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PLoS Computational Biology May 2017Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism...
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline. Transcriptomics has been defined by repeated technological innovations that transform the field. There are two key contemporary techniques in the field: microarrays, which quantify a set of predetermined sequences, and RNA sequencing (RNA-Seq), which uses high-throughput sequencing to capture all sequences. Measuring the expression of an organism's genes in different tissues, conditions, or time points gives information on how genes are regulated and reveals details of an organism's biology. It can also help to infer the functions of previously unannotated genes. Transcriptomic analysis has enabled the study of how gene expression changes in different organisms and has been instrumental in the understanding of human disease. An analysis of gene expression in its entirety allows detection of broad coordinated trends which cannot be discerned by more targeted assays.
Topics: Animals; Cluster Analysis; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Humans; Image Processing, Computer-Assisted; Mice; Oligonucleotide Array Sequence Analysis; Organ Specificity; RNA; Rats; Sequence Analysis, RNA
PubMed: 28545146
DOI: 10.1371/journal.pcbi.1005457 -
Journal of the American College of... Sep 2016The amyloidoses are a group of protein-folding disorders in which ≥1 organ is infiltrated by proteinaceous deposits known as amyloid. The deposits are derived from 1... (Review)
Review
The amyloidoses are a group of protein-folding disorders in which ≥1 organ is infiltrated by proteinaceous deposits known as amyloid. The deposits are derived from 1 of several amyloidogenic precursor proteins, and the prognosis of the disease is determined both by the organ(s) involved and the type of amyloid. Amyloid involvement of the heart (cardiac amyloidosis) carries the worst prognosis of any involved organ, and light-chain (AL) amyloidosis is the most serious form of the disease. The last decade has seen considerable progress in understanding the amyloidoses. In this review, current and novel approaches to the diagnosis and treatment of cardiac amyloidosis are discussed, with particular reference to AL amyloidosis in the heart.
Topics: Amyloid; Amyloidosis; Decision Trees; Heart Diseases; Heart Transplantation; Humans
PubMed: 27634125
DOI: 10.1016/j.jacc.2016.06.053 -
Clinical Microbiology Reviews Oct 2004Mycoplasma pneumoniae is a unique bacterium that does not always receive the attention it merits considering the number of illnesses it causes and the degree of... (Review)
Review
Mycoplasma pneumoniae is a unique bacterium that does not always receive the attention it merits considering the number of illnesses it causes and the degree of morbidity associated with it in both children and adults. Serious infections requiring hospitalization, while rare, occur in both adults and children and may involve multiple organ systems. The severity of disease appears to be related to the degree to which the host immune response reacts to the infection. Extrapulmonary complications involving all of the major organ systems can occur in association with M. pneumoniae infection as a result of direct invasion and/or autoimmune response. The extrapulmonary manifestations are sometimes of greater severity and clinical importance than the primary respiratory infection. Evidence for this organism's contributory role in chronic lung conditions such as asthma is accumulating. Effective management of M. pneumoniae infections can usually be achieved with macrolides, tetracyclines, or fluoroquinolones. As more is learned about the pathogenesis and immune response elicited by M. pneumoniae, improvement in methods for diagnosis and prevention of disease due to this organism may occur.
Topics: Asthma; Humans; Mycoplasma pneumoniae; Pneumonia, Mycoplasma
PubMed: 15489344
DOI: 10.1128/CMR.17.4.697-728.2004 -
Inflammatory Bowel Diseases Aug 2015Extraintestinal manifestations (EIM) in inflammatory bowel disease (IBD) are frequent and may occur before or after IBD diagnosis. EIM may impact the quality of life for... (Review)
Review
Extraintestinal manifestations (EIM) in inflammatory bowel disease (IBD) are frequent and may occur before or after IBD diagnosis. EIM may impact the quality of life for patients with IBD significantly requiring specific treatment depending on the affected organ(s). They most frequently affect joints, skin, or eyes, but can also less frequently involve other organs such as liver, lungs, or pancreas. Certain EIM, such as peripheral arthritis, oral aphthous ulcers, episcleritis, or erythema nodosum, are frequently associated with active intestinal inflammation and usually improve by treatment of the intestinal activity. Other EIM, such as uveitis or ankylosing spondylitis, usually occur independent of intestinal inflammatory activity. For other not so rare EIM, such as pyoderma gangrenosum and primary sclerosing cholangitis, the association with the activity of the underlying IBD is unclear. Successful therapy of EIM is essential for improving quality of life of patients with IBD. Besides other options, tumor necrosis factor antibody therapy is an important therapy for EIM in patients with IBD.
Topics: Biliary Tract Diseases; Eye Diseases; Humans; Inflammatory Bowel Diseases; Liver Diseases; Musculoskeletal Diseases; Prognosis; Skin Diseases
PubMed: 26154136
DOI: 10.1097/MIB.0000000000000392 -
Genetics Nov 2015Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with...
Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with them a century ago. Work with Drosophila has enabled dramatic advances in cell and developmental biology, neurobiology and behavior, molecular biology, evolutionary and population genetics, and other fields. With more tissue types and observable behaviors than in other short-generation model organisms, and with vast genome data available for many species within the genus, the fly's tractable complexity will continue to enable exciting opportunities to explore mechanisms of complex developmental programs, behaviors, and broader evolutionary questions. This primer describes the organism's natural history, the features of sequenced genomes within the genus, the wide range of available genetic tools and online resources, the types of biological questions Drosophila can help address, and historical milestones.
Topics: Animals; Drosophila; Models, Biological; Models, Genetic
PubMed: 26564900
DOI: 10.1534/genetics.115.183392 -
Biochemistry and Molecular Biology... Mar 2018Disrupting a gene to determine its effect on an organism's phenotype is an indispensable tool in molecular biology. Such techniques are critical for understanding how a... (Review)
Review
Disrupting a gene to determine its effect on an organism's phenotype is an indispensable tool in molecular biology. Such techniques are critical for understanding how a gene product contributes to the development and cellular identity of organisms. The explosion of genomic sequencing technologies combined with recent advances in genome-editing techniques has elevated the possibilities of genetic manipulations in numerous organisms in which these experiments were previously not readily accessible or possible. Introducing the next generation of molecular biologists to these emerging techniques is key in the modern biology classroom. This comprehensive review introduces undergraduates to CRISPR/Cas9 editing and its uses in genetic studies. The goals of this review are to explain how CRISPR functions as a prokaryotic immune system, describe how researchers generate mutations with CRISPR/Cas9, highlight how Cas9 has been adapted for new functions, and discuss ethical considerations of genome editing. Additionally, anticipatory guides and questions for discussion are posed throughout the review to encourage active exploration of these topics in the classroom. Finally, the supplement includes a study guide and practical suggestions to incorporate CRISPR/Cas9 experiments into lab courses at the undergraduate level. © 2018 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 46(2):195-205, 2018.
Topics: CRISPR-Cas Systems; Gene Editing; Molecular Biology; Students; Universities
PubMed: 29381252
DOI: 10.1002/bmb.21108 -
The Journal of Clinical Pediatric... 2018Fluoride, one of the most celebrated ingredients for the prevention of dental caries in the 20th century, has also been controversial for its use in dentifrices and... (Review)
Review
Fluoride, one of the most celebrated ingredients for the prevention of dental caries in the 20th century, has also been controversial for its use in dentifrices and other applications. In the current review, we have concentrated primarily on early-life exposure to fluoride and how it may affect the various organs. The most recent controversial aspects of fluoride are related to toxicity of the developing brain and how it may possibly result in the decrease of intelligence quotient (IQ), autism, and calcification of the pineal gland. In addition, it has been reported to have possible effects on bone and thyroid glands. If nutritional stress is applied during a critical period of growth and development, the organ(s) and/or body will never recover once they pass through the critical period. For example, if animals are force-fed during experiments, they will simply get fat but never reach the normal size. Although early-life fluoride exposure causing fluorosis is well reported in the literature, the dental profession considers it primarily as an esthetic rather than a serious systemic problem. In the current review, we wanted to raise the possibility of future disease as a result of early-life exposure to fluoride. It is not currently known how fluoride will become a cause of future disease. Studies of other nutritional factors have shown that the effects of early nutritional stress are a cause of disease in later life.
Topics: Autistic Disorder; Bone Neoplasms; Brain; Calcinosis; Cariostatic Agents; Fluoridation; Fluorides; Humans; Intelligence Tests; Osteosarcoma; Pineal Gland; Thyroid Hormones
PubMed: 29763350
DOI: 10.17796/1053-4625-42.5.1 -
EFORT Open Reviews Oct 2019Culture-negative periprosthetic joint infections (CN-PJI) pose a significant challenge in terms of diagnosis and management. The reported incidence of CN-PJI is reported... (Review)
Review
Culture-negative periprosthetic joint infections (CN-PJI) pose a significant challenge in terms of diagnosis and management. The reported incidence of CN-PJI is reported to be between 7% and 15%.Fungi and mycobacterium are thought to be responsible for over 85% of such cases with more fastidious bacteria accounting for the rest.With the advent of polymerase chain reaction, mass spectrometry and next generation sequencing, identifying the causative organism(s) may become easier but such techniques are not readily available and are very costly.There are a number of more straightforward and relatively low-cost methods to help surgeons maximize the chances of diagnosing a PJI and identify the organisms responsible.This review article summarizes the main diagnostic tests currently available as well as providing a simple diagnostic clinical algorithm for CN-PJI. Cite this article: 2019;4:585-594. DOI: 10.1302/2058-5241.4.180067.
PubMed: 31754464
DOI: 10.1302/2058-5241.4.180067 -
The New Phytologist Sep 2015985 I. 985 II. 986 III. 987 IV. 988 V. 989 989 References 989 SUMMARY: The development of multicellular organisms depends on correct establishment of symmetry both at... (Review)
Review
985 I. 985 II. 986 III. 987 IV. 988 V. 989 989 References 989 SUMMARY: The development of multicellular organisms depends on correct establishment of symmetry both at the whole-body scale and within individual tissues and organs. Setting up planes of symmetry must rely on communication between cells that are located at a distance from each other within the organism, presumably via mobile morphogenic signals. Although symmetry in nature has fascinated scientists for centuries, it is only now that molecular data to unravel mechanisms of symmetry establishment are beginning to emerge. As an example we describe the genetic and hormonal interactions leading to an unusual bilateral-to-radial symmetry transition of an organ in order to promote reproduction.
Topics: Animals; Plant Development; Plants
PubMed: 26086581
DOI: 10.1111/nph.13526