525 research outputs found
Multiplex quantitative PCR for single-reaction genetically modified (GM) plant detection and identification of false-positive GM plants linked to Cauliflower mosaic virus (CaMV) infection.
BACKGROUND:Most genetically modified (GM) plants contain a promoter, P35S, from the plant virus, Cauliflower mosaic virus (CaMV), and many have a terminator, TNOS, derived from the bacterium, Agrobacterium tumefaciens. Assays designed to detect GM plants often target the P35S and/or TNOS DNA sequences. However, because the P35S promoter is derived from CaMV, these detection assays can yield false-positives from non-GM plants infected by this naturally-occurring virus. RESULTS:Here we report the development of an assay designed to distinguish CaMV-infected plants from GM plants in a single multiplexed quantitative PCR (qPCR) reaction. Following initial testing and optimization via PCR and singleplex-to-multiplex qPCR on both plasmid and plant DNA, TaqMan qPCR probes with different fluorescence wavelengths were designed to target actin (a positive-control plant gene), P35S, P3 (a CaMV-specific gene), and TNOS. We tested the specificity of our quadruplex qPCR assay using different DNA extracts from organic watercress and both organic and GM canola, all with and without CaMV infection, and by using commercial and industrial samples. The limit of detection (LOD) of each target was determined to be 1% for actin, 0.001% for P35S, and 0.01% for both P3 and TNOS. CONCLUSIONS:This assay was able to distinguish CaMV-infected plants from GM plants in a single multiplexed qPCR reaction for all samples tested in this study, suggesting that this protocol is broadly applicable and readily transferrable to any interested parties with a qPCR platform
Methodology for experimental and observational animal studies in cow-calf contact systems
publishedVersio
Fluctuation scaling in complex systems: Taylor's law and beyond
Complex systems consist of many interacting elements which participate in
some dynamical process. The activity of various elements is often different and
the fluctuation in the activity of an element grows monotonically with the
average activity. This relationship is often of the form "", where the exponent is predominantly in
the range . This power law has been observed in a very wide range of
disciplines, ranging from population dynamics through the Internet to the stock
market and it is often treated under the names \emph{Taylor's law} or
\emph{fluctuation scaling}. This review attempts to show how general the above
scaling relationship is by surveying the literature, as well as by reporting
some new empirical data and model calculations. We also show some basic
principles that can underlie the generality of the phenomenon. This is followed
by a mean-field framework based on sums of random variables. In this context
the emergence of fluctuation scaling is equivalent to some corresponding limit
theorems. In certain physical systems fluctuation scaling can be related to
finite size scaling.Comment: 33 pages, 20 figures, 2 tables, submitted to Advances in Physic
Magnetism, FeS colloids, and Origins of Life
A number of features of living systems: reversible interactions and weak
bonds underlying motor-dynamics; gel-sol transitions; cellular connected
fractal organization; asymmetry in interactions and organization; quantum
coherent phenomena; to name some, can have a natural accounting via
interactions, which we therefore seek to incorporate by expanding the horizons
of `chemistry-only' approaches to the origins of life. It is suggested that the
magnetic 'face' of the minerals from the inorganic world, recognized to have
played a pivotal role in initiating Life, may throw light on some of these
issues. A magnetic environment in the form of rocks in the Hadean Ocean could
have enabled the accretion and therefore an ordered confinement of
super-paramagnetic colloids within a structured phase. A moderate H-field can
help magnetic nano-particles to not only overcome thermal fluctuations but also
harness them. Such controlled dynamics brings in the possibility of accessing
quantum effects, which together with frustrations in magnetic ordering and
hysteresis (a natural mechanism for a primitive memory) could throw light on
the birth of biological information which, as Abel argues, requires a
combination of order and complexity. This scenario gains strength from
observations of scale-free framboidal forms of the greigite mineral, with a
magnetic basis of assembly. And greigite's metabolic potential plays a key role
in the mound scenario of Russell and coworkers-an expansion of which is
suggested for including magnetism.Comment: 42 pages, 5 figures, to be published in A.R. Memorial volume, Ed
Krishnaswami Alladi, Springer 201
Geo-social gradients in predicted COVID-19 prevalence in Great Britain: results from 1 960 242 users of the COVID-19 Symptoms Study app
Understanding the geographical distribution of
COVID-19 through the general population is key to
the provision of adequate healthcare services. Using
self-reported data from 1 960 242 unique users in Great
Britain (GB) of the COVID-19 Symptom Study app,
we estimated that, concurrent to the GB government
sanctioning lockdown, COVID-19 was distributed across
GB, with evidence of ’urban hotspots’. We found a
geo-social gradient associated with predicted disease
prevalence suggesting urban areas and areas of higher
deprivation are most affected. Our results demonstrate
use of self-reported symptoms data to provide focus on
geographical areas with identified risk factors
Geo-social gradients in predicted COVID-19 prevalence in Great Britain: results from 1 960 242 users of the COVID-19 Symptoms Study app
Understanding the geographical distribution of
COVID-19 through the general population is key to
the provision of adequate healthcare services. Using
self-reported data from 1 960 242 unique users in Great
Britain (GB) of the COVID-19 Symptom Study app,
we estimated that, concurrent to the GB government
sanctioning lockdown, COVID-19 was distributed across
GB, with evidence of ’urban hotspots’. We found a
geo-social gradient associated with predicted disease
prevalence suggesting urban areas and areas of higher
deprivation are most affected. Our results demonstrate
use of self-reported symptoms data to provide focus on
geographical areas with identified risk factors
Astrobiological Complexity with Probabilistic Cellular Automata
Search for extraterrestrial life and intelligence constitutes one of the
major endeavors in science, but has yet been quantitatively modeled only rarely
and in a cursory and superficial fashion. We argue that probabilistic cellular
automata (PCA) represent the best quantitative framework for modeling
astrobiological history of the Milky Way and its Galactic Habitable Zone. The
relevant astrobiological parameters are to be modeled as the elements of the
input probability matrix for the PCA kernel. With the underlying simplicity of
the cellular automata constructs, this approach enables a quick analysis of
large and ambiguous input parameters' space. We perform a simple clustering
analysis of typical astrobiological histories and discuss the relevant boundary
conditions of practical importance for planning and guiding actual empirical
astrobiological and SETI projects. In addition to showing how the present
framework is adaptable to more complex situations and updated observational
databases from current and near-future space missions, we demonstrate how
numerical results could offer a cautious rationale for continuation of
practical SETI searches.Comment: 37 pages, 11 figures, 2 tables; added journal reference belo
Cancer cells exploit an orphan RNA to drive metastatic progression.
Here we performed a systematic search to identify breast-cancer-specific small noncoding RNAs, which we have collectively termed orphan noncoding RNAs (oncRNAs). We subsequently discovered that one of these oncRNAs, which originates from the 3' end of TERC, acts as a regulator of gene expression and is a robust promoter of breast cancer metastasis. This oncRNA, which we have named T3p, exerts its prometastatic effects by acting as an inhibitor of RISC complex activity and increasing the expression of the prometastatic genes NUPR1 and PANX2. Furthermore, we have shown that oncRNAs are present in cancer-cell-derived extracellular vesicles, raising the possibility that these circulating oncRNAs may also have a role in non-cell autonomous disease pathogenesis. Additionally, these circulating oncRNAs present a novel avenue for cancer fingerprinting using liquid biopsies
Cerebellar Integrity in the Amyotrophic Lateral Sclerosis - Frontotemporal Dementia Continuum
Amyotrophic lateral sclerosis (ALS) and behavioural variant frontotemporal dementia (bvFTD) are multisystem neurodegenerative disorders that manifest overlapping cognitive, neuropsychiatric and motor features. The cerebellum has long been known to be crucial for intact motor function although emerging evidence over the past decade has attributed cognitive and neuropsychiatric processes to this structure. The current study set out i) to establish the integrity of cerebellar subregions in the amyotrophic lateral sclerosis-behavioural variant frontotemporal dementia spectrum (ALS-bvFTD) and ii) determine whether specific cerebellar atrophy regions are associated with cognitive, neuropsychiatric and motor symptoms in the patients. Seventy-eight patients diagnosed with ALS, ALS-bvFTD, behavioural variant frontotemporal dementia (bvFTD), most without C9ORF72 gene abnormalities, and healthy controls were investigated. Participants underwent cognitive, neuropsychiatric and functional evaluation as well as structural imaging using voxel-based morphometry (VBM) to examine the grey matter subregions of the cerebellar lobules, vermis and crus. VBM analyses revealed: i) significant grey matter atrophy in the cerebellum across the whole ALS-bvFTD continuum; ii) atrophy predominantly of the superior cerebellum and crus in bvFTD patients, atrophy of the inferior cerebellum and vermis in ALS patients, while ALS-bvFTD patients had both patterns of atrophy. Post-hoc covariance analyses revealed that cognitive and neuropsychiatric symptoms were particularly associated with atrophy of the crus and superior lobule, while motor symptoms were more associated with atrophy of the inferior lobules. Taken together, these findings indicate an important role of the cerebellum in the ALS-bvFTD disease spectrum, with all three clinical phenotypes demonstrating specific patterns of subregional atrophy that associated with different symptomology
Early-Time Energy Loss in a Strongly-Coupled SYM Plasma
We carry out an analytic study of the early-time motion of a quark in a
strongly-coupled maximally-supersymmetric Yang-Mills plasma, using the AdS/CFT
correspondence. Our approach extracts the first thermal effects as a small
perturbation of the known quark dynamics in vacuum, using a double expansion
that is valid for early times and for (moderately) ultrarelativistic quark
velocities. The quark is found to lose energy at a rate that differs
significantly from the previously derived stationary/late-time result: it
scales like T^4 instead of T^2, and is associated with a friction coefficient
that is not independent of the quark momentum. Under conditions representative
of the quark-gluon plasma as obtained at RHIC, the early energy loss rate is a
few times smaller than its late-time counterpart. Our analysis additionally
leads to thermally-corrected expressions for the intrinsic energy and momentum
of the quark, in which the previously discovered limiting velocity of the quark
is found to appear naturally.Comment: 39 pages, no figures. v2: Minor corrections and clarifications.
References added. Version to be published in JHE
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