1
|
Pandita G, Sharma S, Elsa Oommen I, Madaan N, Bhosale Y, Nagy V, Mukarram Shaikh A, Kovács B. Comprehensive review on the potential of ultrasound for blue food protein extraction, modification and impact on bioactive properties. ULTRASONICS SONOCHEMISTRY 2024; 111:107087. [PMID: 39362033 DOI: 10.1016/j.ultsonch.2024.107087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/26/2024] [Accepted: 09/26/2024] [Indexed: 10/05/2024]
Abstract
Food security for the increasing global population is a significant challenge of the current times particularly highlighting the protein deficiencies. Plant-based proteins could be considered as alternate source of the protein. The digestibility and PDCASS value of these proteins are still a concern. Blue proteins, the new approach of utilizing the proteins from aquatic sources could be a possible solution as it contains all the essential amino acids. However, the conjugation of these proteins with fats and glycogen interferes with their techno-functional properties and consequently their applicability. The application of power ultrasound for extraction and modification of these proteins from aquatic sources to break open the cellular structure, increase extractability, alter the protein structure and consequently provide proteins with higher bioavailability and bioactive properties could be a potential approach for their effective utilization into food systems. The current review focuses on the application of power ultrasound when applied as extraction treatment, alters the sulphite and peptide bond and modifies protein to elevated digestibility. The degree of alteration is influenced by intensity, frequency, and exposure time. The extracted proteins will serve as a source of essential amino acids. Furthermore, modification will lead to the development of bioactive peptides with different functional applications. Numerous studies reveal that blue proteins have beneficial impacts on amino acid availability, and subsequently food security with higher PDCAAS values. In many cases, converted peptides give anti-hypertensive, anti-diabetic, and anti-oxidant activity. Therefore, researchers are concentrating on ultrasound-based extraction, modification, and application in food and pharmaceutical systems.
Collapse
Affiliation(s)
- Ghumika Pandita
- Department of Food Technology and Nutrition, School of Agriculture, Lovely Professional University, Phagwara, Punjab, India
| | | | - Irin Elsa Oommen
- Department of Food Technology and Nutrition, School of Agriculture, Lovely Professional University, Phagwara, Punjab, India
| | - Nishchhal Madaan
- Department of Food Technology and Nutrition, School of Agriculture, Lovely Professional University, Phagwara, Punjab, India
| | - Yuvraj Bhosale
- Research Engineer, Indian Institute of Technology, Kharagpur, India.
| | - Vivien Nagy
- Faculty of Agriculture, Food Science, and Environmental Management, Institute of Food Technology, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary; Doctoral School of Nutrition and Food Sciences, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary.
| | - Ayaz Mukarram Shaikh
- Faculty of Agriculture, Food Science, and Environmental Management, Institute of Food Science, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary; Doctoral School of Nutrition and Food Sciences, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary.
| | - Béla Kovács
- Faculty of Agriculture, Food Science, and Environmental Management, Institute of Food Science, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary; Doctoral School of Nutrition and Food Sciences, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary.
| |
Collapse
|
2
|
Kamberović J, Gligora Udovič M, Kulaš A, Tapolczai K, Orlić S, Jusufović A, Gajić A, Žutinić P, Ahmić A, Kalamujić Stroil B. The Diatom Diversity and Ecological Status of a Tufa-Depositing River through eDNA Metabarcoding vs. a Morphological Approach-A Case Study of the Una River (Bosnia and Herzegovina). Microorganisms 2024; 12:1722. [PMID: 39203564 PMCID: PMC11357282 DOI: 10.3390/microorganisms12081722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/13/2024] [Accepted: 08/18/2024] [Indexed: 09/03/2024] Open
Abstract
Tufa deposits in karst rivers are unique habitats created by mutual interactions between specific environmental and biotope features and inhabited by diatoms as a highly abundant and diverse algal group. This pilot study aimed to investigate the diversity of diatom communities on tufa depositing habitats and assess the Una River's ecological status using a comparative molecular and morphological approach for diatom identification. The 312 base pairs of the rbcL gene were barcoded and analyzed using MiSeq reads and amplicon sequence variants (ASVs) obtained by the DADA2 pipeline. The reference database Diat.barcode v7 was used for taxonomic assignment. The morphological identification of the diatoms was carried out in parallel. In total, the combined dataset revealed 46 taxa identified at genus rank, 125 on the subgenus, and 145 on combined taxonomy rank. The metabarcoding approach mostly leads to a lower number of identified taxa at species rank (58 in molecular vs. 119 in optical inventory), resulting in higher values of beta diversity and heterogeneity in diatom assemblages in samples obtained by morphological approach. Despite the high percentage of taxonomically not assigned diatom ASVs to the species rank, high Shannon diversity index values and a similar number of taxa per locations compared to the morphological approach were obtained. Taxa Achnanthidium minutissimum (Kützing) Czarnecki, Achnanthidium pyrenaicum (Hustedt) H.Kobayasi, Amphora pediculus (Kützing) Grunow, Diatoma vulgaris Bory, Navicula cryptotenella Lange-Bertalot, and Navicula tripunctata (O.F.Müller) Bory were identified at all locations in both inventories. Although limited consistency in the diatom abundances between the two inventory datasets was found, a similar grouping of samples was observed connected to the river's longitudinal gradient. The data obtained using molecular approach in most sites indicated a mostly lower ecological status (good or moderate) compared to the data obtained from the morphological approach (high, good, and moderate). The potential of environmental DNA (eDNA) diatom metabarcoding for water monitoring and diversity studies is undeniable, but to fully realize the benefits of these methods in the future, it is essential to standardize protocols and expand the reference database for species found in specific habitats, such as tufa deposits.
Collapse
Affiliation(s)
- Jasmina Kamberović
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, BA-75000 Tuzla, Bosnia and Herzegovina; (J.K.)
| | - Marija Gligora Udovič
- Department of Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia; (M.G.U.); (A.K.); (P.Ž.)
| | - Antonija Kulaš
- Department of Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia; (M.G.U.); (A.K.); (P.Ž.)
| | - Kálmán Tapolczai
- HUN-REN Balaton Limnological Research Institute, H-8237 Tihany, Hungary
| | - Sandi Orlić
- Institute Ruđer Bošković, HR-10000 Zagreb, Croatia
| | - Amela Jusufović
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, BA-75000 Tuzla, Bosnia and Herzegovina; (J.K.)
| | | | - Petar Žutinić
- Department of Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia; (M.G.U.); (A.K.); (P.Ž.)
| | - Adisa Ahmić
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, BA-75000 Tuzla, Bosnia and Herzegovina; (J.K.)
| | - Belma Kalamujić Stroil
- Society for Genetic Conservation of B&H Endemic and Autochthonous Resources, BA-71000 Sarajevo, Bosnia and Herzegovina;
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, BA-71000 Sarajevo, Bosnia and Herzegovina
| |
Collapse
|
3
|
Ferrante MI, Broccoli A, Montresor M. The pennate diatom Pseudo-nitzschia multistriata as a model for diatom life cycles, from the laboratory to the sea. JOURNAL OF PHYCOLOGY 2023; 59:637-643. [PMID: 37256710 DOI: 10.1111/jpy.13342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 06/02/2023]
Abstract
Phytoplankton dynamics are regulated by external cues, such as light and nutrients, as well as by biotic interactions and endogenous controls linked to life cycle characteristics. The planktonic pennate diatom Pseudo-nitzschia multistriata, with a heterothallic mating system with two opposite mating types (MTs), represents a model for the study of diatom life cycles. P. multistriata is a toxic species, able to produce the neurotoxin domoic acid. First described in Japan in 1993, it was detected at the long-term monitoring station MareChiara (Gulf of Naples, Italy) in 1995. Since then, P. multistriata has been reported from several worldwide coastal sites. A large body of knowledge has been produced on its ecology, genetic diversity, and life cycle characteristics. The availability of these data, the ecological relevance of the Pseudo-nitzschia genus, and its controllable life cycle with a short generation time made it an ideal species to develop a genetic model system for diatoms. To enable functional studies, a 59 Mb genome sequence and several transcriptomic data were produced, and genetic transformation was optimized. These tools allowed the discovery of the first mating-type determining gene for diatoms. Gene expression studies and metabolomics analyses defined genes and molecules underpinning different phases of the process of sexual reproduction. This model system, developed to explore the genetics of diatom life cycles, offers the opportunity to parallel experimental observations in the laboratory using in situ meta-omics analyses along space and time, empowering knowledge on the biology and ecology of the genus.
Collapse
Affiliation(s)
- Maria Immacolata Ferrante
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Andrea Broccoli
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marina Montresor
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| |
Collapse
|
4
|
Zhou H, Deng XW, He H. Gene expression variations and allele-specific expression of two rice and their hybrid in caryopses at single-nucleus resolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1171474. [PMID: 37287712 PMCID: PMC10242081 DOI: 10.3389/fpls.2023.1171474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/26/2023] [Indexed: 06/09/2023]
Abstract
Seeds are an indispensable part of the flowering plant life cycle and a critical determinant of agricultural production. Distinct differences in the anatomy and morphology of seeds separate monocots and dicots. Although some progress has been made with respect to understanding seed development in Arabidopsis, the transcriptomic features of monocotyledon seeds at the cellular level are much less understood. Since most important cereal crops, such as rice, maize, and wheat, are monocots, it is essential to study transcriptional differentiation and heterogeneity during seed development at a finer scale. Here, we present single-nucleus RNA sequencing (snRNA-seq) results of over three thousand nuclei from caryopses of the rice cultivars Nipponbare and 9311 and their intersubspecies F1 hybrid. A transcriptomics atlas that covers most of the cell types present during the early developmental stage of rice caryopses was successfully constructed. Additionally, novel specific marker genes were identified for each nuclear cluster in the rice caryopsis. Moreover, with a focus on rice endosperm, the differentiation trajectory of endosperm subclusters was reconstructed to reveal the developmental process. Allele-specific expression (ASE) profiling in endosperm revealed 345 genes with ASE (ASEGs). Further pairwise comparisons of the differentially expressed genes (DEGs) in each endosperm cluster among the three rice samples demonstrated transcriptional divergence. Our research reveals differentiation in rice caryopsis from the single-nucleus perspective and provides valuable resources to facilitate clarification of the molecular mechanism underlying caryopsis development in rice and other monocots.
Collapse
Affiliation(s)
- Han Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| |
Collapse
|
5
|
Butto T, Mungikar K, Baumann P, Winter J, Lutz B, Gerber S. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells 2023; 12:cells12071051. [PMID: 37048124 PMCID: PMC10093037 DOI: 10.3390/cells12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.
Collapse
Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center Mainz, 55128 Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| |
Collapse
|
6
|
Gene expression during the formation of resting spores induced by nitrogen starvation in the marine diatom Chaetoceros socialis. BMC Genomics 2023; 24:106. [PMID: 36899305 PMCID: PMC9999646 DOI: 10.1186/s12864-023-09175-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/09/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Dormancy is widespread in both multicellular and unicellular organisms. Among diatoms, unicellular microalgae at the base of all aquatic food webs, several species produce dormant cells (spores or resting cells) that can withstand long periods of adverse environmental conditions. RESULTS We present the first gene expression study during the process of spore formation induced by nitrogen depletion in the marine planktonic diatom Chaetoceros socialis. In this condition, genes related to photosynthesis and nitrate assimilation, including high-affinity nitrate transporters (NTRs), were downregulated. While the former result is a common reaction among diatoms under nitrogen stress, the latter seems to be exclusive of the spore-former C. socialis. The upregulation of catabolic pathways, such as tricarboxylic acid cycle, glyoxylate cycle and fatty acid beta-oxidation, suggests that this diatom could use lipids as a source of energy during the process of spore formation. Furthermore, the upregulation of a lipoxygenase and several aldehyde dehydrogenases (ALDHs) advocates the presence of oxylipin-mediated signaling, while the upregulation of genes involved in dormancy-related pathways conserved in other organisms (e.g. serine/threonine-protein kinases TOR and its inhibitor GATOR) provides interesting avenues for future explorations. CONCLUSIONS Our results demonstrate that the transition from an active growth phase to a resting one is characterized by marked metabolic changes and provides evidence for the presence of signaling pathways related to intercellular communication.
Collapse
|
7
|
Zhang T, Huang J, Zhang Z, Lv J, Zhang D, Qing R, Lan L. Flow cytometry and 5-ethynyl-2'-deoxyuridine (EdU) labeling to detect the cell cycle dynamics of Phaeodactylum tricornutum under light. JOURNAL OF PHYCOLOGY 2022; 58:555-567. [PMID: 35352350 DOI: 10.1111/jpy.13250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Cell cycle studies in plants and algae are highly dependent on reliable methods for detecting cellular DNA replication. With its short growth cycle and ease of genetic transformation, Phaeodactylum tricornutum is an important model organism for the study of pennate diatoms. Here we explored two different methods to detect the cell cycle of P. tricornutum, one using SYBR-green I to via flow cytometry, and the other using EdU labeling to observe cell cycle changes under fluorescence microscopy. Both EdU labeling fluorescence microscopy and SYBR-green I staining flow cytometry accurately indicated that the cells of P. tricornutum enter the G2/M phase after 12 h of light exposure. The results indicate that SYBR Green I was an adequate detection method for nuclear DNA quantitation in cells of P. tricornutum using a flow cytometer and without RNase A treatment. In addition, EdU can be applied to P. tricornutum to reliably detect cell proliferation. Besides, Mg-ProtoIX was able to reverse the cell cycle division inhibition of P. tricornutum and allow the nuclear DNA replication to proceed normally. Taken together, the photoperiodic division time point was clearly identified, which sheds light on the regulation of cell division mechanism in P. tricornutum.
Collapse
Affiliation(s)
- Ting Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jingyi Huang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Zhixia Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jie Lv
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Dongqun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Renwei Qing
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Liqiong Lan
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| |
Collapse
|
8
|
Kulaš A, Gligora Udovič M, Tapolczai K, Žutinić P, Orlić S, Levkov Z. Diatom eDNA metabarcoding and morphological methods for bioassessment of karstic river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154536. [PMID: 35304150 DOI: 10.1016/j.scitotenv.2022.154536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/20/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Karst ecosystems play a unique role as exceptional natural habitats in sustaining biodiversity. This study focuses on diatoms, a diverse group of microeukaryotes in the periphytic community of a karstic river. In a multi-microhabitat study along the Krka River (Croatia), our goal was to obtain a detailed overview of diatom diversity and community structure using morphological and molecular approaches, and to assess the applicability of eDNA metabarcoding as a reliable tool for biomonitoring assessment. The results revealed a relatively low agreement in the diatom community composition between the two approaches, but also provided complementary information, with no differences in beta diversity detected between microhabitats. The SIMPER analysis underlined the importance of the molecular approach in identifying diatom community composition, due to errors in distinguishing between deposited diatom cells that occurred in the morphological analysis. In contrast, the morphological approach indicated a clear diatom community separation along the river with a strong location effect. Despite certain differences, both approaches provided a feasible assessment of the ecological status according to the relationship to environmental pressures, classifying the Krka River as High (morphological approach) or Good (molecular approach) throughout the most of its course. Moreover, diatom diversity based on both approaches provides a reliable dataset applicable in routine monitoring assessment and offers a deeper understanding of the presented ecological status. The incompleteness of a reference database presents one major drawback of the molecular approach, which needs further updating in order to improve routine diatom metabarcoding.
Collapse
Affiliation(s)
- Antonija Kulaš
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia.
| | - Marija Gligora Udovič
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Kálmán Tapolczai
- Premium Postdoctoral Research Program, Hungarian Academy of Sciences, Budapest, Hungary; Research Group of Limnology, Center for Natural Science, University of Pannonia, Egyetem u. 10, H-8200 Veszprém, Hungary; Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Klebelsberg Kuno u. 3, Tihany, Hungary
| | - Petar Žutinić
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Sandi Orlić
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean Region (STIM), HR-10000 Zagreb, Croatia
| | - Zlatko Levkov
- Institute of Biology, Faculty of Natural Science, Ss Cyril and Methodius University, Skopje, Macedonia
| |
Collapse
|