Time-course transcriptome analysis identifies rewiring patterns of transcriptional regulatory networks in rice under Rhizoctonia solani infection.

Sheath Blight (SB) disease in rice is caused by the infection from the fungal pathogen Rhizoctonia solani (R. solani). SB is one of the most severe rice diseases that can cause up to 50% yield losses in rice. Naturally occurring rice varieties resistant to SB have not been reported yet. We have performed a Time-Series RNA-Seq analysis on a widely cultivated rice variety BPT-5204 for identifying transcriptome level response signatures during R. solani infection at 1st, 2nd and 5th day post infection (dpi). In total, 428, 3225 and 1225 genes were differentially expressed in the treated rice plants on 1, 2 and 5 dpi, respectively. GO and KEGG enrichment analysis identified significant processes and pathways differentially altered in the rice plants during the fungal infection. Machine learning and network based integrative approach was used to construct rice Transcriptional Regulatory Networks (TRNs) for the three time points. TRN analysis identified SUB1B, MYB30 and CCA1 as important regulatory hub transcription factors in rice during R. solani infection. Jasmonic acid, salicylic acid, ethylene biogenesis and signaling were induced on infection. SAR was up regulated, while photosynthesis and carbon fixation processes were significantly down regulated. Involvement of MAPK, CYPs, peroxidase, PAL, chitinase genes were also observed in response to the fungal infection. The integrative analysis identified seven putative SB resistance genes differentially regulated in rice during R. solani infection.

Transcriptomic data of MCF-7 breast cancer cells treated with G1, a G-protein coupled estrogen receptor (GPER) agonist.

Besides short-term non-genomic effects, the G-protein coupled estrogen receptor (GPER) also mediates long-term genomic effects of estrogen. The genomic effects of GPER activation are not completely understood. G1 is a selective GPER agonist, which is popularly used for addressing the effects of GPER activation. Here, we present transcriptomic (RNA-seq) data on MCF-7 cells treated with 100 nM, or 1 µM G1 for a period of 48 h. The data are available from GEO (accession number GSE188706).

Advances in flux balance analysis by integrating machine learning and mechanism-based models.

The availability of multi-omics data sets and genome-scale metabolic models for various organisms provide a platform for modeling and analyzing genotype-to-phenotype relationships. Flux balance analysis is the main tool for predicting flux distributions in genome-scale metabolic models and various data-integrative approaches enable modeling context-specific network behavior. Due to its linear nature, this optimization framework is readily scalable to multi-tissue or -organ and even multi-organism models. However, both data and model size can hamper a straightforward biological interpretation of the estimated fluxes. Moreover, flux balance analysis simulates metabolism at steady-state and thus, in its most basic form, does not consider kinetics or regulatory events. The integration of flux balance analysis with complementary data analysis and modeling techniques offers the potential to overcome these challenges. In particular machine learning approaches have emerged as the tool of choice for data reduction and selection of most important variables in big data sets. Kinetic models and formal languages can be used to simulate dynamic behavior. This review article provides an overview of integrative studies that combine flux balance analysis with machine learning approaches, kinetic models, such as physiology-based pharmacokinetic models, and formal graphical modeling languages, such as Petri nets. We discuss the mathematical aspects and biological applications of these integrated approaches and outline challenges and future perspectives.

A clinico-radiological study of bicondylar tibial plateau fractures managed with dual locking plates.

BACKGROUND: Treatment of bicondylar intra-articular tibial plateau fractures due to high energy trauma is complex and highly prone to complications due to fracture patterns and extensive soft tissue damage. AIM: The study's objective was to evaluate the clinical, radiological and functional outcome, including the complications in closed Schatzker type V and VI tibial plateau fractures managed with dual locking plates using less extensile approaches and indirect reduction techniques. MATERIALS AND METHODS: Thirty-four patients of closed Schatzker Type V and VI treated with pre-contoured locking plates were evaluated clinically and radiologically. Dual plating was done using a less extensile anterolateral approach for lateral plate and medial/open posteromedial approach for medial plate. Functional results were evaluated using the Knee Society Score (KSS) and radiological results by the Modified Rasmussen score (MRS) for radiological assessment. RESULTS: The mean age of patients in our study was 45 years (range = 26-60 years) with a male predominance of 84.4%. The average time difference between trauma and surgery was 7.6 days (range = 5-14 days) with an average length of hospital stay of 8.5 days (range = 7-18 days). Autologous bone grafting from the iliac crest was done in 10 patients (29.4%) with a sizeable metaphyseal void. The study has a mean follow-up period of 22.6 months. The complete union was seen at an average of 17.4 weeks. The average knee ROM at the last follow-up was 110.75°. Three patients had complications, 2 with wound dehiscence and 1 with deep infection. CONCLUSION: Internal fixation with dual locking plates is biomechanically strong and stable and gives excellent to good functional outcomes. However, the timing of internal fixation is essential in such complex injuries to prevent soft tissue complications and failure. The use of rigid fixation by less extensile approaches and indirect reduction techniques helps prevent wound healing problems and allows early knee mobilization.

Temperature differentially modulates the transcriptome response in Oryza sativa to Xanthomonas oryzae pv. oryzae infection.

Bacterial blight is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Genome scale integrative analysis on the interaction of high and low temperatures on the molecular response signature in rice during the Xoo infection has not been conducted yet. We have analysed a unique RNA-Seq dataset generated on the susceptible rice variety IR24 under combined exposure of Xoo with low 29/21 °C (day/night) and high 35/31 °C (day/night) temperatures. Differentially regulated key genes and pathways in rice plants during both the stress conditions were identified. Differential dynamics of the regulatory network topology showed that WRKY and ERF families of transcription factors play a crucial role during signal crosstalk events in rice plants while responding to combined exposure of Xoo with low temperature vs. Xoo with high temperatures. Our study suggests that upon onset of high temperature, rice plants tend to switch its focus from defence response towards growth and reproduction.

Integrative network analysis identifies differential regulation of neuroimmune system in Schizophrenia and Bipolar disorder.

Background: Neuropsychiatric disorders such as Schizophrenia (SCZ) and Bipolar disorder (BPD) pose a broad range of problems with different symptoms mainly characterized by some combination of abnormal thoughts, emotions, behaviour, etc. However, in depth molecular and pathophysiological mechanisms among different neuropsychiatric disorders have not been clearly understood yet. We have used RNA-seq data to investigate unique and overlapping molecular signatures between SCZ and BPD using an integrative network biology approach. Methods: RNA-seq count data were collected from NCBI-GEO database generated on post-mortem brain tissues of controls (n = 24) and patients of BPD (n = 24) and SCZ (n = 24). Differentially expressed genes (DEGs) were identified using the consensus of DESeq2 and edgeR tools and used for downstream analysis. Weighted gene correlation networks were constructed to find non-preserved (NP) modules for SCZ, BPD and control conditions. Topological analysis and functional enrichment analysis were performed on NP modules to identify unique and overlapping expression signatures during SCZ and BPD conditions. Results: We have identified four NP modules from the DEGs of BPD and SCZ. Eleven overlapping genes have been identified between SCZ and BPD networks, and they were found to be highly enriched in inflammatory responses. Among these eleven genes, TNIP2, TNFRSF1A and AC005840.1 had higher sum of connectivity exclusively in BPD network. In addition, we observed that top five genes of NP module from SCZ network were downregulated which may be a key factor for SCZ disorder. Conclusions: Differential activation of the immune system components and pathways may drive the common and unique pathogenesis of the BPD and SCZ.

A prospective study to evaluate the efficacy of ultrasound-guided ganglion impar block in patients with chronic perineal pain.

BACKGROUND: The blockade of the ganglion impar has been described to relieve the intractable perineal pain of sympathetic origin in patients with coccydynia. Chronic perineal pain (CPP) has been effectively managed by ganglion impar block. The feasibility, safety, and efficacy of ultrasound (US)-guided ganglion impar block by transsacrococcygeal approach was analyzed in the present study. METHODS: A total of 15 patients with CPP were administered US-guided ganglion impar block using out of plane approach. Patients were followed for VAS and quality of life using Karnofsky performance status (KS), Linear Analog Scale Assessment (LASA), and constipation score up to 2 months at different time intervals. Time required to perform the procedure, number of attempts, and any complications were also noted. RESULTS: The mean time required to perform the procedure was 7.67 ± 1.23 min. There were no adverse events. All the patients had significant pain relief during 2 month follow-up (P < 0.05 compared to baseline VAS). The KS and LASA score improved post block which was statistically significant. The dose of nonsteroidal anti-inflammatory drugs (NSAIDS) decreased from preblock state with statistically significant difference, while the difference in dose of tramadol and morphine was statistically insignificant. CONCLUSION: US-guided ganglion impar block is technically feasible and safe technique. USG can be used to locate sacrococcygeal junction (SCJ) and facilitate the performance of ganglion impar block. The efficacy and safety of the US-guided ganglion impar blockades needs a proper evaluation in the randomized controlled trials.