The liver undergoes a slow process for lipid deposition during chick embryonic period. However, the underlying physiological and molecular mechanisms are still unclear. Therefore, the aim of the ...current study was to reveal the epigenetic mechanism of hepatic transcriptional reprogramming changes based on the integration analysis of RNA-seq and H3K27ac labeled CUT&Tag. Results showed that lipid contents increased gradually with the embryonic age (E) 11, E15, and E19 based on morphological analysis of Hematoxylin-eosin and Oil Red O staining as well as total triglyceride and cholesterol detection. The hepatic protein level of SREBP-1c was higher in E19 when compared with that in E11 and E15, while H3K27ac and H3K4me2 levels declined from E11 to E19. Differential expression genes (DEGs) among these 3 embryonic ages were determined by transcriptome analysis. A total of 107 and 46 genes were gradually upregulated and downregulated respectively with the embryonic age. Meanwhile, differential H3K27ac occupancy in chromatin was investigated. But the integration analysis of RNA-seq and CUT&Tag data showed that the overlap genes were less between DEGs and target genes of differential peaks in the promoter regions. Further, some KEGG pathways enriched from target genes of typical enhancer were overlapped with those from DEGs in transcriptome analysis such as insulin, FoxO, MAPK signaling pathways which were related to lipid metabolism. DNA motif analysis identify 8 and 10 transcription factors (TFs) based on up and down differential peaks individually among E11, E15, and E19 stages where 7 TFs were overlapped including COUP-TFII, FOXM1, FOXA1, HNF4A, RXR, ERRA, FOXA2. These results indicated that H3K27ac histone modification is involved in the transcriptional reprogramming regulation during embryonic development, which could recruit TFs binding to mediate differential enhancer activation. Differential activated enhancer impels dynamic transcriptional reprogramming towards lipid metabolism to promote the occurrence of special phenotype of hepatic lipid deposition.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The Hybrid Mouse Diversity Panel (HMDP) is a collection of approximately 100 well-characterized inbred strains of mice that can be used to analyze the genetic and environmental factors underlying ...complex traits. While not nearly as powerful for mapping genetic loci contributing to the traits as human genome-wide association studies, it has some important advantages. First, environmental factors can be controlled. Second, relevant tissues are accessible for global molecular phenotyping. Finally, because inbred strains are renewable, results from separate studies can be integrated. Thus far, the HMDP has been studied for traits relevant to obesity, diabetes, atherosclerosis, osteoporosis, heart failure, immune regulation, fatty liver disease, and host-gut microbiota interactions. High-throughput technologies have been used to examine the genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes of the mice under various environmental conditions. All of the published data are available and can be readily used to formulate hypotheses about genes, pathways and interactions.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Annulus fibrosus (AF) injuries can lead to substantial deterioration of intervertebral disc (IVD) which characterizes degenerative disc disease (DDD). However, treatments for AF repair/regeneration ...remain challenging due to the intrinsic heterogeneity of AF tissue at cellular, biochemical, and biomechanical levels. In this study, we isolated and characterized a sub-population of cells from rabbit AF tissue which formed colonies in vitro and could self-renew. These cells showed gene expression of typical surface antigen molecules characterizing mesenchymal stem cells (MSCs), including CD29, CD44, and CD166. Meanwhile, they did not express negative markers of MSCs such as CD4, CD8, and CD14. They also expressed Oct-4, nucleostemin, and SSEA-4 proteins. Upon induced differentiation they showed typical osteogenesis, chondrogenesis, and adipogenesis potential. Together, these AF-derived colony-forming cells possessed clonogenicity, self-renewal, and multi-potential differentiation capability, the three criteria characterizing MSCs. Such AF-derived stem cells may potentially be an ideal candidate for DDD treatments using cell therapies or tissue engineering approaches.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Anterior cervical corpectomy and fusion (ACCF) and anterior cervical discectomy and fusion (ACDF) are 2 effective and safe surgical treatments of degenerative cervical pathologies and are associated ...with a high percentage of excellent clinical outcomes when a graft or device must be used during the surgery, such as an allograft, autograft, nano-hydroxyapatite/polyamide cages, poly-ether-ether-ketone (PEEK) cages, and titanium mesh cages (TMCs). Although TMCs have been used in cervical surgeries for almost 2 decades, no specific reviews have been performed introducing the state of this material. Thus, in the present review, we discuss the status of using TMCs in anterior cervical surgeries. Studies that tested the usage of TMCs in treating degenerative cervical pathologies were included in this review. The development and progress of TMCs, the biomechanical analysis of TMCs, the radiological and clinical assessment of TMCs, the advantages and disadvantages of using TMCs, and their prospects for future applications as a device of ACCF and ACDF in treating degenerative cervical pathologies are discussed. Studies included in this review showed that TMCs can provide sufficient biomechanical stability. Furthermore, the TMCs used in anterior cervical fusion avoid the donor-site morbidity and achieve a solid bony fusion. However, there are some shortcomings. The structural characteristics and the design of TMCs cause the TMC subsidence rate to remain high, thus resulting in multiple related complications. We believe that due to the virtues of TMCs, they are worthy of application and promotion. However, the structure of TMCs should be further optimized to reduce the TMC subsidence rate and subsidence-related complications, ultimately achieving excellent clinical results.
Ficus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its ...coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.
Mimosa bimucronata originates from tropical America and exhibits distinctive leaf movement characterized by a relative slow speed. Additionally, this species possesses the ability to fix nitrogen. ...Despite these intriguing traits, comprehensive studies have been hindered by the lack of genomic resources for M. bimucronata.
To unravel the intricacies of leaf movement and nitrogen fixation, we successfully assembled a high-quality, haplotype-resolved, reference genome at the chromosome level, spanning 648 Mb and anchored in 13 pseudochromosomes. A total of 32,146 protein-coding genes were annotated. In particular, haplotype A was annotated with 31,035 protein-coding genes, and haplotype B with 31,440 protein-coding genes. Structural variations (SVs) and allele specific expression (ASE) analyses uncovered the potential role of structural variants in leaf movement and nitrogen fixation in M. bimucronata. Two whole-genome duplication (WGD) events were detected, that occurred ~ 2.9 and ~ 73.5 million years ago. Transcriptome and co-expression network analyses revealed the involvement of aquaporins (AQPs) and Ca
-related ion channel genes in leaf movement. Moreover, we also identified nodulation-related genes and analyzed the structure and evolution of the key gene NIN in the process of symbiotic nitrogen fixation (SNF).
The detailed comparative genomic and transcriptomic analyses provided insights into the mechanisms governing leaf movement and nitrogen fixation in M. bimucronata. This research yielded genomic resources and provided an important reference for functional genomic studies of M. bimucronata and other legume species.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background
Primary cilia influence cell function and tissue development. Ciliary signaling is mediated by two intraflagellar transport (IFT) protein complexes, IFT‐A and IFT‐B. The IFT‐A complex is ...responsible for retrograde transport, and IFT140 is a core protein in the A complex. Mutations in IFT140 cause a variety of skeletal disorders. However, the expression and role of IFT140 during bone development remain unclear. In this study, to further explore the potential role of IFT140 in osteogenesis, we used cell lineage tracing and conditional knockout to analyze the distribution and function of IFT140‐positive cells during bone formation.
Results
In newborn Ift140‐creER; R26RtdTomato mice, IFT140‐positive cells were mainly located in the medullary cavity and then migrated to and differentiated on the surface of trabecular and cortical bone. In contrast, the number of IFT140‐positive cells significantly decreased in the adult stage, and these cells were only located in the bone marrow cavity for a short time. In Osx‐cre; Ift140flox/flox mice, the loss of IFT140 in preosteoblasts caused bone loss in the trabecular bone area at 10 weeks.
Conclusion
The results revealed that IFT140‐positive cells mainly contribute to the early stage of bone formation.
Key Findings
IFT140 positive cells mainly take part in early stage of osteoblast differentiation and bone development.
IFT140 positive cells were significantly increased at young age.
Conditional knockout of IFT140 in preosteoblasts results in bone dysplasia.
Full text
Available for:
FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
In multi-label learning, the use of labels correlation is crucial for the improvement of multi-label learning performance. Most of the existing methods for studying labels correlation usually do not ...consider the study of feature-space information. Further study is deserved about how to synchronize rich information contained in features-space and labels-space. In this paper, a multi-label learning algorithm of Non-Equilibrium Labels Completion with Mean Shift (i.e. NeLC-MS) was proposed. The aim of this research was to mine the feature hidden information by reconstructing the features space, and introduce non-equilibrium label correlation information so as to better improve the robustness of multi-label learning classification. First, the mean shift clustering method was used to reconstruct the information between features in the feature space to obtain the hidden information between features. Then, the new information entropy was used to measure the correlation between labels which gets the basic labels confidence matrix. Then the basic labels confidence matrix was improved to construct a Non-equilibrium labels completion matrix by the non-equilibrium parameters. Finally, the new training set was constructed by using the reconstructed features space and the Non-equilibrium Labels Completion matrix, and the existing linear classifier was used for predicting the new training set. The experimental results of the proposed algorithm in the opening benchmark multi-label datasets showed that the NeLC-MS algorithm would have some advantages over other comparative multi-label learning algorithms, and the effectiveness of the proposed method was further illustrated by the use of statistical hypothesis test and stability analysis.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Despite the clear association between myocardial injury, heart failure and depressed myocardial energetics, little is known about upstream signals responsible for remodeling myocardial metabolism ...after pathological stress. Here, we report increased mitochondrial calmodulin kinase II (CaMKII) activation and left ventricular dilation in mice one week after myocardial infarction (MI) surgery. By contrast, mice with genetic mitochondrial CaMKII inhibition are protected from left ventricular dilation and dysfunction after MI. Mice with myocardial and mitochondrial CaMKII overexpression (mtCaMKII) have severe dilated cardiomyopathy and decreased ATP that causes elevated cytoplasmic resting (diastolic) Ca
concentration and reduced mechanical performance. We map a metabolic pathway that rescues disease phenotypes in mtCaMKII mice, providing insights into physiological and pathological metabolic consequences of CaMKII signaling in mitochondria. Our findings suggest myocardial dilation, a disease phenotype lacking specific therapies, can be prevented by targeted replacement of mitochondrial creatine kinase or mitochondrial-targeted CaMKII inhibition.
We designed a unique nanocapsule for efficient single CRISPR-Cas9 capsuling, noninvasive brain delivery and tumor cell targeting, demonstrating an effective and safe strategy for glioblastoma gene ...therapy. Our CRISPR-Cas9 nanocapsules can be simply fabricated by encapsulating the single Cas9/sgRNA complex within a glutathione-sensitive polymer shell incorporating a dual-action ligand that facilitates BBB penetration, tumor cell targeting, and Cas9/sgRNA selective release. Our encapsulating nanocapsules evidenced promising glioblastoma tissue targeting that led to high PLK1 gene editing efficiency in a brain tumor (up to 38.1%) with negligible (less than 0.5%) off-target gene editing in high-risk tissues. Treatment with nanocapsules extended median survival time (68 days versus 24 days in nonfunctional sgRNA-treated mice). Our new CRISPR-Cas9 delivery system thus addresses various delivery challenges to demonstrate safe and tumor-specific delivery of gene editing Cas9 ribonucleoprotein for improved glioblastoma treatment that may potentially be therapeutically useful in other brain diseases.
PDF
