Search results for: root microbiome

Authors: Asmaa Al Shafiee, Erdin Ibraim

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Stabilizing slopes by using vegetation is considered as a cost-effective and eco-friendly alternative to the conventional methods. The main aim of this study is to investigate the mechanical effect of analogue root systems on the shear strength of different soil types. Three objectives were defined to achieve the main aim of this paper. Firstly, explore the effect of root architectural design to shear strength parameters. Secondly, study the effect of root area ratio (RAR) on the shear strength of two different soil types. Finally, to investigate how different kinds of soil can affect the behavior of the roots during shear failure. 3D printing tool was used to develop different analogue tap root models with different architectural designs. Direct shear tests were performed on Leighton Buzzard (LB) fraction B sand, which represents a coarse sand and Huston sand, which represent medium-coarse sand. All tests were done with the same relative density for both kinds of sand. The results of the direct shear test indicated that using plant roots will increase both friction angle and cohesion of soil. Additionally, different root designs affected differently the shear strength of the soil. Furthermore, the directly proportional relationship was found between root area ratio for the same root design and shear strength parameters of soil. Finally, the root area ratio effect should be combined with branches penetrating the shear plane to get the highest results.

Keywords: leighton buzzard sand, root area ratio, rooted soil, shear strength, slope stabilization

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Authors: Muhammad Ashfaq, Muhammad Saleem Haider, Muhammad Ali, Muhammad Sajjad, Amna Ali, Urooj Mubashar

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Phenotypic diversity was confirmed by measuring different morphological traits i.e. seed traits (seed length, seed width, seed thickness, seed length-width ratio, 1000 grain weight) and root-shoot traits (shoot length, root length, shoot fresh weight, root fresh weight, root-shoot ratio, root numbers and root thickness). Variance and association study of desirable traits determine the genotypic differences among the rice germplasm. All the traits showed significant differences among the genotypes. The traits were studied in Randomized complete block design (RCBD) at different water levels. Some traits showed positive correlation with each other and beneficial for increasing the yield and production of the crop. Seed thickness has positive correlation with seed length and seed width (r= 0.104**, r=0.246**). On the other hand, various root shoot traits showed positive highly significant association at different water levels i.e. root length, fresh root weight, root thickness, shoot thickness and root numbers. Our main focus to study the performance/correlation of root shoots traits under stress condition. Fresh root weight, shoot thickness and root numbers showed positive significant association with shoot length, root length, fresh root and shoot weight (r=0.2530**, r=0.2891**, r=0.4626**, r=0.4515**, r=0.5781**, r=0.7164**, r=0.0603**, r= 0.5570**, r=0.5824**). Long root length genotypes favors and suitable for drought stress conditions and screening of diverse genotypes for the further development of new plant material that performing well under different environmental conditions. After screening genetic diversity of potential rice, lines were studied to check the polymorphism by using some SSR markers. DNA was extracted, and PCR analyses were done to study PIC values and allelic diversity of the genotypes. The main objective of this study is to screen out the genotypes on the basis of various genotypic and phenotypic traits.

Keywords: rice, morphological traits, association, germplasm, genetic diversity, water levels, variation

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Authors: Kang Huang, Wanting Zhou, Shiwei Yuan, Lei Li

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Since information technology develops rapidly, the security issue has become an increasingly critical for computer system. In particular, as cloud computing and the Internet of Things (IoT) continue to gain widespread adoption, computer systems need to new security threats and attacks. The Root of Trust (RoT) is the foundation for providing basic trusted computing, which is used to verify the security and trustworthiness of other components. Design a reliable Root of Trust and guarantee its own security are essential for improving the overall security and credibility of computer systems. In this paper, we discuss the implementation of self-security technology based on the RISC-V Root of Trust at the hardware level. To effectively safeguard the security of the Root of Trust, researches on security safeguard technology on the Root of Trust have been studied. At first, a lightweight and secure boot framework is proposed as a secure mechanism. Secondly, two kinds of memory protection mechanism are built to against memory attacks. Moreover, hardware implementation of proposed method has been also investigated. A series of experiments and tests have been carried on to verify to effectiveness of the proposed method. The experimental results demonstrated that the proposed approach is effective in verifying the integrity of the Root of Trust’s own boot rom, user instructions, and data, ensuring authenticity and enabling the secure boot of the Root of Trust’s own system. Additionally, our approach provides memory protection against certain types of memory attacks, such as cache leaks and tampering, and ensures the security of root-of-trust sensitive information, including keys.

Keywords: root of trust, secure boot, memory protection, hardware security

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Authors: Matthew Cardeiro, Amalia D. Ardeljan, Lexi Frankel, Dianela Prado Escobar, Catalina Molnar, Omar M. Rashid

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Introduction: Enterococci comprise the natural flora of nearly all animals and are ubiquitous in food manufacturing and probiotics. However, its role in the microbiome remains controversial. The gut microbiome has shown to play an important role in immunology and cancer. Further, recent data has suggested a relationship between gut microbiota and breast cancer. These studies have shown that the gut microbiome of patients with breast cancer differs from that of healthy patients. Research regarding enterococcus infection and its sequala is limited, and further research is needed in order to understand the relationship between infection and cancer. Enterococcus may prevent the development of breast cancer (BC) through complex immunologic and microbiotic adaptations following an enterococcus infection. This study investigated the effect of enterococcus infection and the incidence of BC. Methods: A retrospective study (January 2010- December 2019) was provided by a Health Insurance Portability and Accountability Act (HIPAA) compliant national database and conducted using a Humans Health Insurance Database. International Classification of Disease (ICD) 9th and 10th codes, Current Procedural Terminology (CPT), and National Drug Codes were used to identify BC diagnosis and enterococcus infection. Patients were matched for age, sex, Charlson Comorbidity Index (CCI), antibiotic treatment, and region of residence. Chi-squared, logistic regression, and odds ratio were implemented to assess the significance and estimate relative risk. Results: 671 out of 28,518 (2.35%) patients with a prior enterococcus infection and 1,459 out of 28,518 (5.12%) patients without enterococcus infection subsequently developed BC, and the difference was statistically significant (p<2.2x10⁻¹⁶). Logistic regression also indicated enterococcus infection was associated with a decreased incidence of BC (RR=0.60, 95% CI [0.57, 0.63]). Treatment for enterococcus infection was analyzed and controlled for in both enterococcus infected and noninfected populations. 398 out of 11,523 (3.34%) patients with a prior enterococcus infection and treated with antibiotics were compared to 624 out of 11,523 (5.41%) patients with no history of enterococcus infection (control) and received antibiotic treatment. Both populations subsequently developed BC. Results remained statistically significant (p<2.2x10-16) with a relative risk of 0.57 (95% CI [0.54, 0.60]). Conclusion & Discussion: This study shows a statistically significant correlation between enterococcus infection and a decrease incidence of breast cancer. Further exploration is needed to identify and understand not only the role of enterococcus in the microbiome but also the protective mechanism(s) and impact enterococcus infection may have on breast cancer development. Ultimately, further research is needed in order to understand the complex and intricate relationship between the microbiome, immunology, bacterial infections, and carcinogenesis.

Keywords: breast cancer, enterococcus, immunology, infection, microbiome

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Authors: Abdul Malik Dawlatzai, Shafiqullah Rahmani

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Plant cultivars of the same species differ in their Fe efficiency. This paper studied the Fe influx and root-shoot relations of Fe at different growth stages in wheat. The four wheat cultivars (HD 2967, PDW 233, PBW 550 and PDW 291) were grown in pots in Badam Bagh agricultural researching farm, Kabul under two Fe treatments: (i) 0 mg Fe kg⁻¹ soil (soil with 2.7 mg kg⁻¹ of DTPA-extractable Fe) and (ii) 50 mg Fe kg⁻¹ soil. Root length (RL), shoot dry matter (SDM), Fe uptake, and soil parameters were measured at tillering and anthesis. Application of Fe significantly increased RL, root surface area, SDM, and Fe uptake in all wheat cultivars. Under Fe deficiency, wheat cv. HD 2967 produced 90% of its maximum RL and 75% of its maximum SDM. However, PDW 233 produced only 69% and 60%, respectively. Wheat cultivars HD 2967, and PDW 233 exhibited the highest and lowest value of root surface area and Fe uptake, respectively. The concentration difference in soil solution Fe between bulk soil and root surface (ΔCL) was maximum in wheat cultivar HD 2967, followed by PBW 550, PDW 291, and PDW 233. More depletion at the root surface causes steeper concentration gradients, which result in a high influx and transport of Fe towards root. Fe influx in all the wheat cultivars increased with the Fe application, but the increase was maximum, i.e., 4 times in HD 2967 and minimum, i.e., 2.8 times in PDW 233. It can be concluded that wheat cultivars HD 2967 and PBW 550 efficiently utilized Fe as compared to other cultivars. Additionally, iron efficiency of wheat cultivars depends upon uptake of each root segment, i.e., the influx, which in turn depends on depletion of Fe in the rhizosphere during vegetative phase and higher utilization efficiency of acquired Fe during reproductive phase that governs the ultimate grain yield.

Keywords: Fe efficiency, Fe influx, Fe uptake, Rhizosphere

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Authors: Vinod Kumar Gupta, Narendrakumar M. Chaudhari, Suchismitha Iskepalli, Chitra Dutta

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Background-The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference draft genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium. Results-The analysis reveals the exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from the human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. The pan-genome for Prevotella remains “open”. Distribution of various functional COG categories differs appreciably among the habitat-specific genes, within Prevotella pan-genome and between the GIT-derived Bacteroides and Prevotella. The skin and GIT isolates of Prevotella are enriched in singletons involved in Signal transduction mechanisms, while the UGT and oral isolates show higher representation of the Defense mechanisms category. No niche-specific variations could be observed in the distribution of KEGG pathways. Conclusion-Prevotella may have developed distinct genetic strategies for adaptation to different anatomical habitats through selective, niche-specific acquisition and elimination of suitable gene-families. In addition, individual microorganisms tend to develop their own distinctive adaptive stratagems through large repertoires of singletons. Such in situ, habitat-driven refurbishment of the genetic makeup can impart substantial intra-lineage genome diversity within the microbes without perturbing their general taxonomic heritage.

Keywords: body niche adaptation, human microbiome, pangenome, Prevotella

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Authors: Liang Jiansheng, Zhu Wei

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Light and brassinosteroids are essential external and internal cues for plant survival. Although the coordination of light with phytohormone signals is crucial for plant growth and development, the molecular connection between light and brassinosteroid signaling during root soil penetration remains elusive. Here, we reveal that light-stabilized RACK1 couples a brassinosteroid signaling cascade to drive cell division in root meristems. RACK1 family scaffold proteins positively regulate light-induced the promotion of root elongation during soil penetration. Under the light condition, RACK1A interacts with both phyB and SPA1, then reinforces the phyB-SPA1 association to accumulate its abundance in roots. In response to brassinosteroid signals, RACK1A competes with BKI1 to attenuate the BRI1-BKI1 interaction, thereby leading to activating BRI1 actions in root development. Furthermore, RACK1A binds to BES1 to repress its DNA binding activity toward the target gene CYCD3;1. This ultimately allows to release the inhibition of CYCD3;1 transcription, and promotes cell division during root growth. Our study illustrates a new mechanistic model of how plants engage scaffold proteins in transducing light information to facilitate brassinosteroid signaling for root growth in the soil.

Keywords: root growth, cell division, light signaling, brassinosteroid signaling, soil penetration, scaffold protein, RACK1

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Authors: Thomas Slunecko Karat

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The years since 9/11 2001 have given us a plethora of research papers with the word ‘terrorism’ in the title. Yet only a small subset of these papers has produced new data, which explains why more than 20 years of research since 9/11 have done little to increase our understanding of the mechanisms that lead to terrorism. Specifically, terrorism scholars are divided by political, temporal, geographical and financial demarcation lines which prevent a clear definition of terrorism. As a consequence, the true root causes of terrorism remain unexamined. Instead, the psychopathological conditions of the individual have been emphasized despite ample empirical evidence pointing in a different direction. This paper examines the underlying reasons and motives that prevent open discourse about the root causes of terrorism and proposes that terrorism is linked to the current international system of resource allocation and systematic violations of human rights.

Keywords: terrorism, root causes of terrorism, prevention of terrorism, racism, human rights violations

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Authors: Eszter Repasi, Akos Koller

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Our genetic information determines our look, physiology, sports performance and all our features. Maximizing the performances of athletes have adopted a science-based approach to the nutritional support. Nowadays genetics studies have blended with nutritional sciences, and a dynamically evolving, new research field have appeared. Nutritional genomics is needed to be used by nutritional experts. This is a recent field of nutritional science, which can provide a solution to reach the best sport performance using correlations between the athlete’s genome, nutritions, molecules, included human microbiome (links between food, microbiome and epigenetics), nutrigenomics and nutrigenetics. Nutritional genomics has a tremendous potential to change the future of dietary guidelines and personal recommendations. Experts need to use new technology to get information about the athletes, like nutritional genomics profile (included the determination of the oral and gut microbiome and DNA coded reaction for food components), which can modify the preparation term and sports performance. The influence of nutrients on the genes expression is called Nutrigenomics. The heterogeneous response of gene variants to nutrients, dietary components is called Nutrigenetics. The human microbiome plays a critical role in the state of health and well-being, and there are more links between food or nutrition and the human microbiome composition, which can develop diseases and epigenetic changes as well. A nutritional genomics-based profile of athletes can be the best technic for a dietitian to make a unique sports nutrition diet plan. Using functional food and the right food components can be effected on health state, thus sports performance. Scientists need to determine the best response, due to the effect of nutrients on health, through altering genome promote metabolites and result changes in physiology. Nutritional biochemistry explains why polymorphisms in genes for the absorption, circulation, or metabolism of essential nutrients (such as n-3 polyunsaturated fatty acids or epigallocatechin-3-gallate), would affect the efficacy of that nutrient. Controlled nutritional deficiencies and failures, prevented the change of health state or a newly discovered food intolerance are observed by a proper medical team, can support better sports performance. It is important that the dietetics profession informed on gene-diet interactions, that may be leading to optimal health, reduced risk of injury or disease. A special medical application for documentation and monitoring of data of health state and risk factors can uphold and warn the medical team for an early action and help to be able to do a proper health service in time. This model can set up a personalized nutrition advice from the status control, through the recovery, to the monitoring. But more studies are needed to understand the mechanisms and to be able to change the composition of the microbiome, environmental and genetic risk factors in cases of athletes.

Keywords: gene-diet interaction, multidisciplinary team, microbiome, diet plan

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Authors: Shalini TV, Gangadharan GG, Sriranjini S Jaideep, ASN Seshasayee, Awadhesh Pandit

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Introduction: Prakriti (body-mind constitution of an individual) is a conventional, customized and unique understanding of which is essential for the personalized medicine described in Ayurveda, Indian System of Medicine. Based on the Doshas( functional, bio humoral unit in the body), individuals are categorized into three major Prakriti- Vata, Pitta, and Kapha. The human gut microbiome hosts plenty of highly diverse and metabolically active microorganisms, mainly dominated by the bacteria, which are known to influence the physiology of an individual. Few researches have shown the correlation between the Prakriti and the biochemical parameters. In this study, an attempt was made to explore any correlation between the Prakriti (phenotype of an individual) with the Genetic makeup of the gut microbiome in healthy individuals. Materials and methods: 270 multi-ethnic, healthy volunteers of both sex with the age group between 18 to 40 years, with no history of antibiotics in the last 6 months were recruited into three groups of Vata, Pitta, and Kapha. The Prakriti of the individual was determined using Ayusoft, a software designed by CDAC, Pune, India. The volunteers were subjected to initial screening for the assessment of their height, weight, Body Mass Index, Vital signs and Blood investigations to ensure they are healthy. The stool and saliva samples of the recruited volunteers were collected as per the standard operating procedure developed, and the bacterial DNA was isolated using Qiagen kits. The extracted DNA was subjected to 16s rRNA sequencing using the Illumina kits. The sequencing libraries are targeting the variable V3 and V4 regions of the 16s rRNA gene. Paired sequencing was done on the MiSeq system and data were analyzed using the CLC Genomics workbench 11. Results: The 16s rRNA sequencing of the V3 and V4 regions showed a diverse pattern in both the oral and stool microbial DNA. The study did not reveal any specific pattern of bacterial flora amongst the Prakriti. All the p-values were more than the effective alpha values for all OTUs in both the buccal cavity and stool samples. Therefore, there was no observed significant enrichment of an OTU in the patient samples from either the buccal cavity or stool samples. Conclusion: In healthy volunteers of multi-ethnicity, due to the influence of the various factors, the correlation between the Prakriti and the gut microbiome was not seen.

Keywords: gut microbiome, ayurveda Prakriti, sequencing, multi-ethnic urban population

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Authors: Rasha Sharaf, Nehal Sharaf

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Pulpectomy of primary teeth aims to remove the necrotic pulp tissue from the infected root canal and clean the root canal walls from any remnant of pulp tissue. Different irrigant activation systems have been recently used, and one of these devices is the Eddy which helps in removal of smear layer and improves the intimate contact between the filling material and the root canal wall. Aim: To evaluate the efficacy of Eddy in cleanliness of the root canal during pulpectomy of primary teeth. Materials and methods: 45 freshly extracted primary anterior teeth were divided into 3 equal groups, in the 1st group sodium hypochlorite only was used during pulpectomy, in the 2nd group irrigation using sodium hypochlorite with file agitation was performed and in the 3rd group sodium hypochlorite was used with Eddy for irrigant activation. All samples were sectioned longitudinally and scanned using scanning electron microscope to evaluate the cleanliness of the root canals. Results: It was found that Eddy showed high efficacy in removal of smear layer during pulpectomy of primary teeth.

Keywords: Eddy, irrigant activation, irrigation, pulpectomy

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Authors: Pravaree Phuneerub, Chanida Palanuvej, Nijsiri Ruangrungsi

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Cymbopogon nardus Rendel (Family Gramineae) is commonly known as citronella grass. The dried root of C. nardus is used for antipyretic, anti-inflammation, anti-analgesic and anticancer in traditional Thai medicine. Transverse sectional and pulverized C. nardus root were illustrated. The volatile oil was extracted from oil gland by hydrodistillation and analysed by GC/MS. Cymbopogon nardus root was exhaustively extracted by continuously maceration in ethanol and water respectively. The mutagenic and antimutagenic properties of the ethanol extract and fractionated water extract of C. nardus root were evaluated by Ames assay using the S. typhimurium strains TA98 and TA100 as the models. The result indicated that the anatomical character of root transverse section displayed epidermis, parenchyma, oil gland, phloem, xylem vessel, endodermis and pith. Histological characters of root powder showed parenchyma containing oleoresin, parenchyma in longitudinal view, reticulate vessel, annular vessel, starch granules and fragment of fiber. The root volatile oil was rich in sesquiterpenes dominated by elemol (22.87%) and alpha-eudesmol (16.09%). For mutagenic activity, the both extracts of C. nardus were no mutagenic toward S. typhimurium strains TA98 and TA100. Furthermore, the ethanol extract and fractionated water extract of C. nardus root demonstrated strong antimutagenic effect against of nitrite treated 1-aminopyrene to S. typhimurium strains TA98 and TA100. This present investigation suggested that the dried root extract of C. nardus can be further developed as promising antimutagenic agent.

Keywords: Cymbopogon nardus, volatile oil analysis, mutagenic, antimutagenic effect, Ames Salmonella assay

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Authors: Danyi Wang, Andrew Schriefer, Dennis O'Rourke, Brajendra Kumar, Yang Liu, Fei Zhong, Juergen Scheuenpflug, Zheng Feng

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Purpose: It has been recognized that the microbiome plays critical roles in disease pathogenesis, including cancer, autoimmune disease, and multiple sclerosis. To develop a clinical-grade assay for exploring microbiome-derived clinical biomarkers across disease areas, a two-phase approach is implemented. 1) Identification of the optimal sample preparation reagents using pre-mixed bacteria and healthy donor stool samples coupled with proprietary Sigma-Aldrich® bioinformatics solution. 2) Exploratory analysis of patient samples for enabling precision medicine. Study Procedure: In phase 1 study, we first compared the 16S sequencing results of two ATCC® microbiome standards (MSA 2002 and MSA 2003) across five different extraction kits (Kit A, B, C, D & E). Both microbiome standards samples were extracted in triplicate across all extraction kits. Following isolation, DNA quantity was determined by Qubit assay. DNA quality was assessed to determine purity and to confirm extracted DNA is of high molecular weight. Bacterial 16S ribosomal ribonucleic acid (rRNA) amplicons were generated via amplification of the V3/V4 hypervariable region of the 16S rRNA. Sequencing was performed using a 2x300 bp paired-end configuration on the Illumina MiSeq. Fastq files were analyzed using the Sigma-Aldrich® Microbiome Platform. The Microbiome Platform is a cloud-based service that offers best-in-class 16S-seq and WGS analysis pipelines and databases. The Platform and its methods have been extensively benchmarked using microbiome standards generated internally by MilliporeSigma and other external providers. Data Summary: The DNA yield using the extraction kit D and E is below the limit of detection (100 pg/µl) of Qubit assay as both extraction kits are intended for samples with low bacterial counts. The pre-mixed bacterial pellets at high concentrations with an input of 2 x106 cells for MSA-2002 and 1 x106 cells from MSA-2003 were not compatible with the kits. Among the remaining 3 extraction kits, kit A produced the greatest yield whereas kit B provided the least yield (Kit-A/MSA-2002: 174.25 ± 34.98; Kit-A/MSA-2003: 179.89 ± 30.18; Kit-B/MSA-2002: 27.86 ± 9.35; Kit-B/MSA-2003: 23.14 ± 6.39; Kit-C/MSA-2002: 55.19 ± 10.18; Kit-C/MSA-2003: 35.80 ± 11.41 (Mean ± SD)). Also, kit A produced the greatest yield, whereas kit B provided the least yield. The PCoA 3D visualization of the Weighted Unifrac beta diversity shows that kits A and C cluster closely together while kit B appears as an outlier. The kit A sequencing samples cluster more closely together than both the other kits. The taxonomic profiles of kit B have lower recall when compared to the known mixture profiles indicating that kit B was inefficient at detecting some of the bacteria. Conclusion: Our data demonstrated that the DNA extraction method impacts DNA concentration, purity, and microbial communities detected by next-generation sequencing analysis. Further microbiome analysis performance comparison of using healthy stool samples is underway; also, colorectal cancer patients' samples will be acquired for further explore the clinical utilities. Collectively, our comprehensive qualification approach, including the evaluation of optimal DNA extraction conditions, the inclusion of positive controls, and the implementation of a robust qualified bioinformatics pipeline, assures accurate characterization of the microbiota in a complex matrix for deciphering the deep biology and enabling precision medicine.

Keywords: 16S rRNA sequencing, analytical validation, bioinformatics pipeline, metagenomics

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Authors: H. El-Messiry, M. El-Zainy, D. Abdelkhalek

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Cone-beam computed tomography (CBCT) provides high-quality 3-dimensional images of dental structures because of its high spatial resolution. The study of dental morphology is important in research as it provides information about diversities within a population. Many studies have shown different shapes and numbers of roots canals among different races, especially in molars. The aim of this study was to determine the morphology of root canals of mandibular first and third molars in a sample of Egyptian population using CBCT scanning. Fifty mandibular first Molars (M1) and fifty mandibular third (M3) extracted molars were collected. Thick rectangular molds were made using pink wax to hold the samples. Molars were embedded in the wax mold by aligning them in rows leaving arbitrary 0.5cm space between them. The molds with the samples in were submitted for CBCT scan. The number and morphology of root canals were assessed and classified according to Vertucci's classification. The mesial and the distal roots were examined separately. Finally, data was analyzed using Fisher exact test. The most prevalent mesial root canal frequency in M1 was type IV (60%) and type II (40 %), while M3 showed prevalence of type I (40%) and II (40%). Distal root canal morphology showed prevalence of type I in both M1 (66%) and M3 (86%). So, it can be concluded that CBCT scanning provides supplemental information about the root canal configurations of mandibular molars in a sample of Egyptian population. This study may help clinicians in the root canal treatment of mandibular molars.

Keywords: cone beam computed tomography, mandibular first molar, mandibular third molar, root canal morphology

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Authors: M. Imran Hamid, Muzammil Hussain, Yunpeng Wu, Meichun Xiang, Xingzhong Liu

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The rhizosphere microbiome elucidate multiple functioning in the soil suppressiveness against plant pathogens. Soybean rhizosphere microbial communities may involve in the natural suppression of soybean cyst nematode (SCN) populations in disease suppressive soils. To explore these ecological mechanisms of microbes, a long term monoculture suppressive soil were taken into account for further investigation to test the disease suppressive ability by using different treatments. The designed treatments are as, i) suppressive soil (S), ii) conducive soil (C), iii) conducive soil mixed with 10% (w/w) suppressive soil (CS), iv) suppressive soil treated at 80°C for 1 hr (S80), and v) suppressive soil treated with formalin (SF). By using an ultra-high-throughput sequencing approach, we identified the key bacterial and fungal taxa involved in SCN suppression. The Phylum-level investigation of bacteria revealed that Actinobacteria, Bacteroidetes, and Proteobacteria in the rhizosphere soil of soybean seedlings were more abundant in the suppressive soil than in the conducive soil. The phylum-level analysis of fungi in rhizosphere soil indicated that relative abundance of Ascomycota was higher in suppressive soil than in the conducive soil, where Basidiomycota was more abundant. Transferring suppressive soil to conducive soil increased the population of Ascomycota in the conducive soil by lowering the populations of Basidiomycota. The genera, such as, Pochonia, Purpureocillium, Fusarium, Stachybotrys that have been well documented as bio-control agents of plant nematodes were far more in the disease suppressive soils. Our results suggested that the plants engage a subset of functional microbial groups in the rhizosphere for initial defense upon nematode attack and protect the plant roots later on by nematodes to response for suppression of SCN in disease-suppressive soils.

Keywords: disease suppressive soil, high-throughput sequencing, rhizosphere microbiome, soybean cyst nematode

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Authors: Sofia Sehli, Zainab El Ouafi, Casey Eddington, Soumaya Jbara, Kasambula Arthur Shem, Islam El Jaddaoui, Ayorinde Afolayan, Olaitan I. Awe, Allissa Dillman, Hassan Ghazal

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The ability to promptly sequence whole genomes at a relatively low cost has revolutionized the way we study the microbiome. Microbiologists are no longer limited to studying what can be grown in a laboratory and instead are given the opportunity to rapidly identify the makeup of microbial communities in a wide variety of environments. Analyzing whole genome sequencing (WGS) data is a complex process that involves multiple moving parts and might be rather unintuitive for scientists that don’t typically work with this type of data. Thus, to help lower the barrier for less-computationally inclined individuals, TAXAPRO was developed at the first Omics Codeathon held virtually by the African Society for Bioinformatics and Computational Biology (ASBCB) in June 2021. TAXAPRO is an advanced metagenomics pipeline that accurately assembles organelle genomes from whole-genome sequencing data. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents organism abundance information in both a tabular and graphical format. TAXAPRO was evaluated using COVID-19 patient gut microbiome data. Analysis performed by TAXAPRO demonstrated a high abundance of Clostridia and Bacteroidia genera and a low abundance of Proteobacteria genera relative to others in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings derived using a different analysis methodology. This provides crucial evidence that the TAXAPRO workflow dispenses reliable organism abundance information overnight without the hassle of performing the analysis manually.

Keywords: metagenomics, shotgun metagenomic sequence analysis, COVID-19, pipeline, bioinformatics

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Authors: Anuj Tyagi, Balwinder Singh, Naveen Kumar B. T., Niraj K. Singh

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Characterization of diverse microbial communities in specific environment plays a crucial role in the better understanding of their functional relationship with the ecosystem. It is now well established that gut microbiome of fish is not the simple replication of microbiota of surrounding local habitat, and extensive species, dietary, physiological and metabolic variations in fishes may have a significant impact on its composition. Moreover, overuse of antibiotics in human, veterinary and aquaculture medicine has led to rapid emergence and propagation of antibiotic resistance genes (ARGs) in the aquatic environment. Microbial communities harboring specific ARGs not only get a preferential edge during selective antibiotic exposure but also possess the significant risk of ARGs transfer to other non-resistance bacteria within the confined environments. This phenomenon may lead to the emergence of habitat-specific microbial resistomes and subsequent emergence of virulent antibiotic-resistant pathogens with severe fish and consumer health consequences. In this study, gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. Metagenomic DNA, extracted from the fish gut, was subjected to sequencing on Illumina NextSeq to generate paired-end (PE) 2 x 150 bp sequencing reads. After the QC of raw sequencing data by Trimmomatic, taxonomic analysis by Kraken2 taxonomic sequence classification system revealed the presence of 36 phyla, 326 families and 985 genera in the fish gut microbiome. At phylum level, Proteobacteria accounted for more than three-fourths of total bacterial populations followed by Actinobacteria (14%) and Cyanobacteria (3%). Commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) were found to be very less prevalent in fish gut. After sequencing data assembly by MEGAHIT v1.1.2 assembler and PROKKA automated analysis pipeline, pathway analysis revealed the presence of 1,608 Metacyc pathways in the fish gut microbiome. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy-metabolism (4%) and fermentation (2%). Almost one-third (33%) of biosynthesis pathways were involved in the synthesis of secondary metabolites. Metabolic pathways for the biosynthesis of 35 antibiotic types were also present, and these accounted for 5% of overall metabolic pathways in the fish gut microbiome. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. More than 90% ARGs in fish gut microbiome were against beta-lactams (penicillins, cephalosporins, penems, and monobactams). Resistance against tetracycline, macrolides, fluoroquinolones, and phenicols ranged from 0.7% to 1.3%. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment.

Keywords: antibiotic resistance, fish gut, metabolic pathways, microbial diversity

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Authors: Barbara Torres Rives

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Uveitis. Non-infectious anterior uveitis is a polygenic inflammatory eye disease, and it is suggested that mediated processes by the immune system (autoimmune or not) are the main mechanisms proposed in the pathogenesis of this type of uveitis. A relationship between infectious processes, digestive disorders, and a dysbiosis of the microbiome was recently described. In addition, alterations in the immune response associated with the initiation and progression of the disease have been described. Objective: The aim of this study was to identify factors related to the immune system associated with complicated non-infectious anterior uveitis. Methods: A cross-sectional observational analytical study was carried out. The universe consisted of all patients attending the ocular inflammation service of the Cuban Institute of Ophthalmology Ramón Pando Ferrer. The sample consisted of 213 patients diagnosed with non-infectious anterior uveitis. Results: Of the 213 patients with non-infectious anterior uveitis, the development of ophthalmologic complications predominated 56.3% (p=0.0094). In patients with complications was more frequent the presence of human leukocyte antigen-B27 allele (49.2%) (p<0.0001), decreased immunoglobulin G (24.2%, p=0.0124), increased immunoglobulin A (14.2%, p=0.0024), history of recurrent sepsis (59.2%, p=0.0018), recurrent respiratory infections (44.2%, p=0.0003), digestive alterations (40%, p=0.0013) and spondyloarthropathies (30%, p=0.0314). By logistic regression, it was observed that, for each completed year, the elevated risk for developing complicated non-infectious anterior uveitis in human leukocyte antigen-B27 allele positive patients (OR: 4.22, p=0.000), Conclusions: The control of recurrent sepsis at mucosal level and immunomodulation could prevent complications in non-infectious anterior uveitis. Therefore, the microbiome becomes the target of treatment and prevention of complications in non-infectious anterior uveitis.

Keywords: non-infectious anterior uveitis, immune system disorders, recurrent mucosal infections, microbiome

Procedia PDF Downloads 58

Authors: Mosima M. Mabitsela

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Groundnut is preferably grown on light textured soils. Most of these light textured soils tend to be highly weathered and characterized by high soil acidity and low nutrient status. One major soil factor associated with infertility of acidic soils that can negatively depress groundnut yield is aluminium (Al) toxicity. In plants Al toxicity damages root cells, leading to inhibition of root growth as a result of the suppression of cell division, cell elongation and cell expansion in the apical meristem cells of the root. The end result is that roots become stunted and brittle, root hair development is poor, and the root apices become swollen. This study was conducted to determine the effects of aluminium (Al) toxicity on a range of groundnut varieties. Fifteen cultivars were tested in incremental aluminum (Al) supply in an ebb and flow solution culture laid out in a randomized complete block design. There were six aluminium (Al) treatments viz. 0 µM, 1 µM, 5.7 µM, 14.14 µM, 53.18 µM, and 200 µM. At 1 µM there was no inhibitory effect on the growth of groundnut. The inhibition of groundnut growth was noticeable from 5.7 µM to 200 µM, where the severe effect of aluminium (Al) stress was observed at 200 µM. The cultivars varied in their response to aluminium (Al) supply in solution culture. Groundnuts are one of the most important food crops in the world, and its supply is on a decline due to the light-textured soils that they thrive under as these soils are acidic and can easily solubilize aluminium (Al) to its toxic form. Consequently, there is a need to develop groundnut cultivars with high tolerance to soil acidity.

Keywords: aluminium toxicity, cultivars, reduction, root growth

Procedia PDF Downloads 119

Authors: Mira Ezora Zainal Abidin, Siti Fauzuna Othman, Zalina Harun, M. Hafiz M. Pikri

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In a fire incident involving a Nitrogen storage tank that over-pressured and exploded, resulting in a fire in one of the units in a refinery, lack of data and evidence hampered the investigation to determine the root cause. Instrumentation and fittings were destroyed in the fire. To make it worst, this incident occurred during the COVID-19 pandemic, making collecting and testing evidence delayed. In addition to that, the storage tank belonged to a third-party company which requires legal agreement prior to the refinery getting approval to test the remains. Despite all that, the investigation had to be carried out with stakeholders demanding answers. The investigation team had to devise alternative means to support whatever little evidence came out as the most probable root cause. International standards, practices, and previous incidents on similar tanks were referred. To narrow down to just one root cause from 8 possible causes, transient simulations were conducted to simulate the overpressure scenarios to prove and eliminate the other causes, leaving one root cause. This paper shares the methodology used and details how transient simulations were applied to help solve this. The experience and lessons learned gained from the event investigation and from numerous case studies via transient analysis in finding the root cause of the accident leads to the formulation of future mitigations and design modifications aiming at preventing such incidents or at least minimize the consequences from the fire incident.

Keywords: fire, transient, simulation, relief

Procedia PDF Downloads 68

Authors: Baharullah Khattak, Saifullah

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To study the efficacy of the selected Trichoderma isolates, field trials were conducted in the root-knot nematode-infested areas of Dargai and Swat, Pakistan. Four isolates of T. harzianum viz, Th-1, Th-2, Th-9 and Th-15 were tested against root knot nematodes on summer tomatoes under field conditions. The T. harzianum isolates, grown on wheat grains substrate, were applied @ 8 g plant-1, either alone or in different combinations. Root weight of tomato plants was reduced Th-9 as compared to 26.37 g in untreated control. Isolate Th-1 was found to enhance shoot and root lengths to the maximum levels of 78.76 cm and 19.59 cm, respectively. Tomato shoot weight was significantly increased (65.36g) in Th-1-treated plots as compared to 49.66 g in control. Maximum (156) number of flowers plant-1 and highest (48.18%) fruit set plant-1 was observed in Th-1 treated plots, while there were 87 flowers and 35.50% fruit set in the untreated control. Maximum fruit weight (70.97 g) plant-1 and highest (17.99 t ha-1) marketable yield were recorded in the treatments where T. harzianum isolate Th-1 was used, in comparison to 51.33 g tomato fruit weight and 9.90 t ha-1 yield was noted in the control plots. It was observed that T. harzianum isolates significantly reduced the nematode populations. The fungus enhanced plant growth and yield in all the treated plots. Jabban isolate (Th-1) was found as the most effective in nematode suppression followed by Shamozai (Th-9) isolate. It was concluded from the present findings that T. harzianum has a potential bio control capability against root-knot nematodes.

Keywords: biological control, Trichoderma harzianum, root-knot nematode, meloidogyne

Procedia PDF Downloads 463

Authors: N. Thawornwisit, P. Pradoo, S. Nuypree, L. Jarukasetrporn, S. Jitpukdeebodintra

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Objective: The aim of this study was to evaluate the duration of the Enterococcus faecalis (E. faecalis) penetration into the gap between root canal wall and filling material at a 3 to 6 mm distance from the cementoenamel junction (CEJ) in the dislodged temporary filling, in vitro. Material and methods: Thirty-four single root canal mandibular premolars were divided into two experimental groups (N = 15) and one negative control (N = 4). Root canals were prepared and obturated with gutta-percha using lateral condensation technique, X-ray checked, and sterilized. Leakages were set up using the modified bacterial leakage model, and E. faecalis was used as a microbial marker. Leakages were evaluated at 3 and 7 days by culturing gutta-percha and dentine drilled from a 3-6 mm distance from CEJ. Broth turbidity was recorded and compared. Result: All four negative control and the 3-day experimental group showed no broth turbidity. For the 7-day experimental group, there was 33.3% leakage. Conclusion: Penetration of E. faecalis into the gap between root canal wall and filling material at a 3 to 6 mm distance from CEJ in the dislodged temporary filling were not found at three days. However, at seven days of exposure, bacteria could penetrate into the interface of the root canal and filling materials.

Keywords: coronal leakage, bacterial leakage model, enterococcus faecalis

Procedia PDF Downloads 69

Authors: Sallah S. El-Ammari, Mona. S. Hasan

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This research is aimed to study allelopathic effects of two wind breakers Eucalyptus camaldulensis and E.gomphocephala on germination and growth of barley using aqueous extracts of leaves at 0.5, 1, 5, and 10% concentrations for treatment of barley caryopsis in petri dishes incubated in growth chamber. Distilled water was used in the experiment as a control. Seed germination was recorded on daily basis for five days. After ten days measurements of root length, shoot length, fresh and dry weight of root and shoot were taken. With the exception of 0.5% E. gomphocephala extract effect on length and dry weight of barley root, all the tested extract concentrations for both eucalyptus species significantly decreased the percent and speed of germination, root and shoot length, fresh and dry weight of root and shoot of barley compared to the control. For both species the allelopathic effect was significantly increasing with the increase of the extract concentration. Although, higher allelopathic effect was shown by E. camaldulensis, the results indicating that both eucalyptus species should not be recommended as wind breakers for barley fields.

Keywords: allelopathy, eucalyptus, barley, Libya

Procedia PDF Downloads 310

Authors: Young Hee Geum

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In this paper, we present the iterative method and determine the control parameters to converge cubically for solving nonlinear equations. In addition, we derive the asymptotic error constant.

Keywords: asymptotic error constant, iterative method, multiple root, root-finding, order of convergent

Procedia PDF Downloads 265

Authors: Shahriar M. Saadullah, Abdul-Quddoos Abdul-Basith, Zaki K. Abushawish

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As a part of academic research in Islamic Accounting it is important to know how the word Accounting is discussed in the Qur’aan. This paper identifies and analyzes the word Accounting in the Qur’aan, which is significant to know and understand. The paper uses a methodology of identifying the root word of Accounting Hasaba (حسب) in the Qur’aan with the help of Islam 360 software and analyzes the use of the relevant words derived from the root word. Then the paper attempts to connect the findings to the contemporary Accounting issues. The paper finds that the root word of Accounting Hasaba (حسب) appears in the Qur’aan 109 times but it is only used in the sense Account, Accountable, or Accounting 45 times. These words appear in 44 different verses in the Qur’aan, appearing twice in one of the verses. The paper divides these verses into 8 different themes namely, Day of Accounting, without any Accounting, Accounting of Time, Self-Accounting, Swift in Accounting, Accounting is only with God, Awareness and the Good Accounting, and Heedlessness and the Bad Accounting. The way the words Account, Accounting, and Accountable is discussed in the Qur’aan links to the contemporary accounting issues including Ethics, Agency Theory, and Internal Control. The links discovered in the paper clearly shows the timeless nature of the message of the Qur’aan.

Keywords: accounting, contemporary accounting issues, Qur'aan, root word of accounting hasaba

Procedia PDF Downloads 390

Authors: Zakirul Islam, Yugo Kumokawa, Quoc Thinh Tran, Motoki Kubo

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Clubroot is a disease of cruciferous plant caused by soil born pathogen Plasmodiophora brassicae and can significantly limit the production through rapid spreading. The present study was designed to investigate the effect of cultivation practices (chemical and organic soils) on clubroot disease development in Brassica rapa. Disease index and root bacterial composition were investigated for both chemical and organic soils. The bacterial biomass and diversity in organic soil were higher than those in chemical soil. Disease severity was distinct for two different cultivation methods. The number of endophytic bacteria decreased in the infected root for both soils. The increased number of endophytic bacterial number led to reduce the proliferation of pathogen spore inside the root and thus reduced the disease severity in organic plants.

Keywords: clubroot disease, bacterial biomass, root infection, disease index, chemical cultivation, organic cultivation

Procedia PDF Downloads 49

Authors: Ji-Hyon Kil, Kew-Cheol Shim, Kyoung-Ae Park, Kyoungho Kim

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Ambrosia trifida L. is designated as invasive alien species by the Act on the Conservation and Use of Biodiversity by the Ministry of Environment, Korea. The purpose of present paper was to investigate the inhibitory effects of aqueous extracts of A.trifida on the development of root hairs of Triticum aestivum L., and Allium tuberosum Rottler ex Spreng and the electrophoretic protein patterns of their radicles. The development of root hairs was inhibited by increasing of aqueous extract concentrations. Through SDS-PAGE, the electrophoretic protein bands of extracted proteins from their radicles were appeared in controls, but protein bands of specific molecular weight disappeared or weakened in treatments. In conclusion, inhibitory effects of A. trifida made two receptor species changed morphologically, and at the molecular level in early growth stage.

Keywords: Ambrosia trifida L., invasive alien species, inhibitory effect, root hair, electrophoretic protein, radicle

Procedia PDF Downloads 320

Authors: Milind Patil

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Present paper is a discussion on Hindi-Marathi Morphological Analysis and generating rules for Machine Translation on the basis of Machine Readable Dictionary (MRD). This used Transformative Generative Grammar (TGG) rules to design the MRD. As per TGG rules, the suffix of a particular root word is based on its Tense, Aspect, Modality and Voice. That's why the suffix is very important for the word meanings (or root meanings). The Hindi and Marathi Language both have relation with Indo-Aryan language family. Both have been derived from Sanskrit language and their script is 'Devnagari'. But there are lots of differences in terms of semantics and grammatical level too. In Marathi, there are three genders, but in Hindi only two (Masculine and Feminine), the Natural gender is absent in Hindi. Likewise other grammatical categories also differ in their level of use. For MRD the suffixes (or Morpheme) are of particular root word for GNP (Gender, Number and Person) are based on its natural phenomena. A particular Suffix and Morphine change as per the need of person, number and gender. The design of MRD also based on this format. In first, Person, Number, Gender and Tense are key points than root words and suffix of particular Person, Number Gender (PNG). After that the inferences are drawn on the basis of rules that is (V.stem) (Pre.T/Past.T) (x) + (Aux-Pre.T) (x) → (V.Stem.) + (SP.TM) (X).

Keywords: MRD, TGG, stem, morph, morpheme, suffix, PNG, TAM&V, root

Procedia PDF Downloads 293

Authors: S. Mohajer , R. M. Taha, M. Adel

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Developing our knowledge of when pineapple roots grow can lead to improved water, fertilizer applications, and more precise culture management. This paper presents current understanding of morphological traits in pineapple roots, highlighting studies using incubation periods and various solid MS media treated with different sucrose concentrations and pH, which directly assess in vitro environmental factors. Rooting parameters had different optimal sucrose concentrations and incubation periods. All shoots failed to root in medium supplemented with sucrose at 5 g/L and no roots formed within the first 45 days in medium enriched with sucrose at 10 g/L. After 75 days, all shoots rooted in medium enriched with 10 and 20 g/L sucrose. Moreover, MS medium supplied with 20 g/L sucrose resulted in the longest and the highest number of roots with 27.3 mm and 4.7, respectively. Root function, such as capacity for P and N uptake, declined rapidly with root length. As a result, the longer the incubation period, the better the rooting responses would be.

Keywords: environmental factors, in vitro rooting, pineapple, tissue culture

Procedia PDF Downloads 358

Authors: Benjamin Osae Agyei, Hypolite Bayor

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This present experiment was carried out during the 2012 cropping season, at the Farming for the Future Experimental Field of the University for Development Studies, Nyankpala Campus in the Northern Region of Ghana. The objective of the experiment was to determine the carrot growth and yield responses to poultry manure and N.P.K (15:15:15). Six treatments (Control (no amendment), 20 t/ha poultry manure (PM), 40 t/ha PM, 70 t/ha PM, 35 t/ha PM + 0.11t/ha N.P.K and 0.23 t/ha N.P.K) with three replications for each were laid in a Randomized Complete Block Design (RCBD). Data were collected on plant height, number of leaves per plant, canopy spread, root diameter, root weight, and root length. Microsoft Excel and Genstat Statistical Package (9^th edition) were used for the data analysis. The treatment means were compared by using Least Significant Difference at 10%. Generally, the results showed that there were no significant differences (P>0.1) among the treatments with respect to number of leaves per plant, root diameter, root weight, and root length. However, significant differences occurred among plant heights and canopy spreads. Plant height treated with 40 t/ha PM at the fourth week after planting and canopy spread at eight weeks after planting and ten weeks after planting by 70 t/ha PM and 20 t/ha PM respectively showed significant difference (P<0.1). The study recommended that any of the amended treatments can be applied at their recommended rates to plots for carrot production, since there were no significant differences among the treatments.

Keywords: poultry manure, N.P.K., soil amendment, growth, yield, carrot

Procedia PDF Downloads 439