Scaffolding Role Research Articles

Synthesis and molecular docking study of new pyrazole derivatives as potent anti-breast cancer agents targeting VEGFR-2 kinase.

Based on the previous studies that revealed the valuable role of pyrazole scaffold in cancer management and VEGFR-2 inhibition, a new set of pyrazole conjugated with pyrazoline, triazolopyrimidine and pyrazolone moieties were synthesized and investigated for their anticancer efficiency against human breast cancer MCF-7. The anticancer screening revealed the significant sensitivity of breast carcinoma towards compounds 4b, 5c, 6c, 7b, 7c and 12c with IC50 values ranging from 16.50 - 26.73µM in comparison with tamoxifen (IC50=23.31µM). Moreover, the new analogues were further examined for their VEGFR-2 inhibitory activity, among the tested derivatives 5c, 6c, 7b, 7c and 12c displayed prominent inhibitory efficiency versus VEGFR-2 kinase with % inhibition ranging from 70 to 79%. Compounds 6c, 7c and 12c revealed inhibitory efficiency in nanomolar level with IC50 (913.51, 225.17 and 828.23nM, respectively) comparing to sorafenib (IC50=186.54nM). Flow cytometric analysis revealed that the promising compound 12c prompted pre-G1 apoptosis and cell growth cessation at G2/M phase and stimulated apoptosis via activation of caspase-3. Moreover, molecular docking study of the promising derivatives was performed to highlight their binding modes and interactions with the amino acid residues of VEGFR-2 enzyme.

Insight into delivery of dermal fibroblast by non-biodegradable bacterial nanocellulose composite hydrogel on wound healing

In skin tissue engineering, a biodegradable scaffold is usually used where cells grow, produce its own cytokines, growth factors, and extracellular matrix, until the regenerated tissue gradually replaces the scaffold upon its degradation. However, the role of non-biodegradable scaffold remains unexplored. This study investigates the potential of a non-biodegradable bacterial nanocellulose/acrylic acid (BNC/AA) hydrogel to transfer human dermal fibroblasts (HDF) to the wound and the resulting healing effects of transferred HDF in athymic mice. Results demonstrated that the fabricated hydrogel successfully transferred >50% of HDF onto the wound site within 24 h, with evidence of HDF detected on day 7. The gene and protein study unveiled faster wound healing in the hydrogel with HDF group and characterized more mature newly formed skin microstructure on day 7, despite no visible differences. These findings give a new perspective regarding the role of non-biodegradable materials in skin tissue engineering, in the presence of exogenous cells, mainly at the molecular level.

Invented spelling activities in kindergarten: the role of instructional scaffolding and collaborative learning

ABSTRACT There is considerable evidence on the connections between emergent literacy-related skills in preschool-age and successful reading and writing. The purpose of this double-designed experimental/descriptive study was to analyse the impact of invented spelling activities on kindergarten children’s spelling performance and to explore adult mediation and peer collaboration processes that occurred within a sample of intervention sessions. Data was collected with 52 participants divided into an experimental group and a control group who were submitted to a pre/post-test assessment. The global quantitative analysis revealed the strong impact of the intervention on children’s word spelling progress scores. The descriptive qualitative data of 2304 verbal interventions of a small-scale sample suggested that significant and diverse mediation scaffolding strategies were incorporated by the children in a shared dialogical learning approach. Our findings point to the need for delivering group interaction activities combining early literacy contents in kindergarten contexts as a vehicle for responding to the challenge of reading and writing acquisition at the beginning of schooling.

How to build complexity

Summary The ribosome is the most complex molecular machine shared by all cellular life forms. Details of its evolution from an RNA world precursor are still encrypted in its molecular sequences, which are gradually yielding information beyond the reach of phylogenetic trees. Meanwhile, researchers can now study the assembly of the structure in real time, yielding further insights into the origins of complexity. Michael Gross reports.

Targeting the scaffolding role of LSD1 (KDM1A) poises acute myeloid leukemia cells for retinoic acid-induced differentiation.

The histone demethylase LSD1 is deregulated in several tumors, including leukemias, providing the rationale for the clinical use of LSD1 inhibitors. In acute promyelocytic leukemia (APL), pharmacological doses of retinoic acid (RA) induce differentiation of APL cells, triggering degradation of the PML-RAR oncogene. APL cells are resistant to LSD1 inhibition or knockout, but targeting LSD1 sensitizes them to physiological doses of RA without altering of PML-RAR levels, and extends survival of leukemic mice upon RA treatment. The combination of RA with LSD1 inhibition (or knockout) is also effective in other non-APL, acute myeloid leukemia (AML) cells. Nonenzymatic activities of LSD1 are essential to block differentiation, while RA with targeting of LSD1 releases a differentiation gene expression program, not strictly dependent on changes in histone H3K4 methylation. Integration of proteomic/epigenomic/mutational studies showed that LSD1 inhibitors alter the recruitment of LSD1-containing complexes to chromatin, inhibiting the interaction between LSD1 and the transcription factor GFI1.

FANCJ helicase promotes DNA end resection by facilitating CtIP recruitment to DNA double-strand breaks.

FANCJ helicase mutations are known to cause hereditary breast and ovarian cancers as well as bone marrow failure syndrome Fanconi anemia. FANCJ plays an important role in the repair of DNA inter-strand crosslinks and DNA double-strand breaks (DSBs) by homologous recombination (HR). Nonetheless, the molecular mechanism by which FANCJ controls HR mediated DSB repair is obscure. Here, we show that FANCJ promotes DNA end resection by recruiting CtIP to the sites of DSBs. This recruitment of CtIP is dependent on FANCJ K1249 acetylation. Notably, FANCJ acetylation is dependent on FANCJ S990 phosphorylation by CDK. The CDK mediated phosphorylation of FANCJ independently facilitates its interaction with BRCA1 at damaged DNA sites and promotes DNA end resection by CtIP recruitment. Strikingly, mutational studies reveal that ATP binding competent but hydrolysis deficient FANCJ partially supports end resection, indicating that in addition to the scaffolding role of FANCJ in CtIP recruitment, its helicase activity is important for promoting end resection. Together, these data unravel a novel function of FANCJ helicase in DNA end resection and provide mechanistic insights into its role in repairing DSBs by HR and in genome maintenance.

Facilitating Episodic Simulation in Anxiety: Role of Sensory Scaffolding and Scenario Modality

Cognitive bias modification of interpretation style (CBM-I) is a family of cognitive training programs that seek to reduce anxious thinking by training people to assign relatively more positive meanings to ambiguous situations. CBM-I’s effects may be enhanced by encouraging more vivid imagery-based episodic simulation of events and by increasing engagement with the training materials. This study investigated the role of sensory scaffolding (whether pictures, or pictures + sound were added) and verbal scenario modality (whether scenarios were delivered visually or aurally) on episodic simulation (Vivid; Plausible; Changing Perspective ratings) and user engagement (Relatable, Comprehensible, Enjoyable ratings). Amazon Mechanical Turk workers (N = 187) with varied anxiety symptom severity read or listened to brief scenarios that varied by sensory scaffolding and verbal scenario modality. Results were somewhat mixed. Generally, picture scaffolding tended to facilitate both episodic simulation and user engagement (relative to no scaffolding), irrespective of scenario modality and anxiety level.

The Type 1 Blue Copper Site: From Electron Transfer to Biological Function.

Cupredoxins host in their scaffold one of the most studied and interesting metal sites in biology: the type 1 (T1) or blue Cu center. Blue Cu proteins have evolved to play key roles in biological electron transfer and have the ability to react with a wide variety of redox partners. The inner coordination sphere of T1 Cu sites conserves two histidines and one cysteine with a short Cu-S(Cys) bond as ligands in a trigonal arrangement, with a variable axial ligand that modulates the electronic structure and reactivity. The structural, electronic and geometric features of T1 Cu centers provide the basis for a site that can be optimized by the protein structure for each biological function. This chapter highlights the properties that make this unique Cu center in biology an efficient and tunable electron transfer site. The contributions of the first coordination shell and the high covalency of the Cu-S(Cys) bond in the T1 Cu site to its distinctive geometric and spectroscopic features are discussed, as well as the role of the protein scaffold in imposing an 'entatic' state with a distorted tetrahedral geometry that minimizes geometric changes upon redox cycling. The analysis of naturally occurring perturbed blue Cu sites provides further insights into how the protein scaffold can tune the properties of the T1 Cu site. Blue Cu sites display a wide range of reduction potentials, as these are tuned to be consistent with their physiologically relevant electron donors and acceptors. The different properties of the protein matrix that play important roles in finetuning the reduction potential of T1 Cu sites are also discussed, including the nature of the axial ligand and outer coordination sphere effects. These concepts are further illustrated by the discussion of examples of biosynthetic blue Cu proteins. Finally, the different features of the T1 Cu site that make it an optimal site for electron transfer (ET) are discussed, in terms of Markus theory for intra- and inter-molecular ET. The active site in multicopper oxidases is used as an example to illustrate the contributions of the anisotropic covalency of the blue Cu site to an efficient ET, while the diverse reactivity of the T1 Cu sites in these enzymes is discussed to dissect the different properties provided by the protein that help tune these unique sites for biological ET.

Cyclin B1 scaffolds MAD1 at the kinetochore corona to activate the mitotic checkpoint

Cyclin B:CDK1 is the master kinase regulator of mitosis. We show here that, in addition to its kinase functions, mammalian Cyclin B also scaffolds a localised signalling pathway to help preserve genome stability. Cyclin B1 localises to an expanded region of the outer kinetochore, known as the corona, where it scaffolds the spindle assembly checkpoint (SAC) machinery by binding directly to MAD1. In vitro reconstitutions map the key binding interface to a few acidic residues in the N‐terminal region of MAD1, and point mutations in this sequence abolish MAD1 corona localisation and weaken the SAC. Therefore, Cyclin B1 is the long‐sought‐after scaffold that links MAD1 to the corona, and this specific pool of MAD1 is needed to generate a robust SAC response. Robustness arises because Cyclin B1:MAD1 localisation loses dependence on MPS1 kinase after the corona has been established, ensuring that corona‐localised MAD1 can still be phosphorylated when MPS1 activity is low. Therefore, this study explains how corona‐MAD1 generates a robust SAC signal, and it reveals a scaffolding role for the key mitotic kinase, Cyclin B1:CDK1, which ultimately helps to inhibit its own degradation.

The membrane periodic skeleton is an actomyosin network that regulates axonal diameter and conduction.

Neurons have a membrane periodic skeleton (MPS) composed of actin rings interconnected by spectrin. Here, combining chemical and genetic gain- and loss-of-function assays, we show that in rat hippocampal neurons the MPS is an actomyosin network that controls axonal expansion and contraction. Using super-resolution microscopy, we analyzed the localization of axonal non-muscle myosin II (NMII). We show that active NMII light chains are colocalized with actin rings and organized in a circular periodic manner throughout the axon shaft. In contrast, NMII heavy chains are mostly positioned along the longitudinal axonal axis, being able to crosslink adjacent rings. NMII filaments can play contractile or scaffolding roles determined by their position relative to actin rings and activation state. We also show that MPS destabilization through NMII inactivation affects axonal electrophysiology, increasing action potential conduction velocity. In summary, our findings open new perspectives on axon diameter regulation, with important implications in neuronal biology.

Simultaneous multiple allelic replacement in the malaria parasite enables dissection of PKG function.

Over recent years, a plethora of new genetic tools has transformed conditional engineering of the malaria parasite genome, allowing functional dissection of essential genes in the asexual and sexual blood stages that cause pathology or are required for disease transmission, respectively. Important challenges remain, including the desirability to complement conditional mutants with a correctly regulated second gene copy to confirm that observed phenotypes are due solely to loss of gene function and to analyse structure-function relationships. To meet this challenge, here we combine the dimerisable Cre (DiCre) system with the use of multiple lox sites to simultaneously generate multiple recombination events of the same gene. We focused on the Plasmodium falciparum cGMP-dependent protein kinase (PKG), creating in parallel conditional disruption of the gene plus up to two allelic replacements. We use the approach to demonstrate that PKG has no scaffolding or adaptor role in intraerythrocytic development, acting solely at merozoite egress. We also show that a phosphorylation-deficient PKG is functionally incompetent. Our method provides valuable new tools for analysis of gene function in the malaria parasite.

Do two heads think better than one?

Introduction: This study examines how 13 bachelor students on Faculty of Medicine and Health Sciences experience collaborative learning on campus at NTNU. My purpose was to find out how students reflect upon collaborative learning face to face on Campus, especially according to learning outcome. The findings are based on empirical data. I investigate how they handle collaborative learning, problems they meet and choices they make while collaborating. My findings will be presented in five different main themes. 
 Method: I analyzed three focus group interviews with 13 students using SDI-model and Nvivo12. I focused on the student’s descriptions and reflections of collaborative learning and learning outcome. 
 Results: The students have a lot of reflections about collaborative learning in akademia. The analysis resulted in five different themes named ‘the teacher’s role’, ‘the role of friction’, ‘the role of being prepared’, ‘consciousness’ and ‘meaning making’. 
 Conclusion: The study implies that to achieve desired effect of learning from collaborative learning the universities should continue to encourage active learning strategies. Especially important to succeed is the teacher’s role in scaffolding, the role of friction and the role of being prepared. The role of consciousness and meaning-making is also important in constructing and creating knowledge. 
 This presentation main message is to show the role of collaborative learning on Campus according to why universities should continue to focus on a change in practice which include active learning strategies to succeed teaching.

Room-Temperature Excitation-Emission Spectra of Single LH2 Complexes Show Remarkably Little Variation.

Excitation spectroscopy gives direct insight into the excited state manifold, energy transfer, transient intermediates, vibrations, and so on. Unfortunately, excitation spectroscopy of single molecules under ambient conditions has remained challenging. Here we present excitation spectra alongside emission spectra of the same individual light-harvesting complex LH2 of the purple bacteria Rps. acidophila. The acquisition of both the excited and ground state spectra allows us to quantify disorder and interband correlations, which are key variables for the interpretation of observed long-lasting coherences. We have overcome the low photostability and small fluorescence quantum yield that are inherent to many biologically relevant systems by combining single-molecule Fourier transform spectroscopy, low excitation intensities, and effective data analysis. We find that LH2 complexes show little spectral variation (130-170 cm-1), that their two absorption bands (B800-B850) are uncorrelated, and that the Stokes shift is not constant. The low amount of spectral disorder underlines the protective role of the protein scaffold, benefiting the efficient energy transport throughout the light-harvesting membrane.

E-portfolios and the development of students’ reflective thinking at a Hong Kong University

E-portfolios have been adopted by higher education institutions as assessment for learning tools to develop students’ reflective thinking and their ownership of learning. This paper examines how e-portfolios are integrated in an undergraduate course at a Hong Kong university to develop students’ reflective thinking. Based on the qualitative data collected and analysed from both the teacher and students in the course, this paper first discusses the different levels of reflective thinking that the students developed as they were working on their e-portfolios. It then identifies the factors that facilitate and hinder students’ development of reflective thinking, how the facilitating factors are enabled and what the hindering factors need to be addressed. These key findings highlight the pivotal role of the teacher as a learning facilitator and guide, the scaffolding role of the toolkit to support both teachers and students, and the necessity of the technical capacity building and support in the implementation of e-portfolios in higher education.

Cargo hold and delivery: Ankyrins, spectrins, and their functional patterning of neurons.

The highly polarized, typically very long, and nonmitotic nature of neurons present them with unique challenges in the maintenance of their homeostasis. This architectural complexity serves a rich and tightly controlled set of functions that enables their fast communication with neighboring cells and endows them with exquisite plasticity. The submembrane neuronal cytoskeleton occupies a pivotal position in orchestrating the structural patterning that determines local and long-range subcellular specialization, membrane dynamics, and a wide range of signaling events. At its center is the partnership between ankyrins and spectrins, which self-assemble with both remarkable long-range regularity and micro- and nanoscale specificity to precisely position and stabilize cell adhesion molecules, membrane transporters, ion channels, and other cytoskeletal proteins. To accomplish these generally conserved, but often functionally divergent and spatially diverse, roles these partners use a combinatorial program of a couple of dozens interacting family members, whose code is not fully unraveled. In a departure from their scaffolding roles, ankyrins and spectrins also enable the delivery of material to the plasma membrane by facilitating intracellular transport. Thus, it is unsurprising that deficits in ankyrins and spectrins underlie several neurodevelopmental, neurodegenerative, and psychiatric disorders. Here, I summarize key aspects of the biology of spectrins and ankyrins in the mammalian neuron and provide a snapshot of the latest advances in decoding their roles in the nervous system.

Investigating the Antiparasitic Potential of the Marine Sesquiterpene Avarone, Its Reduced form Avarol, and the Novel Semisynthetic Thiazinoquinone Analogue Thiazoavarone.

The chemical analysis of the sponge Dysidea avara afforded the known sesquiterpene quinone avarone, along with its reduced form avarol. To further explore the role of the thiazinoquinone scaffold as an antiplasmodial, antileishmanial and antischistosomal agent, we converted the quinone avarone into the thiazinoquinone derivative thiazoavarone. The semisynthetic compound, as well as the natural metabolites avarone and avarol, were pharmacologically investigated in order to assess their antiparasitic properties against sexual and asexual stages of Plasmodium falciparum, larval and adult developmental stages of Schistosoma mansoni (eggs included), and also against promastigotes and amastigotes of Leishmania infantum and Leishmania tropica. Furthermore, in depth computational studies including density functional theory (DFT) calculations were performed. A toxic semiquinone radical species which can be produced starting both from quinone- and hydroquinone-based compounds could mediate the anti-parasitic effects of the tested compounds.

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

BackgroundLong noncoding RNAs (lncRNAs) have roles in gene regulation, epigenetics, and molecular scaffolding and it is hypothesized that they underlie some mammalian evolutionary adaptations. However, for many mammalian species, the absence of a genome assembly precludes the comprehensive identification of lncRNAs. The genome of the American beaver (Castor canadensis) has recently been sequenced, setting the stage for the systematic identification of beaver lncRNAs and the characterization of their expression in various tissues. The objective of this study was to discover and profile polyadenylated lncRNAs in the beaver using high-throughput short-read sequencing of RNA from sixteen beaver tissues and to annotate the resulting lncRNAs based on their potential for orthology with known lncRNAs in other species.ResultsUsing de novo transcriptome assembly, we found 9528 potential lncRNA contigs and 187 high-confidence lncRNA contigs. Of the high-confidence lncRNA contigs, 147 have no known orthologs (and thus are putative novel lncRNAs) and 40 have mammalian orthologs. The novel lncRNAs mapped to the Oregon State University (OSU) reference beaver genome with greater than 90% sequence identity. While the novel lncRNAs were on average shorter than their annotated counterparts, they were similar to the annotated lncRNAs in terms of the relationships between contig length and minimum free energy (MFE) and between coverage and contig length. We identified beaver orthologs of known lncRNAs such as XIST, MEG3, TINCR, and NIPBL-DT. We profiled the expression of the 187 high-confidence lncRNAs across 16 beaver tissues (whole blood, brain, lung, liver, heart, stomach, intestine, skeletal muscle, kidney, spleen, ovary, placenta, castor gland, tail, toe-webbing, and tongue) and identified both tissue-specific and ubiquitous lncRNAs.ConclusionsTo our knowledge this is the first report of systematic identification of lncRNAs and their expression atlas in beaver. LncRNAs—both novel and those with known orthologs—are expressed in each of the beaver tissues that we analyzed. For some beaver lncRNAs with known orthologs, the tissue-specific expression patterns were phylogenetically conserved. The lncRNA sequence data files and raw sequence files are available via the web supplement and the NCBI Sequence Read Archive, respectively.

Calix[4]API-s: fully functionalized calix[4]arene-based facial active pharmaceutical ingredients.

This mini-review covers 25 fully functionalized facial calix[4]arene-based symmetrical and conical cyclic tetramers with significant (comparable to established therapeutic agents) anticancer and anti-infective activities. The main role of the calixarene scaffold in these calix[4]arene-based active pharmaceutical ingredients (calix[4]API-s) is to replicate embedded phenolic units in the cyclic tetramers. So, probably owing to the multivalency, facial, conical structures of calix[4]API-s and synergistic effect of their four replicated units, they can be considered as effective bioactive agents.

The Role of Epistemology and Epistemic Games in Mediating the Use of Mathematics in Chemistry: Implications for Mathematics Instruction and Research on Undergraduate Mathematics Education

Mathematics is used in the physical sciences to describe and model phenomena, resulting in a unique interface between mathematics and disciplines such as chemistry and physics. This paper focuses on themes emerging from a larger project that investigated how students understand and use mathematics in chemical kinetics, a field of study concerned with monitoring the rate of chemical reactions. The primary data source for this study involved a subset of the data from the larger project, focusing on semi-structured interviews with 40 students sampled from a second-semester general chemistry course. During the interviews students were asked to work through chemical kinetics problems that could be solved without calculations (using relationships between quantities and chemistry principles) or they could be solved algorithmically (using equations and the provided data). The interviews were analyzed using the construct of epistemic games, which describe a collection of resources and an associated structure that define and guide problem-solving and reflect epistemological commitments. Findings indicate students have productive resources and approaches for engaging in problem-solving, reflected by the observed shared set of epistemic games. Implications emphasize the role of scaffolding and explicit questioning to prevent compartmentalization of chemistry and mathematics, suggesting the need for more support to help students productively apply the knowledge and skills learned in mathematics courses to contexts such as chemistry.

The Role of Muscle-Derived Stem Cell-Enriched Scaffolds for Treating Volumetric Muscle Defects

The Role of Muscle-Derived Stem Cell-Enriched Scaffolds for Treating Volumetric Muscle Defects