Biology

3 pages, 203 KiB

Open AccessEditorial

Coronavirus Disease 2019 (COVID-19)

by Mohamad Goldust

Biology 2022, 11(8), 1250; https://doi.org/10.3390/biology11081250 - 22 Aug 2022

Cited by 2 | Viewed by 1392

Abstract

The coronavirus disease 2019 (COVID-19) pandemic has affected almost all aspects of daily life [...] Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

20 pages, 6362 KiB

Open AccessArticle

Perturbation by Antimicrobial Bacteria of the Epidermal Bacterial Flora of Rainbow Trout in Flow-Through Aquaculture

by Hajime Nakatani, Naoki Yamada, Naoki Hashimoto, Fumiyoshi Okazaki, Tomoko Arakawa, Yutaka Tamaru and Katsutoshi Hori

Biology 2022, 11(8), 1249; https://doi.org/10.3390/biology11081249 - 22 Aug 2022

Cited by 1 | Viewed by 3119

Abstract

The bacterial flora of the epidermal mucus of fish is closely associated with the host’s health and susceptibility to pathogenic infections. In this study, we analyzed the epidermal mucus bacteria of rainbow trout (Oncorhynchus mykiss) reared in flow-through aquaculture under environmental [...] Read more.

The bacterial flora of the epidermal mucus of fish is closely associated with the host’s health and susceptibility to pathogenic infections. In this study, we analyzed the epidermal mucus bacteria of rainbow trout (Oncorhynchus mykiss) reared in flow-through aquaculture under environmental perturbations. Over ~2 years, the bacteria present in the skin mucus and water were analyzed based on the 16S rDNA sequences. The composition of the mucus bacterial community showed significant monthly fluctuations, with frequent changes in the dominant bacterial species. Analysis of the beta- and alpha-diversity of the mucus bacterial flora showed the fluctuations of the composition of the flora were caused by the genera Pseudomonas, Yersinia, and Flavobacterium, and some species of Pseudomonas and Yersinia in the mucus were identified as antimicrobial bacteria. Examination of the antimicrobial bacteria in the lab aquarium showed that the natural presence of antimicrobial bacteria in the mucus and water, or the purposeful addition of them to the rearing water, caused a transition in the mucus bacteria community composition. These results demonstrate that specific antimicrobial bacteria in the water or in epidermal mucus comprise one of the causes of changes in fish epidermal mucus microflora. Full article

(This article belongs to the Section Infection Biology)

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11 pages, 1680 KiB

Open AccessArticle

A Simple Fluorescent Cholesterol Labeling Method to Cryoprotect and Detect Plasma Lipoprotein-X

by Edward B. Neufeld, Lita A. Freeman, Vinay Durbhakula, Maureen L. Sampson, Robert D. Shamburek, Sotirios K. Karathanasis and Alan T. Remaley

Biology 2022, 11(8), 1248; https://doi.org/10.3390/biology11081248 - 22 Aug 2022

Cited by 4 | Viewed by 2146

Abstract

Lipoprotein-X (LpX) are abnormal nephrotoxic lipoprotein particles enriched in free cholesterol and phospholipids. LpX with distinctive lipid compositions are formed in patients afflicted with either familial LCAT deficiency (FLD) or biliary cholestasis. LpX is difficult to detect by standard lipid stains due to [...] Read more.

Lipoprotein-X (LpX) are abnormal nephrotoxic lipoprotein particles enriched in free cholesterol and phospholipids. LpX with distinctive lipid compositions are formed in patients afflicted with either familial LCAT deficiency (FLD) or biliary cholestasis. LpX is difficult to detect by standard lipid stains due to the absence of a neutral lipid core and because it is unstable upon storage, particularly when frozen. We have recently reported that free cholesterol-specific filipin staining after agarose gel electrophoresis sensitively detects LpX in fresh human plasma. Herein, we describe an even more simplified qualitative method to detect LpX in both fresh and frozen–thawed human FLD or cholestatic plasma. Fluorescent cholesterol complexed to fatty-acid-free BSA was used to label LpX and was added together with trehalose in order to cryopreserve plasma LpX. The fluorescent cholesterol bound to LpX was observed with high sensitivity after separation from other lipoproteins by agarose gel electrophoresis. This methodology can be readily developed into a simple assay for the clinical diagnosis of FLD and biliary liver disease and to monitor the efficacy of treatments intended to reduce plasma LpX in these disease states. Full article

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14 pages, 2389 KiB

Open AccessArticle

Thermostable and O₂-Insensitive Pyruvate Decarboxylases from Thermoacidophilic Archaea Catalyzing the Production of Acetaldehyde

by Faisal Alharbi, Thomas Knura, Bettina Siebers and Kesen Ma

Biology 2022, 11(8), 1247; https://doi.org/10.3390/biology11081247 - 22 Aug 2022

Cited by 1 | Viewed by 3998

Abstract

Pyruvate decarboxylase (PDC) is a key enzyme involved in ethanol fermentation, and it catalyzes the decarboxylation of pyruvate to acetaldehyde and CO₂. Bifunctional PORs/PDCs that also have additional pyruvate:ferredoxin oxidoreductase (POR) activity are found in hyperthermophiles, and they are mostly oxygen-sensitive [...] Read more.

Pyruvate decarboxylase (PDC) is a key enzyme involved in ethanol fermentation, and it catalyzes the decarboxylation of pyruvate to acetaldehyde and CO₂. Bifunctional PORs/PDCs that also have additional pyruvate:ferredoxin oxidoreductase (POR) activity are found in hyperthermophiles, and they are mostly oxygen-sensitive and CoA-dependent. Thermostable and oxygen-stable PDC activity is highly desirable for biotechnological applications. The enzymes from the thermoacidophiles Saccharolobus (formerly Sulfolobus) solfataricus (Ss, T_opt = 80 °C) and Sulfolobus acidocaldarius (Sa, T_opt = 80 °C) were purified and characterized, and their biophysical and biochemical properties were determined comparatively. Both enzymes were shown to be heterodimeric, and their two subunits were determined by SDS-PAGE to be 37 ± 3 kDa and 65 ± 2 kDa, respectively. The purified enzymes from S. solfataricus and S. acidocaldarius showed both PDC and POR activities which were CoA-dependent, and they were thermostable with half-life times of 2.9 ± 1 and 1.1 ± 1 h at 80 °C, respectively. There was no loss of activity in the presence of oxygen. Optimal pH values for their PDC and POR activity were determined to be 7.9 and 8.6, respectively. In conclusion, both thermostable SsPOR/PDC and SaPOR/PDC catalyze the CoA-dependent production of acetaldehyde from pyruvate in the presence of oxygen. Full article

(This article belongs to the Special Issue Thermostable Acetaldehyde-Producing Enzymes: Characterization and Applications)

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21 pages, 3312 KiB

Open AccessArticle

Mutational Analyses of the Cysteine-Rich Domain of Yvh1, a Protein Required for Translational Competency in Yeast

by Hannah Zang, Robert Shackelford, Alice Bewley and Alexander E. Beeser

Biology 2022, 11(8), 1246; https://doi.org/10.3390/biology11081246 - 22 Aug 2022

Viewed by 1958

Abstract

Ribosome assembly is a complex biological process facilitated by >200 trans-acting factors (TAFs) that function as scaffolds, place-holders or complex remodelers to promote efficient and directional ribosomal subunit assembly but are not themselves part of functional ribosomes. One such yeast TAF is [...] Read more.

Ribosome assembly is a complex biological process facilitated by >200 trans-acting factors (TAFs) that function as scaffolds, place-holders or complex remodelers to promote efficient and directional ribosomal subunit assembly but are not themselves part of functional ribosomes. One such yeast TAF is encoded by Mrt4 which assembles onto pre-60S complexes in the nuclear compartment and remains bound to pre-60S complexes as they are exported into the cytoplasm. There, Mrt4 is displaced from pre-60S complexes facilitating the subsequent addition of the ribosomal stalk complex (P0/P1/P2). Ribosomal stalk proteins interact with translational GTPases (trGTPase) which facilitate and control protein synthesis on the ribosome. The rRNA-binding domain of Mrt4 is structurally similar to P0, with both proteins binding to the same interface of pre-60S subunits in a mutually exclusive manner; the addition of the ribosomal stalk therefore requires the displacement of Mrt4 from pre-60S subunits. Mrt4 removal requires the C-terminal cysteine-rich domain (CRD) of the dual-specificity phosphatase Yvh1. Unlike many other TAFs, yeast lacking Yvh1 are viable but retain Mrt4 on cytoplasmic pre-60S complexes precluding ribosomal stalk addition. Although Yvh1’s role in Mrt4 removal is well established, how Yvh1 accomplishes this is largely unknown. Here, we report an unbiased genetic screen to isolate Yvh1 variants that fail to displace Mrt4 from pre-60S ribosomes. Bioorthogonal non-canonical amino acid tagging (BONCAT) approaches demonstrate that these YVH1 loss-of-function variants also display defects in nascent protein production. The further characterization of one LOF variant, Yvh1F283L, establishes it as an expression-dependent, dominant-negative variant capable of interfering with endogenous Yvh1 function, and we describe how this Yvh1 variant can be used as a novel probe to better understand ribosome maturation and potentially ribosome heterogeneity in eukaryotes. Full article

(This article belongs to the Section Cell Biology)

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13 pages, 2430 KiB

Open AccessReview

New Insights into the Diversity of Branchiomeric Muscle Development: Genetic Programs and Differentiation

by Imadeldin Yahya, Dorit Hockman, Beate Brand-Saberi and Gabriela Morosan-Puopolo

Biology 2022, 11(8), 1245; https://doi.org/10.3390/biology11081245 - 22 Aug 2022

Viewed by 2718

Abstract

Branchiomeric skeletal muscles are a subset of head muscles originating from skeletal muscle progenitor cells in the mesodermal core of pharyngeal arches. These muscles are involved in facial expression, mastication, and function of the larynx and pharynx. Branchiomeric muscles have been the focus [...] Read more.

Branchiomeric skeletal muscles are a subset of head muscles originating from skeletal muscle progenitor cells in the mesodermal core of pharyngeal arches. These muscles are involved in facial expression, mastication, and function of the larynx and pharynx. Branchiomeric muscles have been the focus of many studies over the years due to their distinct developmental programs and common origin with the heart muscle. A prerequisite for investigating these muscles’ properties and therapeutic potential is understanding their genetic program and differentiation. In contrast to our understanding of how branchiomeric muscles are formed, less is known about their differentiation. This review focuses on the differentiation of branchiomeric muscles in mouse embryos. Furthermore, the relationship between branchiomeric muscle progenitor and neural crest cells in the pharyngeal arches of chicken embryos is also discussed. Additionally, we summarize recent studies into the genetic networks that distinguish between first arch-derived muscles and other pharyngeal arch muscles. Full article

(This article belongs to the Section Developmental and Reproductive Biology)

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15 pages, 2801 KiB

Open AccessArticle

Changes in Dendritic Spine Morphology and Density of Granule Cells in the Olfactory Bulb of Anguilla anguilla (L., 1758): A Possible Way to Understand Orientation and Migratory Behavior

by Riccardo Porceddu, Cinzia Podda, Giovanna Mulas, Francesco Palmas, Luca Picci, Claudia Scano, Saturnino Spiga and Andrea Sabatini

Biology 2022, 11(8), 1244; https://doi.org/10.3390/biology11081244 - 21 Aug 2022

Cited by 1 | Viewed by 3043

Abstract

Olfaction could represent a pivotal process involved in fish orientation and migration. The olfactory bulb can manage olfactive signals at the granular cell (GC) and dendritic spine levels for their synaptic plasticity properties and changing their morphology and structural stability after environmental odour [...] Read more.

Olfaction could represent a pivotal process involved in fish orientation and migration. The olfactory bulb can manage olfactive signals at the granular cell (GC) and dendritic spine levels for their synaptic plasticity properties and changing their morphology and structural stability after environmental odour cues. The GCs’ dendritic spine density and morphology were analysed across the life stages of the catadromous Anguilla anguilla. According to the head and neck morphology, spines were classified as mushroom (M), long thin (LT), stubby (S), and filopodia (F). Total spines’ density decreased from juvenile migrants to no-migrant stages, to increase again in the adult migrant stage. Mean spines’ density was comparable between glass and silver eels as an adaptation to migration. At non-migrating phases, spines’ density decreased for M and LT, while M, LT, and S density increased in silver eels. A great dendritic spine development was found in the two migratory phases, regressing in trophic phases, but that could be recreated in adults, tracing the migratory memory of the routes travelled in juvenile phases. For its phylogenetic Elopomorph attribution and its complex life cycle, A. anguilla could be recommended as a model species to study the development of dendritic spines in GCs of the olfactory bulb as an index of synaptic plasticity involved in the modulation of olfactory stimuli. If olfaction is involved in the orientation and migration of A. anguilla and if eels possess a memory, these processes could be influenced by the modification of environmental stimuli (ocean alterations and rapid climate change) contributing to threatening this critically endangered species. Full article

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18 pages, 5736 KiB

Open AccessArticle

Using DeepLabCut as a Real-Time and Markerless Tool for Cardiac Physiology Assessment in Zebrafish

by Michael Edbert Suryanto, Ferry Saputra, Kevin Adi Kurnia, Ross D. Vasquez, Marri Jmelou M. Roldan, Kelvin H.-C. Chen, Jong-Chin Huang and Chung-Der Hsiao

Biology 2022, 11(8), 1243; https://doi.org/10.3390/biology11081243 - 21 Aug 2022

Cited by 8 | Viewed by 5324

Abstract

DeepLabCut (DLC) is a deep learning-based tool initially invented for markerless pose estimation in mammals. In this study, we explored the possibility of adopting this tool for conducting markerless cardiac physiology assessment in an important aquatic toxicology model of zebrafish (Danio rerio [...] Read more.

DeepLabCut (DLC) is a deep learning-based tool initially invented for markerless pose estimation in mammals. In this study, we explored the possibility of adopting this tool for conducting markerless cardiac physiology assessment in an important aquatic toxicology model of zebrafish (Danio rerio). Initially, high-definition videography was applied to capture heartbeat information at a frame rate of 30 frames per second (fps). Next, 20 videos from different individuals were used to perform convolutional neural network training by labeling the heart chamber (ventricle) with eight landmarks. Using Residual Network (ResNet) 152, a neural network with 152 convolutional neural network layers with 500,000 iterations, we successfully obtained a trained model that can track the heart chamber in a real-time manner. Later, we validated DLC performance with the previously published ImageJ Time Series Analysis (TSA) and Kymograph (KYM) methods. We also evaluated DLC performance by challenging experimental animals with ethanol and ponatinib to induce cardiac abnormality and heartbeat irregularity. The results showed that DLC is more accurate than the TSA method in several parameters tested. The DLC-trained model also detected the ventricle of zebrafish embryos even in the occurrence of heart abnormalities, such as pericardial edema. We believe that this tool is beneficial for research studies, especially for cardiac physiology assessment in zebrafish embryos. Full article

(This article belongs to the Special Issue AI Deep Learning Approach to Study Biological Questions)

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17 pages, 3210 KiB

Open AccessArticle

Soil Microbial Diversity and Community Composition in Rice–Fish Co-Culture and Rice Monoculture Farming System

by Noppol Arunrat, Chakriya Sansupa, Praeploy Kongsurakan, Sukanya Sereenonchai and Ryusuke Hatano

Biology 2022, 11(8), 1242; https://doi.org/10.3390/biology11081242 - 20 Aug 2022

Cited by 38 | Viewed by 4438

Abstract

Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity [...] Read more.

Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility. Full article

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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23 pages, 2625 KiB

Open AccessArticle

Microglia Are Necessary to Regulate Sleep after an Immune Challenge

by Rachel K. Rowe, Tabitha R. F. Green, Katherine R. Giordano, J. Bryce Ortiz, Sean M. Murphy and Mark R. Opp

Biology 2022, 11(8), 1241; https://doi.org/10.3390/biology11081241 - 19 Aug 2022

Cited by 8 | Viewed by 3162

Abstract

Microglia play a critical role in the neuroimmune response, but little is known about the role of microglia in sleep following an inflammatory trigger. Nevertheless, decades of research have been predicated on the assumption that an inflammatory trigger increases sleep through microglial activation. [...] Read more.

Microglia play a critical role in the neuroimmune response, but little is known about the role of microglia in sleep following an inflammatory trigger. Nevertheless, decades of research have been predicated on the assumption that an inflammatory trigger increases sleep through microglial activation. We hypothesized that mice (n = 30) with depleted microglia using PLX5622 (PLX) would sleep less following the administration of lipopolysaccharide (LPS) to induce inflammation. Brains were collected and microglial morphology was assessed using quantitative skeletal analyses and physiological parameters were recorded using non-invasive piezoelectric cages. Mice fed PLX diet had a transient increase in sleep that dissipated by week 2. Subsequently, following a first LPS injection (0.4 mg/kg), mice with depleted microglia slept more than mice on the control diet. All mice were returned to normal rodent chow to repopulate microglia in the PLX group (10 days). Nominal differences in sleep existed during the microglia repopulation period. However, following a second LPS injection, mice with repopulated microglia slept similarly to control mice during the dark period but with longer bouts during the light period. Comparing sleep after the first LPS injection to sleep after the second LPS injection, controls exhibited temporal changes in sleep patterns but no change in cumulative minutes slept, whereas cumulative sleep in mice with repopulated microglia decreased during the dark period across all days. Repopulated microglia had a reactive morphology. We conclude that microglia are necessary to regulate sleep after an immune challenge. Full article

(This article belongs to the Section Neuroscience)

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12 pages, 736 KiB

Open AccessReview

Experience, Principles and Parameters in the Sturgeon Quality Assessment by Anomalies in Early Ontogenesis (A Review)

by Saule Zh. Assylbekova, Ekaterina V. Mikodina, Kuanysh B. Isbekov and Gulmira M. Shalgimbayeva

Biology 2022, 11(8), 1240; https://doi.org/10.3390/biology11081240 - 19 Aug 2022

Cited by 3 | Viewed by 2576

Abstract

Purpose: Review the experience, principles and parameters of the sturgeon assessment quality by anomalies in early ontogeny. Results: Maintaining the number of sturgeon fish in the transboundary Caspian Sea is provided by five states (Russia, Iran, Azerbaijan, Turkmenistan, Kazakhstan) at 16 Sturgeon hatcheries, [...] Read more.

Purpose: Review the experience, principles and parameters of the sturgeon assessment quality by anomalies in early ontogeny. Results: Maintaining the number of sturgeon fish in the transboundary Caspian Sea is provided by five states (Russia, Iran, Azerbaijan, Turkmenistan, Kazakhstan) at 16 Sturgeon hatcheries, where their artificial reproduction is carried out. FAO recognizes Russia’s leadership in creating the basic technology for the sturgeon artificial reproduction, but the other four Caspian states also make a significant contribution to its modern optimizations. There is almost a century of tradition behind the technological development of artificial reproduction in sturgeons. During the artificial reproduction of sturgeons, anomalies in the structure and functions may occur, such as deformities, defects in organs and tissues, edema, hematomas, etc. The sturgeon anomalies classification is based on structural and functional principles. Identification of anomalies is carried out on the basis of a previously created classification, divided into nine large classes. Identification of sturgeon anomalies during the period of their artificial reproduction makes it possible to clarify the real value of replenishment of their stock. Methods: Analysis of professional scientific literature and practical guides. Conclusions: The presence and number of Sturgeon anomalies make it possible to determine their death percentage to calculate the real number of replenishment of the Caspian Sturgeon stock. Full article

(This article belongs to the Special Issue Aquatic Biodiversity and Conservation Biology)

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14 pages, 1982 KiB

Open AccessArticle

Plasma Proteomic Profiling Reveals the Regulatory Factors of Milk Protein Synthesis in Holstein Cows

by Xinling Wang, Jie Xu and Zhaoyu Han

Biology 2022, 11(8), 1239; https://doi.org/10.3390/biology11081239 - 19 Aug 2022

Cited by 4 | Viewed by 1819

Abstract

Milk protein concentrations in dairy cows are considered to be related to some plasma biomolecules. However, the characteristics of plasma biomolecules in dairy cows with different long-term milk protein concentrations are not fully elucidated. This study was conducted to understand the mechanism of [...] Read more.

Milk protein concentrations in dairy cows are considered to be related to some plasma biomolecules. However, the characteristics of plasma biomolecules in dairy cows with different long-term milk protein concentrations are not fully elucidated. This study was conducted to understand the mechanism of plasma proteins in milk protein synthesis by the comparative analysis of the plasma proteomics of cows with different milk protein concentrations. Three groups of Holstein cows (per group = 10) with low (LMP), medium (MMP), and high long-term milk protein concentrations (HMP) were selected for the experiment to determine plasma hormones, biochemical parameters, and proteome. We found that HMP cows had higher concentrations of plasma insulin-like growth factor 1 (IGF-1), glucose, prolactin, insulin, and growth hormone than LMP cows. Additionally, plasma proteomic identified 91 differential proteins, including IGF-1 between the LMP and HMP groups, and the mTOR pathway was enriched. In vitro, IGF-1 treatment increased β-casein expression and simultaneously activated S6K1 and mTOR phosphorylation in bovine mammary epithelial cells. Taken together, these data demonstrate the differences in plasma hormones, biochemical parameters, and proteome of cows with different milk protein concentrations and indicate that IGF-1 enhanced milk protein synthesis, associated with activation of the mTOR signaling pathway. Full article

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34 pages, 4150 KiB

Open AccessSystematic Review

Potential of Whole-Body Vibration in Parkinson’s Disease: A Systematic Review and Meta-Analysis of Human and Animal Studies

by Y. Laurisa Arenales Arauz, Gargi Ahuja, Ype P. T. Kamsma, Arjan Kortholt, Eddy A. van der Zee and Marieke J. G. van Heuvelen

Biology 2022, 11(8), 1238; https://doi.org/10.3390/biology11081238 - 19 Aug 2022

Cited by 14 | Viewed by 3872

Abstract

(1) Background: When the severity of Parkinson’s Disease (PD) increases, patients often have difficulties in performing exercises. Whole-Body Vibration (WBV) may be a suitable alternative. This systematic review aims to clarify if WBV shows potential as rehabilitative therapy for PD patients. (2) Methods: [...] Read more.

(1) Background: When the severity of Parkinson’s Disease (PD) increases, patients often have difficulties in performing exercises. Whole-Body Vibration (WBV) may be a suitable alternative. This systematic review aims to clarify if WBV shows potential as rehabilitative therapy for PD patients. (2) Methods: We searched several databases for controlled trials investigating the effects of WBV (1) on PD populations and (2) PD neuropathological mechanisms. We included both human and animal studies and performed meta-analyses. (3) Results: The studies on PD populations (14 studies) show an overall significant, but small, effect in favor of WBV (Hedges’ g = 0.28), for which the effects on stability (Hedges’ g = 0.39) and balance (Hedges’ g = 0.30) are the most prominent. The studies on the neuropathological mechanisms (18 studies) show WBV effects on neuroinflammation (Hedges’ g = –1.12) and several specific WBV effects on neurotransmitter systems, growth factors, neurogenesis, synaptic plasticity and oxidative stress. (4) Conclusions: The effects of WBV on human PD patients remains inconclusive. Nevertheless, WBV protocols with sufficient duration (≥3 weeks), session frequency (≥3 sessions/week) and vibration frequency (≥20 Hz) show potential as a treatment method, especially for motor function. The potential of WBV for PD patients is confirmed by the effects on the neuropathological mechanisms in mostly non-PD populations. We recommend high-quality future studies on both PD patients and PD mouse models to optimize WBV protocols and to examine the neuropathological mechanisms in PD populations. Full article

(This article belongs to the Special Issue Human Bodywork: Applications in Health, Disease, and Rehabilitation)

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26 pages, 1248 KiB

Open AccessReview

Adipokines in Non-Alcoholic Fatty Liver Disease: Are We on the Road toward New Biomarkers and Therapeutic Targets?

by Vera Francisco, Maria Jesus Sanz, José T. Real, Patrice Marques, Maurizio Capuozzo, Djedjiga Ait Eldjoudi and Oreste Gualillo

Biology 2022, 11(8), 1237; https://doi.org/10.3390/biology11081237 - 19 Aug 2022

Cited by 43 | Viewed by 5013

Abstract

Non-alcoholic fatty liver disease (NAFLD) has become the major cause of chronic hepatic illness and the leading indication for liver transplantation in the future decades. NAFLD is also commonly associated with other high-incident non-communicable diseases, such as cardiovascular complications, type 2 diabetes, and [...] Read more.

Non-alcoholic fatty liver disease (NAFLD) has become the major cause of chronic hepatic illness and the leading indication for liver transplantation in the future decades. NAFLD is also commonly associated with other high-incident non-communicable diseases, such as cardiovascular complications, type 2 diabetes, and chronic kidney disease. Aggravating the socio-economic impact of this complex pathology, routinely feasible diagnostic methodologies and effective drugs for NAFLD management are unavailable. The pathophysiology of NAFLD, recently defined as metabolic associated fatty liver disease (MAFLD), is correlated with abnormal adipose tissue–liver axis communication because obesity-associated white adipose tissue (WAT) inflammation and metabolic dysfunction prompt hepatic insulin resistance (IR), lipid accumulation (steatosis), non-alcoholic steatohepatitis (NASH), and fibrosis. Accumulating evidence links adipokines, cytokine-like hormones secreted by adipose tissue that have immunometabolic activity, with NAFLD pathogenesis and progression; however, much uncertainty still exists. Here, the current knowledge on the roles of leptin, adiponectin, ghrelin, resistin, retinol-binding protein 4 (RBP4), visfatin, chemerin, and adipocyte fatty-acid-binding protein (AFABP) in NAFLD, taken from preclinical to clinical studies, is overviewed. The effect of therapeutic interventions on adipokines’ circulating levels are also covered. Finally, future directions to address the potential of adipokines as therapeutic targets and disease biomarkers for NAFLD are discussed. Full article

(This article belongs to the Special Issue Immunometabolic Crosstalk in Inflammation and Metabolic Syndrome: New Biomarkers and Therapeutic Tools)

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11 pages, 1438 KiB

Open AccessArticle

Goitered Gazelle Gazella subgutturosa Responded to Human Disturbance by Increasing Vigilance Rather than Changing the Group Size

by Wenxuan Xu, Muyang Wang, David Blank, António Alves da Silva, Weikang Yang, Kathreen E. Ruckstuhl and Joana Alves

Biology 2022, 11(8), 1236; https://doi.org/10.3390/biology11081236 - 19 Aug 2022

Viewed by 2285

Abstract

Nonlethal human disturbances have been confirmed to have a negative effect on wildlife in a variety of ways, including on behaviors. In many studies, the impact of human disturbances on gregarious species of wildlife is assessed through changes in their social organization and [...] Read more.

Nonlethal human disturbances have been confirmed to have a negative effect on wildlife in a variety of ways, including on behaviors. In many studies, the impact of human disturbances on gregarious species of wildlife is assessed through changes in their social organization and vigilance. In our study in the Kalamaili Nature Reserve, China, we wanted to estimate the impacts of differing levels of human disturbances on two different group types (mixed-sex and all-male) of goitered gazelle, Gazella subgutturosa, living in three functional zones (experimental, buffer, and core zones), which represent high, medium, and low human disturbance levels, respectively. In addition, we studied the time spent vigilant as a function of group size with different levels of human disturbances in the three zones. In general, mixed-sex gazelle groups were of similar sizes in the three different zones, while all-male groups slightly differed in their sizes between the experimental and buffer zones. This may indicate that human disturbances have varying effects on the different group types, with smaller-sized, single-sex groups being more significantly affected by human disturbances than larger-sized, mixed-sex groups. Goitered gazelle showed higher vigilance levels in the experimental zone than in the two other zones. A trend of decreasing vigilance varying linearly with group size was also found in the three zones, and the rate of decrease was higher in the experimental zone. Increased habitat fragmentation and human activities brought goitered gazelle and humans closer together in the core zone. Therefore, stopping mining activities and returning the reserve to a continuous habitat with fewer environmental disturbances is the best way to establish and protect a stable population of this endangered species of gazelle. Full article

(This article belongs to the Special Issue Advances in Animal Social Behavior and Social Evolution)

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21 pages, 6780 KiB

Open AccessArticle

Ventral Morphology of the Non-Trilobite Artiopod Retifacies abnormalis Hou, Chen & Lu, 1989, from the Early Cambrian Chengjiang Biota, China

by Maoyin Zhang, Yu Liu, Xianguang Hou, Javier Ortega-Hernández, Huijuan Mai, Michel Schmidt, Roland R. Melzer and Jin Guo

Biology 2022, 11(8), 1235; https://doi.org/10.3390/biology11081235 - 19 Aug 2022

Cited by 7 | Viewed by 3403

Abstract

The artiopodans represent a diverse group of euarthropods with a typically flattened dorsal exoskeleton that covers numerous pairs of biramous ventral appendages, and which are ubiquitous faunal components of the 518-million-year-old Chengjiang Lagerstätte in South China. Despite their abundance, several Chengjiang artiopodans remain [...] Read more.

The artiopodans represent a diverse group of euarthropods with a typically flattened dorsal exoskeleton that covers numerous pairs of biramous ventral appendages, and which are ubiquitous faunal components of the 518-million-year-old Chengjiang Lagerstätte in South China. Despite their abundance, several Chengjiang artiopodans remain poorly known, such as the large euarthropoda Retifacies abnormalis, Hou, Chen & Lu, 1989, which is distinguished by the presence of mesh-like ornamentation on its dorsal exoskeleton. Although only a few ventral details were described in a single study in 25 years, it has been frequently featured in phylogenetic analyses that explore the relationships between Cambrian euarthropods. Here, we employ micro-CT and fluorescent microphotography to investigate the exceptionally preserved ventral morphology of R. abnormalis and explore its phylogenetic implications through maximum parsimony and Bayesian inference. Detailed morphology revealed here better supports R. abnormalis as a sister group to the diminutive artiopod Pygmaclypeatus daziensis, also known from Chengjiang, and strengthens the close relationship of these taxa that have been suggested by previous studies as early-branching representatives of Trilobitomorpha. Cephalic appendages suggest this animal might be a scavenger, possibly feeding on soft-bodied organisms. Different pairs of pygidial appendages suggest an anamorphic post-embryonic ontogeny, which adds to the understanding of the developmental mode of Cambrian artiopods, and further supports the statement that post-hatching segment addition occurred in the ancestor of Euarthropoda. Full article

(This article belongs to the Special Issue Cambrian Explosion and Construction of the First Animal Consumer-Driven Marine Ecosystem on Earth)

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10 pages, 1473 KiB

Open AccessArticle

Attack and Defense Performance in Goalball: A Proposal for Throwing, Balance and Acoustic Reaction Evaluation

by A. Vanessa Bataller-Cervero, Pablo J. Bascuas, Juan Rabal-Pelay, Héctor Gutiérrez, Eduardo Piedrafita and César Berzosa

Biology 2022, 11(8), 1234; https://doi.org/10.3390/biology11081234 - 18 Aug 2022

Cited by 3 | Viewed by 2660

Abstract

Goalball is a sport for visually impaired athletes, where the roles of attack and defense change continuously during the game. Performance evaluation should consider the variables that determine the throwing and the stop and clearance of the ball. The aim of this study [...] Read more.

Goalball is a sport for visually impaired athletes, where the roles of attack and defense change continuously during the game. Performance evaluation should consider the variables that determine the throwing and the stop and clearance of the ball. The aim of this study is to evaluate the precision and velocity of the ball throwing in goalball, besides core stability and balance as variables that determine an optimal throwing. Moreover, a novel acoustic reaction time is applied to analyze the defense performance. Eight goalball players (33 ± 9 years old; 77.8 ± 22.7 kg; 174 ± 13 cm; 10 ± 5 years of experience) were recruited to assess ball velocity, with a radar gun, and throwing accuracy. Anthropometry, static balance, and core stability were assessed using a computerized pressure platform. Acoustic reaction time was measured with a photoelectric system. A significant positive correlation was found between throwing speed and the years of experience (Ƿ = 0.714, p = 0.047), height (Ƿ = 0.786, p = 0.021), dominant leg surface area of the stabilogram (Ƿ = 0.738, p = 0.037), and non-dominant leg center of pressure mean velocity (Ƿ = 0.714, p = 0.017). In the present pilot study, height and years of experience are correlated to throwing velocity. This is also the first test proposal to assess throwing precision and complex acoustic reaction in goalball players, which could be used to assess the level of performance in future studies. Full article

(This article belongs to the Special Issue New Frontiers of Sport, Exercise and Physical Activity for Health and Human Performance)

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27 pages, 6046 KiB

Open AccessArticle

Hypoxia Affects HIF-1/LDH-A Signaling Pathway by Methylation Modification and Transcriptional Regulation in Japanese Flounder (Paralichthys olivaceus)

by Binghua Liu, Haishen Wen, Jun Yang, Xiaohui Li, Guangling Li, Jingru Zhang, Shuxian Wu, Ian AE Butts and Feng He

Biology 2022, 11(8), 1233; https://doi.org/10.3390/biology11081233 - 18 Aug 2022

Cited by 3 | Viewed by 2898

Abstract

Japanese flounder (Paralichthys olivaceus) responsive mechanisms to hypoxia are still not fully understood. Therefore, we performed an acute hypoxic treatment (dissolved oxygen at 2.07 ± 0.08 mg/L) on Japanese flounder. It was confirmed that the hypoxic stress affected the physiological phenotype [...] Read more.

Japanese flounder (Paralichthys olivaceus) responsive mechanisms to hypoxia are still not fully understood. Therefore, we performed an acute hypoxic treatment (dissolved oxygen at 2.07 ± 0.08 mg/L) on Japanese flounder. It was confirmed that the hypoxic stress affected the physiological phenotype through changes in blood physiology (RBC, HGB, WBC), biochemistry (LDH, ALP, ALT, GLU, TC, TG, ALB), and hormone (cortisol) indicators. Hypoxia inducible factor-1 (HIF-1), an essential oxygen homeostasis mediator in organisms consisting of an inducible HIF-1α and a constitutive HIF-1β, and its target gene LDH-A were deeply studied. Results showed that HIF-1α and LDH-A genes were co-expressed and significantly affected by hypoxic stress. The dual-luciferase reporter assay confirmed that transcription factor HIF-1 transcriptionally regulated the LDH-A gene, and its transcription binding sequence was GGACGTGA located at −2343~−2336. The DNA methylation status of HIF-1α and LDH-A genes were detected to understand the mechanism of environmental stress on genes. It was found that hypoxia affected the HIF-1α gene and LDH-A gene methylation levels. The study uncovered HIF-1/LDH-A signaling pathway responsive mechanisms of Japanese flounder to hypoxia in epigenetic modification and transcriptional regulation. Our study is significant to further the understanding of environmental responsive mechanisms as well as providing a reference for aquaculture. Full article

(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)

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9 pages, 1565 KiB

Open AccessArticle

Highly Efficient Use of Infrared Spectroscopy (ATR-FTIR) to Identify Aphid Species

by Roma Durak, Beata Ciak and Tomasz Durak

Biology 2022, 11(8), 1232; https://doi.org/10.3390/biology11081232 - 18 Aug 2022

Cited by 10 | Viewed by 4135

Abstract

Aphids are commonly considered to be serious pests for trees, herbaceous and cultivated plants. Recognition and identification of individual species is very difficult and is based mainly on morphological features. The aims of the study were to suggest the possibility of identifying aphids [...] Read more.

Aphids are commonly considered to be serious pests for trees, herbaceous and cultivated plants. Recognition and identification of individual species is very difficult and is based mainly on morphological features. The aims of the study were to suggest the possibility of identifying aphids through the use of Fourier-transform infrared (FTIR) spectroscopy, and to determine which absorption peaks are the most useful to separate aphid species. Using FTIR spectroscopy, based on the chemical composition of the body, we were able to distinguish 12 species of aphid. We have shown that using nine distinct peaks corresponding to the molecular vibrations from carbohydrates, lipids, amides I and II, it is possible to accurately identify aphid species with an efficiency of 98%. Full article

(This article belongs to the Section Zoology)

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22 pages, 1114 KiB

Open AccessReview

Mechanisms and Biomarker Potential of Extracellular Vesicles in Stroke

by Nikita Ollen-Bittle, Austyn D. Roseborough, Wenxuan Wang, Jeng-liang D. Wu and Shawn N. Whitehead

Biology 2022, 11(8), 1231; https://doi.org/10.3390/biology11081231 - 18 Aug 2022

Cited by 11 | Viewed by 3693

Abstract

Stoke is a prevalent and devastating neurologic condition with limited options for therapeutic management. Since brain tissue is rarely accessible clinically, peripheral biomarkers for the central nervous system’s (CNS’s) cellular response to stroke may prove critical for increasing our understanding of stroke pathology [...] Read more.

Stoke is a prevalent and devastating neurologic condition with limited options for therapeutic management. Since brain tissue is rarely accessible clinically, peripheral biomarkers for the central nervous system’s (CNS’s) cellular response to stroke may prove critical for increasing our understanding of stroke pathology and elucidating novel therapeutic targets. Extracellular vesicles (EVs) are cell-derived, membrane-enclosed vesicles secreted by all cell types within the CNS that can freely pass the blood-brain barrier (BBB) and contain unique markers and content linked to their cell of origin. These unique qualities make brain-derived EVs novel candidates for non-invasive blood-based biomarkers of both cell specificity and cell physiological state during the progression of stroke and recovery. While studies are continuously emerging that are assessing the therapeutic potential of EVs and profiling EV cargo, a vast minority of these studies link EV content to specific cell types. A better understanding of cell-specific EV release during the acute, subacute, and chronic stages of stroke is needed to further elucidate the cellular processes responsible for stroke pathophysiology. Herein, we outline what is known about EV release from distinct cell types of the CNS during stroke and the potential of these EVs as peripheral biomarkers for cellular function in the CNS during stroke. Full article

(This article belongs to the Special Issue Roles and Use of Extracellular Vesicles in Health and Disease)

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15 pages, 7291 KiB

Open AccessArticle

Identification of 11-Hydroxytephrosin and Torosaflavone A as Potential Inhibitors of 3-Phosphoinositide-Dependent Protein Kinase 1 (PDPK1): Toward Anticancer Drug Discovery

by Akhtar Atiya, Fahad A. Alhumaydhi, Sharaf E. Sharaf, Waleed Al Abdulmonem, Abdelbaset Mohamed Elasbali, Maher M. Al Enazi, Anas Shamsi, Talha Jawaid, Badrah S. Alghamdi, Anwar M. Hashem, Ghulam Md. Ashraf and Moyad Shahwan

Biology 2022, 11(8), 1230; https://doi.org/10.3390/biology11081230 - 18 Aug 2022

Cited by 3 | Viewed by 2558

Abstract

The 3-phosphoinositide-dependent protein kinase 1 (PDPK1) has a significant role in cancer progression and metastasis as well as other inflammatory disorders, and has been proposed as a promising therapeutic target for several malignancies. In this work, we conducted a systematic virtual screening of [...] Read more.

The 3-phosphoinositide-dependent protein kinase 1 (PDPK1) has a significant role in cancer progression and metastasis as well as other inflammatory disorders, and has been proposed as a promising therapeutic target for several malignancies. In this work, we conducted a systematic virtual screening of natural compounds from the IMPPAT database to identify possible PDPK1 inhibitors. Primarily, the Lipinski rules, ADMET, and PAINS filter were applied and then the binding affinities, docking scores, and selectivity were carried out to find effective hits against PDPK1. Finally, we identified two natural compounds, 11-Hydroxytephrosin and Torosaflavone A, bearing substantial affinity with PDPK1. Both compounds showed drug-likeness as predicted by the ADMET analysis and their physicochemical parameters. These compounds preferentially bind to the ATP-binding pocket of PDPK1 and interact with functionally significant residues. The conformational dynamics and complex stability of PDPK1 with the selected compounds were then studied using interaction analysis and molecular dynamics (MD) simulations for 100 ns. The simulation results revealed that PDPK1 forms stable docked complexes with the elucidated compounds. The findings show that the newly discovered 11-Hydroxytephrosin and Torosaflavone A bind to PDPK1 in an ATP-competitive manner, suggesting that they could one day be used as therapeutic scaffolds against PDPK1-associated diseases including cancer. Full article

(This article belongs to the Special Issue Protein Drug Targets and Drug Design)

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19 pages, 1252 KiB

Open AccessReview

Neuraminidases—Key Players in the Inflammatory Response after Pathophysiological Cardiac Stress and Potential New Therapeutic Targets in Cardiac Disease

by Maren Heimerl, Thomas Gausepohl, Julia H. Mueller and Melanie Ricke-Hoch

Biology 2022, 11(8), 1229; https://doi.org/10.3390/biology11081229 - 17 Aug 2022

Cited by 5 | Viewed by 2992

Abstract

Glycoproteins and glycolipids on the cell surfaces of vertebrates and higher invertebrates contain α-keto acid sugars called sialic acids, terminally attached to their glycan structures. The actual level of sialylation, regulated through enzymatic removal of the latter ones by NEU enzymes, highly affects [...] Read more.

Glycoproteins and glycolipids on the cell surfaces of vertebrates and higher invertebrates contain α-keto acid sugars called sialic acids, terminally attached to their glycan structures. The actual level of sialylation, regulated through enzymatic removal of the latter ones by NEU enzymes, highly affects protein-protein, cell-matrix and cell-cell interactions. Thus, their regulatory features affect a large number of different cell types, including those of the immune system. Research regarding NEUs within heart and vessels provides new insights of their involvement in the development of cardiovascular pathologies and identifies mechanisms on how inhibiting NEU enzymes can have a beneficial effect on cardiac remodelling and on a number of different cardiac diseases including CMs and atherosclerosis. In this regard, a multitude of clinical studies demonstrated the potential of N-acetylneuraminic acid (Neu5Ac) to serve as a biomarker following cardiac diseases. Anti-influenza drugs i.e., zanamivir and oseltamivir are viral NEU inhibitors, thus, they block the enzymatic activity of NEUs. When considering the improvement in cardiac function in several different cardiac disease animal models, which results from NEU reduction, the inhibition of NEU enzymes provides a new potential therapeutic treatment strategy to treat cardiac inflammatory pathologies, and thus, administrate cardioprotection. Full article

(This article belongs to the Special Issue Cardiomyopathies—from Basic Mechanisms to Novel Therapeutic Approaches)

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11 pages, 918 KiB

Open AccessArticle

Liver Graft MicroRNAs Expression in Different Etiology of Acute Jaundice after Living Donor Liver Transplantation

by Shu-Hsien Lin, Kun-Ta Wu, Chih-Chi Wang, Kuang-Tzu Huang, Kuang-Den Chen, Li-Wen Hsu, Hock-Liew Eng and King-Wah Chiu

Biology 2022, 11(8), 1228; https://doi.org/10.3390/biology11081228 - 17 Aug 2022

Cited by 2 | Viewed by 1741

Abstract

Background: Acute jaundice remains a critical problem following liver transplantation. MicroRNAs (miRNAs) are involved in regulating gene expression related to various disease phenotypes and statuses. Aims: To differentiate acute jaundice etiology after living donor liver transplantation (LDLT), we examined the hepatic miRNA expression [...] Read more.

Background: Acute jaundice remains a critical problem following liver transplantation. MicroRNAs (miRNAs) are involved in regulating gene expression related to various disease phenotypes and statuses. Aims: To differentiate acute jaundice etiology after living donor liver transplantation (LDLT), we examined the hepatic miRNA expression patterns in several liver graft pathologies. Methods: Eighty liver transplant recipients undergoing post-LDLT graft biopsy for the evaluation of acute jaundice were enrolled in this 1-year prospective study. Using a real-time quantitative reverse transcription-polymerase chain reaction profiling assay, we identified hepatic miRNA (miRNA-122, miRNA-301, miRNA-133a, and miRNA-21) signatures in various allografts pathologies. Results: Pathologic findings of the 80 recipients were as follows: acute cholangitis (AC), 37 (46%); acute rejection (AR), 20 (25%); recurrent hepatitis (RH), 12 (15%); non-specific pathological change, 6 (8%); and fatty change (FC), 5 (6%). None of these identified hepatic miRNAs expression pattern was significantly correlated with serum parameters, including neutrophil-lymphocyte ratio. In AC, hepatic miRNA-122, miRNA-301, miRNA-133a, and miRNA-21 expression was significantly downregulated (p < 0.05). MicroRNA-122 expression was elevated in cases of AR and RH (p < 0.05); miRNA-301 and miRNA-21 expression was higher in RH than in AC (p < 0.05); and miRNA-133a expression was higher in FC than in AR (p < 0.05). Conclusions: Our study suggests that specific hepatic miRNA expression patterns as a checklist may be useful for differential diagnosis of acute jaundice following liver transplantation. Full article

(This article belongs to the Special Issue Recent Advances in the Diagnosis and Treatment of Liver Disease)

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14 pages, 12829 KiB

Open AccessArticle

Automated Computer-Assisted Image Analysis for the Fast Quantification of Kidney Fibrosis

by Esteban Andrés Sánchez-Jaramillo, Luz Elena Gasca-Lozano, José María Vera-Cruz, Luis Daniel Hernández-Ortega and Adriana María Salazar-Montes

Biology 2022, 11(8), 1227; https://doi.org/10.3390/biology11081227 - 17 Aug 2022

Cited by 5 | Viewed by 2345

Abstract

Chronic kidney disease (CKD) is a common and worldwide health problem and one of the most important causes of morbidity and mortality. Most primary research on this disease requires evaluating the fibrosis index in animal model kidneys, specifically using Masson’s trichrome stain. Different [...] Read more.

Chronic kidney disease (CKD) is a common and worldwide health problem and one of the most important causes of morbidity and mortality. Most primary research on this disease requires evaluating the fibrosis index in animal model kidneys, specifically using Masson’s trichrome stain. Different programs are used to calculate the percentage of fibrosis; however, the analysis is time-consuming since one image must be performed at a time. CellProfiler™ is a program designed to analyze data obtained from biological samples and can process multiple images through pipelines, and the results can be exported to databases. This article explains how CellProfiler™ can be used to automatically analyze kidney histology photomicrographs from samples stained with Masson’s trichrome stain to assess the percentage of fibrosis in an experimental animal model of CKD. A pipeline was created to analyze Masson’s trichrome-stained slides in a model of CDK induced by adenine at doses of 50 mg/kg and 100 mg/kg, in addition to samples with the vehicle (75% glycerin). The results were compared with those obtained by ImageJ, and no significant differences were found between both programs. The CellProfiler™ pipeline made here is a reliable, fast, and easy alternative for kidney fibrosis analysis and quantification in experimental animal models. Full article

(This article belongs to the Section Bioinformatics)

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18 pages, 2189 KiB

Open AccessFeature PaperArticle

Putative Protein Discovery from Microalgal Genomes as a Synthetic Biology Protein Library for Heavy Metal Bio-Removal

by Toungporn Uttarotai, Nilita Mukjang, Natcha Chaisoung, Wasu Pathom-Aree, Jeeraporn Pekkoh, Chayakorn Pumas and Pachara Sattayawat

Biology 2022, 11(8), 1226; https://doi.org/10.3390/biology11081226 - 17 Aug 2022

Cited by 1 | Viewed by 2891

Abstract

Synthetic biology is a principle that aims to create new biological systems with particular functions or to redesign the existing ones through bioengineering. Therefore, this principle is often utilized as a tool to put the knowledge learned to practical use in actual fields. [...] Read more.

Synthetic biology is a principle that aims to create new biological systems with particular functions or to redesign the existing ones through bioengineering. Therefore, this principle is often utilized as a tool to put the knowledge learned to practical use in actual fields. However, there is still a great deal of information remaining to be found, and this limits the possible utilization of synthetic biology, particularly on the topic that is the focus of the present work—heavy metal bio-removal. In this work, we aim to construct a comprehensive library of putative proteins that might support heavy metal bio-removal. Hypothetical proteins were discovered from Chlorella and Scenedesmus genomes and extensively annotated. The protein structures of these putative proteins were also modeled through Alphafold2. Although a portion of this workflow has previously been demonstrated to annotate hypothetical proteins from whole genome sequences, the adaptation of such steps is yet to be done for library construction purposes. We also demonstrated further downstream steps that allow a more accurate function prediction of the hypothetical proteins by subjecting the models generated to structure-based annotation. In conclusion, a total of 72 newly discovered putative proteins were annotated with ready-to-use predicted structures available for further investigation. Full article

(This article belongs to the Special Issue Synthetic Biology Aided by Artificial Intelligence)

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22 pages, 1815 KiB

Open AccessReview

The Effects of Tamoxifen on Tolerogenic Cells in Cancer

by Ros Akmal Mohd Idris, Ali Mussa, Suhana Ahmad, Mohammad A. I. Al-Hatamleh, Rosline Hassan, Tengku Ahmad Damitri Al Astani Tengku Din, Wan Faiziah Wan Abdul Rahman, Norhafiza Mat Lazim, Jennifer C. Boer, Magdalena Plebanski and Rohimah Mohamud

Biology 2022, 11(8), 1225; https://doi.org/10.3390/biology11081225 - 17 Aug 2022

Cited by 6 | Viewed by 3695

Abstract

Tamoxifen (TAM) is the most prescribed selective estrogen receptor modulator (SERM) to treat hormone-receptor-positive breast cancer patients and has been used for more than 20 years. Its role as a hormone therapy is well established; however, the potential role in modulating tolerogenic cells [...] Read more.

Tamoxifen (TAM) is the most prescribed selective estrogen receptor modulator (SERM) to treat hormone-receptor-positive breast cancer patients and has been used for more than 20 years. Its role as a hormone therapy is well established; however, the potential role in modulating tolerogenic cells needs to be better clarified. Infiltrating tumor-microenvironment-regulatory T cells (TME-Tregs) are important as they serve a suppressive function through the transcription factor Forkhead box P3 (Foxp3). Abundant studies have suggested that Foxp3 regulates the expression of several genes (CTLA-4, PD-1, LAG-3, TIM-3, TIGIT, TNFR2) involved in carcinogenesis to utilize its tumor suppressor function through knockout models. TAM is indirectly concomitant via the Cre/loxP system by allowing nuclear translocation of the fusion protein, excision of the floxed STOP cassette and heritable expression of encoding fluorescent protein in a cohort of cells that express Foxp3. Moreover, TAM administration in breast cancer treatment has shown its effects directly through MDSCs by the enrichment of its leukocyte populations, such as NK and NKT cells, while it impairs the differentiation and activation of DCs. However, the fundamental mechanisms of the reduction of this pool by TAM are unknown. Here, we review the vital effects of TAM on Tregs for a precise mechanistic understanding of cancer immunotherapies. Full article

(This article belongs to the Topic Immunotherapy and Targeted Therapy in Breast Cancer)

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23 pages, 2811 KiB

Open AccessArticle

The First Comprehensive Biodiversity Study of Culturable Fungal Communities Inhabiting Cryoconite Holes in the Werenskiold Glacier on Spitsbergen (Svalbard Archipelago, Arctic)

by Justyna Borzęcka, Jakub Suchodolski, Bartłomiej Dudek, Lena Matyaszczyk, Klaudyna Spychała and Rafał Ogórek

Biology 2022, 11(8), 1224; https://doi.org/10.3390/biology11081224 - 16 Aug 2022

Cited by 7 | Viewed by 3170

Abstract

Cryoconite holes on glacier surfaces are a source of cold-adapted microorganisms, but little is known about their fungal inhabitants. Here, we provide the first report of distinctive fungal communities in cryoconite holes in the Werenskiold Glacier on Spitsbergen (Svalbard Archipelago, Arctic). Due to [...] Read more.

Cryoconite holes on glacier surfaces are a source of cold-adapted microorganisms, but little is known about their fungal inhabitants. Here, we provide the first report of distinctive fungal communities in cryoconite holes in the Werenskiold Glacier on Spitsbergen (Svalbard Archipelago, Arctic). Due to a combination of two incubation temperatures (7 °C and 24 ± 0.5 °C) and two media during isolation (PDA, YPG), as well as classical and molecular identification approaches, we were able to identify 23 different fungi (21 species and 2 unassigned species). Most of the fungi cultured from cryoconite sediment were ascomycetous filamentous micromycetes. However, four representatives of macromycetes were also identified (Bjerkandera adusta, Holwaya mucida, Orbiliaceae sp., and Trametes versicolor). Some of the described fungi possess biotechnological potential (Aspergillus pseudoglaucus, A. sydowii, Penicillium expansum, P. velutinum, B. adusta, and T. versicolor), thus, we propose the Arctic region as a source of new strains for industrial applications. In addition, two phytopathogenic representatives were present (P. sumatraense, Botrytis cinerea), as well as one potentially harmful to humans (Cladosporium cladosporioides). To the best of our knowledge, we are the first to report the occurrence of A. pseudoglaucus, C. allicinum, C. ramotenellum, P. sumatraense, P. velutinum, P. cumulodentata, B. adusta, and T. versicolor in polar regions. In all likelihood, two unassigned fungus species (Orbiliaceae and Dothideomycetes spp.) might also be newly described in such environments. Additionally, due to experimenting with 10 sampling sites located at different latitudes, we were able to conclude that the number of fungal spores decreases as one moves down the glacier. Considering the prevalence and endangerment of glacial environments worldwide, such findings suggest their potential as reservoirs of fungal diversity, which should not be overlooked. Full article

(This article belongs to the Special Issue Polar Ecosystem: Response of Organisms to Changing Climate)

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9 pages, 677 KiB

Open AccessArticle

Acute Effects of Different Overspeed Loads with Motorized Towing System in Young Athletes: A Pilot Study

by Pau Cecília-Gallego, Adrián Odriozola, José Vicente Beltrán-Garrido and Jesús Álvarez-Herms

Biology 2022, 11(8), 1223; https://doi.org/10.3390/biology11081223 - 16 Aug 2022

Cited by 1 | Viewed by 2958

Abstract

Overspeed is a training method used to improve running speed, although its effects are not supported by consensual scientific evidence. The overspeed stimulus can be boosted by several methods, including motorized towing devices. Our objectives were to analyze the acute effects of three [...] Read more.

Overspeed is a training method used to improve running speed, although its effects are not supported by consensual scientific evidence. The overspeed stimulus can be boosted by several methods, including motorized towing devices. Our objectives were to analyze the acute effects of three overspeed loads in young athletes and to select optimal loads for training periods. Eight young athletes (16.73 ± 1.69 years) performed one unassisted sprint and three assisted sprints, and kinematic and biomechanical data were compared. Significant increases (p < 0.05) in step velocity and step length were found with 2, 4, and 5.25 kg in maximum running speed, flight time and horizontal distance from the first contact to the vertical projection of the center of mass with 4 and 5.25 kg. Significant time decreases were found in 5 m flying sprint and contact time with 4 and 5.25 kg, and no significant changes were observed in step rate. The individually recommended loads would be between 3.47 ± 0.68% and 6.94 ± 1.35% body weight. Even having limitations, we can understand this work and its results as a pilot study to replicate the methodology and the use of new devices to more broadly investigate the effects of overspeed. Full article

(This article belongs to the Special Issue New Frontiers of Sport, Exercise and Physical Activity for Health and Human Performance)

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23 pages, 2827 KiB

Open AccessArticle

The Protective Performance of Process Operators’ Protective Clothing and Exposure Limits under Low Thermal Radiation Conditions

by Ronald Heus, Boris R. M. Kingma, Birgit M. A. van Berlo, Douwe Mol, Hein A. M. Daanen and Kalev Kuklane

Biology 2022, 11(8), 1222; https://doi.org/10.3390/biology11081222 - 16 Aug 2022

Cited by 2 | Viewed by 3092

Abstract

During the early stage of a fire, a process operator often acts as the first responder and may be exposed to high heat radiation levels. The present limit values of long- (>15 min) and short-term exposure (<5 min), 1.0 and 1.5 kW/m² [...] Read more.

During the early stage of a fire, a process operator often acts as the first responder and may be exposed to high heat radiation levels. The present limit values of long- (>15 min) and short-term exposure (<5 min), 1.0 and 1.5 kW/m², respectively, have been set using physiological models and manikin measurements. Since human validation is essentially lacking, this study investigated whether operators’ protective clothing offers sufficient protection during a short-term deployment. Twelve professional firefighters were exposed to three radiation levels (1.5, 2.0, and 2.5 kW/m²) when wearing certified protective clothing in front of a heat radiation panel in a climatic chamber (20 °C; 50% RH). The participants wore only briefs (male) or panties and a bra (female) and a T-shirt under the operators’ clothing. Skin temperatures were continuously measured at the chest, belly, forearm, thigh, and knee. The test persons had to stop if any skin temperature reached 43 °C, at their own request, or when 5 min of exposure was reached. The experiments showed that people in operators’ clothing can be safely exposed for 5 min to 1.5 kW/m², up to 3 min to 2.0 kW/m², and exposure to 2.5 kW/m² or above must be avoided unless the clothing can maintain an air gap. Full article

(This article belongs to the Special Issue Effects of Environmental Factors on Human Health and Performance)

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20 pages, 2673 KiB

Open AccessReview

by Bahaj Adil, Safae Lhazmir, Mounir Ghogho and Houda Benbrahim

Biology 2022, 11(8), 1221; https://doi.org/10.3390/biology11081221 - 16 Aug 2022

Cited by 1 | Viewed by 1974

Abstract

The urgency of the COVID-19 pandemic caused a surge in the related scientific literature. This surge made the manual exploration of scientific articles time-consuming and inefficient. Therefore, a range of exploratory search applications have been created to facilitate access to the available literature. [...] Read more.

The urgency of the COVID-19 pandemic caused a surge in the related scientific literature. This surge made the manual exploration of scientific articles time-consuming and inefficient. Therefore, a range of exploratory search applications have been created to facilitate access to the available literature. In this survey, we give a short description of certain efforts in this direction and explore the different approaches that they used. Full article

(This article belongs to the Special Issue Intelligent Computing in Biology and Medicine)

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