Beet Soil-Borne Virus Is a Helper Virus for the Novel Beta vulgaris Satellite Virus 1A

Sugar beet (Beta vulgaris) is grown in temperate regions around the world as a source of sucrose used for natural sweetening. Sugar beet is susceptible to a number of viral diseases, but identification of the causal agent(s) under field conditions is often difficult due to mixtures of viruses that may be responsible for disease symptoms. In this study, the application of RNAseq to RNA extracted from diseased sugar beet roots obtained from the field and from greenhouse-reared plants grown in soil infested with the virus disease rhizomania (causal agent beet necrotic yellow vein virus; BNYVV) yielded genome-length sequences from BNYVV, as well as beet soil-borne virus (BSBV). The nucleotide identities of the derived consensus sequence of BSBV RNAs ranged from 99.4 to 96.7% (RNA1), 99.3 to 95.3% (RNA2), and 98.3 to 95.9% (RNA3) compared with published BSBV sequences. Based on the BSBV genome consensus sequence, clones of the genomic RNAs 1, 2, and 3 were obtained to produce RNA copies of the genome through in vitro transcription. Capped RNA produced from the clones was infectious when inoculated into leaves of Chenopodium quinoa and B. vulgaris, and extracts from transcript-infected C. quinoa leaves could infect sugar beet seedling roots through a vortex inoculation method. Subsequent exposure of these infected sugar beet seedling roots to aviruliferous Polymyxa betae, the protist vector of both BNYVV and BSBV, confirmed that BSBV derived from the infectious clones could be transmitted by the vector. Co-inoculation of BSBV synthetic transcripts with transcripts of a cloned putative satellite virus designated Beta vulgaris satellite virus 1A (BvSat1A) resulted in the production of lesions on leaves of C. quinoa similar to those produced by inoculation with BSBV alone. Nevertheless, accumulation of genomic RNA and the encoded protein of the satellite virus in co-inoculated leaves was readily detected on Northern and Western blots, respectively, whereas no accumulation of satellite virus products occurred when satellite virus RNA was inoculated alone. The predicted sequence of the detected protein encoded by BvSat1A bears hallmarks of coat proteins of other satellite viruses, and virions of a size consistent with a satellite virus were observed in samples testing positive for the virus. The results demonstrate that BSBV is a helper virus for the novel satellite virus BvSat1A.

First report of Pepper yellow dwarf strain of Beet curly top virus and Spinach curly top Arizona virus in red table beet in Idaho, United States

In the fall 2021, red table beet plants (Beta vulgaris L. cv 'Eagle') exhibiting stunted growth with shorter petioles were observed at an incidence of 10 to 15 percent in a production field in Payette County, Idaho, United States. In addition to stunting, beet leaves displayed yellowing and mild curling and crumpling, and the roots exhibited hairy root symptoms (sFig.1). To identify potential causal viruses, total RNA was isolated from the leaf and root tissue using RNeasy Plant Mini Kit (Qiagen, Valencia, CA) and subjected to high-throughput sequencing (HTS). Two libraries were prepared, one for the leaf sample and another for the root sample using a ribo-minus TruSeq Stranded Total RNA Library Prep kit (Illumina, San Diego, CA). HTS was performed with 150 bp paired-end sequencing on a NovaSeq 6000 (Novogene, Sacramento, CA). Following adapter trimming and removal of host transcripts, 5.9 and 16.2 million reads were obtained from the leaf and root samples, respectively. These reads were de novo assembled using the SPAdes assembler (Bankevitch et al., 2012; Prjibelski et al., 2020). The assembled leaf sample contigs were aligned to the NCBI non-redundant database to identify contigs matching known viruses. A single contig of 2845 nts that shared 96% coverage and 95.6% sequence identity to the pepper yellow dwarf strain of beet curly top virus (BCTV-PeYD, EU921828; Varsani et al., 2014), and 98% coverage and 98.39% identity with an isolate of BCTV-PeYD (KX529650) from Mexico, was identified in the leaf sample (GenBank Accession OP477336). To validate the HTS detection of BCTV-PeYD, total DNA was isolated from the leaf sample and a 454 bp fragment of the C1 gene (replication-associate protein) was PCR amplified and Sanger sequencing of the amplicon revealed 99.7% identity to the HTS assembled BCTV-PeYD sequence. In addition to the PeYD strain of BCTV, the Worland strain of BCTV (BCTV-Wor) was detected as a single 2930 nt contig with 100% coverage and 97.3% identity to the BCTV-Wor isolate CTS14-015 (KX867045) known to infect sugar beet in Idaho. Of note, there are 11 strains of BCTV and among those, the BCTV-Wor strain induces mild symptoms in sugar beet (Strausbaugh et al., 2017), whereas BCTV-PeYD was found only in pepper from New Mexico. Further, two contigs of 2201 nts and 523 nts were assembled generating a nearly complete genome of spinach curly top Arizona virus (SpCTAV) in the leaf sample with 99% coverage and 99.3% identity (GenBank Accession OQ703946) to the reference genome of SpCTAV (HQ443515; Hernandez-Zepeda et al., 2013). To validate the HTS results, total DNA was isolated from the leaf tissue and PCR amplified a 442 bp fragment that overlaps the V1, V2, and V3 ORFs and its sequence revealed 100% identity with the HTS assembled SpCTAV. The roots sample also showed HTS reads corresponding to BCTV-PeYD and SpCTAV. In addition, beet necrotic yellow vein virus (BNYVV) was detected in the root sample with 30% coverage, but no sequence reads matching to BNYVV was detected in the leaf sample. BNYVV is known to infect sugar beet causing rhizomania (Tamada et al., 1973; Schirmer et al., 2005). To further confirm the BNYVV HTS results, total RNA was extracted separately from the root and leaf tissue, and RT-PCR was performed with primers that were designed to amplify portions of BNYVV RNAs (Weiland et al., 2020). RT-PCR analysis generated the appropriate amplicons with expected sequences corresponding to the RNA-1, RNA-2, RNA-3, and RNA-4 of BNYVV as determined by Sanger sequencing implying BNYVV the causal agent of hairy root symptoms. Similar to observations seen for BNYVV infection in conventional sugar beet varieties, no amplification was detected for BNYVV in the RNA extracted from leaf tissue, indicating that the RT-PCR results are consistent with the HTS analysis. This is the first report of BCTV-PeYD and SpCTAV observed naturally infecting red table beet in Idaho suggesting the geographical expansion of these viruses. The co-existence of BCTV-PeYD and SpCTAV with limited host range needs to be investigated to determine the actual cause of the observed foliar symptoms. This report provides the basis for further research to understand the pathogenic nature of these viruses and their potential threat to red table beet and sugar beet production in Idaho.

First report of Tomato bushy stunt virus naturally infecting sugar beet in the United States

Sugar beet (Beta vulgaris L.) is an important crop grown for its sucrose content used in sugar production around the world. Tomato bushy stunt virus (TBSV) is an RNA virus that belongs to the Tombusvirus genus of the family Tombusviridae (Hearne et al., 1990). The virus was first isolated from tomato, and it is known to infect a wide range of plants (Smith, 1935; Martelli et al., 1988; Hafez et al., 2010). In 1980, a natural infection of TBSV was reported in sugar beet leaves with chlorotic and necrotic ring spots and line pattern symptoms based on serological affinity to TBSV anti-sera in Czechoslovakia (Novak and Lanzova, 1980). In March 2021, sugarbeet plants showing stunted and bushy growth with yellowing and necrotic leaves were observed in a production field in the Imperial Valley of California. Harvested roots exhibited stunted and abnormal growth compared to roots from healthy plants (sFig. 1A). These symptoms prompted a screen for potential infection by TBSV. Root-tissue harvested from the symptomatic sugar beet was initially screened using a TBSV double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA; Agdia, Inc., Elkhart, IN), which reacted positive for TBSV. To obtain the full-length sequence of TBSV and potentially other viruses in the sample, total RNA isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) from the root-tissue was subjected to high-throughput sequencing (HTS). Libraries were prepared using the TruSeq Stranded Total RNA Library Prep kit (Illumina, San Diego, CA) and sequenced using Illumina NovoSeq 6000 paired-end platform (Novogene, Sacramento, CA). A total of 52 million reads were obtained after removing the adapters and reads mapping to the host genome. These high-quality reads were de novo assembled into 75,891 contigs that are larger than 500 base pairs using the SPAdes assembler (Bankevitch et al., 2012; Prjibelski et al., 2020). The resulting contigs were searched for matching sequences to known viruses using the NCBI non-redundant database. A single contig of 4770 nts representing the full-length genome of TBSV was generated (Accession number OP477335), which showed 100% coverage to previously reported TBSV isolates 'statice' (AJ249740.1) and 'nipplefruit' (AY579432.1) with 92.19% and 91.25% nucleotide sequence identities, respectively, and thus confirming the presence of TBSV in sugar beet root-tissue. However, it showed 74% coverage with only 87% nucleotide identity to a previously reported Lettuce necrotic stunt virus (LNSV) from sugar beet, a tombusvirus that was re-classified as Moroccan pepper virus (MPV) due to high degree (>97%) of sequence identity (Obermeier et al., 2001; Wintermantel and Anchieta, 2012; Wintermantel and Hladky, 2013). The coat protein is conserved within species in tombusvirus, and it plays a significant role by providing serological relationships to tombusvirus taxonomy. The coat protein of TBSV-isolate of this study shared 98.45% and 96.91% identities at amino acid level with TBSV 'nipplefruit' (AY579432.1) and TBSV 'statice' (AJ249740.1) isolates, respectively. In contrast, it showed only 61.56% identity with the coat protein of MPV as shown in the phylogenetic tree indicating that the TBSV-isolate reported here is different from MPV (sFig. 2). To confirm the presence of TBSV, reverse-transcription (RT)-PCR was performed using the total RNA isolated from the root-tissue with primers (VR306: 5'-CGCTCACGAGCCCAGCATCCTTGA-3' and VR297: 5'-ACACCGCCACAGGAGCCATGATTG-3') designed based on the HTS data to amplify a portion of the TBSV genome. Sequencing of the RT-PCR product confirmed the presence of TBSV sequence with 99.1% identity to the TBSV-isolate identified in this study. Further, mechanical inoculation of total RNA isolated from the symptomatic sugar beet roots produced local lesions and systemic necrosis symptoms on the leaves of Chenopodium quinoa (sFig. 1B). Sequencing of the amplicon obtained using RT-PCR with primers VR306 and VR297 confirmed the presence of TBSV in C. quinoa. In addition to TBSV, several viral contigs representing Beet necrotic yellow vein virus were identified in the root-tissue indicating mixed infection in the field. To our knowledge, this is the first report that documents the occurrence of TBSV in sugar beet in the United States. Since TBSV is a soil-borne virus, our findings indicate the need for further studies focused on the frequency and coexistence of the TBSV with BNYVV in sugar beet production fields to understand the disease complexity resulting from potential mixed infections.

CRISPR-Based Isothermal Next-Generation Diagnostic Method for Virus Detection in Sugarbeet

Rhizomania is a disease of sugarbeet caused by beet necrotic yellow vein virus (BNYVV) that significantly affects sugarbeet yield globally. Accurate and sensitive detection methods for BNYVV in plants and field soil are necessary for growers to make informed decisions on variety selection to manage this disease. A recently developed CRISPR-Cas-based detection method has proven highly sensitive and accurate in human virus diagnostics. Here, we report the development of a CRISPR-Cas12a-based method for detecting BNYVV in the roots of sugarbeet. A critical aspect of this technique is the identification of conditions for isothermal amplification of viral fragments. Toward this end, we have developed a reverse transcription (RT) recombinase polymerase amplification (RPA) for detecting BNYVV in sugarbeet roots. The RT-RPA product was visualized, and its sequence was confirmed. Subsequently, we designed and validated the cutting efficiency of guide RNA targeting BNYVV via in vitro activity assay in the presence of Cas12a. The sensitivity of CRISPR-Cas12a trans reporter-based detection for BNYVV was determined using a serially diluted synthetic BNYVV target sequence. Further, we have validated the developed CRISPR-Cas12a assay for detecting BNYVV in the root-tissue of sugarbeet bait plants reared in BNYVV-infested field soil. The results revealed that BNYVV detection is highly sensitive and specific to the infected roots relative to healthy control roots as measured quantitatively through the reporter signal. To our knowledge, this is the first report establishing isothermal RT-RPA- and CRISPR-based methods for virus diagnostic approaches for detecting BNYVV from rhizomania diseased sugarbeet roots.

Childlessness among Muthuvan Tribes of Tamil Nadu, India: An Exploratory Study

Introduction:

Childlessness is a global concern and it has serious demographic, social, and health implications. The declining Muthuvan child population may reduce their population on the whole.

Objective:

The study explored the prevalence of childlessness and its underlying reasons in the Muthuvan tribes of Tamil Nadu.

Subjects and Methods:

The study applied the mixed-method design, and the snowball technique was adopted to identify eight Muthuvan hamlets. Descriptive and thematic analysis was done for the collected quantitative and qualitative information.

Results:

The study found the prevalence of childlessness among Muthuvan couples as 30.65%. The underlying reasons were their cultural practices of confinement during menstruation and restriction on engaging in productive work and family care, which gave them the idea of regular intake of oral contraceptive pills and lessen their desire to have children.

Conclusion:

The study concludes that the comfort of their daily life has taken over more important than the consequences of objects used for comfort, to their health and future generations.

Images super-resolution by optimal deep AlexNet architecture for medical application: A novel DOCALN1

In the last decade, numerous researches have been focused on Image Super-Resolution (SR); this recreation or improvement model is vital in different research areas. Recently, deep learning algorithm finds useful to advance in the resolution of the medical output. Here, we devise a novel Deep Convolutional Network model along with the optimal learning rate of the Rectified Linear Unit (ReLU) intended for Medical Image Super-Resolution (MISR). For getting the optimal values of Deep Learning AlexNet structure, Modified Crow Search (MCS) is utilized, which is mainly depends on the behavior of crow sets. The chosen Alexnet lacks in a sort of suitable supervision for upgrading execution of the proposed model that effectively aims to overfit. The proposed design, i.e., MISR, named Deep Optimal Convolutional AlexNet (DOCALN), derives the optimal values of learning rates of the ReLU activation function. Based on this optimal deep learning structure, the Low Resolution (LR) medical images can be applied. Experimentation results of our proposed model are compared with variants of Convolution Neural Networks (CNN) concerning different measures such as image quality assessment, SR efficiency analysis, and execution time.

Hirschsprung’s Disease: Two Cases of Total Intestinal Aganglionosis

Introduction/Objective

Hirschsprung’s disease is a disorder associated with an absence of ganglion cells in a segment of the bowel. Total colonic and small bowel aganglionosis occurs in less than 1% of all Hirschsprung’s disease patients. Even rarer is the finding of Haddad syndrome, the coexistence of congenital central hypoventilation syndrome and Hirschsprung’s disease. Congenital central hypoventilation syndrome has approximately 1,000 reported cases, with colonic aganglionosis being associated with 15-20% of those cases. The prevalence of Hirschsprung’s disease with congenital renal anomalies may be another underreported finding.

Methods

Here, we report two rare cases of Hirschsprung’s disease with significant extension in the small bowel. One case involves a 38-week gestational age male infant admitted for apnea and another case involves 39-week gestational age female infant admitted for vomiting.

Results

Both infants had rectal suction biopsies confirming the absence of ganglion cells. The male infant had mapping biopsies which histologically showed hypertrophic nerve fibers and an absence of ganglion cells in the colon extending up to 70 cm proximal to the ileocecal valve. Calretinin immunostaining confirmed aganglionsis. Genetic testing showed a PHOX2B gene mutation carrying 32 polyalanine repeat mutations, confirming a diagnosis of congenital central hypoventilation syndrome coexisting with Hirschsprung’s disease. The female infant had intraoperative frozen sections that identified ganglion cells throughout the colon. On permanent sections, there was an absence of ganglion cells in the upper rectum extending up to 65 cm proximal to the ileocecal valve. She also was noted to have agenesis of the left kidney and a urachal remnant. Genetic testing was negative for RET mutations.

Conclusion

Overall, these cases provide further information on a rare variant of Hirschsprung’s disease that includes significant portions of the small bowel. Additionally, this study adds to the documented reports of Haddad syndrome and the connections between renal anomalies with Hirschsprung’s disease. Last, this series alludes to the difficulties of frozen section diagnosis of this disease.

Space time analysis of dengue fever diagnosed through a network of laboratories in India from 2014-2017

BACKGROUND & OBJECTIVES

The Department of Health Research and the Indian Council of Medical Research, Government of India, have established Virus Research and Diagnostic Laboratory Network (VRDLN) to strengthen the laboratory capacity in the country for providing timely diagnosis of disease outbreaks. Fifty-one VRDLs were functional as on December 2017 and had reported about dengue fever across Indian states. The objectives of the study were to detect space time clusters and purely temporal clusters of dengue using Kulldorff's SaTScan statistics using patient level information; and to identify regions at greater risk of developing the disease using Kriging technique aggregating at district level.

METHODS

A total of 211,432 patients from 51 VRDLs were investigated for IgM antibodies or NS1 antigen against dengue virus during the period from 1 January 2014 to 31 December 2017 and among them 60,096 (28.4%) were found to be positive. Kulldorff's space time analysis was used to identify significant clusters over space and time. Kriging technique was used to interpolate dengue data for areas not physically sampled using the relationship in the spatial arrangement of the data set. Maps obtained using both the methods were overlaid to identify the regions at greater risk of developing the disease.

RESULTS

Kulldorff Space time Scan Statistics using the Bernoulli model with monthly precision revealed eight statistically significant clusters (P <0.001) for the time period, 1 January 2014 to 31 December 2017. Eight significant clusters identified were districts of Nagpur, Jhunjhunu, Gadag, Dakshin Kannada, Kancheepuram, Sivaganga, Ernakulam and Malda. The purely temporal clusters occurred during the last quarter of 2015 and 2016. The Kriging technique identified north eastern part of the country (Arunachal Pradesh, Nagaland and Manipur) and Gujarat.

INTERPRETATION & CONCLUSION

Dengue fever has spread in all directions in the country. Hence, it is need of the hour to perform an in-depth investigation.

World War against COVID-19: How strong is our armamentarium?

No abstract provided.

Determinants of periodontitis among a rural Indian population: A case control study

OBJECTIVES

Identify the determinants of periodontitis in a rural Indian population aged 35-44 years.

BASIC RESEARCH DESIGN

Case-control clinical and questionnaire study in a cluster sample of 50 villages.

METHODS

A total of 3000 persons were screened for the presence of periodontitis using the CDC case definition in full mouth examination. Equal numbers of cases (604 persons with periodontitis) and controls (604 without periodontitis) were recruited and interviewed with a piloted questionnaire. Univariate and multivariate analysis estimated crude and adjusted odds ratios (aOR) respectively with 95% confidence limits.

RESULTS

Six factors were determined by multivariate analysis to predict periodontitis: education less than or equal to twelve years of schooling (aOR=2.51, 95% CI=1.18-5.34), alcohol consumption (aOR= 1.7, 95% CI=1.16-2.49), consuming a non-vegetarian diet (aOR=1.38, 95% CI=1.08-1.76), not drinking milk (aOR=1.7, 95% CI= 1.29-2.24), not using a toothbrush for cleaning of teeth (aOR=2.98, 95% CI =1.71-5.21) and not cleaning teeth at least once a day (aOR=2.13, 95% CI=1.58-2.87).

CONCLUSION

Risk factors for periodontitis in a rural Indian population were identified. Further studies should validate these findings and appropriate recommendations should be developed to decrease the prevalence and burden of periodontitis in this population.

Epidemiology of Hepatitis A and Hepatitis E Based on Laboratory Surveillance Data-India, 2014-2017

Hepatitis A and hepatitis E viruses (HAV and HEV) are the most common etiologies of viral hepatitis in India. To better understand the epidemiology of these infections, laboratory surveillance data generated during 2014-2017, by a network of 51 virology laboratories, were analyzed. Among 24,000 patients tested for both HAV and HEV, 3,017 (12.6%) tested positive for HAV, 3,865 (16.1%) for HEV, and 320 (1.3%) for both HAV and HEV. Most (74.6%) HAV patients were aged ≤ 19 years, whereas 76.9% of HEV patients were aged ≥ 20 years. These laboratories diagnosed 12 HAV and 31 HEV clusters, highlighting the need for provision of safe drinking water and improvements in sanitation. Further expansion of the laboratory network and continued surveillance will provide data necessary for informed decision-making regarding introduction of hepatitis-A vaccine into the immunization program.

Promotion of HepG2 cell apoptosis by flower of Allium atroviolaceum and the mechanism of action

Background

Liver cancer is a high incidence and fatal disease, the fifth most frequent cancer worldwide that is usually diagnosed at an advanced stage. The number of deaths from liver cancer has not declined even following various therapies. Plant secondary metabolites and their semi-synthetic derivatives play a principal role in anti-cancer drug therapy, since they are effective in the treatment of specific characteristics while also reducing side effects. Allium atroviolaceum, a plant of the genus Allium has been used in folk medicine to protect against several diseases. However, cytotoxicity and the anti-proliferative effect of Allium atroviolaceum remain unclear. This work aims to investigate the anticancer properties of Allium atroviolaceum and the mechanism of action.

Methods

To evaluate the in vitro cytotoxicity of flower of Allium atroviolaceum, methanol extract at a dose range from 100 to 3.12 μg/ml was assessed against the HepG2 hepatocarcinoma cell line, and also on normal 3T3 cells, by monitoring proliferation using the MTT assay method. A microscopy study was undertaken to observe morphological changes of HepG2 cells after treatment and cell cycle arrest and apoptosis were studied using flow cytometry. The apoptosis mechanism of action was assessed by the level of caspase-3 activity and expression of apoptosis related genes, Bcl-2, Cdk1 and p53. The combination effect of the methanolic extract with doxorubicin was also investigated by determination of a combination index.

Results

The results demonstrated growth inhibition of cells in both dose- and time-dependent manners, while no cytotoxic effect on normal cell 3T3 was found. The results revealed the occurrence of apoptosis, illustrated by sub-G0 cell cycle arrest, the change in morphological feature and annexin-V and propidium iodide staining, which is correlated with Bcl-2 downregulation and caspase-3 activity, but p53-independent. In addition, a combination of Allium atroviolaceum and doxorubicin led to a significant synergistic effect.

Conclusion

These findings suggest that Allium atroviolaceum flower extract has potential as a potent cytotoxic agent against HepG2 cell lines, as it has commendable anti-proliferative activities against human hepatocarcinoma and it can be considered as an effective adjuvant therapeutic agent after the clinical trials.

Association between the C34T polymorphism of the AMPD1 gene and essential hypertension in Malaysian patients

The aim of this study was to determine whether C34T, a common polymorphism of the adenosine monophosphate deaminase 1 gene (AMPD1), is associated with essential hypertension (EH). We hypothesize that C34T is associated with the development of EH. A case-control design was used for this study. The DNA was extracted using a commercial kit from the whole blood of 200 patients with hypertension and 200 subjects without hypertension from selected Malaysian ethnicities (Malays, Chinese, and Indians). Polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) and agarose gel electrophoresis were used for genotyping. The C34T gene polymorphism of AMPD1 was significantly associated with EH in the Malaysian subjects (P < 0.0001). The genotype frequencies of CC, CT, and TT were 6%, 79%, and 15%, respectively, among hypertensive subjects, while no TT genotypes were observed in the normotensive subjects. Further, the frequency of hypertension was higher among T allele carriers than C carriers (OD = 9.94; 95%CI = 6.851-14.434). There were significant differences in the systolic blood pressure, diastolic blood pressure, and pulse pressure (P ˂ 0.05) between the normotensive and hypertensive Malaysian subjects; we believe those difference were caused by the C34T polymorphism. For the first time in Malaysia, the current study provides evidence that a common polymorphism of the AMPD1 gene (C34T) is strongly associated with EH.

Glucose uptake through translocation and activation of GLUT4 in PI3K/Akt signaling pathway by asiatic acid in diabetic rats

In this study, we examined the in vivo effect and the mechanism of asiatic acid (AA) on glucose uptake in an insulin target skeletal muscle. Diabetic rats showed significantly increased levels of plasma glucose, thiobarbituric acid reactive substances, and lipid hydroperoxides, decreased levels of insulin and antioxidants, and impairment in insulin-signaling proteins such as insulin receptor (IR), insulin receptor substrate (IRS)-1/2, phosphoinositide 3-kinase (PI3K), Akt, and glucose transporter 4 (GLUT4) proteins. Oral treatment with AA (20 mg/kg body weight) showed near-normalized levels of plasma glucose, lipid peroxidation products, and antioxidants and improved insulin, IR, IRS-1/2, PI3K, Akt, and GLUT4 proteins. These findings suggest that AA improves glucose response by increasing GLUT4 in skeletal muscle through Akt and antioxidant defense in plasma and it also improves glucose homeostasis.

Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis

3’ uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes. 2’-O-methylation on the 3’ terminal ribose protects micro(mi)RNAs from 3’ truncation and 3’ uridylation in Arabidopsis. Previously, we identified HESO1 as the nucleotidyl transferase that uridylates most unmethylated miRNAs in vivo, but substantial 3’ tailing of miRNAs still remains in heso1 loss-of-function mutants. In this study, we found that among nine other potential nucleotidyl transferases, UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) is the single most predominant nucleotidyl transferase that tails miRNAs. URT1 and HESO1 prefer substrates with different 3’ end nucleotides in vitro and act cooperatively to tail different forms of the same miRNAs in vivo. Moreover, both HESO1 and URT1 exhibit nucleotidyl transferase activity on AGO1-bound miRNAs. Although these enzymes are able to add long tails to AGO1-bound miRNAs, the tailed miRNAs remain associated with AGO1. Moreover, tailing of AGO1-bound miRNA165/6 drastically reduces the slicing activity of AGO1-miR165/6, suggesting that tailing reduces miRNA activity. However, monouridylation of miR171a by URT1 endows the miRNA the ability to trigger the biogenesis of secondary siRNAs. Therefore, 3’ tailing could affect the activities of miRNAs in addition to leading to miRNA degradation.

The tailing of RNAs with non-templated uridines, known as uridylation, is often associated with RNA degradation. We previously identified HESO1 as a nucleotidyl transferase that uridylates microRNAs (miRNAs) to lead to their degradation in Arabidopsis. But HESO1 cannot account for all the miRNA uridylation activity in vivo. Here, we have uncovered UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) as another nucleotidyl transferase that uridylates miRNAs. HESO1 and URT1 have different substrate preferences and act cooperatively to tail miRNAs. We show that both enzymes are able to act on ARGONAUTE1 (AGO1)-bound miRNAs and that the tailed miRNAs stay bound by AGO1. We show that URT1-mediated tailing affects the activities of miR165/6 and miR171a differently. This study reveals intricate miRNA uridylation processes as well as functional outcomes of miRNA uridylation.

A genome-wide association study of saturated, mono- and polyunsaturated red blood cell fatty acids in the Framingham Heart Offspring Study

Most genome-wide association studies have explored relationships between genetic variants and plasma phospholipid fatty acid proportions, but few have examined apparent genetic influences on the membrane fatty acid profile of red blood cells (RBC). Using RBC fatty acid data from the Framingham Offspring Study, we analyzed over 2.5 million single nucleotide polymorphisms (SNPs) for association with 14 RBC fatty acids identifying 191 different SNPs associated with at least 1 fatty acid. Significant associations (p<1×10(-8)) were located within five distinct 1MB regions. Of particular interest were novel associations between (1) arachidonic acid and PCOLCE2 (regulates apoA-I maturation and modulates apoA-I levels), and (2) oleic and linoleic acid and LPCAT3 (mediates the transfer of fatty acids between glycerolipids). We also replicated previously identified strong associations between SNPs in the FADS (chromosome 11) and ELOVL (chromosome 6) regions. Multiple SNPs explained 8-14% of the variation in 3 high abundance (>11%) fatty acids, but only 1-3% in 4 low abundance (<3%) fatty acids, with the notable exception of dihomo-gamma linolenic acid with 53% of variance explained by SNPs. Further studies are needed to determine the extent to which variations in these genes influence tissue fatty acid content and pathways modulated by fatty acids.

Self Regressing Epitheloid Haemangioendothelioma of Tibia in an Infant-A rare case report and review of literature

INTRODUCTION

Epitheloid hemangioendothelioma is a rare vascular soft tissue tumour of intermediate malignant potential. The tumor affects any age group, and liver is the commonest internal organ affected. Bones as calvarium, spine, tibia and femur may also be affected. The lesion can be multifocal in the liver or the same bone itself and can metastasise to lungs. Here we report a rare case of epithelioid hemangioendothelioma involving tibia in a male infant, which regressed by itself without any treatment, after incisional biopsy over a period of one and half years.

CASE REPORT

A 7 month old male baby was presented with incessant cry, fever and swelling in left upper leg of 2 weeks duration. X-ray of leg showed a well demarcated lytic lesion in the meta diaphysial region of left tibia. Magnetic resonance imaging showed an irregular lytic lesion with intramedullary extension. Incisional biopsy showed a vascular tumor, epithelioid hemangioendothelioma grade 1. Meanwhile the patient became asymptomatic and subsequent follow ups showed regression in the size of the tumor and complete disappearance after one and half years. This points towards the need of a wait and watch policy in such intermediate grade vascular tumours even though the lesion is so extensive. This is the first case report of an extensive self regressing epithelioid hemangioendothelioma of tibia in an infant to our knowledge.

CONCLUSION

Intermediate grade vascular tumors can undergo spontaneous regression which points towards the need of a wait and watch policy in such tumors thus avoiding extensive surgeries, especially in young patients.

Surface Reconstruction during Molecular Beam Epitaxial Growth of GaN (0001)

Surface reconstructions during homoepitaxial growth of GaN (0001) are studied using reflection high-energy electron diffraction and scanning tunneling microscopy. In agreement with previous workers, a distinct transition from rough to smooth morphology is seen as a function of Ga to N ratio during growth. However, in contrast to some prior reports, no evidence for a 2×2 reconstruction during GaN growth is observed. Observations have been made using four different nitrogen plasma sources, with similar results in each case. A 2×2 structure of the surface can be obtained, but only during nitridation of the surface in the absence of a Ga flux.

Evaluation of transgenic tobacco plants expressing a bacterial Co-Ni transporter for acquisition of cobalt

Phytoremediation is a viable strategy for management of toxic wastes in a large area/volume with low concentrations of toxic elemental pollutants. With increased industrial use of cobalt and its alloys, it has become a major metal contaminant in soils and water bodies surrounding these industries and mining sites with adverse effects on the biota. A bacterial Co-Ni permease was cloned from Rhodopseudomonas palustris and introduced into Nicotiana tabacum to explore its potential for phytoremediation and was found to be specific for cobalt and nickel. The transgenic plants accumulated more cobalt and nickel as compared to control, whereas no significant difference in accumulation of other divalent ions was observed. The transgenic plants were evaluated for cobalt content and showed increased acquisition of cobalt (up to 5 times) as compared to control. The plants were also assessed for accumulation of nickel and found to accumulate up to 2 times more nickel than control. At the same initial concentration of cobalt and nickel, transgenic plant preferentially accumulated cobalt as compared to nickel. The present study is perhaps the first attempt to develop transgenic plants expressing heterologous Co transporter with an improved capacity to uptake cobalt.

The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation

MicroRNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs) impact numerous biological processes in eukaryotes. In addition to biogenesis, turnover contributes to the steady-state levels of small RNAs. One major factor that stabilizes miRNAs and siRNAs in plants as well as siRNAs and piRNAs in animals is 2'-O-methylation on the 3' terminal ribose by the methyltransferase HUA ENHANCER1 (HEN1) [1-6]. Genetic studies with Arabidopsis, Drosophila, and zebrafish hen1 mutants show that 2'-O-methylation protects small RNAs from 3'-to-5' truncation and 3' uridylation, the addition of nontemplated nucleotides, predominantly uridine [2, 7, 8]. Uridylation is a widespread phenomenon that is not restricted to small RNAs in hen1 mutants and is often associated with their reduced accumulation ([7, 9, 10]; reviewed in [11]). The enzymes responsible for 3' uridylation of small RNAs when they lack methylation in plants or animals have remained elusive. Here, we identify the Arabidopsis HEN1 SUPPRESSOR1 (HESO1) gene as responsible for small RNA uridylation in hen1 mutants. HESO1 exhibits terminal nucleotidyl transferase activity, prefers uridine as the substrate nucleotide, and is completely inhibited by 2'-O-methylation. We show that uridylation leads to miRNA degradation, and the degradation is most likely through an enzyme that is distinct from that causing the 3' truncation in hen1 mutants.

Chronic exposure of colorectal cancer cells to bevacizumab promotes compensatory pathways that mediate tumour cell migration

BACKGROUND

Bevacizumab (Bev), a monoclonal antibody to vascular endothelial growth factor (VEGF), is used in combination with chemotherapy for the treatment of metastatic colorectal cancer (CRC). The effects of Bev on angiogenesis have been well described, but the direct effect of Bev on tumour cells is unknown. This study was carried out to determine the molecular and phenotypic changes in CRC cells after chronic Bev exposure in vitro.

METHODS

Human CRC cell lines were chronically exposed (3 months) to Bev in vitro to develop Bev-adapted (Bev-A) cell lines. Vascular endothelial growth factor family members were determined by reverse transcription-polymerase chain reaction and western blotting. Migration and invasion was determined using standard in vitro assays. Intravenous injection of tumour cells was carried out to evaluate metastatic potential in mice.

RESULTS

Bevacizumab-adapted cells were found to be more migratory and invasive than control cells (P<0.001). Bevacizumab-adapted cells showed higher levels of VEGF-A, -B, -C, placental growth factor (PlGF), VEGF receptor-1 (VEGFR-1) and phosphorylation of VEGFR-1. Furthermore, treatment with SU5416, a VEGFR protein tyrosine kinase inhibitor, led to significantly decreased cell migration in vitro (P<0.001). Bevacizumab-adapted cells were more metastatic in vivo (P<0.05).

CONCLUSION

Chronic exposure of CRC cells to Bev (1) increased expression of VEGF-A, -B, -C, PlGF, VEGFR-1 and VEGFR-1 phosphorylation, (2) increased tumour cell migration and invasion, and (3) metastatic potential in vivo. Our study shows the functional significance of autocrine VEGF signalling in CRC cells.

Glutathione transferase from Trichoderma virens enhances cadmium tolerance without enhancing its accumulation in transgenic Nicotiana tabacum

BACKGROUND

Cadmium (Cd) is a major heavy metal pollutant which is highly toxic to plants and animals. Vast agricultural areas worldwide are contaminated with Cd. Plants take up Cd and through the food chain it reaches humans and causes toxicity. It is ideal to develop plants tolerant to Cd, without enhanced accumulation in the edible parts for human consumption. Glutathione transferases (GST) are a family of multifunctional enzymes known to have important roles in combating oxidative stresses induced by various heavy metals including Cd. Some GSTs are also known to function as glutathione peroxidases. Overexpression/heterologous expression of GSTs is expected to result in plants tolerant to heavy metals such as Cd.

RESULTS

Here, we report cloning of a glutathione transferase gene from Trichoderma virens, a biocontrol fungus and introducing it into Nicotiana tabacum plants by Agrobacterium-mediated gene transfer. Transgenic nature of the plants was confirmed by Southern blot hybridization and expression by reverse transcription PCR. Transgene (TvGST) showed single gene Mendelian inheritance. When transgenic plants expressing TvGST gene were exposed to different concentrations of Cd, they were found to be more tolerant compared to wild type plants, with transgenic plants showing lower levels of lipid peroxidation. Levels of different antioxidant enzymes such as glutathione transferase, superoxide dismutase, ascorbate peroxidase, guiacol peroxidase and catalase showed enhanced levels in transgenic plants expressing TvGST compared to control plants, when exposed to Cd. Cadmium accumulation in the plant biomass in transgenic plants were similar or lower than wild-type plants.

CONCLUSION

The results of the present study suggest that transgenic tobacco plants expressing a Trichoderma virens GST are more tolerant to Cd, without enhancing its accumulation in the plant biomass. It should be possible to extend the present results to crop plants for developing Cd tolerance and in limiting Cd availability in the food chain.

Antioxidant Enzyme Activities in Arbuscular Mycorrhizal (Glomus intraradices) Fungus Inoculated and Non-inoculated Maize Plants Under Zinc Deficiency

A greenhouse experiment was conducted to examine the changes in antioxidant enzyme activities of arbuscular mycorrhizal (AM) fungus Glomus intraradices Schenck and Smith inoculated (M+) and non-inoculated (M-) maize (Zea mays L.) plants (variety COHM5) under varying levels of zinc (0, 1.25, 2.5, 3.75 and 5.0 mg kg(-1)). Roots and shoots sampled at 45 days after sowing (DAS) were estimated for its antioxidant enzymes (superoxide dismutase, peroxidase) IAA oxidase, polyphenol oxidase, acid phosphatase and nutritional status especially P and Zn concentrations. Mycorrhizal inoculation significantly (P ≤ 0.01) increased all the four antioxidant enzymes in both roots and shoots at 45 DAS regardless of Zn levels. All enzyme activities except SOD increased progressively with increasing levels of Zn under M+ and M- conditions. The SOD activity got decreased in roots and shoots at 2.5 and 3.75 mg Zn kg(-1). Acid phosphatase activity in M+ roots and shoots were higher in all levels of Zn but the values decreased with increasing levels of Zn particularly in roots. Mycorrhizal fungus inoculated plants had higher P and Zn concentrations in both stages in comparison to non-inoculated plants. Our overall data suggest that mycorrhizal symbiosis plays a vital role in enhancing activities of antioxidant enzymes and nutritional status that enables the host plant to sustain zinc deficient conditions.

Copper tolerance and response of antioxidative enzymes in axenically grown Brassica juncea (L.) plants

Copper is an essential element for proper functioning of all living organisms including plants, but it can cause toxicity at elevated concentrations. In the present study, two varieties of Brassica juncea L. i.e. Pusa JK and TM 4 grown axenically were compared for Cu tolerance and accumulation ability. For further detailed biochemical studies, var. TM 4 was used because of its fast growth and better Cu accumulation in shoots. Toxic effects of Cu were manifested by a reduction in photosynthetic pigments and an increase in the levels of thiobarbituric acid reactive substances. The activities of antioxidant enzymes such as superoxide dismutase, ascorbate peroxidase, guaiacol peroxidase and catalase showed an increase in a concentration and exposure time dependent manner in roots of B. juncea exposed to copper, indicating that they play an important role in combating copper stress in this species.

Adsorption and removal kinetics of phosphonate from water using natural adsorbents

The removal of phosphonate from water was studied using some natural adsorbents. Potassium phosphonate is a fungicide used for the control of Phytophthora capsici, which is prevalent in black pepper (Piper nigrum L.). Batch adsorption kinetic experiments were conducted on the adsorption of phosphonate onto the adsorbents. The concentration of phosphonate was measured on a high-performance liquid chromatograph fitted with a conductivity detector. The percentage removal of phosphonate by powdered laterite stone (PLS) from water was 40.4%, within a residence time of 15 minutes. The mechanisms of the rate of adsorption were analyzed and compared using the pseudo-second-order, Elovich, and intraparticle diffusion models. The experimental data was found to correlate well with the pseudo-second-order kinetic model, indicating adsorption as a chemisorption process. A possible reaction in the phosphonate-PLS system also has been proposed. The PLS can be used as a low-cost natural adsorbent for phosphonate removal from water.