Quartet Model Research Articles

Genome-wide identification of the MADS-box gene family and SEP1 target genes regulating young embryo development in hazel (Corylus spp.) via ChIP sequencing

Hazel (Corylus spp.) is a nut-producing species with important cultivation value. The purpose of this study was to identify important MADS genes involved in the ovule and embryo development of hazel and explore the possible mechanism of MADS regulation on embryo development. After identifying all MADS-box gene members and differentially expressed genes in the hazel genome, we further verified the expression characteristics of important differentially expressed genes (DEGs) using in situ hybridization, and verified the interaction between important proteins using yeast two-hybrid analyses. Finally, ChIP-Seq analysis of ChSEP1 was conducted to identify its target genes. In total, 59 ChMADSs were identified across all 11 chromosomes, and protein length was predicted to vary between 89 and 524 amino acids. All ChMADSs were divided into Type I and Type II MADS-box genes with 14 subgroups. Most ChMADSs showed low expression, and 11 Type II ChMADSs were highly and differentially expressed in the ovule. Of these, floral quartet model genes, both ChMADS11 (AG-like) and ChMADS37 (SEP1) were highly expressed in young embryos at the rapid ovule growth stage and interacted with each other, indicating that they might coordinate embryo development through protein-protein interactions. In total, 4,143 ChSEP1 differential target genes were identified through ChIP-Seq. Important ChSEP1 target genes included ChSEP1/3, ChAG, ChSHP, and ChSTK as well as ChAGL6, ChAP1, ChFUL1, and ChTT16–2, indicating that ChSEP1 might regulate ovule development by cooperating with and mediating ChMADSs. Overall, our study provides new insights into the molecular mechanisms of hazel ovule development.

The Pedagogical Manifestations: A Driver of Teachers’ Practices in Teaching Algebraic Equations

<p style="text-align: justify;">Mathematics teachers’ instructional strategies lack in-depth knowledge of algebraic systems and hold misconceptions about solving two algebraic equations simultaneously. This study aimed to gain an in-depth analysis of teachers’ knowledge and perceptions about the promotion of conceptual learning and effective teaching of algebraic equations. The main question was, ‘How do junior secondary school mathematics teachers manifest their pedagogical practices when teaching algebraic equations? This article reports on a qualitative, underpinned by the knowledge quartet model study, that sought to explore how junior secondary school teachers’ pedagogical practices manifested in the teaching of algebraic equations. Data were collected from observations, semi-structured interviews, and document analysis of two mathematics teachers purposely selected from two schools. The collected data were analysed using a statistical analysis software called Atlas-ti. (Version 8) and triangulated through thematic analysis. The study revealed that teachers’ choices of representations, examples, and tasks used did not expose learners to hands-on activities that promote understanding and making connections from the underlying algebraic equation concepts. The study proposed Penta-Knowledge Collaborative Planning and Reflective Teaching and Learning Models to enable teachers to collaborate with their peers from the planning stage to lesson delivery reflecting on good practices and strategies for teaching algebraic equations.</p>

The protein–protein interaction landscape of transcription factors during gynoecium development in Arabidopsis

Flowers are composed of organs whose identity is defined by the combinatorial activity of transcription factors (TFs). The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development. The gynoecium is the flower's female reproductive part, crucial for fruit and seed production and, hence, for reproductive success. After the establishment of carpel identity, many tissues arise to form a mature gynoecium. TFs have been described as regulators of gynoecium development, and some interactions and complexes have been identified. However, broad knowledge about the interactions among these TFs and their participation during development remains scarce. In this study, we used a systems biology approach to understand the formation of a complex reproductive unit-as the gynoecium-by mapping binary interactions between well-characterized TFs. We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions (PPIs), resulting in a process-specific interaction map. Topological analyses suggest hidden functions and novel roles for many TFs. In addition, we observed a close relationship between TFs involved in auxin and cytokinin-signaling pathways and other TFs. Furthermore, we analyzed the network by combining PPI data, expression, and genetic data, which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes. Finally, we generated an extended PPI network that predicts new players in gynoecium development. Taken together, all these results serve as a valuable resource for the plant community.

Comparison of Pre-service Elementary Teachers’ Mathematical Knowledge in Teaching for Length Measurement: Turkey and the United States

This study investigates pre-service elementary teachers’ mathematical knowledge in teaching for length measurement. More specifically, this study compares the foundation and transformation knowledge of pre-service elementary teachers from Turkey and the United States. The current study examines similarities and differences between them by applying the codes of the Knowledge Quartet model with 40 pre-service teachers selected from Turkey and the United States. This study used a test assessing pre-service teachers’ mathematical knowledge in teaching about the students’ mistakes, difficulties, misconceptions, the reasons for them, and their strategies to overcome them related to the topic of length measurement. The findings indicated that while US pre-service teachers had more secure foundation knowledge in identifying the possible errors, Turkish pre-service teachers showed greater foundation knowledge in identifying the possible reasons for these errors. On the other hand, the pre-service teachers in both countries have similar transformation knowledge to suggest strategies to correct students’ errors. These findings might provide some insights about how pre-service teachers’ mathematical knowledge may be similar or different in different countries. Furthermore, these similarities and differences might help researchers and teacher educators emphasize the importance of the quality of teacher education programs.

KRIFS Quartet Model Improving Livelihoods and Fueling Tourism in Kitagwenda District,Western Uganda

Kyabwanswa Rural Integrated Farming Systems (KRIFS) is a Community Based Organization (CBO) with its Head Office in Kitagwenda Town Council. KRIFS quartet model involves emphasis of integrating four agricultural activities namely: Apiculture, agro-forestry, coffee and at least one type of livestock. The paper utilizes data obtained from January 2017 surveys, interviews, focus group discussions and observations by the authors. The authors observe that the four activities are symbiotic income generating enterprises. The quartet model has greatly contributed in reducing poverty, increasing agricultural productivity, facilitating value addition, conserving the environment, halting biodiversity loss and mitigating climate change. The model is strongly hinged on training of farmers in organized groups more especially the youth and the women.The involvement of KRIFS in integrated farming that involves introducing new innovations to improve production and productivity in agriculture through improved breeds of livestock and crops as well as environmental conservation being pivotal in its operations, has culminated to agro-tourism in the district. The authors recommend that the model be implemented in the whole of Uganda. Apiculture should be included in the priority commodity list for the parish model. Agro-tourism is yet another economi cactivity that should be exploited to reduce unemployment, conserve the environment and reduce effects of climate change.

Distance-based measurement determines the coexistence of B protein hetero- and homodimers in lily tepal and stamen tetrameric complexes.

The floral quartet model proposes that plant MADS box proteins function as higher order tetrameric complexes. However, in planta evidence for MADS box tetramers remains scarce. Here, we applied a strategy using in vivo fluorescence resonance energy transfer (FRET) based on thedistance change and distance symmetry of stable tetrameric complexes in tobacco (Nicotiana benthamiana) leaf cells to improve the accuracy of the estimation of heterotetrameric complex formation. This measuring system precisely verified the stable state of Arabidopsis petal (AP3/PI/SEP3/AP1) and stamen (AP3/PI/SEP3/AG) complexes and showed that the lily (Lilium longiflorum) PI co-orthologs LMADS8 and LMADS9 likely formed heterotetrameric petal complexes with Arabidopsis AP3/SEP3/AP1, which rescued petal defects of pi mutants. However, L8/L9 did not form heterotetrameric stamen complexes with Arabidopsis AP3/SEP3/AG to rescue the stamen defects of the pi mutants. Importantly, this system was applied successfully to find complicated tepal and stamen heterotetrameric complexes in lily. We found that heterodimers of B function AP3/PI orthologs (L1/L8) likely coexist with the homodimers of PI orthologs (L8/L8, L9/L9) to form five (two most stable and three stable) tepal- and four (one most stable and three stable) stamen-related heterotetrameric complexes with A/E and C/E function proteins in lily. Among these combinations, L1 preferentially interacted with L8 to form the most stable heterotetrameric complexes, and the importance of the L8/L8 and L9/L9 homodimers in tepal/stamen formation in lily likely decreased to a minor part during evolution. The system provides substantial improvements for successfully estimating the existence of unknown tetrameric complexes in plants.

Shell-like quarteting in heavy nuclei: Algebraic approaches based on the pseudo- and proxy-SU(3) schemes

Background: The semimicroscopic algebraic quartet model (SAQM) generates the excitation spectra of shell-like quartets, formed by two protons and two neutrons in a well-defined shell configuration. It is based on the SU(3) symmetry, which is valid only in light nuclei. Algebraic quartet models have been proposed for heavy nuclei, too, but their shell model background is not known.

Exploring the methylation status of selected flowering genes in healthy and phyllody infected sesame plants

Phytoplasmas, plant pathogenic Mollicutes are associated with retrograde metamorphosis in phyllody affected sesame plants showing reversion of flowering shoots to leaf-like structures. The molecular mechanism responsible for these dramatic alterations has become an active research area. Recently, the role of phytoplasma secreted effector molecules in the disruption of normal activities of genes comprising floral quartet model has been suggested. However, the mechanism delineating the precise level at which interference of the normal gene expression is caused is far from being understood. DNA methylation is an epigenetic phenomenon that plays a significant role in altering the plant genome machinery in the presence of abiotic and biotic stresses including bacterial infections. The cytosine methylation status of selected key regulatory genes namely UNUSUAL FLORAL ORGANS (UFO), FLORICAULA/LFY (FLO), FLOWERING LOCUS T- like (FLT) and SUPERMAN (SUP), involved in flower development, were chosen for investigating their cytosine methylation status using the McrBC assay. Genic regions located in the sesame orthologs of the selected genes were identified for the primer design. Expected amplicons were obtained in healthy and phyllody infected sesame plants that did not reveal differential methylation. Nevertheless, considering the constraints of the McrBC assay in detecting the methylation, the need for comprehensive studies targeting more genes and higher coverage of the putative methylated regions is suggested before ruling out the involvement of epigenetic manipulation by phytoplasmas.

α clustering from the quartet model

$\ensuremath{\alpha}$ clustering in nuclei is considered with the quartet model (QM) where four valence nucleons (the quartet) move on the top of the core (daughter) nucleus. In the QM approach, it is assumed that the intrinsic wave function of the quartet is changed from the pure cluster configuration to the shell-model configuration when it crosses some critical radius and enters into the core nucleus. The QM approach could give not only the level scheme, the electromagnetic transition, and the nuclear radius but also the $\ensuremath{\alpha}$-cluster formation probability. Numerical results are calculated for $^{20}\mathrm{Ne}$, $^{44}\mathrm{Ti}$, and $^{212}\mathrm{Po}$, where a quartet moves on top of a double magic nucleus. Good agreement with experimental data and previous theoretical studies is obtained. The QM approach is a useful complement to the present phenomenological and microscopic models and could help deepen our understanding of $\ensuremath{\alpha}$ clustering across the nuclide chart.

An in-service primary teacher’s implementation of mathematical tasks: the case of length measurement and perimeter instruction

ABSTRACTThe purpose of this paper is to examine the cognitive demand levels of tasks used by an in-service primary teacher during length measurement and perimeter instruction and to examine a possible link between these tasks and the teacher’s mathematical knowledge in teaching. For this purpose, a case study approach was used and the data was drawn from classroom observations, semi-structured interviews, and field notes. Specific tasks from length measurement and perimeter instruction were presented and analyzed according to the Mathematical Tasks Framework. Then, how these tasks gave information about the teacher’s mathematical knowledge in teaching in the length measurement and perimeter topics was examined according to the Knowledge Quartet model. According to the findings of the study, the tasks used during length measurement and perimeter instruction were mostly categorized as low-level tasks. In addition, teacher’s mathematical knowledge in teaching affected the implementation of the tasks.

The Analysis of a Novice Primary Teacher's Mathematical Knowledge in Teaching: Area Measurement

The purpose of this paper is to investigate a novice primary teacher's mathematical knowledge in teaching on area measurement. Data was collected from a novice primary teacher of fourteen students in a primary school located in Ankara, Turkey using field notes, video recordings of lessons, and audio recordings of interviews before and after her teaching. Her teaching were analyzed according to dimensions of Knowledge Quartet (KQ) model which included Foundation, Transformation, Connection, and Contingency. Results revealed that the KQ model is an alternative and effective tool for the primary mathematics teaching. Specifically, the novice primary teacher's mathematical knowledge in teaching for area measurement was found to be effective regarding the Foundation and Contingency dimensions. However, she lacked the ability to make connections and use appropriate representations and examples regarding the Connection and Transformation dimensions respectively. Implications and suggestions for the improvement of teachers' mathematical knowledge in teaching are presented.

Identification of genes regulating ovary differentiation after pollination in hazel by comparative transcriptome analysis

BackgroundHazel (Corylus spp.) exhibits ovary differentiation and development that is initiated from the ovary primordium after pollination, conferring the plant with a unique delayed fertilization. Failure of development of the ovary and ovule after pollination can lead to ovary abortion and blank fruit formation, respectively, with consequent yield loss. However, the genes involved in ovary and ovule differentiation and development are largely unknown.ResultsIn unpollinated pistillate inflorescences (stage F), the stigma shows an extension growth pattern. After pollination, a rudimentary ovary begins to form (stage S), followed by ovule differentiation (stage T) and growth (stage FO). Total RNA was obtained from pistillate inflorescences or young ovaries at stage F, S, T and FO, and sequencing was carried out on a HiSeq 4000 system. De novo assembly of sequencing data yielded 62.58 Gb of nucleotides and 90,726 unigenes; 5524, 3468, and 8714 differentially expressed transcripts were identified in F-vs-S, S-vs-T, and T-vs-FO paired comparisons, respectively. An analysis of F-vs-S, S-vs-T, and T-vs-FO paired comparisons based on annotations in the Kyoto Encyclopedia of Genes and Genomes revealed six pathways that were significantly enriched during ovary differentiation, including ko04075 (Plant hormone signal transduction). Auxin level increased after pollination, and an immunohistochemical analysis indicated that auxin was enriched at the growth center of pistillate inflorescences and young ovaries. These results indicate that genes related to auxin biosynthesis, transport, signaling, the floral quartet model, and flower development may regulate ovary and ovule differentiation and development in hazel.ConclusionsOur findings provide insight into the molecular mechanisms of ovary differentiation and development after pollination in this economically valuable plant.

Isovector and isoscalar pairing in odd–odd N = Z nuclei within a quartet approach

The quartet condensation model (QCM) is extended for the treatment of isovector and isoscalar pairing in odd-odd N=Z nuclei. In the extended QCM approach the lowest states of isospin T=1 and T=0 in odd-odd nuclei are described variationally by trial functions composed by a proton-neutron pair appended to a condensate of 4-body operators. The latter are taken as a linear superposition of an isovector quartet, built by two isovector pairs coupled to the total isospin T=0, and two collective isoscalar pairs. In all pairs the nucleons are distributed in time-reversed single-particle states of axial symmetry. The accuracy of the trial functions is tested for realistic pairing Hamiltonians and odd-odd N=Z nuclei with the valence nucleons moving above the cores $^{16}$O, $^{40}$Ca and $^{100}$Sn. It is shown that the extended QCM approach is able to predict with high accuracy the energies of the lowest T=0 and T=1 states. The present calculations indicate that in these states the isovector and the isoscalar pairing correlations coexist together, with the former playing a dominant role.

MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution.

The floral quartet model of floral organ specification poses that different tetramers of MIKC-type MADS-domain transcription factors control gene expression and hence the identity of floral organs during development. Here, we provide a brief history of the floral quartet model and review several lines of recent evidence that support the model. We also describe how the model has been used in contemporary developmental and evolutionary biology to shed light on enigmatic topics such as the origin of land and flowering plants. Finally, we suggest a novel hypothesis describing how floral quartet-like complexes may interact with chromatin during target gene activation and repression.

IgG subclass co-expression brings harmony to the quartet model of murine IgG function.

A model of murine IgG function is presented in which the co-expression of the IgG subclasses is a central feature, class switching occurs before the commencement of somatic hypermutation, and there is little switching between subclasses. It is named the quartet model to emphasize the harmony that comes from the simultaneous presence of the four subclasses. In this model, IgG3 and IgG2b antibodies are particularly important early in the response, when T-cell help may be limiting. IgG3 initiates inflammation through complement fixation, whereas IgG2b provides early FcγR-mediated effector functions. As T-cell help strengthens, IgG2a antibodies increase the power of the response, whereas IgG1 production helps limit the inflammatory drive and limits immunopathology. The model highlights the fact that murine IgG subclasses function quite differently to human IgG subclasses. This allows them to serve the special immunological needs of a species that is vulnerable because of its small size.

Optimizing the cut off grade in Sarcheshmeh copper mine using Lane Quartet Model

Lane Algorithm is used to determine optimum cut off grade for a mining operation. There may be three parts in each operation: mining, concentration and refining. In Sarcheshmeh Copper Mine the concentrate coming from the stock has the average grade in addition to the production rate and cost. Therefore, the grade distribution is affected by production rate and cost parameters. The calculation of the cut off grade is done using a modified Lane Algorithm. Therefore, a mix of blending stock received from outside and the concentrate from the mine was considered in the Lane Algorithm. Initially, the profit objective function was taken into account with the addition of the stock limitations; then, the Lane Quartet Model was used and the cut off grade determined. The model uses the technical and economical data of different parts to determine the cut off grade. The result of the model was a cut off grade of (0.1408%), which brings about an increase of848051645 US dollars as profit, in comparison to the cut off grade (0.1617%) that was obtained by the Lane tripartite model.

Lepton flavor violation in the inert scalar model with higher representations

We investigate the lepton flavor violation (LFV) in the inert scalar model with higher representations. We generalize the inert doublet model with right handed neutrino by using higher scalar and fermion representation of $SU(2)_{L}$. As the generalized model and the inert doublet model have the same parameter space, we compare the rates of $\mu\rightarrow e\gamma$, $\mu\rightarrow ee\overline{e}$ and $\mu-e$ conversion in nuclei in the doublet and its immediate extension, the quartet model. We show that the corresponding rates are larger in the case of higher representation compared to the Inert doublet for the same region of parameter space. This implies that such extended models are more constrained by current LFV bounds and will have better prospects in future experiments.

Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach.

Flowering is one of the important defining features of angiosperms. The initiation of flower development and the formation of different floral organs are the results of the interplays among numerous genes. But until now, just fewer genes have been found linked with flower development. And the functions of lots of genes of Arabidopsis thaliana are still unknown. Although, the quartet model successfully simplified the ABCDE model to elaborate the molecular mechanism by introducing protein-protein interactions (PPIs). We still don't know much about several important aspects of flower development. So we need to discriminate even more genes involving in the flower development. In this study, we identified seven differentially modules through integrating the weighted gene co-expression network analysis (WGCNA) and Support Vector Machine (SVM) method to analyze co-expression network and PPIs using the public floral and non-floral expression profiles data of Arabidopsis thaliana. Gene set enrichment analysis was used for the functional annotation of the related genes, and some of the hub genes were identified in each module. The potential floral organ morphogenesis genes of two significant modules were integrated with PPI information in order to detail the inherent regulation mechanisms. Finally, the functions of the floral patterning genes were elucidated by combining the PPI and evolutionary information. It was indicated that the sub-networks or complexes, rather than the genes, were the regulation unit of flower development. We found that the most possible potential new genes underlining the floral pattern formation in A. thaliana were FY, CBL2, ZFN3, and AT1G77370; among them, FY, CBL2 acted as an upstream regulator of AP2; ZFN3 activated the flower primordial determining gene AP1 and AP2 by HY5/HYH gene via photo induction possibly. And AT1G77370 exhibited similar function in floral morphogenesis, same as ELF3. It possibly formed a complex between RFC3 and RPS15 in cytoplasm, which regulated TSO1 and CPSF160 in the nucleus, to control the floral organ morphogenesis. This process might also be fine tuning by AT5G53360 in the nucleus.

Evolutionary perspectives on emotions and their link to intentions, dispositions and behavior: Comment on “The quartet theory of human emotions: An integrative and neurofunctional model” by S. Koelsch et al.

Koelsch and coworkers present a sophisticated neuroanatomical model of emotions comprising four affect-systems and four output-systems, each bound to a specific brain area [1]. Moreover, they suggest the emergence of distinct components of subjective feelings or “emotion percepts” due to integration of the activation across these subsystems. Incorporating numerous neurobiological, psychological and philosophical findings on human emotions, the model reflects an extensive interdisciplinary approach. Considering an evolutionary perspective, however, we would like to address some issues concerning emotions and their link to intentions, dispositions and behavior that are not fully covered by the Quartet Model. Charles Darwin pointed out that individuals that are better adapted to their environment have increased chances of survival and reproduction. Therefore, natural selection leads to a rising prevalence of properties offering a survival benefit across generations [2]. To better understand the biological functions of emotions we propose to ask the question: How do emotions provide a benefit for survival and reproduction? Considering the characterized four affect systems the following benefits can be identified: The brainstem (WAKEsystem) improves survival by matching the arousal level to environmental demands. The diencephalon (SEEK-system) does so by reinforcement of the regulation of homeostatic needs. The hippocampus (CARE-system) offers a survival benefit by strengthening the relations to close relatives, especially cohabitants and offspring. The orbitofrontal cortex (NORM-system) does this by reinforcing adherence to social rules. However, there seem to be many more ways in which emotions contribute to survival:

Isovector pairing in a formalism of quartets forN=Znuclei

We describe the ground state of the isovector pairing Hamiltonian in self-conjugate nuclei by a product of collective quartets of different structures built from two neutrons and two protons coupled to total isospin $T=0$. The structure of the collective quartets is determined by an iterative variational procedure based on a sequence of diagonalizations of the pairing Hamiltonian in spaces of reduced size. The accuracy of the quartet model is tested for $N=Z$ nuclei carrying valence nucleons outside the $^{16}O$, $^{40}\mathrm{Ca}$, and $^{100}\mathrm{Sn}$ cores. The comparison with the exact solutions of the pairing Hamiltonian, obtained by shell model diagonalization, shows that the quartet model is able to describe the isovector pairing energy with very high precision. The predictions of the quartet model are also compared to those of the simpler quartet condensation model in which all the collective quartets are assumed to be identical.