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The advent of artificial intelligence (AI) holds great promise for revolutionizing the fields of plant tissue culture and genome editing. Plant tissue culture is recognized as a powerful tool for rapid multiplication and crop improvement. However, the complex interactions between genetic and environmental factors generate large volumes of data, posing challenges for traditional statistical analysis methods. To address this, researchers are now employing machine learning (ML)-based and artificial neural networks (ANN) approaches to predict and optimize culture protocols thereby improving precision, sustainability, and efficiency. Integrating AI technologies such as machine learning (ML), artificial neural networks (ANN), and deep learning (DL) can significantly advance the development of data-driven models for CRISPR/Cas9 genome editing. Today, AI-driven methods are routinely applied to enhance precision in predicting on- and off-target sequence locations and editing outcomes. Additionally, predicting protein structures can provide a directed evolution framework that facilitates the creation of improved gene editing tools. However, the application of AI-based CRISPR modeling in plants is not yet fully explored. In this context, we aim to examine representative ML/DL/ANN models of CRISPR/Cas based editing employed in various organisms. This review significantly compiles a diverse set of studies and provides a clear overview of how AI is transforming the fields of plant tissue culture and genome editing. It emphasizes AI's potential to increase the efficiency and precision of biotechnological practices, making them more accessible and cost-effective. While outlining current findings, the paper sets the stage for future research, encouraging further exploration into the integration of AI with plant biotechnology.

Doc number: 52 Abstract Background: Fungi are important players in the turnover of plant biomass because they produce a broad range of degradative enzymes. Aspergillus nidulans, a well-studied saprophyte and close homologue to industrially important species such as A. niger and A. oryzae , was selected for this study. Results: A. nidulans was grown on sorghum stover under solid-state culture conditions for 1, 2, 3, 5, 7 and 14 days. Based on analysis of chitin content, A. nidulans grew to be 4-5% of the total biomass in the culture after 2 days and then maintained a steady state of 4% of the total biomass for the next 12 days. A hyphal mat developed on the surface of the sorghum by day one and as seen by scanning electron microscopy the hyphae enmeshed the sorghum particles by day 5. After 14 days hyphae had penetrated the entire sorghum slurry. Analysis (1-D PAGE LC-MS/MS) of the secretome of A. nidulans , and analysis of the breakdown products from the sorghum stover showed a wide range of enzymes secreted. A total of 294 extracellular proteins were identified with hemicellulases, cellulases, polygalacturonases, chitinases, esterases and lipases predominating the secretome. Time course analysis revealed a total of 196, 166, 172 and 182 proteins on day 1, 3, 7 and 14 respectively. The fungus used 20% of the xylan and cellulose by day 7 and 30% by day 14. Cellobiose dehydrogenase, feruloyl esterases, and CAZy family 61 endoglucanases, all of which are thought to reduce the recalcitrance of biomass to hydrolysis, were found in high abundance. Conclusions: Our results show that A. nidulans secretes a wide array of enzymes to degrade the major polysaccharides and lipids (but probably not lignin) by 1 day of growth on sorghum. The data suggests simultaneous breakdown of hemicellulose, cellulose and pectin. Despite secretion of most of the enzymes on day 1, changes in the relative abundances of enzymes over the time course indicates that the set of enzymes secreted is tailored to the specific substrates available. Our findings reveal that A. nidulans is capable of degrading the major polysaccharides in sorghum without any chemical pre-treatment.

In an effort to understand how fungi degrade biomass, we grew Phanerochaete chrysosporium on sorghum stover and chronicled the growth of the fungus over the course of 14 days. The fungal mass grew steadily until the fifth day, reaching 0.06 mg of cells per milligram of dry mass, which fell by the seventh day and stayed at nearly the same level until day 14. After 1 day, hemicellulases, cellulases, and polygalacturonases were detected in the extracellular fluid at 1.06, 0.34, and 0.20 U/ml, respectively. Proteomic studies performed with the extracellular fluid using liquid chromatography-tandem mass spectrometry identified 57, 116, and 102 degradative enzymes targeting cellulose, hemicellulose, pectin, lignin, proteins, and lipids on days 1, 7, and 14, respectively. Significant concentrations of breakdown products of the sorghum polysaccharides were detected in the extracellular fluid indicating that the enzymes were breaking the polysaccharides, and after 14 days, almost 39% of the sorghum sugars had been used by the fungus. Our results suggest that P. chrysosporium produces a set of enzymes to degrade the components of lignocellulose from the beginning of its growth, but modifies the complement of enzymes it secretes over time to adapt to the particular substrate available.[PUBLICATION ABSTRACT]

Repetitive rounds of differential subtraction screening, followed by nucleotide sequence determination and northern-blot analysis, identified 84 salt-regulated (160 mM NaCl for 4 h) genes in Arabidopsis wild-type (Col-0 gl1) seedlings. Probes corresponding to these 84 genes and ACP1, RD22BP1, MYB2, STZ, and PAL were included in an analysis of salt responsive gene expression profiles in gl1 and the salt-hypersensitive mutant sos3. Six of 89 genes were expressed differentially in wild-type and sos3 seedlings; steady-state mRNA abundance of five genes (AD06C08/unknown, AD05E05/vegetative storage protein 2 [VSP2], AD05B11/S-adenosyl-L-Met:salicylic acid carboxyl methyltransferase [SAMT], AD03D05/cold regulated 6.6/inducible2 [COR6.6/KIN2], and salt tolerance zinc finger [STZ]) was induced and the abundance of one gene (AD05C10/circadian rhythm-RNA binding1 [CCR1]) was reduced in wild-type plants after salt treatment. The expression of CCR1, SAMT, COR6.6/KIN2, and STZ was higher in sos3 than in wild type, and VSP2 and AD06C08/unknown was lower in the mutant. Salt-induced expression of VSP2 in sos1 was similar to wild type, and AD06C08/unknown, CCR1, SAMT, COR6.6/KIN2, and STZ were similar to sos3. VSP2 is regulated presumably by SOS2/3 independent of SOS1, whereas the expression of the others is SOS1 dependent. AD06C08/unknown and VSP2 are postulated to be effectors of salt tolerance whereas CCR1, SAMT, COR6.6/KIN2, and STZ are determinants that must be negatively regulated during salt adaptation. The pivotal function of the SOS signal pathway to mediate ion homeostasis and salt tolerance implicates AD06C08/unknown, VSP2, SAMT, 6.6/KIN2, STZ, and CCR1 as determinates that are involved in salt adaptation.

A method has been developed to obtain kinetic rate equations in integrated form for reactions involving two or three different types of reactant with different stoichiometries. The integrated rate equation of a reaction of desired order has been shown to be generated in a stepwise manner with the help of the integrated rate law(s) of lower order(s) by this procedure. The beauty of this procedure is that it is devoid of complicated integrations. This method has a particular mathematical importance, in that it can be used to solve first-order differential equations that involve different terms, each of which is associated with some arbitrary power.

Tobacco is the most commonly used plant for expression of transgenes from a variety of organisms because it can be easily grown and transformed, it provides abundant amounts of fresh tissue and has a well-established cell culture system. As bacterial enzymes can be synthesized in tobacco, here we explore the possibility of in planta expression of staphylococcal protein-A(PA) which is an antibody, an important group among biopharmaceuticals. In our study we have shown that the tobacco plants harboring PA gene could combat the crown gall infection and also effective in resisting abiotic stress conditions. Transgenic plants when subjected to interact with wild variety of Agrobacterium shows its enhanced capability to resist the gall formation. And when transgenic tobacco plants were grown in presence of 200mM NaCl and/or MG(Methylglyoxal) solution, shows their increased tolerance towards salinity stress and high MG stress. So far transgenic tobacco plants are concerned, improvements in the expression of recombinant proteins and their recovery from tobacco may also enhance production and commercial use of this protein.

Scope and method of study. The construction of cDNA libraries is useful for understanding gene expression in organisms under different conditions, but random sequencing of unbiased cDNA collections is laborious and gives rise to high redundancy. We aimed to isolate cDNAs of messages specifically induced by switching Aspergillus nidulans from growth on glucose to growth on selected polysaccharides. We devised a Negative Subtraction Hybridization (NSH) method and tested it in A. nidulans. NSH entails screening a plasmid library made from cDNAs prepared from cells grown under a selected physiological condition with labeled cDNA probes prepared from another physiological condition. Plasmids with inserts that failed to hybridize to cDNA probes through two rounds of screening (i.e. negatives) represent transcripts present at low concentration in the labeled probe pool. Findings and conclusions. In a screen for transcripts induced by switching the carbon source from glucose to 12 selected polysaccharides, 3,532 negatives were isolated from approximately 100,000 surveyed colonies using this method. Single-channel microarray hybridization experiments done with 1184 ESTs confirmed that the majority of the negatives were indeed differentially induced by one or more complex carbohydrates. To gain insight into the extent of the regulation, we used microarrays to identify gene expression changes following a shift from glucose as a carbon source to pectin or glucose starvation. Of the 1184 cDNAs investigated, 312 were significantly upregulated or downregulated during the first 12 hours following the switch from glucose to pectin or glucose starvation. Approximately one third of the transcripts were specifically upregulated or downregulated in glucose starvation, another third in both glucose starvation and pectin, and the remaining third specifically in pectin. Examination of cDNAs encoding polypeptides of known function, suggest that glucose starvation results in upregulation of phosphoenolpyruvate carboxykinase, pyruvate dikinase, and some transcription factors followed by a general downregulation of metabolic processes. Expression profiling of the glucose to pectin switch initially resembled glucose starvation with the exception of upregulated transcripts for degradation and metabolism of pectin, but later, transcripts involved in growth and metabolism were upregulated.

This paper examines and evaluates Virtual Laboratories (VLabs) in consideration of technology design, educational pedagogy, and outcome in tertiary education context for ICT courses. There is a growing demand for VLabs in tertiary education to support remote, flexible, and equitable learning. Most of the universities in Australia offer distance education to students who do not attend on-campus classes. On-line labs allowing access via an internet connection can offer learners the required infrastructure to complete their lab tasks without attending physical lab facilities. The onset of COVID-19 pandemic in early 2020 has seen further spike in demand for VLabs as accessing online lab facilities to undertake hands on activities from anywhere and anytime was imperative during lockdown periods. Despite their benefits, it is complex to choose an appropriate VLab design or type that ensures effective and improved learning process. This paper presents two case studies using commercial and custom-made VLabs that are analyzed through the lens of learning theories. The outcome of the analysis informs the readers that the teachers’ support (human mediator) and VLabs (teaching tool) are interlinked together in a dialectical way which is an important consideration to achieve successful learning outcome. This study will help educators to make an informed decision in choosing an appropriate VLab design for their teaching content to ensure effective learning outcome.

Plant Growth-Promoting Rhizobacteria (PGPR) and compost present promising solutions for bolstering agricultural sustainability by stimulating plant growth and yield while lessening dependence on chemical inputs. Our investigation delved into the combined effects of PGPR and compost on spinach cultivation, conducted at Amity University’s Organic Farm. Employing a Randomized Block Design (RBD) with six treatments and three replications, we evaluated how these treatments influenced spinach growth parameters and photosynthetic pigment levels. Results showed that treatment T5 (AIOA Strain + Compost) outperformed others, significantly boosting plant height, leaf breadth, root length, and leaf count per plant. Furthermore, T5 exhibited elevated chlorophyll and carotenoid levels, indicating enhanced photosynthetic function and overall plant vigor. These outcomes underscore the potential synergy between PGPR and compost in fostering sustainable crop production. By diminishing reliance on chemical fertilizers and pesticides while enhancing soil health and nutrient cycling, integrating PGPR and compost-based biofertilizers offers an economical and environmentally friendly avenue for augmenting agricultural productivity and mitigating environmental hazards. Further exploration into optimization techniques and underlying mechanisms is crucial to fully harness the potential of these microbial and organic interventions across varied agroecological settings. Overall, this study contributes to advancing our knowledge of employing microbial and organic methods in sustainable agriculture, crucial for addressing global challenges in food security and environmental conservation.