Harnessing the potential of non-coding RNA: An insight into its mechanism and interaction in plant biotic stress

Plants have developed diverse physical and chemical defence mechanisms to ensure their continued growth and well-being in challenging environments. Plants also have evolved intricate molecular mechanisms to regulate their responses to biotic stress. Non-coding RNA (ncRNA) plays a crucial role in this process that affects the expression or suppression of target transcripts. While there have been numerous reviews on the role of molecules in plant biotic stress, few of them specifically focus on how plant ncRNAs enhance resistance through various mechanisms against different pathogens. In this context, we explored the role of ncRNA in exhibiting responses to biotic stress endogenously as well as cross-kingdom regulation of transcript expression. Furthermore, we address the interplay between ncRNAs, which can act as suppressors, precursors, or regulators of other ncRNAs. We also delve into the regulation of ncRNAs in response to attacks from different organisms, such as bacteria, viruses, fungi, nematodes, oomycetes, and insects. Interestingly, we observed that diverse microorganisms interact with distinct ncRNAs. This intricacy leads us to conclude that each ncRNA serves a specific function in response to individual biotic stimuli. This deeper understanding of the molecular mechanisms involving ncRNAs in response to biotic stresses enhances our knowledge and provides valuable insights for future research in the field of ncRNA, ultimately leading to improvements in plant traits.

Antidiabetic and hepato-renal protective effects of medicinal plants in STZ induced diabetic rats

Abstract The antidiabetic and hepato-renal protective effects of Citrullus colocynthis and Momordica charantia ethanol extracts were investigated in streptozotocin (STZ) induced diabetic male albino rats. Diabetic rats were treated with C. colocynthis, M. charantia or C. colocynthis + M. charantia mixed extract at a dose of 250 mg /kg body weight per oral per day for 21 days. The mean body weight of all the diabetic rat groups on day 1 of treatment (day 10 of diabetes) was significantly lower than the normal control rat group (P<0.05). The blood glucose level of all the diabetic rat groups on day 1 of treatment (day 10 of diabetes) was significantly (P<0.05) higher (> 200 mg/dl) than the normal control rat group (95.5 ± 2.7). At the end of treatment (day 21), the diabetic rats treated with plant extracts showed significant increase (P<0.05) in body weight and significant (P<0.05) reduction in blood glucose level when compared to diabetic control animals. Significant increase (< 0.05) was observed in the serum bilirubin, alanine transaminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP), urea and creatinine levels of diabetic control rat group. The serum levels of these liver and kidney-related parameters of diabetic rats treated with plant extract were significantly lower when compared to diabetic control rat group (p < 0.05). Photomicrographs of liver and kidney microsections from diabetic rats treated with these plant extracts showed amelioration in the hepato-renal histoarchitectures. It was concluded that the C. colocynthis and M. charantia methanol extracts are antidiabetic and hepato-renal protective in STZ induced diabetic male rats. Treatment of the diabetic rats with C. colocynthis + M. charantia mixed extract is more effective in the amelioration of diabetes and hepato-renal injuries in STZ induced diabetic male rats.

Auger Shake-Up Assisted Electron Recapture

The presence of doubly excited states (DESs) above the core-hole ionization threshold nontrivially modulates the x-ray absorption because the participator Auger decay couples DESs to the underlying low-energy core-hole continuum. We show that coupling also affects the high-energy continuum populated by the spectator Auger decay of DESs. For the K-L_{23}^{2} Auger decay of the 1s^{-1}3p^{-1}4s^{2}^{1}P state in argon, the competing nonresonant path is assigned to the recapture of the 1s photoelectron caused by emission of the fast electron from the shake-up K-L_{23}^{2} decay of the 1s^{-1} ion.

Ocular manifestations of HIV infection at Chris Hani Baragwanath Academic Hospital, Johannesburg, South Africa

BACKGROUND

The pattern of HIV-associated eye disease has changed with ongoing advancements in highly active antiretroviral therapy (HAART). HIV-infected individuals now live longer, enabling us to observe the long-term effects of HIV and HAART on the eye. There are few recent studies on HIV-related ocular disease in sub-Saharan Africa.

OBJECTIVES

To describe the ocular manifestations of HIV in patients attending the Nthabiseng HIV clinic at Chris Hani Baragwanath Academic Hospital, Johannesburg, South Africa.

METHODS

A cross-sectional study was conducted in 2021 and 2022 using convenience sampling of patients at the HIV clinic. The participants' clinical history was taken, their files were reviewed, and they underwent ocular examination. Correlation between eyes was managed by taking disease in one eye as the presence of disease in the participant. Descriptive statistics were used to summarise participant characteristics. Univariate and multivariate logistic regression models were used to assess the odds ratio (OR) of developing HIV-associated ocular diseases, and a p-value of <0.05 was used to define statistical significance.

RESULTS

There were 182 participants (139 females and 43 males), with a mean (standard deviation) age of 48.9 (10.6) years. The most common anterior segment diagnoses were conjunctival microangiopathy (34.6%), pinguecula (31.3%) and cataracts (30.2%), while the most common posterior segment finding was peripheral retinal scarring with features in keeping of previous cytomegalovirus retinitis (24.2%). Notably, only 1.1% of patients had HIV retinopathy. A CD4 count <200 cells/μL showed an increased OR for cataracts (OR 4.24; p=0.003) and any anterior segment diagnoses (OR 10.05; p=0.029), while a CD4 count ≥200 cells/μL showed an increased risk of conjunctival microangiopathy (OR 2.14; p=0.017).

CONCLUSION

With the advent of HAART, ocular manifestations of HIV are changing and the incidence of severe ocular opportunistic infections and HIV retinopathy has decreased precipitously. Although this study has shown that patients with a CD4 count <200 cells/μL are at increased risk of developing anterior ocular manifestations of HIV, including cataracts, these diseases are relatively innocuous or easily treatable. Routine ocular screening of HIV patients seems to be substantially less important now than it was in the pre-HAART era.

Isotope effects in dynamics of water isotopologues induced by core ionization at an x-ray free-electron laser

Dynamical response of water exposed to x-rays is of utmost importance in a wealth of science areas. We exposed isolated water isotopologues to short x-ray pulses from a free-electron laser and detected momenta of all produced ions in coincidence. By combining experimental results and theoretical modeling, we identify significant structural dynamics with characteristic isotope effects in H2O2+, D2O2+, and HDO2+, such as asymmetric bond elongation and bond-angle opening, leading to two-body or three-body fragmentation on a timescale of a few femtoseconds. A method to disentangle the sequences of events taking place upon the consecutive absorption of two x-ray photons is described. The obtained deep look into structural properties and dynamics of dissociating water isotopologues provides essential insights into the underlying mechanisms.

Persicaria minor F-box Gene Pmf-box1 Indirectly Affects Arabidopsis thaliana LOX-HPL Pathway for Green Leaf Volatile Production

Green leaf volatiles (GLVs) play an essential role in plant defence, plant-plant interaction and plant-insect interaction. The plant releases GLVs and inhibits the growth and propagation of plant pathogens. In this study, overexpression of PmF-box1 in wild type A. thaliana showed the downregulation of genes involved in the lipoxygenase-hydroperoxide lyase (LOX-HPL) pathway, which contributes to the biosynthesis of GLVs. It resulted in a marked reduction of hexanal production in the PmF-box1-overexpressing plant. The expression pattern of LOX-HPL branch genes in the kelch-repeat modified PmF-box1 (KMF)-overexpressing plant showed a pattern much closer to the expression of LOX-HPL branch genes in the vector control (VC) plant. It was shown that the functional KMF protein sequence was not responsible for the significant reduction of all GLVs including hexanal, 1-hexanol, (Z)-3-hexen-1-ol, and the carbon 5 (C5) volatile, 1-penten-3-ol, in plants overexpressing KMF. Furthermore, this study also showed that the relative proportion of production of 1-penten-3-ol to hexanal was higher in the PmF-box1-overexpressing plant. Based on the current comparative literature search, PmF-box1 does not appear to interact directly with the proteins or transcription factors of the LOX-HPL pathway. On the other hand, PmF-box1 interacts with SAMS1, which subsequently influences the HPL pathway enzyme genes. Thus, this study highlights the potential roles of PmF-box1 in the manipulation of GLV productions.

Clinical and radiological outcomes of SARS-CoV-2 related organising pneumonia in COVID-19 survivors

INTRODUCTION

COVID-19 patients frequently demonstrate radiological organising pneumonia (OP) pattern. The longterm outcome and treatment options for this group of patients remain uncertain. We aim to describe the clinical and radiological outcomes of patients with COVID-19-related OP and identify possible clinical factors associated with inferior radiological outcome.

MATERIALS AND METHODS

Post-COVID-19 clinic attendees, consisting of post-COVID-19 patients discharged from major hospitals in the state of Selangor during the third pandemic wave of COVID-19 in Malaysia, were enrolled in this retrospective study for 6 months. Physician-scored Modified Medical Research Council (mMRC), patient self-reported quality of life (EQ-VAS) score and follow-up CT scan were evaluated.

RESULTS

Our cohort comprised 131 patients, with a median age of 52 (IQR 39-60) years and median BMI of 29.40 (IQR 25.59-34.72). Majority (72.5%) had co-morbidities, and 97.7% had severe disease requiring supplementary oxygen support during the acute COVID-19 episode. 56.5% required intensive care; among which one-third were invasively ventilated. Median equivalent dose of methylprednisolone prescribed was 2.60 (IQR 1.29-5.18) mg/kg during admission, while the median prednisolone dose upon discharge was 0.64 (IQR 0.51-0.78) mg/kg. It was tapered over a median of 8.0 (IQR 5.8-9.0) weeks. Upon follow-up at 11 (IQR 8-15) weeks, one-third of patients remained symptomatic, with cough, fatigue and dyspnoea being the most reported symptoms. mMRC and EQ-VAS scores improved significantly (p<0.001) during follow-up. Repeat CT scans were done in 59.5% of patients, with 94.8% of them demonstrating improvement. In fact, 51.7% had complete radiological resolution. Intensive care admission and mechanical ventilation are among the factors which were associated with poorer radiological outcomes, p<0.05.

CONCLUSION

Approximately one-third of patients with SARSCoV- 2-related OP remained symptomatic at 3 months of follow-up. Majority demonstrated favourable radiological outcomes at 5-month reassessment, except those who required intensive care unit admission and mechanical ventilation.

Overview of Repressive miRNA Regulation by Short Tandem Target Mimic (STTM): Applications and Impact on Plant Biology

The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. To date, various studies have been conducted to understand the molecular mimic mechanism and to improve the efficiency of this technology. As a result, several mimic tools have been developed: target mimicry (TM), short tandem target mimic (STTM), and molecular sponges (SPs). STTM is the most-developed tool due to its stability and effectiveness in decoying miRNA. This review discusses the application of STTM technology on the loss-of-function studies of miRNA and members from diverse plant species. A modified STTM approach for studying the function of miRNA with spatial-temporal expression under the control of specific promoters is further explored. STTM technology will enhance our understanding of the miRNA activity in plant-tissue-specific development and stress responses for applications in improving plant traits via miRNA regulation.

First (e,e) coincidence measurements on solvated sodium benzoate in water using a magnetic bottle time-of-flight spectrometer

Sodium benzoate molecules solvated in water are studied using coincidence electron spectroscopy coupled with a liquid microjet device.

A modified magnetic bottle electron spectrometer for the detection of multiply charged ions in coincidence with all correlated electrons: decay pathways to Xe3+ above xenon-4d ionization threshold

Single-photon multiple photoionization results from electron correlations that make this process possible beyond the independent electron approximation. To study this phenomenon experimentally, the detection in coincidence of all emitted electrons is the most direct approach. It provides the relative contribution of all possible multiple ionization processes, the energy distribution between electrons that can reveal simultaneous or sequential mechanisms, and, if possible, the angular correlations between electrons. In the present work, we present a new magnet design of our magnetic bottle electron spectrometer that allows the detection of multiply charged Xeⁿ⁺ ions in coincidence with n electrons. This new coincidence detection allows more efficient extraction of minor channels that are otherwise masked by random coincidences. The proof of principle is provided for xenon triple ionization.

Design and analysis of water quality monitoring and filtration system for different types of water in Malaysia

Water pollution always occurs in Malaysia due to industrial, construction, agriculture, and household activities. River pollution can disturb water supply that eventually affects business and household activities. Thus, water quality monitoring system is needed to detect contaminated water. We developed a water quality monitoring and filtration system controlled by Arduino. The proposed system was designed in Proteus software and ThingSpeak platform was used for real-time monitoring. The main objective of the study was to compare water quality of river, lake and tap water in terms of pH, temperature, turbidity, electrical conductivity and oxidation-reduction potential. If the water quality was not satisfied, the water sample would be filtered through filtration system. Water turbidity level, pH, temperature, electrical conductivity, and oxidation-reduction potential for filtered and nonfiltered water were compared and analyzed according to international and national water quality standard. Besides that, statistical analysis such as box plot and one-way analysis of variance test was applied to validate data from the system. The real-time water quality monitoring system was implemented through data storage, data transfer, and data processing. The system was connected to wireless fidelity whereas the output data was sent to the user and monitored by ThingSpeak. The system can be further upgraded and scaled up to be applied in the main tank at our home or factory. The outcome of this research can be used as a reference for further study on lake and river pollution monitoring system.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13762-022-04192-x.

The O K-2V spectrum of CO: the influence of the second core-hole

Using synchrotron radiation in the tender X-ray regime, a photoelectron spectrum showing the formation of single site double-core-hole pre-edge states, involving the K shell of the O atom in CO, has been recorded by means of high-resolution electron spectroscopy. The experimentally observed structures have been simulated, interpreted and assigned, employing state-of-the-art ab initio quantum chemical calculations, on the basis of a theoretical model, accounting for their so-called direct or conjugate character. Features appearing above the double ionization threshold have been reproduced by taking into account the strong mixing between multi-excited and continuum states. The shift of the σ* resonance below the double ionization threshold, in combination with the non-negligible contributions of multi-excited configurations in the final states reached, gives rise to a series of avoided crossings between the different potential energy curves.

Optimal set of microsatellite markers required to detect illegitimate progenies in selected oil palm (Elaeis guineensis Jacq.) breeding crosses

Oil palm is continually being improved via controlled crossing of selected palms to ensure sustainable yields and productivity. As such, correct parental assignment is important as the presence of illegitimates will compromise the progress of improvement. In the present study, we determined the optimal number of microsatellite (SSR) markers for detection of illegitimates in selected oil palm crosses with high confidence. Determining the optimal number of markers to assign parentage will ensure that the DNA fingerprinting will be cost effective for routine use as a quality control tool in oil palm improvement programs. Here, we evaluated a wide range of crosses that included a cross derived from wild germplasm palm. The results revealed that markers with high PIC are informative and detect most of the alleles present in a cross, including those exhibited by the illegitimates. A larger number of optimum sets of markers are needed to detect all illegitimates for crosses with higher levels of genetic diversity. The optimal number of polymorphic SSR markers determined in the present study can ensure that appropriate quality control is implemented for oil palm improvement programs.

Sequence and Phylogenetic Analysis of the First Complete Genome of Ricetungro spherical virus in Malaysia

Background:

Rice tungro disease (RTD) is a viral disease mainly affecting rice in Asia. RTD caused by Rice tungro bacilliform virus and Rice tungro spherical virus. To date, there are only 5 RTSV isolates have been reported.

Objectives:

In this study, we aimed to report the complete nucleotide sequence of Malaysian isolate of Rice tungro spherical virus Seberang Perai (RTSV-SP) for the first time. RTSV-SP was characterized and its evolutionary relationship with previously reported Indian and Philippines isolates were elucidated.

Materials and Methods:

RTSV-SP isolate was isolated from a recent outbreak in a paddy field in Seberang Perai zone of Malaysia. Its complete genome was amplified by RT-PCR, cloned and sequenced.

Results:

Sequence analysis indicated that the genome of RTSV-SP consisted of 12,173 nucleotides (nt). Comparative analysis of 6 complete genome sequences using Clustal Omega showed that Seberang Perai isolate shared the highest nucleotide identity (96.04%) with Philippine-A isolate, except that the sORF-2 of RTSV-SP is shorter than RTSV Philippine-A by 27 amino acid residues. RTSV-SP found to cluster in Southeast Asia (SEA) group based on the whole genome sequence phylogenetic analysis using MEGA X software.

Conclusions:

Phylogenetic classification of RTSV isolates based on the complete nucleotide sequences showed more distinctive clustering pattern with the addition of RTSV-SP whole genome to the available isolates. Present study described the isolation and molecular characterization of RTSV-SP.

Application of Reverse Genetics in Functional Genomics of Potyvirus

Numerous potyvirus studies, including virus biology, transmission, viral protein function, as well as virus–host interaction, have greatly benefited from the utilization of reverse genetic techniques. Reverse genetics of RNA viruses refers to the manipulation of viral genomes, transfection of the modified cDNAs into cells, and the production of live infectious progenies, either wild-type or mutated. Reverse genetic technology provides an opportunity of developing potyviruses into vectors for improving agronomic traits in plants, as a reporter system for tracking virus infection in hosts or a production system for target proteins. Therefore, this review provides an overview on the breakthroughs achieved in potyvirus research through the implementation of reverse genetic systems.

Diverse and dynamic roles of F-box proteins in plant biology

The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.

Pulse Crop Genetics for a Sustainable Future: Where We Are Now and Where We Should Be Heading

The last decade has witnessed dramatic changes in global food consumption patterns mainly because of population growth and economic development. Food substitutions for healthier eating, such as swapping regular servings of meat for protein-rich crops, is an emerging diet trend that may shape the future of food systems and the environment worldwide. To meet the erratic consumer demand in a rapidly changing world where resources become increasingly scarce due largely to anthropogenic activity, the need to develop crops that benefit both human health and the environment has become urgent. Legumes are often considered to be affordable plant-based sources of dietary proteins. Growing legumes provides significant benefits to cropping systems and the environment because of their natural ability to perform symbiotic nitrogen fixation, which enhances both soil fertility and water-use efficiency. In recent years, the focus in legume research has seen a transition from merely improving economically important species such as soybeans to increasingly turning attention to some promising underutilized species whose genetic resources hold the potential to address global challenges such as food security and climate change. Pulse crops have gained in popularity as an affordable source of food or feed; in fact, the United Nations designated 2016 as the International Year of Pulses, proclaiming their critical role in enhancing global food security. Given that many studies have been conducted on numerous underutilized pulse crops across the world, we provide a systematic review of the related literature to identify gaps and opportunities in pulse crop genetics research. We then discuss plausible strategies for developing and using pulse crops to strengthen food and nutrition security in the face of climate and anthropogenic changes.

Hard x-ray spectroscopy and dynamics of isolated atoms and molecules: a review

We present here a review of the most significant recent achievements in the field of HAXPES (hard x-ray photoelectron spectroscopy) on isolated atoms and molecules, and related spectroscopies. The possibility of conducting hard x-ray photoexcitation and photoionization experiments under state-of-the art conditions in terms of photon and electron kinetic energy resolution has become available only in the last few years. HAXPES has then produced structural and dynamical information at the level of detail already reached in the VUV and soft-x-ray ranges. The much improved experimental conditions have allowed extending to the hard x-ray range some methods well established in soft x-ray spectroscopies. Investigations of electron and nuclear dynamics in the femtosecond (fs, 10^-15 s) and even attosecond (as, 10^-18 s) regime have become feasible. Complex relaxation phenomena following deep-core ionization can now be enlightened in great detail. Other phenomena like e.g. recoil-induced effects are much more important in fast photoelectron emission, which can be induced by hard x-rays. Furthermore, a new kind of ionic states with double core holes can be observed by x-ray single-photon absorption. Future perspectives are also discussed.

Tree Physiology Optimization in Benchmark Function and Traveling Salesman Problem

Nature has the ability of sustainability and improvisation for better survival. This unique characteristic reflects a pattern of optimization that inspires the computational intelligence toward different scopes of optimization: a nondeterministic optimization approach or a nature-inspired metaheuristic algorithm. To date, there are many metaheuristic algorithms introduced with good promising results and also becoming a powerful method for solving numerous optimization problems. In this paper, a new metaheuristic algorithm inspired from a plant growth system is proposed, which is defined as tree physiology optimization (TPO). A plant growth consists of two main counterparts: plant shoots and roots. Shoots extend to find better sunlight for the photosynthesis process that converts light and water supplied from the roots into energy for plant growth; at the same time, roots elongate in the opposite way in search for water and nutrients for shoot survival. The collaboration from both systems ensures plant sustainability. This idea is transformed into an optimization algorithm: shoots with defined branches find the potential solution with the help of roots variable. The shoots-branches extension enhances the search diversity and the root system amplifying the search via evaluated fitness. To demonstrate its effectiveness, two different classes of problem are evaluated: (1) a continuous benchmark test function compared to particle swarm optimization (PSO) and genetic algorithm (GA) and (2) an NP-hard problem with the traveling salesman problem (TSP) compared to GA and nearest-neighbor (NN) algorithm. The simulation results show that TPO outperforms PSO and GA in all problem characteristics (flat surface and steep-drop with a combination of many local minima and plateau). In the TSP, TPO has a comparable result to GA.

Dosimetric response of fabricated Ge-doped optical fibres in computed tomography RQT beam quality x-ray beams

Novel germanium (Ge)-doped silica glass fibres tailor-made in Malaysia are fast gaining recognition as potential media for thermoluminescence (TL) dosimetry, with active research ongoing into exploitation of their various beneficial characteristics. Investigation is made herein of the capability of these media for use in diagnostic imaging dosimetry, specifically at the radiation dose levels typically obtained in conduct of Computed Tomography (CT). As a first step within such efforts, there is need to investigate the performance of the fibres using tightly defined spectra, use being made of a Philips constant potential industrial x-ray facility, Model MG165, located at the Malaysian Nuclear Agency Secondary Standards Dosimetry Lab (SSDL). Standard radiation beam qualities (termed RQT) have been established for CT, in accord with IEC 61267: 2003 and IAEA Technical Reports Series No. 457: 2007. A calibrated ionisation chamber has also been utilised, forming a component part of the SSDL equipment. The fabricated fibres used in this study are 2.3 mol% flat fibre (FF) of dimensions 643 × 356 μm² and 2.3 mol% cylindrical fibre (CF) of 481 μm diameter, while the commercial fibre used is 4 mol% with core diameter of 50 μm. The dopant concentrations are nominal preform values. The fibres have been irradiated to doses of 20, 30 and 40 milligray (mGy) for each of the beam qualities RQT 8, RQT 9 and RQT 10. For x-rays generated at constant potential values from 100 to 150 kV, a discernible energy-dependent response is seen, comparisons being made with that of lithium fluoride (LiF) thermoluminescence dosimeters (TLD-100). TL yield versus dose has also been investigated for x-ray doses from 2 to 40 mGy, all exhibiting linearity. Compared to TLD-100, greater sensitivity is observed for the fibres.

Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

Background

Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food industries. Although the terpenoids of P. minor have been studied thoroughly, the involvement of microRNA (miRNA) in terpenoid regulation remains poorly understood and needs to be explored. In this study, P. minor plants were inoculated with the pathogenic fungus Fusarium oxysporum for terpenoid induction.

Result

SPME GC-MS analysis showed the highest terpenoid accumulation on the 6th day post-inoculation (dpi) compared to the other treatment time points (0 dpi, 3 dpi, and 9 dpi). Among the increased terpenoid compounds, α-cedrene, valencene and β-bisabolene were prominent. P. minor inoculated for 6 days was selected for miRNA library construction using next generation sequencing. Differential gene expression analysis showed that 58 miRNAs belonging to 30 families had significantly altered regulation. Among these 58 differentially expressed genes (DEGs), 33 miRNAs were upregulated, whereas 25 miRNAs were downregulated. Two putative novel pre-miRNAs were identified and validated through reverse transcriptase PCR. Prediction of target transcripts potentially involved in the mevalonate pathway (MVA) was carried out by psRobot software, resulting in four miRNAs: pmi-miR530, pmi-miR6173, pmi-miR6300 and a novel miRNA, pmi-Nov_13. In addition, two miRNAs, miR396a and miR398f/g, were predicted to have their target transcripts in the non-mevalonate pathway (MEP). In addition, a novel miRNA, pmi-Nov_12, was identified to have a target gene involved in green leaf volatile (GLV) biosynthesis. RT-qPCR analysis showed that pmi-miR6173, pmi-miR6300 and pmi-nov_13 were downregulated, while miR396a and miR398f/g were upregulated. Pmi-miR530 showed upregulation at 9 dpi, and dynamic expression was observed for pmi-nov_12. Pmi-6300 and pmi-miR396a cleavage sites were detected through degradome sequence analysis. Furthermore, the relationship between miRNA metabolites and mRNA metabolites was validated using correlation analysis.

Conclusion

Our findings suggest that six studied miRNAs post-transcriptionally regulate terpenoid biosynthesis in P. minor. This regulatory behaviour of miRNAs has potential as a genetic tool to regulate terpenoid biosynthesis in P. minor.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5954-0) contains supplementary material, which is available to authorized users.

Agarwood Induction: Current Developments and Future Perspectives

Agarwood is a resinous part of the non-timber Aquilaria tree, which is a highly valuable product for medicine and fragrance purposes. To protect the endangered Aquilaria species, mass plantation of Aquilaria trees has become a sustainable way in Asian countries to obtain the highly valuable agarwood. As only physiologically triggered Aquilaria tree can produce agarwood, effective induction methods are long sought in the agarwood industry. In this paper, we attempt to provide an overview for the past efforts toward the understanding of agarwood formation, the evolvement of induction methods and their further development prospects by integrating it with high-throughput omics approaches.

Data on Fourier transform-infrared of Cosmos caudatus Kunth. tissues analyzed with chemometric analysis

In this dataset, we differentiate four different tissues of Cosmos caudatus Kunth (leaves, flowers, stem and root) obtained from UKM Bangi plot, based on Fourier transform-infrared spectroscopy. Different tissues of C. caudatus demonstrated the position and intensity of characteristic peaks at 4000–450 cm⁻¹. Principal component analysis (PCA) shows three main groups were formed. The samples from leaves and flowers were found to be clustered together in one group, while the samples from stems and roots were clustered into two separate groups, respectively. This data provides an insight into the fingerprint identification and distribution of metabolites in the different organs of this species.

Maize Dwarf Mosaic Virus: From Genome to Disease Management

Maize dwarf mosaic virus (MDMV) is a serious maize pathogen, epidemic worldwide, and one of the most common virus diseases for monocotyledonous plants, causing up to 70% loss in corn yield globally since 1960. MDMV belongs to the genus Potyvirus (Potyviridae) and was first identified in 1964 in Illinois in corn and Johnsongrass. MDMV is a single stranded positive sense RNA virus and is transmitted in a non-persistent manner by several aphid species. MDMV is amongst the most important virus diseases in maize worldwide. This review will discuss its genome, transmission, symptomatology, diagnosis and management. Particular emphasis will be given to the current state of knowledge on the diagnosis and control of MDMV, due to its importance in reducing the impact of maize dwarf mosaic disease, to produce an enhanced quality and quantity of maize.

Data on degradome sequencing and analysis from mock-inoculated and Fusarium oxysporum treated leaves samples in Persicaria minor

Degradome sequencing referred as parallel analysis of RNA ends (PARE) by modifying 5′-rapid amplification of cDNA ends (RACE) with deep sequencing method. Deep sequencing of 5’ products allow the determination of cleavage sites through the mapping of degradome fragments against small RNAs (miRNA or siRNA) on a large scale. Here, we carried out degradome sequencing in medicinal plant, Persicaria minor, to identify cleavage sites in small RNA libraries in control (mock-inoculated) and Fusarium oxysporum treated plants. The degradome library consisted of both control and treated samples which were pooled together during library preparation and named as D4. The D4 dataset have been deposited at GenBank under accession number SRX3921398, https://www.ncbi.nlm.nih.gov/sra/SRX3921398.

Energy Transfer into Molecular Vibrations and Rotations by Recoil in Inner-Shell Photoemission

A mixture of CF_{4} and CO gases is used to study photoelectron recoil effects extending into the tender x-ray region. In CF_{4}, the vibrational envelope of the C 1s photoelectron spectrum becomes fully dominated by the recoil-induced excitations, revealing vibrational modes hidden from Franck-Condon excitations. In CO, using CF_{4} as an accurate energy calibrant, we determine the partitioning of the recoil-induced internal excitation energy between rotational and vibrational excitation. The observed rotational recoil energy is 2.88(28) times larger than the observed vibrational recoil energy, well in excess of the ratio of 2 predicted by the basic recoil model. The experiment is, however, in good agreement with the value of 2.68 if energy transfer via Coriolis coupling is included.

Experimental setup for the study of resonant inelastic X-ray scattering of organometallic complexes in gas phase

A new setup has been designed and built to study organometallic complexes in gas phase at the third-generation Synchrotron radiation sources. This setup consists of a new homemade computer-controlled gas cell that allows us to sublimate solid samples by accurately controlling the temperature. This cell has been developed to be a part of the high-resolution X-ray emission spectrometer permanently installed at the GALAXIES beamline of the French National Synchrotron Facility SOLEIL. To illustrate the capabilities of the setup, the cell has been successfully used to record high-resolution Kα emission spectra of gas-phase ferrocene Fe(C₅H₅)₂ and to characterize their dependence with the excitation energy. This will allow to extend resonant X-ray emission to different organometallic molecules.

Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome

In current era, majority of microRNA (miRNA) are being discovered through computational approaches which are more confined towards model plants. Here, for the first time, we have described the identification and characterization of novel miRNA in a non-model plant, Persicaria minor (P. minor) using computational approach. Unannotated sequences from deep sequencing were analyzed based on previous well-established parameters. Around 24 putative novel miRNAs were identified from 6,417,780 reads of the unannotated sequence which represented 11 unique putative miRNA sequences. PsRobot target prediction tool was deployed to identify the target transcripts of putative novel miRNAs. Most of the predicted target transcripts (mRNAs) were known to be involved in plant development and stress responses. Gene ontology showed that majority of the putative novel miRNA targets involved in cellular component (69.07%), followed by molecular function (30.08%) and biological process (0.85%). Out of 11 unique putative miRNAs, 7 miRNAs were validated through semi-quantitative PCR. These novel miRNAs discoveries in P. minor may develop and update the current public miRNA database.

Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis

Geraniol degradation pathway has long been elucidated in microorganisms through bioconversion studies, yet weakly characterised in plants; enzyme with specific nerol-oxidising activity has not been reported. A novel cDNA encodes nerol dehydrogenase (PmNeDH) was isolated from Persicaria minor. The recombinant PmNeDH (rPmNeDH) is a homodimeric enzyme that belongs to MDR (medium-chain dehydrogenases/reductases) superfamily that catalyses the first oxidative step of geraniol degradation pathway in citral biosynthesis. Kinetic analysis revealed that rPmNeDH has a high specificity for allylic primary alcohols with backbone ≤10 carbons. rPmNeDH has ∼3 fold higher affinity towards nerol (cis-3,7-dimethyl-2,6-octadien-1-ol) than its trans-isomer, geraniol. To our knowledge, this is the first alcohol dehydrogenase with higher preference towards nerol, suggesting that nerol can be effective substrate for citral biosynthesis in P. minor. The rPmNeDH crystal structure (1.54 Å) showed high similarity with enzyme structures from MDR superfamily. Structure guided mutation was conducted to describe the relationships between substrate specificity and residue substitutions in the active site. Kinetics analyses of wild-type rPmNeDH and several active site mutants demonstrated that the substrate specificity of rPmNeDH can be altered by changing any selected active site residues (Asp²⁸⁰, Leu²⁹⁴ and Ala³⁰³). Interestingly, the L294F, A303F and A303G mutants were able to revamp the substrate preference towards geraniol. Furthermore, mutant that exhibited a broader substrate range was also obtained. This study demonstrates that P. minor may have evolved to contain enzyme that optimally recognise cis-configured nerol as substrate. rPmNeDH structure provides new insights into the substrate specificity and active site plasticity in MDR superfamily.

Recent Development in Omics Studies

The central dogma of molecular biology (DNA, RNA, protein and metabolite) has engraved our understanding of genetics in all living organisms. While the concept has been embraced for many decades, the development of high-throughput technologies particularly omics (genomics, transcriptomics, proteomics and metabolomics) has revolutionised the field to incorporate big data analysis including bioinformatics and systems biology as well as synthetic biology area. These omics approaches as well as systems and synthetic biology areas are now increasingly popular as seen by the growing numbers of publication throughout the years. Several journals which have published most of these related fields are also listed in this chapter to overview their impact and target journals.