Beta Elements Research Articles

Reassessing the exon–foldon correspondence using frustration analysis

Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across a set of 38 abundant and conserved protein families. Taking advantage of genomic exon-intron organization and extensive protein sequence data, we explore exon boundary conservation and assess the foldon-like behavior of exons using energy landscape theoretic measurements. We found deviations in the exon size distribution from exponential decay indicating selection in evolution. We show that when taken together there is a pronounced tendency to independent foldability for segments corresponding to the more conserved exons, supporting the idea of exon-foldon correspondence. While 45% of the families follow this general trend when analyzed individually, there are some families for which other stronger functional determinants, such as preserving frustrated active sites, may be acting. We further develop a systematic partitioning of protein domains using exon boundary hotspots, showing that minimal common exons correspond with uninterrupted alpha and/or beta elements for the majority of the families but not for all of them.

Radiolysis of myoglobin concentrated gels by protons: specific changes in secondary structure and production of carbon monoxide

While particle therapy has been used for decades for cancer treatment, there is still a lack of information on the molecular mechanisms of biomolecules radiolysis by accelerated ions. Here, we examine the effects of accelerated protons on highly concentrated native myoglobin, by means of Fourier transform infrared and UV–Visible spectroscopies. Upon irradiation, the secondary structure of the protein is drastically modified, from mostly alpha helices conformation to mostly beta elements at highest fluence. These changes are accompanied by significant production of carbon monoxide, which was shown to come from heme degradation under irradiation. The radiolytic yields of formation of denatured protein, carbon monoxide, and of heme degradation were determined, and found very close to each other: G+denatured Mb ≈ G+CO ≈ G-heme = 1.6 × 10–8 ± 0.1 × 10–8 mol/J = 0.16 ± 0.01 species/100 eV. The denaturation of the protein to a beta structure and the production of carbon monoxide under ion irradiation are phenomena that may play an important role in the biological effects of ionizing radiation.

Isolation, Identification and Determination of Effective Substances of Three plants, Yarrow, False Chamomile and Fennel

This research was conducted in order to determine the amount of effective substances of yarrow, false chamomile and fennel in Hamadan region. First, the alcoholic extract of the three above-mentioned plants was obtained by maceration method. In this way, the body of the desired plant is dried and crushed and immersed in 70% alcohol and left in the same state for 14 days, and then the mixture is filtered and the dried extract was weighed and the ratio of the weight of the liquid extract to the weight of the dry plant was obtained. Also, the numerical amount of total ash and ash insoluble in acid was determined to determine the amount of solutes. Also, the amount of protein, calcium and phosphorus was obtained in three plants. By performing TLC chromatography (paper method), the type of active substances in three plants was determined and the pH of each of the manufactured products was also determined, and the results are as follows: The amount of insoluble ash in fennel acid was 1.6%, yarrow 2.8% and false chamomile 6.8%, and the amount of total ash was 12.9%, 13.7% and 7.4%, respectively. The percentage of calcium and phosphorus in fennel is 0.4% and 0.13%, in yarrow 0.98% and 0.5%, and in false chamomile is 0.74% and 0.39%. The amount of protein in fennel was 4.8%, in yarrow 24.5% and in false chamomile 19.2%. The pH of the products was as follows: the product prepared from fennel is 85/6, yarrow 80/4 and false chamomile 80/5. The results of paper chromatography of three plant samples are as follows: In fennel, in the vicinity of solvent 1 (Rf = 0.6 and 0.51), which is related to antole, and in the vicinity of solvent 2 (Rf = 0.84 and 0.76), which is related to fanchon. In yarrow plant, Rf = 0.86 is related to betapinene, Rf = 0.72 is related to sineon, and finally Rf = 0.1 is related to Borneon's special substance. In the false chamomile plant, Rf = 0.21 is related to gamma element, Rf = 0.30 to beta element, and Rf = 0.39 to the effective substance transmatricaria ester. By performing these steps and comparing the results obtained from previous researches on these plants, a step was taken towards the realization of the aforementioned goals, which is to determine the amount and type of effective substances of these three plants in Hamadan region.

Some thoughts on thinking space and linking in couple analytic therapy

In this article, I discuss the significant clinical meaning of the thinking space and its elements in the service of understanding the patient and the couple, and establishing a deep human link, based on Bion's containment theory and his idea on Transformation in O, or T (O). I also try to apply it to discuss the thinking space related to the couple state of mind in couple analytic therapy. It is crucial for the analyst to keep an open mind with a space for reverie, to receive and identify with beta elements, and transform them both in psychoanalysis and in couple analytic therapy.

Gamma elements as protomental representations: Suggestions for expanding W. R. Bion’s theory of elements

ABSTRACT W. R. Bion developed various models and theories to describe the formation of mental representations. This article introduces an expansion of the model of alpha and beta elements by a new category, termed “gamma elements”. Despite being transformable, gamma elements are characterized by an excessive feeling of reality, such that the subject must evacuate them. We are dealing here with visions, pseudohallucinations, scenarios in nightmares that are as terrible as they are sensorily charged, flashbacks, or overwhelming physical feelings interspersed with hypochondriacal anxieties. Using the “theory of maternal semiotics” (Kristeva), the author traces how the child’s projectiles, i.e. beta experiences projected into the maternal container, are transformed into alpha and gamma elements. In this respect, gamma elements are more or less precise indicators of the analytic process: they indicate the extent to which the analysand is capable of enduring and transforming frustrating experiences in the here-and-now. The expansion of Bion’s model of elements, therefore, has direct clinical relevance, in that gamma elements can be understood both as imaginative creations and as indications of disorganizing processes.

Dreaming About You as We Speak: Waking Dreams and Their Significance in Clinical Work

“Waking dreams,” a particular form of reverie, was first identified by neo-Bionians. They contend that our mind processes raw stimuli by associating the sensory impressions (beta elements) with mental images, thereby creating so-called alpha elements (i.e., pictograms). The images then form an ongoing dream-flow outside of awareness, continually producing a personal, preconscious understanding of what is taking place in and around us. Pictograms are our first, rudimentary interpretations; they serve as the first step toward verbalizing our affective experiences. Waking dreams are (composites of) pictograms that unexpectedly emerge into consciousness during session. Waking dreams shift our focus from content to process in session; they provide a new understanding of the transference-countertransference dynamic of the clinical moment; they alter the affect in the room; and open the door to new experience and new interpretation. We will demonstrate the clinical significance of waking dreams by an in-depth discussion of a relevant case.

Performance characteristics of a tungsten collimator and UVTRON flame sensor in the detection of alpha-induced radioluminescence

It has been established that the UVTRON flame sensor (Hamamatsu) can detect alpha-induced radioluminescence, but that the presence of gamma and beta radiation both interfere with this detection. A UVTRON was placed inside a tungsten collimator and exposed to a range of radioisotopes, 210Po, 241Am, 137Cs, 90Sr and 60Co, to investigate the effect of shielding the UVTRON. The collimator is a cylinder with a hole in the curved wall to allow light and particles to access the interior, without providing a direct shine path to the UVTRON sensor. Ultraviolet C (wavelength 180–280 nm) radioluminescence is reflected onto the UVTRON sensor using a UVC reflecting mirror. It was found that the collimator does not affect the low background count of the UVTRON, but that it does greatly reduce the UVC signal reaching the UVTRON from an alpha source. For example, the collimator reduced the signal by 94% at 60 mm, and 78% at 120 mm, where the signals were still far greater than the background (88 and 84 times background respectively). Beta particles entering the collimator, although not directly impacting on the UVTRON, do increase the count, likely due to bremsstrahlung radiation. The collimator attenuates gamma radiation dependent on the gamma energy, but as expected, does not block it. When using more than one source, the count is cumulative and therefore it may be possible to determine the presence of UVC radioluminescence through subtraction of the gamma and beta element of the signal. The results and findings of the experiments carried out are presented herewithin.

A note on the products $\alpha_1\beta_2\gamma_t$ and $\beta_1^{r+1}\beta_2\gamma_t$ in the stable homotopy of spheres

In the stable homotopy groups of spheres, we have Greek letter elements due to J. F. Adams [2], L. Smith [12] and H. Toda [13]. Here we study the nontriviality of certain products of the first alpha element, the first and the second beta elements and a gamma element in the homotopy groups.

Inconscient digital, excitation des limites, écran bêta

ContextThe psychological and environmental effects of digital culture are increasingly challenging contemporary researchers and thinkers confronted with an unprecedented context. The analyses necessarily involve several layers of disciplinary understanding. One of the main characteristics that emerges from the work at our disposal is the paradox of the effects: we are in the presence of objects that are both creative and destructive. In the psychoanalytical approach, to this day, there is no consideration of the bidirectionality of effects: what the subject implements in the digital realm and, above all, what the latter produces in the subject's unconscious. ObjectivesThis work, which opens the “Digital Subject” debate proposed by the journal In Analysis, attempts to isolate the effects produced by digital hyper-stimulation in the normal subject in order to identify a series of unconscious particularities; it also aims to demonstrate the interest of the psychoanalytical conceptual framework in understanding the side effects of digital life. In this context, we will first describe the phenomenon of ordinary addiction and its relationship with the concept of trauma. This will lead us to decipher the redesign of the psychic limits through (perverse) excitation, pollution, and data extraction that goes beyond the classical logic of psychic functioning. The last theoretical point to be clarified concerns the beta screen (Bion) and its modifications when confronted with sensory agglomerations. MethodThis theoretical research explores a series of works mainly through psychoanalysis, sociology, psychosociology, and epidemiology, which allows for the understanding of the psychoanalytical concept of limit and the reworking that it seems to undergo in the digital age. Other inseparable concepts are defined and questioned: trauma, perversion, and the beta screen. ResultsOur theoretical and experimental data suggest the presence of a set of digital side effects that touch the psychic limits: the trend towards ordinary addiction, the increase in depression and anxiety around the world, the increase in screen time, etc. From a psychoanalytical perspective, the data suggest: the weakening of limits in the case of traumatic or even perverse excitation; the tendency towards regression and narcissistic withdrawal; the failure of transitionality; the tendency to build a beta screen (weakening of the contact barrier dividing the conscious and the unconscious) due to sensory agglomerations similar to the beta elements (in the Bionic sense); the blurring of psychic screens and hallucinatory doses. According to a psychosociological approach, we see the emphasis on a perverse individual-digital relationship, voluntarily structured by companies aiming at unlimited consumption and the economic exploitation of data. ConclusionThe observed effects, discussed here in an analogy with the environmental crisis, could be integrated into clinical and research work at the intersection of the psychoanalytical approach and other disciplines, allowing for a better understanding of digital complexity. We also propose a postmodern engagement of psychoanalytical reflections that integrates the plurality of powers and factors at play in the digital age.

La rêverie in Psicoanalisi e la teoria del Sé in Gestalt: un lavoro di integrazione attraverso lo studio delle esperienze immaginative in psicoterapia.

The imaginative world, asemerges from the relationaldynamic, appears to be the connectingelementbetweenthoughts and emotions, and constitutes a factor of greatcommunicativeefficacy. Bion’s work on the concept of reverie, on the alphafunctionanalysis and on the role of beta elements, shows common standpoints with the Theory of the Self developed by Pearls. This work intends to bringintosharper focus the role of the Imaginationasunconsciouscommunicationinstrument, by trying to classify the imaginativeexperiences with which the therapistisconfrontedthroughout the course of the relationship with the patient. A Type 1 image and a Type 2 image will be identified: the formerorigins from the therapist’sregister of memory, the latterresults from an originalconstruction. Two differente ways will be described, throughwhich the therapistsmindsatisfiesitsownneed of imaginingwhatcomes from the experiencetold by the patient. Thesetwodifferentrepresentationswill be treated from threedifferentpoints of view: Bion’spsychoanalytic work, Gestalt’spsychotherapy and Pearl’s work. By puttingtogetherdifferentmodels of the countertransferencefunction, this work makes an attempt to describehowbothapproachesaddressthisspecificfunction of the mind, evenifthroughdifferentlanguages. The work emphasisesneverthelesshow the Imagination can be used in the clinicalpracticeas a connectinginstrumentbetween the twoactors of the therapeuticalrelationship.

A Chrnb3-Cre BAC transgenic mouse line for manipulation of gene expression in retinal ganglion cells.

The mechanisms by which retinal ganglion cells (RGCs) make specific connections during development is an intense area of research and have served as a model for understanding the general principles of circuit wiring. As such, genetic tools allowing for specific recombination in RGCs are critical to further our understanding of the cell-specific roles of different genes during these processes. However, many RGC-specific Cre lines have drawbacks, due to their broad expression in other cell types and/or retinorecipient regions or lack of expression in broad swaths of the retina. Here, we characterize a Cre BAC transgenic line driven by elements of the cholinergic receptor nicotinic beta 3 subunit (Chrnb3). We show that Cre expression is restricted to RGCs in the retina and sparsely expressed in the brain, importantly excluding retinorecipient regions. Furthermore, Chrnb3-Cre mice label a wide variety of RGCs distributed throughout the retina and Cre activity is detected embryonically, shortly following RGC differentiation. Finally, we find that Chrnb3-Cre-labeled RGCs innervate multiple retinorecipient areas that serve both image-forming and nonimage forming functions. Thus, this genetic tool will be of broad use to investigators studying the RGC-specific contributions of genes to visual circuit development.

Forkhead box O3 promotes cell proliferation and inhibits myotube differentiation in chicken myoblast cells

ABSTRACT1. In the poultry industry, growth performance is important due to its effects on economic value. Much effort has been put forth to achieve introgression of specific genes and DNA markers related to muscle proliferation and differentiation in selective breeding approaches.2. This study investigated the biological functions of the gene Forkhead box O3 (FOXO3) during myogenic differentiation in chicken myoblast cells. FOXO3 was downregulated in primary chicken myoblast (pCM) cells by the piggyBac transposon-mediated microRNA (miRNA) knock-down (KD) system.3. The pCM cells that were stably integrated into the FOXO3 KD expression vector showed significant downregulation of FOXO3 protein and mRNA levels. Expression levels of paired box protein Pax7 (Pax7) and target genes such as CCAAT/enhancer binding protein beta and serum response element decreased in FOXO3 KD pCM cells. In addition, in the undifferentiated myoblast stage, there were no significant differences in cell morphology; however, proliferation rate in FOXO3 KD pCM cells was significantly lower during d 4 and 5 of in vitro culture. By contrast, when myotube differentiation was induced, FOXO3 KD pCM cells exhibited rapid initiation of myotube formation, higher expression of myogenin and desmin as myogenic indicators and a further differentiated phenotype than observed in regular pCM cells.4. These results demonstrated that FOXO3 promotes cell proliferation and inhibits myotube differentiation in chicken myoblast cells. Therefore, the regulation of FOXO3 could be applied to improve muscle differentiation in commercial poultry.

I'm All Ears—Thoughts on Psychoanalysis: The Musical Reverie

In this article I describe one dimension of the reverie phenomenon, which I term the “musical reverie,” whereby the therapist experiences a kind of daydreaming that includes songs with both lyrics and tunes. In early development, the reverie function permits a transformation of the baby's unprocessed and unmetabolized materials within the mother's psyche, so that once they are returned to the infant, it will be possible to contain them in a manner that neither overwhelms nor fragments the child. Likewise, this may operate in psychoanalytic treatment. This article suggests that the auditory dimension, where lyrics and tunes exist successfully, captures both the symbolic and the presymbolic, and bridges the two. I further suggest that the music serves the analyst in early, hopeless, and fragmented moments as a companion to reignite the psychic movement that has halted in both the patient's and the analyst's mind. The therapist's ability to process beta elements—the unmetabolized (unprocessed affective experience)—into alpha elements (thoughts that can be thought by the thinker) will enable the renewed movement and rehabilitation of the mind, even in barren, dead areas.

Assessment of gross alpha and beta activity levels and element concentrations in spa waters from Siirt and Şırnak, Turkey

Gross α and β activity contents and element concentrations in well-known spa waters from the Siirt and the Şirnak cities were determined and assessed by MPC-9604 multi-detector α/β counting system and by wavelength dispersive X-ray fluorescence spectrometry. The 0.05–5.64 gross α and 0.06–2.76 Bq L−1 gross β activity levels and element concentrations found in samples were compared with recommended values given by the World Health Organization, the US Environmental Protection Agency, Turkish Standards and literature results. Principal component and cluster analysis were also used to classify the spa waters due to element concentrations and three principal components calculated were about 91 % of the total variance in the data.

The Child Outside the Door: Primal Scene, Caesura, and the Primary Trauma of Race

ABSTRACTWe are supposedly a “postracial” America, yet we cannot contain our own excess, cannot keep the unmetabolized beta elements of our racial history out of the bedroom or let race stay in the bedroom so the mature genital couple can do what it pleases. Not only do we surveil, police, and monitor race’s own primal scene but also we continuously break and enter into its most intimate chambers, guns drawn, tanks crashing in, in order to prevent the primal scene from ever taking place. This article explores the idea of race in America as denied its own primal scene and the ways in which, contrary to the importance to Bion (1991) of preventing “someone who KNOWS from filling the empty space” (p. 578), we cannot allow race to hold open its own empty space, find its own manifestations of O. I draw from the work of Wilfred Bion, Fred Moten, Jean Laplanche, and others to attempt to theorize the complexities of “postracial” America’s relationship with race vis-à-vis the primal scene.

Navigating in the Protein Universe

How are proteins related to each other? Which physicochemical considerations affect protein evolution, and how? Forming a global picture of the protein universe can help address these, and similar, questions. We study the evolutionary relationships among a representative set of 9,710 protein domains, taken from the SCOP database. We align all-against-all domains, searching for significantly-sized shared segments, referred to as motifs. These motifs have similar sequence and structure, and thus are indicative of evolutionary relationships among the proteins. The results are presented as a similarity network, in which edges connect domains that share a motif. Using reasonable similarity thresholds, the network manifests a large connected component, as well as many isolated ‘islands’, revealing the complex nature of protein space, which includes continuous and discrete regions. Overall SCOP domains of the all-alpha, all-beta and alpha+beta classes, in which alpha and beta elements do not mix, populate the discrete region, while alpha/beta domains, with their alternating alpha and beta elements, populate the continuous one. The network can be interpreted as a collection of evolutionary paths in protein space. The large amount of paths within the alpha/beta class suggests that it is particularly easy to add and delete motifs between them. Apparently, evolution took advantage of this property in order to design new proteins with novel functions. This is the first study that combines sequence and structural similarity between proteins within the context of a network to provide a bird's eye view of the protein universe. The network offers a natural way to organize and search in protein space; we provide tools to this end by integrating Cytoscape with PyMOL and other molecular viewers. They could be used to theorize about protein evolution, suggest evolutionary pathways between domains, and maybe also strategies for protein design.

Global view of the protein universe.

To explore protein space from a global perspective, we consider 9,710 SCOP (Structural Classification of Proteins) domains with up to 70% sequence identity and present all similarities among them as networks: In the "domain network," nodes represent domains, and edges connect domains that share "motifs," i.e., significantly sized segments of similar sequence and structure. We explore the dependence of the network on the thresholds that define the evolutionary relatedness of the domains. At excessively strict thresholds the network falls apart completely; for very lax thresholds, there are network paths between virtually all domains. Interestingly, at intermediate thresholds the network constitutes two regions that can be described as "continuous" versus "discrete." The continuous region comprises a large connected component, dominated by domains with alternating alpha and beta elements, and the discrete region includes the rest of the domains in isolated islands, each generally corresponding to a fold. We also construct the "motif network," in which nodes represent recurring motifs, and edges connect motifs that appear in the same domain. This network also features a large and highly connected component of motifs that originate from domains with alternating alpha/beta elements (and some all-alpha domains), and smaller isolated islands. Indeed, the motif network suggests that nature reuses such motifs extensively. The networks suggest evolutionary paths between domains and give hints about protein evolution and the underlying biophysics. They provide natural means of organizing protein space, and could be useful for the development of strategies for protein search and design.

Bion and Tustin: The autistic phenomena

This article examines the implications of the proposal of autistic transformations within the general context of Bion's theory of Transformations. The aim is to confirm the coherence of this proposal of autistic transformations within the overall structure of Bion's theory of Transformations. She examines the relation between emotional links and their negatives, particularly –K. She questions in which of the dimensions of the mind the autistic phenomena are located, the relation between autistic phenomena and beta elements, and where to place them in the Grid.The author tries to form metapsychological support for the incorporation of the autistic area in Bion's theory of Transformations. She argues that, despite the incongruence and imprecision of this incorporation, such autistic phenomena cannot be excluded from the complexus of the human mind and should therefore be accounted for in Bion's transformations. She discusses the idea that the theory of transformations includes the field of the neurosis and psychosis and deals with emotions, whereas the autistic area is dominated by sensations. The author asks how to add the autistic area to Bion's theory. Clinical material of a child for whom the non‐psychotic part of the personality predominates and who presents autistic nuclei provides material for the discussion.

An Essay on Bion's Beta Function

Among the major theorists studying the effect of the external world on the individual, none had a more ambiguous relationship to the psychic manifestations of the environment than Wilfred Bion. On the one hand his theory of the mind contained a new concept, beta elements, to depict the intrusion of the material world into the mental sphere, while on the other he radically opposed the use of sensory perception as a source for clinical insight. The author examines this dichotomy as an outgrowth of her interest in the place of external reality in psychoanalytic theory. As a result, this essay is an attempt to clarify the source for Bion's theorizing, in order to be more specific about the applicability of his concepts and his precepts.

Plato's Theory of “Form” and Homeomorphic Transformation of Pre-Conceptual Traumas, Using Bion's Model of Container–Contained

I define psychic traumas as pre-concepts resulting when a transient event changes into a permanent one that will remain constantly conjoined(1) and is structured as an unconscious emotional narrative that compulsively repeats. I refer to pre-conceptual traumas because they represent events that took place at a time when there was not a mind capable of containing them. All forms of existing psychopathology are, in summary, the result of the way that explicit pre-conceptual traumas have eroded and outlined the Oedipus complex. Thus, the superego is not heir to the Oedipus complex alone, as Freud (1923, pp. 34-36) once remarked, but heir to an Oedipus complex specifically chiseled and modified by the precise pre-conceptual trauma experienced; a condition I refer as the "mark of Cain." Thle unconscious sequence of events that structure the "pre-conceptual" trauma follows a logic based on a kind of pseudo-causality or chain of beta elements (Bion, 1963, p. 40) in wait for a mind that could change them into a meaningful "concept." This form of pseudo-causality, considered as a minus knowledge (-K) (Bion, 1962, pp. 97-99), is the consequence of a continuous association of no-things or absences, that are modified with time: the appearance, form, or container, changes, but the meaning, or contained, remains the same. It is similar to the way that primary objects transform as the child grows, from breast to thumb, to a security blanket, to sexual acting out, smoking, obesity, drugs, and so forth. I have referred to this mechanism as "homeomorphic symbolization" (homos = same and morphus = form). It is similar to Plato's concept of the Form, in the sense that the external shape (thumb-blanket-obesity …), the phenomenon, changes, but the noumenon, the "thing-in-itself," (breast) remains. When the mind is contained by the psychotic (traumatized) part of the personality, the projection or atomization of pre-conceptual traumas could reach such a power of density and distension that the individual could live completely submerged-like in a dream-in a world of his or her own, without being aware of it. In The Republic, Plato referred to the Allegory of the Cave, where he described a specific condition that all men find themselves living in, where things as they are perceived by the senses might not be exactly what they are, and where the real world can only be apprehended intellectually. Clinical material from analytical patients is presented.