Saurabh Gupta

Curtin University · Curtin Health Innovation Research Institute (CHIRI)

Short-read RNA-Seq analyses of grafted plants have led to the proposal that large numbers of mRNAs move over long distances between plant tissues, acting as potential signals. The detection of transported transcripts by RNA-Seq is both experimentally and computationally challenging, requiring successful grafting, delicate harvesting, rigorous conta...

In Arabidopis a high number of distinct mRNAs move from shoot to root. We previously reported on the correlation of m ⁵ C-methylation and lack of mRNA transport in juvenile plants depending on the RNA methyltransferases DNMT2 NSUN2B . However, to our surprise we uncovered that lack of DNMT2 NSUN2B (writer) activity did not abolished transport of TC...

Chickpea (Cicer arietinum L.)—an important legume crop cultivated in arid and semiarid regions—has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer...

Haberlea rhodopensis, a resurrection species, is the only plant known to be able to survive multiple extreme environments, including desiccation, freezing temperatures, and long-term darkness. However, the molecular mechanisms underlying tolerance to these stresses are poorly studied. Here, we present a high-quality genome of Haberlea and found tha...

Onco-fetal reprogramming of the tumor ecosystem induces fetal developmental signatures in the tumor microenvironment, leading to immunosuppressive features. Here, we employed single-cell RNA sequencing, spatial transcriptomics and bulk RNA sequencing to delineate specific cell subsets involved in hepatocellular carcinoma (HCC) relapse and response...

The environment is seldom optimal for plant growth and changes in abiotic and biotic signals, including temperature, water availability, radiation and pests, induce plant responses to optimise survival. The New Zealand native plant species and close relative to Arabidopsis thaliana, Pachycladon cheesemanii, grows under environmental conditions that...

The environment is seldom optimal for plant growth and changes in abiotic and biotic signals, including temperature, water availability, radiation and pests, induce plant responses to optimise survival. The New Zealand native plant species and close relative to Arabidopsis thaliana, Pachycladon cheesemanii grows under environmental conditions that...

The long-distance transport of messenger RNAs (mRNAs) has been shown to be important for several developmental processes in plants. A popular method for identifying travelling mRNAs is to perform RNA-Seq on grafted plants. This approach depends on the ability to correctly assign sequenced mRNAs to the genetic background from which they originated....

The spatial organisation of cells defines the biological functions of tissue ecosystems from development to disease. Recently, an array of technologies have been developed to query gene expression in a spatial context. These include techniques such as employing barcoded oligonucleotides, single-molecule fluorescence in situ hybridization (smFISH),...

Although several large-scale single-cell RNA sequencing (scRNAseq) studies addressing the root of Arabidopsis (Arabidopsis thaliana) have been published, there is still need for a de novo reference map for both root and especially above-ground cell types. As the plants’ transcriptome substantially changes throughout the day, shaped by the circadian...

Introduction Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly base...

The phytohormones gibberellins (GAs) play fundamental roles in almost every aspect of plant growth and development. Although there is good knowledge about GA biosynthetic and signaling pathways, factors contributing to the mechanisms homeostatically controlling GA levels remain largely unclear. Here, we demonstrate that homeobox transcription facto...

In viticulture, grafting is used to propagate Phylloxera-susceptible European grapevines, thereby using resistant American rootstocks. Although scion–rootstock reciprocal signaling is essential for the formation of a proper vascular union and for coordinated growth, our knowledge of graft partner interactions is very limited. In order to elucidate...

In plants, the shoot apical meristem (SAM) is essential for the growth of above-ground organs. However, little is known about its molecular responses to abiotic stresses. Here, we show that the SAM of Arabidopsis thaliana displays an autonomous heat stress (HS) memory of a previous non-lethal HS, allowing the SAM to regain growth after exposure to...

The Target of Rapamycin (TOR) kinase pathway integrates energy and nutrient availability into metabolism promoting growth in eukaryotes. The overall higher efficiency on nutrient use translated into faster growth rates in C4 grass plants led to the investigation of differential transcriptional and metabolic responses to short-term chemical TOR comp...

The phytohormones gibberellins (GAs) play fundamental roles in almost every aspect of plant growth and development. Although there is good knowledge about GA biosynthetic and signaling pathways, factors contributing to the mechanisms homeostatically controlling GA levels remain largely unclear. Here, we demonstrate that homeobox transcription facto...

Drought represents a major threat to plants in natural ecosystems and agricultural settings. The biostimulant Super Fifty (SF), produced from the brown alga Ascophyllum nodosum, enables ecologically friendly stress mitigation. We investigated the physiological and whole-genome transcriptome responses of Arabidopsis thaliana to drought stress after...

In flowering plants, sugars act as carbon sources providing energy for developing embryos and seeds. Although most studies focus on carbon metabolism in whole seeds, knowledge about how particular sugars contribute to the developmental transitions during embryogenesis is scarce. To develop a quantitative understanding of how carbon composition chan...

Although we have a good understanding of the development of shoot apical meristems (SAM) in higher plants, and the function of the stem cells (SCs) embedded in the SAM, there is surprisingly little known of its molecular responses to abiotic stresses. Here, we show that the SAM of Arabidopsis thaliana senses heat stress (HS) and retains an autonomo...

Leaf senescence is the final stage of leaf development and is induced by the gradual occurrence of Age-Related Changes (ARCs). The process of leaf senescence has been well described but the cellular events leading to this process are still poorly understood. By analysis of progressively ageing, but not yet senescing Arabidopsis thaliana rosette lea...

Oxidative stress can lead to plant growth retardation, yield loss, and death. The atr7 mutant of Arabidopsis thaliana exhibits pronounced tolerance to oxidative stress. Using positional cloning, confirmed by knockout and RNA interference (RNAi) lines, we identified the atr7 mutation and revealed that ATR7 is a previously uncharacterized gene with o...

Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were...

Background: Pachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand. It grows at altitudes of up to 1000 m where it is subject to relatively high levels of ultraviolet (UV)-B radiation. To gain first insights into how Pachycladon copes with U...

Abiotic stress is one of the major threats to plant crop yield and productivity. When plants are exposed to stress, production of reactive oxygen species (ROS) increases, which could lead to extensive cellular damage and hence crop loss. During evolution, plants have acquired antioxidant defense systems which can not only detoxify ROS but also adju...

Background: Clinical trial registries have been established as a form of public accountability. Sponsors ought to register their trials promptly and accurately, but this is not always done. Some of the problems include non-registration of trials, registration of trials with incomplete information, and non-reporting of trial results on time. In thi...

Ageing as a natural process of plant development is provoked by both, internal and external factors and results in the onset of the final phase of plant life known as senescence. The progressive changes that occur during leaf development are termed as age-related changes (ARCs). Leaf senescence, is thus achieved by the gradual occurrence of ARCs. T...

Background Pachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand. It grows at altitudes of up to 1000m where it is subject to relatively high levels of ultraviolet (UV)-B radiation. To gain first insights into how Pachycladon copes with UV-B...

The desiccation-tolerant plant can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated severa...

Ageing as a natural process of plant development is provoked by both, internal and external factors and results in the onset of the final phase of plant life known as senescence. The progressive changes that occur during the time course of growth and development in plants are termed as age-related changes (ARCs). It has been reported by multiple st...

Although a common cause of disease, copy number variants (CNVs) have not routinely been identified from next-generation sequencing (NGS) data in a clinical context. This study aimed to examine the sensitivity and specificity of a widely used software package, ExomeDepth, to identify CNVs from targeted NGS data sets. We benchmarked the accuracy of C...

Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of the plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using addition...

Background: Clinical trials have been criticized on various counts. Any attempt to improve how trials are conducted or reported requires-amongst other things-an understanding of the number, the nature and the location of those that sponsor them or collaborate on them. Here we sought to identify the nature and location of each sponsor/collaborator....

The unique sponsors. The 12,823 unique sponsors and the number of trials sponsored by each. (XLS)

Categorization of the sponsors of six or more trials. The 2,266 organizations sorted into (a) corporates (951 entities), (b) non-corporates (1,145) and (c) unclassified entities (170). (XLS)

Sponsors of six or more trials. The 2,266 organizations that sponsored six or more trials and the number of trials sponsored by each. (XLS)

The base country of sponsors. For the (a) corporates and (b) non-corporates, the number of sponsors based in a particular country is listed. The percentage hosted by a given country and the cumulative percentage is also provided for each category. (XLS)

Expanded methods. (A) A note on the records downloaded, (B) Determining the number of sponsors, (C) Classifying each organization, and (D) Determining each organization's location. (DOC)

Head and neck squamous cell carcinoma (HNSCC) are a heterogeneous group of cancers affecting multiple subsites, including oral cavity. Oral or anterior tongue tumors (OTSCC) are an aggressive group of squamous cell carcinomas, characterized by their early spread to lymph nodes and higher rate of regional failure compared to other oral cavity cancer...

Neem ( Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of the plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using additio...

Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (<50yrs) is on the rise; many of whom lack the typical associated risk factors of alcohol and/or tobacco...

Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (<50yrs) is on a rise; many of who lack the typical associated risk factors of alcohol and/or tobacco exp...

Recently, large numbers of normal human tissues have been profiled for non-coding RNAs and more than fourteen thousand long intergenic non-coding RNAs (lincRNAs) are found expressed in normal human tissues. The functional roles of these normal lincRNAs (nlincRNAs) in the regulation of protein coding genes in normal and disease biology are yet to be...

Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essential amino acids in cereals and C4 photosynthesis being one of the most sought-after phenotypes in protein-rich legume crops, the genome of one of the grain amaranths is likely to play a critical role in crop research. We have sequen...

The rapid advancements in the field of genome sequencing are aiding our understanding on many biological systems. In the last five years, computational biologists and bioinformatics specialists have come up with newer, better and more efficient tools towards the discovery, analysis and interpretation of different genomic variants from high-throughp...

High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous amount of data (often terabytes of raw data in a month) that requires efficient analysis, management and interpre...

High-throughput DNA sequencers are becoming indispensible in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous amount of data (often terabytes of raw data in a month) that requires efficient analysis, management and interpre...

Never before has a single 'omics technology been able to challenge two decades of widely used genomics technologies as the next generation RNA sequencing(RNA-seq). The ability of RNA-seq technologies to generate hundreds of millions of short transcriptome reads from biological samples has made it a one-stop-shop for obtaining a pantheon of 'omics i...

Grain amaranths, members of Amaranthaceae family of plants, are C4 dicots that are known to produce edible seeds with lysine content as high as milk. Given the obscurity during modern times, it is hard to believe that grain amaranths were domesticated for human consumption some thousands of years ago during the Aztec and the Inca civilization. Lysi...