A rapid molecular diagnostic tool to discriminate alleles of avirulence genes and haplotypes of Phytophthora sojae using high-resolution melting analysis

Effectors encoded by avirulence genes (Avr) interact with the Phytophthora sojae resistance gene (Rps) products to generate incompatible interactions. The virulence profile of P. sojae is rapidly evolving as a result of the large-scale deployment of Rps genes in soybean. For a successful exploitation of Rps genes, it is recommended that soybean growers use cultivars containing the Rps genes corresponding to Avr genes present in P. sojae populations present in their fields. Determination of the virulence profile of P. sojae isolates is critical for the selection of soybean cultivars. High-resolution melting curve (HRM) analysis is a powerful tool, first applied in medicine, for detecting mutations with potential applications in different biological fields. Here, we report the development of an HRM protocol, as an original approach to discriminate effectors, to differentiate P. sojae haplotypes for six Avr genes. An HRM assay was performed on 24 P. sojae isolates with different haplotypes collected from soybean fields across Canada. The results clearly confirmed that the HRM assay discriminated different virulence genotypes. Moreover, the HRM assay was able to differentiate multiple haplotypes representing small allelic variations. HRM-based prediction was validated by phenotyping assays. This HRM assay provides a unique, cost-effective and efficient tool to predict virulence pathotypes associated with six different Avr (1b, 1c, 1d, 1k, 3a and 6) genes from P. sojae, which can be applied in the deployment of appropriate Rps genes in soybean fields.

A unique effector secreted by Pseudozyma flocculosa mediates its biocontrol activity

BACKGROUND

Pseudozyma flocculosa is a highly efficient biocontrol agent (BCA) of powdery mildews whose mode of action remains elusive. It is known to secrete unique effectors during its interaction with powdery mildews but effectors have never been shown to be part of the arsenal of a BCA. Here, we characterize the role of the effector Pf2826 released by Pseudozyma flocculosa during its tripartite interaction with barley and the pathogen fungus Blumeria graminis f. sp. hordei.

RESULTS

We utilized CRISPR-Cas9-based genome editing and confirmed that secreted P. flocculosa effector Pf2826 is required for full biocontrol activity. We monitored the localization of the effector Pf2826 with C-terminal mCherry tag and found it localized around the haustoria and on powdery mildew spores. His-tagged Pf2826 recombinant protein was expressed, purified, and used as bait in a pull-down assay from total proteins extracted during the tripartite interaction. Potential interactors were identified by LC-MS/MS analysis after removing unspecific interactions found in the negative controls. A two-way yeast two-hybrid assay validated that Pf2826 interacted with barley pathogenesis-related (PR) proteins HvPR1a and chitinase and with an effector protein from powdery mildew.

CONCLUSIONS

In contrast to the usual modes of action of competition, parasitism, and antibiosis ascribed to BCAs, this study shows that effector pf2826 plays a vital role in the biocontrol activity of P. flocculosa by interacting with plant PR proteins and a powdery mildew effector, altering the host-pathogen interaction.

Progress and Challenges in Elucidating the Functional Role of Effectors in the Soybean-Phytophthora sojae Interaction

Phytophthora sojae, the agent responsible for stem and root rot, is one of the most damaging plant pathogens of soybean. To establish a compatible-interaction, P. sojae secretes a wide array of effector proteins into the host cell. These effectors have been shown to act either in the apoplastic area or the cytoplasm of the cell to manipulate the host cellular processes in favor of the development of the pathogen. Deciphering effector-plant interactions is important for understanding the role of P. sojae effectors in disease progression and developing approaches to prevent infection. Here, we review the subcellular localization, the host proteins, and the processes associated with P. sojae effectors. We also discuss the emerging topic of effectors in the context of effector-resistance genes interaction, as well as model systems and recent developments in resources and techniques that may provide a better understanding of the soybean-P. sojae interaction.

RXLR effector gene Avr3a from Phytophthora sojae is recognized by Rps8 in soybean

The use of resistance genes in elite soybean cultivars is one of the most widely used methods to manage Phytophthora sojae. This method relies on effector-triggered immunity, where a Resistant to P. sojae (Rps) gene product from the plant recognizes a specific effector from the pathogen, encoded by an avirulence (Avr) gene. Many Avr genes from P. sojae have been identified in the last decade, allowing a better exploitation of this type of resistance. The objective of the present study was to identify the Avr gene triggering immunity derived from the soybean resistance gene Rps8. The analysis of a segregating F2 progeny coupled with a genotyping-by-sequencing approach led to the identification of a putative Avr8 locus. The investigation of this locus using whole-genome sequencing data from 31 isolates of P. sojae identified Avr3a as the likely candidate for Avr8. Long-read sequencing also revealed that P. sojae isolates can carry up to five copies of the Avr3a gene, compared to the four previously reported. Haplotype and transcriptional analyses showed that amino acid changes and absence of Avr3a transcripts from P. sojae isolates caused changes in virulence towards Rps8. Functional analyses using CRISPR/Cas9 knockout and constitutive expression demonstrated that Rps8 interacted with Avr3a. We also showed that a specific allele of Avr3a is recognized by Rps3a but not Rps8. While Rps3a and Rps8 have been previously described as closely linked, this is the first report of a clear distinction hitherto undefined between these two resistance genes.

Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole-genome sequencing reveals a major QTL

In the last decade, more than 70 quantitative trait loci (QTL) related to soybean [Glycine max (L.) Merr.] partial resistance (PR) against Phytophthora sojae have been identified by genome-wide association studies (GWAS). However, most of them have either a minor effect on the resistance level or are specific to a single phenotypic variable or one isolate, thereby limiting their use in breeding programs. In this study, we have used an analytical approach combining (a) the phenotypic characterization of a diverse panel of 357 soybean accessions for resistance to P. sojae captured through a single variable, corrected dry weight; (b) a new hydroponic assay allowing the inoculation of a combination of P. sojae isolates covering the spectrum of commercially relevant Rps genes; and (c) exhaustive genotyping through whole-genome resequencing (WGS). This led to the identification of a novel P. sojae resistance QTL with a relatively major effect compared with the previously reported QTL. The QTL interval, spanning ∼500 kb on chromosome (Chr) 15, does not colocalize with previously reported QTL for P. sojae resistance. Plants carrying the favorable allele at this QTL were 60% more resistant. Eight genes were found to reside in the linkage disequilibrium (LD) block containing the peak single-nucleotide polymorphism (SNP) including Glyma.15G217100, which encodes a major latex protein (MLP)-like protein, with a functional annotation related to pathogen resistance. Expression analysis of Glyma.15G217100 indicated that it was nearly eight times more highly expressed in a group of plant introductions (PIs) carrying the resistant (R) allele compared with those carrying the susceptible (S) allele within a short period after inoculation. These results offer new and valuable options to develop improved soybean cultivars with broad resistance to P. sojae through marker-assisted selection.

Knowledge, Awareness and Practice of Periodontal Therapy during Pregnancy among Dental Professionals

Aim: To assess the knowledge, awareness and practice of periodontal therapy during pregnancy among dental professionals Materials and Methods: This cross-sectional study was conducted among 100 dental professionals in and around Chennai. A well-structured questionnaire consisted of 18 questions which were used to assess the awareness of periodontal therapy during pregnancy among dental professionals. Simple randomised sampling method was used to categories the sample population (online survey participants).The knowledge, awareness, scores were calculated for the correct answers to the questions. Based on their response data were statistically analysed. Results: Based on statistical analysis results were tabulated. Around 74% of participants were undergraduates and 26% were postgraduates. Around 64% of the participants were aware of adverse pregnancy outcomes associated with periodontal disease. 80% of the participants were aware that pregnant patients must be turned to the left side on a dental chair for any dental examination and treatment. Conclusion: The results of the present study showed that knowledge and awareness of periodontal therapy during pregnancy among dental professionals are appreciable among postgraduates than undergraduates. The attitude of the dental professionals, particularly undergraduates toward bringing the facts into clinical practice needs to be improved through integrated programs which can provide better and safe treatment to pregnant patients.

Impact of polystyrene microplastics on major marine primary (phytoplankton) and secondary producers (copepod)

The effect of microplastic adsorption on marine microalgae Tetraselmis suecica, Amphora subtropica, and copepod Pseudodiaptomus annandalei was investigated in the present study. Fluorescence microscopic images were used to evaluate MP interactions with algae and copepods. T. suecica growth rate decreased with effects of 0.1 µm polystyrene exposure to 75 µl/100 ml (0.899 to 0.601 abs), 50 µl/100 ml (0.996 to 0.632 abs) and 25 µl/100 ml (0.996 to 0.632 abs), respectively. On the other hand, at 10th day of experiment, the control T. suecica showed the highest growth rate (0.965 abs), chlorophyll concentration (Chl-'a' = 21.36 µg/L; Chl-'b' = 13.65 µg/L), and cell density (3.3 × 10⁶ cells/ml). A marine diatom A. subtropica absorbed 2.0 μm microplastics, and the maximal inhibition rate increased at higher MP concentration until 10th day. The highest MPs (75 μl/100 ml) treatment resulted in decreased growth rate of A. subtropica from 0.163 to 0.096 abs. A. subtropica (without MPs) had the highest lipid concentration of 27.15%, whereas T. suecica had the lowest lipid concentration of 11.2% (without MP). The maximum survival (80%) of P. annandalei was found in control on 15th day whereas on 12th day, the microplastics ingested copepod had the lowest survival rate (0%). On 15th day, the maximum Nauplii Production Rate (NPR) (19.33) female^-1 was observed in control, whereas the minimum (17.33) female^-1 NPR was observed in copepod ingested with MPs. The maximum lipid production (17.33% without MPs) was reported in control, whereas MPs fed copepods had the lowest lipid production (16%). Long-term exposure to polystyrene microplastics significantly reduced algae growth and chlorophyll concentration and also NPR and lipid concentration rate of copepod. We inferred that microplastic exposure of algae and copepods might results in persistent decreases in ingested carbon biomass over time.

Biodegradation of low-density polyethylene and polypropylene by microbes isolated from Vaigai River, Madurai, India

The present study aimed to evaluate the microplastic degradation efficiency of bacterial isolates collected from Vaigai River, Madurai, India. The isolates were processed with proper methods and incorporated in to the UV-treated polyethylene (PE) and polypropylene (PP) degradation. Based on preliminary screening, four bacterial isolates such as Bacillus sp. (BS-1), Bacillus cereus (BC), Bacillus sp. (BS-2), and Bacillus paramycoides (BP) were proceed to further degradation experiment for 21 days. The microplastics were filled with bacterial isolates which is use microplastic (PE, PP) as carbon source for their growth and proceed for shake flask experiment were carried out by two approaches with control. The microplastic degradation was confirmed through their weight loss, increasing fragmentations and changes of surface area against control experiments (microplastic without isolates) also confirms degrading efficiency of isolated bacterial strains through non-changes in their weight and surface area. The highest degradation of PP and PE were observed in BP (78.99 ± 0.005%), and BC (63.08 ± 0.009%) in single approach, while in combined approach BC & BP recorded the highest degradation in both PP (78.62 ± 2.16%), and PE (72.50 ± 20.53%). The formation of new functional groups is confirming the biofilm formation in the surface area of microplastics by isolates and proving their efficiency in degrade the microplastics. The degradation of microplastic experiments should be cost effective and zero waste which is helpful to save the environment and the present findings could reveal the way to degrade the microplastics and prevent the microplastic pollution in aquatic environment.

A reassessment of flocculosin-mediated biocontrol activity of Pseudozyma flocculosa through CRISPR/Cas9 gene editing

Pseudozyma flocculosa is an epiphytic yeast with powerful antagonistic activity against powdery mildews. This activity has been associated with the production of a rare antifungal glycolipid, flocculosin. In spite of the discovery of a specific gene cluster for flocculosin synthesis, attempts to ascribe a functional role to the molecule have been hampered by the inability to efficiently transform P. flocculosa. In this study, two different approaches, target gene replacement by homologous recombination (HR) and CRISPR-Cas9 based genome-editing, were utilized to decipher the role of flocculosin in the biocontrol activity of P.flocculosa. It was possible to alter the production of flocculosin through edition of fat1 by HR, but such mutants displayed abnormal phenotypes and the inability to produce sporidia. Sequencing analyses revealed that transformation by HR led to multiple insertions in the genome explaining the pleiotrophic effects of the approach. On the other hand, CRISPR-Cas9 transformation yielded one mutant that was altered specifically in the proper synthesis of flocculosin. Notwithstanding the loss of flocculosin production, such mutant was phenotypically similar to the wild-type, and when tested for its biocontrol activity against powdery mildew, displayed the same efficacy. These results offer strong evidence that flocculosin-mediated antibiosis is not responsible for the mode of action of P. flocculosa and highlight the potential of CRISPR-Cas9 for functional studies of otherwise difficult-to-transform fungi such as P. flocculosa.

Growth, biochemical, antioxidants, metabolic enzymes and hemocytes population of the shrimp Litopenaeus vannamei exposed to acidified seawater

Acidification in the marine environment has become a global issue that creates serious threats to marine organisms. In the present study, we evaluated the effect of CO₂ driven acidification on the shrimp Litopenaeus vannamei post-larvae (PL). L. vannamei PL were exposed to six different CO₂ driven acidified seawater, such as 8.2 (control), pH 7.8 (IPCC-predicted ocean pH by 2100), 7.6, 7.4, 7.2 and 7.0 with corresponding pCO₂ level of 380.66, 557.53, 878.55, 1355.48, 2129.46, and 3312.12 μatm for seven weeks. At the end of the acidification experiment, results revealed that the survival, growth, feed index, biochemical constituents, chitin, minerals (Na, K, and Ca), and hemocyte populations of shrimps were found to be significantly decreased in CO₂ driven acidified seawater which indicates the negative impacts of acidified seawater on these parameters in L. vannamei. Further, the level of antioxidants, lipid peroxidation, and metabolic enzymes were significantly higher in the muscle of shrimps exposed to acidified seawater suggests that the L. vannamei under oxidative stress and metabolic stress. Among the various acidified seawater tested, pH 7.6 to 7.0 produced a significantly adverse effect on shrimps. Hence, the present study concluded that the elevated level of seawater acidification can produce harmful effects on the biology and physiology of the commercially important shrimp L. vannamei PL.

Silicon influences the localization and expression of Phytophthora sojae effectors in interaction with soybean

In plant-pathogen interactions, expression and localization of effectors in the aqueous apoplastic region play a crucial role in the establishment or suppression of pathogen development. Silicon (Si) has been shown to protect plants in several host-pathogen interactions, but its mode of action remains a source of debate. Its deposition in the apoplastic area of plant cells suggests that it might interfere with receptor-effector recognition. In this study, soybean plants treated or not with Si were inoculated with Phytophthora sojae and differences in the ensuing infection process were assessed through different microscopy techniques, transcript analysis of effector and defense genes, and effector (Avr6) localization through immunolocalization and fluorescence labeling. In plants grown without Si, the results showed the rapid (4 d post-inoculation) host recognition by P. sojae through the development of haustorium-like bodies, followed by expression and release of effectors into the apoplastic region. In contrast, Si treatment resulted in limited pathogen development, and significantly lower expression and presence of Avr6 in the apoplastic region. Based on immunolocalization and quantification of Avr6 through fluorescence labeling, our results suggest that the presence of Si in the apoplast interferes with host recognition and/or limits receptor-effector interactions, which leads to an incompatible interaction.

Baseline assessment of water quality and ecological indicators in Penaeus vannamei farm wastewater along the Southeast coast of India

The present study aimed to investigate the water quality characteristics and the ecological indicators of wastewater of white legged shrimp Penaeus vannamei ponds along the Southeast coast of India. The wastewater samples were collected from 15 shrimp farms covering 11 districts located along the coastal line of Tamil Nadu and Puducherry, India. By adopting standard methods, the collected samples were subjected to analyses of physico-chemical and biological characteristics, especially the microbial load and metal and plankton composition. The nitrate-nitrogen, ammonia-nitrogen, THB, TCB, and Cu concentrations of the samples were found to exceed the permissible limit as recommended by WHO, USEPA, CPCB, and CAA. Principal component analysis and canonical correspondence analysis have suggested that the phosphate, nitrate, silicate, ammonia, and total phosphorus are the important chemical factors. The generated data would be of interest to farmers for their shrimp crop management vis-à-vis culture pond wastewater treatment.

Assessment of Heavy Metals Pollution in Noyyal and Chinnar Rivers, Western Ghats of Tamil Nadu, India with Reference to Crabs (Gecarcinucidae)-A Baseline Study

In the present study, heavy metals (Cd, Cu, Pb, and Zn) level in the water, sediment, and crabs were analyzed from Noyyal and Chinnar Rivers of the Western Ghats in Tamil Nadu, India. Based on our results, Noyyal River is considered as polluted environment due to the discharge of contaminants by various anthropogenic activities, whereas, Chinnar River maintained as unpolluted one due to its tributary nature of Noyyal River located in Western Ghats hills. The results showed that the heavy metals in water and sediments were higher in Noyyal River. Also, the level of bioaccumulation of studied metals and biochemical constituents were higher in the crab Spiralothelphusa hydrodroma sampled from Noyyal River than Barytelphusa cunicularis collected from Chinnar River. The present findings revealed that the crab sampled from Noyyal River had elevated heavy metals which lead to a significant increase in biochemical constituents to overcome the stress.

Structural and Volumetric Brain MRI Findings in Mild Traumatic Brain Injury

BACKGROUND AND PURPOSE

Routine MR imaging findings are frequently normal following mild traumatic brain injury and have a limited role in diagnosis and management. Advanced MR imaging can assist in detecting pathology and prognostication but is not readily available outside research settings. However, 3D isotropic sequences with ∼1-mm³ voxel size are available on community MR imaging scanners. Using such sequences, we compared radiologists' findings and quantified regional brain volumes between a mild traumatic brain injury cohort and non-brain-injured controls to describe structural imaging findings associated with mild traumatic brain injury.

MATERIALS AND METHODS

Seventy-one military personnel with persistent symptoms and 75 controls underwent 3T MR imaging. Three neuroradiologists interpreted the scans using common data elements. FreeSurfer was used to quantify regional gray and white matter volumes.

RESULTS

WM hyperintensities were seen in 81% of the brain-injured group versus 60% of healthy controls. The odds of ≥1 WM hyperintensity in the brain-injured group was about 3.5 times the odds for healthy controls (95% CI, 1.58-7.72; P = .002) after adjustment for age. A frontal lobe-only distribution of WM hyperintensities was more commonly seen in the mild traumatic brain injury cohort. Furthermore, 7 gray matter, 1 white matter, and 2 subcortical gray matter regions demonstrated decreased volumes in the brain-injured group after multiple-comparison correction. The mild traumatic brain injury cohort showed regional parenchymal volume loss.

CONCLUSIONS

White matter findings are nonspecific and therefore a clinical challenge. Our results suggest that prior trauma should be considered in the differential diagnosis of multifocal white matter abnormalities with a clinical history of mild traumatic brain injury, particularly when a frontal predilection is observed.

Larvicidal potency of marine actinobacteria isolated from mangrove environment against Aedes aegypti and Anopheles stephensi

The marine soil samples were collected from different locations of Parangipettai mangrove ecosystem, Vellar estuary, southeast coast of India. Totally 30 different marine actinobacteria were isolated by serial dilution plate technique on starch casein agar medium. The isolated actinobacteria were investigated for their larvicidal activity against Aedes aegypti and Anopheles stephensi mosquitoes. Streptomyces fungicidicus, S. griseus, S. albus, S. alboflavus and S. rochei were identified as potential biocide producers. Based on the antimicrobial activity, five strains were chosen for larvicidal and pupicidal activity. Among the crude extracts tested, the S. alboflavus extract showed significant activity against Ae. aegypti (LC₅₀ 1.48 ± 0.09 and LC₉₀ 3.33 ± 0.22) and An. stephensi (LC₅₀ 1.30 ± 0.09 and LC₉₀ 3.13 ± 0.21). Five isolates have shown a most significant mortality rate of the Ae. aegypti and An. stephensi mosquito larvae. This is an ideal eco-friendly approach for the control of Japanese encephalitis vectors, Ae. aegypti and malarial vector An. stephensi.

Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae

The initial interaction of a pathogenic fungus with its host is complex and involves numerous metabolic pathways and regulatory proteins. Considerable attention has been devoted to proteins that play a crucial role in these interactions, with an emphasis on so-called effector molecules that are secreted by the invading microbe to establish the symbiosis. However, the contribution of other types of molecules, such as glycans, is less well appreciated. Here, we present a random genetic screen that enabled us to identify 58 novel candidate genes that are involved in the pathogenic potential of the fungal pathogen Verticillium dahliae, which causes vascular wilt diseases in over 200 dicotyledonous plant species, including economically important crops. One of the candidate genes that was identified concerns a putative biosynthetic gene involved in nucleotide sugar precursor formation, as it encodes a putative nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER). This enzyme has homology to bacterial enzymes involved in the biosynthesis of the nucleotide sugar deoxy-thymidine diphosphate (dTDP)-rhamnose, a precursor of L-rhamnose, which has been shown to be required for virulence in several human pathogenic bacteria. Rhamnose is known to be a minor cell wall glycan in fungi and has therefore not been suspected as a crucial molecule in fungal-host interactions. Nevertheless, our study shows that deletion of the VdNRS/ER gene from the V. dahliae genome results in complete loss of pathogenicity on tomato and Nicotiana benthamiana plants, whereas vegetative growth and sporulation are not affected. We demonstrate that VdNRS/ER is a functional enzyme in the biosynthesis of uridine diphosphate (UDP)-rhamnose, and further analysis has revealed that VdNRS/ER deletion strains are impaired in the colonization of tomato roots. Collectively, our results demonstrate that rhamnose, although only a minor cell wall component, is essential for the pathogenicity of V. dahliae.

Diagnostic whole body scan (pre-therapy scan) in differentiated thyroid cancer: A single center community hospital experience

OBJECTIVE

Diagnostic whole body scan (pre-therapy scan) with either I-123 or I-131 (radioactive isotopes of iodine) is performed to assess the extent of thyroid cancer especially distant metastasis prior to administering the therapeutic dose of I-131. Our aim of the following study was to determine the utility of the diagnostic pre-therapy scan in the management of differentiated thyroid cancer.

MATERIALS AND METHODS

It was a case-control study carried out by retrospective chart review, of a randomly selected 100 patients with differentiated thyroid cancer who had followed in our community hospital over the course of 1 year. We collected data on multiple variables in the subjects - including age, gender, pre-operative size of the nodules, diagnosis, stage of the malignancy, size of the tumor, multifocality, lymphovascular invasion, dose of radioiodine used for remnant ablation, recurrence rates and persistence rates. Continuous variables were compared using the independent sample Mann-Whitney U-test whereas the Chi-square test was used for nominal variables.

RESULTS

The mean dose of radioactive iodine administered was 97.56 (±27.98) in the pre-therapy scan group and it was 97.23 (±32.40) in the control group. There was no difference between the two groups (P - 0.45). There was also no difference in the recurrence rates between the groups (P = 1.0). There was a trend toward a higher degree of persistent cancer in the group that had the pre-therapy scans (P - 0.086).

CONCLUSION

Pre-therapy scan may not affect the dose of radio-iodine I-131 used for remnant ablation of differentiated thyroid cancer and does not influence the recurrence rates. This was especially true with respect to I-131 remnant ablation for low risk tumors.

Biodecolorization and Bioremediation of Denim Industrial Wastewater by Adapted Bacterial Consortium Immobilized on Inert Polyurethane Foam (PUF) Matrix: A First Approach with Biobarrier Model

The present experiments were studied on bioremediation of denim industry wastewater by using polyurethane foam (PU foam) immobilized bacterial cells. About 30 indigenous adapted bacterial strains were isolated from denim textile effluent out of which only four isolates were found to be efficient against crude indigo carmine degradation using broth decolorization method. The selected bacterial strains were identified as Actinomyces sp., (PK 07), Pseudomonas sp., (PK 18), Stenotrophomonas sp., (PK 23) and Staphylococcus sp., (PK 28) based on microscopic and biochemical characteristics. The bacterial immobilized cells have the highest number of viable cells (PK07, PK18, PK23 and PK28 appeared to be 1 × 108, 1 × 109, 1 × 106 and 1 × 107 CFU/ml respectively) and maximum attachment efficiency of 92% on PU foam. The complete degradation using a consortium of PU foam immobilized cells was achieved at pH 6, 27°C, 100% of substrate concentration and allowed to develop biofilm for one day (1.5% W/V). In SEM analysis, it was found that immobilization of bacterial cells using PUF stably maintained the production of various extracellular enzymes at levels higher than achieved with suspended forms. Finally, isatin and anthranilic acid were found to be degradation products by NMR and TLC. The decolorized dye was not toxic to monkey kidney cell (HBL 100) at a concentration of 50 µl and 95% of cell viability was retained. A mathematical model that describes bacterial transport with biodegradation involves a set of coupled reaction equations with non-standard numerical approach based on the time step scheme.

Phytoremediation of dye contaminated soil by Leucaena leucocephala (subabul) seed and growth assessment of Vigna radiata in the remediated soil

The present study was investigated for soil bioremediation through sababul plant biomass (Leucaena leucocephala). The soil contaminated with textile effluent was collected from Erode (chithode) area. Various physico-chemical characterizations like N, P, and K and electrical conductivity were assessed on both control and dye contaminated soils before and after remediation. Sababul (L. leucocephala) powder used as plant biomass for remediation was a tool for textile dye removal using basic synthetic dyes by column packing and eluting. The concentration of the dye eluted was compared with its original concentration of dye and were analyzed by using UV-vis spectrophotometer. Sababul plant biomass was analyzed for its physico-chemical properties and active compounds were detected by GC-MS, HPTLC and FTIR. Plant growth was assessed with green gram on the textile contaminated soil and sababul had the potential of adsorbing the dye as the contaminated soil and also check the growth of green gram.

Seasonal variations in physico-chemical characteristics of pond and ground water of Tiruchirapalli, India

The aim of this study was to assess the open pond and groundwater quality of Tiruchirapalli city of Tamil Nadu, India. The groundwater quality viz., pH, electrical conductivity, total hardness, calcium ion, magnesium ion, chloride, carbonate, bicarbonate, inorganic nitrate, nitrite, phosphate, ammonia and reactive silicate were analysed with respect to various seasons and recorded in the range of 7.1 to 8.1, 97.67 to 533.67 mhos cm(-1), 7.07 to 186 mg l(-1), 4.67 and 112.0 mg l(-1), 2.40 to 92.80 mg l(-1), 15.23 to 661.73 mg l(-1), 60 to 480 mg l(-1), 22.7 to 544.9 mg l(-1), 15.33 to 68.00 mg l(-1), 0.001 to 0.480 mg l(-1), 0.01 to 0.42 mg l(-1), 0.02 to 0.75 mg l(-1) and 1.1 to 2.96 mg l(-1) respectively. The present findings concluded that the quality of ground waters can be considered suitable for human consumption. But the pond water available in and around Tiruchirappalli city was not fit for human usage, agricultural or industrial purposes.

Effect of temperature and algal food on egg production and hatching of copepod, Paracalanus parvus

There are relatively few reports on the influence of environmental factors on the development and reproduction of calanoid copepods. In this study, we establish over the 12 days culture experiment at different temperature (18, 20, 25, 30 degrees C) and different algal cell densities 1000, 5000, 10,000, 20,000 cells ml(-1). The results revealed that the high egg production (42.33 eggs female(-1) day(-1)) and hatching rate (92.65%) was reported in the temperature of 25 degrees C. It is understood that the egg production of P. parvus clearly affected by temperature was supported by ANOVA value (F = 4.792909) while the egg production and hatching rate was found to be high as 53.5 +/- 4.94 eggs female(-1) day(-1), 96.26% respectively with 20,000 cells ml(-1), The temperature of 25 degrees C and algal concentration was positively supported by ANOVA. The present study concluded that the temperature of 25 degrees C and food concentration of 20,000 cells ml(-1) was found to be favorable water temperature and algal food concentration to obtain high fecundity and hatching success in copepod, P. parvus.

Evidence for functional diversification within a fungal NEP1-like protein family

In this study, we functionally analyzed the gene family encoding necrosis- and ethylene-inducing-like proteins (NLP) of the vascular wilt pathogen Verticillium dahliae. We show that the composition of the NLP gene family varies little among V. dahliae isolates. The cytotoxic activity of NLP family members of a tomato-pathogenic V. dahliae strain was determined, demonstrating that only two of the seven NLP induced plant cell death. The genes encoding these cytotoxic NLP were found to be induced in V. dahliae upon colonization of tomato. Interestingly, targeted deletion of either of the two genes in V. dahliae significantly compromised virulence on tomato as well as on Arabidopsis plants, whereas deletion of only one of the two genes affected virulence on Nicotiana benthamiana. This could be attributed to differential induction of the two NLP genes in V. dahliae upon N. benthamiana colonization, revealing that the in planta induction of NLP genes varies between plant hosts. Intriguingly, one of the NLP genes appears to also affect vegetative growth and conidiospore production, because the corresponding deletion strain produced significantly fewer conidiospores and developed extensive aerial mycelium. In conclusion, we demonstrate that the expanded V. dahliae NLP family shows functional diversification, revealing not only differential cytotoxicity between family members but also that the cytotoxic NLP play a role in vegetative growth and asexual reproduction in addition to their contribution to virulence.

Verticillium dahliae Sge1 differentially regulates expression of candidate effector genes

The ascomycete fungus Verticillium dahliae causes vascular wilt diseases in hundreds of dicotyledonous plant species. However, thus far, only few V. dahliae effectors have been identified, and regulators of pathogenicity remain unknown. In this study, we investigated the role of the V. dahliae homolog of Sge1, a transcriptional regulator that was previously implicated in pathogenicity and effector gene expression in Fusarium oxysporum. We show that V. dahliae Sge1 (VdSge1) is required for radial growth and production of asexual conidiospores, because VdSge1 deletion strains display reduced radial growth and reduced conidia production. Furthermore, we show that VdSge1 deletion strains have lost pathogenicity on tomato. Remarkably, VdSge1 is not required for induction of Ave1, the recently identified V. dahliae effector that activates resistance mediated by the Ve1 immune receptor in tomato. Further assessment of the role of VdSge1 in the induction of the nine most highly in-planta-induced genes that encode putative effectors revealed differential activity. Although the expression of one putative effector gene in addition to Ave1 was not affected by VdSge1 deletion, VdSge1 appeared to be required for the expression of six putative effector genes, whereas two of the putative effectors genes were found to be negatively regulated by VdSge1. In conclusion, our data suggest that VdSge1 differentially regulates V. dahliae effector gene expression.

Copepod population in Vellar estuary, Parangipettai coast in relation to environmental conditions

Distribution and abundance of copepods were studied in relation to environmental conditions at two different ecosystems viz: Neritic (Bay of Bengal) and estuarine (Vellar estuary) of Parangipettai coast from September, 1998 toAugust, 2000. Over the study period, total 85 species of copepods were reported. Among these, the calanoid copepods constituted the major component with 63.52% followed by cyclopoids (29.41%) and harpacticoids (7.05%). The copepods population density was found to be high (2, 53,000 org l(-1)) in estuarine water, while the species diversity was higher (5.47) in neritic water. The observed spatio-temporal variations in the population density and species diversity of copepods were more related to the environmental state of respective study area.

Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing

Fungal plant pathogens secrete effector molecules to establish disease on their hosts, and plants in turn use immune receptors to try to intercept these effectors. The tomato immune receptor Ve1 governs resistance to race 1 strains of the soil-borne vascular wilt fungi Verticillium dahliae and Verticillium albo-atrum, but the corresponding Verticillium effector remained unknown thus far. By high-throughput population genome sequencing, a single 50-Kb sequence stretch was identified that only occurs in race 1 strains, and subsequent transcriptome sequencing of Verticillium-infected Nicotiana benthamiana plants revealed only a single highly expressed ORF in this region, designated Ave1 (for Avirulence on Ve1 tomato). Functional analyses confirmed that Ave1 activates Ve1-mediated resistance and demonstrated that Ave1 markedly contributes to fungal virulence, not only on tomato but also on Arabidopsis. Interestingly, Ave1 is homologous to a widespread family of plant natriuretic peptides. Besides plants, homologous proteins were only found in the bacterial plant pathogen Xanthomonas axonopodis and the plant pathogenic fungi Colletotrichum higginsianum, Cercospora beticola, and Fusarium oxysporum f. sp. lycopersici. The distribution of Ave1 homologs, coincident with the presence of Ave1 within a flexible genomic region, strongly suggests that Verticillium acquired Ave1 from plants through horizontal gene transfer. Remarkably, by transient expression we show that also the Ave1 homologs from F. oxysporum and C. beticola can activate Ve1-mediated resistance. In line with this observation, Ve1 was found to mediate resistance toward F. oxysporum in tomato, showing that this immune receptor is involved in resistance against multiple fungal pathogens.

Random insertional mutagenesis in fungal genomes to identify virulence factors

Agrobacterium tumefaciens-mediated transformation (ATMT) has become an important tool for functional genomics in fungi. ATMT-based approaches such as random insertional mutagenesis and targeted knockout are widely used for gene functional analysis in plant-pathogen interactions. Here, we describe a protocol for the identification of pathogenicity and virulence genes through random insertional mutagenesis using the fungal wilt pathogen Verticillium dahliae as an example for the protocol.

Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens

The vascular wilt fungi Verticillium dahliae and V. albo-atrum infect over 200 plant species, causing billions of dollars in annual crop losses. The characteristic wilt symptoms are a result of colonization and proliferation of the pathogens in the xylem vessels, which undergo fluctuations in osmolarity. To gain insights into the mechanisms that confer the organisms' pathogenicity and enable them to proliferate in the unique ecological niche of the plant vascular system, we sequenced the genomes of V. dahliae and V. albo-atrum and compared them to each other, and to the genome of Fusarium oxysporum, another fungal wilt pathogen. Our analyses identified a set of proteins that are shared among all three wilt pathogens, and present in few other fungal species. One of these is a homolog of a bacterial glucosyltransferase that synthesizes virulence-related osmoregulated periplasmic glucans in bacteria. Pathogenicity tests of the corresponding V. dahliae glucosyltransferase gene deletion mutants indicate that the gene is required for full virulence in the Australian tobacco species Nicotiana benthamiana. Compared to other fungi, the two sequenced Verticillium genomes encode more pectin-degrading enzymes and other carbohydrate-active enzymes, suggesting an extraordinary capacity to degrade plant pectin barricades. The high level of synteny between the two Verticillium assemblies highlighted four flexible genomic islands in V. dahliae that are enriched for transposable elements, and contain duplicated genes and genes that are important in signaling/transcriptional regulation and iron/lipid metabolism. Coupled with an enhanced capacity to degrade plant materials, these genomic islands may contribute to the expanded genetic diversity and virulence of V. dahliae, the primary causal agent of Verticillium wilts. Significantly, our study reveals insights into the genetic mechanisms of niche adaptation of fungal wilt pathogens, advances our understanding of the evolution and development of their pathogenesis, and sheds light on potential avenues for the development of novel disease management strategies to combat destructive wilt diseases.

Non-fluent aphasia and neural reorganization after speech therapy: insights from human sleep electrophysiology and functional magnetic resonance imaging

Stroke is associated with long-term functional deficits. Behavioral interventions are often effective in promoting functional recovery and plastic changes. Recent studies in normal subjects have shown that sleep, and particularly slow wave activity (SWA), is tied to local brain plasticity and may be used as a sensitive marker of local cortical reorganization after stroke. In a pilot study, we assessed the local changes induced by a single exposure to a therapeutic session of IMITATE (Intensive Mouth Imitation and Talking for Aphasia Therapeutic Effects), a behavioral therapy used for recovery in patients with post-stroke aphasia. In addition, we measured brain activity changes with functional magnetic resonance imaging (fMRI) in a language observation task before, during and after the full IMITATE rehabilitative program. Speech production improved both after a single exposure and the full therapy program as measured by the Western Aphasia Battery (WAB) Repetition subscale. We found that IMITATE induced reorganization in functionally-connected, speech-relevant areas in the left hemisphere. These preliminary results suggest that sleep hd-EEGs, and the topographical analysis of SWA parameters, are well suited to investigate brain plastic changes underpinning functional recovery in neurological disorders.

Biochemical composition of wild copepods, Acartia spinicauda and Oithona similis, from Parangipettai coastal waters in relation to environmental parameters

Percentage composition of protein, lipid, carbohydrate and amino acids of copepods, Acartia spinicauda and Oithona similis collected from Parangipettai coastal waters were estimated following standard methodologies. Of the principal biochemical constituents, protein formed the major component followed bylipid and carbohydrate. Biochemical composition analysis of wild copepods indicated their nutritional rank. The ranges of protein, lipid and carbohydrate (%) contents (of A. spinicauda and O. similis) were 67.33-75.45; 12.42-16.58; 6.69-7.98 (Stn 1); 68.10-74.62; 12.65-17.81; 4.41-7.34 (Stn 2); 68.65-74.93; 14.55-17.69; 4.01-7.90 (Stn3) and 59.53-69.61; 10.76-17.68; 3.43-6.59 (Stn 1); 62.39-67.09; 10.26-15.65; 3.78-5.85 (Stn 2) and 59.57-67.60; 9.89-15.44; 3.71-5.72 (Stn 3) respectively. Totally 16 amino acids were observed in these wild copepods, with threonine, glutamic acid, alanine, aspartic acid, serine, valine and methionine as the dominant ones. The minimum and maximum values of atmospheric and surface water temperatures (degrees C), salinity (%), pH and dissolved oxygen (ml l(-1)) were 28.5-35; 28.7-34.2; 14.5-35.7; 7.4-8.6 and 3.0-7.2 respectively. The ranges (microM) of nitrate, nitrite, phosphate and silicate were 7.9-52.9; 0.6-9.6; 0.5-7.5 and 8.2-140.5 respectively. The results supported the view that protein may function as a metabolic reserve in copepods and that the availabilityof a constant supply of food may render large amount of lipid storage unnecessary in tropical copepods.

Generation of a 3D indexed Petunia insertion database for reverse genetics

BLAST searchable databases containing insertion flanking sequences have revolutionized reverse genetics in plant research. The development of such databases has so far been limited to a small number of model species and normally requires extensive labour input. Here we describe a highly efficient and widely applicable method that we adapted to identify unique transposon-flanking genomic sequences in Petunia. The procedure is based on a multi-dimensional pooling strategy for the collection of DNA samples; up to thousands of different templates are amplified from each of the DNA pools separately, and knowledge of their source is safeguarded by the use of pool-specific (sample) identification tags in one of the amplification primers. All products are combined into a single sample that is subsequently used as a template for unidirectional pyrosequencing. Computational analysis of the clustered sequence output allows automatic assignment of sequences to individual DNA sources. We have amplified and analysed transposon-flanking sequences from a Petunia transposon insertion library of 1000 individuals. Using 30 DNA isolations, 70 PCR reactions and two GS20 sequencing runs, we were able to allocate around 10 000 transposon flanking sequences to specific plants in the library. These sequences have been organized in a database that can be BLAST-searched for insertions into genes of interest. As a proof of concept, we have performed an in silico screen for insertions into members of the NAM/NAC transcription factor family. All in silico-predicted transposon insertions into members of this family could be confirmed in planta.