bacteria associated to the ANGs were characterized morphologically and molecularly by complementary approaches: culture dependent (isolation of bacterial strains) and culture independent (direct tissue extraction, sequence comparison of gene for 16S rRNA and fluorescent in situ hybridization). Populations of alpha- and gamma-proteobacteria, Gram-positive bacteria, and Cytophaga-Flavobacteria-Bacteroides were detected in five families of European, Asian and Australian decabrachian cephalopods. In order to obtain bacterial strains difficult to propagate artificially from the host, we have established co-cultures of Sepia officinalis ANG cells with their native bacteria. Cells were maintained viable over one month and the co-cultures contained bacterial strains which could not be cultured in classic microbiological media. Cephalopod cell culture can be used as a new tool to study bacteria-host interactions and their role in the physiology of each partner. Riassunto Le ghiandole nidamentali accessorie (ANGs) del sistema riproduttivo delle femmine delle famiglie Myopsidae e Sepioidae (Cephalopoda) ospitano nei loro tubuli una densa comunita batterica. I batteri associati alle ANGs sono stati caratterizzati morfologicamente e molecolarmente mediante approcci complementari: coltura dipendenti (isolamento di ceppi batterici) e coltura dipendenti (estrazione diretta dal tessuto, confronto della sequenza del gene 16S rRNA e ibridizzazione in situ a fluorescenza). Sono state scoperte popolazioni di proteobatteri-alfa e gamma, batteri Gram-positivi, e di Cytophaga-Flavobacteria-Bacteroides in cinque famiglie di cefalopodi decabrachiati dell’Europa, dell’Asia e dell’Australia. Al fine di ottenere ceppi batterici difficili da propagare artificialmente dall’ospite, si sono fondate co-colture di cellule ANG di Sepia officinalis con i loro batteri originari. Le cellule sono state mantenute vitali per piu di un mese e le loro cocolture contenevano ceppi batterici che non potrebbero essere tenuti in coltura con i classici metodi microbiologi. La coltura delle cellule di cefalopodi puo essere usata come un nuovo strumento di studio tra le interazioni batteri-ospite e il loro ruolo nella fisiologia di ogni partner.
Assessment of Accumulation and Potential Health Risk of Cr, Mn, Fe, Cu, and Zn in Fish from North-Eastern Mediterranean Sea

Heavy metal accumulation in aquatic organisms has been an important issue due to environmental pollution resulting from anthropogenic activities. In this study, Cr, Mn, Fe, Cu, and Zn in the selected fish species (Mullus barbatus, Solea solea, and Siganus rivulatus) from three consecutive bays (Iskenderun, Mersin, and Antalya from North-Eastern Mediterranean Sea) were considered to provide some information on heavy metal accumulation level and assessment of their health risk on both general and fishermen populations. There were some significant differences inter- and intra- species/ tissues/bays. The stability in heavy metal accumulation in fish tissues varied and the most stable tissue for Cr, Cu, Fe, Mn and Zn were determined as skin, muscle, liver, liver and, muscle, respectively. In general, the lowest heavy metal values were observed in the fish muscle. The Target Hazard Quotients (THQ) and Total Target Hazard Quotients (TTHQ) values based on muscle were not exceeded 1.00. Therefore, these results suggest that both general and fishermen populations are not subjected to the significant potential health risk from those bays.
Prevalence and seasonal periodicity of endophytic coelomycetous fungi in Tamil Nadu, India

The present study reports 2,644 endophytic isolates; only 74 different morphospecies of coelomycetes have been isolated and identified from 14,400 segments of healthy tissues such as leaves (4,800), stem (4,800) and bark (4,800). Each plant tissue with 300 segments was studied in a Petri dish containing 10 segments; totally, 30 plates were studied with four seasons. Totally, 74 coelomycetes were isolated and identified to belong to 16 genera by classical taxonomy. Interestingly, thePestalotiopsis spp. was found to be dominant as compared to other genera in all the collection spots in the four different seasons. Key words: Coelomycetes, endophytes, parasites, morphospecies, colony frequency, pestalotiopsis, relative percentage occurrence.
FEULGEN MICROSPECTROPHOTOMETRIC STUDIES OF PANDORINA MORUM AND OTHER VOLVOCALES (CHLOROPHYCEAE) 1 2

The nuclear DNA content during normal vegetative growth and division has been examined in three species of Volvocales, Chlamydomonas reinhardtii Dangeard, Pandorina morum Bory, and Volvox carteri f. nagariensis Iyengar. The results are consistent with the nuclear cycle reported in the literature for Eudorina. Nuclear DNA content does not increase during the prolonged cell growth phase. At the time of colony formation, nuclear DNA doubles, the nucleus divides, and this alternation continues until the final 2n complement of progeny nuclei is formed. The 4‐ and 8‐nucleate stages of dividing gonidia of V. carteri have a nuclear DNA content in the same range as the somatic cells; they are not polyploid or polytene. Four normal clones of Pandorina, having 2, 5 or 12 chromosomes, all had similar amounts of DNA per nucleus, suggesting that the species has a nuclear genome of fairly constant size rather than consisting of many strains representing a polyploid series. One unique clone, a hybrid with double the chromosome number of either its parents, had twice as much DNA as the normal clones. The Feulgen spectrophotometric method is sufficiently sensitive to detect 2‐fold differences in DNA content at the level of 2 × 10−13 g of DNA /nucleus, and its use avoids the complications associated with the presence of organelle DNA.
Fluctuating Asymmetry in the Eurasian Spur-Thighed Tortoise, Testudo graeca ibera Linneaus, 1758 (Testudines: Testudinidae)

Abstract We studied plastron-shaped asymmetry of the Eurasian Spur-Thighed Tortoise, Testudo graeca ibera, as related to life stage, gender, and distribution. Our analyses of 523 individuals showed that fluctuating asymmetry (FA) in plastron shape varied with gender (males exhibited higher levels of FA than did females) and across populations, whereas life stage had no significant effect. Although we could not identify the potential sources of variation responsible for the observed patterns of developmental instability, our study shows the value of FA as a method for studies of developmental instability in turtles.
Separate introductions but lack of genetic variability in the invasive clam Corbicula spp. in Swiss lakes

This study documents the spread of the invasive clam Corbicula spp. in Switzerland since its first record in the River Rhine in 1995. Clams were newly recorded in several Swiss lowland lakes whose interconnecting rivers have not yet been colonized. We present evidence for separate introductions of an identical haplotype of Corbicula fluminea into five lakes in Switzerland in the years 2003–2010 based on the mitochondrial DNA-sequence of the COI in specimens sampled. This suggests passive dispersal of the clam by human activities and/or waterfowl. All but one of the 72 genetically analysed individuals were assigned to a single haplotype FW5 and to the species name C. fluminea. Recent records of specimens, which were not genetically analysed, displayed all the shell morphology of C. fluminea, confirming the dominance of this clam in Swiss rivers and lakes.
Efecto de las alcamidas como inductores de tolerancia al estrés biótico en tomate

El objetivo de este estudio fue conocer los efectos histologicos y los relacionados a vigor con la aplicacion del extracto de Heliopsis longipes sobre plantulas de tomate inoculadas con Fusarium oxysporum f. sp. lycopersici (FOL). El extracto de H. longipes se asperjo a una concentracion de 300 mgL-1 en plantulas de tomate, posteriormente se realizo la inoculacion con FOL por inmersion de raices. Veinte dias despues se tomaron los datos de incidencia y severidad, encontrandose que la aplicacion del extracto provoco una disminucion de 15% y 80% respectivamente para estas variables mientras que para altura de la planta se presento un incremento de 14.3%. En longitud de raiz y peso seco de hojas y tallo se observo un decremento en los resultados; sin embargo, estos valores estuvieron por encima de los obtenidos para plantas inoculadas con FOL. Se encontraron cambios histologicos ocurridos por la infeccion de FOL asi como por la aplicacion del extracto, que consistieron en la modificacion de la distribucion de los haces vasculares en la raiz, asi como en el incremento del area relativa del cortex de raiz y tallo y la disminucion del numero de vasos del xilema de la raiz. Estos resultados indican que la aplicacion del extracto tiene un efecto sobre los sintomas de marchitamiento causados por FOL.
Avoiding offshore transport of competent larvae during upwelling events: The case of the gastropod Concholepas concholepas in Central Chile

The coast of central Chile is characterized by the occurrence of coastal upwelling during the austral spring and summer seasons, which probably has important consequences for the cross‐shelf transport of larval stages of many species. Three cruises were conducted off the locality of El Quisco during upwelling‐favorable wind periods to determine the surface distribution of epineustonic competent larvae of the gastropod Concholepas concholepas during such events. Contrary to the predictions of a traditional model, where neustonic‐type larvae are transported offshore under such conditions, competent larvae of this species were exclusively found in the area between the shore and the upwelling front. Two additional cruises were conducted during calm periods to determine diel variation in the vertical distribution of C. concholepas competent larvae. The absence of competent larvae at the surface during early night hours suggests a reverse vertical migration. Thus, the retention of C. concholepas competent larvae in the upwelled waters could be the result of the interaction between their reverse diel vertical migration and the typical two‐layer upwelling dynamics.
Internal Cysteine Accelerates Thioester-Based Peptide Ligation

Thioester-mediated peptide coupling reactions are powerful tools in protein synthesis. The fragment coupling occurs extremely fast at ligation sites that contain an N-terminal cysteine residue. This native chemical ligation involves a capture step that affixes the acyl component in the immediate vicinity of the N-terminal amino group. The subsequent intramolecular S,N-acyl transfer step proceeds via an entropically favored five-membered ring intermediate. In this study we investigated whether sequence internal cysteine residues that lead to the formation of macrocyclic intermediates are also able to accelerate the rate of thioester-based fragment couplings. It was the aim to identify distance requirements that enable internal cysteine-mediated ligation reactions to proceed at synthetically useful rates. It was found that appropriately positioned cysteine residues can induce up to 25-fold rate enhancements compared to a cysteine-lacking control peptide. Highest ligation rates and yields were obtained when the internal thiol amino acid was incorporated at the fifth or sixth position from the N-terminus of the C-terminal coupling segment. The findings reveal a correlation between the size of the macrocyclic ring intermediate and the ease of the peptide ligation. Internal cysteine ligation may provide the opportunity to shift amino acid cysteine bonds that are difficult to access through native chemical ligation (such as Pro–Cys bonds) by 4–5 amino acids to the N-terminus. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Sodium Channel Mutations and Epilepsy

Voltage-gated sodium channels initiate action potentials in brain neurons, and sodium channel blockers are used in therapy of epilepsy. Mutations in sodium channels are responsible for genetic epilepsy syndromes with a wide range of severity. Generalized Epilepsy with Febrile Seizures Plus (GEFS+) is caused by missense mutations in NaV1.1 channels, which have variable functional effects on sodium channels expressed in non-neuronal cells, but may primarily cause loss of function when expressed in mice. Complete loss-of-function mutations in NaV1.1 cause Severe Myoclonic Epilepsy of Infancy (SMEI or Dravet Syndrome), which involves severe, intractable epilepsy and co-morbidities of ataxia, sleep disturbance, and cognitive impairment. Mice with loss-of-function mutations in NaV1.1 channels have severely impaired sodium currents and action potential firing in hippocampal GABAergic inhibitory neurons without detectable effect on the excitatory pyramidal neurons, which would cause hyperexcitability and contribute to seizures in SMEI. Similarly, sodium currents and action potential firing are impaired in the GABAergic Purkinje neurons in the cerebellum, which likely contributes to ataxia, and in the reticular nucleus of the thalamus and the suprachiasmatic nucleus of the hypothalamus, which likely contribute to circadian rhythm disturbances and sleep disorder. The imbalance between excitatory and inhibitory transmission can be partially corrected by compensatory loss-of-function mutations of NaV1.6 channels, and thermally induced seizures in these mice can be prevented by drug combinations that enhance GABAergic neurotransmission. Familial Febrile Seizures are also caused by mild loss-of-function mutations in NaV1.1 channels. We have proposed a unified loss-of-function hypothesis for the spectrum of epilepsy syndromes caused by genetic changes in NaV1.1 channels: mild impairment predisposes to febrile seizures, intermediate impairment leads to GEFS+ epilepsy, and severe loss of function causes the intractable seizures and co-morbidities of SMEI. Surprisingly, mutations in other sodium channels that cause epilepsy are rare, but Benign Neonatal Infantile Seizures is caused by mutations in NaV1.2 channels, and mutations in those channels can also lead to more severe epilepsy syndromes. Understanding the molecular and cellular mechanisms that underlie these genetic epilepsies is yielding much information about non-genetic epilepsy syndromes as well.