Article
Biochemical Research Methods
Leena M. Patil, David H. Parkinson, Nathan R. Zuniga, Hsien-Jung L. Lin, Bradley C. Naylor, John C. Price
Summary: Offline peptide separation using HPLC is commonly used to enhance protein detection in LC-MS/MS. We developed a robust intact protein separation (IPS) method and found that it is especially effective in serum, while traditional peptide separation (PS) is more effective in tissues. Combining IPS and PS methods significantly increases protein detection, peptide sequence coverage, and detection of post-translational modifications.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Agriculture, Multidisciplinary
Mahya Bahmani, Angela Juhasz, Utpal Bose, Mitchell G. Nye-Wood, Malcolm Blundell, Crispin A. Howitt, Michelle L. Colgrave
Summary: In this study, the proteome profile of barley grain and malt samples was investigated using SWATH-MS proteomics. The results showed that the C-hordein-reduced lines had a more significant impact on proteome level changes during malting. Upregulated proteins in C-hordein-reduced lines were mainly involved in the tricarboxylic acid cycle and fatty acid peroxidation processes. Proteomics approaches in hordein-reduced barley lines after malting also revealed additional changes in the proteome driven by the genetic background. These findings provide valuable insights for barley breeders and maltsters to optimize gluten-free grains in malt products.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemical Research Methods
Rui Sun, Mengge Lyu, Shuang Liang, Weigang Ge, Yingrui Wang, Xuan Ding, Cheng Zhang, Yan Zhou, Shanjun Chen, Lirong Chen, Tiannan Guo
Summary: Prostate cancer, the most common cancer in males worldwide, has shown great potential in targeted proteomic analysis using mass spectrometry. A comprehensive tissue-specific spectral library has been developed for prostate tissue samples, containing a large number of precursors, peptides, and unique proteins. This library has been successfully applied in prostate specimens.
Article
Medicine, General & Internal
Zohaib Iqbal, Helene A. Fachim, J. Martin Gibson, Ivona Baricevic-Jones, Amy E. Campbell, Bethany Geary, Rachelle P. Donn, Dashne Hamarashid, Akheel Syed, Anthony D. Whetton, Handrean Soran, Adrian H. Heald
Summary: Bariatric surgery induces metabolic pathway recalibration, potentially contributing to the remission of type 2 diabetes mellitus. Analysis of plasma samples identified several proteins that may serve as biomarkers for T2DM remission after surgery.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Agriculture, Multidisciplinary
Mahya Bahmani, Angela Juhasz, James Broadbent, Utpal Bose, Mitchell G. Nye-Wood, Ian B. Edwards, Michelle L. Colgrave
Summary: This study analyzed the proteome and malt characteristics of three barley lines grown in different locations in Western Australia using LC-MS. The results showed a correlation between genetics, growing locations, proteins, and traits such as malt yield.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemical Research Methods
Xin Wei, Liang Cao, Mingrui Zhou, Jiana Huang, Xiaoyan Liang, Nijie Li, Yanan Pan, Renli Yin, Huashou Li, Adela Jing Li
Summary: This study developed an efficient and sensitive method to simultaneously analyze 16 NEOs and nine UPs in human follicular fluid. The method showed good performance and detected the presence of some pesticides, highlighting the importance of understanding the potential risks of these pesticides to human health.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Aleksandra E. Lewandowska, Anna Fel, Marcel Thiel, Paulina Czaplewska, Krzysztof Lukaszuk, Jacek R. Wisniewski, Stanislaw Oldziej
Summary: Two label-free quantitative workflows based on different high-resolution mass spectrometers and LC setups were presented for the analysis of human follicular fluid proteome, with around 1000 proteins identified in each workflow. The concentration values obtained from both workflows showed significant correlation, leading to unified lists of proteins linked to oocyte maturity and blastocyst development. The Quad-Orbitrap workflow is suitable for in-depth analysis of low abundant proteome without extensive fractionation, while the Triple Quad-TOF workflow offers a more robust approach with potential for effectiveness with increasing number of analyzed samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Parasitology
Ricardo Perez-Sanchez, Angel Carnero-Moran, M. Luz Valero, Ana Oleaga
Summary: Using a proteomics informed by transcriptomics (PIT) approach, the researchers successfully obtained and characterized the proteome of the saliva of Ornithodoros erraticus adult ticks. They identified novel salivary proteins and functions, and found significant differences between sexes in the saliva proteome of O. erraticus ticks. These findings improve our understanding of feeding physiology in O. erraticus ticks and will contribute to the development of vaccines for controlling O. erraticus infestations and the diseases it transmits.
PARASITES & VECTORS
(2022)
Article
Environmental Sciences
Cong-Cong Shen, Mo-Xian Chen, Tian Xiao, Cheng Zhang, Jun Shang, Kai-Lu Zhang, Fu-Yuan Zhu
Summary: The study utilized SWATH-MS technology to analyze the proteome changes in poplar seedling roots following Pb treatment. Results showed that the lignin and flavonoid biosynthesis pathways were activated upon Pb exposure, while cell wall-related proteins exhibited increased abundances. Glutathione metabolism pathway may play a protective role in mitigating Pb-induced oxidative damages.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Reproductive Biology
Yanna Ban, Haiying Ran, Ying Chen, Li Ma
Summary: The study aimed to investigate changes in lipids in the follicular fluid of PCOS patients with normal weight. Through lipidomic analysis, 32 lipids were found to be significantly different between PCOS patients and the control group, potentially serving as candidate biomarkers and therapeutic targets for PCOS.
JOURNAL OF OVARIAN RESEARCH
(2021)
Article
Cell Biology
Helene A. Fachim, Zohaib Iqbal, J. Martin Gibson, Ivona Baricevic-Jones, Amy E. Campbell, Bethany Geary, Akheel A. Syed, Antony Whetton, Handrean Soran, Rachelle P. Donn, Adrian H. Heald
Summary: After metabolic bariatric surgery, changes in inflammatory markers and circulating proteins were observed, with some proteins correlating with alterations in IL6, TNF alpha, and CRP. Further studies are required to elucidate the mechanisms by which MBS reduces low-grade inflammation.
Article
Plant Sciences
Utpal Bose, Angela Juhasz, Ronald Yu, Mahya Bahmani, Keren Byrne, Malcolm Blundell, James A. Broadbent, Crispin A. Howitt, Michelle L. Colgrave
Summary: This study investigated the regulatory effect of the lys3 mutation in barley, revealing its impact on storage protein accumulation and critical processes in cereal seeds. The results provide insights into how the lys3 mutation remodels cellular functions and impacts phenotype, offering potential applications in selective breeding for favorable agronomic traits.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Applied
Arineh Tahmasian, James A. Broadbent, Angela Juhasz, Mitchell Nye-Wood, Thao T. Le, Utpal Bose, Michelle L. Colgrave
Summary: Lupin is seen as a potential contributor to future food security due to its nutritional and nutraceutical attributes linked to seed proteins. Evaluating four protein extraction procedures using liquid chromatography-tandem mass spectrometry revealed differences in protein identifications based on the extraction buffer used. Variations in protein abundance data and cultivar proteomes were observed, showing the need to optimize protein extraction conditions for accurate biological interpretation.
Article
Food Science & Technology
Stanley H. Chen, Utpal Bose, James A. Broadbent, Narelle Fegan, Richard Wilson, Chawalit Kocharunchitt, Michelle L. Colgrave, Lesley L. Duffy, John P. Bowman
Summary: Peracetic acid (PAA) can reduce the number of Campylobacter on poultry carcasses. However, previous experiments showed that Campylobacter survived better when pre-treated with a thermal stress equivalent to poultry processing prior to chilling with PAA. In this study, the proteomes of C. jejuni poultry strain 2704 were measured after exposure to PAA to understand how Campylobacter responds to the treatment.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Horticulture
Akram Hafizi, Foad Fatehi, Rambod Pakzad
Summary: In this study, the effect of salt exposure on the proteome of the hybrid pistachio rootstock UCB-1 was investigated using SWATH-MS technology. A total of 1150 proteins were quantified, with 459 proteins significantly impacted by salt exposure. Functional enrichment and pathway analysis revealed the upregulation of proteins associated with salt stress response and the downregulation of ribosomal subunits. Centrality analysis highlighted several proteins that may contribute to enhanced salt tolerance in UCB-1. Integration of proteomics and protein-protein interaction analysis can greatly facilitate the identification of potential biomarkers and reduce the need for costly and time-consuming experimental validation.
SCIENTIA HORTICULTURAE
(2023)
Article
Endocrinology & Metabolism
Patrycja Skowronska, Michal Kunicki, Ewa Pastuszek, Lucyna Konieczna, Tomasz Baczek, Blazej Meczekalski, Roman Smolarczyk, Krzysztof Lukaszuk
Summary: The study found that vitamin D concentration in follicular fluid varies with the developmental stage of the oocyte and correlates with embryo development status on day 3; AMH concentration in follicular fluid is not correlated with the developmental potential of an oocyte, but AMH and vitamin D levels in follicular fluid are positively correlated. Further research with larger sample sizes and testing of additional components in follicular fluid is recommended.
GYNECOLOGICAL ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Aleksandra E. Lewandowska, Anna Fel, Marcel Thiel, Paulina Czaplewska, Krzysztof Lukaszuk, Jacek R. Wisniewski, Stanislaw Oldziej
Summary: Two label-free quantitative workflows based on different high-resolution mass spectrometers and LC setups were presented for the analysis of human follicular fluid proteome, with around 1000 proteins identified in each workflow. The concentration values obtained from both workflows showed significant correlation, leading to unified lists of proteins linked to oocyte maturity and blastocyst development. The Quad-Orbitrap workflow is suitable for in-depth analysis of low abundant proteome without extensive fractionation, while the Triple Quad-TOF workflow offers a more robust approach with potential for effectiveness with increasing number of analyzed samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Marta J. Fiolka, Paulina Czaplewska, Sylwia Wojcik-Mieszawska, Aleksandra Lewandowska, Kinga Lewtak, Weronika Sofinska-Chmiel, Tomasz Buchwald
Summary: The protein-polysaccharide fraction AAF from Dendrobaena veneta earthworm coelomic fluid shows effective activity against Candida albicans yeast, causing abnormal cell division and morphology, as well as disturbance in organelle structures such as the nucleus and mitochondria, leading to apoptosis. AAF also influences the expression of fungal proteins and oxidative stress, as demonstrated by various microscopic and proteomic methods.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Bartosz Karaszewski, Anna Gojska-Grymajlo, Paulina Czaplewska, Bartosz Jablonski, Aleksandra E. Lewandowska, Daria Ossowska, Adam Wyszomirski, Marek Halas, Edyta Szurowska
Summary: Intravenous recombinant tissue plasminogen activator (rtPA) is the highest class evidence based reperfusion treatment for acute ischemic stroke (AIS), but symptomatic intracranial hemorrhage (sICH) remains a major concern. Blood proteomic and peptide analysis revealed differences in pre-treatment blood profiles of 15 proteins between patients who developed rtPA-associated ICH and those who did not. SWATH-MS quantification of serum or plasma proteins could potentially improve the prospective assessment of rtPA-associated ICH beyond clinical and neuroimaging characteristics alone.
SCIENTIFIC REPORTS
(2021)
Article
Neurosciences
Kinga Grabowska, Katarzyna Macur, Sarah Zieschang, Lubaba Zaman, Nicole Haverland, Andrew Schissel, Brenda Morsey, Howard S. Fox, Pawel Ciborowski
Summary: This study investigates the impact of Meth on the expression of galectins in HIV-1 infected human monocyte-derived macrophages (hMDM), providing insights into the molecular mechanisms underlying the cellular pathology of hMDM resulting from viral infection and Meth abuse.
JOURNAL OF NEUROVIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Krzysztof Lukaszuk, Amira Podolak
Summary: This retrospective case control study found that mtDNA copy number is higher in aneuploid embryos compared to euploid embryos, but no significant differences were observed in relation to embryo morphology, genetic sex, maternal age, or implantation ability. Therefore, mtDNA has the potential to serve as an additional independent biomarker for embryo selection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Marta Makara-Studzinska, Agnieszka Limanin, Agnieszka Anusiewicz, Paula Janczyk, Dorota Raczkiewicz, Anita Wdowiak-Filip, Michal Filip, Iwona Bojar, Krzysztof Lukaszuk, Artur Wdowiak
Summary: This study aimed to assess the quality of life of men treated for infertility in Poland, revealing that factors such as treatment methods, type of reproductive problems, and living environment can influence the quality of life of affected men.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Immunology
Krzysztof Lukaszuk, Amira Podolak, Paulina Malinowska, Jakub Lukaszuk, Grzegorz Jakiel
Summary: Media reports have affected confidence in the AstraZeneca COVID-19 vaccine, leading many previously vaccinated individuals to refuse further doses. However, there is a shortage of mRNA vaccines due to increased demand, and there have been cases of individuals receiving the AstraZeneca vaccine after the first dose of the Pfizer/BioNTech vaccine. Only 10% of people in low-income countries have received at least one dose of the COVID-19 vaccine.
Review
Medicine, General & Internal
Joanna Kufel-Grabowska, Amira Podolak, Daniel Maliszewski, Mikolaj Bartoszkiewicz, Rodryg Ramlau, Krzysztof Lukaszuk
Summary: Breast cancer is the most common cancer worldwide, and young women with breast cancer account for a small percentage of cases. The availability of next-generation sequencing has improved the diagnosis and treatment of breast cancer, but the treatment of young breast cancer patients may impact their fertility. Therefore, in addition to oncological treatment, patients need to receive genetic counseling, fertility preservation, and psychological support.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Medicine, Research & Experimental
Bartosz Wojciuk, Aleksandra Bogucka, Paulina Czaplewska, Patrycja Okulewicz, Iwona Wojciechowska-Koszko, Kazimierz Ciechanowski, Joanna Kabat-Koperska
Summary: Kidney transplantation is the preferred treatment for patients with end-stage kidney disease, but the understanding of chronic kidney allograft injury is limited. Pregnancy is more common after kidney transplantation than during dialysis, but comprehensive studies on the impact of immunosuppressive regimens on pregnancy are challenging due to ethical issues. This study investigated the proteomic status of lymphocytes from pregnant rats under immunosuppressive treatment and found that these lymphocytes exhibited sustained proinflammatory status with decreased ability to regulate translation, potentially affecting pregnancy and immunity.
CTS-CLINICAL AND TRANSLATIONAL SCIENCE
(2023)
Article
Multidisciplinary Sciences
M. A. Zabielska-Kaczorowska, A. E. Bogucka, K. Macur, P. Czaplewska, S. A. Watson, F. Perbellini, C. M. Terracciano, R. T. Smolenski
Summary: In this study, a special in vitro model using ultrathin cardiac slices was used to investigate the proteomic changes in response to electromechanical stimulation. The findings revealed significant alterations related to mitochondrial respiration, energy metabolism, and muscle contraction in stretched slices and fresh myocardial slices cultured without electromechanical stimulation.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Wlodzimierz Sieg, Jolanta Kiewisz, Amira Podolak, Grzegorz Jakiel, Izabela Woclawek-Potocka, Jakub Lukaszuk, Krzysztof Lukaszuk
Summary: Inflammatory processes during embryo implantation play a crucial role in the successful establishment of pregnancy. However, excessive inflammation can lead to pregnancy complications. Understanding these mechanisms can bring new hope to infertile couples for improved treatments.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Immunology
Adrian Kobiela, Joanna E. Frackowiak, Anna Biernacka, Lilit Hovhannisyan, Aleksandra E. Bogucka, Kinga Panek, Argho Aninda Paul, Joanna Lukomska, Xinwen Wang, Eleni Giannoulatou, Aleksandra Krolicka, Jacek Zielinski, Milena Deptula, Michal Pikula, Susanne Gabrielsson, Graham S. Ogg, Danuta Gutowska-Owsiak
Summary: Research has shown that Candida albicans infection can alter the interaction between small extracellular vesicles (sEVs) and dendritic cells in individuals with atopic dermatitis. This alteration is linked to changes in glycosylation patterns on the surface of sEVs, which may impact the recognition of the pathogen by receptors on dendritic cells. Inhibitory Siglec receptors, specifically Siglec-7 and -9, are involved in the interaction between sEVs and cells, indicating the potential for therapeutic targeting. This study provides new insights into the treatment of skin candidiasis in atopic dermatitis.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Amira Podolak, Joanna Liss, Jolanta Kiewisz, Sebastian Pukszta, Celina Cybulska, Michal Rychlowski, Aron Lukaszuk, Grzegorz Jakiel, Krzysztof Lukaszuk
Summary: This study investigated the correlation between mitochondrial DNA content in embryos and their developmental potential. The findings showed that aneuploid embryos had a higher mitochondrial DNA content compared to euploid embryos.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)