Search results for: bacterial gene clusters

Authors: Zeta Dooly, Aidan Duane

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The collaborative European funded research and development landscape provides prime environmental conditions for multi-disciplinary teams to learn and enhance their knowledge beyond the capability of training and learning within their own organisation cocoons. Whilst the emergence of the academic entrepreneur has changed the focus of educational institutions to that of quasi-businesses, the training and professional development of lecturers and academic staff are often not formalised to the same level as industry. This research focuses on industry and academic collaborative research funded by the European Commission. The impact of research is scalable if an optimum research network is created and managed effectively. This paper investigates network embeddedness, the nature of relationships, links, and nodes within a research network, and the enhancement of the network’s knowledge. The contribution of this paper extends our understanding of establishing and maintaining effective collaborative research networks. The effects of network embeddedness are recognized in the literature as pertinent to innovation and the economy. Network theory literature claims that networks are essential to innovative clusters such as Silicon valley and innovation in high tech industries. This research provides evidence to support the impact collaborative research has on the disparate individuals toward their innovative contributions to their organisations and their own professional development. This study adopts a qualitative approach and uncovers some of the challenges of multi-disciplinary research through case study insights. The contribution of this paper recommends the establishment of scaffolding to accommodate cooperation in research networks, role appointment, and addressing contextual complexities early to avoid problem cultivation. Furthermore, it suggests recommendations in relation to network formation, intra-network challenges in relation to open data, competition, friendships, and competency enhancement. The network capability is enhanced by the adoption of the relevant theories; network theory, open innovation, and social exchange, with the understanding that the network structure has an impact on innovation and social exchange in research networks. The research concludes that there is an opportunity to deepen our understanding of the impact of network reuse and network hoping that provides scaffolding for the network members to enhance and build upon their knowledge using a progressive approach.

Keywords: research networks, competency building, network theory, case study

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Authors: Ghaleb Bin Huraib, Fahad Al Harthi, Misbahul Arfin, Abdulrahman Al-Asmari

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Atopic dermatitis (AD), also known as atopic eczema, is a chronic inflammatory skin disease characterized by severe itching and recurrent relapsing eczema-like skin lesions, affecting up to 20% of children and 10% of adults in industrialized countries. AD is a complex multifactorial disease, and its exact etiology and pathogenesis have not been fully elucidated. The aim of this study was to investigate the impact of gene polymorphisms of T helper cell subtype Th1 and Th2 cytokines, interferon-gamma (IFN-γ), interleukin-6 (IL-6) and transforming growth factor (TGF)-β1on AD susceptibility in a Saudi cohort. One hundred four unrelated patients with AD and 195 healthy controls were genotyped for IFN-γ (874A/T), IL-6 (174G/C) and TGF-β1 (509C/T) polymorphisms using ARMS-PCR and PCR-RFLP technique. The frequency of genotypes AA and AT of IFN-γ (874A/T) differed significantly among patients and controls (P 0.001). The genotype AT was increased while genotype AA was decreased in AD patients as compared to controls. AD patients also had higher frequency of T containing genotypes (AT+TT) than controls (P = 0.001). The frequencies of allele T and A were statistically different in patients and controls (P = 0.04). The frequencies of genotype GG and allele G of IL-6 (174G/C) were significantly higher while genotype GC and allele C were lower in AD patients than controls. There was no significant difference in the frequencies of alleles and genotypes of TGF-β1 (509C/T) polymorphism between patient and control groups. These results showed that susceptibility to AD is influenced by presence or absence of genotypes of IFN-γ (874A/T) and IL-6 (174G/C) polymorphisms. It is concluded that T-allele and T-containing genotypes (AT+TT) of IFN-γ (874A/T) and G-allele and GG genotype ofIL-6 (174G/C) polymorphisms are susceptible to AD in Saudis.On the other hand, the TGF-β1 (509C/T) polymorphism may not be associated with AD risk in Saudi population however further studies with large sample size are required to confirm these findings.

Keywords: atopic dermatitis, interferon-γ, interleukin-6, transforming growth factor-β1, polymorphism

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Authors: Seema Ahlawat, Parul Saxena, Malik Zainul Abdin

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Malaria is a major health problem in many developing countries. The parasite responsible for the vast majority of fatal malaria infections is Plasmodium falciparum. Unfortunately, most Plasmodium strains including P. falciparum have become resistant to most of the antimalarials including chloroquine, mefloquine, etc. To combat this problem, WHO has recommended the use of artemisinin and its derivatives in artemisinin based combination therapy (ACT). Due to its current use in artemisinin based-combination therapy (ACT), its global demand is increasing continuously. But, the relatively low yield of artemisinin in A. annua L. plants and unavailability of economically viable synthetic protocols are the major bottlenecks for its commercial production and clinical use. Chemical synthesis of artemisinin is also very complex and uneconomical. The hairy root system, using the Agrobacterium rhizogenes LBA 9402 strain to enhance the production of artemisinin in A. annua L., is developed in our laboratory. The transgenic nature of hairy root lines and the copy number of trans gene (rol B) were confirmed using PCR and Southern Blot analyses, respectively. The effect of different concentrations of Piriformospora indica on artemisinin production in hairy root cultures were evaluated. 3% P. indica has resulted 1.97 times increase in artemisinin production in comparison to control cultures. The effects of P. indica on artemisinin production was positively correlated with regulatory genes of MVA, MEP and artemisinin biosynthetic pathways, viz. hmgr, ads, cyp71av1, aldh1, dxs, dxr and dbr2 in hairy root cultures of A. annua L. Mass scale cultivation of A. annua L. hairy roots by plant tissue culture technology may be an alternative route for production of artemisinin. A comprehensive investigation of the hairy root system of A. annua L. would help in developing a viable process for the production of artemisinin. The efficiency of the scaling up systems still needs optimization before industrial exploitation becomes viable.

Keywords: A. annua L., artemisinin, hairy root cultures, malaria

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Authors: Karla Cautivo, Thomas Riley, Daniel Knight

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Clostridium difficile infection (CDI) is the most common cause of infectious diarrhea in hospitalised humans. C. difficile colonises the gastrointestinal tract, causes disease in a variety of animal species and can persist as a spore in diverse environments. Genetic overlap between C. difficile strains from human, animal and environmental sources suggests CDI has a zoonotic or foodborne aetiology. In Australia, C. difficile PCR ribotype RT014 (MLST clade 1) and several ST11 (MLST clade 5) RTs are found commonly in livestock. The high prevalence and diversity of ST11 strains in Australian production animals indicates Australia might be the ancestral home for this lineage. This project describes for the first time the ecology of C. difficile in Australian native animals, providing insights into the prevalence, molecular epidemiology and evolution of C. difficile in this unique environment and a possible role in CDI in humans and animals in Australia. Faecal samples were collected from wild/captive reptiles (n=37), mammals (n=104) and birds (n=102) in Western Australia in 2020/21. Anaerobic enrichment culture was performed, and C. difficile isolates were characterised by PCR ribotyping and toxin gene profiling. Seventy isolates of C. difficile were recovered (prevalence of C. difficile in faecal samples 28%, n=68/243); 27 unique RTs were identified, 5 were novel. The prevalence of C. difficile was similar for reptiles and mammals, 46% (n=17/37) and 43%(n=45/104), respectively, but significantly lower in birds (7.8%, n=8/102; p<0.00001 for both reptiles and mammals). Of the 57 isolates available for typing, RT237 (clade 5) and RT002 (clade 2) were the most prevalent, 15.8% (n=9/57) and 14% (n=8/57), respectively. The high prevalence of C. difficile in reptiles and mammals, particularly clade 5 strains, supported by previous studies of C. difficile in Australian soils, suggest that Australia might be the ancestral home of MLST clade 5.

Keywords: Clostridium difficile, zoonosis, molecular epidemiology, ecology and evolution

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Authors: Uchenna Egwu, Paul Jonathan Sallis

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Perennial ryegrass is an abundant renewable lignocellulosic biofuel feedstock for biomethane production through anaerobic digestion (AD). In this study, six anaerobic continuously stirred tank reactors (CSTRs) were set up in three pairs. Each pair of the CSTRs was then used to study the effects of operating temperatures – psychrophilic, mesophilic, and thermophilic, and optimum pH on the specific methane production (SMP) of the ryegrass during AD under discontinuous daily feeding conditions. The reactors were fed at an organic loading rate (OLR) ranging from 1-1.5 kgVS.L⁻¹d⁻¹ and hydraulic residence time, HRT=20 days for 140 days. The pH of the digesters was maintained at the range of 6.8-7.2 using 1 M NH₄HCO₃ solution, but this was replaced with biomass ash-extracts from day 105-140. The results obtained showed that the mean SMP of ryegrass measured between HRT 3 and 4 were 318.4, 425.4 and 335 N L CH₄ kg⁻¹VS.d⁻¹ for the psychrophilic (25 ± 2°C), mesophilic (40 ± 1°C) and thermophilic (60 ± 1°C) temperatures respectively. It was also observed that the buffering ability of the reactors increased with operating temperature, probably due to an increase in the solubility of ammonium bicarbonate (NH₄HCO₃) with temperature. The reactors also achieved a mean VS destruction of 61.9, 68.5 and 63.5%, respectively, which signifies that the mesophilic reactors achieved the highest specific methane production (SMP), while the psychrophilic reactors achieved the lowest. None of the reactors attained steady-state condition due to the discontinuous daily feeding times, and therefore, such feeding practice may not be the most effective for maximum biogas production over long periods of time. The addition of NH₄HCO₃ as supplement provided a good buffering condition in these AD digesters, but the digesters failed in the long run due to inhibition from the accumulation of free ammonia, which later led to decrease in pH, acidification, and souring of the digesters. However, the addition of biomass ash extracts was shown to potentially revive failed AD reactors by providing an adequate buffering and essential trace nutrient supplements necessary for optimal bacterial growth.

Keywords: anaerobic digestion, discontinuous feeding, perennial ryegrass, specific methane production, supplements, temperature

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Authors: Mini P. Singh, Jagat Ram, Archit Kumar, Tripti Rungta, Jasmine Khurana, Amit Gupta, R. K. Ratho

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Introduction: Human adenovirus is the most common agent involved in viral conjunctivitis. The clinical manifestations vary with different serotypes. The identification of the circulating strains followed by phylogenetic analysis can be helpful in understanding the origin and transmission of the disease. The present study aimed to carry out molecular epidemiology of the adenovirus types in the patients with conjunctivitis presenting to the eye centre of a tertiary care hospital in North India. Materials and Methods: The conjunctival swabs were collected from 23 suspected adenoviral conjunctivitis patients between April-August, 2014 and transported in viral transport media. The samples were subjected to nested PCR targeting hexon gene of human adenovirus. The band size of 956bp was eluted and 8 representative positive samples were subjected to sequencing. The sequences were analyzed by using CLUSTALX2.1 and MEGA 5.1 software. Results: The male: female ratio was found to be 3.6:1. The mean age of presenting patients was 43.95 years (+17.2). Approximately 52.1% (12/23) of patients presented with bilateral involvement while 47.8% (11/23) with unilateral involvement of the eye. Human adenovirus DNA could be detected in 65.2% (15/23) of the patients. The phylogenetic analysis revealed presence of serotype 8 in 7 patients and serotype 4 in one patient. The serotype 8 sequences showed 99-100% identity with Tunisian, Indian and Japanese strains. The adenovirus serotype 4 strains had 100% identity with strains from Tunisia, China and USA. Conclusion: Human adenovirus was found be an important etiological agent for conjunctivitis in our set up. The phylogenetic analysis showed that the predominant circulating strains in our epidemic keratoconjunctivitis were serotypes 8 and 4.

Keywords: conjunctivitis, human adenovirus, molecular epidemiology, phylogenetics

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Authors: Idan Chiyanzu, Maruping Mangena

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Crude glycerol, a major by-product from the transesterification of triacylglycerides with alcohol to biodiesel, is known to have a broad range of applications. For example, its bioconversion can afford a wide range of chemicals including alcohols, organic acids, hydrogen, solvents and intermediate compounds. In bacteria, the 2-oxoglutarate dioxygenase (2-OGD) enzymes are widely found among the Pseudomonas syringae species and have been recognized with an emerging importance in ethylene formation. However, the use of optimized enzyme function in recombinant systems for crude glycerol conversion to ethylene is still not been reported. The present study investigated the production of ethylene from crude glycerol using engineered E. coli MG1655 and JM109 strains. Ethylene production with an optimized expression system for 2-OGD in E. coli using a codon optimized construct of the ethylene-forming gene was studied. The codon-optimization resulted in a 20-fold increase of protein production and thus an enhanced production of the ethylene gas. For a reliable bioreactor performance, the effect of temperature, fermentation time, pH, substrate concentration, the concentration of methanol, concentration of potassium hydroxide and media supplements on ethylene yield was investigated. The results demonstrate that the recombinant enzyme can be used for future studies to exploit the conversion of low-priced crude glycerol into advanced value products like light olefins, and tools including recombineering techniques for DNA, molecular biology, and bioengineering can be used to allowing unlimited the production of ethylene directly from the fermentation of crude glycerol. It can be concluded that recombinant E.coli production systems represent significantly secure, renewable and environmentally safe alternative to thermochemical approach to ethylene production.

Keywords: crude glycerol, bioethylene, recombinant E. coli, optimization

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Authors: Sohyoung Won, Heebal Kim, Dajeong Lim

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Genomic prediction is an effective way to measure the abilities of livestock for breeding based on genomic estimated breeding values, statistically predicted values from genotype data using best linear unbiased prediction (BLUP). Using haplotypes, clusters of linked single nucleotide polymorphisms (SNPs), as markers instead of individual SNPs can improve the reliability of genomic prediction since the probability of a quantitative trait loci to be in strong linkage disequilibrium (LD) with markers is higher. To efficiently use haplotypes in genomic prediction, finding optimal ways to define haplotypes is needed. In this study, 770K SNP chip data was collected from Hanwoo (Korean cattle) population consisted of 2506 cattle. Haplotypes were first defined in three different ways using 770K SNP chip data: haplotypes were defined based on 1) length of haplotypes (bp), 2) the number of SNPs, and 3) k-medoids clustering by LD. To compare the methods in parallel, haplotypes defined by all methods were set to have comparable sizes; in each method, haplotypes defined to have an average number of 5, 10, 20 or 50 SNPs were tested respectively. A modified GBLUP method using haplotype alleles as predictor variables was implemented for testing the prediction reliability of each haplotype set. Also, conventional genomic BLUP (GBLUP) method, which uses individual SNPs were tested to evaluate the performance of the haplotype sets on genomic prediction. Carcass weight was used as the phenotype for testing. As a result, using haplotypes defined by all three methods showed increased reliability compared to conventional GBLUP. There were not many differences in the reliability between different haplotype defining methods. The reliability of genomic prediction was highest when the average number of SNPs per haplotype was 20 in all three methods, implying that haplotypes including around 20 SNPs can be optimal to use as markers for genomic prediction. When the number of alleles generated by each haplotype defining methods was compared, clustering by LD generated the least number of alleles. Using haplotype alleles for genomic prediction showed better performance, suggesting improved accuracy in genomic selection. The number of predictor variables was decreased when the LD-based method was used while all three haplotype defining methods showed similar performances. This suggests that defining haplotypes based on LD can reduce computational costs and allows efficient prediction. Finding optimal ways to define haplotypes and using the haplotype alleles as markers can provide improved performance and efficiency in genomic prediction.

Keywords: best linear unbiased predictor, genomic prediction, haplotype, linkage disequilibrium

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Authors: Ferhat Mohamed Amine, Boukhatem Mohamed Nadjib, Chemat Farid

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The Lamiaceae family is widely spread in Algeria. Due to the application of Thymus species growing wild in Algeria as a culinary herb and in folk medicine, the purpose of the present work was to evaluate antimicrobial activities of their essential oils and relate them with their chemical composition, for further application in food and pharmaceutical industries as natural valuable products. The extraction of the Thymus vulgaris L. essential oil (TVEO) was obtained by steam distillation. Chemical composition of the TVEO was determined by Gas Chromatography. A total of thirteen compounds were identified. Carvacrol (83.8%) was the major component, followed by cymene (8.15%) and terpinene (4.96%). Antibacterial action of the TVEO against 23 clinically isolated bacterial strains was determined by using agar disc diffusion and vapour diffusion methods at different doses. By disc diffusion method, TVEO showed potent antimicrobial activity against gram-positive bacteria more than gram-negative strains and antibiotic discs. The Diameter of Inhibition Zone (DIZ) varied from 25 to 60 mm for S. aureus, B. subtilisand E. coli. However, the results obtained by both agar diffusion and vapour diffusion methods were different. Significantly higher antibacterial effect was observed in the vapour phase at lower doses. S. aureus and B. subtilis were the most susceptible strains to the oil vapour. Therefore, smaller doses of EO in the vapour phase can be inhibitory to pathogenic bacteria. There is growing evidence that TVEO in vapour phase are effective antiseptic systems and appears worthy to be considered for practical uses in the treatment of human infections oras air decontaminants in hospital. TVEO has considerable antibacterial activity deserving further investigation for clinical applications. Also whilst the mode of action remains mainly undetermined, this experimental approach will need to continue.

Keywords: antimicrobial drugs, carvacrol, disc diffusion, Thymus vulgaris, vapour diffusion

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Authors: Lindsay Foreman

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Introduction: Goals have become synonymous with the quest for the good life and the pursuit of happiness, with coaching and positive psychology gaining popularity as an approach in recent decades. And yet mental health is on the rise and the leading cause of disability, wellbeing is on the decline, stress is leading to 50-60% of workday absences and the need for action is indisputable and urgent. Purpose: The purpose of this study is to better understand two things we cannot see, but that play the most significant role in these outcomes - what we think and how we feel. With many working on the assumption that positive thinking and an optimistic outlook are necessary or valuable components of goal pursuit, this study uncovers the reality of the ‘inner-game’ from the coachee's perspective. Method: With a mixed methods design using a Q Method study of subjectivity to ‘make the unseen seen’. First, a wide-ranging universe of subjective thoughts and feelings experienced during goal pursuit are explored. These are generated from literature and a Qualtrics survey to create a Q-Set of 40 statements. Then 19 participants in professional and organisational settings offer their perspectives on these 40 Q-Set statements. Each rank them in a semi-forced distribution from ‘most like me’ to ‘least like me’ using Q-Sort software. From these individual perspectives, clusters of perspectives are identified using factor analysis and four distinct viewpoints have emerged. Findings: These Goal Pursuit Viewpoints offer insight into the states and self-talk experienced by coachees and may not reflect the assumption of positive thinking associated with achieving goals. The four Viewpoints are 1) the Optimistic View, 2) the Realistic View 3) The Dreamer View and 4) The Conflicted View. With only a quarter of the Dreamer View, and a third of the Optimistic view going on to achieve their goals, these assumptions need review. And with all the Realistic Views going on to achieve their goals, the role of self-doubt, overwhelm and anxiousness in goal achievement cannot be overlooked. Contribution: This study offers greater insight and understanding of people's inner experiences as they pursue goals and highlights the necessary and normal negative states associated with goal achievement. It also offers a practical tool of the Q-set statements to help coaches and coachees explore the current state and help navigate the journey towards goal achievement. It calls into question whether goals should always be part of coaching and if values, identity, and purpose may play a greater role than goals.

Keywords: coaching, goals, positive psychology, mindset, leadership, mental health, beliefs, cognition, emotional intelligence

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Authors: Chanya Inprasit, Yi-Wen Lin

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Inflammation causes changes of peripheral and central nervous system properties, affecting both neuronal and non-neuronal cells, resulting in inflammatory pain. Acupoint injection (AI) was developed in the 1950s and has been widely used for relieving pain. It is an acupoint-stimulating technique that utilizes anatomically based meridians derived from Chinese medicine theory. AI has been accepted as an effective treatment and is thought to display superior results when compared to traditional acupuncture methods. However, the mechanism of AI needs to be ratified by more scientific evidence in order to support the theory and its therapeutic development. In this study, we explored the effect of AI on the comorbidity of chronic pain and depression. Mice hindpaw was injected by complete Freund’s adjuvant (CFA) to induce the condition of chronic pain. Measurements of mechanical and thermal hyperalgesia and depression-like behavior were analyzed. The results indicated a positive tendency to AI treatment. The comorbidity of chronic pain and depression was investigated with relation to transient receptor potential V1 (TRPV1) mechanism through the use of TRPV1 gene deletion. The expression of nociceptors such as voltage-gated sodium channels (Navs) or TRPV1, was significantly down-regulated by AI. The expression of inflammation-activated molecules: astrocytic marker glial fibrillary acidic protein (GFAP), the microglial marker Iba-1, S100B, and related kinases, were reversed by AI in both the peripheral and central nervous system. Taken together, these data provided a detailed molecular mechanism of AI-induced analgesia and anti-inflammatory properties. This finding may be utilized for clinical practice to treat chronic pain and depression comorbidity.

Keywords: inflammatory pain, acupoint injection, TRPV1, GFAP, S100B

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Authors: Roberto Cassino, Valeria Dissette, Carlo Alberto Bignozzi, Daniele Pazzi

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Background and Aims: The aim of this work was to investigate, both ‘in vitro’ and ‘in vivo’, if the new SCX technology (SiO2-Ag+Chlorex) can easily defeat infections and it is really more effective than SSD (SilverSulfaDiazine). ‘In vitro’ methods: we tested ‘in vitro’ the effectiveness of both silver materials using a pool of 5 strains: Pseudomonas Aeruginosa, Staphylococcus aureus, Escherichia Coli, Enterococcus hirae and Candida Albicans. 100 µl of this pool have been seeded on Petri dishes and kept for 24 hours in incubation at 37 C°. ‘In vivo’ methods: we enrolled patients with multiple infectious chronic wounds (according with cutting & harding criteria for infection); after a qualitative evaluation of the wounds bacterial population, taking a sample by plug, we included in the study 6 patients for a total of 10 wounds, infected by one or more of the microorganisms used for the ‘in vitro’ test. The protocol consisted of a treatment with a spray powder of SSD every 48 hours for 14 days; in case of worsening we should have to start a new treatment with a spray powder containing silicon dioxide, ionic silver and chlorexidine (SiO2-Ag+Chlorex) every 48 hours for 14 days. We evaluated the number of clinical signs of infection and the disappearance or not of the wound edge erithema. ‘In vitro’ results: SSD demonstrated a wide zone of inhibition within 24 hours, but after 5 days there was no more signs of inhibition; on the contrary SCX had a good inhibition ring that lasted more than 5 days. ‘In vivo’ results: all wounds treated with SSD got worse; the signs of infection increased and the wound edge erithema did not disappear. According with the protocol, we treated then all wounds with SCX and they all improved within the period of observation with complete disappearance of clinical signs of infection and no more wound edge erithema. Conclusions: the study demonstrated the effectiveness of SiO2-Ag+Chlorex, especially in terms of long lasting antimicrobial action. We had the same results ‘in vitro’, so that there has been a perfect correspondence between the laboratory outcomes and the clinical ones.

Keywords: chronic wounds, infections, ionic silver, SSD

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Authors: Mohammed Jarrar, Shalini Behl, Nadia Shaheen, Abeer Fatima, Reem Nasab

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Skin aging is a slow multifactorial process influenced by both internal as well as external factors. Ultra-violet radiations (UV), diet, smoking and personal habits are the most common environmental factors that affect skin aging. Fat contents and fibrous proteins as collagen and elastin are core internal structural components. The direct influence of UV on elastin integrity and health is crucial on aging of skin by time. The deposition of abnormal elastic material is a major marker in a photo-aged skin. Searching for compounds that may protect against cutaneous photo-damage is highly valued. Retinoids and Alpha Hydroxy Acids protective and or repairing effects of UV have been endorsed by some researchers. For consolidating a better understanding of anti and protective effects of such anti-aging agents, we evaluated the combinatory effects of various dosages of lactic acid and retinol on the dermal fibroblasts elastin levels exposed to UV. The UV exposed cells showed significant reduction in the elastin levels. A combination of drugs with a higher concentration of lactic acid (30-35 mM) and a lower concentration of retinol (10-15mg/mL) showed to work better in enhancing elastin concentration in UV exposed cells. We assume this enhancement could be the result of increased tropo-elastin gene expression stimulated by retinol and lactic acid probably repaired the UV irradiated damage by enhancing the amount and integrity of the elastin fibers.

Keywords: alpha hydroxy acid, elastin, retinol, ultraviolet radiations

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Authors: Etleva Hamzaraj, Eva Kica, Anila Paparisto, Pranvera Lazo

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Worldwide demographic developments of recent decades have been associated with negative environmental consequences. For this reason, there is a growing interest in assessing the state of natural ecosystems or assessing human impact on them. In this respect, this study aims to evaluate the change in water quality of the Mat River for a period of about ten years to highlight human impact. In one year, period of study, several biological and environmental parameters are determined to evaluate river water quality, and the data collected are compared with those of a similar study in 2007. Samples are collected every month in five stations evenly distributed along the river. Total coliform bacteria, the number of heterotrophic bacteria in water, and benthic macroinvertebrates are used as biological parameters of water quality. The most probable number index is used for evaluation of total coliform bacteria in water, while the number of heterotrophic bacteria is determined by counting colonies on plates with Plate Count Agar, cultivated with 0.1 ml sample after series dilutions. Benthic macroinvertebrates are analyzed by the number of individuals per taxa, the value of biotic index, EPT Richness Index value and tolerance value. Environmental parameters like pH, temperature, and electrical conductivity are measured onsite. As expected, the bacterial load was higher near urban areas, and the pollution increased with the course of the river. The maximum concentration of fecal coliforms was 1100 MPN/100 ml in summer and near the most urbanized area of the river. The data collected during this study show that after about ten years, there is a change in water quality of Mat River. According to a similar study carried out in 2007, the water of Mat River was of ‘excellent’ quality. But, according to this study, the water was classified as of ‘excellent’ quality only in one sampling site, near river source, while in all other stations was of ‘good’ quality. This result is based on biological and environmental parameters measured. The human impact on the quality of water of Mat River is more than evident.

Keywords: water quality, coliform bacteria, MPN index, benthic macroinvertebrates, biotic index

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Authors: Thilini Kananke

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Culinary herbs have long been considered as significant dietary sources of many potential health-promoting compounds. The present research focused on analysis of antimicrobial, antioxidant and physicochemical properties in selected four culinary herbs namely Murraya koenigii (Curry leaves), Pandanus amaryllifolius (Pandan leaves), Cymbopogon citrates (Lemon grass leaves), and Mentha Piperita (Minchi leaves) obtained from several market sites in Ratnapura District, Sri Lanka. The antimicrobial activity of ethanolic, chloroform and distilled water extracts of culinary herbs were evaluated against the strains of Staphylococcus aureus, Salmonella typhi and Shigella spp. Total phenolic content and the radical scavenging activity (using DPPH assay) of culinary herbs were determined. Four heavy metals (Cu, Cd, Pb and Fe) were analyzed in the selected culinary herbs using the atomic absorption spectroscopy (AAS). Proximate compositions of the selected herbs were analyzed using AOAC official methods. Antimicrobial activity of all selected culinary herbs showed relativity high inhibition zones against S. aureus. Pandan leaves showed the least antimicrobial activity against selected bacterial strains compared with other culinary herbs. Both the highest radical scavenging activity (lower IC50 value) and the total phenolic content (25.57 ±3.54µg GAE/100g) were reported in Mentha piperita extract. The highest concentrations of Cu, Fe and Cd were reported in Curry leaves (29.15 mg/kg), Lemon grass leaves (257.98 mg/kg) and Pandan leaves (6.05 mg/kg) respectively. The heavy metal contents detected in all culinary herbs were below the permitted limits set by WHO/FAO, except Cd. The highest moisture (85.00±0.00%) and fiber (10.66± 2.00%) contents were found in Pandan leaves, while the highest protein (8.94±0.29%), fat (12.3± 2.52%) and ash (3.50± 0.17%) contents were reported in curry leaves. The information obtained from this study highlights the importance of further investigation of other antioxidant, antimicrobial and health promoting compounds of culinary herbs available in Sri Lanka for a detailed comparison.

Keywords: antimicrobial, antioxidant, culinary herbs, proximate analysis

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Authors: Ana C. Sousa, Beatriz C. Santos, Fátima N. Serralha

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The Tagus estuary is heavily affected by industrial and urban activities, making bioremediation studies crucial for environmental preservation. Fuel contamination in the area can arise from various anthropogenic sources, such as oil spills from shipping, fuel storage and transfer operations, and industrial discharges. These pollutants can cause severe harm to the ecosystem and the organisms, including humans, that inhabit it. Nonetheless, there are always natural organisms with the ability to resist these pollutants and transform them into non-toxic or harmless substances, which defines the process of bioremediation. Exploring the microbial communities existing in soil and their capacity to break down hydrocarbons has the potential to enhance the development of more efficient bioremediation approaches. The aim of this investigation was to explore the existence of hydrocarbonoclastic microorganisms in six locations within the Tagus estuary, three on the north bank: Trancão River, Praia Fluvial do Cais das Colinas and Praia de Algés, and three on the south bank: Praia Fluvial de Alcochete, Praia Fluvial de Alburrica, and Praia da Trafaria. In all studied locations, native microorganisms of the genus Pseudomonas were identified. The bioremediation rate of common hydrocarbons like gasoline, hexane, and toluene was assessed using the redox indicator 2,6-dichlorophenolindophenol (DCPIP). Effective hydrocarbon-degrading bacterial strains were identified in all analyzed areas, despite adverse environmental conditions. The highest bioremediation rates were achieved for gasoline (68%) in Alburrica, hexane (65%) in Algés, and toluene (79%) in Algés. Generally, the bacteria demonstrated efficient degradation of hydrocarbons added to the culture medium, with higher rates of aerobic biodegradation of hydrocarbons observed. These findings underscore the necessity for further in situ studies to better comprehend the relationship between native microbial communities and the potential for pollutant degradation in soil.

Keywords: biodegradability rate, hydrocarbonoclastic microorganisms, soil bioremediation, tagus estuary

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Authors: Ronald Villamar-Torres, Michael Staudt, Christopher Viot

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Cotton Gossypium hirsutum L. is one of the most important industrial crops, producing the world leading natural textile fiber, but is very prone to arthropod attacks that reduce crop yield and quality. Cotton cultivation, therefore, makes an outstanding use of chemical pesticides. In reaction to herbivorous arthropods, cotton plants nevertheless show natural defense reactions, in particular through volatile organic compounds (VOCs) emissions. These natural defense mechanisms are nowadays underutilized but have a very high potential for cotton cultivation, and elucidating their genetic bases will help to improve their use. Simulating herbivory attacks by mechanical wounding of cotton plants in greenhouse, we studied by qPCR the changes in gene expression for genes of the terpenoids biosynthesis pathway. Differentially expressed genes corresponded to higher levels of the terpenoids biosynthesis pathway and not to enzymes synthesizing particular terpenoids. The genes were mapped on the G. hirsutum L. reference genome; their global relationships inside the general metabolic pathways and the biosynthesis of secondary metabolites were visualized with iPath2. The chromatographic profiles of VOCs emissions indicated first monoterpenes and sesquiterpenes emissions, dominantly four molecules known to be involved in plant reactions to arthropod attacks. As a result, the study permitted to identify potential key genes for the emission of volatile terpenoids by cotton plants in reaction to an arthropod attack, opening possibilities for molecular-assisted cotton breeding in benefit of smallholder cotton growers.

Keywords: biosynthesis pathways, cotton, mechanisms of plant defense, terpenoids, volatile organic compounds

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Authors: Eriselda Simoni, Leonard Simoni, Endri Paparisto, Laureta Flaga, Silvana Bara, Edit Xhajanka, Arjan Harxhi

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Background: Some pathologies are encountered more often in HIV/ AIDS, such as those with bacterial, fungal, viral, and neoplastic causes, but what has been more noticeable in recent years is the increased and more aggressive manifestation of periodontal disease and oral caries. Our purpose is to investigate the correlation between the HIV/AIDS stage and CD4 level with oral health, dentition, and periodontal status. Materials and Methods: We conducted a prospective observational study that included 35 patients newly diagnosed with HIV/AIDS and underwent an oral examination at the University Dental Clinic in Tirana, Albania, in the period April - July 2024. This study evaluated the basic demographic, laboratory characteristics, oral hygiene, and the presence of oral lesions. The dentition status was assessed with the values DT (decay teeth), FT (filled teeth), and MT (missing teeth) presented as DMFT. The periodontal status was evaluated through a periodontal probe measuring CPI (community periodontal index) and LOA (loss of attachment) as recommended by the WHO Oral Health Assessment Form 2013. The Pearson Correlation Coefficient (r) was used to evaluate the relationship between levels of CD4+ and DMF, CD4+ and CPI, and CD4+ and LOA. The P value ≤ 0.05 was considered statistically significant. Results: 80% of patients included were males with a mean age of 35.8 years. 8.6% of patients were categorized as HIV stage I, 28.6% as stage II, and 62.8% as HIV stage III/AIDS. The mean level value of CD4+ was 266.2 cells/mm3 and the rapport CD4+/ WBC (White Blood Cells) was 15.7%. Most patients (57.2%) used toothbrushes less than 1 time a day. An important negative correlation was found between CD4+ and dentition and periodontal status. A lower level of CD4+ was correlated with a higher DMFT, CPI, and LOA, respectively coefficient (r) for CD4/DMFT = -0.52, p =0.01, (r) for CD4/CPI= - 0.38, p=0.024 and (r) for CD4/LOA= - 0.37, p=0.029. Conclusions: In our study, it was documented that patients with HIV/AIDS had worse oral health, an important negative correlation between CD4+ and dentition and periodontal status. A lower level of CD4+ was correlated with a worse dentition status (higher DMFT), and poor periodontal health (higher CPI and LOA). The monitoring and treatment of oral pathologies can be important in early HIV/AIDS diagnoses and treatment.

Keywords: HIV/AIDS, oral health, dentition, periodontal

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Authors: Kidane workelul, Li xu, Xiaoyang Pang, Jiaping Lv

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Dairy products are exceptionally ideal media for the growth of microorganisms because of their high nutritional content. There are several ways that milk might get contaminated throughout the milking process, including how the raw milk is transported and stored, as well as how long it is kept before being processed. Psychrotrophic bacteria are among the one which can deteriorate the quality of milk mainly their heat resistance proteas and lipase enzyme. For this research purpose 8 selected strains of Psychrotrophic bacteria (Entrococcus hirae, Pseudomonas fluorescens, Pseudomonas azotoformans, Pseudomonas putida, Exiguobacterium indicum, Pseudomonas paralactice, Acinetobacter indicum, Serratia liquefacients)are chosen and try to determine their characteristics based on the research methodology protocol. Thus, the 8 selected strains are cultured, plated incubate, extracted their genomic DNA and genome DNA was amplified, the purpose of the study was to identify their Psychrotrophic properties, lipase hydrolysis positive test, their optimal incubation temperature, designed primer using the noble strain P,flourescens conserved region area in target with lipA gene, optimized primer specificity as well as sensitivity and PCR detection for lipase positive strains using the design primers. Based on the findings both the selected 8 strains isolated from stored raw milk are Psychrotrophic bacteria, 6 of the selected strains except the 2 strains are positive for lipase hydrolysis, their optimal temperature is 20 to 30 OC, the designed primer specificity is very accurate and amplifies for those strains only with lipase positive but could not amplify for the others. Thus, the result is promising and could help in detecting the Psychrotrophic bacteria producing heat resistance enzymes (lipase) at early stage before the milk is processed and this will safe production loss for the dairy industry.

Keywords: dairy industry, heat-resistant, lipA, milk, primer and psychrotrophic

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Authors: Seyed Reza Aghili, Tahereh Shokohi, Lotfollah Davoodi, Zahra Kashi, Azam Moslemi, Mahdi Abastabar, Iman Haghani, Sabah Mayahi, Asoudeh A.

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Introduction: In diabetic foot ulcers, if fungal agents such as Candida species penetrate into the cutaneous or depth of ulcer, can increase the degree of the wound and cause Candia infection and make it more difficult to heal. Material & Methods: A cross-sectional study was performed on 100 diabetic foot ulcer patients in 2020 in Sari, Iran. patient's data and wound grade were recorded in a questionnaire. Candida infection was diagnosed with direct microscopic examination and culture of samples. Colony-PCR molecular method was used for ITS region of DNA and then PCR-RFLP with Msp1 enzyme and using HWP1 specific gene to determine species of Candida agent. Results: Of 100 patients, the mean age 62.1 ± 10.8 years, 95% type 2 diabetes, 83%>10 years duration diabetes, 59% male, 66%> poor education level, 99% married, 52% rural, 95% neuropathic symptoms, 88% using antibiotics, 69%HbA1C >9%, and mean ulcer degree 2.6±1.05 were. Candida infection was seen in 13% of the deep tissue of the wound and 7% cutaneous around the wound. The predominant Candida isolated was C. parapsilosis (71.5%), C .albicans (14.3%). Fungal infections caused by mold fungi were not detected. There was a statistically significant relationship between yeast infection and gender, rural, HbA1C and ulcer degree. Conclusion: Mycological evaluations often are ignored. Candida parapsilosis is the most common infectious agent in these patients and may require specific treatment. Therefore, more attention of physicians to Candida infections particularly, early diagnosis and effective treatment can help faster recovery and prevent amputation.

Keywords: diabetic foot ulcer, candida infection, risk factors, c. parapsilosis

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Authors: Minwuyelet Maru, Solomon Habtemariam, Endalamaw Gadissa, Abraham Aseffa

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Background: Tuberculosis is a major public health problem in Ethiopia. The burden of TB is aggravated by emergence and expansion of drug resistant tuberculosis and different lineages of Mycobacterium tuberculosis (M. tuberculosis) have been reported in many parts of the country. Describing strains of Mycobacterial isolates and drug susceptibility pattern is necessary. Method: Sputum samples were collected from smear positive pulmonary TB patients age >= 7 years between October 1, 2012 to September 30, 2013 and Mycobacterial strains isolated on Loweensten Jensen (LJ) media. Each strain was characterized by deletion typing and Spoligotyping. Drug sensitivity testing was determined with the indirect proportion method using Middle brook 7H10 media and association to determine possible risk factors to drug resistance was done. Result: A total of 144 smear positive pulmonary tuberculosis patients were enrolled. The age of participants ranged from 7 to 78 with mean age of 29.22 (±10.77) years. In this study 82.2% (n=97) of the isolates were sensitive to the four first line anti-tuberculosis drugs and resistance to any of the four drugs tested was 17.8% (n=21). A high frequency of any resistance was observed in isoniazid, 13.6%, (n=16) followed by streptomycin, 11.8% (n=14). No significant association of isoniazid resistance with HIV, sex and history of previous TB treatment was observed but there was significant association with age, high between 31-35 years of age (p=0.01). Majority, 89.9% (n=128) of participants were new cases and only 11.1% (n=16) had history of previous TB treatment. No MDR-TB from new cases and 2 MDRTB (13.3%) was isolated from re-treatment cases which was significantly associated with previous TB treatment (p<0.01). Thirty two different types of spoligotype patterns were identified and 74.1% were grouped in to 13 clusters. The dominant strains were SIT 25, 18.1% (n=21), SIT 53, 17.2% (n=20) and SIT 149, 8.6% (n=10). Lineage 4 is the predominant lineage followed by lineage 3 and lineage 7 comprising 65.5% (n=76), 28.4% (n=33) and 6% (n=7) respectively. Majority of strains from lineage 3 and 4 were SIT 25 (63.6%) and SIT 53 (26.3%) whereas SIT 343 was the dominant strain from lineage 7 (71.4%). Conclusion: Wide spread of lineage 3 and lineage 4 of the modern lineage and high number of strain cluster indicates high ongoing transmission. The high proportion resistance to any of the first line anti-tuberculosis drugs may be a potential source in the emergence of MDR-TB. Wide spread of SIT 25 and SIT 53 having a tendency of ease transmission and presence of higher resistance of isoniazid in working and mobile age group, 31-35 years of age may increase risk of drug resistant strains transmission.

Keywords: tuberculosis, drug susceptibility, strain diversity, lineage, Ethiopia, spoligotyping

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Authors: Dana Cassandra Winkler, Delia Leiding, Rene Bergs, Franziska Kaiser, Ramona Kirchhart, Ute Habel

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Background: Violence is a multidimensional phenomenon, affecting people of every age, socio-economic status and gender. Nevertheless, most studies primarily focus on men perpetrating women. Aim of the present study is to identify the likelihood of mental and somatic disorders and risk-taking behavior in male violence affected. In addition, the relationship between age of violence experience and the risk for health-related problems was analyzed. Method: On the basis of current evidence, a questionnaire was developed focusing on demographic background, health status, risk-taking behavior, and active and passive violence exposure. In total, 5221 males (Mean: 56,1 years, SD: 17,6) were consulted. To account for the time of violence experience in an efficient way, age clusters ‘0-12 years’, ‘13-20 years’, ‘21-35 years’, ‘36-65 years’ and ‘over 65 years’ were defined. A binary logistic regression was calculated to reveal differences in violence-affected and non-violence affected males regarding health and risk-taking factors. Males who experienced violence on a daily/ almost daily basis vs. males who reported violence occurrence once/ several times a month/ year were compared with respect to health factors and risk-taking behavior. Data of males, who indicated active and passive violence exposure, were analyzed by a chi²-analysis, to investigate a possible relation between the age of victimization and violence perpetration. Findings: Results imply that general violence experience, independent of active and passive violence exposure increases the likelihood in favor of somatic-, psychosomatic- and mental disorders as well as risk-taking behavior in males. Experiencing violence on a daily or almost daily basis in childhood and adolescence may serve as a predictor for increased health problems and risk-taking behavior. Furthermore, the violence experience and perpetration occur significantly within the same age cluster. This underlines the importance of a near-term intervention to minimize the risk, that victims become perpetrators later. Conclusion: The present study reveals predictors concerning health risk factors as well as risk-taking behavior in males with violence exposure. The results of this study may underscore the benefit of intervention and regular health care approaches in violence-affected males and underline the importance of acknowledging the overlap of violence experience and perpetration for further research.

Keywords: health disease, male, mental health, prevalence, risk-taking behavior, violence

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Authors: Salma Loukman, Reda Benmrid, Najat Bouchmaa, Hicham Hboub, Rachid El Fatimy, Rachid Benhida

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In this study, it use integrated transcriptomic datasets from the GEO repository with the purpose of investigating immune dysregulation in COVID-19. Thus, in this context, we decided to be focused on NK cells and CD14+ monocytes gene expression, considering datasets GSE165461 and GSE198256, respectively. Other datasets with PBMCs, lung, olfactory, and sensory epithelium and lymph were used to provide robust validation for our results. This approach gave an integrated view of the immune responses in COVID-19, pointing out a set of potential biomarkers and therapeutic targets with special regard to standards of physiological conditions. IFI27, MKI67, CENPF, MBP, HBA2, TMEM158, THBD, HBA1, LHFPL2, SLA, and AC104564.3 were identified as key genes from our analysis that have critical biological processes related to inflammation, immune regulation, oxidative stress, and metabolic processes. Consequently, such processes are important in understanding the heterogeneous clinical manifestations of COVID-19—from acute to long-term effects now known as 'long COVID'. Subsequent validation with additional datasets consolidated these genes as robust biomarkers with an important role in the diagnosis of COVID-19 and the prediction of its severity. Moreover, their enrichment in key pathophysiological pathways presented them as potential targets for therapeutic intervention.The results provide insight into the molecular dynamics of COVID-19 caused by cells such as NK cells and other monocytes. Thus, this study constitutes a solid basis for targeted diagnostic and therapeutic development and makes relevant contributions to ongoing research efforts toward better management and mitigation of the pandemic.

Keywords: SARS-COV-2, RNA-seq, biomarkers, severity, long COVID-19, bio analysis

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Authors: Shiv Mohan Singh, Gwyneth Matcher

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To understand the culturable microbial composition and diversity patterns, soil samples were collected from inland nunataks of Jutulsessen and Ahlmannryggen ranges in Dronning Maud Land, Antarctica. 16S rRNA, ITS and the D1/D2 domain sequencing techniques were used for characterization of microbial communities of these geographical areas. The total 37 species of bacteria such as Arthrobacter agilis, Acinetobacter baumannii, Arthrobacter flavus, Arthrobacter ginsengisoli, Arthrobacter oxydans, Arthrobacter oryzae, Arthrobacter polychromogenes, Arthrobacter sulfonivorans, Bacillus altitudinis, Bacillus cereus, Bacillus paramycoides, Brevundimonas vesicularis, Brachybacterium rhamnosum, Curtobacterium luteum, Dermacoccus nishinomiyaensis, Dietzia aerolata, Janibacter indicus, Knoellia subterranean, Kocuria palustris, Kytococcus aerolatus, Lysinibacillus sphaericus, Microbacterium phyllosphaerae, Micrococcus yunnanensis, Methylobacterium rhodesianum, Moraxella osloensis, Paracoccus acridae, Pontibacter amylolyticus, Pseudomonas hunanensis, Pseudarthrobacter siccitolerans, Pseudarthrobacter phenanthrenivorans, Rhodococcus aerolatus, Rhodococcus sovatensis, Sphingomonas daechungensis, Sphingomonas sanguinis, Stenotrophomonas pavanii, Staphylococcus gallinarum, Staphylococcus arlettae and 9 species of fungi such as Candida davisiana, Cosmospora arxii, Geomyces destructans, Lecanicillium muscarium, Memnoniella humicola, Paecilomyces lilacinus, Pseudogymnoascus verrucosus, Phaeophlebiopsis ignerii and Thyronectria caraganae were recorded. Fatty acid methyl esters (FAME) analyses of representative species of each genus have shown predominance branched and unsaturated fatty acids indicate its adaptation strategy in Antarctic cold environment. To the best of our knowledge, this is the first record of culturable bacterial communities from Jutulsessen and Ahlmannryggen ranges in Western Dronning Maud Land, Antarctica.

Keywords: antarctica, microbe, adaptation, polar

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Authors: Michael Dare Asemoloye, Segun Gbolagade Jonathan, Rafiq Ahmad, Odunayo Joseph Olawuyi, D. O. Adejoye

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Fungi have potentials for degrading hydrocarbons through the secretion of different enzymes. Crude oil tolerance and degradation by Trichoderma harzianum was investigated in this study with its ability to produce peroxidase enzymes (LiP and MnP). Many fungal strains were isolated from rhizosphere of grasses growing on a crude oil spilled site, and the most frequent strain based on percentage incidence was further characterized using morphological and molecular characteristics. Molecular characterization was done through the amplification of Ribosomal-RNA regions of 18s (1609-1627) and 28s (287-266) using ITS1 and ITS4 combinations and it was identified using NCBI BLAST tool. The selected fungus was also subjected to an in-vitro tolerance test at crude oil concentrations of 5, 10, 15, 20 and 25% while 0% served as control. In addition, lignin peroxidase genes (lig1-6) and manganese peroxidase gene (mnp) were detected and expressed in this strain using RT-PCR technique, its peroxidase producing activities was also studied in aliquots (U/ml). This strain had highest incidence of 80%, it was registered in NCBI as Trichoderma harzianum asemoJ KY488466. The strain KY488466 responded to crude oil concentrations as it increase, the dose inhibition response percentage (DIRP) increased from 41.67 to 95.41 at 5 to 25 % crude oil concentrations. All the peroxidase genes are present in KY488466, and expressed with amplified 900-1000 bp through RT-PCR technique. In this strain, lig2, lig4 and mnp genes were over-expressed, lig 6 was moderately expressed, while none of the genes was under-expressed. The strain also produced 90±0.87 U/ml lignin peroxidase and 120±1.23 U/mil manganese peroxidase enzymes in aliquots. These results imply that KY488466 can tolerate and survive high crude oil concentration and could be exploited for bioremediation of oil-spilled soils, the produced peroxidase enzymes could also be exploited for other biotechnological experiments.

Keywords: crude oil, enzymes, expression, peroxidase genes, tolerance, Trichoderma harzianum

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Authors: Kyungae Jo, Eun Young Kim, Byungsoo Shin, Kwang Soon Shin, Hyung Joo Suh

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Gamma-aminobutyric acid (GABA) and 5-hydroxytryptophan (5-HTP) are amino acids of digested nutrients or food ingredients and these can possibly be utilized as non-pharmacologic treatment for sleep disorder. We previously investigated the GABA/5-HTP mixture is the principal concept of sleep-promoting and activity-repressing management in nervous system of D. melanogaster. Two experiments in this study were designed to evaluate sleep-promoting effect of GABA/5-HTP mixture, to clarify the possible ratio of sleep-promoting action in the Drosophila invertebrate model system. Behavioral assays were applied to investigate distance traveled, velocity, movement, mobility, turn angle, angular velocity and meander of two amino acids and GABA/5-HTP mixture with caffeine treated flies. In addition, differentially expressed gene (DEG) analyses from next generation sequencing (NGS) were applied to investigate the signaling pathway and functional interaction network of GABA/5-HTP mixture administration. GABA/5-HTP mixture resulted in significant differences between groups related to behavior (p < 0.01) and significantly induced locomotor activity in the awake model (p < 0.05). As a result of the sequencing, the molecular function of various genes has relationship with motor activity and biological regulation. These results showed that GABA/5-HTP mixture administration significantly involved the inhibition of motor behavior. In this regard, we successfully demonstrated that using a GABA/5-HTP mixture modulates locomotor activity to a greater extent than single administration of each amino acid, and that this modulation occurs via the neuronal system, neurotransmitter release cycle and transmission across chemical synapses.

Keywords: sleep, γ-aminobutyric acid, 5-hydroxytryptophan, Drosophila melanogaster

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Authors: Igor Sukhotnik

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Objectives: Notch signaling is thought to act to drive cell versification in the lining of the small intestine. When Notch signaling is blocked, proliferation ceases, and epithelial cells become secretory. The purpose of the present study was to evaluate the role of Notch signaling pathway in stem cell differentiation in a rat model of intestinal ischemia-reperfusion (IR). Methods: Male Sprague-Dawley rats were randomly divided into four experimental groups: Sham-24 and Sham-48 rats underwent laparotomy and were killed 24 or 48 h later, respectively; IR-24 and IR-48 rats underwent occlusion of SMA and portal vein for 30 min followed by 24 or 48 h of reperfusion, respectively. Notch-related gene and protein expression were determined using Real Time PCR, Western blotting and immunohistochemistry. Wax histology and immunohistochemistry was used to determine cell differentiation toward absorptive (enterocytes) or secretory progenitors (goblet cells, enteroendocrine cells or Paneth cells). Results: IR-48 rats exhibited a significant decrease in Notch-1 protein expression (Western blot) that was coincided with a significant decrease in the number of Notch-1 positive cells (immunohistochemistry) in jejunum and ileum as well as Hes-1 positive cells in jejunum and ileum compared to Sham-48 rats. A significant down-regulation of Notch signaling related genes and proteins in IR animals was accompanied by a significant increase in the number of goblet and Paneth cells and decreased number of absorptive cells compared to control rats. Conclusions: Forty-eight hours following intestinal IR in rats, inhibited Notch signaling pathway was accompanied by intestinal stem cells differentiation toward secretory progenitors.

Keywords: Intestine, notch, ischemia-reperfusion, cell differentiation, secretory

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Authors: Deniz Sari, Selahattin İncecik, Nesimi Ozkurt

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Surface ozone, which named as one of the most critical pollutants in the 21th century, threats to human health, forest and vegetation. Specifically, in rural areas surface ozone cause significant influences on agricultural productions and trees. In this study, in order to understand to the surface ozone levels in rural areas we focus on the north-western side of Biga Peninsula which covers by the mountainous and forested area. Ozone concentrations were measured for the first time with passive sampling at 10 sites and two online monitoring stations in this rural area from 2013 and 2015. Using with the daytime hourly O3 measurements during light hours (08:00–20:00) exceeding the threshold of 40 ppb over the 3 months (May, June and July) for agricultural crops, and over the six months (April to September) for forest trees AOT40 (Accumulated hourly O3 concentrations Over a Threshold of 40 ppb) cumulative index was calculated. AOT40 is defined by EU Directive 2008/50/EC to evaluate whether ozone pollution is a risk for vegetation, and is calculated by using hourly ozone concentrations from monitoring systems. In the present study, we performed the trajectory analysis by The Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model to follow the long-range transport sources contributing to the high ozone levels in the region. The ozone episodes observed between 2013 and 2015 were analysed using the HYSPLIT model developed by the NOAA-ARL. In addition, the cluster analysis is used to identify homogeneous groups of air mass transport patterns can be conducted through air trajectory clustering by grouping similar trajectories in terms of air mass movement. Backward trajectories produced for 3 years by HYSPLIT model were assigned to different clusters according to their moving speed and direction using a k-means clustering algorithm. According to cluster analysis results, northerly flows to study area cause to high ozone levels in the region. The results present that the ozone values in the study area are above the critical levels for forest and vegetation based on EU Directive 2008/50/EC.

Keywords: AOT40, Biga Peninsula, HYSPLIT, surface ozone

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Authors: Kumudini Apsara Munasinghe, Devin Gregory Lissau, Ryan Thomas Wade

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Fresh fruits and vegetables are rich in vitamins, minerals, and fibers and help maintain a healthy weight over high-calorie food. Eating fruits and vegetables protects us from free radicals produced by metabolic reactions and safeguards us from cardiovascular disease and cancer. However, there has been an increased concern about foodborne diseases tied to contaminated farmers’ market produce. In addition, very little information is available about the contribution of eating raw fruits and vegetables to human exposure to antibiotic-resistant bacteria. This research aims to identify bacteria isolated from farmers’ market fruits and vegetables and understand their antibiotic resistance. Vegetables and fruits were collected from farmers’ markets around Frostburg and Cumberland areas in Maryland and transported to the microbiology lab at Frostburg State University for the isolation of bacteria. Bacteria were extracted from tomatoes, cucumber, strawberry, and lettuce using Tryptic soy broth overnight at 37°C, and Tryptic Soy agar was used for the streak plate technique to isolate bacteria. Pure cultures were used to identify bacteria using biochemical reactions after conducting Gram staining technique. The research used many biochemical reactions, including Mannitol Salt agar, MacConkey agar, and Eosin Methylene blue agar, for identification. Antibiotic sensitivity was tested for many different types of antibiotics, including amoxicillin, penicillin, tetracycline, ampicillin, and erythromycin. Most prevalent bacteria in the isolates were Staphylococcus, Bacillus, Micrococcus, Enterococcus, Enterobacter, Citrobacter, and other bacteria from the family Enterobacteriaceae. The data obtained from this research will be useful to educate and train farmers and individuals involved in post-harvest processes such as transportation and selling in farmers’ markets. Further results for bacterial antibiotic resistance will be obtained, and unculturable bacteria will be identified by next-generation DNA sequencing.

Keywords: antibiotic resistance, farmers markets, fruits, bacteria, vegetables

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Authors: Kakali Bhadra

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Binding of small molecules to DNA and recently to RNA, continues to attract considerable attention for developing effective therapeutic agents for control of gene expression. This work focuses towards understanding interaction of harmalol, a dihydro beta-carboline alkaloid, with different nucleic acid motifs viz. double stranded CT DNA, single stranded A-form poly(A), double-stranded A-form of poly(C)·poly(G) and clover leaf tRNAphe by different spectroscopic, calorimetric and molecular modeling techniques. Results of this study converge to suggest that (i) binding constant varied in the order of CT DNA > poly(C)·poly(G) > tRNAphe > poly(A), (ii) non-cooperative binding of harmalol to poly(C)·poly(G) and poly(A) and cooperative binding with CT DNA and tRNAphe, (iii) significant structural changes of CT DNA, poly(C)·poly(G) and tRNAphe with concomitant induction of optical activity in the bound achiral alkaloid molecules, while with poly(A) no intrinsic CD perturbation was observed, (iv) the binding was predominantly exothermic, enthalpy driven, entropy favoured with CT DNA and poly(C)·poly(G) while it was entropy driven with tRNAphe and poly(A), (v) a hydrophobic contribution and comparatively large role of non-polyelectrolytic forces to Gibbs energy changes with CT DNA, poly(C)·poly(G) and tRNAphe, and (vi) intercalated state of harmalol with CT DNA and poly(C)·poly(G) structure as revealed from molecular docking and supported by the viscometric data. Furthermore, with competition dialysis assay it was shown that harmalol prefers hetero GC sequences. All these findings unequivocally pointed out that harmalol prefers binding with ds CT DNA followed by ds poly(C)·poly(G), clover leaf tRNAphe and least with ss poly(A). The results highlight the importance of structural elements in these natural beta-carboline alkaloids in stabilizing different DNA and RNA of various motifs for developing nucleic acid based better therapeutic agents.

Keywords: calorimetry, docking, DNA/RNA-alkaloid interaction, harmalol, spectroscopy

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