scholarly journals The Constitutive Proteome of Human Aqueous Humor and Race Specific Alterations

Proteomes ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 34
Author(s):  
Sai Karthik Kodeboyina ◽  
Tae Jin Lee ◽  
Lara Churchwell ◽  
Lane Ulrich ◽  
Kathryn Bollinger ◽  
...  
Keyword(s):  
Aqueous Humor ◽  
Protein Concentration ◽  
State Of The Art ◽  
Sample Volume ◽  
Lipid Binding ◽  
Ion Binding ◽  
Biological Processes ◽  
Liquid Chromatography Mass Spectrometry ◽  
Endopeptidase Activity ◽  
Insight Into

Aqueous humor (AH) is the fluid in the anterior and posterior chambers of the eye that contains proteins regulating ocular homeostasis. Analysis of aqueous humor proteome is challenging, mainly due to low sample volume and protein concentration. In this study, by utilizing state of the art technology, we performed Liquid-Chromatography Mass spectrometry (LC-MS/MS) analysis of 88 aqueous humor samples from subjects undergoing cataract surgery. A total of 2263 unique proteins were identified, which were sub-divided into four categories that were based on their detection in the number of samples: High (n = 152), Medium (n = 91), Low (n = 128), and Rare (n = 1892). A total of 243 proteins detected in at least 50% of the samples were considered as the constitutive proteome of human aqueous humor. The biological processes and pathways enriched in the AH proteins mainly include vesicle mediated transport, acute phase response signaling, LXR/RXR activation, complement system, and secretion. The enriched molecular functions are endopeptidase activity, and various binding functions, such as protein binding, lipid binding, and ion binding. Additionally, this study provides a novel insight into race specific differences in the AH proteome. A total of six proteins were upregulated, and five proteins were downregulated in African American subjects as compared to Caucasians.

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

scholarly journals Fragments of Locusta migratoria apoLp-III provide insight into lipid binding

BBA Advances ◽  
2021 ◽  
pp. 100020
Author(s):  
Blair A. Russell ◽  
James V.C. Horn ◽  
Paul M.M. Weers
Keyword(s):  
Locusta Migratoria ◽  
Lipid Binding ◽  
Insight Into

scholarly journals In vivo interactome profiling by enzyme‐catalyzed proximity labeling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yangfan Xu ◽  
Xianqun Fan ◽  
Yang Hu
Keyword(s):  
State Of The Art ◽  
Catalytic Efficiency ◽  
Biological Processes ◽  
Protein Protein Interaction ◽  
Current State ◽  
Protein Interactome ◽  
Potential Applications ◽  
Protein Protein Interaction Networks ◽  
Temporal And Spatial

AbstractEnzyme-catalyzed proximity labeling (PL) combined with mass spectrometry (MS) has emerged as a revolutionary approach to reveal the protein-protein interaction networks, dissect complex biological processes, and characterize the subcellular proteome in a more physiological setting than before. The enzymatic tags are being upgraded to improve temporal and spatial resolution and obtain faster catalytic dynamics and higher catalytic efficiency. In vivo application of PL integrated with other state of the art techniques has recently been adapted in live animals and plants, allowing questions to be addressed that were previously inaccessible. It is timely to summarize the current state of PL-dependent interactome studies and their potential applications. We will focus on in vivo uses of newer versions of PL and highlight critical considerations for successful in vivo PL experiments that will provide novel insights into the protein interactome in the context of human diseases.

scholarly journals Significance of Mast Cell Formed Extracellular Traps in Microbial Defense

2021 ◽  
Author(s):  
Daniel Elieh Ali Komi ◽  
Wolfgang M. Kuebler
Keyword(s):  
State Of The Art ◽  
Extracellular Dna ◽  
Cellular Mechanisms ◽  
Extracellular Traps ◽  
Synthetic Chemicals ◽  
Dna Strands ◽  
Associated Proteins ◽  
Microbial Defense ◽  
And Function ◽  
Insight Into

AbstractMast cells (MCs) are critically involved in microbial defense by releasing antimicrobial peptides (such as cathelicidin LL-37 and defensins) and phagocytosis of microbes. In past years, it has become evident that in addition MCs may eliminate invading pathogens by ejection of web-like structures of DNA strands embedded with proteins known together as extracellular traps (ETs). Upon stimulation of resting MCs with various microorganisms, their products (including superantigens and toxins), or synthetic chemicals, MCs become activated and enter into a multistage process that includes disintegration of the nuclear membrane, release of chromatin into the cytoplasm, adhesion of cytoplasmic granules on the emerging DNA web, and ejection of the complex into the extracellular space. This so-called ETosis is often associated with cell death of the producing MC, and the type of stimulus potentially determines the ratio of surviving vs. killed MCs. Comparison of different microorganisms with specific elimination characteristics such as S pyogenes (eliminated by MCs only through extracellular mechanisms), S aureus (removed by phagocytosis), fungi, and parasites has revealed important aspects of MC extracellular trap (MCET) biology. Molecular studies identified that the formation of MCET depends on NADPH oxidase-generated reactive oxygen species (ROS). In this review, we summarize the present state-of-the-art on the biological relevance of MCETosis, and its underlying molecular and cellular mechanisms. We also provide an overview over the techniques used to study the structure and function of MCETs, including electron microscopy and fluorescence microscopy using specific monoclonal antibodies (mAbs) to detect MCET-associated proteins such as tryptase and histones, and cell-impermeant DNA dyes for labeling of extracellular DNA. Comparing the type and biofunction of further MCET decorating proteins with ETs produced by other immune cells may help provide a better insight into MCET biology in the pathogenesis of autoimmune and inflammatory disorders as well as microbial defense.

Towards Interconnected Blockchains

2021 ◽  
Vol 54 (7) ◽  
pp. 1-39
Author(s):  
Ankur Lohachab ◽  
Saurabh Garg ◽  
Byeong Kang ◽  
Muhammad Bilal Amin ◽  
Junmin Lee ◽  
...  
Keyword(s):  
State Of The Art ◽  
The State ◽  
Future Research ◽  
Missing Link ◽  
Layered Architecture ◽  
Blockchain Technology ◽  
Wide Scale ◽  
Effective Development ◽  
Insight Into ◽  
Game Changer

Unprecedented attention towards blockchain technology is serving as a game-changer in fostering the development of blockchain-enabled distinctive frameworks. However, fragmentation unleashed by its underlying concepts hinders different stakeholders from effectively utilizing blockchain-supported services, resulting in the obstruction of its wide-scale adoption. To explore synergies among the isolated frameworks requires comprehensively studying inter-blockchain communication approaches. These approaches broadly come under the umbrella of Blockchain Interoperability (BI) notion, as it can facilitate a novel paradigm of an integrated blockchain ecosystem that connects state-of-the-art disparate blockchains. Currently, there is a lack of studies that comprehensively review BI, which works as a stumbling block in its development. Therefore, this article aims to articulate potential of BI by reviewing it from diverse perspectives. Beginning with a glance of blockchain architecture fundamentals, this article discusses its associated platforms, taxonomy, and consensus mechanisms. Subsequently, it argues about BI’s requirement by exemplifying its potential opportunities and application areas. Concerning BI, an architecture seems to be a missing link. Hence, this article introduces a layered architecture for the effective development of protocols and methods for interoperable blockchains. Furthermore, this article proposes an in-depth BI research taxonomy and provides an insight into the state-of-the-art projects. Finally, it determines possible open challenges and future research in the domain.

scholarly journals The apple C2H2-type zinc finger transcription factor MdZAT10 positively regulates JA-induced leaf senescence by interacting with MdBT2

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Kuo Yang ◽  
Jian-Ping An ◽  
Chong-Yang Li ◽  
Xue-Na Shen ◽  
Ya-Jing Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Transcription Factor ◽  
Liquid Chromatography ◽  
Zinc Finger ◽  
Leaf Senescence ◽  
Transcriptional Activity ◽  
Molecular Mechanisms ◽  
Liquid Chromatography Mass Spectrometry ◽  
Zinc Finger Transcription Factor ◽  
Insight Into

AbstractJasmonic acid (JA) plays an important role in regulating leaf senescence. However, the molecular mechanisms of leaf senescence in apple (Malus domestica) remain elusive. In this study, we found that MdZAT10, a C2H2-type zinc finger transcription factor (TF) in apple, markedly accelerates leaf senescence and increases the expression of senescence-related genes. To explore how MdZAT10 promotes leaf senescence, we carried out liquid chromatography/mass spectrometry screening. We found that MdABI5 physically interacts with MdZAT10. MdABI5, an important positive regulator of leaf senescence, significantly accelerated leaf senescence in apple. MdZAT10 was found to enhance the transcriptional activity of MdABI5 for MdNYC1 and MdNYE1, thus accelerating leaf senescence. In addition, we found that MdZAT10 expression was induced by methyl jasmonate (MeJA), which accelerated JA-induced leaf senescence. We also found that the JA-responsive protein MdBT2 directly interacts with MdZAT10 and reduces its protein stability through ubiquitination and degradation, thereby delaying MdZAT10-mediated leaf senescence. Taken together, our results provide new insight into the mechanisms by which MdZAT10 positively regulates JA-induced leaf senescence in apple.

scholarly journals Capsule-LPI: a LncRNA–protein interaction predicting tool based on a capsule network

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ying Li ◽  
Hang Sun ◽  
Shiyao Feng ◽  
Qi Zhang ◽  
Siyu Han ◽  
...  
Keyword(s):  
Protein Interactions ◽  
State Of The Art ◽  
Recognition Performance ◽  
Feature Learning ◽  
Biological Processes ◽  
Multimodal Features ◽  
Learning Architectures ◽  
Motif Information ◽  
Experimental Comparisons ◽  
Better Than

Abstract Background Long noncoding RNAs (lncRNAs) play important roles in multiple biological processes. Identifying LncRNA–protein interactions (LPIs) is key to understanding lncRNA functions. Although some LPIs computational methods have been developed, the LPIs prediction problem remains challenging. How to integrate multimodal features from more perspectives and build deep learning architectures with better recognition performance have always been the focus of research on LPIs. Results We present a novel multichannel capsule network framework to integrate multimodal features for LPI prediction, Capsule-LPI. Capsule-LPI integrates four groups of multimodal features, including sequence features, motif information, physicochemical properties and secondary structure features. Capsule-LPI is composed of four feature-learning subnetworks and one capsule subnetwork. Through comprehensive experimental comparisons and evaluations, we demonstrate that both multimodal features and the architecture of the multichannel capsule network can significantly improve the performance of LPI prediction. The experimental results show that Capsule-LPI performs better than the existing state-of-the-art tools. The precision of Capsule-LPI is 87.3%, which represents a 1.7% improvement. The F-value of Capsule-LPI is 92.2%, which represents a 1.4% improvement. Conclusions This study provides a novel and feasible LPI prediction tool based on the integration of multimodal features and a capsule network. A webserver (http://csbg-jlu.site/lpc/predict) is developed to be convenient for users.

Exploiting native language interference for native language identification

2020 ◽  
pp. 1-31
Author(s):  
Ilia Markov ◽  
Vivi Nastase ◽  
Carlo Strapparava
Keyword(s):  
Second Language ◽  
State Of The Art ◽  
Native Language ◽  
Emotion Expression ◽  
The State ◽  
Language Identification ◽  
Independent Features ◽  
Insight Into

Abstract Native language identification (NLI)—the task of automatically identifying the native language (L1) of persons based on their writings in the second language (L2)—is based on the hypothesis that characteristics of L1 will surface and interfere in the production of texts in L2 to the extent that L1 is identifiable. We present an in-depth investigation of features that model a variety of linguistic phenomena potentially involved in native language interference in the context of the NLI task: the languages’ structuring of information through punctuation usage, emotion expression in language, and similarities of form with the L1 vocabulary through the use of anglicized words, cognates, and other misspellings. The results of experiments with different combinations of features in a variety of settings allow us to quantify the native language interference value of these linguistic phenomena and show how robust they are in cross-corpus experiments and with respect to proficiency in L2. These experiments provide a deeper insight into the NLI task, showing how native language interference explains the gap between baseline, corpus-independent features, and the state of the art that relies on features/representations that cover (indiscriminately) a variety of linguistic phenomena.

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