Article
Chemistry, Analytical
Fatema Bhinderwala, Thao Vu, Thomas G. Smith, Julian Kosacki, Darrell D. Marshall, Yuhang Xu, Martha Morton, Robert Powers
Summary: This article discusses the importance of using multispectral approaches to improve the accuracy and convenience of metabolite assignments, as well as the common experiments used in metabolite assignments. It also explores the impact of 13C-labeled feedstocks like glucose on experimental results and the corresponding improvement methods.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Krzysztof Ossolinski, Tomasz Ruman, Valerie Copie, Brian P. Tripet, Artur Kolodziej, Aneta Plaza-Altamer, Anna Ossolinska, Tadeusz Ossolinski, Anna Nieczaj, Joanna Niziol
Summary: This study investigated polar metabolite profiles in urine samples from BC patients and normal controls using NMR and LDI-MS and identified potential markers for bladder cancer. The metabolites were able to distinguish urine samples from BC and NCs individuals, and correlate with tumor stages and grades. The findings suggest that these metabolite markers may be useful for non-invasive detection and monitoring of bladder cancer.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Article
Biochemical Research Methods
Olatomiwa O. Bifarin, Samyukta Sah, David A. Gaul, Samuel G. Moore, Ruihong Chen, Murugesan Palaniappan, Jaeyeon Kim, Martin M. Matzuk, Facundo M. Fernandez
Summary: Ovarian cancer is a deadly cancer that affects the female reproductive system and is often asymptomatic until later stages. Little is known about the metabolic changes in the early stages of high-grade serous ovarian cancer. This study used a mouse model and machine learning analysis to examine the temporal changes in serum lipidome. The results showed unique alterations in cell membrane stability, proliferation, and survival during cancer development and progression, providing potential targets for early detection and prognosis of ovarian cancer.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Food Science & Technology
Dhara Dixit
Summary: This study reveals the biochemical traits, mineral makeup, and secondary metabolite outline of Iyengaria stellata using untargeted metabolite profiling. A total of 108 putative metabolites were detected, including steroids, terpenoids, ketones, esters, polyphenols, anthraquinones, tocopherol, etc. The study highlights the potential of I. stellata as a natural source in pharmaceutical and nutraceutical compositions.
Review
Cell Biology
Martin Giera, Oscar Yanes, Gary Siuzdak
Summary: Metabolite identification is a significant challenge and opportunity in biochemistry. The characterization and quantification of metabolites in living organisms has resulted in a valuable biochemical knowledgebase and serves as the foundation for metabolism research in the 21st century. However, the characterization of newly discovered metabolites has remained a persistent obstacle. Crystallography, NMR spectroscopy, and mass spectrometry are important techniques in this field, with the latter being particularly useful when coupled with high-performance separation technologies and database solutions. Furthermore, the development of artificial intelligence technologies is rapidly advancing to help overcome the challenges in metabolite identification.
Review
Biochemistry & Molecular Biology
Dhananjaya Pratap Singh, Mansi Singh Bisen, Renu Shukla, Ratna Prabha, Sudarshan Maurya, Yesaru S. Reddy, Prabhakar Mohan Singh, Nagendra Rai, Tribhuwan Chaubey, Krishna Kumar Chaturvedi, Sudhir Srivastava, Mohammad Samir Farooqi, Vijai Kumar Gupta, Birinchi K. Sarma, Anil Rai, Tusar Kanti Behera
Summary: This study discusses the application of metabolomics in vegetable plants, including the identification and quantification of metabolites, the localization of metabolic pathways, the classification of functional biomolecules, and the linkages between metabolic fluxes and genomic regulations. It also explores the role of metabolomics in the domestication, growth, and development of vegetable plants, as well as the impacts of climate, plant-microbe-pest interactions, and anthropogenic activities. Additionally, efforts to identify biomarker metabolites and relevant genes are documented, aiming to improve the nutritional capabilities, disease/pest tolerance, and climate resilience of vegetable crops.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Tibor Nagy, Gergo Roth, Akos Kuki, Miklos Zsuga, Sandor Keki
Summary: This study introduces a novel method for comprehensive screening and filtering of flavonoids based on mass spectrometry analysis. The M-MARA technique is applied for efficient filtering of peak rich spectra in natural herb extracts to determine elemental composition. The method is simple, easy to implement, and suitable for real-time application.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yewei Wang, Zeljka Popovic, Georgia Charkoftaki, Rolando Garcia-Milian, TuKiet T. Lam, David C. Thompson, Ying Chen, Vasilis Vasiliou
Summary: This study identifies the impact of knocking down ALDH1B1 on molecular signatures in colon cancer cells through multi-omics analysis. The findings provide new molecular information associated with the cellular functions of ALDH1B1, which will guide future investigations of colon cancer.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Biochemistry & Molecular Biology
Tao Zhang, Xue Ma, Yuanyuan Zhou, Hui Yang, Yuxin Wang, Taolin Chen, Qincao Chen, Yanli Deng
Summary: This study investigated the non-volatile secondary metabolites in the internal and external petals of different colored tea flowers. A total of 429 metabolites were identified, including flavonoids, phenolic acids, alkaloids, lignans, coumarins, tannins, terpenoids, and other metabolites. The metabolites in the internal and external petals showed significant changes, with higher levels of flavonoids and tannins in the internal petals. Pink tea flowers contained more flavonoids, alkaloids, lignans, coumarins, terpenoids, and tannins compared to white tea flowers. Anthocyanin may be the main reason for the color difference between pink and white tea flowers. The enriched metabolic pathways were involved in flavonoid biosynthesis, amino acid metabolism, glycerophospholipid metabolism, and phenylpropanoid biosynthesis. This study expands our understanding of non-volatile compound changes in tea plants and provides a theoretical foundation for the integrated applications of tea flowers.
Article
Biochemical Research Methods
Jinfeng Zhu, Mengmeng Zhang, Jinxiu Guo, Xueke Wu, Shaomin Wang, Yubing Zhou, Hongmin Liu
Summary: Chondrosarcoma is the second most common bone sarcoma. This study investigated the metabolic profiling of human chondrosarcoma SW-1353 cell line for the first time, evaluating pretreatment methods to obtain precise information. The final protocol provides a simple, robust, and reproducible method for obtaining metabolite information from chondrosarcoma cells.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2021)
Article
Biochemical Research Methods
Marina Creydt, Lea Ludwig, Michael Kohl, Jorg Fromm, Markus Fischer
Summary: The analysis of wood geographical origin using different extraction methods can effectively distinguish the geographic source of wood, helping to prevent illegal logging and timber trade. Multivariate data analysis can extract differences related to geographic origin, and the identification of marker substances reveals metabolic pathways affected by geographical influences.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Biotechnology & Applied Microbiology
Pratigya Subba, Pallabi Saha, Gayathree Karthikkeyan, Mousumi Biswas, Thottethodi Subrahmanya Keshava Prasad, Subhankar Roy-Barman
Summary: The study aimed to investigate the regulatory role of the global regulator MoLAEA in metabolic pathways and metabolites in the plant pathogen M. oryzae. The results showed significant changes in the levels of metabolites involved in various pathways in the mutant strains of MoLAEA compared with the wild type, and overproduced metabolites in the overexpression strain were associated with distinct phenotypic changes. This study reveals new insights into the genetic regulation of secondary metabolism in M. oryzae. Overall, the study is rated 8 out of 10 in importance.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Laura Del Coco, Marco Greco, Alessandra Inguscio, Anas Munir, Antonio Danieli, Luca Cossa, Debora Musaro, Maria Rosaria Coscia, Francesco Paolo Fanizzi, Michele Maffia
Summary: This study analyzed serum samples from Antarctic expedition participants to investigate metabolic changes and adaptations to hypoxia. By using NMR spectroscopy, it was found that during the adaptation period, there was an increase in circulating glutamine and lipids for energy supply, while levels of glutamate and N-acetyl glycoproteins, stress indicators, and proinflammatory markers decreased. Pathway analysis revealed potential perturbations related to physiological adaptation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Multidisciplinary
Mengliang Zhang, Yifei Wang, Roderick Moore, Roy Upton, Peter de B. Harrington, Pei Chen
Summary: A metabolomic ratio rule-based classification method was developed for automated differentiation of cinnamon species. The method achieved high accuracy in classifying cinnamon species and offered great value for the authentication and evaluation of cinnamon samples.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Chemistry, Analytical
Yasin El Abiead, Christoph Bueschl, Lisa Panzenboeck, Mingxun Wang, Maria Doppler, Bernhard Seidl, Juergen Zanghellini, Pieter C. Dorrestein, Gunda Koellensperger
Summary: This study utilized 13C labeled and unlabeled Pichia pastoris extracts to identify heterogeneous multimerization in biological samples and successfully annotated the monomeric partners of these heteromers. Additionally, they created the first MS/MS library that included data from heteromultimers and demonstrated the relevance of these newly annotated ions to other publicly available datasets. Furthermore, their workflow detected metabolite features originating from heterodimers in other datasets as well.
ANALYTICA CHIMICA ACTA
(2022)
Article
Mathematics, Applied
Daniel Irving Bernstein, Grigoriy Blekherman, Kisun Lee
Summary: This study investigates the low-rank matrix completion problem for symmetric matrices, finding that the minimum rank depends on the location of specified entries rather than their values, and provides a combinatorial description of typical ranks. Additionally, the study details when a partial matrix can be minimally completed to rank n and characterizes typical ranks for patterns with low maximal typical rank.
JOURNAL OF PURE AND APPLIED ALGEBRA
(2021)
Article
Computer Science, Software Engineering
Grigoriy Blekherman, Santanu S. Dey, Marco Molinaro, Shengding Sun
Summary: Although semidefinite programming problems are theoretically solvable in polynomial time, solving large SDP instances in practice is often challenging. A technique to address this challenge is to relax the global PSD constraint and only enforce PSD on smaller submatrices. Empirical observations suggest that this approach can produce bounds close to the optimal value of the original SDP.
MATHEMATICAL PROGRAMMING
(2022)
Article
Computer Science, Software Engineering
Grigoriy Blekherman, Bharath Hebbe Madhusudhana
Summary: The problem of determining whether a quantum state is entangled is equivalent to a moment problem in real analysis. Due to experimental limitations, the study of quantum entanglement in many-body systems can be simplified to a truncated moment problem. The necessary and sufficient conditions for membership in the moment cone can be expressed through linear matrix inequalities independent of the number of entities involved.
MATHEMATICAL PROGRAMMING
(2022)
Article
Robotics
Tianyu Wang, Bo Lin, Baxi Chong, Julian Whitman, Matthew Travers, Daniel Goldman, Greg Blekherman, Howie Choset
Summary: Snake robots with multiple internal degrees of freedom are designed for versatile three-dimensional locomotion through a series of continuous backbone curves capturing desired shapes. However, constraints from the geometric arrangement of single-axis rotary joints make it difficult for the robot to reconstruct arbitrary 3D curves.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2021)
Article
Robotics
Baxi Chong, Tianyu Wang, Jennifer M. Rieser, Bo Lin, Abdul Kaba, Grigoriy Blekherman, Howie Choset, Daniel I. Goldman
Summary: Sidewinding locomotion in limbless robots and snakes relies on coordination of horizontal and vertical traveling waves for stability and maneuverability. Modulating the vertical wave can stabilize configurations and generate desired translation and rotation. This approach expands the movement capabilities of sidewinding locomotors on different terrains.
INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH
(2021)
Article
Mathematics, Applied
Grigoriy Blekherman, Rainer Sinn, Gregory G. Smith, Mauricio Velasco
Summary: We establish bounds for the Pythagoras number of a real projective subvariety and introduce a new invariant called quadratic persistence. Our upper bounds are derived from existing methods, while the lower bound depends on the quadratic persistence and its relation to linear syzygies. We also classify projective subvarieties based on their quadratic persistence and determine their Pythagoras numbers.
JOURNAL OF THE EUROPEAN MATHEMATICAL SOCIETY
(2022)
Article
Microbiology
Linda Archambault, Sherli Koshy-Chenthittayil, Angela Thompson, Anna Dongari-Bagtzoglou, Reinhard Laubenbacher, Pedro Mendes
Summary: This study investigates the interaction between Streptococcus oralis and Lactobacillus paracasei in biofilm growth. It suggests that L. paracasei may secrete an inhibitor of S. oralis growth, which could be used to prevent or alleviate mucosal fungal infections. The research highlights the importance of agent-based modeling and experiments in studying multi-species biofilm interactions for mucosal health and disease prevention.
Article
Mathematics, Applied
Grigoriy Blekherman, Santanu S. Dey, Kevin Shu, Shengding Sun
Summary: This study examines a computational approach for enforcing PSD-ness on a collection of submatrices in large-scale positive semidefinite (PSD) programs. It introduces new insights on the eigenvalues of Sn,k matrices and improves known upper bounds on Frobenius distance. The research also demonstrates the tightness of relaxation for the case of k = n-1 and presents a structure theorem on nonsingular matrices in Sn,k.
SIAM JOURNAL ON OPTIMIZATION
(2022)
Article
Mathematics
Grigoriy Blekherman, Annie Raymond, Mohit Singh, Rekha R. Thomas
Summary: The article introduces the tropicalization of graph and hypergraph profiles and computes specific examples. It then uses tropicalization to restrict the power of the sums of squares method in testing graph density inequalities.
TRANSACTIONS OF THE AMERICAN MATHEMATICAL SOCIETY
(2022)
Article
Mathematics
Grigoriy Blekherman, Annie Raymond
Summary: Many important problems in extremal combinatorics can be stated as proving pure binomial inequalities in graph homomorphism numbers. The exponent vectors of valid pure binomial inequalities form a convex cone for a fixed collection of graphs. We observe a polyhedrality phenomenon and use tropicalization techniques to prove results and solve open problems.
ADVANCES IN MATHEMATICS
(2022)
Article
Mathematics
Grigoriy Blekherman, Mario Kummer, Raman Sanyal, Kevin Shu, Shengding Sun
Summary: This study discusses the relationship between linear principal minor polynomials and symmetric matrices. By imposing certain restrictions, a correspondence between multiaffine polynomials and LPM polynomials is established. This provides new techniques for constructing hyperbolic polynomials and generalizing PSD-stable LPM polynomials. The relationships between hyperbolicity cones and eigenvalues of symmetric matrices are investigated, and a conjecture regarding the spectral containment of certain LPM polynomials is proposed.
INTERNATIONAL MATHEMATICS RESEARCH NOTICES
(2022)
Article
Multidisciplinary Sciences
Joseph Masison, Pedro Mendes
Summary: Computational models of cellular iron metabolism can be created more efficiently by using smaller sub-models that represent specific cellular structures. A model for ferritin iron sequestration kinetics was established and validated, and it was found that the concentration of FT has the greatest impact on overall sequestration dynamics. The model's flexibility makes it suitable for use in a variety of specific cell type models of iron metabolism.
Article
Mathematics
Grigoriy Blekherman, Annie Raymond
Summary: Erdos and Simonovits conjectured an inequality between the number of walks of length k and t in graph G(n), where both k and t are odd. In 2018, Saglam proved this conjecture. We provide a new, shorter proof for this result.
GRAPHS AND COMBINATORICS
(2023)
Article
Multidisciplinary Sciences
Baxi Chong, Juntao He, Daniel Soto, Tianyu Wang, Daniel Irvine, Grigoriy Blekherman, Daniel I. Goldman
Summary: This article develops a matter-transport framework based on the principles of information transmission and demonstrates that noninertial locomotion can be reliably generated over complex terrains. Experiments show that serially connected legged robots can achieve reliable transport on such terrain without sensing and control.
Article
Mathematics, Applied
Grigoriy Blekherman, Kevin Shu
Summary: The paper discusses the relationship between nonnegative polynomials and sums of squares on real varieties, as well as their connection to sparse semidefinite programming. Quantitative results are shown on the approximation of nonnegative polynomials by sums of squares, leading to applications in sparse semidefinite programming.
SIAM JOURNAL ON APPLIED ALGEBRA AND GEOMETRY
(2021)
