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Source code for STORE model
Kildekode for STORE-modellen
Thomas A. Adams II
November 15, 2022 (v2)
Subject: Biosystems
Keywords: Computational Biology, Dynamic Modelling, Matlab, Omentum, Particle Swarm Optimization, Stochastic Modelling, Vaccine
This is the source code for the STORE (STochasic Omentum REsponse) model. The model is used to simulate how naive T-cells in the omentum will prime and multiply during the expansion period (8 days) after a T-cell vaccination in a mouse.

This is the matlab source code used in the following paper:

Christian DA, Adams TA II, Smith TA, Shallberg LA, Theisen DJ, Phan AT, Abraha M, Perry J, Ruthel G, Clark JT, Murphy KM, Kedl, RM, Hunter CA. cDC1 coordinate innate and adaptive responses in the omentum required for T cell priming and memory. Science Immunology 7, eabq7432 (2022).

This is fixed legacy code used for the paper for scientific auditing and reproduction purposes. See paper for documentation.
Proprotein Convertase Subtilisin/Kexin Type 9 Gene Variants in Familial Hypercholesterolemia: A Systematic Review and Meta-Analysis
Nang Hoang Pham, Phuong Kim Truong, Thuan Duc Lao, Thuy Ai Huyen Le
November 6, 2022 (v1)
Subject: Biosystems
Keywords: familial hypercholesterolemia, meta-analysis, mutation, PCSK9 gene
Proprotein Convertase Subtilisin Kexin type 9 (PCSK9), comprises 12 exons, encoded for an enzyme which plays a critical role in the regulation of circulating low density lipoprotein. The gain-of-function (GOF) mutations aggravate the degradation of LDL receptors, resulting in familial hypercholesterolemia (FH), while loss-of-function (LOF) mutations lead to higher levels of the LDL receptors, lower the levels of LDL cholesterol, and preventing from cardiovascular diseases. It is noted that, previous publications related to the mutations of PCSK9 were not always unification. Therefore, this study aims to present the spectrum and distribution of PCSK9 gene mutations by a meta-analysis. A systematic literature analysis was conducted based on previous studies published by using different keywords. The weighted average frequency of PCSK9 mutation was calculated and accessed by MedCalc®. A total of 32 cohort studies, that included 19,725 familial hypercholesterolemia blood samples, were enro... [more]
Extracellular Vesicle Transportation and Uptake by Recipient Cells: A Critical Process to Regulate Human Diseases
Zhi Hao Kwok, Chenghao Wang, Yang Jin
October 31, 2022 (v1)
Subject: Biosystems
Keywords: endocytosis, extracellular vesicles, uptake specificity
Emerging evidence highlights the relevance of extracellular vesicles (EVs) in modulating human diseases including but not limited to cancer, inflammation, and neurological disorders. EVs can be found in almost all types of human body fluids, suggesting that their trafficking may allow for their targeting to remote recipient cells. While molecular processes underlying EV biogenesis and secretion are increasingly elucidated, mechanisms governing EV transportation, target finding and binding, as well as uptake into recipient cells remain to be characterized. Understanding the specificity of EV transport and uptake is critical to facilitating the development of EVs as valuable diagnostics and therapeutics. In this mini review, we focus on EV uptake mechanisms and specificities, as well as their implications in human diseases.
Multi-Enzyme Systems in Flow Chemistry
Pedro Fernandes, Carla C. C. R. de Carvalho
October 13, 2022 (v1)
Subject: Biosystems
Keywords: immobilization, microreactor, reaction cascade, scale-up, whole cell
Recent years have witnessed a growing interest in the use of biocatalysts in flow reactors. This merging combines the high selectivity and mild operation conditions typical of biocatalysis with enhanced mass transfer and resource efficiency associated to flow chemistry. Additionally, it provides a sound environment to emulate Nature by mimicking metabolic pathways in living cells and to produce goods through the systematic organization of enzymes towards efficient cascade reactions. Moreover, by enabling the combination of enzymes from different hosts, this approach paves the way for novel pathways. The present review aims to present recent developments within the scope of flow chemistry involving multi-enzymatic cascade reactions. The types of reactors used are briefly addressed. Immobilization methodologies and strategies for the application of the immobilized biocatalysts are presented and discussed. Key aspects related to the use of whole cells in flow chemistry are presented. The... [more]
Biofunctional Peptide-Modified Extracellular Vesicles Enable Effective Intracellular Delivery via the Induction of Macropinocytosis
Ikuhiko Nakase
October 13, 2022 (v1)
Subject: Biosystems
Keywords: biofunctional peptides, exosomes, intracellular delivery systems, macropinocytosis
We previously reported that macropinocytosis (accompanied by actin reorganization, ruffling of the plasma membrane, and engulfment of large volumes of extracellular fluid) is an important process for the cellular uptake of extracellular vesicles, exosomes. Accordingly, we developed techniques to induce macropinocytosis by the modification of biofunctional peptides on exosomal membranes, thereby enhancing their cellular uptake. Arginine-rich cell-penetrating peptides have been shown to induce macropinocytosis via proteoglycans; accordingly, we developed peptide-modified exosomes that could actively induce macropinocytotic uptake by cells. In addition, the activation of EGFR induces macropinocytosis; based on this knowledge, we developed artificial leucine-zipper peptide (K4)-modified exosomes. These exosomes can recognize E3 sequence-fused EGFR (E3-EGFR), leading to the clustering and activation of E3-EGFR by coiled-coil formation (E3/K4), which induces cellular exosome uptake by macrop... [more]
Construction of an Artificial Cell Capable of Protein Expression at Low Temperatures Using a Cell Extract Derived from Pseudomonas fluorescens
Mana Fukumoto, Taishi Tonooka
October 12, 2022 (v1)
Subject: Biosystems
Keywords: artificial cell, cell-free protein expression, liposome, Pseudomonas fluorescens
A liposome-based artificial cell (LBAC) consists of a liposome encapsulating a cell-free protein expression system (CFPES) and protein-encoding DNA. It is surrounded by a lipid bilayer membrane and synthesizes proteins that resemble actual cells. Hence, they have been one of the most studied artificial cells. According to recent studies, they have been able to sense bio-functional molecules by synthesizing fluorescent proteins in response to target molecules. Therefore, they are expected to be used as biosensors. However, previously reported LBACs encapsulated the CFPES derived from Escherichia coli, resulting in the most productive protein expression at 20−40 °C. To broaden the range of their working temperatures to lower temperatures, in this study, we constructed LBACs using a CFPES derived from Pseudomonas fluorescens that grows at a temperature range of 4 °C to 30 °C. We then demonstrated that the constructed LBAC expressed proteins at 8 °C and that, the protein expression capabil... [more]
Identifying Shared Risk Genes between Nonalcoholic Fatty Liver Disease and Metabolic Traits by Cross-Trait Association Analysis
Hongping Guo, Zuguo Yu
January 24, 2022 (v1)
Subject: Biosystems
Keywords: metabolic trait, nonalcoholic fatty liver disease, shared gene
Nonalcoholic fatty liver disease (NAFLD) generally co-occurs with metabolic disorders, but it is unclear which genes have a pleiotripic effect on NAFLD and metabolic traits. We performed a large-scale cross-trait association analysis to identify the overlapping genes between NAFLD and nine metabolic traits. Among all the metabolic traits, we found that obesity and type II diabetes are associated with NAFLD. Then, a multitrait association analysis among NAFLD, obesity and type II diabetes was conducted to improve the overall statistical power. We identified 792 significant variants by a cross-trait meta-analysis involving 100 pleiotripic genes. Moreover, we detected another two common genes by a genome-wide gene test. The results from the pathway enrichment analysis show that the 102 shared risk genes are enriched in cancer, diabetes, insulin secretion, and other related pathways. This study can help us understand the molecular mechanisms underlying comorbid NAFLD and metabolic disorder... [more]
Centrifugal Microfluidic Integration of 4-Plex ddPCR Demonstrated by the Quantification of Cancer-Associated Point Mutations
Franziska Schlenker, Elena Kipf, Nadine Borst, Nils Paust, Roland Zengerle, Felix von Stetten, Peter Juelg, Tobias Hutzenlaub
January 24, 2022 (v1)
Subject: Biosystems
Keywords: centrifugal step emulsification, digital droplet polymerase chain reaction (ddPCR), droplet fluorescence evaluation, droplet stability, microfluidics, multiplexing
We present the centrifugal microfluidic implementation of a four-plex digital droplet polymerase chain reaction (ddPCR). The platform features 12 identical ddPCR units on a LabDisk cartridge, each capable of generating droplets with a diameter of 82.7 ± 9 µm. By investigating different oil−surfactant concentrations, we identified a robust process for droplet generation and stabilization. We observed high droplet stability during thermocycling and endpoint fluorescence imaging, as is required for ddPCRs. Furthermore, we introduce an automated process for four-color fluorescence imaging using a commercial cell analysis microscope, including a customized software pipeline for ddPCR image evaluation. The applicability of ddPCRs is demonstrated by the quantification of three cancer-associated KRAS point mutations (G12D, G12V and G12A) in a diagnostically relevant wild type DNA background. The four-plex assay showed high sensitivity (3.5−35 mutant DNA copies in 15,000 wild type DNA copies) a... [more]
A Fructan Sucrase Secreted Extracellular and Purified in One-Step by Gram-Positive Enhancer Matrix Particles
Jingyue Wang, Huazhi Xiao, Fangkun Zhao, Bo Zhao, Min Xu, Zhijiang Zhou, Ye Han
December 6, 2021 (v1)
Subject: Biosystems
Keywords: Bacillus subtilis, Escherichia coli, fructan sucrase, secretory expression
Fructan sucrase is a kind of biological enzyme that catalyzes the synthesis of fructan, and fructan is a polysaccharide product with important industrial application value. In this study, the Fructan sucrase gene of Bacillus subtilis was cloned to plasmid PET-28A-ACMA-Z, and three clones were obtained after the transformation of Escherichia coli BL21, namely BS-FF, BSO, and BS. The clones BS-FF and BSO secreted the recombinant enzymes outside the cells, while the clone BS expressed them inside the cells. The induction experiment results showed that the optimum IPTG concentration in the medium was 0.5 mM and 1.0 mM for clones BS-FF and BSO, respectively, while the incubation conditions were at 28 °C for 8 h. The recombinant fructan sucrase was purified one step using a material called GEM particles. The results indicated that 95.25% of fructan sucrase expressed by the clone BS-FF could be secreted into the extracellular area, and even 98.78% by the clone BSO. With the above purification... [more]
Set Membership Estimation for Dynamic Flux Balance Models
Xin Shen, Hector Budman
October 21, 2021 (v1)
Subject: Biosystems
Keywords: dynamic flux balance model, multiparametric programming, multiplicity, set membership estimation, variable structure system, weighted primal dual method
A set membership estimator (SME) based on limited number of measurements is proposed for estimating metabolite concentrations using dynamic flux balance models (DFBMs). To deal with multiplicity of solutions of the DFBM, a weighted primal dual method is used to find solutions that best fit the data. Multiparametric nonlinear programming is applied to propagate uncertainty in initial concentrations along a batch/fed-batch operation. The proposed method has been applied to E. coli batch and fed-batch fermentation without noise.
Towards the Development of a Diagnostic Test for Autism Spectrum Disorder: Big Data Meets Metabolomics
Juergen Hahn
October 21, 2021 (v1)
Subject: Biosystems
Keywords: autism spectrum disorder, fisher discriminant analysis, kernel partial least squares
Autism Spectrum Disorders (ASD) are a group of neurological disorders that present with limited social communication/interaction and restricted, repetitive behaviors/interests. The current estimate is that approximately 1.9% of children in the US are diagnosed with ASD. While this is a high prevalence and the economic burden by ASD is significant, there is still considerable debate regarding the underlying pathophysiology of ASD. Because of this lack of biological knowledge, autism diagnoses are restricted to observational behavioral and psychometric tools. This work takes a step towards the goal of incorporating bio-chemical data into ASD diagnosis by analyzing measurements of metabolite concentrations of the folate-dependent one-carbon metabolism and transulfuration pathways. Unlike traditional approaches that are based upon comparing differences in individual metabolite concentrations between children with and without an ASD diagnosis, we made use of multivariate classification via... [more]
Dynamic Modelling of T Cell Vaccination Response
Alisa Douglas, Thomas A Adams II, David A Christian
October 21, 2021 (v1)
Subject: Biosystems
Keywords: Dynamic Modelling, stochastic modelling, T cells, vaccine
In our previous work, a mathematical, agent-based dynamic model was developed which simulates the response of the mammalian omentum to a T cell vaccine injection during the expansion phase. The model tracks how each individual naïve T cell interacts with antigen presenting cells, and subsequently primes and divides over an 8-day period following vaccine injection. The model works from first principles; individual phenomena based on experimental observation and theory are incorporated into the model, and the collection of many such phenomena together create a nuanced model of the system as a whole. In this work, we show that the model works well in other relevant tissues, such as the spleen.
Ozone Sterilization of N95 Masks
Mohammad Irfan Malik, Karen Bechwaty, François Guitzhofer, Inès Esma Achouri
October 21, 2021 (v1)
Subject: Biosystems
Keywords: COVID-19, N95 mask, organic compounds, ozone disinfectant
The rapid spread of the COVID-19 worldwide pandemic at the beginning of 2020 has significantly affect-ed the global economy with severe human and economic losses. Despite the shortage of personal protective equipment, the facemask serves as a fundamental means to protect health care professionals' and re-strict the spread of the coronavirus. However, due to the limited stock of facemasks, many sterilization methods were developed to eliminate the infection and established strategies for fast and repeated reuse without affecting the filtration efficiency. The current study extrapolates the effective utilization of the ozonic sterilization of the N95 mask. First, we demonstrated the potential of ozone as a disinfectant that successfully destructs the organic food colour compounds deposited on the N95 mask; In the quantitative part of this research, the N95 facemask pieces were soaked in diphenylamine solution and later oxidized with ozone under the different intervals of time. Finally,... [more]
Green Synthesis of Copper Oxide Nanoparticles Using Protein Fractions from an Aqueous Extract of Brown Algae Macrocystis pyrifera
Karla Araya-Castro, Tzu-Chiao Chao, Benjamín Durán-Vinet, Carla Cisternas, Gustavo Ciudad, Olga Rubilar
October 14, 2021 (v1)
Subject: Biosystems
Keywords: brown seaweed, copper oxide nanoparticles, green synthesis, proteins, size exclusion chromatography
Amongst different living organisms studied as potential candidates for the green synthesis of copper nanoparticles, algal biomass is presented as a novel and easy-to-handle method. However, the role of specific biomolecules and their contribution as reductant and capping agents has not yet been described. This contribution reports a green synthesis method to obtain copper oxide nanoparticles (CuO-NPs) using separated protein fractions from an aqueous extract of brown algae Macrocystis pyrifera through size exclusion chromatography (HPLC-SEC). Proteins were detected by a UV/VIS diode array, time-based fraction collection was carried out, and each collected fraction was used to evaluate the synthesis of CuO-NPs. The characterization of CuO-NPs was evaluated by Dynamic Light Scattering (DLS), Z-potential, Fourier Transform Infrared (FTIR), Transmission Electron Microscope (TEM) equipped with Energy Dispersive X-ray Spectroscopy (EDS) detector. Low Molecular Weight (LMW) and High Molecular... [more]
Encapsulation of Lactoferrin for Sustained Release Using Particles from Gas-Saturated Solutions
Kento Ono, Hiroki Sakai, Shinichi Tokunaga, Tanjina Sharmin, Taku Michael Aida, Kenji Mishima
October 14, 2021 (v1)
Subject: Biosystems
Keywords: enteric polymer, gastric digestion, lactoferrin, PGSS, shellac
The particles from gas saturated solutions (PGSS) process were performed to encapsulate lactofer-rin, an iron-binding milk glycoprotein, using supercritical carbon dioxide (scCO2). A natural en-teric polymer, shellac, was used as a coating material of lactoferrin carried out by the PGSS pro-cess. Conditions were optimized by applying different temperatures (20−50 °C) and pressures (8−10 MPa) and the particles were evaluated for particle shape and size, lactoferrin encapsulation ef-ficiency, Fourier transform infrared (FTIR) spectroscopy to confirm lactoferrin entrapment and in vitro dissolution studies at different pH values. Particles with an average diameter of 75.5 ± 7 μm were produced with encapsulation efficiency up to 71 ± 2%. Furthermore, particles that showed high stability in low pH (pH 1.2) and a sustained release over time (t2h = 75%) in higher pH (pH 7.4) suggested an effective encapsulation process for the protection of lactoferrin from gastric di-gestion.
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
Outi M. H. Salo-Ahen, Ida Alanko, Rajendra Bhadane, Alexandre M. J. J. Bonvin, Rodrigo Vargas Honorato, Shakhawath Hossain, André H. Juffer, Aleksei Kabedev, Maija Lahtela-Kakkonen, Anders Støttrup Larsen, Eveline Lescrinier, Parthiban Marimuthu, Muhammad Usman Mirza, Ghulam Mustafa, Ariane Nunes-Alves, Tatu Pantsar, Atefeh Saadabadi, Kalaimathy Singaravelu, Michiel Vanmeert
October 14, 2021 (v1)
Subject: Biosystems
Keywords: binding free energy, computational pharmaceutics, computer-aided drug design, conformational ensemble, drug formulations, drug targets, enhanced sampling methods, ligand binding kinetics, membrane interactions, protein flexibility
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels a... [more]
LC-UV and UPLC-MS/MS Methods for Analytical Study on Degradation of Three Antihistaminic Drugs, Ketotifen, Epinastine and Emedastine: Percentage Degradation, Degradation Kinetics and Degradation Pathways at Different pH
Anna Gumieniczek, Izabela Kozak, Paweł Żmudzki, Urszula Hubicka
October 14, 2021 (v1)
Subject: Biosystems
Keywords: degradation in solutions, epinastine and emedastine, ketotifen, LC-UV and UPLC-MS/MS methods, new degradation products, pH and high temperature
Evaluation of pH-dependent reactivity of drugs is an essential component in the pharmaceutical industry. Thus, the stability of three antihistaminic drugs, i.e., ketotifen, epinastine and emedastine, was tested, in solutions of five pH values, i.e., 1.0, 3.0, 7.0, 10.0 and 13.0, at high temperature (70 °C). LC-UV isocratic methods were developed to estimate percentage degradation as well as the kinetics of degradation. Generally, epinastine was shown to be the most stable compound with degradation below 14%. Emedastine was labile in all pH conditions, with degradation in the range 29.26−51.88%. Ketotifen was moderately stable at pH 1−7 (degradation ≤ 14.04%). However, at pH ≥ 10, its degradation exceeded 30%. The kinetics of degradation of ketotifen, epinastine and emedastine was shown as a pseudo-first-order reaction with the rate constants in the range 10−4−10−3 min−1 Finally, the UPLC-MS/MS method was applied to identify the main degradants and suggest degradation pathways. Degradat... [more]
Fabrication and Analysis of Polydimethylsiloxane (PDMS) Microchannels for Biomedical Application
Shahzadi Tayyaba, Muhammad Waseem Ashraf, Zubair Ahmad, Ning Wang, Muhammad Javaid Afzal, Nitin Afzulpurkar
October 11, 2021 (v1)
Subject: Biosystems
Keywords: biocompatibility, curvilinear microchannel, fuzzy, internet of things (IoT), polydimethylsiloxane (PDMS), sterilization
In this research work, Polydimethylsiloxane (PDMS) has been used for the fabrication of microchannels for biomedical application. Under the internet of things (IoT)-based controlled environment, the authors have simulated and fabricated bio-endurable, biocompatible and bioengineered PDMS-based microchannels for varicose veins implantation exclusively to avoid tissue damaging. Five curved ascending curvilinear micro-channel (5CACMC) and five curved descending curvilinear micro-channels (5CDCMC) are simulated by MATLAB (The Math-Works, Natick, MA, USA) and ANSYS (ANSYS, The University of Lahore, Pakistan) with actual environments and confirmed experimentally. The total length of each channel is 1.6 cm. The diameter of both channels is 400 µm. In the ascending channel, the first to fifth curve cycles have the radii of 2.5 mm, 5 mm, 7.5 mm, 10 mm, and 2.5 mm respectively. In the descending channel, the first and second curve cycles have the radii of 12.5 mm and 10 mm respectively. The thir... [more]
Expression of the Thermobifida fusca β-1,3-Glucanase in Yarrowia lipolytica and Its Application in Hydrolysis of β-1,3-Glucan from Four Kinds of Polyporaceae
Wei-Lin Chen, Jo-Chieh Hsu, Chui-Li Lim, Cheng-Yu Chen, Chao-Hsun Yang
October 11, 2021 (v1)
Subject: Biosystems
Keywords: antioxidant activity, Pycnoporus sanguineus, Thermobifida fusca, Wolfiporia cocos, Yarrowia lipolytica, β-1,3-glucanase
The gene encoding a thermostable β-1,3-glucanase was cloned from Thermobifida fusca and expressed constitutively by Yarrowia lipolytica using plasmid pYLSC1. The expression level of the recombinant β-1,3-glucanase reached up to 270 U/mL in the culture medium. After a treatment with endo-β-N-acetyl-glucosaminidase H, the recombinant protein appeared as a single protein band, with a molecular size of approximately 66 kDa on the SDS-polyacrylamide gel. The molecular weight was consistent with the size predicted from the nucleotide sequence. The optimum temperature and pH of the transformant β-1,3-glucanase were 60 °C and pH 8.0, respectively. This β-1,3-glucanase was tolerant to 10% methanol, ethanol, and DMSO, retaining 70% activity. The enzyme markedly hydrolyzed Wolfiporia cocos and Pycnoporus sanguineus glucans. The DPPH and ABTS scavenging potential, reducing power and total phenolic contents of these two Polyporaceae hydrolysates, were significantly increased after 18 h of the enzym... [more]
Reversible Bonding of Thermoplastic Elastomers for Cell Patterning Applications
Byeong-Ui Moon, Keith Morton, Kebin Li, Caroline Miville-Godin, Teodor Veres
October 11, 2021 (v1)
Subject: Biosystems
Keywords: cell migration, cell patterning, reversible bonding, thermoplastic elastomers
In this paper, we present a simple, versatile method that creates patterns for cell migration studies using thermoplastic elastomer (TPE). The TPE material used here can be robustly, but reversibly, bonded to a variety of plastic substrates, allowing patterning of cultured cells in a microenvironment. We first examine the bonding strength of TPE to glass and polystyrene substrates and com-pare it to thermoset silicone-based PDMS under various conditions and demonstrate that the TPE can be strongly and reversibly bonded on commercially available polystyrene culture plates. In cell migration studies, cell patterns are templated around TPE features cored from a thin TPE film. We show that the significance of fibroblast cell growth with fetal bovine serum (FBS)-cell culture media compared to the cells cultured without FBS, analyzed over two days of cell culture. This simple approach allows us to generate cell patterns without harsh manipulations like scratch assays and to avoid damaging th... [more]
Cancer Stem Cell Microenvironment Models with Biomaterial Scaffolds In Vitro
Ghmkin Hassan, Said M. Afify, Shiro Kitano, Akimasa Seno, Hiroko Ishii, Yucheng Shang, Michiya Matsusaki, Masaharu Seno
September 22, 2021 (v1)
Subject: Biosystems
Keywords: biomaterial scaffolds, cancer stem cells, drug screening, tumor microenvironment
Defined by its potential for self-renewal, differentiation and tumorigenicity, cancer stem cells (CSCs) are considered responsible for drug resistance and relapse. To understand the behavior of CSC, the effects of the microenvironment in each tissue are a matter of great concerns for scientists in cancer biology. However, there are many complicated obstacles in the mimicking the microenvironment of CSCs even with current advanced technology. In this context, novel biomaterials have widely been assessed as in vitro platforms for their ability to mimic cancer microenvironment. These efforts should be successful to identify and characterize various CSCs specific in each type of cancer. Therefore, extracellular matrix scaffolds made of biomaterial will modulate the interactions and facilitate the investigation of CSC associated with biological phenomena simplifying the complexity of the microenvironment. In this review, we summarize latest advances in biomaterial scaffolds, which are explo... [more]
Thermophilic Anaerobic Digestion of Second Cheese Whey: Microbial Community Response to H2 Addition in a Partially Immobilized Anaerobic Hybrid Reactor
Giuseppe Lembo, Silvia Rosa, Valentina Mazzurco Miritana, Antonella Marone, Giulia Massini, Massimiliano Fenice, Antonella Signorini
September 22, 2021 (v1)
Subject: Biosystems
Keywords: anaerobic hybrid reactor, cheese whey, in situ hydrogen addition, microbial community, thermophilic anaerobic digestion
In this study, we investigated thermophilic (55 °C) anaerobic digestion (AD) performance and microbial community structure, before and after hydrogen addition, in a novel hybrid gas-stirred tank reactor (GSTR) implemented with a partial immobilization of the microbial community and fed with second cheese whey (SCW). The results showed that H2 addition led to a 25% increase in the methane production rate and to a decrease of 13% in the CH4 concentration as compared with the control. The recovery of methane content (56%) was reached by decreasing the H2 flow rate. The microbial community investigations were performed on effluent (EF) and on interstitial matrix (IM) inside the immobilized area. Before H2 addition, the Anaerobaculaceae (42%) and Lachnospiraceae (27%) families dominated among bacteria in the effluent, and the Thermodesulfobiaceae (32%) and Lachnospiraceae (30%) families dominated in the interstitial matrix. After H2 addition, microbial abundance showed an increase in the ba... [more]
Ideal Feedstock and Fermentation Process Improvements for the Production of Lignocellulolytic Enzymes
Attia Iram, Deniz Cekmecelioglu, Ali Demirci
September 22, 2021 (v1)
Subject: Biosystems
Keywords: cellulase, enzyme production, hemicellulase, lignin modifying enzymes, lignocellulolytic enzymes, lignocellulosic biomass, pretreatment
The usage of lignocellulosic biomass in energy production for biofuels and other value-added products can extensively decrease the carbon footprint of current and future energy sectors. However, the infrastructure in the processing of lignocellulosic biomass is not well-established as compared to the fossil fuel industry. One of the bottlenecks is the production of the lignocellulolytic enzymes. These enzymes are produced by different fungal and bacterial species for degradation of the lignocellulosic biomass into its reactive fibers, which can then be converted to biofuel. The selection of an ideal feedstock for the lignocellulolytic enzyme production is one of the most studied aspects of lignocellulolytic enzyme production. Similarly, the fermentation enhancement strategies for different fermentation variables and modes are also the focuses of researchers. The implementation of fermentation enhancement strategies such as optimization of culture parameters (pH, temperature, agitation,... [more]
Plant-Based Tacca leontopetaloides Biopolymer Flocculant (TBPF) Produced High Removal of Heavy Metal Ions at Low Dosage
Nurul Shuhada Mohd Makhtar, Juferi Idris, Mohibah Musa, Yoshito Andou, Ku Halim Ku Hamid, Siti Wahidah Puasa
September 22, 2021 (v1)
Subject: Biosystems
Keywords: flocculation mechanism, heavy metal, hydroxide ion, polymer flocculant, Tacca leontopetaloides biopolymer flocculant (TBPF)
High removal of heavy metals using plant-based bioflocculant under low concentration is required due to its low cost, abundant source, and nontoxicity for improved wastewater management and utilization in the water industry. This paper presents a treatment of synthetic wastewater using plant-based Tacca leontopetaloides biopolymer flocculant (TBPF) without modification on its structural polymer chains. It produced a high removal of heavy metals (Zn, Pb, Ni, and Cd) at a low concentration of TBPF dosage. In our previous report, TBPF was characterized and successfully reduced the turbidity, total suspended solids, and color for leachate treatment; however, its effectiveness for heavy metal removal has not been reported. The removal of these heavy metals was performed using a standard jar test procedure at different pH values of synthetic wastewater and TBPF dosages. The effects of hydroxide ion, pH, initial TBPF concentration, initial metal ion concentration, and TBPF dosage were examine... [more]
Adsorption of Tetracycline and Sulfadiazine onto Three Different Bioadsorbents in Binary Competitive Systems
Raquel Cela-Dablanca, Manuel Conde-Cid, Gustavo Ferreira-Coelho, Manuel Arias-Estévez, David Fernández-Calviño, Avelino Núñez-Delgado, María J. Fernández-Sanjurjo, Esperanza Álvarez-Rodríguez
September 21, 2021 (v1)
Subject: Biosystems
Keywords: antibiotics, competitive sorption, retention/release, sorbents
Different antibiotics contained in manure, slurry, wastewater or sewage sludge are spread into the environment. The harmful effects of these antibiotics could be minimized by means of immobilization onto bioadsorbent materials. This work investigates the competitive adsorption/desorption of tetracycline (TC) and sulfadiazine (SDZ) onto pine bark, oak ash and mussel shell. The study was carried out using batch-type experiments in binary systems (with both antibiotics present simultaneously), adding 5 equal concentrations of the antibiotics (between 1 and 50 µmol L−1). The adsorption percentages were higher for TC (close to 100% onto pine bark and oak ash, and between 40 and 85% onto mussel shell) than for SDZ (75−100% onto pine bark, and generally less than 10% on oak ash and mussel shell). Pine bark performed as the best adsorbent since TC adsorption remained close to 100% throughout the entire concentration range tested, while it was between 75 and 100% for SDZ. Desorption was always... [more]
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