To see the other types of publications on this topic, follow the link: Developmental sequence model.
Journal articles on the topic 'Developmental sequence model'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 journal articles for your research on the topic 'Developmental sequence model.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.
1
Schnell, Jim. "The Developmental Speech Sequence Model (DSSM)." Speech Communication Teacher 1, no. 2 (1987): 15–16. http://dx.doi.org/10.1080/29945054.1987.12289045.
Full text
2
Yu, Byong-Kyu, and Kyong-Mi Kim. "A Literature Review of Motor DevelopmentalTheory and Dynamical Systems Model." Journal of Clinical Movement Science in Human 4, no. 1 (1999): 121–41. https://doi.org/10.17817/1999.4.1.10.
Full textAbstract:
This paper reviews some of the literature relating to traditional and contemporary motor developmental theories. In particular, focused on reference to dynamical systems model. Current researchhas shown that some of our ideas regarding a normal motor development sequence have been incomplete. A normal motor developmental progression seems not only to move in overlapping sequences but also to demonstrate great variability in the age that a motor milestone emerges. All of the previous research ideas regarding development blend very well with the new dynamic systems theory of motor control. With the dynamic systems theory, there are many circular loops and levels of control that cannot only work independently. But they can also work interactively with each other. This theory suggests an interaction in the progression of all systems and subsystems that determines when a motor skill appears and what the quality from that a motor skill. The theories presented in the original writings regarding these neurophysiological treatment approaches need to be reviewed and updated to foster improvement of our treatment techniques and to better analyser treatment efficacy. And many issues must be considered when determining whether to follow a normal motor developmental sequence for treatment planning and implementation.
3
Chavoshi, Saeid, Maxine Gallander Wintre, Stella Dentakos, and Lorna Wright. "A Developmental Sequence Model to University Adjustment of International Undergraduate Students." Journal of International Students 7, no. 3 (2017): 703–27. https://doi.org/10.5281/zenodo.570029.
Full textAbstract:
The current study proposes a Developmental Sequence Model to University Adjustment and uses a multifaceted measure, including academic, social and psychological adjustment, to examine factors predictive of undergraduate international student adjustment. A hierarchic regression model is carried out on the Student Adaptation to College Questionnaire to examine theoretically pertinent predictors arranged in a developmental sequence in determining adjustment outcomes. This model accounted for over 60% of the variance in adjustment scores, and highlighted the importance of ecological factors in relation to student adjustment, such as social support, relationship with parents, and perceived institutional support as more useful than static measures of achievement such as high school GPA. Implications of these findings, including the important role of campus services, are discussed.
4
Chavoshi, Saeid, Maxine Gallander Wintre, Stella Dentakos, and Lorna Wright. "A Developmental Sequence Model to University Adjustment of International Undergraduate Students." Journal of International Students 7, no. 3 (2018): 703–27. http://dx.doi.org/10.32674/jis.v7i3.295.
Full textAbstract:
The current study proposes a Developmental Sequence Model to University Adjustment and uses a multifaceted measure, including academic, social and psychological adjustment, to examine factors predictive of undergraduate international student adjustment. A hierarchic regression model is carried out on the Student Adaptation to College Questionnaire to examine theoretically pertinent predictors arranged in a developmental sequence in determining adjustment outcomes. This model accounted for over 60% of the variance in adjustment scores, and highlighted the importance of ecological factors in relation to student adjustment, such as social support, relationship with parents, and perceived institutional support as more useful than static measures of achievement such as high school GPA. Implications of these findings, including the important role of campus services, are discussed.
5
Thomas, Kathleen M., Ruskin H. Hunt, Nathalie Vizueta, et al. "Evidence of Developmental Differences in Implicit Sequence Learning: An fMRI Study of Children and Adults." Journal of Cognitive Neuroscience 16, no. 8 (2004): 1339–51. http://dx.doi.org/10.1162/0898929042304688.
Full textAbstract:
Prevailing theories of implicit or unaware learning propose a developmental invariance model, with implicit function maturing early in infancy or childhood despite prolonged improvements in explicit or intentional learning and memory systems across childhood. Neuroimaging studies of adult visuomotor sequence learning have associated fronto-striatal brain regions with implicit learning of spatial sequences. Given evidence of continued development in these brain regions during childhood, we compare implicit sequence learning in adults and 7- to 11-year-old children to examine potential developmental differences in the recruitment of fronto-striatal circuitry during implicit learning. Participants performed a standard serial reaction time task. Stimuli alternately followed a fixed 10-step sequence of locations or were presented in a pseudorandom order of locations. Adults outperformed children, achieving a significantly larger sequence learning effect and showing learning more quickly than children. Age-related differences in activity were observed in the premotor cortex, putamen, hippocampus, inferotemporal cortex, and parietal cortex. We observed differential recruitment of cortical and subcortical motor systems between groups, presumably reflecting age differences in motor response execution. Adults showed greater hippocampal activity for sequence trials, whereas children demonstrated greater signal during random trials. Activity in the right caudate correlated significantly with behavioral measures of implicit learning for both age groups, although adults showed greater signal change than children overall, as would be expected given developmental differences in sequence learning magnitude. These results challenge the idea of developmental invariance in implicit learning and instead support a view of parallel developments in implicit and explicit learning systems.
6
Opitz, Bertram, Daniel Brady, and Hayley C. Leonard. "Motor and non-motor sequence prediction is equally affected in children with developmental coordination disorder." PLOS ONE 15, no. 11 (2020): e0232562. http://dx.doi.org/10.1371/journal.pone.0232562.
Full textAbstract:
Children with Developmental Coordination Disorder (DCD) are diagnosed based on motor difficulties. However, they also exhibit difficulties in several other cognitive domains, including visuospatial processing, executive functioning and attention. One account of the difficulties seen in DCD proposes an impairment in internal forward modelling, i.e., the ability to (i) detect regularities of a repetitive perceptual or motor pattern, (ii) predict future outcomes of motor actions, and (iii) adapt behaviour accordingly. Using electroencephalographic recordings, the present study aimed to delineate these different aspects of internal forward modelling across several domains. To this end, 24 children with DCD and 23 typically-developing children (aged 7–10 years) completed a serial prediction task in the visual, temporal, spatial and motor domains. This task required them to learn short sequences and to indicate whether a sequence was disrupted towards its end. Analyses revealed that, across all domains, children with DCD showed poorer discrimination between intact and disrupted sequences, accompanied by a delayed late parietal positivity elicited by disrupted sequences. These results indicate an impairment in explicit sequence discrimination in DCD across motor and cognitive domains. However, there is no evidence for an impairment in implicit performance on the visuomotor task in DCD. These results suggest an impairment of the updating of an internal forward model in DCD resulting in a blurred representation of that model and, consequently, in a reduced ability to detect regularities in the environment (e.g., sequences). Such a detailed understanding of internal forward modelling in DCD could help to explain the wide range of co-occurring difficulties experienced by those with a diagnosis of DCD.
7
Pimus, Inna, Mitchell Schertz, and Mor Peleg. "Sequence Mining of Comorbid Neurodevelopmental Disorders Using the SPADE Algorithm." Methods of Information in Medicine 55, no. 03 (2016): 223–33. http://dx.doi.org/10.3414/me15-01-0142.
Full textAbstract:
SummaryObjectives: Understanding the progression of comorbid neurodevelopmental disorders (NDD) during different critical time periods may contribute to our comprehension of the underlying pathophysiology of NDDs. The objective of our study was to identify frequent temporal sequences of developmental diagnoses in noisy patient data.Methods: We used a data set of 2810 patients, documenting NDD diagnoses given to them by an NDD expert at a child developmental center during multiple visits at different ages. Extensive preprocessing steps were developed in order to allow the data set to be processed by an efficient sequence mining algorithm (SPADE).Results: The discovered sequences were validated by cross validation for 10 iterations; all correlation coefficients for support, con -fidence and lift measures were above 0.75 and their proportions were similar. No significant differences between the distributions of sequences were found using KolmogorovSmirnov test.Conclusions: We have demonstrated the feasibility of using the SPADE algorithm for discovery of valid temporal sequences of co-morbid disorders in children with NDDs. The identification of such sequences would be beneficial from clinical and research perspectives. Moreover, these sequences could serve as features for developing a full-fledged temporal predictive model.
8
Almeida, Renata, Alan Norrish, Mark Levick, et al. "From genomes to vaccines: Leishmania as a model." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 357, no. 1417 (2002): 5–11. http://dx.doi.org/10.1098/rstb.2001.0985.
Full textAbstract:
The 35 Mb genome of Leishmania should be sequenced by late 2002. It contains approximately 8500 genes that will probably translate into more than 10 000 proteins. In the laboratory we have been piloting strategies to try to harness the power of the genome–proteome for rapid screening of new vaccine candidate. To this end, microarray analysis of 1094 unique genes identified using an EST analysis of 2091 cDNA clones from spliced leader libraries prepared from different developmental stages of Leishmania has been employed. The plan was to identify amastigote–expressed genes that could be used in high–throughput DNA–vaccine screens to identify potential new vaccine candidates. Despite the lack of transcriptional regulation that polycistronic transcription in Leishmania dictates, the data provide evidence for a high level of post–transcriptional regulation of RNA abundance during the developmental cycle of promastigotes in culture and in lesion–derived amastigotes of Leishmania major . This has provided 147 candidates from the 1094 unique genes that are specifically upregulated in amastigotes and are being used in vaccine studies. Using DNA vaccination, it was demonstrated that pooling strategies can work to identify protective vaccines, but it was found that some potentially protective antigens are masked by other disease–exacerbatory antigens in the pool. A total of 100 new vaccine candidates are currently being tested separately and in pools to extend this analysis, and to facilitate retrospective bioinformatic analysis to develop predictive algorithms for sequences that constitute potentially protective antigens. We are also working with other members of the Leishmania Genome Network to determine whether RNA expression determined by microarray analyses parallels expression at the protein level. We believe we are making good progress in developing strategies that will allow rapid translation of the sequence of Leishmania into potential interventions for disease control in humans.
9
Cathleen Revlock, Therese, Kathleen Wiles, Eileen Kolich, et al. "ADVANCING THE COMPLETION AGENDA IN ADULT DEVELOPMENTAL READING AT THE COMMUNITY COLLEGE LEVEL: A QUANTITATIVE RESEARCH STUDY." International Journal of Advanced Research 10, no. 04 (2022): 881–916. http://dx.doi.org/10.21474/ijar01/14625.
Full textAbstract:
In order to assist community college students in completing their program of study at a more rapid pace, this quantitative, correlational study examined the effectiveness of acceleration as a method to help community college students complete the developmental reading sequence quickly and more successfully. Acceleration is a curricular redesign that includes challenging readings and assignments and reduces the number of required classes in the developmental sequence. Past research does not adequately measure student success in the current community college trend of securing the most efficient pathway possible for attaining an associates degree or career certificate. Students who scored 80 or higher on the post-course, COMPASS reading placement test skipped a developmental class and were eligible to take college-level gateway courses sooner, for the purpose of saving them time and money. Retention and grade-point-average of developmental reading students who pursued an accelerated path was compared to developmental reading students who followed the traditional, two-tiered course sequence to determine first year success. In the college of the study, findings indicated developmental reading intervention, regardless of model, was effective for the students who persisted, as measured by their literacy skill gains.
10
Rakhimov, Oktyabr, Dilrabo Rakhimova, Otabek Mirzaev, and Shavkat Azizov. "Analysis of developmental education models in the ecological education system in Uzbekistan." E3S Web of Conferences 458 (2023): 06020. http://dx.doi.org/10.1051/e3sconf/202345806020.
Full textAbstract:
The article points out the analysis of goals and tasks, models and methods of organization of traditional and developmental education, as well as the cyclic sequence of learning in ecological education. The cyclical model of ecological education, the main stages of the cyclical process of teaching and educational development, the main problems of the reflexive state of the student, the characteristics of educational models, the cyclical sequence of mastering in developmental education have been developed, the form of organizing teaching according to this cycle is considered as a universal mechanism of personal experience and ability development, and the essence of developmental education is revealed. In the higher education system of Uzbekistan, the need for a gradual transition to developmental education based on digital technologies in ecological education is based on the need for independent educational activities in the field of ecology of students to occupy an important place and the necessity of its proper organization.
11
Dragićević, Milan, and Ana Simonović. "Arabinogalactan protein mining and diversity - the case of Centaurium erythraea." Biologia Serbica 43, no. 1 (2021): 4–11. https://doi.org/10.5281/zenodo.5512429.
Full textAbstract:
<strong>Summary. </strong><em>Centaurium erythraea </em>(common centaury) is a medicinal plant with extraordinary developmental plasticity <em>in vitro </em>that is used as a model organism for studying <em>in vitro </em>morphogenesis in our lab. Several experimental lines of evidence have identified arabinogalactan proteins (AGPs) as one of the key players involved in centaury morphogenesis; however, the role of specific genes has yet to be determined. AGPs are ubiquitous plant cell surface glycoproteins associated with various physiological functions. AGP sequences are characterized by the presence of non-continuous hydroxyproline residues, which serve as O-glycosylation anchor sites for branched arabinogalactans. Due to a biased amino acid composition rich in disorder-promoting amino acids, AGP sequences lack a stable structure and consequently have lessened evolutionary constraints. Therefore, homology-based approaches to AGP sequence mining have limited success. We have recently developed a bioinformatics pipeline for AGP sequence mining, ragp, which exploits their key feature – the presence of hydroxyprolines. This pipeline combines estimation of proline hydroxylation based on local sequence context by a machine learning model with a flexible motif search. After applying this pipeline to the centaury transcriptome, AGP regions were found to associate with a variety of conserved domains. Here we introduce a streamlined way to train models for prediction of Pro hydroxylation, analyze important protein sequence features determining Pro hydroxylation status, present some of the AGP types found in centaury and discuss model limitations and future prospects.
12
Yamada, Hiroyuki, Angel X. Bohannon, Alicia Grunow, and Christopher A. Thorn. "Assessing the Effectiveness of Quantway®: A Multilevel Model With Propensity Score Matching." Community College Review 46, no. 3 (2018): 257–87. http://dx.doi.org/10.1177/0091552118771754.
Full textAbstract:
Objective: Quantway is a Carnegie Math Pathways initiative, which redesigns the content, pedagogy, and structure of traditional developmental mathematics courses to simultaneously tackle traditional barriers to student success and support a broad range of developmental students in achieving their mathematics potential. Specifically, Quantway is a quantitative reasoning sequence that is comprised of a single term accelerated developmental mathematics course called Quantway 1 and a college-level mathematics course called Quantway 2. This study assesses the effectiveness of the developmental mathematics course, Quantway 1, during its first six semesters of implementation. Method: We used a hierarchical linear modeling technique to conduct propensity score matching across 37 student characteristics to compare the course performance of Quantway 1 students with matched comparison students from traditional developmental mathematics courses. Results: Quantway 1 students demonstrated significantly higher odds of success in fulfilling developmental mathematics course requirements and enrolling in college mathematics courses in the following year than matched comparison students. In addition, Quantway 1 effects were positive across all sex and race/ethnicity subgroups as well as in nearly all classrooms and colleges. Contributions: This study provides robust evidence that Quantway 1 increases student success in fulfilling developmental mathematics requirements and advances equity in student outcomes. Implications of and future directions for the Pathways are discussed.
13
Hirnyak, Andriy, and Halyna Hirnyak. "METHODOLOGICAL MODEL OF PSYCHOLOGICAL COGNITION IN MODULAR-DEVELOPMENTAL EDUCATIONAL INTERACTION." PSYCHOLOGICAL JOURNAL 8, no. 1 (57) (2022): 49–60. http://dx.doi.org/10.31108/1.2022.8.1.4.
Full textAbstract:
The study concerns a systematic methodological substantiation of a fundamentally new psychological solution to the scientific problem of the step-by-step deployment of modular-developmental educational interaction in the space of modern higher education institutions. It was stated that a higher school has a multi-parameter structure, multi-level organization and functionally optimizes personal growth and professional development of participants in the educational process. The strategic direction of a successful solution to this problem was the expansion of the object-subject format of scientific research. On the one hand, the understanding of the educational process is a psychologically based system of goals, tasks, forms, content, technologies, methods and tools of professionally organized education, on the other hand, the determination of psychological characteristics in a modular manner means a developmental interaction of participants in the educational process of higher education as a sequence of four periods of its innovative psycho-content support. Methodologically, it is argued that modular-developmental interaction in the conditions of higher education activates the sequence of four types of exchange (informational-knowledge, normative-volitional, cyclical-meaningful, spiritual-meaningful) and their corresponding styles of developmental interaction (inhibitory, facilitative, moderating, spontaneous) of training participants as carriers of subjective reality in the ontological hypostases of the subject, personality, individuality, universe, forms of their mental activity (behavior, activity, learning, self-creation), psychological mechanisms of deployment of polydialogic interaction (activation, intensification, actualization, self-actualization), which are grounded in the epistemic framework of principles modular-developmental interaction (mentality, modularity, development, spirituality) and the psychological content of periods of a complete educational cycle and stages of the act of psychological cognition (informational-cognitive – situation, normative-regulatory – motivation, value-reflective – action, spiritual-creative – after-action). Thus, the modular development system is based on an innovative scientific paradigm, which comes from a deep (purely psychological) and most progressive awareness of the process of socialization as a vita-cultural phenomenon. The subject of scientific knowledge here is the whole world of the psychocultural experience of mankind, in which numerous national traditions are related to the universal stereotypes, the essential characteristics of the spiritual life of society are diversified by abstract and logical forms of native culture, and scientific rationalism (laws, axioms, etc.) is organically combined with vitacultural taxa, aesthetic images and multivariate material meanings.
14
Yuan, Hong Qi, Si Ming Gai, and Ying Hua Yu. "Discussion along Source Onlap Sequence Stratigraphy Model from Putaohua Oil Layer of Songfang Oilfield in the Northern Songliao Basin." Applied Mechanics and Materials 295-298 (February 2013): 2786–89. http://dx.doi.org/10.4028/www.scientific.net/amm.295-298.2786.
Full textAbstract:
The stratigraphy developmental model for Putaohua oil layer of Songfang oilfield in the northern Songliao basin are studied by using the data of core, well log, mud log and regional geology. The possible developmental models for target oil layer are each layer onlap thinning, each layer gradually thinning, truncated thinning and early foreset later structural uplift. And Putaohua oil layer is proved to be the each layer onlap thinning model with along source onlap features.
15
Hudson, Thom. "Nothing Does Not Equal Zero." Studies in Second Language Acquisition 15, no. 4 (1993): 461–93. http://dx.doi.org/10.1017/s0272263100012389.
Full textAbstract:
During the past decade and a half, a great deal of research has posited a developmental sequence approach in second language acquisition. Much of this research has proposed that certain linguistic structures are acquired in a natural immutable order while other linguistic structures are acquired variably as a result of a learner's orientation (Clahsen, Meisel, & Pienemann, 1983; Meisel, Clahsen, & Pienemann, 1981; Pienemann, 1984, 1985, 1987; Pienemann & Johnston, 1987). Proposals have been made for extending the model into language assessment and pedagogy (Clahsen, 1985; Pienemann, 1984, 1992; Pienemann & Johnston, 1987). The present study reexamines the original social-psychological research upon which the multidimensional model is based and shows that it is incorrect due to faulty analyses. Further, it examines the limited applicability and generalizability of the developmental sequence approach for assessment and pedagogy.
16
Samollow, Paul B. "Status and applications of genomic resources for the gray, short-tailed opossum, Monodelphis domestica, an American marsupial model for comparative biology." Australian Journal of Zoology 54, no. 3 (2006): 173. http://dx.doi.org/10.1071/zo05059.
Full textAbstract:
Owing to its small size, favourable reproductive characteristics, and simple husbandry, the gray, short-tailed opossum, Monodelphis domestica, has become the most widely distributed and intensively utilised laboratory-bred research marsupial in the world today. This article provides an overview of the current state and future projections of genomic resources for this species and discusses the potential impact of this growing resource base on active research areas that use M. domestica as a model system. The resources discussed include: fully arrayed, bacterial artificial chromosome (BAC) libraries; an expanding linkage map; developing full-genome BAC-contig and chromosomal fluorescence in situ hybridisation maps; public websites providing access to the M. domestica whole-genome-shotgun sequence trace database and the whole-genome sequence assembly; and a new project underway to create an expressed-sequence database and microchip expression arrays for functional genomics applications. Major research areas discussed span a variety of genetic, evolutionary, physiologic, reproductive, developmental, and behavioural topics, including: comparative immunogenetics; genomic imprinting; reproductive biology; neurobiology; photobiology and carcinogenesis; genetics of lipoprotein metabolism; developmental and behavioural endocrinology; sexual differentiation and development; embryonic and fetal development; meiotic recombination; genome evolution; molecular evolution and phylogenetics; and more.
17
Negriff, Sonya. "Developmental pathways from maltreatment to risk behavior: Sexual behavior as a catalyst." Development and Psychopathology 30, no. 2 (2017): 683–93. http://dx.doi.org/10.1017/s0954579417001201.
Full textAbstract:
AbstractAlthough delinquency, substance use, and sexual activity are established to be highly intercorrelated, the extant research provides minimal evidence in support of one particular sequence of risk behavior or on the cascade effects from maltreatment. The present study tested a longitudinal model incorporating maltreatment, deviant peers, sexual behavior, delinquency, and substance use to elucidate the sequential pathway(s) from maltreatment to each specific risk behavior throughout adolescence. Data came from a longitudinal study on the effects of maltreatment on adolescent development (N = 454) with four study assessments from early (Time 1 M age = 10.98) to late adolescence (Time 4 M age = 18.22). Results from the cross-lagged model showed a sequence from maltreatment to sexual behavior (Time 1), to delinquency (Time 2), to sexual behavior (Time 3), to substance use and delinquency (Time 4). These findings support sexual behavior as the initial risk behavior that is the catalyst for engagement in more advanced risk behaviors across adolescence.
18
Carre, Wilfrid, Xiaofei Wang, Tom E. Porter, et al. "Chicken genomics resource: sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index." Physiological Genomics 25, no. 3 (2006): 514–24. http://dx.doi.org/10.1152/physiolgenomics.00207.2005.
Full textAbstract:
Its accessibility, unique evolutionary position, and recently assembled genome sequence have advanced the chicken to the forefront of comparative genomics and developmental biology research as a model organism. Several chicken expressed sequence tag (EST) projects have placed the chicken in 10th place for accrued ESTs among all organisms in GenBank. We have completed the single-pass 5′-end sequencing of 37,557 chicken cDNA clones from several single and multiple tissue cDNA libraries and have entered 35,407 EST sequences into GenBank. Our chicken EST sequences and those found in public databases (on July 1, 2004) provided a total of 517,727 public chicken ESTs and mRNAs. These sequences were used in the CAP3 assembly of a chicken gene index composed of 40,850 contigs and 79,192 unassembled singlets. The CAP3 contigs show a 96.7% match to the chicken genome sequence. The University of Delaware (UD) EST collection (43,928 clones) was assembled into 19,237 nonredundant sequences (13,495 contigs and 5,742 unassembled singlets). The UD collection contains 6,223 unique sequences that are not found in other public EST collections but show a 76% match to the chicken genome sequence. Our chicken contig and singlet sequences were annotated according to the highest BlastX and/or BlastN hits. The UD CAP3 contig assemblies and singlets are searchable by nucleotide sequence or key word ( http://cogburn.dbi.udel.edu ), and the cDNA clones are readily available for distribution from the chick EST website and clone repository ( http://www.chickest.udel.edu ). The present paper describes the construction and normalization of single and multiple tissue chicken cDNA libraries, high-throughput EST sequencing from these libraries, the CAP3 assembly of a chicken gene index from all public ESTs, and the identification of several nonredundant chicken gene sets for production of custom DNA microarrays.
19
Penin, Aleksey A., Anna V. Klepikova, Artem S. Kasianov, Evgeny S. Gerasimov, and Maria D. Logacheva. "Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum." Genes 10, no. 1 (2019): 50. http://dx.doi.org/10.3390/genes10010050.
Full textAbstract:
The knowledge of gene functions in model organisms is the starting point for the analysis of gene function in non-model species, including economically important ones. Usually, the assignment of gene functions is based on sequence similarity. In plants, due to a highly intricate gene landscape, this approach has some limitations. It is often impossible to directly match gene sets from one plant species to another species based only on their sequences. Thus, it is necessary to use additional information to identify functionally similar genes. Expression patterns have great potential to serve as a source of such information. An important prerequisite for the comparative analysis of transcriptomes is the existence of high-resolution expression maps consisting of comparable samples. Here, we present a transcriptome atlas of tomato (Solanum lycopersicum) consisting of 30 samples of different organs and developmental stages. The samples were selected in a way that allowed for side-by-side comparison with the Arabidopsis thaliana transcriptome map. Newly obtained data are integrated in the TraVA database and are available online, together with tools for their analysis. In this paper, we demonstrate the potential of comparing transcriptome maps for inferring shifts in the expression of paralogous genes.
20
Southern, E. "Structural features of the Y chromosome." Development 101, Supplement (1987): 75. http://dx.doi.org/10.1242/dev.101.supplement.75.
Full textAbstract:
Sex determination, as a model for the developmental process in mammals, is undoubtedly the principal reason for the intense activity of research on the Y chromosome. As the smallest human chromosome it also offers a simple system for studying those aspects of the human genome that are less well understood than genes and the control of their expression. These include functional regions, such as the kinetochores and telomeres involved in chromosome segregation and integrity. The regions associated with these functions contain the simple-sequence DNAs discovered more than 25 years ago but whose roles are still not understood. The association of simple-sequence DNA with the more broadly defined heterochromatic regions of the genome is nowhere better seen than in the long arm of the Y chromosome. The four papers that follow describe studies of sequences in the Y chromosome in the region of the telomere of the short arm, in the region of the centromere and within the heterochromatin present on the long arm.
21
Corkins, Mark E., Bridget D. DeLay, and Rachel K. Miller. "Tissue-Targeted CRISPR–Cas9-Mediated Genome Editing of Multiple Homeologs in F0-Generation Xenopus laevis Embryos." Cold Spring Harbor Protocols 2022, no. 3 (2021): pdb.prot107037. http://dx.doi.org/10.1101/pdb.prot107037.
Full textAbstract:
Xenopus laevis frogs are a powerful developmental model that enables studies combining classical embryology and molecular manipulation. Because of the large embryo size, ease of microinjection, and ability to target tissues through established fate maps, X. laevis has become the predominant amphibian research model. Given that their allotetraploid genome has complicated the generation of gene knockouts, strategies need to be established for efficient mutagenesis of multiple homeologs to evaluate gene function. Here we describe a protocol to use CRISPR–Cas9-mediated genome editing to target either single alleles or multiple alloalleles in F0X. laevis embryos. A single-guide RNA (sgRNA) is designed to target a specific DNA sequence encoding a critical protein domain. To mutagenize a gene with two alloalleles, the sgRNA is designed against a sequence that is common to both homeologs. This sgRNA, along with the Cas9 protein, is microinjected into the zygote to disrupt the genomic sequences in the whole embryo or into a specific blastomere for tissue-targeted effects. Error-prone repair of CRISPR–Cas9-generated DNA double-strand breaks leads to insertions and deletions creating mosaic gene lesions within the embryos. The genomic DNA isolated from each mosaic F0 embryo is sequenced, and software is applied to assess the nature of the mutations generated and degree of mosaicism. This protocol enables the knockout of genes within the whole embryo or in specific tissues in F0X. laevis embryos to facilitate the evaluation of resulting phenotypes.
22
Liu, Guoqing, Zhi Zhang, Biyu Dong, and Jia Liu. "DNA Sequence-Dependent Properties of Nucleosome Positioning in Regions of Distinct Chromatin States in Mouse Embryonic Stem Cells." International Journal of Molecular Sciences 23, no. 22 (2022): 14488. http://dx.doi.org/10.3390/ijms232214488.
Full textAbstract:
Chromatin architecture is orchestrated, and plays crucial roles during the developmental process by regulating gene expression. In embryonic stem cells (ESCs), three types of chromatin states, including active, repressive and poised states, were previously identified and characterized with specific chromatin modification marks and different transcription activity, but it is largely unknown how nucleosomes are organized in these chromatin states. In this study, by using a DNA deformation energy model, we investigated the sequence-dependent nucleosome organization within the chromatin states in mouse ESCs. The results revealed that: (1) compared with poised genes, active genes are characterized with a higher level of nucleosome occupancy around their transcription start sites (TSS) and transcription termination sites (TTS), and both types of genes do not have a nucleosome-depleted region at their TTS, contrasting with the MNase-seq based result; (2) based on our previous DNA bending energy model, we developed an improved model capable of predicting both rotational positioning and nucleosome occupancy determined by a chemical mapping approach; (3) DNA bending-energy-based analyses demonstrated that the fragile nucleosomes positioned at both gene ends could be explained largely by enhanced rotational positioning signals encoded in DNA, but nucleosome phasing around the TSS of active genes was not determined by sequence preference; (4) the nucleosome occupancy landscape around the binding sites of some developmentally important transcription factors known to bind with different chromatin contexts, was also successfully predicted; (5) the difference of nucleosome occupancy around the TSS between CpG-rich and CpG-poor promoters was partly captured by our sequence-dependent model. Taken together, by developing an improved deformation-energy-based model, we revealed some sequence-dependent properties of the nucleosome arrangements in regions of distinct chromatin states in mouse ESCs.
23
Parisi, Maria-Giovanna, Mylène Toubiana, Valentina Mangano, Nicolò Parrinello, Matteo Cammarata, and Philippe Roch. "MIF from mussel: Coding sequence, phylogeny, polymorphism, 3D model and regulation of expression." Developmental & Comparative Immunology 36, no. 4 (2012): 688–96. http://dx.doi.org/10.1016/j.dci.2011.10.014.
Full text
24
Kertil, Mahmut, Ayhan Kursat Erbas, and Bulent Cetinkaya. "Developing prospective teachers’ covariational reasoning through a model development sequence." Mathematical Thinking and Learning 21, no. 3 (2019): 207–33. http://dx.doi.org/10.1080/10986065.2019.1576001.
Full text
25
Postberg, Weil, and Pembaur. "Biogenesis of Developmental Master Regulatory 27nt-RNAs in Stylonychia—Can Coding RNA Turn into Non-Coding?" Genes 10, no. 11 (2019): 940. http://dx.doi.org/10.3390/genes10110940.
Full textAbstract:
In the ciliate Stylonychia, somatic macronuclei differentiate from germline micronuclei during sexual reproduction, accompanied by developmental sequence reduction. Concomitantly, over 95% of micronuclear sequences adopt a heterochromatin structure characterized by the histone variant H3.4 and H3K27me3. RNAi-related genes and histone variants dominate the list of developmentally expressed genes. Simultaneously, 27nt-ncRNAs that match sequences retained in new macronuclei are synthesized and bound by PIWI1. Recently, we proposed a mechanistic model for ‘RNA-induced DNA replication interference’ (RIRI): during polytene chromosome formation PIWI1/27nt-RNA-complexes target macronucleus-destined sequences (MDS) by base-pairing and temporarily cause locally stalled replication. At polytene chromosomal segments with ongoing replication, H3.4K27me3-nucleosomes become selectively deposited, thus dictating the prospective heterochromatin structure of these areas. Consequently, these micronucleus-specific sequences become degraded, whereas 27nt-RNA-covered sites remain protected. However, the biogenesis of the 27nt-RNAs remains unclear. It was proposed earlier that in stichotrichous ciliates 27nt-RNA precursors could derive from telomere-primed bidirectional transcription of nanochromosomes and subsequent Dicer-like (DCL) activity. As a minimalistic explanation, we propose here that the 27nt-RNA precursor could rather be mRNA or pre-mRNA and that the transition of coding RNA from parental macronuclei to non-coding RNAs, which act in premature developing macronuclei, could involve RNA-dependent RNA polymerase (RDRP) activity creating dsRNA intermediates prior to a DCL-dependent pathway. Interestingly, by such mechanism the partition of a parental somatic genome and possibly also the specific nanochromosome copy numbers could be vertically transmitted to the differentiating nuclei of the offspring.
26
Chiesa, Morgane, Romain Nardou, Natalia Lozovaya, et al. "Enhanced Glutamatergic Currents at Birth in Shank3 KO Mice." Neural Plasticity 2019 (July 3, 2019): 1–11. http://dx.doi.org/10.1155/2019/2382639.
Full textAbstract:
Autism spectrum disorders (ASD) are neurodevelopmental disorders induced by genetic and environmental factors. In our recent studies, we showed that the GABA developmental shifts during delivery and the second postnatal week are abolished in two rodent models of ASD. Maternal treatment around birth with bumetanide restored the GABA developmental sequence and attenuated the autism pathogenesis in offspring. Clinical trials conducted in parallel confirmed the usefulness of bumetanide treatment to attenuate the symptoms in children with ASD. Collectively, these observations suggest that an alteration of the GABA developmental sequence is a hallmark of ASD. Here, we investigated whether similar alterations occur in the Shank3 mouse model of ASD. We report that in CA3 pyramidal neurons, the driving force and inhibitory action of GABA are not different in naïve and Shank3-mutant age-matched animals at birth and during the second postnatal week. In contrast, the frequency of spontaneous excitatory postsynaptic currents is already enhanced at birth and persists through postnatal day 15. Therefore, in CA3 pyramidal neurons of Shank3-mutant mice, glutamatergic but not GABAergic activity is affected at early developmental stages, hence reflecting the heterogeneity of mechanisms underlying the pathogenesis of ASD.
27
Crayton III, Mack E., Carll E. Ladd, Martin Sommer, Gregory Hampikian, and Linda D. Strausbaugh. "An Organizational Model of Transcription Factor Binding Sites for a Histone Promoter in D. melanogaster." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 4, no. 4 (2004): 537–48. https://doi.org/10.3233/isb-00155.
Full textAbstract:
The Drosophila H2A-H2B histone spacer, a small region that functions as a bidirectional promoter for the gene pair, was used as a test sequence for generation of a computationally derived organizational model of transcription factor (TF) binding sites. Expression studies of the spacer revealed that it contains the necessary sequences to confer replication-dependent transcription in partially synchronized cells in culture. Informatics analysis of the spacer uncovered a number of binding sites for specific TFs, none of which had been previously associated with this particular promoter. Each of the TFs in the promoter organizational model are also known to participate in stages of fly development that are characterized by DNA replication and/or cell division, thus providing a biologically functional rationale for an association. Moreover, phylogenetic analysis of the binding sites provides evidence for evolutionary conservation of the essential features of the organizational model. The model, if correct, provides information about the molecules that couple developmental specific demands and histone gene transcription.
28
Moore, Jordan M., and Timothy J. DeVoogd. "Concerted and mosaic evolution of functional modules in songbird brains." Proceedings of the Royal Society B: Biological Sciences 284, no. 1854 (2017): 20170469. http://dx.doi.org/10.1098/rspb.2017.0469.
Full textAbstract:
Vertebrate brains differ in overall size, composition and functional capacities, but the evolutionary processes linking these traits are unclear. Two leading models offer opposing views: the concerted model ascribes major dimensions of covariation in brain structures to developmental events, whereas the mosaic model relates divergent structures to functional capabilities. The models are often cast as incompatible, but they must be unified to explain how adaptive changes in brain structure arise from pre-existing architectures and developmental mechanisms. Here we show that variation in the sizes of discrete neural systems in songbirds, a species-rich group exhibiting diverse behavioural and ecological specializations, supports major elements of both models. In accordance with the concerted model, most variation in nucleus volumes is shared across functional domains and allometry is related to developmental sequence. Per the mosaic model, residual variation in nucleus volumes is correlated within functional systems and predicts specific behavioural capabilities. These comparisons indicate that oscine brains evolved primarily as a coordinated whole but also experienced significant, independent modifications to dedicated systems from specific selection pressures. Finally, patterns of covariation between species and brain areas hint at underlying developmental mechanisms.
29
Sasaki, Shunya, Maaya Nishiko, Takuma Sakamoto, Michael R. Kanost, and Hiroko Tabunoki. "cDNA Cloning and Partial Characterization of the DJ-1 Gene from Tribolium castaneum." Antioxidants 10, no. 12 (2021): 1970. http://dx.doi.org/10.3390/antiox10121970.
Full textAbstract:
The DJ-1 gene is highly conserved across a wide variety of organisms and it plays a role in anti-oxidative stress mechanisms in cells. The red flour beetle, Tribolium castaneum, is widely used as a model insect species because it is easy to evaluate gene function in this species using RNA interference (RNAi). The T. castaneum DJ-1 (TcDJ-1) sequence is annotated in the T. castaneum genome database; however, the function and characteristics of the TcDJ-1 gene have not been elucidated. Here, we investigated the cDNA sequence of TcDJ-1 and partially characterized its function. First, we examined the TcDJ-1 amino acid sequence and found that it was highly conserved with sequences from other species. TcDJ-1 mRNA expression was higher in the early pupal and adult developmental stages. We evaluated oxidant tolerance in TcDJ-1 knockdown adults using paraquat and found that adults with TcDJ-1 knockdown exhibited increased sensitivity to paraquat. Our findings show that TcDJ-1 has an antioxidant function, as observed for DJ-1 from other insects. Therefore, these results suggest that TcDJ-1 protects against oxidative stress during metamorphosis.
30
Kelly, Linda. "Developmental Patterns in Zimbabwean Children with HIV+ Serology: A Guide to Planning a Service Delivery Model." British Journal of Occupational Therapy 57, no. 4 (1994): 121–23. http://dx.doi.org/10.1177/030802269405700403.
Full textAbstract:
The sequelae of AIDS are presenting a worldwide challenge, both in numbers and in the presentation of symptoms, and more children are being affected. Seventy-five children ranging from one month to 4 years were assessed on the Gesell Developmental Schedules in a paediatric clinic for follow-up of children with HIV+ serology in Zimbabwe. When children are deficient in their developmental milestones, it is of concern to their parents. Therapists are involved in the stimulation, adaptation and remediation of the deficits and problems encountered. Combining the parents' concerns with the child's needs can be a challenge with children who, in the long run, will face death. Four patterns emerged which required different levels of intervention. The levels may be described in a graded sequence that increases with disability, beginning with no developmental delay, then increasing from mild to moderate to severe developmental delays. Handicapping conditions vary within this framework. Within the severe category, there are children who have a range of neurological deficits, including dystonia, hypotonia and tongue thrust. Intervention requires strategies that use a variety of techniques, dependent on the presentation of symptoms. The level of illness in the parents must also be taken into account because they too may need intervention. Intervention strategies are outlined according to the pattern of delay.
31
Robb, Elizabeth A., and Mary E. Delany. "Case Study of Sequence Capture Enrichment Technology: Identification of Variation Underpinning Developmental Syndromes in an Amniote Model." Genes 3, no. 2 (2012): 233–47. http://dx.doi.org/10.3390/genes3020233.
Full text
32
Huang, Kenneth, Suela Xhani, Amanda V. Albrecht, Van L. T. Ha, Shingo Esaki, and Gregory M. K. Poon. "Mechanism of cognate sequence discrimination by the ETS-family transcription factor ETS-1." Journal of Biological Chemistry 294, no. 25 (2019): 9666–78. http://dx.doi.org/10.1074/jbc.ra119.007866.
Full textAbstract:
Functional evidence increasingly implicates low-affinity DNA recognition by transcription factors as a general mechanism for the spatiotemporal control of developmental genes. Although the DNA sequence requirements for affinity are well-defined, the dynamic mechanisms that execute cognate recognition are much less resolved. To address this gap, here we examined ETS1, a paradigm developmental transcription factor, as a model for which cognate discrimination remains enigmatic. Using molecular dynamics simulations, we interrogated the DNA-binding domain of murine ETS1 alone and when bound to high-and low-affinity cognate sites or to nonspecific DNA. The results of our analyses revealed collective backbone and side-chain motions that distinguished cognate versus nonspecific as well as high- versus low-affinity cognate DNA binding. Combined with binding experiments with site-directed ETS1 mutants, the molecular dynamics data disclosed a triad of residues that respond specifically to low-affinity cognate DNA. We found that a DNA-contacting residue (Gln-336) specifically recognizes low-affinity DNA and triggers the loss of a distal salt bridge (Glu-343/Arg-378) via a large side-chain motion that compromises the hydrophobic packing of two core helices. As an intact Glu-343/Arg-378 bridge is the default state in unbound ETS1 and maintained in high-affinity and nonspecific complexes, the low-affinity complex represents a unique conformational adaptation to the suboptimization of developmental enhancers.
33
Danes, Sharon M., Martha A. Rueter, Hee-Kyung Kwon, and William Doherty. "Family FIRO Model: An Application to Family Business." Family Business Review 15, no. 1 (2002): 31–43. http://dx.doi.org/10.1111/j.1741-6248.2002.00031.x.
Full textAbstract:
This study applies the Family FIRO model, one of interpersonal dynamics and change, to family businesses (specifically, to family farming couples). It empirically tests the developmental sequence of three dimensions of the model: inclusion, control, and integration. Findings indicate that both a sense of inclusion in a family business and the manner in which control issues are managed have important influences on family business integration. Because inclusion predicts control dynamics, effective control may not be diminished without adequate levels of inclusion. The study offers practitioners a theory-based approach to working with the complex dynamics within family businesses. Family businesses will remain more resilient in times of change if the leaders understand and reassess patterns of inclusion when change is initiated.
34
Kantak, A. G., R. M. Goldblum, M. Z. Schwartz, S. Rajaraman, C. T. Ladoulis, and A. S. Goldman. "Fetal intestinal transplants in syngeneic rats: a developmental model of intestinal immunity." Journal of Immunology 138, no. 10 (1987): 3191–96. http://dx.doi.org/10.4049/jimmunol.138.10.3191.
Full textAbstract:
Abstract We conducted a longitudinal study of the development of lymphoid tissue in fetal small intestine transplanted to a subcutaneous site in adult syngeneic Fischer strain rats. Fetal jejunoileal segments obtained between 18 and 21 days of gestation were transplanted to a dorsal subcutaneous site on syngeneic adult rats. Three weeks later, intestinal segments greater than 2.5 cm in length were found in 70% of recipients. Each week for 6 wk post-transplantation, a full-thickness biopsy was obtained for histologic and immunohistologic examination. At the time of transplantation, fetal rat intestine did not display Peyer's patches, intraepithelial lymphocytes, lymphoid follicles, or IgA-containing plasma cells. These lymphoid structures reached adult levels by 4 wk after transplantation, and the sequence of development of the lymphoid structures in the transplants appeared to match the postnatal development of normal small intestine. After immunizing the in situ intestine or the transplanted fetal intestine with cholera toxin, the number of cells producing specific antibodies to the immunogen increased significantly in intestinal transplants and in situ intestine. In contrast, few if any cells synthesizing antibodies to cholera toxin developed in the transplants after i.p. immunization. This study suggests that fetal intestinal transplants behave as part of the mucosal immune system. This model may provide useful approaches to studying the development of mucosal immunity.
35
Robinson, G., and C. M. Rutten. "Early Literacy: A Developmental and Comparative Analysis." Australasian Journal of Special Education 20, no. 1 (1996): 49–60. http://dx.doi.org/10.1017/s1030011200023599.
Full textAbstract:
In two experiments, the acquisition of literacy skills by three to six year olds was examined to (1) assess a possible developmental sequence of knowledge about print and word reading, and (2) compare the skill levels of good and poor six year old readers using a developmental model.The first experiment involved 30 three, four and five year olds from a preschool and primary school who were assessed on a battery of tasks designed to measure five aspects of awareness of print and word reading concepts. The five aspects assessed were concepts about print, graphic awareness, phonemic awareness, grapheme-phoneme correspondence knowledge and word reading. Analysis of the data showed a developmental expansion of print related concepts and skills with age.In the second experiment, using similar methodology, 25 good six year old readers performed significantly better than 22 poor six year old readers across all component measures and a developmental lag reading disability model was thus implied.
36
Wang, Jun, and Liangjiang Wang. "Deep learning of the back-splicing code for circular RNA formation." Bioinformatics 35, no. 24 (2019): 5235–42. http://dx.doi.org/10.1093/bioinformatics/btz382.
Full textAbstract:
Abstract Motivation Circular RNAs (circRNAs) are a new class of endogenous RNAs in animals and plants. During pre-RNA splicing, the 5′ and 3′ termini of exon(s) can be covalently ligated to form circRNAs through back-splicing (head-to-tail splicing). CircRNAs can be conserved across species, show tissue- and developmental stage-specific expression patterns, and may be associated with human disease. However, the mechanism of circRNA formation is still unclear although some sequence features have been shown to affect back-splicing. Results In this study, by applying the state-of-art machine learning techniques, we have developed the first deep learning model, DeepCirCode, to predict back-splicing for human circRNA formation. DeepCirCode utilizes a convolutional neural network (CNN) with nucleotide sequence as the input, and shows superior performance over conventional machine learning algorithms such as support vector machine and random forest. Relevant features learnt by DeepCirCode are represented as sequence motifs, some of which match human known motifs involved in RNA splicing, transcription or translation. Analysis of these motifs shows that their distribution in RNA sequences can be important for back-splicing. Moreover, some of the human motifs appear to be conserved in mouse and fruit fly. The findings provide new insight into the back-splicing code for circRNA formation. Availability and implementation All the datasets and source code for model construction are available at https://github.com/BioDataLearning/DeepCirCode. Supplementary information Supplementary data are available at Bioinformatics online.
37
Wharton, K. A., R. G. Franks, Y. Kasai, and S. T. Crews. "Control of CNS midline transcription by asymmetric E-box-like elements: similarity to xenobiotic responsive regulation." Development 120, no. 12 (1994): 3563–69. http://dx.doi.org/10.1242/dev.120.12.3563.
Full textAbstract:
Central nervous system midline cells constitute a discrete group of Drosophila embryonic cells with numerous functional and developmental roles. Corresponding to their separate identity, the midline cells display patterns of gene expression distinct from the lateral central nervous system. A conserved 5 base pair sequence (ACGTG) was identified in central nervous system midline transcriptional enhancers of three genes. Germ-line transformation experiments indicate that this motif forms the core of an element required for central nervous system midline transcription. The central nervous system midline element is related to the mammalian xenobiotic response element, which regulates transcription of genes that metabolize aromatic hydrocarbons. These data suggest a model whereby related basic-helix-loop-helix-PAS proteins interact with asymmetric E-box-like target sequences to control these disparate processes.
38
Garofalo, Giancarlo, Tyson Nielsen, and Samuel Caito. "Expression Profiling of Adipogenic and Anti-Adipogenic MicroRNA Sequences following Methylmercury Exposure in Caenorhabditis elegans." Toxics 11, no. 11 (2023): 934. http://dx.doi.org/10.3390/toxics11110934.
Full textAbstract:
MicroRNA (miRNA) are important regulators of gene expression that respond not only to developmental and pathological cues, but also to environmental stimuli. Dyslipidemia is a hallmark of metabolic conditions and has been shown to significantly affect the expression of circulating miRNA sequences. Recently, our lab has shown that the environmental toxicant methylmercury (MeHg) causes dyslipidemia in the Caenorhabditis elegans model organism. While 10 and 20 μM MeHg increases the expression of adipogenic transcription factors and lipid-binding proteins in worms, there is limited information on how the toxicant affects the miRNA regulators of these genes. We hypothesized that MeHg would increase the expression of adipogenic miRNA sequences and/or decrease the expression of anti-adipogenic miRNA sequences. We further hypothesized that the target mRNA sequences for the miRNAs affected by MeHg would be consequently altered. We selected three potentially adipogenic (mir-34, mir-124, and mir-355) and three potentially anti-adipogenic (mir-240, mir-786, and let-7) miRNA sequences homologous to known human miRNA sequences altered in obesity, and quantified their levels 24 h and 48 h post MeHg treatment. At 24 h post exposure, MeHg significantly increased expression of both the adipogenic and anti-adipogenic miRNA sequences 1.5–3x above untreated control. By 48 h post exposure, only the adipogenic miRNA sequences were elevated, while the anti-adipogenic miRNA sequences were decreased by 50% compared to untreated control. These data suggest that there are developmental changes in miRNA expression over time following MeHg exposure. We next selected one target mRNA sequence for each miRNA sequence based on miRNA–mRNA relationships observed in humans. MeHg altered the gene expression of all the target genes assayed. Except for mir-34, all the tested miRNA–mRNA sequences showed a conserved relationship between nematode and humans. To determine whether the selected miRNA sequences were involved in lipid accumulation in response to MeHg, lipid storage was investigated in transgenic worm strains that lacked the specific miRNA strains. Of the six strains investigated, only the mir-124 and let-7 mutant worms had lipid storage levels that were statistically different from wild type, suggesting that these two sequences can be potential mediators of MeHg-induced lipid dysregulation.
39
Zheng, Jinshui, Donghai Peng, Ling Chen, et al. "The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes." Proceedings of the Royal Society B: Biological Sciences 283, no. 1835 (2016): 20160942. http://dx.doi.org/10.1098/rspb.2016.0942.
Full textAbstract:
Plant-parasitic nematodes were found in 4 of the 12 clades of phylum Nematoda. These nematodes in different clades may have originated independently from their free-living fungivorous ancestors. However, the exact evolutionary process of these parasites is unclear. Here, we sequenced the genome sequence of a migratory plant nematode, Ditylenchus destructor . We performed comparative genomics among the free-living nematode, Caenorhabditis elegans and all the plant nematodes with genome sequences available. We found that, compared with C. elegans , the core developmental control processes underwent heavy reduction, though most signal transduction pathways were conserved. We also found D. destructor contained more homologies of the key genes in the above processes than the other plant nematodes. We suggest that Ditylenchus spp. may be an intermediate evolutionary history stage from free-living nematodes that feed on fungi to obligate plant-parasitic nematodes. Based on the facts that D. destructor can feed on fungi and has a relatively short life cycle, and that it has similar features to both C. elegans and sedentary plant-parasitic nematodes from clade 12, we propose it as a new model to study the biology, biocontrol of plant nematodes and the interaction between nematodes and plants.
40
Han, Jian, Chunlin Wang, Catherine Sanders, et al. "Comprehensive and semi-quantitative TCR repertoire analysis with a novel multiplex PCR method and 454 sequencing (85.3)." Journal of Immunology 184, no. 1_Supplement (2010): 85.3. http://dx.doi.org/10.4049/jimmunol.184.supp.85.3.
Full textAbstract:
Abstract CDR3 sequences, composed by V(D)J combination, form the center of the antigen binding site where they often play a critical role in defining the affinity and specificity of the receptor for individual peptide-MHC complexes of both the TCRα and TCRβ chains. The goal of our study was to produce comprehensive, unrestricted profiles of TCR diversity among key developmental and effector subsets of T cells isolated from the blood of a single, healthy donor at sequence-level resolution using a novel multiplex PCR method combined with Roche 454 Life Sciences high-throughput sequencing technology. From the sequence reads, about 1.48 million CDR3 intervals were identified, totaling 169,977 and 113,290 unique CDR3 intervals for TCRα and for TCRβ, respecitively. Our data also show numerous examples of identical CDR3 sequences shared by different T subsets. Using the compound Poisson process model, we estimated that the diversity of the TCRα and β chains expressed by our donor is around 0.47 x 106 and 0.35 x 106 unique CDR3 nucleotide sequences, respectively. Our comprehensive data demonstrates that our new method has overcome past challenges in studying the T cell immune repertoire and is highly sensitive, repeatable, and semi-quantitative. This approach provides a useful tool for assessing immune competence, tracking T cell expansion kinetics, assessing vaccine efficiency, and detecting antigen-specific T cell clones in patients with infection or cancer.
41
Balcı, Ali Tuğrul, Mark Maher Ebeid, Panayiotis V. Benos, Dennis Kostka, and Maria Chikina. "An intrinsically interpretable neural network architecture for sequence-to-function learning." Bioinformatics 39, Supplement_1 (2023): i413—i422. http://dx.doi.org/10.1093/bioinformatics/btad271.
Full textAbstract:
Abstract Motivation Sequence-based deep learning approaches have been shown to predict a multitude of functional genomic readouts, including regions of open chromatin and RNA expression of genes. However, a major limitation of current methods is that model interpretation relies on computationally demanding post hoc analyses, and even then, one can often not explain the internal mechanics of highly parameterized models. Here, we introduce a deep learning architecture called totally interpretable sequence-to-function model (tiSFM). tiSFM improves upon the performance of standard multilayer convolutional models while using fewer parameters. Additionally, while tiSFM is itself technically a multilayer neural network, internal model parameters are intrinsically interpretable in terms of relevant sequence motifs. Results We analyze published open chromatin measurements across hematopoietic lineage cell-types and demonstrate that tiSFM outperforms a state-of-the-art convolutional neural network model custom-tailored to this dataset. We also show that it correctly identifies context-specific activities of transcription factors with known roles in hematopoietic differentiation, including Pax5 and Ebf1 for B-cells, and Rorc for innate lymphoid cells. tiSFM’s model parameters have biologically meaningful interpretations, and we show the utility of our approach on a complex task of predicting the change in epigenetic state as a function of developmental transition. Availability and implementation The source code, including scripts for the analysis of key findings, can be found at https://github.com/boooooogey/ATAConv, implemented in Python.
42
Gilligan, Carol. "Reprint: In a Different Voice: Women's Conceptions of Self and of Morality." Harvard Educational Review 94, no. 1 (2024): 55–91. http://dx.doi.org/10.17763/1943-5045-94.1.55.
Full textAbstract:
As theories of developmental psychology continue to define educational goals and practice, it has become imperative for educators and researchers to scrutinize not only the underlying assumptions of such theories but also the model of adulthood toward which they point. Carol Gilligan examines the limitations of several theories, most notably Kohlberg's stage theory of moral development, and concludes that developmental theory has not given adequate expression to the concerns and experience of women. Through a review of psychological and literary sources, she illustrates the feminine construction of reality. From her own research data, interviews with women contemplating abortion, she then derives an alternative sequence for the development of women's moral judgments. Finally, she argues for an expanded conception of adulthood that would result from the integration of the “feminine voice” into developmental theory.
43
Winward, John. "The state of the article." Linguistic Variation 14, no. 1 (2014): 46–68. http://dx.doi.org/10.1075/lv.14.1.03win.
Full textAbstract:
English articles represent one of the most challenging areas of second language acquisition for learners whose L1 lacks articles. The two studies presented here examine the developmental sequence of acquisition, the first through a cross-sectional analysis of Thai learners at different levels of overall English proficiency, the second through a longitudinal experiment in which learners were exposed to semantically-tailored tokens of article use, but without any explicit or meta-linguistic instruction. It is argued that the data do not show evidence of abrupt parameter resetting. Instead, the developmental patterns fit well with Yang’s variational model of acquisition. Keywords: L2 acquisition; article systems; determiners; definiteness; specificity
44
Saint-Georges, Zacharie, and Tracy Vaillancourt. "The temporal sequence of depressive symptoms, peer victimization, and self-esteem across adolescence: Evidence for an integrated self-perception driven model." Development and Psychopathology 32, no. 3 (2019): 975–84. http://dx.doi.org/10.1017/s0954579419000865.
Full textAbstract:
AbstractDepression is associated with a multiplicity of adverse outcomes in adolescence, including peer victimization and low self-esteem. Depressive symptoms, peer victimization, and self-esteem are linked in cross-sectional studies, but no longitudinal study has been conducted assessing their developmental pathways in one integrated model across adolescence. We explored their temporal sequencing in a normative sample of 612 Canadian adolescents (54% girls) assessed annually over 5 years (Grade 7 to Grade 11). Potential confounders such as biological sex, ethnicity/race, and parent income and education were statistically controlled. We found evidence for the vulnerability model (self-esteem predicting depression) and the symptoms-driven model (depression predicting peer victimization). Our findings also supported the integration of these pathways into a self-perception driven model characterized by the indirect effect of self-esteem on later peer victimization via depressive symptoms. Specifically, poor self-esteem initiated a developmental cascade that led to poor mood and poor peer relations. These results highlight the importance of helping youth form a healthy identity that promotes positive mental health and peer relations, and the need to intervene with depressed, victimized, and at-risk adolescents to instill positive self-regard. Our results also emphasize the central role that self-perceptions play in the onset and maintenance of poor outcomes.
45
Barribeau, Seth M., Jandouwe Villinger, and Bruce Waldman. "Ecological immunogenetics of life-history traits in a model amphibian." Biology Letters 8, no. 3 (2011): 405–7. http://dx.doi.org/10.1098/rsbl.2011.0845.
Full textAbstract:
Major histocompatibility complex (MHC) genes determine immune repertoires and social preferences of vertebrates. Immunological regulation of microbial assemblages associated with individuals influences their sociality, and should also affect their life-history traits. We exposed Xenopus laevis tadpoles to water conditioned by adult conspecifics. Then, we analysed tadpole growth, development and survivorship as a function of MHC class I and class II peptide-binding region amino acid sequence similarities between tadpoles and frogs that conditioned the water to which they were exposed. Tadpoles approached metamorphosis earlier and suffered greater mortality when exposed to immunogenetically dissimilar frogs. The results suggest that developmental regulatory cues, microbial assemblages or both are specific to MHC genotypes. Tadpoles may associate with conspecifics with which they share microbiota to which their genotypes are well adapted.
46
Li, Yan, and R. E. Burke. "Developmental Changes in Short-Term Synaptic Depression in the Neonatal Mouse Spinal Cord." Journal of Neurophysiology 88, no. 6 (2002): 3218–31. http://dx.doi.org/10.1152/jn.00406.2002.
Full textAbstract:
We examined age-dependent changes in short-term synaptic depression of monosynaptic excitatory postsynaptic potentials (EPSPs) recorded in lumbar motoneurons in hemisected spinal cords of neonatal Swiss-Webster mice between postnatal day 2 (P2) and 12 (P12). We used four paradigms that sample the input-output dependence on stimulation history in different but complementary ways: 1) paired-pulse depression; 2) steady-state depression during constant frequency trains; 3) modulation during irregular stimulation sequences; and 4) recovery after high-frequency conditioning trains. Paired-pulse synaptic depression declined more than steady-state depression during 10-pulse trains at frequencies from 0.125 to 8 Hz in this age range. Depression during sequences of irregular stimulations that more closely mimic physiological activation also declined with postnatal age. On the other hand, the overall rate of synaptic recovery after a 4-Hz conditioning train exhibited surprisingly little change between P2 and P12. Control experiments indicated that these observations depend primarily, if not exclusively, on changes in presynaptic transmitter release. The data were examined using quantitative models that incorporate factors that have been suggested to exist at more specialized central synapses. The model that best predicted the observations included two presynaptic compartments that are depleted during activation, plus two superimposed processes that enhance transmitter release by different mechanisms. One of the latter produced rapidly-decaying enhancement of transmitter release fraction. The other mechanism indirectly enhanced the rate of renewal of one of the depleted presynaptic compartments. This model successfully predicted the constant frequency and irregular sequence data from all age groups, as well as the recovery curves following short, high-frequency tetani. The results suggest that a reduction in release fraction accounts for much of the decline in synaptic depression during early postnatal development, although changes in both enhancement processes also contribute. The time constants of resource renewal showed surprisingly little change through the first 12 days of postnatal life.
47
Pos, Robert. "A Developmental Theory of Personality Producing Two Time Orientations." KronoScope 6, no. 1 (2006): 83–104. http://dx.doi.org/10.1163/156852406777505327.
Full textAbstract:
AbstractThis paper describes a theory of genetically determined personality development, including the development of two mutually exclusive time orientations: alphas preferentially relate to their present, often being inattentive to their past and future; betas preferentially relate to their future and past, and tend to be inattentive to their present. These time orientations or perspectives derive from two types of autobiographic memory materializing around age 6, which cause two types of personality. For example, the theory views alphas as extroverted and betas as introverted although there are significant differences between Jung's view of these traits and the theory's definitions. Beginning at birth, the amalgam of inborn motivational contexts induces a context-specific partitioning of reality. This is left intact when an alpha child's autobiographic memory, which is free of trans-contextual sequencing of memories, becomes active and the child's identity becomes therefore multi-focal (situational), as represented by Jung's personality model. By contrast, a beta child spontaneously produces a trans-contextual sequence of memories. The youngster's partitioned reality fuses, leading to a singular, monofocal identity, as represented by Freud's personality model. Self-reflection in adolescence makes both implicit identities self-conscious. The underlying genes possibly belong to the X-chromosome, the alpha gene being dominant and the beta gene recessive.
48
Ziegler, Paul. "The Developmental Cycle of Spirodela polyrhiza Turions: A Model for Turion-Based Duckweed Overwintering?" Plants 13, no. 21 (2024): 2993. http://dx.doi.org/10.3390/plants13212993.
Full textAbstract:
Duckweeds are widely distributed small, simply constructed aquatic higher plants (the Lemnaceae) found on quiet freshwater surfaces. Species inhabiting temperate climates may have to cope with long periods of severe cold during the winter season. Several duckweeds form compact resting structures from the assimilatory fronds of the growing season that can bridge inhospitable conditions in a quiescent state. Of these, turions separate from the mother fronds and overwinter on the water body bottom in a dormant state. They can surface, germinate, and sprout to resume active growth upon warming in the spring. The turions of the largest duckweed, Spirodela polyrhiza, have been intensively examined as to ultrastructure, the factors governing their formation and release from dormancy, and the signals driving their germination and sprouting and the accompanying starch degradation. Comparative transcriptomics of assimilatory fronds and dormant turions are revealing the molecular features of this developmental cycle. The results illustrate an elegant sequence of reactions that ensures aquatic survival of even severe winters by frost avoidance in a vegetative mode. Since little is known about other duckweed resting fronds, the S. polyrhiza turion developmental cycle cannot be considered to be representative of duckweed resting fronds in general but can serve as a reference for corresponding investigations.
49
Bednarek, Piotr Tomasz, Renata Orłowska, Dariusz Rafał Mańkowski, Sylwia Oleszczuk, and Jacek Zebrowski. "Structural Equation Modeling (SEM) Analysis of Sequence Variation and Green Plant Regeneration via Anther Culture in Barley." Cells 10, no. 10 (2021): 2774. http://dx.doi.org/10.3390/cells10102774.
Full textAbstract:
The process of anther culture involves numerous abiotic stresses required for cellular reprogramming, microspore developmental switch, and plant regeneration. These stresses affect DNA methylation patterns, sequence variation, and the number of green plants regenerated. Recently, in barley (Hordeum vulgare L.), mediation analysis linked DNA methylation changes, copper (Cu2+) and silver (Ag+) ion concentrations, sequence variation, β-glucans, green plants, and duration of anther culture (Time). Although several models were used to explain particular aspects of the relationships between these factors, a generalized complex model employing all these types of data was not established. In this study, we combined the previously described partial models into a single complex model using the structural equation modeling approach. Based on the evaluated model, we demonstrated that stress conditions (such as starvation and darkness) influence β-glucans employed by cells for glycolysis and the tricarboxylic acid cycle. Additionally, Cu2+ and Ag+ ions affect DNA methylation and induce sequence variation. Moreover, these ions link DNA methylation with green plants. The structural equation model also showed the role of time in relationships between parameters included in the model and influencing plant regeneration via anther culture. Utilization of structural equation modeling may have both scientific and practical implications, as it demonstrates links between biological phenomena (e.g., culture-induced variation, green plant regeneration and biochemical pathways), and provides opportunities for regulating these phenomena for particular biotechnological purposes.
50
Rösner, Janin, Benedikt Wellmeyer, and Hans Merzendorfer. "Tribolium castaneum: A Model for Investigating the Mode of Action of Insecticides and Mechanisms of Resistance." Current Pharmaceutical Design 26, no. 29 (2020): 3554–68. http://dx.doi.org/10.2174/1381612826666200513113140.
Full textAbstract:
The red flour beetle, Tribolium castaneum, is a worldwide insect pest of stored products, particularly food grains, and a powerful model organism for developmental, physiological and applied entomological research on coleopteran species. Among coleopterans, T. castaneum has the most fully sequenced and annotated genome and consequently provides the most advanced genetic model of a coleopteran pest. The beetle is also easy to culture and has a short generation time. Research on this beetle is further assisted by the availability of expressed sequence tags and transcriptomic data. Most importantly, it exhibits a very robust response to systemic RNA interference (RNAi), and a database of RNAi phenotypes (iBeetle) is available. Finally, classical transposonbased techniques together with CRISPR/Cas-mediated gene knockout and genome editing allow the creation of transgenic lines. As T. castaneum develops resistance rapidly to many classes of insecticides including organophosphates, methyl carbamates, pyrethroids, neonicotinoids and insect growth regulators such as chitin synthesis inhibitors, it is further a suitable test system for studying resistance mechanisms. In this review, we will summarize recent advances in research focusing on the mode of action of insecticides and mechanisms of resistance identified using T. castaneum as a pest model.