A deep learning approach to measure stress level in plants due to Nitrogen deficiency
یک روش یادگیری عمیق برای اندازه گیری سطح تنش در گیاهان به دلیل کمبود نیتروژن-2021
Stress due to nutrients deficiency in plants can reduce the agricultural yield significantly. Nitrogen, an essential nutrient, is a crucial growth-limiting factor and is the prime component of amino acids, proteins, nucleic acids, and chlorophyll. Nitrogen deficiency affects certain visible plant traits such as area, color, the number of leaves and plant height, etc. With the recent advancements in imaging technology, computer vision-based plant phenomics has become a promising field of plant research and management. Such imaging-based techniques are non-destructive and much faster with higher levels of automation. In this work, we have proposed an automatic image-based plant phenotyping approach for stress classification in plant shoot images. In this proposed phenotyping approach, a 23-layered deep learning technique is proposed and compared with traditional Machine Learning techniques and few other deep architectures. Results reveal that a simple 23-layered deep learning architecture is comparable to the established state of art deep learning architectures like ResNet18 and NasNet Large (having millions of trainable parameters) in yielding ceiling level stress classification from plant shoot images. In addition, the proposed model also outperforms traditional Machine Learning techniques by achieving an average of 8.25% better accuracy.
Keywords: Computer vision | Deep learning | Nitrogen stress | Plant phenotyping
Classification of fermented cocoa beans (cut test) using computer vision
طبقه بندی دانه های کاکائو تخمیر شده (تست برش) با استفاده از بینایی ماشین-2021
Fermentation of cocoa beans is a critical step for chocolate manufacturing, since fermentation influences the development of flavour, affecting components such as free amino acids, peptides and sugars. The degree of fermentation is determined by visual inspection of changes in the internal colour and texture of beans, through the cut-test. Although considered standard for evaluation of fermentation in cocoa beans, this method is time consuming and relies on specialized personnel. Therefore, this study aims to classify fermented cocoa beans using computer vision as a fast and accurate method. Imaging and image analysis provides hand-crafted features computed from the beans, that were used as predictors in random decision forests to classify the samples. A total of 1800 beans were classified into four grades of fermentation. Concerning all image features, 0.93 of accuracy was obtained for validation of unbalanced dataset, with precision of 0.85, recall of 0.81. Although the unbalanced dataset represents actual variation of fermentation, the method was tested for a balanced dataset, to investigate the influence of a smaller number of samples per class, obtaining 0.92, 0.92 and 0.90 for accuracy, precision and recall, respectively. The technique can evolve into an industrial application with a proper integration framework, substituting the traditional method to classify fermented cocoa beans.
Keywords: Chocolate | Cut-test | Food quality | Analytical method | Image analysis | Random decision forest
Biometric, chemical, and microbiological evaluation of common wheat ( Triticum aestivum L:) seedlings fertilized with mealworm ( Tenebrio molitor L:) larvae meal
ارزیابی بیومتریک ، شیمیایی و میکروبیولوژیکی نهال گندم معمولی (Triticum aestivum L:) بارور شده با پودر لارو کرم غذایی (Tenebrio molitor L:)-2021
Alternative organic fertilizers are being developed to minimize the adverse environmental impact of chemical plant protection agents. The interest in industrial-scale insect farming has increased in recent years. Mealworm larvae are a rich source of protein and fatty acids. This study focuses on mealworm larvae, which are characterized by a rapid increase in biomass and a high nutritional value. In the present experiment, mealworm larvaewere processed into fertilizer with a high content of organic nitrogen. The fertilizer’s effect on wheat growth, soiland rhizosphere microorganisms, including phytopathogenic fungi of the genus Fusarium, and N-cycle, was analyzed. Mineral nitrogen fertilizer and mealworm larvae meal used as fertilizer caused a similar increase (~40%) in the total nitrogen content of the soil. Due to its mineral content, mealworm larvae meal contributed to an increase in the concentrations of P, K, and Mg in soil. The amino acid quality was high (0.89). Increasing the load of Bacillus spp. after using the meal was negatively correlated with the Fusarium spp. load in the wheat rhizosphere. In the case of meal fertilization, ammonification was noticed, and organic nitrogen was successively mineralized. The fertilizer produced from mealworm larvae offers a viable alternative to mineral fertilizers. It improves the health and nutrient status of wheat seedlings and stimulates the growth of Bacillus bacteria that enhance the availability of soil nutrients to plants and prevent seedling damping off. Further research is needed to confirm the applicability of the mealworm fertilizer in other field crops.
Keywords: Insect meal | Amino acids | Rhizosphere microorganisms | Biometry | Nitrogen
Identification of the absorbed components and metabolites ofXiao-Ai-Jie-Du decoction and their distribution in rats using ultrahigh-performance liquid chromatography/quadrupole time-of-flightmass spectrometry
شناسایی اجزای جذب شده و متابولیتهای جوشانده Xiao-Ai-Jie-Du و توزیع آنها در موشهای صحرایی با استفاده از کروماتوگرافی مایع با عملکرد فوق العاده / طیف سنجی ماد پرواز چهارگانه-2020
Xiao-Ai-Jie-Du decoction (XAJDD), a traditional Chinese medicine formula, has long been used forthe treatment of hepatocarcinoma, gastric cancer and colorectal cancer. It is composed of six herbalmedicines, including Scutellariae Barbatae Herba, Pseudostellariae Radix, Ophiopogonis Radix, Cremastrae Pseudobulbus, Curcumae Rhizoma and Akebiae Fructus. Despite the in-depth study on its pharmacologicaleffects on cancer prevention and treatment, the comprehensive analysis of the chemical components andthe absorbed bioactive constituents are not well studied. Thus, an ultra-high-performance liquid chro-matography/quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) method was establishedto detect and identify the chemical constituents in XAJDD. The absorbed components and metabolitesafter oral administration of XAJDD in rats were also studied. In total, 102 components were identified ortentatively characterized in XAJDD, including 30 flavonoids, 19 triterpenoids, 12 organic acids, 9 steroidalsaponins, 9 cyclic peptides, 7 phenanthrenes, 5 amino acids, 3 alkaloids and 8 other compounds. Afteranalysing the metabolites in rat plasma and urine after oral administration of XAJDD, a total of 70 com-pounds were identified, including 15 primary components and 55 metabolites, and metabolic pathways,including hydrogenation, hydroxylation, methylation, sulfonation, and glucuronidation were evaluated.Among these, methylation and glucuronidation were the main metabolic pathways. In conclusion, thedeveloped UHPLC-Q-TOF-MS method with high sensitivity and resolution is suitable for identifying andcharacterizing the chemical constituents of XAJDD in vitro and characterizing the primary componentsand their metabolites in vivo; moreover, the results will provide essential data for further studying therelationship between the chemical components and pharmacological activity of XAJDD.
Keywords: Absorbed components | Metabolites | Identification | UHPLC-Q-TOF-MS | Xiao-Ai-Jie-Du formula
A lab-on-a-carbon nanodot sensor array for simultaneous pattern recognition of multiple antibiotics
مجموعه ای از سنسورهای نانودوت کربن بر روی یک کربن برای تشخیص الگوی همزمان آنتی بیوتیک های متعدد-2019
Carbon nanodots (CDs) have gained extremely consideration in recent years as a result of their predominant fluorescence properties. Combining these unique advantages, herein, a “lab-on-a-carbon nanodot” based crossreactive sensor array for multiple antibiotics discrimination was introduced. Four types of CDs which were synthesized by simply mixing diphosphorus pentoxide, different amino acids (isoleucine, leucine and histidine) and water, were used as sensing receptors. Eight antibiotics can be well distinguished on account of the different fluorescence responses by linear discrimination analysis (LDA). Isothermal titration calorimetry (ITC) results indicated that the main interaction force between CDs and antibiotics are hydrogen bonding and van der waals forces. More importantly, binary and ternary antibiotics mixtures can also be adequately recognized in real samples such as human urine.
Keywords: Sensor array | Carbon nanodots | Antibiotics | Lab-on-a-carbon nanodot | Statistical analysis
A novel globular C1q domain containing protein (C1qDC-7) from Crassostrea gigas acts as pattern recognition receptor with broad recognition spectrum
A novel globular C1q domain containing protein (C1qDC-7) from Crassostrea gigas acts as pattern recognition receptor with broad recognition spectrum-2019
The globular C1q domain containing (C1qDC) proteins are a family of versatile pattern recognition receptors (PRRs) to bind various ligands by their globular C1q (gC1q) domain. In the present study, a novel globular C1qDC (CgC1qDC-7) was characterized from Pacific oyster Crassostrea gigas. The open reading frame of CgC1qDC-7 was of 555 bp, encoding a polypeptide of 185 amino acids. Phylogenetic analysis indicated that CgC1qDC-7 shared high homology with C1qDCs from Crassostrea virginica, Mytilus galloprovincialis, and Mizuhopecten yessoensis. The mRNA transcripts of CgC1qDC-7 were widely expressed in all the tested tissues including mantle, gonad, gills, adductor muscle, hemocytes, hepatopancreas and labial palps, with the highest expression level in hemocytes and gills. The recombinant protein of CgC1qDC-7 (rCgC1qDC-7) exhibited binding activity towards Gram-negative bacteria (Vibrio splendidus, V. anguillarum, Escherichia coli, V. alginolyticus, and Aeromonas hydrophila), Gram-positive bacteria (Micrococcus luteus and Staphylococcus aureus) and fungi (Pichia pastoris and Yarrowia lipolytica), and displayed strongest binding affinity towards Gram-negative bacteria V. splendidus and V. anguillarum. It also exhibited affinity to vital pathogen-associated molecular patterns (PAMPs), such as lipopolysaccharide (LPS), peptidoglycan (PGN), mannan (MAN) and Poly (I:C) with high affinity towards LPS and PGN, and low affinity to MAN and Poly (I:C). These results collectively indicated that CgC1qDC-7 was a novel PRR in C. gigas with high binding affinity towards LPS and PGN as well as Gram-negative bacteria
Keywords: Crassostrea gigas | C1q domain containing proteins | Pattern recognition receptors | Gram-negative bacteria recognition
Molecular cloning and expression analysis of C-type lectin (RpCTL) in Manila clam Ruditapes philippinarum after lipopolysaccharide challenge
کلونینگ مولکولی و تجزیه و تحلیل بیان لکتین از نوع C (RpCTL) در مانیل clam Ruditapes Philippinarum پس از چالش لیپوپلی ساکارید-2019
The Manila clam, Ruditapes philippinarum, is one of the most commercially important marine bivalves. C-type lectins (CTLs) are pattern recognition receptors (PRRs) that play important roles in the identification and elimination of pathogens by the innate immune system. In this study, a new CTL (RpCTL) was identified in the Manila clam, R. philippinarum. The full-length RpCTL cDNA is 802 bp, with an open reading frame of 591 bp, encoding 196 amino acids, including an N-terminal signal peptide and a carbohydrate recognition domain (CRD). RpCTL contains conserved CRD disulfide bonds involving four cysteine residues (Cys30–Cys104, Cys124, and Cys132), and the EPN (Glu94–Pro95–Asn96) and WND (Trp119–Asn120–Asp121) motifs. Quantitative reverse transcription (RT)–PCR detected RpCTL transcripts mainly in the gill, siphon, and hepatopancreas in three shellcolor strains (zebra, white, and white–zebra strains) and two unselected populations of R. philippinarum, and the gene was highly expressed in the hepatopancreas after lipopolysaccharide treatment. Antimicrobial activity assays of recombinant RpCTL against both Gram-positive and Gram-negative bacteria showed that RpCTL inhibits microorganismal growth. In a survival test, RpCTL inhibited and killed Vibrio anguillarum in R. philippinarum. These results suggest that RpCTL participates in the pathogen identification process of R. philippinarum as a PRR and in its immune defense system.
Keywords: Ruditapes philippinarum | C-type lectin | Immune defense | Expression profile | Pattern recognition receptor
Molecular cloning, characterization, and expression of a C-type lectin from Scylla paramamosain, which might be involved in the innate immune response
کلونینگ مولکولی ، خصوصیات و بیان یک لکتین از نوع C از پاراماموسین Scylla ، که ممکن است در پاسخ ایمنی ذاتی درگیر باشد-2019
C-type lectins (CTLs) have characteristic carbohydrate recognition domains (CRDs) and play important roles in the immune system. In the present study, a new CTL, SpCTL5, was identified from the hepatopancreas of the mud crab Scylla paramamosain. The open reading frame of SpCTL5 comprised 762 bp, encoding a polypeptide of 253 amino acids with a putative signaling peptide of 20 amino acids. The predicted SpCTL5 protein contained a single CRD. SpCTL5 transcripts were distributed in all examined tissues, with the highest level being detected in the hepatopancreas. Upon challenging with Vibrio alginolyticus, the mRNA levels of SpCTL5 in the hepatopancreas were up-regulated. The recombinant protein of SpCTL5 could agglutinate three Gram-positive bacteria and three Gram-negative bacteria in the presence of Ca2+. Furthermore, hemagglutination analysis showed that the recombinant protein of SpCTL5 can agglutinate rabbit erythrocytes. This study indicated that SpCTL5 acts as a pattern recognition receptor for the innate immune response which protects S. paramamosain from bacterial infection. Moreover, these findings also provide information to further our understanding of the innate immunology of invertebrates.
Keywords: C-type lectin | Scylla paramamosain | Agglutinating activity | Innate immunity
A sialic acid-binding lectin with bactericidal and opsonic activities from Ruditapes philippinarum
لکتین با اسید سیالیک با فعالیتهای ضد باکتری و اپسونیک از Ruditapes Philippinarum-2019
In the present study, a sialic acid-binding lectin was cloned and characterized from Manila clam Ruditapes philippinarum (designed as RpSabl). The open reading frame of RpSabl encoded a polypeptide of 162 amino acids with a calculated molecular mass of 17.7 kDa. Analysis of the conserved domain suggested that RpSabl was a new member of the sialic acid-binding lectins family. In non-stimulated clams, RpSabl transcripts were constitutively expressed in all five tested tissues, especially in hepatopancreas. After Vibrio anguillarum challenge, the expression of RpSabl mRNA in hepatopancreas was significantly up-regulated at 3 h (3.8-fold, P < 0.05), 6 h (4.9-fold, P < 0.05), 12 h (12.3-fold, P < 0.01) and 24 h (9.7-fold, P < 0.01), while RpSabl transcripts in hemocytes was only significantly up-regulated at 6 h (8.5-Fold, P < 0.01). RNAi-mediated knockdown of RpSabl transcripts affected the survival rates of Manila clam against V. anguillarum, perhaps mainly due to the inhibited expression of antibacterial effectors (e.g. lysozyme and defensin). Moreover, recombinant protein of RpSabl (rRpSabl) possessed binding activities towards lipopolysaccharides (LPS), peptidoglycan (PGN) and glucan in vitro. Coinciding with the Pathogen-associated molecular patterns (PAMPs) binding assay, rRpSabl displayed broad bacterial-agglutination properties towards Vibrio harveyi, Vibrio splendidus, V. anguillarum, Enterobacter cloacae and Aeromonas hydrophila. Meanwhile, the phagocytosis and encapsulation ability of hemocytes could be significantly enhanced by rRpSabl incubation. All these results showed that RpSabl could function as a versatile molecule involved in the innate immune responses of R. philippinarum.
Keywords: Ruditapes philippinarum | Sialic acid-binding lectin | Pattern recognition receptor | Immune recognition
Molecular characterization of a pattern recognition protein LGBP highly expressed in the early stages of mud crab Scylla paramamosain
خصوصیات مولکولی پروتئین به رسمیت شناختن الگوی LGBP که در مراحل اولیه خرچنگ گلی Scylla paramamosain بیان شده است-2019
The early developmental stages of the mud crab Scylla paramamosain suffer from high mortality caused by pathogen infections; however, few immune associated factors are known. Lipopolysaccharide and β-1,3-glucanbinding protein (LGBP) functions as a typical pathogen recognition receptor and plays an important role in the innate immune system of invertebrates. In this study we characterized a LGBP gene (SpLGBP) which was highly expressed in the late embryonic, zoea I larval stage and hepatopancreas of S. paramamosain.. It encodes 364 amino acids, composed of several conserved domains like the bacterial glucanase motif. The recombinant SpLGBP protein (rSpLGBP) was obtained through the E.coli expression system, in which two 6◊His-tags were added to both C and N terminals during vector construction for the improvement of purification efficiency. In vivo the study showed that the SpLGBP mRNA was significantly up-regulated under Vibrio parahaemolyticus and a lipopolysaccharide (LPS) challenge in the hemocytes and hepatopancreas. The ELISA binding assay in vitro indicated that the rSpLGBP was capable of binding to LPSs and peptidoglycan (PGN). The rSpLGBP could agglutinate both G+ and G- bacteria in the presence of Ca2+. Our results suggest that SpLGBP may play an immunological role against pathogenic infection in the early developmental stages of S. paramamosain.
Keywords: Ca2+ dependent | Lipopolysaccharide and β-1,3-glucan-binding | protein (LGBP) | LPS | Recognition | Scylla paramamosain | Vibro parahaemolyticus