Transcriptome analysis of waterlogging-induced adventitious root and control taproot of Mentha arvensis.

KEY MESSAGE: The present study reports differentially expressed transcripts in the waterlogging-induced adventitious root (AR) of Mentha arvensis; the identified transcripts will help to understand AR development and improve waterlogging stress response. Waterlogging notably hampers plant growth in areas facing waterlogged soil conditions. In our previous findings, Mentha arvensis was shown to adapt better in waterlogging conditions by initiating the early onset of adventitious root development. In the present study, we compared the transcriptome analysis of adventitious root induced after the waterlogging treatment with the control taproot. The biochemical parameters of total carbohydrate, total protein content, nitric oxide (NO) scavenging activity and antioxidant enzymes, such as catalase activity (CAT) and superoxide dismutase (SOD) activity, were enhanced in the adventitious root compared with control taproot. Analysis of differentially expressed genes (DEGs) in adventitious root compared with the control taproot were grouped into four functional categories, i.e., carbohydrate metabolism, antioxidant activity, hormonal regulation, and transcription factors that could be majorly involved in the development of adventitious roots. Differential expression of the upregulated and uniquely expressing thirty-five transcripts in adventitious roots was validated using qRT-PCR. This study has generated the resource of differentially and uniquely expressing transcripts in the waterlogging-induced adventitious roots. Further functional characterization of these transcripts will be helpful to understand the development of adventitious roots, leading to the resistance towards waterlogging stress in Mentha arvensis.

Barriers and enablers of breastfeeding in mother-newborn dyads in institutional settings during the COVID-19 pandemic: A qualitative study across seven government hospitals of Delhi, India.

Introduction: The COVID-19 pandemic disrupted newborn care and breastfeeding practices across most healthcare facilities. We undertook this study to explore the barriers and enablers for newborn care and breastfeeding practices in hospitals in Delhi, India for recently delivered mother (RDM)-newborn dyads during the first wave of the COVID-19 pandemic (2020) and inductively design a "pathway of impaction" for informing mitigatory initiatives during the current and future pandemics, at least in the initial months. Materials and methods: We used an exploratory descriptive design (qualitative research method) and collected information from seven leading public health facilities in Delhi, India. We conducted separate interviews with the head and senior faculty from the Departments of Pediatrics/Neonatology (n = 12) and Obstetrics (n = 7), resident doctors (n = 14), nurses (labor room/maternity ward; n = 13), and RDMs (n = 45) across three profiles: (a) COVID-19-negative RDM with healthy newborn (n = 18), (b) COVID-19-positive RDM with healthy newborn (n = 19), and (c) COVID-19 positive RDM with sick newborn needing intensive care (n = 8) along with their care-giving family members (n = 39). We analyzed the data using grounded theory as the method and phenomenology as the philosophy of our research. Results: Anxiety among clients and providers, evolving evidence and advisories, separation of the COVID-positive RDM from her newborn at birth, providers' tendency to minimize contact duration and frequency with COVID-positive mothers, compromised counseling on breastfeeding, logistic difficulties in expression and transportation of COVID-positive mother's milk to her baby in the nursery, COVID restrictions, staff shortage and unavailable family support in wards and nursery, and inadequate infrastructure were identified as major barriers. Keeping the RDM-newborn together, harmonization of standard operating procedures between professional associations and within and between departments, strategic mobilization of resources, optimization of human resources, strengthening client-provider interaction, risk triaging, leveraging technology, and leadership-in-crisis-situations were notable enablers. Conclusion: The separation of the RDM and newborn led to a cascade of disruptions to newborn care and breastfeeding practices in the study institutions. Separating the newborn from the mother should be avoided during public health emergencies unless there is robust evidence favoring the same; routine institutional practices should be family centered.

Nurturing Beyond the Womb - Early Intervention Practices in Newborn Care Unit.

The survival of small and sick babies has increased over the last two decades, though at the cost of increasing the burden of neuro-morbidities. Early intervention (EI) capitalises on the unique characteristic of neuroplasticity that ameliorates the effect of insult to the developing brain during fetal and early infancy period. EI provides positive sensorimotor experiences and promotes neuro-behavioural maturation which can greatly mitigate adverse outcomes for these at-risk babies. EI includes nurturing care delivered through the antenatal period continuing into a developmentally supportive environment and family centred care for the small and sick baby in the new-born care unit and continuing up to 3 years of life. Although the concept is now well understood, these practices still lack consistency and standardization across the units.

Foley catheter with noble metal alloy coating for preventing catheter-associated urinary tract infections: a large, multi-center clinical trial.

BACKGROUND: Catheter-associated urinary tract infections (CAUTI) are among the most frequent healthcare-associated infections in the world. They are associated with increased mortality, prolonged hospital stay and increased healthcare costs. The objective of this study was to evaluate the efficacy of the noble metal alloy (NMA) coated BIP Foley Catheter in preventing the incidence of symptomatic CAUTI in a large cohort of patients in India. METHODS: This multi-center, prospective study included 1000 adult patients admitted to six hospitals across India for urology, surgery and ICU requiring urethral catheterization and admission for ≥ 48 h. Patients were allocated to the NMA-coated BIP Foley Catheter group or a non-coated control catheter group, with a randomization ratio of 3:1. CAUTI surveillance was conducted at study entry, upon catheter removal, and 2 days after catheter removal. For statistical analysis, categorical data (e.g. gender) were compared using the chi-square or Fischer test, and numerical data were compared using the two-sample t-test. Associations were evaluated using logistic regression. RESULTS AND CONCLUSIONS: The incidence of symptomatic CAUTI was reduced by 69% in the BIP Foley Catheter group compared to the control group (6.5 vs 20.8 CAUTI/1000 catheter days), with an incidence rate ratio of 0.31 (95% confidence interval: 0.21-0.46; p < 0.001). A reduction in the cumulative CAUTI incidence was evident in the BIP Foley Catheter group within 3 days after catheterization; this reduction was maintained up to ~ 30 days, and the largest reductions were seen between 3 and 11 days. There were no serious adverse events related to either catheter, and the percentage of patients with ≥ 1 adverse event was significantly lower in the NMA-coated BIP Foley Catheter group than in the control group (21.6% vs. 48.4%; p = 0.001). In conclusion, the NMA-coated BIP Foley Catheter was effective in reducing CAUTI and was well tolerated, with a lower incidence of adverse events compared to the uncoated catheter. Trial registration This study was registered prospectively (28 September 2015) in the Clinical Trials Registry of India (trial number CTRI/2015/09/006220; http://ctri.nic.in/Clinicaltrials/showallp.php?mid1=12631&EncHid=&userName=bactiguard ).

Familial Hemophagocytic Lymphohistiocytosis: A Rare Mutation of STXBP2 in Exon 19.

Familial hemophagocytic lymphohistiocytosis (FHLH) is a fulminant rapidly progressive disorder characterized by uncontrolled immune system activation. Over the last decade, STXBP2 mutations have been reported as causative. We report a baby with typical clinical features and supportive laboratory findings, who had a homozygous missense variation in exon 19 of STXBP2 that results in an amino acid substitution of aspartic acid for glycine. Adding to the currently scant literature on this variation may contribute to the database pool and help to confirm assertion of pathogenicity in FHLH.

Negative Pressure Wound Therapy With Instillation and Dwell Time and Standard Negative Pressure Wound Therapy in Complex Wounds: Are They Complementary or Competitive?

INTRODUCTION: Advanced wound management of complex surgical wounds remains a significant challenge as more patients are being admitted to the hospital with infected wounds. Reducing recurrent infections and promoting granulation tissue formation are essential to overall wound healing. Negative pressure wound therapy (NPWT) has been widely practiced for 2 decades for the management of such wounds, but NPWT with instillation and dwell time (NPWTi-d) is a relatively recent adjunctive treatment of wounds that require serial debridements. OBJECTIVE: This study evaluates the advantages and disadvantages of NPWTi-d alone as well as NPWTi-d as an adjunct to standard NPWT in the treatment of complex wounds in patients with serious comorbidities. MATERIALS AND METHODS: In this case series, the NPWTi-d group was given instillation therapy only. In the combined group, instillation therapy was applied and then, as the bioburden in the wound decreased, NPWT therapy was substituted. Repeated volumetric measurements and photographs of the wounds were taken. An approximate 50% decrease in wound dimensions, clearance of slough and necrotic tissue, and the appearance of healthy granulation tissue in the wound bed were considered as the endpoint of therapy. RESULTS: Four cases in which only NPWTi-d was applied reached the endpoint with 1 to 3 dressings. In the other 4 cases, after NPWTi-d was applied, the bioburden was reduced to a great extent but the wound did not reach the end point. There were a few episodes of troubleshooting (eg, leakage alarm and blocking of the drainage tubes) in the system, and surrounding skin showed maceration. Hence, 2 to 4 courses of NPWT were substituted for the wound to reach the endpoint. CONCLUSIONS: In this study, NPWTi-d proved to be more effective in clearing the bioburden and reducing the number of surgeries for debridement. Complementing it with NPWT led to reduced episodes of troubleshooting and proved to be more cost-effective. Thus, NPWT may be considered as an adjunct therapy in select cases of complex wounds. However, more evidence is required.

Outcome of Very Preterm Infants With Early Optimal Nutrition Strategy: A Comparative Cohort Study.

BACKGROUND: Aggressive nutrition may benefit early growth; nevertheless, effects on neurodevelopmental outcomes are unclear. We planned a descriptive analytical study to compare survival without neurodevelopment disability (NDD) at 1 year in 2 groups during 2 time epochs-before and after implementation of early optimal nutrition strategies. NDD was defined as any one of the following: mental and/or motor development quotient < 85 at 12 months of age, corrected for prematurity; Denver Developmental Screening Test abnormal/suspect in even 1 domain out of the 4 domains; seizures; requirement of hearing aid; or blindness in 1 or both eyes. We also compared mortality, survival without bronchopulmonary dysplasia, necrotizing enterocolitis (NEC), retinopathy of prematurity (ROP), intraventricular hemorrhage, periventricular leukomalacia, sepsis, metabolic bone disease (MBD), and extrauterine growth restriction (EUGR). METHODS: Preterm neonates born between 27 and 32 weeks' gestation were included. The prospective study group (AO) was recruited after implementation of early optimal nutrition policy. The comparative retrospective cohort (BO) received nutrition based on clinicians' decisions. Both groups were followed up using a structured plan till 1 year corrected age. RESULTS: 137 neonates were enrolled in AO and 151 in the BO cohort. There was no statistically significant difference in survival without NDD at 1 year-75.5% in AO vs 72.1% in BO, odds ratio 0.84 (95% CI 0.5-1.6). Babies who received early optimal nutrition had less NEC, EUGR, and ROP requiring laser therapy but more MBD. CONCLUSION: There was no difference in survival without NDD in early optimal nutrition cohort compared to the cohort before implementation of the nutrition strategy. Short-term benefits themselves may justify the need for early optimal nutrition.

Asparagus racemosus bZIP transcription factor-regulated squalene epoxidase (ArSQE) promotes germination and abiotic stress tolerance in transgenic tobacco.

A. racemosus is a rich source of pharmacologically active steroidal saponins. Most of the studies are related to its chemistry and pharmacology, but the pathway involved in the biosynthesis of steroidal saponin is not much emphasized. Squalene epoxidase acts as a rate-limiting enzyme in this biosynthesis. In this study, we have selected root specific squalene epoxidase ArSQE from A. racemosus for its characterization. ArSQE was able to complement ergosterol auxotrophy in erg1 yeast mutants. Mutants were sensitive to the antifungal drug terbinafine, whereas ArSQE complementation made them tolerant to the same drug. ArSQE plays a significant role in early germination in transgenic tobacco. The transgenic tobacco seedlings overexpressing ArSQE were tolerant to terbinafine and abiotic stress. Expression analysis of transcripts in ArSQE transgenic lines suggests that it mostly affects ABA, GA, stress, and sterol related functions in transgenic tobacco. Further, root specific MeJA responsive A. racemosus bZIP transcription factors (TFs), ArTGA1 and ArTGA2, were identified that bind to MeJA responsive cis-element present in the promoter region of ArSQE. Characterization of ArSQE of A. racemosus provides new information about its regulation through MeJA responsive bZIP TF along with its role in the development and abiotic stress response in transgenic tobacco.

Retrograde response by reactive oxygen/nitrogen species in plants involving different cellular organelles.

During oxidative and nitrosative stress conditions cellular organelles convey information to the nucleus to express specific sets of genes to withstand the stress condition and to reorganize their growth and developmental pattern. This organelle to nucleus communication is termed retrograde signaling. In the plant system chloroplast and peroxisomes are mainly involved with little involvement of mitochondria and other organelles in oxidative stress-mediated retrograde signaling. In this review, we will discuss retrograde signaling in plant systems with factors that regulate this signaling cascade.

Recent advances in steroidal saponins biosynthesis and in vitro production.

MAIN CONCLUSION: Steroidal saponins exhibited numerous pharmacological activities due to the modification of their backbone by different cytochrome P450s (P450) and UDP glycosyltransferases (UGTs). Plant-derived steroidal saponins are not sufficient for utilizing them for commercial purpose so in vitro production of saponin by tissue culture, root culture, embryo culture, etc, is necessary for its large-scale production. Saponin glycosides are the important class of plant secondary metabolites, which consists of either steroidal or terpenoidal backbone. Due to the existence of a wide range of medicinal properties, saponin glycosides are pharmacologically very important. This review is focused on important medicinal properties of steroidal saponin, its occurrence, and biosynthesis. In addition to this, some recently identified plants containing steroidal saponins in different parts were summarized. The high throughput transcriptome sequencing approach elaborates our understanding related to the secondary metabolic pathway and its regulation even in the absence of adequate genomic information of non-model plants. The aim of this review is to encapsulate the information related to applications of steroidal saponin and its biosynthetic enzymes specially P450s and UGTs that are involved at later stage modifications of saponin backbone. Lastly, we discussed the in vitro production of steroidal saponin as the plant-based production of saponin is time-consuming and yield a limited amount of saponins. A large amount of plant material has been used to increase the production of steroidal saponin by employing in vitro culture technique, which has received a lot of attention in past two decades and provides a way to conserve medicinal plants as well as to escape them for being endangered.

Comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri identifies potential genes related to triterpenoid saponin biosynthesis.

BACKGROUND: Bacopa monnieri commonly known as Brahmi is utilized in Ayurveda to improve memory and many other human health benefits. Bacosides enriched standardized extract of Bacopa monnieri is being marketed as a memory enhancing agent. In spite of its well known pharmacological properties it is not much studied in terms of transcripts involved in biosynthetic pathway and its regulation that controls the secondary metabolic pathway in this plant. The aim of this study was to identify the potential transcripts and provide a framework of identified transcripts involved in bacosides production through transcriptome assembly. RESULTS: We performed comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri in two independent biological replicate and obtained 22.48 million and 22.0 million high quality processed reads in shoot and root respectively. After de novo assembly and quantitative assessment total 26,412 genes got annotated in root and 18,500 genes annotated in shoot sample. Quality of raw reads was determined by using SeqQC-V2.2. Assembled sequences were annotated using BLASTX against public database such as NR or UniProt. Searching against the KEGG pathway database indicated that 37,918 unigenes from root and 35,130 unigenes from shoot were mapped to 133 KEGG pathways. Based on the DGE data we found that most of the transcript related to CYP450s and UDP-glucosyltransferases were specifically upregulated in shoot tissue as compared to root tissue. Finally, we have selected 43 transcripts related to secondary metabolism including transcription factor families which are differentially expressed in shoot and root tissues were validated by qRT-PCR and their expression level were monitored after MeJA treatment and wounding for 1, 3 and 5 h. CONCLUSIONS: This study not only represents the first de novo transcriptome analysis of Bacopa monnieri but also provides information about the identification, expression and differential tissues specific distribution of transcripts related to triterpenoid sapogenin which is one of the most important pharmacologically active secondary metabolite present in Bacopa monnieri. The identified transcripts in this study will establish a foundation for future studies related to carrying out the metabolic engineering for increasing the bacosides biosynthesis and its regulation for human health benefits.

Comparative transcriptome analysis reveals candidate genes for the biosynthesis of natural insecticide in Tanacetum cinerariifolium.

BACKGROUND: Pyrethrins are monoterpenoids and consist of either a chrysanthemic acid or pyrethric acid with a rethrolone moiety. Natural pyrethrins are safe and eco-friendly while possessing strong insecticidal properties. Despite such advantages of commercial value coming with the eco-friendly tag, most enzymes/genes involved in the pyrethrin biosynthesis pathway remain unidentified and uncharacterized. Since the flowers of Tanacetum cinerariifolium are rich in major pyrethrins, next generation transcriptome sequencing was undertaken to compare the flowers and the leaves of the plant de novo to identify differentially expressed transcripts and ascertain which among them might be involved in and responsible for the differential accumulation of pyrethrins in T. cinerariifolium flowers. RESULTS: In this first tissue specific transcriptome analysis of the non-model plant T. cinerariifolium, a total of 23,200,000 and 28,500,110 high quality Illumina next generation sequence reads, with a length of 101 bp, were generated for the flower and leaf tissue respectively. After functional enrichment analysis and GO based annotation using public protein databases such as UniRef, PFAM, SMART, KEGG and NR, 4443 and 8901 unigenes were identified in the flower and leaf tissue respectively. These could be assigned to 13344 KEGG pathways and the pyrethrin biosynthesis contextualized. The 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was involved in the biosynthesis of acid moiety of pyrethrin and this pathway predominated in the flowers as compared to the leaves. However, enzymes related to oxylipin biosynthesis were found predominantly in the leaf tissue, which suggested that major steps of pyrethrin biosynthesis occurred in the flowers. CONCLUSIONS: Transcriptome comparison between the flower and leaf tissue of T. cinerariifolium provided an elaborate list of tissue specific transcripts that was useful in elucidating the differences in the expression of the biosynthetic pathways leading to differential presence of pyrethrin in the flowers. The information generated on genes, pathways and markers related to pyrethrin biosynthesis in this study will be helpful in enhancing the production of these useful compounds for value added breeding programs. Related proteome comparison to overlay our transcriptome comparison can generate more relevant information to better understand flower specific accumulation of secondary metabolites in general and pyrethrin accumulation in particular.

The Role of Strigolactones and Their Potential Cross-talk under Hostile Ecological Conditions in Plants.

The changing environment always questions the survival mechanism of life on earth. The plant being special in the sense of their sessile habit need to face many of these environmental fluctuations as they have a lesser escape option. To counter these adverse conditions, plants have developed efficient sensing, signaling, and response mechanism. Among them the role of phytohormones in the management of hostile ecological situations is remarkable. The strigolactone, a newly emerged plant hormone has been identified with many functions such as growth stimulant of parasitic plants, plant architecture determinant, arbuscular mycorrhiza symbiosis promoter, and also in many other developmental and environmental cues. Despite of their immense developmental potential, the strigolactone research in the last few years has also established their significance in adverse environmental condition. In the current review, its significance under drought, salinity, nutrient starvation, temperature, and pathogenic assail has been discussed. This review also opens the research prospects of strigolactone to better manage the crop loss under hostile ecological conditions.

De novo leaf and root transcriptome analysis identified novel genes involved in steroidal sapogenin biosynthesis in Asparagus racemosus.

BACKGROUND: Saponins are mainly amphipathic glycosides that posses many biological activities and confer potential health benefits to humans. Inspite of its medicinal attributes most of the triterpenes and enzymes involved in the saponin biosynthesis remains uncharacterized at the molecular level. Since the major steroidal components are present in the roots of A. racemosus our study is focussed on the comparative denovo transcriptome analysis of root versus leaf tissue and identifying some root specific transcripts involved in saponin biosynthesis using high-throughput next generation transcriptome sequencing. RESULTS: After sequencing, de novo assembly and quantitative assessment, 126861 unigenes were finally generated with an average length of 1200 bp. Then functional annotation and GO enrichment analysis was performed by aligning all-unigenes with public protein databases including NR, SwissProt, and KEGG. Differentially expressed genes in root were initially identified using the RPKM method using digital subtraction between root and leaf. Twenty seven putative secondary metabolite related transcripts were experimentally validated for their expression in root or leaf tissue using q-RT PCR analysis. Most of the above selected transcripts showed preferential expression in root as compared to leaf supporting the digitally subtracted result obtained. The methyl jasmonate application induces the secondary metabolite related gene transcripts leading to their increased accumulation in plants. Therefore, the identified transcripts related to saponin biosynthesis were further analyzed for their induced expression after 3, 5 and 12 hours of exogenous application of Methyl Jasmonate in tissue specific manner. CONCLUSIONS: In this study, we have identified a large set of cDNA unigenes from A. racemosus leaf and root tissue. This is the first transcriptome sequencing of this non-model species using Illumina, a next generation sequencing technology. The present study has also identified number of root specific transcripts showing homology with saponin biosynthetic pathway. An integrated pathway of identified saponin biosynthesis transcripts their tissue specific expression and induced accumulation after methyl jasmonate treatment was discussed.

Identification, occurrence, and validation of DRE and ABRE Cis-regulatory motifs in the promoter regions of genes of Arabidopsis thaliana.

Plants posses a complex co-regulatory network which helps them to elicit a response under diverse adverse conditions. We used an in silico approach to identify the genes with both DRE and ABRE motifs in their promoter regions in Arabidopsis thaliana. Our results showed that Arabidopsis contains a set of 2,052 genes with ABRE and DRE motifs in their promoter regions. Approximately 72% or more of the total predicted 2,052 genes had a gap distance of less than 400 bp between DRE and ABRE motifs. For positional orientation of the DRE and ABRE motifs, we found that the DR form (one in direct and the other one in reverse orientation) was more prevalent than other forms. These predicted 2,052 genes include 155 transcription factors. Using microarray data from The Arabidopsis Information Resource (TAIR) database, we present 44 transcription factors out of 155 which are upregulated by more than twofold in response to osmotic stress and ABA treatment. Fifty-one transcripts from the one predicted above were validated using semiquantitative expression analysis to support the microarray data in TAIR. Taken together, we report a set of genes containing both DRE and ABRE motifs in their promoter regions in A. thaliana, which can be useful to understand the role of ABA under osmotic stress condition.