Biological Foundations Research Articles

Dynamical modules in metabolism, cell and developmental biology.

Modularity is an essential feature of any adaptive complex system. Phenotypic traits are modules in the sense that they have a distinguishable structure or function, which can vary (quasi-)independently from its context. Since all phenotypic traits are the product of some underlying regulatory dynamics, the generative processes that constitute the genotype–phenotype map must also be functionally modular. Traditionally, modular processes have been identified as structural modules in regulatory networks. However, structure only constrains, but does not determine, the dynamics of a process. Here, we propose an alternative approach that decomposes the behaviour of a complex regulatory system into elementary activity-functions. Modular activities can occur in networks that show no structural modularity, making dynamical modularity more widely applicable than structural decomposition. Furthermore, the behaviour of a regulatory system closely mirrors its functional contribution to the outcome of a process, which makes dynamical modularity particularly suited for functional decomposition. We illustrate our approach with numerous examples from the study of metabolism, cellular processes, as well as development and pattern formation. We argue that dynamical modules provide a shared conceptual foundation for developmental and evolutionary biology, and serve as the foundation for a new account of process homology, which is presented in a separate contribution by DiFrisco and Jaeger to this focus issue.

Psychic Trauma Disturbs Networks of Meaning and Constitutes a Linguistic Wound

Psychic Trauma Disturbs Networks of Meaning and Constitutes a Linguistic Wound

Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data.

Accurate reference genome sequences provide the foundation for modern molecular biology and genomics as the interpretation of sequence data to study evolution, gene expression, and epigenetics depends heavily on the quality of the genome assembly used for its alignment. Correctly organising sequenced fragments such as contigs and scaffolds in relation to each other is a critical and often challenging step in the construction of robust genome references. We previously identified misoriented regions in the mouse and human reference assemblies using Strand-seq, a single cell sequencing technique that preserves DNA directionality Here we demonstrate the ability of Strand-seq to build and correct full-length chromosomes by identifying which scaffolds belong to the same chromosome and determining their correct order and orientation, without the need for overlapping sequences. We demonstrate that Strand-seq exquisitely maps assembly fragments into large related groups and chromosome-sized clusters without using new assembly data. Using template strand inheritance as a bi-allelic marker, we employ genetic mapping principles to cluster scaffolds that are derived from the same chromosome and order them within the chromosome based solely on directionality of DNA strand inheritance. We prove the utility of our approach by generating improved genome assemblies for several model organisms including the ferret, pig, Xenopus, zebrafish, Tasmanian devil and the Guinea pig.

Comprehensive comparative morphology and developmental staging of final instar larvae toward metamorphosis in the insect order Odonata

The order Odonata (dragonflies and damselflies) is among the most ancestral groups of winged insects with drastic morphological changes upon metamorphosis, and thus important for understanding evo-devo aspects of insects. However, basic developmental descriptions of Odonata have been scarce. In an attempt to establish the foundation of developmental and experimental biology of Odonata, we present an unprecedentedly comprehensive survey of dragonflies and damselflies, in total 158 larvae representing 49 species and 14 families, wherein morphological changes of all the final and/or penultimate instar larvae were photographed and monitored everyday. Although their morphology and development were diverse, we consistently identified two visually recognizable morphogenetic events in the final larval instar, namely start of wing expansion and onset of melanization on the wing sheaths, thereby categorizing the final instar into three stages. While the duration of the first stage ranged 4–66 days across diverse Odonata species, the second or third stages exhibited relatively small variation ranging 3–22 days or 1–8 days, respectively, probably reflecting the steady and irreversible metamorphosis process after stage 2. We also described other characteristic morphological changes during the larval development, although they were observed only in some Odonata species and lineages.

Aneuploidy and loss of heterozygosity as risk markers for malignant transformation in oral mucosa.

The ability to predict malignant transformation in oral potentially malignant disorders would inform targeted treatment, provide prognostic information and allow secondary prevention. DNA ploidy and loss of heterozygosity assays are already in clinical use, and loss of heterozygosity has been used in prospective clinical trials. This review appraises published evidence of predictive ability and explores interpretation of heterogeneous studies, with different diagnostic methods, criteria and intention. Both methods have a sound biological foundation and have predictive value independent of dysplasia grading and clinical parameters. The application of these two techniques cannot be directly compared because of differences in expression of results and application to populations of different risk. Predicting malignant transformation accurately on an individual patient basis is not yet possible with either technique. However, they are valuable applications to stratify patients for inclusion in trials, identify the lowest risk patients and exclude risk when biopsy results are indeterminate for dysplasia.

Shared biological foundations of post-traumatic headache and migraine.

Shared biological foundations of post-traumatic headache and migraine.

Evaluation of a U.S. National Cohort to Determine Utilization in Colectomy Rates for Ulcerative Colitis Among Ethnicities.

Colectomy is the curative management for ulcerative colitis (UC). Multiple studies have reported racial disparities for colectomy before the advent of anti-TNF alpha agents. The aim of this study was to describe racial and geographic differences in colectomy rates among hospitalized patients with UC after anti-TNF therapy was introduced. We examined all patients discharged from the hospital between 2010 and 2014 with a primary diagnosis of UC or of complications of UC. The data were evaluated for race and colectomy rates among the hospitalized patients with UC. The unadjusted national colectomy rate among hospitalized patients with UC between 2010 and 2014 was 3.90 per 1000 hospitalization days (95% confidence interval, 3.72-4.08). The undajusted colectomy rates in African American (2.33 vs 4.35; P < 0.001) and Hispanic patients (3.99 vs 4.35; P ≤ 0.009) were considerably lower than those for White patients. After adjustment for confounders, the incidence rate ratio for African American as compared to White patients was 0.43 (95% confidence interval, 0.32-0.58; P < 0.001). Geographic region of the United States also showed significant variation in colectomy rates, with western regions having the highest rate (4.76 vs 3.20; P < 0.001). Racial and geographical disparities persist for the rate of colectomy among hospitalized patients with UC. The national database analysis reveals that colectomy rates for hospitalized African American and Hispanic patients were lower than those for White patients. Further studies are important to determine the social and biologic foundations of these disparities.

Systems Biology and Multi‐Omics

Systems Biology and Multi‐Omics

Philosophical and Biological Foundation of Brain Based Learning: A Phenomenological Approach

This investigation was undertaken to look at the philosophical and biological foundation of brain based learning through phenomenological approach. Subjective method of investigation was used. Interviews were taken through semi-structures procedure in which 12 instructors were involved as a sample. Two topics of the examination were assessed and it was discovered that authenticity, optimism, realism, dualism, naturalism, cognizant and oblivious part of cerebrum and constructivism were straightforwardly related with brain oriented learning approach. Correspondingly, Brain is not organically comprehended by the educator completely in light of the fact because cerebrum discovery is tranquil as a young ground of teaching learning process. Instructor have been rehearsing cerebrum based adapting normally yet they are not ready to express a reasonable balanced for their activity yet the educators still practice the mind based adapting adequately.&#x0D; Keywords: Brain-Based Learning, Philosophical and Biological Foundation, Phenomenological Study

Le traumatisme psychique constitue une blessure du langage par atteinte des réseaux de significations

Le traumatisme psychique constitue une blessure du langage par atteinte des réseaux de significations

BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts.

Synthetic biology seeks to create new biological parts, devices, and systems, and to reconfigure existing natural biological systems for custom-designed purposes. The standardized BioBrick parts are the foundation of synthetic biology. The incomplete and flawed metadata of BioBrick parts, however, are a major obstacle for designing genetic circuit easily, quickly, and accurately. Here, a database termed BioMaster http://www.biomaster-uestc.cn was developed to extensively complement information about BioBrick parts, which includes 47,934 items of BioBrick parts from the international Genetically Engineered Machine (iGEM) Registry with more comprehensive information integrated from 10 databases, providing corresponding information about functions, activities, interactions, and related literature. Moreover, BioMaster is also a user-friendly platform for retrieval and analyses of relevant information on BioBrick parts.

Jeannine Cavender-Bares.

Jeannine Cavender-Bares.

Deciphering the genetic code of DNA methylation.

DNA methylation plays crucial roles in many biological processes and abnormal DNA methylation patterns are often observed in diseases. Recent studies have shed light on cis-acting DNA elements that regulate locus-specific DNA methylation, which involves transcription factors, histone modification and DNA secondary structures. In addition, several recent studies have surveyed DNA motifs that regulate DNA methylation and suggest potential applications in diagnosis and prognosis. Here, we discuss the current biological foundation for the cis-acting genetic code that regulates DNA methylation. We review the computational models that predict DNA methylation with genetic features and discuss the biological insights revealed from these models. We also provide an in-depth discussion on how to leverage such knowledge in clinical applications, particularly in the context of liquid biopsy for early cancer diagnosis and treatment.

Biocultural theory and the problem of human editing

The transition from an irregular understanding of nature as a given to the regulatory concepts of human development is one of the central philosophical and socio-humanitarian issues in the development of not only biotechnologies, but also society as a whole. In the theory of philosophy of biomedicine, the discussion is structured as the positioning of various problematic approaches, modeled using the principles of bioethics and philosophical ethics, taking into account the actual experience of the application and social perception of biomedical technologies. The status of problematic approaches is determined not only by philosophical ethics, but also by the willingness of society to accept something new as its own future. At the same time, accepting the future is impossible without rooting the future in the past - the beliefs and expectations that legitimize the future. The correlation of such concepts as the authentic autonomy of J. Habermas and the expansion of utilitarianism into the problems of editing the human genome, the conflict associated with challenges requiring collective moral action, and the rigidity of traditional moral mechanisms lead to the search for such a sociobiological language that would be formed from competitively coexisting old, traditional, and new, bioengineering, concepts of human development. The idea of biocultural theory as a form of connection between culture and biological foundation is associated with the work of A. Buchanan and R. Powell, who propose a systemic definition of biocultural theory as a mutual biological and cultural transformation of a person. Biocultural theory is aimed at shaping such a philosophical horizon, where the body, not only carnal, such as organs, but also personal - the awareness of its own bioidentity, becomes open and understandable due to the expansion of the connection between biology and culture, but at the same time acquires problems that becomes the subject of philosophy and ethics, since now a person, comprehended as a body, receives a variability that is no longer associated exclusively with culture. The goal of the article is to show that editing a person is not so much a traditionally understood risk as a transformation of the understanding of the cultural and biological conditions for the formation of his bioidentity.

Non-scalable functions as biological object boundary models

This article considers the possibility of creating an algorithm for universal image preprocessing that would simplify its segmentation and is suitable for any type of medical or biological study methods. The authors propose a number of equally applicable functions that describe the changes in the parameters of a raster image along the normal to the border of an arbitrary biological object and at the same time doesn’t depend on the instrumental method of image acquisition. The work also determines the absence of any parametric adaptation as the boundary condition for reducing the subjective contribution to the final scientific and practical result. Methods. Based on the biological foundations, the following three simple mathematical expressions were chosen for changing brightness on the border of a biological object: All the functions participating in calculations were not scaled, their size corresponded to the coordinates expressed as raster image dots. The Pearson’s correlation without reliability assessment was used to describe the probabilities of the object’s border being present in the coordinate x=0, and to assess its affinity with properties of the proposed synthetic functions. The basis of functions was tested using digital images of three fundamentally-different objects obtained with different physical detectors: sagittal section of the MRI scan of human head capturing the hippocampus area (Siemens Magnetom Skyra, Germany); optical section of eye cornea (Pentacam, Oculus, Japan); image of transverse histological section of human skin stained with hematoxylin and eosin obtained with microscope (Olympus BX65, Olympus, Japan). In addition, practical evaluation of the applicability of the developed approach was done by processing 100 two-dimensional images of different arbitrarily selected brain MRI sections. A field of probability of the presence of “biological border” in each dot of the image was built for each image. Results. The best affinity — with significant outperformance — to all kinds of digital images of biological objects’ borders was found in the compound function described by the formula. Its affinity to object’s borders on the MRI images was 0.87–0.99; for the borders of biological objects on the images obtained with optical methods it was lower than 0.99 only in two out of seven tests (0.95 and 0.97). Discussion. The high affinity of the proposed compound function may be associated with the fact that the three members of this synthetic expression correspond to three individual additive physical phenomena manifesting its biological basis. The first member is responsible for general biological contrast differentiation — the delineation of tissues appears sharpest at the borders of the organs. The second member describes the conventional membrane present in all healthy organized biological structures, including epithelial lining of the esophagus, muscle fascia, developed mucous membrane etc. The third member of the proposed function characterizes the blurred junction of arbitrarily-uniform structures. The proposed mathematical apparatus describes the formation of scalar field of probabilities for selected borders of biological structures and can easily be transformed into vector representation. Additional advantage of the developed and tested mathematical apparatus is the fact that the formulated approach can be used for determining the orientation of brightness increment gradient. This, in turn, allows distinguishing additional properties of biological objects based on calculation of the direction of development and growth of the tissue and structural anisotropy.

Etudes in Light and Harmony: An Interdisciplinary Workbook for Creative Dialogue and Discovery

This workbook of etudes offers a collection of experimental texts for communal dialogue and discovery that crosses multiple academic disciplines, including: foundations of physics, metaphysics, theoretical biology, semiotics, cognitive science, linguistics, phenomenology, logic & mathematics, poetry and theology. Each etude probes limits, horizons and boundaries by implicitly bring into relation foundational issues that characterize different academic disciplines or systems of meaning formation. Some formal techniques are deployed the etudes. Most notable is the use of the “logic of three” to overcome falsely totalizing images and inexorable dualities. This technique involves a particular kind of attunement to the “betweenness” of mediation that is not common in modern science. The attunement draws on the formal and precise movements of analysis in concert with the metaphoric and singular movements of synthesis.

Epidemiological and Clinical Aspects of Autoimmune Dysthyroidism in Internal Medicine at Aristide Le Dantec Hospital

Introduction: Autoimmune thyroiditis is relatively common in medicine. However, comprehensive studies are few in number, especially in Africa and particularly in Senegal. The aim of this study was therefore to determine the epidemiological, clinical, profile of Autoimmune Thyroid Diseases (OITD). Materials and Methods: This was a retrospective descriptive study from 2016 to 2019 of the records of patients who consulted or were hospitalised for autoimmune dysthyroidism in the internal medicine department of the Aristide Le Dantec Hospital. During this period, 1227 new consultations were recorded; they concerned three specialized consultations including endocrinology. The autoimmune origin was confirmed in 159 patients, i.e. in 45.69% of cases the AIDM then 12.96% of all consultations. The autoimmune origin was established on clinical, biological and immunological grounds. The data were collected from the medical records of the patients and recorded on a pre-established individual survey sheet taking into account the objectives of the study. The data collected was entered into the Sphinx V5 software on an established form. The analysis was carried out with the following software: Excel 2010 and Epi info 7.2. Results: Among this dysthyroidism, 159 patients had a confirmed autoimmune thyroid disease. On all new consultations, OITD represented 12.96% of internal medicine consultations. The sex ratio M/F was 0.18. The majority of our patients (57.86%) were aged between 25 and 44 years with extremes ranging from 11 to 63 years. In Graves’ disease, the notion of an irritative spine was found in 60.27% of cases. Signs of thyrotoxicosis were present in 92.7% of cases. There was a goiter in 81.1% of cases with a vascular character in 76.47% of cases. Anti-THR antibodies were positive in 96.15% of cases. Complications were noted in 9 patients (6.5%) such as cardiothyreosis in 8 patients (5.7%) and malignant orbitopathy noted in 1 patient (0.8%). In Hashimoto’s thyroiditis, signs of hypometabolism were evident in 87.50% of patients. Anti-TPO antibodies were positive in all patients. All patients had received thyroid hormone supplementation. Thyroid autoimmune disease was associated with other autoimmune diseases in 6.2% of cases. Conclusion: Autoimmune thyroiditis is common in our daily practice in Senegal; it is dominated by Grave’s disease. Hypothyroidism was the most common manifestation of Hashimoto’s thyroiditis. The inaccessibility of antithyroid antibody testing is an obstacle to the diagnosis and management of these conditions.

Max Scheler’s Biologievorlesung (1908/09)

The text, known as Biologievorlesung (1908/09), written by the German phenomenologist Max Scheler appeared in 1993 in volume XIV of the Schelerian Gesammelte Werke by M.S. Frings. It collects the surviving fragments of the notes on the “Gnoseological foundations of biology” elaborated by Scheler for the cycle of lectures, which were held as Privatdozent at the University of Munich in the winter semester of the academic year 1908-1909. Despite being interesting in many respects, the text is still largely unexplored to the very day. In this article I intend to focus on two points: 1) demonstrate the relatively advanced state of progress of the proposal expressed therein by the author compared to his real first phenomenological production between the publication in 1912 of the long article Über Selbsttäuschungen and 1922, the year that marks Scheler's open detachment from the Catholic cultural horizon hitherto embraced, and 2) bring out the systematic unity of the epistemological, ontological and phenomenological themes, articulated here, in a first attempt to develop an ontology of modern science, understood as the product of a vision of a historically located world, through a descriptive analysis of the intentional structures of consciousness implicated in intellectual knowledge.

Treatment Process for Neuropathy Involving Science-Based Clinical Research and Medical Technology Combinations

we will demonstrate the ability of multiple and specific alternative medical technologies used in combination that support the body’s natural ability to repair peripheral nerves in neuropathy patients. This paper looks to review currently known biological foundations for the regenerative effects of Low-Level Laser Therapy, Pulsed Electromagnetic Field Therapy, Infrared and Near Infrared Therapy, and Nutritional Protocols to demonstrate the significant potential to repair peripheral nerve injuries. There is favorable evidence to expand functional recovery in diverse types of peripheral nerve injuries. The conclusion from this study indicates using a specific combination of technologies that scientifically enhances the body’s ability to repair nerves is more effective in helping patients with neuropathies than the normal standard of care.

Biological and Anthropological Foundations of Arnold Gehlen’s Political Theory

The problem of the body-soul separation has long been the subject of both philosophy and science. There is no doubt that man is a biological being. What is not certain is how human biology influences our actions and decision processes. Does it constitute humanity or is it just an excess. At the beginning of the twentieth century, Arnold Gehlen, who laid the foundations of the institutional theory, stated that man is a being marked by a deficiency. This statement was derived precisely from man’s biological deficiencies. At the same time, those influenced the human’s ability to create complex institutional systems. From the biological foundations of the analysis of man as a psychophysical being, Gehlen derived the need to establish a system of rules and norms that helps us to survive. This article will primarily discuss the biological foundations of Gehlen's theory. It will show how this 20th century anthropologist moved from researching the biological aspects of individuals to the cultural challenges faced by modern humans.