Corrigendum: Integrated transcriptomics and miRNAomics provide insights into the complex multi-tiered regulatory networks associated with coleoptile senescence in rice

[This corrects the article DOI: 10.3389/fpls.2022.985402.].

Integrated transcriptomics and miRNAomics provide insights into the complex multi-tiered regulatory networks associated with coleoptile senescence in rice

Coleoptile is the small conical, short-lived, sheath-like organ that safeguards the first leaf and shoot apex in cereals. It is also the first leaf-like organ to senesce that provides nutrition to the developing shoot and is, therefore, believed to play a crucial role in seedling establishment in rice and other grasses. Though histochemical studies have helped in understanding the pattern of cell death in senescing rice coleoptiles, genome-wide expression changes during coleoptile senescence have not yet been explored. With an aim to investigate the gene regulation underlying the coleoptile senescence (CS), we performed a combinatorial whole genome expression analysis by sequencing transcriptome and miRNAome of senescing coleoptiles. Transcriptome analysis revealed extensive reprogramming of 3439 genes belonging to several categories, the most prominent of which encoded for transporters, transcription factors (TFs), signaling components, cell wall organization enzymes, redox homeostasis, stress response and hormone metabolism. Small RNA sequencing identified 41 known and 21 novel miRNAs that were differentially expressed during CS. Comparison of gene expression and miRNA profiles generated for CS with publicly available leaf senescence (LS) datasets revealed that the two aging programs are remarkably distinct at molecular level in rice. Integration of expression data of transcriptome and miRNAome identified high confidence 140 miRNA-mRNA pairs forming 42 modules, thereby demonstrating multi-tiered regulation of CS. The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

Long-read-based draft genome sequence of Indian black gram IPU-94-1 'Uttara': Insights into disease resistance and seed storage protein genes

Black gram [Vigna mungo (L.) Hepper var. mungo] is a warm-season legume highly prized for its protein content along with significant folate and iron proportions. To expedite the genetic enhancement of black gram, a high-quality draft genome from the center of origin of the crop is indispensable. Here, we established a draft genome sequence of an Indian black gram cultivar, 'Uttara' (IPU 94-1), known for its high resistance to mungbean yellow mosaic virus. Pacific Biosciences of California, Inc. (PacBio) single-molecule real-time (SMRT) and Illumina sequencing assembled a draft reference-guided assembly with a cumulative size of ∼454.4 Mb, of which, 444.4 Mb was anchored on 11 pseudomolecules corresponding to 11 chromosomes. Uttara assembly denotes features of a high-quality draft genome illustrated through high N50 value (42.88 Mb), gene completeness (benchmarking universal single-copy ortholog [BUSCO] score 94.17%) and low levels of ambiguous nucleotides (N) percent (0.0005%). Gene discovery using transcript evidence predicted 28,881 protein-coding genes, from which, ∼95% were functionally annotated. A global survey of genes associated with disease resistance revealed 119 nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, while 23 genes encoding seed storage proteins (SSPs) were discovered in black gram. A large set of microsatellite loci were discovered for marker development in the crop. Our draft genome of an Indian black gram provides the foundational genomic resources for the improvement of important agronomic traits and ultimately will help in accelerating black gram breeding programs.

Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani

Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.

The Signature Amino Acid Residue Serine 31 of HIV-1C Tat Potentiates an Activated Phenotype in Endothelial Cells

The natural cysteine to serine variation at position 31 of Tat in HIV-1C disrupts the dicysteine motif attenuating the chemokine function of Tat. We ask if there exists a trade-off in terms of a gain of function for HIV-1C Tat due to this natural variation. We constructed two Tat-expression vectors encoding Tat proteins discordant for the serine 31 residue (CS-Tat vs. CC-Tat), expressed the proteins in Jurkat cells under doxycycline control, and performed the whole transcriptome analysis to compare the early events of Tat-induced host gene expression. Our analysis delineated a significant enrichment of pathways and gene ontologies associated with the angiogenic signaling events in CS-Tat stable cells. Subsequently, we validated and compared angiogenic signaling events induced by CS- vs. CC-Tat using human umbilical vein endothelial cells (HUVEC) and the human cerebral microvascular endothelial cell line (hCMEC/D3). CS-Tat significantly enhanced the production of CCL2 from HUVEC and induced an activated phenotype in endothelial cells conferring on them enhanced migration, invasion, and in vitro morphogenesis potential. The ability of CS-Tat to induce the activated phenotype in endothelial cells could be of significance, especially in the context of HIV-associated cardiovascular and neuronal disorders. The findings from the present study are likely to help appreciate the functional significance of the SAR (signature amino acid residues) influencing the unique biological properties.

Transcriptomic changes in the pre-parasitic juveniles of Meloidogyne incognita induced by silencing of effectors Mi-msp-1 and Mi-msp-20

Plant-parasitic root-knot nematode Meloidogyne incognita uses an array of effector proteins to establish successful plant infections. Mi-msp-1 and Mi-msp-20 are two known effectors secreted from nematode subventral oesophageal glands; Mi-msp-1 being a putative secretory venom allergen AG5-like protein, whereas Mi-msp-20 is a pioneer gene with a coiled-coil motif. Expression of specific effector is known to cause disturbances in the expression of other effectors. Here, we used RNA-Seq to investigate the pleiotropic effects of silencing Mi-msp-1 and Mi-msp-20. A total of 25.1-51.9 million HQ reads generated from Mi-msp-1 and Mi-msp-20 silenced second-stage juveniles (J2s) along with freshly hatched J2s were mapped to an already annotated M. incognita proteome to understand the impact on various nematode pathways. As compared to control, silencing of Mi-msp-1 caused differential expression of 29 transcripts, while Mi-msp-20 silencing resulted in differential expression of a broader set of 409 transcripts. In the Mi-msp-1 silenced J2s, cytoplasm (GO:0005737) was the most enriched gene ontology (GO) term, whereas in the Mi-msp-20 silenced worms, embryo development (GO:0009792), reproduction (GO:0000003) and nematode larval development (GO:0002119) were the most enriched terms. Limited crosstalk was observed between these two effectors as a sheer 5.9% of the up-regulated transcripts were common between Mi-msp-1 and Mi-msp-20 silenced nematodes. Our results suggest that in addition to the direct knock-down caused by silencing of Mi-msp-1 and Mi-msp-20, the cascading effect on other genes might also be contributing to a reduction in nematode's parasitic abilities.

Meloidogyne incognita (Nematoda: Meloidogynidae) sterol-binding protein Mi-SBP-1 as a target for its management

Meloidogyne incognita is a polyphagous plant-parasitic nematode that causes considerable yield loss in agricultural and horticultural crops. The management options available for M. incognita are extremely limited. Here we identified and characterised a M. incognita homolog of Caenorhabditis elegans sterol-binding protein (Mi-SBP-1), a transcriptional regulator of several lipogenesis pathway genes, and used RNA interference-mediated gene silencing to establish its utility as a target for the management of M. incognita. Mi-sbp-1 is predicted to be a helix-loop-helix domain containing DNA binding transcription factor, and is present in the M. incognita genome in three copies. The RNA-Seq analysis of Mi-sbp-1 silenced second stage juveniles confirmed the key role of this gene in lipogenesis regulation in M. incognita. In vitro and host-induced gene silencing of Mi-sbp-1 in M. incognita second stage juveniles resulted in loss of nematodes' ability to utilise the stored fat reserves, slower nematode development, and reduced parasitism on adzuki bean and tobacco plants. The multiplication factor for the Mi-sbp-1 silenced nematodes on adzuki bean plants was reduced by 51% compared with the control nematodes in which Mi-sbp-1 was not silenced. Transgenic expression of the double-stranded RNA construct of the Mi-sbp-1 gene in tobacco plants caused 40-45% reduction in M. incognita multiplication, 30-43.8% reduction in the number of egg masses, and 33-54% reduction in the number of eggs per egg mass compared with the wild type control plants. Our results confirm that Mi-sbp-1 is a key regulator of lipogenesis in M. incognita and suggest that it can be used as an effective target for its management. The findings of this study can be extended to develop methods to manage other economically important parasitic nematodes.

Nematode Genome Announcement: A Draft Genome for Rice Root-Knot Nematode, Meloidogyne graminicola

The rice root-knot nematode Meloidogyne graminicola has emerged as a devastating pest of rice in South-East Asian countries. Here we present a draft genome sequence for M. graminicola , assembled using data from short and long insert libraries sequenced on Illumina GAIIx sequencing platform.

A comprehensive annotation for the root-knot nematode Meloidogyne incognita proteome data

Root-knot nematodes are devastating pathogens of crop plants. The draft genome of southern root-knot nematode Meloidogyne incognita was published in 2008 and additional genome and transcriptome data became available later on. However, lack of a publically available annotation for M. incognita genome and transcriptome(s) limits the use of this data for functional and comparative genomics by the interested researchers. Here we present a comprehensive annotation for the M. incognita proteome data available at INRA Meloidogyne Genomic Resources page (https://meloidogyne.inra.fr/Downloads/Meloidogyne-incognita-V2-2017) and European Nucleotide Archive (ENA) (accession number: ERP009887) using a multi-pronged approach.

Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler

Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays.

Global gene expression profiling data analysis reveals key gene families and biological processes inhibited by Mithramycin in sarcoma cell lines

The role of Mithramycin as an anticancer drug has been well studied. Sarcoma is a type of cancer arising from cells of mesenchymal origin. Though incidence of sarcoma is not of significant percentage, it becomes vital to understand the role of Mithramycin in controlling tumor progression of sarcoma. In this article, we have analyzed the global gene expression profile changes induced by Mithramycin in two different sarcoma lines from whole genome gene expression profiling microarray data. We have found that the primary mode of action of Mithramycin is by global repression of key cellular processes and gene families like phosphoproteins, kinases, alternative splicing, regulation of transcription, DNA binding, regulation of histone acetylation, negative regulation of gene expression, chromosome organization or chromatin assembly and cytoskeleton.

Ketodex, a combination of dexmedetomidine and ketamine for upper gastrointestinal endoscopy in children: a preliminary report

A combination of dexmedetomidine and ketamine for upper gastrointestinal endoscopies (UGIE) was studied in 46 children aged 2-12 years over a 6-month period. Dexmedetomidine 1 μg/kg and ketamine 2 mg/kg were given as a bolus over 5 min. Heart rate (HR), mean arterial pressure (MAP), oxygen saturation (SpO2), and sedation scores were noted before induction as baseline and then every 5 min until recovery. The duration and ease of the procedure, time to recovery, and adverse effects, if any, were also recorded. UGIE could be performed with ease in 41 of the 46 cases. The HR, MAP, and SpO2 did not change significantly from the baseline. No airway intervention was required in any patient. There was no laryngospasm or shivering in any of the children, and one, four, and 11 children had hiccup, vomiting, and increased salivation, respectively. The Pediatric Anesthesia Emergence Delirium score was <4 in all except for two cases. The results of this case series show that this drug combination not only promises to be clinically effective but also safe for UGIE in children. Further randomized controlled trials with standard sedation protocols will be required to draw definite conclusions.

Local anesthetic systemic toxicity (LAST) - Should we not be concerned?

Local anesthetics are one of the most commonly used drugs in the field of medicine. Yet little is known about the systemic toxicity that can occur with their overdose. In the last few years, a lot of research has taken place understanding the etiology of the Local anesthetics systemic toxicity (LAST) and the role of lipid emulsion in treating it. There is a need to increase the awareness about LAST and establish a protocol to treat any serious neuro or cardiotoxicity.

Significance of free radicals in chronic tonsillitis

The present study was carried on adolescents suffering from chronic tonsillitis. Blood (pre and post tonsillectomy) as well as tonsil samples were evaluated for -MDA, SOD and Catalase. Our results showed a decrease in level of MDA and increase in SOD and Catalase levels post tonsillectomy. Presence of MDA and SOD in tonsillar tissue reinforce involvement of oxidative stress in pathophysiology of chronic tonsillitis.

Platelet ionic calcium and serum total calcium in essential hypertension

A total of 44 cases comprising hypertensive (31) and normotensive group (13) were studied. Serum total calcium concentrations remained unaltered in hypertensives. Platelet cytosolic calcium in hypertensive group was significantly higher as compared to the normotensive controls. Platelet cytosolic calcium correlated with systolic and diastolic blood pressure and mean arterial pressure significantly.

Platelet serotonergic mechanisms and glomerulonephritis

Proven cases (28) of glomerulonephritis (GN) were evaluated for clinico-biochemical profile, bleeding time, platelet count, platelet aggregation and platelet serotonergic mechanisms. Inordinate increase in platelet aggregation and altered platelet serotonergic mechanisms (reduced 5-HT, uptake, reduced intraplatelet 5-HT and increased plasma 5-HT) were demonstrated in some histopathological types of GN. The mechanisms and importance of these alterations have been discussed.

Tick-borne rickettsioses in Pune district, Maharashtra, India

An extensive study on tick-borne rickettsioses in the Pune district of Maharashtra revealed that Indian tick typhus exists as a zoonosis, which only occasionally causes disease in man. By sero-conversion in guinea pigs, presumptive isolates of Rickettsia conori and Coxiella burnetii were recovered from 4 of the 11 species of ticks examined. Boophilus microplus and Rhipicephalus haemaphysalis were found to be harbouring R. conori whereas C. burnetii was isolated from Haemaphysalis intermedia and Hyalomma hussaini in addition to the above mentioned 2 tick species. Complement fixation tests carried out on sera from various species of rodents and gerbils revealed the presence of antibodies against the R. conori antigen in the sera of Rattus blanfordi, R.r. rufescens and Suncus murinus. In the case of large mammals, similar antibodies were detected in the sera from dog, cow, horse and sheep. C. burnetii infection was found to exist in both the sylvan and domestic cycle, as evidenced from the involvement of ticks, large and small mammals and man in its natural history.

Ontogeny of alpha-foetoprotein in human foetal brain

Alpha-foetoprotein (AFP) was found to be present in human foetal brain during early embryonic life. Antigenically and electrophoretically foetal brain AFP is similar to that found in human foetal serum. Like serum AFP it did not bind oestradiol. Developmental profile of the proteins in foetal brain was distinct from that observed in foetal serum, amniotic fluid and maternal serum compartments. Peak levels of brain AFP were obtained in foetuses in the 20th week of gestation. These levels decreased rapidly and no AFP could be detected in foetal brains derived from the third trimester of pregnancy. The origin of AFP and its possible role in foetal brain development is discussed.

Protein and lipid concentration in the haemolymph of Danais chrysippus. Linn

Proteins and lipids in the haemolymph in both the sexes of the Danais chrysippus has been observed during the first gonotropic cycle. The concentration fluctuations in these haemolymph metabolites are correlated with the physiological state of the insect. The total protein and lipid concentration in the haemolymph of unmated females have been found to be low than the concentration found for the normal females although it followed the same type of oscillations in the concentration as have been observed for normal females.