Article
Nutrition & Dietetics
Seiichiro Aoe, Chiemi Yamanaka, Kento Mio
Summary: The study demonstrated that supplementation of a high fat diet with paramylon improved lipid metabolism by suppressing the digestion and absorption pathway in the ileum and activating the hepatic PPAR signaling pathway. This led to reduced abdominal fat accumulation and serum LDL cholesterol concentrations. Additionally, paramylon intake may enhance serum secretory immunoglobulin A concentrations through the promotion of the immunoglobulin production pathway in the ileum.
Article
Multidisciplinary Sciences
Faryal Ijaz, Ryota Nakazato, Mitsutoshi Setou, Koji Ikegami
Summary: This study developed a simple genotyping method called DST-PCR to screen potential mutation clones in CRISPR/Cas9-engineered knockout (KO) cells. The method is simple, fast, and capable of detecting both insertion and deletion mutations.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Joung Sug Kim, SongHwa Chae, Kyong Mi Jun, Gang-Seob Lee, Jong-Seong Jeon, Kyung Do Kim, Yeon-Ki Kim
Summary: The study successfully identified the DNA-binding sequences of OsWOX13, OsSMF1, and OsWRKY34, along with the respective numbers of putative feature genes. This method could be applicable in analyzing DNA-binding motifs for TFs in the promoter and 5' upstream CDS regions, facilitating the construction of gene networks.
Article
Genetics & Heredity
Yi-Chiao Cheng, Po-Hsien Wu, Yen-Ju Chen, Cing-Han Yang, Jhen-Li Huang, Yu-Ching Chou, Pi-Kai Chang, Chia-Cheng Wen, Shu-Wen Jao, Hsin-Hui Huang, Yi-Hsuan Tsai, Tun-Wen Pai
Summary: This study developed a novel approach in biomarker selection by integrating genome-wide DNA methylation profiles and CRC comorbidity analytics, selecting suitable biomarkers for CRC screening tests. These biomarkers showed significantly higher methylation levels in CRC patients compared to normal subjects, achieving high sensitivity and specificity for CRC detection when integrated.
Article
Biochemical Research Methods
Hannes P. Eggertsson, Bjarni Halldorsson
Summary: Reliable data is essential for data analysis, and sample contamination is a common issue in genetics. In diploid species like humans, DNA contamination from the same species can be detected by the number of haplotypes between polymorphic SNPs. An effective tool called read_haps is available for detecting sample contamination from short read whole genome sequencing data.
Article
Environmental Sciences
Marissa S. Giroux, Jay R. Reichman, Troy Langknecht, Robert M. Burgess, Kay T. Ho
Summary: This study investigated the effects of nanoplastics on benthic micro- and meiofaunal community diversity using a metabarcoding approach. The results showed that the highest concentration of nanoplastics exposure led to increased diversity and significant changes in community composition, driven by differential abundance of specific protists and arthropods.
ENVIRONMENTAL POLLUTION
(2023)
Article
Chemistry, Analytical
Bailey C. Buchanan, Babak Safavinia, Lillian Wu, Jeong-Yeol Yoon
Summary: This study developed a method to detect bacteria on laboratory surfaces using low-cost components and a smartphone, without the need for culturing or staining. The presence of Escherichia coli, Salmonella Typhimurium, and Staphylococcus aureus was successfully detected, and the method could also distinguish from tap water, protein, and NaCl solutions.
Article
Immunology
Yunqi Li, Francois Lefebvre, Edith Nakku-Joloba, Allan Ronald, Glenda Gray, Guy de Bruyn, James Kiarie, Connie Celum, Mark J. Cameron, Jairam R. Lingappa, Romel D. Mackelprang
Summary: In individuals exposed to HIV-1, higher expression of PTPRC (CD45 antigen) and interferon-response pathways may indicate an increased risk of acquiring HIV-1.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Multidisciplinary Sciences
Tanay Thakar, Ashna Dhoonmoon, Joshua Straka, Emily M. Schleicher, Claudia M. Nicolae, George-Lucian Moldovan
Summary: This study reveals that lagging strand ssDNA gaps interfere with nucleosome assembly and drive replication fork degradation in BRCA-deficient cells. Correcting PCNA unloading defects and activating a compensatory histone deposition pathway can restore fork stability in BRCA-deficient cells.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Brittany G. Sullivan, Angelina Lo, Jingjing Yu, Amber Gonda, Farideh Dehkordi-Vakil, Farshid Dayyani, Maheswari Senthil
Summary: This study found that peritoneal carcinomatosis (PC) is associated with lower levels of circulating tumor DNA (ctDNA) compared to other metastatic sites in gastrointestinal cancers. The researchers also caution that interpretation of ctDNA results in patients with PC should be done with caution due to lower sensitivity for detecting actionable mutations.
ANNALS OF SURGICAL ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ayuba Sunday Buru, Vasantha Kumari Neela, Kavitha Mohandas, Mallikarjuna Rao Pichika
Summary: Staphylococcus aureus is a highly adaptable human pathogen with rapid antibiotic resistance, prompting the search for more effective antibacterial agents. This study investigates the mechanism of action of eugenol against MRSA and identifies potential drug targets for the development of efficacious antimicrobial agents.
Article
Environmental Sciences
Yu-Cheng Zhu, Yuzhe Du, Jianxiu Yao, Xiaofen F. F. Liu, Yanhua Wang
Summary: Frequent sprays on cotton led to resistance development in tarnished plant bugs (TPBs). Understanding global gene regulation is crucial for comprehending resistance mechanisms and developing molecular tools for resistance monitoring. Microarray analysis of 6688 genes revealed significant up- or down-regulation of 3080 genes in TPBs treated with permethrin. Over-expression of oxidase enzymes, along with a specific GST gene, was identified as a novel resistance mechanism in permethrin-treated TPBs. Other enzymes such as reductases and dehydrogenases may indirectly contribute to permethrin detoxification.
Review
Oncology
Naomie Devico Marciano, Gianna Kroening, Farshid Dayyani, Jason A. Zell, Fa-Chyi Lee, May Cho, Jennifer Goldstein Valerin
Summary: This article discusses the impact of genetic mutations on the development and treatment of pancreatic cancer, particularly focusing on the role of BRCA1 and BRCA2 genes. These mutations affect various aspects of cellular function and may provide new targets for pancreatic cancer treatment. Patients with BRCA mutations show increased sensitivity to certain treatments, but resistance can also occur. Therefore, the development of novel therapies is urgently needed.
Review
Oncology
Marjolijn M. Ladan, Dik C. van Gent, Agnes Jager
Summary: Effective cancer treatment requires selecting patients based on tumor characteristics, including those with BRCA1/2 mutations or defects in the homologous recombination repair pathway. The challenge lies in identifying patients with BRCA-like tumors and selecting appropriate treatment strategies. Germline BRCA mutations result in HRD phenotype, making tumors sensitive to DNA double strand break-inducing agents.
Article
Chemistry, Analytical
Chuo-Ying Mai, Yu-Fen Lai, Li Zou
Summary: This study developed an enzyme-free colorimetric biosensor for the determination of the BRCA-1 gene, allowing detection of target DNA at low concentrations with colorimetric readout. The biosensor showed excellent selectivity and applicability in human serum samples, holding great potential in genetic analysis and clinical diagnosis.
CHINESE JOURNAL OF ANALYTICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Alisha Prasad, Syed Mohammad Abid Hasan, Manas Ranjan Gartia
Review
Nanoscience & Nanotechnology
Nishir Mehta, Sushant P. Sahu, Shahensha Shaik, Ram Devireddy, Manas Ranjan Gartia
Summary: Nanomaterials are crucial in cancer diagnosis and treatment, with Dark-field hyperspectral imaging (DF-HSI) offering a cost-effective and minimally invasive method for studying the cellular transport and toxicity effects of these materials.
WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Alisha Prasad, Sushant P. Sahu, Sara Karoline Figueiredo Stofela, Ardalan Chaichi, Syed Mohammad Abid Hasan, Wokil Bam, Kanchan Maiti, Kevin M. McPeak, Gang Logan Liu, Manas Ranjan Gartia
Summary: Phosphate is a major nonpoint source pollutant in Louisiana and the Gulf of Mexico, contributing to global water eutrophication. This study aims to monitor phosphate levels in local watersheds using an electrochemical sensor, evaluate its performance, and potentially identify hot spots contributing to downstream nutrient loading.
Article
Chemistry, Multidisciplinary
Sushant P. Sahu, Subarna Kole, Christopher G. Arges, Manas Ranjan Gartia
Summary: This study reports an electrochemical sensor with a selective perfluorinated anion exchange ionomer (PFAEI) coating for direct sensing of a type of PFAS called perfluorooctanoic acid (PFOA). The sensor operates without redox probes and has a low detection limit.
Article
Chemistry, Analytical
Eloghosa Ikponmwoba, Okezzi Ukorigho, Parikshit Moitra, Dipanjan Pan, Manas Ranjan Gartia, Opeoluwa Owoyele
Summary: This study investigates predictive diagnosis of COVID-19 infection using surface-enhanced Raman scattering (SERS) and machine learning approaches. It provides high-throughput rapid testing, with the need for confirmation through follow-up PCR in cases of model uncertainty.
Article
Neurosciences
D. Parker Kelley, Ardalan Chaichi, Alexander Duplooy, Dhirendra Singh, Manas Ranjan Gartia, Joseph Francis
Summary: Stress and trauma alter oxidative and lipid homeostasis, and PTSD is associated with changes in lipid species in plasma. However, there is limited research on stress-induced lipidomic changes in the brain. In this study, Raman imaging was used to quantify lipid species in the hippocampus, revealing increased cholesterol, altered lipid concentrations, increased free radical production, and reduced oxidized polyunsaturated fatty acids (PUFAs) after traumatic stress.
NEUROBIOLOGY OF STRESS
(2022)
Review
Chemistry, Analytical
Sreyashi Das, Ram Devireddy, Manas Ranjan Gartia
Summary: A biomarker is a physiological observable marker that can predict clinically significant outcomes. Diagnostic biomarkers are more convenient and cost-effective for measuring clinical outcomes. Surface plasmon resonance (SPR) is a promising technique for the quick and less invasive screening of biomarkers, such as ctDNA, miRNA, CTCs, lipids, and proteins. This review focuses on advancements in SPR biosensing technologies for cancer detection.
Article
Biology
Kevin J. Tu, Sanjit K. Roy, Zachery Keepers, Manas R. Gartia, Hem D. Shukla, Nrusingh C. Biswal
Summary: The study investigates the effectiveness and molecular characteristics of the combination therapy of Docetaxel (DXL) and radiation in vitro. The results suggest that DXL sensitizes castration-resistant prostate cancer (CRPC) cells to radiation by downregulating CAV-1.
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
(2023)
Article
Engineering, Biomedical
Elnaz Sheikh, Kirti Agrawal, Sanjit Roy, David Burk, Fabrizio Donnarumma, Young H. Ko, Praveen Kumar Guttula, Nrusingh C. Biswal, Hem D. Shukla, Manas Ranjan Gartia
Summary: This study demonstrates the simultaneous profiling of three protein biomarkers using SERS nanotags and antibody-functionalized nanoparticles in a syngeneic mouse model of pancreatic cancer. The multimodal imaging techniques used provide comprehensive information about biomarkers and TAM alterations before and after treatment. The study reveals the efficacy of 3-BP in treating pancreatic cancer and identifies drug treatment-induced lipid species remodeling and associated pathways through bioinformatics analysis.
ADVANCED HEALTHCARE MATERIALS
(2023)
Review
Chemistry, Analytical
Mohan Kumar Dey, Maria Iftesum, Ram Devireddy, Manas Ranjan Gartia
Summary: Integrating new technologies and reagents could improve lateral flow assays' sensitivity and accuracy while minimizing the complexity and potential for false positives.
ANALYTICAL METHODS
(2023)
Article
Chemistry, Physical
Chintan P. Chavda, Ashok Srivastava, Erin Vaughan, Jianwei Wang, Manas Ranjan Gartia, Georgios Veronis
Summary: Two-dimensional transition metal dichalcogenides (2D-TMDs) have promising optoelectronic properties for space applications. This study investigates the effect of gamma irradiation on a monolayer of MoS2, a 2D-TMD. Raman spectroscopy and X-ray photoelectron spectroscopy (XPS) analysis reveal the presence of point defects after gamma irradiation, and density functional theory (DFT) calculations suggest that the conductivity of the monolayer may increase due to the creation of additional defect states.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Nishir Mehta, Amirreza Mahigir, Georgios Veronis, Manas Ranjan Gartia
Summary: Rotational dynamics at the molecular level provides additional data for protein diffusion and cytoskeleton formation at the cellular level. Metal nanoparticles can be used for sensing rotational motion and offer better biocompatibility and stability compared to conventional fluorescent molecules for orientation imaging.
NANOSCALE ADVANCES
(2022)
Article
Chemistry, Analytical
Ardalan Chaichi, Syed Mohammad Abid Hasan, Nishir Mehta, Fabrizio Donnarumma, Philip Ebenezer, Kermit K. Murray, Joseph Francis, Manas Ranjan Gartia
Summary: Post-traumatic stress disorder (PTSD) is a severe psychiatric injury that can lead to life-threatening symptoms. A novel method utilizing Raman mapping provides quantitative results on lipid alterations in the brain region affected by PTSD, offering valuable insights into the mechanisms of this disorder.