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Frontiers in Molecular Neuroscience 2022Noncoding RNAs (ncRNAs) occupy ~98% of the transcriptome in human, and are usually not translated into proteins. Among ncRNAs, long non-coding RNAs (lncRNAs, >200...
Noncoding RNAs (ncRNAs) occupy ~98% of the transcriptome in human, and are usually not translated into proteins. Among ncRNAs, long non-coding RNAs (lncRNAs, >200 nucleotides) are important regulators to modulate gene expression, and are involved in many biological processes (e.g., cell development). To study lncRNA regulation, many computational approaches or tools have been proposed by using bulk transcriptomics data. Nevertheless, previous bulk data-driven methods are mostly limited to explore the lncRNA regulation regarding all of cells, instead of the lncRNA regulation specific to cell developmental stages. Fortunately, recent advance in single-cell sequencing data has provided a way to investigate cell developmental stage-specific lncRNA regulation. In this work, we present a novel computational method, CDSlncR (Cell Developmental Stage-specific lncRNA regulation), which combines putative lncRNA-target binding information with single-cell transcriptomics data to infer cell developmental stage-specific lncRNA regulation. For each cell developmental stage, CDSlncR constructs a cell developmental stage-specific lncRNA regulatory network in the cell developmental stage. To illustrate the effectiveness of CDSlncR, we apply CDSlncR into single-cell transcriptomics data of the developing human neocortex for exploring lncRNA regulation across different human neocortex developmental stages. Network analysis shows that the lncRNA regulation is unique in each developmental stage of human neocortex. As a case study, we also perform particular analysis on the cell developmental stage-specific lncRNA regulation related to 18 known lncRNA biomarkers in autism spectrum disorder. Finally, the comparison result indicates that CDSlncR is an effective method for predicting cell developmental stage-specific lncRNA targets. CDSlncR is available at https://github.com/linxi159/CDSlncR.
PubMed: 36710930
DOI: 10.3389/fnmol.2022.1037565 -
Antonie Van Leeuwenhoek Jan 2022Bacterial symbionts of insects have been shown to play important roles in host fitness. However, little is known about the bacterial community of Tessaratoma papillosa...
Bacterial symbionts of insects have been shown to play important roles in host fitness. However, little is known about the bacterial community of Tessaratoma papillosa which is one of the most destructive pests of the well-known fruits Litchi chinensis Sonn and Dimocarpus longan Lour in Oriental Region, especially in South-east Asia and adjacent areas. In this study, we surveyed the bacterial community diversity and dynamics of T. papillosa in all developmental stages with both culture-dependent and culture-independent methods by the third-generation sequencing technology. Five bacterial phyla were identified in seven developmental stages of T. papillosa. Proteobacteria was the dominant phylum and Pantoea was the dominant genus of T. papillosa. The results of alpha and beta diversity analyses showed that egg stage had the most complex bacterial community. Some of different developmental stages showed similarities, which were clustered into three phases: (1) egg stage, (2) early nymph stages (instars 1-3), and (3) late nymph stages (instars 4-5) and adult stage. Functional prediction indicated that the bacterial community played different roles in these three phases. Furthermore, 109 different bacterial strains were isolated and identified from various developmental stages. This study revealed the relationship between the symbiotic bacteria and the development of T. papillosa, and may thus contribute to the biological control techniques of T. papillosa in the future.
Topics: Animals; Bacteria; Fruit; Heteroptera; Litchi; Symbiosis
PubMed: 34843017
DOI: 10.1007/s10482-021-01685-6 -
Comparative Biochemistry and... Jun 2019Bradysia odoriphaga is a serious pest of the Chinese chive; however, detailed information regarding the developmental stage-specific gene expression patterns of B....
Bradysia odoriphaga is a serious pest of the Chinese chive; however, detailed information regarding the developmental stage-specific gene expression patterns of B. odoriphaga is not yet available. In this study, RNA sequencing (RNA-seq) was performed to determine the gene expression patterns of developmental stages including the eggs, second instar larvae, fourth instar larvae, pupae, and adults of B. odoriphaga. Analysis of 15 samples revealed an average of 89.56% of the clean reads could be mapped onto the assembled UniGene database. Cluster tree analysis showed that the expression patterns were stage-specific and that samples of the second and fourth instar larvae clustered in one group, while those of eggs, pupae, and adults clustered in another group. Differential expression unigenes (DEUs) for sequential developmental stages were between 3314 and 10,632. A total of 1910-7756 DEUs of sequential developmental stages were assigned into 45-56 gene ontology categories and 1165-3845 DEUs were mapped into Kyoto Encyclopedia of Genes and Genomes pathways. The expression of DEUs related to growth and development showed that hormone receptors highly expressed in the pupal stage, while chitinases were highly expressed in the larval stage. The results of quantitative real time polymerase chain reaction (qRT-PCR) and RNA-seq expression agreed well for 12 growth- and development-related unigenes. This study identified DEUs for sequential developmental stages of B. odoriphaga. Gene Ontology classifications and KEGG pathway identification of DEUs not only provide information useful for understanding insect growth and development but also for exploring novel approaches to control B. odoriphaga.
Topics: Animals; Diptera; Female; Gene Expression Profiling; Gene Expression Regulation, Developmental; Insect Proteins; Male; Sequence Analysis, RNA; Transcriptome
PubMed: 30776755
DOI: 10.1016/j.cbd.2019.02.003 -
Glycoconjugate Journal Dec 2017Cell surface glycans are tissue-specific and developmentally regulated. They function as essential modulators in cell-cell interactions, cell-extracellular matrix... (Review)
Review
Cell surface glycans are tissue-specific and developmentally regulated. They function as essential modulators in cell-cell interactions, cell-extracellular matrix interactions, and ligand-receptor interactions, binding to various ligands, including Wnt, fibroblast growth factors, and bone morphogenetic proteins. Embryonic stem (ES) cells, originally derived from the inner cell mass of blastocysts, have the essential characteristics of pluripotency and self-renewal. Recently, it has been proposed that mouse and human conventional ES cells are present in different developmental stages, namely pre-implantation blastocyst and post-implantation blastocyst stages, also called the naïve state and the primed state, respectively. They therefore require different extrinsic signals for the maintenance of self-renewal and pluripotency, and also appear to require different surface glycans. Understanding of molecular mechanisms involving glycans in self-renewal and pluripotency of ES cells is increasingly important for potential clinical applications, as well as for basic research. This review focuses on the roles of glycans in the two different states of pluripotent stem cells, namely the naïve state and the primed state, and the transition between these two states.
Topics: Animals; Cell Differentiation; Embryonic Stem Cells; Humans; Polysaccharides; Signal Transduction
PubMed: 27796614
DOI: 10.1007/s10719-016-9740-9 -
AORN Journal Feb 2023Pediatric patients do not undergo procedures exclusively at pediatric specialty facilities. Many perioperative nurses will care for a pediatric patient at some point in...
Pediatric patients do not undergo procedures exclusively at pediatric specialty facilities. Many perioperative nurses will care for a pediatric patient at some point in their career. Children and their caregivers often experience elevated levels of anxiety during the perioperative experience. Possessing knowledge of the child's age and developmental stage and using effective communication techniques can decrease this anxiety. This article presents insights into the stages of pediatric cognitive and psychosocial development and special pediatric health care considerations. Approaching and interacting with a child in a manner appropriate for their age and developmental stage can foster a more trusting nurse-child-caregiver relationship and reassure the caregiver that the perioperative team is providing their child with safe, high-quality care. Also included are five hypothetical case studies that illustrate effective communication styles and developmentally appropriate techniques that personnel can apply during the pediatric patient's perioperative experience.
Topics: Child; Humans; Patients; Anxiety; Caregivers
PubMed: 36705448
DOI: 10.1002/aorn.13863 -
Medical Image Analysis May 2021Spermatogenesis in mammals is a cyclic process of spermatogenic cell development in the seminiferous epithelium that can be subdivided into 12 subsequent stages....
Spermatogenesis in mammals is a cyclic process of spermatogenic cell development in the seminiferous epithelium that can be subdivided into 12 subsequent stages. Histological staging analysis of testis sections, specifically of seminiferous tubule cross-sections, is the only effective method to evaluate the quality of the spermatogenic process and to determine developmental defects leading to infertility. Such staging analysis, however, is tedious and time-consuming, and it may take a long time to become proficient. We now have developed a Computerized Staging system of Spermatogenesis (CSS) for mouse testis sections through learning of an expert with decades of experience in mouse testis staging. The development of the CSS system comprised three major parts: 1) Developing computational image analysis models for mouse testis sections; 2) Automated classification of each seminiferous tubule cross-section into three stage groups: Early Stages (ES: stages I-V), Middle Stages (MS: stages VI-VIII), and Late Stages (LS: stages IV-XII); 3) Automated classification of MS into distinct stages VI, VII-mVIII, and late VIII based on newly developed histomorphological features. A cohort of 40 H&E stained normal mouse testis sections was built according to three modules where 28 cross-sections were leveraged for developing tubule region segmentation, spermatogenic cells types and multi-concentric-layers segmentation models. The rest of 12 testis cross-sections, approximately 2314 tubules whose stages were manually annotated by two expert testis histologists, served as the basis for developing the CSS system. The CSS system's accuracy of mean and standard deviation (MSD) in identifying ES, MS, and LS were 0.93 ± 0.03, 0.94 ± 0.11, and 0.89 ± 0.05 and 0.85 ± 0.12, 0.88 ± 0.07, and 0.96 ± 0.04 for one with 5 years of experience, respectively. The CSS system's accuracy of MSD in identifying stages VI, VII-mVIII, and late VIII are 0.74 ± 0.03, 0.85 ± 0.04, and 0.78 ± 0.06 and 0.34 ± 0.18, 0.78 ± 0.16, and 0.44 ± 0.25 for one with 5 years of experience, respectively. In terms of time it takes to collect these data, it takes on average 3 hours for a histologist and 1.87 hours for the CSS system to finish evaluating an entire testis section (computed with a PC (I7-6800k 4.0 GHzwith 32GB of RAM & 256G SSD) and a Titan 1080Ti GPU). Therefore, the CSS system is more accurate and faster compared to a human histologist in staging, and further optimization and development will not only lead to a complete staging of all 12 stages of mouse spermatogenesis but also could aid in the future diagnosis of human infertility. Moreover, the top-ranking histomorphological features identified by the CSS classifier are consistent with the primary features used by histologists in discriminating stages VI, VII-mVIII, and late VIII.
Topics: Animals; Male; Mice; Seminiferous Epithelium; Seminiferous Tubules; Spermatogenesis; Testis
PubMed: 33676102
DOI: 10.1016/j.media.2020.101835 -
The Laryngoscope Oct 2020Congenital auricular anomalies are common. Additionally, the auricle plays an important role in the staging of human embryos. However, little is known about the...
OBJECTIVES/HYPOTHESIS
Congenital auricular anomalies are common. Additionally, the auricle plays an important role in the staging of human embryos. However, little is known about the embryological development of the auricle. The most commonly reproduced developmental theory by His (1885) describes six hillocks; three on the first and three on the second pharyngeal arch. The aim of this study was to assess the validity of this theory by modern techniques and to expand the knowledge of the embryological development and morphology of the auricle.
STUDY DESIGN
22 human embryos from the Carnegie collection between Carnegie stage 13 and 23 (28-60 days) were selected based on their histological quality.
METHODS
Histological sections of the selected embryos were examined. Three-dimensional (3D) reconstructions were prepared. Additionally, literature research was performed.
RESULTS
The hillocks were absent in most stages. Contrary to common knowledge, the auricle is almost entirely innervated by branches of the facial nerve. The branches of the trigeminal nerve only innervate the tragus and the anterior external auditory meatus (EAM). Consequently, this indicates that almost the entire auricle is derived from the second pharyngeal arch, with the exception of the tragus and the anterior EAM.
CONCLUSIONS
The 3D reconstructions show the anatomy and development of the auricle to be different from concepts presented in current textbooks. As a consequence, we propose that preauricular sinuses should be classified as first pharyngeal arch anomalies.
LEVEL OF EVIDENCE
NA Laryngoscope, 130:2467-2474, 2020.
Topics: Cadaver; Ear Auricle; Humans; In Vitro Techniques; Organogenesis
PubMed: 31825094
DOI: 10.1002/lary.28456 -
The Saudi Dental Journal Jan 2018The present study was designed to evaluate the efficacy of using the developmental stages of the canines and third molars to predict the timing of skeletal maturity in...
AIMS
The present study was designed to evaluate the efficacy of using the developmental stages of the canines and third molars to predict the timing of skeletal maturity in the Saudi population.
MATERIAL AND METHODS
The lateral cephalometric radiographs and orthopantograms of 239 Saudi patients, 106 males and 133 females, aged 9 to 21 years, were collected from several dental centers. Orthopantograms were used to assess the developmental stages of the upper and lower canine teeth and third molars using two popular methods: that of Nolla and that of Demirjian. Cervical vertebral maturation (CVM) stage was assessed on the lateral cephalometric images according to the method of Baccetti et al. Trained observers with no knowledge of patient age or gender performed assessments. Data were analyzed with Spearman's rank correlation coefficient at a significance level of ≤ .05.
RESULT
Skeletal CVM stages III and IV had a stronger correlation with mandibular left canine developmental stage than with maxillary canine developmental stage in the two methods used (correlation with Nolla stage 10 and Demirjian stage H: root completely formed with apex closed), especially for male patients (r = 0.700, < .001). In contrast, the maxillary third molars at Nolla stages 5 and 7 (crown completed to 1/3 of the root formed) showed an association with CVM stages III and IV (r = 0.540 for females and r = 0.639 for males, ≤ .001 for both and with Demirjian stages D, E, and F. Males had slightly higher correlation values than females (r = 0.578 and 0.5010, respectively; ≤ .001) at CVM stages III and IV. Interestingly, canine teeth showed a stronger correlation than third molars with skeletal maturation in Saudi children.
CONCLUSION
Dental developmental stages were highly correlated with CVM stages III and IV among Saudi subjects.
PubMed: 30166875
DOI: 10.1016/j.sdentj.2017.11.003 -
Genes Feb 2020Two genes, and , both encoding indole-3-glycerol phosphate lyase (IGL), are believed to control the conversion of indole-3-glycerol phosphate (IGP) to indole. The first...
Two genes, and , both encoding indole-3-glycerol phosphate lyase (IGL), are believed to control the conversion of indole-3-glycerol phosphate (IGP) to indole. The first of these has generally been supposed to be regulated developmentally, being expressed at early stages of plant development with the indole being used in the benzoxazinoid (BX) biosynthesis pathway. In contrast, it has been proposed that the second one is regulated by stresses and that the associated free indole is secreted as a volatile. However, our previous results contradicted this. In the present study, we show that the gene takes over the role of at later developmental stages, between the 42nd and 70th days after germination. In the majority of plants with silenced expression, was either expressed at a significantly higher level than or it was the only gene with detectable expression. Therefore, we postulate that the synthesis of indole used in BX biosynthesis in rye is controlled by both and , which are both regulated developmentally and by stresses. In silico and in vivo analyses of the promoter sequences further confirmed our hypothesis that the roles and modes of regulation of the and genes are similar.
Topics: Benzoxazines; Biosynthetic Pathways; Gene Expression Regulation, Plant; Genes, Plant; Germination; Glycerophosphates; Indoles; Lyases; Plant Proteins; Promoter Regions, Genetic; Secale
PubMed: 32093268
DOI: 10.3390/genes11020223 -
Philosophical Transactions of the Royal... Mar 2023Viruses are obligate pathogens that entirely rely on their hosts to complete their infectious cycle. The outcome of viral infections depends on the status of the host....
Viruses are obligate pathogens that entirely rely on their hosts to complete their infectious cycle. The outcome of viral infections depends on the status of the host. Host developmental stage is an important but sometimes overlooked factor impacting host-virus interactions. This impact is especially relevant in a context where climate change and human activities are altering plant development. To better understand how different host developmental stages shape virus evolution, we experimentally evolved turnip mosaic virus (TuMV) on at three different developmental stages: vegetative (juvenile), bolting (transition) and reproductive (mature). After infecting plants with an -naive or an -well-adapted TuMV isolate, we observed that hosts in later developmental stages were prone to faster and more severe infections. This observation was extended to viruses belonging to different genera. Thereafter, we experimentally evolved lineages of the naive and the well-adapted TuMV isolates in plants from each of the three developmental stages. All evolved viruses enhanced their infection traits, but this increase was more intense in viruses evolved in younger hosts. The genomic changes of the evolved viral lineages revealed mutation patterns that strongly depended on the founder viral isolate as well as on the developmental stage of the host wherein the lineages were evolved. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.
Topics: Humans; Arabidopsis; RNA, Plant; Potyvirus; Plant Viruses; Plant Diseases
PubMed: 36744567
DOI: 10.1098/rstb.2022.0005