Article
Biotechnology & Applied Microbiology
Shelly Gupta, Karan Paul, Ayan Roy
Summary: The fungal genus Cryptococcus includes several diverse species, with Cryptococcus neoformans and Cryptococcus gattii species complex having significant clinical importance globally. Factors such as compositional bias, translational selection, and gene expression were found to influence codon and amino acid usage bias in pathogenic and non-pathogenic species. Statistical analysis based on codon usage data led to discrete clustering of pathogens and non-pathogens, in line with their phylogenetic distribution.
Article
Genetics & Heredity
Anders Fuglsang
Summary: This study systematically investigates intragenic variations in codon usage by analyzing over 1100 proteobacteria. The research reveals a correlation between genome size and codon usage biases, as well as a uniform pattern of codon usage near gene termini. Furthermore, translational selection, genome shrinkage, and IS expansion are shown to result in characteristic patterns in intragenic codon usage.
Article
Virology
Wei Liu, Junhua Li, Hongli Du, Zhihua Ou
Summary: By investigating the genomes of HPV16, it was found that there are conserved mutation sites in different lineages and sublineages, as well as differences in glycosylation and codon usage preference. This study helps increase our understanding of the diversity of HPV16 and its adaptation mechanisms in human cells.
Article
Cell Biology
Sandeep Appunni, Muni Rubens, Venkataraghavan Ramamoorthy, Vivek Anand, Madhuram Khandelwal, Alpana Sharma
Summary: Biglycan, as a class I SLRP, is a key component of the ECM involved in scaffolding collagen fibrils and mediating cell signaling. Dysregulation of its expression can lead to various clinical conditions including metabolic disorders, inflammatory disorders, musculoskeletal defects, and malignancies. Biglycan interacts with TLR-2 and TLR-4 on immune cells to induce inflammation, and its dysregulation is also observed in inflammatory metabolic conditions and cancer, where high expression levels facilitate tumor growth and metastasis.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2021)
Article
Cell Biology
Romain Rivet, Rajas Mallenahalli Rao, Pierre Nizet, Nicolas Belloy, Louise Huber, Manuel Dauchez, Laurent Ramont, Stephanie Baud, Stephane Brezillon
Summary: This study characterized the structure and dynamics of four SLRPs using in silico 3D modeling, and evaluated their capacity to bind to MMP-14 and regulate its activity. The results demonstrated that each SLRP exhibited significant inhibition of MMP-14 activity, which was related to the core protein conformation as well as the glycan chain structures and dynamics.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2023)
Article
Dermatology
Xue Xu, Pin Ha, Emily Yen, Chenshuang Li, Zhong Zheng
Summary: Small leucine-rich proteoglycans (SLRPs) play a crucial role in regulating tendon structure and biomechanics, offering a promising method for tendon injury management. However, current knowledge on the role of SLRPs in tendon development and regeneration is limited, requiring further investigations.
ADVANCES IN WOUND CARE
(2022)
Article
Cell Biology
Ravi Adusmalli, Hans-Christian Asheim, Vladimir Lupashin, Jessica B. Blackburn, Kristian Prydz
Summary: The absence of individual COG subunits impacts GAG synthesis of proteoglycans, potentially explaining the variability in severity of COG associated CDGs.
Review
Biochemistry & Molecular Biology
Shermaine W. Y. Low, Thomas B. Connor, Iris S. Kassem, Deborah M. Costakos, Shyam S. Chaurasia
Summary: Small leucine-rich proteoglycans (SLRPs) serve a crucial role in maintaining retinal homeostasis by participating in the organization of extracellular matrix, regulation of cell growth, and cell-matrix interactions in several upstream signaling pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Neurosciences
Sherif Rashad, Shane R. Byrne, Daisuke Saigusa, Jingdong Xiang, Yuan Zhou, Liyin Zhang, Thomas J. Begley, Teiji Tominaga, Kuniyasu Niizuma
Summary: This study investigated the impact of blocking transcription or translation on Erastin (Class I) or RSL3 (Class II) induced ferroptosis. It was found that blocking transcription or translation protected cells against Erastin but was detrimental against RSL3. The study also revealed divergent mRNA stability changes and codon usage biases in cellular response to Erastin or RSL3. Additionally, the role of a tRNA modifying enzyme in the ferroptosis stress response was evaluated.
Article
Clinical Neurology
Shanmuganathan Rajasekaran, Dilip Chand Raja Soundararajan, Chitraa Tangavel, Sharon Miracle Nayagam, Sri K. S. Vijayanand, R. Sunmathi, Monica Steffi Matchado, Raveendran Muthurajan, Ajoy Prasad Shetty, Rishi Mugesh Kanna, K. Dharmalingam
Summary: This study utilized proteomic analysis to compare the expression of SLRPs in fetal, healthy adult, and degenerated discs. The results showed a universal decrease in SLRPs abundance in degenerated discs, associated with an increase in MMPs and a reduction in TIMPs. Fetal discs were mainly engaged in ribosomal pathways, while healthy adult discs primarily participated in ECM maintenance and basic metabolic pathways.
Review
Oncology
Aikaterini Berdiaki, Eirini-Maria Giatagana, George Tzanakakis, Dragana Nikitovic
Summary: Cancer is a complex disease involving changes in cells and the surrounding environment. The tumor microenvironment consists of tumor cells, normal tissue cells, blood vessels, immune system cells, stromal cells, and the extracellular matrix (ECM). Small leucine-rich proteoglycans (SLRPs) are molecules released by cells into the surrounding matrix. They can interact with cell surface molecules and secreted biomolecules, altering signaling pathways and regulating cell behavior. This review focuses on the roles of two SLRP members, biglycan and lumican, and their impact on cancer cell survival, growth, and metastasis.
Review
Biochemistry & Molecular Biology
Chidambra D. Halari, Michael Zheng, Peeyush K. Lala
Summary: This review highlights the important roles of two small leucine-rich proteoglycans in the placenta and fetal membranes, discussing their alterations and associations with pregnancy-related diseases. The expression and actions of these proteoglycans in pathological pregnancies are explored, along with unanswered questions for further research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Geyang Dai, Yue Sun, Rui Wei, Ling Xi
Summary: PODNL1, a member of SLRP family, plays a crucial role in the tumor microenvironment and has significant correlations with prognosis and immunotherapeutic responses in various cancers. It is closely associated with cancer-associated fibroblast infiltration levels and participates in the complex regulation network of tumor progression, indicating its potential as a biomarker for cancer treatment and prognosis.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Biology
Maneenop Yimyaem, Kunlakanya Jitobaom, Prasert Auewarakul
Summary: This study found that rare codons at the beginning of dengue virus do not necessarily result in low overall CAI, but there is a significant drop in CAI around the 50th codon. This suggests the presence of a translational checkpoint at this site, and the rare codon usage upstream to this checkpoint may not be related to translational control.
BMC RESEARCH NOTES
(2023)
Article
Biochemistry & Molecular Biology
Guillermo Lamolle, Andres Iriarte, Hector Musto
Summary: This study reanalyzed the codon usage in Schistosoma mansoni and discovered a significant increase of G/C-ending codons in highly expressed genes. Moreover, the synonymous distance was significantly lower in highly expressed genes compared to lowly expressed sequences. Therefore, the codon usage in S. mansoni is influenced by both mutational bias and translational selection.
MOLECULAR AND BIOCHEMICAL PARASITOLOGY
(2022)
Article
Pharmacology & Pharmacy
Cecile Lambert, Gaelle Bellemere, Gaetan Boyer, Frank Ponelle, Thierry Bauer, Marie-Christine Legeny, Caroline Baudouin, Yves Henrotin
Summary: This study compared the composition and pharmacological activity of seven commercially available ASU products on human osteoarthritis chondrocytes. It was found that PIASCLEDINE-ExpASU(R) had a specific composition and exhibited better pharmacological activity, including higher inhibitory effect on pro-inflammatory factors.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Cell Biology
Yvenn Sermeus, Jef Vangheel, Liesbet Geris, Bart Smeets, Przemko Tylzanowski
Summary: Early limb bud development has attracted significant interest in embryological development and morphogenesis, with a focus on biochemical signaling rather than cell biomechanics. However, the role of cellular and tissue mechanics, as well as the feedback between gene regulation and the biomechanical environment, are crucial for tissue shape changes.
Article
Oncology
Sophie Bekisz, Louis Baudin, Florence Buntinx, Agnes Noel, Liesbet Geris
Summary: Lymphangiogenesis, the formation of new lymphatic vessels, plays a crucial role in various diseases, particularly cancer. Studying lymphangiogenesis through biological and computational models, as well as imaging techniques, provides valuable insights into the molecular mechanisms and dysregulation of this process. This review discusses the different models used to study lymphangiogenesis, their advantages and limitations, and the importance of integrating in vivo and in silico approaches. Overall, these models contribute to advancing lymphangiogenesis research.
Article
Orthopedics
M. A. Holden, B. Metcalf, B. J. Lawford, R. S. Hinman, M. Boyd, K. Button, N. J. Collins, E. Cottrell, Y. Henrotin, J. B. Larsen, H. Master, S. T. Skou, L. M. Thoma, R. Rydz, E. Wellsandt, D. K. White, K. Bennell
Summary: This study developed evidence-informed recommendations for the delivery of best practice therapeutic exercise for people with knee and/or hip osteoarthritis. The final recommendations comprised 54 specific proposition statements across 11 broad domains.
OSTEOARTHRITIS AND CARTILAGE
(2023)
Article
Orthopedics
Thierry Conrozier, Demirhan Diracoglu, Jordi Monfort, Xavier Chevalier, Herve Bard, Dominique Baron, Joerg Jerosch, Alberto Migliore, Pascal Richette, Yves Henrotin
Summary: This study provides recommendations for decision-making in knee Viscosupplementation (VS) based on literature review and expert opinions. It includes recommendations on pain assessment, the necessity of imaging tests, treatment goals, etc. These recommendations are helpful for physicians to make informed decisions.
Article
Rheumatology
Belinda J. Lawford, Hiral Master, Jesper B. Larsen, Cecilie Bartholdy, Patrick Corrigan, Elisabeth Ginnerup-Nielsen, Christina Le, Anthony Teoli, Kim L. Bennell, Ben Metcalf, Rana S. Hinman, Kate Button, Natalie J. Collins, Elizabeth Cottrell, Yves Henrotin, Soren T. Skou, Louise M. Thoma, Elizabeth Wellsandt, Daniel K. White, Melanie A. Holden
Summary: This study aimed to identify important components and practical resources for a toolkit to aid exercise delivery for people with hip/knee osteoarthritis. An online survey involving clinicians, patients, and researchers yielded nine broad domains of resources, including accessibility, quality, stakeholder involvement, different modes of information delivery, resources for exercise and non-exercise self-management, recommended exercises and progression, motivation and progress tracking tools, individual tailoring, and access to professional and peer support. These findings lay the foundation for developing a toolkit aligned with international recommendations.
MUSCULOSKELETAL CARE
(2023)
Review
Developmental Biology
Caroline Caetano da Silva, Agnes Ostertag, Ratish Raman, Marc Muller, Martine Cohen-Solal, Corinne Collet
Summary: Wnt signaling plays a crucial role in osteoblast differentiation and mineralization through canonical and noncanonical pathways. The zebrafish silberblick mutant with a wnt11f2 mutation shows defects in embryonic morphogenesis, and this review aims to summarize its characterization and role in skeletal development. In addition to early developmental defects and craniofacial dysmorphia, the heterozygous mutant also exhibits increased tissue mineral density, suggesting a potential role of wnt11f2 in high bone mass phenotypes.
Article
Environmental Sciences
Gustavo Guerrero-Limon, Renaud Nivelle, Nguyen Bich-Ngoc, Dinh Duy-Thanh, Marc Muller
Summary: Persistent organic pollutants (POPs) pose significant threats to the environment and health due to their stability, prevalence, and ability to accumulate in organisms. While most studies focus on single chemicals, our research examines the effects of an environmentally relevant POP mixture on zebrafish larvae. The larvae exposed to this mixture exhibited growth retardation, edemas, impaired swim bladder inflation, hyperactive swimming behavior, and other malformations. Our findings highlight the harmful effects of certain compounds in the mixture and provide insights into the potential mechanisms underlying these effects, emphasizing the need for further investigation.
Article
Engineering, Biomedical
Pieter Ansoms, Mojtaba Barzegari, Jos Vander Sloten, Liesbet Geris
Summary: This study presents an in silico strategy for designing and studying biodegradable metal implants for fracture fixation. By combining three separate models, patient-specific biodegradable fixation implants can be designed to deliver the desired mechanical behavior in coordination with bone regeneration.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2023)
Review
Orthopedics
Katherine B. Crump, Ahmad Alminnawi, Paola Bermudez-Lekerika, Roger Compte, Francesco Gualdi, Terence McSweeney, Estefano Munoz-Moya, Andrea Nuesch, Liesbet Geris, Stefan Dudli, Jaro Karppinen, Jerome Noailly, Christine Le Maitre, Benjamin Gantenbein
Summary: The cartilaginous endplates (CEP) play a vital role in the intervertebral disc (IVD) by maintaining nutrition, distributing mechanical loads, and preventing bulging. Degeneration of the CEP is linked to IVD degeneration and low back pain. However, there is limited data on the CEP and its distinct properties. Furthermore, current IVD regeneration therapies often overlook the importance of the CEP. Therefore, further research and consideration of the CEP are necessary for sustainable treatments.
Article
Engineering, Biomedical
Ehsan Sadeghian Dehkord, Greet Kerckhofs, Philippe Compere, France Lambert, Liesbet Geris
Summary: Facial trauma, cancer bone resection, periodontal diseases, and bone atrophy after tooth extraction often result in alveolar bone defects, which require bone regeneration for dental function restoration. Guided bone regeneration using synthetic biomaterials has been proposed as an alternative to autologous bone grafts. This study aimed to develop an empirical model for evaluating the bone regeneration potential of new biomaterials based on their physico-chemical characteristics, potentially guiding the design of new dental biomaterials. A quantitative dataset of physico-chemical characteristics of seven commercially available intra-oral bone biomaterials and their in vivo response was constructed. The empirical model identified the construct parameters that drive optimized bone formation, providing insights for the design of bone biomaterials.
JOURNAL OF FUNCTIONAL BIOMATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Marc Joiret, Frederic Kerff, Francesca Rapino, Pierre Close, Liesbet Geris
Summary: The study established a minimal geometrical model to quantitatively estimate the electrostatic potential and electric field experienced by the ribosome during the peptidyl transfer reaction. The theoretical calculations are consistent with experimental results and shed light on the functional role of the electrostatic profile in ribosome elongation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Cell & Tissue Engineering
Jeremie Zappia, Qiao Tong, Renee Van der Cruyssen, Frederique M. F. Cornelis, Cecile Lambert, Tiago Pinto Coelho, Juliane Grisart, Erika Kague, Rik J. Lories, Marc Muller, Dirk Elewaut, Chrissy L. Hammond, Christelle Sanchez, Yves Henrotin
Summary: Abnormal subchondral bone remodeling leading to sclerosis is a main feature of osteoarthritis. Osteomodulin (OMD), a proteoglycan, is associated with the sclerotic phenotype. This study found that OMD binds to RANKL and inhibits osteoclastogenesis, thus regulating bone remodeling and contributing to bone and cartilage homeostasis. Targeting OMD may be a promising personalized approach for osteoarthritis.
Meeting Abstract
Biochemistry & Molecular Biology
G. Kausel, G. E. Valenzuela Nieto, F. Stolzenbach, S. O. Alhassan, M. Muller
