Segmental Identity Research Articles

Investigating the universality of consonant and vowel co-occurrence restrictions

Certain phonotactic constraints on the co-occurrence of segments appear to be much more common across the world’s languages than others. In many languages, similar consonant co-occurrence is restricted through Obligatory Contour Principle (OCP) effects, while there are some exceptions for identical consonants. In vowels, the opposite pattern appears to hold: many languages have vowel harmony processes, where vowels within a domain are required to share some feature. Languages that encourage similar consonant co-occurrence or restrict similar vowel co-occurrence appear to be exceedingly uncommon. However, evidence of this pattern so far only comes from studies of individual languages or families, or of only consonants or vowels. We investigate patterns of co-occurrence in vowels and consonants in 107 Northern Eurasian languages across 21 families using Bayesian negative binomial regression to explicitly model the effects of aggregate similarity and segment identity on co-occurrence counts (the results of which can be interpreted similarly to observed/expected ratios). We find that the effect of similarity is remarkably consistent across languages: Similar consonant co-occurrence is disfavored, while aggregate similarity has no effect on vowel co-occurrence. Identical segment co-occurrence effects are much more variable across languages, with a tendency towards disfavoring identical consonants, and favoring identical vowels. We also find larger effects in consonants than in vowels, suggesting that consonant co-occurrence is more strongly constrained than vowel co-occurrence. We also find that there is no evidence for or against any correlations between vowel and consonant co-occurrence, suggesting that more data is needed to evaluate this possibility.

CRISPR/Cas9-mediated knockout of the abdominal-B homeotic gene in the global pest, fall armyworm (Spodoptera frugiperda).

The Homeotic complex (Hox) genes play a crucial role in determining segment identity and appendage morphology in bilaterian animals along the antero-posterior axis. Recent studies have expanded to agricultural pests such as fall armyworm (FAW), scientifically known as Spodoptera frugiperda J. E. Smith (Lepidoptera: Noctuidae), which significantly threatens global agricultural productivity. However, the specific role of the hox gene Sfabd-B in FAW remains unexplored. This research investigates the spatial and temporal expression patterns of Sfabd-B in various tissues at different developmental stages using quantitative real-time polymerase chain reaction (qRT-PCR). Additionally, we explored the potential function of the Sfabd-B gene located in the FAW genome using CRISPR/Cas9 technology. The larval mutant phenotypes can be classified into three subgroups as compared with wild-type individuals, that is, an excess of pedis in the posterior abdomen, deficient pedis due to segmental fusion and deviations in the posterior abdominal segments. Importantly, significant differences in mutant phenotypes between male and female individuals were also evident during the pupal and adult phases. Notably, both the decapentaplegic (dpp) and cuticular protein 12 (cp 12) genes displayed a substantial marked decrease in expression levels in the copulatory organ of male mutants and the ovipositor of female mutants compared with the wild type. These findings highlight the importance of Sfabd-B in genital tract patterning, providing a potential target for improving genetic control.

Suppletion of numerals ‘one’ and ‘two’ in Mandarin Chinese

In many languages numerals may appear in different forms depending on the context, which Greenberg (1978) called the contextual and absolute forms respectively. Greenberg made the universal generalization that if a numeral has two forms, then all the lower numerals also do. He then mentioned Mandarin Chinese as an exception because while its numeral ‘2’ has two forms, he thinks that the lower numeral ‘1’ doesn’t. This paper argues for a different view about Mandarin ‘1’–that is, ‘1’ actually has two forms just like ‘2’, despite their segmental identity. Then I argue that the two forms of ‘1’ and ‘2’ are not distinguished by use as Greenberg claimed for ‘2’, but rather by the morphophonological context: the contextual form appears when followed by overt material at the point of vocabulary insertion of the numeral, otherwise the absolute form appears. This generalization, together with the key assumption that vocabulary insertion proceeds bottom-up, leads to a particular structure for enumerating numerals like liǎng gè nv̌hái ‘two girls’, where the Cardinal head liǎng ‘two’ takes the Classifier Phrase gè nv̌hái as its complement. This paper also provides novel evidence suggesting that in Mandarin a complex enumerating numeral like ‘125 pears’ merges the complex cardinal phrase ‘125’ with the Classifier Phrase, supporting He (2015) and challenging Ionin & Matushansky (2016, 2018).

A chromatin code for limb segment identity in axolotl limb regeneration

The salamander limb correctly regenerates missing limb segments because connective tissue cells have segment-specific identities, termed "positional information". How positional information is molecularly encoded at the chromatin level has been unknown. Here, we performed genome-wide chromatin profiling in mature and regenerating axolotl limb connective tissue cells. We find segment-specific levels of histone H3K27me3 as the major positional mark, especially at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. In the hand, the permissive chromatin state of the homeoprotein gene HoxA13 engages with the regeneration program bypassing the upper limb program. Comparison of regeneration regulatory elements with those found in other regenerative animals identified a core shared set of transcription factors, supporting an ancient, conserved regeneration program.

Prolonging somatic cell proliferation through constitutive hox gene expression in C. elegans

hox genes encode a conserved family of homeodomain transcription factors that are essential to determine the identity of body segments during embryogenesis and maintain adult somatic stem cells competent to regenerate organs. In contrast to higher organisms, somatic cells in C. elegans irreversibly exit the cell cycle after completing their cell lineage and the adult soma cannot regenerate. Here, we show that hox gene expression levels in C. elegans determine the temporal competence of somatic cells to proliferate. Down-regulation of the central hox gene lin-39 in dividing vulval cells results in their premature cell cycle exit, whereas constitutive lin-39 expression causes precocious Pn.p cell and sex myoblast divisions and prolongs the proliferative phase of the vulval cells past their normal point of arrest. Furthermore, ectopic expression of hox genes in the quiescent anchor cell re-activates the cell cycle and induces proliferation until young adulthood. Thus, constitutive expression of a single hox transcription factor is sufficient to prolong somatic cell proliferation beyond the restriction imposed by the cell lineage. The down-regulation of hox gene expression in most somatic cells at the end of larval development may be one cause for the absence of cell proliferation in adult C. elegans.

Maltese as a merger of two worlds: A cross-language approach to phonotactic classification.

Maltese is a prime example of a language that emerged through extensive language contact, joining the two linguistic worlds of Semitic and Italo-Romance languages. Previous studies have shown this shared origin on the basis of hands-on comparative methods. However, such approaches may be biased by the researchers perspective and the selected material. To avoid this bias, we employed a naive computational method that classifies words on the basis of their phonotactics. Specifically, we trained a simple two-layer neural network on Tunisian and Italian nouns, i.e. the languages that Maltese emerged from. We used the trained network to classify Maltese nouns based on their phonotactic characteristics as either of Tunisian or of Italian origin. Overall, the network is capable of correctly classifying Maltese nouns as belonging to either of the original languages. Moreover, we find that the classification depends on whether a noun has a sound or broken plural. By manipulating the segment identity in the training input, we found that consonants are more important for the classification of Maltese nouns than vowels. While our results replicate previous comparative studies, they also demonstrate that a more fine grained classification of a language's origin can be based on individual words and morphological classes.

The Drosophila Fab-7 boundary modulates Abd-B gene activity by guiding an inversion of collinear chromatin organization and alternate promoter use

Hox genes encode transcription factors that specify segmental identities along the anteroposterior body axis. These genes are organized in clusters, where their order corresponds to their activity along the body axis, a feature known as collinearity. In Drosophila, the BX-C cluster contains the three most posterior Hox genes, where their collinear activation incorporates progressive changes in histone modifications, chromatin architecture, and use of boundary elements and cis-regulatory regions. To dissect functional hierarchies, we compare chromatin organization in cell lines and larvae, with a focus on the Abd-B gene. Our work establishes the importance of the Fab-7 boundary for insulation between 3D domains carrying different histone modifications. Interestingly, we detect a non-canonical inversion of collinear chromatin dynamics at Abd-B, with the domain of active histone modifications progressively decreasing in size. This dynamic chromatin organization differentially activates the alternative promoters of the Abd-B gene, thereby expanding the possibilities for fine-tuning of transcriptional output.

A viral metagenomic protocol for nanopore sequencing of group A rotavirus

AimDevelopment of an unbiased methodology using Oxford Nanopore Technology (ONT) sequencing to obtain whole-genome sequences (WGS) of Rotavirus A (RVA) from clinical samples. Methods157 RVA qRT-PCR positive faecal samples were enriched by virus-like particle (VLP) purification and host nuclease digestion to enhance the detection of viral nucleic acids and cDNA generated as per the NetoVIR protocol. ONT sequencing was then performed using the ONT Native Barcoding kit (SQK-LSK-109) on the GridION platform. Data was basecalled, demultiplexed and assembled into near complete RVA genomes. The accuracy and quality of the obtained sequences was assessed by comparing to Sanger sequencing and RVA reference genomes. ResultsThe developed protocol generated 146 near-complete RVA WGS out of the 157 RVA-positive clinical samples. The quality of the assembled genomes was assessed by comparison against publicly-available sequences with results showing 98.76 % ± 0.03 % similarity and > 90 % genome coverage. A concordance assessment was performed comparing the identity of partial RVA VP7 and VP4 segments obtained by Sanger sequencing (n = 51) against corresponding nanopore sequences which demonstrated an overall identity of 100.0 % ± 0.02 %. ConclusionsThe nanopore protocol generated both high quality and accurate RVA WGS extracted from faecal samples. This protocol can be extended to other viral agents in other sample types.

An Identity Preference in Ngbaka Vowels

In a large Ngbaka dictionary (Henrix et al. 2015), segmental identity between vowels is systematically overrepresented: cases of identity like [kɔkɔ] 'to cover oneself' and [ɓɛnɛ] 'to consult an oracle' occur significantly more often than predicted by the frequencies of the individual vowels alone. I show that the best-fit statistical model of the lexical data includes a predictor for identity: non-identical vowels are dispreferred. The implication of this finding is that the phonological grammar must be able to reference identity directly (following MacEachern 1999, Coetzee & Pater 2008, Gallagher & Coon 2009, Gallagher 2013, 2014, a.o.).

Harmonic Gradience in Greek Rap Rhymes

This study investigates the gradience in mismatch acceptability in Greek rap Imperfect Rhyme. We consider that the rhyme domains of a rhyming pair are in a Base-Reduplicant correspondence relationship, requiring segmental identity in Place of Articulation, Manner of Articulation and voicing, and manifesting a gradient acceptability of featural mismatches. Analysis shows that voicing mismatches are highly marked in Greek rap rhyme, implying a high perceptual salience, which seems to be language-specific. Mismatches only in Place of Articulation seem to be the most harmonic and frequent mismatch pattern, while Harmony and similarity decrease in inverse proportion to the number of mismatching features. Mismatches in Greek rap rhyme are, in principle, accepted between unmarked corresponding consonants. Obstruents, mainly Stops mismatch in Place of Articulation, and Coronals mismatch in Manner of Articulation. In general, mainly Coronal Obstruents and, to a lesser extent, Nasals are involved in mismatches. Due to the attested high avoidance of voicing mismatches, which are acoustically non-salient, we propose that, in Standard Modern Greek, perceptual salience is not purely phonetic, as it seems to be also based on the language-specific phonological grammar.

Expression of Abdominal-B in the brine shrimp, Artemia franciscana, expands our evolutionary understanding of the crustacean abdomen

The brine shrimp, Artemia franciscana, has a body plan composed of 11 thoracic segments, followed by 2 genital segments, and then 6 additional abdominal segments. Previous studies of Artemia reported that expression of the posterior-most Hox gene, Abdominal-B (Abd-B), is restricted to the genital segments and is not observed posteriorly in the abdomen at any developmental stage. This report was remarkable because it suggested that the Artemia abdomen posterior to the genital segments was a novel body region of 6 segments that bore no homology to any region in other crustaceans and was unique amongst arthropods in being a Hox-free segmented domain outside of the head. In this study, we used RT-PCR, antibody staining, and in situ hybridization on various stages of Artemia nauplii to show that Abd-B mRNA and protein are in fact expressed throughout the abdominal segments during Artemia development, but this expression later retracts to the two genital segments (G1, G2) and the T11 appendages. This suggests that Abd-B does play a role in specifying abdominal segment identity in all crustaceans that have been examined and suggests a common evolutionary origin for the crustacean abdomen.

Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus

Oribatid mites are a specious order of microarthropods within the Chelicerata, compromising about 11,000 described species. They are ubiquitously distributed across different microhabitats in all terrestrial ecosystems around the world and were among the first animals colonizing terrestrial habitats as decomposers and scavengers. Despite their species richness and ecological importance genomic resources are lacking for oribatids. Here, we present a 143-Mb chromosome-level genome assembly of the clonal, all-female oribatid mite species Archegozetes longisetosus Aoki, a model species used by numerous laboratories for the past 30 years. Comparative genomic and transcriptional analyses revealed patterns of reduced body segmentation and loss of the segmental identity gene abd-A within Acariformes, and unexpected expression of key eye development genes in these eyeless mites across developmental stages. Consistent with their soil dwelling lifestyle, investigation of sensory genes revealed a species-specific expansion of gustatory receptors, and evidence of horizontally transferred genes related to cell wall degradation of plant and fungal matter, both components of Archegozetes’ diet. Oribatid mites are also noted for their biosynthesis capacities and biochemical diversity. Using biochemical and genomic data, we were able to delineate the backbone biosynthesis of monoterpenes, an important class of compounds found in the major exocrine gland system of Oribatida – the oil glands. Given the mite’s strength as an experimental model, the new high-quality resources provided here will serve as the foundation for molecular research in Oribatida and will enable a broader understanding of chelicerate evolution.

The Hox gene Abdominal-B regulates the appendage development during the embryogenesis of scorpionflies.

The Homeotic Complex (Hox) genes encode conserved homeodomain transcription factors that specify segment identity and appendage morphology along the antero-posterior axis in bilaterian animals. The Hox gene Abdominal-B (Abd-B) is mainly expressed in the posterior segments of the abdomen and plays an important role in insect organogenesis. In Mecoptera, the potential function of this gene remains unclear yet. Here, we performed a de novo transcriptome assembly and identified an Abd-B ortholog in the scorpionfly Panorpa liui. Quantitative real-time reverse transcription PCR showed that Abd-B expression increased gradually in embryos 76 h post oviposition, and was mainly present in the more posterior abdominal segments. Embryonic RNA interference of Abd-B resulted in a set of abnormalities, including developmental arrest, malformed suckers and misspecification of posterior segment identity. These results suggest that Abd-B is required for the proper development of the posterior abdomen. Furthermore, in Abd-B RNAi embryos, the expression of the appendage marker Distal-less (Dll) was up-regulated and was additionally present on abdominal segments IX and X compared with wild embryos, suggesting that scorpionfly Abd-B may act to suppress proleg development and has gained the ability to repress Dll expression on the more posterior abdominal segments. This study provides additional information on both the functional and evolutionary roles of Abd-B across different insects.

How body patterning might have worked in the evolution of arthropods-Acase study of the mystacocarid Derocheilocaris remanei (Crustacea, Oligostraca).

Body organization within arthropods is enormously diverse, but a fusion of segments into "functional groups" (tagmatization) is found in all species. Within Tetraconata/Pancrustacea, an anterior head, a locomotory thorax region, and a posterior, mostly limbless tagma known as the abdomen is present. The posterior-most tagma in crustaceans is frequently confused with the malacostracan, for example,decapod pleon often misleadingly termed abdomen, however, its evolutionary and developmental origin continues to pose a riddle, especially the completely limbless abdomen of the "entomostracan morphotype" (e.g., fairy shrimps). Since the discovery of Hox genes and their involvement in specifying the morphology or identity of segments, tagmata, or regions along the anteroposterior axis of an organism, only a few studies have focused on model organisms representing the "entomostracan morphotype" and used a variety of dedicated Hox genes and their transcription products to shine light on abdomen formation. The homeotic genes or the molecular processes that determine the identity of the entomostracan abdomen remain unknown to date.This study focuses on the "entomostracan morphotype" representative Derocheilocaris remanei (Mystacocarida). We present a complete overview of development throughout larval stages and investigate homeotic gene expression data using the antibody FP6.87 that binds specifically to epitopes of Ultrabithorax/Abdominal-A proteins.Our results suggest that the abdomen in Mystacocarida is bipartite (abdomen I + abdomen II). We suggest that the limbless abdomen is an evolutionary novelty that evolved several times independently within crustaceans and which might be the result of a progressive reduction of former thoracic segments into abdominal segments.

Serial Homology and Segment Identity in the Arthropod Head.

SynopsisThe anterior-most unit of the crown-group arthropod body plan includes three segments, the pre-gnathal segments, that contain three neuromeres that together comprise the brain. Recent work on the development of this anterior region has shown that its three units exhibit many developmental differences to the more posterior segments, to the extent that they should not be considered serial homologs. Building on this revised understanding of the development of the pre-gnathal segments, we suggest a novel scenario for arthropod head evolution. We posit an expansion of an ancestral single-segmented head at the transition from Radiodonta to Deuteropoda in the arthropod stem group. The expanded head subdivided into three segmental units, each maintaining some of the structures of the ancestral head. This scenario is consistent with what we know of head evolution from the fossil record and helps reconcile some of the debates about early arthropod evolution.

Segmentation of collaborative consumption consumers: Social identity theory perspective

AbstractThe aim of this study is to show how consumers' pursuit of social identity drives collaborative consumption. A survey conducted among active participants in various forms of collaborative consumption found four types of users with clearly distinguishable characteristics: Social Followers, Distrustful Prosumers, Doubtful Laggards and Traditional Spenders. We use social identity theory to explain why those users who engage in collaborative consumption because of sociability and seeking excitement are also highly environmentally conscious (Social Followers), while very frugal users show the least trust towards what collaborative consumption has to offer (Distrustful Prosumers). We observe favourable social identity for collaborative consumption in the Social Followers segment and unfavourable social identity in the Doubtful Laggards segment. Our findings suggest that social identity plays an important role in forming consumers’ intentions to participate in collaborative consumption. At the general level of collaborative consumption, our study confirms previous findings that social values outweigh environmental and economic values. However, this study contributes to the discussion and closes the research gap by explaining that each component may predominate depending on the type of collaborative consumption user.

Identification of Hox genes and their expression profiles during embryonic development of the emerging model organism, Macrobrachium olfersii.

Hox genes encode transcription factors that specify the body segment identity during development, including crustaceans, such as amphipods and decapods, that possess a remarkable diversity of segments and specialized appendages. In amphipods, alterations of specialized appendages have been obtained using knockout experiment of Hox genes, which suggests that these genes are involved in the evolution of morphology within crustaceans. However, studies of Hox genes in crustaceans have been limited to a few species. Here, we identified the homeodomain of nine Hox genes: labial (lab), proboscipedia (pb), Deformed (Dfd), Sex combs reduced (Scr), fushi tarazu (ftz), Antennapedia (Antp), Ultrabithorax (Ubx), abdominal-A (abdA), and Abdominal-B (AbdB), and evaluated their expression by RT-qPCR and RT-PCR in the ovary, during embryonic development, and at the first larval stage (Zoea I) of the decapod Macrobrachium olfersii. The transcript levels of lab, Dfd, and ftz decreased and transcripts of pb, Scr, Antp, Ubx, abdA, and AbdB increased during embryonic development. Hox genes were expressed in mature ovaries and Zoea I larval stages, except Scr and ftz, respectively. In addition, isoforms of Dfd, Scr, Ubx, and abdA, which have been scarcely reported in crustaceans, were described. New partial sequences of 87 Hox genes from other crustaceans were identified from the GenBank database. Our results are interesting for future studies to determine the specific function of Hox genes and their isoforms in the freshwater prawn M. olfersii and to contribute to the understanding of the diversity and evolution of body plans and appendages in Crustaceans.

UV-C radiation-induced changes in the legs and trichoid sensilla of the red flour beetle Tribolium castaneum Herbst (Coleoptera: Tenebrionidae)

Since various kind of receptors in insects are mainly located on their legs. We estimate the influence of ultraviolet-C on the leg morphology and trichoid sensilla of Tribolium castaneum (Herbst, 1797) (Coleoptera: Tenebrionidae), zero-day-old pupae were irradiated with UV-C at a distance of 35 cm for 1, 2, 4, 8, 16, 32, and 64 min. Changes in leg morphologies and trichoid sensilla were determined using light and scanning electron microscopes. UV-C radiation caused the abnormalities of an adult’s legs that were classified into three levels; mild, moderate, and strong. Legs of the resulting adults were developed into malformed structures that lacked clear segmental identity. The severity of leg abnormalities was recorded in a dose-dependent manner. UV-C significantly decreased the length and width of the femur, tibia, and tarsus. In the strongly affected level, the femur was reduced in size while the tibia and tarsus were completely deleted, and there was no evidence of claws. Scanning electron microscopy showed the wrinkled cuticle on the leg segment, and the sensilla of the resulting adults appeared less in number. After UV-C radiation, the trichoid sensilla on the femur became longer and wider, but the trichoid sensilla on the tibia were shorter and narrower. Taken together, UV-C irradiation during pupal stage interfered development of legs and brought about specific malformation features.

Identification and characterization of homeobox gene clusters in harpacticoid and calanoid copepods.

In this study, we have identified the entire complement of typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) in harpacticoid and calanoid copepods and compared them with the cyclopoid copepod Paracyclopina nana. The harpacticoid copepods Tigriopus japonicus and Tigriopus kingsejongensis have seven Hox genes (Lab, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and the Pb and Ftz genes are also present in the cyclopoid copepod P. nana. In the Hox gene cluster of the calanoid copepod Eurytemora affinis, all the Hox genes were present linearly in the genome but the Antp gene was duplicated. Of the three representative copepods, the P. nana Hox gene cluster was the most compact due to its small genome size. The Hox gene expression profile patterns in the three representative copepods were stage-specific. The Lab, Dfd, Scr, Pb, Ftz, and Hox3 genes showed a high expression in early developmental stages but Antp, Ubx, Abd-A, and Abd-B genes were mostly expressed in later developmental stages, implying that these Hox genes may be closely associated with the development of segment identity during early development.

Mechanisms Underlying Hox-Mediated Transcriptional Outcomes.

Metazoans differentially express multiple Hox transcription factors to specify diverse cell fates along the developing anterior-posterior axis. Two challenges arise when trying to understand how the Hox transcription factors regulate the required target genes for morphogenesis: First, how does each Hox factor differ from one another to accurately activate and repress target genes required for the formation of distinct segment and regional identities? Second, how can a Hox factor that is broadly expressed in many tissues within a segment impact the development of specific organs by regulating target genes in a cell type-specific manner? In this review, we highlight how recent genomic, interactome, and cis-regulatory studies are providing new insights into answering these two questions. Collectively, these studies suggest that Hox factors may differentially modify the chromatin of gene targets as well as utilize numerous interactions with additional co-activators, co-repressors, and sequence-specific transcription factors to achieve accurate segment and cell type-specific transcriptional outcomes.