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The closest relatives of Cercozoa are the Retaria (Foraminifera and Radiozoa; Cavalier-Smith 1999). Radiozoa are all marine unicellular organisms with microtubule-supported axopodia; they comprise the classical polycystine Radiolaria (with silica skeletons), the Acantharea (with strontium sulphate skeletons), which both also possess axopodia, and the curious floating and axopodially swimming Sticholonche which is not mineralized. Radiozoa now excludes the Phaeodarea, which despite their silica skeleton and axopodia, clearly belong in Cercozoa. Phaeodarea appear to be related to the filosan group known as Thecofilosea, which includes filose testate amoebae without silica scales and also the exclusively marine ebriid flagellates, which like the Phaeodarea have a hollow silica endoskeleton, which might therefore have been a common ancestral character for both groups. A hollow silica endoskeleton is unknown in any other eukaryotes. Two groups of Cercozoa (the euglyphid testate amoebae and the ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=http://www.nrbook.com/b/bookcpdf.php>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
Our laboratory uses molecular biological and computational methods to study the genes and genomes of prokaryotic and eukaryotic (nucleus-containing) microorganisms. Using a comparative genomics approach, we are interested in (1) the pivotal molecular and biochemical events that have shaped the evolution of eukaryotes; (2) understanding the evolutionary relationships amongst eukaryotic microbes; (3) how endosymbionts become organelles; and (4) understanding how eukaryotic genes, genomes and proteins change over time. We currently study the spread of photosynthetic organelles (chloroplasts) in eukaryotes and the extent to which lateral (horizontal) gene transfer has impacted the gene content of nuclear genomes.. ...
When senior Saudi cleric Abdulaziz al-Tarifi told his almost one million Twitter followers that musical instruments were ungodly, it helped spark a hashtag among like-minded Saudis that
As your question rightfully emphasizes - the optimizations of sample preparation (and handling) is crucially important for getting meaningful data from your single cell sequencing assay - if you dont have the cells going into the assay you will not be able to profile them. Worse yet, if you dont know you lost them, you could risk making a conclusion based on the composition of cells in the sample. In this case, you know what cells are important in your samples and are concerned that you may lose them in the processing. To assay whether your protocol is optimized for retention of a particular cell type, we usually recommend folks who have access to flow cytometry and a reliable flow panel to use this to identify the composition of cell types and their viability. This ends up being a strong indicator of what you will see in the single cell sequencing data. If you have other ways to mark the cells of interest, simple cell counting or qualitative assessments on a standard microscope are also ...
Mechanical micromanipulation is a classic method to isolate uncultivated microorganisms or early embryos, and it involves using a capillary pipette to suck up a single cell from a cell suspension with visual inspection of cellular morphology and coloring characteristics under a microscope [13, 14] (Fig. 1b). The drawback of mechanical micromanipulation is that it is low-throughput and time-consuming and can cause cellular injury from mechanical shearing during manipulation [15]. Additionally, it often leads to a failure for an unskilled manipulator or misidentification of the cellular morphology under the microscope.. FACS is the most efficient and economical method to isolate hundreds of thousands of individual cells per minute based on their size, granularity and fluorescence properties [4] (Fig. 1c). The high-throughput, time-saving and automatic properties are the main advantage of FACS. Additionally, it allows researchers to isolate specific individual cells from heterogeneous cell samples ...
Figure 5. Dose-response analysis of an EGFR‐amplified case. Enriched gene sets (WEBGESTALT, DAVID, adj. P‐value , 0.05) correlated to EGFR. Distributions of in‐pathway genes in individual cells, sorted from low EGFR to high EGFR (top panel). An interaction network (generated via geneMANIA) of physical and genetic interactions of transcription factors, whose recognition motifs are overrepresented (OPOSSUM, z‐score ≥ 10, Fisher score ≥ 7) in correlated genes. Physical interactions are interactions between the protein product, identified from proteomics experiments. Genetic interactions are changes in gene expression that occur when another gene is suppressed in a knockdown experiment. ...
Single-cell transcriptome sequencing is commonly referred to as single-cell RNA sequencing (scRNA-seq). It is used to analyze single-cell-level cell type differences and gene expression profiles in complex biological systems.
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Researchers from the Institute of Food Research and the University of East Anglia have discovered how the beneficial bacteria in our guts communicate
NovaDigm Therapeutics, a pharmaceutical company specializing in vaccines to fight fungal and bacterial infections, recently announced positive results from a phase I study of a vaccine to against the fungus Candida and the bacterium Staphylococcus aureus.
Research Description. The liver is the primary filter for drugs, environmental toxins and chemicals and as such protects the body against harmful chemical exposures. This work will aid the differentiation, maturation and culture of hepatocytes in vitro. It will improve both the quality and quantity of hepatocytes for use in in-vitro toxicological screening of drugs and other compounds. Using Single Cell sequencing and WaveCrest, an algorithm that can minimize the Euclidian distance between the transcriptomes of the cells, we aim to spatially recreate the periportal to perivenous axis of the hepatocytes allowing us to understand region differences within the liver. Many toxins (such as acetaminophen) have a zone specific toxicity profile. By being blind to the zonation of hepatocytes on culture we could mischaracterize toxic compounds due to the fact that the sensitive population of cells might not be present in the culture.. ...
See the latest publications using 10x Genomics. Read about exciting discoveries in single cell sequencing for gene expression profiling, immune profiling, epigenetics, and more.
See the latest publications using 10x Genomics. Read about exciting discoveries in single cell sequencing for gene expression profiling, immune profiling, epigenetics, and more.
Adl, S.M., Simpson, A.G., Farmer, M.A., Andersen, R.A., Anderson, O.R., Barta, J.R., Bowser, S.S., Brugerolle, G., Fensome, R.A., Fredericq, S., James, T.Y., Karpov, S., Kugrens, P., Krug, J., Lane, C.E., Lewis, L.A., Lodge, J., Lynn, D.H., Mann, D.G., McCourt, R.M., Mendoza, L., Moestrup, O., Mozley-Standridge, S.E., Nerad, T.A., Shearer, C.A., Smirnov, A.V., Spiegel, F.W. and Taylor, M.F. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol., 52, 399-451.. Andersson, S.G. and Kurland, C.G. (1999) Origins of mitochondria and hydrogenosomes. Curr. Opin. Microbiol., 2, 535-541.. Archibald, J.M. (2005) Jumping genes and shrinking genomes--probing the evolution of eukaryotic photosynthesis with genomics. IUBMB Life, 57, 539-547.. Archibald, J.M., Longet, D., Pawlowski, J. and Keeling, P.J. (2002) A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol., 20, ...
Adl, S.M., Simpson, A.G., Farmer, M.A., Andersen, R.A., Anderson, O.R., Barta, J.R., Bowser, S.S., Brugerolle, G., Fensome, R.A., Fredericq, S., James, T.Y., Karpov, S., Kugrens, P., Krug, J., Lane, C.E., Lewis, L.A., Lodge, J., Lynn, D.H., Mann, D.G., McCourt, R.M., Mendoza, L., Moestrup, O., Mozley-Standridge, S.E., Nerad, T.A., Shearer, C.A., Smirnov, A.V., Spiegel, F.W. and Taylor, M.F. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol., 52, 399-451.. Andersson, S.G. and Kurland, C.G. (1999) Origins of mitochondria and hydrogenosomes. Curr. Opin. Microbiol., 2, 535-541.. Archibald, J.M. (2005) Jumping genes and shrinking genomes--probing the evolution of eukaryotic photosynthesis with genomics. IUBMB Life, 57, 539-547.. Archibald, J.M., Longet, D., Pawlowski, J. and Keeling, P.J. (2002) A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol., 20, ...
Plastids have a tremendous importance in plants as they are the photosynthetic organelles. But their importance extends way beyond this physiological role, as they are also part of the regulatory network that controls the life cycle of the entire plant. Our research is focussed on the integration of the cell organelles (plastids as well as mitochondria) into cellular response regulation of plants with a particular focus on dually targeted proteins.
From BioPortfolio: Complex biological systems are fundamentally determined by the coordinated functions of individual cells. The transcriptional heterogeneity that drives this com...
Diagnosis of an infection with Marteiliodes chungmuensis requires identification of the protozoan through laboratory tests. Not all infected molluscs show signs of disease
Visit Healthgrades for information on Dr. Gabriel Garcia, MD Find Phone & Address information, medical practice history, affiliated hospitals and more.
ABSTRACT Marine phytomyxids (Cercozoa: Phytomyxea) represent a group of obligate biotrophic eukaryotes known for infecting several algae and oomycetes and counted among three taxa generally reported to behave as seagrass-pathogens. Due to their low-key nature, they are observed only sporadically and very limited information about their diversity, life cycles or distribution is available. In order to extend the knowledge of this enigmatic group of marine protists, an extensive research on a phytomyxid found in the invasive seagrass Halophila stipulacea was carried out. In situ observations, light and scanning electron microscopy and molecular methods were used to approach the species ecology, geographical range and phylogenetic placement within the class Phytomyxea. The organism was confirmed to be present in the Red, the Mediterreanean and the Caribbean Sea, suggesting a potential case of a host-parasite comigration on a global scale. Phylogenetically it represents the first and so far the only ...
The Rhizaria are a species-rich supergroup of mostly unicellular[1] eukaryotes.[2] Except from the Chlorarachniophyte and three species in the genus Paulinella in the phylum Cercozoa, they are all non-photosyntethic, but many foraminifers have a symbiotic relationship with unicellular algae. A multicellular form, Guttulinopsis vulgaris, a cellular slime mold, has also been described.[3] This supergroup was proposed by Cavalier-Smith in 2002. Being described mainly from rDNA sequences, they vary considerably in form, having no clear morphological distinctive characters (synapomorphies), but for the most part they are amoeboids with filose, reticulose, or microtubule-supported pseudopods. Many produce shells or skeletons, which may be quite complex in structure, and these make up the vast majority of protozoan fossils. Nearly all have mitochondria with tubular cristae. ...
Identification of rare cells or molecules from a mixture population is important in biology such as identification of rare cancer cells or nucleic acid in early stage cancer diagnosis. Recent advances in droplet-based microfluidics and hydrogel barcoded microsphere to capture all the mRNA molecules in each cell in a single step enables scientists to identify cells based on their whole transcriptome information. However, due to the large number of sequencing reads required to cover the whole transcriptome, this limits the number of cells processed in one sequencing run. We address this problem by using a stepwise approach by first encapsulating single cell and lysis buffer together in a water-in-oil picoliter droplet, then amplifying only the target DNA/RNA molecule of interest in each droplet, pico-inject hydrogel barcoded microsphere into each droplet to tag the amplicons prior to next generation sequencing. We demonstrated the use of this technology by applying it to study how single tumor ...
Researchers at the British Columbia Cancer Agency in Vancouver have developed a directional single-cell sequencing method that allows them to selectively sequence the original DNA template strand a daughter cell has inherited from its parent.
The Antarctic nematode Panagrolaimus davidi can survive intracellular freezing. Genetic studies indicate the culture strain (now designated as Panagrolaimus sp. DAW1) is a different species to the P. davidi of field origin. This paper reports further attempts both to isolate DAW1 from Antarctic soils and to culture P. davidi itself. Sequencing of the 18S rRNA gene of 151 individuals indicates that DAW1 is rare in the field, but characterising two new isolates shows that, nevertheless, it is present. Panagrolaimus davidi is common in the field, but cannot be cultured using the media tested here. These two species are difficult to distinguish morphologically, apart from the absence of males in DAW1 and its longer recurved tail. Whilst it is possible that DAW1 is an introduced species, the sites at Shackletons hut at Cape Royds are dominated by P. davidi, which is clearly an endemic species.
Penicillin-binding protein 3 (PBP3) of Pseudomonas aeruginosa is the primary target of beta-lactams used to treat pseudomonas infections. Meanwhile, structure change and overproduction of PBP3 play important roles in the drug resistance of P. aeruginosa. Therefore, studies on the gene and structure of PBP3 are urgently needed. P. aeruginosa CMCC 10104 is a type culture strain common used in China. However, there is no report on its genomic and proteomic profiles. In this study, based on ftsl of P. aeruginosa PAO1, the gene encoding PBP3 was cloned from CMCC 10104. A truncated version of the ftsl gene, omitting the bases encoding the hydrophobic leader peptide (amino acids 1-34), was amplified by PCR. The cloned DNA shared 99.76% identity with frsl from PAO1. Only four bases were different (66 C-A, 1020 T-C, 1233 T-C, and 1527 T-C). However, there were no differences between their deduced amino acid sequences. The recombinant PBP3 (rPBP3), containing a 6-histidine tag, was expressed in ...
At cultivation of |i|Chlorella vulgaris|/i| Beijer. culture (strains LARG-3, HPDP-120) in close system at medium saturation by CO|sub|2|/sub| it was stated that...
Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are important regulators of eukaryotic gene expression by guiding mRNA cleavage, translational inhibition or chromatin modification. We utilize genomics, genetics, molecular and biochemical approaches to identify and functionally characterize infection-regulated small RNAs, including those from plant hosts and from eukaryotic pathogens. My lab provided the first example of a plant endogenous siRNA that regulates plant immune responses. We further discovered that some small RNAs from aggressive fungal pathogens are delivered into host cells to hijack host RNAi machinery to suppress host immunity genes. These studies have added small RNAs to the list of pathogen effectors, which unveiled a novel virulence mechanism in aggressive eukaryotic pathogens. The transport of small RNAs from fungal pathogens to plant hosts also represents a naturally occurring cross-kingdom RNAi event. We recently show that such cross-kingdom ...
Cysts of free-living protozoa have an impact on the ecology and epidemiology of bacteria because they may act as a transmission vector or shelter the bacteria against hash environmental conditions. Detection and localization of intracystic bacteria and examination of the en- and excystment dynamics is a major challenge because no detailed protocols for ultrastructural analysis of cysts are currently available. Transmission electron microscopy ...
View Notes - IMG_0004_NEW from BISC 333 at Simon Fraser. Wr *&{ ffi{Tnffi m{w rnmdtfr** during wv*ltst**n and tries to explain the morphological diversity of plants and animals in this context.
a research entomologist with the U.S. Department of Agriculture.. You just wonder … do all animals have that potential?. ---. (c) 2010, Los Angeles Times.. Visit the Los Angeles Times on the Internet at http://www.latimes.com/ Distributed by McClatchy-Tribune Information Services.. ...
Endosulfan is a synthetic cyclodiene non-systemic insecticide and acaricide with both contact and stomach activity. Microorganisms play a key role in removal of xenobiotics like endosulfan from the contaminanted sites because of their dynamic, complex, and complicated enzymatic systems which degrade these chemical. In this study, endosulfan was degraded by indigenous bacteria strains of Pseudomonas aeruginosa and Staphylococcus aureus. The biodegradation process was carried out according to the method established by Buff et al., 1992. The results obtained showed that the bacterial strains efficiently degraded endosulfan by consuming more than 90 % of 40 mg/l of the minimal media within 7 days of incubation. Maximum biodegration by these two selected bacterial stains was observed at an initial pH of 8.0 at an incubation temperature of 30 °C. The findings from present study suggest that these bacterial strains could be potentially promising as a low cost effective technology in the biodegradation ...
Lactobacillus sakei is an important food-associated lactic acid bacterium commonly used as starter culture for industrial meat fermentation, and with great potential as a biopreservative in meat and fish products. Understanding the metabolic mechanisms underlying the growth performance of a strain to be used for food fermentations is important for obtaining high-quality and safe products. Proteomic analysis was used to study the primary metabolism in ten food isolates after growth on glucose and ribose, the main sugars available for L. sakei in meat and fish. Proteins, the expression of which varied depending on the carbon source were identified, such as a ribokinase and a D-ribose pyranase directly involved in ribose catabolism, and enzymes involved in the phosphoketolase and glycolytic pathways. Expression of enzymes involved in pyruvate and glycerol/glycerolipid metabolism were also affected by the change of carbon source. Interestingly, a commercial starter culture and a protective culture strain
1. Immune sera produced in rabbits by treatment with our Culture Strain A of Treponema pallidum agglutinated not only the homologous strain, but also the Noguchi strains, and indicate a close group relationship of other non-pathogenic treponemata. Absorption experiments confirmed this, indicating a close relationship between the pallidum and the calligyrum.. 2. Culture treponemata are not agglutinated to a much greater extent by the sera of syphilitic rabbits than they are by those of normal rabbits.. 3. Culture treponemata are not agglutinated to any considerable extent by the sera of rabbits immunized with virulent treponemata.. 4. The sera of syphilitic patients, especially those in the tertiary stages, agglutinate culture pallidum to a slightly greater extent than do those of normal individuals, but the culture pallidum is agglutinated to an almost equal degree by the sera of many individuals with diseases other than syphilis. We do not think that we could definitely distinguish the ...
Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, Cell Biology, BIOCHEMISTRY & MOLECULAR BIOLOGY, CELL BIOLOGY, RHOPALOSIPHUM-PADI VIRUS, HEPATITIS-C VIRUS, TRANSLATION INITIATION-FACTORS, TRACT-BINDING-PROTEIN, FACTOR 4G EIF4G, ENCEPHALOMYOCARDITIS VIRUS, PREINITIATION COMPLEXES, INDEPENDENT INITIATION, MEDIATED TRANSLATION, PURIFIED COMPONENTS ...
Partek Flow is a web-based application for the data analysis of next generation sequencing including RNA, small RNA, and DNA sequencing. With an easy-to-use graphical interface and the ability to build custom analysis pipelines or download existing ones, Partek Flow enables bench top researchers to carry out routine NGS data analysis using dozens of popular algorithms without writing codes or running command lines tools. The software features streamlined workflows for RNA-seq, DNA-seq, ChIP-seq, and Single cell sequencing data analysis. that uses popular algorithms for NGS raw data QA/QC, alignment, visualization, as well as RNA quantification and variant detection. Partek Flow has been implemented on both HPCC-NML Custom Condo and NML Bioinformatics Workstations.. ...
Our group develops single-cell analysis methods and microfluidic systems to improve measurement functionality, accuracy, and throughput and applies these tools to problems in signaling, immunity and cellular information processing. We are particularly interested in multiplexed proteomic and transcriptomic methods at the single-cell level, with applications to intact tissue. In this project, we will develop single cell sequencing and single-cell proteomics methods where the spatial position of every cell in the tissue is recorded along with the measurement of its genome, transcriptome, and proteome. Such a measurement capability will allow us to discover new cell types and functional states, create a Human Cell Atlas, and broadly impact a range of fields in Systems Biology and Medicine.. ...
Biorealm}} {, width=50 cellpadding=5 , height=69 bgcolor=#FFDF95 , NCBI:,br />[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=238777&lvl=3&lin=f&keep=1&srchmode=1&unlock Phaeodaria],br />[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=65582&lvl=3&lin=f&keep=1&srchmode=1&unlock Polycistinea] Genome ,} [[Image:81102D.jpg,frame,right,Various Radiolaria tests. [http://www.denniskunkel.com/index.php Dennis Kunkel Microscopy, Inc.]]] ==Classification== ===Higher order taxa=== Eukaryota; Cercozoa ===Species=== Halesium triacanthum,br />Pterocanium praetaxum,br /> Collozoum inerme ==Description and Significance== [[Image:radi032.gif,thumb,200px,right,Acanthoicircus tympanum. [http://www.ucl.ac.uk/GeolSci/micropal/radiolaria.html University College London Micropalaeontology Unit].]] Radiolaria are planktonic protists. They are among the few protistan groups with comprehensive fossil records available for study. Radiolaria ...
A novel DAMP molecule has been identified in plants that triggers an immune response after tissue damage. Knowledge of this protein and its human equivalent give us a cross-kingdom understanding of how humans and plants fight off infections ...
A global phylogeny of major eukaryotic lineages is a significant and ongoing challenge to molecular phylogenetics. Currently, there are five hypothesized major lineages or supergroups' of eukaryotes. One of these, the chromalveolates, represents a large fraction of protist and algal diversity. The chromalveolate hypothesis was originally based on similarities between the photosynthetic organelles (plastids) found in many of its members and has been supported by analyses of plastid-related genes. However, since plastids can move between eukaryotic lineages, it is important to provide additional support from data generated from the nuclear-cytosolic host lineage. Genes coding for six different cytosolic proteins from a variety of chromalveolates (yielding 68 new gene sequences) have been characterized so that multiple gene analyses, including all six major lineages of chromalveolates, could be compared and concatenated with data representing all five hypothesized supergroups. Overall support for
TTP Labtech, a global leader in the design and development of automated instrumentation and consumables for life science applications, and the University of California San Diego (UC San Diego), have announced that their collaboration has resulted in a new workflow for single cell sequencing, which reduces the cost of sample preparation by 90%.. The workflow, which has been published in the Journal of Laboratory Automation, was developed through the combination of UC San Diegos expertise in genomics and the use of TTP Labtechs mosquito liquid handlers, which can pipette nanolitre to microlitre volumes with high accuracy and reproducibility, to miniaturise and automate the process.. Although single-cell genomics is advancing rapidly, researchers face challenges linked with reproducibility, sensitivity, scalability and cost, particularly when trying to miniaturize high-throughput applications. To maximize accuracy and precision, library prep protocols recommend volumes that are within the range ...
The generation of single cell sequencing data from human tissues is transforming our understanding of biological mechanisms. This is particularly true for poorly studied organs and tissues that are difficult to obtain. One such tissue is the human male genital duct, the epididymis and vas deferens, which have a pivotal role in sperm maturation and hence maintenance of the species. Most models of epididymis function are based upon other mammals, which show substantial anatomic and functional diversity. Here, we construct a single cell atlas of the human proximal epididymis, which reveals detailed molecular characterization of both common and rare cell types, and hence may advance our understanding of mechanisms of male fertility.. The key functions of the epididymis are performed by the cells lining the lumen of the duct, which maintain a low pH environment necessary for sperm quiescence. These cells also secrete a wide spectrum of proteins, peptides, and RNAs that provide the necessary cues for ...
My thesis intended to develop methods to facilitate the study of soil eukaryotic microbes as well as to enhance the understanding of their ecological role in the soil food web and nutrient cycles of agroecosystems. A cell extraction method was first developed and evaluated for its quantitative and qualitative ability to recover eukaryotic microbial cells in a particle free suspension. Cells were sorted based on their natural fluorescence by mean of flow cytometry, thus allowing the separation of photo-autotrophic and heterotrophic organisms. Deep molecular characterisation based on a multiple barcoding approach was also applied to assess the long term effect of crop fertilisation on the diversity and community composition of different groups of soil eukaryotic microbes. The comparison between group specific barcodes and a universal eukaryotic barcode further aimed to challenge the accuracy of the latter approach to measure soil microbial eukaryotic diversity. At a final stage, the diversity and ...
This blog was created as an online diary to capture some of the things I love or experience in life. Anyway, I hope we will all learn to appreciate the simple things in life, cherish our loved ones and make the most of our lives ...
Rapid methods of identifying Lancefield group B streptococci were compared to the standard Fullers extraction method. Such tests as sodium hippurate hydrolysis, bile tolerance, aesculin hydrolysis, pyruvate fermentation, Camp factor, pigmentation, and bacitracin haemolysis were tested on both routine clinical specimens and National Collection of Type Culture strains. The results show that pigmentation on Islamss medium was the most definitive test available rapidly to identify group B streptococci.. ...
human-diploid fibroblast cell cultures (strain WI-38)…fetal bovine serum…monosodium glutamate [MSG]…human serum albumin…magnesium stearate…FD&C Yellow #6 aluminum lake dye…acetone…castor oil…aluminum phosphate…formaldehyde…casein…inorganic salts…Fenton medium containing a bovine extract…aluminum hydroxide…polysorbate 80 (Tween 80)…VERO cells, a continuous line of monkey kidney cells…calf serum…neomycin sulfate…polymyxin B…ammonium sulfate…modified Mueller-Miller casamino acid medium without beef heart infusion…MRC-5 cells…normal human diploid cells…CMRL 1969 medium supplemented with calf serum…Medium 199 without calf serum…2-phenoxyethanol…synthetic medium…formalin…complex fermentation medium…soy peptone…mineral salts…potassium aluminum sulfate…amorphous aluminum hydroxyphosphate sulfate…sodium borate…non-viral protein…bovine albumin…aminoglycoside antibiotic…yeast protein…L-histidine…squalene…thimerosal…egg ...
A fundamental fact in biology states that genes do not operate in isolation, and yet, methods that infer regulatory networks for single cell gene expression data have been slow to emerge. With single cell sequencing methods now becoming accessible, general network inference algorithms that were initially developed for data collected from bulk samples may not be suitable for single cells. Meanwhile, although methods that are specific for single cell data are now emerging, whether they have improved performance over general methods is unknown. In this study, we evaluate the applicability of five general methods and three single cell methods for inferring gene regulatory networks from both experimental single cell gene expression data and in silico simulated data. Standard evaluation metrics using ROC curves and Precision-Recall curves against reference sets sourced from the literature demonstrated that most of the methods performed poorly when they were applied to either experimental single cell data, or
TY - JOUR. T1 - Data descriptor. T2 - Single cell RNA sequencing of stem cell-derived retinal ganglion cells. AU - Daniszewski, Maciej. AU - Senabouth, Anne. AU - Nguyen, Quan H.. AU - Crombie, Duncan E.. AU - Lukowski, Samuel W.. AU - Kulkarni, Tejal. AU - Sluch, Valentin M.. AU - Jabbari, Jafar S.. AU - Chamling, Xitiz. AU - Zack, Donald J.. AU - Pébay, Alice. AU - Powell, Joseph E.. AU - Hewitt, Alex W.. PY - 2018/2/13. Y1 - 2018/2/13. N2 - We used single cell sequencing technology to characterize the transcriptomes of 1,174 human embryonic stem cell-derived retinal ganglion cells (RGCs) at the single cell level. The human embryonic stem cell line BRN3B-mCherry (A81-H7), was differentiated to RGCs using a guided differentiation approach. Cells were harvested at day 36 and prepared for single cell RNA sequencing. Our data indicates the presence of three distinct subpopulations of cells, with various degrees of maturity. One cluster of 288 cells showed increased expression of genes involved in ...
To date, almost all the pathogen effectors studied or discovered have been proteins, said lead author Hailing Jin, a professor of plant pathology and microbiology. Ours is the first study to add the RNA molecule to the list of effectors. We expect our work will help in the development of new means to control aggressive pathogens.. Small RNAs guide gene silencing in a wide range of eukaryotic organisms. In the case of Botrytis cinerea, small RNAs silence the expression of host defense genes, resulting in the host plant cells being less able to resist the fungal attack. The process is similar to how protein effectors weaken host immunity in the case of most pathogens.. What we have discovered is a naturally-occurring cross-kingdom RNAi phenomenon between a fungal pathogen and a plant host that serves as an advanced virulence mechanism, Jin said.. RNA interference or RNAi is a conserved gene regulatory mechanism that is guided by small RNAs for silencing (or suppressing) genes.. Next, Jin and ...
In situ sequencing differs from previous sequencing generations in two respects, both of which are relevant for its use in research and diagnostics. First, the spatial distribution of the sequencing reads over the sample can be seen, adding an important level of information. We demonstrated in our article how this information can be used to visualize tissue heterogeneity based on a number of known molecular markers.. Lee and colleagues showed that subcellular resolution can be achieved with their method, an interesting feature that would allow the study of regulatory elements such as non-coding RNA species in complex populations of cells, for example, in brain tissue. A second difference is the throughput in terms of the number of cells it is possible to simultaneously analyze. Single-cell RNA sequencing methods have been developed to work robustly with just a few picograms of starting material, and there has been an increase in the rate of cell sequencing as well as a decrease in cost [9]. ...