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406 results for “amniotes”
Electronic supporting information for: Evolution of posture in amniotes–diving into the trabecular architecture of the femoral head
<p>Extant amniotes show remarkable postural diversity. Broadly speaking, limbs with erect (strongly adducted, more vertically oriented) posture are found in mammals that are particularly heavy (graviportal) or show good running skills (cursorial), while crouched (highly flexed) limbs are found in taxa with more generalized locomotion. In Reptilia, crocodylians have a "semi-erect" (somewhat adducted) posture, birds have more crouched limbs and lepidosaurs have sprawling (well-abducted) limbs. Both synapsids and reptiles underwent a postural transition from sprawling to more erect limbs during the Mesozoic Era. In Reptilia, this postural change is prominent among archosauriforms in the Triassic Period. However, limb posture in many key Triassic taxa remains poorly known. In Synapsida, the chronology of this transition is less clear, and competing hypotheses exist. On land, the limb bones are subject to various stresses related to body support that partly shape their external and internal morphology. Indeed, bone trabeculae (lattice-like bony struts that form the spongy bone tissue) tend to orient themselves along lines of force. Here, we study the link between femoral posture and the femoral trabecular architecture using phylogenetic generalized least squares. We show that microanatomical parameters measured on bone cubes extracted from the femoral head of a sample of amniote femora depend strongly on body mass, but not on femoral posture or lifestyle. We reconstruct ancestral states of femoral posture and various microanatomical parameters to study the "sprawling-to-erect" transition in reptiles and synapsids, and obtain conflicting results. We tentatively infer femoral posture in several hypothetical ancestors using phylogenetic flexible discriminant analysis from maximum likelihood estimates of the microanatomical parameters. In general, the trabecular network of the femoral head is not a good indicator of femoral posture. However, ancestral state reconstruction methods hold great promise for advancing our understanding of the evolution of posture in amniotes.</p>
Gene expression counts from amniotic fluid cells
<p><strong>File description:</strong></p> <ol> <li> <p>Gene-level counts using the gtf file from the release 29 of GENCODE <a href="https://www.gencodegenes.org/human/release_29">https://www.gencodegenes.org/human/release_29</a></p> </li> <li> <p>Split counts spanning from one exon to another using an annotation-free algorithm, therefore capturing new splice sites</p> </li> <li> <p>Non-split counts covering exon-intron boundaries</p> </li> <li> <p>Sample annotation describing each sample from the dataset</p> </li> <li> <p>Description file with global information from the dataset</p> </li> </ol> <p><strong>Use: </strong>The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired end specifications match. Afterwards, the DROP pipeline can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>).</p> <p><strong>Maintainer: </strong>Vicente A. Yépez, <a href="mailto:yepez@in.tum.de">yepez@in.tum.de</a></p> <p><strong>Title:</strong> Gene expression and splicing counts from amniotic fluid cells<br> <strong>Number of samples:</strong> 56<br> <strong>Tissue:</strong> Amniotic fluid cells<br> <strong>Organism:</strong> Homo sapiens<br> <strong>Genome assembly:</strong> hg19<br> <strong>Gene annotation:</strong> gencode29<br> <strong>Disease ICD-10</strong>: Q89: F2100984A and F2100985, Q23: F1901567 and Q74: F2000845<br> <strong>Strand specific</strong>: False<br> <strong>Paired end</strong>: True<br> <strong>Cite as</strong>: Cite both the resource using Zenodo's citation and the publication under References<br> <strong>Dataset contact</strong>: Brian Chung bhychung@hku.hk<br> <strong>Comments</strong>: A total of 56 RNA-seq samples were used for running pipeline. Out of those, 52 samples were included in the manuscript.</p>
Inference-of-the-genes-in-the-ancestor-of-amniotes-and-the-genomic-basis-for-the-origin-of-the-egg
<p><strong>Inference of the genes in the ancestor of amniotes and the genomic basis for the origin of the egg</strong></p> <p>Amniotes are the first fully terrestrial vertebrate animals with several evolutionary innovations in their common ancestor that allowed them to become fully independent of the aquatic environment, including a more complex egg with shell and additional structures. During evolution, organisms’ form and functions evolve, and so do their genomes, which are the ultimately responsible for the observed changes. In fact, genomes are evolutionarily labile and experience changes in gene content and structure. This project aims to investigate the genomic basis for the origin of amniotes and their evolutionary innovations. From a bioinformatic point of view, this work involves: (i). choosing the highest quality vertebrate genomes to use in our analysis; (ii). estimating the genes that originated in the common ancestor of reptiles, birds and mammals by searching for sequence similarity and clustering of homologous genes; (iii). functionally characterizing the novel genes that originated in the common ancestor of amniotes and identifying any relationship with the origin of the amniote egg.</p> <p> </p> <p>Structure followed of the data published:</p> <p>-Selection_Of_Species</p> <p> *Genomes.tar.gz</p> <p> *all_proteomes_db.tar.gz</p> <p>-Phylogenetic_Aware_Parsing_Script</p> <p> *Searching_Protein_Sequence_Similarities_With_DIAMOND</p> <p> +all_blastp_output.tar.gz</p> <p> *Gene_Clustering_In_HGs_With_MCL</p> <p> +mcxdeblast_all_blastp_output.tar.gz</p> <p> +mcl_all_blastp_output.tar.gz</p> <p> *Preparation_Of_PAPS_and_Inferring_Ancestral_And_Novel_Genes</p> <p> +Ancestral_Novel_HGs.tar.gz</p> <p>-Removal_Of_False_Positives</p> <p> *Amniota_novel_seq.fa.tar.gz</p> <p>-Annotation_With_GO_terms.tar.gz</p> <p> </p>
microRNA profiling of amniotic fluid samples from CAKUT fetuses
<p><strong>Summary</strong></p> <p>Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) is the leading cause of childhood end-stage renal disease and a significant cause of chronic kidney disease in adults. Genetic and environmental factors have been shown to influence CAKUT development, but the known disease mechanism remains incomplete. Our goal is to identify affected pathways and networks in CAKUT through multi-omics analysis, including miRNome, peptidome and proteome data. The peptidome and proteome data of the corresponding samples were previously published [pmid: 32750455, pmid: 33987838].</p> <p><strong>Study design</strong></p> <p>Amniotic fluid samples were collected in a prospective multicenter observational study focusing on fetal bilateral CAKUT as part of a <a title="clinical trial" href="https://clinicaltrials.gov/ct2/show/NCT02675686">clinical trial</a>. In addition, 21 samples were collected from non-CAKUT individuals. The severity was defined based on the renal status after 2 years of postnatal clinical follow-up.</p> <p>The total RNA was isolated using the Agilent RNA 6000 Pico kit protocol (5067-1513) and microRNAs were profiled using Agilent microRNA slides (Sanger miRBase release 21). The samples were labelled and hybridized according to the Agilent's microRNA Complete Labeling and Hybridization Kit protocol (5190-0456), followed by Spike-ins with the Agilent's microRNA Spike-In Kit protocol (5190-1934) and analyzed using Aligent's High-Resolution Microarray Scanner GS2505_C. Features were called using the Agilent Feature Extraction software (version 11.0.1.1) and sample intensities were normalized using quantile normalization (RMA).</p>
Determination of Abnormal Fetal Growth or Amniotic Fluid With Third Trimester Ultrasounds in Uncomplicated Pregnancies: A Randomized Trial
ClinicalTrials.gov study NCT02702999. IPD Sharing: NO. Countries: 1. Publications: 1.
Safety and Feasibility of Amniotic Fluid as a Treatment for COVID-19 Patients
ClinicalTrials.gov study NCT04497389. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Coupling and uncoupling of midline morphogenesis and cell flow in amniote gastrulation
Open the record for dataset details and reuse information.
Data from: Phylogenetic paradigm shifts in early amniote evolution
Open the record for dataset details and reuse information.
Electronic supporting information for: Evolution of posture in amniotes–diving into the trabecular architecture of the femoral head
Open the record for dataset details and reuse information.
The limits of convergence: the roles of phylogeny and dietary ecology in shaping non-avian amniote skulls
Cranial morphology is remarkably varied in living amniotes, ranging from short-faced mammals to the elongate snouts of crocodylians. This diversity of shapes is thought to correspond with feeding ecology, a relationship repeatedly demonstrated at smaller phylogenetic scales, but one that remains untested across amniote phylogeny. Using a combination of 2D geometric and linear morphometrics, we investigate the links between phylogenetic relationships, diet, and skull shape in an expansive dataset of extant amniotes with teeth: mammals, lepidosaurs, and crocodylians. We find that both phylogeny and diet have statistically significant effects on skull shape, although these effects differ depending on the dataset analyzed. The three major clades largely partition morphospace, each plotting in separate regions with limited overlap. Mammals and squamates extensively diversify within their respective regions. Among all three groups, dietary generalists often occupy clade-specific central regions of morphospace. Some parallel changes in skull shape occur in clades with distinct evolutionary histories but similar diets. However, members of a given clade often present distinct skull shape solutions for a given diet, and the vast majority of species retain the unique aspects of their ancestral skull plan, underscoring the limits of morphological convergence due to ecology in amniotes. These data demonstrate that certain skull shapes may provide functional advantages suited to particular diets, but accounting for both phylogenetic history and ecology can provide a more nuanced approach for inferring the ecology and functional morphology of cryptic or extinct amniotes.
Data from: Inner ear morphology of diadectomorphs and seymouriamorphs (Tetrapoda) uncovered by high-resolution x-ray microcomputed tomography, and the origin of the amniote crown group
The origin of amniotes was a key event in vertebrate evolution, enabling tetrapods to break their ties with water and invade terrestrial environments. Two pivotal clades of early tetrapods, the diadectomorphs and the seymouriamorphs, have played an unsurpassed role in debates about the ancestry of amniotes for over a century, but their skeletal morphology has provided conflicting evidence for their affinities. Using high-resolution X-ray microcomputed tomography, we reveal the three-dimensional architecture of the well preserved endosseous labyrinth of the inner ear in representative species belonging to both groups. Data from the inner ear are coded in a new cladistic matrix of stem and primitive crown amniotes. Both maximum parsimony and Bayesian inference analyses retrieve seymouriamorphs as derived non-crown amniotes and diadectomorphs as sister group to synapsids. If confirmed, this sister group relationship invites re-examination of character polarity near the roots of the crown amniote radiation. Major changes in the endosseous labyrinth and adjacent braincase regions are mapped across the transition from non-amniote to amniote tetrapods, and include: a ventral shift of the cochlear recess relative to the vestibule and the semicircular canals; cochlear recess (primitively housed exclusively within the opisthotic) accommodated within both the prootic and the opisthotic; development of a distinct fossa subarcuata. The inner ear of seymouriamorphs foreshadows conditions of more derived groups, whereas that of diadectomorphs shows a mosaic of plesiomorphic and apomorphic traits, some of which are unambiguously amniote-like, including a distinct and pyramid-like cochlear recess.
FIG. 4 in Extended embryo retention, caecilian oviparity and amniote origins
FIG. 4. Stages in the early development of the oviparous Sri Lankan caecilian Ichthyophis glutinosus (reproduced from Sarasin and Sarasin [1887 –1890]). All of the stages illustrated were observed in eggs that had been laid.
FIG. 3 in Extended embryo retention, caecilian oviparity and amniote origins
FIG. 3. Alternative tetrapod phylogeny with the binary character, extended egg retention 'present' or 'absent', mapped on to the tree by MacClade (Maddison and Maddison, 1992). With caecilians coded present as in Laurin and Reisz (1997) but placed as the sister group of the salamanders (Urodela), the parsimonious interpretation is unambiguous and indicates the absence of EER in the ancestral amniote.
FIG. 1 in Extended embryo retention, caecilian oviparity and amniote origins
FIG. 1. Tetrapod phylogeny (after Laurin and Reisz, 1997) with the binary character, extended egg retention 'present' or 'absent', mapped on to the tree by MacClade (Maddison and Maddison, 1992). With caecilians coded 'present', as in Laurin and Reisz (1997), the condition of ancestral amniotes with respect to this character is ambiguous.
The Collection and Application of Autologous Amniotic Fluid At Cesarean Delivery Closure.
ClinicalTrials.gov study NCT04359472. IPD Sharing: NO. Countries: 1. Publications: 10.
An Amniotic Membrane Injection Comparing Two Doses (1 mL and 2 mL Injection) and a Placebo (Sterile Saline) in the Treatment of Osteoarthritis of the Knee
ClinicalTrials.gov study NCT04612023. IPD Sharing: NO. Countries: 1. Publications: 2.
Comparing Infectious Morbidity Among Women With Meconium-stained Amniotic Fluid at Term, Between Those Treated With Prophylactic Antibiotics Zinacef vs. Placebo
ClinicalTrials.gov study NCT06849037. IPD Sharing: YES. Countries: 1. Publications: 5.
Surgical Result of Pterygium Extended Removal Followed by Fibrin Glue Assisted Amniotic Membrane Transplantation
ClinicalTrials.gov study NCT02015000. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Amniotic Membrane Graft In Syntomathic Bullous Keratopathy
ClinicalTrials.gov study NCT01926535. IPD Sharing: Not stated. Countries: 1. Publications: 20.
Evaluation of Laparotomy With Trans-Amniotic Suture Placement in TTTS Surgery
ClinicalTrials.gov study NCT06991400. IPD Sharing: NO. Countries: 1. Publications: 2.
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