Search results for: gene diversity

Authors: Ashkan Asgari, Korous Khoshbakht, Saeid Soufizadeh

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Various factors including land lots can affect biodiversity indices in Agricultural systems. Field study conducted to evaluate factors affecting crop diversity in Sarpolzahab in 2012. Required data were collected through direct observation of farms and filling questionnaires. Total numbers of 140 questionnaires were filled, SAS Software was used to analyse data and Ecological Methodology Program was applied to calculate Shannon-Winner index, subsequently. Results of study indicated that average number of land lots for each farmer was 2.78 and various from 2.2 in Rikhak Olia Village to 4.31 in Golam Kaboud Olia Village which shows small size of land lots due to separating larger lots by children of deceased farmers. The correlation between number of land lots and species biodiversity (0.308**) was significant and Shannon-Winner index was (0.262**). Therefore, according to the mentioned results one can assume that increase in number of land lots results in improving of the target index. Multiple land lots allow farmers to cultivate various crops which results in increasing biodiversity of crops in agro ecosystem. Subsequently, this increase will facilitate economic sustainability of the farmers and distribution of work force in the region throughout the year. The correlation of seasonal workers with biodiversity of crop species (0.256**) and Shannon-Winner (0.286**) was statistically significant and increasing number of seasonal work forces had resulted in improving crop biodiversity and decreasing dominant species or single crop farming systems. Vegetable farms which have a significant diversity, require a significant number of work forces which describes correlation between number of workers and diversity of species.

Keywords: agricultural systems, biodiversity indices, Shannon-Winner index, sustainability, rural

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Authors: Amirreza Razzaghipour Sorkhab

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One of the most common disorders among humans is hearing impairment. This paper provides an evidence base that recovers understanding of Meniere’s disease and highlights the physical and mental health correlates of the disorder. Meniere's disease is more common in the elderly. The term idiopathic endolymphatic hydrops has been attributed to this disease by some in the previous. Meniere’s disease demonstrations a genetic tendency, and a family history is found in 10% of cases, with an autosomal dominant inheritance pattern. The COCH gene may be one of the hereditary factors contributing to Meniere’s disease, and the possibility of a COCH mutation should be considered in patients with Meniere’s disease symptoms. Should be considered Missense mutations in the COCH gene cause the autosomal dominant sensorineural hearing loss and vestibular disorder. Meniere’s disease is a complex, heterogeneous disorder of the inner ear and that is characterized by episodes of vertigo lasting from minutes to hours, fluctuating sensorineural hearing loss, tinnitus, and aural fullness. The existing evidence supports the suggestion that age and sleep disorder are risk factors for Meniere's disease. Many factors have been reported to precipitate the progress of Menier, including endolymphatic hydrops, immunology, viral infection, inheritance, vestibular migraine, and altered intra-labyrinthine fluid dynamics. Although there is currently no treatment that has a proven helpful effect on hearing levels or on the long-term evolution of the disease, however, in the primary stages, the hearing may improve among attacks, but a permanent hearing loss occurs in the majority of cases. Current publications have proposed a role for the intratympanic use of medicine, mostly aminoglycosides, for the control of vertigo. more than 85% of patients with Meniere's disease are helped by either changes in lifestyle and medical treatment or minimally aggressive surgical procedures such as intratympanic steroid therapy, intratympanic gentamicin therapy, and endolymphatic sac surgery. However, unilateral vestibular extirpation methods (intratympanic gentamicin, vestibular nerve section, or labyrinthectomy) are more predictable but invasive approaches to control the vertigo attacks. Medical therapy aimed at reducing endolymph volume, such as low-sodium diet, diuretic use, is the typical initial treatment.

Keywords: meniere's disease, endolymphatic hydrops, hearing loss, vertigo, tinnitus, COCH gene

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Authors: Rini Rahul, Manoj Kumar

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Cadmium (Cd) is a poisonous trace metal, which is responsible for excess reactive oxygen species generation (ROS) in plants, thereby adversely affecting their productivity and commercial potential. Ricinus communis (castor) is an industry-efficient non-edible bioenergy crop used for phytoremediation and re-vegetation. We have determined the total Cd content in castor genotypes and established a relationship between the Cd tolerance mechanism and physiological parameters like chlorophyll fluorescence, the total photosynthetic activity, chlorophyll and carotenoid content as well as ROS generation and malondialdehyde content. This study is an effort to comprehend the interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), nicotianamine synthase (NAS) and Natural resistance-associated macrophage protein (NRAMP) gene. The antioxidant enzyme activity increased for WM hence conferring Cd toxicity in this genotype. RcNRAMP genes showed differential expression in GCH2 and WM genotypes; this can also be one of the reasons for Cd toxicity and sensitivity in WM and GCH2, respectively. The cause of pronounced Cd tolerance in WM leaves can be because of enhanced expression of RcNAS1, RcNAS2 and RcNAS3 genes. Our results demonstrate that there is an interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), NAS and NRAMP gene.

Keywords: ricinus communis, cadmium, reactive oxygen species, nicotianamine synthase, NRAMP, malondialdehyde

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Authors: Kinnsley Travis, Camerron M. Crowder

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Mapk8ip3 (Mitogen-Activated Protein Kinase 8 Interacting Protein 3) is a gene that codes for the JIP3 protein, which is a part of the JIP scaffolding protein family. This protein is involved in axonal vesicle transport, elongation and regeneration. Variants in the Mapk8ip3 gene are associated with a rare-genetic condition that results in a neurodevelopmental disorder that can cause a range of phenotypes including global developmental delay and intellectual disability. Currently, there are 18 known individuals diagnosed to have sequenced confirmed Mapk8ip3 genetic disorders. This project focuses on examining the impact of a subset of missense patient variants on the Jip3 protein function by overexpressing the mRNA of these variants in a zebrafish knockout model for Jip3. Plasmids containing cDNA with individual missense variants were reverse transcribed, purified, and injected into single-cell zebrafish embryos (Wild Type, Jip3 -/+, and Jip3 -/-). At 6-days post mRNA microinjection, morphological, behavioral, and microscopic phenotypes were examined in zebrafish larvae. Morphologically, we compared the size and shape of the zebrafish during their development over a 5-day period. Total locomotive activity was assessed using the Microtracker assay and patterns of movement over time were examined using the DanioVision assay. Lastly, we used confocal microscopy to examine sensory axons for swelling and shortened length, which are phenotypes observed in the loss-of-function knockout Jip3 zebrafish model. Using these assays during embryonic development, we determined the impact of various missense variants on Jip3 protein function, compared to knockout and wild-type zebrafish embryo models. Variants in the gene Mapk8ip3 cause rare-neurodevelopmental disorders due to an essential role in axonal vesicle transport, elongation and regeneration. A subset of missense variants was examined by overexpressing the mRNA of these variants in a Jip3 knock-out zebrafish. Morphological, behavioral, and microscopic phenotypes were examined in zebrafish larvae. Using these assays, the spectrum of disorders can be phenotypically determined and the impact of variant location can be compared to knockout and wild-type zebrafish embryo models.

Keywords: rare disease, neurodevelopmental disorders, mrna overexpression, zebrafish research

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Authors: Reem Alajmi, Hind Al Harbi, Tahany Ayaad, Zainab Al Musawi

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Hard ticks Hyalomma spp. (family: Ixodidae) are obligate ectoparasite in their all life stages on some domestic animals mainly camels and cattle. Ticks may lead to many economic and public health problems because of their blood feeding behavior. Also, they act as vectors for many bacterial, viral and protozoan agents which may cause serious diseases such as tick-born encephalitis, Rocky-mountain spotted fever, Q-fever and Lyme disease which can affect human and/or animals. In the present study, molecular identification of ticks that attack camels in Riyadh region, Saudi Arabia based on the partial sequence of mitochondrial 16s rRNA gene was applied. Also, the present study aims to detect natural infections of collected camel ticks with Rickessia spp. and Borelia spp. using PCR/hybridization of Citrate synthase encoding gene present in bacterial cells. Hard ticks infesting camels were collected from different camels located in a farm in Riyadh region, Saudi Arabia. Results of the present study showed that the collected specimens belong to two species: Hyalomma dromedari represent 99% of the identified specimens and Hyalomma marginatum which account for 1 % of identified ticks. The molecular identification was made through blasting the obtained sequence of this study with sequences already present and identified in GeneBank. All obtained sequences of H. dromedarii specimens showed 97-100% identity with the same gene sequence of the same species (Accession # L34306.1) which was used as a reference. Meanwhile, no intraspecific variations of H. marginatum mesured because only one specimen was collected. Results also had shown that the intraspecific variability between individuals of H. dromedarii obtained in 92 % of samples ranging from 0.2- 6.6%, while the remaining 7 % of the total samples of H. dromedarii showed about 10.3 % individual differences. However, the interspecific variability between H. dromedarii and H. marginatum was approximately 18.3 %. On the other hand, by using the technique of PCR/hybridization, we could detect natural infection of camel ticks with Rickettsia spp. and Borrelia spp. Results revealed the natural presence of both bacteria in collected ticks. Rickettsial spp. infection present in 29% of collected ticks, while 35% of collected specimen were infected with Borrelia spp. The valuable results obtained from the present study are a new record for the molecular identification of camel ticks in Riyadh, Saudi Arabia and their natural infection with both Rickettsia spp. and Borrelia spp. These results may help scientists to provide a good and direct control strategy of ticks in order to protect one of the most important economic animals which are camels. Also results of this project spotlight on the disease that might be transmitted by ticks to put out a direct protective plan to prevent spreading of these dangerous agents. Further molecular studies are needed to confirm the results of the present study by using other mitochondrial and nuclear genes for tick identification.

Keywords: Camel ticks, Rickessia spp. , Borelia spp. , mitochondrial 16s rRNA gene

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Authors: Ana Handel, Jamal Ellerbe, Sarah Kanzaki, Natalie White, Nathan Ousey, Sean Gallagher

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A sense of belonging is the ability for individuals to feel they are a necessary part of whatever organization or community they find themselves in. In an academic setting, a sense of belonging is key to a student’s success. The collected research points to this sense of belonging in academic settings as a significant contributor of students’ levels of engagement and trust. When universities leverage the arts, students are provided with more opportunities to engage and feel confident in their surroundings. This allows for greater potential to develop within academic and social settings. The arts also call for the promotion of diversity, equity, and inclusion by showcasing works of artists from all different backgrounds, thus allowing students to gain cultural knowledge and be able to embrace differences. Equity, diversity, and inclusion are all emotional facets of belonging. Equity relates to the concept of making the conscious choice to recognize opportunities to incorporate inclusive and diverse ideals into different thought processes and collaboration. Inclusion involves providing equal access to opportunities and resources for people of all ‘ingroups. In an inclusive culture, individuals are able to maximize their potential with the confidence they have gained through an accepting environment. A variety of members in academic communities have noted it may be beneficial to make certain events surrounding the arts to be built into course requirements in order to ensure students are expanding their horizons and exposing themselves to the arts. These academics also recommend incorporating the arts into extracurricular activities, such as Greek life, in order to appeal to large groups of students. Once students have an understanding of the rich knowledge cultivated through exploring the arts, they will feel more comfortable in their surroundings and thus more confident to become involved in other areas of their university. A number of universities, including West Chester and Carnegie Mellon, have instituted programs aiming to provide students with the necessary tools and resources to feel comfortable in their educational settings. Different programs include references to hotlines for discrimination and office for diversity, equity, and inclusion. Staff members have also been provided with means of combating biases and increasing feelings of belongingness in order to properly support and communicate with students. These tools have successfully allowed universities to foster inviting environments for students of all backgrounds to feel belong as well as strengthening the community’s diversity, equity, and inclusion. Through demonstrating concepts of diversity, equity, and inclusion by introducing the arts into learning spaces, students can find a sense of belonging within their academic environments. It is essential to understand these topics and how they work together to achieve a common goal. The efforts of universities have made much progress in shedding light on different cultures and ideas to show students their full potential and opportunities. Once students feel more comfortable within their organizations, engagement will increase substantially.

Keywords: arts, belonging, engagement, inclusion

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Authors: Alina Beraudi, Simona Catalani, Dalila De Pasquale, Eva Bianconi, Umberto Santoro, Susanna Stea, Pietro Apostoli

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Recently the European Community, in line with the international scientific community such as with the Consensus Statement, has determined to stop the use of metal-on-metal big head stemmed hip prosthesis. Among the factors accounted as responsible for the high failure rates of these hip implants are the release and accumulation of metal ions. Many studies have correlated the presence of these ions, besides other factors, with the induction of oxidative stress response. In our study on 12 subjects, we observed the patient specific capability to eliminate metal ions after revision surgery. While for cobalt all the patients were able to completely excrete cobalt ions within 5-7 months after metal-on-metal bearing removal, for chromium ions it didn’t happen. If on the one hand the toxicokinetic differences between the two types of ions are confirmed by toxicological and occupational studies, on the other hand, this peculiar way of exposition represents a novel and important point of view. Thus, two different approaches were performed to better understand the subject specific capability to transport metal ions (albumin study) and to manage the response to them (heme-oxygenase-1 study): - a mutational screening of ALBUMIN gene was conducted in 30 MoM prosthetic patients resulting in the absence of nucleotidic changes compared with the ALB reference sequence. To this study was also added the analysis of expression of modified albumin protein; - a gene and protein expression study on 44 patients of heme-oxygenase-1, that is one of the most important antioxidant enzyme induced by metallic ions, was performed. This study resulted in no statistically significant differences in the expression of the gene and protein heme-oxygenase-1 between prosthetic and non-prosthetic patients, as well as between patients with high and low ions levels. Our results show that the protein studied (albumin and heme-oxygenase-1) seem to be not involved in determining chromium and cobalt ions level. On the other hand, achromium and cobalt elimination rates are different, but similar in all patients analyzed, suggesting that this process could be not patient-related. We support the importance of researching more about ions transport within the organism once released by hip prosthesis, about the chemical species involved, the districts where they are contained and the mechanisms of elimination, not excluding the existence of a subjective susceptibility to these metals ions.

Keywords: chromium, cobalt, hip prosthesis, individual susceptibility

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Authors: Zhenfeng Xie

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Acute gastroenteritis (AGE) is a common cause of morbidity and mortality in infants and young children worldwide, especially in developing countries. Enterovirus(EVs) have been identified in patients with AGE in many countries around the world, and some studies have revealed that EV infection is associated with gastrointestinal symptoms and plays a role in AGE. As a potential causative pathogen of AGE in humans, continuous detection and identification of EVs in pediatric patients with AGE is needed. In this study, we aimed to investigate the prevalence, seasonal distribution, and molecular characteristics of EVs circulating in pediatric patients with AGE in Thailand from 2019 to 2022. A total of 1422 stool specimens were collected for this study. RT-PCR amplification of the 5'UTR was used to screen for EV positive samples. EV genotyping was determined based on nucleotide sequence and phylogenetic analysis of the VP1 sequences. EV prevalence in pediatric AGE patients was 8.3% (118 out of 1,422). Among these, 35.6% of EV infection cases were caused by species A, followed by species C and B (33.1% and 30.5%, respectively). A total of 26 EV genotypes were identified in this study. Poliovirus 3 and coxsackievirus A2 were the predominant genotypes detected(14% and 13%, respectively). EV was detected all year round with higher prevalence between July and December. In summary, this study reports EV's prevalence and genotype diversity in pediatric patients with AGE in Thailand during 2019-2022.

Keywords: enterovirus, epidemiology, acute gastroenteritis, genotype

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Authors: Zewdneh Zana Zate

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The study focuses on the evolutionary and ecological genomics of both wild and cultivated Coffea arabica L. at its center of origin, Ethiopia, aiming to uncover how this vital species may withstand future climate changes. Utilizing bioclimatic models, we project the future distribution of Arabica under varied climate scenarios for 2050 and 2080, identifying potential conservation zones and immediate risk areas. Through whole-genome resequencing of accessions from Ethiopian gene banks, this research assesses genetic diversity and divergence between wild and cultivated populations. It explores relationships, demographic histories, and potential hybridization events among Coffea arabica accessions to better understand the species' origins and its connection to parental species. This genomic analysis also seeks to detect signs of natural or artificial selection across populations. Integrating these genomic discoveries with ecological data, the study evaluates the current and future ecological and genomic vulnerabilities of wild Coffea arabica, emphasizing necessary adaptations for survival. We have identified key genomic regions linked to environmental stress tolerance, which could be crucial for breeding more resilient Arabica varieties. Additionally, our ecological modeling predicted a contraction of suitable habitats, urging immediate conservation actions in identified key areas. This research not only elucidates the evolutionary history and adaptive strategies of Arabica but also informs conservation priorities and breeding strategies to enhance resilience to climate change. By synthesizing genomic and ecological insights, we provide a robust framework for developing effective management strategies aimed at sustaining Coffea arabica, a species of profound global importance, in its native habitat under evolving climatic conditions.

Keywords: coffea arabica, climate change adaptation, conservation strategies, genomic resilience

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Authors: Charalabos Antonatos, Mariza Panoutsopoulou, Georgios K. Georgakilas, Evangelos Evangelou, Yiannis Vasilopoulos

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The extended tissue damage and severe clinical outcomes of autoimmune diseases, accompanied by the high annual costs to the overall health care system, highlight the need for an efficient therapy. Increasing knowledge over the pathophysiology of specific chronic inflammatory diseases, namely Psoriasis (PsO), Inflammatory Bowel Diseases (IBD) consisting of Crohn’s disease (CD) and Ulcerative colitis (UC), and Rheumatoid Arthritis (RA), has provided insights into the underlying mechanisms that lead to the maintenance of the inflammation, such as Tumor Necrosis Factor alpha (TNF-α). Hence, the anti-TNFα biological agents pose as an ideal therapeutic approach. Despite the efficacy of anti-TNFα agents, several clinical trials have shown that 20-40% of patients do not respond to treatment. Nowadays, high-throughput technologies have been recruited in order to elucidate the complex interactions in multifactorial phenotypes, with the most ubiquitous ones referring to transcriptome quantification analyses. In this context, a random effects meta-analysis of available gene expression cDNA microarray datasets was performed between responders and non-responders to anti-TNFα therapy in patients with IBD, PsO, and RA. Publicly available datasets were systematically searched from inception to 10th of November 2020 and selected for further analysis if they assessed the response to anti-TNFα therapy with clinical score indexes from inflamed biopsies. Specifically, 4 IBD (79 responders/72 non-responders), 3 PsO (40 responders/11 non-responders) and 2 RA (16 responders/6 non-responders) datasetswere selected. After the separate pre-processing of each dataset, 4 separate meta-analyses were conducted; three disease-specific and a single combined meta-analysis on the disease-specific results. The MetaVolcano R package (v.1.8.0) was utilized for a random-effects meta-analysis through theRestricted Maximum Likelihood (RELM) method. The top 1% of the most consistently perturbed genes in the included datasets was highlighted through the TopConfects approach while maintaining a 5% False Discovery Rate (FDR). Genes were considered as Differentialy Expressed (DEGs) as those with P ≤ 0.05, |log2(FC)| ≥ log2(1.25) and perturbed in at least 75% of the included datasets. Over-representation analysis was performed using Gene Ontology and Reactome Pathways for both up- and down-regulated genes in all 4 performed meta-analyses. Protein-Protein interaction networks were also incorporated in the subsequentanalyses with STRING v11.5 and Cytoscape v3.9. Disease-specific meta-analyses detected multiple distinct pro-inflammatory and immune-related down-regulated genes for each disease, such asNFKBIA, IL36, and IRAK1, respectively. Pathway analyses revealed unique and shared pathways between each disease, such as Neutrophil Degranulation and Signaling by Interleukins. The combined meta-analysis unveiled 436 DEGs, 86 out of which were up- and 350 down-regulated, confirming the aforementioned shared pathways and genes, as well as uncovering genes that participate in anti-inflammatory pathways, namely IL-10 signaling. The identification of key biological pathways and regulatory elements is imperative for the accurate prediction of the patient’s response to biological drugs. Meta-analysis of such gene expression data could aid the challenging approach to unravel the complex interactions implicated in the response to anti-TNFα therapy in patients with PsO, IBD, and RA, as well as distinguish gene clusters and pathways that are altered through this heterogeneous phenotype.

Keywords: anti-TNFα, autoimmune, meta-analysis, microarrays

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Authors: Dilani Wimalasiri, Robert Brkljaca, Sylvia Urban, Terrence Piva, Tien Huynh

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Momordica cochinchinensis (Cucurbitaceae) is used as food and traditional medicine in South East Asia and is commonly known as Red Gac. The fruit aril consists 70 times higher lycopene and 10 times higher β-carotene than all known fruits and vegetables. Despite its nutritional value there is little information available on its genetic variation and its influence on nutritional value. In this study; genetic and nutritional variation (lycopene and β-carotene) was investigated among 47 M. cochinchinensis samples collected from Australia, Thailand and Vietnam using molecular markers (RAPD and ISSR) and HPLC, respectively. UPGMA based cluster analysis of genetic data grouped Northern and Central Vietnam samples together but were separated from Australia, Thailand and Southern Vietnam samples. The concentration of lycopene was significantly higher among the samples collected from Central Vietnam (p<0.05) and the concentration of β-carotene was significantly higher among the samples collected from Northern Vietnam (p<0.05) indicating the existence of best varieties. This study provides vital information in genetic diversity and facilitates the selection and breeding for nutritious M. cochinchinensis varieties.

Keywords: momordica cochinchinensis, lycopene, beta carotene, genetic diversity

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Authors: Kapse Swapnil, K. Shankar

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Aiming at optimizing the weight and deflection of cantilever beam subjected to maximum stress and maximum deflection, Multi-objective Particle Swarm Optimization (MOPSO) with Utopia Point based local search is implemented. Utopia point is used to govern the search towards the Pareto Optimal set. The elite candidates obtained during the iterations are stored in an archive according to non-dominated sorting and also the archive is truncated based on least crowding distance. Local search is also performed on elite candidates and the most diverse particle is selected as the global best. This method is implemented on standard test functions and it is observed that the improved algorithm gives better convergence and diversity as compared to NSGA-II in fewer iterations. Implementation on practical structural problem shows that in 5 to 6 iterations, the improved algorithm converges with better diversity as evident by the improvement of cantilever beam on an average of 0.78% and 9.28% in the weight and deflection respectively compared to NSGA-II.

Keywords: Utopia point, multi-objective particle swarm optimization, local search, cantilever beam

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Authors: Meilisha Putri Pertiwi, Mufti Petala Patria

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Mangrove forest often categorized as a productive ecosystem in trophic water and the highest carbon storage among all the forest types. Mangrove-derived organic matter determines the food web of fish and invertebrates. In Indonesia trophic water ecosystem, 80% commersial fish caught in coastal area are high related to food web in mangrove forest ecosystem. Based on the previous research in Panjang Island, Bojonegara, Banten, Indonesia, removed mangrove litterfall to the sea water were 9,023 g/m³/s for two stations (west station–5,169 g/m³/s and north station-3,854 g/m³/s). The vegetation were dominated from Rhizophora apiculata and Rhizopora stylosa. C element is the highest content (27,303% and 30,373%) than N element (0,427% and 0,35%) and P element (0,19% and 0,143%). The aim of research also to know the diversity of fish inhabit in mangrove forest. Fish sampling is by push net. Fish caught are collected into plastics, total length measured, weigh measured, and individual and total counted. Meanwhile, the 3 modified pipes (1 m long, 5 inches diameter, and a closed one hole part facing the river by using a nylon cloth) set in the water channel connecting mangrove forest and sea water for each stasiun. They placed for 1 hour at low tide. Then calculate the speed of water flow and volume of modified pipes. The fish and mangrove litter will be weigh for wet weight, dry weight, and analyze the C, N, and P element content. The sampling data will be conduct 3 times of month in full moon. The salinity, temperature, turbidity, pH, DO, and the sediment of mangrove forest will be measure too. This research will give information about the fish diversity in mangrove forest, the removed mangrove litterfall to the sea water, the composition of sediment, the total element content (C, N, P) of fish and mangrove litter, and the correlation of element content absorption between fish and mangrove litter. The data will be use for the fish and mangrove ecosystem conservation.

Keywords: fish diversity, mangrove forest, mangrove litter, carbon element, nitrogen element, P element, conservation

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Authors: Chia-Jung Li, Li-Te Lin, Kuan-Hao Tsui

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The study identifies SPP1 as a potential gene associated with ovarian aging, revealing a significant decline in its expression in aged ovaries. SPP1, also known as osteopontin (OPN), is a multifunctional glycoprotein involved with regulatory proteins and pro-inflammatory immune chemokines. However, its genetic links to ovarian aging have not been extensively explored. Spatial transcriptomic analyses were conducted on ovaries from young and aged female mice, along with a sample from a 73-year-old individual. Additionally, single-cell RNA sequencing analysis was performed to identify associations between SPP1 and key genes. The study focused on crucial genes, including ITGAV, ITGB1, CD44, MMP3, and FN1, with a particular emphasis on the correlation between SPP1 and ITGB1. The findings indicate a significant decline in SPP1 expression in aged ovaries, which was consistent in the 73-year-old sample. Single-cell RNA sequencing unveiled associations between SPP1 and key genes, emphasizing a strong co-expression correlation between SPP1 and ITGB1. While the study provides valuable insights, further research is necessary to understand the broader implications and potential applications of SPP1 in ovarian aging. Translating these findings to clinical settings requires careful consideration. The identification of SPP1 as a gene implicated in ovarian aging opens new avenues for advancing precision medicine and refining treatment strategies for conditions related to ovarian aging.

Keywords: SPP1, ovarian aging, spatial transcriptomic, single-cell RNA sequencing

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Authors: Ouabel Habib, Taleb Mohamed Lamine, Ben Zohra Mohamed Nadjib

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The Tissemsilt Province occupies a natural transitional zone and is dedicated to cereal production, dry forage, and livestock farming. It encompasses an agricultural domain covering an area of 181,097 hectares, of which 143,451 hectares are considered arable land. A field study was conducted along a west-to-east transect, covering six zones within the province, including Maacem, Ammari, Tissemsilt, Khemisti, Laayoune, Theniet el Had, and Taza. Random soil samples were collected from each region for laboratory analyses to assess soil types and quality, ultimately aiming to identify soil diversity within the Tissemsilt Province. Within the agricultural zones, approximately 40 soil samples were collected, revealing that the province contains moderately high-quality clayey soils, semi-rich in organic matter. However, as one moves southward, this richness diminishes. This leads us to predict that the agricultural zone is an ideal region for cereal cultivation. Nonetheless, this situation is challenged by the decreasing precipitation, which affects overall yields.

Keywords: soil, biodiversity, semi-arid, agriculture

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Authors: Teresa Leary Handy

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As awareness of the importance of diversity has increased in society, higher education has also begun to recognize the importance of supporting faculty of color. In the university setting, faculty women of color specifically encounter barriers that impact their level of job satisfaction, retention rates, and pedagogical practices. These barriers and challenges not only undermine faculty diversity efforts but also hinder the ability of colleges and universities to provide a supportive environment that fosters students' academic success and sense of belonging. Faculty who are marginalized and on the periphery in higher education institutions need support so that they can feel confident in building a student’s sense of belonging which can impact a student’s academic success and goal of earning a college degree. This study examined and sought to understand the importance of supporting faculty of color, specifically women faculty of color, and how this type of faculty support can impact student academic success and a student’s sense of belonging. The study furthered original research on strategies to move an institution forward on the equity spectrum to support belonging and inclusions as core culture elements.

Keywords: equity, inclusion, belonging, women, faculty support

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Authors: Sadaf Ilyas, Saba Riaz

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The extensive use of antibiotics has led to increases emergence of antibiotic-resistant organisms. Pseudomonas is a notorious opportunistic pathogen involoved in nosocomial infections and exhibit innate resistance to many antibiotics. The present study was conducted to assess the prevalence, levels of antimicrobial susceptibility and resistance mechanisms of Pseudomonas. A total of thirty clinical strains of Pseudomonas were isolated from different clinical sites of infection. All clinical specimens were collected from Chughtais Lahore Lab. Jail road, during 8-07-2010 to 11-01-2011. Biochemical characterization was done using routine biochemical tests. Antimicrobial susceptibility was determined by Kirby-Baeur method. The plasmids were isolated from all the strains and digested with restriction enzyme PstI and EcoRI. Transfer of Multi-resistance plasmid was checked via transformation and conjugation to confirm the plasmid mediated resistance to antibiotics. The prevalence of Pseudomonas in clinical specimens was found out to be 14% of all bacterial infections. IPM has shown to be the most effective drug against Pseudomonas followed by CES, PTB and meropenem, wheareas most of the Pseudomonas strains have developed significant resistance against Penicillins and some Cephalasporins. Antibiotic resistance determinants were carried by plasmids, as they conferred resistance to transformed K1 strains. The isolates readily undergo conjugation, transferring the resistant genes to other strains, illustrating the high rates of cross infection and nosocomial infection in the immunocompromised patients.

Keywords: pseudomonas, antibiotics, drug resistance, horizontal gene transfer

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Authors: Jamal Ayour, Mohamed Benichou

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Fruit quality is one of the main concerns of consumers, producers, and distributors. The evolution of apricot fruits undergoes a strong acceleration during maturation, and the rapidity of post-harvest evolution of the ripe fruit is particularly selective in the apricot. The objective of this study is to identify new cultivars with an interesting quality as well as a better yield allowing a more prolonged production over time. The evaluation of the fruit quality of new apricot cultivars from the Marrakech region was carried out by analyzing their physical and biochemical attributes during ripening. The results obtained clearly show a great diversity of the physicochemical attributes of the selected clones. Also, some genotypes of apricots showed contents of sugars, organic acids (vitamin C) and β carotene significantly higher than those of the most famous varieties of Morocco: Canino, Delpatriarca, and Maoui. Principal component analysis (PCA), taking into account the maturity stage and the diversity of cultivars, made it possible to define three groups with similar physicochemical attributes. The results of this study are of great use, particularly for the selection of genotypes with a better quality of fruit, both for consumption or industrial processing and with important contents of physicochemical attributes.

Keywords: apricot, acidity, carotenoids, color, sugar, quality, vitamin C

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Authors: Laura Gantley, Vanessa M. Conn, Stuart Webb, Kirsty Kirk, Marta Gabryelska, Duncan Holds, Brett W. Stringer, Simon J. Conn

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Trinucleotide repeat disorders comprise ~20 severe, inherited human neuromuscular and neurodegenerative disorders, which are a result of an abnormal expansion of repetitive sequences in the DNA. The most common of these, Huntington’s disease, results from the expansion of the CAG repeat region in exon 1 of the HTT gene via an unknown mechanism. Non-coding RNAs have been implicated in the initiation and progression of many diseases; thus, we focus on one circular RNA (circRNA) molecule arising from non-canonical splicing (back splicing) of HTT pre-mRNA. This circRNA and its mouse orthologue were transgenically overexpressed in human cells (SHSY-5Y and HEK293T) and mouse cells (Mb1), respectively. High-content imaging and flow cytometry demonstrated the overexpression of this circRNA reduces cell proliferation, reduces nuclear size independent of cellular size, and alters cell cycle progression. Analysis of protein by western blot and immunofluorescence demonstrated no change to HTT protein levels but altered nuclear-cytoplasmic distribution without impacting the expansion of the HTT repeat region. As these phenotypic and genotypic changes are found in Huntington’s disease patients, these results may suggest that this circRNA may play a functional role in the progression of Huntington’s disease.

Keywords: cell biology, circular RNAs, Huntington’s disease, molecular biology, neurodegenerative disorders

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Authors: Keunhong Chae, Seokho Yoon

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Recently, the global navigation satellite system (GNSS) such as Galileo and GPS is employing more satellites to provide a higher degree of accuracy for the location service, thus calling for a more efficient signaling scheme among the satellites used in the overall GNSS network. In that the network throughput is improved, the spatial diversity can be one of the efficient signaling schemes; however, it requires multiple antenna that could cause a significant increase in the complexity of the GNSS. Thus, a diversity scheme called the cooperative signaling was proposed, where the virtual multiple-input multiple-output (MIMO) signaling is realized with using only a single antenna in the transmit satellite of interest and with modeling the neighboring satellites as relay nodes. The main drawback of the cooperative signaling is that the relay nodes receive the transmitted signal at different time instants, i.e., they operate in an asynchronous way, and thus, the overall performance of the GNSS network could degrade severely. To tackle the problem, several modified cooperative signaling schemes were proposed; however, all of them are difficult to implement due to a signal decoding at the relay nodes. Although the implementation at the relay nodes could be simpler to some degree by employing the time-reversal and conjugation operations instead of the signal decoding, it would be more efficient if we could implement the operations of the relay nodes at the source node having more resources than the relay nodes. So, in this paper, we propose a novel cooperative signaling scheme, where the data signals are combined in a unique way at the source node, thus obviating the need of the complex operations such as signal decoding, time-reversal and conjugation at the relay nodes. The numerical results confirm that the proposed scheme provides the same performance in the cooperative diversity and the bit error rate (BER) as the conventional scheme, while reducing the complexity at the relay nodes significantly. Acknowledgment: This work was supported by the National GNSS Research Center program of Defense Acquisition Program Administration and Agency for Defense Development.

Keywords: global navigation satellite network, cooperative signaling, data combining, nodes

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Authors: Suganiya Rama Rao, Yoon-Yen Yow, Thor-Seng Liew, Shyamala Ratnayeke

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Invasive snails in the genus Pomacea have spread across Southeast Asia including Peninsular Malaysia. Apart from significant economic costs to wetland crops, very little is known about the snails’ effects on native species, and wetland function through their alteration of macrophyte communities. This study was conducted to establish diagnostic characteristics of Pomacea species in the Malaysian environment using genetic and morphological criteria. Snails were collected from eight localities in northern and central regions of Peninsular Malaysia. The mitochondrial COI gene of 52 adult snails was amplified and sequenced. Maximum likelihood analysis was used to analyse species identity and assess phylogenetic relationships among snails from different geographic locations. Shells of the two species were compared using geometric morphometric analysis and covariance analyses. Shell height accounted for most of the observed variation between P. canaliculata and P. maculata, with the latter possessing a smaller mean ratio of shell height: aperture height (p < 0.0001) and shell height to shell width (give p < 0.0001). Genomic and phylogenetic analysis demonstrated the presence of two monophyletic taxa, P. canaliculata and P. maculata, in Peninsular Malaysia samples. P. maculata co-occurred with P. canaliculata in 5 localities, but samples from 3 localities contained only P. canaliculata. This study is the first to confirm the presence of two of the most invasive species of Pomacea in Peninsular Malaysia using a genomic approach. P. canaliculata appears to be the more widespread species. Despite statistical differences, both quantitative and qualitative morphological characteristics demonstrate much interspecific overlap and intraspecific variability; thus morphology alone cannot reliably verify species identity. Molecular techniques for distinguishing between these two highly invasive Pomacea species are needed to understand their specific ecological niches and develop effective protocols for their management.

Keywords: Pomacea canaliculata, Pomacea maculata, invasive species, phylog enetic analysis, geometric morphometric analysis

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Authors: Seyed Esmail Seyedi Bariran, Khairul Salleh Mohamed Sahari

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In multi-echelon supply chain networks, optimal supplier selection significantly depends on the accuracy of suppliers’ performance prediction. Different methods of multi criteria decision making such as ANN, GA, Fuzzy, AHP, etc have been previously used to predict the supplier performance but the “black-box” characteristic of these methods is yet a major concern to be resolved. Therefore, the primary objective in this paper is to implement an artificial intelligence-based gene expression programming (GEP) model to compare the prediction accuracy with that of ANN. A full factorial design with %95 confidence interval is initially applied to determine the appropriate set of criteria for supplier performance evaluation. A test-train approach is then utilized for the ANN and GEP exclusively. The training results are used to find the optimal network architecture and the testing data will determine the prediction accuracy of each method based on measures of root mean square error (RMSE) and correlation coefficient (R2). The results of a case study conducted in Supplying Automotive Parts Co. (SAPCO) with more than 100 local and foreign supply chain members revealed that, in comparison with ANN, gene expression programming has a significant preference in predicting supplier performance by referring to the respective RMSE and R-squared values. Moreover, using GEP, a mathematical function was also derived to solve the issue of ANN black-box structure in modeling the performance prediction.

Keywords: Supplier Performance Prediction, ANN, GEP, Automotive, SAPCO

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Authors: Mohammed Abdelsabour-Khalaf, F. Yusuf , B Brand-Saberi

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Purpose: Applications of nanotechnology nowadays extended to include a wide range of scientific areas such electron micrscopy and gene expression. The aim of the current study was to investigate the developmental expression pattern of genes involved in human glomerulo-nephropathies associated with massive proteinuria and podocyte differentiation using the chicken mesonephros as a model system. Method: We performed in situ hybridization using chicken specific mRNA probes for genes expressed in the early nephron and slit diaphragm genes. The probes used were cNeph1, cNeph2, cSim1, cLmx1b, and cAtoh8. Chicken embryos from Hamburger Hamilton developmental stage HH19 (E3) to HH 34 (E9) were used for the in situ hybridization (ISH). ISH was performed on whole mount embryos which were sectioned by vibratome. Results: Our result show that Neph1, Neph2, Sim1. Lmx1b and Atoh8 genes are dynamically expressed during nephron morphogenesis and Neph1 and Atoh8 are also specifically expressed in the podocytes during late stages of differentiation. Conclusion: We conclude from our results that the genes implicated in congenital and acquired glomerulo-nephropathies like Neph1 and Neph2 are dynamically expressed during mesonephros development pointing towards a role in the formation of the filtration barrier and the differentiation of the mesonephric podocytes. Thus the avian mesonephros could serve as a model to study human kidney diseases.

Keywords: mesonephros, chicken embryo, gene expression, immunohistochemistry

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Authors: Dani Sukkar, Ali Kanso, Philippe Laval-Gilly, Jairo Falla-Angel

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The honeybees' immune system is challenged by different risk factors that induce various responses. However, complex scenarios where bees are exposed to different pesticides simultaneously with immune activation are not well evaluated. The Toll pathway is one of the main signaling pathways studied in invertebrate immune responses, and it is a good indicator of the effect of such complex interactions in addition to key signaling elements of other pathways like Relish of the immune deficiency (IMD) pathway or Eater, the phagocytosis receptor or vitellogenin levels. Honeybee hemocytes extracted from 5th instar larvae were exposed to imidacloprid and/or amitraz with or without the presence of the zymosan a as an immune activator. The gene expression of multiple immune related genes were studied, including spaetzle, Toll, myD88, relish, eater and vitellogenin, by real-time polymerase chain reaction after RNA extraction. The results demonstrated that the Toll pathway is mainly affected by the pesticides; imidacloprid and amitraz, especially by their different combinations. Furthermore, immune activation by zymosan A, a fungal cell-wall component, acts to mitigate to some extent the effect of pesticides on the different levels of the Toll pathway. In addition, imidacloprid, amitraz, and zymosan A have complex and context-specific interactions depending on the levels of immune activation and the pathway evaluated affecting immune-gene expression differently.

Keywords: toll pathway, immune modulation, β-glucan, imidacloprid, amitraz, honeybees, immune genes

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Authors: Zina Nasr, Faiek Errouissi

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Forest ecosystems are known for its ability to contain a large diversity of fauna especially insects that represent a huge taxonomic group. A portion of forest insects are recognized as saproxylic including the group of organisms that ‘depend on dead or dying wood’ about them, 20% are beetles. We focused our study on saproxylic beetles in an old urban park ‘the park of Belvedere’, located in the north west of Tunis (36° 49'21’ N 10°10'24’ W). The vegetation is dominated by old trees (Eucalyptus, Olea, Aberia, Pinus) and many fallen wood exist. Saproxylic beetles were collected using three interception traps set in the park over one year (from June 2014 to May 2015) and recovered monthly. In total, we collected 189 beetles belonging to 20 families and 57 species. Several saproxylic families (Bostrichidae, Cerambycidae, Curculionidae, Melyridae, Nitidulidae, Staphylinidae), and well known genus (Rhizopertha, Thrychoplerus, Otiorhychus, Dolichosoma, Epuraea, Anotylus) are recorded. We have retained the largest activity of beetles in spring and a very low richness in winter with zero insect per traps. This result was certainly caused by the variation of meteorological factors that mainly influenced the activity of these organisms. Therefore, we were interested on the saproxylic diversity in an urban ‘forest’, and these results will be more interesting when they are compared in the future with other works from natural forest.

Keywords: saproxylic beetles, seasons, urban park, wood

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Authors: Aswini M. S.

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Tomato (Solanum lycopersicum L.) is one of the most significant vegetable crops in terms of its economic benefits. Both fresh and processed tomatoes are consumed. Tomatoes have a limited genetic base, which makes breeding extremely challenging. Plant breeding has become much simpler and more effective with genome editing tools of CRISPR and CRISPR-associated 9 protein (CRISPR/Cas9), which address the problems with traditional breeding, chemical/physical mutagenesis, and transgenics. With the use of CRISPR/Cas9, a number of tomato traits have been functionally distinguished and edited. These traits include plant architecture as well as flower characters (leaf, flower, male sterility, and parthenocarpy), fruit ripening, quality and nutrition (lycopene, carotenoid, GABA, TSS, and shelf-life), disease resistance (late blight, TYLCV, and powdery mildew), tolerance to abiotic stress (heat, drought, and salinity) and resistance to herbicides. This study explores the potential of CRISPR/Cas9 genome editing for enhancing yield in tomato plants. The study utilized the CRISPR/Cas9 genome editing technology to functionally edit various traits in tomatoes. The de novo domestication of elite features from wild cousins to cultivated tomatoes and vice versa has been demonstrated by the introgression of CRISPR/Cas9. The CycB (Lycopene beta someri) gene-mediated Cas9 editing increased the lycopene content in tomato. Also, Cas9-mediated editing of the AGL6 (Agamous-like 6) gene resulted in parthenocarpic fruit development under heat-stress conditions. The advent of CRISPR/Cas has rendered it possible to use digital resources for single guide RNA design and multiplexing, cloning (such as Golden Gate cloning, GoldenBraid, etc.), creating robust CRISPR/Cas constructs, and implementing effective transformation protocols like the Agrobacterium and DNA free protoplast method for Cas9-gRNAs ribonucleoproteins (RNPs) complex. Additionally, homologous recombination (HR)-based gene knock-in (HKI) via geminivirus replicon and base/prime editing (Target-AID technology) remains possible. Hence, CRISPR/Cas facilitates fast and efficient breeding in the improvement of tomatoes.

Keywords: CRISPR-Cas, biotic and abiotic stress, flower and fruit traits, genome editing, polygenic trait, tomato and trait introgression

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Authors: Judith Mogouong, Philippe Constant, Robert Lavallee, Claude Guertin

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The emerald ash borer (EAB) is an exotic wood borer insect native from China, which is associated with important environmental and economic damages in North America. Beetles are known to be vectors of microbial communities related to their adaptive capacities. It is now established that environmental stress factors may induce physiological events on the host trees, such as phytochemical changes. Consequently, that may affect the establishment comportment of herbivorous insect. Considering the number of insects collected on ash trees (insects’ density) as an abiotic factor related to stress damage, the aim of our study was to explore the dynamic of EAB gut microbial community genome (microbiome) when facing that factor and to monitor its diversity. Insects were trapped using specific green Lindgren© traps. A gradient of the captured insect population along the St. Lawrence River was used to create three levels of insects’ density (low, intermediate, and high). After dissection, total DNA extracted from insect guts of each level has been sent for amplicon sequencing of bacterial 16S rRNA gene and fungal ITS2 region. The composition of microbial communities among sample appeared largely diversified with the Simpson index significantly different across the three levels of density for bacteria. Add to that; bacteria were represented by seven phyla and twelve classes, whereas fungi were represented by two phyla and seven known classes. Using principal coordinate analysis (PCoA) based on Bray Curtis distances of 16S rRNA sequences, we observed a significant variation between the structure of the bacterial communities depending on insects’ density. Moreover, the analysis showed significant correlations between some bacterial taxa and the three classes of insects’ density. This study is the first to present a complete overview of the bacterial and fungal communities associated with the gut of EAB base on culture-independent methods, and to correlate those communities with a potential stress factor of the host trees.

Keywords: gut microbiome, DNA, 16S rRNA sequences, emerald ash borer

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Authors: O. Ubani, H. I. Atagana, M. S. Thantsha, R. Adeleke

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The oil sludge components (polycyclic aromatic hydrocarbons, PAHs) have been found to be cytotoxic, mutagenic and potentially carcinogenic and microorganisms such as bacteria and fungi can degrade the oil sludge to less toxic compounds such as carbon dioxide, water and salts. In the present study, we isolated different bacteria with PAH-degrading potentials from the co-composting of oil sludge and different animal manure. These bacteria were isolated on the mineral base medium and mineral salt agar plates as a growth control. A total of 31 morphologically distinct isolates were carefully selected from 5 different compost treatments for identification using polymerase chain reaction (PCR) of the 16S rDNA gene with specific primers (16S-P1 PCR and 16S-P2 PCR). The amplicons were sequenced and sequences were compared with the known nucleotides from the gene bank database. The phylogenetical analyses of the isolates showed that they belong to 3 different clades namely Firmicutes, Proteobacteria and Actinobacteria. These bacteria identified were closely related to genera Bacillus, Arthrobacter, Staphylococcus, Brevibacterium, Variovorax, Paenibacillus, Ralstonia and Geobacillus species. The results showed that Bacillus species were more dominant in all treated compost piles. Based on their characteristics these bacterial isolates have high potential to utilise PAHs of different molecular weights as carbon and energy sources. These identified bacteria are of special significance in their capacity to emulsify the PAHs and their ability to utilize them. Thus, they could be potentially useful for bioremediation of oil sludge and composting processes.

Keywords: bioaugmentation, biodegradation, bioremediation, composting, oil sludge, PAHs, animal manures

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Authors: Van Thinh Bui, Anh Tuan Tran, Quoc Viet Ngo, The Bao Pham

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Video retrieval is a searching problem on videos or clips based on content in which they are relatively close to an input image or video. The application of this retrieval consists of selecting video in a folder or recognizing a human in security camera. However, some recent approaches have been in challenging problem due to the diversity of video types, frame transitions and camera positions. Besides, that an appropriate measures is selected for the problem is a question. In order to overcome all obstacles, we propose a content-based video retrieval system in some main steps resulting in a good performance. From a main video, we process extracting keyframes and principal objects using Segmentation of Aggregating Superpixels (SAS) algorithm. After that, Speeded Up Robust Features (SURF) are selected from those principal objects. Then, the model “Bag-of-words” in accompanied by SVM classification are applied to obtain the retrieval result. Our system is performed on over 300 videos in diversity from music, history, movie, sports, and natural scene to TV program show. The performance is evaluated in promising comparison to the other approaches.

Keywords: video retrieval, principal objects, keyframe, segmentation of aggregating superpixels, speeded up robust features, bag-of-words, SVM

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Authors: Dedy Pratama, Akhmadu Muradi, Hilman Ibrahim, Patrianef Darwis, Alexander Jayadi Utama, Raden Suhartono, D. Suryandari, Luluk Yunaini, Tom Ch Adriani

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Objective: Diabetic Foot Ulcer (DFU) is one of the complications of Type 2 Diabetes Mellitus (T2DM) that can lead to disability and death. Inadequate vascularization condition will affect healing process of DFU. Therefore, we investigated the expression of polymorphism TGF- β1 in the relation of the occurrence of DFU in T2DM. Methods: We designed a case-control study to investigate the polymorphism TGF- β1 gene 1800469 C > T and 1982073 C > T in T2DM in Cipto Mangunkusumo National Hospital (RSCM) Jakarta from June to December 2016. We used PCR techniques and compared the results in a group of T2DM patients with DFU as the case study and without DFU as the control group. Results: There were 203 patients, 102 patients with DFU and 101 patients control without DFU. 49,8% is male and 50,2% female with mean age about 56 years. Distribution of wild-type genotype TGF-B1 1800469 C > T wild type CC was found in 44,8%, the number of mutant heterozygote CT was 10,8% and mutant homozygote is 11,3%. Distribution of TGF-B1 1982073 C>T wild type CC was 32,5%, mutant heterozygote is 38,9% and mutant homozygote 25,1%. Conclusion: Distribution of alleles from TGF-B1 1800469 C > T is C 75% and T 25% and from TGF-B1 1982073 C > T is C53,8% and T 46,2%. In the other word polymorphism TGF- β1 plays a role in the occurrence and healing process of the DFU in T2DM patients.

Keywords: diabetic foot ulcers, diabetes mellitus, polymorphism, TGF-β1

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