Combining meta-QTL with RNA-seq data to identify candidate genes of kernel row number trait in maize

Kernel row number is an important component of grain yield in maize. With development of classical quantitative trait loci (QTL) mapping and modern RNA-seq, numerous QTL and tissue-specific gene expression data were accumulated in previous studies. In this paper, a total of initial 373 QTL for grain yield (GY) and kernel row number (KRN) were collected based on 29 previous literatures. Fifty-four meta-QTL (MQTL) were detected via the meta-analysis method with IBM2 2008 Neighbors as a reference map, including 19 for GY and 35 for KRN. These MQTL were unevenly distributed on all 10 chromosomes. Chromosome 1 harbored the most initial QTL and MQTL, and chromosome 7 contained the least. Three MQTL for KRN have been overlapped with MQTL for GY on chromosomes 1 and 3. A total of 1,588 (46.07%) out of 3,447 genes located in the KRN MQTL regions were identified by gene expression data, and categorized into 101 significant GO terms. Meanwhile, six candidate genes were identified from MQTL regions, which are homologous to three functionally characterized genes found to participate in plant inflorescence development. The identified MQTL could be applied to marker-assisted selection (MAS) to facilitate yield architecture, QTL fine mapping and gene cloning in the maize community. Furthermore, the identified candidate genes could enhance the selection efficiency by MAS directly, and could illuminate molecular mechanisms of grain yield in maize

SIRT1 silencing confers neuroprotection through IGF-1 pathway activation

The following study demonstrated that, in in vitro differentiated neurons, SIRT1 silencing induced an increase of IGF-1 protein expression and secretion and of IGF-1R protein levels which, in turn, prolonged neuronal cell survival in presence of an apoptotic insult. On the contrary, SIRT1 overexpression increased cell death. In particular, IGF-1 and IGF-1R expression levels were negatively regulated by SIRT1. In SIRT1 silenced cells, the increase in IGF-1 and IGF-1R expression was associated to an increase in AKT and ERK1/2 phosphorylation. Moreover, neuronal differentiation was reduced in SIRT1 overexpressing cells and increased in SIRT1 silenced cells. We conclude that SIRT1 silenced neurons appear more committed to differentiation and more resistant to cell death through the activation of IGF-1 survival pathway. J. Cell. Physiol. 228: 17541761, 2013. (c) 2013 Wiley Periodicals, Inc

Predictive value of the resistance of the probe to pass through the lesion in the diagnosis of peripheral pulmonary lesions using radial probe endobronchial ultrasound with a guide sheath

BackgroundTransbronchial lung biopsy guided by radial probe endobronchial ultrasonography with a guide sheath (EBUS-GS-TBLB) is becoming a significant approach for diagnosing peripheral pulmonary lesions (PPLs). We aimed to explore the clinical value of the resistance of the probe to pass through the lesion in the diagnosis of PPLs when performing EBUS-GS-TBLB, and to determine the optimum number of EBUS-GS-TBLB.MethodsWe performed a prospective, single-center study of 126 consecutive patients who underwent EBUS-GS-TBLB for solid and positive-bronchus-sign PPLs where the probe was located within the lesion from September 2019 to May 2022. The classification of probe resistance for each lesion was carried out by two bronchoscopists independently, and the final result depended on the bronchoscopist responsible for the procedures. The primary endpoint was the diagnostic yield according with the resistance pattern. The secondary endpoints were the optimum number of EBUS-GS-TBLB and factors affecting diagnostic yield. Procedural complications were also recorded.ResultsThe total diagnostic yield of EBUS-GS-TBLB was 77.8%, including 83.8% malignant and 67.4% benign diseases (P=0.033). Probe resistance type II displayed the highest diagnostic yield (87.5%), followed by type III (81.0%) and type I (61.1%). A significant difference between the diagnostic yield of malignant and benign diseases was detected in type II (P = 0.008), whereas others did not. Although most of the malignant PPLs with a definitive diagnosis using EBUS-GS-TBLB in type II or type III could be diagnosed in the first biopsy, the fourth biopsy contributed the most sufficient biopsy samples. In contrast, considerably limited tissue specimens could be obtained for each biopsy in type I. The inter-observer agreement of the two blinded bronchoscopists for the classification of probe resistance was excellent (κ = 0.84).ConclusionThe probe resistance is a useful predictive factor for successful EBUS-GS-TBLB diagnosis of solid and positive-bronchus-sign PPLs where the probe was located within the lesion. Four serial biopsies are appropriate for both probe resistance type II and type III, and additional diagnostic procedures are needed for type I

Identifying long-term stable refugia for dominant Castanopsis species of evergreen broad-leaved forests in East Asia: A tool for ensuring their conservation

Identifying and protecting refugia is a priority for conservation management under projected anthropogenic climate change. We have two main objectives: the first is to explore the spatial (East Asia) and temporal (Last Glacial Maximum to year 2070) distribution patterns of dominant Castanopsis species of evergreen broad-leaved forests, also the relation with their niche breadths; the second is to identify long-term stable refugia for preserving these species and provide a framework of conservation strategies. We find that there is an extraordinary richness with 32 dominant Castanopsis species, and they form both a geographically and climatically almost unbroken connection from ca. 5°N to 38°N, having thus ecological significance. During the Mid-Holocene and, particularly, the Last Glacial Maximum, the predicted suitable areas of the species as a whole were larger than those in the present. By 2070, potentially suitable areas with high richness of dominant Castanopsis species will be reduced by 94.5 % on average. No correlation between species niche breadths and distribution ranges is found, which could be due to regional climate stability. Mountains of southwestern and southern Yunnan in China are identified as climatically long-term stable refugia for 7¿9 Castanopsis species. We recommend that these refugia have the highest priority of conservation to prevent their extinction. Our suggested urgent measures include improving the effectiveness of currently protected Castanopsis species and expanding the network of protected areas to cover a larger fraction of the refugia, as well as ensuring Castanopsis species natural regeneration potential in fragmented and natural secondary forest areas.This study received financial support from the Major Program for Basic Research Project of Yunnan Province, China (202101BC070002), the Science and Technology Department of Yunnan University, China (2019YNU002), the Ministry of Science and Technology of China (2015FY210200-15), the Spanish Ministry of Science and Innovation (grant PID2020-119163GB-I00 funded by MCIN/AEI/10.13039/501100011033), the Environment Research and Technology Development Fund of the Environmental Restoration and Conservation Agency of Japan (JPMEERF20202002), and the Northeastern Research Institute of Petrified Wood and Mineral Resources, Nakhon Ratchasima Rajabhat University, Thailand.Keywords 1. Introduction 2. Materials and methods 2.1. Data collection and notations 2.2. Ecological niche modeling 2.3. Data analyses 3. Results 3.1. Dominant Castanopsis species in East Asia today: richness and distribution patterns 3.2. Richness of dominant Castanopsis species shaped by climate change 3.3. Niche groups and niche breadths of dominant Castanopsis species 3.4. Climatically long-term stable refugia 4. Discussion 4.1. Richness of dominant Castanopsis species shaped by climate change 4.2. Niche groups and niche breadths of dominant Castanopsis species 4.3. Long-term stable refugia and conservation strategies 5. Conclusions CRediT authorship contribution statement Declaration of competing interest Acknowledgements Appendix A. Supplementary material Reference

Cellular Mechanism Underlying Hydrogen Sulfide Mediated Epithelial K+ Secretion in Rat Epididymis

As a novel gasotransmitter, hydrogen sulfide (H2S) elicits various physiological actions including smooth muscle relaxation and promotion of transepithelial ion transport. However, the pro-secretory function of H2S in the male reproductive system remains largely unclear. The aim of this study is to elucidate the possible roles of H2S in modulating rat epididymal intraluminal ionic microenvironment essential for sperm storage. The results revealed that endogenous H2S-generating enzymes cystathionine β-synthetase (CBS) and cystathionine γ-lyase (CSE) were both expressed in rat epididymis. CBS located predominantly in epithelial cells whilst CSE expressed primarily in smooth muscle cells. The relative expression level of CBS and CSE escalated from caput to cauda regions of epididymis, which was paralleled to the progressively increasing production of endogenous H2S. The effect of H2S on epididymal epithelial ion transportation was investigated using short-circuit current (ISC), measurement of intracellular ion concentration and in vivo rat epididymal microperfusion. Our data showed that H2S induced transepithelial K+ secretion via adenosine triphosphate-sensitive K+ (KATP) channel and large conductance Ca2+-activated K+ (BKCa) channel. Transient receptor potential vanilloid 4 (TRPV4) channel-mediated Ca2+ influx was implicated in the activation of BKCa channel. In vivo studies further demonstrated that H2S promoted K+ secretion in rat epididymal epithelium. Inhibition of endogenous H2S synthesis caused a significant decrease in K+ concentration of cauda epididymal intraluminal fluid. Moreover, our data demonstrated that high extracellular K+ concentration actively depressed the motility of cauda epididymal sperm in a pH-independent manner. Collectively, the present study demonstrated that H2S was vital to the formation of high K+ concentration in epididymal intraluminal fluid by promoting the transepithelial K+ secretion, which might contribute to the maintenance of the cauda epididymal sperm in quiescent dormant state before ejaculation

Photocatalytic Degradation of Organic Pollutants in Water Using Graphene Oxide Composite

Developing sustainable and less-expensive technique is always challenging task in water treatment process. This chapter explores the recent development of photocatalysis technique in organic pollutant removal from the water. Particularly, advantages of graphene oxide in promoting the catalytic performance of semiconductor, metal nanoparticle and polymer based photocatalyst materials. Owing to high internal surface area and rapid electron conducting property of graphene oxide fostering as backbone scaffold for effective hetero-photocatalyst loading, and rapid photo-charge separation enables effective degradation of pollutant. This chapter summaries the recent development of graphene oxide composite (metal oxide, metal nanoparticle, metal chalcogenides, and polymers) in semiconductor photocatalysis process towards environmental remediation application

Comparative Analyses by Sequencing of Transcriptomes during Skeletal Muscle Development between Pig Breeds Differing in Muscle Growth Rate and Fatness

Understanding the dynamics of muscle transcriptome during development and between breeds differing in muscle growth is necessary to uncover the complex mechanism underlying muscle development. Herein, we present the first transcriptome-wide longissimus dorsi muscle development research concerning Lantang (LT, obese) and Landrace (LR, lean) pig breeds during 10 time-points from 35 days-post-coitus (dpc) to 180 days-post-natum (dpn) using Solexa/Illumina's Genome Analyzer. The data demonstrated that myogenesis was almost completed before 77 dpc, but the muscle phenotypes were still changed from 77 dpc to 28 dpn. Comparative analysis of the two breeds suggested that myogenesis started earlier but progressed more slowly in LT than in LR, the stages ranging from 49 dpc to 77 dpc are critical for formation of different muscle phenotypes. 595 differentially expressed myogenesis genes were identified, and their roles in myogenesis were discussed. Furthermore, GSK3B, IKBKB, ACVR1, ITGA and STMN1 might contribute to later myogenesis and more muscle fibers in LR than LT. Some myogenesis inhibitors (ID1, ID2, CABIN1, MSTN, SMAD4, CTNNA1, NOTCH2, GPC3 and HMOX1) were higher expressed in LT than in LR, which might contribute to more slow muscle differentiation in LT than in LR. We also identified several genes which might contribute to intramuscular adipose differentiation. Most important, we further proposed a novel model in which MyoD and MEF2A controls the balance between intramuscular adipogenesis and myogenesis by regulating CEBP family; Myf5 and MEF2C are essential during the whole myogenesis process while MEF2D affects muscle growth and maturation. The MRFs and MEF2 families are also critical for the phenotypic differences between the two pig breeds. Overall, this study contributes to elucidating the mechanism underlying muscle development, which could provide valuable information for pig meat quality improvement

Business analytics in industry 4.0: a systematic review

Recently, the term “Industry 4.0” has emerged to characterize several Information Technology and Communication (ICT) adoptions in production processes (e.g., Internet-of-Things, implementation of digital production support information technologies). Business Analytics is often used within the Industry 4.0, thus incorporating its data intelligence (e.g., statistical analysis, predictive modelling, optimization) expert system component. In this paper, we perform a Systematic Literature Review (SLR) on the usage of Business Analytics within the Industry 4.0 concept, covering a selection of 169 papers obtained from six major scientific publication sources from 2010 to March 2020. The selected papers were first classified in three major types, namely, Practical Application, Reviews and Framework Proposal. Then, we analysed with more detail the practical application studies which were further divided into three main categories of the Gartner analytical maturity model, Descriptive Analytics, Predictive Analytics and Prescriptive Analytics. In particular, we characterized the distinct analytics studies in terms of the industry application and data context used, impact (in terms of their Technology Readiness Level) and selected data modelling method. Our SLR analysis provides a mapping of how data-based Industry 4.0 expert systems are currently used, disclosing also research gaps and future research opportunities.The work of P. Cortez was supported by FCT - Fundação para a Ciência e Tecnologia within the R&D Units Project Scope: UIDB/00319/2020. We would like to thank to the three anonymous reviewers for their helpful suggestions