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Biology, Volume 9, Issue 11 (November 2020) – 67 articles

Cover Story (view full-size image): Cells, life’s smallest units, are defined within the enclosure of thin, continuous membranes. These confine the molecular machinery required for life and replication of cells. Membrane proteins establish and maintain electrical and solute gradients, vital to normal cellular functions, and are key pharmacological targets. Despite major advances in crystallography and cryo-electron microscopy, structural studies of membrane proteins remain challenging. Nuclear magnetic resonance is an advanced tool for membrane protein structural studies in mimetics and membranes at the atomic level of detail. We discuss the applications of solution and solid-state NMR to structural and interaction studies of membrane proteins, alongside new developments in signal and sensitivity enhancement through dynamic nuclear polarization. View this paper.
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Open AccessReview
Sustainable Antibiotic-Free Broiler Meat Production: Current Trends, Challenges, and Possibilities in a Developing Country Perspective
Biology 2020, 9(11), 411; https://doi.org/10.3390/biology9110411 - 23 Nov 2020
Viewed by 360
Abstract
Antibiotic-free broiler meat production is becoming increasingly popular worldwide due to consumer perception that it is superior to conventional broiler meat. Globally, broiler farming impacts the income generation of low-income households, helping to alleviate poverty and secure food in the countryside and in [...] Read more.
Antibiotic-free broiler meat production is becoming increasingly popular worldwide due to consumer perception that it is superior to conventional broiler meat. Globally, broiler farming impacts the income generation of low-income households, helping to alleviate poverty and secure food in the countryside and in semi-municipal societies. For decades, antibiotics have been utilized in the poultry industry to prevent and treat diseases and promote growth. This practice contributes to the development of drug-resistant bacteria in livestock, including poultry, and humans through the food chain, posing a global public health threat. Additionally, consumer demand for antibiotic-free broiler meat is increasing. However, there are many challenges that need to be overcome by adopting suitable strategies to produce antibiotic-free broiler meat with regards to food safety and chicken welfare issues. Herein, we focus on the importance and current scenario of antibiotic use, prospects, and challenges in the production of sustainable antibiotic-free broiler meat, emphasizing broiler farming in the context of Bangladesh. Moreover, we also discuss the need for and challenges of antibiotic alternatives and provide a future outlook for antibiotic-free broiler meat production. Full article
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Open AccessArticle
First De Novo Transcriptome of the Copepod Rhincalanus gigas from Antarctic Waters
Biology 2020, 9(11), 410; https://doi.org/10.3390/biology9110410 - 23 Nov 2020
Viewed by 246
Abstract
Antarctic waters are the largest almost untapped diversified resource of our planet. Molecular resources for Antarctic organisms are very limited and mostly represented by sequences used for species genotyping. In this study, we present the first transcriptome for the copepod Rhincalanus gigas, [...] Read more.
Antarctic waters are the largest almost untapped diversified resource of our planet. Molecular resources for Antarctic organisms are very limited and mostly represented by sequences used for species genotyping. In this study, we present the first transcriptome for the copepod Rhincalanus gigas, one of the predominant zooplankton species of Antarctic waters. This transcriptome represents also the first molecular resource for an eucalanoid copepod. The transcriptome is of high quality and completeness. The presence of three predicted genes encoding antifreeze proteins and gene duplication within the glutathione metabolism pathway are suggested as possible adaptations to cope with this harsh environment. The R. gigas transcriptome represents a powerful new resource for investigating the molecular basis associated with polar biological processes and ecology. Full article
(This article belongs to the Section Marine Biology)
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Open AccessReview
Interaction between Laser Light and Osteoblasts: Photobiomodulation as a Trend in the Management of Socket Bone Preservation—A Review
Biology 2020, 9(11), 409; https://doi.org/10.3390/biology9110409 - 23 Nov 2020
Viewed by 291
Abstract
Bone defects are the main reason for aesthetic and functional disability, which negatively affect patient’s quality of life. Particularly, after tooth extraction, the bone of the alveolar process resorbs, limiting the optimal prosthetic implant placement. One of the major pathophysiological events in slowly- [...] Read more.
Bone defects are the main reason for aesthetic and functional disability, which negatively affect patient’s quality of life. Particularly, after tooth extraction, the bone of the alveolar process resorbs, limiting the optimal prosthetic implant placement. One of the major pathophysiological events in slowly- or non-healing tissues is a blood supply deficiency, followed by a significant decrease in cellular energy amount. The literature shows that photons at the red and infrared wavelengths can interact with specific photoacceptors located within the cell. Through this mechanism, photobiomodulation (PBM) can modify cellular metabolism, by increasing mitochondrial ATP production. Here, we present a review of the literature on the effect of PBM on bone healing, for the management of socket preservation. A search strategy was developed in line with the PRISMA statement. The PubMed and Scholar electronic databases were consulted to search for in vivo studies, with restrictions on the year (<50 years-old), language (English), bone socket preservation, and PBM. Following the search strategy, we identified 269 records, which became 14, after duplicates were removed and titles, abstract and inclusion-, exclusion-criteria were screened. Additional articles identified were 3. Therefore, 17 articles were included in the synthesis. We highlight the osteoblast–light interaction, and the in vivo therapeutic tool of PBM is discussed. Full article
(This article belongs to the Special Issue Multidisciplinary Insights on Bone Healing)
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Open AccessArticle
Transcriptional Responses of the Heat Shock Protein 20 (Hsp20) and 40 (Hsp40) Genes to Temperature Stress and Alteration of Life Cycle Stages in the Harmful Alga Scrippsiella trochoidea (Dinophyceae)
Biology 2020, 9(11), 408; https://doi.org/10.3390/biology9110408 - 21 Nov 2020
Viewed by 317
Abstract
The small heat shock protein (sHsp) and Hsp40 are Hsp members that have not been intensively investigated but are functionally important in most organisms. In this study, the potential roles of a Hsp20 (StHsp20) and a Hsp40 (StHsp40) in [...] Read more.
The small heat shock protein (sHsp) and Hsp40 are Hsp members that have not been intensively investigated but are functionally important in most organisms. In this study, the potential roles of a Hsp20 (StHsp20) and a Hsp40 (StHsp40) in dinoflagellates during adaptation to temperature fluctuation and alteration of different life stages were explored using the representative harmful algal blooms (HABs)-causative dinoflagellate species, Scrippsiella trochoidea. We isolated the full-length cDNAs of the two genes via rapid amplification of cDNA ends (RACE) and tracked their differential transcriptions via real-time qPCR. The results revealed StHsp20 and StHsp40 exhibited mRNA accumulation patterns that were highly similar in response to heat stress but completely different toward cold stress, which implies that the mechanisms underlying thermal and cold acclimation in dinoflagellates are regulated by different sets of genes. The StHsp20 was probably related to the heat tolerance of the species, and StHsp40 was closely involved in the adaptation to both higher and lower temperature fluctuations. Furthermore, significantly higher mRNA abundance of StHsp40 was detected in newly formed resting cysts, which might be a response to intrinsic stress stemmed from encystment. This finding also implied StHsp40 might be engaged in resting cyst formation of S. trochoidea. Our findings enriched the knowledge about possible cross-talk of different Hsp members in dinoflagellates and provided clues to further explore the molecular underpinnings underlying resting cyst production and broad temperature tolerance of this group of HABs contributors. Full article
(This article belongs to the Section Marine Biology)
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Open AccessReview
Insights on the Quest for the Structure–Function Relationship of the Mitochondrial Pyruvate Carrier
Biology 2020, 9(11), 407; https://doi.org/10.3390/biology9110407 - 19 Nov 2020
Viewed by 492
Abstract
The molecular identity of the mitochondrial pyruvate carrier (MPC) was presented in 2012, forty years after the active transport of cytosolic pyruvate into the mitochondrial matrix was first demonstrated. An impressive amount of in vivo and in vitro studies has since revealed an [...] Read more.
The molecular identity of the mitochondrial pyruvate carrier (MPC) was presented in 2012, forty years after the active transport of cytosolic pyruvate into the mitochondrial matrix was first demonstrated. An impressive amount of in vivo and in vitro studies has since revealed an unexpected interplay between one, two, or even three protein subunits defining different functional MPC assemblies in a metabolic-specific context. These have clear implications in cell homeostasis and disease, and on the development of future therapies. Despite intensive efforts by different research groups using state-of-the-art computational tools and experimental techniques, MPCs’ structure-based mechanism remains elusive. Here, we review the current state of knowledge concerning MPCs’ molecular structures by examining both earlier and recent studies and presenting novel data to identify the regulatory, structural, and core transport activities to each of the known MPC subunits. We also discuss the potential application of cryogenic electron microscopy (cryo-EM) studies of MPC reconstituted into nanodiscs of synthetic copolymers for solving human MPC2. Full article
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Open AccessFeature PaperReview
Nanoparticles Coated with Cell Membranes for Biomedical Applications
Biology 2020, 9(11), 406; https://doi.org/10.3390/biology9110406 - 18 Nov 2020
Viewed by 295
Abstract
Nanoparticles designed for diagnosing and treating different diseases have impacted the scientific research in biomedicine, and are expected to revolutionize the clinic in the near future through a new area called nanomedicine. In the last few years, a new approach in this field [...] Read more.
Nanoparticles designed for diagnosing and treating different diseases have impacted the scientific research in biomedicine, and are expected to revolutionize the clinic in the near future through a new area called nanomedicine. In the last few years, a new approach in this field has emerged: the use of cell membranes for coating nanoparticles in an attempt to mimic the ability of cells to interface and interact with physiological environments. Although such functions have been replicated through synthetic techniques, many research groups are now employing naturally derived cell membranes to coat different types of nanoparticles in an attempt to improve their performance for a wide range of applications. This review summarizes the literature on nanoparticles coated with cell membranes and, more importantly, aims at inspiring and encouraging new developments to this technology in the biomedical area. Full article
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Open AccessReview
Organismal Fructose Metabolism in Health and Non-Alcoholic Fatty Liver Disease
Biology 2020, 9(11), 405; https://doi.org/10.3390/biology9110405 - 18 Nov 2020
Viewed by 269
Abstract
NAFLD has alarmingly increased, yet FDA-approved drugs are still lacking. An excessive intake of fructose, especially in liquid form, is a dietary risk factor of NAFLD. While fructose metabolism has been studied for decades, it is still controversial how fructose intake can cause [...] Read more.
NAFLD has alarmingly increased, yet FDA-approved drugs are still lacking. An excessive intake of fructose, especially in liquid form, is a dietary risk factor of NAFLD. While fructose metabolism has been studied for decades, it is still controversial how fructose intake can cause NAFLD. It has long been believed that fructose metabolism solely happens in the liver and accordingly, numerous studies have investigated liver fructose metabolism using primary hepatocytes or liver cell lines in culture. While cultured cells are useful for studying detailed signaling pathways and metabolism in a cell-autonomous manner, it is equally important to understand fructose metabolism at the whole-body level in live organisms. In this regard, recent in vivo studies using genetically modified mice and stable isotope tracing have tremendously expanded our understanding of the complex interaction between fructose-catabolizing organs and gut microbiota. Here, we discuss how the aberrant distribution of fructose metabolism between organs and gut microbiota can contribute to NAFLD. We also address potential therapeutic interventions of fructose-elicited NAFLD. Full article
(This article belongs to the Special Issue Non-Alcoholic Liver Injury)
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Open AccessReview
Allergies to Titanium Dental Implants: What Do We Really Know about Them? A Scoping Review
Biology 2020, 9(11), 404; https://doi.org/10.3390/biology9110404 - 18 Nov 2020
Viewed by 319
Abstract
The purpose of this scoping review was to describe the current state of knowledge and understanding of allergies to titanium dental implants. A scoping review was conducted following the Prisma Extension for Scoping Reviews checklist. An electronic search was performed in five databases [...] Read more.
The purpose of this scoping review was to describe the current state of knowledge and understanding of allergies to titanium dental implants. A scoping review was conducted following the Prisma Extension for Scoping Reviews checklist. An electronic search was performed in five databases complemented by manual and grey literature searches. Fifty-two relevant papers were included for final review. Titanium particles can be released from the surfaces of dental implants in a process called tribocorrosion, which may contribute to bone loss due to inflammatory reaction. Diverse mechanisms have been described that may trigger allergy to titanium, as well as the clinical signs that manifest as the allergy develops. Allergies to titanium are uncommon but represent a real possibility that should not be overlooked in patients requiring prosthodontic rehabilitation with dental implants. Allergy can trigger a range of symptoms. Patients who have already been diagnosed with allergies to other metals will be more predisposed to suffering an allergy to titanium. Further investigation is needed in order to measure the true scope of these allergies. Full article
(This article belongs to the Special Issue New Trends in Bioengineering in Osseointegration and Dental Implants)
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Open AccessReview
Fascin in Cell Migration: More Than an Actin Bundling Protein
Biology 2020, 9(11), 403; https://doi.org/10.3390/biology9110403 - 17 Nov 2020
Viewed by 322
Abstract
Fascin, an actin-binding protein, regulates many developmental migrations and contributes to cancer metastasis. Specifically, Fascin promotes cell motility, invasion, and adhesion by forming filopodia and invadopodia through its canonical actin bundling function. In addition to bundling actin, Fascin has non-canonical roles in the [...] Read more.
Fascin, an actin-binding protein, regulates many developmental migrations and contributes to cancer metastasis. Specifically, Fascin promotes cell motility, invasion, and adhesion by forming filopodia and invadopodia through its canonical actin bundling function. In addition to bundling actin, Fascin has non-canonical roles in the cell that are thought to promote cell migration. These non-canonical functions include regulating the activity of other actin-binding proteins, binding to and regulating microtubules, mediating mechanotransduction to the nucleus via interaction with the Linker of the Nucleoskeleton and Cytoskeleton (LINC) Complex, and localizing to the nucleus to regulate nuclear actin, the nucleolus, and chromatin modifications. The many functions of Fascin must be coordinately regulated to control cell migration. While much remains to be learned about such mechanisms, Fascin is regulated by post-translational modifications, prostaglandin signaling, protein–protein interactions, and transcriptional means. Here, we review the structure of Fascin, the various functions of Fascin and how they contribute to cell migration, the mechanisms regulating Fascin, and how Fascin contributes to diseases, specifically cancer metastasis. Full article
(This article belongs to the Special Issue Reviews in Actin Cytoskeletal Dynamics)
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Open AccessReview
Fluorescent PSC-Derived Cardiomyocyte Reporter Lines: Generation Approaches and Their Applications in Cardiovascular Medicine
Biology 2020, 9(11), 402; https://doi.org/10.3390/biology9110402 - 16 Nov 2020
Viewed by 405
Abstract
Recent advances have made pluripotent stem cell (PSC)-derived cardiomyocytes an attractive option to model both normal and diseased cardiac function at the single-cell level. However, in vitro differentiation yields heterogeneous populations of cardiomyocytes and other cell types, potentially confounding phenotypic analyses. Fluorescent PSC-derived [...] Read more.
Recent advances have made pluripotent stem cell (PSC)-derived cardiomyocytes an attractive option to model both normal and diseased cardiac function at the single-cell level. However, in vitro differentiation yields heterogeneous populations of cardiomyocytes and other cell types, potentially confounding phenotypic analyses. Fluorescent PSC-derived cardiomyocyte reporter systems allow specific cell lineages to be labelled, facilitating cell isolation for downstream applications including drug testing, disease modelling and cardiac regeneration. In this review, the different genetic strategies used to generate such reporter lines are presented with an emphasis on their relative technical advantages and disadvantages. Next, we explore how the fluorescent reporter lines have provided insights into cardiac development and cardiomyocyte physiology. Finally, we discuss how exciting new approaches using PSC-derived cardiomyocyte reporter lines are contributing to progress in cardiac cell therapy with respect to both graft adaptation and clinical safety. Full article
(This article belongs to the Special Issue Pluripotent Stem Cells, Cell Reprogramming and Tissue Modelling)
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Open AccessReview
Changes in Membrane Protein Structural Biology
Biology 2020, 9(11), 401; https://doi.org/10.3390/biology9110401 - 16 Nov 2020
Viewed by 411
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is [...] Read more.
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome. Full article
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Open AccessArticle
Probing Membrane Protein Assembly into Nanodiscs by In Situ Dynamic Light Scattering: A2A Receptor as a Case Study
Biology 2020, 9(11), 400; https://doi.org/10.3390/biology9110400 - 13 Nov 2020
Cited by 1 | Viewed by 371
Abstract
Membrane proteins play a crucial role in cell physiology by participating in a variety of essential processes such as transport, signal transduction and cell communication. Hence, understanding their structure–function relationship is vital for the improvement of therapeutic treatments. Over the last decade, based [...] Read more.
Membrane proteins play a crucial role in cell physiology by participating in a variety of essential processes such as transport, signal transduction and cell communication. Hence, understanding their structure–function relationship is vital for the improvement of therapeutic treatments. Over the last decade, based on the development of detergents, amphipoles and styrene maleic-acid lipid particles (SMALPs), remarkable accomplishments have been made in the field of membrane protein structural biology. Nevertheless, there are still many drawbacks associated with protein–detergent complexes, depending on the protein in study or experimental application. Recently, newly developed membrane mimetic systems have become very popular for allowing a structural and functional characterisation of membrane proteins in vitro. The nanodisc technology is one such valuable tool, which provides a more native-like membrane environment than detergent micelles or liposomes. In addition, it is also compatible with many biophysical and biochemical methods. Here we describe the use of in situ dynamic light scattering to accurately and rapidly probe membrane proteins’ reconstitution into nanodiscs. The adenosine type 2A receptor (A2AR) was used as a case study. Full article
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Open AccessReview
Development of the Biomechanical Technologies for the Modeling of Major Segments of the Human Body: Linking the Past with the Present
Biology 2020, 9(11), 399; https://doi.org/10.3390/biology9110399 - 13 Nov 2020
Viewed by 301
Abstract
The knowledge of human body proportions and segmental properties of limbs, head and trunk is of fundamental importance in biomechanical research. Given that many methods are employed, it is important to know which ones are currently available, which data on human body masses, [...] Read more.
The knowledge of human body proportions and segmental properties of limbs, head and trunk is of fundamental importance in biomechanical research. Given that many methods are employed, it is important to know which ones are currently available, which data on human body masses, lengths, center of mass (COM) location, weights and moment of inertia (MOI) are available and which methods are most suitable for specific research purposes. Graphical, optical, x-ray and derived techniques, MRI, laser, thermography, has been employed for in-vivo measurement, while direct measurements involve cadaveric studies with dissection and various methods of acquiring shape and size of body segments. The present review examines the literature concerning human body segments’ properties for biomechanical purposes starting with a historical examination. It emerges that data obtained in studies on cadaveric specimens are still accurate in comparison to more recent technologies, whilst technological tools currently available are manifolds, each one with proper advantages and disadvantages. Classical studies were focused mainly on white men, while in recent years, the available data on body segments have been extended to children, women, and other races. Additionally, data on special populations (obese, pregnant women) are starting to appear in the scientific literature. Full article
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Open AccessArticle
Deficiency of Splicing Factor 1 (SF1) Reduces Intestinal Polyp Incidence in ApcMin/+ Mice
Biology 2020, 9(11), 398; https://doi.org/10.3390/biology9110398 - 13 Nov 2020
Viewed by 293
Abstract
Background: Splicing factor 1 (SF1) is a conserved alternative splicing factor expressed in many different mammalian cell types. The genetically modified Sf1+/− (or Sf1β-geo/+) mice express reduced levels of SF1 protein in mouse tissues, including in cells of the intestines. Mutational [...] Read more.
Background: Splicing factor 1 (SF1) is a conserved alternative splicing factor expressed in many different mammalian cell types. The genetically modified Sf1+/− (or Sf1β-geo/+) mice express reduced levels of SF1 protein in mouse tissues, including in cells of the intestines. Mutational inactivation of human adenomatous polyposis coli (APC) gene deregulates the Wnt signaling pathway and is a frequent genetic event in colon cancers. Mice with a point mutation in the Apc gene (ApcMin/+) also develop numerous intestinal polyps at a young age. Our aim was to determine the effect of reduced SF1 levels on polyp development due to the strong driver ApcMin/+ mutation. Methods: We utilized mice genetically deficient for expression of SF1 to assess how SF1 levels affect intestinal tumorigenesis. We crossed ApcMin/+ to Sf1+/− mice to generate a cohort of heterozygous mutant ApcMin/+;Sf1+/− mice and compared intestinal polyp development in these mice to that in a control cohort of sibling ApcMin/+ mice. We compared total polyp numbers, sizes of polyps and gender differences in polyp numbers between ApcMin/+;Sf1+/− and ApcMin/+ mice. Results: Our results showed that ApcMin/+ mice with lower SF1 expression developed 25–30% fewer intestinal polyps compared to their ApcMin/+ siblings with normal SF1 levels. Interestingly, this difference was most significant for females (ApcMin/+;Sf1+/− and ApcMin/+ females developed 39 and 55 median number of polyps, respectively). Furthermore, the difference in polyp numbers between ApcMin/+;Sf1+/− and ApcMin/+ mice was significant for smaller polyps with a size of 2 mm or less, whereas both groups developed similar numbers of larger polyps. Conclusions: Our results suggest that lower SF1 levels likely inhibit the rate of initiation of polyp development due to ApcMin/+ driver mutation in the mouse intestine. Thus, therapeutic lowering of SF1 levels in the intestine could attenuate intestinal polyp development. Full article
(This article belongs to the Special Issue Genetics of cancer)
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Open AccessArticle
Integration of Real-Time Image Fusion in the Robotic-Assisted Treatment of Hepatocellular Carcinoma
Biology 2020, 9(11), 397; https://doi.org/10.3390/biology9110397 - 12 Nov 2020
Viewed by 259
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide, with its mortality rate correlated with the tumor staging; i.e., early detection and treatment are important factors for the survival rate of patients. This paper presents the development of a [...] Read more.
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide, with its mortality rate correlated with the tumor staging; i.e., early detection and treatment are important factors for the survival rate of patients. This paper presents the development of a novel visualization and detection system for HCC, which is a composing module of a robotic system for the targeted treatment of HCC. The system has two modules, one for the tumor visualization that uses image fusion (IF) between computerized tomography (CT) obtained preoperatively and real-time ultrasound (US), and the second module for HCC automatic detection from CT images. Convolutional neural networks (CNN) are used for the tumor segmentation which were trained using 152 contrast-enhanced CT images. Probabilistic maps are shown as well as 3D representation of HCC within the liver tissue. The development of the visualization and detection system represents a milestone in testing the feasibility of a novel robotic system in the targeted treatment of HCC. Further optimizations are planned for the tumor visualization and detection system with the aim of introducing more relevant functions and increase its accuracy. Full article
(This article belongs to the Special Issue Computational Biology)
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Open AccessReview
Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR
Biology 2020, 9(11), 396; https://doi.org/10.3390/biology9110396 - 12 Nov 2020
Viewed by 356
Abstract
Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise [...] Read more.
Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells. Full article
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Open AccessReview
Emerging Roles of Liver Sinusoidal Endothelial Cells in Nonalcoholic Steatohepatitis
Biology 2020, 9(11), 395; https://doi.org/10.3390/biology9110395 - 12 Nov 2020
Viewed by 388
Abstract
Nonalcoholic steatohepatitis (NASH) has become a growing public health problem worldwide, yet its pathophysiology remains unclear. Liver sinusoidal endothelial cells (LSEC) have unique morphology and function, and play a critical role in liver homeostasis. Emerging literature implicates LSEC in many pathological processes in [...] Read more.
Nonalcoholic steatohepatitis (NASH) has become a growing public health problem worldwide, yet its pathophysiology remains unclear. Liver sinusoidal endothelial cells (LSEC) have unique morphology and function, and play a critical role in liver homeostasis. Emerging literature implicates LSEC in many pathological processes in the liver, including metabolic dysregulation, inflammation, angiogenesis, and carcinogenesis. In this review, we highlight the current knowledge of the role of LSEC in each of the progressive phases of NASH pathophysiology (steatosis, inflammation, fibrosis, and the development of hepatocellular carcinoma). We discuss processes that have important roles in NASH progression including the detrimental transformation of LSEC called “capillarization”, production of inflammatory and profibrogenic mediators by LSEC as well as LSEC-mediated angiogenesis. The current review has a special emphasis on LSEC adhesion molecules, and their key role in the inflammatory response in NASH. Moreover, we discuss the pathogenic role of extracellular vesicles and their bioactive cargos in liver intercellular communication, inflammation, and fibrosis. Finally, we highlight LSEC-adhesion molecules and derived bioactive product as potential therapeutic targets for human NASH. Full article
(This article belongs to the Special Issue Non-Alcoholic Liver Injury)
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Open AccessArticle
Mathematical Modeling and Robustness Analysis to Unravel COVID-19 Transmission Dynamics: The Italy Case
Biology 2020, 9(11), 394; https://doi.org/10.3390/biology9110394 - 11 Nov 2020
Viewed by 367
Abstract
This study started from the request of providing predictions on hospitalization and Intensive Care Unit (ICU) rates that are caused by COVID-19 for the Umbria region in Italy. To this purpose, we propose the application of a computational framework to a SEIR-type (Susceptible, [...] Read more.
This study started from the request of providing predictions on hospitalization and Intensive Care Unit (ICU) rates that are caused by COVID-19 for the Umbria region in Italy. To this purpose, we propose the application of a computational framework to a SEIR-type (Susceptible, Exposed, Infected, Removed) epidemiological model describing the different stages of COVID-19 infection. The model discriminates between asymptomatic and symptomatic cases and it takes into account possible intervention measures in order to reduce the probability of transmission. As case studies, we analyze not only the epidemic situation in Umbria but also in Italy, in order to capture the evolution of the pandemic at a national level. First of all, we estimate model parameters through a Bayesian calibration method, called Conditional Robust Calibration (CRC), while using the official COVID-19 data of the Italian Civil Protection. Subsequently, Conditional Robustness Analysis (CRA) on the calibrated model is carried out in order to quantify the influence of epidemiological and intervention parameters on the hospitalization rates. The proposed pipeline properly describes the COVID-19 spread during the lock-down phase. It also reveals the underestimation of new positive cases and the need of promptly isolating asymptomatic and presymptomatic cases. The results emphasize the importance of the lock-down timeliness and provide accurate predictions on the current evolution of the pandemic. Full article
(This article belongs to the Special Issue Theories and Models on COVID-19 Epidemics)
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Open AccessReview
Application of Proteomic Technologies to Assess the Quality of Raw Pork and Pork Products: An Overview from Farm-To-Fork
Biology 2020, 9(11), 393; https://doi.org/10.3390/biology9110393 - 11 Nov 2020
Viewed by 333
Abstract
The quality assurance of pork meat and products includes the study of factors prior to slaughter such as handling practices, diet and castration, and others during the post-mortem period such as aging, storage, and cooking. The development over the last two decades of [...] Read more.
The quality assurance of pork meat and products includes the study of factors prior to slaughter such as handling practices, diet and castration, and others during the post-mortem period such as aging, storage, and cooking. The development over the last two decades of high-throughput techniques such as proteomics offer great opportunities to examine the molecular mechanisms and study a priori the proteins in the living pigs and main post-mortem changes and post-translational modifications during the conversion of the muscle into the meat. When the most traditional crossbreeding and rearing strategies to improve pork quality were assessed, the main findings indicate that metabolic pathways early post-mortem were affected. Among the factors, it is well documented that pre-slaughter stress provokes substantial changes in the pork proteome that led to defective meat, and consequently, novel protein biomarkers should be identified and validated. Additionally, modifications in pork proteins had a strong effect on the sensory attributes due to the impact of processing, either physical or chemical. Maillard compounds and protein oxidation should be monitored in order to control proteolysis and volatile compounds. Beyond this, the search of bioactive peptides is becoming a paramount goal of the food and nutraceutical industry. In this regard, peptidomics is a major tool to identify and quantify these peptides with beneficial effects for human health. Full article
(This article belongs to the Section Proteomics)
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Open AccessArticle
Global Picture of Genetic Relatedness and the Evolution of Humankind
Biology 2020, 9(11), 392; https://doi.org/10.3390/biology9110392 - 10 Nov 2020
Viewed by 427
Abstract
We performed an exhaustive pairwise comparison of whole-genome sequences of 3120 individuals, representing 232 populations from all continents and seven prehistoric people including archaic and modern humans. In order to reveal an intricate picture of worldwide human genetic relatedness, 65 million very rare [...] Read more.
We performed an exhaustive pairwise comparison of whole-genome sequences of 3120 individuals, representing 232 populations from all continents and seven prehistoric people including archaic and modern humans. In order to reveal an intricate picture of worldwide human genetic relatedness, 65 million very rare single nucleotide polymorphic (SNP) alleles have been bioinformatically processed. The number and size of shared identical-by-descent (IBD) genomic fragments for every pair of 3127 individuals have been revealed. Over 17 million shared IBD fragments have been described. Our approach allowed detection of very short IBD fragments (<20 kb) that trace common ancestors who lived up to 200,000 years ago. We detected nine distinct geographical regions within which individuals had strong genetic relatedness, but with negligible relatedness between the populations of these regions. The regions, comprising nine unique genetic components for mankind, are the following: East and West Africa, Northern Europe, Arctica, East Asia, Oceania, South Asia, Middle East, and South America. The level of admixture in every studied population has been apportioned among these nine genetic components. Genetically, long-term neighboring populations are strikingly similar to each other in spite of any political, religious, and cultural differences. The topmost admixture has been observed at the center of Eurasia. These admixed populations (including Uyghurs, Azerbaijanis, Uzbeks, and Iranians) have roughly equal genetic contributions from the Middle East, Europe, China, and India, with additional significant traces from Africa and Arctic. The entire picture of relatedness of all the studied populations unfolds and presents itself in the form of shared number/size of IBDs. Full article
(This article belongs to the Special Issue Computational Biology)
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Open AccessArticle
The Tumor–Fat Interface Volume of Breast Cancer on Pretreatment MRI Is Associated with a Pathologic Response to Neoadjuvant Chemotherapy
Biology 2020, 9(11), 391; https://doi.org/10.3390/biology9110391 - 10 Nov 2020
Viewed by 359
Abstract
Adipocytes are active sources of numerous adipokines that work in both a paracrine and endocrine manner. It is not known that the direct contact between tumor and neighboring fat measured by pretreatment breast magnetic resonance imaging (MRI) affects treatment outcomes to neoadjuvant chemotherapy [...] Read more.
Adipocytes are active sources of numerous adipokines that work in both a paracrine and endocrine manner. It is not known that the direct contact between tumor and neighboring fat measured by pretreatment breast magnetic resonance imaging (MRI) affects treatment outcomes to neoadjuvant chemotherapy (NAC) in breast cancer patients. A biomarker quantifying the tumor–fat interface volume from pretreatment MRI was proposed and used to predict pathologic complete response (pCR) in breast cancer patients treated with NAC. The tumor–fat interface volume was computed with data-driven clustering using multiphasic MRI. Our approach was developed and validated in two cohorts consisting of 1140 patients. A high tumor–fat interface volume was significantly associated with a non-pCR in both the development and validation cohorts (p = 0.030 and p = 0.037, respectively). Quantitative measurement of the tumor–fat interface volume based on pretreatment MRI may be useful for precision medicine and subsequently influence the treatment strategy of patients. Full article
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Open AccessReview
Lymphotropic Viruses: Chronic Inflammation and Induction of Cancers
Biology 2020, 9(11), 390; https://doi.org/10.3390/biology9110390 - 10 Nov 2020
Viewed by 296
Abstract
Inflammation induced by transcription factors, including Signal Transducers and Activators of Transcription (STATs) and NF-κB, in response to microbial pathogenic infections and ligand dependent receptors stimulation are critical for controlling infections. However, uncontrolled inflammation induced by these transcription factors could lead to immune [...] Read more.
Inflammation induced by transcription factors, including Signal Transducers and Activators of Transcription (STATs) and NF-κB, in response to microbial pathogenic infections and ligand dependent receptors stimulation are critical for controlling infections. However, uncontrolled inflammation induced by these transcription factors could lead to immune dysfunction, persistent infection, inflammatory related diseases and the development of cancers. Although the induction of innate immunity and inflammation in response to viral infection is important to control virus replication, its effects can be modulated by lymphotropic viruses including human T-cell leukemia virus type 1 (HTLV-1), Κaposi’s sarcoma herpesvirus (KSHV), and Epstein Barr virus (EBV) during de novo infection as well as latent infection. These lymphotropic viruses persistently activate JAK-STAT and NF-κB pathways. Long-term STAT and NF-κB activation by these viruses leads to the induction of chronic inflammation, which can support the persistence of these viruses and promote virus-mediated cancers. Here, we review how HTLV-1, KSHV and EBV hijack the function of host cell surface molecules (CSMs), which are involved in the regulation of chronic inflammation, innate and adaptive immune responses, cell death and the restoration of tissue homeostasis. Thus, better understanding of CSMs-mediated chronic activation of STATs and NF-κB pathways in lymphotropic virus-infected cells may pave the way for therapeutic intervention in malignancies caused by lymphotropic viruses. Full article
(This article belongs to the Special Issue Inflammation in Cancer: A Target for Prevention and Therapy)
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Open AccessCommunication
Development of Open-Field Behaviour in the Medaka, Oryzias latipes
Biology 2020, 9(11), 389; https://doi.org/10.3390/biology9110389 - 10 Nov 2020
Viewed by 342
Abstract
The use of juvenile and larval fish models has been growing in importance for several fields. Accordingly, the evaluation of behavioural tests that can be applied to larvae and juveniles is becoming increasingly important. We tested medaka at four different ages (1, 10, [...] Read more.
The use of juvenile and larval fish models has been growing in importance for several fields. Accordingly, the evaluation of behavioural tests that can be applied to larvae and juveniles is becoming increasingly important. We tested medaka at four different ages (1, 10, 30, and 120 dph) in the open field test, one of the most commonly used behavioural assays, to investigate its suitability for larvae and juveniles of this species. We also explored ontogenetic variation in behaviour during this test. On average, adult 120-day-old medaka showed higher locomotor activity in terms of distance moved compared with younger fish. Our analysis suggests that this effect was derived from both quantitative changes in locomotion related to the ontogenetic increase in fish size as well as qualitative changes in two aspects of locomotor behaviour. Specifically, time spent moving was similar between 1- and 10-day-old medaka, but progressively increased with development. In addition, we revealed that adult medaka showed constant levels of activity, whereas younger medaka progressively reduced their activity over the course of the entire experiment. The thigmotaxis behaviour typically used to assess anxiety in the open field test emerged at 120 days post-hatching, even though a difference in the temporal pattern of spatial preference emerged earlier, between 10 and 30 days post-hatching. In conclusion, some measures of the open field test such as total distance moved allow behavioural phenotyping in the medaka of all ages, although with some degree of quantitative and qualitative developmental variation. In contrast, immature medaka appear not to exhibit thigmotactic behaviour. Full article
(This article belongs to the Section Behavior Biology)
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Open AccessArticle
Evaluation for the Genetic Association between Store-Operated Calcium Influx Pathway (STIM1 and ORAI1) and Human Hepatocellular Carcinoma in Patients with Chronic Hepatitis B Infection
Biology 2020, 9(11), 388; https://doi.org/10.3390/biology9110388 - 09 Nov 2020
Viewed by 375
Abstract
Hepatocellular carcinoma (HCC) often develops from chronic hepatitis B (CHB) through replication of hepatitis B virus (HBV) infection. Calcium (Ca2+) signaling plays an essential role in HBV replication. Store-operated calcium (SOC) channels are a major pathway of Ca2+ entry into [...] Read more.
Hepatocellular carcinoma (HCC) often develops from chronic hepatitis B (CHB) through replication of hepatitis B virus (HBV) infection. Calcium (Ca2+) signaling plays an essential role in HBV replication. Store-operated calcium (SOC) channels are a major pathway of Ca2+ entry into non-excitable cells such as immune cells and cancer cells. The basic components of SOC signaling include the STIM1 and ORAI1 genes. However, the roles of STIM1 and ORAI1 in HBV-mediated HCC are still unclear. Thus, long-term follow-up of HBV cohort was carried out in this study. This study recruited 3631 patients with chronic hepatitis (345 patients with HCC, 3286 patients without HCC) in a Taiwanese population. Genetic variants of the STIM1 and ORAI1 genes were detected using an Axiom CHB1 genome-wide array. Clinical associations of 40 polymorphisms were analyzed. Three of the STIM1 single-nucleotide polymorphisms (SNPs) (rs6578418, rs7116520, and rs11030472) and one SNP of ORAI1 (rs6486795) showed a trend of being associated with HCC disease (p < 0.05). However, after correction for multiple testing, none of the SNPs reached a significant level (q > 0.05); in contrast, neither STIM1 nor ORAI1 showed a significant association with HCC progression in CHB patients. Functional studies by both total internal reflection fluorescence images and transwell migration assay indicated the critical roles of SOC-mediated signaling in HCC migration. In conclusion, we reported a weak correlation between STIM1/ORAI1 polymorphisms and the risk of HCC progression in CHB patients. Full article
(This article belongs to the Section Genetics and Genomics)
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Open AccessArticle
Prognostic Implication of SOX2 Expression Associated with p16 in Oropharyngeal Cancer: A Study of Consecutive Tissue Microarrays and TCGA
Biology 2020, 9(11), 387; https://doi.org/10.3390/biology9110387 - 09 Nov 2020
Viewed by 241
Abstract
For oropharyngeal squamous cell carcinoma (OPSCC), there are not enough additional robust biomarkers for subgrouping after the distinct classification using p16. As SOX2 is an emerging biomarker for cancer treatment, its clinical implication in OPSCC was evaluated using a consecutive tissue microarray (TMA) [...] Read more.
For oropharyngeal squamous cell carcinoma (OPSCC), there are not enough additional robust biomarkers for subgrouping after the distinct classification using p16. As SOX2 is an emerging biomarker for cancer treatment, its clinical implication in OPSCC was evaluated using a consecutive tissue microarray (TMA) cohort consisting of 111 patients who underwent surgery as an initial treatment from May 2002 to December 2016 and 79 patients in The Cancer Genome Atlas (TCGA) dataset. In both datasets, p16+/SOX2High (HPV+/SOX2High in TCGA) showed the best prognosis among the four groups classified by SOX2 and p16 for 5-year overall survival (OS) and recurrence (all p < 0.05), but SOX2 did not make a significant difference in the prognosis of the p16− group. In the TMA cohort, SOX2High was significantly correlated with response to radiotherapy and lower pathologic T classification in the p16+ group (p = 0.001). In TCGA, correlations between SOX2 and tumor stage classification or radiotherapy were not observed; however, HPV+/SOX2High had a significantly low tumor mutation burden among the four groups (all p < 0.05). In summary, SOX2 was proven to be a potential marker to predict overall survival and recurrence in p16+ OPSCC. However, the role of SOX2 has not yet been confirmed in p16− OPSCC patients. Full article
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Open AccessArticle
Fer1L5, a Dysferlin Homologue Present in Vesicles and Involved in C2C12 Myoblast Fusion and Membrane Repair
Biology 2020, 9(11), 386; https://doi.org/10.3390/biology9110386 - 09 Nov 2020
Viewed by 357
Abstract
Fer1L5 is a dysferlin and myoferlin related protein, which has been predicted to have a role in vesicle trafficking and muscle membrane fusion events. Mutations in dysferlin and otoferlin genes cause heredity diseases: muscular dystrophy and deafness in humans, respectively. Dysferlin is implicated [...] Read more.
Fer1L5 is a dysferlin and myoferlin related protein, which has been predicted to have a role in vesicle trafficking and muscle membrane fusion events. Mutations in dysferlin and otoferlin genes cause heredity diseases: muscular dystrophy and deafness in humans, respectively. Dysferlin is implicated in membrane repair. Myoferlin has a role in myogenesis. In this study, we investigated the role of the Fer1L5 protein during myoblast fusion and membrane repair. To study the functions of Fer1L5 we used confocal microscopy, biochemical fractionation, Western blot analysis and multiphoton laser wounding assay. By immunolabelling, Fer1L5 was detected in vesicular structures. By biochemical fractionation Fer1L5 was observed in low density vesicles. Our studies show that the membranes of Fer1L5 vesicles are non-resistant to non-ionic detergent. Partial co-staining of Fer1L5 with other two ferlin vesicles, respectively, was observed. Fer1L5 expression was highly detected at the fusion sites of two apposed C2C12 myoblast membranes and its expression level gradually increased at D2 and reached a maximum at day 4 before decreasing during further differentiation. Our studies showed that Fer1L5 has fusion defects during myoblast fusion and impaired membrane repair when the C2C12 cultures were incubated with inhibitory Fer1L5 antibodies. In C2C12 cells Fer1L5 vesicles are involved in two stages, the fusion of myoblasts and the formation of large myotubes. Fer1L5 also plays a role in membrane repair. Full article
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Open AccessReview
Cytoskeletal Remodeling in Cancer
Biology 2020, 9(11), 385; https://doi.org/10.3390/biology9110385 - 07 Nov 2020
Viewed by 563
Abstract
Successful metastasis depends on cell invasion, migration, host immune escape, extravasation, and angiogenesis. The process of cell invasion and migration relies on the dynamic changes taking place in the cytoskeletal components; actin, tubulin and intermediate filaments. This is possible due to the plasticity [...] Read more.
Successful metastasis depends on cell invasion, migration, host immune escape, extravasation, and angiogenesis. The process of cell invasion and migration relies on the dynamic changes taking place in the cytoskeletal components; actin, tubulin and intermediate filaments. This is possible due to the plasticity of the cytoskeleton and coordinated action of all the three, is crucial for the process of metastasis from the primary site. Changes in cellular architecture by internal clues will affect the cell functions leading to the formation of different protrusions like lamellipodia, filopodia, and invadopodia that help in cell migration eventually leading to metastasis, which is life threatening than the formation of neoplasms. Understanding the signaling mechanisms involved, will give a better insight of the changes during metastasis, which will eventually help targeting proteins for treatment resulting in reduced mortality and longer survival. Full article
(This article belongs to the Section Cancer Biology)
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Open AccessFeature PaperArticle
Loss of Class III Phosphoinositide 3-Kinase Vps34 Results in Cone Degeneration
Biology 2020, 9(11), 384; https://doi.org/10.3390/biology9110384 - 07 Nov 2020
Viewed by 443
Abstract
The major pathway for the production of the low-abundance membrane lipid phosphatidylinositol 3-phosphate (PI(3)P) synthesis is catalyzed by class III phosphoinositide 3-kinase (PI3K) Vps34. The absence of Vps34 was previously found to disrupt autophagy and other membrane-trafficking pathways in some sensory neurons, but [...] Read more.
The major pathway for the production of the low-abundance membrane lipid phosphatidylinositol 3-phosphate (PI(3)P) synthesis is catalyzed by class III phosphoinositide 3-kinase (PI3K) Vps34. The absence of Vps34 was previously found to disrupt autophagy and other membrane-trafficking pathways in some sensory neurons, but the roles of phosphatidylinositol 3-phosphate and Vps34 in cone photoreceptor cells have not previously been explored. We found that the deletion of Vps34 in neighboring rods in mouse retina did not disrupt cone function up to 8 weeks after birth, despite diminished rod function. Immunoblotting and lipid analysis of cones isolated from the cone-dominant retinas of the neural retina leucine zipper gene knockout mice revealed that both PI(3)P and Vps34 protein are present in mouse cones. To determine whether Vps34 and PI(3)P are important for cone function, we conditionally deleted Vps34 in cone photoreceptor cells of the mouse retina. Overall retinal morphology and rod function appeared to be unaffected. However, the loss of Vps34 in cones resulted in the loss of structure and function. There was a substantial reduction throughout the retina in the number of cones staining for M-opsin, S-opsin, cone arrestin, and peanut agglutinin, revealing degeneration of cones. These studies indicate that class III PI3K, and presumably PI(3)P, play essential roles in cone photoreceptor cell function and survival. Full article
(This article belongs to the Section Cell Biology)
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Open AccessArticle
Acute Physiological Responses to High-Intensity Resistance Circuit Training vs. Traditional Strength Training in Soccer Players
Biology 2020, 9(11), 383; https://doi.org/10.3390/biology9110383 - 07 Nov 2020
Viewed by 391
Abstract
The aim of this study was to evaluate and compare the cardiorespiratory and metabolic responses induced by high-intensity resistance circuit-based (HRC) and traditional strength (TS) training protocols. Ten amateur soccer players reported to the laboratory on four occasions: (1) protocol familiarization and load [...] Read more.
The aim of this study was to evaluate and compare the cardiorespiratory and metabolic responses induced by high-intensity resistance circuit-based (HRC) and traditional strength (TS) training protocols. Ten amateur soccer players reported to the laboratory on four occasions: (1) protocol familiarization and load determination; (2) maximal oxygen consumption test; (3) and (4) resistance training protocols (HRC and TS), completed in a cross-over randomized order. In both protocols, the same structure was used (two blocks of 3 sets × 3 exercises, separated by a 5-min rest), with only the time between consecutive exercises differing: TS (3 min) and HRC (~35 s, allowing 3 min of local recovery). To test for between-protocol differences, paired t-tests were applied. Results showed that oxygen consumption and heart rate during HRC were 75% and 39% higher than TS, respectively (p < 0.001). After the training sessions, blood lactate concentration at 1.5, 5 and 7 min and excess post-exercise oxygen consumption were higher in HRC. The respiratory exchange ratio was 6.7% greater during HRC, with no between-group differences found post-exercise. The energy cost of HRC was ~66% higher than TS. In conclusion, HRC training induces greater cardiorespiratory and metabolic responses in soccer players and thus may be a time-effective training strategy. Full article
(This article belongs to the Section Physiology)
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Open AccessArticle
Antimicrobial Activity of Chrysoeriol 7 and Chochlioquinone 9, White-Backed Planthopper-Resistant Compounds, Against Rice Pathogenic Strains
Biology 2020, 9(11), 382; https://doi.org/10.3390/biology9110382 - 07 Nov 2020
Viewed by 316
Abstract
As environmental damage caused by chemical pesticides appears worldwide, eco-friendly agriculture is increasing, and finding eco-friendly pesticide materials has become very important. Chrysoeriol and cochlioquinone, two flavonoids, act as an antibacterial and antioxidant, and increase the resistance of rice to the white-backed planthopper [...] Read more.
As environmental damage caused by chemical pesticides appears worldwide, eco-friendly agriculture is increasing, and finding eco-friendly pesticide materials has become very important. Chrysoeriol and cochlioquinone, two flavonoids, act as an antibacterial and antioxidant, and increase the resistance of rice to the white-backed planthopper (WBPH). In this experiment, chrysoeriol 7 (C7) and cochlioquinone 9 (C9) were extracted from rice inoculated with the WBPH using MeOH, and cultivars with high extraction efficiency were selected. In addition, the antimicrobial activity of C7 and C9 against various pathogens causing disease in rice was tested. The results show that C7 has antifungal activity against Fusarium graminearum and Pythium graminicola, and C9 show antifungal activity against Cladosporium herbarum, Cladosporium cladosporioides, Gibberella zeae, Fusarium graminearum and Pythium graminicola. When both substances were treated at a concentration of 1000 ppm, they showed high inhibition rates of 62.3% and 36.2% against P.graminicola, respectively. After that, a phylogenetic tree was created to clarify the relationship between the microorganisms whose growth was inhibited and divided into three groups. This result can contribute to the study of biopesticide materials that can control pests and pathogens. Full article
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