Tissue Patterning Research Articles

A Decade of Progress in Ultrasound Assessments of Subcutaneous and Total Body Fat: A Scoping Review

Body composition assessment by ultrasonography is a vivid research field. Ultrasound (US) can be used to quantify subcutaneous and visceral fat, to evaluate the quantity and quality of skeletal muscle, and to infer intracellular fat content. This scoping review aimed to summarize recent advancements in subcutaneous fat estimation using US and related applications. A systematic search was conducted on PubMed, MEDLINE, Scopus, Google Scholar, and Web of Science to identify original articles published in English between 1 January 2014 and 20 December 2024. A total of 1869 articles were screened based on their titles and abstracts, and 283 were retrieved for full-text evaluation. Our search and selection strategy resulted in 89 eligible documents. The literature discussed in this review suggests that US is a reliable and valid technique for measuring subcutaneous fat thickness at selected anatomic locations. Standardized measurement protocols enabled accurate subcutaneous adipose tissue (SAT) patterning in various populations (e.g., athletes, children, adults, and patients with anorexia nervosa). Further research is warranted to establish clinically relevant cutoff values. US-derived SAT thicknesses can also provide whole-body fat estimates of fat mass (FM), fat-free mass (FFM), and body fat percentage (%BF). To this end, prediction formulas were developed to ensure agreement with criterion measures given by laboratory techniques, or multicompartment models based on combinations thereof. The resulting assessments of global adiposity were reliable but inaccurate in certain populations (e.g., overweight and obese). Nevertheless, due to its high reliability, US might be used to track changes in body fat content during nutritional and/or lifestyle interventions. Future investigations will be needed to evaluate its accuracy in this respect and to improve the validity of whole-body fat estimation compared to multicompartment models.

Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS)

To explore the impact of epigenetic modifications on egg-laying traits in geese, we employed genome-wide bisulfite sequencing (WGBS) to analyze DNA methylation patterns in pituitary tissues of high-(HYP) and low-yield (LYP) Sichuan White geese. We achieved high-quality sequencing data (mean 19.09 Gb raw reads, 15.49 Gb clean reads, 79.1% unique mapping rate) with a bisulfite conversion efficiency of 99.88%. Comparative analysis revealed 2394 differentially methylated regions (DMRs) and 422 differentially methylated genes (DMGs) between HYP and LYP groups. We identified five key differentially methylated candidate genes (BMPER, INHA, NMBR, NK3R, and DSG2) linked to egg-laying traits in Sichuan White geese. Integrated GO and KEGG enrichment analysis conducted to explore the role of regulatory networks of epigenetic modification on egg-laying traits in Sichuan White geese identified multiple metabolic pathways associated with egg-laying traits (promoting egg transport, ovulation, and yolk protein synthesis and secretion), thus providing a basis for subsequent functional verification.

Flexible analysis of spatial transcriptomics data (FAST): a deconvolution approach

MotivationSpatial transcriptomics is a state-of-art technique that allows researchers to study gene expression patterns in tissues over the spatial domain. As a result of technical limitations, the majority of spatial transcriptomics techniques provide bulk data for each sequencing spot. Consequently, in order to obtain high-resolution spatial transcriptomics data, performing deconvolution becomes essential. Most existing deconvolution methods rely on reference data (e.g., single-cell data), which may not be available in real applications. Current reference-free methods encounter limitations due to their dependence on distribution assumptions, reliance on marker genes, or the absence of leveraging histology and spatial information. Consequently, there is a critical need for the development of highly flexible, robust, and user-friendly reference-free deconvolution methods capable of unifying or leveraging case-specific information in the analysis of spatial transcriptomics data.ResultsWe propose a novel reference-free method based on regularized non-negative matrix factorization (NMF), named Flexible Analysis of Spatial Transcriptomics (FAST), that can effectively incorporate gene expression data, spatial, and histology information into a unified deconvolution framework. Compared to existing methods, FAST imposes fewer distribution assumptions, utilizes the spatial structure information of tissues, and encourages interpretable factorization results. These features enable greater flexibility and accuracy, making FAST an effective tool for deciphering the complex cell-type composition of tissues and advancing our understanding of various biological processes and diseases. Extensive simulation studies have shown that FAST outperforms other existing reference-free methods. In real data applications, FAST is able to uncover the underlying tissue structures and identify the corresponding marker genes.

Inter- and Transgenerational Effects of In Ovo Stimulation with Bioactive Compounds on Cecal Tonsils and cecal Mucosa Transcriptomes in a Chicken Model

Backgroub/Objectives: Exploring how early-life nutritional interventions may impact future generations, this study examines the inter- and transgenerational effects of in ovo injection of bioactive compounds on gene expression in the cecal tonsils and cecal mucosa using a chicken model. Methods: Synbiotic PoultryStar® (Biomin) and choline were injected in ovo on the 12th day of egg incubation. Three experimental groups were established in the generation F1: (1) a control group (C) receiving 0.9% physiological saline (NaCl), (2) a synbiotic group (SYN) receiving 2 mg/embryo, and (3) a combined synbiotic and choline group (SYNCH) receiving 2 mg synbiotic and 0.25 mg choline per embryo. For the generations F2 and F3, the SYN and SYNCH groups were each divided into two subgroups: (A) those injected solely in F1 (SYNs and SYNCHs) and (B) those injected in each generation (SYNr and SYNCHr). At 21 weeks posthatching, cecal tonsil and cecal mucosa samples were collected from F1, F2, and F3 birds for transcriptomic analysis. Results: Gene expression profiling revealed distinct intergenerational and transgenerational patterns in both tissues. In cecal tonsils, a significant transgenerational impact on gene expression was noted in the generation F3, following a drop in F2. In contrast, cecal mucosa showed more gene expression changes in F2, indicating intergenerational effects. While some effects carried into F3, they were less pronounced, except in the SYNs group, which experienced an increase compared to F2. Conclusions: The study highlights that transgenerational effects of epigenetic modifications are dynamic and unpredictable, with effects potentially re-emerging in later generations under certain conditions or fading or intensifying over time. This study provides valuable insights into how epigenetic nutritional stimulation during embryonic development may regulate processes in the cecal tonsils and cecal mucosa across multiple generations. Our findings provide evidence supporting the phenomenon of epigenetic dynamics in a chicken model.

Genome-Wide Analysis, Identification, and Transcriptional Profile of the Response to Abiotic Stress of the Purple Acid Phosphatases (PAP) Gene Family in Apple

Purple acid phosphatases (PAPs) play a significant role in plant phosphorus nutrition and can not only release phosphorus from the soil but also regulate the distribution of phosphorus in plants throughout their entire growth and development process. Moreover, members of the PAP protein family exert a more extensive influence on plant mineral homeostasis, developmental processes, and stress responses. Three clusters of purple acid phosphatases, including 31 putative genes, were identified in apples (Malus domestica) by searching the Genome Database for Rosaceae. The structure, chromosomal distribution and location, phylogeny, motifs, and cis-acting elements in the gene promoter regions of the MdPAP gene family are reviewed. These genes exhibit different expression patterns in different tissues. For example, almost all MdPAP genes are strongly expressed in the roots, except for MdPAP10, MdPAP12, and MdPAP27. Similarily, all MdPAPs were expressed in the leaves while the transcript levels of MdPAP7, MdPAP10, MdPAP15, MdPAP21, MdPAP24, MdPAP26, MdPAP29, and MdPAP30 were highest in apple flowers. Overall, the expression of the 31 genes significantly changed in either the roots or leaves following the application of phosphorus and/or drought stress. These results indicate that MdPAP family members play a role in plant adaptation to adverse environments. This work explores the adaptative responses to phosphorus and/or drought conditions in apple and establishes a foundation for an enhanced comprehension of the evolution of PAP families and the exploration of the genes of interest.

Genome-wide analysis of TCP family genes and their constitutive expression pattern analysis in the melon (Cucumis melo).

TCP proteins are plant-specific transcription factors that play essential roles in various developmental processes, including leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, a comprehensive analysis of genome-wide TCP genes and their expression patterns in melon is yet to be done. The present study aims to identify and analyze the TCP genes in the melon genome and understand their putative functions. The chromosomal location, gene structure, conserved motifs, protein domains, structural homology, cis-regulating elements, transcript expression patterns, and potential protein-protein interactions were analyzed using various databases and webtools. A total of 29 putative TCP genes are identified in melon. These genes were classified into two classes: Class-I (13 genes) and Class-II (16 genes). The results revealed that the putative CmTCP genes are distributed across nine of the twelve melon chromosomes and exhibit diverse expression patterns in different tissues which mostly indicates their potential role in floral organ development, lateral branching, growth and development. Phylogenetic analysis suggests that some CmTCP genes may have similar functions to their homologs in other plant species, while others may have undergone functional diversification. This study paves the way for future investigations into the specific roles of individual CmTCP genes in melon and for elucidating the mechanisms by which TCP proteins regulate leaf elongation, floral development, and lateral branching.

Evaluating biomarkers in canine cytotoxic interface dermatitis reactions to account for clinical and histopathological similarities and differences.

Cytotoxic interface dermatitis (CID) is a pattern reaction predominantly at the dermo-epidermal junction that encapsulates numerous chronic non-communicable inflammatory skin conditions in which the basal keratinocytes are attacked by T-cell infiltrate leading to apoptosis, lymphocytic satellitosis and vacuolar degeneration. Though many diseases include CID, the type of clinical presentation and tissue patterns expressed from disease to disease varies. In this study, we evaluate the commonalities and discrepancies in significantly expressed biomarkers across several CID conditions to examine their impact on clinical presentations in canines. Among the uniquely expressed genes in each disease, we observed significantly expressed IFNG in Discoid Lupus Erythematosus, TRAT1 in Epitheliotropic Lymphoma, and CXCL8 and CSF3R in pemphigus affected dogs. With this knowledge, we may be able to use molecular signatures in combination with current treatment practices to develop a more targeted treatment plan for patients with CID.

Screening potential diagnostic biomarkers for PLA2R‑associated idiopathic membranous nephropathy by WGCNA analysis and LASSO algorithm

Adult nephrotic syndrome is primarily caused by membranous nephropathy (MN), with idiopathic membranous nephropathy (IMN) being a prominent subtype. The onset of phospholipase A2 receptor (PLA2R1)-associated IMN is critically linked to M-type PLA2R1 exposure, yet the mechanism underlying glomerular injury remains unclear. In this study, membranous nephropathy datasets (GSE115857, GSE200828) were retrieved from GEO. Differential gene expression was analyzed using the ‘limma’ R package. WGCNA filtered PLA2R-related modules and intersected genes. LASSO regression, evaluated by ROC analysis, identified characteristic genes. Binomial logistic regression assessed their association with IMN. Validation was performed in the GSE133288 dataset. IHC and qRT-PCR detected characteristic gene expression in PLA2R-positive patients. This study identified elevated PLA2R expression in IMN patients among 117 DEGs. PPI analysis suggested enrichment in Golgi membranes, co-regulation, and glucocorticoid responsiveness, implicating the PPAR pathway by KEGG. WGCNA revealed a 440-gene brown module associated with IMN-PLA2R, with ECM1, SLC19A2, RASD1, FOSB, KDELR3, ZFP36, and ELF4 highlighted as diagnostic markers by ROC analysis. Clinical validation confirmed ECM1 upregulation increased IMN risk, while upregulation of SLC19A2, ZFP36, RASD1, and FOSB decreased it. ECM1 positively correlated with PLA2R, whereas SLC19A2, ZFP36, and FOSB negatively correlated. IHC analysis demonstrated consistent gene expression patterns in IMN tissues, with podocyte exposure to PLA2R-positive serum reducing viability and increasing apoptosis. Functional studies, prompted by RASD1 downregulation, revealed enhanced cell activity and reduced apoptosis upon RASD1 overexpression compared to the Serum + Ov-NC control. Collectively, this study identified diagnostic markers for PLA2R-related IMN, offering novel therapeutic targets for the treatment of IMN.

Genome-wide Characterization of the MBF1 Gene Family and Its Expression Pattern in Different Tissues and Under Stresses in Medicago truncatula and Medicago sativa.

Multiprotein bridging factor 1 (MBF1) is a transcription factor family playing crucial roles in plant development and stress responses. In this study, we analyzed MBF1 genes in Medicago truncatula and Medicago sativa under abiotic stresses, revealing evolutionary patterns and functional differences. Four MBF1 genes were identified in M. truncatula and two in M. sativa, with conserved MBF1 and HTH domains, similar exon/intron structures, and stress-related cis-elements in their promoters. Subcellular localization showed that MtMBF1a.1 is predominantly localized in the nucleus, while MtMBF1a.2, MtMBF1b, MtMBF1c, and MsMBF1a localize to both the nucleus and cytoplasm. In contrast, MsMBF1c is exclusively localized in the cytoplasm. An expression analysis revealed distinct stress responses: salt stress-induced MtMBF1b and MtMBF1c expression but repressed MsMBF1a and MsMBF1c. In contrast, PEG stress did not affect M. truncatula MBF1 genes but repressed both M. sativa MBF1 genes. These findings provide insights into MBF1-mediated stress adaptation and inform strategies for the molecular breeding of stress-tolerant alfalfa.

Degenerative Disease Diagnosis and Analysis Based on Tissue Specificity of DNA Methylation.

The tissue specificity of DNA methylation refers to the significant differences in DNA methylation patterns in different tissues. This specificity regulates gene expression, thereby supporting the specific functions of each tissue and the maintenance of normal physiological activities. Abnormal tissue-specific patterns of DNA methylation are closely related to age-related diseases. This abnormal methylation pattern affects the regulation of gene expression, which may lead to changes in cell function and promote the occurrence of pathological conditions. By analyzing the differences in these methylation patterns, key CpG sites for disease diagnosis can be effectively screened. The main goal of this paper is to use the characteristics associated with tissue-specific abnormal expression and disease to construct an age-related disease diagnosis model. First, we combined chi-square tests and logistic regression to identify tissue-specific and disease-specific CpG sites, laying the foundation for accurate medical diagnosis, and verified the biological relevance of these CpG sites through enrichment analysis. Then we used the Transformer model to fit these CpG sites and realized the automatic diagnosis of age-related diseases. Our work proves that the tissue specificity of DNA methylation has the potential to diagnose age-related diseases, and proves the scientific nature of our proposed diagnostic method from a biological perspective.

Genome-Wide Study of Plant-Specific PLATZ Transcription Factors and Functional Analysis of OsPLATZ1 in Regulating Caryopsis Development of Rice (Oryza sativa L.).

Plant A/T-rich sequence- and zinc-binding protein (PLATZ) is a type of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. This family is essential for plant growth, development, and stress response. In this study, 15 OsPLATZs were identified in the rice genome with complete PLATZ-conserved domains by CD-search, similar to those found in angiosperms. Multi-species phylogenetic analysis showed that PLATZs were conserved in photosynthetic organisms, and an evolutionary branch unique to angiosperms was identified among members of the PLATZ family. Fifteen OsPLATZs were represented by five groups, each with distinct characteristics. An analysis of protein structures and sequence motifs showed that OsPLATZs were similar within groups, but varied between them. The expression profile and qRT-PCR results showed that OsPLATZs had distinct expression patterns in different tissues, with some responding to stress induction. Most of the OsPLATZs localized to the nuclei, and were predicted to bind to DNA sequences by AlphaFold3, suggesting that they likely function as conventional transcription factors. We also identified OsPLATZ1, a caryopsis-specific gene that regulates grain filling and caryopsis development in rice. This research lays the foundation for exploring the structural diversity, evolutionary traits, expression profile, and possible roles of PLATZ transcription factors in rice.

Single cell RNA sequencing reveals shifts in cell maturity and function of endogenous and infiltrating cell types in response to acute intervertebral disc injury.

The intervertebral disc (IVD) is a spinal joint that accumulates damage with age but has limited tissue repair capabilities. IVD injuries progress into degeneration, and IVD degeneration is a leading cause of lower back pain. Understanding the cell populations that change and respond to injury will uncover targets to restore IVD function. Mesenchymal stem cells (MSCs) are cells within the IVD that can potentially replenish the cells lost after IVD damage. To better understand how IVD cell populations are affected by tissue damage, we performed single cell RNA sequencing of IVD tissue 7 days post injury and analyzed the differences in gene regulation. We identified diverse cells populations such as IVD, immune cells, vascular cells, and MSCs. We discovered the presence of Saa2 and Grem1 expressing MSCs that become less stem cell-like and express higher levels of IVD gene markers after injury. We also determined that Saa2 and Grem1 have varying gene expression patterns in IVD tissues that becomes attenuated after injury. These MSCs could be targeted for future stem cell therapies to prevent IVD degeneration.

The Identification of Auxin Response Factors and Expression Analyses of Different Floral Development Stages in Roses.

Background/Objectives:Auxin response factors (ARFs) are important in plant growth and development, especially flower development. However, there is limited research on the comprehensive identification and characterization of ARF genes in roses. Methods: We employed bioinformatics tools to identify the ARF genes of roses. These genes were characterized for their phylogenetic relationships, chromosomal positions, conserved motifs, gene structures, and expression patterns. Results: In this study, a total of 17 ARF genes were identified in the genomes of Rosa chinensis 'OB', R. chinensis 'CH', R. rugosa, and R. wichurana. Based on RNA-seq analyses, we found that the ARF genes had diverse transcript patterns in various tissues and cultivars. In 'CH', the expression levels of RcCH_ARFs during different flower-development stages were classified into four clusters. In cluster 3 and cluster 4, RcCH_ARFs were specifically high and low in different stages of floral evocation. Gene expression and phylogenetic analyses showed that RcCH_ARF3, RcCH_ARF4, and RcCH_ARF18 were likely to be the key genes for rose flower development. Conclusions: The identification and characterization of ARF genes in Rosa were investigated. The results presented here provide a theoretical basis for the molecular mechanisms of ARF genes in plant development and flowering for roses, with a broader application for other species in the rose family and for the development of novel cultivars.

Unsupervised spatio-temporal classification of deformation patterns of embryonic tissues matches their fate map

Unsupervised spatio-temporal classification of deformation patterns of embryonic tissues matches their fate map

Segmentation of Breast Lesion using Fuzzy Thresholding and Deep Learning

Breast cancer is a major cause of morbidity and mortality in women. In breast cancer screening, Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI) has shown promise as a technique, providing enhanced temporal patterns of breast tissues. This study proposes an enhanced segmentation method for identifying breast lesions. The proposed experiments are done using the breast DCE-MRI images of 123 slices from seven patients in The Cancer Image Archive database. The three methods proposed and tested to segment the lesions are: i) Fuzzy C-mean Thresholding (FCMTH) with morphological operations ii) deep learning networks trained with original images iii) deep learning networks trained with three types of preprocessed images: the core breast image, the filtered core breast image, and the fuzzy thresholded image. In this study, the deep learning networks are trained with preprocessed images generated from the FCMTH technique, resulting in higher segmentation accuracy. FCMTH achieves Dice and Jaccard coefficients of 0.8458 and 0.7471, while DeepLabv3+ with MobileNetv2 trained by preprocessed images achieves 0.9468 and 0.8990, respectively. Thus, the combination of deep learning and FCMTH techniques provides the best performance for lesion detection.

Noninvasive Grading of Liver Fibrosis Based on Texture Analysis From MRI-Derived Radiomics.

Given the increasing global prevalence of metabolic syndrome, this study aimed to assess the potential of MRI-derived radiomics in noninvasively grading fibrosis. The study included 79 prospectively enrolled participants who had undergone MRE due to known or suspected liver disease between November 2022 and September 2023. Among them, 48 patients were diagnosed with histopathologically confirmed liver fibrosis. A total of 107 radiomic features per patient were extracted from MRI imaging. The dataset was then divided into training and test sets for model development and validation. Stepwise feature reduction was employed to identify the most relevant features and subsequently used to train a gradient-boosted tree model. The gradient-boosted tree model, trained on the training cohort with identified radiomic features to differentiate fibrosis grades, exhibited good performances, achieving AUC values from 0.997 to 0.998. In the independent test cohort of 24 patients, the radiomics model demonstrated AUC values ranging from 0.617 to 0.830, with the highest AUC of 0.830 (95% CI 0.520-0.830) for classifying fibrosis grade 2. Incorporating ADC values did not improve the model's performance. In conclusion, our study emphasizes the significant promise of using radiomics analysis on MRI images for noninvasively staging liver fibrosis. This method provides valuable insights into tissue characteristics and patterns, enabling a retrospective liver fibrosis severity assessment from nondedicated MRI scans.

Clinical confocal laser endomicroscopy for imaging of autofluorescence signals of human brain tumors and non-tumor brain

PurposeAnalysis of autofluorescence holds promise for brain tumor delineation and diagnosis. Therefore, we investigated the potential of a commercial confocal laser scanning endomicroscopy (CLE) system for clinical imaging of brain tumors.MethodsA clinical CLE system with fiber probe and 488 nm laser excitation was used to acquire images of tissue autofluorescence. Fresh samples were obtained from routine surgeries (glioblastoma n = 6, meningioma n = 6, brain metastases n = 10, pituitary adenoma n = 2, non-tumor from surgery for the treatment of pharmacoresistant epilepsy n = 2). Additionally, in situ intraoperative label-free CLE was performed in three cases. The autofluorescence images were visually inspected for feature identification and quantification. For reference, tissue cryosections were prepared and further analyzed by label-free multiphoton microscopy and HE histology.ResultsLabel-free CLE enabled the acquisition of autofluorescence images for all cases. Autofluorescent structures were assigned to the cytoplasmic compartment of cells, elastin fibers, psammoma bodies and blood vessels by comparison to references. Sparse punctuated autofluorescence was identified in most images across all cases, while dense punctuated autofluorescence was most frequent in glioblastomas. Autofluorescent cells were observed in higher abundancies in images of non-tumor samples. Diffuse autofluorescence, fibers and round fluorescent structures were predominantly found in tumor tissues.ConclusionLabel-free CLE imaging through an approved clinical device was able to visualize the characteristic autofluorescence patterns of human brain tumors and non-tumor brain tissue ex vivo and in situ. Therefore, this approach offers the possibility to obtain intraoperative diagnostic information before resection, importantly independent of any kind of marker or label.

Click chemistry-based dual nanosystem for microRNA-122 detection with single-base specificity from tumour cells

MicroRNAs (miRNAs) have been recognised as potential biomarkers due to their specific expression patterns in different biological tissues and their changes in expression under pathological conditions. MicroRNA-122 (miR-122) is a vertebrate-specific miRNA that is predominantly expressed in the liver and plays an important role in liver metabolism and development. Dysregulation of miR-122 expression is associated with several liver-related diseases, including hepatocellular carcinoma and drug-induced liver injury (DILI). Given the potential of miR-122 as a biomarker, its effective detection is important for accurate diagnosis. However, miRNA detection methods still face challenges, particularly in terms of accurately identifying miRNA isoforms that may differ by only a single base. Here, with the aim of advancing accessible methods for the detection of miRNAs with single-base specificity, we have developed a robust dual nanosystem that leverages the simplicity of click chemistry reactions. Using the dual nanosystem, we successfully detected miR-122 at single-base resolution using flow cytometry and analysed its expression in various tumour cell lines with high specificity and strong correlation with TaqMan assay results. We also detected miR-122 in serum and identified four single nucleotide variations in its sequence. The chemistry employed in this dual nanosystem is highly versatile and offers a promising opportunity to develop nanoparticle-based strategies that incorporate click chemistry and bioorthogonal chemistry for the detection of miRNAs and their isoforms.Graphical

Histomorphometry of Gastrointestinal Tract Mucosae of Sonali and Indigenous Chickens in Bangladesh

The study was conducted to provide a histomorphmetric comparison between the mucosa of the gastrointestinal tract (GUT) and the distribution pattern of gutassociated lymphoid tissue (GALT) in two types of chickens in Bangladesh: Sonali and Indigenous chickens. The study included 20 male Sonali and indigenous chickens aged 10 to 11 weeks, divided evenly into two groups of 10 chickens each. Following humane slaughter, various segments of the GUT were collected for histomorphometric analysis with hematoxylin and eosin staining. The histological investigation revealed that the epithelial lining and mucosal layer of the esophagus were thicker in the Sonali than in the Indigenous chickens. Nonetheless, the Indigenous chickens had a bigger number of lymphocytes. Indigenous chickens had thicker lining epithelium in the proventriculus, whereas Sonali chickens had thicker mucosa. Indigenous chickens showed greater lymphocyte populations than Sonali. Indigenous chickens exhibited taller duodenal and jejunal villi, but Sonali chickens had taller ileal villi. The Sonali possessed wider duodenal and jejunal villi, while Indigenous chickens had wider ileal villi. Because of their scavenging activity, Indigenous people have greater lymphocyte populations in the small intestine. The Sonali possessed the most lymphatic nodules in Meckel's diverticulum, as well as a higher crypt depth and lymphocyte density. Indigenous chickens had thicker mucosa and Lieberkühn crypts in the caecum, whereas Sonali had a greater lymphocyte count. Indigenous chickens showed larger lymphatic nodules and crypts in the cecal tonsil, whereas Sonali had thicker mucosa, deeper crypts, and a higher lymphocyte population in the colon. Lymphocytes were found scattered throughout the tissues of Sonali and Indigenous chickens. The cells were primarily detected within the lamina propria. Further research with other types of chickens could be undertaken to measure lymphocytes, intraepithelial lymphocytes, and lymphatic nodules. J. of Sci. and Tech. Res. 6(1): 33-44, 2024

Timely TGFβ signalling inhibition induces notochord

The formation of the vertebrate body involves the coordinated production of trunk tissues from progenitors located in the posterior of the embryo. Although in vitro models using pluripotent stem cells replicate aspects of this process1, 2, 3, 4, 5, 6, 7, 8, 9–10, they lack crucial components, most notably the notochord—a defining feature of chordates that patterns surrounding tissues11. Consequently, cell types dependent on notochord signals are absent from current models of human trunk formation. Here we performed single-cell transcriptomic analysis of chick embryos to map molecularly distinct progenitor populations and their spatial organization. Guided by this map, we investigated how differentiating human pluripotent stem cells develop a stereotypical spatial organization of trunk cell types. We found that YAP inactivation in conjunction with FGF-mediated MAPK signalling facilitated WNT pathway activation and induced expression of TBXT (also known as BRA). In addition, timely inhibition of WNT-induced NODAL and BMP signalling regulated the proportions of different tissue types, including notochordal cells. This enabled us to create a three-dimensional model of human trunk development that undergoes morphogenetic movements, producing elongated structures with a notochord and ventral neural and mesodermal tissues. Our findings provide insights into the mechanisms underlying vertebrate notochord formation and establish a more comprehensive in vitro model of human trunk development. This paves the way for future studies of tissue patterning in a physiologically relevant environment.