Article
Chemistry, Multidisciplinary
Zacharias G. Fthenakis
Summary: In this study, we expand our previously proposed nomenclature scheme for porous graphene structures to include graphene flakes and edges. We also investigate the geometric characteristics of these structures using ideas from graph theory and the pore-flake duality. Furthermore, we develop an algorithm for the systematic generation, identification, and numbering of graphene pores, flakes, and edges, which can be applied to similar honeycomb systems.
Review
Mathematics
Jose A. Saez
Summary: This paper presents the first review of noise models in classification, covering both label and attribute noise, and reveals the lack of a unified nomenclature in this field. The authors propose a tripartite nomenclature based on the structural analysis of existing noise models and revise the current taxonomies to better reflect the nature of any model. Finally, a categorization of noise models is proposed from a practical point of view depending on the characteristics of noise and the study purpose.
Article
Chemistry, Multidisciplinary
Guoxiu Wang, Wenjuan Lv, Congjie Pan, Hongli Chen, Xingguo Chen
Summary: A novel chiral COF, DA-TD COF, was synthesized and used as a chiral stationary phase for open-tubular capillary electrochromatography, showing excellent enantioseparation efficiency and stability. The enantioseparation mechanism was also studied in this work.
CHEMICAL COMMUNICATIONS
(2022)
Review
Nutrition & Dietetics
Nair Cunha, Vanda Andrade, Paula Ruivo, Paula Pinto
Summary: This systematic review provides an update on the impact of insect consumption on human health. The study shows that consuming insect protein can increase post-prandial amino acid levels and has similar effects on essential amino acid values compared to other protein sources. In terms of muscle protein synthesis, there were no significant differences observed. Insulin levels were lower after consuming insect-based products. Allergenicity assessments revealed sensitisation and cross-reactivity between insect allergens and known allergens. Thermal processing can partially reduce cross-allergenicity. Insect protein is a promising and adequate protein source, but further research is needed to understand its full potential and optimize its inclusion in the human diet.
Review
Biotechnology & Applied Microbiology
Yoichi Toyokawa, Jirasin Koonthongkaew, Hiroshi Takagi
Summary: BCAT catalyzes transamination between BCAAs and BCKAs in the cell. Eukaryotic cells have mitochondrial BCAT (BCATm) and cytosolic BCAT (BCATc) isozymes, which have similar enzymatic functions but differences in physiological functions and regulatory mechanisms. The variations of BCAT could have significant implications for research into the relationship between their primary structures and protein functions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Medicinal
Andrea Petreni, Sameh M. Osman, Fatmah A. Alasmary, Tahani M. Almutairi, Alessio Nocentini, Claudiu T. Supuran
Summary: This study presents the first structural analysis comparing two opposite classes of modulators binding to the target carbonic anhydrases, showing that coumarin derivatives act as prodrug CA inhibitors while CA activators belonging to the amine and amino acid types enhance CA activity by increasing the efficiency of the rate-determining proton shuttling step in the CA catalytic cycle. The analysis of crystallographic data reveals that both types of CA modulators bind in the same region of the enzyme active site, interacting with superimposable amino acid residues and involving a plethora of water molecules in the formation of adducts. Additionally, the study highlights the importance of certain chemical groups in compound structure to produce an activating rather than inhibitory action, with multiple nitrogen- and oxygen-based moieties capable of shuttling protons or forming extended H-bond networks nearby the proton shuttle residue. This unique finding showcases the significant pharmacological implications of having an identical binding site for both inhibitors and activators in enzymes.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Review
Agriculture, Dairy & Animal Science
Shemil P. Macelline, Mehdi Toghyani, Peter Chrystal, Peter H. Selle, Sonia Yun Liu
Summary: This review aims to consolidate published data on amino acid requirements of layer hens and proposes new recommendations based on these data. Inconsistencies in recommendations for various amino acids have been found, with factors such as breed, age, basal diet composition, and assessment method contributing to the discrepancies. The development of reduced-protein diets for layer hens is gaining attention for sustainable production, involving changes in diet composition with inclusions of nonbound amino acids that may influence amino acid requirements.
Article
Chemistry, Multidisciplinary
Beryl X. Li, Daniel K. Kim, Steven Bloom, Richard Y. -C. Huang, Jennifer X. Qiao, William R. Ewing, Daniel G. Oblinsky, Gregory D. Scholes, David W. C. MacMillan
Summary: This study presents a novel method for site-selective tyrosine bioconjugation using photoredox catalysis, which allows for chemically modifying native proteins with high site-selectivity. The water-soluble photocatalyst lumiflavin has been demonstrated to induce oxidative coupling between a phenoxazine dialdehyde tag and a single tyrosine site on native proteins, even in the presence of multiple tyrosyl side chains, enabling the synthesis of structurally defined fluorescent conjugates.
Review
Biochemistry & Molecular Biology
Mark J. Pallen, Andrea Telatin, Aharon Oren
Summary: Latin binomials, popularized by Linnaeus in the 18th century, have provided a stable and clear system of nomenclature in biology. However, with the increasing exploration of the microbial world, there is a need for a large number of new names for Archaea and Bacteria. To address this issue, an automated approach using Latin and Greek roots for creating linguistically correct names has been proposed, demonstrating the potential for creating millions of new names for Bacteria and Archaea.
TRENDS IN MICROBIOLOGY
(2021)
Article
Medicine, Research & Experimental
Nneka Southwell, Guido Primiano, Viraj Nadkarni, Nabeel Attarwala, Emelie Beattie, Dawson Miller, Sumaitaah Alam, Irene Liparulo, Yevgeniya Shurubor, Maria Lucia Valentino, Valerio Carelli, Serenella Servidei, Steven S. Gross, Giovanni Manfredi, Qiuying Chen, Marilena D'Aurelio
Summary: Mitochondrial diseases are a group of disorders caused by impaired oxidative phosphorylation, which often affects skeletal muscle due to its high energy dependency. However, the metabolic drivers of muscle degeneration in these diseases are not well understood, leading to a lack of effective treatments. This study identifies systemic metabolic mechanisms underlying mitochondrial myopathies and potential new targets for intervention.
EMBO MOLECULAR MEDICINE
(2023)
Article
Pharmacology & Pharmacy
Gregory Gauthier-Coles, Angelika Broer, Malcolm Donald McLeod, Amee J. George, Ross D. Hannan, Stefan Broer
Summary: SNAT2 is an important amino acid transporter involved in amino acid accumulation, cellular osmolarity, and cell growth. A potent inhibitor of SNAT2 has been identified through high-throughput screening, with selectivity against other transporters. Combined with a glucose transport inhibitor, this compound can halt the proliferative growth of cancer cells.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Wen-Ling Liao, Yu-Fan Liu, Tsung-Ho Ying, Jia-Ching Shieh, Yueh-Tzu Hung, Huei-Jane Lee, Chen-Yang Shen, Chun-Wen Cheng
Summary: In this study, it was found that ursolic acid (UA) inhibits the proliferation of breast cancer cells and reduces the proportion of cancer stem cells (CSCs). UA alters the invasion and migration capacities of cancer cells by regulating the expression levels of stemness biomarkers and epithelial-to-mesenchymal transition (EMT) proteins. Furthermore, UA decreases the levels of oncogenic miRNAs by down-modulating AGO2 in breast cancer cells. These findings suggest that UA has potential in improving the clinical practice of breast cancer by interrupting EMT programming and targeting CSCs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Carol M. Sheppard, Daniel H. Goldhill, Olivia C. Swann, Ecco Staller, Rebecca Penn, Olivia K. Platt, Ksenia Sukhova, Laury Baillon, Rebecca Frise, Thomas P. Peacock, Ervin Fodor, Wendy S. Barclay
Summary: This study reveals that human ANP32A and ANP32B are redundant host factors for influenza virus genome replication. By investigating the evolution of influenza virus in cells lacking ANP32A and ANP32B, the researchers discovered mutations that enable the virus to utilize ANP32E, a novel host factor, and observed increased virulence in mice.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Juan Ni, Wumin Dai, Chun Liu, Yutian Ling, Hanzhou Mou
Summary: Through analysis of the TCGA and GEO databases, it was found that SLC1A5 is over-expressed in multiple types of cancer and elevated expression is associated with poor prognosis in many cancers. The study also revealed the important role of SLC1A5 in tumorigenesis and its involvement in central carbon metabolism in cancer. Additionally, elevated SLC1A5 expression is associated with immune cell infiltration.
Article
Environmental Sciences
Guozhu Ye, Han Gao, Xu Zhang, Xinyu Liu, Jinsheng Chen, Xu Liao, Han Zhang, Qiansheng Huang
Summary: Exposure to polycyclic aromatic hydrocarbon BaP accelerates lung cancer initiation and progression through AHR signaling and metabolic reprogramming. The study reveals that amino acid and fatty acid metabolism, along with AHR and PPAR-FATP1 signaling, could be potential therapeutic targets for intervening BaP-induced toxicity and related diseases. The novel findings of fatty acid accumulation and high correlations of AHR signaling with amino acid and fatty acid metabolism in BaP-exposed lung epithelial cells are highlighted.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Sonia Missiroli, Mariasole Perrone, Roberta Gafa, Francesco Nicoli, Massimo Bonora, Giampaolo Morciano, Caterina Boncompagni, Saverio Marchi, Magdalena Lebiedzinska-Arciszewska, Bianca Vezzani, Giovanni Lanza, Franz Kricek, Alessandro Borghi, Francesco Fiorica, Keisuke Ito, Mariusz R. Wieckowski, Francesco Di Virgilio, Luigi Abelli, Paolo Pinton, Carlotta Giorgi
Summary: Uncontrolled inflammatory response from the tumor microenvironment significantly contributes to cancer progression. A trimeric complex at the mitochondria-associated membranes, involving P2X7 receptor-NLRP3 inflammasome interaction, is regulated by the tumor suppressor PML. Downregulation of PML leads to an exacerbated immune response and boosted tumor growth. Mislocalization of PML results in uncontrolled NLRP3 activation and cytokine production, fueling cancer development and worsening prognosis in various human cancers. Mechanistic insights into the PML-P2X7R-NLRP3 axis provide new opportunities for targeted therapeutic approaches in human carcinogenesis.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Biochemistry & Molecular Biology
Leire Torices, Janire Mingo, Isabel Rodriguez-Escudero, Teresa Fernandez-Acero, Sandra Luna, Caroline E. Nunes-Xavier, Jose Lopez, Fatima Mercadillo, Maria Curras, Miguel Urioste, Maria Molina, Victor J. Cid, Rafael Pulido
Summary: Heterozygous germline mutations in PTEN gene are associated with hamartomas, tumors, and neurodevelopmental disorders. PTEN acts as a phosphatase, counteracting the pro-oncogenic function of PI3K. This study characterized several PTEN variants found in PHTS patients and observed complex patterns of loss of function, altered localization, and altered cleavage by caspase-3.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Oncology
James E. Barrett, Allison Jones, Iona Evans, Chiara Herzog, Daniel Reisel, Adeola Olaitan, Tim Mould, Nicola MacDonald, Konstantinos Doufekas, Claire Newton, Emma J. Crosbie, Line Bjorge, Nicoletta Colombo, Lukas Dostalek, Laura Costas, Paula Peremiquel-Trillas, Jordi Ponce, Xavier Matias-Guiu, Michal Zikan, David Cibula, Jiangrong Wang, Karin Sundstroem, Joakim Dillner, Martin Widschwendter
Summary: To reduce the morbidity caused by aggressive treatment for advanced endometrial cancer, it is necessary to identify women at risk and detect the cancer earlier. A new test called WID-EC based on DNA methylation was developed and validated in different sets of samples, showing promising results in identifying women with or at risk of endometrial cancer.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Cell Biology
Yaiza Jung-Garcia, Oscar Maiques, Joanne Monger, Irene Rodriguez-Hernandez, Bruce Fanshawe, Marie-Charlotte Domart, Matthew J. Renshaw, Rosa M. Marti, Xavier Matias-Guiu, Lucy M. Collinson, Victoria Sanz-Moreno, Jeremy G. Carlton
Summary: Metastasis involves cancer cells spreading from the primary tumor to other sites. Researchers discovered increased expression of the protein LAP1 in metastatic melanoma cells, primary melanoma tumors, and metastases. They found that a shorter isoform of LAP1, LAP1C, supports constrained cell migration and invasion by allowing a weaker coupling between the nuclear envelope and the nuclear lamina. This suggests that LAP1 contributes to melanoma aggressiveness.
NATURE CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Valentino Bezzerri, Valentina Gentili, Martina Api, Alessia Finotti, Chiara Papi, Anna Tamanini, Christian Boni, Elena Baldisseri, Debora Olioso, Martina Duca, Erika Tedesco, Sara Leo, Monica Borgatti, Sonia Volpi, Paolo Pinton, Giulio Cabrini, Roberto Gambari, Francesco Blasi, Giuseppe Lippi, Alessandro Rimessi, Roberta Rizzo, Marco Cipolli
Summary: As an inherited disorder characterized by severe pulmonary disease, cystic fibrosis could be considered a comorbidity for coronavirus disease 2019. However, current clinical evidence suggests that cystic fibrosis may actually protect against SARS-CoV-2 infection. The expression of SARS-CoV-2 receptors in primary airway epithelial cells is regulated by the CFTR channel, and dysfunctional CFTR channels in cystic fibrosis cells result in reduced viral entry and replication.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Maria Livia Sassano, Alexander R. R. van Vliet, Ellen Vervoort, Sofie Van Eygen, Chris van den Haute, Benjamin Pavie, Joris Roels, Johannes V. V. Swinnen, Marco Spinazzi, Leen Moens, Kristina Casteels, Isabelle Meyts, Paolo Pinton, Saverio Marchi, Leila Rochin, Francesca Giordano, Blanca Felipe-Abrio, Patrizia Agostinis
Summary: ER-mitochondria appositions play a critical role in the transfer of ions and phospholipids between these organelles and impact mitochondrial bioenergetics. However, the molecular mechanisms involved in this process are not well understood. This study reveals that PERK acts as an adaptor to recruit the lipid transfer protein E-Syt1 at ER-mitochondria contact sites, enabling lipid transport and maintaining mitochondrial homeostasis. These findings provide insights into the molecular components and functions of the lipid trafficking machinery at ER-mitochondria contact sites.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Chemistry, Medicinal
Valentina Albanese, Sonia Missiroli, Mariasole Perrone, Martina Fabbri, Caterina Boncompagni, Salvatore Pacifico, Tiziano De Ventura, Antonella Ciancetta, Giulio Dondio, Franz Kricek, Paolo Pinton, Remo Guerrini, Delia Preti, Carlotta Giorgi
Summary: A series of aryl sulfonamide derivatives (ASDs) were designed and synthesized to inhibit the activation of the NLRP3 inflammasome. Compounds 6c, 7n, and 10 specifically inhibited NLRP3 activation at nanomolar concentrations without affecting the activation of other inflammasomes. These compounds were also found to reduce IL-1 beta production in vivo and attenuate melanoma tumor growth. The findings suggest that these potent NLRP3 inflammasome inhibitors could be considered for future therapeutic approaches in NLRP3 inflammasome-driven cancer.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Javier Plou, Pablo S. Valera, Isabel Garcia, David Vila-Liarte, Carlos Renero-Lecuna, Jesus Ruiz-Cabello, Arkaitz Carracedo, Luis M. Liz-Marzan
Summary: During the response to stress, damaged cells release metabolites and secretomes, which can be utilized in anticancer therapies and biomarker predictions. However, monitoring these processes is challenging, leading to the development of noninvasive secretome screening tools. Machine learning methods and microfluidic chips were used to identify secretome variations and classify cell death, allowing for faster implementation of surface-enhanced Raman scattering (SERS) into cell secretome classification.
Review
Cell Biology
Gokhan Burcin Kubat, Esmaa Bouhamida, Oner Ulger, Ibrahim Turkel, Gaia Pedriali, Daniela Ramaccini, Ozgur Ekinci, Berkay Ozerklig, Ozbeyen Atalay, Simone Patergnani, Beyza Nur Sahin, Giampaolo Morciano, Meltem Tuncer, Elena Tremoli, Paolo Pinton
Summary: Skeletal muscle is a dynamic and plastic tissue that plays a vital role in movement, posture, and force production. It functions as an endocrine organ capable of producing and secreting bioactive molecules. Various pathological conditions can disrupt the balance between muscle protein synthesis and degradation, leading to skeletal muscle atrophy.
Article
Biochemistry & Molecular Biology
Raquel Garcia-Vilchez, Ana M. M. Anazco-Guenkova, Sabine Dietmann, Judith Lopez, Virginia Moron-Calvente, Silvia D'Ambrosi, Paz Nombela, Kepa Zamacola, Isabel Mendizabal, Saioa Garcia-Longarte, Amaia Zabala-Letona, Ianire Astobiza, Sonia Fernandez, Alejandro Paniagua, Borja Miguel-Lopez, Virginie Marchand, Diego Alonso-Lopez, Angelika Merkel, Ignacio Garcia-Tunon, Aitziber Ugalde-Olano, Ana Loizaga-Iriarte, Isabel Lacasa-Viscasillas, Miguel Unda, Mikel Azkargorta, Felix Elortza, Laura Barcena, Monika Gonzalez-Lopez, Ana M. M. Aransay, Tomas Di Domenico, Manuel A. A. Sanchez-Martin, Javier De Las Rivas, Sonia Guil, Yuri Motorin, Mark Helm, Pier Paolo Pandolfi, Arkaitz Carracedo, Sandra Blanco
Summary: New evidence suggests that epitranscriptomic marks play an important role in cancer development, but the role and implications of altered epitranscriptome deposition in prostate cancer are largely unknown. This study demonstrates that the transfer RNA N-7-methylguanosine (m(7)G) transferase METTL1 is highly expressed in prostate tumors and its depletion leads to the loss of m(7)G tRNA methylation and the formation of small non-coding RNAs derived from 5'tRNA fragments. These small RNAs regulate translation control and favor the synthesis of key regulators and immune effectors, impacting tumor growth suppression and response to immunotherapy in prostate cancer models.
Article
Chemistry, Multidisciplinary
Raul Navaridas, Maria Vidal-Sabanes, Anna Ruiz-Mitjana, Gisela Altes, Aida Perramon-Guell, Andree Yeramian, Joaquim Egea, Mario Encinas, Sonia Gatius, Xavier Matias-Guiu, Xavier Dolcet
Summary: Simultaneous deletion of Pten and p53 in endometrial epithelial cells is sufficient to trigger epithelial-to-mesenchymal transition, leading to the development of metastatic uterine carcinosarcomas.
Article
Geriatrics & Gerontology
Ines Marin, Manuel Serrano, Federico Pietrocola
Summary: Recent reports provide strong evidence that senescent cells undergo surveillance by CD8 T cell-mediated adaptive immunity in both oncological and non-oncological experimental setups. These findings also reveal the mechanisms of sensitizing senescent cells to CD8 T cell-dependent killing and the mechanisms of senescent cell evasion from CD8 T cell immunosurveillance. Understanding the interplay between cellular senescence and the adaptive immune system could potentially lead to new strategies for mitigating aging and aging-associated diseases.
Article
Biochemical Research Methods
Jaime Martinez de Villarreal, Mark Kalisz, Gabriel Piedrafita, Osvaldo Grana-Castro, Dafni Chondronasiou, Manuel Serrano, Francisco X. Real
Summary: Transposable elements have played a major role in shaping mammalian genomes, but little is known about their cell-type-specific expression. A cost-efficient single-cell-resolution TE expression analytical approach is needed.
Article
Oncology
Jonathan S. Berek, Xavier Matias-Guiu, Carien Creutzberg, Christina Fotopoulou, David Gaffney, Sean Kehoe, Kristina Lindemann, David Mutch, Endometrial Canc Staging Subcomm, FIGO Womens Canc Comm
Summary: Since the 2009 update of the FIGO staging system, there have been significant advances in understanding the pathologic and molecular features of endometrial cancer. The new staging system aims to better define prognostic groups and create substages to guide more appropriate treatment.
JOURNAL OF GYNECOLOGIC ONCOLOGY
(2023)
Article
Chemistry, Analytical
Erin E. Hickey, Austin Shigemoto, Arne Gericke, Shawn C. Burdette
Summary: This study presents two Zn2+ photocages and one photocage based on Sanger's reagent, and their binding affinities were measured using isothermal titration calorimetry (ITC). The results demonstrate that ITC is an effective measurement tool and consistent with UV-vis titration data.
ANALYSIS & SENSING
(2023)