CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane.

Gene editing technologies have opened up the possibility of manipulating the genome of any organism in a predicted way. CRISPR technology is the most used genome editing tool and, in agriculture, it has allowed the expansion of possibilities in plant biotechnology, such as gene knockout or knock-in, transcriptional regulation, epigenetic modification, base editing, RNA editing, prime editing, and nucleic acid probing or detection. This technology mostly depends on tissue culture and genetic transformation/transfection protocols, which sometimes become the major challenges for its application in different crops.

What Is the CRISPR System and How It Is Used?

CRISPR is a revolutionary gene editing technology that has enabled scientists worldwide to explore the cell's genetic blueprint in an unprecedented easy way. In this chapter, we will briefly present the history behind the development of this innovative tool, how it emerged from a natural bacterial mechanism for antiviral defense, its key components (Cas9 endonuclease and single guide RNA), mode of action (DNA cleavage and repair via NHEJ or HDR), and versatility (acting on single- or double-stranded DNA or RNA) for diverse purposes beyond gene editing such as stochastic marking, digital encoding, high-fidelity SNP genotyping, programmed chromosome fission/fusion, gene mapping, nucleic acid detection, regulation of gene expression, DNA/RNA labeling or tracking, and more.

Drought-triggered leaf transcriptional responses disclose key molecular pathways underlying leaf water use efficiency in sugarcane ( spp.).

Drought is a major constraint to sugarcane ( spp.) production and improving the water use efficiency (WUE) is a critical trait for the sustainability of this bioenergy crop. The molecular mechanism underlying WUE remains underexplored in sugarcane.

Designing optimized drug candidates with Generative Adversarial Network.

Drug design is an important area of study for pharmaceutical businesses. However, low efficacy, off-target delivery, time consumption, and high cost are challenges and can create barriers that impact this process. Deep Learning models are emerging as a promising solution to perform de novo drug design, i.

Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions.

Drought is the most detrimental abiotic stress to sugarcane production. Nevertheless, transcriptomic analyses remain scarce for field-grown plants. Here we performed comparative transcriptional profiling of two contrasting sugarcane genotypes, 'IACSP97-7065' (drought-sensitive) and 'IACSP94-2094' (drought-tolerant) grown in a drought-prone environment.

MicroRNAs in Prion Diseases-From Molecular Mechanisms to Insights in Translational Medicine.

MicroRNAs (miRNAs) are small non-coding RNA molecules able to post-transcriptionally regulate gene expression via base-pairing with partially complementary sequences of target transcripts. Prion diseases comprise a singular group of neurodegenerative conditions caused by endogenous, misfolded pathogenic (prion) proteins, associated with molecular aggregates. In humans, classical prion diseases include Creutzfeldt-Jakob disease, fatal familial insomnia, Gerstmann-Sträussler-Scheinker syndrome, and kuru.

An Animal Able To Tolerate D O.

It is possible to gain a deeper insight into the role of water in biology by using physicochemical variant molecules, such as deuterium oxide (D O); however, D O is toxic to multicellular organisms in high concentrations. By using a unique desiccation-rehydration process, we demonstrate that the anhydrobiotic nematode Panagrolaimus superbus is able to tolerate and proliferate in 99 % D O. Moreover, we analysed P.

tolerates hypoxia within Gallium metal cage: implications for the understanding of the phenomenon of anhydrobiosis.

nematodes are able to tolerate desiccation by entering into a peculiar state of suspended animation known as anhydrobiosis. When desiccated, anhydrobiotic organisms are also able to tolerate other physical stresses, as high and low levels of temperature and pressure. Here, we decided to investigate the tolerance of desiccated to an unprecedented double stress - hypoxia within 99.

SSD - a free software for designing multimeric mono-, bi- and trivalent shRNAs.

RNA interference (RNAi) is a powerful gene silencing technology, widely used in analyses of reverse genetics, development of therapeutic strategies and generation of biotechnological products. Here we present a free software tool for the rational design of RNAi effectors, named siRNA and shRNA designer (SSD). SSD incorporates our previously developed software Strand Analysis to construct template DNAs amenable for the large scale production of mono-, bi- and trivalent multimeric shRNAs, via in vitro rolling circle transcription.

MicroRNA dysregulation interplay with childhood abdominal tumors.

Abdominal tumors (AT) in children account for approximately 17% of all pediatric solid tumor cases, and frequently exhibit embryonal histological features that differentiate them from adult cancers. Current molecular approaches have greatly improved the understanding of the distinctive pathology of each tumor type and enabled the characterization of novel tumor biomarkers. As seen in abdominal adult tumors, microRNAs (miRNAs) have been increasingly implicated in either the initiation or progression of childhood cancer.

Lack of Standardization in Commercial Thickeners Used in the Management of Dysphagia.

Introduction: Oral feeding safety is necessary to provide nutrition, hydration, and eating pleasure for patients with dysphagia. Commercial thickeners are prescribed for these patients to change food viscosity and may alter the proper preparation of modified food.

Objective: Analyze composition, employed terminology, preparation instructions, recommended amount and weight of provided measuring spoons, nutritional information, and viscosity of 7 commercial thickeners.

Consistencies and terminologies - the use of the International Dysphagia Diet Standardization Initiative.

Introduction: this study aimed to verify the ability of speech therapists to identify, sort and name the different consistencies used in neurogenic oropharyngeal dysphagia (NOD) management, and to compare the results with the terms proposed by the International Dysphagia Diet Standardization Initiative (IDDSI). Methods: this research was approved by the ethics committee. Sixty speech therapists who work with NOD patients sorted 5 commercial foods from thinnest to thickest to match IDDSI levels 0 to 4, and then used a term to designate each consistency.

Relationship between mouth breathing etiology and maximum tongue pressure.

Purpose: To verify the relationship between maximum tongue pressure and the etiology of oral breathing in oral breathing children attended at the Oral Respiratory Outpatient Clinic.

Methods: A descriptive and analytical cross-sectional study was accomplished with 59 mouth breathing children aged 3 to 12 years (mean age 6.5 years and SD: standard deviation= 2.

Caenorhabditis elegans Tolerates Hyperaccelerations up to 400,000 x g.

One of the most important laboratory animal species is the nematode Caenorhabditis elegans, which has been used in a range of research fields such as neurobiology, body development, and molecular biology. The scientific progress obtained by employing C. elegans as a model in these areas has encouraged its use in new fields.

Multiple genes contribute to anhydrobiosis (tolerance to extreme desiccation) in the nematode Panagrolaimus superbus.

The molecular basis of anhydrobiosis, the state of suspended animation entered by some species during extreme desiccation, is still poorly understood despite a number of transcriptome and proteome studies. We therefore conducted functional screening by RNA interference (RNAi) for genes involved in anhydrobiosis in the holo-anhydrobiotic nematode Panagrolaimus superbus. A new method of survival analysis, based on staining, and proof-of-principle RNAi experiments confirmed a role for genes involved in oxidative stress tolerance, while a novel medium-scale RNAi workflow identified a further 40 anhydrobiosis-associated genes, including several involved in proteostasis, DNA repair and signal transduction pathways.

New mechanisms of disease and parasite-host interactions.

An unconventional interaction between a patient and parasites was recently reported, in which parasitic cells invaded host's tissues, establishing several tumors. This finding raises various intriguing hypotheses on unpredicted forms of interplay between a patient and infecting parasites. Here we present four unusual hypothetical host-parasite scenarios with intriguing medical consequences.

Effects of RNA interference therapy against herpes simplex virus type 1 encephalitis.

Background: Herpetic encephalitis (HSE) is caused mainly by herpes simplex virus type 1 (HSV-1) with an annual incidence of 1-4 cases/million inhabitants. Currently, HSE treatment faces difficulties such as the use of antivirals with elevated toxicity, metabolic side effects and HSV-1 resistance. An alternative to antivirals is the use of small interfering RNA (siRNA) as a viral replication inhibitor.

The new world of RNAs.

One of the major developments that resulted from the human genome sequencing projects was a better understanding of the role of non-coding RNAs (ncRNAs). NcRNAs are divided into several different categories according to size and function; however, one shared feature is that they are not translated into proteins. In this review, we will discuss relevant aspects of ncRNAs, focusing on two main types: i) microRNAs, which negatively regulate gene expression either by translational repression or target mRNA degradation, and ii) small interfering RNAs (siRNAs), which are involved in the biological process of RNA interference (RNAi).

Applications of RNA Interference in Schistosomiasis: Gene Function Identification and Development of New Therapies.

The study of Schistosoma species has undergone a dramatic change in recent years mainly due to transcriptome, proteome, and genome analyses. In order to better understand the biology of the parasite and to develop new and more efficient/specific drugs, scientists have now the task to translate genetic information into functional data. The present paper aims to review the use of RNA interference (RNAi), a versatile technique used in gene silencing, for the dissection of the cellular/molecular biology of Schistosoma spp.

Analysis of energetically biased transcripts of viruses and transposable elements.

RNA interference (RNAi) is a natural endogenous process by which double-stranded RNA molecules trigger potent and specific gene silencing in eukaryotic cells and is characterized by target RNA cleavage. In mammals, small interfering RNAs (siRNAs) are the trigger molecules of choice and constitute a new class of RNA-based antiviral agents. In an efficient RNAi response, the antisense strand of siRNAs must enter the RNA-induced silencing complex (RISC) in a process mediated by thermodynamic features.