Search results for: human genome sequencing

Authors: Salman Naveed, Nitant Gandhi, Grant Billings, Zachary Jones, B. Todd Campbell, Michael Jones, Sachin Rustgi

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Cotton (Gossypium spp.) is the primary source of natural fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified markers associated with the gene expression traits via genome-wide association analysis using a 63K SNP Array (Hulse-Kemp et al. 2015 G3 5:1187). Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed association with expression traits. Out of these 396 markers, 159 mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated via virus-induced gene silencing.

Keywords: cotton, GWAS, QTL, expression traits

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Authors: Pouira Askary

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Indeed, in our globalized world which is facing with various international crises, the transnational corporations and other business enterprises have the capacity to foster economic well-being, development, technological improvement and wealth, as well as causing adverse impacts on human rights. The UN Human Rights Council declared that although the primary responsibility to protect human rights lie with the State but the transnational corporations and other business enterprises have also a responsibility to respect and protect human rights in the framework of corporate social responsibility. In 2011, the Human Rights Council endorsed the Guiding Principles on Business and Human Rights, a set of guidelines that define the key duties and responsibilities of States and business enterprises with regard to business-related human rights abuses. In UN’s view, the Guiding Principles do not create new legal obligations but constitute a clarification of the implications of existing standards, including under international human rights law. In 2014 the UN Human Rights Council decided to establish a working group on transnational corporations and other business enterprises whose mandate shall be to elaborate an international legally binding instrument to regulate, in international human rights law, the activities of transnational corporations and other business enterprises. Extremely difficult task for the working group to codify a legally binding document to regulate the behavior of corporations on the basis of the norms of international law! Concentration of this paper is on the origins of those human rights applicable on business enterprises. The research will discuss that the social and ethical roots of the CSR are much more institutionalized and elaborated than the legal roots. Therefore, the first step is to determine whether and to what extent corporations, do have an ethical responsibility to respect human rights and if so, by which means this ethical and social responsibility is convertible to legal commitments.

Keywords: CSR, ethics, international law, human rights, development, sustainable business

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

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

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

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Authors: Timothy Fwa Yerima

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This paper evaluates the development of human rights jurisprudence in Africa by the ECOWAS Court of Justice. It traces that though ECOWAS was not established with the aim of promoting and protecting human rights as the African Court of Human and Peoples’ Rights, no doubt, the 1991 ECOWAS Court Protocol and the 1993 ECOWAS Revised Treaty give the ECOWAS Court its human rights mandate. The paper, however, points out that despite the availability of these two Laws, the ECOWAS Court had difficulty in its human rights mandate, in view of the twin problems of lack of access to the Court by private parties and personal jurisdiction of the Court to entertain cases filed by private parties. The paper considers the 2005 Supplementary Protocol, not only as an effective legal framework in West African Sub-Region that tackles these problems in human rights cases but also a strong foundation upon which the Court has been developing human rights jurisprudence in Africa through the interpretation and application of this Law and other sources of Law of the Court. After a thorough analysis of some principles laid down by the ECOWAS Court so far, the paper observes that human rights jurisprudence in Africa is growing rapidly; depicting that though the ECOWAS Court initially had difficulty in its human rights mandate, today it has a bright and visionary landing. The paper concludes that West African Sub-Region will witness a more effective performance of the ECOWAS Court if some of its challenges are tackled.

Keywords: access, African human rights, ECOWAS court of justice, jurisprudence, personal jurisdiction

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Authors: Simona Perga, Chiara Beltramo, Floriana Fruscione, Isabella Martini, Federica Cavallo, Federica Riccardo, Paolo Buracco, Selina Iussich, Elisabetta Razzuoli, Katia Varello, Lorella Maniscalco, Elena Bozzetta, Angelo Ferrari, Paola Modesto

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Introduction: Human and canine melanoma have common clinical, histologic characteristics making dogs a good model for comparative oncology. The identification of specific genes and a better understanding of the genetic landscape, signaling pathways, and tumor–microenvironmental interactions involved in the cancer onset and progression is essential for the development of therapeutic strategies against this tumor in both species. In the present study, the differential expression of genes in spontaneously occurring canine melanoma and in paired normal tissue was investigated by targeted RNAseq. Material and Methods: Total RNA was extracted from 17 canine malignant melanoma (CMM) samples and from five paired normal tissues stored in RNA-later. In order to capture the greater genetic variability, gene expression analysis was carried out using two panels (Qiagen): Human Immuno-Oncology (HIO) and Mouse-Immuno-Oncology (MIO) and the miSeq platform (Illumina). These kits allow the detection of the expression profile of 990 genes involved in the immune response against tumors in humans and mice. The data were analyzed through the CLCbio Genomics Workbench (Qiagen) software using the Canis lupus familiaris genome as a reference. Data analysis were carried out both comparing the biologic group (tumoral vs. healthy tissues) and comparing neoplastic tissue vs. paired healthy tissue; a Fold Change greater than two and a p-value less than 0.05 were set as the threshold to select interesting genes. Results and Discussion: Using HIO 63, down-regulated genes were detected; 13 of those were also down-regulated comparing neoplastic sample vs. paired healthy tissue. Eighteen genes were up-regulated, 14 of those were also down-regulated comparing neoplastic sample vs. paired healthy tissue. Using the MIO, 35 down regulated-genes were detected; only four of these were down-regulated, also comparing neoplastic sample vs. paired healthy tissue. Twelve genes were up-regulated in both types of analysis. Considering the two kits, the greatest variation in Fold Change was in up-regulated genes. Dogs displayed a greater genetic homology with humans than mice; moreover, the results have shown that the two kits are able to detect different genes. Most of these genes have specific cellular functions or belong to some enzymatic categories; some have already been described to be correlated to human melanoma and confirm the validity of the dog as a model for the study of molecular aspects of human melanoma.

Keywords: animal model, canine melanoma, gene expression, spontaneous tumors, targeted RNAseq

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Authors: Selisha A. Sooklal, Phelelani Mpangase, Shaun Aron, Karl Rumbold

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Organically bound fluorine (C-F bond) is extremely rare in nature. Despite this, the first fluorinated secondary metabolite, fluoroacetate, was isolated from the plant Dichapetalum cymosum (commonly known as Gifblaar). However, the enzyme responsible for fluorination (fluorinase) in Gifblaar was never isolated and very little progress has been achieved in understanding this process in higher plants. Fluorinated compounds have vast applications in the pharmaceutical, agrochemical and fine chemicals industries. Consequently, an enzyme capable of catalysing a C-F bond has great potential as a biocatalyst in the industry considering that the field of fluorination is virtually synthetic. As with any biocatalyst, a range of these enzymes are required. Therefore, it is imperative to expand the exploration for novel fluorinases. This study aimed to gain molecular insights into secondary metabolite biosynthesis in Gifblaar using a high-throughput sequencing-based approach. Mechanical wounding studies were performed using Gifblaar leaf tissue in order to induce expression of the fluorinase. The transcriptome of the wounded and unwounded plant was then sequenced on the Illumina HiSeq platform. A total of 26.4 million short sequence reads were assembled into 77 845 transcripts using Trinity. Overall, 68.6 % of transcripts were annotated with gene identities using public databases (SwissProt, TrEMBL, GO, COG, Pfam, EC) with an E-value threshold of 1E-05. Sequences exhibited the greatest homology to the model plant, Arabidopsis thaliana (27 %). A total of 244 annotated transcripts were found to be differentially expressed between the wounded and unwounded plant. In addition, secondary metabolic pathways present in Gifblaar were successfully reconstructed using Pathway tools. Due to lack of genetic information for plant fluorinases, a transcript failed to be annotated as a fluorinating enzyme. Thus, a local database containing the 5 existing bacterial fluorinases was created. Fifteen transcripts having homology to partial regions of existing fluorinases were found. In efforts to obtain the full coding sequence of the Gifblaar fluorinase, primers were designed targeting the regions of homology and genome walking will be performed to amplify the unknown regions. This is the first genetic data available for Gifblaar. It has provided novel insights into the mechanisms of metabolite biosynthesis and will allow for the discovery of the first eukaryotic fluorinase.

Keywords: biocatalyst, fluorinase, gifblaar, transcriptome

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Authors: S. J. Higgs, E. Van Eck, K. Heynis, S. H. Broadberry

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Engagement with non-human animals is a rapidly-growing field of study within the animal science and social science sectors, with human-interactions occurring in many forms; interactions, encounters and animal-assisted therapy. To our knowledge, there has been a wide array of research published on domestic and livestock human-animal interactions, however, there appear to be fewer publications relating to zoo animals and the effect these interactions have on the animal, human and establishment. The aim of this study was to identify if there were any perceivable benefits from the human-animal interaction for the cheetah, the human and the establishment. Behaviour data were collected before, during and after the interaction on the behaviour of the cheetah and the human participants to highlight any trends with nine interactions conducted. All 35 participants were asked to fill in a questionnaire prior to the interaction and immediately after to ascertain if their perceptions changed following an interaction with the cheetah. An online questionnaire was also distributed for three months to gain an understanding of the perceptions of human-animal interactions from members of the public, gaining 229 responses. Both questionnaires contained qualitative and quantitative questions to allow for specific definitive answers to be analysed, but also expansion on the participants perceived perception of human-animal interactions. In conclusion, it was found that participants’ perceptions of human-animal interactions saw a positive change, with 64% of participants altering their opinion and viewing the interaction as beneficial for the cheetah (reduction in stress assumed behaviours) following participation in a 15-minute interaction. However, it was noted that many participants felt the interaction lacked educational values and therefore this is an area in which zoological establishments can work to further improve upon. The results highlighted many positive benefits for the human, animal and establishment, however, the study does indicate further areas for research in order to promote positive perceptions of human-animal interactions and to further increase the welfare of the animal during these interactions, with recommendations to create and regulate legislation.

Keywords: Acinonyx jubatus, encounters, human-animal interactions, perceptions, zoological establishments

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Authors: Alhaji Khuzaima Mohammed Osman, Zaeem Sheikh Abdul Wadudi Haruna

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This article aims to explore the crucial link between counter-terrorism efforts and the preservation of human security. As acts of terrorism continue to pose significant threats to societies worldwide, it is imperative to develop effective strategies that mitigate risks while safeguarding the rights and well-being of individuals. This paper discusses key aspects of counter-terrorism and human security, emphasizing the need for a comprehensive approach that integrates intelligence, prevention, response, and resilience-building measures. By highlighting successful case studies and lessons learned, this article provides valuable insights for policymakers, law enforcement agencies, and practitioners in their quest to address terrorism and foster human security.

Keywords: human security, risk mitigation, terrorist activities, civil liberties

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Authors: Jerry John T. M., Sylas V. P., Shijo Joy

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Hydrogen is the most essential gas that can be used for many purposes. During the production of hydrogen using raw materials like Soil and leftover cooked rice water (kanjivellam), the major by-product formed is water. Soil is collected from three different places in kottayam district: Kallara, Meenachilar, and Athirampuzha. Collected samples are mixed with rice water and tested for traces of hydrogen using a biohydrogen sensor after 72 hours. The result was the presence of hydrogen in all the 3 samples. After streaking, PCR and gel electrophoresis detected the bacteria which produced the hydrogen. RGCB Thiruvananthapuram conducted the sequencing of the PCR resultant. And identified the bacterial strains. Five variants of Bacillus bacteria ( (1) Bacillus cereus strain JTM GenBank: OP278839.1 (2) Bacillus toyonensis strain JTM2 GenBank: OP278841.1 (3) Bacillus anthracis strain JTM_SR2989-3-R_H08 GenBank: OP278960.1 (4) Bacillus thuringiensis strain JRY1 GenBank: OP278976.1 (5) Bacillus anthracis strain JTM_SR2989-3-F_H07 GenBank: OP278959.1 ) are identified and successfully registered in NCBI Gen bank. These Bacillus bacteria are major types of Rhizobacteria that can form spores and can survive in the soil for a long time period under harsh environmental conditions. Also, plant growth is enhanced by PGPR (Plant growth promoting rhizobacteria) through the induction of systemic resistance, antibiosis, and competitive omission. The molecular sequencing was submitted to the NCBI Gen Bank, and the accession numbers were allotted for the bacterial cultures.

Keywords: bio hydrogen production, bacterial bio hydrogen production, plant related to bacillus bacteria., bacillus bacteria study

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Authors: Seyed Reza Aghili, Tahereh Shokohi, Shirin Sadat Hashemi Fesharaki, Mohammad Ali Boroumand, Bahar Salmanian

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Introduction: Intravenous catheter-associated fungal infection as nosocomial infection continue to be a deep problem among hospitalized patients, decreasing quality of life and adding healthcare costs. The capacity of catheters in the spread of candidemia in heart failure patients is obvious. The aim of this study was to evaluate the prevalence and genetic identification of Candida species in heart disorder patients. Material and Methods: This study was conducted in Tehran Hospital of Cardiology Center (Tehran, Iran, 2014) during 1.5 years on the patients hospitalized for at least 7 days and who had central or peripheral vein catheter. Culture of catheters, blood and skin of the location of catheter insertion were applied for detecting Candida colonies in 223 patients. Identification of Candida species was made on the basis of a combination of various phenotypic methods and confirmed by sequencing the ITS1-5.8S-ITS2 region amplified from the genomic DNA using PCR and the NCBI BLAST. Results: Of the 223 patients samples tested, we identified totally 15 Candida isolates obtained from 9 (4.04%) catheter cultures, 3 (1.35%) blood cultures and 2 (0.90%) skin cultures of the catheter insertion areas. On the base of ITS region sequencing, out of nine Candida isolates from catheter, 5(55.6%) C. albicans, 2(22.2%) C. glabrata, 1(11.1%) C. membranifiaciens and 1 (11.1%) C. tropicalis were identified. Among three Candida isolates from blood culture, C. tropicalis, C. carpophila and C. membranifiaciens were identified. Non-candida yeast isolated from one blood culture was Cryptococcus albidus. One case of C. glabrata and one case of Candida albicans were isolated from skin culture of the catheter insertion areas in patients with positive catheter culture. In these patients, ITS region of rDNA sequence showed a similarity between Candida isolated from the skin and catheter. However, the blood samples of these patients were negative for fungal growth. We report two cases of catheter-related candidemia caused by C. membranifiaciens and C. tropicalis on the base of genetic similarity of species isolated from blood and catheter which were treated successfully with intravenous fluconazole and catheter removal. In phenotypic identification methods, we could only identify C. albicans and C. tropicalis and other yeast isolates were diagnosed as Candida sp. Discussion: Although more than 200 species of Candida have been identified, only a few cause diseases in humans. There is some evidence that non-albicans infections are increasing. Many risk factors, including prior antibiotic therapy, use of a central venous catheter, surgery, and parenteral nutrition are considered to be associated with candidemia in hospitalized heart failure patients. Identifying the route of infection in candidemia is difficult. Non-albicans candida as the cause of candidemia is increasing dramatically. By using conventional method, many non-albicans isolates remain unidentified. So, using more sensitive and specific molecular genetic sequencing to clarify the aspects of epidemiology of the unknown candida species infections is essential. The positive blood and catheter cultures for candida isolates and high percentage of similarity of their ITS region of rDNA sequence in these two patients confirmed the diagnosis of intravenous catheter-associated candidemia.

Keywords: catheter-associated infections, heart failure patient, molecular genetic sequencing, ITS region of rDNA, Candidemia

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Authors: Varinder Singh

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The primitive man had not known anything like human rights. In the later centuries of human progress with the development of scientific and technological knowledge, the growth of population and the tremendous changes in the human environment, the laws of nature that maintained the Eco-balance crumbled. The race for better and comfortable life landed mankind in a vicious circle. It created environmental imbalance, unplanned and uneven development, breakdown of self-sustaining village economy, mushrooming of shanty towns and slums, widening the chasm between the rich and the poor, over-exploitation of natural resources, desertification of arable lands, pollution of different kinds, heating up of earth and depletion of ozone layer. Modem International Life has been deeply marked and transformed by current endeavors to meet the needs and fulfill the requirements of protection of human person and of the environment. Such endeavors have been encouraged by the widespread recognition that protection of human being and the environment reflects common superior values and constitutes a common concern of mankind. The parallel evolutions of human rights protection and environmental protection disclose some close affinities. There was the occurrence of process of internationalization of both human rights protection and environmental protection, the former beginning with the 1948 Universal Declaration of Human Rights, the latter with the 1972 Stockholm Declaration on the Human Environment.It is now well established that it is the basic human right of every individual to live in a pollution free environment with full human dignity. The judiciary has so far pronounced a number of judgments in this regard. The Supreme Court in view of various laws relating to environment protection and the constitutional provision has held that right to pollution free environment. Article-21 is the heart of the fundamental rights and has received expanded meanings from time to time.

Keywords: human rights, law, environment, polluter

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Authors: Fatemeh Jalalvand

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The critical human rights problems such as extreme poverty, hunger, inequalities and gender discrimination need to be addressed by powerful and influential actors in the world. In today’s globalization, corporations have become one of the potent agents in the society. They are capable of generating economic growth, reducing poverty, and increasing the well-being of individuals, thereby contributing to the betterment of a broad spectrum of human rights. However, the discussion on how business can contribute to human rights has primarily focused on not violating them (reactive approach) rather than improving the conditions and solving the problems of human rights (proactive approach). In particular, the role of corporate social responsibility (CSR) in bringing proactivity of business in human rights has gained less attention. This paper develops a conceptual framework to examine the role of different categories of CSR, including discretionary, ethical, legal, instrumental and political CSR in encouraging the proactive contribution of corporations to the betterment of human rights. The five propositions, related to the conceptual framework, outline the relationships between five categories of CSR and proactivity of corporations in human rights. The findings indicate that discretionary CSR with voluntary nature might not be able to motivate any contribution of business in human rights. Moreover, ethical CSR and legal CSR might lead to reactive strategies of business toward human rights. Meanwhile, the economic incentives behind the notion of instrumental CSR could result in partial proactive engagement of corporations in human rights. Finally, the internal motives as profit and power besides the external duties might lead to the highest level of proactivity of corporations in human rights under the context of political CSR. The model developed offers a map for business to adopt proactive human rights strategies more systematically maintaining key profit-drivers like power and profit. In sum, instrumental and political categories of CSR might lead corporations to improve the conditions of human rights proactively.

Keywords: CSR, human rights, proactive approach, reactive approach

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Authors: Santiago Martínez Hernández

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The establishment of the European Union signified the culmination of the supra-national power addressing economic, political, legal and humanitarian matters within and above a national territory. Human rights have taken a protagonist role as one of the pressing concerns that the EU addresses, and one of the most critical problems is that of human trafficking. This multi-billion dollar criminal business represents $31.6 per year made out of 2.5 million trafficked persons worldwide, making it one of the most crucial human rights problems in the world to address. The EU has developed strategies to tackle this issue through supra-national governance, however, how have they fared? What is the impact of its development on the issue? This paper will address the direct and indirect impact of the formation of the European Union as a supranational political and economic entity on the illicit industry of human trafficking in Europe. It attempts to analyse first, the situation of human trafficking in Europe, as an attempt to understand its importance in the region, addressing its root causes and the role of the states addressed. Second, the paper will examine the impact of the EU on human breaking down its policy-making at a supranational level, the role of the economic integration of the region, and the change of migration patterns since its inception.

Keywords: human trafficking, human rights, European union, criminal business

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Authors: Ayyoub Jamali, Alena Kozlova

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The Russian invasion of Ukraine has tested the mettle of the international community, prompting not only States but also non-state actors to take deterrent action in response. Indeed, international sports organisations, namely FIFA and UEFA, have been rather successful in shifting the power dynamics by introducing a complete ban on the Russian national and club teams. This article aims to inquire into the human rights implications of such actions taken by international sports organisations. First, the article departs from an assessment of the legal status of FIFA and UEFA under international law and reflects on how a legal link could be established vis-à-vis their human rights obligations. Second, it examines the human rights aspects of the impugned measures by FIFA and UEFA on the part of the Russian athletes, further scrutinising them against the international human rights law principle of non-discrimination through a proportionality test. Last, it draws basic pathways for how possible human rights violations committed in the context of measures adopted by such organisations could be remedied, outlining the challenges of arbitration and litigation in Switzerland.

Keywords: FIFA, UEFA, FUR, ban, human rights, Russia, Ukraine, non-state actors

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Authors: Vun Yee Thien, Kenneth Francis Rodrigues, Clemente Michael Vui Ling Wong, Wilson Thau Lym Yong

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Transcriptomes associated with the process of photosynthesis have offered insights into the mechanism of gene regulation in terrestrial plants; however, limited information is available as far as macroalgae are concerned. This investigation aims to decipher the underlying mechanisms associated with photosynthesis in the red alga, Kappaphycus alvarezii, by performing a differential expression analysis on a de novo assembled transcriptomes. Comparative analysis of gene expression was designed to examine the alteration of light qualities and its effect on physiological mechanisms in the red alga. High-throughput paired-end RNA-sequencing was applied to profile the transcriptome of K. alvarezii irradiated with different wavelengths of light (blue 492-455 nm, green 577-492 nm and red 780-622 nm) as compared to the full light spectrum, resulted in more than 60 million reads individually and assembled using Trinity and SOAPdenovo-Trans. The transcripts were annotated in the NCBI non-redundant (nr) protein, SwissProt, KEGG and COG databases with a cutoff E-value of 1e-5 and nearly 30% of transcripts were assigned to functional annotation by Blast searches. Differential expression analysis was performed using edgeR. The DEGs were designated to six categories: BL (blue light) regulated, GL (green light) regulated, RL (red light) regulated, BL or GL regulated, BL or RL regulated, GL or RL regulated, and either BL, GL or RL regulated. These DEGs were mapped to terms in KEGG database and compared with the whole transcriptome background to search for genes that regulated by light quality. The outcomes of this study will enhance our understanding of molecular mechanisms underlying light-induced responses in red algae.

Keywords: de novo transcriptome sequencing, differential gene expression, Kappaphycus alvareziired, red alga

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Authors: Huajuan Shi

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Background: The biopsy of the preimplantation embryo may increase the potential risk and concern of embryo viability. Clinically discarded spent embryo medium (SEM) has entered the view of researchers, sparking an interest in noninvasive embryo screening. However, one of the major restrictions is the extremelty low quantity of cf-RNA, which is difficult to efficiently and unbiased amplify cf-RNA using traditional methods. Hence, there is urgently need to an efficient and low bias amplification method which can comprehensively and accurately obtain cf-RNA information to truly reveal the state of SEM cf-RNA. Result: In this present study, we established an agarose PCR amplification system, and has significantly improved the amplification sensitivity and efficiency by ~90 fold and 9.29 %, respectively. We applied agarose to sequencing library preparation (named AG-seq) to quantify and characterize cf-RNA in SEM. The number of detected cf-RNAs (3533 vs 598) and coverage of 3' end were significantly increased, and the noise of low abundance gene detection was reduced. The increasing percentage 5' end adenine and alternative splicing (AS) events of short fragments (< 400 bp) were discovered by AG-seq. Further, the profiles and characterizations of cf-RNA in spent cleavage medium (SCM) and spent blastocyst medium (SBM) indicated that 4‐mer end motifs of cf-RNA fragments could remarkably differentiate different embryo development stages. Significance: This study established an efficient and low-cost SEM amplification and library preparation method. Not only that, we successfully described the characterizations of SEM cf-RNA of preimplantation embryo by using AG-seq, including abundance features fragment lengths. AG-seq facilitates the study of cf-RNA as a noninvasive embryo screening biomarker and opens up potential clinical utilities of trace samples.

Keywords: cell-free RNA, agarose, spent embryo medium, RNA sequencing, non-invasive detection

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Authors: B. Arend, P. Sunnen, P. Caire

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In a single case study, we show how a conversation analysis (CA) approach can shed light onto the sequential unfolding of human-robot interaction. Relying on video data, we are able to show that CA allows us to investigate the respective turn-taking systems of humans and a NAO robot in their dialogical dynamics, thus pointing out relevant differences. Our fine grained video analysis points out occurring breakdowns and their overcoming, when humans and a NAO-robot engage in a multimodally uttered multi-party communication during a sports guessing game. Our findings suggest that interdisciplinary work opens up the opportunity to gain new insights into the challenging issues of human robot communication in order to provide resources for developing mechanisms that enable complex human-robot interaction (HRI).

Keywords: human robot interaction, conversation analysis, dialogism, breakdown, museum

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Authors: Lamis Naddaf, Yuval Tabach

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In this research, we identified the missense genetic variants that have the potential to enhance resistance against cancer. Such field has not been widely explored, as researchers tend to investigate mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution, and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and can have significant implications on improved risk estimation, diagnostics, prognosis and even for personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and picked up the alleles that showed a correlation with the species’ cancer resistance. We predicted 250 protecting variants (PVs) with a 0.01 false discovery rate and more than 20 thousand PVs with a 0.25 false discovery rate. Cancer resistance in Mammals and reptiles was significantly predicted by the number of PVs a species has. Moreover, Genes enriched with the protecting variants are enriched in pathways relevant to tumor suppression like pathways of Hedgehog signaling and silencing, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are more abundant in healthy people compared to cancer patients within different human races.

Keywords: comparative genomics, machine learning, cancer resistance, cancer-protecting alleles

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Authors: Shantanu Prakash, Suruchi Shukla, Amita Jain

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Introduction: The hepatitis C virus (HCV) is a major public health problem and a leading cause of chronic liver disease. Injection drug use and individuals receiving blood and blood products are the primary modes of HCV transmission. Our study aims to establish the prevalent genotypes/ subtypes of HCV circulating in Uttar Pradesh, North India, as reported from a tertiary care hospital. Methods: It is a retrospective observational analysis of consecutive 404 HCV RNA positive cases referred to our hospital during September 2014 to April 2017. The study was approved by an institutional ethics committee. Written informed consent was taken from each participant. Clinical and demographic details of these patients were recorded using predesigned questionnaires. All the laboratory testing was carried on stored serum sample of enrolled cases. Genotyping of all 404 strains was done by Sanger’s sequencing of the core region. The phylogenetic analysis of 179 HCV strains with high -quality sequencing data was performed. Results: The distribution of prevalent genotypes/ subtypes as noted in the present study was; Genotype (GT)1a [n-101(25%)], GT1b [n-12(2.9%)], GT1c [1(0.25%)], GT3a [275(68.07%)], GT3b [9(2.2%)], GT3g [2(0.49%)], GT3i [3(0.74%)], and GT4a [1(0.24%)]. HCV genotypes GT2, GT5 and GT6 were not detected from our region. Sequence analysis showed high genotypic variability in HCV GT3. Phylogenetic analysis showed that HCV GT3 and GT1 circulating in our region were related to Indian strains reported earlier. Conclusions: HCV genotypes 3a and 1a are commonest circulating genotypes in Uttar Pradesh (UP), India.

Keywords: Hepatitis C virus, genetic variation, bioinformatics, genotype, HCV

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Authors: Neziha Jaouedi, Noureddine Boujnah, Mohamed Salim Bouhlel

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In the framework of human machine interaction systems enhancement, we focus throw this paper on human behavior analysis and action recognition. Human behavior is characterized by actions and reactions duality (movements, psychological modification, verbal and emotional expression). It’s worth noting that many information is hidden behind gesture, sudden motion points trajectories and speeds, many research works reconstructed an information retrieval issues. In our work we will focus on motion extraction, tracking and action recognition using wavelet network approaches. Our contribution uses an analysis of human subtraction by Gaussian Mixture Model (GMM) and body movement through trajectory models of motion constructed from kalman filter. These models allow to remove the noise using the extraction of the main motion features and constitute a stable base to identify the evolutions of human activity. Each modality is used to recognize a human action using wavelets of derived beta distributions approach. The proposed approach has been validated successfully on a subset of KTH and UCF sports database.

Keywords: feautures extraction, human action classifier, wavelet neural network, beta wavelet

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Authors: Madhusudana S. N., Reeta Mani, Ashwini S. Satishchandra P., Netravati, Udhani V., Fiaz A., Karande S.

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Rabies is an acute encephalitis which is considered 100% fatal despite occasional reports of survivors. However, in recent times more cases of human rabies survivors are being reported. In the last 5 years, there are six laboratories confirmed human rabies survivors in India alone. All cases were children below 15 years and all contracted the disease by dog bites. All of them also had received the full or partial course of rabies vaccination and 4 out of 6 had also received rabies immunoglobulin. All cases were treated in intensive care units in hospitals at Bangalore, Mumbai, Chandigarh, Lucknow and Goa. We report here the results of immunological and virological studies conducted at our laboratory on these patients. The clinical samples that were obtained from these patients were Serum, CSF, nuchal skin biopsy and saliva. Serum and CSF samples were subjected to standard RFFIT for estimation of rabies neutralizing antibodies. Skin biopsy, CSF and saliva were processed by TaqMan real-time PCR for detection of viral RNA. CSF, saliva and skin homogenates were also processed for virus isolation by inoculation of suckling mice. The PBMCs isolated from fresh blood was subjected to ELISPOT assay to determine the type of immune response (Th1/Th2). Both CSF and serum were also investigated for selected cytokines by Luminex assay. The level of antibodies to virus G protein and N protein were determined by ELISA. All survivors had very high titers of RVNA in serum and CSF 100 fold higher than non-survivors and vaccine controls. A five-fold rise in titer could be demonstrated in 4 out of 6 patients. All survivors had a significant increase in antibodies to G protein in both CSF and serum when compared to non-survivors. There was a profound and robust Th1 response in all survivors indicating that interferon gamma could play an important factor in virus clearance. We could isolate viral RNA in only one patient four years after he had developed symptoms. The partial N gene sequencing revealed 99% homology to species I strain prevalent in India. Levels of selected cytokines in CSF and serum did not reveal any difference between survivors and non-survivors. To conclude, survival from rabies is mediated by virus-specific immune responses of the host and clearance of rabies virus from CNS may involve the participation of both Th2 and Th1 immune responses.

Keywords: rabies, rabies treatment, rabies survivors, immune reponse in rabies encephalitis

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Authors: S. Hannah Elizabeth, A. Panneerselvam

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Objective: The main objective was to evaluate the degradative properties of Bacillus cereus sp TUHP2 isolated from TNT-Polluted soils in the Vellore District, Tamil Nadu, India. Methods: Among the 3 bacterial genera isolated from different soil samples, one potent TNT degrading strain Bacillus cereus sp TUHP2 was identified. The morphological, physiological and the biochemical properties of the strain Bacillus cereus sp TUHP2 was confirmed by conventional methods and genotypic characterization was carried out using 16S r-DNA partial gene amplification and sequencing. The broken down by products of DNT in the extract was determined by Gas Chromatogram- Mass spectrometry (GC-MS). Supernatant samples from the broth studied at 24 h interval were analyzed by HPLC analysis and the effect on various nutritional and environmental factors were analysed and optimized for the isolate. Results: Out of three isolates one strain TUHP2 were found to have potent efficiency to degrade TNT and revealed the genus Bacillus. 16S rDNA gene sequence analysis showed highest homology (98%) with Bacillus cereus and was assigned as Bacillus cereus sp TUHP2. Based on the energy of the predicted models, the secondary structure predicted by MFE showed the more stable structure with a minimum energy. Products of TNT Transformation showed colour change in the medium during cultivation. TNT derivates such as 2HADNT and 4HADNT were detected by HPLC chromatogram and 2ADNT, 4ADNT by GC/MS analysis. Conclusion: Hence this study presents the clear evidence for the biodegradation process of TNT by strain Bacillus cereus sp TUHP2.

Keywords: bioremediation, biodegradation, biotransformation, sequencing

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Authors: Yin Cheung Lam

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In 1949, the ratification of the Geneva Conventions heralded the international community’s adoption of a new universal and non-discriminatory approach to human rights in situations of conflict. However, with the proliferation of international terrorism after the 9/11 attacks on the United States (U.S.), the international community’s uneven and contradictory implementations of international humanitarian law (IHL) questioned its agenda of universal human rights. Specifically, the derogation from IHL has never been so pronounced in the U.S. led ‘War on Terror’. While an extensive literature has ‘assessed the impact’ of the implementation of the Geneva Conventions, limited attention has been paid to interrogating the ways in which the Geneva Conventions and its resulting implementation have functioned to discursively reproduce certain understandings of human rights between states and non-state actors. Through a discursive analysis of the Geneva Conventions and the conceptualization of human rights in relation to terrorism, this thesis problematises the way in which the U.S. has understood and reproduced understandings of human rights. Using the U.S. ‘War on Terror’ as an example, it seeks to extend previous analyses of the U.S.’ practice of IHL through a qualitative discursive analysis of the human rights content that appears in the Geneva Conventions in addition to the speeches and policy documents on the ‘War on Terror’.

Keywords: discursive analysis, human rights, non-state actors, war on terror

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Authors: Lamis Naddaf, Yuval Tabach

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We identified missense genetic variants with the potential to enhance resistance against cancer. Such a field has not been widely explored as researchers tend to investigate the mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and have significant implications for improved risk estimation, diagnostics, prognosis, and even personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and selected the alleles that showed a correlation with the species’ cancer resistance. Interestingly, we found several amino acids that are more generally preferred (like the Proline) or avoided (like the Cysteine) by the resistant species. Furthermore, Cancer resistance in mammals and reptiles is significantly predicted by the number of the predicted protecting variants (PVs) a species has. Moreover, PVs-enriched-genes are enriched in pathways relevant to tumor suppression. For example, they are enriched in the Hedgehog signaling and silencing pathways, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are mostly more abundant in healthy people compared to cancer patients within different human races.

Keywords: cancer resistance, protecting variant, naked mole rat, comparative genomics

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Authors: Jiahe Liu, Hongyang Yu, Feng Qian, Miao Luo

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SMPL-X was a powerful parametric human body model that included male, neutral, and female models, with significant gender differences between these three models. During the process of 3D human body reconstruction, the correct selection of standard templates was crucial for obtaining accurate results. To address this issue, we developed an efficient gender classification algorithm to automatically select the appropriate template for 3D human body reconstruction. The key to this gender classification algorithm was the precise analysis of human body features. By using the SMPL-X model, the algorithm could detect and identify gender features of the human body, thereby determining which standard template should be used. The accuracy of this algorithm made the 3D reconstruction process more accurate and reliable, as it could adjust model parameters based on individual gender differences. SMPL-X and the related gender classification algorithm have brought important advancements to the field of 3D human body reconstruction. By accurately selecting standard templates, they have improved the accuracy of reconstruction and have broad potential in various application fields. These technologies continue to drive the development of the 3D reconstruction field, providing us with more realistic and accurate human body models.

Keywords: gender classification, joint detection, SMPL-X, 3D reconstruction

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Authors: Rachel Danielson, Brendan Bohannan, S.M. Tsai, Kyle Meyer, Jorge L.M. Rodrigues

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The Amazon Rainforest is a global diversity hotspot and crucial carbon sink, but approximately 20% of its total extent has been deforested- primarily for the establishment of cattle pasture. Understanding the impact of this large-scale disturbance on soil microbial community composition and activity is crucial in understanding potentially consequential shifts in nutrient or greenhouse gas cycling, as well as adding to the body of knowledge concerning how these complex communities respond to human disturbance. In this study, surface soils (0-10cm) were collected from three forests and three 45-year-old pastures in Rondonia, Brazil (the Amazon state with the greatest rate of forest destruction) in order to determine the impact of forest conversion on microbial communities involved in nitrogen fixation. Soil chemical and physical parameters were paired with measurements of microbial activity and genetic profiles to determine how community composition and process rates relate to environmental conditions. Measuring both the natural abundance of 15N in total soil N, as well as incorporation of enriched 15N2 under incubation has revealed that conversion of primary forest to cattle pasture results in a significant increase in the rate of nitrogen fixation by free-living diazotrophs. Quantification of nifH gene copy numbers (an essential subunit encoding the nitrogenase enzyme) correspondingly reveals a significant increase of genes in pasture compared to forest soils. Additionally, genetic sequencing of both nifH genes and transcripts shows a significant increase in the diversity of the present and metabolically active diazotrophs within the soil community. Levels of both organic and inorganic nitrogen tend to be lower in pastures compared to forests, with ammonium rather than nitrate as the dominant inorganic form. However, no significant or consistent differences in total, extractable, permanganate-oxidizable, or loss-on-ignition carbon are present between the two land-use types. Forest conversion is associated with a 0.5- 1.0 unit pH increase, but concentrations of many biologically relevant nutrients such as phosphorus do not increase consistently. Increases in free-living diazotrophic community abundance and activity appear to be related to shifts in carbon to nitrogen pool ratios. Furthermore, there may be an important impact of transient, low molecular weight plant-root-derived organic carbon on free-living diazotroph communities not captured in this study. Preliminary analysis of nitrogenase gene variant composition using NovoSeq metagenomic sequencing indicates that conversion of forest to pasture may significantly enrich vanadium-based nitrogenases. This indication is complemented by a significant decrease in available soil molybdenum. Very little is known about the ecology of diazotrophs utilizing vanadium-based nitrogenases, so further analysis may reveal important environmental conditions favoring their abundance and diversity in soil systems. Taken together, the results of this study indicate a significant change in nitrogen cycling and diazotroph community composition with the conversion of the Amazon Rainforest. This may have important implications for the sustainability of cattle pastures once established since nitrogen is a crucial nutrient for forage grass productivity.

Keywords: free-living diazotrophs, land use change, metagenomic sequencing, nitrogen fixation

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Authors: Stephanie K. Douglas, Gordon R. Haley

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Organizations face increasing disruptions, changes, and uncertainties through the rapid shifts in the economy and business environment. A capacity for resilience is necessary for organizations to survive and thrive in such adverse conditions. Learning is an essential component of an organization's capability for building resilience. Strategic human resource management is a principal component of learning and organizational resilience. To achieve organizational resilience, human resource management strategies must support individual knowledge, skills, and ability development through organizational learning. This study aimed to contribute to the comprehensive knowledge of the relationship between strategic human resource management and organizational learning to build organizational resilience. The organizational learning dimensions of knowledge acquisition, knowledge distribution, knowledge interpretation, and organizational memory can be fostered through human resource management strategies and then aggregated to the organizational level to build resilience.

Keywords: human resource development, human resource management, organizational learning, organizational resilience

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Authors: Lottie Lane

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It is habitually assumed and stated that the World Bank should engage and comply with international human rights standards. However, the basis for holding the Bank to such standards is unclear. Most advocates of the idea invoke aspects of international law to argue that the Bank has existing obligations to act in compliance with human rights standards. The Bank itself, however, does not appear to accept such arguments, despite having endorsed the importance of human rights for a considerable length of time. A substantial challenge is that under the current international human rights law framework, the World Bank is considered a non-state actor, and as such, has no direct human rights obligations. In the absence of clear legal duties for the Bank, it is necessary to look at the tools available beyond the international human rights framework to encourage the Bank to comply with human rights standards. This article critically examines several bases for arguing that the Bank should comply and engage with human rights through its policies and practices. Drawing on the Bank’s own ‘good governance’ approach as well as the United Nations’ ‘human rights-based-approach’ to development, a new basis is suggested. First, the relationship between the World Bank and human rights is examined. Three perspectives are considered: (1) the legal position – what the status of the World Bank is under international human rights law, and whether it can be said to have existing legal human rights obligations; (2) the Bank’s own official position – how the Bank envisages its relationship with and role in the protection of human rights; and (3) the relationship between the Bank’s policies and practices and human rights (including how its attitudes are reflected in its policies and how the Bank’s operations impact human rights enjoyment in practice). Here, the article focuses on two examples – the (revised) 2016 Environmental and Social Safeguard Policies and the 2012 case-study regarding Gambella, Ethiopia. Both examples are widely considered missed opportunities for the Bank to actively engage with human rights. The analysis shows that however much pressure is placed on the Bank to improve its human rights footprint, it is extremely reluctant to do so explicitly, and the legal bases available are insufficient for requiring concrete, ex ante action by the Bank. Instead, the Bank’s own ‘good governance’ approach to development – which it has been advocating since the 1990s – can be relied upon. ‘Good governance’ has been used and applied by many actors in many contexts, receiving numerous different definitions. This article argues that human rights protection can now be considered a crucial component of good governance, at least in the context of development. In doing so, the article explains the relationship and interdependence between the two concepts, and provides three rationales for the Bank to take a ‘human rights-based approach’ to good governance. Ultimately, this article seeks to look beyond international human rights law and take a governance approach to provide a convincing basis upon which to argue that the World Bank should comply with human rights standards.

Keywords: World Bank, international human rights law, good governance, human rights-based approach

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Authors: Yustina Trihoni Nalesti Dewi

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Gross violations of human rights consisting of crime against humanity, genocide and war crime, are serious international crimes. Prohibition such crimes have obtain to the level of international norms of jus cogens based on conventions and customary international law. Therefore, the duty of the state to punish the crimes is obligatory. The legal consequence of jus cogens is obligation erga omnes which are a matter of state responsibility. When a state is not willing or neglects to do so in its national law, it results in state responsibility to be imposed by international human rights and humanitarian law. This article reviews the concept of jus cogens and obligatio erga omnes that appear as two sides of the same coin. It also explains how international human rights and humanitarian law set down the duty of the state to punish gross violations of human rights.

Keywords: duty of states, gross violations of human rights, jus cogens, obligatio erga omnes

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Authors: Tereza Branyšová, Martina Kračmarová, Kateřina Demnerová, Michal Ďurovič, Hana Stiborová

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Microbial deterioration threatens all objects of cultural heritage, including audio-visual materials. Fungi are commonly known to be the main factor in audio-visual material deterioration. However, although being neglected, bacteria also play a significant role. In addition to microbial contamination of materials, it is also essential to analyse air as a possible contamination source. This work aims to identify bacterial species in the archives of the Czech Republic that occur on audio-visual materials as well as in the air in the archives. For sampling purposes, the smears from the materials were taken by sterile polyurethane sponges, and the air was collected using a MAS-100 aeroscope. Metagenomic DNA from all collected samples was immediately isolated and stored at -20 °C. DNA library for the 16S rRNA gene was prepared using two-step PCR and specific primers and the concentration step was included due to meagre yields of the DNA. After that, the samples were sent to the University of Fairbanks, Alaska, for Illumina MiSeq sequencing. Subsequently, the analysis of the sequences was conducted in R software. The obtained sequences were assigned to the corresponding bacterial species using the DADA2 package. The impact of air contamination and the impact of different photosensitive layers that audio-visual materials were made of, such as gelatine, albumen, and collodion, were evaluated. As a next step, we will take a deeper focus on air contamination. We will select an appropriate culture-dependent approach along with a culture-independent approach to observe a metabolically active species in the air. Acknowledgment: This project is supported by grant no. DG18P02OVV062 of the Ministry of Culture of the Czech Republic.

Keywords: cultural heritage, Illumina MiSeq, metagenomics, microbial identification

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