Exploring Socially Shared Regulation Processes in Peer Tutoring: Focusing on the Functions of Tutor Utterances

This study quantitatively and qualitatively examined socially shared regulation processes in peer tutoring. Participants were 22 teacher-candidate university students assigned to 11 peer-tutoring pairs. Peer tutoring included two sessions, in which one student was the tutor and another the tutee. Participants completed a socially shared regulation of learning (SSRL) scale before peer tutoring and an academic engagement measurement afterward. Moreover, peer tutoring sessions were videotaped. Students were divided into two groups, based on high and low SSRL scores, and verbal protocols were analyzed. Tutoring utterances were analyzed and categorized by the following social regulation functions, namely “orientation,” “monitoring,” and “evaluation,” while distinguishing between deep- or surface-level. Tutors in high-SSRL groups adopted deep-level orientation more than low-SSRL groups. Qualitative analysis indicated deep-level orientation played a key role in peer tutoring. Additionally, regarding motivational factors, high-SSRL groups showed stronger agentic and cognitive engagement than low-SSRL groups. The implications for teacher-candidate university education are discussed.

Sosialisasi dan Pendampingan Materi Pembelajaran IPA Berbasis Metakognisi pada Mahasiswa Magister Pendidikan IPA Universitas Mataram

Community service activities have been carried out for master students of Science Education at the University of Mataram which aimed to provide understanding to students about the development of science teaching materials that can develop students' metacognition. Teaching materials that are able to develop metacognitive abilities are needed by students in the current era of globalization. With the ability of metacognition, it will raise students' awareness of what they really know and one's cognition-regulation functions to regulate their cognitive activities effectively. Knowledge-cognition contains declarative, procedural, and conditional knowledge, while metacognition skills include four skills, namely problem solving skills, decision-making skills, critical thinking skills, and creative thinking skills. Activity participants can understand the material presented which was shown by the ability to answer questions during the discussion. An understanding of proper metacognition was also measured by its ability to fill out a questionnaire that was distributed after the service was complete. A good understanding of metacognition is expected to be a guide in developing metacognition-based teaching materials so that students can develop metacognition abilities.

Toward a Taxonomy of Virus-ncRNAs Interactions in an RNA World for Disentangling Some Tiny Secrets of Dengue Virus

In recent years, the role of non-coding RNAs (ncRNAs) in regulating cell physiology has begun to be better understood. Recent discoveries in viral molecular biology have revealed that such cellular functions are disturbed during viral infections mainly due to host cell ncRNAs, cellular factors, and virus-derived ncRNAs. Apart from the interplay between those molecules, other interactions derive from the specific folding of RNA virus genomes. These fulfill canonical regulation functions such as replication, translation, and viral packaging. In some cases, folds serve as precursors of small viral RNAs whose biogenesis is not yet clearly understood. Since ncRNAs and RNA viral genomes modulate complex molecular and cellular processes in viral infections, a new taxonomy is being proposed here overarching three main categories, considering the current information about ncRNA interactions in some well-known viral infections. The first category shows examples of host ncRNAs associated with the trigger of the immune response under viral infections. The second category describes interactions between the virus and host ncRNAs. The last category shows how the shape of the RNA viral genome is essential in processing RNAs derived from viruses. Finally, we introduce evidence of how these three categories can also work as a framework in order to organize known interactions of ncRNAs and cellular factors under DENV infection. This new taxonomy of interactions provides a comprehensive framework for organizing the ncRNA regulatory roles in the context of viral interactions and an RNA world.

Expanding the Disorder-Function Paradigm in the C-Terminal Tails of Erbbs

ErbBs are receptor tyrosine kinases involved not only in development, but also in a wide variety of diseases, particularly cancer. Their extracellular, transmembrane, juxtamembrane, and kinase folded domains were described extensively over the past 20 years, structurally and functionally. However, their whole C-terminal tails (CTs) following the kinase domain were only described at atomic resolution in the last 4 years. They were shown to be intrinsically disordered. The CTs are known to be tyrosine-phosphorylated when the activated homo- or hetero-dimers of ErbBs are formed. Their phosphorylation triggers interaction with phosphotyrosine binding (PTB) or Src Homology 2 (SH2) domains and activates several signaling pathways controling cellular motility, proliferation, adhesion, and apoptosis. Beyond this passive role of phosphorylated domain and site display for partners, recent structural and function studies unveiled active roles in regulation of phosphorylation and interaction: the CT regulates activity of the kinase domain; different phosphorylation states have different compaction levels, potentially modulating the succession of phosphorylation events; and prolines have an important role in structure, dynamics, and possibly regulatory interactions. Here, we review both the canonical role of the disordered CT domains of ErbBs as phosphotyrosine display domains and the recent findings that expand the known range of their regulation functions linked to specific structural and dynamic features.

Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy

G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force–spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins.

Assessment of Water Quality Regulation Functions in Southwestern Europe Watersheds

Estimation at large scale of the water quality regulation services is still lacking. It is essential to develop methodological approaches to quantify nutrient-related functions’ distribution. The present study aims to quantify nitrate-related ecological functions through nitrate net balance (NNB), nitrate removal (NR), and nitrate production (NP). This study explores the spatiotemporal dynamics of these indicators in South-Western Europe (SUDOE, 216 subsystems over 81 basins) at a monthly scale from 2000 to 2010. We use the Soil and Water Assessment Tool model to simulate nutrient transfer at the subsystem scale (~3000 km2) and calculate ecological functions. The modeled NNB is validated at the subsystem scale by comparing with NNB predicted at the water body scale (~60 km2) over the Garonne watershed (France). Hot spots of NR are located in the south of SUDOE, characterized by a warmer and dryer climate, whereas NP hot spots are located in the most anthropized streams. The mean NNB (the balance between NP and NR) at the subsystem scale for the SUDOE territory reaches −3.5 and −2.8 gN m−2 day−1 during the most active seasons. The results highlight drivers influencing NR such as streamflow, river slope, and hydrological alteration. Getting an overview of where and when these nitrate regulation functions (NP and NR) occur is essential for socio-ecosystem sustainability and this study highlights its sensitivity to anthropogenic stressors.

When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes

The degree of proteins structural organization ranges from highly structured, compact folding to intrinsic disorder, where each degree of self-organization corresponds to specific functions: well-organized structural motifs in enzymes offer a proper environment for precisely positioned functional groups to participate in catalytic reactions; at the other end of the self-organization spectrum, intrinsically disordered proteins act as binding hubs via the formation of multiple, transient and often non-specific interactions. This review focusses on cases where structurally organized proteins or domains associate with highly disordered protein chains, leading to the formation of interfaces with varying degrees of fuzziness. We present a review of the computational methods developed to provide us with information on such fuzzy interfaces, and how they integrate experimental information. The discussion focusses on two specific cases, microtubules and homologous recombination nucleoprotein filaments, where a network of intrinsically disordered tails exerts regulatory function in recruiting partner macromolecules, proteins or DNA and tuning the atomic level association. Notably, we show how computational approaches such as molecular dynamics simulations can bring new knowledge to help bridging the gap between experimental analysis, that mostly concerns ensemble properties, and the behavior of individual disordered protein chains that contribute to regulation functions.

Conserved Structure and Evolution of DPF Domain of PHF10—The Specific Subunit of PBAF Chromatin Remodeling Complex

Transcription activation factors and multisubunit coactivator complexes get recruited at specific chromatin sites via protein domains that recognize histone modifications. Single PHDs (plant homeodomains) interact with differentially modified H3 histone tails. Double PHD finger (DPF) domains possess a unique structure different from PHD and are found in six proteins: histone acetyltransferases MOZ and MORF; chromatin remodeling complex BAF (DPF1–3); and chromatin remodeling complex PBAF (PHF10). Among them, PHF10 stands out due to the DPF sequence, structure, and functions. PHF10 is ubiquitously expressed in developing and adult organisms as four isoforms differing in structure (the presence or absence of DPF) and transcription regulation functions. Despite the importance of the DPF domain of PHF10 for transcription activation, its structure remains undetermined. We performed homology modeling of the human PHF10 DPF domain and determined common and distinct features in structure and histone modifications recognition capabilities, which can affect PBAF complex chromatin recruitment. We also traced the evolution of DPF1–3 and PHF10 genes from unicellular to vertebrate organisms. The data reviewed suggest that the DPF domain of PHF10 plays an important role in SWI/SNF-dependent chromatin remodeling during transcription activation.

Age and Behavior-Dependent Differential miRNAs Expression in the Hypopharyngeal Glands of Honeybees (Apis mellifera L.)

This study aims to investigate the expression differences of miRNAs in the hypopharyngeal glands (HPGs) of honeybees at three developmental stages and to explore their regulation functions in the HPGs development. Small RNA sequencing was employed to analyze the miRNA profiles of HPGs in newly-emerged bees (NEB), nurse bees (NB), and forager bees (FB). Results showed that a total of 153 known miRNAs were found in the three stages, and ame-miR-276-3p, ame-miR-375-3p, ame-miR-14-3p, ame-miR-275-3p, and ame-miR-3477-5p were the top five most abundant ones. Furthermore, the expression of 11 miRNAs, 17 miRNAs, and 18 miRNAs were significantly different in NB vs. FB comparison, NB vs. NEB comparison, and in FB vs. NEB comparison, respectively, of which ame-miR-184-3p and ame-miR-252a-5p were downregulated in NB compared with that in both the FB and NEB, while ame-miR-11-3p, ame-miR-281-3p, and ame-miR-31a-5p had lower expression levels in FB compared with that in both the NB and NEB. Bioinformatic analysis showed that the potential target genes of the differentially expressed miRNAs (DEMs) were mainly enriched in several key signaling pathways, including mTOR signaling pathway, MAPK signaling pathway-fly, FoxO signaling pathway, Hippo signaling pathway-fly. Overall, our study characterized the miRNA profiles in the HPGs of honeybees at three different developmental stages and provided a basis for further study of the roles of miRNAs in HPGs development.