Search results for: bacterial gene clusters

Authors: Noshaba Dilbar, Aisha Tahir, Amer Jamil

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During the last decade, DNA barcoding proved to be an authentic tool for discovery and identification of plants. In the present study, DNA barcoding of two species, Fagonia arabica and Fagonia indica was done for differentiation by using matK region. matK gene is considered as a universal barcode because of its easy alignment and high discrimination ability. In this study, matK yielded 100% sequencing results. The sequences from both plants were aligned at clustal W and observed that there is no nucleotide variation and polymorphism among both sequences. This was further analysed by BLAST which showed the similar sequences from different plants belonging to same family but didn’t find sequence of both species. Considering this, the resulted sequence was submitted by the name of Fagonia arabica with accession number KM276890. In the end, we analysed the results from BOLD which gave us the final conclusion that both plants are same as their matK sequences are 100% identical. In literature, both Fagonia indica and Fagonia arabica names are used for this plant but there is no clear differentiation has been observed in these plants. Results evaluate that Fagonia indica and Fagonia arabica are the alternative names of same plant.

Keywords: DNA barcoding, Fagonia arabica, Fagonia indica, matK

Procedia PDF Downloads 153

Authors: Seyed Hassan Moosa-kazemi, Jalal Mohammadi Soleimani, Hassan Vatandoost, Mohammad Hassan Shirazi, Sara Hajikhani, Roonak Bakhtiari, Morteza Akbari, Siamak Hydarzadeh

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Malaria is an infectious disease and considered most important health problems in the southeast of Iran. Iran is elimination malaria phase and new tool need to vector control. Paraterasgenesis is a new way to cut of life cycle of the malaria parasite. In this study, the microflora of the surface and gut of various stages of Anopheles fluviatilis James as one of the important malaria vector was studied using biochemical and molecular techniques during 2013-2014. Twelve bacteria species were found including; Providencia rettgeri, Morganella morganii, Enterobacter aerogenes, Pseudomonas oryzihabitans, Citrobacter braakii، Citrobacter freundii، Aeromonas hydrophila، Klebsiella oxytoca, Citrobacter koseri, Serratia fonticola، Enterobacter sakazakii and Yersinia pseudotuberculosis. The species of Alcaligenes faecalis, Providencia vermicola and Enterobacter hormaechei were identified in various stages of the vector and confirmed by biochemical and molecular techniques. We found Providencia rettgeri proper candidate for paratransgenesis.

Keywords: Anopheles fluviatilis, bacteria, malaria, Paraterasgenesis, Southern Iran

Procedia PDF Downloads 491

Authors: Jose A. Aznar-Moreno, Xi Jiang, Stefan Burén, Luis M. Rubio

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Integration of prokaryotic nitrogen fixation (nif) genes into the plastid genome for expression of functional nitrogenase components could render plants capable of assimilating atmospheric N2 making their crops less dependent of nitrogen fertilizers. The nitrogenase Fe protein component (NifH) has been used as proxy for expression and targeting of Nif proteins within plant and yeast cells. Here we use tobacco plants with the Azotobacter vinelandii nifH and nifM genes integrated into the plastid genome. NifH and its maturase NifM were constitutively produced in leaves, but not roots, during light and dark periods. Nif protein expression in transplastomic plants was stable throughout development. Chloroplast NifH was soluble, but it only showed in vitro activity when isolated from leaves collected at the end of the dark period. Exposing the plant extracts to elevated temperatures precipitated NifM and apo-NifH protein devoid of [Fe4S4] clusters, dramatically increasing the specific activity of remaining NifH protein. Our data indicate that the chloroplast endogenous [Fe-S] cluster biosynthesis was insufficient for complete NifH maturation, albeit a negative effect on NifH maturation due to excess NifM in the chloroplast cannot be excluded. NifH and NifM constitutive expression in transplastomic plants did not affect any of the following traits: seed size, germination time, germination ratio, seedling growth, emergence of the cotyledon and first leaves, chlorophyll content and plant height throughout development.

Keywords: NifH, chloroplast, nitrogen fixation, crop improvement, transplastomic plants, fertilizer, biotechnology

Procedia PDF Downloads 162

Authors: I. V. Pinto, M. R. Sooriyarachchi

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It can be frequently observed that the data arising in our environment have a hierarchical or a nested structure attached with the data. Multilevel modelling is a modern approach to handle this kind of data. When multilevel modelling is combined with a binary response, the estimation methods get complex in nature and the usual techniques are derived from quasi-likelihood method. The estimation methods which are compared in this study are, marginal quasi-likelihood (order 1 & order 2) (MQL1, MQL2) and penalized quasi-likelihood (order 1 & order 2) (PQL1, PQL2). A statistical model is of no use if it does not reflect the given dataset. Therefore, checking the adequacy of the fitted model through a goodness-of-fit (GOF) test is an essential stage in any modelling procedure. However, prior to usage, it is also equally important to confirm that the GOF test performs well and is suitable for the given model. This study assesses the suitability of the GOF test developed for binary response multilevel models with respect to the method used in model estimation. An extensive set of simulations was conducted using MLwiN (v 2.19) with varying number of clusters, cluster sizes and intra cluster correlations. The test maintained the desirable Type-I error for models estimated using PQL2 and it failed for almost all the combinations of MQL. Power of the test was adequate for most of the combinations in all estimation methods except MQL1. Moreover, models were fitted using the four methods to a real-life dataset and performance of the test was compared for each model.

Keywords: goodness-of-fit test, marginal quasi-likelihood, multilevel modelling, penalized quasi-likelihood, power, quasi-likelihood, type-I error

Procedia PDF Downloads 142

Authors: Waseem Al Talalwah, Shorok Al Dorazi, Roger Soames

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Persistent sciatic artery is a rare anatomical vascular variation resulting from a lack of regression of the embryonic dorsal axial artery. The axial artery is the main artery supplying the lower limb during development in the first trimester. The current research includes 206 sciatic artery cases in 171 patients between 1864 and 2012. It aims to identify the risk factor of sciatic artery aneurysm in congenital limb anomalies. Sciatic artery aneurysm was diagnosed incidentally in amniotic band syndrome (ABS) existing with no congenital anomaly in 0.7% or with double knee in 0.7%, with the tibia in 0.7% and with hemihypertrophy or soft tissue hypertrophy in 1.4%. Therefore, the current study indicates a relationship the same gene responsible for the congenital limb deformities may be responsible for non-regression of the sciatic artery. Furthermore, pediatricians should refer cases of congenital limb anomalies for vascular evaluation prior to corrective surgical intervention.

Keywords: amniotic band syndrome, congenital limb deformities, double knee, sciatic artery, sciatic artery aneurysm , soft tissue hypertrophy

Procedia PDF Downloads 376

Authors: Erin Curtis, Avraham Schwiger

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Neuropsychological testing and evaluation is a crucial step in providing patients with effective diagnoses and treatment while in clinical care. The variety of batteries used in these evaluations can help clinicians better understand the nuanced declivities in a patient’s cognitive, behavioral, or emotional functioning, consequently equipping clinicians with the insights to make intentional choices about a patient’s care. Despite the knowledge these batteries can yield, some aspects of neuropsychological testing remain largely inaccessible to certain patient groups as a result of fundamental cultural, educational, or social differences. One such battery includes the Dot Counting Test (DCT), during which patients are required to count a series of dots on a page as rapidly and accurately as possible. As the battery progresses, the dots appear in clusters that are designed to be easily multiplied. This task evaluates a patient’s cognitive functioning, attention, and level of effort exerted on the evaluation as a whole. However, there is evidence to suggest that certain social groups, particularly Latinx groups, may perform worse on this task as a result of cultural or educational differences, not reduced cognitive functioning or effort. As such, this battery fails to account for baseline differences among patient groups, thus creating questions surrounding the accuracy, generalizability, and value of its results. Accessibility and cultural sensitivity are critical considerations in the testing and treatment of marginalized groups, yet have been largely ignored in the literature and in clinical settings to date. Implications and improvements to applications are discussed.

Keywords: culture, latino, neuropsychological assessment, neuropsychology, accessibility

Procedia PDF Downloads 113

Authors: Jamal S. M. Sabir, Edward C. Theriot, Schonna R. Manning, Abdulrahman L. Al-Malki, Mohammad, Mumdooh J. Sabir, Dwight K. Romanovicz, Nahid H. Hajrah, Robert K. Jansen, Matt P. Ashworth

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The diatom Phaeodactylum tricornutum has been used as a model for cell biologists and ecologists for over a century. We have incorporated several new raphid pennates into a three-gene phylogenetic dataset (SSU, rbcL, psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with 100% BS support. This is the first time a close relative has been identified for P. tricornutum with robust statistical support. We test and reject a succession of hypotheses for other relatives. Our molecular data are statistically significantly incongruent with placement of either or both species among the Cymbellales, an order of diatoms with which both have been associated. We believe that further resolution of the phylogenetic position of P. tricornutum will rely more on increased taxon sampling than increased genetic sampling. Gomphonemopsis is a benthic diatom, and its phylogenetic relationship with P. tricornutum is congruent with the hypothesis that P. tricornutum is a benthic diatom with specific adaptations that lead to active recruitment into the plankton. We hypothesize that other benthic diatoms are likely to have similar adaptations and are not merely passively recruited into the plankton.

Keywords: benthic, diatoms; ecology, Phaeodactylum tricornutum, phylogeny, tychoplankton

Procedia PDF Downloads 238

Authors: A. Dali-Ali, F. Agag, H. Beldjilali, A. Oukebdane, K. Meddeber, R. Dali-Yahia, N. Midoun

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The ability of Acinetobacter baumannii to develop multiple resistances towards to the majority of antibiotics explains the therapeutic difficulties encountered in severe infections. Furthermore, its persistence in the humid or dry environment promotes cross-contamination in intensive care units. The aim of our study was to describe the epidemiological and bacterial resistance profiles of hospital-acquired infections caused by Acinetobacter baumannii in the intensive care unit of our teaching hospital. During the study period (June 3, 2012 to December 31, 2013), 305 patients having duration of hospitalization equal or more than 48 hours were included in the study. Among these, 36 had developed, at least, one health-care associated infection caused by Acinetobacter baumannii. The rate of infected patients was equal to 11.8% (36/305). The rate of cumulative incidence of hospital-acquired pneumonia was the highest (9.2%) followed by central venous catheter infection (1.3%). Analysis of the various antibiotic resistance profile shows that 93.8% of the strains were resistant to imipenem. The nosocomial infection control committee set up a special program not only to reduce the high rates of incidence of these infections but also to descrease the rate of imipenem resistance.

Keywords: Acinetobacer baumannii, epidemiological profile, hospital acquired infections, intensive care unit

Procedia PDF Downloads 331

Authors: Boxiang Zhuang

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This study analyzes the clinical manifestations, hearing rehabilitation methods and outcomes of a complex case of neurofibromatosis type II (NF2). Methods: The clinical manifestations, medical history, clinical data, surgical methods and postoperative hearing rehabilitation outcomes of an NF2 patient were analyzed to determine the hearing reconstruction method and postoperative effect for a special type of NF2 acoustic neuroma. Results: The patient had bilateral acoustic neuromas with profound sensorineural hearing loss in both ears. Peripheral blood genetic testing did not reveal pathogenic gene mutations, suggesting mosaicism. The patient had an intracochlear schwannoma in the right ear and severely impaired vision in both eyes. Cochlear implantation with tumor retention was performed in the right ear. After 2 months of family-based auditory and speech rehabilitation, the Categories of Auditory Performance (CAP) score improved from 0 to 5. Conclusion: NF2 has complex clinical manifestations and poor prognosis. For NF2 patients with intracochlear tumors, cochlear implantation with tumor retention can be used to reconstruct hearing.

Keywords: NF2, intracochlear schwannoma, hearing reconstruction, cochlear implantation

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Authors: Ikram Mohamed Eltayeb Elsiddig, Abdel Khalig Muddather, Hiba Abdel Rahman Ali, Saad Mohamed Hussein Ayoub

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Anogeissusleiocarpus (Combretaceae) is well known for its medicinal uses in African traditional medicine, for treating many human diseases mainly skin diseases and infections.Mycetoma disease is a fungal and/ or bacterial skin infection, mainly cause by Madurella mycetomatis fungus.This study was carried out in vitro to investigate the antifungal activity of Anogeissusleiocarpus leaf extracts against the isolated pathogenicMadurellamycetomatis, by using the NCCLS modified method compared to Ketoconazole standard drug and MTT assay. The bioactive fraction was subjected to chemical analysis implementing different chromatographic analytical methods (TLC, HPLC, and LC-MS/MS). The results showed significance antifungal activity of A. leiocarpus leaf extractsagainst the isolated pathogenicM. mycetomatis, compared to negative and positive controls. The chloroform fraction showed the highest antifungal activity.The chromatographic analysis of the chloroform fraction with the highest activity showed the presence of important bioactive compounds such as ellagic and flavellagic acids derivatives, flavonoids and stilbenoid, which are well known for their antifungal activity.

Keywords: Anogeissus leiocarpus, crude extracts and fractions of Anogeissus leiocarpus, in vitrosusceptibility of Madurella mycetomatis, Madurella mycetomatis

Procedia PDF Downloads 622

Authors: Muhammad Raqib Rasul, Tavga Sulaiman Rashid

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Fertilization increases efficiency and obtains better quality of product recovery in agricultural activities. However, fertilizer consumption increased exponentially throughout the world, causing severe environmental problems. Biofertilizers can be a practical approach to minimize chemical fertilizer sources and ultimately develop soil fertility. This study was carried out to isolate, identify and characterize bacteria from medicinal plant (Rumex tuberosus L. and Verbascum sp.) rhizosphere for in vivo screening. 25 bacterial isolates were isolated and several biochemical tests were performed. Two isolates that were positive for most biochemical tests were chosen for the field experiment. The isolates were identified as Go1 Alcaligenes faecalis (Accession No. OP001725) and T11 (Bacillus sp.) based on the 16S rRNA sequence analysis that was compared with related bacteria in GenBank database using MEGA 6.1. For the field trial isolate GO1 and T11 (separately and mixed), NPK as a positive control was used. Both isolates increased plant height, chlorophyll content, number of tubers, and tuber’s weight. The results demonstrated that these two isolates of bacteria can potentially replace with chemical fertilizers for potato production.

Keywords: biofertilizer, Bacillus subtilis, Alcaligenes faecalis, potato tubers, in vivo screening

Procedia PDF Downloads 103

Authors: Qasim HamaKhurshid HamaMurad, Normal Mat Jusoh, Uznir Ujang

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The concept of the city with an infrastructure of (information and communication) Technology embraces several definitions depending on the meanings of the word "smart" are (intelligent city, smart city, knowledge city, ubiquitous city, sustainable city, digital city). Many definitions of the city exist, but this chapter explores which one has been universally acknowledged. From literature analysis, it emerges that Smart City is the most used terminologies in literature through the digital database to indicate the smartness of a city. This paper share exploration the research from main seven website digital databases and journal about Smart City from "January 2015 to the February of 2020" to (a) Time research, to examine the causes of the Smart City phenomenon and other concept literature in the last five years (b) Review of words, to see how and where the smart city specification and relation different definition And(c) Geographical research to consider where Smart Cities' greatest concentrations are in the world and are Malaysia has interacting with the smart city, and (d) how many papers published from all Malaysia from 2015 to 2020 about smart citie. Three steps are followed to accomplish the goal. (1)The analysis covered publications Build a systematic literature review search strategy to gather a representative sub-set of papers on Smart City and other definitions utilizing (GoogleScholar, Elsevier, Scopus, ScienceDirect, IEEEXplore, WebofScience, Springer) January2015-February2020. (2)A bibliometric map was formed based on the bibliometric evaluation using the mapping technique VOSviewer to visualize differences. (3)VOSviewer application program was used to build initial clusters. The Map of Bibliometric Visualizes the analytical findings which targeted the word harmony.

Keywords: bibliometric research, smart city, ICT, VOSviewer, urban modernization

Procedia PDF Downloads 202

Authors: Wendy Flory, Kazi Czarnecki, Matthijs Mercy, Mark Joswiak, Mary Beth Seasholtz

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Polyurethane Materials are present in a wide range of industrial segments such as Furniture, Building and Construction, Composites, Automotive, Electronics, and more. Dow is one of the leaders for the manufacture of the two main raw materials, Isocyanates and Polyols used to produce polyurethane products. Dow is also a key player for the manufacture of Polyurethane Systems/Formulations designed for targeted applications. In 1990, the first analytical chemometric models were developed and deployed for use in the Dow QC labs of the polyols business for the quantification of OH, water, cloud point, and viscosity. Over the years many models have been added; there are now over 140 models for quantification and hundreds for product identification, too many to be reasonable for support. There are 29 global models alone for the quantification of OH across > 70 products at many sites. An attempt was made to consolidate these into a single model. While the consolidated model proved good statistics across the entire range of OH, several products had a bias by ASTM E1655 with individual product validation. This project summary will show the strategy for global model updates for OH, to reduce the number of models for quantification from over 140 to 5 or less using chemometric methods. In order to gain an understanding of the best product groupings, we identify clusters by reducing spectra to a few dimensions via Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP). Results from these cluster analyses and a separate validation set allowed dow to reduce the number of models for predicting OH from 29 to 3 without loss of accuracy.

Keywords: hydroxyl, global model, model maintenance, near infrared, polyol

Procedia PDF Downloads 135

Authors: Babak Sadeghi, Parisa Ghayomipour

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ZnO/Ag nanocomposites coated with polyvinyl chloride (PVC) were prepared by chemical reduction method, for anti-infection biomaterial application. There is a growing interest in attempts in using biomolecular as the templates to grow inorganic nanocomposites in controlled morphology and structure. By optimizing the experiment conditions, we successfully fabricated high yield of ZnO/Ag nanocomposite with full coverage of high-density polyvinyl chloride (PVC) coating. More importantly, ZnO/Ag nanocomposites were shown to significantly inhibit the growth of S. aureus in solution. It was further shown that ZnO/Ag nanocomposites induced thiol depletion that caused death of S. aureus. The coatings were fully characterized using techniques such as scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray diffraction (XRD). Most importantly, compared to uncoated metals, the coatings on PVC promoted healthy antibacterial activity. Importantly, compared to ZnO-Ag -uncoated PVC, the ZnO/Ag nanocomposites coated was approximately triplet more effective in preventing bacteria attachment. The result of Thermal Gravimetric Analysis (TGA) indicates that, the ZnO/Ag nanocomposites are chemically stable in the temperature range from 50 to 900 ºC. This result, for the first time, demonstrates the potential of using ZnO/Ag nanocomposites as a coating material for numerous anti-bacterial applications.

Keywords: nanocomposites, antibacterial activity, scanning electron microscopy (SEM), x-ray diffraction (XRD)

Procedia PDF Downloads 473

Authors: Tatiana Butkova, Nikolai Kibrik, Kristina Malsagova, Alexander Izotov, Alexander Stepanov, Anna Kaysheva

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Relevance. The genetic risk of developing schizophrenia is determined by two factors: single nucleotide polymorphisms and gene copy number variations. The search for serological markers for early diagnosis of schizophrenia is driven by the fact that the first five years of the disease are accompanied by significant biological, psychological, and social changes. It is during this period that pathological processes are most amenable to correction. The aim of this study was to analyze single nucleotide polymorphisms (SNPs) that are hypothesized to potentially influence the onset and development of the endogenous process. Materials and Methods It was analyzed 73 single nucleotide polymorphism variants. The study included 48 patients undergoing inpatient treatment at "Psychiatric Clinical Hospital No. 1" in Moscow, comprising 23 females and 25 males. Inclusion criteria: - Patients aged 18 and above. - Diagnosis according to ICD-10: F20.0, F20.2, F20.8, F21.8, F25.1, F25.2. - Voluntary informed consent from patients. Exclusion criteria included: - The presence of concurrent somatic or neurological pathology, neuroinfections, epilepsy, organic central nervous system damage of any etiology, and regular use of medication. - Substance abuse and alcohol dependence. - Women who were pregnant or breastfeeding. Clinical and psychopathological assessment was complemented by psychometric evaluation using the PANSS scale at the beginning and end of treatment. The duration of observation during therapy was 4-6 weeks. Total DNA extraction was performed using QIAamp DNA. Blood samples were processed on Illumina HiScan and genotyped for 652,297 markers on the Infinium Global Chips Screening Array-24v2.0 using the IMPUTE2 program with parameters Ne=20,000 and k=90. Additional filtration was performed based on INFO>0.5 and genotype probability>0.5. Quality control of the obtained DNA was conducted using agarose gel electrophoresis, with each tested sample having a volume of 100 µL. Results. It was observed that several SNPs exhibited gender dependence. We identified groups of single nucleotide polymorphisms with a membership of 80% or more in either the female or male gender. These SNPs included rs2661319, rs2842030, rs4606, rs11868035, rs518147, rs5993883, and rs6269.Another noteworthy finding was the limited combination of SNPs sufficient to manifest clinical symptoms leading to hospitalization. Among all 48 patients, each of whom was analyzed for deviations in 73 SNPs, it was discovered that the combination of involved SNPs in the manifestation of pronounced clinical symptoms of schizophrenia was 19±3 out of 73 possible. In study, the frequency of occurrence of single nucleotide polymorphisms also varied. The most frequently observed SNPs were rs4849127 (in 90% of cases), rs1150226 (86%), rs1414334 (75%), rs10170310 (73%), rs2857657, and rs4436578 (71%). Conclusion. Thus, the results of this study provide additional evidence that these genes may be associated with the development of schizophrenia spectrum disorders. However, it's impossible cannot rule out the hypothesis that these polymorphisms may be in linkage disequilibrium with other functionally significant polymorphisms that may actually be involved in schizophrenia spectrum disorders. It has been shown that missense SNPs by themselves are likely not causative of the disease but are in strong linkage disequilibrium with non-functional SNPs that may indeed contribute to disease predisposition.

Keywords: gene polymorphisms, genotyping, single nucleotide polymorphisms, schizophrenia.

Procedia PDF Downloads 80

Authors: Apichai Sawisit, Sirima Suvarnakuta Jantama, Sunthorn Kanchanatawee, Lonnie O. Ingram, Kaemwich Jantama

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Escherichia coli KJ122 was engineered to produce succinate from glucose using the wild type GalP for glucose uptake instead of the native phosphotransferase system (ptsI mutation). This strain ferments 10% (w/v) xylose poorly. Mutants were selected by serial transfers in AM1 mineral salts medium with 10% (w/v) xylose. Evolved mutants exhibited a similar improvement, co-fermentation of an equal mixture of xylose and glucose. One of these, AS1600a, produced 84.26±1.37 g/L succinate, equivalent to that produced by the parent (KJ122) strain from 10% glucose (85.46±1.78 g/L). AS1600a was sequenced and found to contain a mutation in galactose permease (GalP, G236D). Expressing the galP* mutation gene in KJ122ΔgalP resembled the xylose utilization phenotype of the mutant AS1600a. The strain AS1600a and KJ122ΔgalP (pLOI5746; galP*) also co-fermented a mixture of glucose, xylose, arabinose, and galactose in sugarcane bagasse hydrolysate for succinate production.

Keywords: xylose, furfural, succinat, sugarcane bagasse, E. coli

Procedia PDF Downloads 450

Authors: John N. Idenyi, Hadimundeen Abdallah, Abigeal D. Adeyemi, Jonathan C. Eya

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Gut microbiomes play a significant role in the growth, metabolism, and health of fish. However, we know very little about the interactive effects of variations in dietary composition and temperature on rainbow trout gut microbiota. Exactly 288 rainbow trout weighing 45.6g ± 0.05 (average ± SD) were fed four isocaloric, isolipidic, and isonitrogenous diets comprising 40% crude protein and 20% crude lipid and formulated as 100 % animal-based protein (AP) and a blend of 50 fish oil (FO)/50 camelina oil (CO), 100 % AP and100 % CO, 100 % plant-based protein (PP) and a blend of 50FO/50CO or 100 % PP and 100 % CO in 14 or 18°C for 150 days. Gut content was analyzed using 16S rRNA gene and shotgun sequencing. The most abundant phyla identified regardless of diet were Tenericutes, Firmicutes, Proteobacteria, Spirochaetes, Bacteroidetes, and Actinobacteria, while Aeromonadaceae and Enterobacteriaceae were dominant families in 18°C. Moreover, gut microbes were dominated by genes relating to an amino acid, carbohydrate, fat, and energy metabolisms and influenced by temperature. The shared functional profiles for all the diets suggest that plant protein sources in combination with CO could be as good as the fish meal with 50/50 FO & CO in rainbow trout farming.

Keywords: aquafeed, aquaculture, microbiome, rainbow trout

Procedia PDF Downloads 91

Authors: E. L. Albuquerque, U. L. Fulco, G. S. Ourique

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The focus of this work is on the numerical investigation of the charge transport properties of the de novo-designed alpha3 polypeptide, as well as in its variants, all of them probed by gene engineering. The theoretical framework makes use of a tight-binding model Hamiltonian, together with ab-initio calculations within quantum chemistry simulation. The alpha3 polypeptide is a 21-residue with three repeats of the seven-residue amino acid sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala, forming an alpha–helical bundle structure. Its variants are obtained by Ala→Gln substitution at the e (5th) and g (7th) position, respectively, of the alpha3 polypeptide amino acid sequence. Using transmission electron microscopy and atomic force microscopy, it was observed that the alpha3 polypeptide and one of its variant do have the ability to form fibrous assemblies, while the other does not. Our main aim is to investigate whether or not the biased alpha3 polypeptide and its variants can be also identified by quantum charge transport measurements through current-voltage (IxV) curves as a pattern to characterize their fibrous assemblies. It was observed that each peptide has a characteristic current pattern, which may be distinguished by charge transport measurements, suggesting that it might be a useful tool for the development of biosensors.

Keywords: charge transport properties, electronic transmittance, current-voltage characteristics, biological sensor

Procedia PDF Downloads 665

Authors: Ricardo Alberto Chiong Zevallos, Eduardo Moraes Rego Reis

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Pancreatic adenocarcinoma (PDAC) patients have a less than 10% 5-year survival rate. PDAC has no defined diagnostic and prognostic biomarkers. Gemcitabine is the first-line drug in PDAC and several other cancers. Long non-coding RNAs (lncRNAs) contribute to the tumorigenesis and are potential biomarkers for PDAC. Although lncRNAs aren’t translated into proteins, they have important functions. LncRNAs can decoy or recruit proteins from the epigenetic machinery, act as microRNA sponges, participate in protein translocation through different cellular compartments, and even promote chemoresistance. The chromatin remodeling enzyme EZH2 is a histone methyltransferase that catalyzes the methylation of histone 3 at lysine 27, silencing local expression. EZH2 is ambivalent, it can also activate gene expression independently of its histone methyltransferase activity. EZH2 is overexpressed in several cancers and interacts with lncRNAs, being recruited to a specific locus. EZH2 can be recruited to activate an oncogene or silence a tumor suppressor. The lncRNAs misregulation in cancer can result in the differential recruitment of EZH2 and in a distinct epigenetic landscape, promoting chemoresistance. The relevance of the EZH2-lncRNAs interaction to chemoresistant PDAC was assessed by Real Time quantitative PCR (RT-qPCR) and RNA Immunoprecipitation (RIP) experiments with naïve and gemcitabine-resistant PDAC cells. The expression of several lncRNAs and EZH2 gene targets was evaluated contrasting naïve and resistant cells. Selection of candidate genes was made by bioinformatic analysis and literature curation. Indeed, the resistant cell line showed higher expression of chemoresistant-associated lncRNAs and protein coding genes. RIP detected lncRNAs interacting with EZH2 with varying intensity levels in the cell lines. During RIP, the nuclear fraction of the cells was incubated with an antibody for EZH2 and with magnetic beads. The RNA precipitated with the beads-antibody-EZH2 complex was isolated and reverse transcribed. The presence of candidate lncRNAs was detected by RT-qPCR, and the enrichment was calculated relative to INPUT (total lysate control sample collected before RIP). The enrichment levels varied across the several lncRNAs and cell lines. The EZH2-lncRNA interaction might be responsible for the regulation of chemoresistance-associated genes in multiple cancers. The relevance of the lncRNA-EZH2 interaction to PDAC was assessed by siRNA knockdown of a lncRNA, followed by the analysis of the EZH2 target expression by RT-qPCR. The chromatin immunoprecipitation (ChIP) of EZH2 and H3K27me3 followed by RT-qPCR with primers for EZH2 targets also assess the specificity of the EZH2 recruitment by the lncRNA. This is the first report of the interaction of EZH2 and lncRNAs HOTTIP and PVT1 in chemoresistant PDAC. HOTTIP and PVT1 were described as promoting chemoresistance in several cancers, but the role of EZH2 is not clarified. For the first time, the lncRNA LINC01133 was detected in a chemoresistant cancer. The interaction of EZH2 with LINC02577, LINC00920, LINC00941, and LINC01559 have never been reported in any context. The novel lncRNAs-EZH2 interactions regulate chemoresistant-associated genes in PDAC and might be relevant to other cancers. Therapies targeting EZH2 alone weren’t successful, and a combinatorial approach also targeting the lncRNAs interacting with it might be key to overcome chemoresistance in several cancers.

Keywords: epigenetics, chemoresistance, long non-coding RNAs, pancreatic cancer, histone modification

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Authors: Adenike Adesanya, Nonthaphat Wong, Xiang-Yun Lan, Shea Ping Yip, Chien-Ling Huang

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Background: The most challenging mutation of the oncokinase BCR-ABL protein T315I, which is commonly known as the “gatekeeper” mutation and is notorious for its strong resistance to almost all tyrosine kinase inhibitors (TKIs), especially imatinib. Therefore, this study aims to identify T315I-dependent downstream microRNA (miRNA) pathways associated with drug resistance in chronic myeloid leukemia (CML) for prognostic and therapeutic purposes. Methods: T315I-carrying K562 cell clones (K562-T315I) were generated by the CRISPR-Cas9 system. Imatinib-treated K562-T315I cells were subjected to small RNA library preparation and next-generation sequencing. Putative lncRNA-miRNA-mRNA networks were analyzed with (i) DESeq2 to extract differentially expressed miRNAs, using Padj value of 0.05 as cut-off, (ii) STarMir to obtain potential miRNA response element (MRE) binding sites of selected miRNAs on lncRNA H19, (iii) miRDB, miRTarbase, and TargetScan to predict mRNA targets of selected miRNAs, (iv) IntaRNA to obtain putative interactions between H19 and the predicted mRNAs, (v) Cytoscape to visualize putative networks, and (vi) several pathway analysis platforms – Enrichr, PANTHER and ShinyGO for pathway enrichment analysis. Moreover, mitochondria isolation and transcript quantification were adopted to determine the new mechanism involved in T315I-mediated resistance of CML treatment. Results: Verification of the CRISPR-mediated mutagenesis with digital droplet PCR detected the mutation abundance of ≥80%. Further validation showed the viability of ≥90% by cell viability assay, and intense phosphorylated CRKL protein band being detected with no observable change for BCR-ABL and c-ABL protein expressions by Western blot. As reported by several investigations into hematological malignancies, we determined a 7-fold increase of H19 expression in K562-T315I cells. After imatinib treatment, a 9-fold increment was observed. DESeq2 revealed 171 miRNAs were differentially expressed K562-T315I, 112 out of these miRNAs were identified to have MRE binding regions on H19, and 26 out of the 112 miRNAs were significantly downregulated. Adopting the seed-sequence analysis of these identified miRNAs, we obtained 167 mRNAs. 6 hub miRNAs (hsa-let-7b-5p, hsa-let-7e-5p, hsa-miR-125a-5p, hsa-miR-129-5p, and hsa-miR-372-3p) and 25 predicted genes were identified after constructing hub miRNA-target gene network. These targets demonstrated putative interactions with H19 lncRNA and were mostly enriched in pathways related to cell proliferation, senescence, gene silencing, and pluripotency of stem cells. Further experimental findings have also shown the up-regulation of mitochondrial transcript and lncRNA MALAT1 contributing to the lncRNA-miRNA-mRNA networks induced by BCR-ABL T315I mutation. Conclusions: Our results have indicated that lncRNA-miRNA regulators play a crucial role not only in leukemogenesis but also in drug resistance, considering the significant dysregulation and interactions in the K562-T315I cell model generated by CRISPR-Cas9. In silico analysis has further shown that lncRNAs H19 and MALAT1 bear several complementary miRNA sites. This implies that they could serve as a sponge, hence sequestering the activity of the target miRNAs.

Keywords: chronic myeloid leukemia, imatinib resistance, lncRNA-miRNA-mRNA, T315I mutation

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Authors: Aigul Abduldayeva, Gulnar Tuleshova

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Osteoporosis (OP) is a major socio-economic problem and is a major cause of disability, reduced quality of life and premature death of elderly people. In Astana, the study involved 93 respondents, of whom 17 were men (18.3%), and 76 were women (81.7%). Age distribution of the respondents is as follows: 40-59 (66.7%), 60-75 (29.0%), 75-90 (4.3%). In the city of Astana general breach of bone mass (CCM) was determined in 83.8% (nationwide figure - RRP - 79.0%) of the patients, and normal levels of ultrasound densitometry were detected in 16.1% (RRP 21.0%) of the patients. OP was diagnosed in 20.4% of people over 40 (RRP for citizens is 19.0%), 25.4% in the group older than 50 (23.4% PIU), 22,6% in the group older than 60 (RRP 32.6%), 25.0% in the group older than 70 (47.6% of RRP). OPN was detected in 63.4% (RRP 59.6%) of the surveyed population. These data indicate that, there is no sharp difference between Astana and other cities in the country regarding the incidence of OP, that is, the situation with the OP is not aggravated by any regional characteristics. In the distribution of respondents by clusters it was found that 80.0% of the respondents with CCM were in the "best urban cluster", 93.8% were in "average urban cluster", and 77.4% were in a "poor urban cluster". There is a high rate construction of new buildings in Astana, presumably, that the new settlers inhabit the outskirts of the city, and very difficult to trace the socio-economic differences there. Based on these data the following conclusions can be made: 1. According to the ultrasound densitometry of the calcaneus the prevalence rate of NCM among the residents of Astana is 83.3%, OP - 20.4%, which generally coincides with data elsewhere in the country. 2. The urban population of Astana is under a high degree of risk for low energetic fracture, 46.2% of the population had medium and high risks of fracture, while the nationwide index is 26.7%. 3. In the development of CCM residents of Akmola region play a significant role gender, age, ethnic factors. According to the ultrasound densitometry women are more prone to Astana OP - 22.4% of respondents than men - 11.8% of respondents.

Keywords: nutrition, osteoporosis, elderly, urban population

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Authors: Salma M. Wakil

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Advances in the field of genetics overwhelmed detecting large number of inherited disorders at the molecular level and directed to the development of innovative technologies. These innovations have led to gene sequencing, prenatal mutation detection, pre-implantation genetic diagnosis; population based carrier screening and genome wide analyses using microarrays. Microarrays are widely used in establishing clinical and diagnostic setup for genetic anomalies at a massive level, with the advent of cytoscan molecular karyotyping as a clinical utility card for detecting chromosomal aberrations with high coverage across the entire human genome. Unlike a regular karyotype that relies on the microscopic inspection of chromosomes, molecular karyotyping with cytoscan constructs virtual chromosomes based on the copy number analysis of DNA which improves its resolution by 100-fold. We have been investigating a large number of patients with Developmental Delay and Intellectual disability with this platform for establishing micro syndrome deletions and have detected number of novel CNV’s in the Arabian population with the clinical relevance.

Keywords: microarrays, molecular karyotyping, developmental delay, genetics

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Authors: Pablo Vidal, Misael Martinez, Carlos Hernandez, Ananta R. Adhikari, Luis Materon, Yuanbing Mao, Karen Lozano

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Conjugated polymers are smart materials that show tremendous practical applications in diverse subjects. Polydiacetylenes are conjugated polymers with special optical properties. In response to the environmental changes such as pH and molecular binding, it changes its color. Such an interesting chromic and emissive behavior of polydiacetylenes make them a highly popular polymer in wide areas, including biomedicine such as a biosensor. In this research, we used polyvinyl butyrate as a matrix to fibrillate polydiacetylenes. We initially prepared polyvinyl butyrate/diacetylene matrix using forcespinning technique. They were then polymerized to form polyvinyl butyrate/polydiacetylene (PVB/PDA). These matrices then studied for their bio-sensing response to gram-positive and gram-negative bacteria. The sensing ability of the PVB/PDA biosensor was observed as early as 30 min in the presence of bacteria at 37°C. Now our effort is to decrease this effective temperature to room temperature to make this device applicable in the general daily life. These chromic biosensors will find extensive application not only alert the infection but also find other promising applications such as wearable sensors and diagnostic systems.

Keywords: smart material, conjugated polymers, biosensor, polyvinyl butyrate/polydiacetylene

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Authors: Hafsa Raheel

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Background: Adolescents who suffer from depression early in life, have an increase in suicidal tendency, anxiety, conduct disorders, substance abuse, and continue to be depressed, later on in life. This study was conducted to identify the prevalence and correlates of depression among adolescent girls in Riyadh city in order to carry out early intervention. Methods: A cross‑sectional, school‑based survey was conducted among 1028 adolescent girls aged 15–19 years in secondary schools of Riyadh city. Riyadh was divided into clusters and within each cluster, both public and private schools were enrolled. From the selected schools students from grade 10–12 were surveyed. Survey was conducted using a structured questionnaire including the beck depression inventory‑II, and questions exploring the correlates of depression. Results: About 30% of participants were found to be depressed. Depression was more prevalent among female adolescents whose household income was inferior to 12,000 Saudi Riyal/month (odds ratio [OR] 2.17, confidence interval [CI] 0.97–6.84), did not have a good relationship with peers and family members (OR 4.63, CI 2.56–8.41), lived with single parent or alone (OR 1.77, CI 0.97–3.23), had been emotionally abused (OR 3.45, CI 2.56–8.41), and those who had been subjected to physical violence at least once (OR 3.34, CI 1.89–5.91). Conclusions: Strategies need to be developed to identify early signs and symptoms of depression among Saudi female adolescents. Training can be given to groups of students to help their peers, and also to the teachers to identify, and help students identify early signs of depression and provide them with better‑coping strategies to combat progression of depression and anxiety among such adolescents.

Keywords: adolescents, depression, Saudi Arabia, mental health

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Authors: Eugene Stepanov, Arkadi Ponossov

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Many mathematical models used in biological and other applications are ill-posed. The reason for that is the nature of differential equations, where the nonlinearities are assumed to be step functions, which is done to simplify the analysis. Prominent examples are switched systems arising from gene regulatory networks and neural field equations. This simplification leads, however, to theoretical and numerical complications. In the presentation, it is proposed to apply the theory of hybrid feedback controls to regularize the problem. Roughly speaking, one attaches a finite state control (‘automaton’), which follows the trajectories of the original system and governs its dynamics at the points of ill-posedness. The construction of the automaton is based on the classification of the attractors of the specially designed adjoint dynamical system. This ‘hybridization’ is shown to regularize the original switched system and gives rise to efficient hybrid numerical schemes. Several examples are provided in the presentation, which supports the suggested analysis. The method can be of interest in other applied fields, where differential equations contain step-like nonlinearities.

Keywords: hybrid feedback control, ill-posed problems, singular perturbation analysis, step-like nonlinearities

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Authors: Júlia Cristina Bonaldo, Christophe L. Martin, Martiniano Piccico, Keith Beale, Roop Kishore, Severine Romero-Baivier

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Refractory composite materials employed in steel casting applications are prone to cracking and material damage because of the very high operating temperature (thermal shock) and mismatched properties of the constituent phases. The fracture behavior of a model MgO-C composite refractory is investigated to quantify and characterize its thermal shock resistance, employing a cold crushing test and Brazilian test with fractographic analysis. The discrete element method (DEM) is used to generate numerical refractory composites. The composite in DEM is represented by an assembly of bonded particle clusters forming perfectly spherical aggregates and single spherical particles. For the stresses to converge with a low standard deviation and a minimum number of particles to allow reasonable CPU calculation time, representative volume element (RVE) numerical packings are created with various numbers of particles. Key microscopic properties are calibrated sequentially by comparing stress-strain curves from crushing experimental data. Comparing simulations with experiments also allows for the evaluation of crack propagation, fracture energy, and strength. The crack propagation during Brazilian experimental tests is monitored with digital image correlation (DIC). Simulations and experiments reveal three distinct types of fracture. The crack may spread throughout the aggregate, at the aggregate-matrix interface, or throughout the matrix.

Keywords: refractory composite, fracture mechanics, crack propagation, DEM

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Authors: Huijie Wang, Bin Zhang

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In China, the middle reaches of the Yangtze River are well-developed, boasting a wealth of different types of watershed landscape. In this regard, landscape character assessment (LCA) can serve as a basis for protection, management and planning of trans-regional watershed landscape types. For this study, we chose the middle reaches of the Yangtze River in Wuhan metropolitan area as our study site, wherein the water system consists of rich variety in landscape types. We analyzed trans-regional data to cluster and identify types of landscape characteristics at two levels. 55 basins were analyzed as variables with topography, land cover and river system features in order to identify the watershed landscape character types. For watershed landscape, drainage density and degree of curvature were specified as special variables to directly reflect the regional differences of river system features. Then, we used the principal component analysis (PCA) method and hierarchical clustering algorithm based on the geographic information system (GIS) and statistical products and services solution (SPSS) to obtain results for clusters of watershed landscape which were divided into 8 characteristic groups. These groups highlighted watershed landscape characteristics of different river systems as well as key landscape characteristics that can serve as a basis for targeted protection of watershed landscape characteristics, thus helping to rationally develop multi-value landscape resources and promote coordinated development of trans-regions.

Keywords: GIS, hierarchical clustering, landscape character, landscape typology, principal component analysis, watershed

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Authors: Apichai Sawisit, Sirima Suvarnakuta Jantama, Sunthorn Kanchanatawee, Lonnie O. Ingram, Kaemwich Jantama

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Escherichia coli KJ122 was engineered to produce succinate from glucose using the wild type GalP for glucose uptake instead of the native phosphotransferase system (ptsI mutation). This strain ferments 10% (w/v) xylose poorly. Mutants were selected by serial transfers in AM1 mineral salts medium with 10% (w/v) xylose. Evolved mutants exhibited a similar improvement, co-fermentation of an equal mixture of xylose and glucose. One of these, AS1600a, produced 84.26±1.37 g/L succinate, equivalent to that produced by the parent (KJ122) strain from 10% glucose (85.46±1.78 g/L). AS1600a was sequenced and found to contain a mutation in galactose permease (GalP, G236D). Expressing the galP* mutation gene in KJ122ΔgalP resembled the xylose utilization phenotype of the mutant AS1600a. The strain AS1600a and KJ122ΔgalP (pLOI5746; galP*) also co-fermented a mixture of glucose, xylose, arabinose, and galactose in sugarcane bagasse hydrolysate for succinate production.

Keywords: xylose, furfural, succinate, sugarcane bagasse, E. coli

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Authors: Alexis John de Britto

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Studies were performed to select the superior genotypes based on intra-specific variations, caused by phytogeographical, climatic and edaphic parameters of three anti cancer drug yielding mangrove plants such as Acanthus ilicifolius L., Calophyllum inophyllum L. and Excoecaria agallocha L. using ISSR (Inter Simple Sequence Repeats) markers and phytochemical analysis such as preliminary phytochemical tests, TLC, HPTLC, HPLC and antioxidant tests. The plants were collected from five different geographical locations of the East Coast of south India. Genetic heterozygosity, Nei’s gene diversity, Shannon’s information index and Percentage of polymorphism between the populations were calculated using POPGENE software. Cluster analysis was performed using UPGMA algorithm. AMOVA and correlations between genetic diversity and soil factors were analyzed. Combining the molecular and phytochemical variations superior genotypes were selected. Conservation constraints and methods of efficient exploitation of the species are discussed.

Keywords: anti-cancer drug yielding plants, DNA fingerprinting, phytochemical analysis, selection of superior genotypes

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Authors: Gómez Romero Jacob, García Peña Elvia Inés

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The co-digestion process of crude cheese whey (CCW) with fruit vegetable waste (FVW) for biohydrogen production was investigated in batch and continuous systems, in stirred 1.8 L bioreactors at 37°C. Five different C/N ratios (7, 17, 21, 31, and 46) were tested in batch systems. While, in continuous system eight conditions were evaluated, hydraulic retention time (from 60 to 10 h) and organic load rate (from 21.96 to 155.87 g COD/L d). Data in batch tests showed a maximum specific biohydrogen production rate of 10.68 mmol H2/Lh and a biohydrogen yield of 449.84 mL H2/g COD at a C/N ratio of 21. In continuous co-digestion system, the optimum hydraulic retention time and organic loading rate were 17.5 h and 80.02 g COD/L d, respectively. Under these conditions, the highest volumetric production hydrogen rate (VPHR) and hydrogen yield were 11.02 mmol H2/L h, 800 mL H2/COD, respectively. A pyrosequencing analysis showed that the main acclimated microbial communities for co-digestion studies consisted of Bifidobacterium, with 85.4% of predominance. Hydrogen producing bacteria such as Klebsiella (9.1%), Lactobacillus (0.97%), Citrobacter (0.21%), Enterobacter (0.27%), and Clostridium (0.18%) were less abundant at this culture period. The microbial population structure was correlated with the lactate, acetate, and butyrate profiles obtained. Results demonstrated that the co-digestion of CCW with FVW improves biohydrogen production due to a better nutrient balance and improvement of the system’s buffering capacity.

Keywords: acclimatation, biohydrogen, co-digestion, microbial community

Procedia PDF Downloads 556