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58 pages, 5907 KiB  
Review
The Transformation Experiment of Frederick Griffith II: Inclusion of Cellular Heredity for the Creation of Novel Microorganisms
by Günter A. Müller
Bioengineering 2025, 12(5), 532; https://doi.org/10.3390/bioengineering12050532 - 15 May 2025
Cited by 1 | Viewed by 967
Abstract
So far, synthetic biology approaches for the construction of artificial microorganisms have fostered the transformation of acceptor cells with genomes from donor cells. However, this strategy seems to be limited to closely related bacterial species only, due to the need for a “fit” [...] Read more.
So far, synthetic biology approaches for the construction of artificial microorganisms have fostered the transformation of acceptor cells with genomes from donor cells. However, this strategy seems to be limited to closely related bacterial species only, due to the need for a “fit” between donor and acceptor proteomes and structures. “Fitting” of cellular regulation of metabolite fluxes and turnover between donor and acceptor cells, i.e. cybernetic heredity, may be even more difficult to achieve. The bacterial transformation experiment design 1.0, as introduced by Frederick Griffith almost one century ago, may support integration of DNA, macromolecular, topological, cybernetic and cellular heredity: (i) attenuation of donor Pneumococci of (S) serotype fosters release of DNA, and hypothetically of non-DNA structures compatible with subsequent transfer to and transformation of acceptor Pneumococci from (R) to (S) serotype; (ii) use of intact donor cells rather than of subcellular or purified fractions may guarantee maximal diversity of the structural and cybernetic matter and information transferred; (iii) “Blending” or mixing and fusion of donor and acceptor Pneumococci may occur under accompanying transfer of metabolites and regulatory circuits. A Griffith transformation experiment design 2.0 is suggested, which may enable efficient exchange of DNA as well as non-DNA structural and cybernetic matter and information, leading to unicellular hybrid microorganisms with large morphological/metabolic phenotypic differences and major features compared to predeceding cells. The prerequisites of horizontal gene and somatic cell nuclear transfer, the molecular mechanism of transformation, the machineries for the biogenesis of bacterial cytoskeleton, micelle-like complexes and membrane landscapes are briefly reviewed on the basis of underlying conceptions, ranging from Darwin’s “gemmules” to “stirps”, cytoplasmic and “plasmon” inheritance, “rhizene agency”, “communicology”, “transdisciplinary membranology” to up to Kirschner’s “facilitated variation”. Full article
(This article belongs to the Section Biochemical Engineering)
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11 pages, 6705 KiB  
Case Report
Unveiling Secondary Mutations in Blended Phenotypes: Dual ERCC4 and OTOA Pathogenic Variants Through WES Analysis
by Pinella Failla, Lucia Saccuzzo, Ornella Galesi, Donatella Greco, Vincenza Barresi, Silvestra Amata, Corrado Romano and Marco Fichera
Int. J. Mol. Sci. 2024, 25(24), 13471; https://doi.org/10.3390/ijms252413471 - 16 Dec 2024
Viewed by 925
Abstract
This study describes two siblings from consanguineous parents who exhibit intellectual disability, microcephaly, photosensitivity, bilateral sensorineural hearing loss, numerous freckles, and other clinical features that suggest a potential disruption of the nucleotide excision repair (NER) pathway. Whole exome sequencing (WES) identified a novel [...] Read more.
This study describes two siblings from consanguineous parents who exhibit intellectual disability, microcephaly, photosensitivity, bilateral sensorineural hearing loss, numerous freckles, and other clinical features that suggest a potential disruption of the nucleotide excision repair (NER) pathway. Whole exome sequencing (WES) identified a novel homozygous missense variant in the ERCC4 gene, which was predicted to be pathogenic. However, a subsequent peculiar audiometric finding prompted further investigation, revealing a homozygous deletion in the OTOA gene linked to neurosensorial hearing loss. Both variants were located within a run of homozygosity (ROH) on chromosome 16p13.12-p12.2, implicating a complex genetic basis for the observed phenotype. While this study reports a potentially novel ERCC4 variant, it underscores the importance of comprehensive analysis and deep phenotyping in WES data to improve diagnostic accuracy. Our findings advocate for an expanded approach in WES analysis, ensuring more precise diagnoses and improved genetic counseling, particularly when specialized tests for structural variant analysis are unavailable. Full article
(This article belongs to the Collection Feature Papers in Molecular Genetics and Genomics)
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14 pages, 2280 KiB  
Article
Response of Morphological Plasticity of Quercus variabilis Seedlings to Different Light Quality
by Zhengning Wang, Hang Luo, Baoxuan Liu, Shangwen Song, Xiao Zhang, Yushuang Song and Bo Liu
Forests 2024, 15(12), 2153; https://doi.org/10.3390/f15122153 - 6 Dec 2024
Cited by 1 | Viewed by 878
Abstract
This experiment explores the regulatory mechanisms of various light qualities on the phenotypic plasticity of Quercus variabilis seedlings during their growth. The light conditions included blue light (BL), red light (RL), far-red light (FrL), a blend of RL and FrL with a ratio [...] Read more.
This experiment explores the regulatory mechanisms of various light qualities on the phenotypic plasticity of Quercus variabilis seedlings during their growth. The light conditions included blue light (BL), red light (RL), far-red light (FrL), a blend of RL and FrL with a ratio of 1:1 (RFr1:1L), and a blend of RL and FrL with a ratio of 1:2 (RFr1:2L), alongside a broad-spectrum white light (WL) as the control. Each treatment was maintained at a consistent photosynthetic photon flux density of 400 µmol·m−2·s−1. Results indicate significant morphological variations in Q. variabilis seedlings under different light qualities. Compared to white light treatment, all light quality treatments enhance seedling height, with the FrL treatment exhibiting the most pronounced effect. Seedling ground diameter elongation is stimulated by all light quality treatments, except for the BL treatment. Although the BL treatment promotes leaf morphology in Q. variabilis seedlings, it inhibits root growth, leading to reduced biomass accumulation and a lower root-to-shoot ratio. FrL can mitigate the effects of RL. Under the FrL treatment, Q. variabilis seedlings exhibit a greater increase in plant height and a higher height-to-diameter ratio. While the leaf morphology of RFr1:1L treatment does not show significant advantages, it demonstrates substantial root growth, resulting in the highest biomass accumulation. Quercus variabilis displays the strongest morphological plasticity in its root system, showing greater sensitivity to variations in light quality compared to leaf morphology and biomass accumulation. Strategically optimizing light spectrum and wavelength can significantly boost economic yields and improve the quality of forestry products. Full article
(This article belongs to the Section Forest Ecophysiology and Biology)
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20 pages, 7283 KiB  
Article
Composite Polycaprolactone/Gelatin Nanofiber Membrane Scaffolds for Mesothelial Cell Culture and Delivery in Mesothelium Repair
by Darshan Tagadur Govindaraju, Hao-Hsi Kao, Yen-Miao Chien and Jyh-Ping Chen
Int. J. Mol. Sci. 2024, 25(18), 9803; https://doi.org/10.3390/ijms25189803 - 11 Sep 2024
Cited by 2 | Viewed by 1654
Abstract
To repair damaged mesothelium tissue, which lines internal organs and cavities, a tissue engineering approach with mesothelial cells seeded to a functional nanostructured scaffold is a promising approach. Therefore, this study explored the uses of electrospun nanofiber membrane scaffolds (NMSs) as scaffolds for [...] Read more.
To repair damaged mesothelium tissue, which lines internal organs and cavities, a tissue engineering approach with mesothelial cells seeded to a functional nanostructured scaffold is a promising approach. Therefore, this study explored the uses of electrospun nanofiber membrane scaffolds (NMSs) as scaffolds for mesothelial cell culture and transplantation. We fabricated a composite NMS through electrospinning by blending polycaprolactone (PCL) with gelatin. The addition of gelatin enhanced the membrane’s hydrophilicity while maintaining its mechanical strength and promoted cell attachment. The in vitro study demonstrated enhanced adhesion of mesothelial cells to the scaffold with improved morphology and increased phenotypic expression of key marker proteins calretinin and E-cadherin in PCL/gelatin compared to pure PCL NMSs. In vivo studies in rats revealed that only cell-seeded PCL/gelatin NMS constructs fostered mesothelial healing. Implantation of these constructs leads to the regeneration of new mesothelium tissue. The neo-mesothelium is similar to native mesothelium from hematoxylin and eosin (H&E) and immunohistochemical staining. Taken together, the PCL/gelatin NMSs can be a promising scaffold for mesothelial cell attachment, proliferation, and differentiation, and the cell/scaffold construct can be used in therapeutic applications to reconstruct a mesothelium layer. Full article
(This article belongs to the Special Issue Nanoparticles: From Synthesis to Applications 2.0)
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14 pages, 5805 KiB  
Technical Note
Soft Tissue Retraction Maneuver in Cone Beam Computed Tomography Prior to Crown-Lengthening Procedure—A Technical Note
by Paulina Adamska, Marcin Stasiak, Wojciech Dąbrowski, Dorota Pylińska-Dąbrowska, Łukasz Jan Adamski, Adam Zedler, Ewa Kozłowska and Michał Studniarek
J. Clin. Med. 2024, 13(13), 3668; https://doi.org/10.3390/jcm13133668 - 24 Jun 2024
Cited by 2 | Viewed by 1351
Abstract
Background: An accurate determination of the biological width and the relationship of the cemento-enamel junction with the border of the alveolar bone is crucial during a clinical crown-lengthening (CCL) procedure. The aim of this study was to present a technical note about the [...] Read more.
Background: An accurate determination of the biological width and the relationship of the cemento-enamel junction with the border of the alveolar bone is crucial during a clinical crown-lengthening (CCL) procedure. The aim of this study was to present a technical note about the retraction techniques in cone beam computed tomography (CBCT) prior to CCL, highlighting the significant enhancement in procedural accuracy and predictability that these techniques offer. Methods: Clinical and radiological examinations should be performed before a CCL procedure. It is necessary to determine the length of the tooth crowns, the periodontal pockets’ depth, and the phenotype of the gingiva. The ideal CBCT examination should be performed with soft tissue retraction. This can be achieved using retractors or cotton rolls. Results: Retraction of the lips, cheeks, and tongue allows one to assess the marginal gingiva, the cemento-enamel junction, and the alveolar bone. A detailed plan of the CCL procedure, which involves retraction, ensures both the aesthetic appeal and the achievement of a newly defined gingival zenith, enhancing the overall visual harmony. Conclusions: Compared with conventional radiographic imaging, the soft tissue retraction maneuver in CBCT prior to CCL surgery offers an effective approach to the evaluation and diagnosis of soft and hard tissue. This is because of the detailed planning of the aesthetic CCL procedure. Such an approach leads to superior aesthetic outcomes in dentistry, contributing to the advancement of aesthetic dentistry through a harmonious blend of art and science. Full article
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17 pages, 4439 KiB  
Article
Lon1 Inactivation Downregulates Autophagic Flux and Brassinosteroid Biogenesis, Modulating Mitochondrial Proportion and Seed Development in Arabidopsis
by Ce Song, Yuqi Hou, Tiantian Li, Yinyin Liu, Xian-Ao Wang, Wumei Qu and Lei Li
Int. J. Mol. Sci. 2024, 25(10), 5425; https://doi.org/10.3390/ijms25105425 - 16 May 2024
Cited by 2 | Viewed by 1500
Abstract
Mitochondrial protein homeostasis is crucially regulated by protein degradation processes involving both mitochondrial proteases and cytosolic autophagy. However, it remains unclear how plant cells regulate autophagy in the scenario of lacking a major mitochondrial Lon1 protease. In this study, we observed a notable [...] Read more.
Mitochondrial protein homeostasis is crucially regulated by protein degradation processes involving both mitochondrial proteases and cytosolic autophagy. However, it remains unclear how plant cells regulate autophagy in the scenario of lacking a major mitochondrial Lon1 protease. In this study, we observed a notable downregulation of core autophagy proteins in Arabidopsis Lon1 knockout mutant lon1-1 and lon1-2, supporting the alterations in the relative proportions of mitochondrial and vacuolar proteins over total proteins in the plant cells. To delve deeper into understanding the roles of the mitochondrial protease Lon1 and autophagy in maintaining mitochondrial protein homeostasis and plant development, we generated the lon1-2atg5-1 double mutant by incorporating the loss-of-function mutation of the autophagy core protein ATG5, known as atg5-1. The double mutant exhibited a blend of phenotypes, characterized by short plants and early senescence, mirroring those observed in the individual single mutants. Accordingly, distinct transcriptome alterations were evident in each of the single mutants, while the double mutant displayed a unique amalgamation of transcriptional responses. Heightened severity, particularly evident in reduced seed numbers and abnormal embryo development, was observed in the double mutant. Notably, aberrations in protein storage vacuoles (PSVs) and oil bodies were evident in the single and double mutants. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of genes concurrently downregulated in lon1-2, atg5-1, and lon1-2atg5-1 unveiled a significant suppression of genes associated with brassinosteroid (BR) biosynthesis and homeostasis. This downregulation likely contributes to the observed abnormalities in seed and embryo development in the mutants. Full article
(This article belongs to the Section Molecular Plant Sciences)
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22 pages, 16578 KiB  
Article
YOLOv8-RMDA: Lightweight YOLOv8 Network for Early Detection of Small Target Diseases in Tea
by Rong Ye, Guoqi Shao, Yun He, Quan Gao and Tong Li
Sensors 2024, 24(9), 2896; https://doi.org/10.3390/s24092896 - 1 May 2024
Cited by 24 | Viewed by 3471
Abstract
In order to efficiently identify early tea diseases, an improved YOLOv8 lesion detection method is proposed to address the challenges posed by the complex background of tea diseases, difficulty in detecting small lesions, and low recognition rate of similar phenotypic symptoms. This method [...] Read more.
In order to efficiently identify early tea diseases, an improved YOLOv8 lesion detection method is proposed to address the challenges posed by the complex background of tea diseases, difficulty in detecting small lesions, and low recognition rate of similar phenotypic symptoms. This method focuses on detecting tea leaf blight, tea white spot, tea sooty leaf disease, and tea ring spot as the research objects. This paper presents an enhancement to the YOLOv8 network framework by introducing the Receptive Field Concentration-Based Attention Module (RFCBAM) into the backbone network to replace C2f, thereby improving feature extraction capabilities. Additionally, a mixed pooling module (Mixed Pooling SPPF, MixSPPF) is proposed to enhance information blending between features at different levels. In the neck network, the RepGFPN module replaces the C2f module to further enhance feature extraction. The Dynamic Head module is embedded in the detection head part, applying multiple attention mechanisms to improve multi-scale spatial location and multi-task perception capabilities. The inner-IoU loss function is used to replace the original CIoU, improving learning ability for small lesion samples. Furthermore, the AKConv block replaces the traditional convolution Conv block to allow for the arbitrary sampling of targets of various sizes, reducing model parameters and enhancing disease detection. the experimental results using a self-built dataset demonstrate that the enhanced YOLOv8-RMDA exhibits superior detection capabilities in detecting small target disease areas, achieving an average accuracy of 93.04% in identifying early tea lesions. When compared to Faster R-CNN, MobileNetV2, and SSD, the average precision rates of YOLOv5, YOLOv7, and YOLOv8 have shown improvements of 20.41%, 17.92%, 12.18%, 12.18%, 10.85%, 7.32%, and 5.97%, respectively. Additionally, the recall rate (R) has increased by 15.25% compared to the lowest-performing Faster R-CNN model and by 8.15% compared to the top-performing YOLOv8 model. With an FPS of 132, YOLOv8-RMDA meets the requirements for real-time detection, enabling the swift and accurate identification of early tea diseases. This advancement presents a valuable approach for enhancing the ecological tea industry in Yunnan, ensuring its healthy development. Full article
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17 pages, 7737 KiB  
Article
AC R-CNN: Pixelwise Instance Segmentation Model for Agrocybe cylindracea Cap
by Hua Yin, Shenglan Yang, Wenhao Cheng, Quan Wei, Yinglong Wang and Yilu Xu
Agronomy 2024, 14(1), 77; https://doi.org/10.3390/agronomy14010077 - 28 Dec 2023
Cited by 2 | Viewed by 1767
Abstract
The popularity of Agrocybe cylindracea is increasing due to its unique flavor and nutritional value. The Agrocybe cylindracea cap is a key aspect of the growth process, and high-throughput observation of cap traits in greenhouses by machine vision is a future development trend [...] Read more.
The popularity of Agrocybe cylindracea is increasing due to its unique flavor and nutritional value. The Agrocybe cylindracea cap is a key aspect of the growth process, and high-throughput observation of cap traits in greenhouses by machine vision is a future development trend of smart agriculture. Nevertheless, the segmentation of the Agrocybe cylindracea cap is extremely challenging due to its similarity in color to the rest of the mushroom and the occurrence of mutual occlusion, presenting a major obstacle for the effective application of automation technology. To address this issue, we propose an improved instance segmentation network called Agrocybe cylindracea R-CNN (AC R-CNN) based on the Mask R-CNN model. AC R-CNN incorporates hybrid dilated convolution (HDC) and attention modules into the feature extraction backbone network to enhance the segmentation of adhesive mushroom caps and focus on the segmentation objects. Furthermore, the Mask Branch module is replaced with PointRend to improve the network’s segmentation accuracy at the edges of the mushroom caps. These modifications effectively solve the problems of the original algorithm’s inability to segment adhesive Agrocybe cylindracea caps and low accuracy in edge segmentation. The experimental results demonstrate that AC R-CNN outperforms the original Mask R-CNN in terms of segmentation performance. The average precision (AP) is improved by 12.1%, and the F1 score is improved by 13.7%. Additionally, AC R-CNN outperforms other networks such as Mask Scoring R-CNN and BlendMask. Therefore, the research findings of this study can meet the high-precision segmentation requirements of Agrocybe cylindracea caps and lay a theoretical foundation for the development of subsequent intelligent phenotyping devices and harvesting robots. Full article
(This article belongs to the Section Precision and Digital Agriculture)
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13 pages, 2841 KiB  
Article
Modified TPP-MoS2 QD Blend as a Bio-Functional Model for Normalizing Microglial Dysfunction in Alzheimer’s Disease
by Ohoud A. Alomari, Safaa Qusti, Maha Balgoon, Fadwa Aljoud, Khalid A. Alamry and Mahmoud A. Hussein
Neurol. Int. 2023, 15(3), 954-966; https://doi.org/10.3390/neurolint15030061 - 8 Aug 2023
Cited by 4 | Viewed by 2575
Abstract
Alzheimer’s disease (AD) is the most prevalent neurodegenerative disease of old age. Accumulation of β-amyloid peptide (Aβ) and mitochondrial dysfunction results in chronic microglial activation, which enhances neuroinflammation and promotes neurodegeneration. Microglia are resident macrophages of the brain and spinal cord which play [...] Read more.
Alzheimer’s disease (AD) is the most prevalent neurodegenerative disease of old age. Accumulation of β-amyloid peptide (Aβ) and mitochondrial dysfunction results in chronic microglial activation, which enhances neuroinflammation and promotes neurodegeneration. Microglia are resident macrophages of the brain and spinal cord which play an important role in maintaining brain homeostasis through a variety of phenotypes, including the pro-inflammatory phenotype and anti-inflammatory phenotypes. However, persistently activated microglial cells generate reactive species and neurotoxic mediators. Therefore, inhibitors of microglial activation are seen to have promise in AD control. The modified TPP/MoS2 QD blend is a mitochondrion-targeted nanomaterial that exhibits cytoprotective activities and antioxidant properties through scavenging free radicals. In the present study, the cell viability and cytotoxicity of the DSPE-PEG-TPP/MoS2 QD blend on microglial cells stimulated by Aβ were investigated. The levels of reactive oxygen species (ROS) and mitochondrial membrane potential (MMP) were also assessed. In addition, pro-inflammatory and anti-inflammatory cytokines, such as tumor necrosis factor α (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), transforming growth factor beta (TGF-β), inducible nitric oxide synthase (iNOS) and arginase-1 (Arg-I) were measured in the presence or absence of the DSPE-PEG-TPP/MoS2 QD blend on an immortalized microglia cells activated by accumulation of Aβ. We found that the DSPE-PEG-TPP/MoS2 QD blend was biocompatible and nontoxic at specific concentrations. Furthermore, the modified TPP/MoS2 QD blend significantly reduced the release of free radicals and improved the mitochondrial function through the upregulation of MMP in a dose-dependent manner on microglial cells treated with Aβ. In addition, pre-treatment of microglia with the DSPE-PEG-TPP/MoS2 QD blend at concentrations of 25 and 50 μg/mL prior to Aβ stimulation significantly inhibited the release and expression of pro-inflammatory cytokines, such as IL-1β, IL-6, TNF-α, and iNOS. Nevertheless, the anti-inflammatory cytokines TGF-β and Arg-I were activated. These findings suggest that the modified TPP/MoS2 QD blend reduced oxidative stress, inflammation and improved the mitochondrial function in the immortalized microglial cells (IMG) activated by Aβ. Overall, our research shows that the DSPE-PEG-TPP/MoS2 QD blend has therapeutic promise for managing AD and can impact microglia polarization. Full article
(This article belongs to the Collection Advances in Neurodegenerative Diseases)
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28 pages, 3433 KiB  
Article
Triazine Herbicide and NPK Fertilizer Exposure: Accumulation of Heavy Metals and Rare Earth Elements, Effects on Cuticle Melanization, and Immunocompetence in the Model Species Tenebrio molitor
by Attilio Naccarato, Maria Luigia Vommaro, Domenico Amico, Francesca Sprovieri, Nicola Pirrone, Antonio Tagarelli and Anita Giglio
Toxics 2023, 11(6), 499; https://doi.org/10.3390/toxics11060499 - 1 Jun 2023
Cited by 17 | Viewed by 3358
Abstract
The increasing use of agrochemicals, including fertilizers and herbicides, has led to worrying metal contamination of soils and waters and raises serious questions about the effects of their transfer to different levels of the trophic web. Accumulation and biomagnification of essential (K, Na, [...] Read more.
The increasing use of agrochemicals, including fertilizers and herbicides, has led to worrying metal contamination of soils and waters and raises serious questions about the effects of their transfer to different levels of the trophic web. Accumulation and biomagnification of essential (K, Na, Mg, Zn, Ca), nonessential (Sr, Hg, Rb, Ba, Se, Cd, Cr, Pb, As), and rare earth elements (REEs) were investigated in newly emerged adults of Tenebrio molitor exposed to field-admitted concentrations of a metribuzin-based herbicide and an NPK blend fertilizer. Chemical analyses were performed using inductively coupled plasma tandem mass spectrometry (ICP-MS/MS) supported by unsupervised pattern recognition techniques. Physiological parameters such as cuticle melanization, cellular (circulating hemocytes), and humoral (phenoloxidase enzyme activity) immune responses and mass loss were tested as exposure markers in both sexes. The results showed that NPK fertilizer application is the main cause of REE accumulation in beetles over time, besides toxic elements (Sr, Hg, Cr, Rb, Ba, Ni, Al, V, U) also present in the herbicide-treated beetles. The biomagnification of Cu and Zn suggested a high potential for food web transfer in agroecosystems. Gender differences in element concentrations suggested that males and females differ in element uptake and excretion. Differences in phenotypic traits show that exposure affects metabolic pathways involving sequestration and detoxification during the transition phase from immature-to-mature beetles, triggering a redistribution of resources between sexual maturation and immune responses. Our findings highlight the importance of setting limits for metals and REEs in herbicides and fertilizers to avoid adverse effects on species that provide ecosystem services and contribute to soil health in agroecosystems. Full article
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38 pages, 10981 KiB  
Article
UAV Multisensory Data Fusion and Multi-Task Deep Learning for High-Throughput Maize Phenotyping
by Canh Nguyen, Vasit Sagan, Sourav Bhadra and Stephen Moose
Sensors 2023, 23(4), 1827; https://doi.org/10.3390/s23041827 - 6 Feb 2023
Cited by 34 | Viewed by 6340
Abstract
Recent advances in unmanned aerial vehicles (UAV), mini and mobile sensors, and GeoAI (a blend of geospatial and artificial intelligence (AI) research) are the main highlights among agricultural innovations to improve crop productivity and thus secure vulnerable food systems. This study investigated the [...] Read more.
Recent advances in unmanned aerial vehicles (UAV), mini and mobile sensors, and GeoAI (a blend of geospatial and artificial intelligence (AI) research) are the main highlights among agricultural innovations to improve crop productivity and thus secure vulnerable food systems. This study investigated the versatility of UAV-borne multisensory data fusion within a framework of multi-task deep learning for high-throughput phenotyping in maize. UAVs equipped with a set of miniaturized sensors including hyperspectral, thermal, and LiDAR were collected in an experimental corn field in Urbana, IL, USA during the growing season. A full suite of eight phenotypes was in situ measured at the end of the season for ground truth data, specifically, dry stalk biomass, cob biomass, dry grain yield, harvest index, grain nitrogen utilization efficiency (Grain NutE), grain nitrogen content, total plant nitrogen content, and grain density. After being funneled through a series of radiometric calibrations and geo-corrections, the aerial data were analytically processed in three primary approaches. First, an extended version normalized difference spectral index (NDSI) served as a simple arithmetic combination of different data modalities to explore the correlation degree with maize phenotypes. The extended NDSI analysis revealed the NIR spectra (750–1000 nm) alone in a strong relation with all of eight maize traits. Second, a fusion of vegetation indices, structural indices, and thermal index selectively handcrafted from each data modality was fed to classical machine learning regressors, Support Vector Machine (SVM) and Random Forest (RF). The prediction performance varied from phenotype to phenotype, ranging from R2 = 0.34 for grain density up to R2 = 0.85 for both grain nitrogen content and total plant nitrogen content. Further, a fusion of hyperspectral and LiDAR data completely exceeded limitations of single data modality, especially addressing the vegetation saturation effect occurring in optical remote sensing. Third, a multi-task deep convolutional neural network (CNN) was customized to take a raw imagery data fusion of hyperspectral, thermal, and LiDAR for multi-predictions of maize traits at a time. The multi-task deep learning performed predictions comparably, if not better in some traits, with the mono-task deep learning and machine learning regressors. Data augmentation used for the deep learning models boosted the prediction accuracy, which helps to alleviate the intrinsic limitation of a small sample size and unbalanced sample classes in remote sensing research. Theoretical and practical implications to plant breeders and crop growers were also made explicit during discussions in the studies. Full article
(This article belongs to the Special Issue Unmanned Aerial Vehicles in Smart Agriculture)
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11 pages, 1084 KiB  
Case Report
Dual Molecular Diagnoses of Recessive Disorders in a Child from Consanguineous Parents: Case Report and Literature Review
by Gabriela Roldão Correia-Costa, Ana Mondadori dos Santos, Nicole de Leeuw, Sumara Zuanazi Pinto Rigatto, Vera Maria Santoro Belangero, Carlos Eduardo Steiner, Vera Lúcia Gil-da-Silva-Lopes and Társis Paiva Vieira
Genes 2022, 13(12), 2377; https://doi.org/10.3390/genes13122377 - 16 Dec 2022
Cited by 4 | Viewed by 2873
Abstract
The widespread use of whole exome sequencing (WES) resulted in the discovery of multilocus pathogenic variations (MPV), defined as two or more distinct or overlapping Mendelian disorders occurring in a patient, leading to a blended phenotype. In this study, we report on a [...] Read more.
The widespread use of whole exome sequencing (WES) resulted in the discovery of multilocus pathogenic variations (MPV), defined as two or more distinct or overlapping Mendelian disorders occurring in a patient, leading to a blended phenotype. In this study, we report on a child with autosomal recessive primary microcephaly-5 (MCPH5) and nephropathic cystinosis. The proband is the first child of consanguineous parents, presenting a complex phenotype including neurodevelopmental delay, microcephaly, growth restriction, significant delay of bone maturation, lissencephaly, and abnormality of neuronal migration, photophobia, and renal tubular acidosis. WES revealed two pathogenic and homozygous variants: a c.4174C>T variant in the ASPM gene and a c.382C>T variant in the CTNS gene, explaining the complex phenotype. The literature review showed that most of the patients harboring two variants in recessive disease genes are born to consanguineous parents. To the best of our knowledge, the patient herein described is the first one harboring pathogenic variants in both the ASPM and CTNS genes. These findings highlight the importance of searching for MPV in patients with complex phenotypes investigated by genome-wide testing methods, especially for those patients born to consanguineous parents. Full article
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10 pages, 479 KiB  
Article
A Note on the Conditioning of the H−1 Matrix Used in Single-Step GBLUP
by Mohammad Ali Nilforooshan
Animals 2022, 12(22), 3208; https://doi.org/10.3390/ani12223208 - 19 Nov 2022
Viewed by 1675
Abstract
The single-step genomic BLUP (ssGBLUP) is used worldwide for the simultaneous genetic evaluation of genotyped and non-genotyped animals. It is easily extendible to all BLUP models by replacing the pedigree-based additive genetic relationship matrix (A) with an augmented pedigree–genomic relationship matrix [...] Read more.
The single-step genomic BLUP (ssGBLUP) is used worldwide for the simultaneous genetic evaluation of genotyped and non-genotyped animals. It is easily extendible to all BLUP models by replacing the pedigree-based additive genetic relationship matrix (A) with an augmented pedigree–genomic relationship matrix (H). Theoretically, H does not introduce any artificially inflated variance. However, inflated genetic variances have been observed due to the incomparability between the genomic relationship matrix (G) and A used in H. Usually, G is blended and tuned with A22 (the block of A for genotyped animals) to improve its numerical condition and compatibility. If deflation/inflation is still needed, a common approach is weighting G1A221 in the form of τG1ωA221, added to A1 to form H1. In some situations, this can violate the conditional properties upon which H is built. Different ways of weighting the H1 components (A1, G1, A221, and H1 itself) were studied to avoid/minimise the violations of the conditional properties of H. Data were simulated on ten populations and twenty generations. Responses to weighting different components of H1 were measured in terms of the regression of phenotypes on the estimated breeding values (the lower the slope, the higher the inflation) and the correlation between phenotypes and the estimated breeding values (predictive ability). Increasing the weight on H1 increased the inflation. The responses to weighting G1 were similar to those for H1. Increasing the weight on A1 (together with A221) was not influential and slightly increased the inflation. Predictive ability is a direct function of the slope of the regression line and followed similar trends. Responses to weighting G1A221 depend on the inflation/deflation of evaluations from A1 to H1 and the compatibility of the two matrices with the heritability used in the model. One possibility is a combination of weighting G1A221 and weighting H1. Given recent advances in ssGBLUP, conditioning H1 might become an interim solution from the past and then not be needed in the future. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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17 pages, 4300 KiB  
Article
Electrospun Chitosan–Polyvinyl Alcohol Nanofiber Dressings Loaded with Bioactive Ursolic Acid Promoting Diabetic Wound Healing
by Hongyu Lv, Meng Zhao, Yiran Li, Kun Li, Shaojuan Chen, Wenwen Zhao, Shaohua Wu and Yantao Han
Nanomaterials 2022, 12(17), 2933; https://doi.org/10.3390/nano12172933 - 25 Aug 2022
Cited by 68 | Viewed by 5483
Abstract
The design and development of novel dressing materials are urgently required for the treatment of chronic wounds caused by diabetic ulcers in clinics. In this study, ursolic acid (UA) extracted from Chinese herbal plants was encapsulated into electrospun nanofibers made from a blend [...] Read more.
The design and development of novel dressing materials are urgently required for the treatment of chronic wounds caused by diabetic ulcers in clinics. In this study, ursolic acid (UA) extracted from Chinese herbal plants was encapsulated into electrospun nanofibers made from a blend of chitosan (CS) and polyvinyl alcohol (PVA) to generate innovative CS-PVA-UA dressings for diabetic wound treatment. The as-prepared CS-PVA-UA nanofiber mats exhibited randomly aligned fiber morphology with the mean fiber diameters in the range of 100–200 nm, possessing great morphological resemblance to the collagen fibrils which exist in the native skin extracellular matrix (ECM). In addition, the CS-PVA-UA nanofiber mats were found to possess good surface hydrophilicity and wettability, and sustained UA release behavior. The in vitro biological tests showed that the high concentration of UA could lead to slight cytotoxicity. It was also found that the CS-PVA-UA nanofiber dressings could significantly reduce the M1 phenotypic transition of macrophages that was even stimulated by lipopolysaccharide (LPS) and could effectively restore the M2 polarization of macrophages to shorten the inflammatory period. Moreover, the appropriate introduction of UA into CS-PVA nanofibers decreased the release levels of TNF-α and IL-6 inflammatory factors, and suppressed oxidative stress responses by reducing the generation of reactive oxygen species (ROS) as well. The results from mouse hepatic hemorrhage displayed that CS-PVA-UA nanofiber dressing possessed excellent hemostatic performance. The in vivo animal experiments displayed that the CS-PVA-UA nanofiber dressing could improve the closure rate, and also promote the revascularization and re-epithelization, as well as the deposition and remodeling of collagen matrix and the regeneration of hair follicles for diabetic wounds. Specifically, the mean contraction rate of diabetic wounds using CS-PVA-UA nanofiber dressing could reach 99.8% after 18 days of treatment. In summary, our present study offers a promising nanofibrous dressing candidate with multiple biological functions, including anti-inflammation, antioxidation, pro-angiogenesis, and hemostasis functions, for the treatment of hard-to-heal diabetic wounds. Full article
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18 pages, 5015 KiB  
Article
Polycaprolactone/Chitosan Composite Nanofiber Membrane as a Preferred Scaffold for the Culture of Mesothelial Cells and the Repair of Damaged Mesothelium
by Hao-Hsi Kao, Chang-Yi Kuo, Darshan Tagadur Govindaraju, Kuo-Su Chen and Jyh-Ping Chen
Int. J. Mol. Sci. 2022, 23(17), 9517; https://doi.org/10.3390/ijms23179517 - 23 Aug 2022
Cited by 24 | Viewed by 3477
Abstract
Mesothelial cells are specific epithelial cells lining the serosal cavity and internal organs. Nonetheless, few studies have explored the possibility to culture mesothelial cells in a nanostructure scaffold for tissue engineering applications. Therefore, this study aims to fabricate nanofibers from a polycaprolactone (PCL) [...] Read more.
Mesothelial cells are specific epithelial cells lining the serosal cavity and internal organs. Nonetheless, few studies have explored the possibility to culture mesothelial cells in a nanostructure scaffold for tissue engineering applications. Therefore, this study aims to fabricate nanofibers from a polycaprolactone (PCL) and PCL/chitosan (CS) blend by electrospinning, and to elucidate the effect of CS on the cellular response of mesothelial cells. The results demonstrate that a PCL and PCL/CS nanofiber membrane scaffold could be prepared with a comparable fiber diameter (~300 nm) and porosity for cell culture. Blending CS with PCL influenced the mechanical properties of the scaffold due to interference of PCL crystallinity in the nanofibers. However, CS substantially improves scaffold hydrophilicity and results in a ~6-times-higher cell attachment rate in PCL/CS. The mesothelial cells maintain high viability in both nanofiber membranes, but PCL/CS provides better maintenance of cobblestone-like mesothelial morphology. From gene expression analysis and immunofluorescence staining, the incorporation of CS also results in the upregulated expression of mesothelial marker genes and the enhanced production of key mesothelial maker proteins, endorsing PCL/CS to better maintain the mesothelial phenotype. The PCL/CS scaffold was therefore chosen for the in vivo studies, which involved transplanting a cell/scaffold construct containing allograft mesothelial cells for mesothelium reconstruction in rats. In the absence of mesothelial cells, the mesothelium wound covered with PCL/CS showed an inflammatory response. In contrast, a mesothelium layer similar to native mesothelium tissue could be obtained by implanting the cell/scaffold construct, based on hematoxylin and eosin (H&E) and immunohistochemical staining. Full article
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