cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.825941.v2
title: Molecular fingerprinting of some <i>Mentha</i> species by sequencing and RFLP analysis of the 5S-rRNA non-transcribed spacer region

description: The genus <i>Mentha</i> is of particular economic importance. The development of new methods for the characterisation of <i>Mentha</i> species is crucial for their unequivocal identification. Amplification of the non-transcribed spacer (NTS) of the 5S-rRNA gene was used to characterise some <i>Mentha</i> species, which revealed a high-specific variability. Cloning and sequencing of all amplified NTS fragments enabled the discrimination among almost all species. <i>In silico</i> and experimental analyses identified specific restriction sites on the amplified 5S-NTS regions, facilitating the rapid and unambiguous discrimination of all the different species by polymerase chain reaction–restriction fragment length polymorphism. A direct comparison between essential oil composition and DNA fingerprinting confirmed a relationship between chemical and molecular data.
DOI: 10.6084/m9.figshare.825937
title: Patterns of floristic composition of Mediterranean meadows and mesophytic grasslands in eastern Continental Portugal

description: It is becoming increasingly necessary to gain a deeper understanding of the ecological gradients underlying the floristic pattern of meadows and grasslands, because their distribution area and dynamics may be affected by the increased dryness resulting from climate change. Thus, the objectives are (1) to identify community types in <i>Molinio–Arrhenatheretea</i> meadows and <i>Stipo giganteae–Agrostietea castellanae</i> grasslands in Eastern Continental Portugal; (2) to recognize those communities that configure habitat types of the European Union Habitats Directive; (3) to establish environmental gradients underlying their spatial variation. Combining the Braun–Blanquet approach with numerical analysis, 292 relevés and 448 species were classified and ordered using two-way indicator species analysis (Twinspan classification) and canonical correspondence analysis (CCA). Partial CCA was applied to assess the relative influence of land use factors. About 17 community types were identified and those floristic patterns were mainly related to environmental gradients linked to pedological factors and humidity gradients. Based on biogeography and the determination of diagnostic species, four new phytosociological associations were proposed: <i>Mentho pulegii–Cyperetum badii</i> ass. nova hoc loco; <i>Trifolio resupinati–Menthetum suaveolentis</i> ass. nova hoc loco; <i>Mentho suaveolentis–Holcetum lanati</i> ass. nova hoc loco and <i>Festuco amplae–Brachypodietum phoenicoidis</i> ass. nova hoc loco.
DOI: 10.6084/m9.figshare.825940.v2
title: Proteomic investigation of glucosinolate systematically changes in <i>Arabidopsis</i> Rosette leaves to exogenous methyl jasmonate

description: Defense responses of plants are activated not only in the wounded tissues but also in the remote parts of the plants. Two different methyl jasmonate (MeJA) treatments were conducted, i.e., MeJA solution spraying of entire rosettes leaves and pasting leaf surface with lanolin squares containing MeJA. Glucosinolate profiles in leaves were similar using the two methods of MeJA treatment except for indole glucosinolates. The glucosinolate profiles in local and systemic leaves showed that the accumulation of glucosinolates in systemic leaves were delayed comparing with those in local treated leaves. Comparative proteomics were used to investigate the molecular processes underlying the glucosinolate changes in response to local and systemic MeJA induction. A total of 83 unique proteins were detected as differentially expressed between the local and systemic leaves. Functional analysis showed that redirection of metabolism from growth to defense was differentially regulated in local and systemic MeJA induction. The higher contents of indole glucosinolates in systemic leaves might arise from the induction of a long-distance signal produced in local leaves as well as from JA synthesized in systemic leaves.
DOI: 10.6084/m9.figshare.825935
title: Structural and functional characterization of the MERIT40 to understand its role in DNA repair

description: <i>MERIT40</i> (MEdiator of RAP80 Interaction and Targeting 40) is a novel associate of the BRCA1-complex and plays an essential role in DNA damage repair. It is the least characterized protein of BRCA1-complex and mainly responsible for maintaining the complex integrity. However, its structural and functional aspects of regulating the complex stability still remain elusive. Here, we carried out a comprehensive examination of MERIT40 biophysical properties and identified its novel interacting partner which would help to understand its role in BRCA1-complex. The recombinant protein was purified by affinity chromatography and unfolding pathway was determined using spectroscopic and calorimetric methods. Molecular model was generated using combinatorial approaches of modeling, and monomer–monomer docking was carried out to identify dimeric interface. Disordered region of MERIT40 was hatchet using trypsin and chymotrypsin to illustrate the existence of stable domain whose function was speculated through DALI search. Our findings suggest that MERIT40 forms a dimer in a concentration-independent manner. Its central region shows remarkable stability towards the protease digestion and has structural similarity with vWA-like region, a domain mainly present in complement activation factors. MERIT40 undergoes a three-state unfolding transition pathway with a dimeric intermediate. It interacts with adaptor molecule of BRCA1-complex, called ABRAXAS, thus help in extending the bridging interaction among various members which further stabilizes the whole complex. The results presented in this paper provide first-hand information on structural and folding behavior of MERIT40. These findings will help in elucidating the role of protein–protein interactions in stabilization of BRCA1-complex.
DOI: 10.6084/m9.figshare.825941.v3
title: Molecular fingerprinting of some <i>Mentha</i> species by sequencing and RFLP analysis of the 5S-rRNA non-transcribed spacer region

description: The genus <i>Mentha</i> is of particular economic importance. The development of new methods for the characterisation of <i>Mentha</i> species is crucial for their unequivocal identification. Amplification of the non-transcribed spacer (NTS) of the 5S-rRNA gene was used to characterise some <i>Mentha</i> species, which revealed a high-specific variability. Cloning and sequencing of all amplified NTS fragments enabled the discrimination among almost all species. <i>In silico</i> and experimental analyses identified specific restriction sites on the amplified 5S-NTS regions, facilitating the rapid and unambiguous discrimination of all the different species by polymerase chain reaction–restriction fragment length polymorphism. A direct comparison between essential oil composition and DNA fingerprinting confirmed a relationship between chemical and molecular data.
DOI: 10.6084/m9.figshare.825935.v2
title: Structural and functional characterization of the MERIT40 to understand its role in DNA repair

description: <i>MERIT40</i> (MEdiator of RAP80 Interaction and Targeting 40) is a novel associate of the BRCA1-complex and plays an essential role in DNA damage repair. It is the least characterized protein of BRCA1-complex and mainly responsible for maintaining the complex integrity. However, its structural and functional aspects of regulating the complex stability still remain elusive. Here, we carried out a comprehensive examination of MERIT40 biophysical properties and identified its novel interacting partner which would help to understand its role in BRCA1-complex. The recombinant protein was purified by affinity chromatography and unfolding pathway was determined using spectroscopic and calorimetric methods. Molecular model was generated using combinatorial approaches of modeling, and monomer–monomer docking was carried out to identify dimeric interface. Disordered region of MERIT40 was hatchet using trypsin and chymotrypsin to illustrate the existence of stable domain whose function was speculated through DALI search. Our findings suggest that MERIT40 forms a dimer in a concentration-independent manner. Its central region shows remarkable stability towards the protease digestion and has structural similarity with vWA-like region, a domain mainly present in complement activation factors. MERIT40 undergoes a three-state unfolding transition pathway with a dimeric intermediate. It interacts with adaptor molecule of BRCA1-complex, called ABRAXAS, thus help in extending the bridging interaction among various members which further stabilizes the whole complex. The results presented in this paper provide first-hand information on structural and folding behavior of MERIT40. These findings will help in elucidating the role of protein–protein interactions in stabilization of BRCA1-complex.
DOI: 10.6084/m9.figshare.825938.v1
title: Study of the vegetation in the Multiple Use Natural Reserve of Monterrico (Guatemala)

description: The Multiple Use Natural Reserve of Monterrico lies on the Pacific coast of the southwest Guatemala in the Chiapas Sector of the Chiapaneca-Hondureña Province. It belongs to the Guatemalan System of Protected Areas and has a predominantly estuarine and coastal marine ecosystem. We took 218 vegetation relevés that contained 72 species belonging to 138 genera and 69 plant families. Multivariate analysis techniques have led to the determination of seven different associations. Three of them are mangrove swamp associations (<i>Lagunculario-Rhizophoretum manglis</i>; <i>Lagunculario-Avicennietum germinantis</i> Peinado, Alcaraz, Delgadillo, De la Cruz, Álvarez and Aguirre, 1994; <i>Rhizophoretum manglis</i> Cuatrecasas, 1958). Three new associations are proposed. These are one reed–bulrush association (<i>Typho domingensis-Phragmitetum australis</i><i>ass. nova</i>) and two sand-dwelling associations, one made up of evergreen grasses dominated by <i>Canavalia rosea</i> which grows on mobile dunes (<i>Thephrosio-Canavalietum roseae</i><i>ass. nova</i>) and a dry forest phytocoenosis dominated by deciduous and some evergreen species, such as <i>Pithecellobium dulce</i>, that grow on more consolidated sandy soils (<i>Gliricidio-Pithecellobietum dulcis</i><i>ass. nova</i>). Finally, special mention must be made of the presence of the pleustohelophytic association <i>Eichhornietum crassipedis</i> Samek and Moncada, 1971. This is the first time that these mangrove swamp associations and this hydrophytic association have been recorded in Guatemala.
DOI: 10.6084/m9.figshare.825941.v5
title: Molecular fingerprinting of some <i>Mentha</i> species by sequencing and RFLP analysis of the 5S-rRNA non-transcribed spacer region

description: The genus <i>Mentha</i> is of particular economic importance. The development of new methods for the characterisation of <i>Mentha</i> species is crucial for their unequivocal identification. Amplification of the non-transcribed spacer (NTS) of the 5S-rRNA gene was used to characterise some <i>Mentha</i> species, which revealed a high-specific variability. Cloning and sequencing of all amplified NTS fragments enabled the discrimination among almost all species. <i>In silico</i> and experimental analyses identified specific restriction sites on the amplified 5S-NTS regions, facilitating the rapid and unambiguous discrimination of all the different species by polymerase chain reaction–restriction fragment length polymorphism. A direct comparison between essential oil composition and DNA fingerprinting confirmed a relationship between chemical and molecular data.
DOI: 10.6084/m9.figshare.825937.v1
title: Patterns of floristic composition of Mediterranean meadows and mesophytic grasslands in eastern Continental Portugal

description: It is becoming increasingly necessary to gain a deeper understanding of the ecological gradients underlying the floristic pattern of meadows and grasslands, because their distribution area and dynamics may be affected by the increased dryness resulting from climate change. Thus, the objectives are (1) to identify community types in <i>Molinio–Arrhenatheretea</i> meadows and <i>Stipo giganteae–Agrostietea castellanae</i> grasslands in Eastern Continental Portugal; (2) to recognize those communities that configure habitat types of the European Union Habitats Directive; (3) to establish environmental gradients underlying their spatial variation. Combining the Braun–Blanquet approach with numerical analysis, 292 relevés and 448 species were classified and ordered using two-way indicator species analysis (Twinspan classification) and canonical correspondence analysis (CCA). Partial CCA was applied to assess the relative influence of land use factors. About 17 community types were identified and those floristic patterns were mainly related to environmental gradients linked to pedological factors and humidity gradients. Based on biogeography and the determination of diagnostic species, four new phytosociological associations were proposed: <i>Mentho pulegii–Cyperetum badii</i> ass. nova hoc loco; <i>Trifolio resupinati–Menthetum suaveolentis</i> ass. nova hoc loco; <i>Mentho suaveolentis–Holcetum lanati</i> ass. nova hoc loco and <i>Festuco amplae–Brachypodietum phoenicoidis</i> ass. nova hoc loco.
DOI: 10.6084/m9.figshare.825938.v3
title: Study of the vegetation in the Multiple Use Natural Reserve of Monterrico (Guatemala)

description: The Multiple Use Natural Reserve of Monterrico lies on the Pacific coast of the southwest Guatemala in the Chiapas Sector of the Chiapaneca-Hondureña Province. It belongs to the Guatemalan System of Protected Areas and has a predominantly estuarine and coastal marine ecosystem. We took 218 vegetation relevés that contained 72 species belonging to 138 genera and 69 plant families. Multivariate analysis techniques have led to the determination of seven different associations. Three of them are mangrove swamp associations (<i>Lagunculario-Rhizophoretum manglis</i>; <i>Lagunculario-Avicennietum germinantis</i> Peinado, Alcaraz, Delgadillo, De la Cruz, Álvarez and Aguirre, 1994; <i>Rhizophoretum manglis</i> Cuatrecasas, 1958). Three new associations are proposed. These are one reed–bulrush association (<i>Typho domingensis-Phragmitetum australis</i><i>ass. nova</i>) and two sand-dwelling associations, one made up of evergreen grasses dominated by <i>Canavalia rosea</i> which grows on mobile dunes (<i>Thephrosio-Canavalietum roseae</i><i>ass. nova</i>) and a dry forest phytocoenosis dominated by deciduous and some evergreen species, such as <i>Pithecellobium dulce</i>, that grow on more consolidated sandy soils (<i>Gliricidio-Pithecellobietum dulcis</i><i>ass. nova</i>). Finally, special mention must be made of the presence of the pleustohelophytic association <i>Eichhornietum crassipedis</i> Samek and Moncada, 1971. This is the first time that these mangrove swamp associations and this hydrophytic association have been recorded in Guatemala.
DOI: 10.6084/m9.figshare.825941.v4
title: Molecular fingerprinting of some <i>Mentha</i> species by sequencing and RFLP analysis of the 5S-rRNA non-transcribed spacer region

description: The genus <i>Mentha</i> is of particular economic importance. The development of new methods for the characterisation of <i>Mentha</i> species is crucial for their unequivocal identification. Amplification of the non-transcribed spacer (NTS) of the 5S-rRNA gene was used to characterise some <i>Mentha</i> species, which revealed a high-specific variability. Cloning and sequencing of all amplified NTS fragments enabled the discrimination among almost all species. <i>In silico</i> and experimental analyses identified specific restriction sites on the amplified 5S-NTS regions, facilitating the rapid and unambiguous discrimination of all the different species by polymerase chain reaction–restriction fragment length polymorphism. A direct comparison between essential oil composition and DNA fingerprinting confirmed a relationship between chemical and molecular data.
DOI: 10.6084/m9.figshare.825934
title: Role of ELA region in auto-activation of mutant KIT receptor: a molecular dynamics simulation insight

description: KIT receptor is the prime target in gastrointestinal stromal tumor (GISTs) therapy. Second generation inhibitor, Sunitinib, binds to an inactivated conformation of KIT receptor and stabilizes it in order to prevent tumor formation. Here, we investigated the dynamic behavior of wild type and mutant D816H KIT receptor, and emphasized the extended A-loop (EAL) region (805–850) by conducting molecular dynamics simulation (∼100 ns). We analyzed different properties such as root mean square cutoff or deviation, root mean square fluctuation, radius of gyration, solvent-accessible surface area, hydrogen bonding network analysis, and essential dynamics. Apart from this, clustering and cross-correlation matrix approach was used to explore the conformational space of the wild type and mutant EAL region of KIT receptor. Molecular dynamics analysis indicated that mutation (D816H) was able to alter intramolecular hydrogen bonding pattern and affected the structural flexibility of EAL region. Moreover, flexible secondary elements, specially, coil and turns were dominated in EAL region of mutant KIT receptor during simulation. This phenomenon increased the movement of EAL region which in turn helped in shifting the equilibrium towards the active kinase conformation. Our atomic investigation of mutant KIT receptor which emphasized on EAL region provided a better insight into the understanding of Sunitinib resistance mechanism of KIT receptor and would help to discover new therapeutics for KIT-based resistant tumor cells in GIST therapy.
DOI: 10.6084/m9.figshare.825935.v1
title: Structural and functional characterization of the MERIT40 to understand its role in DNA repair

description: <i>MERIT40</i> (MEdiator of RAP80 Interaction and Targeting 40) is a novel associate of the BRCA1-complex and plays an essential role in DNA damage repair. It is the least characterized protein of BRCA1-complex and mainly responsible for maintaining the complex integrity. However, its structural and functional aspects of regulating the complex stability still remain elusive. Here, we carried out a comprehensive examination of MERIT40 biophysical properties and identified its novel interacting partner which would help to understand its role in BRCA1-complex. The recombinant protein was purified by affinity chromatography and unfolding pathway was determined using spectroscopic and calorimetric methods. Molecular model was generated using combinatorial approaches of modeling, and monomer–monomer docking was carried out to identify dimeric interface. Disordered region of MERIT40 was hatchet using trypsin and chymotrypsin to illustrate the existence of stable domain whose function was speculated through DALI search. Our findings suggest that MERIT40 forms a dimer in a concentration-independent manner. Its central region shows remarkable stability towards the protease digestion and has structural similarity with vWA-like region, a domain mainly present in complement activation factors. MERIT40 undergoes a three-state unfolding transition pathway with a dimeric intermediate. It interacts with adaptor molecule of BRCA1-complex, called ABRAXAS, thus help in extending the bridging interaction among various members which further stabilizes the whole complex. The results presented in this paper provide first-hand information on structural and folding behavior of MERIT40. These findings will help in elucidating the role of protein–protein interactions in stabilization of BRCA1-complex.
DOI: 10.6084/m9.figshare.825937.v3
title: Patterns of floristic composition of Mediterranean meadows and mesophytic grasslands in eastern Continental Portugal

description: It is becoming increasingly necessary to gain a deeper understanding of the ecological gradients underlying the floristic pattern of meadows and grasslands, because their distribution area and dynamics may be affected by the increased dryness resulting from climate change. Thus, the objectives are (1) to identify community types in <i>Molinio–Arrhenatheretea</i> meadows and <i>Stipo giganteae–Agrostietea castellanae</i> grasslands in Eastern Continental Portugal; (2) to recognize those communities that configure habitat types of the European Union Habitats Directive; (3) to establish environmental gradients underlying their spatial variation. Combining the Braun–Blanquet approach with numerical analysis, 292 relevés and 448 species were classified and ordered using two-way indicator species analysis (Twinspan classification) and canonical correspondence analysis (CCA). Partial CCA was applied to assess the relative influence of land use factors. About 17 community types were identified and those floristic patterns were mainly related to environmental gradients linked to pedological factors and humidity gradients. Based on biogeography and the determination of diagnostic species, four new phytosociological associations were proposed: <i>Mentho pulegii–Cyperetum badii</i> ass. nova hoc loco; <i>Trifolio resupinati–Menthetum suaveolentis</i> ass. nova hoc loco; <i>Mentho suaveolentis–Holcetum lanati</i> ass. nova hoc loco and <i>Festuco amplae–Brachypodietum phoenicoidis</i> ass. nova hoc loco.
DOI: 10.6084/m9.figshare.825938.v2
title: Study of the vegetation in the Multiple Use Natural Reserve of Monterrico (Guatemala)

description: The Multiple Use Natural Reserve of Monterrico lies on the Pacific coast of the southwest Guatemala in the Chiapas Sector of the Chiapaneca-Hondureña Province. It belongs to the Guatemalan System of Protected Areas and has a predominantly estuarine and coastal marine ecosystem. We took 218 vegetation relevés that contained 72 species belonging to 138 genera and 69 plant families. Multivariate analysis techniques have led to the determination of seven different associations. Three of them are mangrove swamp associations (<i>Lagunculario-Rhizophoretum manglis</i>; <i>Lagunculario-Avicennietum germinantis</i> Peinado, Alcaraz, Delgadillo, De la Cruz, Álvarez and Aguirre, 1994; <i>Rhizophoretum manglis</i> Cuatrecasas, 1958). Three new associations are proposed. These are one reed–bulrush association (<i>Typho domingensis-Phragmitetum australis</i><i>ass. nova</i>) and two sand-dwelling associations, one made up of evergreen grasses dominated by <i>Canavalia rosea</i> which grows on mobile dunes (<i>Thephrosio-Canavalietum roseae</i><i>ass. nova</i>) and a dry forest phytocoenosis dominated by deciduous and some evergreen species, such as <i>Pithecellobium dulce</i>, that grow on more consolidated sandy soils (<i>Gliricidio-Pithecellobietum dulcis</i><i>ass. nova</i>). Finally, special mention must be made of the presence of the pleustohelophytic association <i>Eichhornietum crassipedis</i> Samek and Moncada, 1971. This is the first time that these mangrove swamp associations and this hydrophytic association have been recorded in Guatemala.