GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis

Big genomic data and artificial intelligence (AI) are ushering in an era of precision medicine, providing opportunities to study previously under-represented subtypes and rare diseases rather than categorize them as variances. However, clinical researchers face challenges in accessing such novel technologies as well as reliable methods to study small datasets or subcohorts with unique phenotypes. To address this need, we developed an integrative approach, GAiN, to capture patterns of gene expression from small datasets on the basis of an ensemble of generative adversarial networks (GANs) while leveraging big population data. Where conventional biostatistical methods fail, GAiN reliably discovers differentially expressed genes (DEGs) and enriched pathways between two cohorts with limited numbers of samples (n = 10) when benchmarked against a gold standard. GAiN is freely available at GitHub. Thus, GAiN may serve as a crucial tool for gene expression analysis in scenarios with limited samples, as in the context of rare diseases, under-represented populations, or limited investigator resources.

SCCA1/SERPINB3 suppresses anti-tumor immunity and blunts therapy-induced T cell responses via STAT-dependent chemokine production

Cancer patients with high serum squamous cell carcinoma antigen (SCCA1/SERPINB3) are commonly associated with treatment resistance and poor prognosis. Despite being a clinical biomarker, the modulation of SERPINB3 in tumor immunity is poorly understood. We found positive correlations of SERPINB3 with CXCL1/8, S100A8/A9 and myeloid cell infiltration through RNAseq analysis of human primary cervix tumors. Induction of SERPINB3 resulted in increased CXCL1/8 and S100A8/A9, which promoted monocyte and MDSC migration in vitro. In mouse models, Serpinb3a-tumors showed increased MDSC and TAM infiltration contributing to T cell inhibition and this was further augmented upon radiation. Intratumoral knockdown of Serpinb3a demonstrated tumor growth inhibition and reduced CXCL1, S100A8/A9, MDSC, and M2 macrophage infiltration. These changes led to enhanced cytotoxic T cell function and sensitized tumors to radiotherapy. We further revealed SERPINB3 promoted STAT-dependent suppressive chemokine expression, whereby inhibiting STAT activation by ruxolitinib or siRNA abrogated CXCL1/8 and S100A8/A9 in SERPINB3 cells. Patients with elevated pre-treatment SCCA and high pSTAT3 had increased intratumoral CD11b+ myeloid cell compared to patients with low SCCA and pSTAT3 cohort that had overall improved survival after radiotherapy. These findings provide a preclinical rationale for targeting SERPINB3 in tumors to counteract the immunosuppression and improve response to radiation.

SCCA1/SERPINB3 promotes suppressive immune environment via STAT-dependent chemokine production, blunting the therapy-induced T cell responses

Radiotherapy is a commonly used cancer treatment; however, patients with high serum squamous cell carcinoma antigen (SCCA1/SERPINB3) are associated with resistance and poor prognosis. Despite being a strong clinical biomarker, the modulation of SERPINB3 in tumor immunity is poorly understood. We investigated the microenvironment of SERPINB3 high tumors through RNAseq of primary cervix tumors and found that SERPINB3 was positively correlated with CXCL1/8, S100A8/A9 and myeloid cell infiltration. Induction of SERPINB3 in vitro resulted in increased CXCL1/8 and S100A8/A9 production, and supernatants from SERPINB3-expressing cultures attracted monocytes and MDSCs. In murine tumors, the orthologue mSerpinB3a promoted MDSC, TAM, and M2 macrophage infiltration contributing to an immunosuppressive phenotype, which was further augmented upon radiation. Radiation-enhanced T cell response was muted in SERPINB3 tumors, whereas Treg expansion was observed. A STAT-dependent mechanism was implicated, whereby inhibiting STAT signaling with ruxolitinib abrogated suppressive chemokine production. Patients with elevated pre-treatment serum SCCA and high pSTAT3 had increased intratumoral CD11b+ myeloid cell compared to patients with low SCCA and pSTAT3 cohort that had overall improved cancer specific survival after radiotherapy. These findings provide a preclinical rationale for targeting STAT signaling in tumors with high SERPINB3 to counteract the immunosuppressive microenvironment and improve response to radiation.

Endogenous Retrovirus RNA Expression Differences between Race, Stage and HPV Status Offer Improved Prognostication among Women with Cervical Cancer

Endogenous human retroviruses (ERVs) are remnants of exogenous retroviruses that have integrated into the human genome. Using publicly available RNA-seq data from 63 cervical cancer patients, we investigated the expression of ERVs in cervical cancers. Four aspects of cervical cancer were investigated: patient ancestral background, tumor HPV type, tumor stage and patient survival. Between the racial subgroups, 74 ERVs were significantly differentially expressed, with Black Americans having 30 upregulated and 44 downregulated (including MER21C, HERV9-int, and HERVH-int) ERVs when compared to White Americans. We found that 3313 ERVs were differentially expressed between HPV subgroups, including MER41A, HERVH-int and HERVK9. There were 28 downregulated (including MLT1D and HERVH-int) and 61 upregulated (including MER41A) ERVs in locally advanced-stage compared to early-stage samples. Tissue microarrays of cervical cancer patients were used to investigate the protein expression of ERVs with protein coding potential (i.e., HERVK and ERV3). Significant differences in protein expression of ERV3 (p = 0.000905) were observed between early-stage and locally advanced-stage tumors. No significant differential expression at the protein level was found for HERVK7 (p = 0.243). We also investigated a prognostic model, supplementing a baseline prediction model using FIGO stage, age and HPV positivity with ERVs data. The expression levels of all ERVs in the HERVd were input into a Lasso-Cox proportional hazards model, developing a predictive 67-ERV panel. When ERVs expression levels were supplemented with the clinical data, a significant increase in prognostic power (p = 9.433 × 10-15) relative to that obtained with the clinical parameters alone (p = 0.06027) was observed. In summary, ERV RNA expression in cervical cancer tumors is significantly different among racial cohorts, HPV subgroups and disease stages. The combination of the expression of certain ERVs in cervical cancers with clinical factors significantly improved prognostication compared to clinical factors alone; therefore, ERVs may serve as future prognostic biomarkers and therapeutic targets. Novelty and Impact: When endogenous retroviral (ERV) expression signatures were combined with currently employed clinical prognosticators of relapse of cervical cancer, the combination outperformed prediction models based on clinical prognosticators alone. ERV expression signatures in tumor biopsies may therefore be useful to help identify patients at greater risk of recurrence. The novel ERV expression signatures or adjacent genes possibly impacted by ERV expression described here may also be targets for the development of future therapeutic interventions.

Monounsaturated and Diunsaturated Fatty Acids Sensitize Cervical Cancer to Radiation Therapy

Obesity induces numerous physiological changes that can impact cancer risk and patient response to therapy. Obese patients with cervical cancer have been reported to have superior outcomes following chemoradiotherapy, suggesting that free fatty acids (FFA) might enhance response to radiotherapy. Here, using preclinical models, we show that monounsaturated and diunsaturated FFAs (uFFA) radiosensitize cervical cancer through a novel p53-dependent mechanism. UFFAs signaled through PPARγ and p53 to promote lipid uptake, storage, and metabolism after radiotherapy. Stable isotope labeling confirmed that cervical cancer cells increase both catabolic and anabolic oleate metabolism in response to radiotherapy, with associated increases in dependence on mitochondrial fatty acid oxidation for survival. In vivo, supplementation with exogenous oleate suppressed tumor growth in xenografts after radiotherapy, an effect that could be partially mimicked in tumors from high fat diet-induced obese mice. These results suggest that supplementation with uFFAs may improve tumor responses to radiotherapy, particularly in p53 wild-type tumors.

SIGNIFICANCE

Metabolism of monounsaturated and diunsaturated fatty acids improves the efficacy of radiotherapy in cancer through modulation of p53 activity. See related commentary by Jungles and Green, p. 4513.

Loss of H3K27 trimethylation promotes radiotherapy resistance in medulloblastoma and induces an actionable vulnerability to BET inhibition

Medulloblastoma has been categorized into four subgroups based on genetic, epigenetic, and transcriptional profiling. Radiation is used for treating medulloblastoma regardless of the subgroup. A better understanding of the molecular pathways determining radiotherapy response could help improve medulloblastoma treatment. Here, we investigated the role of the EZH2-dependent histone H3K27 trimethylation in radiotherapy response in medulloblastoma. The tumors in 47.2% of group 3 and 4 medulloblastoma patients displayed H3K27me3 deficiency. Loss of H3K27me3 was associated with a radioresistant phenotype, high relapse rates, and poor overall survival. In H3K27me3-deficient medulloblastoma cells, an epigenetic switch from H3K27me3 to H3K27ac occurred at specific genomic loci, altering the transcriptional profile. The resulting upregulation of EPHA2 stimulated excessive activation of the pro-survival AKT signaling pathway, leading to radiotherapy resistance. BET inhibition overcame radiation resistance in H3K27me3-deficient medulloblastoma cells by suppressing H3K27ac levels, blunting EPHA2 overexpression, and mitigating excessive AKT signaling. Additionally, BET inhibition sensitized medulloblastoma cells to radiation by enhancing the apoptotic response through suppression of Bcl-xL and upregulation of Bim. This work demonstrates a novel mechanism of radiation resistance in medulloblastoma and identifies an epigenetic marker predictive of radiotherapy response. Based on these findings, we propose an epigenetically guided treatment approach targeting radiotherapy resistance in medulloblastoma patients.

DANSR: A Tool for the Detection of Annotated and Novel Small RNAs

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17-35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36-200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17-200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.

EMBR-04. BET INHIBITION TARGETS RADIOTHERAPY RESISTANCE IN H3K27ME3-DEFICIENT GROUP 3 MEDULLOBLASTOMA

Medulloblastoma has been categorized into four subgroups based on genetic, epigenetic and transcriptional profiling. However, molecular pathways determining radiotherapy response in this tumor remain elusive. Here, we investigated the role of the EZH2-dependent histone H3K27 tri-methylation in radiotherapy response in medulloblastoma. We demonstrate that 47.2% of group 3 and 4 medulloblastoma patients have H3K27me3-deficient tumors. Loss of H3K27me3 was associated with a radioresistant phenotype, high relapse rates and poor overall survival. We show that an epigenetic switch from H3K27me3 to H3K27ac occurs at specific genomic loci in H3K27me3-deficient medulloblastoma cells altering the transcriptional profile. The resulting up-regulation of EPHA2 (ephrin type-A receptor 2) stimulates an excessive activation of the pro-survival AKT signaling pathway leading to radiotherapy resistance. We show that BET inhibition targets radiation resistance in H3K27me3-deficient medulloblastoma by suppressing H3K27ac levels, blunting EPHA2 overexpression and mitigating the excessive AKT signaling. Additionally, BET inhibition sensitizes medulloblastoma cells to radiation by enhancing apoptotic response through suppression of Bcl-XL and up-regulation of Bim expression. Our work demonstrates a novel mechanism of radiation resistance in medulloblastoma and identifies an epigenetic marker predictive of radiotherapy response. Based on these findings we propose an epigenetically guided treatment approach targeting radiotherapy resistance in medulloblastoma patients.

Standardized Uptake Value for 18F-Fluorodeoxyglucose Is a Marker of Inflammatory State and Immune Infiltrate in Cervical Cancer

PURPOSE

Chemoradiotherapy for locally advanced cervical cancer fails in over a third of patients. Biomarkers with therapeutic implications are therefore needed. We investigated the relationship between an established prognostic marker, maximum standardized uptake value (SUV_max) on ¹⁸F-fluorodeoxyglucose positron emission tomography, and the inflammatory and immune state of cervical cancers.

EXPERIMENTAL DESIGN

An SUV_max most prognostic for freedom from progression (FFP) was identified and compared with known prognostic clinical variables in a cohort of 318 patients treated with definitive radiation with prospectively collected clinical data. Gene set enrichment analysis (GSEA) and CIBERSORT of whole-transcriptome data from 68 patients were used to identify biological pathways and immune cell subpopulations associated with high SUV_max. IHC using a tissue microarray (TMA, N = 82) was used to validate the CIBERSORT findings. The impact of macrophages on cervical cancer glucose metabolism was investigated in coculture experiments.

RESULTS

SUV_max <11.4 was most prognostic for FFP (P = 0.001). The GSEA showed that high SUV_max is associated with increased gene expression of inflammatory pathways, including JAK/STAT3 signaling. CIBERSORT and CD68 staining of the TMA showed high SUV_max tumors are characterized by a monocyte-predominant immune infiltrate. Coculture of cervical cancer cells with macrophages or macrophage-conditioned media altered glucose uptake, and IL6 and JAK/STAT3 signaling contribute to this effect.

CONCLUSIONS

SUV_max is a prognostic marker in cervical cancer that is associated with activation of inflammatory pathways and tumor infiltration of myeloid-derived immune cells, particularly macrophages. Macrophages contribute to changes in cervical cancer glucose metabolism.See related commentary by Williamson et al., p. 4136.

Integrating imaging and RNA-seq improves outcome prediction in cervical cancer

Approaches using a single type of data have been applied to classify human tumors. Here we integrate imaging features and transcriptomic data using a prospectively collected tumor bank. We demonstrate that increased maximum standardized uptake value on pretreatment 18F-fluorodeoxyglucose-positron emission tomography correlates with epithelial-to-mesenchymal transition (EMT) gene expression. We derived and validated 3 major molecular groups, namely squamous epithelial, squamous mesenchymal, and adenocarcinoma, using prospectively collected institutional (n = 67) and publicly available (n = 304) data sets. Patients with tumors of the squamous mesenchymal subtype showed inferior survival outcomes compared with the other 2 molecular groups. High mesenchymal gene expression in cervical cancer cells positively correlated with the capacity to form spheroids and with resistance to radiation. CaSki organoids were radiation-resistant but sensitive to the glycolysis inhibitor, 2-DG. These experiments provide a strategy for response prediction by integrating large data sets, and highlight the potential for metabolic therapy to influence EMT phenotypes in cervical cancer.

Quinalphos Tolerant Endophytic Bacillus sp. Fcl1 and its Toxicity-Alleviating Effect in Vigna unguiculata

In order to meet the agricultural requirement for the expanding population, pesticides have been used regularly even with their severe threat. The uncontrolled use of these pesticides can cause irreparable damage to both soil and plant-associated microbiome. Therefore, an environment friendly alternative to enhance plant productivity and yield is highly important. Here comes the importance of endophytic microorganisms with multi-plant beneficial mechanisms to protect plants from the biotic and abiotic stress factors. However, their performance can be negatively affected under pesticide exposure. Hence the present study was conducted to analyse the tolerating ability of a Bacillus sp. Fcl1 which was originally isolated from the rhizome of Curcuma longa towards the pesticide quinalphos and also its ability to reduce the quinalphos-induced toxicity in Vigna unguiculata. The results revealed that the viability of endophytic Bacillus sp. Fcl1 depended on the concentration of quinalphos used for the study. Further, Fcl1 supplementation was found to alleviate the quinalphos-induced toxicity in Vigna unguiculata seedlings. The study is environmentally significant due to the pesticide tolerating and alleviating effect of Bacillus sp. Fcl1 in quinalphos-induced plant toxicity. This could suggest the application of microbes of endophytic origin as an efficient bioinoculant for field application even in the presence of pesticide residues.

Glutaminase Inhibitors Induce Thiol-Mediated Oxidative Stress and Radiosensitization in Treatment-Resistant Cervical Cancers

The purpose of this study was to determine if radiation (RT)-resistant cervical cancers are dependent upon glutamine metabolism driven by activation of the PI3K pathway and test whether PI3K pathway mutation predicts radiosensitization by inhibition of glutamine metabolism. Cervical cancer cell lines with and without PI3K pathway mutations, including SiHa and SiHa PTEN^-/- cells engineered by CRISPR/Cas9, were used for mechanistic studies performed in vitro in the presence and absence of glutamine starvation and the glutaminase inhibitor, telaglenastat (CB-839). These studies included cell survival, proliferation, quantification of oxidative stress parameters, metabolic tracing with stable isotope-labeled substrates, metabolic rescue, and combination studies with L-buthionine sulfoximine (BSO), auranofin (AUR), and RT. In vivo studies of telaglenastat ± RT were performed using CaSki and SiHa xenografts grown in immune-compromised mice. PI3K-activated cervical cancer cells were selectively sensitive to glutamine deprivation through a mechanism that included thiol-mediated oxidative stress. Telaglenastat treatment decreased total glutathione pools, increased the percent glutathione disulfide, and caused clonogenic cell killing that was reversed by treatment with the thiol antioxidant, N-acetylcysteine. Telaglenastat also sensitized cells to killing by glutathione depletion with BSO, thioredoxin reductase inhibition with AUR, and RT. Glutamine-dependent PI3K-activated cervical cancer xenografts were sensitive to telaglenastat monotherapy, and telaglenastat selectively radiosensitized cervical cancer cells in vitro and in vivo These novel preclinical data support the utility of telaglenastat for glutamine-dependent radioresistant cervical cancers and demonstrate that PI3K pathway mutations may be used as a predictive biomarker for telaglenastat sensitivity.

4-4' Diaponeurosporenic Acid, the C30 Carotenoid Pigment in Endophytic Pseudomonas Mendocina with Squalene Cyclase Activity

Even though organisms with squalene hopene cyclase activity involved in hopanoid synthesis has been reported earlier, their existence along with carotenoid synthesis is rarely reported. Here, we report the existence of hopanoid and C₃₀ carotenoid biosynthetic pathway in Pseudomonas mendocina, the squalene hopene cyclase producing endophyte of the medicinal plant Murraya koenigii. The enzyme squalene hopene cyclase from Pseudomonas mendocina is involved in the synthesis of dehydrosqualene-mediated alternate pathway for carotenoid biosynthesis. The hopanoids are involved in membrane stability and integrity, and the carotene chromophores are involved in the photo protection of the cell. The orange-colored C₃₀ carotenoid pigment 4-4' diaponeurosporenic acid in the extracellular extract of Pseudomonas mendocina with squalene cyclase activity was detected by the combination of UV/Vis spectrometry, FTIR, and Mass Spectrometry. 4-4' diaponeurosporenic acid could be traced as the end product of the carotenoid pathway and belonged to the xanthophyll group of carotenoids.

A novel three-stage bioreactor for the effective detoxification of sodium dodecyl sulphate from wastewater

Anionic surfactants like sodium dodecyl sulphate (SDS), due to its extensive disposal to water bodies cause detrimental effects to the ecosystem. Among the various attempts to reduce the after effects of these toxicants, microbial induced bioremediation serves as a promising strategy. The current study aimed to develop a three stage bioreactor to remediate anionic surfactants in wastewater using effective bacterial isolates. Screening of effective SDS biodegraders led to isolation of Pseudomonas aeruginosa (MTCC 10311). Treatment of synthetic effluent with an immobilized packed bed reactor at a flow rate of 5 mL h^-1 resulted in 81 ± 2% SDS eliminations and 70 ± 1% reduction in chemical oxygen demand (COD) in five cycles (6 h per cycle). The hydraulic retention time of the reactor was found to be 6 h. Combinatorial usage of a three stage bioreactor, involving aeration, adsorption with low cost scrap rubber granules and treatment with immobilized Pseudomonas aeruginosa, successfully reduced SDS concentrations and COD of wastewater to 99.8 ± 0.1% and 99 ± 1%, respectively, in 18 h by continuous treatment. Half-life of the three stage bioreactor was 72 h. In addition to reducing the surfactant concentrations, this novel bioreactor could resolve the surfactant associated foaming problems in treatment plants, which make it more unique.

Hypokalaemic paralysis and normocalcaemic tetany--a rare presentation of Sjogren's syndrome

38 year old woman was admitted with acute onset of quadriplegia. Biochemical investigation revealed severe hypokalaemia with hyperchloraemic metabolic acidosis, alkaline urine, and positive urinary anion gap which are the hallmark of distal tubular acidosis. In addition she also had hypophosphataemia, normoglycaemic glycosuria, aminoaciduria, and hyperphosphaturia suggestive of proximal tubular dysfunction. Further evaluation confirmed the diagnosis of Sjogren's syndrome. Interestingly our patient also had carpopedal spasm despite normal calcium and magnesium level. Quadriplegia and carpopedal spasm improved with correction of hypokalaemia and acidosis. Proximal tubular abnormalities (except albuminuria) were normalised at the time of discharge. Distal tubular acidosis is a well known renal manifestation of Sjogren's syndrome. But this type of transient proximal tubular dysfunction with distal tubular acidosis in Sjogren's syndrome is very rare and hypokalaemic tetany also deserves mention.

Production and characterization of rhamnolipid biosurfactant from waste frying coconut oil using a novel Pseudomonas aeruginosa D

AIM

To improve biosurfactant production economics by the utilization of potential low-cost materials.

METHODS AND RESULTS

In an attempt to utilize cost-effective carbon sources in the fermentative production of biosurfactants, various pure and waste frying oils were screened by a standard biosurfactant producing strain. Considering the regional significance, easy availability and the economical advantages, waste frying coconut oil was selected as the substrate for further studies. On isolation of more competent strains that could use waste frying coconut oil efficiently as a carbon source, six bacterial strains were isolated on cetyltrimethyl ammonium bromide-methylene blue agar plate, from a soil sample collected from the premises of a coconut oil mill. Among these, Pseudomonas aeruginosa D was selected as the potential producer of rhamnolipid. Spectrophotometric method, TLC, methylene blue active substance assay, drop collapse technique, surface tension measurement by Du Nouy ring method and emulsifying test confirmed the rhamnolipid producing ability of the selected strain and various process parameters were optimized for the production of maximum amount of biosurfactant. Rhamnolipid components purified and separated by ethyl acetate extraction, preparative silica gel column chromatography, HPLC and TLC were characterized by fast atom bombardment mass spectrometry as a mixture of dirhamnolipids and monorhamnolipids. The rhamnolipid homologues detected were Rha-Rha-C(10) -C(10) , Rha-C(12) -C(10) and Rha-C(10) -C(8) /Rha-C(8) -C(10) .

CONCLUSION

These results indicated the possibility of waste frying coconut oil to be used as a very effective alternate substrate for the economic production of rhamnolipid by a newly isolated Ps. aeruginosa D.

SIGNIFICANCE AND IMPACT OF THE STUDY

Results of this study throws light on the alternate use of already used cooking oil as high-energy source for producing a high value product like rhamnolipid. This would provide options for the food industry other than the recycling and reuse of waste frying oils in cooking and also furthering the value of oil nuts.

Microbial degradation of microcystin in Florida's freshwaters

Presence of microcystin (MC), a predominant freshwater algal toxin and a suspected liver carcinogen, in Florida's freshwaters poses serious health threat to humans and aquatic species. Being recalcitrant to conventional physical and chemical water treatment methods, biological methods of MC removal is widely researched. Water samples collected from five sites of Lake Okeechobee (LO) frequently exposed to toxic Microcystis blooms were used as inoculum for enrichment with microcystin LR (MC-LR) supplied as sole C and N source. After 20 days incubation, MC levels were analyzed using high performance liquid chromatography (HPLC). A bacterial consortium consisting of two isolates DC7 and DC8 from the Indian Prairie Canal sample showed over 74% toxin degradation at the end of day 20. Optimal temperature requirement for biodegradation was identified and phosphorus levels did not affect the MC biodegradation. Based on 16S rRNA sequence similarity the isolate DC8 was found to have a match with Microbacterium sp. and the DC7 isolate with Rhizobium gallicum (AY972457).

Lung and lupus vulgaris

Lupus vulgaris is chronic, postprimary, paucibacillary cutaneous tuberculosis found in individuals with moderate immunity and high degree of tuberculin sensitivity. Eighty percent of the lesions are on the head and neck. We present the case of a 38 year old lady who was admitted with complaints of worsening breathlessness and low grade fever of one month duration. Examination showed multiple, nontender skin ulcers on bilateral lumbar areas, two oozing serosanguinous discharge and others scarred in the centre. Respiratory system examination and chest X-ray revealed right sided pleural effusion. On investigation, pleural fluid was tuberculous in nature. Skin biopsy from the edge of ulcer was also suggestive of tuberculosis. Patient is doing well on antituberculous drugs. This case highlights the importance of cutaneous manifestations of systemic disease and is an example of the unusual presentation of lupus vulgaris in a case of pleural effusion.

Kikuchi-Fujimoto's disease: a report of five cases

Kikuchi Fujimoto's disease is a rare, self limiting disorder characterized by fever and cervical lymphadenitis. It is often an incidental finding in a patient suspected to have tuberculosis or lymphoproliferative disorder. We diagnosed this disease in a young 23-year-old female who was suffering from prolonged fever, cervical lymphadenopathy, anemia, leucopenia and mild splenomegaly; based on histopathological study of the excised lymphnode. We reviewed the clinical records and histopathologic findings of four more patients of Kikuchi-Fujimoto's disease, who were treated by others at our institute. All five patients improved with NSAIDS (non steroidal anti inflammatory drugs). Histopathological finding of histiocytic necrotizing lymphadenitis or Kikuchi's disease proved invaluable in characterization of these cases.

Endophytic Penicillium citrinum Thom. from Scoparia dulcis Linn

Scoparia dulcis of Scrophulariaceae is an annual herb distributed through out the tropics. Penicillium citrinum was obtained from apparently healthy roots, stem, leaves and fruits of this plant. Callus and multiple shoots produced during micropropagation from various explants were also symptomless but showed occurrence of Penicillium citrinum when cultured in Murashige & Skoog liquid medium for the production of secondary metabolites.

Analysis of rhamnolipid biosurfactants produced through submerged fermentation using orange fruit peelings as sole carbon source

The fermentative production of rhamnolipid biosurfactant from Pseudomonas aeruginosa MTCC 2297 was carried out by submerged fermentation using various cost-effective waste materials such as orange peelings, carrot peel waste, lime peelings, coconut oil cake, and banana waste. The orange peel was found to be the best substrate generating 9.18 g/l of rhamnolipid biosurfactant with a surface tension reduction up to 31.3 mN/m. The production was growth independent, and optimum conditions were standardized. The emulsifying activity was highest against kerosene (73.3%). Rhamnolipid components were purified and separated by ethyl acetate extraction, preparative silica gel column chromatography, high-performance liquid chromatography and thin-layer chromatography. The major rhamnolipid components were characterized, by fast atom bombardment mass spectrometry, as a mixture of dirhamnolipids and monorhamnolipids.

Treatment of paper factory effluent using a phenol degrading Alcaligenes sp. under free and immobilized conditions

Treatment of the paper factory effluent was done with free and immobilized cells of a phenol degrading Alcaligenes sp. d(2). The free cells could bring a maximum of 99% reduction in phenol and 40% reduction in chemical oxygen demand (COD) after 32 and 20 h of treatment, respectively. In the case of immobilized cells, a maximum of 99% phenol reduction and 70% COD reduction was attained after 20 h of treatment under batch process. In the continuous mode of operation using packed bed reactor, the strain was able to give 99% phenol removal and 92% COD reduction in 8h of residence time The optimum flow rate was 2.5 ml/h and the half life period was 76 h. Even after the complete removal of phenol, the strain could further enhance reduction in chemical oxygen demand, which clearly indicated that in the paper factory effluent, this strain could also oxidize organic matter other than phenol.

Presence of arbuscular mycorrhizal fungi in South Florida native plants

The roots of 27 species of South Florida plants in 15 families (including one cycad, six palms, one Smilax, and 19 dicotyledons) native to pine rockland and tropical hardwood hammock communities were examined for arbuscular mycorrhizal fungi (AMF). These plants grow in the biologically diverse but endangered Greater Everglades habitat. Roots from field-grown and potted plants were cleared and stained. All 27 species had AMF and include 14 species having an endangered or threatened status. The Paris-type colonization occurred in two species in the families Annonaceae and Smilacaceae. The Arum-type occurred in 22 species in the families Anacardiaceae, Arecaceae (Palmae), Boraginaceae, Cactaceae (questionable), Euphorbiaceae, Fabaceae, Lauraceae, Melastomataceae, Polygalaceae, Rubiaceae, Simaroubaceae, Ulmaceae, and Zamiaceae. Three species in the families Fabaceae, Lauraceae, and Simaroubaceae had a mix of Paris- and Arum-types. The results have implications for the restoration of these endangered plant communities in the Everglades.

Phosphorus in periphyton mats provides the best metric for detecting low-level P enrichment in an oligotrophic wetland

Growing concern over the ecological consequence of phosphorus (P) enrichment in freshwater wetlands has elicited considerable debate over the concentration of water column P associated with eutrophication. In the oligotrophic Everglades, the displacement of native communities by enriched ones is widespread and has occurred at sites experiencing only minimal elevations in P input. To help define regulatory criteria for P inputs to the Everglades, we constructed an experiment that mimics P input to the natural system by continuously delivering P at concentrations elevated 5, 15 and 30 microgl(-1) above ambient to 100-m long flow-through channels. We compared patterns of P accumulation in the water, periphyton, detritus and soils among the channel treatments and also along a 16 km transect from an enriched canal that inflows to the interior of the same marsh. Water column TP and SRP were unrelated to input TP concentration in both the experiment and the marsh transect. However, concentrations of TP in periphyton mats were significantly elevated at all levels of experimental enrichment and as far as 2 km downstream from water inputs into the marsh. Elevated periphyton TP was associated with significant loss of periphyton biomass. In oligotrophic wetlands, traditional measures of water column SRP and TP will substantially underestimate P loading because biotically incorporated P is displaced from the water column to benthic surfaces. Using periphyton TP as a metric of P enrichment is uncomplicated and analogous to pelagic TP assessments in lakes where most P is sequestered in phytoplankton.

Treatment of Dairy Wastewater Using a Selected Bacterial Isolate, Alcaligenes sp. MMRR7

Physicochemical and biologic analysis of dairy wastewater showed that the effluent had a high organic load (chemical oxygen demand [COD]: 5095 mg/L), an acidic pH (6.4), and a high probability of coliforms (most probable number [MPN] >1100). The various bacterial strains isolated and purified were identified as Sporolactobacillus sp., Citrobacter sp., Pseudomonas sp., Alcaligenes sp., Bacillus sp., Staphylococcus sp., and Proteus sp., as per the Bergey's manual of systematic bacteriology. Among the five selected bacterial strains, the strain designated as MMRR7 and identified as Alcaligenes sp. was found to give a maximum reduction in COD (62%) in 5 d of incubation. Chemical coagulation using alum at a concentration of 0.5 g/100 mL was found to be effective in the primary treatment of the effluent. Studies on free-cell treatment of the coagulated effluent with the selected bacterial strain Alcaligenes sp. MMRR7 gave a maximum COD reduction of 91% in 120 h. This study clearly indicates the possibility of using Alcaligenes sp. MMRR7 for the effective treatment of dairy wastewater.

Chromium transport, oxidation, and adsorption in manganese-coated sand

We examine how the processes of advection, dispersion, oxidation-reduction, and adsorption combine to affect the transport of chromium through columns packed with pyrolusite (beta-MnO2)-coated sand. We find that beta-MnO2 effectively oxidizes Cr(III) to Cr(VI) and that the extent of oxidation is sensitive to changes in pH, pore water velocity, and influent concentrations of Cr(III). Cr(III) oxidation rates, although initially high, decline well before the supply of beta-MnO2 is depleted, suggesting that a reaction product inhibits the conversion of Cr(III) to Cr(VI). Rate-limited reactions govern the weak adsorption of each chromium species, with Cr(III) adsorption varying directly with pH and Cr(VI) adsorption varying inversely with pH. The breakthrough data on chromium transport can be matched closely by calculations of a simple model that accounts for (1) advective-dispersive transport of Cr(III), Cr(VI), and dissolved oxygen, (2) first-order kinetics adsorption of the reduced and oxidized chromium species, and (3) nonlinear rate-limited oxidation of Cr(III) to Cr(VI). Our work supplements the limited database on the transport of redox-sensitive metals in porous media and provides a means for quantifying the coupled processes that contribute to this transport.

Kinetics of chromium (VI) reduction by a type strain Shewanella alga under different growth conditions

We conducted kinetic batch experiments to determine the reduction of Chromium(VI) by a type strain of Shewanella alga (BrY-MT) ATCC 55627. Chromium(VI) was reduced to Chromium(III) by BrY-MT grown in three different substrates: BHIB (brain heart infusion broth), TSB (tryptic soy broth), and M9 (minimum broth). Four different Cr(VI) concentrations 4.836, 10.00, 37.125, and 260.00 mg l-1 were reduced at different rates by BrY-MT in both aerobic and anaerobic conditions. BrY-MT grown in BHIB reduced the maximum amount of Cr(VI) followed by TSB and M9. Carbondioxide produced from bacterial respiration varied with and without Cr(VI) under both aerobic and anaerobic conditions. The Cr(VI) reduction data under anaerobic condition was fitted by a monod model to determine the bacterial kinetic parameters. The kinetic parameters determined by fitting the anaerobic experimental data were used to run a forward simulation for experiments conducted under aerobic conditions. The monod model was modified to account for an inhibition parameter for the Cr(VI) experiment at 260 mg l-1. All the parameters varied within a narrow range, and were distinct for different substrates. Our studies show that, successful in situ bioremediation of Cr(VI) is depended on the type of substrates (electron donors) and the concentration of Cr(VI) in geologic medium.

Biodegradation of atrazine by Agrobacterium radiobacter J14a and use of this strain in bioremediation of contaminated soil

We examined the ability of a soil bacterium, Agrobacterium radiobacter J14a, to degrade the herbicide atrazine under a variety of cultural conditions, and we used this bacterium to increase the biodegradation of atrazine in soils from agricultural chemical distribution sites. J14a cells grown in nitrogen-free medium with citrate and sucrose as carbon sources mineralized 94% of 50 microgram of [14C-U-ring]atrazine ml-1 in 72 h with a concurrent increase in the population size from 7.9 x 10(5) to 5.0 x 10(7) cells ml-1. Under these conditions cells mineralized the [ethyl-14C]atrazine and incorporated approximately 30% of the 14C into the J14a biomass. Cells grown in medium without additional carbon and nitrogen sources degraded atrazine, but the cell numbers did not increase. Metabolites produced by J14a during atrazine degradation include hydroxyatrazine, deethylatrazine, and deethyl-hydroxyatrazine. The addition of 10(5) J14a cells g-1 into soil with a low indigenous population of atrazine degraders treated with 50 and 200 microgram of atrazine g-1 soil resulted in two to five times higher mineralization than in the noninoculated soil. Sucrose addition did not result in significantly faster mineralization rates or shorten degradation lag times. However, J14a introduction (10(5) cells g-1) into another soil with a larger indigenous atrazine-mineralizing population reduced the atrazine degradation lag times below those in noninoculated treatments but did not generally increase total atrazine mineralization.

Acute pancreatitis with disseminated intravascular coagulation

Acute Pancreatitis is seen very frequently. We report a case of acute pancreatitis with a rare complication of disseminated intravascular coagulation (DIC), who recovered completely.