Sense in antisense?

A correspondence between open reading frames in sense and antisense strands is expected from the hypothesis that the prototypic triplet code was of general form RNY, where R is a purine base, N is any base, and Y is a pyrimidine. A deficit of stop codons in the antisense strand (and thus long open reading frames) is predicted for organisms with high G + C percentages; however, two bacteria (Azotobacter vinelandii, Rhodobacter capsulatum) have larger average antisense strand open reading frames than predicted from (G + C)%. The similar Codon frequencies found in sense and antisense strands can be attributed to the wide distribution of inverted repeats (stem-loop potential) in natural DNA sequences.     

On Primordial Sense–Antisense Coding

The genetic code is implemented by aminoacyl-tRNA synthetases (aaRS). These 20 enzymes are divided into two classes that, despite performing same functions, have nothing common in structure. The mystery of this striking partition of aaRSs might have been concealed in their sterically complementary modes of tRNA recognition that, as we have found recently, protect the tRNAs with complementary anticodons from confusion in translation. This finding implies that, in the beginning, life increased its coding repertoire by the pairs of complementary codons (rather than one-by-one) and used both complementary strands of genes as templates for translation. The class I and class II aaRSs may represent one of the most important examples of such primordial sense–antisense (SAS) coding (Rodin and Ohno, Orig Life Evol Biosph 25:565–589, 1995). In this report, we address the issue of SAS coding in a wider scope. We suggest a variety of advantages that such coding would have had in exploring a wider sequence space before translation became highly specific. In particular, we confirm that in Achlya klebsiana a single gene might have originally coded for an HSP70 chaperonin (class II aaRS homolog) and an NAD-specific GDH-like enzyme (class I aaRS homolog) via its sense and antisense strands. Thus, in contrast to the conclusions in Williams et al. (Mol Biol Evol 26:445–450, 2009), this could indeed be a “Rosetta stone” gene (Carter and Duax, Mol Cell 10:705–708, 2002) (eroded somewhat, though) for the SAS origin of the two aaRS classes.     

How Do Neurons Sense a Spike Burst?

In this issue of Neuron, Xu et al. (2012) show that knock down of Syt1, a major Ca(2+) sensor, impairs synaptic transmission similarly in different brain regions but with unexpected, region-specific behavioral outcomes.     

Why and How Do Plant Cells Sense Sugars?

The ability to sense sugars is crucial for the modulation ofgene expression in plants. Despite the importance of this phenomenon,our knowledge of sugar sensing in plants is scant. Several valuablehypotheses have been put forward based on the extensive knowledgeof sugar sensing in yeast. In recent years, tests of these hypotheseshave shown that hexokinase and sucrose-non-fermenting- (SNF-)related proteins appear to be involved in sugar sensing andtransduction, not only in yeast but also in higher plants. However,even if plants share with yeast some elements involved in sugarsensing, several aspects of sugar perception are likely to bepeculiar to higher plants. Plants should be able to sense notonly glucose but also other hexoses, such as fructose and disaccharides(sucrose, maltose and others). In this Botanical Briefing weoutline recent discoveries in this field, with emphasis on arabidopsisand cereals. The use of transgenic plants and mutants to identifysugar sensor(s) and elements in the signalling pathways andtheir cross-talk with the hormonal signalling is discussed.Copyright2001 Annals of Botany Company Abscisic acid, Arabidopsis thaliana, cereals, hexokinase, sugar sensing     

Animal Cognition: An Insect's Sense of Time?

For Immanuel Kant, time was the very form of the inner sense, the bedrock of our consciousness and also the origin of arithmetic ability. New research on bumblebees has shown that even an invertebrate with a brain the size of a pinhead can actively sense the passage of elapsed time, allowing it to predict when certain salient events will occur in the future.     

How Do Stomata Sense Reductions in Atmospheric Relative Humidity？

Dear Editor, It has been known since the work of Francis Darwin that, in response to a reduction in atmospheric relative humidity （rh）, stomatal aperture decreases. Screening for Arabidopsis mutants compromised in stomatal responses to reduced rh resulted in the identification of two genes, OST1 and ABA2, that are involved in stomatal response to low rh conditions. Interestingly both encode proteins previously known to be involved in ABA signaling （Xie et al., 2006, and references therein）. These findings strongly suggested that, at least in part, the stomatal response to low rh is mediated by ABA and the intracellular ABA signaling pathway. Our most recent data show that low rh-induced stomatal closure can pro- ceed by guard cell autonomous ABA synthesis （Bauer et al., 2013）,     

Does Combination T4 And T3 Therapy Make Sense?

ObjectiveTo evaluate the existing evidence regarding the combined use of levothyroxine and liothyronine to treat hypothyroidism.MethodsEleven published randomized controlled trials evaluating the efficacy and safety of combined levo- thyroxine and liothyronine therapy for hypothyroidism were reviewed and summarized. Related basic and clinical research findings were also incorporated for perspective.ResultsAn initial randomized controlled trial reported symptomatic improvement in hypothyroid patients taking combined levothyroxine and liothyronine therapy compared with those taking levothyroxine therapy alone. Subsequently, multiple relatively small randomized controlled trials failed to demonstrate any subjective or objective benefit from combined levothyroxine and liothy- ronine therapy. A polymorphism (Thr92Ala) in the gene encoding the deiodinase 2 (D2) enzyme that converts thy- roxine to triiodothyronine in the brain was later identified in about 16% of hypothyroid persons. This polymorphism may impair brain deiodinase activity in the presence of low brain thyroxine levels. One randomized controlled trial found that patients with the D2 Thr92Ala polymorphism had more baseline symptoms than those with the wild type D2 and experienced significantly greater symptomatic improvement in response to combined levothyroxine and liothyronine therapy.ConclusionsMost hypothyroid patients experience rapid symptomatic relief after institution of levothyroxine replacement therapy, but persistent symptoms remain in some despite what appears to be adequate levothyroxine therapy with normalization of the serum thyrotropin level. A thorough investigation is warranted in these patients to detect and treat other responsible lifestyle issues, medical conditions, and endocrine conditions. A subset of hypo- thyroid patients has a polymorphism in the gene encoding the D2 enzyme that may prevent full resolution of symp- toms with levothyroxine therapy alone; these patients may benefit from combination levothyroxine and liothyronine therapy. (Endocr Pract. 2012;18:750-757)     

Response to commentaries on “The Transmission Sense of Information”

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a shallow notion of correlation, the so-called “causal sense” of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a “semantic sense,” whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence.     

Impaired Sense of Smell in a Drosophila Parkinson’s Model

Parkinson’s disease (PD) is one of the most common neurodegenerative disease characterized by the clinical triad: tremor, akinesia and rigidity. Several studies have suggested that PD patients show disturbances in olfaction at the earliest onset of the disease. The fruit fly Drosophila melanogaster is becoming a powerful model organism to study neurodegenerative diseases. We sought to use this system to explore olfactory dysfunction, if any, in PINK1 mutants, which is a model for PD. PINK1 mutants display many important diagnostic symptoms of the disease such as akinetic motor behavior. In the present study, we describe for the first time, to the best of our knowledge, neurophysiological and neuroanatomical results concerning the olfactory function in PINK1 mutant flies. Electroantennograms were recorded in response to synthetic and natural volatiles (essential oils) from groups of PINK1 mutant adults at three different time points in their life cycle: one from 3–5 day-old flies, from 15–20 and from 27–30 days. The results obtained were compared with the same age-groups of wild type flies. We found that mutant adults showed a decrease in the olfactory response to 1-hexanol, α-pinene and essential oil volatiles. This olfactory response in mutant adults decreased even more as the flies aged. Immunohistological analysis of the antennal lobes in these mutants revealed structural abnormalities, especially in the expression of Bruchpilot protein, a marker for synaptic active zones. The combination of electrophysiological and morphological results suggests that the altered synaptic organization may be due to a neurodegenerative process. Our results indicate that this model can be used as a tool for understanding PD pathogensis and pathophysiology. These results help to explore the potential of using olfaction as a means of monitoring PD progression and developing new treatments.     

The Path to Enlightenment： Making Sense of Genomic and Proteomic Information

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.     

Does It Make Sense to Restore Wildland Fire in Changing Climate?

Forest restoration guided by historical reference conditions of fire regime, forest structure, and composition has been increasingly and successfully applied in fire‐adapted forests of western North America. But because climate change is expected to alter vegetation distributions and foster severe disturbances, does it make sense to restore the ecological role of wildland fire through management burning and related activities such as tree thinning? I suggest that some site‐ and date‐specific historical conditions may be less relevant, but reference conditions in the broad sense are still useful. Reference conditions encompass not only the recent past but also evolutionary history, reflecting the role of fire as a selective force over millennia. Taking a long‐term functional view of historical reference conditions as the result of evolutionary processes can provide insights into past forest adaptations and migrations under various climates. As future climates change, historical reference data from lower, southerly, and drier sites may be useful in places that are higher, northerly, and currently wetter. Almost all models suggest that the future will have substantial increases in wildfire occurrence, but prior to recent human‐caused fire exclusion, fire‐adapted pine forests of western North America were among the most frequently burned in the world. Restoration of patterns of burning and fuels/forest structure that reasonably emulate historical conditions prior to fire exclusion is consistent with reducing the susceptibility of these ecosystems to catastrophic loss. Priorities may include fire and thinning treatments of upper elevation ecotones to facilitate forest migration, whereas vulnerable low‐elevation forests may merit less management investment.     

The mechanobiology of NK cells- ‘Forcing NK to Sense’ target cells

Natural killer (NK) cells are innate immune lymphocytes that recognize and kill cancer and infected cells, which makes them unique ‘off-the-shelf’ candidates for a new generation of immunotherapies. Biomechanical forces in homeostasis and pathophysiology accrue additional immune regulation for NK immune responses. Indeed, cellular and tissue biomechanics impact NK receptor clustering, cytoskeleton remodeling, NK transmigration through endothelial cells, nuclear mechanics, and even NK-dendritic cell interaction, offering a plethora of unexplored yet important dynamic regulation for NK immunotherapy. Such events are made more complex by the heterogeneity of human NK cells. A significant question remains on whether and how biochemical and biomechanical cues collaborate for NK cell mechanotransduction, a process whereby mechanical force is sensed, transduced, and translated to downstream mechanical and biochemical signalling. Herein, we review recent advances in understanding how NK cells perceive and mechanotransduce biophysical cues. We focus on how the cellular cytoskeleton crosstalk regulates NK cell function while bearing in mind the heterogeneity of NK cells, the direct and indirect mechanical cues for NK anti-tumor activity, and finally, engineering advances that are of translational relevance to NK cell biology at the systems level.     

Functional MRI To Evaluate “Sense of Self” following Perforator Flap Breast Reconstruction

Background

Breast reconstruction is associated with high levels of patient satisfaction. Previous patient satisfaction studies have been subjective. This study utilizes functional magnetic resonance imaging (fMRI) to objectively evaluate “sense of self” following deep inferior epigastric perforator (DIEP) flap breast reconstruction in an attempt to better understand patient perception.

Methods

Prospective fMRI analysis was performed on four patients before and after delayed unilateral DIEP flap breast reconstruction, and on four patients after immediate unilateral DIEP flap breast reconstruction. Patients were randomly cued to palpate their natural breast, mastectomy site or breast reconstruction, and external silicone models. Three regions of interest (ROIs) associated with self-recognition were examined using a general linear model, and compared using a fixed effects and random effects ANOVA, respectively.

Results

In the delayed reconstruction group, activation of the ROIs was significantly lower at the mastectomy site compared to the natural breast (p<0.01). Ten months following reconstruction, activation of the ROIs in the reconstructed breast was not significantly different from that observed with natural breast palpation. In the immediate reconstruction group, palpation of the reconstructed breast was also similar to the natural breast. This activity was greater than that observed during palpation of external artificial models (p<0.01).

Conclusions

Similar activation patterns were observed during palpation of the reconstructed and natural breasts as compared to the non-reconstructed mastectomy site and artificial models. The cognitive process represented by this pattern may be a mechanism by which breast reconstruction improves self-perception, and thus patient satisfaction following mastectomy.     

The Best of Both Worlds——Building Gardens With a Sense of Place

The last decade in China has been a period of great growth and renewal. More and more public garden has been built, many those gardens are built with Western-influenced styles and lack of Chinese factor. A garden with a strong sense of place will clearly put the visitor in a specific locality by astute use of design to support a distinctive regional character. Here the author gives several examples of famous gardens about how to keep the sense of place and try to give some useful suggestion on Chinese garden build.     

The Best of Both Worlds——Building Gardens With a Sense of Place

The last decade in China has been a period of great growth and renewal. More and more public garden has been built, many those gardens are built with Western-influenced styles and lack of Chinese factor. A garden with a strong sense of place will clearly put the visitor in a specific locality by astute use of design to support a distinctive regional character. Here the author gives several examples of famous gardens about how to keep the sense of place and try to give some useful suggestion on Chinese garden build.     

Cdc42p,GTP Hydrolysis and the Cell’s Sense of Direction

The GTPase Cdc42p is essential for polarity establishment in animals and fungi.1 Human Cdc42p can functionally replace yeast Cdc42p,2 indicating a high degree of evolutionary conservation. Current models of Cdc42p action generally follow the signaling paradigm established for Ras, in which receptors responding to an initiating stimulus cause guanine nucleotide exchange factors (GEFs) to trigger GTP-loading of Ras, leading to engagement of downstream effectors and ensuing cell proliferation. Key support for the Ras paradigm came from the finding that oncogenic forms of Ras, unable to hydrolyze GTP and therefore constitutively GTP-bound, mimicked the effect of constitutive signaling by the upstream receptors even in the absence of stimuli. Attempts to assess whether or not this paradigm is valid for Cdc42p-induced polarization of yeast cells have yielded conflicting results.3-6 Here, we discuss the available information on this issue and conclude that unlike Ras signaling, Cdc42p directed polarity establishment additionally requires cycling between GTP- and GDP-bound forms. We suggest that such cycling is critical for a little-studied “function” of Cdc42p: its ability to designate a unique portion of the cell cortex to become the polarization site, and to become concentrated at that site.     

Do Implicit and Explicit Measures of the Sense of Agency Measure the Same Thing?

The sense of agency (SoA) refers to perceived causality of the self, i.e. the feeling of causing something to happen. The SoA has been probed using a variety of explicit and implicit measures. Explicit measures include rating scales and questionnaires. Implicit measures, which include sensory attenuation and temporal binding, use perceptual differences between self- and externally generated stimuli as measures of the SoA. In the present study, we investigated whether the different measures tap into the same self-attribution processes by determining whether individual differences on implicit and explicit measures of SoA are correlated. Participants performed tasks in which they triggered tones via key presses (operant condition) or passively listened to tones triggered by a computer (observational condition). We replicated previously reported effects of sensory attenuation and temporal binding. Surprisingly the two implicit measures of SoA were not significantly correlated with each other, nor did they correlate with the explicit measures of SoA. Our results suggest that some explicit and implicit measures of the SoA may tap into different processes.     

Do Cells Sense Stress or Strain? Measurement of Cellular Orientation Can Provide a Clue

We predict theoretically the steady-state orientation of cells subject to dynamical stresses that vary more quickly than the cell relaxation time. We show that the orientation is a strong function of the Poisson's ratio, ν, of the matrix when cell activity is governed by the matrix strain; if cell activity is governed by the matrix stress, the orientation depends only weakly on ν. These results can be used to differentiate systems in which the strain or the stress determine the setpoint for the mechanosensitivity of cells.     

Seeing,Hearing and Speaking: Morality and Sense among the Panará in Central Brazil

Based on the ethnographic example of the Panará, a Gê-group in central Brazil, this paper examines the significance of vision and visibility. For Gê-speaking groups it has been suggested that while hearing and speaking are socially privileged faculties, contributing to the mature status of an individual, seeing has been considered to be an anti-social faculty and is largely associated with the exercise of negative mystical power. While not wishing to deny the appropriateness of this association, I argue that seeing and being seen, as well as the particular visual qualities of phenomena play an important role in an Amazonian lived world.     

A Sense of Belonging and Exclusion: ‘Touchability’ and ‘Untouchability’ in Tamil Nadu

In India, touch is a prime marker of status and social relations. Those who are impure are ‘untouchable’,1 The terms ‘Untouchable’ and ‘Untouchability’ have been abandoned due to the humiliating meaning these terms confer, therefore I use them in inverted commas. The politically correct and common terms today are Scheduled Castes, in short sc, or Dalits, or sometimes Harijan. I use them here synonymously. but those who are of a relatively higher purity are also, depending on the context, either ‘untouchable’ or ‘touchable’ only under certain fixed rules. In this paper, I will explore the contexts in which body contact and touch can be part of personal relations. I describe how these body contacts signify important social relations and establish community identity. Further, I will analyse how patterns of body contact on the one hand change during childhood, and on the other hand produce changes in the status of a social persona. The last point to be investigated is the meaning of touch as a sign for public representations.