Troponin I 1 (TNNI1) encodes the slow skeletal isoform of troponin I and is essential for the regulation of contraction in slow-twitch skeletal muscle. However, the developmental and tissue-specific expression of TNNI1-related genes across vertebrates remains incompletely characterized. In zebrafish, multiple tnni genes have been identified, including four tnni1-related paralogs (tnni1a, tnni1b, tnni1c, and tnni1d), which share high sequence similarity. While individual tnni genes have been partially characterized, a systematic comparison of the spatial and temporal expression patterns of these tnni1 paralogs during embryogenesis remains lacking. Here, we analyzed and compared the spatial and temporal expression patterns of the four tnni1 paralogs during zebrafish embryogenesis to assess their potential functional divergence. Multiple sequence alignment revealed that proteins encoded by zebrafish Tnni1 paralogs are highly conserved relative to mammalian TNNI1, with paralog-specific divergence primarily in the N-terminal region. Whole-mount in situ hybridization showed that tnni1a is first detected in the embryonic heart and was later expressed in cranial and hypaxial muscles. tnni1b was expressed in bilateral cardiac precursor cells, exhibited the strongest and most sustained cardiac expression among the paralogs, and was subsequently expressed in extraocular, craniofacial, hypaxial, and trunk muscles. In contrast, tnni1c and tnni1d were initially expressed in somites, displayed weaker or transient cardiac expression, and were later broadly expressed in extraocular, craniofacial, and hypaxial muscles. Taken together, these findings indicate that zebrafish tnni1 paralogs exhibit distinct yet partially overlapping spatiotemporal expression profiles, supporting partial subfunctionalization following gene duplication during cardiac and skeletal muscle development.
Heat Shock Protein (HSP) 90 is a molecular chaperone that contributes to a broad range of cellular processes in nearly all tissues including the brain. HSP90 has two isoforms, namely HSP90α and HSP90β, that have highly similar amino-acid sequences and have therefore been assumed to perform redundant functions, although their roles may be distinct in certain cellular contexts. In both the developing brain and adult brain, it remains unclear whether HSP90α and HSP90β have unique functions. Here we demonstrate that these two isoforms are differentially distributed in the mouse cerebral cortex, as evidenced by immunofluorescence staining, fluorescence in situ hybridization, and single-cell RNA sequencing data. HSP90α was strongly expressed in layer 5 excitatory neurons, inhibitory neurons across all layers, and a subset of oligodendrocytes. In addition to the populations expressing HSP90α, HSP90β was strongly expressed in layer 6 neurons. Moreover, HSP90β was preferentially enriched in distal portions of neurites compared with HSP90α. These results suggest unique roles for HSP90α and HSP90β in certain cell types of the cerebral cortex.
Melanoma differentiation-associated gene 5 (MDA5) is a prime member of the RIG-I-like receptor (RLR) family that recognises viral RNA in the cytoplasm and triggers antiviral innate immunity mainly via the MAVS-dependent signalling cascade. This study reports the molecular cloning and characterization of MDA5 in Labeo rohita (LrMDA5), a commercially important major carp in India and Southeast Asia. The LrMDA5 has 3000bp open reading frame (ORF) encoding a 1000-amino acid protein of molecular weight (mw) 240.764 kDa and isoelectric point (pI) of ∼4.84. It's structural domain analysis identified two CARDs, a DEXDc, a helicase, and a C-terminal domain. Phylogenetically, LrMDA5 is closest to the Cyprinus carpio, and the ontogenic expression profiling revealed maximal expression at neurula stage {12h post-fertilization (h.p.f)}. It was ubiquitously expressed across all tested organs/tissues, and in specialised cells such as mucosal RBCs (red blood cells) and PBLs (peripheral blood leukocytes). LrMDA5 gene transcripts along with its adaptor molecule, MAVS, and the cytokines (IL-8 and IL-1β) gene expression were significantly upregulated both in-vivo and in-vitro against poly I:C and LPS-stimulations, and infections with Aeromonas hydrophila and Edwardsiella tarda. These data together highlight the important immune role of MDA5 in fish.
The developmental mechanisms by which neurons are generated and migrate to their final locations within the developing spinal cord are not fully understood. Expression of Rap1, a small GTPase, has been previously implicated in cellular differentiation and migration across multiple tissues in various model organisms. Therefore, we investigated Rap1 expression in the embryonic chicken spinal cord at times when progenitor cells within the ventricular zone give rise to differentiated neurons that migrate towards the lateral surface of the spinal cord. Our results indicate that Rap1 is broadly expressed within the developing spinal cord across the dorsal-ventral axis during neurogenesis, including expression within neuronal progenitors in the ventricular zone and laterally within migrating neurons. We also observed Rap1 expression in spinal commissural axons and within the floor plate, where commissural axons cross the midline. In addition to the spinal cord, we observed expression of Rap1 within the developing dorsal root ganglia and ventral motor axons. Our expression analysis suggests that Rap1 may play a role in determination of progenitor cellular identity, production and migration of neurons, and commissural axons within the spinal cord.
The transmembrane channel-like (TMC) gene family encodes membrane proteins required for hair cell mechanotransduction. While TMC1 and TMC2 are indispensable for mammalian hearing, the functions of other paralogs remain poorly defined. Using zebrafish, we examined nine TMC genes (tmc1, tmc2a, tmc2b, tmc3, tmc4, tmc5, tmc6a, tmc6b, and tmc8) through phylogenetic, transcriptomic, and spatiotemporal expression analyses. tmc1, tmc2a, and tmc2b were robustly expressed in hair cells of the otic vesicle and neuromasts, supporting their early roles in hair cell differentiation. tmc3 and tmc6a showed clear expression by in situ hybridization but were underrepresented in transcriptomic datasets. tmc4 and tmc5 were more broadly expressed, including vestibular hair cells and neuromasts from 72 to 96 h post-fertilization (hpf). Several TMC genes were also detected in non-sensory tissues, suggesting potential roles in other developmental processes. Together, this study provides the first comprehensive atlas of TMC gene expression during zebrafish embryogenesis and reveals divergent expression patterns among paralogs.
During the evolution of vertebrate heads, the emergence of dorso-ventrally segmented facial skeletal elements in the jaw and branchial basket structures is a key feature invented in jawed fish. The segmental development begins from the two distinct prechondrogenic condensations in the dorsal and ventral regions of the respective pharyngeal arches in facial skeletal formation. Interestingly, in zebrafish, a single barx1-expressing prechondrogenic condensation occurs in the posterior arches, in which the ventral ceratobranchial cartilages of the branchial basket form. While the single condensation is expected to cover the ventral regions in the posterior arches for the development of the ventral cartilage, the location of the condensation domain in the arches has not been evaluated yet. Here, we mapped the location of the barx1-expressing condensation domain in the arches through comparative gene expression analyses. The single barx1-expressing condensation domain occupied the whole ventral area and expanded to the middle region of the intermediate area of the respective arches. From the dorsal regions of the condensation domain, the sox9a-expressing chondrocytes for the ventral ceratobranchial cartilages initially arose, with the sox9a expression sustained in the dorsal ends of the developed ceratobranchial cartilages. Our results suggest that the single condensation domain covers not only the ventral but also intermediate regions of the arches, consequently resulting in the dorsal areas of the ventral ceratobranchial cartilages probably originating from the intermediate regions of the arches.
To investigate the immunological function of TRIM13 in zebrafish (Danio rerio), we cloned the zebrafish TRIM13 homolog (DrTRIM13) and obtained its complete coding sequence (CDS) and3 '-untranslated region (3 '-UTR) through sequencing and sequence assembly. Reverse transcription PCR was used to examine the tissue distribution of DrTRIM13. Additionally, fluorescence microscopy was performed to visualize protein localization. Our results demonstrate that the cloned DrTRIM13 cDNA consists of a 276-bp 3 '-UTR and a 1215-bp open reading frame (ORF), encoding a 404-amino acid protein. Phylogenetic analysis indicated that DrTRIM13 shares the highest homology and closest evolutionary relationship with carp (Cyprinus carpio). Subcellular localization in HeLa cells confirmed predominant cytoplasmic distribution. These findings provide a theoretical framework for mitigating viral diseases in aquaculture.
Glaucoma is a group of optic neuropathic conditions in which the progressive degeneration of retinal ganglion cells (RGC) occurs, ultimately leading to irreversible vision loss. Despite our understanding of pathophysiology, potential biomarkers and early detection are still very limited. Hence, there is an urgent need to find the potent molecular biomarker of Glaucoma so that early diagnosis and personalised glaucoma treatment can be possible. In this study, we performed comparative transcriptomic analyses to discern differentially expressed genes (DEGs) linked with Glaucoma. The aim is to find a robust candidate biomarker to facilitate early diagnosis and characterisation of Glaucoma. Advanced feature selections are performed by employing DEG identification and machine learning algorithms, enabling the selection of highly prognostic relevance genes. Furthermore, Artificial neural network (ANN) models were developed to recognise the complicated nonlinear patterns within high-dimensional data and identify the most promising genes having a potent role in glaucoma progression and risk prediction. After the analysis, NPM1P51 turned out to be the most significant contributor after performing multiple analyses, suggesting it to be a strong pseudogene biomarker. Further, CACNG7 showed moderate results in Garson and Olden plots, but better in Generalised weight plots. It encodes a subunit of the voltage-gated calcium channel complex, aligning with already established roles in the mechanisms of neurodegeneration in glaucoma, particularly in apoptosis of retinal ganglion cells through calcium dysregulation. These results provide a foundation for further experimental validations and therapeutic interventions.
The orphan G protein coupled receptor GPR101, which is implicated in X-linked acrogigantism (X-LAG), a rare pituitary disorder characterized by rapid growth a few years after birth, has received significant attention for its expression pattern in adult vertebrate tissues. However, the characterization of GPR101 expression during early embryonic development is poorly characterized. In this study, we investigated the spatiotemporal expression patterns of Gpr101 during early embryonic mouse development (E7.5-E15.5) using a global Gpr101 knock-in mouse model with an inserted LacZ reporter, Gpr101tm1b(KOMP)Mbp. Similar to previously published studies using adult tissues, we found that LacZ reporter expression was largely restricted to regions of the central nervous system. Expression was not detected until E10.5 in a region near the telencephalic vesicle. In contrast to what has been reported in adult tissues, Gpr101 expression was absent in the hypothalamus and pituitary gland during the developmental timepoints assessed. These novel observations provide a more comprehensive characterization of GPR101's expression and may offer insights into its role in growth and development across species.
The regeneration of amputated body parts depends on the activation and inactivation of signaling pathways that regulate various cellular processes, such as proliferation, migration, differentiation, apoptosis, etc. In the case of annelids, gene expression of several members of the canonical Wnt pathway has been detected during regeneration of the primary body axis and it has been determined that alteration of its activity results in deficiencies in blastema and central nervous system formation, as well as in body segmentation. However, most studies have been carried out at very specific times of regeneration, in a few species and mainly in anterior regeneration. In this work, we analyzed the expression of β-catenin throughout anterior and posterior regeneration in Lumbriculus variegatus, using it as a marker for the potential activation of the pathway. We also carried out pharmacological inhibition and overactivation assays of the pathway during blastema formation and growth. We determined that the expression of β-catenin changes in anterior and posterior regeneration in a highly dynamic manner, both in its intensity and in the tissue in which it is expressed as the process progresses. We also described its potential role in chaeta regeneration. In addition, we showed that inhibition and overactivation of the pathway negatively affect blastema formation and do so differently in the anterior and posterior sections. These findings suggest that the canonical Wnt pathway participates in several cellular processes within annelid regeneration and that its activity must be finely regulated to allow the transition between one process and another.
Shroom3 is an actin binding protein integral to apical constriction and apical-basal elongation during mammalian morphogenesis. Shroom3 function has been demonstrated in the development of the heart, neural tube, gut tube, eye, thyroid bud, and kidneys, with mutations linked to human congenital defects including anencephaly, spina bifida, cleft lip and palate, and ventricular septal defects. Genome-wide association studies implicate Shroom3 in human conditions such as chronic kidney disease and heterotaxy. While this suggests that Shroom3 expression continues postnatally, the extent of adult expression patterns remain unexplored. To address this, we first harvested organs from adult mice heterozygous for a LacZ reporter inserted into the Shroom3 allele (Shroom3+/Gt). Organs were stained in wholemount with X-gal and cleared in glycerol to identify which tissues expressed Shroom3 and to localize the expression within the tissue. Wildtype organs were then harvested and fluorescently stained to localize Shroom3 protein in tissue sub-structures. From this, we have characterized previously unknown Shroom3 expression in many adult organs including the bladder and reproductive systems, as well as established postnatal Shroom3 expression in organs thought to only have developmental expression including the eye and whisker pad. Our results also demonstrate organs which did not show Shroom3 expression, including the liver and pancreas. This data suggests that Shroom3 has roles in a wider number of tissues than previously thought and provides a foundation for future hypotheses regarding the biological and pathological significance of Shroom3.
The SH2B family, which includes SH2B1, SH2B2, and SH2B3, consists of adaptor proteins that possess conserved Src homology 2 (SH2) and pleckstrin homology (PH) domains, playing essential roles as signaling mediators. However, the gene expression patterns of this family during embryonic development are still mostly unclear. In this study, we first investigated the evolutionary conservation of SH2B across multiple species using phylogenetic analysis, which revealed high sequence homology between zebrafish Sh2b and its orthologs in other vertebrates. Subsequently, we examined the expression patterns of sh2b during zebrafish embryogenesis through whole mount in situ hybridization. The findings revealed that all sh2b genes are expressed during the early developmental stages of zebrafish embryos, with a significant concentration in the brain, eyes, and spinal cord. Additionally, sh2b1 was found to be expressed in the lateral line neuromast (lln) support cells. In conclusion, our results suggest that the sh2b family is mainly localized in the brain and eyes, with sh2b1 specifically expressed in the lln support cells. This study offers important insights into the role of the sh2b family in zebrafish embryonic development.
CWC27 is a member of cyclophilin-type peptidyl-prolyl cis-trans isomerase family and takes part in the pre-mRNA splicing. The mutation of its gene, Cwc27, has been verified to be related to cancer, craniofacial and skeletal anomalies, retinal degeneration, and hearing loss. However, expression pattern of Cwc27 in the development of inner ear has not been fully understood. In this study, we studied the spatiotemporal expression of Cwc27 mRNA and CWC27 protein in the mouse inner ear from embryonic day (E) 9 to postnatal 0-day by in situ hybridization and immunohistochemistry staining, respectively. The expression level of Cwc27 was analyzed by quantitative reverse transcription polymerase chain reaction. We found that Cwc27 was expressed early in the otocyst at E9. At E13, Cwc27 was expressed in the cochlear duct, spiral ganglion area, and vestibular organ. The expression level of Cwc27 mRNA reached its maximum level at E13. From E14 onward, Cwc27 was expressed in the sensory epithelium in the cochlear duct and spiral ganglion area. From E18 onward, the distribution of CWC27 protein became more limited to the organ of Corti. Our study revealed Cwc27 might play an important part on promoting the development of developing inner ear.
This correspondence addresses several inconsistencies identified in the article "Kurdish Handwritten Character Recognition Using Deep Learning Techniques," published in Gene Expression Patterns. We commend the authors for their contribution to Kurdish handwriting recognition using deep learning methods. However, critical discrepancies are evident in the model architecture description, class labeling, and model summary. This letter outlines these concerns in detail and suggests revisions to enhance transparency and reproducibility.
Axon guidance signaling pathways, including the Eph/ephrin, Semaphorin, and Slit/Robo pathways, have been found to play crucial roles in cardiac development. Netrin signaling is another well-studied signaling pathway important for axon guidance, but its role in the developing heart has not been investigated. Here, we describe the novel expression pattern of Netrin-1 in the developing murine heart. Transcriptomic analysis of embryonic mouse hearts shows dynamic Netrin-1 expression from E8.5 through E14.5, where Netrin-1 expression preferentially co-localizes with developing trabecular cardiomyocytes. We further demonstrate the spatiotemporal expression pattern of Netrin-1 using a combination of RNA in situ hybridization and Netrin-1Bgeo/+ reporter mice. Netrin-1 is expressed in the developing cardiomyocytes with the highest degree of expression within the left ventricular trabecular myocardium, which has not been previously recognized. Additionally, Netrin-1 expression is observed at lower levels in the cardiomyocytes of the right ventricle and atria. This expression pattern supports a role for Netrin signaling in the developing murine myocardium requiring further functional characterization.
The lateral plate mesoderm of vertebrates, which borders the other mesodermal territories, develops during embryogenesis into a variety of tissues and organs such as blood, heart, vasculature, kidney and smooth muscles. This mesoderm compartment, as well as the unsegmented pharyngeal mesoderm which gives rise to head muscles and part of the heart, have been proposed as vertebrate innovations. Indeed, in the two other chordate clades, the tunicates and the cephalochordates, no such mesoderm regions are formed during development. However, in ascidians, the most studied tunicate group, some cells in the larva which participate to siphon muscles and heart formation are thought to be homologous to the cardiopharyngeal field of vertebrates. Moreover, in the cephalochordate amphioxus, lateral plate and pharyngeal mesoderm marker genes were shown to be expressed in different regions of the fully segmented paraxial mesoderm. In this work, we decided to look at the embryonic expression in amphioxus of several of these mesoderm marker genes, that could give new insights into the putative homology between cephalochordate somite regions and vertebrates' mesoderm compartments. Here, we describe the expression pattern of Erg/Fli1a, Erg/Fli1b, Lmo2, Mesp, Npas4/4l, Osr1/2a, Osr1/2b, Tcf21/Msc and Tcf21/Mscb. Our results highlight the presence of a putative hematopoietic field in the first somite pair as previously proposed, and suggest that some genes were probably specifically recruited during vertebrate evolution for the development of pharyngeal or lateral plate mesoderm derivatives.
BACKGROUND:Recently, transcriptomic analysis has been key in identifying therapeutic targets in cardiovascular regeneration. The postnatal loss of cardiomyocyte proliferative capacity has been linked to the transition from glycolysis to fatty acid oxidation in rodent models of acute myocardial infarction (AMI). However, the transcriptomic profile of these processes in large mammals more similar to humans is still unknown. The aim of this study was to examine the transcriptomic profile, from the proliferative fetal stage to the non-regenerative infarcted adult stage, in an ovine AMI model. METHODS:Samples consisted of fetal sheep hearts sequenced in our laboratory and adult sheep hearts (healthy, infarct, and infarct border) from the Gene Expression Omnibus repository (GSE164245). RESULTS:Fetal tissue showed changes in epigenetic regulation and a predominance of glycolytic metabolism, whereas in the adult infarct core and border zones, there was a partial activation of glycolysis and a reduction in the expression of genes associated with β-oxidation of fatty acids. Myocardial infarction in adult sheep triggers metabolic changes that partially mimic fetal regenerative processes. CONCLUSIONS:These findings will allow for a more precise understanding of the mechanisms underlying cardiac regeneration and facilitate the translation of regenerative therapies for clinical application in humans.
Chchd10 protein is crucial for sustaining mitochondrial dynamics, physiology and functions, and has been reported to be most abundantly in myocardial cells and skeletal muscle. However, nothing is known for the expression pattern of Chchd10 in gonadal development. Here, we characterized the expression patterns of Chchd10 gene during embryonic gonad development and postnatal testis development in mice, as well as the expression pattern of Chchd10 gene in human puberty testis and young adult testis using publicly available datasets. Besides, we investigated the expression and distribution of Chchd10 in mice testis by RT-qPCR and immunofluorescence and analyzed the possible role and mechanism of Chchd10 in the testis. We noticed that Chchd10 showed abundant expression in embryonic testis compared to ovaries and dynamically expressed during embryonic and postnatal testis development in mice. In addition, Chchd10 was highly abundant within testicular Sertoli cells populations both in embryonic and postnatal mice and mainly located in the mitochondria of Sertoli cells in mice. Furthermore, CHCHD10 was not only enriched in Sertoli cells, but also highly expressed in tMΦ of human puberty testis and adult testis. CHCHD10 may participate in testicular development by regulating multiple biological processes of Sertoli cells. Taken together, our data indicated that Chchd10 appears to be important during testicular development, particularly in the functional modulation of Sertoli cells. Our study revealed the expression profile of Chchd10 gene during testicular development for the first time and will provide new ideas for further studying the function and molecular mechanism of Chchd10.
Deafness is a common genetic disorder, where mutations,in the OTOF gene can disrupt the normal functionof the Otoferlin protein, leading to impaired neurotransmitter release in the inner ear and subsequent deafness. Despite the complexity of the pathogenic mechanism,it is not fully understood. Zebrafish are an excellent model for studying genetically-induced deafness,but there have been no previous reports on the pathogenesis of OTOF in zebrafish.This study successfully established a zebrafish model with mutated OTOF genes using CRISPR/Cas9 gene editing technology to investigate the molecular basis of OTOF-induced deafness. Compared to AB wild type zebrafish, those with low otof expression showed injury and apoptosis of hair cells in the posterior lateral neuromasts along with significant increase in the number of macrophages and apoptotic cells in this region. Additionally, these mutants exhibited a reduction in body length. To further elucidate differences at 5dpf (days post-fertilization) between mutant and wild type zebrafish embryos, RNA-seq analysis was conducted to examine differentially expressed genes (DEGs).A total of 334 up-regulated DEGs and 111 down-regulated DEGs were identified in mutants compared to wild types.KEGG and GO enrichment analyses were performed on these DEGs to identify key signaling pathways and hub DEGs. The findings revealedan increased expression of several genes involved in the HSP70 oxidative stress system, suggesting that OTOF may protect cochlear hair cell from apoptosis induced by oxidative stress through regulation of MAPK signal and HSP70 expression.In summary, the establishment of a zebrafish model with OTOF knockout provides a valuable tool for investigating the function of Otoferlin and understanding the role of the OTOF gene in deafness. These potential molecular insights offer significant contributions towards understanding the pathogenesis of deafness experimental models and serves as a foundation for comprehending the involvement of the OTOF gene.
