Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Article
Plant Sciences
Jiu-Xia Zhao, Shu Wang, Jiazhi Liu, Xiao-Dong Jiang, Jing Wen, Zhi-Quan Suo, Jie Liu, Mi-Cai Zhong, Qin Wang, Zhirong Gu, Changning Liu, Yunfei Deng, Jin-Yong Hu, De-Zhu Li
Summary: This study generated a transcriptome resource for two Strobilanthes species, providing valuable information for understanding the molecular mechanisms of perennial monocarpic mass flowering. The differential expression of transcription factors potentially involved in the photoperiod and circadian-clock pathway suggests their role in regulating flowering time diversity.
Article
Ecology
Aliona S. Rosca, Joana Castro, Angela Franca, Mario Vaneechoutte, Nuno Cerca
Summary: Bacterial vaginosis (BV) is a common bacterial vaginal infection with an unknown etiology, characterized by structured polymicrobial biofilms primarily formed by Gardnerella spp. and other anaerobic species. The study compared triple-species biofilms using pre-conditioned and competitive models, finding more significant synergistic growth interactions in the competitive model. Despite model differences, G. vaginalis consistently dominated the biofilm composition, emphasizing its relevance in BV.
Article
Biotechnology & Applied Microbiology
Jiyue Huang, Hongkuan Wang, Yingxiang Wang, Gregory P. Copenhaver
Summary: This study compared the transcriptomes of msh4 and mus81 mutants under thermal stress, revealing the impact of heat stress on gene expression in meiotic-stage anthers and the differential responses of different genotypes to heat stress. The results showed up-regulation of multiple genes related to meiosis in all three genotypes, along with the identification of novel unannotated transcripts associated with meiotic recombination hotspot motifs in their promoter regions. This transcriptomic analysis enhances understanding of how meiotic CO pathways respond to environmental temperature stress and offers potential strategies to manipulate recombination levels in plants.
Article
Biochemistry & Molecular Biology
Weiguang Kong, Guangyi Ding, Peng Yang, Yuqing Li, Gaofeng Cheng, Chang Cai, Jun Xiao, Hao Feng, Zhen Xu
Summary: This study compared the infections of three genotypes of grass carp reovirus (GCRV) in Ctenopharyngodon idella kidney (CIK) cells. The results showed that GCRV-I and GCRV-III induced cytopathic effects (CPE), while GCRV-II did not. Additionally, all three genotypes activated immune responses in CIK cells, with GCRV-II inducing a more intense response. Interestingly, infected CIK cells exhibited a widespread down-regulation of metabolism processes. These findings provide a theoretical basis for understanding the pathogenesis and prevention and control methods of GCRV.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Jianshuang Li, Likang Lyu, Haishen Wen, Yun Li, Xiaojie Wang, Ying Zhang, Yijia Yao, Xin Qi
Summary: By using histology and RNA-seq, key pathways and genes involved in gonadal development and gamete maturation in black rockfish were characterized and differentially expressed genes were identified in testes and ovaries. The study provides comprehensive insight into black rockfish gonadal development, highlighting important pathways and genes for further reproductive physiology and molecular biology research in ovoviviparity teleosts.
Article
Plant Sciences
Amparo Primo-Capella, Maria Angeles Forner-Giner, Mary-Rus Martinez-Cuenca, Javier Terol
Summary: The long-term effects of cold stress on the transcriptome and metabolome of Valencia sweet orange were studied, and ABA signaling was found to play a crucial role in mediating the cold hardiness or sensitivity of the plant when grafted onto different rootstocks.
Article
Microbiology
Kundi Zhang, Mengyao Lu, Yuxin Qiu, Xiaoxuan Zhu, Hongwei Wang, Yan Huang, Hongjie Dong, Lichuan Gu
Summary: Gardnerella vaginalis is the main pathogen causing bacterial vaginosis. In a healthy vaginal microecological environment, lactobacilli produce lactate and hydrogen peroxide to inhibit the growth of G. vaginalis. This study simulated the co-culture of lactobacilli and G. vaginalis by adding lactate and hydrogen peroxide to a G. vaginalis culture medium, and identified the stress response genes of G. vaginalis using transcriptomics and proteomics. The findings suggest potential new drug targets for G. vaginalis and the development of novel therapies for bacterial vaginosis.
Article
Infectious Diseases
Heng Kang Ng, Suat Moi Puah, Cindy Shuan Ju Teh, Nuryana Idris, Kek Heng Chua
Summary: This study investigated the transcriptomic profiles of pellicle cells from carbapenem-resistant Acinetobacter baumannii strains. The analysis identified 366 differentially expressed genes (DEGs) in pellicle cells, including potential genes involved in fatty acid degradation (ABUW_1624, ABUW_1550) and a methionine transporter system gene (ABUW_2820). Upregulation of two-component systems (CusSR, KdpDE) related to copper and potassium ion regulation during CRAB pellicle formation was also observed. These findings provide insights into gene expression regulation in CRAB pellicle formation and potential targets for eradicating CRAB infections.
Article
Multidisciplinary Sciences
Pengliang Liu, Diyan Li, Jiaman Zhang, Mengnan He, Yan Li, Rui Liu, Mingzhou Li
Summary: The storage of lipids as energy in adipose tissue is conserved, but there are substantial differences in the physiological activities of adipose tissues among species. This study characterized the transcriptional and lipidomic profiles of subcutaneous and visceral adipose tissues across 15 vertebrate species, spanning more than 300 million years of evolution. The data revealed greater variation in AT transcriptome and lipidome among species than within the same species, providing a resource for future studies on functional differences among adipose tissues in vertebrate species.
Article
Genetics & Heredity
Xin Liu, Jing Zhang, Danyao Nie, Kun Zeng, Huiling Hu, Jinjun Tie, Liangnan Sun, Ling Peng, Xinhua Liu, Jiantao Wang
Summary: Transcriptome analysis of pterygium tissues identified differential expression of 579 mRNAs, 275 lncRNAs, and 21 circRNAs, which are associated with extracellular matrix organization, blood vessel morphogenesis, and focal adhesion. Key genes such as FN1, VCAM1, and MMP2, as well as lncRNAs like MIR4435-2HG and LINC00968, were identified to potentially play a role in the pathogenesis of pterygium. Additionally, circRNAs such as hsa_circ_0007482 and hsa_circ_001730 were found to be involved in the development of pterygium.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Abrahan Hernandez-Hernandez, Tayde Lopez-Santaella, Aranxa Torres-Caballero, Amarantha Serrato, Ulises Torres-Flores, Diego Montesinos-Valencia, Fernando Chico-Ponce De Leon, Vicente Gonzalez-Carranza, Samuel Torres-Garcia, Rosa Rebollar-Vega, Inti Alberto De la Rosa-Velazquez, Rosario Ortiz, Monserrat Perez-Ramirez, Normand Garcia-Hernandez, Antonio Garcia-Mendez, Francisco Arenas-Huertero
Summary: Central nervous system tumors are common in childhood and contribute to cancer-related mortality. This study explored the transcriptomic landscape of pediatric astrocytoma, focusing on the genetic alterations associated with tumorigenesis. The findings provide insights into the biological functions and pathways involved in astrocytoma, and establish a transcriptional signature for identifying different grades of the tumor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Shouping Zhao, Qi Zhang, Wendan Xiao, De Chen, Jing Hu, Na Gao, Miaojie Huang, Xuezhu Ye
Summary: Cd is still a major contaminant in rice production. Study on the mechanism of genotypic differences in Cd enrichment in rice is necessary to regulate Cd enrichment. Two rice cultivars (low Cd, ZZ143; and high Cd, YX409) showed different transcriptomic profile patterns under 100 μmol/L Cd stress. The identified DEGs and enriched pathways suggest that ZZ143 has a stronger ability for sulfur assimilation and Cys synthesis, while YX409 has a stronger ability to maintain cell wall stability, which may contribute to their different Cd concentrations.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Microbiology
Yue Zhang, Huijie Chen, Jia Yu, Rui Feng, Zhao Chen, Xiaolin Zhang, Yudong Ren, Guijun Yang, Xiaodan Huang, Guangxing Li
Summary: This study isolated and characterized an epidemic strain of porcine epidemic diarrhea virus (PEDV) from China and investigated its genomic expression profile in infected pig intestinal cells. The study found that the isolated strain could activate anti-viral innate immune response and inflammation more intensively than a classical strain, suggesting its high pathogenicity. The results contribute to understanding the pathogenesis mechanism of PEDV variants and can aid in the prevention and control of PEDV infection.
VETERINARY MICROBIOLOGY
(2022)
Article
Environmental Sciences
J. Bjorneset, P. Blevin, P. M. Bjornstad, R. A. Dalmo, A. Goksoyr, M. Harju, G. Limonta, C. Panti, A. H. Rikardsen, A. Y. M. Sundaram, F. Yadetie, H. Routti
Summary: Populations of killer whales contain highly polluted animals, but the understanding of the effects of chemical pollutants on this species is limited. In this study, skin biopsies were collected from killer whales in the Northern Norwegian fjords, and primary fibroblast cell cultures were established. The cells were exposed to a mixture of persistent organic pollutants (POPs) found in Norwegian killer whales, and the transcriptional responses were analyzed. The study found significant downregulation of CYP1A1 and non-significant upregulation of genes involved in endocrine functions. Bioinformatic analysis revealed differentially expressed genes related to lipid metabolism, myogenesis, and glucocorticoid receptor regulation. These findings provide cause-effect relationships and are relevant for chemical and environmental management.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Ecology
Aliona S. Rosca, Joana Castro, Angela Franca, Mario Vaneechoutte, Nuno Cerca
Summary: Bacterial vaginosis (BV) is a common bacterial vaginal infection with an unknown etiology, characterized by structured polymicrobial biofilms primarily formed by Gardnerella spp. and other anaerobic species. The study compared triple-species biofilms using pre-conditioned and competitive models, finding more significant synergistic growth interactions in the competitive model. Despite model differences, G. vaginalis consistently dominated the biofilm composition, emphasizing its relevance in BV.
Article
Immunology
Vania Gaio, Tania Lima, Manuel Vilanova, Nuno Cerca, Angela Franca
Summary: The mazEF homologue does not play a role in VBNC cell formation, antimicrobial susceptibility, virulence factor expression, or immune cell response in S. epidermidis strain 1457.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Editorial Material
Pharmacology & Pharmacy
Nuno Cerca
EXPERT OPINION ON PHARMACOTHERAPY
(2023)
Article
Infectious Diseases
Aliona S. Rosca, Joana Castro, Lucia G. Sousa, Angela Franca, Mario Vaneechoutte, Nuno Cerca
Summary: This study investigated the role of interactions between bacterial species in multi-species biofilms in bacterial vaginosis (BV) in relation to antimicrobial tolerance. The results showed that when these species were co-cultured, they could synergistically increase resistance to antibiotics.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2022)
Article
Biochemical Research Methods
Nuno Cerca, Angela Lima, Angela Franca
Summary: qPCR absolute quantification requires evaluating the efficiency of the PCR reaction. This is achieved by diluting gDNA in a series. In this study, we demonstrate that when quantifying bacterial load in mixed samples, the calibration curve should not solely be based on reaction efficiency, as neglecting gDNA isolation efficiency significantly impacts the quantification results.
JOURNAL OF MICROBIOLOGICAL METHODS
(2022)
Article
Multidisciplinary Sciences
Lucia G. Sousa, Joana Castro, Carlos Cavaleiro, Ligia Salgueiro, Mariana Tomas, Rita Palmeira-Oliveira, Jose Martinez-Oliveira, Nuno Cerca
Summary: Bacterial vaginosis (BV) is a common vaginal infection in women worldwide. This study found that Thymbra capitata essential oils (EOs), specifically carvacrol and rho-cymene, have a strong synergistic antimicrobial effect against Gardnerella spp., the main bacteria causing BV. These EOs also effectively eliminate biofilm cells without cytotoxicity, highlighting their potential as alternative therapeutic options for BV treatment.
SCIENTIFIC REPORTS
(2022)
Article
Immunology
Aliona S. Rosca, Joana Castro, Lucia G. V. Sousa, Angela Franca, Carlos Cavaleiro, Ligia Salgueiro, Nuno Cerca
Summary: This study characterized the first polymicrobial biofilm consisting of six BV-associated species and found that Thymbra capitata essential oil exhibited a high antibacterial effect against the polymicrobial biofilm. The findings provide important insights for the development of antimicrobial agents against BV.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Microbiology
Christina A. Muzny, Nuno Cerca, Jacob H. Elnaggar, Christopher M. Taylor, Jack D. Sobel, Barbara van der Pol
Summary: Bacterial vaginosis (BV) is a common cause of vaginal discharge in women of reproductive age and is associated with various negative health outcomes, including increased risk of HIV and other STIs, as well as adverse birth outcomes. The exact cause of BV, a dysbiosis of the vaginal microbiota, is still unknown. This mini-review provides an updated overview of the diagnostic tests used for BV in clinical and research settings, focusing on traditional and molecular diagnostics. It highlights the use of molecular diagnostic assays such as 16S rRNA gene sequencing, shotgun metagenomic sequencing, and FISH, as well as multiplex NAATs, in studying the vaginal microbiota and BV pathogenesis.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Veterinary Sciences
D. Araujo, J. Castro, F. Matos, R. Oliveira, C. Ramos, C. Almeida, S. Silva
Summary: This study investigated the prevalence and antibiotic resistance of Klebsiella spp. in clinically ill cats and dogs in veterinary clinics in the North of Portugal. The results showed that multidrug-resistant Klebsiella is widely disseminated in companion animals, and carries extended-spectrum beta-lactamase genes. This highlights the potential role of dogs and cats as a reservoir of resistant Klebsiella spp. that have the potential to be transmitted to humans.
RESEARCH IN VETERINARY SCIENCE
(2023)
Article
Immunology
Jacob H. Elnaggar, Caleb M. Ardizzone, Nuno Cerca, Evelyn Toh, Pawel Laniewski, Rebecca A. Lillis, Melissa M. Herbst-Kralovetz, Alison J. Quayle, Christina A. Muzny, Christopher M. Taylor
Summary: Bacterial vaginosis (BV) is the most common vaginal dysbiosis characterized by the formation of a polymicrobial biofilm on vaginal epithelial cells. The standard method for quantifying the bacterial burden of BV biofilm using Escherichia coli as a reference has limitations. A novel qPCR standard using different combinations of vaginal bacteria was proposed to accurately quantify bacterial burden in vaginal microbial communities, which showed superior accuracy compared to the traditional E. coli reference standard.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Lucia G. V. Sousa, Carina Almeida, Christina A. Muzny, Nuno Cerca
Summary: Bacterial vaginosis (BV) is a common vaginal infection worldwide. A peptide nucleic acid (PNA) probe targeting Prevotella bivia, a common BV-associated bacteria, was developed, and a multiplex approach for detection of Gardnerella spp., P. bivia, and Fannyhessea vaginae was optimized. The P. bivia PNA probe specifically detected the target species, and the optimized multiplex approach could identify the presence of these three species in multi-species BV biofilms.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Review
Biotechnology & Applied Microbiology
Lucia G. V. Sousa, Sofia A. Pereira, Nuno Cerca
Summary: Bacterial vaginosis (BV) is a common cause of vaginal discharge and is often problematic in pregnant women. BV is caused by an imbalance in the vaginal microbiota, leading to the overgrowth of bacteria that produce lactic acid and hydrogen peroxide. The treatment of BV with antibiotics is often associated with high recurrence rates. Various alternative strategies including probiotics, acidifying agents, antiseptics, and plant-based products are being studied to improve treatment success.
MICROBIAL BIOTECHNOLOGY
(2023)
Review
Infectious Diseases
Maria Margarida Barros, Joana Castro, Daniela Araujo, Ana Maria Campos, Ricardo Oliveira, Sonia Silva, Divanildo Outor-Monteiro, Carina Almeida
Summary: This review summarizes the epidemiological challenge of swine colibacillosis caused by Escherichia coli, highlighting the role of antibiotic use in animal practices in the emergence of multidrug-resistant strains. It discusses the diversity, resistance, and virulence profiles of pathogenic ETEC strains and emphasizes their importance as zoonotic agents.
Article
Polymer Science
Mariana Tomas, Lucia G. V. Sousa, Ana Sofia Oliveira, Carolina P. P. Gomes, Ana Palmeira-de-Oliveira, Carlos Cavaleiro, Ligia Salgueiro, Nuno Cerca, Jose Martinez-de-Oliveira, Rita Palmeira-de-Oliveira
Summary: We aimed to incorporate Thymbra capitata essential oil (TCEO), a potent antimicrobial natural product against BV-related bacteria, in a suitable drug delivery system. Vaginal sheets were used as the dosage form to provide immediate relief for BV symptoms. The vaginal sheets containing TCEO showed promising bioadhesive profiles, flexibility, and structure, and were able to significantly reduce bacterial load. Although toxicity was observed at certain concentrations, the short treatment period may limit or reverse this toxicity.
Article
Veterinary Sciences
Alice Ferreira, Daniela Silva, Carina Almeida, Maria Elisa Rodrigues, Sonia Silva, Joana Castro, Dalila Mil-Homens, Isidro Garcia-Menino, Azucena Mora, Mariana Henriques, Ana Oliveira
Summary: This study evaluated the efficacy of phage vB_EcoM_FJ1 (FJ1) in reducing the load of pathogenic Escherichia coli (ETEC) and found that encapsulated FJ1 in microparticles significantly reduced the quantity of ETEC. Bacteriophage-insensitive mutants (BIMs) displayed weaker adaptability in the pig model.
VETERINARY RESEARCH
(2023)