Article
Biochemical Research Methods
Yumeng Yan, Sheng-You Huang
Summary: DeepHomo, a deep learning model for predicting inter-protein residue-residue contacts, integrates various information sources and achieves high precision, outperforming existing methods on both experimentally determined structures and simulated targets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Wei-Chun Huang, Wai-Ting Chen, Yueh-Chen Chen, Shiuh-Bin Fang, Tzu-Wen Huang, Pei-Ru Chang, Yu-Chu Chang
Summary: Protein oligomerization is crucial for the pathogenesis of Salmonella Typhimurium. YqiC forms a homotrimer and its mutations result in reduced colonization and invasion to host cells. It interacts with subunits of the electron transport chain and ATP synthase, suggesting its role in energy modulation and virulence factor assembly.
Article
Biochemistry & Molecular Biology
Shogo Inoue, Yohei Ikeda, Saki Fujiyama, Tadashi Ueda, Yoshito Abe
Summary: DNA replication stops when DNA is damaged. Repairing genomic DNA and reloading replication helicase are crucial for restarting DNA replication. The Escherichia coli primosome is responsible for reloading replication helicase DnaB. Protein DnaT in the primosome complex contains two functional domains. The N-terminal domain of DnaT has a dimeric antitoxin structure, which plays a role in replication restart in Escherichia coli.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2023)
Article
Microbiology
Lun Hu, Xiaojuan Wang, Yu-An Huang, Pengwei Hu, Zhu-Hong You
Summary: Proteins play a crucial role in carrying out various physiological functions in cells through interactions, making the prediction of protein-protein interactions essential for understanding biological processes. Computational prediction algorithms have become popular due to the time-consuming and labor-intensive nature of laboratory-based experiments. This study introduces a novel algorithm based on prior information and biological data to accurately predict PPIs.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shifeng Xiao, Qiuping Wu, Xuanbao Yao, Jiahao Zhang, Weicong Zhong, Junyi Zhao, Qiong Liu, Mohan Zhang
Summary: Isobavachalcone is a promising compound for potential preventive and therapeutic medicine for Alzheimer's disease, as it can inhibit tau protein aggregation and disaggregation, as well as regulate tau phosphorylation.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Sucharita Dey, Emmanuel D. Levy
Summary: An accurate understanding of protein quaternary structure is crucial for studying biomolecular mechanisms and diseases. By comparing structures and compositions of hetero-oligomers, using QS conservation across homologs, the study annotates complexes with a high accuracy exceeding 94%. The research provides high-quality annotations and a large benchmark dataset for hetero-assemblies.
Article
Biotechnology & Applied Microbiology
Chris Gaiteri, David R. Connell, Faraz A. Sultan, Artemis Iatrou, Bernard Ng, Boleslaw K. Szymanski, Ada Zhang, Shinya Tasaki
Summary: Clustering molecular data into informative groups is essential for extracting robust conclusions from big data. This study compares popular clustering algorithms on synthetic and real biological datasets, finding that no single method is universally optimal. The SpeakEasy2 algorithm generally provides robust, scalable, and informative clusters for various applications.
Review
Computer Science, Information Systems
Xiangmao Meng, Wenkai Li, Xiaoqing Peng, Yaohang Li, Min Li
Summary: This paper provides a comprehensive survey on the characteristics of protein interaction networks (PINs), including centrality, modularity, and dynamics, and discusses their applications in complex diseases as well as future research directions.
FRONTIERS OF COMPUTER SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Anne Chouquet, Andrea J. Pinto, Julia Hennicke, Wai Li Ling, Isabelle Bally, Linda Schwaigerlehner, Nicole M. Thielens, Renate Kunert, Jean-Baptiste Reiser
Summary: In this study, recombinant production of two IgM models was successfully achieved, and their polymer distribution was evaluated using various biophysical methods. The results showed that both purified IgMs were able to activate complement and possessed similar C1q-binding properties as IgMs purified from human plasma.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Physiology
Maria Steene Eriksen, Clive R. Bramham
Summary: Arc is a pivotal protein regulating synaptic plasticity, memory, and cognitive flexibility. It acts as a protein interaction hub and dynamic regulator of intra-cellular signaling in neurons, but can also self-assemble into retrovirus-like capsids for intercellular RNA transfer. Understanding the molecular basis and relationship between these functions are crucial for progress.
Article
Biology
Hua Leonhard Tan, Stefanie Bungert-Plumke, Daniel Kortzak, Christoph Fahlke, Gabriel Stoelting
Summary: The oligomeric state of plasma membrane proteins is crucial for their function and can be determined using super-resolution microscopy techniques. The dual-color colocalization (DCC) approach we developed allows for accurate counting of protein subunits and simplifies data processing.
Article
Ecology
Hai-Xia Hu, Ting Shen, Dong-Li Quan, Akihiro Nakamura, Liang Song
Summary: This study investigated the network structures between epiphytic bryophytes and their hosts in tropical and subtropical forests, revealing nested relationships, low modularity, and specialization levels. The vertical distribution of bryophyte species showed structured modules within tree basal and crown zones. The high nestedness may stabilize ecological networks, while low modularity and specialization suggest less colonization of specific host species by epiphytes.
FRONTIERS IN FORESTS AND GLOBAL CHANGE
(2021)
Article
Biochemistry & Molecular Biology
Mohd Imran K. Khan, Ramya Chandar M. Charles, Reshma Ramachandran, Somlee Gupta, Gayathri Govindaraju, Rashmi Mishra, Arumugam Rajavelu, Mohane Selvaraj Coumar, Sreenivas Chavali, Arunkumar Dhayalan
Summary: The study found that the ribosomal protein eL21 interacts with the lysine methyltransferase SMYD2, regulating its levels and contributing to cell proliferation, with potential implications for tumorigenesis. This highlights a novel extra-ribosomal function of eL21 and suggests that ribosomal proteins may regulate various cellular functions through protein-protein interactions beyond their role in translation.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Jiarui Cui, Jiaming Zhang
Summary: Cartilage oligomeric matrix protein (COMP) plays a critical role in collagen assembly and ECM stability in the extracellular matrix. Mutations in COMP can lead to endoplasmic reticulum stress and chondrocyte apoptosis, resulting in rare skeleton diseases. COMP acts as a bridging molecule with its bouquet-like structure, regulating cellular phenotype and function by interacting with ECM components, cellular receptors, and growth factors. Recent studies suggest that COMP may also be involved in other skeleton diseases, malignancy, cardiovascular diseases, and tissue fibrosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Neharika Chamachi, Andreas Hartmann, Mai Quynh Ma, Anna Svirina, Georg Krainer, Michael Schlierf
Summary: This study investigates the essential role of periplasmic chaperones, 17-kilodalton protein (Skp) and survival factor A (SurA), in outer membrane protein (OMP) biogenesis. The researchers use single-molecule fluorescence spectroscopy to analyze the conformational dynamics and thermodynamics of Skp and SurA binding to unfolded OmpX and study their disaggre-gase activities. The findings provide insights into the multifaceted functionalities of Skp and SurA and shed light on the balance between conformational flexibility and underlying ener-getics in aiding chaperone action during OMP biogenesis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Environmental Sciences
Ilan Levy, Isabella Karakis, Tamar Berman, Moshe Amitay, Zohar Barnett-Itzhaki
ENVIRONMENTAL MONITORING AND ASSESSMENT
(2020)
Article
Genetics & Heredity
Zohar Barnett-Itzhaki, Miriam Elbaz, Rachely Butterman, Devora Amar, Moshe Amitay, Catherine Racowsky, Raoul Orvieto, Russ Hauser, Andrea A. Baccarelli, Ronit Machtinger
JOURNAL OF ASSISTED REPRODUCTION AND GENETICS
(2020)
Article
Environmental Sciences
Zohar Barnett-Itzhaki, Adi Levi
Summary: The study found that long-term exposure to air pollutants concentrations exceeding WHO guidelines, such as PM2.5 and NOx, may exacerbate morbidity and mortality rates from COVID-19. The models also highlighted the importance of the relative number of hospital beds in decreasing the morbidity and mortality of COVID-19.
ENVIRONMENTAL RESEARCH
(2021)
Article
Environmental Sciences
Maya Negev, Tamar Berman, Shula Goulden, Shay Reicher, Zohar Barnett-Itzhaki, Ruti Ardi, Yaniv Shammai, Miriam L. Diamond
Summary: The study found that the proportion of children's jewelry samples exceeding the ASTM lead standard decreased to 17% in 2018, with a lower average lead content. The swift implementation of the new standard was attributed to scientific and regulatory consensus. However, enforcement challenges may reduce the standard's impact.
JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY
(2022)
Article
Obstetrics & Gynecology
Zohar Barnett-Itzhaki, Sarah Knapp, Chaya Avraham, Catherine Racowsky, Russ Hauser, Valentina Bollati, Andrea A. Baccarelli, Ronit Machtinger
Summary: The study found that phthalate metabolite concentrations are associated with the expression of extracellular vesicle microRNAs (EV-miRNAs) in follicular fluid, potentially impacting pathways related to oocyte development, maturation, and fertilization.
HUMAN REPRODUCTION
(2021)
Article
Environmental Sciences
Adi Levi, Zohar Barnett-Itzhaki
Summary: The study found an association between chronic exposure to air pollutants in Israeli cities and towns and COVID-19 morbidity rates during two of the three morbidity waves. The third wave with higher morbidity was more related to socioeconomic factors, emphasizing the need for attention to socioeconomically vulnerable populations.
ENVIRONMENTAL RESEARCH
(2021)
Article
Ophthalmology
Guy Barnett-Itzhaki, Zohar Barnett-Itzhaki, Noa Ela-Dalman
Summary: The study showed that the Dyop eye chart is a valid measure of visual acuity in children aged 4-17 with visual acuity ranging from 20/16 to 20/200, but it tends to underestimate visual acuity compared to the Lea numbers chart.
Article
Psychiatry
Dekel Taliaz, Amit Spinrad, Ran Barzilay, Zohar Barnett-Itzhaki, Dana Averbuch, Omri Teltsh, Roy Schurr, Sne Darki-Morag, Bernard Lerer
Summary: This study utilized machine learning algorithms to analyze genetic, clinical, and demographic factors in patients with major depressive disorder, generating an accurate predictive algorithm for antidepressant response. The results showed improved accuracy in individualized antidepressant prescription, supporting the feasibility of using ML algorithms applied to large datasets to enhance treatment selection.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Health Policy & Services
Shirly Bar-Lev, Shahar Reichman, Zohar Barnett-Itzhaki
Summary: Vaccines have significantly reduced morbidity and mortality from vaccine-preventable diseases, especially in children. However, vaccine hesitancy is listed as one of the top ten threats to world health by the World Health Organization (WHO) in 2019. This study found an association between social media traffic and vaccine hesitancy, suggesting the importance of utilizing social media as a main communication channel during health crises, and encouraging health officials and experts to actively engage in social media discussions to optimize vaccination efforts and improve public health.
ISRAEL JOURNAL OF HEALTH POLICY RESEARCH
(2021)
Article
Environmental Sciences
Maya Negev, Zohar Barnett-Itzhaki, Tamar Berman, Shay Reicher, Naor Cohen, Ruti Ardi, Yaniv Shammai, Tamar Zohar, Miriam L. Diamond
Summary: The review of literature and regulations revealed potential health risks associated with synthetic surface materials containing toxic chemicals. Testing results showed that a majority of synthetic playground and grass surfaces exceeded relevant standards for trace metals, indicating potential risks of exposure for children.
JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY
(2022)
Article
Health Policy & Services
Zohar Barnett-Itzhaki, Daniel Ehrlich, Aron M. Troen, Efrat Rorman, Luda Groismann, Moran Blaychfeld-Magnazi, Ronit Endevelt, Tamar Berman
Summary: The lack of mandatory salt fortification policy in Israel, heavy reliance on desalination and low iodine intake from dairy products and seafood have led to iodine deficiency in the population. Despite the inadequacy identified in the 2016 iodine survey, there has been no improvement in the population's iodine status in the past five years. Compared to other countries, Israel and Lebanon are the only ones with median urinary iodine concentrations (UIC) below the WHO adequacy range. Therefore, there is an urgent need for mandatory salt fortification in Israel.
ISRAEL JOURNAL OF HEALTH POLICY RESEARCH
(2022)
Article
Environmental Sciences
Jose V. Tarazona, Irene Cattaneo, Lars Niemann, Susana Pedraza-Diaz, Maria Carmen Gonzalez-Caballero, Mercedes de Alba-Gonzalez, Ana Canas, Noelia Dominguez-Morueco, Marta Esteban-Lopez, Argelia Castano, Teresa Borges, Andromachi Katsonouri, Konstantinos C. Makris, Ilse Ottenbros, Hans Mol, Annelies De Decker, Bert Morrens, Tamar Berman, Zohar Barnett-Itzhaki, Nicole Probst-Hensch, Samuel Fuhrimann, Janja Snoj Tratnik, Milena Horvat, Loic Rambaud, Margaux Riou, Greet Schoeters, Eva Govarts, Marike Kolossa-Gehring, Till Weber, Petra Apel, Sonia Namorado, Tiina Santonen
Summary: Pyrethroids are commonly used insecticides that can be monitored in humans. A tiered approach was used to assess the risk of pyrethroid exposure, starting with a conservative screening and followed by probabilistic approaches and substance-specific assessments. The study analyzed data from various countries and found that some metabolites exceeded the screening value in children populations, but were below the human biomonitoring guidance values. Overall, the study suggests a low health concern at the population level, although a potential risk for highly exposed children cannot be completely excluded.
Article
Environmental Sciences
Jose Tarazona, Maria del Carmen Gonzalez-Caballero, Mercedes de Alba-Gonzalez, Susana Pedraza-Diaz, Ana Canas, Noelia Dominguez-Morueco, Marta Esteban-Lopez, Irene Cattaneo, Andromachi Katsonouri, Konstantinos C. Makris, Thorhallur Halldorsson, Kristin Olafsdottir, Jan-Paul Zock, Jonatan Dias, Annelies De Decker, Bert Morrens, Tamar Berman, Zohar Barnett-Itzhaki, Christian Lindh, Liese Gilles, Eva Govarts, Greet Schoeters, Till Weber, Marike Kolossa-Gehring, Tiina Santonen, Argelia Castano
Summary: The risk assessment of pesticide residues in food is a key priority in food safety. Most jurisdictions have implemented pre-marketing authorization processes and large monitoring programs, resulting in reduced exposure levels of European consumers to the organophosphate insecticide chlorpyrifos.
Article
Environmental Sciences
Zohar Barnett-Itzhaki, Adi Levi
Summary: Studies have shown positive associations between chronic exposure to air pollution and COVID-19 morbidity. In Israel, population density, ratio of elderly people, and air pollutants were found to be related to COVID-19 morbidity rates. These findings emphasize the importance of reducing air pollution and highlight vulnerable populations during the pandemic.
Article
Oncology
Yael Inbar, Ronit Machtinger, Zohar Barnett-Itzhaki, Avishai Goldblatt, Eti Stoler, Jaron Rabinovici
Summary: The study found that women with abdominal scars had lower non-perfused volume (NPV) during MRgFUS treatment compared to women without scars. However, no serious adverse events were reported in both groups. Linear regression models indicated that fibroids' volume, stopping the treatment due to severe pain, and the presence of abdominal scars had a statistically negative effect on NPV, while the number of sonications had a statistically positive effect on NPV.
INTERNATIONAL JOURNAL OF HYPERTHERMIA
(2021)