Gene Expressions
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2021 ◽  
Vol 51 (3) ◽  
pp. 311-320
Author(s):  
Iris Adriana Hernández-López ◽  
Dariel Tovar-Ramírez ◽  
Susana De la Rosa-García ◽  
Carina Shianya Álvarez-Villagómez ◽  
Gloria Gertrudys Asencio-Alcudia ◽  
...  

Tropical gar, Atractosteus tropicus Gill, 1863, is an ancient freshwater fish that is commercially cultivated in southern Mexico. Currently, there is a specific diet for its culture; however, the addition of probiotics has not been investigated. The objective of this study was to evaluate the supplementation of live yeast Debaryomyces hansenii for A. tropicus juveniles on growth, productive parameters, survival, somatic index, digestive enzyme activity, and immune system gene expressions (interleukin 10, il-10, Transforming growth factor β1, tgf-β1, and β2 microglobulin, b2m). Three experimental diets increased the dose of live yeast (0.5, 1.0, and 1.5%; 1014, 1015, and 1016CFU g diet–1, respectively) and a control diet (CD; without yeast) were designed. Daily weight gain and specific growth rate were higher in fish fed with CD and 0.5% D. hansenii. High activities of trypsin, chymotrypsin LAP, and α-amylase, as well as overexpression of il-10 in the spleen, were detected in fish feed 0.5% D. hansenii. The inclusion of D. hansenii had no positive effect on aquaculture for A. tropicus, lower doses should be tested to optimize the diet.


2021 ◽  
Vol 51 (3) ◽  
pp. 311-320
Author(s):  
Iris Adriana Hernández-López ◽  
Dariel Tovar-Ramírez ◽  
Susana De la Rosa-García ◽  
Carina Shianya Álvarez-Villagómez ◽  
Gloria Gertrudys Asencio-Alcudia ◽  
...  

Tropical gar, Atractosteus tropicus Gill, 1863, is an ancient freshwater fish that is commercially cultivated in southern Mexico. Currently, there is a specific diet for its culture; however, the addition of probiotics has not been investigated. The objective of this study was to evaluate the supplementation of live yeast Debaryomyces hansenii for A. tropicus juveniles on growth, productive parameters, survival, somatic index, digestive enzyme activity, and immune system gene expressions (interleukin 10, il-10, Transforming growth factor β1, tgf-β1, and β2 microglobulin, b2m). Three experimental diets increased the dose of live yeast (0.5, 1.0, and 1.5%; 1014, 1015, and 1016CFU g diet–1, respectively) and a control diet (CD; without yeast) were designed. Daily weight gain and specific growth rate were higher in fish fed with CD and 0.5% D. hansenii. High activities of trypsin, chymotrypsin LAP, and α-amylase, as well as overexpression of il-10 in the spleen, were detected in fish feed 0.5% D. hansenii. The inclusion of D. hansenii had no positive effect on aquaculture for A. tropicus, lower doses should be tested to optimize the diet.


2021 ◽  
Author(s):  
Haoxiang Gao ◽  
Kui Hua ◽  
Sijie Chen ◽  
Qijin Yin ◽  
Rui Jiang ◽  
...  

AbstractThe goal of big projects like Human Cell Atlas (HCA) and Human BioMedical Atlas Program (HuBMAP) is to build maps that comprehensively define and describe all cell types and their molecular features in a healthy human being. Just like geographical maps must have coordinates, a key task in building cell maps is to provide coordinate systems for cells. A well-designed coordinate system helps better understand the highly orchestrated function and organization of different cells. Cells could be depicted by external information like their spatial locations in the body and organ, the sex and race of the donor, and multiple endogenous attributes of cells such as their types, states, functions, developing trajectory, etc. These heterogeneities are encoded in or can be predicted with transcriptomics and other omics data. Cell heterogeneities are multifaceted, including three major types: continuous values or scores, categorical groups and structured annotations. Here we propose to a unified multidimensional coordinate system UniCoord to represent the multifaceted heterogeneities of cells. It is based on a general deep learning framework, with a supervised VAE structure to learn the mapping relationship between gene expressions and the generated coordinates in a low-dimensional space that encode multiple cell attributes of the three types. Experiment results on several datasets showed that UniCoord was able to represent a variety of cell heterogeneous properties that are discrete, continuous or of hierarchical structures. The trained UniCoord model can be used to automatically label attributes of cells and generate the corresponding expression data. Experiments showed that UniCoord is a feasible coordinates framework for representing multifaceted cell heterogeneity in comprehensive cell atlases.


2021 ◽  
Vol 13 (3) ◽  
pp. 303-9
Author(s):  
Imam Megantara ◽  
Ronny Lesmana ◽  
Nova Sylviana ◽  
Sunarjati Soedigdoadi ◽  
Teti Madiadipoera

BACKGROUND: The lic1A gene is an important virulence factor for non-typeable H. influenzae (NTHi), which allows its translocation from the nasopharynx into the sinonasal cavity and modulates more severe inflammatory processes. This study is aimed for identifying the potential correlation between the NTHi lic1A gene expressions and the severity of post-viral acute rhinosinusitis.METHODS: Sixty patients who were diagnosed with post-viral acute rhinosinusitis, were recruited from an ENT clinic in a referral hospital, in Bandung, West Java, Indonesia. All patients underwent a historical assessment and ENT examination. The nasal specimen was taken from the patient’s middle meatal. The NTHi lic1A gene expression was detected using Polymerase Chain Reaction (PCR).RESULTS: We observed that eight patients had the NTHi lic1A (+), with a strong correlation toward the dominant symptoms (nasal obstruction and discharge). In addition, the symptom’s duration of the NTHi lic1A (+) was twice longer than patients with the NTHi lic1A (-). Its severity was significantly more different between the two groups (p=0.034).CONCLUSION: Taken together, the presence of the NTHi lic1A gene is significantly associated with the severity of the disease and the symptom’s duration. Thus, the NTHi lic1A gene could potentially be a good marker for assessing the severity of post-viral acute rhinosinusitis cases in the future.KEYWORDS: H. influenzae, rhinosinusitis, nasal obstruction, virulence factors


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Masayuki Nakajima ◽  
Masashi Matsuyama ◽  
Mio Kawaguchi ◽  
Sosuke Matsumura ◽  
Takumi Kiwamoto ◽  
...  

AbstractThe programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) pathway could affect antimicrobial immune responses by suppressing T cell activity. Several recent studies demonstrated that blocking of the PD-1/PD-L1 pathway exacerbated Mycobacterium tuberculosis infection. However, the effect of blocking this pathway in pulmonary Mycobacterium avium–intracellulare complex (MAC) infection is not fully understood. Wild-type, PD-1-deficient mice, and PD-L1-deficient mice were intranasally infected with Mycobacterium avium bacteria. Depletion of PD-1 or PD-L1 did not affect mortality and bacterial burden in MAC-infected mice. However, marked infiltration of CD8-positive T lymphocytes was observed in the lungs of PD-1 and PD-L1-deficient mice compared to wild-type mice. Comprehensive transcriptome analysis showed that levels of gene expressions related to Th1 immunity did not differ according to the genotypes. However, genes related to the activity of CD8-positive T cells and related chemokine activity were upregulated in the infected lungs of PD-1 and PD-L1-deficient mice. Thus, the lack of change in susceptibility to MAC infection in PD-1 and PD-L1-deficient mice might be explained by the absence of obvious changes in the Th1 immune response. Furthermore, activated CD8-positive cells in response to MAC infection in these mice seemed to not be relevant in the control of MAC infection.


2021 ◽  
Author(s):  
Enze Liu ◽  
Xue Wu ◽  
Lei Wang ◽  
Yang Huo ◽  
Lang Li ◽  
...  

Cancer is a complex disease with usually multiple disease mechanisms. Target combination is a better strategy than a single target in developing cancer therapies. However, target combinations are generally more difficult to be predicted. Current CRISPR-cas9 technology enables genome-wide screening for potential targets, but only a handful of genes have been screened as target combinations. Thus, an effective computational approach for selecting candidate target combinations is highly desirable. Selected target combinations also need to be translational between cell lines and cancer patients. We have therefore developed DSCN (Double-target Selection guided by CRISPR screening and Network), a method that matches expression levels in patients and gene essentialities in cell lines through spectral-clustered protein-protein interaction (PPI) network. In DSCN, a sub-sampling approach is developed to model first-target knockdown and its impact on the PPI network, and it also facilitates the selection of a second target. Our analysis first demonstrated high correlation of the DSCN sub-sampling-based gene knockdown model and its predicted differential gene expressions using observed gene expression in 22 pancreatic cell lines before and after MAP2K1 and MAP2K2 inhibition. In our DSCN algorithm, various scoring schemes were evaluated. The 'diffusion-path'; method showed the most significant statistical power of differentiation known synthetic lethal (SL) versus non-SL gene pairs in pancreatic cancer. The superior performance of DSCN over existing network-based algorithms, such as OptiCon[1] and VIPER[2], in the selection of target combinations is attributable to its ability to calculate combinations for any gene pairs, whereas other approaches focus on the combinations among optimized regulators in the network. DSCN's computational speed is also at least ten times faster than that of other methods. Finally, in applying DSCN to predict target combinations and drug combinations for individual samples (DSCNi), we showed high correlation of DSCNi predicted target combinations with synergistic drug combinations (P = 1e-5) in pancreatic cell lines. In summary, DSCN is a highly effective computational method for the selection of target combinations.


2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Wen-jing Ning ◽  
Ren-jun Lv ◽  
Ning Xu ◽  
Xun-yao Hou ◽  
Chao Shen ◽  
...  

Objective. To investigate the effects of lycopene-loaded microemulsion (LME) on the cognitive function and neurogenesis in the dentate gyrus (DG) of the hippocampus and subventricular (SVZ) region of rats with amyloid β- (Aβ-) induced Alzheimer’s disease (AD) and its mechanism based on the Wnt/β-catenin pathway. Methods. Healthy Wistar rats were divided into four groups: the blank control (CON), AD control, traditional lycopene (LOO), and LME groups. The CON and AD groups were fed with normal saline, while the LOO group was fed with traditional lycopene, and the LME group was fed with lycopene-loaded microemulsion. Behavioral tests were performed after three weeks of gastric administration. Immunofluorescence-labeled cells were used to observe the differentiation and maturation of new nerve cells in the DG of the hippocampus and SVZ region. qRT-PCR and Western blotting detected the expression of neurogenesis genes and Wnt/β-catenin pathway-related proteins, respectively. Results. On the Morris water maze test, LME rats had significantly shortened movement trajectory on the searching platform, reduced escape latency time, and increased residence time on the original platform quadrant. In addition, more LME rats crossed the platform when it was removed. Thus, LME can improve the spatial learning and memory of Aβ-induced AD rats. On qRT-PCR, LME significantly increased Reelin, Nestin, and Pax6 gene expressions, which regulate neurogenesis. Immunofluorescence showed that LME could significantly increase BrdU+, Dcx+, BrdU+/Neun+, BrdU+/Dcx+ cells in the DG and SVZ regions, thus promoting neurogenesis. LME also reduced the number of Iba1+ and Iba1+/BrdU+ cells, thus reducing the neuroinflammatory response. On Western blot, LME upregulated the Wnt/β-catenin pathway by upregulating Wnt3a, β-catenin, Disheveled (Dvl), and p-GSK3β and downregulating p-β-catenin and GSK3β. Conclusion. LME attenuates cognitive impairment in Aβ-induced AD rats by promoting neurogenesis in the hippocampus and SVZ region through upregulating the Wnt/β-catenin pathway.


2021 ◽  
pp. 074823372110429
Author(s):  
Kaiyue Wang ◽  
Dongyan Huang ◽  
Ping Zhou ◽  
Xin Su ◽  
Rongfu Yang ◽  
...  

As a typical environmental endocrine disruptor (EED), bisphenol A (BPA) can induce pathological hyperplasia of the prostatic epithelium and stroma. This study concentrates mainly on the effect and underlying mechanisms of BPA on prostatic hyperplasia, which is based on the culture of primary human prostate epithelial cells (HPEpiC) and human prostate fibroblasts (HPrF). In an effect to screen the optimal pro-survival BPA levels, HPEpiC and HPrF were, respectively, exposed to concentration gradients of BPA (10−12 M–10−4 M) solution diluted with two corresponding medium and incubated for 72 h at 37°C. CCK-8 assay showed that 10−9 M–10−5 M BPA could facilitate the proliferation of HPEpiC, while similar proliferative effect of HPrF only needed 10−11 M–10−7 M BPA. HPrF were more sensitive to BPA than HPEpiC. The qualification of PCNA gene expression measured using quantitative real-time polymerase chain reaction (qRT-PCR) also mirrored the BPA-induced cell proliferation. Additionally, our results considered that androgen receptor (AR), estrogen receptor (ERα, ERβ), and NFKB1 gene expressions exhibited up-regulation in HPEpiC treated with 10−9 M BPA for 72 h. However, in HPrF, the identical BPA treatment could activate ERα, ERβ, and NFKB1 gene expressions and down-regulated the expression of AR levels. It is further confirmed that low-dose BPA can indeed promote the proliferation of human prostate cells in vitro, and the mechanisms of BPA for prostatic epithelial and stromal hyperplasia may not be consistent.


2023 ◽  
Vol 83 ◽  
Author(s):  
S. M. S. Shah ◽  
F. Ullah

Abstract MicroRNAs (miRNAs) are essential nonprotein-coding genes. In a range of organisms, miRNAs has been reported to play an essential role in regulating gene expressions at post-transcriptional level. They participate in most of the stress responsive processes in plants. Drought is an ultimate abiotic stress that affects the crop production. Therefore understanding drought stress responses are essential to improve the production of agricultural crops. Throughout evolution, plants have developed their own defense systems to cope with the adversities of environmental stresses. Among defensive mechanisms include the regulations of gene expression by miRNAs. Drought stress regulates the expression of some of the functionally conserved miRNAs in different plants. The given properties of miRNAs provide an insight to genetic alterations and enhancing drought resistance in cereal crops. The current review gives a summary to regulatory mechanisms in plants as well as miRNAs response to drought stresses in cereal crops. Some possible approaches and guidelines for the exploitation of drought stress miRNA responses to improve cereal crops are also described.


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