Biology

16 pages, 4485 KiB

Open AccessArticle

Soil Geochemical Properties Influencing the Diversity of Bacteria and Archaea in Soils of the Kitezh Lake Area, Antarctica

by Qinxin Li, Nengfei Wang, Wenbing Han, Botao Zhang, Jiaye Zang, Yiling Qin, Long Wang, Jie Liu and Tao Zhang

Biology 2022, 11(12), 1855; https://doi.org/10.3390/biology11121855 - 19 Dec 2022

Cited by 3 | Viewed by 1878

Abstract

It is believed that polar regions are influenced by global warming more significantly, and because polar regions are less affected by human activities, they have certain reference values for future predictions. This study aimed to investigate the effects of climate warming on soil [...] Read more.

It is believed that polar regions are influenced by global warming more significantly, and because polar regions are less affected by human activities, they have certain reference values for future predictions. This study aimed to investigate the effects of climate warming on soil microbial communities in lake areas, taking Kitezh Lake, Antarctica as the research area. Below-peak soil, intertidal soil, and sediment were taken at the sampling sites, and we hypothesized that the diversity and composition of the bacterial and archaeal communities were different among the three sampling sites. Through 16S rDNA sequencing and analysis, bacteria and archaea with high abundance were obtained. Based on canonical correspondence analysis and redundancy analysis, pH and phosphate had a great influence on the bacterial community whereas pH and nitrite had a great influence on the archaeal community. Weighted gene coexpression network analysis was used to find the hub bacteria and archaea related to geochemical factors. The results showed that in addition to pH, phosphate, and nitrite, moisture content, ammonium, nitrate, and total carbon content also play important roles in microbial diversity and structure at different sites by changing the abundance of some key microbiota. Full article

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

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19 pages, 8801 KiB

Open AccessArticle

Cultivars Resistance Assay for Maize Late Wilt Disease

by Ofir Degani, Ran Yifa, Asaf Gordani, Paz Becher and Assaf Chen

Biology 2022, 11(12), 1854; https://doi.org/10.3390/biology11121854 - 19 Dec 2022

Cited by 5 | Viewed by 2083

Abstract

Magnaporthiopsis maydis late wilt disease (LWD) in corn is considered to be the most severe in Israel and Egypt and poses a significant threat in other countries. Research efforts extending over a period of five decades led to the development of chemical, biological, [...] Read more.

Magnaporthiopsis maydis late wilt disease (LWD) in corn is considered to be the most severe in Israel and Egypt and poses a significant threat in other countries. Research efforts extending over a period of five decades led to the development of chemical, biological, agrotechnical, physical (solar disinfection) and other means for controlling late wilt disease. Today, some applications can reduce damage even in severe cases. However, cultivating disease-resistant maize varieties is the primary means for reducing the disease’s impact. The current work uses a rapid (six days) laboratory seedling pathogenicity test and a full-season open encloser semi-field conditioned pots assay (101 days) to classify maize varieties according to their LWD resistance. To better evaluate differences between the cultivars, a real-time based molecular assay was applied to track the pathogen’s presence in the plants’ tissues, and visible light aerial imaging was used in parallel. The findings show that in cases of extreme sensitivity or tolerance (for example, in the highly susceptible Megaton cultivar (cv.) or the resistant Hatai cv.), a similarity in the results exists between the different methods. Thus, a reliable estimate of the varieties’ sensitivity can be obtained in a seed assay without the need for a test carried out throughout an entire growing season. At the same time, in most situations of partial or reduced LWD sensitivity/resistance, there is no match between the various tests, and only the entire growing season can provide the most reliable results. Tracking the amount of M. maydis DNA in the plants’ bodies is a precise, sensitive scientific tool of great importance for studying the development of the disease and the factors affecting it. Yet, no complete overlap exists between the fungal DNA amount and symptom severity. Such a correlation exists in high sensitivity or resistance cases but not in intermediate situations. Still, the valuation of the pathogen’s establishment in asymptomatic corn hybrids can indicate the degree of LWD immunity and the chance of susceptibility development. Full article

(This article belongs to the Special Issue Plant–Fungi Interaction: Two-Edged Sword for Plant Growth, Production and Storage)

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15 pages, 2983 KiB

Open AccessArticle

A Comparative Study of Mesenchymal Stem Cell-Derived Extracellular Vesicles’ Local and Systemic Dose-Dependent Administration in Rat Spinal Cord Injury

by Alexander Kostennikov, Ilyas Kabdesh, Davran Sabirov, Anna Timofeeva, Alexander Rogozhin, Ilya Shulman, Albert Rizvanov and Yana Mukhamedshina

Biology 2022, 11(12), 1853; https://doi.org/10.3390/biology11121853 - 19 Dec 2022

Cited by 8 | Viewed by 2160

Abstract

Spinal cord injury (SCI) is a serious neurological condition that causes severe disability. One of the approaches to overcoming the complications of SCI is stem cell-derived extracellular vesicle (EV) therapy. In this research, we performed a comparative evaluation of rat spinal cord post-traumatic [...] Read more.

Spinal cord injury (SCI) is a serious neurological condition that causes severe disability. One of the approaches to overcoming the complications of SCI is stem cell-derived extracellular vesicle (EV) therapy. In this research, we performed a comparative evaluation of rat spinal cord post-traumatic regeneration efficacy using different methods of mesenchymal stem cell-derived EV transplantation (local vs. systemic) followed by evaluation of their minimal therapeutic dose. The results suggested that MSC-EV therapy could improve locomotor activity over 60 days after the SCI, showing a dose-dependent effect on the recovery of spinal cord motor pathways. We also established the possibility of maintaining a population of mature oligodendrocytes by MSC-EVs. It was observed that in the spinal cord injury area, intravenous transplantation of MSC-EVs showed more pronounced therapeutic effects compared to the treatment of fibrin matrix-encapsulated MSC-EVs. Full article

(This article belongs to the Section Neuroscience)

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15 pages, 1703 KiB

Open AccessArticle

Paramecium bursaria as a Potential Tool for Evaluation of Microplastics Toxicity

by Jianhua Zhang, Changhong Li, Xiangrui Chen, Yunqian Li, Chenjie Fei and Jiong Chen

Biology 2022, 11(12), 1852; https://doi.org/10.3390/biology11121852 - 19 Dec 2022

Cited by 4 | Viewed by 2517

Abstract

Microplastics (MPs) are normally defined as small plastic wastes with a size of 1 μm to 5 mm in diameter. This tiny plastic debris is abundant in aquatic systems and poses a great threat to aquatic biota. To date, toxicological assessment of MPs [...] Read more.

Microplastics (MPs) are normally defined as small plastic wastes with a size of 1 μm to 5 mm in diameter. This tiny plastic debris is abundant in aquatic systems and poses a great threat to aquatic biota. To date, toxicological assessment of MPs is predominantly dependent on metazoan animals, although their applications are sometimes limited due to the high cost, narrow ecological niche, or ethical considerations. In this regard, unicellular eukaryotes (i.e., protozoa) that are ubiquitously present in nature represent a promising alternative for evaluating the toxicity of MPs. In this study, we selected Paramecium bursaria (P. bursaria) as a representative of protozoa and further investigated behavioral and molecular changes in MPs-exposed P. bursaria. Our results showed that following MPs uptake, P. bursaria exhibited various changes, including anomalies in swimming patterns, reduction in moving speed, impairment of avoidance behavior, elevation of oxidative stress, and potential disturbance of endosymbiosis. These elicited changes in P. bursaria in response to MPs exposure were pronounced and measurable. Overall, this study demonstrated that P. bursaria could serve as a promising alternative for the toxicological assessment of MPs and may be further applied to evaluate the toxicity of other environmental contaminants. Full article

(This article belongs to the Section Toxicology)

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22 pages, 6085 KiB

Open AccessArticle

RETRACTED: Identify Biomarkers and Design Effective Multi-Target Drugs in Ovarian Cancer: Hit Network-Target Sets Model Optimizing

by Amir Abbas Esmaeilzadeh, Mahdis Kashian, Hayder Mahmood Salman, Marwa Fadhil Alsaffar, Mustafa Musa Jaber, Siamak Soltani, Ahmet Ilhan and Abolfazl Bahrami

Biology 2022, 11(12), 1851; https://doi.org/10.3390/biology11121851 - 19 Dec 2022

Cited by 3 | Viewed by 3542 | Retraction | Correction

Abstract

Epithelial ovarian cancer (EOC) is highly aggressive with poor patient outcomes, and a deeper understanding of ovarian cancer tumorigenesis could help guide future treatment development. We proposed an optimized hit network-target sets model to systematically characterize the underlying pathological mechanisms and intra-tumoral heterogeneity [...] Read more.

Epithelial ovarian cancer (EOC) is highly aggressive with poor patient outcomes, and a deeper understanding of ovarian cancer tumorigenesis could help guide future treatment development. We proposed an optimized hit network-target sets model to systematically characterize the underlying pathological mechanisms and intra-tumoral heterogeneity in human ovarian cancer. Using TCGA data, we constructed an epithelial ovarian cancer regulatory network in this study. We use three distinct methods to produce different HNSs for identification of the driver genes/nodes, core modules, and core genes/nodes. Following the creation of the optimized HNS (OHNS) by the integration of DN (driver nodes), CM (core module), and CN (core nodes), the effectiveness of various HNSs was assessed based on the significance of the network topology, control potential, and clinical value. Immunohistochemical (IHC), qRT-PCR, and Western blotting were adopted to measure the expression of hub genes and proteins involved in epithelial ovarian cancer (EOC). We discovered that the OHNS has two key advantages: the network’s central location and controllability. It also plays a significant role in the illness network due to its wide range of capabilities. The OHNS and clinical samples revealed the endometrial cancer signaling, and the PI3K/AKT, NER, and BMP pathways. MUC16, FOXA1, FBXL2, ARID1A, COX15, COX17, SCO1, SCO2, NDUFA4L2, NDUFA, and PTEN hub genes were predicted and may serve as potential candidates for new treatments and biomarkers for EOC. This research can aid in better capturing the disease progression, the creation of potent multi-target medications, and the direction of the therapeutic community in the optimization of effective treatment regimens by various research objectives in cancer treatment. Full article

(This article belongs to the Special Issue Bioinformatics and Machine Learning for Cancer Biology (Volume II))

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21 pages, 3390 KiB

Open AccessArticle

Oral Processing of Three Guenon Species in Taï National Park, Côte d’Ivoire

by Erin E. Kane, Taylor Polvadore, Ferdinand Ouro Bele, Eloi Anderson Bitty, Ernest Kamy, Frederic Gnepa Mehon, David J. Daegling and William Scott McGraw

Biology 2022, 11(12), 1850; https://doi.org/10.3390/biology11121850 - 19 Dec 2022

Cited by 1 | Viewed by 2030

Abstract

Three guenon species in Taï National Park frequently form and maintain stable polyspecific associations despite significant feeding competition. This dietary overlap provides an opportunity to examine how closely related and anatomically similar taxa process the same foods. Our research examines whether the oral-processing [...] Read more.

Three guenon species in Taï National Park frequently form and maintain stable polyspecific associations despite significant feeding competition. This dietary overlap provides an opportunity to examine how closely related and anatomically similar taxa process the same foods. Our research examines whether the oral-processing behaviors of these guenons differ when they consume the same foods. Methods: Data on oral-processing behavior were collected on one habituated group each of Cercopithecus campbelli, C. diana, and C. petaurista in Taï National Park, Côte d’Ivoire from January 2016 to December 2018. We recorded the frequency with which foods were introduced to the mouth (ingestive action) and the frequency with which foods were processed using incisors, canines, and postcanine teeth. Oral-processing profiles for species-specific plant foods, fungi, and invertebrates were compared using Monte Carlo resampling. We quantified oral-processing behavior during a total of 2316 five-minute focal periods. Diana monkeys use their incisors significantly more per ingestive action than Campbell’s monkeys or Lesser spot-nosed guenons. Lesser spot-nosed guenons use their incisors more than Campbell’s monkeys. Diana monkeys also use significantly more post-canine chews per ingestive action than Campbell’s monkeys and Lesser spot-nosed guenons. Lesser spot-nosed guenons generally use fewer post-canine chews than Diana monkeys but more than Campbell’s monkeys. Canine use during feeding was rare in all three taxa. The three study species use different oral-processing profiles when consuming the same foods. These results are intriguing given the overall similarity in dental and cranial anatomy in these taxa. The oral-processing profiles we report do not encompass the full dietary breadth of all species; however, the behavioral diversity demonstrated during consumption of the same foods suggests that insight into feeding behavior is more likely obtained by examining oral processing of individual foods rather than broad food categories. Furthermore, these results underscore that important variation in feeding behavior is not necessarily associated with morphological differences in dental or craniofacial anatomy. Full article

(This article belongs to the Section Ecology)

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16 pages, 22730 KiB

Open AccessArticle

Genome-Wide Association Study Revealed the Effect of rs312715211 in ZNF652 Gene on Abdominal Fat Percentage of Chickens

by Yuting Zhu, Xiaojing Liu, Yongli Wang, Lu Liu, Yidong Wang, Guiping Zhao, Jie Wen and Huanxian Cui

Biology 2022, 11(12), 1849; https://doi.org/10.3390/biology11121849 - 19 Dec 2022

Cited by 1 | Viewed by 1759

Abstract

Abdominal fat percentage (AFP) is an important economic trait in chickens. Intensive growth selection has led to the over-deposition of abdominal fat in chickens, but the genetic basis of AFP is not yet clear. Using 520 female individuals from selection and control lines [...] Read more.

Abdominal fat percentage (AFP) is an important economic trait in chickens. Intensive growth selection has led to the over-deposition of abdominal fat in chickens, but the genetic basis of AFP is not yet clear. Using 520 female individuals from selection and control lines of Jingxing yellow chicken, we investigated the genetic basis of AFP using a genome-wide association study (GWAS) and fixation indices (F_ST). A 0.15 MB region associated with AFP was located on chromosome 27 and included nine significant single nucleotide polymorphisms (SNPs), which could account for 3.34–5.58% of the phenotypic variation. In addition, the π value, genotype frequency, and dual-luciferase results identified SNP rs312715211 in the intron region of ZNF652 as the key variant. The wild genotype was associated with lower AFP and abdominal fat weight (AFW), but higher body weight (BW). Finally, annotated genes based on the top 1% SNPs were used to investigate the physiological function of ZNF652. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that ZNF652 may reduce AFW and BW in broilers through the TGF-β1/SMad2/3 and MAPK/FoxO pathways via EGFR and TGFB1. Our findings elucidated the genetic basis of chicken AFP, rs312715211 on the ZNF652 gene, which can affect BW and AFW and was the key variant associated with AFP. These data provide new insight into the genetic mechanism underlying AF deposition in chickens and could be beneficial in breeding chickens for AF. Full article

(This article belongs to the Section Genetics and Genomics)

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16 pages, 1949 KiB

Open AccessArticle

Cardiac Magnetic Resonance Findings in Patients Recovered from COVID-19 Pneumonia and Presenting with Persistent Cardiac Symptoms: The TRICITY-CMR Trial

by Dagmara Wojtowicz, Karolina Dorniak, Marzena Ławrynowicz, Piotr Wąż, Jadwiga Fijałkowska, Dorota Kulawiak-Gałąska, Joanna Rejszel-Baranowska, Robert Knut, Maciej Haberka, Edyta Szurowska and Marek Koziński

Biology 2022, 11(12), 1848; https://doi.org/10.3390/biology11121848 - 18 Dec 2022

Cited by 5 | Viewed by 2460

Abstract

The prevalence and clinical consequences of coronavirus disease 2019 (COVID-19)-related non-ischemic cardiac injury are under investigation. The main purpose of this study was to determine the occurrence of non-ischemic cardiac injury using cardiac magnetic resonance (CMR) imaging in patients with persistent cardiac symptoms [...] Read more.

The prevalence and clinical consequences of coronavirus disease 2019 (COVID-19)-related non-ischemic cardiac injury are under investigation. The main purpose of this study was to determine the occurrence of non-ischemic cardiac injury using cardiac magnetic resonance (CMR) imaging in patients with persistent cardiac symptoms following recovery from COVID-19 pneumonia. We conducted a single-center, cross-sectional study. Between January 2021 and May 2021, we enrolled 121 patients with a recent COVID-19 infection and persistent cardiac symptoms. Study participants were divided into those who required hospitalization during the acute phase of SARS-CoV-2 infection (n = 58; 47.9%) and those non-hospitalized (n = 63; 52.1%). Non-ischemic cardiac injury (defined as the presence of late gadolinium enhancement (LGE) lesion and/or active myocarditis in CMR) was detected in over half of post-COVID-19 patients (n = 64; 52.9%). LGE lesions were present in 63 (52.1%) and active myocarditis in 10 (8.3%) post-COVID-19 study participants. The majority of LGE lesions were located in the left ventricle at inferior and inferolateral segments at the base. There were no significant differences in the occurrence of LGE lesions (35 (60.3%) vs. 28 (44.4%); p = 0.117) or active myocarditis (6 (10.3%) vs. 4 (6.3%); p = 0.517) between hospitalized and non-hospitalized post-COVID-19 patients. However, CMR imaging revealed lower right ventricular ejection fraction (RVEF; 49.5 (44; 54) vs. 53 (50; 58) %; p = 0.001) and more frequent presence of reduced RVEF (60.3% vs. 33.3%; p = 0.005) in the former subgroup. In conclusion, more than half of our patients presenting with cardiac symptoms after a recent recovery from COVID-19 pneumonia had CMR imaging abnormalities indicating non-ischemic cardiac injury. The most common finding was LGE, while active myocarditis was detected in the minority of patients. CMR imaging abnormalities were observed both in previously hospitalized and non-hospitalized post-COVID-19 patients. Further research is needed to determine the long-term cardiovascular consequences of COVID-19 infection and the optimal management of patients with suspected post-COVID-19 non-ischemic cardiac injury. Full article

(This article belongs to the Special Issue New Advances and Insights in Inflammatory Cardiomyopathy)

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12 pages, 1114 KiB

Open AccessArticle

Association between Thyroid Function and Ocular Parameters

by Mirjana Babić Leko, Nikolina Pleić, Mladen Lešin, Ivana Gunjača, Vesela Torlak, Jelena Škunca Herman, Zoran Vatavuk, Ante Punda, Ozren Polašek, Caroline Hayward and Tatijana Zemunik

Biology 2022, 11(12), 1847; https://doi.org/10.3390/biology11121847 - 18 Dec 2022

Cited by 1 | Viewed by 2437

Abstract

During development, thyroid hormones play an important role in eye development, while in adults, some pathological thyroid conditions can affect the normal functioning of the eyes. Thyroid eye disease is the most well-known eye pathology caused by a pathological thyroid condition. Few studies [...] Read more.

During development, thyroid hormones play an important role in eye development, while in adults, some pathological thyroid conditions can affect the normal functioning of the eyes. Thyroid eye disease is the most well-known eye pathology caused by a pathological thyroid condition. Few studies have investigated the association between ocular parameters and thyroid function. Thus, in this study, we aimed to examine whether thyroid activity affects ocular parameters. This cross-sectional study included 4633 healthy adults recruited within the 10,001 Dalmatians project of the Croatian Biobank. The plasma levels of thyroid-stimulating hormone (TSH), free triiodothyronine (fT3), free thyroxine (fT4), thyroglobulin (Tg), thyroglobulin antibodies (TgAb), and thyroid peroxidase antibodies (TPOAb) were measured by an immunoassay. We determined 20 ocular parameters for each participant (10 for each eye, including corneal radius, corneal thickness, anterior chamber depth, anterior chamber angle, lens thickness, posterior chamber length, axial length, intraocular lens power (IOL), spherical power, and cylinder power). Patients with hyperthyroidism had thicker corneas compared to euthyroid individuals. Corneal thickness was also negatively associated with plasma TSH levels. Intra-ocular lens power was higher in patients with clinical hypothyroidism, while spherical power was higher in euthyroid individuals with positive antibodies compared to euthyroid individuals. Intra-ocular lens power negatively correlated with fT4 levels, while spherical power positively correlated with TgAb, TPOAb, and Tg levels and negatively correlated with TSH levels. The anterior chamber angle was positively associated with plasma TSH levels and TPOAb levels and negatively associated with plasma fT4 levels. These findings suggest an interesting interplay between ophthalmic measures and thyroid status, detectable even in the general adult population. Full article

(This article belongs to the Section Medical Biology)

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17 pages, 2789 KiB

Open AccessArticle

Human J-Domain Protein DnaJB6 Protects Yeast from [PSI⁺] Prion Toxicity

by Richard E. Dolder III, Jyotsna Kumar, Michael Reidy and Daniel C. Masison

Biology 2022, 11(12), 1846; https://doi.org/10.3390/biology11121846 - 18 Dec 2022

Viewed by 2473

Abstract

Human J-domain protein (JDP) DnaJB6 has a broad and potent activity that prevents formation of amyloid by polypeptides such as polyglutamine, A-beta, and alpha-synuclein, related to Huntington’s, Alzheimer’s, and Parkinson’s diseases, respectively. In yeast, amyloid-based [PSI⁺] prions, which rely on [...] Read more.

Human J-domain protein (JDP) DnaJB6 has a broad and potent activity that prevents formation of amyloid by polypeptides such as polyglutamine, A-beta, and alpha-synuclein, related to Huntington’s, Alzheimer’s, and Parkinson’s diseases, respectively. In yeast, amyloid-based [PSI⁺] prions, which rely on the related JDP Sis1 for replication, have a latent toxicity that is exposed by reducing Sis1 function. Anti-amyloid activity of DnaJB6 is very effective against weak [PSI⁺] prions and the Sup35 amyloid that composes them, but ineffective against strong [PSI⁺] prions composed of structurally different amyloid of the same Sup35. This difference reveals limitations of DnaJB6 that have implications regarding its therapeutic use for amyloid disease. Here, we find that when Sis1 function is reduced, DnaJB6 represses toxicity of strong [PSI⁺] prions and inhibits their propagation. Both Sis1 and DnaJB6, which are regulators of protein chaperone Hsp70, counteract the toxicity by reducing excessive incorporation of the essential Sup35 into prion aggregates. However, while Sis1 apparently requires interaction with Hsp70 to detoxify [PSI⁺], DnaJB6 counteracts prion toxicity by a different, Hsp70-independent mechanism. Full article

(This article belongs to the Special Issue 10th Anniversary of Biology: Amyloid Interaction in Regulation of Protein Function, Prion Propagation, and Cell Death)

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14 pages, 2163 KiB

Open AccessArticle

Characterization of Acinetobacter baumannii Isolated from Raw Milk

by Hams M. A. Mohamed, Hanan H. Abd-Elhafeez, Omar A. Al-Jabr and Mona A. El-Zamkan

Biology 2022, 11(12), 1845; https://doi.org/10.3390/biology11121845 - 18 Dec 2022

Cited by 6 | Viewed by 3380

Abstract

Acinetobacter baumannii (A. baumannii) is an opportunistic pathogen associated with nosocomial infections. In this study, 100 raw milk samples were collected from Qena, Egypt, and subjected to conventional and molecular assays to determine the presence of A. baumannii and investigate their antimicrobial resistance [...] Read more.

Acinetobacter baumannii (A. baumannii) is an opportunistic pathogen associated with nosocomial infections. In this study, 100 raw milk samples were collected from Qena, Egypt, and subjected to conventional and molecular assays to determine the presence of A. baumannii and investigate their antimicrobial resistance and biofilm formation. Our findings revealed that, among the 100 samples, Acinetobacter spp. were found in 13 samples based on CHROM agar results. We further characterized them using rpoB and 16S-23SrRNA sequencing and gyrB multiplex PCR analysis and confirmed that 9 out of the 13 Acinetobacter spp. isolates were A. baumannii and 4 were other species. The A. baumannii isolates were resistant to β-lactam drugs, including cefotaxime (44%), ampicillin-sulbactam and levofloxacin (33.3% for each), imipenem, meropenem and aztreonam (22.2% for each). We observed different antimicrobial resistance patterns, with a multi-antibiotic resistant (MAR) index ranging from 0.2 to 0.3. According to the PCR results, bla_OXA-51 and bla_OXA-23 genes were amplified in 100% and 55.5% of the A. baumannii isolates, respectively, while the bla_OXA-58 gene was not amplified. Furthermore, the metallo-β-lactamases (MBL) genes bla_IMP and bla_NDM were found in 11.1% and 22.2% of isolates, respectively, while bla_VIM was not amplified. Additionally, eight A. baumannii isolates (88.8%) produced black-colored colonies on Congo red agar, demonstrating their biofilm production capacity. These results showed that, besides other foodborne pathogens, raw milk should also be examined for A. baumannii, which could be a public health concern. Full article

(This article belongs to the Special Issue Microbial Diversity and Microbial Resistance)

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23 pages, 1880 KiB

Open AccessArticle

Foliar Spray or Soil Drench: Microalgae Application Impacts on Soil Microbiology, Morpho-Physiological and Biochemical Responses, Oil and Fatty Acid Profiles of Chia Plants under Alkaline Stress

by Samah M. Youssef, Rasha S. El-Serafy, Kholoud Z. Ghanem, Abeer Elhakem and Azza A. Abdel Aal

Biology 2022, 11(12), 1844; https://doi.org/10.3390/biology11121844 - 17 Dec 2022

Cited by 13 | Viewed by 6832 | Correction

Abstract

Alkaline soil inhibits the growth and productivity of chia plants (Salvia hispanica L.). Microalgae as biofertilizers have been reported to induce alkalinity tolerance and enhance yield and quality. However, limited information is known concerning the influence of microalgae application on medical plants, [...] Read more.

Alkaline soil inhibits the growth and productivity of chia plants (Salvia hispanica L.). Microalgae as biofertilizers have been reported to induce alkalinity tolerance and enhance yield and quality. However, limited information is known concerning the influence of microalgae application on medical plants, including chia. Our experiments were performed to evaluate the effect of microalgae strains of Arthrospira platensis, Chlorella vulgaris, Nostoc muscorum, and Anabaena azollae with two application methods, foliar spray and soil drench, on morpho-physiological and biochemical parameters, yield, seed and oil quality, and fatty acid profiles of chia plants cultivated under alkaline soil conditions, as well as the on soil microbial activity. The results obtained reveal that both application methods positively influenced the growth and productivity of chia plants. However, the foliar application showed significant differences in the herb’s fresh and dry weights and leaf pigments, whereas the drenching application caused more effect than the foliar spray application at the reproductive stage. Untreated chia plants showed a slight decline in the growth, productivity, and antioxidant level with an increase in Na content. However, microalgae applications significantly ameliorated these impacts as they induced an enhancement in the growth, leaf pigments, total protein and carbohydrate contents, nutrient content, seed and oil yields, as well as an increase in linolenic and linoleic fatty acids, with a reduction in saturated fatty acids, namely, palmitic and lauric acid. Soil drenching generated an improvement in the soil microbial activity and caused a reduction in the pH. The treatment of A. platensis with drenching application resulted in higher seed and oil yield, with an increase of 124 and 263.3% in seed and oil yield, respectively. Full article

(This article belongs to the Collection Abiotic Stress in Plants and Resilience: Recent Advances)

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15 pages, 1237 KiB

Open AccessArticle

Does Caffeine Supplementation Associated with Paralympic Powerlifting Training Interfere with Hemodynamic Indicators?

by Jainara Lima Menezes, Felipe J. Aidar, Georgian Badicu, Stefania Cataldi, Roberto Carvutto, Ana Filipa Silva, Filipe Manuel Clemente, Claudia Cerulli, Joseane Barbosa de Jesus, Lucio Marques Vieira-Souza, Eliana Tranchita, Ciro José Brito, Francesco Fischetti and Gianpiero Greco

Biology 2022, 11(12), 1843; https://doi.org/10.3390/biology11121843 - 16 Dec 2022

Cited by 2 | Viewed by 2632

Abstract

Exercise, including resistance exercise with high loads, has positive hemodynamic responses such as reduced systolic blood pressure (SBP), diastolic blood pressure (DBP), heart rate (HR), Pressure Product Rate (PPR), and estimated myocardial oxygen volume (MVO₂). Caffeine (CA), used to improve performance, [...] Read more.

Exercise, including resistance exercise with high loads, has positive hemodynamic responses such as reduced systolic blood pressure (SBP), diastolic blood pressure (DBP), heart rate (HR), Pressure Product Rate (PPR), and estimated myocardial oxygen volume (MVO₂). Caffeine (CA), used to improve performance, tends to interfere with BP and HR. This study aimed to analyze the effects of CA supplementation on hemodynamic indicators in Paralympic weightlifting (PP). The exercise was performed on 14 male athletes (32.4 ± 8.5 years; 81.7 ± 21.9 kg) for three weeks. Two conditions were evaluated: supplementation with CA Anhydrous 9 mg/kg and with placebo (PL). The adapted bench press was used, with 5 × 5 at 80% 1RM. We evaluated BP, HR, PPR, and MVO₂, before, after, 5, 10, 20, 30, 40, 50, 60 min, and 24 h later. The CA presented higher absolute values in the pressure indicators than the PL, and after 24 h there was an inversion. The HR was higher in the CA and showed a reduction after 10 min. The PPR and MVO₂ in the CA presented absolute values greater than the PL, and 24 h later there was an inversion. There was no hypotensive effect, but the use of CA did not present risks related to PPR and MVO₂, demonstrating the safe use of this supplement in adapted strength sports. 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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18 pages, 884 KiB

Open AccessReview

Plasticity in Chemical Host Plant Recognition in Herbivorous Insects and Its Implication for Pest Control

by Sylvia Anton and Anne-Marie Cortesero

Biology 2022, 11(12), 1842; https://doi.org/10.3390/biology11121842 - 16 Dec 2022

Cited by 7 | Viewed by 2602

Abstract

Chemical communication is very important in herbivorous insects, with many species being important agricultural pests. They often use olfactory cues to find their host plants at a distance and evaluate their suitability upon contact with non-volatile cues. Responses to such cues are modulated [...] Read more.

Chemical communication is very important in herbivorous insects, with many species being important agricultural pests. They often use olfactory cues to find their host plants at a distance and evaluate their suitability upon contact with non-volatile cues. Responses to such cues are modulated through interactions between various stimuli of biotic and abiotic origin. In addition, the response to the same stimulus can vary as a function of, for example, previous experience, age, mating state, sex, and morph. Here we summarize recent advances in the understanding of plant localization and recognition in herbivorous insects with a focus on the interplay between long- and short-range signals in a complex environment. We then describe recent findings illustrating different types of plasticity in insect plant choice behavior and the underlying neuronal mechanisms at different levels of the chemosensory pathway. In the context of strong efforts to replace synthetic insecticides with alternative pest control methods, understanding combined effects between long- and close-range chemical cues in herbivore–plant interactions and their complex environment in host choice are crucial to develop effective plant protection methods. Furthermore, plasticity of behavioral and neuronal responses to chemical cues needs to be taken into account to develop effective sustainable pest insect control through behavioral manipulation. Full article

(This article belongs to the Section Ecology)

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19 pages, 16054 KiB

Open AccessArticle

Simulation Palynologists for Pollinosis Prevention: A Progressive Learning of Pollen Localization and Classification for Whole Slide Images

by Lin-Na Zhao, Jian-Qiang Li, Wen-Xiu Cheng, Su-Qin Liu, Zheng-Kai Gao, Xi Xu, Cai-Hua Ye and Huan-Ling You

Biology 2022, 11(12), 1841; https://doi.org/10.3390/biology11121841 - 16 Dec 2022

Cited by 6 | Viewed by 1985

Abstract

Existing API approaches usually independently leverage detection or classification models to distinguish allergic pollens from Whole Slide Images (WSIs). However, palynologists tend to identify pollen grains in a progressive learning manner instead of the above one-stage straightforward way. They generally focus on two [...] Read more.

Existing API approaches usually independently leverage detection or classification models to distinguish allergic pollens from Whole Slide Images (WSIs). However, palynologists tend to identify pollen grains in a progressive learning manner instead of the above one-stage straightforward way. They generally focus on two pivotal problems during pollen identification. (1) Localization: where are the pollen grains located? (2) Classification: which categories do these pollen grains belong to? To perfectly mimic the manual observation process of the palynologists, we propose a progressive method integrating pollen localization and classification to achieve allergic pollen identification from WSIs. Specifically, data preprocessing is first used to cut WSIs into specific patches and filter out blank background patches. Subsequently, we present the multi-scale detection model to locate coarse-grained pollen regions (targeting at “pollen localization problem”) and the multi-classifiers combination to determine the fine-grained category of allergic pollens (targeting at “pollen classification problem”). Extensive experimental results have demonstrated the feasibility and effectiveness of our proposed method. Full article

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

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9 pages, 1383 KiB

Open AccessArticle

Differential Expression of Dickkopf 1 and Periostin in Mouse Strains with High and Low Bone Mass

by Katharina Kerschan-Schindl, Victoria Schramek, Maria Butylina, Ursula Föger-Samwald and Peter Pietschmann

Biology 2022, 11(12), 1840; https://doi.org/10.3390/biology11121840 - 16 Dec 2022

Cited by 1 | Viewed by 1771

Abstract

By expressing different genes and proteins that regulate osteoclast as well as osteoblast formation, osteocytes orchestrate bone metabolism. The aim of this project was the evaluation of the differences in the osteocytes’ secretory activity in the low bone mass mouse strain C57BL/6J and [...] Read more.

By expressing different genes and proteins that regulate osteoclast as well as osteoblast formation, osteocytes orchestrate bone metabolism. The aim of this project was the evaluation of the differences in the osteocytes’ secretory activity in the low bone mass mouse strain C57BL/6J and the high bone mass strain C3H/J. The femura of eight- and sixteen-week-old male C57BL/6J and C3H/J mice—six animals per group—were analyzed. Using immunohistochemistry, osteocytes expressing dickkopf 1, sclerostin, periostin, fibroblast growth factor 23 (FGF23), and osteoprotegerin were detected. By means of the OsteoMeasure-System, 92.173 osteocytes were counted. At the age of eight weeks, approximately twice as many cortical and trabecular osteocytes from the C57BL/6J mice compared to the C3H/J mice expressed dickkopf 1 (p < 0.005). The number of cortical osteocytes expressing sclerostin was also higher in the C57BL/6J mice (p < 0.05). In contrast, the cortical and trabecular osteocytes expressing periostin were twice as high in the C3H/J mice (p < 0.005). The dickkopf 1 expressing osteocytes of the C57BL/6J mice decreased with age and showed a strain-specific difference only in cortical bone by 16 weeks of age (p < 0.05). In the C3H/J mice, the amount of osteocytes expressing periostin tended to increase with age. Thus, strain-related differences were maintained in 16-week-old rodents (p < 0.005). No strain-specific differences in the expression of FGF23 or osteoprotegerin in the cortical compartment could be detected. This experimental study showed that the osteocytes’ protein expression reflects differences in bone characteristics and strain-related differences during skeletal maturation. Besides the osteocytes’ expression of sclerostin, their expression of dickkopf 1 and periostin seems to be important for bone properties as well. Full article

(This article belongs to the Section Cell Biology)

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13 pages, 3160 KiB

Open AccessArticle

The Nature of Functional Features of Different Classes of G-Protein-Coupled Receptors

by Ke An, Xiaohong Zhu and Chen Bai

Biology 2022, 11(12), 1839; https://doi.org/10.3390/biology11121839 - 16 Dec 2022

Cited by 6 | Viewed by 2532

Abstract

G-protein-coupled receptors (GPCRs) are a critical family in the human proteome and are involved in various physiological processes. They are also the most important drug target, with approximately 30% of approved drugs acting on such receptors. The members of the family are divided [...] Read more.

G-protein-coupled receptors (GPCRs) are a critical family in the human proteome and are involved in various physiological processes. They are also the most important drug target, with approximately 30% of approved drugs acting on such receptors. The members of the family are divided into six classes based on their structural and functional characteristics. Understanding their structural–functional relationships will benefit us in future drug development. In this article, we investigate the features of protein function, structure, and energy that describe the dynamics of the GPCR activation process between different families. GPCRs straddle the cell membrane and transduce signals from outside the membrane into the cell. During the process, the conformational change in GPCRs that is activated by the binding of signal molecules is essential. During the binding process, different types of signal molecules result in different signal transfer efficiencies. Therefore, the GPCR classes show a variety of structures and activation processes. Based on the experimental crystal structures, we modeled the activation process of the β2 adrenergic receptor (β2AR), glucagon receptor (GCGR), and metabotropic glutamate receptor 2 (mGluR2), which represent class A, B, and C GPCRs, respectively. We calculated their activation free-energy landscapes and analyzed the structure–energy–function relationship. The results show a consistent picture of the activation mechanisms between different types of GPCRs. This could also provide us a way to understand other signal transduction proteins. Full article

(This article belongs to the Special Issue New Sights in Odorant-Binding Proteins)

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29 pages, 4568 KiB

Open AccessArticle

Geographically Disperse, Culturable Seed-Associated Microbiota in Forage Plants of Alfalfa (Medicago sativa L.) and Pitch Clover (Bituminaria bituminosa L.): Characterization of Beneficial Inherited Strains as Plant Stress-Tolerance Enhancers

by Marla Niza-Costa, Ana Sofía Rodríguez-dos Santos, Inês Rebelo-Romão, María Victoria Ferrer, Cristina Sequero López and Juan Ignacio Vílchez

Biology 2022, 11(12), 1838; https://doi.org/10.3390/biology11121838 - 16 Dec 2022

Cited by 6 | Viewed by 2742

Abstract

Agricultural production is being affected by increasingly harsh conditions caused by climate change. The vast majority of crops suffer growth and yield declines due to a lack of water or intense heat. Hence, commercial legume crops suffer intense losses of production (20–80%). This [...] Read more.

Agricultural production is being affected by increasingly harsh conditions caused by climate change. The vast majority of crops suffer growth and yield declines due to a lack of water or intense heat. Hence, commercial legume crops suffer intense losses of production (20–80%). This situation is even more noticeable in plants used as fodder for animals, such as alfalfa and pitch trefoil, since their productivity is linked not only to the number of seeds produced, but also to the vegetative growth of the plant itself. Thus, we decided to study the microbiota associated with their seeds in different locations on the Iberian Peninsula, with the aim of identifying culturable bacteria strains that have adapted to harsh environments and that can be used as biotreatments to improve plant growth and resistance to stress. As potentially inherited microbiota, they may also represent a treatment with medium- and long-term adaptative effects. Hence, isolated strains showed no clear relationship with their geographical sampling location, but had about 50% internal similarity with their model plants. Moreover, out of the 51 strains isolated, about 80% were capable of producing biofilms; around 50% produced mid/high concentrations of auxins and grew notably in ACC medium; only 15% were characterized as xerotolerant, while more than 75% were able to sporulate; and finally, 65% produced siderophores and more than 40% produced compounds to solubilize phosphates. Thus, Paenibacillus amylolyticus BB B2-A, Paenibacillus xylanexedens MS M1-C, Paenibacillus pabuli BB Oeiras A, Stenotrophomonas maltophilia MS M1-B and Enterobacter hormaechei BB B2-C strains were tested as plant bioinoculants in lentil plants (Lens culinaris Medik.), showing promising results as future treatments to improve plant growth under stressful conditions. Full article

(This article belongs to the Special Issue 18th SEFIN Meeting and 1st Spanish-Portuguese Congress on Beneficial Plant-Microorganism Interactions)

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11 pages, 1315 KiB

Open AccessArticle

In Silico Study of Mangostin Compounds and Its Derivatives as Inhibitors of α-Glucosidase Enzymes for Anti-Diabetic Studies

by Ahmad Fariz Maulana, Sriwidodo Sriwidodo, Yaya Rukayadi and Iman Permana Maksum

Biology 2022, 11(12), 1837; https://doi.org/10.3390/biology11121837 - 16 Dec 2022

Cited by 7 | Viewed by 2316

Abstract

Diabetes is a chronic disease with a high mortality rate worldwide and can cause other diseases such as kidney damage, narrowing of blood vessels, and heart disease. The concomitant use of drugs such as metformin, sulfonylurea, miglitol, and acarbose may cause side effects [...] Read more.

Diabetes is a chronic disease with a high mortality rate worldwide and can cause other diseases such as kidney damage, narrowing of blood vessels, and heart disease. The concomitant use of drugs such as metformin, sulfonylurea, miglitol, and acarbose may cause side effects with long-term administration. Therefore, natural ingredients are the best choice, considering that their long-term side effects are not significant. One of the compounds that can be used as a candidate antidiabetic is mangostin; however, information on the molecular mechanism needs to be further analyzed through molecular docking, simulating molecular dynamics, and testing the in silico antidiabetic potential. This study focused on modeling the protein structure, molecular docking, and molecular dynamics simulations and analyses. This process produces RMSD values, free energies, and intermolecular hydrogen bonding. Based on the analysis results, all molecular dynamics simulations can occur under physiological conditions, and γ-mangostin is the best among the test compounds. Full article

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

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18 pages, 8781 KiB

Open AccessArticle

In Vitro Antimicrobial and Anticancer Peculiarities of Ytterbium and Cerium Co-Doped Zinc Oxide Nanoparticles

by Essia Hannachi, Firdos Alam Khan, Yassine Slimani, Suriya Rehman, Zayneb Trabelsi, Sultan Akhtar and Ebtesam A. Al-Suhaimi

Biology 2022, 11(12), 1836; https://doi.org/10.3390/biology11121836 - 16 Dec 2022

Cited by 6 | Viewed by 2543

Abstract

Zinc oxide nanoparticles (ZnO NPs) are a promising platform for their use in biomedical research, especially given their anticancer and antimicrobial activities. This work presents the synthesis of ZnO NPs doped with different amounts of rare-earth ions of ytterbium (Yb) and cerium (Ce) [...] Read more.

Zinc oxide nanoparticles (ZnO NPs) are a promising platform for their use in biomedical research, especially given their anticancer and antimicrobial activities. This work presents the synthesis of ZnO NPs doped with different amounts of rare-earth ions of ytterbium (Yb) and cerium (Ce) and the assessment of their anticancer and antimicrobial activities. The structural investigations indicated a hexagonal wurtzite structure for all prepared NPs. The particle size was reduced by raising the amount of Ce and Yb in ZnO. The anticancer capabilities of the samples were examined by the cell viability MTT assay. Post 48-h treatment showed a reduction in the cancer cell viability, which was x = 0.00 (68%), x = 0.01 (58.70%), x = 0.03 (80.94%) and x = 0.05 (64.91%), respectively. We found that samples doped with x = 0.01 and x = 0.05 of Yb and Ce showed a better inhibitory effect on HCT-116 cancer cells than unadded ZnO (x = 0.00). The IC₅₀ for HCT-116 cells of Ce and Yb co-doped ZnO nanoparticles was calculated and the IC₅₀ values were x = 0.01 (3.50 µg/mL), x = 0.05 (8.25 µg/mL), x = 0.00 (11.75 µg/mL), and x = 0.03 (21.50 µg/mL). The treatment-doped ZnO NPs caused apoptotic cell death in the HCT-116 cells. The nanoparticles showed inhibitory action on both C. albicans and E. coli. It can be concluded that doping ZnO NPs with Yb and Ce improves their apoptotic effects on cancer and microbial cells. Full article

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10 pages, 1946 KiB

Open AccessArticle

Modification of Antibiotic Activity by Fixed Oil of the Artocarpus heterophyllus Almond against Standard and Multidrug-Resistant Bacteria Strains

by Cícera Janayne Ferreira Dias, António Raposo, Cícera Dayane Thais de Sousa, José Bezerra de Araújo-Neto, Saulo Relison Tintino, Cícera Datiane de Morais Oliveira-Tintino, Isaac Moura Araújo, Henrique Douglas Melo Coutinho, Mayra Garcia Maia Costa, Cleidiane Gomes Lima, Mairlane Silva de Alencar, Conrado Carrascosa, Ariana Saraiva and Erlânio Oliveira de Sousa

Biology 2022, 11(12), 1835; https://doi.org/10.3390/biology11121835 - 16 Dec 2022

Cited by 4 | Viewed by 2135

Abstract

Artocarpus heterophyllus (jackfruit) is an evergreen tree distributed in tropical regions and is among the most studied species of the genus Artocarpus. The jackfruit almond has been highlighted in relation to phytochemical studies, biological properties, and application in the development of food [...] Read more.

Artocarpus heterophyllus (jackfruit) is an evergreen tree distributed in tropical regions and is among the most studied species of the genus Artocarpus. The jackfruit almond has been highlighted in relation to phytochemical studies, biological properties, and application in the development of food products. This study aimed to analyze jackfruit fixed oil regarding chemical components, antibacterial property alone, and in association with antibiotics against standard and MDR bacteria strains. In the analysis of the oil by gas chromatography coupled to a flame ionization detector (GC-FID), a high content of saturated fatty acids (78.51%) was identified in relation to unsaturated fatty acids (17.07%). The main fatty acids identified were lauric acid (43.01%), myristic acid (11.10%), palmitic acid (6.95%), and oleic acid (15.32%). In the antibacterial analysis, broth microdilution assays were used. The oil presented minimum inhibitory concentration (MIC) ≥ 1024 μg/mL in antibacterial analysis for standard and MDR bacterial strains. The oil showed synergistic effects in the association with gentamicin, ofloxacin, and penicillin against MDR strains, with significant reductions in the MIC of antibiotics. The results suggest that the fixed oil of A. heterophyllus has fatty acids with the potential to synergistically modify antibiotic activity. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety)

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12 pages, 2030 KiB

Open AccessArticle

Evaluation of Gastrocnemius Motor Evoked Potentials Induced by Trans-Spinal Magnetic Stimulation Following Tibial Nerve Crush in Rats

by Pauline Michel-Flutot, Isley Jesus, Arnaud Mansart, Marcel Bonay, Kun-Ze Lee, Karine Auré and Stéphane Vinit

Biology 2022, 11(12), 1834; https://doi.org/10.3390/biology11121834 - 16 Dec 2022

Cited by 3 | Viewed by 1887

Abstract

Peripheral nerve injuries induce long-lasting physiological and severe functional impairment due to motor, sensory, and autonomic denervation. Preclinical models allow us to study the process of nerve damage, evaluate the capacity of the peripheral nervous system for spontaneous recovery, and test diagnostic tools [...] Read more.

Peripheral nerve injuries induce long-lasting physiological and severe functional impairment due to motor, sensory, and autonomic denervation. Preclinical models allow us to study the process of nerve damage, evaluate the capacity of the peripheral nervous system for spontaneous recovery, and test diagnostic tools to assess the damage and subsequent recovery. Methods: In this study on Sprague–Dawley rats, we: (1) compared the use of two different anesthetics (isoflurane and urethane) for the evaluation of motor evoked potentials (MEPs) induced by trans-spinal magnetic stimulation (TSMS) in gastrocnemius and brachioradialis muscles; (2) monitored the evolution of gastrocnemius MEPs by applying paired-pulse stimulation to evaluate the neuromuscular junction activity; and (3) evaluated the MEP amplitude before and after left tibialis nerve crush (up to 7 days post-injury under isoflurane anesthesia). The results showed that muscle MEPs had higher amplitudes under isoflurane anesthesia, as compared with urethane anesthesia in the rats, demonstrating higher motoneuronal excitability under isoflurane anesthesia evaluated by TSMS. Following tibial nerve crush, a significant reduction in gastrocnemius MEP amplitude was observed on the injured side, mainly due to axonal damage from the initial crush. No spontaneous recovery of MEP amplitude in gastrocnemius muscles was observed up to 7 days post-crush; even a nerve section did not induce any variation in residual MEP amplitude, suggesting that the initial crush effectively severed the axonal fibers. These observations were confirmed histologically by a drastic reduction in the remaining myelinated fibers in the crushed tibial nerve. These data demonstrate that TSMS can be reliably used to noninvasively evaluate peripheral nerve function in rats. This method could therefore readily be applied to evaluate nerve conductance in the clinical environment. Full article

(This article belongs to the Section Physiology)

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9 pages, 472 KiB

Open AccessArticle

Outnumbered: Control Prothrombin Time in Maddrey’s Discriminant Function Impacts Steroid Use but Not Mortality in Alcoholic Hepatitis

by Marcus Healey and Richard K. Sterling

Biology 2022, 11(12), 1833; https://doi.org/10.3390/biology11121833 - 16 Dec 2022

Cited by 1 | Viewed by 2047

Abstract

Background and aims: In alcoholic hepatitis (AH), increases in the total bilirubin (TB) and the prothrombin time (PT), which are included in the Maddrey’s discriminant function (MDF) and the model for end-stage liver disease (MELD), are associated with poor outcomes. However, the impact [...] Read more.

Background and aims: In alcoholic hepatitis (AH), increases in the total bilirubin (TB) and the prothrombin time (PT), which are included in the Maddrey’s discriminant function (MDF) and the model for end-stage liver disease (MELD), are associated with poor outcomes. However, the impact of which control PT in the MDF to use compared to the MELD on the outcomes in AH is unknown. Our aim is to determine whether the choice of the control PT used in the MDF calculations has any impact on steroid use and survival when compared to the MELD in those with AH. Methods: Through retrospective chart review, we analyzed 882 subjects who were admitted from 2012 to 2020 with acute AH. Their MDF was calculated [(TB + 4.6 × (PT–control)] using the following three different control PTs: 12, 13.5, and 14.8 s, and was compared to the MELD. The primary outcomes were steroid use and 30-day survival. Results: When it was stratified by the control PT, the percentage of MDF ≥ 32 (the threshold for steroids) decreased with increasing control PT (70%, 61%, and 52%, respectively), along with decreased steroid use (91%, 84%, and 75%, respectively). Those who received steroids were not shown to have improved 30-day survival compared to those who did not receive steroids (p = 0.41). The ability of the MDF for each control PT threshold to predict 30-day survival was similar (AUROC 0.735), and was lower compared to the MELD (0.767). Conclusion: While the choice of PT control in the MDF impacted the use of steroids in AH, the use of steroids and the choice of PT control used did not impact the overall survival. Regardless of which control PT was used in the MDF, the MELD was better at predicting 30-day survival. Important information: Background: Treatment with steroids is indicated in alcoholic hepatitis (AH) with Maddrey discriminant function (MDF) ≥ 32 and the model for end-stage liver disease (MELD) ≥ 20. The impact that the control prothrombin time (PT) value that is used in MDF has on steroid use and survival in AH is poorly understood. Findings: The choice of control PT that is used when calculating the MDF impacts the use of steroids but does not impact mortality. The MELD was better than the MDF at any control PT used in predicting survival in acute AH. Implications for patient care: Providers should be aware that higher control PT’s have an effect on treatment decisions but should not generally impact survival in this population. The MELD appears to better predict 30-day survival in this population. Full article

(This article belongs to the Special Issue Non-alcoholic and Alcohol-Associated Liver Injury)

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17 pages, 1961 KiB

Open AccessArticle

Assessment of Fish Diversity in the Ma’an Archipelago Special Protected Area Using Environmental DNA

by Yuqing Wang, Xunmeng Li, Xu Zhao, Jianqu Chen, Zhenhua Wang, Lili Chen, Shouyu Zhang and Kai Wang

Biology 2022, 11(12), 1832; https://doi.org/10.3390/biology11121832 - 15 Dec 2022

Cited by 3 | Viewed by 2561

Abstract

This study aimed to investigate the practical validity of the environmental DNA (eDNA) method for evaluating fish composition and diversity in different habitats. We evaluated the fish composition and diversity characteristics of seven different habitats in the Ma’an Archipelago Special Protected Area in [...] Read more.

This study aimed to investigate the practical validity of the environmental DNA (eDNA) method for evaluating fish composition and diversity in different habitats. We evaluated the fish composition and diversity characteristics of seven different habitats in the Ma’an Archipelago Special Protected Area in April 2020. The results showed that a total of twenty-seven species of fishes belonging to six orders, eighteen families, and twenty-three genera of the Actinopterygii were detected in the marine waters of the Ma’an Archipelago Special Protected Area. The dominant species in each habitat were Larimichthys crocea, Paralichthys olivaceus, and Lateolabrax maculatus. The mussel culture area had the highest number of species, with 19 fish species, while the offshore bulk load shedding platform had the lowest number of species, with 12 fish species. The rest of the habitat was not significantly different. The results showed that the mussel culture area had the highest diversity index (average value of 2.352 ± 0.161), and the offshore bulk load shedding platform had the lowest diversity index (average value of 1.865 ± 0.127); the rest of the habitat diversity indices did not differ significantly. A comparison with historical surveys showed that the eDNA technique can detect species not collected by traditional methods such as gillnets and trawls. Our study demonstrates the role of eDNA technology in obtaining fish diversity in different habitats and provides a theoretical basis for the continuous monitoring and management of fish biodiversity in protected areas. Full article

(This article belongs to the Section Conservation Biology and Biodiversity)

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15 pages, 19584 KiB

Open AccessArticle

Ability of the Right Ventricle to Serve as a Systemic Ventricle in Response to the Volume Overload at the Neonatal Stage

by Chunxia Zhou, Debao Li, Qing Cui, Qi Sun, Yuqing Hu, Yingying Xiao, Chuan Jiang, Lisheng Qiu, Haibo Zhang, Lincai Ye and Yanjun Sun

Biology 2022, 11(12), 1831; https://doi.org/10.3390/biology11121831 - 15 Dec 2022

Cited by 2 | Viewed by 1711

Abstract

Background: In children with hypoplastic left heart syndrome (HLHS), volume overload (VO) is inevitable, and the right ventricle (RV) pumps blood into the systemic circulation. Understanding the molecular differences and their different responses to VO between the RV and left ventricle (LV) at [...] Read more.

Background: In children with hypoplastic left heart syndrome (HLHS), volume overload (VO) is inevitable, and the right ventricle (RV) pumps blood into the systemic circulation. Understanding the molecular differences and their different responses to VO between the RV and left ventricle (LV) at the neonatal and highly plastic stages may improve the long-term management of children with HLHS. Methods and Results: A neonatal rat ventricular VO model was established by the creation of a fistula between the inferior vena cava and the abdominal aorta on postnatal day 1 (P1) and confirmed by echocardiographic and histopathological analyses. Transcriptomic analysis demonstrated that some of the major differences between a normal neonatal RV and LV were associated with the thyroid hormone and insulin signaling pathways. Under the influence of VO, the levels of insulin receptors and thyroid hormone receptors were significantly increased in the LV but decreased in the RV. The transcriptomic analysis also demonstrated that under the influence of VO, the top two common enriched pathways between the RV and LV were the insulin and thyroid hormone signaling pathways, whereas the RV-specific enriched pathways were primarily associated with lipid metabolism and arrhythmogenic right ventricular cardiomyopathy (ARVC); further, the LV-specific enriched pathways were primarily associated with nucleic acid metabolism and microRNAs in cancer. Conclusions: Insulin and thyroid hormones may play critical roles in the differences between a neonatal RV and LV as well as their common responses to VO. Regarding the isolated responses to VO, the RV favors an ARVC change and the LV favors a reduction in microRNAs in cancer. The current study suggests that insulin, thyroid hormone, and cancer-associated microRNAs are potential therapeutic targets that should be explored by basic science studies to improve the function of the RV to match that of the LV. Full article

(This article belongs to the Special Issue Animal Disease Models and Patient-iPS Cell Derived In Vitro Disease Models for Cardiovascular Biology—How Close to Disease?)

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18 pages, 3356 KiB

Open AccessArticle

Knocking Out the Transcription Factor OsNAC092 Promoted Rice Drought Tolerance

by Bo Wang, Yiheng Wang, Wancong Yu, Luping Wang, Qingkuo Lan, Yong Wang, Chengbin Chen and Yong Zhang

Biology 2022, 11(12), 1830; https://doi.org/10.3390/biology11121830 - 15 Dec 2022

Cited by 10 | Viewed by 1936

Abstract

Environmental drought stress threatens rice production. Previous studies have reported that related NAC (NAM, ATAF1/2, and CUC) transcription factors play an important role in drought stress. Herein, we identified and characterized OsNAC092, encoding an NAC transcription factor that is highly expressed [...] Read more.

Environmental drought stress threatens rice production. Previous studies have reported that related NAC (NAM, ATAF1/2, and CUC) transcription factors play an important role in drought stress. Herein, we identified and characterized OsNAC092, encoding an NAC transcription factor that is highly expressed and induced during drought tolerance. OsNAC092 knockout lines created using the clustered regularly interspaced palindromic repeats (CRISPR)-associated protein 9 (Cas9) system exhibited increased drought resistance in rice. RNA sequencing showed that the knockout of OsNAC092 caused a global expression change, and differential gene expression is chiefly associated with “response to light stimulus,” “MAPK signaling pathway,” “plant hormone signal transduction,” “response to oxidative stress,” “photosynthesis,” and “water deprivation.” In addition, the antioxidants and enzyme activities of the redox response were significantly increased. OsNAC092 mutant rice exhibited a higher ability to scavenge more ROS and maintained a high GSH/GSSG ratio and redox level under drought stress, which could protect cells from oxidant stress, revealing the importance of OsNAC092 in the rice’s response to abiotic stress. Functional analysis of OsNAC092 will be useful to explore many rice resistance genes in molecular breeding to aid in the development of modern agriculture. Full article

(This article belongs to the Collection Abiotic Stress Tolerance in Cereals)

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17 pages, 3936 KiB

Open AccessArticle

Transcriptomic Analysis on the Effects of Altered Water Temperature Regime on the Fish Ovarian Development of Coreius guichenoti under the Impact of River Damming

by Ting Li, Qiuwen Chen, Qi Zhang, Tao Feng, Jianyun Zhang, Yuqing Lin, Peisi Yang, Shufeng He and Hui Zhang

Biology 2022, 11(12), 1829; https://doi.org/10.3390/biology11121829 - 15 Dec 2022

Cited by 8 | Viewed by 2134

Abstract

Field investigation indicated that the reduction in fish spawning was associated with the alteration in water temperatures, even a 2–3 °C monthly difference due to reservoir operations. However, the physiological mechanism that influences the development of fish ovary (DFO) remains unclear. Thus, experiments [...] Read more.

Field investigation indicated that the reduction in fish spawning was associated with the alteration in water temperatures, even a 2–3 °C monthly difference due to reservoir operations. However, the physiological mechanism that influences the development of fish ovary (DFO) remains unclear. Thus, experiments of Coreius guichenoti were conducted at three different temperatures, optimal temperature (~20 °C, N) for fish spawning, lower (~17 °C, L), and higher (~23 °C, H), to reveal the effects of altered water temperature on the DFO. Comparisons were made between the L and N (LvsN) conditions and H and N (HvsN) conditions. Transcriptomic analysis differentially expressed transcripts (DETs) related to heat stress were observed only in LvsN conditions, indicating that the DFO showed a stronger response to changes in LvsN than in HvsN conditions. Upregulation of DETs of vitellogenin receptors in N temperature showed that normal temperature was conducive to vitellogenin entry into the oocytes. Other temperature-sensitive DETs, including microtubule, kinesin, dynein, and actin, were closely associated with cell division and material transport. LvsN significantly impacted cell division and nutrient accumulation in the yolk, whereas HvsN only influenced cell division. Our results highlight the impact of altered water temperature on the DFO, thereby providing insights for future reservoir operations regarding river damming and climate change and establishing fish conservation measures. Full article

(This article belongs to the Special Issue Physiological Ecology of Aquatic Animals under Extreme Environments)

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17 pages, 4848 KiB

Open AccessArticle

Characterization of a Stress-Enhanced Promoter from the Grass Halophyte, Spartina alterniflora L.

by Sonali Sengupta, Necla Pehlivan, Venkata Mangu, Kanniah Rajasekaran and Niranjan Baisakh

Biology 2022, 11(12), 1828; https://doi.org/10.3390/biology11121828 - 15 Dec 2022

Cited by 6 | Viewed by 1956

Abstract

Stress-inducible promoters are vital for the desirable expression of genes, especially transcription factors, which could otherwise compromise growth and development when constitutively overexpressed in plants. Here, we report on the characterization of the promoter region of a stress-responsive gene SaAsr1 from monocot halophyte [...] Read more.

Stress-inducible promoters are vital for the desirable expression of genes, especially transcription factors, which could otherwise compromise growth and development when constitutively overexpressed in plants. Here, we report on the characterization of the promoter region of a stress-responsive gene SaAsr1 from monocot halophyte cordgrass (Spartina alterniflora). Several cis-acting elements, such as ABRE (ABA-responsive element), DRE-CRT (dehydration responsive-element/C-Repeat), LTRE (low temperature-responsive element), ERE (ethylene-responsive element), LRE (light-responsive element), etc. contributed at varying degrees to salt-, drought- and ABA-enhanced expression of gusA reporter gene in Arabidopsis thaliana under the full-length promoter, pAsr1₁₈₇₅ and its deletion derivatives with an assortment of cis-regulatory motifs. The smallest promoter, pAsr1₄₉₁, with three cis-acting elements (a CCAAT box-heat responsive, an LRE, and a copper responsive element) conferred drought-enhanced expression of gusA; pAsr1₇₅₅ (with an ABRE and a DRE) presented the highest expression in ABA and drought; and pAsr1₉₉₄ with seven ABREs and two DREs conferred optimal induction of gusA, especially under drought and ABA. Arabidopsis transgenics expressing a known abiotic stress-responsive gene, SaADF2 (actin depolymerization factor 2), under both pAsr1₁₈₇₅ and p35S promoters outperformed the wild type (WT) with enhanced drought and salt tolerance contributed by higher relative water content and membrane stability with no significant difference between pAsr1₁₈₇₅:SaADF2 or p35S:SaADF2 lines. However, pAsr1₁₈₇₅:SaADF2 lines produced healthy plants with robust shoot systems under salt stress and control compared to slightly stunted growth of the p35S:SaADF2 plants. This reestablished the evidence that transgene expression under a stress-inducible promoter is a better strategy for the genetic manipulation of crops. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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18 pages, 1522 KiB

Open AccessArticle

Drug Repurposing Using Gene Co-Expression and Module Preservation Analysis in Acute Respiratory Distress Syndrome (ARDS), Systemic Inflammatory Response Syndrome (SIRS), Sepsis, and COVID-19

by Ryan Christian Mailem and Lemmuel L. Tayo

Biology 2022, 11(12), 1827; https://doi.org/10.3390/biology11121827 - 15 Dec 2022

Cited by 12 | Viewed by 2936

Abstract

SARS-CoV-2 infections are highly correlated with the overexpression of pro-inflammatory cytokines in what is known as a cytokine storm, leading to high fatality rates. Such infections are accompanied by SIRS, ARDS, and sepsis, suggesting a potential link between the three phenotypes. Currently, little [...] Read more.

SARS-CoV-2 infections are highly correlated with the overexpression of pro-inflammatory cytokines in what is known as a cytokine storm, leading to high fatality rates. Such infections are accompanied by SIRS, ARDS, and sepsis, suggesting a potential link between the three phenotypes. Currently, little is known about the transcriptional similarity between these conditions. Herein, weighted gene co-expression network analysis (WGCNA) clustering was applied to RNA-seq datasets (GSE147902, GSE66890, GSE74224, GSE177477) to identify modules of highly co-expressed and correlated genes, cross referenced with dataset GSE160163, across the samples. To assess the transcriptome similarities between the conditions, module preservation analysis was performed and functional enrichment was analyzed in DAVID webserver. The hub genes of significantly preserved modules were identified, classified into upregulated or downregulated, and used to screen candidate drugs using Connectivity Map (CMap) to identify repurposed drugs. Results show that several immune pathways (chemokine signaling, NOD-like signaling, and Th1 and Th2 cell differentiation) are conserved across the four diseases. Hub genes screened using intramodular connectivity show significant relevance with the pathogenesis of cytokine storms. Transcriptomic-driven drug repurposing identified seven candidate drugs (SB-202190, eicosatetraenoic-acid, loratadine, TPCA-1, pinocembrin, mepacrine, and CAY-10470) that targeted several immune-related processes. These identified drugs warrant further study into their efficacy for treating cytokine storms, and in vitro and in vivo experiments are recommended to confirm the findings of this study. Full article

(This article belongs to the Special Issue Single Cell Omics and Integrative Biology: Selected Papers from ICBCB 2022)

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12 pages, 785 KiB

Open AccessArticle

Mesothelin Gene Variants Affect Soluble Mesothelin-Related Protein Levels in the Plasma of Asbestos-Exposed Males and Mesothelioma Patients from Germany

by Hans-Peter Rihs, Swaantje Casjens, Irina Raiko, Jens Kollmeier, Martin Lehnert, Kerstin Nöfer, Kerstin May-Taube, Nina Kaiser, Dirk Taeger, Thomas Behrens, Thomas Brüning and Georg Johnen

Biology 2022, 11(12), 1826; https://doi.org/10.3390/biology11121826 - 14 Dec 2022

Cited by 1 | Viewed by 1961

Abstract

Malignant mesothelioma (MM) is a severe disease mostly caused by asbestos exposure. Today, one of the best available biomarkers is the soluble mesothelin-related protein (SMRP), also known as mesothelin. Recent studies have shown that mesothelin levels are influenced by individual genetic variability. This [...] Read more.

Malignant mesothelioma (MM) is a severe disease mostly caused by asbestos exposure. Today, one of the best available biomarkers is the soluble mesothelin-related protein (SMRP), also known as mesothelin. Recent studies have shown that mesothelin levels are influenced by individual genetic variability. This study aimed to investigate the influence of three mesothelin (MSLN) gene variants (SNPs) in the 5′-untranslated promoter region (5′-UTR), MSLN rs2235503 C > A, rs3764246 A > G, rs3764247 A > C, and one (rs1057147 G > A) in the 3′-untranslated region (3′-UTR) of the MSLN gene on plasma concentrations of mesothelin in 410 asbestos-exposed males without cancer and 43 males with prediagnostic MM (i.e., with MM diagnosed later on) from the prospective MoMar study, as well as 59 males with manifest MM from Germany. The mesothelin concentration differed significantly between the different groups (p < 0.0001), but not between the prediagnostic and manifest MM groups (p = 0.502). Five to eight mutations of the four SNP variants studied were associated with increased mesothelin concentrations (p = 0.001). The highest mesothelin concentrations were observed for homozygous variants of the three promotor SNPs in the 5′-UTR (p < 0.001), and the highest odds ratio for an elevated mesothelin concentration was observed for MSLN rs2235503 C > A. The four studied SNPs had a clear influence on the mesothelin concentration in plasma. Hence, the analysis of these SNPs may help to elucidate the diagnostic background of patients displaying increased mesothelin levels and might help to reduce false-positive results when using mesothelin for MM screening in high-risk groups. Full article

(This article belongs to the Special Issue Examining the Biology of Mesothelin in Normal Physiology, Cancer and Therapeutic Development)

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Biology, Volume 11, Issue 12 (December 2022) – 168 articles

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