The Functional Sequence Above QP

2021 ◽  
pp. 93-157
Author(s):  
Éva Dékány
Keyword(s):  
Functional Sequence

Syncretism and Containment in Spatial Deixis

2018 ◽  
Author(s):  
Eric Lander ◽  
Liliane Haegeman
Keyword(s):  
Universal Grammar ◽  
Functional Sequence ◽  
Wide Range ◽  
Spatial Deixis

This chapter investigates spatial-deictic systems (e.g. English this vs. that, or Latin hīc vs. iste vs. ille) from a wide range of typologically diverse languages. We propose that spatial deixis is encoded as a three-way contrast in Universal Grammar (UG): Proximal ‘close to speaker,’ Medial ‘close to hearer,’ and Distal ‘far from speaker and hearer.’ The empirical core of the chapter focuses on two phenomena: (i) syncretism and (ii) morphological containment. It is shown that only certain kinds of syncretism patterns are attested crosslinguistically: Syncretism cannot target Proximal and Distal without also targeting Medial (a case of *ABA). Furthermore, the cases of morphological containment we have found show that Distal contains Medial, which, in turn, contains Proximal. A functional sequence of three heads is posited that captures our generalizations in a simple and effective way.

scholarly journals EpicPCR 2.0: Technical and Methodological Improvement of a Cutting-Edge Single-Cell Genomic Approach

2021 ◽  
Vol 9 (8) ◽  
pp. 1649
Author(s):  
Véronica L. Roman ◽  
Christophe Merlin ◽  
Marko P. J. Virta ◽  
Xavier Bellanger
Keyword(s):  
Microbial Communities ◽  
Single Cell ◽  
Operational Taxonomic Unit ◽  
Rrna Gene ◽  
Environmental Matrices ◽  
Taxonomic Assignment ◽  
Integrative And Conjugative Elements ◽  
Functional Sequence ◽  
Methodological Improvement ◽  
New Gene

EpicPCR (Emulsion, Paired Isolation and Concatenation PCR) is a recent single-cell genomic method based on a fusion-PCR allowing us to link a functional sequence of interest to a 16S rRNA gene fragment and use the mass sequencing of the resulting amplicons for taxonomic assignment of the functional sequence-carrying bacteria. Although it is interesting because it presents the highest efficiency for assigning a bacterial host to a marker, epicPCR remains a complex multistage procedure with technical difficulties that may easily impair the approach depth and quality. Here, we described how to adapt epicPCR to new gene targets and environmental matrices while identifying the natural host range of SXT/R391 integrative and conjugative elements in water microbial communities from the Meurthe River (France). We notably show that adding a supplementary PCR step allowed us to increase the amplicon yield and thus the number of reads obtained after sequencing. A comparison of operational taxonomic unit (OTU) identification approaches when using biological and technical replicates demonstrated that, although OTUs can be validated when obtained from three out of three technical replicates, up to now, results obtained from two or three biological replicates give a similar and even a better confidence level in OTU identification, while allowing us to detect poorly represented SXT/R391 hosts in microbial communities.

scholarly journals Decomposing Complementizers

2018 ◽  
Author(s):  
Lena Baunaz
Keyword(s):  
Long Distance ◽  
Modern Greek ◽  
Functional Sequence ◽  
Relativized Minimality ◽  
Embedded Clauses

This chapter discusses the morphosyntax of French, Modern Greek, Serbo-Croatian, and Bulgarian complementizers equivalent to English that. From long-distance wh-extractions across complementizers in these languages, it is shown that (i) the morpheme complementizer is composed of features that are hierarchically ordered according to a functional sequence (fseq) (see Baunaz 2015, 2016a; Baunaz and Lander to appear); (ii) the complementizer morpheme lexicalizes structures of different sizes; (iii) the distribution of complementizers is governed by veridicality (see Baunaz 2015, 2016a); (iv) the complementizer morpheme is syntactically active. The basic template for complementizers that I argue for is F4 > F3 > F2 > F1. Evidence in favor of this template comes from crosslinguistic patterns of syncretism and featural Relativized Minimality (Starke 2001; Rizzi 2004; Haegeman 2010, among others). Evidence in favor of different realizations of the complementizer is provided by means of long-distance extractions across declarative embedded clauses.

scholarly journals Cigarette Smoking-Associated Isoform Switching and 3-prime UTR Lengthening Via Alternative Polyadenylation

2021 ◽  
Author(s):  
Zhonghui Xu ◽  
John Platig ◽  
Sool Lee ◽  
Adel Boueiz ◽  
Rob Chase ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Cigarette Smoking ◽  
Differential Expression ◽  
Alternative Polyadenylation ◽  
The United States ◽  
Biological Pathways ◽  
Differentially Expressed ◽  
Gtpase Activity ◽  
Functional Sequence ◽  
Sequence Elements

Cigarette smoking accounts for approximately one in five deaths in the United States. Previous genomic studies have primarily focused on gene level differential expression to identify related molecular signatures and pathways, but the genome-wide effects of smoking on alternative isoform regulation and posttranscriptional modulation have not yet been described. We conducted RNA sequencing (RNA-seq) in whole-blood samples of 454 current and 767 former smokers in COPDGene Study. We assessed the association of current smoking with differential expression of genes and isoforms and differential usage of isoforms and exons. At 10% FDR, we detected 3,167 differentially expressed genes, 2,014 differentially expressed isoforms, 945 differentially used isoforms and 160 differentially used exons. Genes containing differentially used isoforms were enriched in biological pathways involving GTPase activity and innate immunity. The majority of these genes were not differentially expressed, thus not identifiable from conventional differential gene expression analysis. Isoform switch analysis revealed for the first time widespread 3-prime UTR lengthening associated with cigarette smoking, where current smokers were found to have higher expression and usage of isoforms with markedly longer 3-prime UTRs. The lengthening of 3-prime UTRs appears to be mediated through alternative usage of distal polyadenylation sites, and these extended 3-prime UTR regions are significantly enriched with functional sequence elements including adenylate-uridylate (AU)-rich elements, microRNA and RNA-protein binding sites. Expression quantitative trait locus analyses on differentially used 3-prime UTRs identified 79 known GWAS variants associated with multiple smoking-related human diseases and traits. Smoking elicits widespread transcriptional and posttranscriptional alterations with disease implications. It induces alternative polyadenylation (APA) events resulting in a switch towards the usage of isoforms with strikingly longer 3-prime UTRs in genes related to multiple biological pathways including GTPase activity and innate immunity. The extended 3-prime UTR regions are enriched with functional sequence elements facilitating post-transcriptional regulation of protein expression and mRNA stability. These findings warrant further studies on APA events as potential biomarkers and novel therapeutic targets for smoking-related diseases.

scholarly journals Ecomorphological analysis of the astragalo-calcaneal complex in rodents and inferences of locomotor behaviours in extinct rodent species

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2393 ◽  
Author(s):  
Samuel Ginot ◽  
Lionel Hautier ◽  
Laurent Marivaux ◽  
Monique Vianey-Liaud
Keyword(s):  
Rodent Species ◽  
A Posteriori ◽  
Linear Discriminant ◽  
Extinct Species ◽  
Postcranial Morphology ◽  
Functional Sequence ◽  
Extant Species ◽  
Discriminant Analyses ◽  
Osteological Characters

Studies linking postcranial morphology with locomotion in mammals are common. However, such studies are mostly restricted to caviomorphs in rodents. We present here data from various families, belonging to the three main groups of rodents (Sciuroidea, Myodonta, and Ctenohystrica). The aim of this study is to define morphological indicators for the astragalus and calcaneus, which allow for inferences to be made about the locomotor behaviours in rodents. Several specimens were dissected and described to bridge the myology of the leg with the morphology of the bones of interest. Osteological characters were described, compared, mechanically interpreted, and correlated with a “functional sequence” comprising six categories linked to the lifestyle and locomotion (jumping, cursorial, generalist, fossorial, climber and semi-aquatic). Some character states are typical of some of these categories, especially arboreal climbers, fossorial and “cursorial-jumping” taxa. Such reliable characters might be used to infer locomotor behaviours in extinct species. Linear discriminant analyses (LDAs) were used on a wider sample of species and show that astragalar and calcaneal characters can be used to discriminate the categories among extant species whereasa posterioriinferences on extinct species should be examined with caution.

scholarly journals Directed Evolution Reveals the Functional Sequence Space of an Adenylation Domain Specificity Code

2019 ◽  
Vol 14 (9) ◽  
pp. 2044-2054 ◽  
Author(s):  
Kurt Throckmorton ◽  
Vladimir Vinnik ◽  
Ratul Chowdhury ◽  
Taylor Cook ◽  
Marc G. Chevrette ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Sequence Space ◽  
Domain Specificity ◽  
Adenylation Domain ◽  
Functional Sequence
Sign in / Sign up

Export Citation Format

Share Document