Plant genomes contain large numbers of cell surface leucine-rich repeat (LRR) and intracellular nucleotide binding (NB)-LRR immune receptors encoded by resistance (R) genes that recognize specific pathogen effectors and trigger resistance responses. The unregulated expression of NB-LRR genes can trigger autoimmunity in the absence of pathogen infection and inhibit plant growth. Despite the potential serious consequence on agricultural production, the mechanisms regulating R-gene expression are not well understood. We identified microRNA (miRNA) progenitor genes precursor transcripts, and two miRNAs [nta-miR6019 (22-nt) and ntamiR6020 (21-nt)] that guide cleavage of transcripts of the Toll and Interleukin-1 receptor-NB-LRR immune receptor N from tobacco that confers resistance to tobacco mosaic virus (TMV). We further showed that cleavage by nta-miR6019 triggers RNA-dependent RNA polymerase 6-and ribonuclease Dicer-like 4-dependent biogenesis of 21-nt secondary siRNAs "in phase" with the 22-nt miR6019 cleavage site. Furthermore, we found that processing of the 22-nt nta-miR6019 depended on an asymmetric bulge caused by mismatch in the nta-miR6019 precursor. Interestingly, coexpression of N with nta-miR6019 and nta-miR6020 resulted in attenuation of N-mediated resistance to TMV, indicating that these miRNAs have functional roles in NB-LRR regulation. Using a bioinformatics approach, we identified six additional 22-nt miRNA and two 21-nt miRNA families from three Solanaceae species-tobacco, tomato, and potato. We show that members of these miRNA families cleave transcripts of predicted functional R genes and trigger production of phased secondary 21-nt siRNAs. Our results demonstrate a conserved role for miRNAs and secondary siRNAs in NB-LRR/LRR immune receptor gene regulation and pathogen resistance in Solanaceae.

No abstract

MicroRNAs (miRNAs) are important regulators of gene expression and have great potential as biomarkers, prognostic indicators, and therapeutic targets. Determining the expression patterns of these molecules is essential for elucidating their biogenesis, regulation, relation to disease, and response to therapy. Although PCR-based assays are commonly used for expression profiling of miRNAs, the small size, sequence heterogeneity, and (in some cases) end modifications of miRNAs constrain the performance of existing PCR methods. Here we introduce miR-ID, a novel method that avoids these constraints while providing superior sensitivity and sequence specificity at a lower cost. It also has the unique ability to differentiate unmodified small RNAs from those carrying 29-OMe groups at their 39-ends while detecting both forms. miR-ID is comprised of the following steps: (1) circularization of the miRNA by a ligase; (2) reverse transcription of the circularized miRNA (RTC), producing tandem repeats of a DNA sequence complementary to the miRNA; and (3) qPCR amplification of segments of this multimeric cDNA using 59-overlapping primers and a nonspecific dye such as SYBR Green. No chemically modified probes (e.g., TaqMan) or primers (e.g., LNA) are required. The circular RNA and multimeric cDNA templates provide unmatched flexibility in the positioning of primers, which may include straddling the boundaries between these repetitive miRNA sequences. miR-ID is based on new findings that are themselves of general interest, including reverse transcription of small RNA circles and the use of 59-overlapping primers for detection of repetitive sequences by qPCR.

Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)—microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker “retinoic acid” in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5′–AGGTCA–3′) in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and embryological features are in favor of our hypothesis, additional studies including animal models are warranted to validate our proposition. Such studies are likely to unfold ZIKV-microcephaly association and may help in devising methods to combat it.

Bacterial blight caused by Xanthomonas axonopodis pv. punicae is a major disease of pomegranate. Bacterial blight drastically reduces the yield and quality of fruits, which are critical for pomegranate production. Precise and early diagnosis of bacterial blight is crucial for active surveillance and effective management of the disease. Symptoms based disease diagnostic methods are labor-intensive, time-consuming and may not detect disease on asymptomatic plants. DNA-based disease diagnostics using polymerase chain reaction (PCR) are reliable, precise, accurate and quick. PCR coupled with agarose gel electrophoresis (PCR-AGE), PCR coupled with capillary electrophoresis (PCR-CE) and real-time PCR (qPCR) were applied for the early and accurate diagnosis of bacterial blight in pomegranate. PCR-CE and qPCR were capable of diagnosing bacterial blight 6 to 10 days before symptom appearance, with detection limits of 100 fg and 10 fg of bacterial DNA respectively. However, conventional PCR-AGE detected pathogen at the onset of disease symptoms with a detection limit of 10 pg of bacterial DNA. qPCR detected bacterial blight in orchards that did not show any disease symptoms. Our data demonstrate that qPCR is more sensitive than other PCR methods along with being reliable for early diagnosis.

The present study was conducted to document the rearing practices of village chicken production in the Northern midlands, agro-ecological zone comprising Kannur and Kozhikode districts of Kerala state, India. Data was generated from 65 and 63 chicken farming families of Kozhikode and Kannur districts respectively. The system of chicken rearing is extensive, with the provision of shelter only during the night. The birds are being managed mostly by women (89.06%). The decision on the sale of birds and eggs is made by women and the proceeds of sales go directly to them. It was found that as many as 43.75% of the chicken farmers in these areas have no other animal husbandry activities. The average flock size is 5.62 birds. Natural incubation using locally available materials as a nest box and sand as the nesting material is the common practice. The average number of eggs set under the broody hen for hatching is 10.41. Chicken coops are placed at an average distance of 5.45m from the house and elevated 0.39 m from the ground. The average floor area of the coops is 0.757 m 2 and the night shelter provided per bird is 830.39 cm 2 . The walls and floor of the coops are made of wood and the roof with tiles or thatch in most of cases. Rice grain is commonly fed as supplementary feed with mostly no specific timing in feeding. Farmers depend on an array of herbs rather than chemotherapeutic agents and vaccines for the treatment and control of diseases. Most of the surplus males (59.38%) are discarded before one year of age, whereas females are less commonly culled (21.87%). The average culling age of males and females was 11.05 and 36.64 months, respectively. It was discovered that as high as 52.15% of the eggs and 59.38% of the cockerels produced are consumed in the

Background: The etiology of schizophrenia is extensively debated, and multiple factors have been contended to be involved. A panoramic view of the contributing factors in a genome-wide study can be an effective strategy to provide a comprehensive understanding of its causality. Materials and Methods: GSE53987 dataset downloaded from GEO-database, which comprised mRNA expression data of post-mortem brain tissue across three regions from control (C) and age-matched subjects (T) of schizophrenia (N = Hippocampus [HIP]: C-15, T-18, Prefrontal cortex [PFC]: C-15, T-19, Associative striatum [STR]: C-18, T-18). Bio-conductor-affy-package used to compute mRNA expression, and further t-test applied to investigate differential gene expression. The analysis of the derived genes performed using the PANTHER Classification System and NCBI database. Further, a protein interactome analysis of the derived gene set was performed using STRING v10 database (https://string-db.org/). Results: A set of 40 genes showed significantly altered (p < 0.01) expression across all three brain regions. The analyses unraveled genes implicated in biological processes and events, and molecular pathways relating basic neuronal functions. Conclusions: The aberrant expression of genes maintaining basic cell machinery explains compromised neuronal processing in SCZ.

A survey to document the behaviour characteristics and mortality pattern of indigenous chicken of Kerala and a field egg recording study to record egg production characteristics of these birds were conducted. Flight distance and height was 13.29 and 3.97 m, respectively. The territory radius of cocks was 121.15 m. The chick survivability at 4 weeks of age was 64.98 percent. The day-old and 8 th week body weights were 28.83 and 347.24 g, respectively. The 20 th and 40 th week body weight of males were 1,428.42 and 1,936.67 g and that of females were 1,114.04 and 1,445.63 g, respectively. The mortality up to 72 weeks was 69.38 percent and major cause of mortality during chick, grower and layer stage were mongoose (44.63 percent), wolf (24.29 percent) and diseases (52.18 percent) respectively. The fertility was 71.22 percent and hatchability on total and fertile egg set were 62.26 and 87.42 percent, respectively. There were 2.13 clutches in a laying cycle with inter-clutch intervals of 1.11 days. The average clutch size and number of eggs per cycle were 7.27 and 14.32, respectively. The egg number up to 72 weeks on hen-day and hen-housed basis was 116.81 and 85.84, respectively and the eggs were laid in 7.7 cycles. The age at first egg and average age at sexual maturity were 155 and 199.26 days, respectively. The egg weight at 28, 40 and 72 weeks of age was 37.80, 40.74 and 43.31 g, respectively, and egg mass per bird was 4,659.04 g. The broodiness and incubation pause were 26.03 and 121.75 days, respectively.