Stacking Chairs: Local Sense and Global Nonsense.
Ontology highlight
ABSTRACT:
SUBMITTER: Scott-Samuel NE
PROVIDER: S-EPMC5777564 | biostudies-other | 2018 Jan-Feb
REPOSITORIES: biostudies-other
Publications
Stacking Chairs: Local Sense and Global Nonsense.
Scott-Samuel Nicholas E NE Ashida Hiroshi H Lovell P George PG Meese Tim S TS Schwarzkopf D Samuel DS
i-Perception 20180119 1
We report a confusing stimulus which demonstrates the power of local interpretation of three-dimensional structure to disrupt a coherent global perception. ...[more]
Similar Datasets
Project description:All three translation termination codons, or nonsense codons, contain a uridine residue at the first position of the codon. Here, we demonstrate that pseudouridylation (conversion of uridine into pseudouridine (?), ref. 4) of nonsense codons suppresses translation termination both in vitro and in vivo. In vivo targeting of nonsense codons is accomplished by the expression of an H/ACA RNA capable of directing the isomerization of uridine to ? within the nonsense codon. Thus, targeted pseudouridylation represents a novel approach for promoting nonsense suppression in vivo. Remarkably, we also show that pseudouridylated nonsense codons code for amino acids with similar properties. Specifically, ?AA and ?AG code for serine and threonine, whereas ?GA codes for tyrosine and phenylalanine, thus suggesting a new mode of decoding. Our results also suggest that RNA modification, as a naturally occurring mechanism, may offer a new way to expand the genetic code.
| S-EPMC3381908 | biostudies-literature
Project description:BackgroundThe well-established left hemisphere specialisation for language processing has long been claimed to be based on a low-level auditory specialization for specific acoustic features in speech, particularly regarding 'rapid temporal processing'.MethodologyA novel analysis/synthesis technique was used to construct a variety of sounds based on simple sentences which could be manipulated in spectro-temporal complexity, and whether they were intelligible or not. All sounds consisted of two noise-excited spectral prominences (based on the lower two formants in the original speech) which could be static or varying in frequency and/or amplitude independently. Dynamically varying both acoustic features based on the same sentence led to intelligible speech but when either or both acoustic features were static, the stimuli were not intelligible. Using the frequency dynamics from one sentence with the amplitude dynamics of another led to unintelligible sounds of comparable spectro-temporal complexity to the intelligible ones. Positron emission tomography (PET) was used to compare which brain regions were active when participants listened to the different sounds.ConclusionsNeural activity to spectral and amplitude modulations sufficient to support speech intelligibility (without actually being intelligible) was seen bilaterally, with a right temporal lobe dominance. A left dominant response was seen only to intelligible sounds. It thus appears that the left hemisphere specialisation for speech is based on the linguistic properties of utterances, not on particular acoustic features.
| S-EPMC3184092 | biostudies-literature
Project description:A stop or nonsense codon is an in-frame triplet within a messenger RNA that signals the termination of translation. One common feature shared among all three nonsense codons (UAA, UAG, and UGA) is a uridine present at the first codon position. It has been recently shown that the conversion of this uridine into pseudouridine (?) suppresses translation termination, both in vitro and in vivo. Furthermore, decoding of the pseudouridylated nonsense codons is accompanied by the incorporation of two specific amino acids in a nonsense codon-dependent fashion. ? differs from uridine by a single N¹H group at the C5 position; how ? suppresses termination and, more importantly, enables selective decoding is poorly understood. Here, we provide molecular rationales for how pseudouridylated stop codons are selectively decoded. Our analysis applies crystal structures of ribosomes in varying states of translation to consider weakened interaction of ? with release factor; thermodynamic and geometric considerations of the codon-anticodon base pairs to rank and to eliminate mRNA-tRNA pairs; the mechanism of fidelity check of the codon-anticodon pairing by the ribosome to evaluate noncanonical codon-anticodon base pairs and the role of water. We also consider certain tRNA modifications that interfere with the ?-coordinated water in the major groove of the codon-anticodon mini-helix. Our analysis of nonsense codons enables prediction of potential decoding properties for ?-modified sense codons, such as decoding ?UU potentially as Cys and Tyr. Our results provide molecular rationale for the remarkable dynamics of ribosome decoding and insights on possible reprogramming of the genetic code using mRNA modifications.
| S-EPMC3285925 | biostudies-literature
Project description:Expectations are high that increasing knowledge of the genetic basis of cardiovascular disease will eventually lead to personalised medicine-to preventive and therapeutic interventions that are targeted to at-risk individuals on the basis of their genetic profiles. Most cardiovascular diseases are caused by a complex interplay of many genetic variants interacting with many non-genetic risk factors such as diet, exercise, smoking and alcohol consumption. Since several years, genetic susceptibility testing for cardiovascular diseases is being offered via the internet directly to consumers. We discuss five reasons why these tests are not useful, namely: (1) the predictive ability is still limited; (2) the risk models used by the companies are based on assumptions that have not been verified; (3) the predicted risks keep changing when new variants are discovered and added to the test; (4) the tests do not consider non-genetic factors in the prediction of cardiovascular disease risk; and (5) the test results will not change recommendations of preventive interventions. Predictive genetic testing for multifactorial forms of cardiovascular disease clearly lacks benefits for the public. Prevention of disease should therefore remain focused on family history and on non-genetic risk factors as diet and physical activity that can have the strongest impact on disease risk, regardless of genetic susceptibility.
| S-EPMC3040348 | biostudies-literature
Project description:The invasion of cancer is brought about by continuous interaction of malignant cells with their surrounding tissue microenvironment. Investigating the remodeling of local extracellular matrix (ECM) by invading cells can thus provide fundamental insights into the dynamics of cancer progression. In this paper, we use an active untethered nanomechanical tool, realized as magnetically driven nanomotors, to locally probe a 3D tissue culture environment. We observed that nanomotors preferentially adhere to the cancer-proximal ECM and magnitude of the adhesive force increased with cell lines of higher metastatic ability. We experimentally confirmed that sialic acid linkage specific to cancer-secreted ECM makes it differently charged, which causes this adhesion. In an assay consisting of both cancerous and non-cancerous epithelia, that mimics the in vivo histopathological milieu of a malignant breast tumor, we find that nanomotors preferentially decorate the region around the cancer cells.
| S-EPMC7756332 | biostudies-literature
Project description:Preserving global public goods, such as the planet's ecosystem, depends on large-scale cooperation, which is difficult to achieve because the standard reciprocity mechanisms weaken in large groups. Here we demonstrate a method by which reciprocity can maintain cooperation in a large-scale public goods game (PGG). In a first experiment, participants in groups of on average 39 people play one round of a Prisoner's Dilemma (PD) with their two nearest neighbours on a cyclic network after each PGG round. We observe that people engage in "local-to-global" reciprocity, leveraging local interactions to enforce global cooperation: Participants reduce PD cooperation with neighbours who contribute little in the PGG. In response, low PGG contributors increase their contributions if both neighbours defect in the PD. In a control condition, participants do not know their neighbours' PGG contribution and thus cannot link play in the PD to the PGG. In the control we observe a sharp decline of cooperation in the PGG, while in the treatment condition global cooperation is maintained. In a second experiment, we demonstrate the scalability of this effect: in a 1,000-person PGG, participants in the treatment condition successfully sustain public contributions. Our findings suggest that this simple "local-to-global" intervention facilitates large-scale cooperation.
| S-EPMC5093714 | biostudies-literature
Project description:Surveillance and isolation for the prevention of methicillin-resistant Staphylococcus aureus (MRSA) has become a controversial topic, one that causes heated debate and appears to be surrounded by both politics and industrial conflicts-of-interest. There have been calls from numerous authors for a movement away from rigid mandates and toward an evidence-based medicine approach. However, much of the evidence can be viewed with an entirely different interpretation. Two major studies with negative findings have had an adverse impact on recommendations regarding active detection and isolation (ADI) for MRSA. However the negative findings in these studies can be explained by shortcomings in study implementation rather than the ineffectiveness of ADI. The use of daily chlorhexidine bathing has also been proposed as an alternative to ADI in ICU settings. There are shortcomings regarding the evidence in the literature concerning the effectiveness of daily chlorhexidine bathing. One of the major concerns with universal daily chlorhexidine bathing is the development of bacterial resistance. The use of surveillance and isolation to address epidemics and common dangerous pathogens should solely depend upon surveillance and isolation's ability to prevent further spread to and infection of other patients through indirect contact. At present, there is a preponderance of evidence in the literature to support continuing use of surveillance and isolation to prevent the spread of MRSA.
| S-EPMC4345038 | biostudies-other
Project description:Here, we report on the surface conductivity of WSe2 and Mo xW1- xSe2 (0 ? x ? 1) crystals investigated with conductive atomic force microscopy. We found that stacking faults, defects, and chemical heterogeneities form distinct two-dimensional and one-dimensional conduction paths on the transition metal dichalcogenide surface. In the case of WSe2, in addition to step edges, we find a significant amount of stacking faults (formed during the cleaving process) that strongly influence the surface conductivity. These regions are attributed to the alternation of the 2H and 3R polytypism. The stacking faults form regular 2D patterns by alternation of the underlying stacking order, with a periodicity that varies significantly between different regions and samples. In the case of Mo xW1- xSe2, its conductivity has a localized nature, which depends on the underlying chemical composition and the Mo/W ratio. Segregation to W-rich and Mo-rich regions during the growth process leads to nonuniform conduction paths on the surface of the alloy. We found a gradual change of the conductivity moving from one region to the other, reminiscent of lateral band bending. Our results demonstrate the use of C-AFM as a nanoscopic tool to probe the electrical properties of largely inhomogeneous samples and show the complicated nature of the surface conductivity of TMDC alloys.
| S-EPMC5909175 | biostudies-literature
Project description:High-entropy alloys (HEAs) are an intriguing new class of metallic materials due to their unique mechanical behavior. Achieving a detailed understanding of structure-property relationships in these materials has been challenged by the compositional disorder that underlies their unique mechanical behavior. Accordingly, in this work, we employ first-principles calculations to investigate the nature of local chemical order and establish its relationship to the intrinsic and extrinsic stacking fault energy (SFE) in CrCoNi medium-entropy solid-solution alloys, whose combination of strength, ductility, and toughness properties approaches the best on record. We find that the average intrinsic and extrinsic SFE are both highly tunable, with values ranging from -43 to 30 mJ?m-2 and from -28 to 66 mJ?m-2, respectively, as the degree of local chemical order increases. The state of local ordering also strongly correlates with the energy difference between the face-centered cubic (fcc) and hexagonal close-packed (hcp) phases, which affects the occurrence of transformation-induced plasticity. This theoretical study demonstrates that chemical short-range order is thermodynamically favored in HEAs and can be tuned to affect the mechanical behavior of these alloys. It thus addresses the pressing need to establish robust processing-structure-property relationships to guide the science-based design of new HEAs with targeted mechanical behavior.
| S-EPMC6130406 | biostudies-literature
Project description:BackgroundThe balance of the benefits and risks of long term use of hormone replacement therapy (HRT) have been a matter of debate for decades. In Europe, HRT requires medical prescription and its advertising is only permitted when aimed at health professionals (direct to consumer advertising is allowed in some non European countries). The objective of this study is to analyse the appropriateness and quality of Internet advertising about HRT in Spain.MethodsA search was carried out on the Internet (January 2009) using the eight best-selling HRT drugs in Spain. The brand name of each drug was entered into Google's search engine. The web sites appearing on the first page of results and the corresponding companies were analysed using the European Code of Good Practice as the reference point.ResultsFive corporate web pages: none of them included bibliographic references or measures to ensure that the advertising was only accessible by health professionals. Regarding non-corporate web pages (n = 27): 41% did not include the company name or address, 44% made no distinction between patient and health professional information, 7% contained bibliographic references, 26% provided unspecific information for the use of HRT for osteoporosis and 19% included menstrual cycle regulation or boosting feminity as an indication. Two online pharmacies sold HRT drugs which could be bought online in Spain, did not include the name or contact details of the registered company, nor did they stipulate the need for a medical prescription or differentiate between patient and health professional information.ConclusionsEven though pharmaceutical companies have committed themselves to compliance with codes of good practice, deficiencies were observed regarding the identification, information and promotion of HRT medications on their web pages. Unaffected by legislation, non-corporate web pages are an ideal place for indirect HRT advertising, but they often contain misleading information. HRT can be bought online from Spain, without a medical consultation or prescription constituting a serious issue for public health. In our information society, it is the right and obligation of public health bodies to ensure that such information is not misleading.
| S-EPMC2850342 | biostudies-literature