Advances In Proteomics Research Research Articles

Unveiling the power of proteomics in advancing tropical animal health and production.

Proteomics, the large-scale study of proteins in biological systems has emerged as a pivotal tool in the field of animal and veterinary sciences, mainly for investigating local and rustic breeds. Proteomics provides valuable insights into biological processes underlying animal growth, reproduction, health, and disease. In this review, we highlight the key proteomics technologies, methodologies, and their applications in domestic animals, particularly in the tropical context. We also discuss advances in proteomics research, including integration of multi-omics data, single-cell proteomics, and proteogenomics, all of which are promising for improving animal health, adaptation, welfare, and productivity. However, proteomics research in domestic animals faces challenges, such as sample preparation variation, data quality control, privacy and ethical considerations relating to animal welfare. We also provide recommendations for overcoming these challenges, emphasizing the importance of following best practices in sample preparation, data quality control, and ethical compliance. We therefore aim for this review to harness the full potential of proteomics in advancing our understanding of animal biology and ultimately improve animal health and productivity in local breeds of diverse animal species in a tropical context.

Advances in proteomic research on plant responses to metal-based nanomaterial stress

Soil is gradually becoming the main sink of metal-based nanomaterials (MNMs) in the environment. Plants, as a vital component in the ecosystem, play a critical role in determining the fate of nanomaterials. Previous studies showed that MNMs could affect the growth and development of various plant species via altering protein expression. In this review, we described the differences in plant protein expression caused by various typical MNM stresses, and summarized the impact factors including physicochemical properties of MNMs, plant characteristics and stress conditions on plant protein response under the stress of MNMs. Moreover, the response mechanisms of plant protein to MNMs stress were reviewed, including energy synthesis and metabolic response, amino acid synthesis and information transmission response, and oxidative stress and defense response. Finally, further research directions were proposed.

Proteomic insights into floral biology

The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics — a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

FTDR 2.0: A Tool To Achieve Sub-ppm Level Recalibrated Accuracy in Routine LC–MS Analysis

Advances in proteomics research involve the use of high-precision and high-resolution mass spectrometry instruments. Although hardware improvements are the main impetus for the acquisition of high-quality data, enhancements in software tools are also needed. In this study, recalibration was verified as an important way to improve data accuracy. A new version tool, known as FTDR 2.0, was developed to recalibrate the mass-to-charge ratio error of most observed parent ions to the sub part per million level in routine experiments. First, many new parameters were introduced and screened as features online to reduce systematic error and to adapt to various data sets. Second, a support vector regression model was trained to characterize the complex nonlinear maps from features to mass-to-charge ratio measurement errors. Third, a specific mass-to-charge ratio error tolerance for each parent ion was estimated by considering the impact of signal intensity. FTDR 2.0 is a user-friendly tool that supports most commonly used data standards and formats. A C++ library and the source code are provided to support the redevelopment and integration into other mass spectrometry data processing tools. The performance of FTDR 2.0 was verified using several experimental data sets from different research programs. Recalibration with FTDR 2.0 has been proved to improve the peptide identification in qualitative, quantitative, and post-translational modification analyses.

Polyionic and cysteine-containing fusion peptides as versatile protein tags

In response to advances in proteomics research and the use of proteins in medical and biotechnological applications, recombinant protein production and the design of specific protein characteristics and functions has become a widely used technology. In this context, protein fusion tags have been developed as indispensable tools for protein expression, purification, and the design of functionalized surfaces or artificially bifunctional proteins. Here we summarize how positively or negatively charged polyionic fusion peptides with or without an additional cysteine can be used as protein tags for protein expression and purification, for matrix-assisted refolding of aggregated protein, and for coupling of proteins either to technologically relevant matrices or to other proteins. In this context we used cysteine-containing polyionic fusion peptides for the design of immunotoxins. In general, polyionic fusion tags can be considered as a multifunctional module in protein technology.

Nitric Oxide-Dependent Posttranslational Modification in Plants: An Update

Nitric oxide (NO) has been demonstrated as an essential regulator of several physiological processes in plants. The understanding of the molecular mechanism underlying its critical role constitutes a major field of research. NO can exert its biological function through different ways, such as the modulation of gene expression, the mobilization of second messengers, or interplays with protein kinases. Besides this signaling events, NO can be responsible of the posttranslational modifications (PTM) of target proteins. Several modifications have been identified so far, whereas metal nitrosylation, the tyrosine nitration and the S-nitrosylation can be considered as the main ones. Recent data demonstrate that these PTM are involved in the control of a wide range of physiological processes in plants, such as the plant immune system. However, a great deal of effort is still necessary to pinpoint the role of each PTM in plant physiology. Taken together, these new advances in proteomic research provide a better comprehension of the role of NO in plant signaling.

The cerebrospinal fluid: regulator of neurogenesis, behavior, and beyond

The cerebrospinal fluid (CSF) has attracted renewed interest as an active signaling milieu that regulates brain development, homeostasis, and disease. Advances in proteomics research have enabled an improved characterization of the CSF from development through adulthood, and key neurogenic signaling pathways that are transmitted via the CSF are now being elucidated. Due to its immediate contact with neural stem cells in the developing and adult brain, the CSF's ability to swiftly distribute signals across vast distances in the central nervous system is opening avenues to novel and exciting therapeutic approaches. In this review, we will discuss the development of the choroid plexus-CSF system, and review the current literature on how the CSF actively regulates mammalian brain development, behavior, and responses to traumatic brain injury.

Proteomics-based discovery of biomarkers and therapeutic targets in neurodegenerative diseases: perspective of microglia and neuroinflammation

Proteomics is a field of study that characterises a complete profile of proteins present in a given cell, tissue or biological system. Recent advances in proteomics research made possible the identification of novel biomarkers and therapeutic targets in neurodegenerative diseases. The field of neurodegenerative diseases is particularly well suited for proteomic analysis, given the multifactorial nature of the diseases and complexity of the nervous system. As increasing evidence indicates that microglia-associated chronic neuroinflammation plays an important role in the pathophysiology of neurodegenerative diseases, microglial activation may be a potential drug target in CNS disorders. On the basis of both the neuroprotective and neurotoxic role of microglia, the proteomic analysis of microglial signalling and neuroinflammation may thus be used for the identification and validation of novel drug targets as well as for the discovery of useful biomarkers of disease diagnosis and progression in the CNS.

High throughput production of mouse monoclonal antibodies using antigen microarrays

Recent advances in proteomics research underscore the increasing need for high-affinity monoclonal antibodies, which are still generated with lengthy, low-throughput antibody production techniques. Here we present a semi-automated, high-throughput method of hybridoma generation and identification. Monoclonal antibodies were raised to different targets in single batch runs of 6-10 wk using multiplexed immunisations, automated fusion and cell-culture, and a novel antigen-coated microarray-screening assay. In a large-scale experiment, where eight mice were immunized with ten antigens each, we generated monoclonal antibodies against 68 of the targets (85%), within 6 wk of the primary immunization.

Design, construction, and characterization of a large synthetic human antibody phage display library

Advances in proteomic research allow the identification of several hundred protein components in complex biological specimens. Structural information is typically lost during proteomic investigations. For this reason, the rapid isolation of monoclonal antibodies specific to proteins of interest would allow the study of structurally intact biological specimens, thus providing complementary proteomic information. Here, we describe the design, construction, characterization, and use of a large synthetic human antibody phage display library (ETH-2-Gold) containing three billion individual antibody clones. A large repertoire of antibodies with similar biochemical properties was produced by appending short variable complementarity-determining region 3 (CDR3) onto three antibody germline segments (DP47, DPK22, and DPL16), which are frequently found in human antibodies. The ETH-2-Gold library exhibits efficient display of antibody fragments on filamentous phage, as assessed by immunoblot. Furthermore, the library is highly functional, since >90% of clones express soluble antibodies in bacteria and since good quality monoclonal antibodies have been isolated against 16 different antigens. The usefulness of the library as a tool for generating monoclonal antibodies for biomedical applications was tested using the C-domain of tenascin-C (a marker of angiogenesis) as antigen and showing that specific antibodies to this target were able to stain vascular structures in tumor sections.

A clinical overview of carcinoid tumors: Perspectives for improvement in treatment using peptide analogs (Review)

Carcinoid tumors were first described more than a century ago, but the treatment of patients with advanced disease remains a challenge to physicians. The etiology of carcinoid tumors, the biologic determinants of the growth of these malignancies, as well as the high frequency of multiple carcinoid and/or non-carcinoid tumors in patients with this disease also remain to be elucidated. A 5-decade analysis of 13,715 carcinoid tumors in the USA showed that distant metastases were demonstrated at the time of diagnosis in 12.9% of patients with this neoplasia. The overall 5-year survival rate for all patients with carcinoids regardless of the site, was reported to be 67.2%. The prognosis of patients with early stage disease is good and surgical resection is the standard form of treatment. The resection of local or regional metastases can result in cure for some cases. However, patients with metastatic dissemination have poor outcomes since chemotherapy is generally ineffective. Surgical resection of isolated hepatic metastases, surgical hepatic artery ligation or embolization produce responses in selected patients. Radiation therapy may ease the pain of bone metastases. The administration of long acting analogs of somatostatin can control the symptoms of diarrhea and flushing in patients with the malignant carcinoid syndrome. However, a complete regression of metastatic carcinoid tumors following the administration of somatostatin analog octreotide has been reported so far in only 3 cases. Other modalities of treatment, including liver transplantation and the administration of radiolabeled somatostatin analogs have likewise been applied in patients with advanced disease. It is expected that advances in proteomics research will contribute to our understanding of the mechanisms of diseases and aid in designing new drugs.