Transcriptome reveals genes involving in black skin color formation of ducks

Lei Wang,Hehe Liu,Bo Hu,Jiwei Hu,Hengyong Xu,Hua He,Chunchun Han,Bo Kang,Lili Bai,Rongping Zhang,Jiwen Wang,Shengqiang Hu,Liang Li 한국유전학회 2021 Genes & Genomics Vol.43 No.2

Background Skin color is colorful for birds, which has been reported to be associated with multi-biological functions, such as crypsis, camoufage, social signaling and mate choice, but little is known about its underlying molecular mechanism. Objective Studies on the major genes afecting the black skin color of ducks. Methods For this purpose, Silver ammonia staining and RNA-seq analysis were carried out to identify the diferences in tissue morphology and gene expressions between black and yellow skin ducks. Results The silver ammonia dyes slice results showed that in the development of black duck, the content of melanin in black skin gradually increased and then decreased, and the content of melanin in yellow and black skin was signifcantly diferent. Through transcriptome, a total of 102 and 84 diferentially expressed genes (DEGs) were identifed in beak skin and web skin, respectively. These DEGs were enriched in melanin biosynthesis and play a critical role in melanogenesis pathway. Co-expression analysis showed that EDNRB2 was the only gene associated with black skin color in DEGs, which was also consistent with qRT-PCR. Conclusions The melanin synthesis pathway dominated by EDNRB2 up-regulated the amount of melanin synthesis, leading to the formation of black skin in ducks.

Prognostic Significance of Beclin-1 Expression in Colorectal Cancer: a Meta-analysis

Han, Ye,Xue, Xiao-Feng,Shen, Hu-Gang,Guo, Xiao-Bo,Wang, Xu,Yuan, Bin,Guo, Xing-Po,Kuang, Yu-Ting,Zhi, Qiao-Ming,Zhao, Hong Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.11

Objective: Beclin-1 has recently been observed as an essential marker of autophagy in several cancers. However, the prognostic role of Beclin-1 in colorectal neoplasia remains controversial. Our study aimed to evaluate the potential association between Beclin-1 expression and the outcome of colorectal cancer patients. Materials and Methods: All related studies were systematically searched in Pubmed, Embase, Springer and Chinese National Knowledge Infrastructure databases (CNKI), and then a meta-analysis was performed to determine the association of Beclin-1 expression with clinical outcomes. Finally, a total of 6 articles were included in our analysis. Results: Our data showed that high Beclin-1 expression in patients with CRC was associated with poor prognosis in terms of tumor distant metastasis (OR=2.090, 95%CI=1.061-4.119, p=0.033) and overall survival (RR=1.422, 95%CI=1.032-1.959, p=0.031). However, we did not found any correlation between Beclin-1 over-expression and tumor differentiation (OR=1.711, 95%CI=0.920-3.183, p=0.090). In addition, there was no evidence of publication bias as suggested by Egger's tests for tumor distant metastasis (p=1.000), differentiation (p=1.000) and OS (p=0.308). Conclusions: Our present meta-analysis indicated that elevated Beclin-1 expression iss associated with tumor metastasis and a poor prognosis in patients with CRC. Beclin-1 might serve as an efficient prognostic indicator in CRC, and could be a new molecular target in CRC therapy.

Investigation of the strength of concrete-like material with waste rock and aeolian sand as aggregate by machine learning

Hu Yafei,Li Keqing,Zhang Bo,Han Bin 한국CDE학회 2022 Journal of computational design and engineering Vol.9 No.5

Solid waste filling is an important development direction for filling mining technology. This paper proposes to use waste rock and aeolian sand as aggregates to fill the underground extraction area in order to reduce the environmental damage of related waste solid. The experiments are optimized by response surface methodology and multivariate nonlinear response models are constructed to investigate the effects of different factors on uniaxial compressive strength (UCS) of concrete-like material (CLM). The performance of different swarm intelligence optimization algorithms is analyzed and combined with support vector regression model (SVR) to construct an intelligent prediction model for UCS. The results show that the packing density has a maximum value of 0.74 when the proportion of waste rock is around 0.6. The response model constructed in this paper has a P-value < 0.01 and R2 > 0.8, which indicates its high significance and goodness of fit. The UCS of CLM increases with the increase of cement content and slurry mass fraction, while it also increases and then decreases with the increase of proportion of waste rock. The ratio of waste rock and aeolian sand will affect the compactness of cemented structure. The better the ratio, the higher the average grey value of the cemented structure, the more compactness the cemented structure. The whale optimization algorithm-SVR model constructed in this paper has a prediction accuracy of more than 99% for UCS of CLM, which achieves high accuracy and fast prediction of UCS under multifactor conditions.

Immunoprofiling of the Tryptophan-Rich Antigen Family in <i>Plasmodium vivax</i>

Wang, Bo,Lu, Feng,Cheng, Yang,Chen, Jun-Hu,Jeon, Hye-Yoon,Ha, Kwon-Soo,Cao, Jun,Nyunt, Myat Htut,Han, Jin-Hee,Lee, Seong-Kyun,Kyaw, Myat Phone,Sattabongkot, Jetsumon,Takashima, Eizo,Tsuboi, Takafumi,H American Society for Microbiology 2015 Infection and immunity Vol.83 No.8

<P>Tryptophan-rich antigens (TRAgs) are an antigen family that has been identified in human and rodent malaria parasites. TRAgs have been proposed as candidate antigens for potential vaccines. The <I>Plasmodium vivax</I> TRAg (PvTRAg) family includes 36 members. Each PvTRAg contains a tryptophan-rich (TR) domain in the C-terminal region. In this study, we recombinantly expressed all 36 PvTRAgs using a cell-free expression system, and, for the first time, profiled the IgG antibody responses against all PvTRAgs in the sera from 96 vivax malaria patients and 40 healthy individuals using protein microarray technology. The mean seropositive rate for all PvTRAgs was 60.3%. Among them, nine PvTRAgs were newly identified in this study and showed a seropositive rate of >50%. Five of them, PvTRAg_13, PvTRAg_15, PvTRAg_16, PvTRAg_26, and PvTRAg_29, produced higher levels of IgG antibody, even in low-endemicity countries. In addition, the results of an immunofluorescence analysis suggest that PvTRAgs are, at least in part, associated with caveola-vesicle complexes, a unique structure of <I>P. vivax</I>-infected erythrocytes. The mechanism of formation and the function of these abundant membrane structures are not known. Further investigation aimed at determining the functions of these proteins would lead to a better understanding of the blood-stage biology of <I>P. vivax</I>.</P>

Food Microbiology and Biotechnology : Gene Cloning and Characterization of an α-Amylase from Alteromonas macleodii B7 for Enteromorpha Polysaccharide Degradation

( Xue Feng Han ),( Bo Kun Lin ),( Gan Ji Ru ),( Zhi Biao Zhang ),( Yan Liu ),( Zhong Hu ) 한국미생물 · 생명공학회 2014 Journal of microbiology and biotechnology Vol.24 No.2

Enteromorpha polysaccharides (EP) extracted from green algae have displayed a wide variety of biological activities. However, their high molecular weight leads to a high viscosity and low solubility, and therefore, greatly restrains their application. To solve this problem, bacteria from the surface of Enteromorpha were screened, and an Alteromonas macleodii strain B7 was found to be able to decrease the molecular weight of EP in culture media. Proteins harvested from the supernatant of the A. macleodii B7 culture were subjected to native gel electrophoresis, and a band corresponding to the Enteromorpha polysaccharide lyase (EPL) was detected by activity staining. The enzyme identity was subsequently confirmed by MALDI-TOF/TOF mass spectrometry as the putative α-amylase reported in A. macleodii ATCC 27126. The amylase gene (amySTU) from A. macleodii B7 was cloned into Escherichia coli, resulting in highlevel expression of the recombinant enzyme with EP-degrading activity. AmySTU was found to be cold-adapted; however, its optimal enzyme activity was detected at 40oC. The α-amylase was highly stable over a broad pH range (5.5-10) with the optimal pH at 7.5-8.0. The highest enzyme activity was detected when NaCl concentration was 2%, which dropped by 50% when the NaCl concentration was increased to 16%, showing an excellent nature of halotolerance. Furthermore, the amylase activity was not significantly affected by tested surfactants or the presence of some organic solvents. Therefore, the A. macleodii strain B7 and its α-amylase can be useful in lowering EP molecular weight and in starch processing.

변형률 속도 효과를 고려한 355㎚ UV 레이저 다중 펄스 미세가공의 전산해석에 관한 연구

이정한(Jung Han Lee),오재용(Jae Yong Oh),박상후(Sang Hu Park),남기중(Gi-Jung Nam),류광현(Gwang-Hyun Ryu),신석훈(Suk-Hun Shin),신보성(Bo-Sung Shin) Korean Society for Precision Engineering 2010 한국정밀공학회지 Vol.27 No.10

Transposon <i>Ac/Ds</i> -induced chromosomal rearrangements at the rice <i>OsRLG5</i> locus

Xuan, Yuan Hu,Piao, Hai Long,Je, Byoung Il,Park, Soon Ju,Park, Su Hyun,Huang, Jin,Zhang, Jian Bo,Peterson, Thomas,Han, Chang-deok Oxford University Press 2011 Nucleic acids research Vol.39 No.22

<P>Previous studies have shown that pairs of closely-linked <I>Ac/Ds</I> transposable elements can induce various chromosomal rearrangements in plant genomes. To study chromosomal rearrangements in rice, we isolated a line (<I>OsRLG5-161)</I> that contains two inversely-oriented <I>Ds</I> insertions in <I>OsRLG5</I> (<I>Oryza sativa</I> Receptor like kinase Gene 5). Among approximately 300 plants regenerated from <I>OsRLG5-161</I> heterozygous seeds, 107 contained rearrangements including deletions, duplications and inversions of various sizes. Most rearrangements were induced by previously identified alternative transposition mechanism. Furthermore, we also detected a new class of rearrangements that contain juxtaposed inversions and deletions on the same chromosome. We propose that these novel alleles were generated by a previously unreported type of alternative transposition reactions involving the 5′ and 3′ termini of two inversely-oriented <I>Ds</I> elements located on the same chromatid. Finally, 11% of rearrangements contained inversions resulting from homologous recombination between the two inverted <I>Ds</I> elements in <I>OsRLG5-161</I>. The high frequency inheritance and great variety of rearrangements obtained suggests that the rice regeneration system results in a burst of transposition activity and a relaxation of the controls which normally limit the transposition competence of individual <I>Ds</I> termini. Together, these results demonstrate a greatly enlarged potential of the <I>Ac/Ds</I> system for plant chromosome engineering.</P>

Privet golden leaves adapt unexpectedly well to light changes

Ming Yuan,Bo Huang,Li-Hua Dong,Qiao-Hong Han,Yong Yang,Chun-Bang Ding,Chao Hu,Yang-Er Chen,Zhong-Wei Zhang,Shu Yuan 한국원예학회 2020 Horticulture, Environment, and Biotechnology Vol.61 No.4

Golden-leaf privet ( Ligustrum × vicaryi ) is widely used as a horticultural shrub because of its upper golden leaves, butits lower leaves are green. However, the putative mechanisms of its upper golden leaves and the leaf color changes inresponse to light shifts have not been well studied so far. Here, chlorophylls (Chl), carotenoids, and Chl precursors from bothgolden and green leaves grown in full sunlight (approximately 1200 μmol photons m −2 s −1 at noon) or low-light conditions(180 μmol m −2 s −1 ) were determined spectrophotometrically. In addition, their gas exchange parameters and Chl fl uorescencewere measured in situ. Metabolic fl ux analysis of chlorophyll intermediates indicated that the conversion of prochlorophyllideto chlorophyllide was signifi cantly blocked in golden leaves when compared with green leaves. Green leaves showed higherphotosynthetic capacity in low light than golden leaves, but golden leaves presented unexpectedly stronger photosyntheticcapacity and lower reactive oxygen species accumulation under the high-light condition. Furthermore, golden leaves showeda higher level of nonphotochemical quenching (NPQ) after the light-to-dark shift and presented a stronger adaptive abilityto a broad range of light environments. Higher NPQ values and less oxidative damage in golden leaves may be correlatedwith their higher carotenoid levels. The results imply that lower chlorophyll levels and higher carotenoid levels in canopyleaves may help privet plants acclimate better to illumination changes. This study demonstrates the key role of irradiance ingenerating the two types of Ligustrum × vicaryi leaves and sheds a light on cultivation of other ornamental foliage plants.

변형률 속도 효과를 고려한 355 ㎚ UV 레이저 구리재질의 싱글 펄스 전산해석

이정한(Jung-Han Lee),오재용(Jae Yong Oh),박상후(Sang Hu Park),신보성(Bo Sung Shin) 한국기계가공학회 2010 한국기계가공학회지 Vol.9 No.3

Recently, UV pulse laser is widely used in micro machining of the research, development and industry field of IT, NT and BT products because the laser short wavelength provides not only micro drilling, micro cutting and micro grooving which has a very fine line width, but also high absorption coefficient which allows a lot of type of materials to be machined more easily. To analyze the dynamic deformation during a very short processing time, which is nearly about several tens nanoseconds, the commercial Finite Element Analysis (FEA) code, LS-DYNA 3D, was employed for the computitional simulation of the UV laser micro machining behavior for thin copper material in this paper. A finite element model considering high strain rate effect is especially suggested to investigate the micro phenomena which are only dominated by mechanically pressure impact in disregard of thennally heat transfer. From these computational results, some of dynamic deformation behaviors such as dent deformation shapes, strains and stresses distributions were observed and compared with previous experimental works. These will help us to understand micro interaction between UV laser beam and material.

Systemic Inflammatory Biomarkers, Especially Fibrinogen to Albumin Ratio, Predict Prognosis in Patients with Pancreatic Cancer

Lin Fang,Fei-Hu Yan,Chao Liu,Jing Chen,Dan Wang,Chun-Hui Zhang,Chang-Jie Lou,Jie Lian,Yang Yao,Bo-Jun Wang,Rui-Yang Li,Shu-Ling Han,Yi-Bing Bai,Jia-Ni Yang,Zhi-Wei Li,Yan-Qiao Zhang 대한암학회 2021 Cancer Research and Treatment Vol.53 No.1

Purpose Systemic inflammatory response is a critical factor that promotes the initiation and metastasis of malignancies including pancreatic cancer (PC). This study was designed to determine and compare the prognostic value of neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR), and fibrinogen-to-albumin ratio (FAR) in resectable PC and locally advanced or metastatic PC. Materials and Methods Three hundred fifty-three patients with resectable PC and 807 patients with locally advan-ced or metastatic PC were recruited in this study. These patients were classified into a training set (n=758) and a validation set (n=402). Kaplan-Meier survival plots and Cox proportional hazards regression models were used to analyze prognosis. Results Overall survival (OS) was significantly better for patients with resectable PC with low preoperative PLR (p=0.048) and MLR (p=0.027). Low FAR, MLR, NLR (p < 0.001), and PLR (p=0.003) were significantly associated with decreased risk of death for locally advanced or metastatic PC patients. FAR (hazard ratio [HR], 1.522; 95% confidential interval [CI], 1.261 to 1.837; p < 0.001) and MLR (HR, 1.248; 95% CI, 1.017 to 1.532; p=0.034) were independent prognostic factors for locally advanced or metastatic PC. Conclusion The prognostic roles of FAR, MLR, NLR, and PLR in resectable PC and locally advanced or metastatic PC were different. FAR showed the most prognostic power in locally advanced or metastatic PC. Low FAR was positively correlated with OS in locally advanced or metastatic PC, which could be used to predict the prognosis.