Landscape functionality in protected and unprotected areas: Case studies from the Czech Republic

Landscape structure not only reflects the natural settings of the landscape but also its history and the impact of human activity. Information about the characteristics of the landscape elements in terms of their structural functionality plays a central role in assessing their ecological quality. Statutory designation of sites plays a key role in conserving and maintaining valuable parts of the landscape.In this study, we investigated whether protection status influences functionality in case studies from the Czech Republic, representing three different landscape types.Landscape structure metrics derived from land cover maps, were used for the assessment of functionality in protected and unprotected regions of the landscape types. Mean functionality was calculated for six different functionality groups. We also focused on the level of protection status and its relationship to functionality.Our results showed that landscape functionality is higher in protected areas as opposed to unprotected areas. In addition, functionality was found to be high for the ‘valuable matrix’ and the ‘connecting corridors’ groups. The results also indicated that the more strictly protected areas tend to have higher functionality.     

Low root functional dispersion enhances functionality of plant growth by influencing bacterial activities in European forest soils

Current studies show that multispecies forests are beneficial regarding biodiversity and ecosystem functionality. However, there are only little efforts to understand the ecological mechanisms behind these advantages of multispecies forests. Bacteria are among the key plant growth-promoting microorganisms that support tree growth and fitness. Thus, we investigated links between bacterial communities, their functionality and root trait dispersion within four major European forest types comprising multispecies and monospecific plots. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggest an increasing bacterial functionality from monospecific to multispecies forest. In multispecies forest plots, the bacterial functionality linked to plant growth activities declined with the increasing functional dispersion of the roots. Our findings indicate that enriched abundant bacterial operational taxonomic units are decoupled from bacterial functionality. We also found direct effects of tree species identity on bacterial community composition but no significant relations with root functional dispersion. Additionally, bacterial network analyses indicated that multispecies forests have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. We identified a potential of root dispersion to facilitate bacterial interactions and consequently, plant growth activities.     

Preparation of chain-end clickable recombinant protein and its bio-orthogonal modification

Introducing unique functional group into protein is an attractive approach for site-selective protein modification applications. In this report, we systemically investigated four site-selective strategies to introduce azide functionality into recombinant thrombomodulin (TM₄₅₆), via direct recombinant expression with unnatural amino acid, chemical, and enzymatic modification for its bio-orthogonal modification application. First, a straightforward recombinant method to express TM₄₅₆ with azide functionality near C-terminus by replacing methionine with azidohomoanlanine from methionine auxotroph Escherichia coli cell was investigated. Next, a sortase-mediated ligation (SML) method to incorporate azide functionality into the C-terminus of recombinant TM₄₅₆ was demonstrated. The third is to add azide functionality to the N-terminal amine of recombinant TM₄₅₆ via amidation chemistry, and the fourth is tyrosine selective three-component Mannich reaction to introduce azide functionality to recombinant TM₄₅₆. Overall, SML of recombinant protein affords the highest overall yield for incorporating azide functionality into the C-terminus recombinant TM₄₅₆ since the key protein expression step uses natural amino acids. Also, single site modification facilitates the highest TM₄₅₆ activity.     

Tumor-induced impairment of TCR signaling results in compromised functionality of tumor-infiltrating regulatory T cells

This study demonstrates, for the first time, that murine regulatory T (Treg) cells in the tumor microenvironment display both enhanced proliferation and reduced functionality. This enhanced proliferation, combined with decreased apoptosis, leads to an intratumoral accumulation of Treg cells with a unique phenotype: CD4(+)CD25(+)FoxP3(+)GITR(high)CD27(low)CD62L(-). The loss of functionality is associated with down-regulation of the TCR signaling complex, including IL-2-inducible T cell kinase. It is also demonstrated that tumor-infiltrating Treg cells have impaired TCR-mediated signaling and calcium influx. Based on these findings, this study supports the hypothesis that 1) tumor-infiltrating Treg cells lose functionality due to their diminished ability to become effectively activated and 2) intratumoral accumulation of Treg cells may compensate for the impaired functionality, thus maintaining immune tolerance to the tumor.     

Immobilization of oligonucleotides on glass surface using an efficient heterobifunctional reagent through maleimide-thiol combination chemistry

An efficient heterobifunctional reagent, N-(3-triethoxysilylpropyl)-4-(N'-maleimidylmethyl) cyclohexanamide (TPMC), was developed for the immobilization of thiol-modified oligonucleotides on an unmodified glass surface. The heterobifunctionality of the reagent was used for the construction of a DNA microarray in which the triethoxysilyl functionality has specificity toward a glass surface, whereas the maleimide functionality has thiol-modified oligonucleotides via a stable thioether linkage. Immobilization of DNA was achieved by two alternative approaches. In the first approach, the reagent TPMC was treated with oligonucleotides to get triethoxysilyl-oligonucleotide conjugate, which was then covalently attached via specific triethoxysilyl functionality to an unmodified glass surface. In the second approach, the reagent was first covalently linked with an unmodified glass surface to get maleimide functionality on a glass surface, which was then used for the immobilization of oligonucleotides via a stable thioether linkage. The applicability of the reagent was explored by hybridization studies with the fluorescein-labeled complementary DNA strand and in mismatch discrimination.     

Mouthpart separation does not impede butterfly feeding

The functionality of butterfly mouthparts (proboscis) plays an important role in pollination systems, which is driven by the reward of nectar. Proboscis functionality has been assumed to require action of the sucking pump in the butterfly's head coupled with the straw-like structure. Proper proboscis functionality, however, also is dependent on capillarity and wettability dynamics that facilitate acquisition of liquid films from porous substrates. Due to the importance of wettability dynamics in proboscis functionality, we hypothesized that proboscides of eastern black swallowtail (Papilio polyxenes asterius Stoll) (Papilionidae) and cabbage butterflies (Pieris rapae Linnaeus) (Pieridae) that were experimentally split (i.e., proboscides no longer resembling a sealed straw-like tube) would retain the ability to feed. Proboscides were split either in the drinking region (distal 6–10% of proboscis length) or approximately 50% of the proboscis length 24 h before feeding trials when butterflies were fed a red food-coloring solution. Approximately 67% of the butterflies with proboscides split reassembled prior to the feeding trials and all of these butterflies displayed evidence of proboscis functionality. Butterflies with proboscides that did not reassemble also demonstrated fluid uptake capabilities, thus suggesting that wild butterflies might retain fluid uptake capabilities, even when the proboscis is partially injured.     

N-(3-triethoxysilylpropyl)-4-(isothiocyanatomethyl)-cyclohexane-1-carboxamide (TPICC): a heterobifunctional reagent for immobilization of biomolecules on glass surface

An efficient heterobifunctional reagent, N-(3-triethoxysilylpropyl)-4-(isothiocyanatomethyl)cyclohexane-1-carboxamide (TPICC) has been developed by a simple 'two step reaction' for the preparation of bioconjugates and immobilization of biomolecules such as oligonucleotides, peptides and proteins on the glass surface. The isothiocyanate functionality at one end of the reagent, TPICC was found specific for the ligands having either aminoalkyl (RNH(2)) or mercaptoalkyl (R-SH) functionality. The synthesis of bioconjugates with the reagent was achieved through its isothiocyanate functionality at one end via the formation of stable thiourea linkage with aminoalkyl and dithiocarbamate linkage with mercaptoalkyl derivatives. The triethoxysilyl functionality of the reagent has been utilized for specific coupling with the virgin glass surface by a very simple methodology.     

Protein Domain Analysis of Genomic Sequence Data Reveals Regulation of LRR Related Domains in Plant Transpiration in Ficus

Predicting protein domains is essential for understanding a protein’s function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.     

Functional lifespans of xylem vessels: Development,hydraulic function,and post‐function of vessels in several species of woody plants

Premise of the Study

Xylem vessels transition through different stages during their functional lifespan, including expansion and development of vessel elements, transition to vessel hydraulic functionality, and eventual transition to post‐functionality. We used information on vessel development and function to develop a model of vessel lifespan for woody plants.

Methods

We examined vessel functional lifespan using repeated anatomical sampling throughout the growing season, combined with active‐xylem staining to evaluate vessel hydraulic transport functionality. These data were combined with a literature review. The transitions between vessel functional lifespans for several species are illustrated, including grapevine (Vitis vinifera L., Vitaceae), English oak (Quercus robur L., Fagaceae), American chestnut [Castanea dentata (Marshall) Borkh.; Fagaceae], and several arid and semi‐arid shrub species.

Key Results

In intact woody plants, development and maturation of vessel elements may be gradual. Once hydraulically functional, vessel elements connect to form a vessel network that is responsible for bulk hydraulic flow through the xylem. Vessels become nonfunctional due to the formation of gas emboli. In some species and under some conditions, vessel functionality of embolized conduits may be restored through refilling. Blockages, such as tyloses, gels, or gums, indicate permanent losses in hydraulic functional capacity; however, there may be some interesting exceptions to permanent loss of functionality for gel‐based blockages.

Conclusions

The gradual development and maturation of vessel elements in woody plants, variation in the onset of functionality between different populations of vessels throughout the growing season, and differences in the timing of vessel transitions to post‐functionality are important aspects of plant hydraulic function.     

A new usage of functionalized oligodeoxynucleotide probe for site-specific modification of a guanine base within RNA

Site-specific modification of RNA is of great significance to investigate RNA structure, function and dynamics. Recently, we reported a new method for sequence- and cytosine-selective chemical modification of RNA based on the functional group transfer reaction of the 1-phenyl-2-methylydene-1,3-diketone unit of the 6-thioguanosine base incorporated in the oligodeoxynucleotide probe. In this study, we describe that the functionality transfer rate is greatly enhanced and the selectivity is shifted to the guanine base when the reaction is performed under alkaline conditions. Detailed investigation indicated that the 2-amino group of the enolate form of rG is the reactant of the functionality transfer reaction. As a potential application of this efficient functionality transfer reaction, a pyrene group as a relatively large fluorescent group was successfully transferred to the target guanine base of RNA with a high guanine and site selectivity. This functionality transfer reaction with high efficiency and high site-selectivity would provide a new opportunity as a unique tool for the study of RNA.     

Expanding the catalytic repertoire of nucleic acid catalysts: simultaneous incorporation of two modified deoxyribonucleoside triphosphates bearing ammonium and imidazolyl functionalities.

Two nucleoside triphosphates, a pyrimidine modified with an ammonium functionality and a purine modified with an imidazolyl functionality are compatible with all conditions for a combinatorial selection of nucleic-acid catalysts. We believe that this work is the first to demonstrate the potential for using not one but two modified nucleotides in tandem. The potential for an enriched catalytic repertoire is envisioned.     

Required functionality of PACS from clinical point of view

Concerning the required functionality of PACS from a clinical point of view this paper describes the functionality during the several phases of the imaging process. A list of general requirements is summarized. To get more information a period of prototype development and testing is needed. During this period the required functionality has to be investigated by questionnaires and automatic registration by the work stations.     

Exercise-Induced Norepinephrine Decreases Circulating Hematopoietic Stem and Progenitor Cell Colony-Forming Capacity

A recent study showed that ergometry increased circulating hematopoietic stem and progenitor cell (CPC) numbers, but reduced hematopoietic colony forming capacity/functionality under normoxia and normobaric hypoxia. Herein we investigated whether an exercise-induced elevated plasma free/bound norepinephrine (NE) concentration could be responsible for directly influencing CPC functionality. Venous blood was taken from ten healthy male subjects (25.3+/−4.4 yrs) before and 4 times after ergometry under normoxia and normobaric hypoxia (F_iO₂<0.15). The circulating hematopoietic stem and progenitor cell numbers were correlated with free/bound NE, free/bound epinephrine (EPI), cortisol (Co) and interleukin-6 (IL-6). Additionally, the influence of exercise-induced NE and blood lactate (La) on CPC functionality was analyzed in a randomly selected group of subjects (n = 6) in vitro under normoxia by secondary colony-forming unit granulocyte macrophage assays. Concentrations of free NE, EPI, Co and IL-6 were significantly increased post-exercise under normoxia/hypoxia. Ergometry-induced free NE concentrations found in vivo showed a significant impairment of CPC functionality in vitro under normoxia. Thus, ergometry-induced free NE was thought to trigger CPC mobilization 10 minutes post-exercise, but as previously shown impairs CPC proliferative capacity/functionality at the same time. The obtained results suggest that an ergometry-induced free NE concentration has a direct negative effect on CPC functionality. Cortisol may further influence CPC dynamics and functionality.     

Membrane protein synthesis in cell-free systems: From bio-mimetic systems to bio-membranes

When taking up the gauntlet of studying membrane protein functionality, scientists are provided with a plethora of advantages, which can be exploited for the synthesis of these difficult-to-express proteins by utilizing cell-free protein synthesis systems. Due to their hydrophobicity, membrane proteins have exceptional demands regarding their environment to ensure correct functionality. Thus, the challenge is to find the appropriate hydrophobic support that facilitates proper membrane protein folding. So far, various modes of membrane protein synthesis have been presented. Here, we summarize current state-of-the-art methodologies of membrane protein synthesis in biomimetic-supported systems. The correct folding and functionality of membrane proteins depend in many cases on their integration into a lipid bilayer and subsequent posttranslational modification. We highlight cell-free systems utilizing the advantages of biological membranes.     

Examining Emergence of Functional Gene Clustering in a Simulated Evolution

Recent research suggests that rather than being random, gene order may be coupled with gene functionality. These findings may be explained by mechanisms that require physical proximity such as co-expression and co-regulation. Alternatively, they may be due to evolutionary-dynamics forces, as expressed in genetic drift or linkage disequilibrium. This paper proposes a biologically plausible model for evolutionary development. Using the model, which includes natural selection and the development of gene networks and cellular organisms, the co-evolution of recombination rate and gene functionality is examined. The results presented here are compatible with previous biological findings showing that functionally related genes are clustered. These results imply that evolutionary pressure in a complex environment is sufficient for the emergence of gene order that is coupled with functionality. They shed further light on the mechanisms that may cause such gene clusters.     

Impact of Physicochemical Environment on the Super Disintegrant Functionality of Cross-Linked Carboxymethyl Sodium Starch: Insight on Formulation Precautions

The aim of this work is to improve the understanding of the physicochemical mechanisms involved in the functionality of cross-linked carboxymethyl sodium starch (CCSS) as a tablet super disintegrant (SD). The behavior and properties of this SD (medium uptake, disintegration times, particle size, and rheology) was investigated in a wetting medium of different physicochemical properties. In particular, the relative permittivity (dielectric constant) of these media was intentionally modified for evaluating its effect on CCSS properties. Results showed different swelling behaviors of CCSS particles according to the relative permittivity of the tested media and allow to propose two underlying mechanisms that explain CCSS functionality. Both the intra-particular swelling and the inter-particular repulsion are affected by the relative permittivity of the media. Finally, disintegration test performed on tablets specially formulated with mannitol (used commonly as an excipient and known to modify relative permittivity) confirmed that the functionality of CCSS and therefore the disintegration of the tablet can be altered according to the mannitol content.KEY WORDS: cross-linked carboxymethyl sodium starch, disintegrant functionality, orally disintegrating tablets, relative permittivity, repulsive layers     

The contributions of dsRNA structure to Dicer specificity and efficiency

Dicer processes long double-stranded RNA (dsRNA) and pre-microRNAs to generate the functional intermediates (short interfering RNAs and microRNAs) of the RNA interference pathway. Here we identify features of RNA structure that affect Dicer specificity and efficiency. The data presented show that various attributes of the 3' end structure, including overhang length and sequence composition, play a primary role in determining the position of Dicer cleavage in both dsRNA and unimolecular, short hairpin RNA (shRNA). We also demonstrate that siRNA end structure affects overall silencing functionality. Awareness of these new features of Dicer cleavage specificity as it is related to siRNA functionality provides a more detailed understanding of the RNAi mechanism and can shape the development of hairpins with enhanced functionality.     

Anticipatory Functions, Digital-Analog Forms and Biosemiotics: Integrating the Tools to Model Information and Normativity in Autonomous Biological Agents

We argue that living systems process information such that functionality emerges in them on a continuous basis. We then provide a framework that can explain and model the normativity of biological functionality. In addition we offer an explanation of the anticipatory nature of functionality within our overall approach. We adopt a Peircean approach to Biosemiotics, and a dynamical approach to Digital-Analog relations and to the interplay between different levels of functionality in autonomous systems, taking an integrative approach. We then apply the underlying biosemiotic logic to a particular biological system, giving a model of the B-Cell Receptor signaling system, in order to demonstrate how biosemiotic concepts can be used to build an account of biological information and functionality. Next we show how this framework can be used to explain and model more complex aspects of biological normativity, for example, how cross-talk between different signaling pathways can be avoided. Overall, we describe an integrated theoretical framework for the emergence of normative functions and, consequently, for the way information is transduced across several interconnected organizational levels in an autonomous system, and we demonstrate how this can be applied in real biological phenomena. Our aim is to open the way towards realistic tools for the modeling of information and normativity in autonomous biological agents.     

Ring-B functionalized androst-4-en-3-ones and ring-C substituted pregn-4-en-3-ones undergo differential transformation in Aspergillus tamarii KITA: ring-A transformation with all C-6 substituted steroids and ring-D transformation with C-11 substituents

The fungus Aspergillus tamarii transforms progesterone 1 into testololactone 5 in high yield through a four-step enzymatic pathway which is flexible to a range of steroidal substrates. To date, no studies have investigated the fate of C-6 (ring-B) and C-11 (ring-C) functionalized steroidal substrates on metabolism. Remarkably all of the C-6 functionalized substrates underwent reductive metabolism on ring-A in contrast to C-11 functionalized steroids where only ring-D oxidative or reductive transformation occurred. In order to discern the precise role of the functional groups in directing metabolism 6-ketoprogesterone 10 with functionality at C-6 and the ring-D methyl ketone underwent reductive and oxidative transformation on both terminal A and D rings showing that this functionality was directing metabolism. Androst-4-en-3,6-dione 12 devoid of ring-D functionality underwent reductive metabolism on ring-A proving that the C-6 functionality was directing metabolism to this ring with the ring-D methyl ketone responsible for generating transformation at this position. Functionality at C-11 exclusively controlled entry into and degree of metabolism on the lactonization pathway. These novel findings may have important bearing in the future understanding of structure activity relationships in revealing new metabolic pathways and further affords a unique opportunity for generation of novel bioactive steroidal compounds.     

Generation of monospecific antibodies based on affinity capture of polyclonal antibodies

A method is described to generate and validate antibodies based on mapping the linear epitopes of a polyclonal antibody followed by sequential epitope-specific capture using synthetic peptides. Polyclonal antibodies directed towards four proteins RBM3, SATB2, ANLN, and CNDP1, potentially involved in human cancers, were selected and antibodies to several non-overlapping epitopes were generated and subsequently validated by Western blot, immunohistochemistry, and immunofluorescence. For all four proteins, a dramatic difference in functionality could be observed for these monospecific antibodies directed to the different epitopes. In each case, at least one antibody was obtained with full functionality across all applications, while other epitope-specific fractions showed no or little functionality. These results present a path forward to use the mapped binding sites of polyclonal antibodies to generate epitope-specific antibodies, providing an attractive approach for large-scale efforts to characterize the human proteome by antibodies.