ARTICLE | doi:10.20944/preprints202212.0249.v1
Subject: Biology, Entomology Keywords: tan; Drosophila; Drosophila guttifera; CRM; cis-regulatory; evo-devo; yellow; transcription factor; cis-regulatory module; cis-regulatory element
Online: 14 December 2022 (06:48:07 CET)
How complex morphological patterns form is an intriguing question in developmental biology. However, the mechanisms that generate complex patterns remain largely unknown. Here we sought to identify the genetic mechanisms that regulate the tan (t) gene in a multi-spotted pigmentation pattern on the abdomen and wings of Drosophila guttifera. Previously, we showed that yellow (y) gene expression completely prefigures the abdominal  and wing  pigment patterns of this species. In the current study, we demonstrate that the t gene is co-expressed with the y gene in nearly identical patterns, both transcripts foreshadowing the adult abdominal and wing melanin spot patterns. We identified cis-regulatory modules (CRMs) of t, one of which drives reporter expression in six longitudinal rows of spots on the developing pupal abdomen, while the second CRM activates the reporter gene in a spotted wing pattern. Comparing the abdominal spot CRMs of y and t, we found a similar composition of putative transcription factor binding sites that are thought to regulate the complex expression patterns of both terminal pigmentation genes y and t. In contrast, the y and t wing spots appear to be regulated by distinct upstream factors. Our results suggest that the D. guttifera abdominal and wing melanin spot patterns have been established through the co-regulation of y and t, shedding light on how complex morphological traits may be regulated through the parallel coordination of downstream target genes.
ARTICLE | doi:10.20944/preprints202012.0503.v1
Subject: Life Sciences, Biochemistry Keywords: Corynebacterium glutamicum; regulatory interactions; regulatory network; curation; network inference; systems; modules; NDA; regulogs
Online: 21 December 2020 (10:52:52 CET)
Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory interactions, which study at the global scale has been challenged by the lack of data integration. Here, we update the manually-curated C. glutamicum transcriptional regulatory network, now including protein-protein interactions having a direct effect on gene transcription. The network model with regulations supported by any experimental evidence increased by 557 interactions regarding the previous (2018) version. 73 interactions supported by directed experiments were also included in a second model. We included 545 sRNA-mediated regulations in a third model with a total of 5164 interactions. We deposited the three network models in Abasy Atlas v2.4. We study the C. glutamicum regulatory structure by comparing it against the networks for more than 40 species, finding it to contrast in several global structural properties. We analyze the system-level components of the networks, finding that the inclusion of the sRNAs regulations changes their proportions, transferring part of the basal machinery to the modular class and increasing the number of modules while decreasing their size. Finally, we use strong networks of three model organisms to provide insights in future directions of the C. glutamicum network characterization.
ARTICLE | doi:10.20944/preprints201909.0204.v1
Subject: Medicine & Pharmacology, Other Keywords: Office of Innovation; novel drugs; novel therapies; regulatory science; Latin American Regulatory landscape
Online: 18 September 2019 (12:51:16 CEST)
Regulatory agencies across the Latin American Region have strengthened the regulatory science through the development of new tools, standards and various other related parameters to evaluate and assess safety, efficacy, quality and performance. The former have been implemented to promote and incorporate new drugs and technologies, which still, are a challenge to well-established regulatory frameworks. Furthermore, in today’s environment, the existing regulatory framework protecting public’s health creates barriers for market entry of novel drugs and medical devices. This article aims to the pioneering work that Cuban Regulatory Agency (CECMED) has been developing with the aim to build a strong regulatory framework geared to accelerated innovation and the successful transition from research and development to clinical development. The Office of Innovation recently established at the CECMED is the first flagship in Latin America and the Caribbean region. Its aim is to play a leading role as a driving force for the national and regional biopharmaceutical innovation. This article will discuss the Office of Innovation its conceptualisation and management taking into account the Latin American regional and national Cuban context.
Subject: Medicine & Pharmacology, Other Keywords: purinergic signaling; regulatory role; neutrophils; inflammation
Online: 8 September 2021 (13:16:11 CEST)
Purinergic signaling is that nucleotides (especially ATP) and adenosine are utilized as transmitter molecules, which play an important role in the immune system. In the extracellular ventricle, ATP plays a significant role of pro-inflammatory molecules mainly through activating P2 receptors, while adenosine plays the role as anti-inflammatory molecule mainly through activating P1 receptors. As we know，neutrophils are the most abundant immune cells in our circulation and have become an essential part of coordinating a series of complex events during inflammatory diseases. However, due to the destruction of inflammatory substances from neutrophils, the activation of neutrophils is fine-tuned, and purinergic signaling is associated with this process. As a matter of fact, altering the balance between P2 and P1 signals is of great importance for neutrophils to exert immune activities properly. Here, we review the role of purinergic signaling in regulatory function of neutrophils during inflammatory disease, and then discuss the potential contribution of targeted purinergic signals in the treatment of the neutrophil during inflammatory diseases.
ARTICLE | doi:10.20944/preprints202107.0300.v1
Online: 13 July 2021 (11:24:23 CEST)
An economic and business history approach is used to show the rise and relative failure of the Spanish wind industry during the period between 2004-2015, when Spain became the fourth country after China, the US and Germany in installed capacity of renewable energies and, in relative terms, the second country after Denmark. This study is unique in that it provides an integrated vision of the reasons for the relative fall of Spain in the world ranking of wind energy producers. The methodology of the economic analysis of industrial policies makes it possible to explain the fall in the relative importance of Spain in the international panorama of wind farms. There were no reasons related to technological obsolescence or inability of the CECRE managing renewable energies to explain the fall.
ARTICLE | doi:10.20944/preprints202110.0270.v1
Subject: Life Sciences, Other Keywords: Biopesticides; Regulations; Risk Assessment; Regulatory Challenge, Sustainability; Nigeria.
Online: 19 October 2021 (10:49:58 CEST)
The global trend towards increased demand for organic food, greener environments, and the integration of biological control agents into pest management strategies has greatly enhanced the need for biological pesticides (biopesticides). Biopesticides are generally environmentally friendly and are made from micro-organisms or other natural substances. Despite their great potential, relatively few have been registered and commercialised in Nigeria compared to other African countries such as South Africa and Kenya. Biological active agents are so diverse such that ap-plying the same safety standards or environmental conditions to all of them is almost impossible. A review of risk assessment processes and comparative assessments of Nigeria's biopesticide regulations with other developing African countries and developed regions was conducted. Prolonged field testing, lack of bridged risk assessments and technical checklists have been identified as key factors hampering the timely development and commercialisation of biopesti-cides in Nigeria. Recommendations on necessary changes to the existing Nigeria biopesticide regulations have been made. Risk assessment matrices for microbial and biochemical biopesti-cides and a scientific/technical checklist have also been developed. Harmonisation and data ex-change among other countries in the region will also enhance the advancement of scientific and technical knowledge for sustainable regulation and cross-border trade.
REVIEW | doi:10.20944/preprints202002.0068.v1
Subject: Life Sciences, Genetics Keywords: cis-regulatory element; developmental modularity; evolutionary modularity; Heliconius
Online: 5 February 2020 (14:02:51 CET)
Developmental modularity has long been viewed as a hierarchical organization that facilitates evolution over macro-evolutionary time through modification or co-option of preexisting modules. More recently, developmental modularity has been proposed as a micro-evolutionary mechanism capable of driving rapid evolution of novel color pattern phenotypes between closely related taxa. In this scenario, swapping allelic variants of modular cis-regulatory elements (CREs) via recombination generates novel phenotypes by shuffling preexisting color pattern modules into new arrangements. Recent evidence from Drosophila and butterflies, however, provides a series of examples in which pleiotropic CREs function in multiple developmental contexts. The potential prevalence of pleiotropy in CRE function is a major barrier to the proposed evolutionary role of CRE modules and encourages us to reconsider the relative importance of modularity for microevolutionary change. Here we first review the case for the apparent frequent exchange of modular color pattern phenotypes as a mechanism facilitating diversification. We then contrast this with recent evidence of CRE pleiotropy and argue that exchange of CRE modules should not be the default assumption, even when phenotypes look modular. Finally, we review experimental data on Heliconius butterfly wing patterns—which appear modular—and introduce the concept of evolutionary modularity as an alternative to developmental modularity. Evolutionary modularity reconciles the appearance of modularity in comparative genomic studies of Heliconius color patterns with experimental data supporting a non-modular architecture. We propose that evolutionary modularity provides a potentially important pathway for exchange of phenotypic elements between hybridizing taxa independent of the underlying developmental architecture.
ARTICLE | doi:10.20944/preprints201810.0030.v2
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: artificial general intelligence, AI policy, self-regulatory organization
Online: 8 November 2018 (10:52:39 CET)
The first group to build artificial general intelligence or AGI stands to gain a significant strategic and market advantage over competitors, so companies, universities, militaries, and other actors have strong incentives to race to build AGI first. An AGI race would be dangerous, though, because it would prioritize capabilities over safety and increase the risk of existential catastrophe. A self-regulatory organization (SRO) for AGI may be able to change incentives to favor safety over capabilities and encourage cooperation rather than racing.
REVIEW | doi:10.20944/preprints202210.0248.v1
Subject: Biology, Other Keywords: Trade-off of survival for reproduction; natural selection of aging; regulatory redundancy; aging’s individual benefit; regulatory molecular biology; Darwin’s dilemma; aging-reproduction trade-off; aging declines force of selection; master gene; holistic regulatory mechanism
Online: 18 October 2022 (04:36:09 CEST)
There is scientific consensus that organismal aging did not evolve by natural selection (NS) because it lacks individual benefit. Nonetheless it exists, leading to much speculation about its origins, and when the diminishing force of selection begins. Both concepts are based upon two misconceptions; that aging occurs in and of itself and is caused by the declining strength of NS during the reproductive lifespan. Although lacking individual benefit, aging evolved by NS as a tradeoff of survival for reproduction. Based upon regulatory dynamics that participate in this tradeoff, aging begins once reproductive success has been achieved through offspring nurturing. Thereafter, the strength of NS wanes to exponentially accelerate aging, leading to death. Assumptions of the theory are that: (1) a life-long, “holistic” regulatory mechanism whose genic expression is modified epigenetically, originates in ontogenesis; (2) the regulatory mechanism of the last developmental stage becomes redundantly expressed during “morphostasis”, a non-aging, life interval of peak vitality to ensure completion of reproduction through nurturing, and (3) thereafter, loss of regulatory redundancy causes aging which reduces the strength of natural selection and allows accumulation of randomly occurring somatic damage.
ARTICLE | doi:10.20944/preprints202210.0286.v1
Subject: Life Sciences, Genetics Keywords: cytokines; haplotypes; immune response; Leishmania; regulatory mechanisms; resistance; susceptibility
Online: 19 October 2022 (11:30:49 CEST)
Background: The Ibizan Hound is a canine breed native to the Mediterranean region, where leishmaniasis is an endemic zoonosis. Several studies indicate a low prevalence of this disease in dogs, whereas other canine breeds present a high prevalence. However, the molecular underlaying mechanisms yet remains unknown. Methods: In this study, we analyze the haplotypes of genes encode cytokines related to immune response of Leishmania infantum infection in twenty-four Boxer and twenty-four Ibizan hound apparently healthy using CanineHD DNA Analysis BeadChip including 165,480 mapped positions. Results: The results show that several haplotypes of genes encoding Interleukin 6 (IL6) and Interferon gamma (IFNG) are related to Interferon gamma (IFN-γ), and Interleukins (IL) 2 and 18 serum levels. Our results indicate that the regulation of immune response is different in the two canine breeds analyzed and are related to the haplotype compositions of the genes encoding these cytokines. Conclusions: Future studies are needed to elucidate whether these differences and haplotypes are related to different phenotypes in immune response and expression gene regulation to L. infantum infection in dogs.
ARTICLE | doi:10.20944/preprints202006.0094.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: CCCP; Mitophagy; Regulatory T cells; Flow cytometry; fluorescence microscopy
Online: 7 June 2020 (15:03:23 CEST)
Objective: To investigate the effects and mechanisms of different concentrations of CCCP on mitophagy in human peripheral blood regulatory T cells. Methods: Tregs were isolated, identified and then grouped, treating with CCCP at a concentration of 2.5 μM, 5 μM, 10 μM, 20 μM and 40 μM for 24h in an incubator. Flow cytometry detected the reactive oxygen species (ROS), mitochondrial membrane potential (MMP), mitochondrial quality, and fluorescence microscopy observed the co-localization of mitochondria and lysosomes in each group. Results: The purity of CD4+CD25+Tregs was (93.36 ± 1.87) %. With the increase of CCCP concentration, the level of ROS gradually increased, while the MMP decreased gradually. About the mitochondria and lysosome fusion, the fluorescence intensity of orange (yellow) was the highest when the concentration of CCCP was in the range of 5-10 μM while decreased with the CCCP concentration continually increasing. The mitochondrial quality decreased with the increase of CCCP concentration. However, there was no significant difference between groups C, D and E. The mitochondrial quality of groups F and G were significantly lower than that of group E. Conclusions: With the concentration of CCCP gradually increased, the level of ROS in Treg cells increased, and MMP decreased, which promoted the mitophagy, mitochondrial quality maintains homeostasis; When ROS accumulated, and MMP decreased significantly, the mitophagy was inhibited, and the mitochondrial quality was significantly decreased.
REVIEW | doi:10.20944/preprints201906.0178.v1
Subject: Life Sciences, Genetics Keywords: Alzheimer's disease; Parkinson's disease; genetics; gene regulatory network; miRNAs
Online: 18 June 2019 (13:07:49 CEST)
Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative disorders related to aging. Though several risk factors are shared between these two diseases, the exact relationship between these two diseases is still unknown. In this paper, we analyzed how these diseases relate to each other from a genomics viewpoint. Using an extensive literature search, we accumulated the list of genes from the major genome-wide association (GWAS) studies. However, we found only one gene (HLA-DRB5) reported in these GWAS studies that are common between AD and PD. We also listed all the miRNAs that have been previously reported for AD and PD. Here we found 15 different miRNAs that were reported in both diseases. In order to get better insights, we predicted the gene coexpression network for both AD and PD. Network analysis on these networks show six clusters of genes related to AD and four clusters of genes related to PD.
ARTICLE | doi:10.20944/preprints201711.0182.v1
Subject: Biology, Other Keywords: RpoS; crystal structure; Legionella pneumophila; intracellular pathogen; regulatory factor
Online: 29 November 2017 (05:04:33 CET)
Legionella pneumophila RpoS (LpRpoS) is an alternative sigma factor of RNA polymerase (RNAP) essential for virulence and stress resistance. To investigate the mechanism of RpoS in the intracellular pathogen L. pneumophila, we determined the high-resolution crystal structure of the LpRpoS (residues 95-194) containing a partial region 1.2 and region 2. The structure of LpRpoS (residues 95-194) reveals that the conserved residues are critical for promoter melting, DNA and core RNAP binding. The differences in regulatory factor binding site between Escherichia coli RpoS and LpRpoS suggest that LpRpoS may employ a distinct mechanism to recruit alternative regulatory factors controlling transcription initiation.
Subject: Life Sciences, Immunology Keywords: allergy; regulatory T cells; IL-2; IL-4; Th2; tolerance
Online: 10 November 2022 (11:09:22 CET)
This manuscript provides a new integrated view of the development of allergen-specific TH2 and the lack of their associated Treg cells in a unified model, justifying the need for IL-2 to correct allergy conditions.
ARTICLE | doi:10.20944/preprints202112.0358.v1
Subject: Engineering, General Engineering Keywords: ecigarette; regulatory science; substantial equivalence; public health; tobacco product comparison.
Online: 22 December 2021 (12:04:52 CET)
This study introduces and demonstrates a comprehensive, accurate, unbiased approach to robust quantitative comparison of Electronic Nicotine Delivery Systems (ENDS) appropriate for establishing substantial equivalence (or lack thereof) between tobacco products. The approach is demonstrated across a family of thirteen pen- and pod-style ENDS products. Methods employed consist of formulating a robust emissions surface regression model, quantifying the empirical accuracy of the model as applied to each product, evaluating relationships between product design characteristics and maximum emissions characteristics, and presenting results in formats useful to researchers, regulators, and consumers. Results provide a response surface to characterize emissions (total particulate matter and constituents thereof) from each ENDS appropriate for use in a computer model and for conducting quantitative exposure comparisons between products. Results demonstrate that emissions vary as a function of puff duration, flow rate, E-Liquid composition, and device operating power. Further, results indicate that regulating design characteristics of ENDS devices and consumables may not achieve desired public health outcomes; it is more effective to regulate maximum permissible emissions directly. Three emissions outcome measures (yield per puff, mass concentration and constituent mass ratio) are recommended for adoption as standard quantities for reporting by manufacturers and research laboratories. The approach provides a means of (a) quantifying and comparing maximal emissions from ENDS products spanning their entire operating envelope, (b) comparative evaluation of ENDS devices and consumable design characteristics, and (c) establishing comparative equivalence of maximal emissions from ENDS. A consumer-oriented product emissions dashboard is proposed for comparative evaluation of ENDS exposure potential. Maximum achievable power dissipated in the coil of ENDS is identified as a potentially effective regulatory parameter.
Subject: Life Sciences, Biochemistry Keywords: circular RNAs (circRNAs); biogenesis; trans-acting proteins; cis-regulatory elements
Online: 16 July 2021 (14:48:13 CEST)
Circular RNAs (circRNAs), which are a class of non-coding RNA with covalently closed loops, play important roles in epigenetics regulation of gene expression at both the transcriptional and post-transcriptional level. Accumulating evidence demonstrated that numerous circRNAs were abnormally expressed in tumors and their dysregulation was involved in the tumorigenesis and metastasis of cancer. Although the functional mechanisms of many circRNAs have been revealed, why circRNAs are dysregulated in cancer remains elusive. CircRNAs are generated by a “backsplicing” process, which is regulated by different cis-regulatory elements and trans-acting proteins. Therefore, how these cis- and trans-elements change during tumorigenesis and how they regulate the biogenesis of circRNAs in cancer are two questions that interest us. In this review, we summarized the pathways for the biogenesis of circRNAs; and then illustrated why circRNAs dysregulated in cancer by discussing the changes of cis-regulatory elements and trans-acting proteins that related to circRNA splicing and maturation in cancer.
ARTICLE | doi:10.20944/preprints202005.0063.v1
Subject: Life Sciences, Molecular Biology Keywords: p53-Mdm2; mutant p53; oncogene; stress; regulatory network; cancer dynamics
Online: 5 May 2020 (05:55:27 CEST)
We study a minimal model of the stress-driven p53 regulatory network that includes competition between active and mutant forms of the tumor-suppressor gene p53. Depending on the nature of the external stress signal, four distinct dynamical states are observed. These states can be distinguished by dierent dynamical properties and correspond to active, apoptotic, pre-malignant and cancer states. Transitions between any two of these states are found to be unidirectional and irreversible if the stress signal is either oscillatory or constant. When the signal decays exponentially, the apoptotic state vanishes, and for low stress the pre-malignant state is bounded by two critical points, allowing the system to transition reversibly from the active to the pre-malignant state. For signicantly large stress, the range of the pre-malignant state expands and the system moves to the cancerous state which is a stable attractor. This suggests that identification of the pre-malignant state may be important both for therapeutic intervention as well as for drug discovery.
ARTICLE | doi:10.20944/preprints202001.0048.v1
Subject: Biology, Horticulture Keywords: cis-regulatory element; data mining; NBS-LRR resistance genes; Zucchini
Online: 5 January 2020 (17:22:10 CET)
Although Cucurbita pepo is one of the most variable species of the plant kingdom, Zucchini morphotype has undergone intensive breeding that has led to a narrow genetic base making the crop vulnerable to pest and diseases. This vulnerability makes the knowledge of resistance genes of utmost importance. In this study, a data mining search of Zucchini summer squash genome database was conducted to identify and annotate members of the NBS-encoding gene family. In order to characterize the retrieved genes in detail, they have been studied in the bases of phylogenetic relationships, structural diversity, conserved protein motifs, gene duplications and promoter region analysis. Our study shows that the NBS-encoding gene family is relatively small in Zucchini (34 members, which are separated into non-TIR- and TIR-NBS-LRR subfamilies) with a significantly lower number of R-genes than in other species. Duplications have not played a major role in the expansion of this type of genes in C. pepo. Among the cis-regulatory elements presented in these sequences, six motifs are over-represented. These elements were reported to be involved in pathogens or plant stress induced responses. These results will contribute to the identification, isolation and characterization of candidate R-genes, thereby providing insight into NBS gene family evolution in the species.
Subject: Life Sciences, Other Keywords: neural differentiation; regulatory motif; feedback regulation; signaling pathway; mathematical models
Online: 24 December 2019 (11:20:25 CET)
Computational simulation using mathematical models is a useful method for understanding the complex behavior of a living system. The majority of studies using mathematical models to reveal biological mechanisms uses one of the two main approaches: the bottom-up or the top-down approach. When we aim to analyze a large-scale network, such as a comprehensive knowledge-integrated model of a target phenomenon, for example a whole-cell model, the variation of analyses is limited to particular kind of analysis because of the size and complexity of the model. To analyze a large-scale regulatory network of neural differentiation, we developed a hybrid method that combines both approaches. To construct a mathematical model, we extracted network motifs, subgraph structures that recur more often in a metabolic network or gene regulatory network than in a random network, from a large-scale regulatory network, detected regulatory motifs among them, and combined these motifs. We confirmed that the model reproduced the known dynamics of HES1 and ASCL1 before and after differentiation, including oscillation and equilibrium of their concentrations. The model also reproduced the effects of overexpression and knockdown of the Id2 gene. Our model suggests that the characteristic change in HES1 and ASCL1 expression in the large-scale regulatory network is controlled by a combination of four feedback loops, including a large loop which has not been focused on. The model extracted by our hybrid method has the potential to reveal the critical mechanisms of neural differentiation. The hybrid method is applicable to other biological events.
ARTICLE | doi:10.20944/preprints201812.0116.v1
Subject: Arts & Humanities, Other Keywords: Available for sale securities, Realized gains and losses, Regulatory capital
Online: 11 December 2018 (09:10:16 CET)
Based on a large sample of publicly listed and non-listed US commercial banks from 1996 to 2011, we find robust evidence consistent with banks using realized available for sale (AFS) securities gains and losses to smooth earnings and increase low regulatory capital. We also find that (i) banks with positive earnings smooth earnings, and banks with negative earnings generally take big baths; (ii) regulatory capital constrains big baths; (iii) banks with more negative earnings and more unrealized beginning-of-quarter losses (gains) take big baths (smooth earnings); and (iv) banks with low regulatory capital and more unrealized gains realize more gains. Also, banks with negative earnings tak big baths (avoid or reduce the earnings loss) if their unrealized gains are insufficient (sufficient) to offset the negative earnings. Our inferences apply to listed and non-listed banks, which indicates that the earnings management incentives do not derive solely from public capital markets. Our findings reveal that the accounting for AFS securities gains and losses enables banks to manage regulatory capital and earnings in a variety of ways.
ARTICLE | doi:10.20944/preprints201804.0352.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: network inference; data integration; regulatory networks; transcription factor; gene expression
Online: 27 April 2018 (06:34:12 CEST)
Data generation using high throughput technologies has led to the accumulation of diverse types of molecular data.These data have different types (discrete,real,string etc.) and occur in various formats and sizes. Datasets including gene expression, miRNA expression, protein-DNA binding data (ChIP-Seq/ChIP-ChIP), mutation data(copy number variation, single nucleotide polymorphisms), GO annotations, protein-protein interaction and disease-gene association data are some of the commonly used genomic datasets to study biological processes. Each of them provides a unique, complementary and partly independent view of the genome and hence embed essential information about their regulatory mechanisms. In order to understand the functions of genes, proteins and analyze mechanisms arising out of their interactions, information provided by each of these datasets individually may not be sufficient. Therefore integrating these multi-omic data and inferring regulatory interactions from the integrated dataset provides a system level biological insights in predicting gene functions and their phenotypic outcomes. To study genome functionality through interaction networks, different methods have been proposed for collective mining of information from an integrated dataset. We survey here data integration approaches using state-of-the-art techniques such as network integration, Bayesian networks, regularized regression (LASSO) and multiple kernel learning methods.
ARTICLE | doi:10.20944/preprints202210.0317.v1
Subject: Life Sciences, Genetics Keywords: Bioinformatics; Biotic stresses; Regulatory mechanisms; Protein structure; Gene expression; Evolution analysis
Online: 21 October 2022 (03:37:45 CEST)
Sulfate transporters (SULTRs) are responsible for the uptake of the sulfate (SO42−) ions in the rhizosphere by the roots and their distribution in plant organs. In this study, SULTR family members in the genome of the two oilseed crops, Camelina sativa, and Brassica napus, were identified and characterized based on their sequence structure, duplication events, phylogenetic relationships, phosphorylation sites, and expression levels. Herein, 36 and 45 putative SULTR genes were recognized from the genome of C. sativa, and B. napus, respectively. SULTR proteins were predicted as basophilic proteins with low hydrophilicity in both studied species. According to phylogenetic relationships, we divided SULTRs into five groups, in which SULTRs 3 showed highest variation. Besides, several duplication events were observed between SULTRs. The first duplication event was predicted approximately five million years ago between three SULTRs 3.1 in C. sativa. Two subunits were indicated in the 3D structure of SULTRs that the active binding sites differed between C. sativa and B. napus. According to available RNA-seq data, SULTRs showed diverse expression in tissues and response to stimuli. SULTRs 3 showed an expression in all tissues. SULTRs 3.1 were more upregulated in response to abiotic stresses in C. sativa, while SULTRs 3.3, and SULTRs 2.1 showed an upregulation in B. napus. Furthermore, SULTRs 3 and SULTRs 4.1 showed an upregulation in response to biotic stresses in B. napus. Based on the distribution of cis-regulatory elements in the promoter region, we speculated that SULTRs might be controlled by phytohormones such as ABA, and MeJA. Therefore, it seems that SULTR genes in C. sativa have been more influenced by evolutionary processes and have acquired more diversity.
REVIEW | doi:10.20944/preprints202105.0507.v1
Subject: Engineering, Energy & Fuel Technology Keywords: Energy storage system, photovoltaic systems, PV-battery, regulatory issues, energy management.
Online: 21 May 2021 (09:29:36 CEST)
Integration of battery energy storage in photovoltaic (PV) systems can reduce the electricity costs and provide desirable flexibility and reliability to these systems decreasing renewable energy fluctuations. This paper presents a review of the PV-battery application in Brazil, highlighting the challenges and prospects based on the state-of-art. A PV-battery systems description is presented in this work, as well as the most applied battery technology and its comparison. The paper also describes the set of applications such as voltage and frequency regulation, renewable energy integration, power quality, etc. In the Brazilian scenario, there are applications of PV-battery systems, most of them part of research and development projects (R&D’s), and some real cases are shown, including its goals, applied equipment, operation modes, strategies, and perspectives. Additionally, this work evaluates the Brazilian scenario regarding the energy storage systems implementation challenges, such as regulatory barriers, business models, and opportunities for R&D in the energy market. In conclusion, it is need develop proper regulatory models to expand PV-battery systems and make them visible to the agents in the electricity sector.
ARTICLE | doi:10.20944/preprints202010.0246.v1
Subject: Life Sciences, Biochemistry Keywords: Interleukin-33; Cytokine; Systemic Lupus Erythematosus; Regulatory B cells; autoimmune disease
Online: 12 October 2020 (14:59:30 CEST)
Interleukin-33 (IL-33), a member of the IL-1 cytokine family has been recently associated with the development of autoimmune diseases, including SLE. IL-33 is an alarmin and a pleiotropic cytokine that affects various types of immune cells via binding to its receptor, ST2. In this study, we determine the impact of intraperitoneal IL-33 treatments in young lupus, NZB/W F1 mice. Mice were treated from the age of 6 to 11 weeks. We then assessed the proteinuria level, renal damage, survival rate, and anti-dsDNA antibodies. The induction of regulatory B (Breg) cells and changes in gene expression were also examined. In comparison to the control group, young NZB/W F1 mice administered with IL-33 had a better survival rate as well as reduced proteinuria level and lupus nephritis. IL-33 treatments significantly induced IgM anti-dsDNA antibody, IL-10 expressing Breg cells, and alternatively induced M2 macrophage gene signatures. These results imply that IL-33 exhibit regulatory roles during lupus onset via the expansion of protective IgM anti-dsDNA as well as regulatory cells such as Bregs and M2 macrophages.
REVIEW | doi:10.20944/preprints201809.0289.v1
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: schizophrenia, immune system, inflammation, cytokines, immune regulatory, CIRS, psychiatry, immunology, psychosis
Online: 17 September 2018 (08:57:53 CEST)
In this paper we propose a novel theoretical framework, which was previously developed for major depression and bipolar disorder, namely the compensatory immune-regulatory reflex system (CIRS), as applied to the neuro-immune pathophysiology of schizophrenia and its phenotypes, including first episode psychosis (FEP), acute relapses, chronic and treatment resistant schizophrenia (TRS), comorbid depression, and deficit schizophrenia. These schizophrenia phenotypes and manifestations are accompanied by increased production of positive acute phase proteins, including haptoglobin and α2-macroglobulin, complement factors, and macrophagic M1 (IL-1β, IL-6 and TNF-α), T helper (Th)-1 (interferon-γ and IL-2R), Th-2 (IL-4, IL-5), Th-17 (IL-17) and T regulatory (Treg; IL-10 and transforming growth factor (TGF)-β1) cytokines, cytokine-induced activation of the tryptophan catabolite (TRYCAT) pathway as well as chemokines, including CCL-11 (eotaxin), CCL-2, CCL-3 and CXCL-8. While the immune profiles in the different schizophrenia phenotypes indicate activation of the immune-inflammatory response system (IRS), there are simultaneous signs of CIRS activation, including increased levels of the IL-1 receptor antagonist (sIL-1RA), sIL-2R and tumor necrosis factor-a receptors, Th-2 and Treg phenotypes with increased IL-4 and IL-10 production, and increased levels of TRYCATs and haptoglobin, α2-macroglobulin and other acute phase reactants, which have immune-regulatory and anti-inflammatory effects. Signs of activated IRS and CIRS pathways are also detected in TRS, chronic and deficit schizophrenia indicating that these conditions are accompanied by a new homeostatic setpoint between upregulated IRS and CIRS components. In FEP, increased baseline CIRS activity is a protective factor which may predict favorable clinical outcomes. Moreover, impairments in the CIRS are associated with deficit schizophrenia and greater impairments in semantic and episodic memory. It is concluded that CIRS plays a key role in the pathophysiology of schizophrenia by negatively regulating the primary IRS and contributing to recovery from the acute phase of illness. Components of the CIRS may offer promising therapeutic targets for schizophrenia.
REVIEW | doi:10.20944/preprints201801.0232.v1
Subject: Biology, Other Keywords: small non-coding RNAs; gene regulation; archaea; stress response; regulatory networks
Online: 25 January 2018 (03:57:55 CET)
Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing, and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3’ UTR, 5’ UTR, CDS-binding). These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved, and how sRNAs integrate with complex regulatory networks.
ARTICLE | doi:10.20944/preprints202205.0251.v1
Subject: Life Sciences, Biotechnology Keywords: Recombinant DNA; scope of legislation; regulatory compliance; analytical capabilities; safety; global harmonization
Online: 19 May 2022 (04:55:19 CEST)
A large variety of fermentation products are used in food and feed production, but also in other industries, and many of these products are produced with genetically modified microorganisms (GMMs). In food and feed production, prominent examples are amino acids, vitamins, food and feed enzymes, colorants, non-caloric sweeteners and human milk oligosaccharides. From a regulatory perspective, fermentation products are typically produced under containment. This means that premises, equipment and work processes need to be designed to prevent or at least minimize release of GMMs into the environment. The fermentation products themselves should not contain any live cells of the GMM. Over the past years, there have been concerning developments, particularly in the European Union, stipulating that also absence of recombinant DNA might be interpreted as a regulatory requirement for fermentation products produced with GMMs. In this paper, we (i) attempt to place these developments into the historical context, (ii) sketch the potential negative repercussions for the food and feed industries, (iii) elaborate on the safety of recombinant DNA, and (iv) postulate that recombinant DNA should remain an integral part of the safety assessment of fermentation products but should not be misconstrued as a criterion for regulatory classification of products of biotechnology.
ARTICLE | doi:10.20944/preprints202203.0297.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: regulatory T cell; tumor-infiltrating lymphocyte; neoadjuvant chemotherapy; triple-negative breast cancer
Online: 22 March 2022 (07:50:45 CET)
Triple-negative breast cancer (TNBC) is characterized by an active immune response. We evalu-ated intratumoral interrelation between FOXP3+ tumor-infiltrating lymphocytes and other cy-tokines in TNBC. Network analysis refined cytokines significantly correlate with FOPX3 in TNBC. Treatment response and prognosis imformation of patients and survival data from the TGCA and METABRIC databases were analyzed according to refined cytokines. Interleukin (IL)-33 was sig-nificantly expressed by TNBC cell lines than luminal cell lines (log2 fold change: 5.31, p <0.001) and IL-33 and TGFB2 showed a strong correlation with FOXP3 in the TNBC cell line. Immunohisto-chemistry demonstrated IL-33 high group was a significant predictor of complete response of neoadjuvant chemotherapy (odds ratio (OR) 4.12, p<0.05) and a favorable survival compared to IL-33 low group (OR 6.48, p<0.05) in TNBC. Survival data from TGCA and METABRIC revealed that FOXP3 was a significantly favorable marker in IL-33 high group com-pared to the low IL-33 low group (hazard ratio (HR) 2.1, p=0.02), and IL-33 high/TGFB2 high subgroup showed significant favorable prognosis in the FOXP3 high group compared to the FOPX3 low group in TNBC (HR 3.5, p=0.01). IL-33 and TGFB2 were key cytokines of intratumoral interrelation among FOXP3 in TNBC.
ARTICLE | doi:10.20944/preprints202103.0250.v1
Subject: Social Sciences, Political Science Keywords: Blockchain; Decentralization; Innovation Policy; National Innovation Systems; Policy Tools; Legal and Regulatory
Online: 9 March 2021 (09:50:38 CET)
Blockchain technology can achieve decentralization, multi-party verification, anti-tampering, anonymity, traceability of transactions, and the application of distributed ledger. Countries around the world continue to seek the blockchain business models, technologies and applications, and have different visions and policies for the development of blockchain. This study conducts a comparative policy framework of theoretical analysis of the blockchain technology between the USA and China. Using the innovative policy tools proposed by Rothwell and Zegveld, the above mentioned governments are analyzed from the viewpoint of twelve policy tools. The results show that the USA and China all prefer to use “Environmental-side” policy. The USA has paid more attention to “Legal and regulatory”, “Public services” and “Procurement”. China has the highest proportion of policies in “Political tools”, followed by “Legal & regulatory”, while “Scientific and technical”, “Education” and “Overseas agent” come in third . The blockchain technology has developed vigorously among industries and its applications have gradually diversified. The results are provided to various stakeholders as a reference for policy planning.
ARTICLE | doi:10.20944/preprints202006.0093.v1
Subject: Medicine & Pharmacology, Clinical Neurology Keywords: myasthenia gravis; thymic stromal lymphopoietin; regulatory T cells; TGF- β; IL-10
Online: 7 June 2020 (15:00:37 CEST)
Thymic stromal lymphopoietin (TSLP) is a cytokine and is closely related to Interleukin (IL) - 7, and hTSLP can activation through the human thymus dendritic cell in thymic to indirectly promote the differentiation of natural Regulatory T cells (Tregs) of the thymus. In this study, we focused on recombinant TSLP to determine its effects on the differentiation of CD4+CD25-T cells separated from the thymus of myasthenia gravis (MG) patients. Our results demonstrated that exogenous TSLP could increase CD4+CD25+T/CD4+T cells ratio, up-regulate the expression of Foxp3 mRNA and protein expression in CD4+CD25+Treg cells. Furthermore, we found that CD4+CD25+ Treg cells induced by exogenous TSLP could secrete IL - 10, Transforming growth factor (TGF) - β and the ability to inhibit CD4+T cell proliferation improved. These results indicate that TSLP may promote the differentiation of thymic CD4+CD25-T cells of MG patient to CD4+CD25+Foxp3+ regulatory T cells and enhance the function of immune suppression.
REVIEW | doi:10.20944/preprints201808.0381.v1
Subject: Life Sciences, Immunology Keywords: CCR6, CCL20, Inflammatory Bowel Disease, Inflammation, Suppression, TH17 cells, Regulatory Treg cells
Online: 21 August 2018 (15:04:43 CEST)
Inflammatory bowel disease (IBD) is a CC chemokine receptor 6 (CCR6) - associated immune mediated disorder which has attracted an extensive superfluity of experimental analyses. IBD has come to the fore of varied scrutinizing owing to its complexity by nature for comprising of two synergistic sub phenotypes; Crohn’s disease (CD) and Ulcerative colitis (UC). Both these disease entities cause potent immune dysregulation followed by intense tissue damage within the gut mucosal system, initiating symptoms which are severely debilitating. Multiple causative factors are said to be responsible for IBD but direct immune dysfunction is kindled by overplay of innate and adaptive immune responses produced against a pathogenic microbial attack through the weakened or leaky gut epithelial barrier. Once immune homeostasis is not achieved by tolerating agents, the self-assertive adaptive immunity mobilize its various T and B cell cohorts initializing their allied immune mechanisms by vigorously deploying them towards the site of infection. CCR6 and its unique solitary ligand CC-chemokine ligand 20 (CCL20) are small protein molecules which are abundantly expressed by T and B lymphocytes and act as chemotactic immune-modulatory envoys that help in the deployment of the effector lymphocyte arm of the immune system, producing two directly opposing outcomes in IBD. This dichotomous immunity consists of either immune tolerance or inflammation which then develops into a chronic state, remaining catatonic to inherent immunity or targeted clinical therapy. In this review, we have chronologically identified a plethora of experimental studies radiating into 14 different compartments highlighted in the visual depiction which have employed both mouse models and clinical subjects spanning a period of nearly two decades. In doing so, we expect the research community would further benefit by tracing through the history, thereby understanding the CCR6 –CCL20 axis in IBD and identifying the gaps in literature which can be fortuitously filled in the future.
REVIEW | doi:10.20944/preprints201806.0206.v2
Subject: Biology, Animal Sciences & Zoology Keywords: lineage determination; patterning; blastomere polarization; compaction; cleavage stages; morula; gene regulatory networks
Online: 25 July 2018 (05:43:59 CEST)
The self-organisation of a fertilised egg to form a blastocyst structure, which consists of three distinct cell lineages (trophoblast, epiblast and hypoblast) arranged around an off-centre cavity, is unique to mammals. While the starting point (the zygote) and endpoint (the blastocyst) are similar in all mammals, the intervening events have diverged. This review examines and compares the descriptive and functional data surrounding embryonic gene activation, symmetry-breaking, first and second lineage establishment, and fate commitment in a wide range of mammalian orders. The exquisite detail known from mouse embryogenesis, embryonic stem cell studies and the wealth of recent single cell transcriptomic experiments are used to highlight the building principles underlying early mammalian embryonic development.
ARTICLE | doi:10.20944/preprints202206.0401.v1
Subject: Biology, Plant Sciences Keywords: abaca (Musa textilis); allelic imbalance; regulatory divergence; banana (M. balbisiana); allele-specific expression
Online: 29 June 2022 (09:34:03 CEST)
The Musa textilis var. Abuab has high fiber quality (FQ) but has low resistance against abaca bunchy top virus (AbBTV); the Musa balbisiana var. Pacol, has low FQ but high resistance against AbBTV. Their backcrosses (BC2 and BC3) possess both desirable traits. Analysis using RNA-seq showed that the regulatory divergence of Abuab and Pacol is largely explained by cis differences with 27.4% and 22.3% if we are to assess it using BC2 and BC3, respectively. Cis differences between the two genotypes are significantly reduced from BC2 to BC3 due to changes in genomic constitution. Trans, on the other hand, is robust to changes in allelic composition. All these are attributed to the loss of heterozygosity in the BC3 relative to BC2. Further analysis showed that both backcrosses exhibited genome-wide preferential expression of Pacol- over Abuab-specific alleles, despite the wider genetic presence of the latter in the hybrids. The ratio of the two genotype-specific expressed transcripts and the ratio of their corresponding genetic make-up are significantly disproportionate, a phenomenon which we refer here as “genome–transcriptome incongruence”. We also observed preferential expression switching in which several genes prefer Abuab- (or Pacol-) specific allele in the BC2 but switched to Pacol- (or Abuab-) specific allele in the BC3 genome.
REVIEW | doi:10.20944/preprints202110.0060.v3
Subject: Biology, Plant Sciences Keywords: RNAi; dsRNA; silencing; encapsulation; liposomes; virus-like particles; polyplex nanoparticles; bio-clay; regulatory
Online: 13 October 2021 (15:39:34 CEST)
RNAi technology is a versatile, effective, safe, and eco-friendly alternative for crop protection. There is plenty of evidence of its use through host-induced gene silencing (HIGS) and spray-induced gene silencing (SIGS) techniques to control viruses, bacteria, fungi, insects, and nematodes. For SIGS, its most significant challenge is achieving stability and avoiding premature degradation of RNAi in the environment or during its absorption by the target organism. One alternative is encapsulation in liposomes, virus-like particles, polyplex nanoparticles, and bioclay, which can be obtained through the recombinant production of RNAi in vectors, transgenesis, and micro/nanoencapsulation. The materials must be safe, biodegradable, and stable in multiple chemical environments, favoring the controlled release of RNAi. Most of the current research on encapsulated RNAi focuses primarily on oral delivery to control insects by silencing essential genes. The regulation of RNAi technology focuses on risk assessment using different approaches; however, this technology has positive economic, environmental, and human health implications for its use in agriculture. The emergence of alternatives combining RNAi gene silencing with the induction of resistance in crops by elicitation and metabolic control is expected, as well as multiple silencing and biotechnological optimization of its large-scale production.
ARTICLE | doi:10.20944/preprints202011.0199.v1
Subject: Life Sciences, Biophysics Keywords: Gene Regulatory Networks; Non-Linear Variable Order Fractional System; Gene Expression; Epigenetic Memory
Online: 4 November 2020 (15:35:24 CET)
Complex diseases such as cancer are caused by changes in the Gene Regulatory Networks. Systems that model the complex dynamics of these networks along with adapting to real gene expression data are closer to reality and can help understand the creation and treatment of cancer. In this paper, for the first time, modelling of gene regulatory networks is performed using delayed nonlinear variable order fractional systems in the state space by a new tool called GENAVOS. This tool uses gene expression time series data to identify and optimize system parameters. This software has several tools for analyzing system dynamics. The results show that the nonlinear variable order fractional systems have very good flexibility in adapting to real data. We found that regulatory networks in cancer cells actually have a larger delay parameter than in normal cells. It is also possible to create chaos, periodic and quasi-periodic oscillations by changing the delay, degradation and synthesis rates. Our findings indicate a profound effect of time-varying order on these networks, which may be related to a type of cellular memory due to epigenetic and environmental factors. We showed that by changing the delay parameter and the variable order function for a normal cell system, its behavior changes and becomes quite similar to the behavior of a cancer cell. This work also confirms the effective role of the miR-17-92 cluster in the cancer cell cycle. GENAVOS is available at https://github.com/hanif-y/GENAVOS with its user guide and MATLAB codes.
ARTICLE | doi:10.20944/preprints201806.0340.v1
Subject: Life Sciences, Immunology Keywords: T-regulatory cells, immune regulation, Foxp3, PPARγ, autoimmune diabetes, NOD mouse, Thiazolidinediones, ciglitazone.
Online: 22 June 2018 (09:33:32 CEST)
Immunomodulation as means of immunotherapy has been studied in major research and clinical laboratories for many years. T-Regulatory (Treg) cell therapy is one of the modulator used in immunotherapy approaches. Similarly, nuclear receptor peroxisome proliferator activated receptor gamma (PPARγ) has extensively been shown to play a role as an immuno-modulator during inflammation. Given their mutual roles in downregulating the immune response, current study examined the influence of PPARγ ligands i.e thiazolidinedione (TZD) class of drugs on Foxp3 expression and possible crosstalk between PPARγ and nTreg cells of NOD and NOR mice. Results showed that TZD drug, ciglitazone and natural ligand of PPARγ 15d-prostaglandin downregulated Foxp3 expression in activated nTreg cells from both NOD and NOR mice. Interestingly, addition of the PPARγ inhibitor, GW9662 further downregulated Foxp3 expression in these cells from both mice. We also found that PPARγ ligands negatively regulate Foxp3 expression in activated nTreg cells via PPARγ-independant mechanism(s). These results demonstrate that both natural and synthetic PPARγ ligands capable of suppressing Foxp3 expression in activated nTreg cells of NOD and NOR mice. This may suggest that the effect of PPARγ ligands in modulating Foxp3 expression in activated nTreg cells is different from their reported effects on effector T cells. Given the capability to suppress foxp3 gene, it is possible to be tested as immunomodulators in cancer-related studies.
REVIEW | doi:10.20944/preprints202210.0397.v1
Subject: Medicine & Pharmacology, Other Keywords: biosimilars; regulatory process; animal studies; clinical efficacy testing; interchangeability; FDA; EMA; MHRA; MENA; cGMP
Online: 26 October 2022 (03:58:16 CEST)
Biological drugs are inaccessible to more than 80% of the world population due mainly to their high costs; this is a significant concern of the World Health Organization. Biosimilars are supposed to reduce the cost burden, but their approval process is complex, including expensive and irrelevant studies. While the Stringent Regulatory Authorities (SRAs) have adopted the guidance of the FDA or EMA, such adoptions are neither necessary nor practical for the rest of the world (ROW). We present a science-driven, rational approach to formulate regulatory guidelines that will enable faster biosimilars' entry into the ROW without compromising their safety and efficacy. The key recommendations include removing animal and safety efficacy testing, making analytical assessment more robust, and cGMP compliance assured through third-party audits. The ROW countries are also recommended to initiate a rapporteur system available in the EU, to overcome the biases and assure state-of-the-science evaluation as the common understanding of the critical quality attributes evolves. It is anticipated that stronger regional agencies like those in the MENA region, with the leadership of the Kingdom of Saudi Arabia, will help propel the idea faster across the globe.
ARTICLE | doi:10.20944/preprints202111.0222.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: Takayasu arteritis; echocardiography; immune cell infiltration; vascular stiffness; T helper like cells; regulatory T lymphocytes
Online: 12 November 2021 (13:40:14 CET)
Background: Takayasu Arteritis (TAK) increases vascular stiffness and arterial resistance. Hypertension and atherosclerosis lead to similar changes. We investigated possible differences in cardiovascular remodeling between these diseases and whether the differences are correlated with immune cell expression. Methods: Patients with active TAK arteritis were compared with age- and sex-matched hypertensive and atherosclerotic patients. In a subpopulation of TAK patients, Treg/Th17 cells were measured before (T0) and after 18 months (T18) of infliximab treatment. Echocardiogram, supraaortic Doppler ultrasound, and lymphocytogram were performed in all patients. Histological and immunohistochemical evaluation of the vessel wall was performed to compare the in vivo results. Results: TAK patients have increased aortic valve dysfunction and diastolic dysfunction. These data have been associated with uric acid levels. A significant increase in aortic stiffness was also noted and associated with peripheral T lymphocyte levels. CD3+CD4+ cell infiltrates were detected in the vessel wall samples of these patients. They had a lower mean percentage of Tregs at T0 than controls, but levels increased significantly at T18. Opposite results were found in Th17 cells. Finally, TAK patients were found to have an increased risk of atherosclerotic cardiovascular disease (ASCVD). Conclusion: Our data suggest that different pathogenic mechanisms of vessel damage, including atherosclerosis, underlie TAK patients compared with control subjects. The increased risk of ASCVD in TAK patients correlates directly with the degree of inflammatory cell infiltration in the vessel wall. Infliximab restores the normal frequency of Tregs/Th17 in TAK patients and allows a possible reduction of steroids and immunosuppressants.
HYPOTHESIS | doi:10.20944/preprints202108.0270.v1
Subject: Biology, Other Keywords: T helper differentiation; T helper polarization; Cross-reactivity; Regulatory T cells; Microbiota; Original Antigenic Sin
Online: 12 August 2021 (08:46:55 CEST)
Naive CD4+ T cells engage cognate peptide MHC-II complexes (pMHC-IIs) to differentiate and acquire one of several T helper (Th) fates whose specific trajectories are guided by a dynamic cytokine milieu that develops in response to antigenic entity. This physiological process is often erroneously conflated with a pathological one termed Th polarization. Using the SPIRAL model, we argue here that unlike Th fate choice, innate signaling alone is insufficient to initiate Th polarization in naive CD4+ T cells, that it instead develops from pre-existing memory CD4+ T cells that express cross-reactive TCRs, and that it inevitably leads to immunopathology.
ARTICLE | doi:10.20944/preprints201809.0200.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: objective clustering; biclustering; gene regulatory networks; reconstruction; validation; gene expression profiles; noise component; systems stability
Online: 11 September 2018 (13:48:12 CEST)
REVIEW | doi:10.20944/preprints202212.0006.v2
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: Reconfigurable intelligent surfaces; 6G; Cascade Channel Decoupling; RIS Regulatory Constraint; RIS System Architecture; True Time Delay.
Online: 26 December 2022 (01:45:18 CET)
It is expected that scholars will continue to strengthen the depth and breadth of theoretical research on RIS, so as to provide a higher theoretical upper bound for the engineering application of RIS. While making breakthroughs in academic research, great progress has been made in engineering application research and industrialization promotion. This article will provide an overview of RIS engineering applications, mainly including the typical features, typical classifications, and typical deployment scenarios of RIS. Then the challenges and candidate solutions of the RIS are systematically and deeply analyzed, involving the cascade channel decoupling for solving the RIS beamforming, the influences and solutions of RIS regulation constraints, RIS system architecture of network controlled mode, the integrated channel regulation and information modulation, TDD mechanism used for RIS. Future trends and challenges are also provided.
ARTICLE | doi:10.20944/preprints202112.0111.v1
Subject: Biology, Plant Sciences Keywords: Durum wheat; heat stress; grain weight; grain quality; RNA-seq; gene regulatory network; DOF transcription factor
Online: 7 December 2021 (23:38:32 CET)
In a changing climate, extreme weather events such as heat waves will be more frequent and could affect grain weight and the quality of crops such as wheat, one of the most significant crops in terms of global food security. In this work, we characterized the response of Triticum turgidum spp. durum wheat to a short-term heat-stress (HS) treatment at transcriptomic and physiological levels during early grain filling in glasshouse experiments. We found a significant reduction in grain weight and size from HS treatment. Grain quality was also affected, showing a decrease in starch content in addition to increments in grain protein levels. Moreover, an RNA-seq analysis of durum wheat grains allowed us to identify 1590 differentially expressed genes related to photosynthesis, response to heat, and carbohydrate metabolic process. A gene regulatory network analysis of HS-responsive genes uncovered novel transcription factors (TFs) controlling the expression of genes involved in abiotic stress response and grain quality, such as a member of the DOF family predicted to regulate glycogen and starch biosynthetic processes in response to HS in grains. In summary, our results provide new insights into the extensive transcriptome reprogramming that occurs during short-term HS in durum wheat grains.
Subject: Life Sciences, Biochemistry Keywords: livestock diseases; miRNAs; biomarkers; regulatory networks; mastitis; PRRSV; foot-and-mouth disease; Marek's disease; RNAi therapy
Online: 31 December 2020 (09:15:19 CET)
MicroRNAs (miRNAs) are small endogenous RNAs that regulate gene expression post-transcriptionally by targeting either the 3′ untranslated or coding regions of genes. They have been reported to play key roles in a wide range of biological processes. The recent remarkable developments of transcriptomics technologies, especially next-generation sequencing technologies and advanced bioinformatics tools, allow more in-depth exploration of messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) including miRNAs. These technologies have offered great opportunities for a deeper exploration of miRNA involvement in farm animal diseases, as well as livestock productivity and welfare. In this review, we provide an overview of the current knowledge of miRNA roles in farm animal diseases with a particular focus on diseases of economic importance. In addition, we discuss the steps and future perspectives of using miRNAs as biomarkers and molecular therapy for livestock disease management as well as the challenges and opportunities for understanding the regulatory mechanisms of miRNAs related to disease pathogenesis.
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Melanoma; Core regulatory network; in silico perturbationSystems pharmacology; Boolean model; Small molecule inhibitors; Virtual screening, ADME, E2F1
Online: 17 August 2021 (11:00:27 CEST)
Skin melanoma presents increasing prevalence and poor outcomes. Progression to aggressive stages is characterized by overexpression of the transcription factor E2F1 and activation of downstream pro-metastatic gene regulatory networks (GRNs). Appropriate therapeutic manipulation of the E2F1-governed GRNs holds potential to prevent metastasis, however these networks entail complex feedback and feedforward regulatory motifs among various regulatory layers, which challenge the characterization of drug targetablemake it difficult to identify druggable components. To this end, computational approaches such as mathematical modeling and virtual screening are important tools to unveil the dynamics of these signaling networks and comprehensively identify critical components that could be further explored as therapeutic targets. Herein, we integrated a well-established E2F1-mediated epithelial-mesenchymal transition (EMT) map with transcriptomics data from E2F1-expressing melanoma cells to reconstruct a core regulatory network underlying aggressive melanoma. Using logic-based in silico perturbation experiments of a core regulatory network, we identifiedy that simultaneous perturbation of AKT1 and MDM2 drastically reduces EMT in metastatic melanoma. Using the structures of the two protein signatures along with virtual screening of lead-like compound library available in ZINC12 database, we identified a number of lead compounds that efficiently inhibit AKT1 and MDM2 without eliciting toxicities. We propose that these compounds could be taken into account in the design of novel therapeutic strategies for the management of aggressive melanoma. were identified using virtual screening of lead-like compound library available in ZINC12 database. Subsequent high-throughput virtual screening of drug library using the structures of the two protein signatures predicted a number of lead compounds that efficiently inhibit AKT1 and MDM2 without eliciting toxicities. These can be experimentally evaluated and further considered as new anti-melanoma metastatic agents, in monotherapies or combination regimens.
ARTICLE | doi:10.20944/preprints202101.0472.v1
Subject: Engineering, Automotive Engineering Keywords: public health; decision-making; evidence; knowledge; translation; Tobacco Regulatory Science; Tobacco Regulation; ecigarette; e-cig; vape; Juul
Online: 25 January 2021 (10:26:40 CET)
The popularity of electronic cigarettes in the United States and around the world has led to a startling rise in youth nicotine use. The Juul e-cigarette was introduced in the U.S. market in 2015 and had captured approximately 13% of the U.S. market by 2017. Unlike many other contemporary electronic cigarette companies, the founders behind the Juul® e-cigarette approached their product launch like a traditional high-tech start-up company, not like a tobacco company. This article presents a case study of Juul’s corporate and product development history in the context of US regulatory actions. The objective of this article is to demonstrate the value of government-curated archives as leading indicators which can (a) provide insight into emergent technologies and (b) inform emergent regulatory science research questions. A variety of sources were used to gather data about the Juul e-cigarette and the corporations that surround it. Sources included government agencies, published academic literature, non-profit organizations, corporate and retail websites, and the popular press. Data was disambiguated, authenticated, and categorized prior to being placed on a timeline of events. A timeline of four significant milestones, nineteen corporate filings and events, twelve US regulatory actions, sixty four patent applications, eighty seven trademark applications, twenty three design patents and thirty two utility patents related to Juul Labs and its associates is presented spanning the years 2004 thought 2020. This work demonstrates the probative value of findings from patent, trademark, and SEC filing literature in establishing a premise for emergent regulatory science research questions which may not yet be supported by traditional archival research literature. The methods presented here can be used to identify key aspects of emerging technologies before products actually enter the market, this shifting policy formulation and problem identification from a paradigm of being reactive in favor of becoming proactive. Such a proactive approach may permit anticipatory regulatory science research and ultimately shorten the elapsed time between market technology innovation and regulatory response.
REVIEW | doi:10.20944/preprints201805.0129.v1
Subject: Medicine & Pharmacology, Gastroenterology Keywords: BET inhibitors; HDAC inhibitors; pancreatic cancer; aberrant transcription; enhancers; transcription factors; distal regulatory elements; MYC; FOXA1; BRD4
Online: 8 May 2018 (10:47:27 CEST)
While the mortality rates of cancer are generally declining, pancreatic cancer persists to be an exception with a 5-year-survival rate of less than 7%. Late diagnosis and resistance to conventional therapies contribute to high mortality rates in spite of the remarkable recent advances in cancer management and research. Consequently, there is an urgent need to find new and unconventional therapeutic targets to improve prognosis and survival of pancreatic cancer patients. In this review, we discuss the transcriptional effects of the most widely used epigenetic inhibitors in pancreatic cancer focusing on Bromodomain and Extraterminal domain (BET) and Histone Deacetylase (HDAC) inhibitors, which are currently highly promising therapeutic options. We suggest that these inhibitors can be better utilized at lower doses which exploit their transcriptional modulatory effects on pancreatic cancer transcriptional programs directed by specific factors such as MYC and FOXA1, rather than simply based on their anti-proliferative effects. This approach can potentially help avoid the intolerable adverse events frequently elicited by the use of these treatments at higher doses. In particular, we underscore the crucial role of distal regulatory elements in mediating the specific effects of these epigenetic inhibitors and propose using them in a more selective and prudent manner.
ARTICLE | doi:10.20944/preprints202301.0343.v1
Subject: Life Sciences, Genetics Keywords: Prostate cancer; Somatic point mutations; Copy number variation; Regulatory variant, Hi-C; Per-sonalized medicine; Biomedical machine learning
Online: 19 January 2023 (02:10:02 CET)
Prostate cancer (PC) is the most frequently diagnosed non-skin cancer in the world. Previous studies showed that genomic alterations represent the most common mechanism for molecular alterations that cause the development and progression of PC. Great efforts have been done to identify common protein-coding genetic variations; however, the impact of non-coding variations including regulatory genetic variants is not still well understood. To gain an understanding of the functional impact of genetic variants, particularly, regulatory variants in PC, we developed an integrative pipeline (AGV) that used whole genome/exome sequences, GWAS SNPs, chromosome conformation capture data, and ChIP-Seq signals to investigate the potential impact of genomic variants on the underlying target genes in PC. We identified 646 putative regulatory variants, of which 30 of them significantly altered the expression of at least one protein-coding gene. Our analysis of chromatin interactions data (Hi-C) revealed that the 30 putative regulatory variants may affect 131 coding and non-coding genes. Interestingly, our study showed the 131 protein-coding genes are involved in disease-related pathways including Reactome and MSigDB in which for most of them targeted treatment options are currently available. Together, our results provide a comprehensive map of genomic variants in PC and revealed their potential contribution to prostate cancer progression and development.
ARTICLE | doi:10.20944/preprints202104.0344.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Lysine; Rice; Amino Acids; Saline Stress; Abiotic Stress; Gene Regulatory Network; Bayesian Network; Parameter Estimation; Inference; RNA Seq
Online: 13 April 2021 (10:52:26 CEST)
Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the human body’s healthy functioning. Rice is a staple food for large proportion of the global population, thus increasing the lysine content in rice will improve its nutritional value. In this paper, we studied the lysine biosynthesis pathway in rice (Oryza Sativa) to identify the regulators of the lysine reporter gene LYSA (LOC_Os02g24354). Genetically intervening at the regulators has the potential to increase the overall lysine content in rice. We modeled the lysine biosynthesis pathway in rice seedlings under normal and saline (NaCl) stress conditions using Bayesian networks. We estimated the model parameters using experimental data and identified the gene DAPF(LOC_Os12g37960) as a positive regulator of the lysine reporter gene LYSA under both normal and saline stress conditions. Based on this analysis, we conclude that the gene DAPF is a potent candidate for genetic intervention. Upregulating DAPF using methods such as CRISPR-Cas9 has the potential to upregulate the lysine reporter gene LYSA and increase the overall lysine content in rice.
ARTICLE | doi:10.20944/preprints202009.0577.v1
Subject: Engineering, Other Keywords: personal protective equipment (PPE); COVID-19; manufacturing; prototyping; 3D-printing; biocompatibility; sterilization; face shields; regulatory sciences; local resilience
Online: 24 September 2020 (10:45:53 CEST)
The disruption of conventional manufacturing, supply, and distribution channels for medical supplies during the COVID-19 pandemic has caused widespread shortages and catalyzed local efforts to use nontraditional, rapid manufacturing to meet urgent healthcare needs. Here we present a crisis-responsive design framework designed to assist with product development under pandemic conditions. The framework utilizes extensive stakeholder engagement, comprehensive and dynamic needs assessment, local manufacturing, and product testing for the accelerated development of healthcare products. We contrast this framework with traditional medical device manufacturing and discuss relevant regulatory policies. We highlight the applicability of the crisis-responsive framework to a successful local program that designed and supplied face shields for a large US academic hospital. Finally, we make recommendations aimed at improving future resilience to healthcare emergencies. These include continued development of open source designs suitable for rapid manufacturing and changes in regulatory policy that strike a balance between rigidity and uncontrolled innovation.
REVIEW | doi:10.20944/preprints201912.0096.v1
Subject: Life Sciences, Other Keywords: brain connectivity; brain development; gut-brain axis; neurodevelopmental diseases; neuronal cytoarchitecture; neuroplasticity; regulatory T cells; serotonin (5-HT)
Online: 7 December 2019 (16:55:39 CET)
Our knowledge on the plastic functions of the serotonin (5-HT) receptor subtype 7 (5-HT7R) in the brain physiology and pathology considerably advanced in the last few years. A wealth of data show that the 5-HT7R is a key player in the establishment and remodeling of neuronal cytoarchitecture during development and in the mature brain, and its dysfunction is linked to neuropsychiatric and neurodevelopmental diseases. The involvement of this receptor in synaptic plasticity is further demonstrated by data showing that its activation allows to rescue long term potentiation (LTP) and long term depression (LTD) deficits in various animal models of neurodevelopmental diseases. In addition, it is becoming clear that the 5-HT7R is involved in inflammatory intestinal diseases, possibly playing a role in the gut-brain axis, and modulates the function of immune cells. In this review, we will mainly focus on recent findings on this receptor’s role in the structural and synaptic plasticity of the mammalian brain, although we will also illustrate novel aspects highlighted in gut and immune system.
Subject: Keywords: bioprocess models; model validation; model calibration; Quality by Design; mechanistical and statistical models; hybrid models; chemometric models; Biopharmaceutical engineering; regulatory guidance
Online: 10 May 2021 (09:57:09 CEST)
In bioprocess engineering the Qualtiy by Design (QbD) initiative encourages the use of models to define design spaces. However, clear guides on how models for QbD are validated are still missing. In this review we provide a comprehensive overview about validation methods, mathematical approaches and metrics currently applied in bioprocess modeling. The methods cover analytics for data used for modeling, model training and selection, measures for predictiveness and model uncertainties. We point out general issues in model validation and calibration for different types of models and put this into context of existing health authority recommendations. This review provides the start-point for developing a guidance for model validation approaches. There is no one-fits-all approach but this review shall help to identify the best fitting validation method or combination of methods for the specific task and type of bioprocess models that is developed.
REVIEW | doi:10.20944/preprints202103.0061.v1
Subject: Medicine & Pharmacology, Dermatology Keywords: vitamin D3, D2, calcitriol, oral, topical, serum 25-hydroxyvitamin D, psoriasis, skin diseases, UVB, phototherapy, sunshine, COVID-19, regulatory T lymphocytes
Online: 2 March 2021 (09:44:17 CET)
Vitamin D, sunshine and UVB phototherapy were first reported in the early 1900s to control psoriasis, cure rickets and cure tuberculosis (TB). Vitamin D also controlled asthma and rheumatoid arthritis with intakes ranging from 60,000 to 600,000 International Units (IU)/day. In the 1980s interest in treating psoriasis with vitamin D rekindled. Since 1985 four different oral forms of vitamin D (D2, D3, 1-hydroxyvitaminD3 (1(OH)D3) and 1,25-dihydroxyvitaminD3 (calcitriol)) and several topical formulations have been reported safe and effective treatments for psoriasis—as has UVB phototherapy and sunshine. In this review we show that many pre-treatment serum 25(OH)D concentrations fall within the current range of normal, while many post-treatment concentrations fall outside the upper limit of this normal (100 ng/ml). Yet, psoriasis patients showed significant clinical improvement without complications using these treatments. Current estimates of vitamin D sufficiency appear to underestimate serum 25(OH)D concentrations required for optimal health in psoriasis patients, while concentrations associated with adverse events appear to be much higher than current estimates of safe serum 25(OH)D concentrations. Based on these observations, the therapeutic index for vitamin D needs to be reexamined in the treatment of psoriasis and other diseases strongly linked to vitamin D deficiency, including COVID-19 infections, which may also improve safely with sufficient vitamin D intake or UVB exposure.
ARTICLE | doi:10.20944/preprints201809.0193.v1
Subject: Biology, Other Keywords: evolutionary innovation, cell type evolution, cellular stress response, evolution of gene regulation, gene regulatory network evolution, decidual cell, evolution of pregnancy
Online: 11 September 2018 (11:41:34 CEST)
Understanding the evolutionary role of environmentally-induced phenotypic variation (i.e., environmental plasticity) is an important issue in developmental evolution. One of the major physiological responses to environmental changes is cellular stress, which is counteracted by a generic stress reaction that detoxifies the cell, refolds proteins, and repairs DNA damage. In this paper, we elaborate on a previous finding suggesting that the cell differentiation cascade of human decidual stromal cells, a cell type critical for embryo implantation and the maintenance of pregnancy, evolved from a cellular stress reaction. We hypothesize that the stress reaction in these cells was elicited ancestrally through the inflammation caused by embryo attachment and invasion. We describe a model, Stress-Induced Evolutionary Innovation (SIEI), whereby ancestral stress reactions and their corresponding pathways can be transformed into novel structural components of body plans, such as new cell types. After reviewing similarities and differences between SIEI and the “plasticity first hypothesis” (PFH) of evolution, we argue that SIEI is a distinct form of plasticity-based evolutionary change because it leads to the origin of novel structures rather than the adaptive transformation of a pre-existing character.
REVIEW | doi:10.20944/preprints201807.0237.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: TRPM7, kinase, inflammation, lymphocytes, calcium signalling, SMAD, TH17, hypersensitivity, regulatory T cells, thrombosis, graft versus host disease, T cells, innate immunity
Online: 13 July 2018 (14:14:56 CEST)
The enzyme-coupled transient receptor potential channel subfamily M member 7, TRPM7, has been associated with immunity and immune cell signalling. Here, we review the role of this remarkable signalling protein in lymphocyte proliferation, differentiation, activation and survival. We also discuss its role in mast cell, neutrophil and macrophage function and highlight the potential of TRPM7 to regulate immune system homeostasis. Further, we shed light on how the cellular signalling cascades involving TRPM7 channel and/or kinase activity culminate in pathologies as diverse as allergic hypersensitivity, arterial thrombosis, and graft versus host disease (GVHD), stressing the need for TRPM7 specific pharmacological modulators.
REVIEW | doi:10.20944/preprints202006.0078.v1
Subject: Life Sciences, Other Keywords: COVID-19; vaccine; vaccine development; vaccine discovery; systems biology; machine learning; platform technologies; adjuvants; smart clinical trials; human genetics; regulatory convergence; real world evidence; vaccines safety
Online: 7 June 2020 (10:11:02 CEST)
The urgency to develop vaccines against Covid-19 is putting pressure on the long and expensive development timelines which are normally required for development of lifesaving vaccines. There is a unique opportunity to take advantage of new technologies, smart and flexible design of clinical trials, and evolving regulatory science to speed up vaccine development against Covid-19 and transform vaccine development altogether.
REVIEW | doi:10.20944/preprints202105.0183.v1
Subject: Life Sciences, Biochemistry Keywords: Intravenous Immunoglobulin (IVIg); Human Leukocyte Antigen-I (HLA-1); Polyreactive mAbs; Monospecific mAbs; Shared epitopes; Immunosuppression; T-cells; B-memory cells; T-regulatory Cells; Blastogenesis, proliferation, Antibody production
Online: 10 May 2021 (12:30:03 CEST)
HLA class-I (HLA-I) polyreactive monoclonal antibodies (mAbs) reacting to all HLA-I alleles were developed by immunizing HLA-E monomeric heavy chain (HC) (Open Conformers, OCs). Two of the mAbs (TFL-006 and TFL-007) bound to the HC’s coated on a solid matrix. The binding was inhibited by a peptide 117AYDGKDY123, present in all alleles of the six HLA-I isoforms but masked by 2-microglobulin -m) in intact HLA-I trimers (Closed Conformers, CCs). Identical HLA-I polyreactivity is observed in IVIg administered to lower anti-HLA antibodies (Abs) in HLA-sensitized patients, but the mechanism is unknown. We hypothesized that the mAbs that mimic IVIg HLA-I polyreactivity might mimic the immunomodulatory functions of IVIg. We tested the relative binding affinity of the mAbs and IVIg for both OCs- and CCs and compared their effects on (a) the phytohemagglutinin (PHA)-activation T-cells, (b) the production of anti-HLA-II antibody (Ab) by B-memory cells, and anti-HLA-I Ab by immortalized B-cells, and (c) the upregulation of CD4+, CD25+, and Fox P3+ T-regs. The mAbs bound only to OCs, whereas IVIg is bound to both CCs and OCs. The mAbs suppressed blastogenesis and proliferation of PHA-activated T-cells, anti-HLA Ab production by B-cells and expanded the T-regs, better than IVIg. We conclude that a humanized version of the TFL-mAbs could be an ideal therapeutic IVIg-mimetic.
REVIEW | doi:10.20944/preprints201901.0039.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: autoimmune sensorineural hearing loss; age-related sensorineural hearing loss; inflammation, immune senescence; interleukin 1 receptor type II -positive T cells; naturally occurring regulatory T cells; immune rejuvenation; thymus
Online: 4 January 2019 (11:37:31 CET)
Although congenital sensorineural hearing loss (SHL) in the bilateral cochleae mainly results from genetic abnormalities, chronic SHL progressing in later life is often influenced by systemic immune disturbances, including autoimmunity, chronic inflammation, and immunosenescence. We have investigated the relationship between the inner ear and systemic immunity and reviewed the possibilities to prevent SHL, including autoimmune SHL and age-related SHL. We also demonstrated two lymphocyte populations, interleukin 1 receptor type II (IL-1R2)-positive T cells (T1R2) and naturally occurring regulatory T cells (nTregs) in CD4+ T cells, which increase with aging, suppress host immune function and promote organ degeneration. Alterations in systemic immunity by fewer microbial antigen challenges in the living environment, elimination of immune suppressive lymphocytes, or immune rejuvenation with a reconstituted thymus may contribute not only to renew the cochlear function in SHL, but also to extend the healthy life of functional organs in a vigorous and youthful body, one of humanity’s greatest dreams.
REVIEW | doi:10.20944/preprints202007.0311.v1
Subject: Biology, Plant Sciences Keywords: fossil; morphology; evo-devo; paleobotany; evolution; development; macroevolution; modularity; hierarchy; structural fingerprint; regulatory module; auxin; polar auxin transport; embryophyte evolution; sporophyte evolution; polysporangiophyte; leaf evolution; secondary growth; secondary xylem; vascular cambium; strobilus; Sphenophyta; Equisetum; Lycophyta; root evolution; Lepidodendrales
Online: 14 July 2020 (13:34:20 CEST)
Fossils constitute the principal repository of data that allow for independent tests of hypotheses of biological evolution derived from observations of the extant biota. Traditionally, transformational series of structure, consisting of sequences of fossils of the same lineage through time, have been employed to reconstruct and interpret morphological evolution. More recently, a move toward an updated paradigm was fueled by the deliberate integration of developmental thinking in the inclusion of fossils in reconstruction of morphological evolution. The vehicle for this is provided by structural fingerprints – recognizable morphological and anatomical structures generated by (and reflective of) the deployment of specific genes and regulatory pathways during development. Furthermore, because the regulation of plant development is both modular and hierarchical in nature, combining structural fingerprints recognized in the fossil record with our understanding of the developmental regulation of those structures produces a powerful tool for understanding plant evolution. This is particularly true when the systematic distribution of specific developmental regulatory mechanisms and modules is viewed within an evolutionary (paleo-evo-devo) framework. Here, we discuss several advances in understanding the processes and patterns of evolution, achieved by tracking structural fingerprints with their underlying regulatory modules across lineages, living and fossil: the role of polar auxin regulation in the cellular patterning of secondary xylem and the parallel evolution of arborescence in lycophytes and seed plants; the morphology and life history of early polysporangiophytes and tracheophytes; the role of modularity in the parallel evolution of leaves in euphyllophytes; leaf meristematic activity and the parallel evolution of venation patterns among euphyllophytes; mosaic deployment of regulatory modules and the diverse modes of secondary growth of euphyllophytes; modularity and hierarchy in developmental regulation and the evolution of equisetophyte reproductive morphology. More generally, inclusion of plant fossils in the evo-devo paradigm has informed discussions on the evolution of growth patterns and growth responses, sporophyte body plans and their homology, sequences of character evolution, and the evolution of reproductive systems.
REVIEW | doi:10.3390/sci2030068
Subject: Keywords: COVID-19; pooling clinical trials; hyperinfection; steroids; treatment; targeted healthcare; population health management; cancer treatment; clinical research; clinical trials; developing vaccines; ranking and rating hospital quality; school closures; interventions for delirium; assessments of COVID-19 death inequities; regulatory safeguards; preventing child abuse and maltreatment; prevalence of health care worker burnout; nursing home ratings; challenging oncology practice; addressing racial; ethnic; social and economic divides; violence against sexual minority adolescents; primary tumors; metastasis; stages of cancer; reforming cancer clinical trials; supporting carers; protection and prevention; benign and malignant tumors; reforming cancer clinical trials; protection of healthcare personnel; comparing excess deaths in NYC; 1918 influenza pandemic; the possibility of full recovery from COVID-19; mental health impact of COVID-19 on young adults; ranking and rating nursing home quali
Online: 21 August 2020 (00:00:00 CEST)
The SARS-CoV-2 virus that causes the COVID-19 disease has wreaked havoc on the world community in terms of every imaginable parameter. The research output on COVID-19 has been nothing short of phenomenal, especially in the medical and biomedical sciences, where the search for a potential vaccine is being conducted in earnest. Much of the advanced research has been distributed in the leading medical journals, including the Journal of the American Medical Association (JAMA), where the latest research is distributed on a daily basis. The purpose of this paper is to provide some perspectives on 44 interesting and highly topical research papers that have been published in JAMA, at the time of writing, within the past two weeks. The diverse topics include public health, general medicine, internal medicine, oncology, paediatrics, geriatrics, and biostatistics.