Article
Biochemistry & Molecular Biology
Jordi Gomez Borrego, Marc Torrent Burgas
Summary: Adhesion and colonization of host cells by pathogenic bacteria rely on protein-protein interactions (PPIs). This study developed a filtering process to obtain a reliable list of domains and motifs participating in PPIs between bacteria and human cells. Structural analysis revealed that human proteins involved in these interactions are rich in alpha helix and disordered regions. The most significant domain-domain interactions were validated, but verifying domain-motif interactions was more challenging. Post-translational modifications, especially phosphorylation, also play a role in these interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Telecommunications
Peppino Fazio, Miralem Mehic, Miroslav Voznak
Summary: In this study, a new approach to mobility prediction by analyzing the effects of a proper mobility sampling frequency was proposed. The spectral content of mobility traces was considered to determine the appropriate sampling frequency, which was found to have significant effects on the characteristics of mobility. Simulation campaigns were performed to observe and evaluate these effects.
DIGITAL COMMUNICATIONS AND NETWORKS
(2023)
Article
Biochemistry & Molecular Biology
Pooppadi Maxin Sayeesh, Mayumi Iguchi, Yusuke Suemoto, Jin Inoue, Kohsuke Inomata, Teppei Ikeya, Yutaka Ito
Summary: Drk, a homologue of human GRB2 in Drosophila, receives signals from outside the cells through the interaction of its SH2 domain with the phospho-tyrosine residues in the intracellular regions of receptor tyrosine kinases (RTKs) and transduces the signals downstream through the association of its N- and C-terminal SH3 domains with proline-rich motifs (PRMs) in Son of Sevenless (Sos) or Daughter of Sevenless (Dos). The affinity of the SH3 domains towards Sos and Dos was assessed using NMR titration experiments, revealing that Sos-S1 binds to Drk-NSH3 with the highest affinity and that the two Sos-derived PRMs favor NSH3 for binding, while the two Dos-derived PRMs show similar affinity for both NSH3 and CSH3. Docking simulations based on chemical shift perturbations caused by Sos and Dos-derived peptides were also performed to further understand the interactions of Drk with Sos/Dos.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Kaitlin Klotz, Yasmine Radwan, Kausik Chakrabarti
Summary: Nucleic acid nanoparticles (NANPs) are programmable particles made of DNA, RNA, or their analogs, which have the potential to prevent, detect, and treat diseases. However, there are challenges in targeting specific cells and tissues and avoiding off-target effects. The development of regulated biological activities and immunorecognition of NANPs hold promise for versatile nucleic acid therapeutics, and they can also assist in fine-tuning the structure-function relationship in basic research.
Article
Chemistry, Applied
Ali Khodayari, Wim Thielemans, Ulrich Hirn, Aart W. Van Vuure, David Seveno
Summary: In this work, the interactions of five different hemicellulose models with cellulose nanocrystals were studied through molecular dynamics simulations. It was found that glucuronoarabinoxylan had the highest binding free energy, while xyloglucan showed the lowest interaction energies. The presence of water molecules was observed to weaken the interactions between hemicellulose and cellulose.
CARBOHYDRATE POLYMERS
(2021)
Article
Biochemistry & Molecular Biology
Kasie Baker, Ethiene Kwok, Patrick Reardon, Diego J. Rodriguez, Amber D. Rolland, Jesse W. Wilson, James S. Prell, Afua Nyarko
Summary: Research has shown that multiple copies of WW domains and PPXY motif sequences can interact to form a variety of complexes with different stoichiometries and binding energetics. These interconverting complexes play a role in promoting the adaptability and versatility of WW domain-PPXY mediated cellular processes.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sergei Rudnizky, Hadeel Khamis, Yuval Ginosar, Efrat Goren, Philippa Melamed, Ariel Kaplan
Summary: The study reveals that linker histone interactions with DNA are extensive and dynamic, crucial for the symmetry of the chromatosome's core. Extensive unzipping of the linker DNA leads to a shift in H1 configuration to asymmetric and triggers nucleosome decompaction.
Article
Chemistry, Medicinal
Xiaorong Liu, Jianhan Chen, Yumeng Zhang
Summary: Intrinsically disordered proteins (IDPs) play crucial roles in cellular regulatory networks. The HyRes II model can semi-quantitatively reproduce the structural properties of IDPs and simulate their dynamic interactions efficiently.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Mahmudul Hasan, Daniel G. S. Capelluto
Summary: This study determined the concurrence of the PH-FYVE module with the polyD motif in Phafin2 protein using bioinformatics tools and resources. It was found that the polyD motif only evolved in Phafin2 and PH- or both PH-FYVE-containing proteins in animals.
Review
Biochemistry & Molecular Biology
Artem Bonchuk, Konstantin Balagurov, Pavel Georgiev
Summary: The article provides a translation of the importance of BTB/POZ domains in eukaryotic organisms, as well as their role in various developmental processes and oncological diseases. Structural studies have revealed the principles of protein-protein interactions mediated by BTB domains and provided a basis for specific inhibition of these interactions. BTB domains originated early in evolution and progressively adapted to perform different functions. The article also proposes an updated structure-based classification of BTB domain families and discusses their evolutionary interconnections.
Article
Biochemistry & Molecular Biology
S. Pankivskyi, D. Pastre, E. Steiner, V Joshi, A. Rynditch, L. Hamon
Summary: SAM68 is an mRNA-binding protein involved in mRNA processing in the nucleus, and its interaction with ITSN1 can enhance its solubility, regulating the processing of a fraction of nuclear mRNAs. ITSN1 and mRNA may act together to promote SAM68 solubilization, which is important for SAM68-controlled splicing events related to higher neuronal functions or cancer progression.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Zhen-Lu Li, Carla Mattos, Matthias Buck
Summary: The article explores the importance of dynamic allostery in protein-protein interactions, revealing the impact of protein fluctuations on protein association processes, and investigates the influence of point mutations and ambient temperature on protein dynamics and interactions.
Article
Biochemistry & Molecular Biology
Sonali Tayal, Venugopal Bhatia, Tanya Mehrotra, Sonika Bhatnagar
Summary: This study curated experimental host-pathogen and host-host protein-protein interactions, annotated the domains and motifs of these proteins, and proposed the concept of mimicry pairs. The results were organized in a web-based resource called ImitateDB, which allows for easy querying of a large number of identified mimicry pairs in interacting host and pathogen proteins.
Editorial Material
Multidisciplinary Sciences
Anne van Schoonhoven, Ralph Stadhouders
Summary: A new technique reveals the interactions of folded chromosomal DNA in the nucleus at the level of single base pairs, providing unprecedented detail about gene regulation. The method monitors 3D genome architecture with high precision.
Article
Biology
Duanzhi Wu, Xin Fang, Kai Luan, Qijin Xu, Shiqi Lin, Shiying Sun, Jiaying Yang, Bingying Dong, Balachandran Manavalan, Zhijun Liao
Summary: In this study, SH2 domain-containing proteins and non-SH2 domain-containing proteins were successfully identified using deep learning technology. The best performing 288-dimensional features were obtained. Additionally, a new motif, YKIR, in the SH2 domain was discovered and its function in signal transduction was analyzed.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
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
Hematology
Hila Fishman, Shreyas Madiwale, Ifat Geron, Vase Bari, Wouter Van Loocke, Yael Kirschenbaum, Itamar Ganmore, Eitan Kugler, Avigail Rein-Gil, Gilgi Friedlander, Ginette Schiby, Yehudit Birger, Sabine Strehl, Jean Soulier, Birgit Knoechel, Adolfo Ferrando, Sharon Noy-Lotan, Arnon Nagler, James C. Mulloy, Pieter Van Vlierberghe, Shai Izraeli
Summary: Mixed-phenotype acute leukemia is a rare subtype of leukemia. The ETV6-NCOA2 fusion gene is associated with the development of T/myeloid leukemia. The study provides mechanistic insights into the initiation of T/myeloid leukemia by ETV6-NCOA2 and the role of Notch1 activating mutations.
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
Biochemistry & Molecular Biology
Maya David, Tsviya Olender, Orel Mizrahi, Shira Weingarten-Gabbay, Gilgi Friedlander, Sara Meril, Nadav Goldberg, Alon Savidor, Yishai Levin, Vered Salomon, Noam Stern-Ginossar, Shani Bialik, Adi Kimchi
Summary: DAP5 is an important translation initiation factor that mediates noncanonical and cap-independent translation. Comparison of ribosome profiles in control and DAP5 knockdown cells revealed decreased translation efficiency of a cohort of genes upon DAP5 silencing. Mass spectrometry confirmed decreased protein abundance of these targets. It was also found that half of the DAP5 target mRNAs contain upstream open reading frames, suggesting a mechanism of leaky scanning and reinitiation.
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
Cell Biology
Keren David, Gilgi Friedlander, Bianca Pellegrino, Lihi Radomir, Hadas Lewinsky, Lin Leng, Richard Bucala, Idit Shachar, Shirly Becker Herman
Summary: This study investigated the transcriptional and regulatory function of CD74-ICD in normal B cells. It was found that CD74-ICD forms a complex with PAX5 and binds to chromatin at a higher number of sites compared to CLL cells. The CD74-ICD:PAX5 complex also downregulates the expression of the tumor-suppressor gene DMTF1 through transcriptional inhibition.
Article
Cell Biology
Anna Kosenko, Tomer Meir Salame, Gilgi Friedlander, Itamar Barash
Summary: Studies have identified macrophages and secreted CSF1 as the energy sensor and paracrine transmitter in the self-renewal of mammary stem cells. Through experiments with conditioned medium and analyses using RNA-Seq, immunohistochemistry, and immunofluorescence, this mechanism was confirmed.
Article
Multidisciplinary Sciences
Yael Aylon, Noa Furth, Giuseppe Mallel, Gilgi Friedlander, Nishanth Belugali Nataraj, Meng Dong, Ori Hassin, Rawan Zoabi, Benjamin Cohen, Vanessa Drendel, Tomer Meir Salame, Saptaparna Mukherjee, Nofar Harpaz, Randy Johnson, Walter E. Aulitzky, Yosef Yarden, Efrat Shema, Moshe Oren
Summary: Breast cancer, the most common cancer in women, exhibits cellular and functional heterogeneity, which is influenced by dynamic changes in the epigenetic landscape of cancer cells. LATS1, a tumor suppressor gene, plays a role in maintaining luminal cell identity and preventing the transition to a basal-like state in breast cancer.
NATURE COMMUNICATIONS
(2022)
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)