Scaffolding Role Research Articles

A comparative in vitro and in vivo study on bone tissue engineering potential of the collagen/nano-hydroxyapatite scaffolds loaded with ginger extract and curcumin

Tissue engineering, a multidisciplinary science which can be used to restore the functions of the damaged tissues and organs, has attracted attention of researchers for the last decades. In this study, due to the importance of the role of scaffold in tissue engineering, optimized collagen-hydroxyapatite (COL-HA) scaffolds have been loaded with different amounts of curcumin (CUR) and hydro-alcoholic ginger extract (GIN) for bone tissue engineering applications. The scaffolds were created by freeze dryer method and the physical and biological properties of the scaffolds were evaluated in vitro and in vivo. The comparison revealed the efficacy of resulting porous 3D structures in both groups of scaffolds with CUR and GIN. Mechanically, CUR increased the tensile strength of the scaffolds, while GIN slightly decreased it. Both CUR and GIN caused higher bioactivity and osteogenesis ability in the COL-HA scaffolds. In vitro biocompatibility, in the presence of mesenchymal stem cells derived from synovial membrane of rats, has been improved by CUR and GIN. In vivo biocompatibility, by subcutaneous implantation of the scaffold in rat animal models for 12 weeks, indicated less inflammatory reactions by the addition of CUR and GIN into the scaffolds. These findings make promising appropriate scaffolds for bone tissue engineering applications.

Distinct PEAK3 interactors and outputs expand the signaling potential of the PEAK pseudokinase family.

The pseudokinase scaffolds PEAK1 and PEAK2 are implicated in cancer cell migration and metastasis. We characterized the regulation and role of the third family member PEAK3 in cell signaling. Similar to PEAK1 and PEAK2, PEAK3 formed both homotypic and heterotypic complexes. In addition, like PEAK1, it bound to the adaptors Grb2 and CrkII. However, unlike PEAK1 and PEAK2, homodimerized PEAK3 also interacted with the ARF GTPase-activating protein ASAP1, the E3 ubiquitin ligase Cbl, and the kinase PYK2. Dimerization and subsequent phosphorylation on Tyr24, likely by a Src family kinase, were required for the binding of PEAK3 to Grb2 and ASAP1. Interactions with Grb2, CrkII, ASAP1, Cbl, and PYK2 exhibited contrasting dynamics upon cell stimulation with epidermal growth factor (EGF), in part due to PEAK3 dephosphorylation mediated by the phosphatase PTPN12. Overexpressing PEAK3 in mesenchymal-like MDA-MB-231 breast cancer cells enhanced cell elongation in a manner dependent on PEAK3 dimerization, and manipulation of PEAK3 expression demonstrated a positive role for this scaffold in regulating cell migration. Overexpressing PEAK3 in PEAK1/2 double-knockout MCF-10A breast epithelial cells enhanced acinar growth, impaired basement membrane integrity, and promoted invasion in three-dimensional cultures, with the latter two effects dependent on the binding of PEAK3 to Grb2 and ASAP1. PEAK1 and PEAK2 quantitatively and temporally influenced PEAK3 function. These findings characterize PEAK3 as an integral, signal-diversifying member of the PEAK family with scaffolding roles that promote cell proliferation, migration, and invasion.

Filament assembly of the C. elegans lamin in the absence of helix 1A

ABSTRACT Lamins are the major constituent of the nuclear lamina, a protein meshwork underlying the inner nuclear membrane. Nuclear lamins are type V intermediate filaments that assemble into ~3.5 nm thick filaments. To date, only the conditions for the in vitro assembly of Caenorhabditis elegans lamin (Ce-lamin) are known. Here, we investigated the assembly of Ce-lamin filaments by cryo-electron microscopy and tomography. We show that Ce-lamin is composed of ~3.5 nm protofilaments that further interact in vitro and are often seen as 6–8 nm thick filaments. We show that the assembly of lamin filaments is undisturbed by the removal of flexible domains, that is, the intrinsically unstructured head and tail domains. In contrast, much of the coiled-coil domains are scaffold elements that are essential for filament assembly. Moreover, our results suggest that Ce-lamin helix 1A has a minor scaffolding role but is important to the lateral assembly regulation of lamin protofilaments.

Forging of nicotine for the effective management of diabetic wounds: A hybrid of scaffold hopping and molecular dynamics simulation approaches

Diabetic wound (DW) is a huge threat to the health care community and is always challenging to treat. The main biochemical culprits in DW recalcitrance are elevated inflammatory mediators, proteases, cell proliferation and migration suppressors, anti-angiogenic factors, and bacterial infections. In this scenario, using a scaffold to target important factors at each stage of pathogenesis can accelerate the healing process. Many shreds of evidence disclosed the role of nicotine scaffold in handling inflammation, infection, proliferation, migration, and angiogenesis. All these factors made us forge nicotine by employing a scaffold hopping approach. The hops were then subjected to molecular docking and binding free energy calculations against Matrix metallopeptidase 9, Glycogen synthase kinase 3 beta, Tumor necrosis factor alpha, MurC and ParE enzymes. Gratifyingly, molecule H1 was found to possess significant inhibitory activity against the selected receptors as evidenced by their high negative glide score and binding energy. Furthermore, 100 ns of molecular dynamics simulation studies (MD) was performed for the five H1/4XCT, H1/5F95, H1/2AZ5, H1/4C13 and H1/4MOT complexes to get insight into the binding modes and stability. The MD results showed significant stability as evidenced by the low conformational changes of the H1 with the chosen receptors. Hence, H1 might be a druggable candidate in the therapeutic management of DW. However, further research is strongly recommended to advance the drug into the therapeutic pipeline.

Tailoring Reaction Selectivity by Modulating a Catalytic Diad on a Foldamer Scaffold.

Use of a tunable molecular scaffold to align a reactive diad for bifunctional catalysis can reveal relationships between functional group identity and reactivity that might otherwise be impossible to identify. Here we use an α/β-peptide helix to show that an aligned pair of primary amine groups is uniquely competent to catalyze crossed aldol condensations with an aryl aldehyde as the electrophile. Geometrically similar diads in which one amine group is secondary, or both are secondary, are good catalysts for other types of aldol condensations but not those involving an aryl aldehyde. Catalytic efficacy requires β-amino acid residues that are preorganized for helix formation via cyclic constraint. Conventional peptides (exclusively α-amino acid residues) that display the primary amine diad are poor catalysts, which highlights the critical role of the foldamer scaffold.

Structural insights into the membrane microdomain organization by SPFH family proteins.

The lateral segregation of membrane constituents into functional microdomains, conceptually known as lipid raft, is a universal organization principle for cellular membranes in both prokaryotes and eukaryotes. The widespread Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are enriched in functional membrane microdomains at various subcellular locations, and therefore were hypothesized to play a scaffolding role in microdomain formation. In addition, many SPFH proteins are also implicated in highly specific processes occurring on the membrane. However, none of these functions is understood at the molecular level. Here we report the structure of a supramolecular complex that is isolated from bacterial membrane microdomains and contains two SPFH proteins (HflK and HflC) and a membrane-anchored AAA+ protease FtsH. HflK and HflC form a circular 24-mer assembly, featuring a laterally segregated membrane microdomain (20 nm in diameter) bordered by transmembrane domains of HflK/C and a completely sealed periplasmic vault. Four FtsH hexamers are embedded inside this microdomain through interactions with the inner surface of the vault. These observations provide a mechanistic explanation for the role of HflK/C and their mitochondrial homologs prohibitins in regulating membrane-bound AAA+ proteases, and suggest a general model for the organization and functionalization of membrane microdomains by SPFH proteins.

Ultrafast 2D-IR spectroscopy of [NiFe] hydrogenase from E. coli reveals the role of the protein scaffold in controlling the active site environment.

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of Escherichia coli Hyd-1 (EcHyd-1) reveals the structural and dynamic influence of the protein scaffold on the Fe(CO)(CN)2 unit of the active site. Measurements on as-isolated EcHyd-1 probed a mixture of active site states including two, which we assign to Nir-SI/II, that have not been previously observed in the E. coli enzyme. Explicit assignment of carbonyl (CO) and cyanide (CN) stretching bands to each state is enabled by 2D-IR. Energies of vibrational levels up to and including two-quantum vibrationally excited states of the CO and CN modes have been determined along with the associated vibrational relaxation dynamics. The carbonyl stretching mode potential is well described by a Morse function and couples weakly to the cyanide stretching vibrations. In contrast, the two CN stretching modes exhibit extremely strong coupling, leading to the observation of formally forbidden vibrational transitions in the 2D-IR spectra. We show that the vibrational relaxation times and structural dynamics of the CO and CN ligand stretching modes of the enzyme active site differ markedly from those of a model compound K[CpFe(CO)(CN)2] in aqueous solution and conclude that the protein scaffold creates a unique biomolecular environment for the NiFe site that cannot be represented by analogy to simple models of solvation.

Exploring the role of scaffolds in problem-based learning (PBL) in an undergraduate chemistry laboratory

The need for shifting the expository laboratory instruction style to inquiry-based approaches is widely acknowledged. Problem-based learning (PBL), one of the inquiry-based approaches, advocates students’ self-directed learning. The literature indicates that scaffolding students’ independent learning is necessary for a PBL environment. In our study, we provided scaffolds such as a precursor task, reading material, and structured group discussion to facilitate the planning of a PBL task on indigo dyeing wastewater treatment. In this paper, we describe how these three scaffolds integrated within the PBL style contributed to students’ learning as per the stages of Kolb's Experiential Learning Cycle (ELC). We analyzed the level of the abstract conceptualization stage of ELC through students’ experimental designs (EDs) of the PBL task. The results of the qualitative analysis of the scaffolded and un-scaffolded groups suggest that scaffolded students’ experimental design scores are higher. The qualitative results indicate that the structured group discussion influences the EDs planned by students more than the precursor task and the reading material. All three scaffolds help in the reflective learning and planning of executable EDs for a PBL task. The study indicates that students transitioning into the inquiry laboratory benefit from the inclusion of scaffolding.

The Role of Scaffolding in LMOOCs for Displaced People

This article presents the results of an analysis of how passive and active scaffolding, as types of structured student learning support, can be provided for refugees and migrants in Language MOOCs (LMOOCs). It focuses on the nature of such scaffolding and what effect it has on learning. After an analysis of the theoretical aspects of supporting refugees and migrants in this type of course a case study is presented. This study focuses on the inclusion of scaffolding in the design, development and running of two Spanish LMOOCs for immediate needs, created within the MOONLITE[1] project in collaboration with support groups for displaced people. The results of the study support the use of scaffolding as a mechanism that improves the course completion rates (increasing from the usual figure of around 10% to 31% and 30% in the respective courses), language learning, and the overall satisfaction and motivation of the students.
 
 [1] Massive Open Online courses eNhancing LInguistic and TransvErsal skills for social inclusion and employability. ERASMUS+ project number: 2016-1-ES01-KA203-025731

Researching the Complexities of the School Subject Swedish as a Second Language: A Linguistic Ethnographic Project in Four Schools

This article focuses on language education policy for language learners in Sweden by building on a synthesis of findings from a research project on the school subject Swedish as a second language (SSL). The project was located in three upper secondary schools and one primary school with a large proportion of migrant students, of whom a majority studied SSL. We present previously published core findings, as well as revisit data for new analyses. The overarching aim is to contribute new knowledge on the complexities of arranging for sustainable, equitable and high-quality language educational provisions that include the teaching and learning of the language of schooling, through the lens of SSL. First, we outline and discuss the relatively unique design of SSL and discourses surrounding the subject, and also make some international comparisons with English as an Additional Language. Secondly, we discuss the role of pedagogical scaffolding of advanced literacy and literary content, and of multilingual aspects in SSL, as well as examine policy frictions in the data. We conclude by reflecting on the role of teacher competences and research methodology. Researching a second language subject is to stand in the crossroad of macro policy, the theory and practice of language education, and equity. All these aspects need to be considered to reach sustainable educational goals.

The Role of Scaffolding through Peer Collaborative Feedback in EFL Literature Students’ Oral Presentation of Short Stories

The Role of Scaffolding through Peer Collaborative Feedback in EFL Literature Students’ Oral Presentation of Short Stories

ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly.

SUMMARYThe ATPase Family AAA Domain Containing 3A (ATAD3A), is a mitochondrial inner membrane protein conserved in metazoans. ATAD3A has been associated with several mitochondrial functions, including nucleoid organization, cholesterol metabolism, and mitochondrial translation. To address its primary role, we generated a neuronal-specific conditional knockout (Atad3 nKO) mouse model, which developed a severe encephalopathy by 5 months of age. Pre-symptomatic mice showed aberrant mitochondrial cristae morphogenesis in the cortex as early as 2 months. Using a multi-omics approach in the CNS of 2-to-3-month-old mice, we found early alterations in the organelle membrane structure. We also show that human ATAD3A associates with different components of the inner membrane, including OXPHOS complex I, Letm1, and prohibitin complexes. Stochastic Optical Reconstruction Microscopy (STORM) shows that ATAD3A is regularly distributed along the inner mitochondrial membrane, suggesting a critical structural role in inner mitochondrial membrane and its organization, most likely in an ATPase-dependent manner.

Structural Evolution of TIR-Domain Signalosomes.

TIR (Toll/interleukin-1 receptor/resistance protein) domains are cytoplasmic domains widely found in animals and plants, where they are essential components of the innate immune system. A key feature of TIR-domain function in signaling is weak and transient self-association and association with other TIR domains. An additional new role of TIR domains as catalytic enzymes has been established with the recent discovery of NAD+-nucleosidase activity by several TIR domains, mostly involved in cell-death pathways. Although self-association of TIR domains is necessary in both cases, the functional specificity of TIR domains is related in part to the nature of the TIR : TIR interactions in the respective signalosomes. Here, we review the well-studied TIR domain-containing proteins involved in eukaryotic immunity, focusing on the structures, interactions and their corresponding functional roles. Structurally, the signalosomes fall into two separate groups, the scaffold and enzyme TIR-domain assemblies, both of which feature open-ended complexes with two strands of TIR domains, but differ in the orientation of the two strands. We compare and contrast how TIR domains assemble and signal through distinct scaffolding and enzymatic roles, ultimately leading to distinct cellular innate-immunity and cell-death outcomes.

Comprehensive in Vitro Characterization of the LSD1 Small Molecule Inhibitor Class in Oncology.

Lysine-specific demethylase 1 (LSD1 or KDM1A) is a chromatin modifying enzyme playing a key role in the cell cycle and cell differentiation and proliferation through the demethylation of histones and nonhistone substrates. In addition to its enzymatic activity, LSD1 plays a fundamental scaffolding role as part of transcription silencing complexes such as rest co-repressor (CoREST) and nucleosome remodeling and deacetylase (NuRD). A host of classical amine oxidase inhibitors such as tranylcypromine, pargyline, and phenelzine together with LSD1 tool compounds such as SP-2509 and GSK-LSD1 have been extensively utilized in LSD1 mechanistic cancer studies. Additionally, several optimized new chemical entities have reached clinical trials in oncology such as ORY-1001 (iadademstat), GSK2879552, SP-2577 (seclidemstat), IMG-7289 (bomedemstat), INCB059872, and CC-90011 (pulrodemstat). Despite this, no single study exists that characterizes them all under the same experimental conditions, preventing a clear interpretation of published results. Herein, we characterize the whole LSD1 small molecule compound class as inhibitors of LSD1 catalytic activity, disruptors of SNAIL/GFI1 (SNAG)-scaffolding protein-protein interactions, inducers of cell differentiation, and potential anticancer treatments for hematological and solid tumors to yield an updated, unified perspective of this field. Our results highlight significant differences in potency and selectivity among the clinical compounds with iadademstat being the most potent and reveal that most of the tool compounds have very low activity and selectivity, suggesting some conclusions derived from their use should be taken with caution.

Genetic and physical interactions between Pol\u03b7 and Rev1 in response to UV-induced DNA damage in mammalian cells

In response to UV irradiation, translesion DNA synthesis (TLS) utilizes specialized DNA polymerases to bypass replication-blocking lesions. In a well-established polymerase switch model, Polη is thought to be a preferred TLS polymerase to insert correct nucleotides across from the thymine dimer, and Rev1 plays a scaffold role through physical interaction with Polη and the Rev7 subunit of Polζ for continual DNA synthesis. Defective Polη causes a variant form of xeroderma pigmentosum (XPV), a disease with predisposition to sunlight-induced skin cancer. Previous studies revealed that expression of Rev1 alone is sufficient to confer enhanced UV damage tolerance in mammalian cells, which depends on its physical interaction with Polζ but is independent of Polη, a conclusion that appears to contradict current literature on the critical roles of Polη in TLS. To test a hypothesis that the Rev1 catalytic activity is required to backup Polη in TLS, we found that the Rev1 polymerase-dead mutation is synergistic with either Polη mutation or the Polη-interaction mutation in response to UV-induced DNA damage. On the other hand, functional complementation of polH cells by Polη relies on its physical interaction with Rev1. Hence, our studies reveal critical interactions between Rev1 and Polη in response to UV damage.

Advances in Skin Wound and Scar Repair by Polymer Scaffolds.

Scars, as the result of abnormal wound-healing response after skin injury, may lead to loss of aesthetics and physical dysfunction. Current clinical strategies, such as surgical excision, laser treatment, and drug application, provide late remedies for scarring, yet it is difficult to eliminate scars. In this review, the functions, roles of multiple polymer scaffolds in wound healing and scar inhibition are explored. Polysaccharide and protein scaffolds, an analog of extracellular matrix, act as templates for cell adhesion and migration, differentiation to facilitate wound reconstruction and limit scarring. Stem cell-seeded scaffolds and growth factors-loaded scaffolds offer significant bioactive substances to improve the wound healing process. Special emphasis is placed on scaffolds that continuously release oxygen, which greatly accelerates the vascularization process and ensures graft survival, providing convincing theoretical support and great promise for scarless healing.

Explaining and drawing activities for learning from multimedia: The role of sequencing and scaffolding

SummaryThis study tested how different implementations of explaining and drawing activities affect learning from a multimedia science lesson. After studying a multimedia slideshow about the human respiratory system, college students (n = 145) were assigned randomly to one of four learning activity conditions: write explanations before drawing pictures (explain‐then‐draw group), draw pictures before writing explanations (draw‐then‐explain group), study provided explanations before drawing pictures (provided explanation‐then‐draw), or study provided pictures before writing explanations (provided drawing‐then‐explain). One week following the learning activity, all students completed post‐tests of their understanding. Results from the learning activity supported the scaffolding hypothesis: students generated better explanations when they used provided (rather than their own) drawings, and they generated better quality drawings when they used provided (rather than their own) explanations. However, this difference in learning activity performance did not correspond to higher performance on the delayed post‐tests. We discuss implications for how to best sequence and scaffold generative activities.

The Expanding Role of Pyridine and Dihydropyridine Scaffolds in Drug Design.

Pyridine-based ring systems are one of the most extensively used heterocycles in the field of drug design, primarily due to their profound effect on pharmacological activity, which has led to the discovery of numerous broad-spectrum therapeutic agents. In the US FDA database, there are 95 approved pharmaceuticals that stem from pyridine or dihydropyridine, including isoniazid and ethionamide (tuberculosis), delavirdine (HIV/AIDS), abiraterone acetate (prostate cancer), tacrine (Alzheimer’s), ciclopirox (ringworm and athlete’s foot), crizotinib (cancer), nifedipine (Raynaud’s syndrome and premature birth), piroxicam (NSAID for arthritis), nilvadipine (hypertension), roflumilast (COPD), pyridostigmine (myasthenia gravis), and many more. Their remarkable therapeutic applications have encouraged researchers to prepare a larger number of biologically active compounds decorated with pyridine or dihydropyridine, expandeing the scope of finding a cure for other ailments. It is thus anticipated that myriad new pharmaceuticals containing the two heterocycles will be available in the forthcoming decade. This review examines the prospects of highly potent bioactive molecules to emphasize the advantages of using pyridine and dihydropyridine in drug design. We cover the most recent developments from 2010 to date, highlighting the ever-expanding role of both scaffolds in the field of medicinal chemistry and drug development.

Writing Play‐Books With Linguistically Diverse Young Learners

AbstractThe article presents a classroom‐based study that engaged linguistically diverse preschool and early school‐age children in illustrating books, jointly composing written narratives to accompany their illustrations, and enacting these child‐authored books through shared sociodramatic play. Findings from story retell tasks show significant improvement in children's narrative language: vocabulary, syntax, accuracy, and text structure. Analysis of collaborative dialogue during book‐making highlights the role of peer and teacher scaffolding in supporting children's literate language and identity development. The article presents an engaging play‐based approach for ECE educators to (1) significantly and equitably increase child‐led literate language interactions; (2) improve early writing instruction, by increasing meaningful composing experience; (3) strengthen culturally sustaining home/community–school partnerships, through authentic dialogue with caregivers about children's writing; and (4) harness the social and multimodal power of play to promote a range of important early learning goals.

Acute myeloid leukemia: Therapy resistance and a potential role for tetraspanin membrane scaffolds.

Acute myeloid leukemia (AML) is characterized by the disruption of myeloid differentiation and accumulation of blast cells in the bone marrow. While AML patients respond favorably to induction chemotherapy, long-term outcomes remain poor due to a high rate of chemoresistance. Advances with targeted therapies, which can be used in combination with conventional chemotherapy, have expanded therapeutic options for patients. However, remission is often short-lived and followed by disease relapse and drug resistance. Therefore, there is a substantial need to improve treatment options by identifying novel molecular and cellular targets that regulate AML chemosensitivity. Membrane scaffolds such as the tetraspanin family of proteins often serve as signaling mediators, translating extracellular signaling cues into intracellular signaling cascades. In this review, we discuss the conventional and targeted treatment strategies for AML and review chemoresistance mechanisms with a focus on the tetraspanin family of membrane scaffold proteins.