Variation and Evolution of Human Centromeres: A Field Guide and Perspective

We are entering a new era in genomics where entire centromeric regions are accurately represented in human reference assemblies. Access to these high-resolution maps will enable new surveys of sequence and epigenetic variation in the population and offer new insight into satellite array genomics and centromere function. Here, we focus on the sequence organization and evolution of alpha satellites, which are credited as the genetic and genomic definition of human centromeres due to their interaction with inner kinetochore proteins and their importance in the development of human artificial chromosome assays. We provide an overview of alpha satellite repeat structure and array organization in the context of these high-quality reference data sets; discuss the emergence of variation-based surveys; and provide perspective on the role of this new source of genetic and epigenetic variation in the context of chromosome biology, genome instability, and human disease.

Sequence organization of autistic children’s play with caregivers: Rethinking follow-in directives

This study is a qualitative investigation of caregiver–child interactions, involving 15 autistic children who are in the early stages of language learning. Data consisted of 15-min videos of free-play interactions recorded in a University clinic. We use conversation analysis to examine the sequence organization of proposal episodes, where the caregiver proposes some course of action regarding the child’s play activity. Prior work has used a speech act theoretical framework to identify follow-in directives, which are similar to proposals, but identified at the utterance level rather than at the level of social action. According to conversation analysis, social actions are implemented over multiple interactional turns and produced in collaboration between interaction partners. Our analysis showed that caregivers design their talk in ways that enable autistic children’s participation in interactional turn-taking by forecasting the upcoming proposal. They also socialize children into expectations around turn-taking, by providing an “interaction envelope” around children’s conduct so that it can be construed as completing interactional sequences. Finally, we show how autistic children can display an orientation to turn-taking by timing their interactive moves to occur at transitional moments in the interaction in ways similar to adult conversational turn-taking. Lay abstract In this article we use a qualitative method, conversation analysis, to examine videos of caregivers interacting with their young autistic children who are in the early phases of language learning. Conversation analysis involves preparation of detailed transcripts of video data, which are then analyzed together to understand how interactional moves (e.g. talk, gestures, and physical conduct) are linked with prior and subsequent interactional moves. We analyzed data from 15 participants, and focused on instances when caregivers made a proposal about something the child was playing with. In previous research, similar instances have been referred to as “follow-in directives.” We found that these proposals were embedded in sequences that had a similar structure, and were prefaced with a ‘pre-proposal’; where the caregiver established the child’s interest in a joint activity and signaled the upcoming proposal. The caregiver’s talk was also provided in such a way that there was a clear “slot” for the child’s turn, which made it easy for the child’s actions to become part of an interactional sequence. In addition, proposal sequences were very negotiable—the caregivers do not usually insist that the child follow through on the proposal, only that they produce an action that could be taken as a response. Finally, there were some instances where the child’s turn was very precisely timed to occur right at the end of a caregiver’s proposal; this precise timing could signal the child’s understanding of how interactional turn-taking works. We suggest that this method of examining caregiver–child interactions provides new insights into how interactions proceed, which could be useful for future intervention research.

Revealing the Patterns of Sequence Organization on Blackpink Interview at Zach Sang Show

Intentionally or not, a conversation between two people or more is a common thing around us. This research will discuss the patterns of sequence organization in the conversation using the qualitative method. The data in this research were words, phrases, sentences in the form of spoken language taken from Youtube entitled "Blackpink Talks 'Kill This Love', Coachella & How They Formed" which premiered on April 17, 2019. The research findings describe the patterns of sequence organization in conversation which consist of adjacency pairs, preference organization, sequence expansion, repair, and topic management. From 1 There were 9 responses from SPP that showed preferred and 8 others indicated dispreferred and 4 repair sessions where all were initiated by other speakers. In addition, which only 1 denotes pre-expansion, 6 denotes insert expansion, and one more denotes post expansion. From the patterns formed in the conversation, finally FPP can bring the flow of the conversation and produce 8 topics FPP begins the conversation by asking about Blackpink performance at Coachella, then interspersed by discussing each member’s life, how their initial meeting, what is their motivation, and talking about songs and choreography.

Hierarchical Structure of Protein Sequence

Most non-infectious diseases are associated with dysfunction of proteins or protein complexes. Аssociation between sequence and structure is analyzed since a long time, and analysis of sequence organization in domains and motifs is actual research area. A mathematical method is proposed here to identify the hierarchical organization of protein sequences. The method is based on pentapeptide as a unit of protein sequences. This method was applied on a non-homologous dataset of protein sequences. The analysis revealed 11 hierarchical levels of protein sequence organization, showing the relationship of these multiple fragments of sequences. Using different examples, we illustrated how the fragments of the spatial structure of protein correspond to the elements of the hierarchical structure of the protein sequence. A hierarchical structure is observed in the protein sequence. This methodology is an interesting basis for mathematically based classification of elements of spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used for biotechnological and medical problems.

CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification

Background Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. Results In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel levels are devoted to catching both non periodic and periodic DNA string features. A dense layer is devoted to their combination to give a final classification. Conclusions Results computed on public data sets of different organisms show that CORENup is a state of the art methodology for nucleosome positioning identification based on a Deep Neural Network architecture. The comparisons have been carried out using two groups of datasets, currently adopted by the best performing methods, and CORENup has shown top performance both in terms of classification metrics and elapsed computation time.

Grammatical conformity in question-answer sequences: The case of meiyou in Mandarin conversation

This article probes into grammatical conformity in Mandarin by examining meiyou, a multifunctional negative form, in question-answer sequences. Using a conversation analysis approach, it discovers that, as a conforming answer to polar questions, meiyou acquiesces to all the terms and constraints of the question and maximizes the progressivity of the sequence. As a non-conforming response to polar questions, it mitigates the disagreement by avoiding a pointed syntactic negation. Meiyou can also respond to Q-word questions, problematizing the inference incorporated in the question. This study not only contributes to the cross-linguistic research on negative particles in talk-in-interaction but also reveals that grammatical conformity is a crucial dimension in Mandarin response design, providing further confirmation of the link between grammar, action, and sequence organization.