scholarly journals The Current Immunoassays and Merging immunogenomic Approaches for Immunomonitoring Cancer and Infectious Diseases

2019 ◽  
Vol 1 (3) ◽  
pp. 1-18
Author(s):  
Xi Zhang ◽  
Xi Zhang ◽  
Yan Wang ◽  
Qin Ouyang ◽  
Hara Levy ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Immune Monitoring ◽  
Clinical Samples ◽  
Rna Seq ◽  
Patients With Cancer ◽  
Data Profiling ◽  
Genome Wide ◽  
Substantial Progress ◽  
Selection Of ◽  
Made In

As remarkable advances have been made in immunotherapies, the overall goal of immunotherapy has become the selection of patients and evaluating the benefits of treatment. One of the major obstacles to develop immunotherapies is the lack of effective immune monitoring. Monitoring of key changes in the immune system during immunotherapy (immunomonitoring) provides important insights into efficacy as well as the immune mechanisms of response at the molecular and cellular levels. Immunomonitoring techniques include traditional immunoassays that use specific antibodies to recognize the analytes of interest, new high-throughput immunoassays that target immune cells and nucleic acids, and less classical immunogenomic approaches that rely on genome-wide profiling and computational analysis on various types of clinical samples. Substantial progress has been made in the application of immunomonitoring strategies to pre-clinical and clinical studies, especially for patients with cancer and infectious diseases. Current and emerging immunoassays performed in clinical practice will be examined herein, and immunogenomic approaches that complement these techniques will be highlighted and compared with traditional methods. Finally, we will discuss several new computational methods for analyzing gene signatures for immunomonitoring, including gene expression data profiling by microarray, the nCounter technique, regular RNA-seq, and single-cell RNA-seq. Novel immunomonitoring techniques, especially immunogenomic approaches, will continue to be developed to facilitate assessment of immunotherapeutic response and predict patient outcomes in cancer and infectious disease.

scholarly journals FAKTOR FAKTOR YANG MEMPENGARUHI KEJADIAN TB PARU DAN UPAYA PENANGGULANGANNYA

2019 ◽  
Author(s):  
Edza Aria Wikurendra
Keyword(s):  
Infectious Disease ◽  
Pulmonary Tuberculosis ◽  
Infectious Diseases ◽  
Influential Factors ◽  
Pulmonary Tb ◽  
Treatment And Prevention ◽  
The World ◽  
Success Of Treatment ◽  
Selection Of ◽  
Made In

Tuberculosis is still the main infectious disease in the world and is increasingly becoming a concern with the presence of HIV / AIDS. In the Ministry of Health's Strategic Plan for 2015-2019, infectious diseases are one of the main priorities that must be addressed to realize a Healthy Indonesia. The number of cases of pulmonary tuberculosis in Indonesia is reported to be 130 / 100,000, every year there are 539,000 new cases and the number of deaths is around 101,000 per year, the incidence rate of pulmonary tuberculosis cases is about 110 / 100,000 people. This paper aims to reveal the problem of influential factors and efforts that must be made in controlling pulmonary TB disease. This paper is made by tracing research reports / articles related to the incidence of pulmonary TB. And then a selection of the collected reports is carried out, so that 20 selected journals / articles can be reviewed. From selected reports, determined aspects that indicate the factors that caused the incidence of pulmonary TB and TB prevention efforts were carried out. Various efforts have been made through various approaches to treat or at least reduce the incidence of TB. Such as network model strategy programs and others are expected to provide healing and prevent transmission. But in the implementation in the field, the success of treatment and prevention with this strategy experienced several obstacles that did not provide maximum results.

scholarly journals Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets

2017 ◽  
Author(s):  
Stefan Wyder ◽  
Michael T. Raissig ◽  
Ueli Grossniklaus
Keyword(s):  
Linear Models ◽  
Real Data ◽  
Rna Seq ◽  
Sequence Coverage ◽  
Reciprocal Crosses ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Allelic Bias ◽  
Generation Sequencing ◽  
Made In

ABSTRACTGenomic imprinting leads to different expression levels of maternally and paternally derived alleles. Over the last years, major progress has been made in identifying novel imprinted candidate genes in plants, owing to affordable next-generation sequencing technologies. However, reports on sequencing the transcriptome of hybrid F1 seed tissues strongly disagree about how many and which genes are imprinted. This raises questions about the relative impact of biological, environmental, technical, and analytic differences or biases. Here, we adopt a statistical approach, frequently used in RNA-seq data analysis, which properly models count overdispersion and considers replicate information of reciprocal crosses. We show that our statistical pipeline outperforms other methods in identifying imprinted genes in simulated and real data. Accordingly, reanalysis of genome-wide imprinting studies in Arabidopsis and maize shows that, at least for the Arabidopsis dataset, an increased agreement across datasets can be observed. For maize, however, consistent reanalysis did not yield in a larger overlap between the datasets. This suggests that the discrepancy across publications might be partially due to different analysis pipelines but that technical, biological, and environmental factors underlie much of the discrepancy between datasets. Finally, we show that the set of genes that can be characterized regarding allelic bias by all studies with minimal confidence is small (~8,000/27,416 genes for Arabidopsis and ~12,000/39,469 for maize). In conclusion, we propose to use biologically replicated reciprocal crosses, high sequence coverage, and a generalized linear model approach to identify differentially expressed alleles in developing seeds.

scholarly journals Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5642 ◽  
Author(s):  
Chenhua Zhang ◽  
Hongying Zheng ◽  
Xinyang Wu ◽  
Heng Xu ◽  
Kelei Han ◽  
...  
Keyword(s):  
Reference Genes ◽  
Bottle Gourd ◽  
Lagenaria Siceraria ◽  
Rna Seq ◽  
Isopentenyl Transferase ◽  
Genome Wide ◽  
Transcriptome Database ◽  
Qpcr Normalization ◽  
Suitable Reference ◽  
Selection Of

Lagenaria siceraria is an economically important cucurbitaceous crop, but suitable reference genes (RGs) to use when the plants are infected by cucumber green mottle mosaic virus (CGMMV) have not been determined. Sixteen candidate RGs of both leaf and fruit and 18 candidate RGs mostly from separate RNA-Seq datasets of bottle gourd leaf or fruit were screened and assessed by RT-qPCR. The expression stability of these genes was determined and ranked using geNorm, NormFinder, BestKeeper and RefFinder. Comprehensive analysis resulted in the selection of LsCYP, LsH3, and LsTBP as the optimal RGs for bottle gourd leaves, and LsP4H, LsADP, and LsTBP for fruits. LsWD, LsGAPDH, and LsH3 were optimal for use in both leaves and fruits under the infection of CGMMV. Isopentenyl transferase (IPT) and DNA-directed RNA polymerase (DdRP) were used to validate the applicability of the most stable identified RGs from bottle gourd in response to CGMMV. All the candidate RGs performed in RT-qPCR consistently with the data from the transcriptome database. The results demonstrated that LsWD, LsGAPDH and LsH3 were the most suitable internal RGs for the leaf, and LsH3, LsGAPDH, LsP4H and LsCYP for the fruit.

Are Three Items Sufficient to Measure Sense of Coherence?

2018 ◽  
Vol 34 (4) ◽  
pp. 229-237 ◽  
Author(s):  
Francesca Chiesi ◽  
Andrea Bonacchi ◽  
Caterina Primi ◽  
Alessandro Toccafondi ◽  
Guido Miccinesi
Keyword(s):  
Sense Of Coherence ◽  
Convergent Validity ◽  
Clinical Sample ◽  
Clinical Samples ◽  
Depression Symptoms ◽  
Time Saving ◽  
Positive Role ◽  
Patients With Cancer ◽  
Measure Sense

Abstract. The present study aimed at evaluating if the three-item sense of coherence (SOC) scale developed by Lundberg and Nystrom Peck (1995) can be effectively used for research purpose in both nonclinical and clinical samples. To provide evidence that it represents adequately the measured construct we tested its validity in a nonclinical (N = 658) and clinical sample (N = 764 patients with cancer). Results obtained in the nonclinical sample attested a positive relation of SOC – as measured by the three-item SOC scale – with Antonovsky’s 13-item and 29-item SOC scales (convergent validity), and with dispositional optimism, sense of mastery, anxiety, and depression symptoms (concurrent validity). Results obtained in the clinical sample confirmed the criterion validity of the scale attesting the positive role of SOC – as measured by the three-item SOC scale – on the person’s capacity to respond to illness and treatment. The current study provides evidence that the three-item SOC scale is a valid, low-loading, and time-saving instrument for research purposes on large sample.

WINTER WHEAT DEVELOPED BY THE UDMURT RESEARCH INSTITUTE OF AGRICULTURE IN COMPETITIVE VARIETY TESTING

2020 ◽  
pp. 5-16
Author(s):  
I.V. TORBINA ◽  
◽  
I.R. FARDEYEVA ◽  
Keyword(s):  
Winter Wheat ◽  
Crop Rotation ◽  
Biological Characteristics ◽  
Commercial Use ◽  
Breeding Material ◽  
Rotation Pattern ◽  
Selection Of ◽  
Variety Testing ◽  
Made In ◽  
Research Institute

The paper assesses the promising varieties of winter wheat in a competitive variety test by the main economic and biological characteristics that determine the suitability of the variety for commercial use. The object of research was the authors’ own breeding material. The experiments on the selection of winter wheat were made in the experimental crop rotation pattern of the Institute.

Evidence-based Assessment

2010 ◽  
pp. 76-98
Author(s):  
John Hunsley ◽  
Eric J. Mash
Keyword(s):  
Decision Making ◽  
Clinical Assessment ◽  
Assessment Process ◽  
Evidence Based ◽  
The Past ◽  
Specific Assessment ◽  
The Many ◽  
Selection Of ◽  
Made In

Evidence-based assessment relies on research and theory to inform the selection of constructs to be assessed for a specific assessment purpose, the methods and measures to be used in the assessment, and the manner in which the assessment process unfolds. An evidence-based approach to clinical assessment necessitates the recognition that, even when evidence-based instruments are used, the assessment process is a decision-making task in which hypotheses must be iteratively formulated and tested. In this chapter, we review (a) the progress that has been made in developing an evidence-based approach to clinical assessment in the past decade and (b) the many challenges that lie ahead if clinical assessment is to be truly evidence-based.

scholarly journals Putative transmembrane transporter modulates higher-level aggression in Drosophila

2017 ◽  
Vol 114 (9) ◽  
pp. 2373-2378 ◽  
Author(s):  
Budhaditya Chowdhury ◽  
Yick-Bun Chan ◽  
Edward A. Kravitz
Keyword(s):  
Causal Effect ◽  
Nerve Terminals ◽  
Rna Seq ◽  
Wild Type ◽  
Temperature Dependent ◽  
Number Of Genes ◽  
Interesting Family ◽  
Solute Carrier ◽  
Transmembrane Transporter ◽  
Selection Of

By selection of winners of dyadic fights for 35 generations, we have generated a hyperaggressive Bully line of flies that almost always win fights against the parental wild-type Canton-S stock. Maintenance of the Bully phenotype is temperature dependent during development, with the phenotype lost when flies are reared at 19 °C. No similar effect is seen with the parent line. This difference allowed us to carry out RNA-seq experiments and identify a limited number of genes that are differentially expressed by twofold or greater in the Bullies; one of these was a putative transmembrane transporter, CG13646, which showed consistent and reproducible twofold down-regulation in Bullies. We examined the causal effect of this gene on the phenotype with a mutant line for CG13646, and with an RNAi approach. In all cases, reduction in expression of CG13646 by approximately half led to a hyperaggressive phenotype partially resembling that seen in the Bully flies. This gene is a member of a very interesting family of solute carrier proteins (SLCs), some of which have been suggested as being involved in glutamine/glutamate and GABA cycles of metabolism in excitatory and inhibitory nerve terminals in mammalian systems.

scholarly journals VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide

Cell Reports ◽  
2021 ◽  
Vol 34 (3) ◽  
pp. 108629
Author(s):  
Kathrin Leppek ◽  
Gun Woo Byeon ◽  
Kotaro Fujii ◽  
Maria Barna
Keyword(s):  
Rna Seq ◽  
Expansion Segment ◽  
Genome Wide

scholarly journals Distinct regulation of hippocampal neuroplasticity and ciliary genes by corticosteroid receptors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karen R. Mifsud ◽  
Clare L. M. Kennedy ◽  
Silvia Salatino ◽  
Eshita Sharma ◽  
Emily M. Price ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Glucocorticoid Receptors ◽  
Acute Stress ◽  
Circadian Variation ◽  
Rna Seq ◽  
Physiological Regulation ◽  
Behavioural Adaptation ◽  
Neuronal Progenitor ◽  
Genome Wide ◽  
Transcriptional Changes

AbstractGlucocorticoid hormones (GCs) — acting through hippocampal mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) — are critical to physiological regulation and behavioural adaptation. We conducted genome-wide MR and GR ChIP-seq and Ribo-Zero RNA-seq studies on rat hippocampus to elucidate MR- and GR-regulated genes under circadian variation or acute stress. In a subset of genes, these physiological conditions resulted in enhanced MR and/or GR binding to DNA sequences and associated transcriptional changes. Binding of MR at a substantial number of sites however remained unchanged. MR and GR binding occur at overlapping as well as distinct loci. Moreover, although the GC response element (GRE) was the predominant motif, the transcription factor recognition site composition within MR and GR binding peaks show marked differences. Pathway analysis uncovered that MR and GR regulate a substantial number of genes involved in synaptic/neuro-plasticity, cell morphology and development, behavior, and neuropsychiatric disorders. We find that MR, not GR, is the predominant receptor binding to >50 ciliary genes; and that MR function is linked to neuronal differentiation and ciliogenesis in human fetal neuronal progenitor cells. These results show that hippocampal MRs and GRs constitutively and dynamically regulate genomic activities underpinning neuronal plasticity and behavioral adaptation to changing environments.

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