REVIEW | doi:10.20944/preprints202007.0328.v3
Subject: Biology And Life Sciences, Other Keywords: Evolution; Speciation; Crossbreeding; Hybridization; Species spectrum; Polyploidization; Somatic cell hybridization; Mutation
Online: 3 March 2022 (10:25:51 CET)
Although Darwin‘s evolutionary mutation theory has been widely accepted, many endeavors have been tried to challenge it. With more and more observation of successful hybridization and hybrids, the sexual isolation between species has become vague. The mechanism of evolution has been expanded from the classical model of evolution to multiple routes of speciation. Furthermore, a fundamental crossbreeding theory has been raised and proved by two lines of evidences: paleopolyploidy and fan-shaped spectrum of species. Ancient genome duplications are widespread throughout eukaryotic lineages, particularly in plants. The genome polyploidization, especially in the somatic cell hybridization, can break through the sexual incompatibility between diploid counterparts to hybridize and produce new species. By comparing characteristics, all species in every taxon, both in the extinct fossil and extant organisms, can be arranged into fan-shaped spectrum according to their similarity: left primitive type-middle advanced type-right primitive type. The species are primitive at the two ends and advanced at the middle. The primitive two species always resemble two types of more primitive species that can be confirmed as their ancestors respectively, and the middle species is half similar to the two ancestors respectively. These suggest that the species in the spectrum come from two different ancestors by crossbreeding and gene combination. As a sum, advanced species originated from crossbreeding of two primitive ancestors, by major method of polyploidization, and proved by results of fan-shaped spectrum of species. Then, sex is the cause, force and opportunity for evolution.
ARTICLE | doi:10.20944/preprints202304.0734.v1
Subject: Computer Science And Mathematics, Computer Networks And Communications Keywords: Federated Learning; Node Selection; Deep Reinforcement Learning; Multi-Objective; Model Performance
Online: 23 April 2023 (03:02:36 CEST)
As a new distributed machine learning (ML) approach, federated learning (FL) shows the great potential to preserve data privacy by enabling distributed data owners to collaboratively build a global model without sharing their raw data. However, the heterogeneity in terms of data distribution and hardware configurations make it hard to select participants from the thousands of nodes. In this paper, we propose a multi-objective node selection approach to improve time-to-accuracy performance while resisting malicious nodes. We firstly design a deep reinforcement learning assisted FL framework. Then the problem of multi-objective node selection under this framework is formulated as a Markov decision process (MDP), which aims to reduce the training time and improve model accuracy simultaneously. Finally, a deep Q-netwok (DQN) based algorithm is proposed to efficiently solve the optimal set of participants for each iteration. Simulation results show that the proposed method not only significantly improves the accuracy and training speed of FL, but has stronger robustness to resist malicious nodes.
ARTICLE | doi:10.20944/preprints202304.0885.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Nanozyme; Metallic nanocomposite; Bisphenol A; Electrochemical sensors
Online: 25 April 2023 (04:23:09 CEST)
A sensitive electrochemical sensor based on AuPtPd trimetallic nanoparticles functionalized multi-walled carbon nanotubes coupled with chitosan modified glassy carbon electrode (GCE/CS/MWCNTs-AuPtPd) for the rapid detection of bisphenol A (BPA) was proposed. AuPtPd trimetallic nanoparticles were first assembled on MWCNTs to obtain MWCNTs-AuPtPd nanocomposite. Then the MWCNTs-AuPtPd was further dispersed on the surface of chitosan modified electrode surface to fabricate the GCE/CS/MWCNTs-AuPtPd sensor. Due to the superior catalytic properties of MWCNTs-AuPtPd and the good film formation of chitosan, the constructed sensor displayed good performances for BPA detection. The structural morphology of CS/MWCNTs-AuPtPd was characterized by many methods, such as SEM, UV-vis and TEM. Under the optimal conditions, the designed sensor showed a linear range from 0.05 to 100 µM for BPA detecting with a low detection limit of 1.4 nM. The designed sensor was further used to realize the determination of BPA in real samples and the recoveries ranged from 94.4% to 103.6%. The results demonstrated that the electrochemical sensor designed by CS/MWCNTs-AuPtPd nanocomposites was reliable and could be a useful tool for the monitoring of food safety.
ARTICLE | doi:10.20944/preprints202309.0989.v1
Subject: Engineering, Bioengineering Keywords: RiPP; marine Streptomyces; phoU (SCO4228); wblA (SCO3579); SCO1712; orrA (SCO3008); gntR (SCO1678)
Online: 15 September 2023 (04:19:06 CEST)
Aborycin is a type I lasso peptide with a stable interlocked structure, offering a favorable framework for drug development. The aborycin biosynthetic gene cluster gul from marine sponge-associated Streptomyces sp. HNS054 was cloned and integrated into the chromosome of S. coelicolor hosts with different copies. The 3-copy gul-integration strains S. coelicolor M1346::3gul showed better production than one-copy or 2-copy gul-integration strains, and the total titer reached approximately 10.4 mg/L, i.e., 2.1 times that of the native strain. Then, five regulatory genes, phoU (SCO4228), wblA (SCO3579), SCO1712, orrA (SCO3008) and gntR (SCO1678), which were reported to have negative effects on secondary metabolism, were further knocked out from the M1346::3gul genome by CRISPR/Cas9 technology. While the ΔSCO1712 mutant showed a significant decrease (4.6 mg/L) and the ΔphoU mutant showed no significant improvement (12.1 mg/L) in aborycin production, the ΔwblA, ΔorrA and ΔgntR mutations significantly improved the aborycin titers to approximately 23.6 mg/L, 56.3 mg/L and 48.2 mg/L, respectively, which were among the highest heterologous yields for lasso peptides in both Escherichia coli systems and Streptomyces systems. Thus, this study provided important clues for future studies on enhancing antibiotic production in Streptomyces systems.
ARTICLE | doi:10.20944/preprints201811.0478.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Japanese encephalitis virus; drug repurposing; systems biology; antiviral agents
Online: 20 November 2018 (04:54:48 CET)
Japanese encephalitis is a zoonotic disease caused by Japanese encephalitis virus (JEV). It is mainly epidemic in Asia with an estimated 69,000 cases occurring per year. However, no approved agents are available for the treatment of JEV infection, and existing vaccines cannot resist various types of JEV strains. Drug repurposing is a new concept for finding new indication of existing drugs, and recently, it has been used to discover new antiviral agents. Identifying host proteins involved in the progress of JEV infection and using these proteins as targets are the center of drug repurposing for JEV infection. In this study, based on the gene expression data of JEV infection and the phenome-wide association study (PheWAS) data, we identified 286 genes participating in the progress of JEV infection using the systems biology methods. The enrichment analysis of these genes suggested that the genes identified by our methods were predominantly related to viral infection pathways and immune response-related pathways. We found that bortezomib which can target these genes may have potential effect on the treatment of JEV infection. Subsequently, we evaluated the antiviral activity of bortezomib using the JEV-infected mice model. The results showed that bortezomib can lower JEV-induced lethality in mice, alleviate suffering in JEV-infected mice and reduce the damage in brains caused by JEV infection. This work provides a new method for the development of antiviral agents.
ARTICLE | doi:10.20944/preprints202211.0176.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: prostate cancer; neuroendocrine prostate cancer; PET; DOTATATE
Online: 9 November 2022 (11:48:56 CET)
Objectives: Prostate cancer is well known to express high levels of somatostatin receptors and preliminary data suggests that PET imaging with the somatostatin analog, 68Ga-DOTATATE, may allow for whole body staging of patients with metastatic castration resistant prostate cancer (mCRPC) and neuroendocrine prostate cancer (NePC). This study explores the utility of 68Ga-DOTATATE PET-CT to identify metastatic deposits in men with mCRPC and NePC and prognosticate disease progression. Methods: 68Ga-DOTATATE PET-CT was performed in 17 patients with mCRPC and of those 2/17 had NePC. Semiquantitative analysis with standardized uptake values (SUV) (e.g. SUVmax, SUVmean) was performed for each metastatic lesion and reference background tissues. 68Ga-DOTATATE uptake in metastatic deposits was further classified as: mild (less than liver), moderate (up to liver average), or marked (greater than liver). Serial prostate-specific antigen measurements and patient survival were followed up to 3 years after PET imaging to assess response to standard of care treatment. Results: All patients had at least one metastic lesion with identifiable 68Ga-DOTATATE uptake. Marked 68Ga-DOTATATE uptake was found in 7/17 patients, including both NePC patients, and all were non-responders to systemic therapy and died within the follow up period, with a mean time to death of 8.1 months. 3 patients had mild 68Ga-DOTATATE uptake, and all were responders to systemic therapy and were alive 36 months after 68Ga-DOTATATE imaging. Conclusions: 68Ga-DOTATATE is able to identify mCRPC and NePC metastatic deposits, and lesions with 68Ga-DOTATATE uptake > liver may portend poor outcomes in patients with mCRPC.
ARTICLE | doi:10.20944/preprints201812.0293.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: human poly(ADP-ribose) polymerase 1 (PARP1), PARP-DNA complex,DNA-protein binding,DNA repair, 5′,8-Cyclopurine-2′-deoxynucleoside, DNA damage , DNA repair efficiency.
Online: 24 December 2018 (16:01:44 CET)
Abstract5′,8-Cyclo-2′-deoxyadenosine (cdA), in the 5′R and 5′Sdiastereomeric forms, are typical non strand-break oxidative DNA lesions, induced by hydroxyl radicals, with emerging importance as a molecular marker. These lesions are exclusively repaired by nucleotide excision repair (NER) mechanism with a low efficiency, thus readily accumulating in the genome. Poly(ADP-ribose) polymerase1 (PARP1) acts as an early responder to DNA damage and plays a key role as a nick sensor in the maintenance of the integrity of the genome by recognizing nicked DNA. So far, it was unknown whether the diastereomeric cdA lesions could induce specific PARP1 binding. Here we provide the first evidence of PARP1 to selectively recognize the diastereomeric lesions 5′S-cdA and 5′R-cdA in vitro as compared to deoxyadenosine in model DNA substrates (23-mers) by using circular dichroism,fluorescence spectroscopy, immunoblotting analysis and gel mobility shift assay. Several features of the recognition of the damaged and undamaged oligonucleotides by PARP1were characterized. Remarkably, PARP1 efficiently binds to both cdA lesions in the double stranded (ds)-oligonucleotides. In particular, PARP1 proved to bind 5′S-cdAwith a higher affinity constant for the 5'S lesion in a model of ds DNA than 5′R-cdA, showing different recognition patterns, also compared with undamaged dA. This new finding highlights the ability of PARP1 to recognize and differentiate the distorted DNA backbone in a biomimetic system caused by different diastereomeric forms of a cdA lesion.