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Pedro Silva
Gold Contributor
24,000 Points

Contributions by role

Author 945
Preprint Author 280
Reviewer 220
Editor 22,555
Preprint Feedback 90
Answers 20

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Biochemistry
Biophysics
Computational Biology
Computational Science
Drugs and Devices
Pharmacology
Theoretical and Computational Chemistry
Photochemistry
Biophysical Chemistry
Catalysis
Physical Organic Chemistry
Bioinformatics
Cognitive Disorders
Physical Chemistry (other)
Cell Biology
Molecular Biology
Histology
Virology
Immunology
Crystallography
Transition Metal Chemistry
Data Mining and Machine Learning
Data Science
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Microbiology
Plant Science
Freshwater Biology
Genomics
Neuroscience
Cardiology
Ecology
Environmental Sciences
Evolutionary Studies
Genetics
Entomology
Marine Biology
Oncology
Biotechnology
Veterinary Medicine
Anesthesiology and Pain Management
Bioengineering
Toxicology
Ecosystem Science
Food Science and Technology
Mathematical Biology
Science and Medical Education
Aquatic and Marine Chemistry
Biological Oceanography
Medical Genetics
Green Chemistry
Infectious Diseases
Diabetes and Endocrinology
Zoology
Neurology
COVID-19
Biodiversity
Mycology
Paleontology
Biogeochemistry
Environmental Contamination and Remediation
Aquaculture, Fisheries and Fish Science
Emergency and Critical Care
Andrology
Gastroenterology and Hepatology
Global Health
Public Health
Soil Science
Dentistry
Developmental Biology
Parasitology
Environmental Impacts
Clinical Trials
Evidence Based Medicine
Urology
Synthetic Biology
Conservation Biology
HIV
Ethical Issues
Nephrology
Epidemiology
Translational Medicine
Orthopedics
Pathology
Pediatrics
Animal Behavior
Geriatrics
Gynecology and Obstetrics
Women's Health
Anatomy and Physiology
Metabolic Sciences
Radiology and Medical Imaging
Surgery and Surgical Specialties
Respiratory Medicine
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Rheumatology
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By Q&A topic

Biochemistry
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Gold Contributor

Pedro J Silva

PeerJ Author & Reviewer

Summary

I was originally raised as en experimental Biochemist. My PhD research (1996-2000) centered on the biochemical characterization of the soluble hydrogenase of the hyperthermophile Pyrococcus furiosus. Eventually, the research focus broadened to include other metalloproteins from P. furiosus, which were characterized by biochemical, electrochemical and spectroscopic methods (electron paramagnetic resonance, UV-Vis spectroscopy, cofactor analysis, bioinformatics, enzymology, etc.).

In 2001, after completing my PhD, I became an Assistant Professor at Universidade Fernando Pessoa (Porto, Portugal). My research focus then moved to the computational study of enzymatic and organic reaction mechanisms using quantum chemistry and molecular dynamics methods. I left that position in August 2023 to become Staff Editor at PeerJ.

I had been an Academic Editor for PeerJ since September 2015, and Section Editor for its "Biochemistry, Biophysics and Molecular Biology" section from its creation in February 2018, to the end of May 2023.

Biochemistry Biophysical Chemistry Cell Biology Microbiology Molecular Biology Physical Organic Chemistry Synthetic Biology Theoretical & Computational Chemistry

Editorial Board Member

Past or current institution affiliations

Universidade do Porto
Universidade Fernando Pessoa

Work details

Researcher

BIOSIM @ UCIBIO
May 2019

Websites

  • ResearcherID
  • ORCID
  • Blog
  • Google Scholar
  • Figshare
  • My approach to editing journal manuscripts

PeerJ Contributions

  • Articles 7
  • Preprints 6
  • Edited 157
  • Reviewed 2
  • Feedback 6
  • Questions 8
  • Answers 2
December 19, 2022
How to tune the absorption spectrum of chlorophylls to enable better use of the available solar spectrum
Pedro J. Silva, Maria Osswald-Claro, Rosário Castro Mendonça
https://doi.org/10.7717/peerj-pchem.26
December 15, 2020
New insights into the mechanism of Schiff base synthesis from aromatic amines in the absence of acid catalyst or polar solvents
Pedro J. Silva
https://doi.org/10.7717/peerj-ochem.4
December 20, 2016
Refining the reaction mechanism of O2 towards its co-substrate in cofactor-free dioxygenases
Pedro J. Silva
https://doi.org/10.7717/peerj.2805 PubMed 28028471
July 28, 2016
Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?
Pedro J. Silva
https://doi.org/10.7717/peerj.2299 PubMed 27547588
July 28, 2015
Mechanistic pathways of mercury removal from the organomercurial lyase active site
Pedro J. Silva, Viviana Rodrigues
https://doi.org/10.7717/peerj.1127 PubMed 26246970
September 2, 2014
With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase
Pedro J. Silva
https://doi.org/10.7717/peerj.551 PubMed 25237602
July 10, 2014
Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition
Carlos E.P. Bernardo, Pedro J. Silva
https://doi.org/10.7717/peerj.470 PubMed 25071993
May 7, 2019 - Version: 1
New insights into the mechanism of Schiff base synthesis from aromatic amines in the absence of acid catalyst or polar solvents
Pedro J Silva
https://doi.org/10.7287/peerj.preprints.27710v1
June 21, 2016 - Version: 1
Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases
Pedro J Silva
https://doi.org/10.7287/peerj.preprints.2145v1
May 18, 2016 - Version: 2
Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?
Pedro J Silva
https://doi.org/10.7287/peerj.preprints.1989v2
March 19, 2015 - Version: 1
Mechanistic pathways of mercury removal from the organomercurial lyase active site
Pedro J Silva, Viviana Rodrigues
https://doi.org/10.7287/peerj.preprints.909v1
August 3, 2014 - Version: 2
With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase
Pedro J Silva
https://doi.org/10.7287/peerj.preprints.302v2
April 1, 2014 - Version: 1
Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition
Pedro J Silva, Carlos E. P. Bernardo
https://doi.org/10.7287/peerj.preprints.348v1

Academic Editor on

July 17, 2023
Immunostimulation of Parasteatoda tepidariorum (Araneae: Theridiidae) in juvenile and adult stages. Immunity reactions to injury with foreign body and Bacillus subtilis infection
Agnieszka Ewa Czerwonka, Marta Katarzyna Sawadro, Jolanta Brożek, Agnieszka Izabela Babczyńska
https://doi.org/10.7717/peerj.15337 PubMed 37483985
June 28, 2023
Hydrogen-rich water treatment targets RT1-Db1 and RT1-Bb to alleviate premature ovarian failure in rats
Xiaoyin Meng, Shuai Zhang, Lu Zhao, Yingmei Wang
https://doi.org/10.7717/peerj.15564 PubMed 37397014
June 22, 2023
Early pain in females is linked to late pathological features in murine experimental osteoarthritis
Natália Valdrighi, Arjen B. Blom, Henk M. van Beuningen, Elly L. Vitters, Monique M. Helsen, Birgitte Walgreen, Peter L.E.M. van Lent, Marije I. Koenders, Peter M. van der Kraan, Fons A.J. van de Loo, Esmeralda N. Blaney Davidson
https://doi.org/10.7717/peerj.15482 PubMed 37366428
May 9, 2023
Factors shaping the gut microbiome of five species of lizards from different habitats
Diana S. Vasconcelos, D. James Harris, Isabel Damas-Moreira, Ana Pereira, Raquel Xavier
https://doi.org/10.7717/peerj.15146 PubMed 37187519
May 9, 2023
Molecular analysis of the 14-3-3 genes in Panax ginseng and their responses to heat stress
Qi Wang, Wenyue Peng, Junbo Rong, Mengyang Zhang, Wenhao Jia, Xiujuan Lei, Yingping Wang
https://doi.org/10.7717/peerj.15331 PubMed 37187526
May 2, 2023
Illuminating the druggable genome through patent bioactivity data
Maria P. Magariños, Anna Gaulton, Eloy Félix, Tevfik Kiziloren, Ricardo Arcila, Tudor I. Oprea, Andrew R. Leach
https://doi.org/10.7717/peerj.15153 PubMed 37151295
April 7, 2023
Identification of human phosphoglycerate mutase 1 (PGAM1) inhibitors using hybrid virtual screening approaches
Numan Yousaf, Rima D. Alharthy, Maryam, Iqra Kamal, Muhammad Saleem, Muhammad Muddassar
https://doi.org/10.7717/peerj.14936 PubMed 37051414
April 3, 2023
SARS-CoV-2 ORF3A interacts with the Clic-like chloride channel-1 (CLCC1) and triggers an unfolded protein response
Hannah N. Gruner, Yaohuan Zhang, Kaavian Shariati, Nicholas Yiv, Zicheng Hu, Yuhao Wang, J. Fielding Hejtmancik, Michael T. McManus, Kevin Tharp, Gregory Ku
https://doi.org/10.7717/peerj.15077 PubMed 37033725
March 21, 2023
Prediction of HIV-1 protease resistance using genotypic, phenotypic, and molecular information with artificial neural networks
Huseyin Tunc, Berna Dogan, Büşra Nur Darendeli Kiraz, Murat Sari, Serdar Durdagi, Seyfullah Kotil
https://doi.org/10.7717/peerj.14987 PubMed 36967989
February 20, 2023
Disinfection efficacy of sodium hypochlorite and glutaraldehyde and their effects on the dimensional stability and surface properties of dental impressions: a systematic review
Yuan Qiu, Jiawei Xu, Yuedan Xu, Zhiwei Shi, Yinlin Wang, Ling Zhang, Baiping Fu
https://doi.org/10.7717/peerj.14868 PubMed 36846444
February 6, 2023
Influence of resin modified glass ionomer cement incorporating protein-repellent and antimicrobial agents on supragingival microbiome around brackets: an in-vivo split-mouth 3-month study
Yansong Ma, Chengjun Su, Hao Yang, Hockin H.K. Xu, Yuxing Bai, Yan Xu, Xiaoxia Che, Ning Zhang
https://doi.org/10.7717/peerj.14820 PubMed 36778151
January 31, 2023
Simultaneous functioning of different light-harvesting complexes—a strategy of adaptation of purple bacterium Rhodopseudomonas palustris to low illumination conditions
Olga Petrovna Serdyuk, Azat Vadimovich Abdullatypov, Lidiya Dmitrievna Smolygina, Aleksandr Aleksandrovich Ashikhmin, Maxim Alexandrovich Bolshakov
https://doi.org/10.7717/peerj.14769 PubMed 36743963
December 5, 2022
Effects of cleaning sports mouthguards with ethylene-vinyl acetate on oral bacteria
Hiroki Hayashi, Yoshikazu Naiki, Masahiro Murakami, Akihiro Oishi, Rihoko Takeuchi, Masayoshi Nakagawa, Suguru Kimoto, Yoshiaki Hasegawa, Akizumi Araki
https://doi.org/10.7717/peerj.14480 PubMed 36523462
November 16, 2022
Functional expression and purification of DoxA, a key cytochrome P450 from Streptomyces peucetius ATCC 27952
Liyan Yang, Dengfeng Yang, Qingyan Wang, Juan Li, Hong-Liang Li, Lixia Pan
https://doi.org/10.7717/peerj.14373 PubMed 36411834
October 19, 2022
Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation
Sobroney Heng, Sawannee Sutheeworapong, Verawat Champreda, Ayaka Uke, Akihiko Kosugi, Patthra Pason, Rattiya Waeonukul, Ruben Michael Ceballos, Khanok Ratanakhanokchai, Chakrit Tachaapaikoon
https://doi.org/10.7717/peerj.14211 PubMed 36281362
October 7, 2022
Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations
Hossam Nada, Ahmed Elkamhawy, Kyeong Lee
https://doi.org/10.7717/peerj.14120 PubMed 36225900
August 17, 2022
The greening reaction of skipjack tuna (Katsuwonus pelamis) metmyoglobin promoted by free cysteine during thermal treatment
Andrés Álvarez-Armenta, Ramón Pacheco-Aguilar, Alonso A. López-Zavala, David O. Corona-Martínez, Rogerio R. Sotelo-Mundo, Karina D. García-Orozco, Juan C. Ramírez-Suárez
https://doi.org/10.7717/peerj.13923 PubMed 35996665
July 22, 2022
Rare earth element geochemistry of Middle Devonian reefal limestones of the Dianqiangui Basin, South China: implications for nutrient sources and expansion of the reef ecosystem
Qi Mao, Shangyi Gu, Huan Li, Gary G. Lash, Tianyi Zhang, Xiaofeng Xie, Zidong Guo
https://doi.org/10.7717/peerj.13663 PubMed 35898942
July 18, 2022
Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris)
Zhangqiang You, Jing Deng, Jialin Liu, Junhua Fu, Huan Xiong, Wei Luo, Jianli Xiong
https://doi.org/10.7717/peerj.13753 PubMed 35873913
July 15, 2022
The efficacy of commercial decontamination agents differs between standardised test settings and research laboratory usage for a variety of bacterial species
Benedict Uy, Hannah Read, Shara van de Pas, Rebecca Marnane, Francesca Casu, Simon Swift, Siouxsie Wiles
https://doi.org/10.7717/peerj.13646 PubMed 35860043
July 4, 2022
Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)
Zhenfan Yu, Dongdong Zhang, Bin Zeng, Xingyue Liu, Jiahui Yang, Wenwen Gao, Xintong Ma
https://doi.org/10.7717/peerj.13491 PubMed 35811825
July 1, 2022
Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae)
Changhong Li, Yu Liu, Furong Lin, Yongqi Zheng, Ping Huang
https://doi.org/10.7717/peerj.13570 PubMed 35795179
May 13, 2022
Genome-wide identification and response stress expression analysis of the BES1 family in rubber tree (Hevea brasiliensis Muell. Arg.)
Bingbing Guo, Hong Yang, Longjun Dai, Xizhu Zhao, Li-feng Wang
https://doi.org/10.7717/peerj.13189 PubMed 35586131
April 19, 2022
Analysis of fungal dynamic changes in the natural fermentation broth of ‘Hongyang’ kiwifruit
Zhiming Zhang, Yuhong Gao, Wenjuan Zhao, Zhuo Wei, Xiaozhen Liu, Hanyao Zhang
https://doi.org/10.7717/peerj.13286 PubMed 35462763
March 29, 2022
Investigating effect of mutation on structure and function of G6PD enzyme: a comparative molecular dynamics simulation study
Sadaf Rani, Fouzia Perveen Malik, Jamshed Anwar, Rehan Zafar Paracha
https://doi.org/10.7717/peerj.12984 PubMed 35368337
March 22, 2022
Mutation breeding of Aspergillus niger by atmospheric room temperature plasma to enhance phosphorus solubilization ability
Qiuju Peng, Yang Xiao, Su Zhang, Changwei Zhou, Ailin Xie, Zhu Li, Aijuan Tan, Lihong Zhou, Yudan Xie, Jinyi Zhao, Chenglin Wu, Lei Luo, Jie Huang, Tengxia He, Ran Sun
https://doi.org/10.7717/peerj.13076 PubMed 35341057
March 16, 2022
Whole-genome analysis of CGS, SAHH, SAMS gene families in five Rosaceae species and their expression analysis in Pyrus bretschneideri
Yang Zhang, Decong Li, Xiaofeng Feng, Xinya Wang, Mengna Wang, Wenlong Han, Muhammad Aamir Manzoor, Guohui Li, Tianzhe Chen, Han Wang, Yongping Cai
https://doi.org/10.7717/peerj.13086 PubMed 35313526
March 8, 2022
Microbial community spatial structures in Luzhou-flavored liquor pit muds with different brewing materials
Jinjin Li, Hongzhao Sun, Qian Wang, Yunfei Cai, Zhu Shi, Jianlei Jia, Lei Zheng, Ru Jiang, Lingmei Gao
https://doi.org/10.7717/peerj.12987 PubMed 35282287
February 21, 2022
Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat
Abdullah Yasin, Mst. Khadiza Begum, Md. Mostavi Enan Eshik, Nusrat Jahan Punom, Shawon Ahmmed, Mohammad Shamsur Rahman
https://doi.org/10.7717/peerj.12808 PubMed 35223199
February 10, 2022
Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum)
Zesheng Liu, Xuejuan Pan, Chunlei Wang, Fahong Yun, Dengjing Huang, Yandong Yao, Rong Gao, Fujin Ye, Xingjuan Liu, Weibiao Liao
https://doi.org/10.7717/peerj.12943 PubMed 35186505
February 1, 2022
B-box containing protein 1 from Malus domestica (MdBBX1) is involved in the abiotic stress response
Yaqing Dai, Ying Lu, Zhou Zhou, Xiaoyun Wang, Hongjuan Ge, Qinghua Sun
https://doi.org/10.7717/peerj.12852 PubMed 35178298
January 24, 2022
Characterization of transcriptional landscape in bone marrow-derived mesenchymal stromal cells treated with aspirin by RNA-seq
Xinpeng Liu, Yuanbo Zhan, Wenxia Xu, Lixue Liu, Xiaoyao Liu, Junlong Da, Kai Zhang, Xinjian Zhang, Jianqun Wang, Ziqi Liu, Han Jin, Bin Zhang, Ying Li
https://doi.org/10.7717/peerj.12819 PubMed 35127290
January 4, 2022
Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola
Chengru Li, Na Dong, Liming Shen, Meng Lu, Junwen Zhai, Yamei Zhao, Lei Chen, Zhiting Wan, Zhongjian Liu, Hui Ren, Shasha Wu
https://doi.org/10.7717/peerj.12558 PubMed 35036123
December 16, 2021
Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C4 grassland soils
Jialin Hu, Jonathan D. Richwine, Patrick D. Keyser, Lidong Li, Fei Yao, Sindhu Jagadamma, Jennifer M. DeBruyn
https://doi.org/10.7717/peerj.12592 PubMed 35003922
November 3, 2021
Genomic diversity of SARS-CoV-2 in Malaysia
Noorliza Mohamad Noordin, Joon Liang Tan, Chee Kheong Chong, Yu Kie Chem, Norazimah Tajudin, Rehan Shuhada Abu Bakar, Selvanesan Sengol, Hannah Yik Phing Phoon, Nurul Aina Murni Che Azid, W Nur Afiza W Mohd Arifin, Zirwatul Adilah Aziz, Hani Hussin, Nurul Syahida Ibrahim, Aziyati Omar, Ushananthiny Ravi, Kamal Hisham Kamarul Zaman, Mohd Asri Yamin, Yun Fong Ngeow
https://doi.org/10.7717/peerj.12449 PubMed 34760404
November 2, 2021
Punicalagin, a pomegranate compound, induces apoptosis and autophagy in acute leukemia
Paweena Subkorn, Chosita Norkaew, Kamolchanok Deesrisak, Dalina Tanyong
https://doi.org/10.7717/peerj.12303 PubMed 34760363
November 1, 2021
Co-culturing Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 allows sustainable denitrifying activities under marine conditions
Alexandra Cucaita, Marianne Piochon, Richard Villemur
https://doi.org/10.7717/peerj.12424 PubMed 34760396
October 20, 2021
Functional analysis of a dihydroflavonol 4-reductase gene in Ophiorrhiza japonica (OjDFR1) reveals its role in the regulation of anthocyanin
Wei Sun, Nana Zhou, Cai Feng, Shiyu Sun, Ming Tang, Xiaoxin Tang, Zhigang Ju, Yin Yi
https://doi.org/10.7717/peerj.12323 PubMed 34721993
October 6, 2021
The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket)
Micaela Schagen, Jason Bosch, Jenny Johnson, Robbert Duker, Pedro Lebre, Alastair J. Potts, Don A. Cowan
https://doi.org/10.7717/peerj.12176 PubMed 34707927
September 24, 2021
Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation
Ashley Ryan Vidad, Stephen Macaspac, Ho Leung Ng
https://doi.org/10.7717/peerj.12219 PubMed 34631323
August 23, 2021
Diclofenac toxicity in susceptible bird species results from a combination of reduced glomerular filtration and plasma flow with subsequent renal tubular necrosis
Bono Nethathe, John Chipangura, Ibrahim Zubairu Hassan, Neil Duncan, Emmanuel Oluwasegun Adawaren, Lauren Havenga, Vinny Naidoo
https://doi.org/10.7717/peerj.12002 PubMed 34513332
July 20, 2021
Network pharmacology to investigate the pharmacological mechanisms of muscone in Xingnaojing injections for the treatment of severe traumatic brain injury
Zhuohang Liu, Hang Li, Wenchao Ma, Shuyi Pan
https://doi.org/10.7717/peerj.11696 PubMed 34322321
June 24, 2021
Alpha- and beta- adrenergic receptors regulate inflammatory responses to acute and chronic sleep fragmentation in mice
Nicholas D. Wheeler, David C. Ensminger, Megan M. Rowe, Zachary S. Wriedt, Noah T. Ashley
https://doi.org/10.7717/peerj.11616 PubMed 34221721
June 14, 2021
Transcriptome analysis associated with polysaccharide synthesis and their antioxidant activity in Cyclocarya paliurus leaves of different developmental stages
Weida Lin, Huanwei Chen, Jianmei Wang, Yongli Zheng, Qiuwei Lu, Ziping Zhu, Na Li, Zexin Jin, Junmin Li, Hongfei Lu
https://doi.org/10.7717/peerj.11615 PubMed 34178473
June 10, 2021
nCov2019: an R package for studying the COVID-19 coronavirus pandemic
Tianzhi Wu, Erqiang Hu, Xijin Ge, Guangchuang Yu
https://doi.org/10.7717/peerj.11421 PubMed 34178436
June 4, 2021
Response of the characteristics of organic carbon mineralization of soft rock and soil composed of sand to soil depth
Wanying Li, Zhen Guo, Juan Li, Jichang Han
https://doi.org/10.7717/peerj.11572 PubMed 34141496
April 30, 2021
Cinnamaldehyde inhibits the growth of Phytophthora capsici through disturbing metabolic homoeostasis
Yinan Wang, Mengke Wang, Min Li, Te Zhao, Lin Zhou
https://doi.org/10.7717/peerj.11339 PubMed 33987017
April 30, 2021
The hypoferremic response to acute inflammation is maintained in thalassemia mice even under parenteral iron loading
Chanita Sanyear, Buraporn Chiawtada, Punnee Butthep, Saovaros Svasti, Suthat Fucharoen, Patarabutr Masaratana
https://doi.org/10.7717/peerj.11367 PubMed 33987030
April 27, 2021
Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries)
Xiaolei Shi, Jianping Wu, Xia Lang, Cailian Wang, Yan Bai, David Greg Riley, Lishan Liu, Xiaoming Ma
https://doi.org/10.7717/peerj.11122 PubMed 33986980
April 22, 2021
The antimicrobial activity of silver acetate against Acinetobacter baumannii in a Galleria mellonella infection model
Eden Mannix-Fisher, Samantha McLean
https://doi.org/10.7717/peerj.11196 PubMed 33981496
April 16, 2021
Antifungal properties of volatile organic compounds produced by Daldinia eschscholtzii MFLUCC 19-0493 isolated from Barleria prionitis leaves against Colletotrichum acutatum and its post-harvest infections on strawberry fruits
Sarunpron Khruengsai, Patcharee Pripdeevech, Chutima Tanapichatsakul, Chanin Srisuwannapa, Priya Esilda D’Souza, Parinya Panuwet
https://doi.org/10.7717/peerj.11242 PubMed 33959421
April 13, 2021
Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation
Asim Kumar Bepari, Hasan Mahmud Reza
https://doi.org/10.7717/peerj.11261 PubMed 33954055
March 9, 2021
Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4
Go Furusawa, Nor Azura Azami, Aik-Hong Teh
https://doi.org/10.7717/peerj.10929 PubMed 33732545
February 15, 2021
Magnetic resonance diffusion tensor imaging applied to rat model of contrast-induced acute kidney injury
Bin Wang, Junjie Li, Yongfang Wang
https://doi.org/10.7717/peerj.10620 PubMed 33628631
February 10, 2021
High throughput virtual screening of 230 billion molecular solar heat battery candidates
Mads Koerstz, Anders S. Christensen, Kurt V. Mikkelsen, Mogens Brøndsted Nielsen, Jan H. Jensen
https://doi.org/10.7717/peerj-pchem.16
February 3, 2021
A novel bicyclic 2,4-diaminopyrimidine inhibitor of Streptococcus suis dihydrofolate reductase
Warangkhana Songsungthong, Sunisa Prasopporn, Louise Bohan, Potjanee Srimanote, Ubolsree Leartsakulpanich, Suganya Yongkiettrakul
https://doi.org/10.7717/peerj.10743 PubMed 33604179
February 2, 2021
Inhibitory effect and mechanism of action (MOA) of hirsutine on the proliferation of T-cell leukemia Jurkat clone E6-1 cells
Jie Meng, Rui Su, Luping Wang, Bo Yuan, Ling Li
https://doi.org/10.7717/peerj.10692 PubMed 33604171
January 22, 2021
Exogenous melatonin improves growth in hulless barley seedlings under cold stress by influencing the expression rhythms of circadian clock genes
Tianliang Chang, Yi Zhao, Hongyan He, Qianqian Xi, Jiayi Fu, Yuwei Zhao
https://doi.org/10.7717/peerj.10740 PubMed 33552735
January 13, 2021
Modeling the bidirectional glutamine/ammonium conversion between cancer cells and cancer-associated fibroblasts
Peter Hinow, Gabriella Pinter, Wei Yan, Shizhen Emily Wang
https://doi.org/10.7717/peerj.10648 PubMed 33520452
December 21, 2020
The effects of the recombinant YeaZ of Vibrio harveyi on the resuscitation and growth of soil bacteria in extreme soil environment
Yanlin Li, Jixiang Chen, Yonggang Wang, Dan Ma, Wenhong Rui
https://doi.org/10.7717/peerj.10342 PubMed 33391864
November 18, 2020
Changes and sex- and age-related differences in the expression of drug metabolizing enzymes in a KRAS-mutant mouse model of lung cancer
Xiaoyan Li, Yiyan Lu, Xiaojun Ou, Sijing Zeng, Ying Wang, Xiaoxiao Qi, Lijun Zhu, Zhongqiu Liu
https://doi.org/10.7717/peerj.10182 PubMed 33240601
October 20, 2020
Isolation and evolutionary analyses of porcine epidemic diarrhea virus in Asia
Wan Liang, Danna Zhou, Chao Geng, Keli Yang, Zhengying Duan, Rui Guo, Wei Liu, Fangyan Yuan, Zewen Liu, Ting Gao, Ling Zhao, Dongwan Yoo, Yongxiang Tian
https://doi.org/10.7717/peerj.10114 PubMed 33150069
September 28, 2020
Pyruvate is required for catecholamine-stimulated growth of different strains of Campylobacter jejuni
Meicen Liu, Mark Lyte
https://doi.org/10.7717/peerj.10011 PubMed 33062434
August 26, 2020
In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis
Carlos Leonardo Araújo, Iago Blanco, Luciana Souza, Sandeep Tiwari, Lino César Pereira, Preetam Ghosh, Vasco Azevedo, Artur Silva, Adriana Folador
https://doi.org/10.7717/peerj.9643 PubMed 32913672
August 11, 2020
Antibacterial activity and mechanism of sanguinarine against Providencia rettgeri in vitro
Qian Zhang, Yansi Lyu, Jingkai Huang, Xiaodong Zhang, Na Yu, Ziping Wen, Si Chen
https://doi.org/10.7717/peerj.9543 PubMed 32864203
August 11, 2020
Evaluation of computational methods for human microbiome analysis using simulated data
Matthieu J. Miossec, Sandro L. Valenzuela, Marcos Pérez-Losada, W. Evan Johnson, Keith A. Crandall, Eduardo Castro-Nallar
https://doi.org/10.7717/peerj.9688 PubMed 32864214
July 29, 2020
Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing
Yeonhwa Jo, Hoseong Choi, Sen Lian, Jin Kyong Cho, Hyosub Chu, Won Kyong Cho
https://doi.org/10.7717/peerj.9588 PubMed 32821540
July 29, 2020
Spermatogenesis is normal in Tex33 knockout mice
Zhendong Zhu, Xin Zhang, Wentao Zeng, Shuqin Zhao, Jianli Zhou, Zuomin Zhou, Mingxi Liu
https://doi.org/10.7717/peerj.9629 PubMed 32821546
July 14, 2020
Siderophore and indolic acid production by Paenibacillus triticisoli BJ-18 and their plant growth-promoting and antimicrobe abilities
Yunzhi Zhang, Jinwei Ren, Wenzhao Wang, Baosong Chen, Erwei Li, Sanfeng Chen
https://doi.org/10.7717/peerj.9403 PubMed 32742769
July 3, 2020
A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains
Swati Tyagi, Jae-A Jung, Jung Sun Kim, So Youn Won
https://doi.org/10.7717/peerj.9448 PubMed 32685287
June 18, 2020
KIT is involved in melanocyte proliferation, apoptosis and melanogenesis in the Rex Rabbit
Shuaishuai Hu, Yang Chen, Bohao Zhao, Naisu Yang, Shi Chen, Jinyu Shen, Guolian Bao, Xinsheng Wu
https://doi.org/10.7717/peerj.9402 PubMed 32596061
June 12, 2020
Potential of rice straw biochar, sulfur and ryegrass (Lolium perenne L.) in remediating soil contaminated with nickel through irrigation with untreated wastewater
Inas A. Hashem, Aonalah Y. Abbas, Abo El-Nasr H. Abd El-Hamed, Haythum M.S. Salem, Omr E.M. El-hosseiny, Mohamed A. Abdel-Salam, Muhammad Hamzah Saleem, Wenbing Zhou, Ronggui Hu
https://doi.org/10.7717/peerj.9267 PubMed 32566397
June 10, 2020
Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips
Yunmin Wei, Caode Jiang, Rongrong Han, Yonghong Xie, Lusheng Liu, Yongxiong Yu
https://doi.org/10.7717/peerj.9312 PubMed 32566407
June 8, 2020
Lycopene alleviates oxidative stress via the PI3K/Akt/Nrf2pathway in a cell model of Alzheimer’s disease
Yinchao Fang, Shanshan Ou, Tong Wu, Lingqi Zhou, Hai Tang, Mei Jiang, Jie Xu, Kaihua Guo
https://doi.org/10.7717/peerj.9308 PubMed 32551202
June 1, 2020
Developments in marine invertebrate primary culture reveal novel cell morphologies in the model bivalve Crassostrea gigas
Robert W.A. Potts, Alejandro P. Gutierrez, Yennifer Cortés-Araya, Ross D. Houston, Tim P. Bean
https://doi.org/10.7717/peerj.9180 PubMed 32547861
May 27, 2020
Purpureocillium lilacinum and Metarhizium marquandii as plant growth-promoting fungi
Noemi Carla Baron, Andressa de Souza Pollo, Everlon Cid Rigobelo
https://doi.org/10.7717/peerj.9005 PubMed 32518715
May 25, 2020
Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods
Hongye Hu, Buran Chen, Danni Zheng, Guanli Huang
https://doi.org/10.7717/peerj.9241 PubMed 32509471
May 14, 2020
Full-length transcriptome and targeted metabolome analyses provide insights into defense mechanisms of Malus sieversii against Agrilus mali
Chuang Mei, Jie Yang, Peng Yan, Ning Li, Kai Ma, Aisajan Mamat, Liqun Han, Qinglong Dong, Ke Mao, Fengwang Ma, Jixun Wang
https://doi.org/10.7717/peerj.8992 PubMed 32461824
May 4, 2020
Antifungal activity of 8-methoxynaphthalen-1-ol isolated from the endophytic fungus Diatrype palmicola MFLUCC 17-0313 against the plant pathogenic fungus Athelia rolfsii on tomatoes
Chutima Tanapichatsakul, Acharavadee Pansanit, Sakon Monggoot, Siraprapa Brooks, Surasak Prachya, Prasat Kittakoop, Parinya Panuwet, Patcharee Pripdeevech
https://doi.org/10.7717/peerj.9103 PubMed 32411538
April 28, 2020
Long-term continuously monocropped peanut significantly changed the abundance and composition of soil bacterial communities
Mingna Chen, Hu Liu, Shanlin Yu, Mian Wang, Lijuan Pan, Na Chen, Tong Wang, Xiaoyuan Chi, Binghai Du
https://doi.org/10.7717/peerj.9024 PubMed 32377450
April 28, 2020
Impact of Phellinus gilvus mycelia on growth, immunity and fecal microbiota in weaned piglets
Yuqing Sun, Shi Zhong, Bo Deng, Qinsheng Jin, Jie Wu, Jinxi Huo, Jianxun Zhu, Cheng Zhang, Yougui Li
https://doi.org/10.7717/peerj.9067 PubMed 32377455
April 10, 2020
The whole body transcriptome of Coleophora obducta reveals important olfactory proteins
Dongbai Wang, Jing Tao, Pengfei Lu, Youqing Luo, Ping Hu
https://doi.org/10.7717/peerj.8902 PubMed 32309046
March 25, 2020
Mitochondria-targeted triphenylphosphonium-based compounds do not affect estrogen receptor α
Ludmila A. Zinovkina, Alina K. Galivondzhyan, Anastasia S. Prikhodko, Ivan I. Galkin, Roman A. Zinovkin
https://doi.org/10.7717/peerj.8803 PubMed 32257641
March 9, 2020
Biocontrol of chocolate spot disease (Botrytis cinerea) in faba bean using endophytic actinomycetes Streptomyces: a field study to compare application techniques
Sahar A. El-Shatoury, Fuad Ameen, Heba Moussa, Omar Abdul Wahid, Ahmed Dewedar, Saleh AlNadhari
https://doi.org/10.7717/peerj.8582 PubMed 32195043
March 6, 2020
The altered gut microbiota of high-purine-induced hyperuricemia rats and its correlation with hyperuricemia
Xiu Liu, Qiulan Lv, Hongyan Ren, Liu Gao, Peng Zhao, Xiaomin Yang, Guanpin Yang, Daxing Xu, Guangtao Wang, Wan Yang, Pengjun Wang, Zenglan Wang, Shichao Xing
https://doi.org/10.7717/peerj.8664 PubMed 32185104
February 17, 2020
The R2R3-MYB transcription factor family in Taxus chinensis: identification, characterization, expression profiling and posttranscriptional regulation analysis
Xinling Hu, Lisha Zhang, Iain Wilson, Fenjuan Shao, Deyou Qiu
https://doi.org/10.7717/peerj.8473 PubMed 32110480
February 5, 2020
Postharvest biochemical characteristics and ultrastructure of Coprinus comatus
Yi Peng, Tongling Li, Huaming Jiang, Yunfu Gu, Qiang Chen, Cairong Yang, Wei liang Qi, Song-qing Liu, Xiaoping Zhang
https://doi.org/10.7717/peerj.8508 PubMed 32071815
January 28, 2020
Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis
Yongguo Zhao, Hua Kong, Yunling Guo, Zhi Zou
https://doi.org/10.7717/peerj.8465 PubMed 32025382
January 20, 2020
Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot
Guiquan Cai, Xuan Yang, Ting Chen, Fangchun Jin, Jing Ding, Zhenkai Wu
https://doi.org/10.7717/peerj.8422 PubMed 31998564
January 16, 2020
Comparative transcriptome analysis revealed genes involved in the fruiting body development of Ophiocordyceps sinensis
Xinxin Tong, Han Zhang, Fang Wang, Zhengyao Xue, Jing Cao, Cheng Peng, Jinlin Guo
https://doi.org/10.7717/peerj.8379 PubMed 31988806
January 2, 2020
Bioactivity of compounds secreted by symbiont bacteria of Nudibranchs from Indonesia
Rhesi Kristiana, Gilles Bedoux, Gerard Pals, I. Wayan Mudianta, Laure Taupin, Christel Marty, Meezan Ardhanu Asagabaldan, Diah Ayuningrum, Agus Trianto, Nathalie Bourgougnon, Ocky Karna Radjasa, Agus Sabdono, Muhammad Hanafi
https://doi.org/10.7717/peerj.8093 PubMed 31915568
December 20, 2019
Heterologous expression, purification and biochemical characterization of a glutamate racemase (MurI) from Streptococcus mutans UA159
Xiangzhu Wang, Chanchan Chen, Ting Shen, Jiangying Zhang
https://doi.org/10.7717/peerj.8300 PubMed 31875162
December 11, 2019
Prosaposin in seminal plasma on the day of oocyte retrieval is associated with normal fertilization and embryo development in in vitro fertilization cycles
Chun Xu, Jiali Cai, Lanlan Liu, Jianzhi Ren
https://doi.org/10.7717/peerj.8177 PubMed 31844578
December 9, 2019
Synthesis of silver nanoparticles using a Mentha spicata extract and evaluation of its anticancer and cytotoxic activity
Yuridia Torres-Martínez, Eder Arredondo-Espinoza, Carlos Puente, Omar González-Santiago, Nayely Pineda-Aguilar, Isaías Balderas-Rentería, Israel López, Mónica A. Ramírez-Cabrera
https://doi.org/10.7717/peerj.8142 PubMed 31844570
October 22, 2019
Exploration of the selective binding mechanism of protein kinase Aurora A selectivity via a comprehensive molecular modeling study
Zhe Zhang, Yafei Xu, Jian Wu, Ying Shen, Hao Cheng, Yiming Xiang
https://doi.org/10.7717/peerj.7832 PubMed 31660263
October 11, 2019
Isolation and molecular characterization of the indigenous Staphylococcus aureus strain K1 with the ability to reduce hexavalent chromium for its application in bioremediation of metal-contaminated sites
Muhammad Tariq, Muhammad Waseem, Muhammad Hidayat Rasool, Muhammad Asif Zahoor, Irshad Hussain
https://doi.org/10.7717/peerj.7726 PubMed 31616584
September 23, 2019
Paenibacillus strains with nitrogen fixation and multiple beneficial properties for promoting plant growth
Xiaomeng Liu, Qin Li, Yongbin Li, Guohua Guan, Sanfeng Chen
https://doi.org/10.7717/peerj.7445 PubMed 31579563
September 17, 2019
Effects of shokyo (Zingiberis Rhizoma) and kankyo (Zingiberis Processum Rhizoma) on prostaglandin E2 production in lipopolysaccharide-treated mouse macrophage RAW264.7 cells
Toshiaki Ara, Masanori Koide, Hiroyuki Kitamura, Norio Sogawa
https://doi.org/10.7717/peerj.7725 PubMed 31576251
September 13, 2019
Screening and identification of SipC-interacting proteins in Salmonella enteritidis using Gal4 yeast two-hybrid system in duck
Yu Zhang, Tiantian Gu, Yang Chen, Guoqiang Zhu, Wanwipa Vongsangnak, Qi Xu, Guohong Chen
https://doi.org/10.7717/peerj.7663 PubMed 31565575
August 28, 2019
The effect of modulating the quantity of enzymes in a model ethanol pathway on metabolic flux in Synechocystis sp. PCC 6803
Paulina Bartasun, Nicole Prandi, Marko Storch, Yarin Aknin, Mark Bennett, Arianna Palma, Geoff Baldwin, Yumiko Sakuragi, Patrik R. Jones, John Rowland
https://doi.org/10.7717/peerj.7529 PubMed 31523505
August 5, 2019
Binding interactions of epididymal protease inhibitor and semenogelin-1: a homology modeling, docking and molecular dynamics simulation study
Changyu Shan, Hongwei Li, Yuping Zhang, Yuyan Li, Yingchun Chen, Wei He
https://doi.org/10.7717/peerj.7329 PubMed 31404433
July 5, 2019
Curcumin ameliorates atrophy of seminal vesicle via reduction of oxidative stress in castrated mice
Rui Li, Hao Li, Ke Rao, Kang Liu, Yan Zhang, Xiaming Liu, Tao Wang, Shaogang Wang, Zhuo Liu, Jihong Liu
https://doi.org/10.7717/peerj.7192 PubMed 31316871
April 24, 2019
Normal spermatogenesis in Fank1 (fibronectin type 3 and ankyrin repeat domains 1) mutant mice
Jintao Zhang, Xin Zhang, Yue Zhang, Wentao Zeng, Shuqin Zhao, Mingxi Liu
https://doi.org/10.7717/peerj.6827 PubMed 31086747
April 17, 2019
Understanding the NaCl-dependent behavior of hydrogen production of a marine bacterium, Vibrio tritonius
Nurhidayu Al-saari, Eri Amada, Yuta Matsumura, Mami Tanaka, Sayaka Mino, Tomoo Sawabe
https://doi.org/10.7717/peerj.6769 PubMed 31024772
April 5, 2019
Evaluation of potential molecular interaction between quorum sensing receptor, LuxP and grouper fatty acids: in-silico screening and simulation
Chen-Fei Low, Mohd Shahir Shamsir, Zeti-Azura Mohamed-Hussein, Syarul Nataqain Baharum
https://doi.org/10.7717/peerj.6568 PubMed 30984478
April 5, 2019
Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica
Nikolay B. Pestov, Daniel V. Kalinovsky, Tatyana D. Larionova, Alia Z. Zakirova, Nikolai N. Modyanov, Irina A. Okkelman, Tatyana V. Korneenko
https://doi.org/10.7717/peerj.6691 PubMed 30984480
February 5, 2019
Genome-wide identification and comparative evolutionary analysis of the Dof transcription factor family in physic nut and castor bean
Zhi Zou, Xicai Zhang
https://doi.org/10.7717/peerj.6354 PubMed 30740272
February 1, 2019
Suppression of hesA mutation on nitrogenase activity in Paenibacillus polymyxa WLY78 with the addition of high levels of molybdate or cystine
Xiaomeng Liu, Xiyun Zhao, Xiaohan Li, Sanfeng Chen
https://doi.org/10.7717/peerj.6294 PubMed 30723617
January 31, 2019
Identification, expression, and phylogenetic analyses of terpenoid biosynthesis-related genes in secondary xylem of loblolly pine (Pinus taeda L.) based on transcriptome analyses
Jipeng Mao, Zidi He, Jing Hao, Tianyi Liu, Jiehu Chen, Shaowei Huang
https://doi.org/10.7717/peerj.6124 PubMed 30723613
January 31, 2019
Transcriptome-wide characterization and functional analysis of MATE transporters in response to aluminum toxicity in Medicago sativa L.
Xueyang Min, Xiaoyu Jin, Wenxian Liu, Xingyi Wei, Zhengshe Zhang, Boniface Ndayambaza, Yanrong Wang
https://doi.org/10.7717/peerj.6302 PubMed 30723620
January 24, 2019
Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube
Ji Qing, Wang Dawei, Zhou Jun, Xu Yulan, Shen Bingqi, Zhou Fan
https://doi.org/10.7717/peerj.6353 PubMed 30697496
January 21, 2019
Molecular mechanism of point mutation-induced Monopolar spindle 1 (Mps1/TTK) inhibitor resistance revealed by a comprehensive molecular modeling study
Yan Han, Yungang Wu, Yi Xu, Wentao Guo, Na Zhang, Xiaoyi Wang
https://doi.org/10.7717/peerj.6299 PubMed 30693152
January 11, 2019
Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)
Kebin Yang, Ying Li, Sining Wang, Xiurong Xu, Huayu Sun, Hansheng Zhao, Xueping Li, Zhimin Gao
https://doi.org/10.7717/peerj.6242 PubMed 30648007
January 3, 2019
Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis
Rumana Ahmad
https://doi.org/10.7717/peerj.6012 PubMed 30627484
October 30, 2018
Adipose tissues of MPC1± mice display altered lipid metabolism-related enzyme expression levels
Shiying Zou, Liye Zhu, Kunlun Huang, Haoshu Luo, Wentao Xu, Xiaoyun He
https://doi.org/10.7717/peerj.5799 PubMed 30397542
September 21, 2018
A secretory hexokinase plays an active role in the proliferation of Nosema bombycis
Yukang Huang, Shiyi Zheng, Xionge Mei, Bin Yu, Bin Sun, Boning Li, Junhong Wei, Jie Chen, Tian Li, Guoqing Pan, Zeyang Zhou, Chunfeng Li
https://doi.org/10.7717/peerj.5658 PubMed 30258733
September 21, 2018
Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes
Cíntia Carreira, Olga Mestre, Rute F. Nunes, Isabel Moura, Sofia R. Pauleta
https://doi.org/10.7717/peerj.5603 PubMed 30258713
September 10, 2018
Effects of resveratrol, exercises and their combination on Farnesoid X receptor, Liver X receptor and Sirtuin 1 gene expression and apoptosis in the liver of elderly rats with nonalcoholic fatty liver
Amir Hajighasem, Parvin Farzanegi, Zohreh Mazaheri, Marjan Naghizadeh, Ghoncheh Salehi
https://doi.org/10.7717/peerj.5522 PubMed 30221089
September 5, 2018
Single mutations in the ε subunit from thermophilic Bacillus PS3 generate a high binding affinity site for ATP
Alexander Krah, Peter J. Bond
https://doi.org/10.7717/peerj.5505 PubMed 30202650
July 31, 2018
Anxiolytic and anti-stress effects of acute administration of acetyl-L-carnitine in zebrafish
Lais Pancotto, Ricieri Mocelin, Matheus Marcon, Ana P. Herrmann, Angelo Piato
https://doi.org/10.7717/peerj.5309 PubMed 30083453
July 12, 2018
Cloning, purification and characterization of trehalose-6-phosphate synthase from Pleurotus tuoliensis
Xiangli Wu, Zhihao Hou, Chenyang Huang, Qiang Chen, Wei Gao, Jinxia Zhang
https://doi.org/10.7717/peerj.5230 PubMed 30013854
June 22, 2018
Prevalence of extended spectrum beta lactamase and plasmid mediated quinolone resistant genes in strains of Klebsiella pneumonia, Morganella morganii, Leclercia adecarboxylata and Citrobacter freundii isolated from poultry in South Western Nigeria
Olajumoke R. Akinbami, Samson Olofinsae, Funmilola A. Ayeni
https://doi.org/10.7717/peerj.5053 PubMed 29942700
June 8, 2018
MipLAAO, a new L-amino acid oxidase from the redtail coral snake Micrurus mipartitus
Paola Rey-Suárez, Cristian Acosta, Uday Torres, Mónica Saldarriaga-Córdoba, Bruno Lomonte, Vitelbina Núñez
https://doi.org/10.7717/peerj.4924 PubMed 29900074
June 5, 2018
Biochemical and genetic analyses of the oomycete Pythium insidiosum provide new insights into clinical identification and urease-based evolution of metabolism-related traits
Theerapong Krajaejun, Thidarat Rujirawat, Teerat Kanpanleuk, Pitak Santanirand, Tassanee Lohnoo, Wanta Yingyong, Yothin Kumsang, Pattarana Sae-Chew, Weerayuth Kittichotirat, Preecha Patumcharoenpol
https://doi.org/10.7717/peerj.4821 PubMed 29888122
May 2, 2018
From in silico to in vitro: a trip to reveal flavonoid binding on the Rattus norvegicus Kir6.1 ATP-sensitive inward rectifier potassium channel
Alfonso Trezza, Vittoria Cicaloni, Piera Porciatti, Andrea Langella, Fabio Fusi, Simona Saponara, Ottavia Spiga
https://doi.org/10.7717/peerj.4680 PubMed 29736333
March 19, 2018
Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8
Lawal Garba, Mohamad Ariff Mohamad Yussoff, Khairul Bariyyah Abd Halim, Siti Nor Hasmah Ishak, Mohd Shukuri Mohamad Ali, Siti Nurbaya Oslan, Raja Noor Zaliha Raja Abd. Rahman
https://doi.org/10.7717/peerj.4347 PubMed 29576935
February 9, 2018
Antitumor activity of Chlorella sorokiniana and Scenedesmus sp. microalgae native of Nuevo León State, México
Raul Reyna-Martinez, Ricardo Gomez-Flores, Ulrico López-Chuken, Ramiro Quintanilla-Licea, Diana Caballero-Hernandez, Cristina Rodríguez-Padilla, Julio Cesar Beltrán-Rocha, Patricia Tamez-Guerra
https://doi.org/10.7717/peerj.4358 PubMed 29441241
January 11, 2018
A streptomycin resistance marker in H. parasuis based on site-directed mutations in rpsL gene to perform unmarked in-frame mutations and to verify natural transformation
Ke Dai, Xintian Wen, Yung-Fu Chang, Sanjie Cao, Qin Zhao, Xiaobo Huang, Rui Wu, Yong Huang, Qigui Yan, Xinfeng Han, Xiaoping Ma, Yiping Wen
https://doi.org/10.7717/peerj.4253 PubMed 29340249
January 10, 2018
Refining amino acid hydrophobicity for dynamics simulation of membrane proteins
Jr, Ronald D. Hills
https://doi.org/10.7717/peerj.4230 PubMed 29340240
October 27, 2017
Immunofluorescence characterization of spinal cord dorsal horn microglia and astrocytes in horses
Constanza Stefania Meneses, Heine Yacob Müller, Daniel Eduardo Herzberg, Benjamín Uberti, Hedie Almagro Bustamante, Marianne Patricia Werner
https://doi.org/10.7717/peerj.3965 PubMed 29085760
October 12, 2017
Cellobiohydrolase B of Aspergillus niger over-expressed in Pichia pastoris stimulates hydrolysis of oil palm empty fruit bunches
James Sy-Keen Woon, Mukram M. Mackeen, Rosli M. Illias, Nor M. Mahadi, William J. Broughton, Abdul Munir Abdul Murad, Farah Diba Abu Bakar
https://doi.org/10.7717/peerj.3909 PubMed 29038760
July 21, 2017
In vitro assessment of anti-proliferative effect induced by α-mangostin from Cratoxylum arborescens on HeLa cells
Aisha I. El habbash, Najihah Mohd Hashim, Mohamed Yousif Ibrahim, Maizatulakmal Yahayu, Fatima Abd Elmutaal Omer, Mashitoh Abd Rahman, Noraziah Nordin, Gwendoline Ee Cheng Lian
https://doi.org/10.7717/peerj.3460 PubMed 28740747
July 5, 2017
13C based proteinogenic amino acid (PAA) and metabolic flux ratio analysis of Lactococcus lactis reveals changes in pentose phosphate (PP) pathway in response to agitation and temperature related stresses
Kamalrul Azlan Azizan, Habtom W. Ressom, Eduardo R. Mendoza, Syarul Nataqain Baharum
https://doi.org/10.7717/peerj.3451 PubMed 28695065
May 23, 2017
Effects of arginine vasopressin on the urine proteome in rats
Manxia An, Yanying Ni, Xundou Li, Youhe Gao
https://doi.org/10.7717/peerj.3350 PubMed 28560103
May 10, 2017
Screening of a natural compound library identifies emodin, a natural compound from Rheum palmatum Linn that inhibits DPP4
Zhaokai Wang, Longhe Yang, Hu Fan, Peng Wu, Fang Zhang, Chao Zhang, Wenjie Liu, Min Li
https://doi.org/10.7717/peerj.3283 PubMed 28507818
April 27, 2017
Lack of riluzole efficacy in the progression of the neurodegenerative phenotype in a new conditional mouse model of striatal degeneration
Grzegorz Kreiner, Katarzyna Rafa-Zabłocka, Piotr Chmielarz, Monika Bagińska, Irena Nalepa
https://doi.org/10.7717/peerj.3240 PubMed 28462043
April 27, 2017
Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling
Steven R. Ahrendt, Edgar Mauricio Medina, Chia-en A. Chang, Jason E. Stajich
https://doi.org/10.7717/peerj.3206 PubMed 28462022
March 1, 2017
Genetic and structural study of DNA-directed RNA polymerase II of Trypanosoma brucei, towards the designing of novel antiparasitic agents
Louis Papageorgiou, Vasileios Megalooikonomou, Dimitrios Vlachakis
https://doi.org/10.7717/peerj.3061 PubMed 28265521
February 28, 2017
Purification and biochemical characterization of recombinant Persicaria minor β-sesquiphellandrene synthase
De-Sheng Ker, Sze Lei Pang, Noor Farhan Othman, Sekar Kumaran, Ee Fun Tan, Thiba Krishnan, Kok Gan Chan, Roohaida Othman, Maizom Hassan, Chyan Leong Ng
https://doi.org/10.7717/peerj.2961 PubMed 28265494
February 23, 2017
Tartrazine induces structural and functional aberrations and genotoxic effects in vivo
Latifa Khayyat, Amina Essawy, Jehan Sorour, Ahmed Soffar
https://doi.org/10.7717/peerj.3041 PubMed 28243541
February 14, 2017
Modafinil decreases anxiety-like behaviour in zebrafish
Adrian Johnson, Trevor James Hamilton
https://doi.org/10.7717/peerj.2994 PubMed 28229024
February 2, 2017
Effects of rhodomyrtone on Gram-positive bacterial tubulin homologue FtsZ
Dennapa Saeloh, Michaela Wenzel, Thanyada Rungrotmongkol, Leendert Willem Hamoen, Varomyalin Tipmanee, Supayang Piyawan Voravuthikunchai
https://doi.org/10.7717/peerj.2962 PubMed 28168121
January 19, 2017
Jellyfish extract induces apoptotic cell death through the p38 pathway and cell cycle arrest in chronic myelogenous leukemia K562 cells
Sun-Hyung Ha, Fansi Jin, Choong-Hwan Kwak, Fukushi Abekura, Jun-Young Park, Nam Gyu Park, Young-Chae Chang, Young-Choon Lee, Tae-Wook Chung, Ki-Tae Ha, Jong-Keun Son, Hyeun Wook Chang, Cheorl-Ho Kim
https://doi.org/10.7717/peerj.2895 PubMed 28133573
January 18, 2017
Species-specific pharmacology of maximakinin, an amphibian homologue of bradykinin: putative prodrug activity at the human B2 receptor and peptidase resistance in rats
Xavier Charest-Morin, Hélène Bachelard, Melissa Jean, Francois Marceau
https://doi.org/10.7717/peerj.2911 PubMed 28133580
December 15, 2016
Discovery of novel inhibitors disrupting HIF-1α/von Hippel–Lindau interaction through shape-based screening and cascade docking
Xin Xue, Ning-Yi Zhao, Hai-Tao Yu, Yuan Sun, Chen Kang, Qiong-Bin Huang, Hao-Peng Sun, Xiao-Long Wang, Nian-Guang Li
https://doi.org/10.7717/peerj.2757 PubMed 27994971
November 24, 2016
Legionella shows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase
Nicholas J. Tobias, Tilman Ahrendt, Ursula Schell, Melissa Miltenberger, Hubert Hilbi, Helge B. Bode
https://doi.org/10.7717/peerj.2720 PubMed 27904811
November 22, 2016
Hypothesis on Serenoa repens (Bartram) small extract inhibition of prostatic 5α-reductase through an in silico approach on 5β-reductase x-ray structure
Paolo Governa, Daniela Giachetti, Marco Biagi, Fabrizio Manetti, Luca De Vico
https://doi.org/10.7717/peerj.2698 PubMed 27904805
August 11, 2016
Prediction of pKa values using the PM6 semiempirical method
Jimmy C. Kromann, Frej Larsen, Hadeel Moustafa, Jan H. Jensen
https://doi.org/10.7717/peerj.2335 PubMed 27602298
May 31, 2016
An explicit-solvent conformation search method using open software
Kari Gaalswyk, Christopher N. Rowley
https://doi.org/10.7717/peerj.2088 PubMed 27280078
May 18, 2016
Symbiotic essential amino acids provisioning in the American cockroach, Periplaneta americana (Linnaeus) under various dietary conditions
Paul A. Ayayee, Thomas Larsen, Zakee Sabree
https://doi.org/10.7717/peerj.2046 PubMed 27231663
April 19, 2016
Exploring the chemical space of influenza neuraminidase inhibitors
Nuttapat Anuwongcharoen, Watshara Shoombuatong, Tanawut Tantimongcolwat, Virapong Prachayasittikul, Chanin Nantasenamat
https://doi.org/10.7717/peerj.1958 PubMed 27114890
April 18, 2016
Structure and stability of recombinant bovine odorant-binding protein: II. Unfolding of the monomeric forms
Olga V. Stepanenko, Denis O. Roginskii, Olesya V. Stepanenko, Irina M. Kuznetsova, Vladimir N. Uversky, Konstantin K. Turoverov
https://doi.org/10.7717/peerj.1574 PubMed 27114857
April 18, 2016
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Bioactivities by a crude extract from the Greenlandic Pseudomonas sp. In5 involves the nonribosomal peptides, nunamycin and nunapeptin
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Provided feedback on

1 vote
11 Feb 2016

Towards a barrier height benchmark set for biologically relevant systems

This is a nice paper, even though the results are frustrating for those who expect that semi-empirical methods will soon become a useful alternative to DFT in real-life application...

10 May 2013

Selective comparability and physiological studies of lactic acid bacteria protease and Calotropis procera (linn) extracts

Minor points: p. 19 "Procerain, a stable cysteine protease […] was found to have a molecular mass of 28.8KDa and an isoelectric point of 9.32." The original paper (Dubey, VK a...

10 May 2013

Selective comparability and physiological studies of lactic acid bacteria protease and Calotropis procera (linn) extracts

Other minor points: Figs 25-35: The xx axis are labeled “enzyme concentration” instead of urea /CaCl2, NaCl, etc… concentration. Are those concentrations final concentrations or (...

10 May 2013

Selective comparability and physiological studies of lactic acid bacteria protease and Calotropis procera (linn) extracts

Other Major points: The data on figs 9-18 are extensively described verbally, which is redundant as proper graphs tell the story much more effectively. An attempt to discuss,...

03 Jan 2014

The sea urchin – the ultimate herbivore and biogeographic variability in its ability to deforest kelp ecosystems

line 120: " the name of either the region, or various localities within the region (e.g., “Ireland” and “England” for the Western Atlantic)." Should it not be Eastern Atlantic?...

23 Sep 2019

New insights into the mechanism of Schiff base synthesis from aromatic amines in the absence of acid catalyst or polar solvents

I found out that the basis set used is insufficient for proper optimizations. I have now redone the whole computations with (aug)-pcseg-1 and computed single points with DSD-BLYP....

8 Questions

0
There seems to be a mistake in the legend to figure 1
about Potential problems of removing one invasive species at a time: a meta-analysis of the interactions between invasive vertebrates and unexpected effects of removal programs
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Shoud the astronauts who performed the measurements in the ISS be mentioned/highlighted in the acknowledgments?
about Growth of 48 built environment bacterial isolates on board the International Space Station (ISS)
0
There is a typo in the Material and Methods section.
about Mechanistic pathways of mercury removal from the organomercurial lyase active site
0
How novel is the taxonomic information presented in this paper?
about Prospecting Russula senecis: a delicacy among the tribes of West Bengal
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The colored county map shown in the PeerJ entry page is not present in the paper. Would it be possible to include it as Supplemental Information?
about Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen
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Is the method compatible with the simultaneous use of $QUANPOL in Gamess US?
about A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+
0
Is there any experimental/computational support to the suggestion that cell differentiation really postpones the initiation of cell division?
about Cancer as a script and possible implications on workings of genome
0
How did the younger co-workers in the retracted papers react to the need for a retraction?

2 Answers

0
After how many days this article would appear in the Web of Science published paper list?
0
accepted Abstract is unable to provide insight into story & results!