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Article: Coevolutionary forces shaping the fitness of SARS-CoV-2 spike glycoprotein against human receptor ACE2

Priya, Prerna / Shanker, Asheesh

Infection, genetics, and evolution. 2021 Jan., v. 87

2021

Abstract: The current global health problem caused by SARS-CoV-2 has challenged the scientific community in various ways. Therefore, worldwide several scientific groups are exploring SARS-CoV-2 from different aspects including its origin, spread, severe ... ...

Abstract	The current global health problem caused by SARS-CoV-2 has challenged the scientific community in various ways. Therefore, worldwide several scientific groups are exploring SARS-CoV-2 from different aspects including its origin, spread, severe infectivity, and also to find a cure. It is now well known that spike glycoprotein helps SARS-CoV-2 to enter inside the human host through a cellular receptor ACE2. However, the role of coevolutionary forces that makes SARS-CoV-2 spike glycoprotein more fit towards its human host remains unexplored. Therefore, in present bioinformatics study we identify coevolving amino acids in spike glycoprotein. Additionally, the effects of coevolution on the stability of the spike glycoprotein as well as its binding with receptor ACE2 were predicted. The results clearly indicate that coevolutionary forces play a pivotal role in increasing the fitness of spike glycoprotein against ACE2.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; bioinformatics ; coevolution ; genetics ; glycoproteins ; humans ; infection ; pathogenicity
Language	English
Dates of publication	2021-01
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2020.104646
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2.

Priya, Prerna / Basit, Abdul / Bandyopadhyay, Pradipta

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 13, Page(s) 6191–6202

Abstract: The SARS-CoV-2 virus has caused high-priority health concerns at a global level. Vaccines have stalled the proliferation of viruses to some extent. Yet, the emergence of newer, potentially more infectious, and dangerous mutants such as Delta and Omicron ... ...

Abstract	The SARS-CoV-2 virus has caused high-priority health concerns at a global level. Vaccines have stalled the proliferation of viruses to some extent. Yet, the emergence of newer, potentially more infectious, and dangerous mutants such as Delta and Omicron are among the major challenges in finding a more permanent solution for this pandemic. The effectiveness of antivirals Molnupiravir and Paxlovid, authorized for emergency use by the FDA, are yet to be assessed on a larger population. Patients with a high risk of disease progression have received treatment with antibody-cocktail. Most of the mutations leading to the new lineage of SARS-CoV-2 are found in the spike protein of this virus that plays a key role in facilitating host entry. The current study has investigated how to modify a promising peptide-based inhibitor of spike protein, LCB3, against common mutations, N501Y and K417N in the target protein so that it retains its efficacy against the spike protein. LCB3 being a prototype for protein-based inhibitors is an ideal testing system to learn about protein-based inhibitors. This study proposes the substitutions of amino acid residues of LCB3 inhibitor using a structure-based approach that considers free energy decomposition of residues, the distance between atoms, and the interaction among amino acids. The binding free energy calculations suggest a possible improvement in the binding affinity of existing inhibitor LCB3 to the mutant forms of the S-protein using simple substitutions at specific positions of the inhibitor. This approach, being general, can be used in different inhibitors and other mutations and help in fighting against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; COVID-19 ; Peptides ; Amino Acids ; Protein Binding ; Mutation
Chemical Substances	nirmatrelvir and ritonavir drug combination ; spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Peptides ; Amino Acids
Language	English
Publishing date	2022-07-26
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2103587
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Article: Neuropalliative Care in India - Barriers, Challenges and Future Directions.

Baruah, Upasana / Sharma, Prerna / Thomas, Priya Treesa / Dhamija, Rajinder K

Annals of Indian Academy of Neurology

2023 Volume 26, Issue 2, Page(s) 107–111

Abstract: Neuropalliative care is an emerging sub-specialty of neurology and palliative care that aims to relieve suffering from symptoms, reduce distress and improve the quality of life of people with life-limiting neurological conditions and their family ... ...

Abstract	Neuropalliative care is an emerging sub-specialty of neurology and palliative care that aims to relieve suffering from symptoms, reduce distress and improve the quality of life of people with life-limiting neurological conditions and their family caregivers. As advances are being made in the prevention, diagnosis, and treatment of neurological illnesses, there is an increasing need to guide and support patients and their families through complex choices involving immense uncertainty and important life-changing outcomes. The unmet need for palliative care in neurological illnesses is high, especially in a low-resource setting like India. This article discusses the scope of neuropalliative care in India, the barriers and challenges that impede the specialty's development, and the factors that could facilitate the development and scale-up delivery of neuropalliative services. The article also attempts to highlight priority areas for advancing neuropalliative care in India which include context-specific assessment tools, sensitization of the healthcare system, identification of intervention outcomes, the need for developing culturally sensitive models based on home-based or community-based care, evidence-based practices, and development of manpower and training resources.
Language	English
Publishing date	2023-03-17
Publishing country	India
Document type	Journal Article
ZDB-ID	2240174-X
ISSN	1998-3549 ; 0972-2327
ISSN (online)	1998-3549
ISSN	0972-2327
DOI	10.4103/aian.aian_1021_22
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Article ; Online: Coevolutionary forces shaping the fitness of SARS-CoV-2 spike glycoprotein against human receptor ACE2.

Priya, Prerna / Shanker, Asheesh

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2020 Volume 87, Page(s) 104646

Abstract	The current global health problem caused by SARS-CoV-2 has challenged the scientific community in various ways. Therefore, worldwide several scientific groups are exploring SARS-CoV-2 from different aspects including its origin, spread, severe infectivity, and also to find a cure. It is now well known that spike glycoprotein helps SARS-CoV-2 to enter inside the human host through a cellular receptor ACE2. However, the role of coevolutionary forces that makes SARS-CoV-2 spike glycoprotein more fit towards its human host remains unexplored. Therefore, in present bioinformatics study we identify coevolving amino acids in spike glycoprotein. Additionally, the effects of coevolution on the stability of the spike glycoprotein as well as its binding with receptor ACE2 were predicted. The results clearly indicate that coevolutionary forces play a pivotal role in increasing the fitness of spike glycoprotein against ACE2.
MeSH term(s)	Angiotensin-Converting Enzyme 2/metabolism ; Biological Evolution ; Humans ; Protein Binding ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; SARS-CoV-2/physiology ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/physiology ; Virulence
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2020-11-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2020.104646
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Article ; Online: Shear stress and microRNAs for better metastatic cancer management.

KrishnaPriya, Siluveru / Nair, Pallavi S / Bhalla, Prerna / Karunagaran, D / Suraishkumar, G K

Biotechnology progress

2023 Volume 40, Issue 1, Page(s) e3396

Abstract: Metastasis is the process by which cancer cells move from the primary location to establish themselves in a new location in the human body. It is still a significant challenge in cancer management because it is responsible for 90% of cancer-related ... ...

Abstract	Metastasis is the process by which cancer cells move from the primary location to establish themselves in a new location in the human body. It is still a significant challenge in cancer management because it is responsible for 90% of cancer-related deaths. In this work, we present an idea to use shear stress encountered by all metastasizing cells as an elegant means to deactivate metastasizing cancer cells. Shear-induced ROS and cross-talk between ROS and miRNA play crucial roles in deactivating metastasizing cancer cells. In addition, there exists a vast therapeutic potential for miRNAs. Therefore, this study explores the effect of shear on miRNAs and reactive oxygen species (ROS), the two molecular mediators in the proposed {shear-stress}-{miRNA}-{metastasizing-cancer-cell-deactivation} approach. In this context, to understand the effect of defined shear on HCT116 colon cancer cells, they were cultivated in a defined shear environment provided by an appropriately designed and fabricated cone-and-plate device. Shear rate affected the culture growth characteristics and the specific intracellular reactive oxygen species level (si-ROS). HCT116 cell growth was observed at 0 and 0.63 s
MeSH term(s)	Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Reactive Oxygen Species/metabolism ; Colonic Neoplasms ; Down-Regulation ; HCT116 Cells ; RNA, Messenger
Chemical Substances	MicroRNAs ; Reactive Oxygen Species ; RNA, Messenger
Language	English
Publishing date	2023-10-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	165657-0
ISSN	1520-6033 ; 8756-7938
ISSN (online)	1520-6033
ISSN	8756-7938
DOI	10.1002/btpr.3396
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Article ; Online: Coevolution based immunoinformatics approach considering variability of epitopes to combat different strains: A case study using spike protein of SARS-CoV-2.

Mishra, Saurav Kumar / Priya, Prerna / Rai, Gyan Prakash / Haque, Rizwanul / Shanker, Asheesh

Computers in biology and medicine

2023 Volume 163, Page(s) 107233

Abstract: In the recent past several vaccines were developed to combat the COVID-19 disease. Unfortunately, the protective efficacy of the current vaccines has been reduced due to the high mutation rate in SARS-CoV-2. Here, we successfully implemented a ... ...

Abstract	In the recent past several vaccines were developed to combat the COVID-19 disease. Unfortunately, the protective efficacy of the current vaccines has been reduced due to the high mutation rate in SARS-CoV-2. Here, we successfully implemented a coevolution based immunoinformatics approach to design an epitope-based peptide vaccine considering variability in spike protein of SARS-CoV-2. The spike glycoprotein was investigated for B- and T-cell epitope prediction. Identified T-cell epitopes were mapped on previously reported coevolving amino acids in the spike protein to introduce mutation. The non-mutated and mutated vaccine components were constructed by selecting epitopes showing overlapping with the predicted B-cell epitopes and highest antigenicity. Selected epitopes were linked with the help of a linker to construct a single vaccine component. Non-mutated and mutated vaccine component sequences were modelled and validated. The in-silico expression level of the vaccine constructs (non-mutated and mutated) in E. coli K12 shows promising results. The molecular docking analysis of vaccine components with toll-like receptor 5 (TLR5) demonstrated strong binding affinity. The time series calculations including root mean square deviation (RMSD), radius of gyration (RGYR), and energy of the system over 100 ns trajectory obtained from all atom molecular dynamics simulation showed stability of the system. The combined coevolutionary and immunoinformatics approach used in this study will certainly help to design an effective peptide vaccine that may work against different strains of SARS-CoV-2. Moreover, the strategy used in this study can be implemented on other pathogens.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/prevention & control ; Molecular Docking Simulation ; COVID-19 Vaccines ; Spike Glycoprotein, Coronavirus/chemistry ; Escherichia coli ; Viral Vaccines/chemistry ; Epitopes, T-Lymphocyte/chemistry ; Vaccines, Subunit/chemistry ; Computational Biology/methods
Chemical Substances	COVID-19 Vaccines ; spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Viral Vaccines ; Epitopes, T-Lymphocyte ; Vaccines, Subunit
Language	English
Publishing date	2023-07-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2023.107233
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Article ; Online: A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2

Priya, Prerna / Basit, Abdul / Bandyopadhyay, Pradipta

bioRxiv

Abstract: SARS-CoV-2 virus has caused high-priority health concerns at a global level. Vaccines have stalled the proliferation of viruses to some extent. Yet, the emergence of newer, potentially more infectious, and dangerous mutants such as delta and omicron are ... ...

Abstract	SARS-CoV-2 virus has caused high-priority health concerns at a global level. Vaccines have stalled the proliferation of viruses to some extent. Yet, the emergence of newer, potentially more infectious, and dangerous mutants such as delta and omicron are among the major challenges in finding a more permanent solution for this pandemic. The effectiveness of antivirals Molnupiravir and Paxlovid, authorized for emergency use by the FDA, are yet to be assessed at larger populations. Patients with a high risk of disease progression or hospitalization have received treatment with a combination of antibodies (antibody-cocktail). Most of the mutations leading to the new lineage of SARS-CoV-2 are found in the spike protein of this virus that plays a key role in facilitating host entry. The current study has investigated how to modify a promising peptide-based inhibitor of spike protein, LCB3, against common mutations in the target protein so that it retains its efficacy against the spike protein. LCB3 being a prototype for protein-based inhibitors is an ideal testing system to learn about protein-based inhibitors. Two common mutations N501Y and K417N are considered in this work. Using a structure-based approach that considers free energy decomposition of residues, distance, and the interactions between amino acids, we propose the substitutions of amino acid residues of LCB3 inhibitors. Our binding free energy calculations suggest a possible improvement in the binding affinity of existing inhibitor LCB3 to the mutant forms of the S-protein using simple substitutions at specific positions of the inhibitor. This approach, being general, can be used in different inhibitors and other mutations and help in fighting against SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2022-02-28
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.02.27.482153
Database	COVID19

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Article ; Online: Impact of D-dimer levels on no-reflow phenomenon following percutaneous coronary intervention for ST-elevation myocardial infarction: a meta-analysis.

Jain, Akhil / Desai, Rupak / Shenwai, Priya / Akah, Ozo / Bansal, Prerna / Ghimire, Samir / Ghimire, Shristee / Vyas, Ankit / Gupta, Puneet / Badheka, Apurva

Acta cardiologica

2022 Volume 78, Issue 8, Page(s) 970–973

MeSH term(s)	Humans ; ST Elevation Myocardial Infarction/diagnosis ; ST Elevation Myocardial Infarction/surgery ; No-Reflow Phenomenon/diagnosis ; No-Reflow Phenomenon/etiology ; Percutaneous Coronary Intervention/adverse effects ; Fibrin Fibrinogen Degradation Products ; Coronary Angiography
Chemical Substances	fibrin fragment D ; Fibrin Fibrinogen Degradation Products
Language	English
Publishing date	2022-07-05
Publishing country	England
Document type	Meta-Analysis ; Journal Article
ZDB-ID	390197-x
ISSN	1784-973X ; 0001-5385
ISSN (online)	1784-973X
ISSN	0001-5385
DOI	10.1080/00015385.2022.2097346
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Article ; Online: The long unstructured region of Bcl-xl modulates its structural dynamics.

Priya, Prerna / Maity, Atanu / Ghosh Dastidar, Shubhra

Proteins

2017 Volume 85, Issue 8, Page(s) 1567–1579

Abstract: Bcl-xl protein has a long unstructured loop attached to its structured region which joins two helices. The necessity to have this unstructured segment in Bcl-xl is not yet well understood. To what extent the unstructured segment can influence the ... ...

Abstract	Bcl-xl protein has a long unstructured loop attached to its structured region which joins two helices. The necessity to have this unstructured segment in Bcl-xl is not yet well understood. To what extent the unstructured segment can influence the dynamics of the structured region of protein, with potential to influence the function, has been investigated in this work. Molecular dynamics simulation and principal component analysis show how the loop affects the internal motions of the protein, particularly its ligand binding pocket. Generally an unstructured region in the structure would promote flexibility resulting entropic stability but in contrary, here it narrows down the conformational space of the structured region of protein that could be hypothesized to impact the functional precision. Effects of the loop propagate to the binding pocket through structural rearrangements of polar side chains. The immediate suspicion of possible impact of phosphorylation to modulate the function of the protein is proven to be a fact, as the phosphorylated S49 and S62 located on the large unstructured region are seen to perturb the electrostatic network of the structure; an observation that validates and clarifies the role of loop as a modulator through biophysical and biochemical mechanisms. Proteins 2017; 85:1567-1579. © 2017 Wiley Periodicals, Inc.
MeSH term(s)	Binding Sites ; Humans ; Ligands ; Molecular Dynamics Simulation ; Phosphorylation ; Principal Component Analysis ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Static Electricity ; Thermodynamics ; bcl-X Protein/chemistry ; bcl-X Protein/metabolism
Chemical Substances	BCL2L1 protein, human ; Ligands ; bcl-X Protein
Language	English
Publishing date	2017-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.25316
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Article ; Online: Physical interaction between nuclear accumulated CC-NB-ARC-LRR protein and WRKY64 promotes EDS1 dependent Fusarium wilt resistance in chickpea.

Chakraborty, Joydeep / Priya, Prerna / Dastidar, Shubhra Ghosh / Das, Sampa

Plant science : an international journal of experimental plant biology

2018 Volume 276, Page(s) 111–133

Abstract: Fusarium wilt is one of the most serious diseases affecting chickpea (Cicer arietinum L.). Here, we identified a putative Resistance Gene Analog (CaRGA) from chickpea, encoding a coiled-coil (CC) nucleotide-binding oligomerization domain (NB-ARC) ... ...

Abstract	Fusarium wilt is one of the most serious diseases affecting chickpea (Cicer arietinum L.). Here, we identified a putative Resistance Gene Analog (CaRGA) from chickpea, encoding a coiled-coil (CC) nucleotide-binding oligomerization domain (NB-ARC) containing leucine-rich repeat (LRR) protein (CC-NLR protein) that confers resistance against Fusarium oxysporum f. sp. ciceri race1 (Foc1). Over-expression and silencing of CaRGA in chickpea resulted in enhanced resistance and hyper-susceptibility, respectively against Foc1. Furthermore, defense response to Foc1 depends on CC-NLR interaction with WRKY64 transcription factor. CaRGA mediated wilt resistance largely compromised when WRKY64 was silenced. We also determined in planta intramolecular interactions and self-association of chickpea CC-NLR protein. The study shows CC domain suppressing auto-activation of the full-length CC-NLR protein in the absence of pathogen through self-inhibitory intramolecular interaction with NB-ARC domain, which is attenuated by self-interactions to LRR domain. Chickpea CC-NLR protein forms homocomplexes and then interacts with WRKY64. CC-NLR protein further phosphorylates WRKY64 thereby, ubiquitination and proteasome mediated degradation are protected. Phosphorylated WRKY64 with increased stability binds to EDS1 promoter and stimulates its transcription that induces in planta ectopic cell-death. The detailed analysis of CC-NLR and WRKY interactions provide a better understanding of the immune regulation by NLR proteins under biotic stresses.
MeSH term(s)	Cicer/genetics ; Cicer/immunology ; Cicer/physiology ; Disease Resistance ; Fusarium/growth & development ; Fusarium/physiology ; Gene Expression Regulation, Plant ; Glucans/metabolism ; Host-Pathogen Interactions ; NLR Proteins/genetics ; NLR Proteins/metabolism ; Phylogeny ; Plant Diseases/immunology ; Plant Diseases/microbiology ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Protein Domains ; Signal Transduction
Chemical Substances	Glucans ; NLR Proteins ; Plant Proteins ; callose (9064-51-1)
Language	English
Publishing date	2018-08-22
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	742010-9
ISSN	1873-2259 ; 0168-9452
ISSN (online)	1873-2259
ISSN	0168-9452
DOI	10.1016/j.plantsci.2018.08.008
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