Biosafety of RNA silencing and genome editing technologies in crop plants: Malaysian and Australian research perspectives

Research in agricultural biotechnology can produce novel solutions to address the ever growing demand for food, feed, renewable materials and renewable energy using increasingly limited resources. Yet research is expensive with long timelines before implementation can disseminate the benefits to society, so there is a need to maximise co-operation and communication between scientists, stakeholders and their governments, to optimise research, its development and the implementation of research outcomes, into mainstream applications. Recognising the impacts of regulations on biosafety, biosecurity and intellectual property policy on strategies for research, senior and early career researchers from two research intensive universities in Malaysia and Australia, held a workshop to identify and to deliberate over two key areas of technology that offer much promise for agriculture, namely RNA silencing and genome editing. A major focus of the workshop was the regulation of new breeding technologies, and how the regulations need to take into account these new technologies. Themes discussed were the need for harmonisation of international legal frameworks and careful use of terminology, standards and guidelines; and the need for good communication and consensus within and between groups of stakeholders and law-makers. This mini-review highlights the deliberations and recommendations from the workshop

Synthesis, gene silencing, and molecular modeling studies of 4 '-C-aminomethyl-2 '-O-methyl modified small interfering RNAs.

The linear syntheses of 4′-C-aminomethyl-2′-O-methyl uridine and cytidine nucleoside phosphoramidites were achieved using glucose as the starting material. The modified RNA building blocks were incorporated into small interfering RNAs (siRNAs) by employing solid phase RNA synthesis. Thermal melting studies showed that the modified siRNA duplexes exhibited slightly lower Tm (1 °C/modification) compared to the unmodified duplex. Molecular dynamics simulations revealed that the 4′-C-aminomethyl-2′-O-methyl modified nucleotides adopt South-type conformation in a siRNA duplex, thereby altering the stacking and hydrogen-bonding interactions. These modified siRNAs were also evaluated for their gene silencing efficiency in HeLa cells using a luciferase-based reporter assay. The results indicate that the modifications are well tolerated in various positions of the passenger strand and at the 3′ end of the guide strand but are less tolerated in the seed region of the guide strand. The modified siRNAs exhibited prolonged stability in human serum compared to unmodified siRNA. This work has implications for the use of 4′-C-aminomethyl-2′-O-methyl modified nucleotides to overcome some of the challenges associated with the therapeutic utilities of siRNAs

Analysis of functional outcome of anterior cruciate ligament reconstruction using quadruple hamstring graft

Background: Anterior cruciate ligament reconstruction is the most commonly reconstructed ligaments of the knee. This study attempts to analyse the functional outcome of ACL reconstruction and the parameters utilized commonly to assess the outcomes.Methods: This is an analysis of 25 patients who underwent ACL reconstruction, who were operated by a single surgeon, and were studied for a period of one year .Analysis was made using standard scoring systems like Lysholm and IKDC score by an independent observer over a period of one year.Results: The injury was commonly noted in the male gender although the sidedness of the injury did not seem to influence the outcome. The larger percentage of cases was operated less than 6 months from the date of injury. The mean graft diameter was 7.9 mm, with a positive correlation to the thickness of the thigh. The preoperative mean Lysholm score of 58.76 improved to 91.16 after surgery. The mean preoperative IKDC score improved from 29.26 to 58.70. One patient had infection and two had stiffness and reduced range of motion. The timing of surgery and rehabilitation influence the outcome largely. Conclusions: Anterior cruciate ligament reconstruction surgery with quadrupled hamstring grafts provides a good outcome to ACL injuries when the surgery is timed well, with sufficient graft thickness and good rehabilitation

The Platelet-activating Factor Receptor Protects Epidermal Cells from Tumor Necrosis Factor (TNF) α and TNF-related Apoptosis-inducing Ligand-induced Apoptosis through an NF-κB-dependent Process

A number of chemical mediators can induce human keratinocytes and epidermal-derived carcinomas to undergo apoptosis, or programmed cell death. Recent evidence suggests pro-inflammatory cytokines, such as interleukin-1β or transforming growth factor α, protects carcinomas from numerous pro-apoptotic stimuli. Platelet-activating factor (1-alkyl-2-acetyl-3-glycerophosphocholine; PAF) is a lipid mediator with pro-inflammatory effects on numerous cell types. Although PAF can be metabolized to other bioactive lipids, the majority of PAF effects occur through activation of a G protein-coupled receptor. Using a model system created by retroviral transduction of the PAF receptor (PAF-R) into the PAF-R-negative human epidermal cell line KB and the PAF-R-expressing keratinocyte cell line HaCaT, we now demonstrate that activation of the epidermal PAF-R results in protection from apoptosis induced by tumor necrosis factor (TNF) α or TNF-related apoptosis-inducing ligand. The PAF-mediated protection was inhibited by PAF-R antagonists, and protection did not occur in PAF-R-negative KB cells. Additionally, we show protection from TNFα- or TRAIL-induced apoptosis by PAF-R activation is dependent on the transcription factor nuclear factor (NF)-κB, because PAF-R activation-induced NF-κB and epidermal cells transduced with a super-repressor form of inhibitor κB were not protected by the PAF-R. These studies provide a mechanism whereby the epidermal PAF-R, and possibly other G protein-coupled receptors, can exert anti-apoptotic effects through an NF-κB-dependent process

Marine ornamental fish culture: Means for economic growth

The marine ornamental fish trade is a sunrise industry that has been expanding in recent years and has grown into a multimillion-dollar enterprise mainly due to the emergence of technologies for captive breeding of fishes, modern aquarium gadgets, setting and maintenance of miniature reef aquaria. Aquarium keeping is amongst the most popular of hobbies with millions of enthusiasts worldwide and the trade of marine ornamentals has been expanding in recent years and has grown into a multimillion-dollar enterprise. The recent emergence of modern aquarium gadgets and technologies for setting and maintenance of miniature reef aquaria made aquarium keeping much easier than previous. Since the marine ornamental trade is operated throughout the tropics, the global marine ornamental trade is estimated at US$ 200-330 million. India is endowed with a vast resource potential of marine ornamentals distributed in the coral seas and rocky coasts with patchy coral formations. In the context of the expanding global scenario and the increasing demand for domestic trade, it appears very lucrative for India to venture into this industr

Genetic and Phenotypic Diversity in Downy-mildew-resistant Sorghum (Sorghum bicolor (L.) Moench) Germplasm

Genetic and phenotypic diversity among randomly selected 36 downy-mildew-resistant sorghum accessions were assessed, the former using 10 simple sequence repeat (SSR) marker loci and the latter using 20 phenotypic traits. The number of alleles (a j ) at individual loci varied from five to 14 with an average of 8.8 alleles per locus. Nei's gene diversity (H j ) varied from 0.59 to 0.92 with an average of 0.81 per locus. High gene diversity and allelic richness were observed in races durra caudatum (H j = 0.76, a j = 4.3) and guinea caudatum (H j = 0.76, a j = 3.8) and in east Africa (H j = 0.78, a j = 7.2). The regions were genetically more differentiated than the races as indicated by Wright's F st. The pattern of SSR-based clustering of accessions was more in accordance with their geographic proximity than with their racial likeness. This clustering pattern matched little with that obtained from phenotypic traits. The inter-accession genetic distance varied from 0.30 to 1.00 with an average of 0.78. Inter-accession phenotypic distance varied from 0.01 to 0.55 with an average of 0.33. Eleven accession-pairs had phenotypic distance of more than 0.50 and genetic distance of more than 0.70. These could be used as potential parents in a sorghum downy mildew resistance-breeding progra

Optimal auctions through deep learning

Designing an incentive compatible auction that maximizes expected revenue is an intricate task. The single-item case was resolved in a seminal piece of work by Myerson in 1981. Even after 30-40 years of intense research the problem remains unsolved for seemingly simple multibidder, multi-item settings. In this work, we initiate the exploration of the use of tools from deep learning for the automated design of optimal auctions. We model an auction as a multi-layer neural network, frame optimal auction design as a constrained learning problem, and show how it can be solved using standard pipelines. We prove generalization bounds and present extensive experiments, recovering essentially all known analytical solutions for multi-item settings, and obtaining novel mechanisms for settings in which the optimal mechanism is unknown

Estradiol-regulated MicroRNAs Control Estradiol Response in Breast Cancer Cells

Estradiol (E2) regulates gene expression at the transcriptional level by functioning as a ligand for estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ). E2-inducible proteins c-Myc and E2Fs are required for optimal ERα activity and secondary estrogen responses, respectively. We show that E2 induces 21 microRNAs and represses seven microRNAs in MCF-7 breast cancer cells; these microRNAs have the potential to control 420 E2-regulated and 757 non-E2-regulated mRNAs at the post-transcriptional level. The serine/threonine kinase, AKT, alters E2-regulated expression of microRNAs. E2 induced the expression of eight Let-7 family members, miR-98 and miR-21 microRNAs; these microRNAs reduced the levels of c-Myc and E2F2 proteins. Dicer, a ribonuclease III enzyme required for microRNA processing, is also an E2-inducible gene. Several E2-regulated microRNA genes are associated with ERα-binding sites or located in the intragenic region of estrogen-regulated genes. We propose that the clinical course of ERα-positive breast cancers is dependent on the balance between E2-regulated tumor-suppressor microRNAs and oncogenic microRNAs. Additionally, our studies reveal a negative-regulatory loop controlling E2 response through microRNAs as well as differences in E2-induced transcriptome and proteome