1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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2. |
- Kar, Rohan, et al.
(författare)
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The FBXW7-NOTCH interactome : A ubiquitin proteasomal system-induced crosstalk modulating oncogenic transformation in human tissues
- 2021
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Ingår i: Cancer Reports. - : John Wiley & Sons. - 2573-8348. ; 4:4
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Forskningsöversikt (refereegranskat)abstract
- Background Ubiquitin ligases or E3 ligases are well programmed to regulate molecular interactions that operate at a post-translational level. Skp, Cullin, F-box containing complex (or SCF complex) is a multidomain E3 ligase known to mediate the degradation of a wide range of proteins through the proteasomal pathway. The three-dimensional domain architecture of SCF family proteins suggests that it operates through a novel and adaptable "super-enzymatic" process that might respond to targeted therapeutic modalities in cancer. Recent findings Several F-box containing proteins have been characterized either as tumor suppressors (FBXW8, FBXL3, FBXW8, FBXL3, FBXO1, FBXO4, and FBXO18) or as oncogenes (FBXO5, FBXO9, and SKP2). Besides, F-box members like beta TrcP1 and beta TrcP2, the ones with context-dependent functionality, have also been studied and reported. FBXW7 is a well-studied F-box protein and is a tumor suppressor. FBXW7 regulates the activity of a range of substrates, such as c-Myc, cyclin E, mTOR, c-Jun, NOTCH, myeloid cell leukemia sequence-1 (MCL1), AURKA, NOTCH through the well-known ubiquitin-proteasome system (UPS)-mediated degradation pathway. NOTCH signaling is a primitive pathway that plays a crucial role in maintaining normal tissue homeostasis. FBXW7 regulates NOTCH protein activity by controlling its half-life, thereby maintaining optimum protein levels in tissue. However, aberrations in the FBXW7 or NOTCH expression levels can lead to poor prognosis and detrimental outcomes in patients. Therefore, the FBXW7-NOTCH axis has been a subject of intense study and research over the years, especially around the interactome's role in driving cancer development and progression. Several studies have reported the effect of FBXW7 and NOTCH mutations on normal tissue behavior. The current review attempts to critically analyze these mutations prognostic value in a wide range of tumors. Furthermore, the review summarizes the recent findings pertaining to the FBXW7 and NOTCH interactome and its involvement in phosphorylation-related events, cell cycle, proliferation, apoptosis, and metastasis. Conclusion The review concludes by positioning FBXW7 as an effective diagnostic marker in tumors and by listing out recent advancements made in cancer therapeutics in identifying protocols targeting the FBXW7-NOTCH aberrations in tumors.
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3. |
- Kar, Sandeep, et al.
(författare)
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Health risks for human intake of aquacultural fish : Arsenic bioaccumulation and contamination
- 2011
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Ingår i: Journal of Environmental Science and Health. Part A. - : Informa UK Limited. - 1093-4529 .- 1532-4117. ; 46:11, s. 1266-1273
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Tidskriftsartikel (refereegranskat)abstract
- Aquacultural tilapia (Oreochromis mossambicus L.) and shrimp (Penaeus monodon L.) from groundwater-cultured ponds in southwestern Taiwan were analyzed to estimate arsenic (As) bioaccumulation and the potential health risk to human intake. Most of aquacultural ponds exhibited higher arsenic than maximum allowed concentrations (50 mu g L(-1)) in pond water of Taiwan. Arsenic levels in tilapia in Budai, Yichu and Beimen were 0.92 +/- 0.52 mu g g(-1), 0.93 +/- 0.19 mu g g(-1) and 0.76 +/- 0.03 mu g g(-1), respectively and in shrimp was 0.36 +/- 0.01 mu g g(-1) in Beimen. Total arsenic in tilapia is highly correlated (R(2) = 0.80) with total arsenic concentration of pond water. Total arsenic in fish showed high correlation with that in bone (R(2) = 0.98), head (R(2) = 0.97) and tissue (R(2) = 0.96). Organic arsenic species (DMA) was found higher relative to inorganic species of As(III) and As(V). The average percent contribution of inorganic arsenic to total arsenic in fish samples was 12.5% and ranged between 11.7 to 14.2%. Bioaccumulation factors (BAFs) for total arsenic in fish ranged from 10.3 to 22.1, whereas BAF for inorganic arsenic ranged from 1.33 to 2.82. The mean human health cancer risk associated with the ingestion of inorganic arsenic in the fish was estimated at 2.36 x 10(-4) +/- 0.99 x 10(-4), which is over 200 times greater than a de Minimus cancer risk of 1 x 10(-6). The mean human health hazard quotient associated with ingesting inorganic arsenic in the fish was 1.22 +/- 0.52, indicating that expected human exposure exceeds the reference dose for non-cancer health effects by 22%. These results suggest that the inhabitants in this region are being subjected to moderately elevated arsenic exposure through the consumption of tilapia and shrimp raised in aquaculture ponds.
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4. |
- Kar, Sandeep, et al.
(författare)
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Role of organic matter and humic substances in the binding and mobility of arsenic in a Gangetic aquifer
- 2011
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Ingår i: Journal of Environmental Science and Health. Part A. - : Informa UK Limited. - 1093-4529 .- 1532-4117. ; 46:11, s. 1231-1238
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Tidskriftsartikel (refereegranskat)abstract
- Arsenic (As) enrichment in groundwater has led to extensive research, particularly on the factors responsible for its release into groundwater. In the Gangetic plain, organic matter driven microbial reduction of Fe-oxyhydroxides is considered as the most plausible mechanism of As release into groundwater. However, the role of organic matter in the aqueous environment is not well known and particularly that of organometallic complex. In this study, we have characterized bulk sediment and groundwater samples, collected from Barasat, West Bengal, India, to understand the effect of organic matter in the binding and mobility of As in the subsurface environment. The results showed a moderate correlation (R(2) = 0.49, p < 0.05) between dissolved organic carbon (DOC) and As in groundwater, suggesting that DOC has a role in releasing As into groundwater. The relative fluorescent intensity (RFI) of the dissolved humic substances in groundwater showed a maximum value of 65 QSU (mean: 47 +/- 8 QSU). FT-IR spectra of the extracted humic acid fractions of the sediment showed COO-, C = O, OH, and C = C (aromatic ring) functional groups, which may act as a chelating agents with the metal(loid)s. FT-IR spectra of the HA-As complex exhibited specific peaks at 1242 and 832 cm(-1) in the fingerprint region. This is similar to the extracted humic acid fractions of the Gangetic sediment, suggesting binding of As with humic substances.
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5. |
- Liu, Chia-Chuan, et al.
(författare)
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Biogeochemical interactions among the arsenic, iron, humic substances, and microbes in mud volcanoes in southern Taiwan
- 2011
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Ingår i: Journal of Environmental Science and Health. Part A. - : Informa UK Limited. - 1093-4529 .- 1532-4117. ; 46:11, s. 1218-1230
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Tidskriftsartikel (refereegranskat)abstract
- Fluid and mud samples collected from Hsiaokunshui (HKS), Wushanting (WST), Yenshuikeng (YSK), Kunshuiping (KSP), Liyushan (LYS), and Sinyangnyuhu (SYNH) mud volcanoes of southwestern Taiwan were characterized for major ions, humic substances (HS) and trace elements concentrations. The relationship between the release of arsenic (As) and activities of sulfate-reducing bacteria has been assessed to understand relevant geochemical processes in the mud volcanoes. Arsenic (0.02-0.06 mg/L) and humic substances (4.13 x 10(-4) to 1.64 x 10(-3) mM) in the fluids of mud volcanoes showed a positive correlation (r = 0.99, p < 0.05) except in Liyushan mud volcano. Arsenic and iron in mud sediments formed two separate groups i) high As, but low Fe in HKS, WST, and SYNH; and ii) low As, but high Fe in the YSK, KSP, and LYS mud volcanoes. The Eh(S.H.E). values of the mud volcano liquids were characterized by mild to strongly reducing conditions. The HKS, SYNH, and WST mud volcanoes (near the Chishan Fault) belongs to strong reducing environment (-33 to -116 mV), whereas the LYS, YSK, and KSP mud volcanoes located near the coastal plain are under mild reducing environment (-11 to 172 mV). At low Eh values mud volcanoes, saturation index (SI) values of poorly crystalline phases such as amorphous ferric hydroxide indicate understaturation, whereas saturation is reached in relatively high Eh(S.H.E.) values mud volcanoes. Arsenic contents in sediments are low, presumably due to its release to fluids (As/Fe ratio in YSK, KSP, and LYS sediment: 4.86 x 10(-4)-6.20 x 10(-4)). At low Eh(S.H.E.) values (mild to strong reducing environment), arsenic may co-precipitate with sulfides as a consequence of sulfate reduction (As/Fe ratios in WST, HKS, and SYNH sediments: 0.42-0.69).
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6. |
- Maity, Jyoti Prakash, et al.
(författare)
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Arsenic-enriched groundwaters of India, Bangladesh and Taiwan-Comparison of hydrochemical characteristics and mobility constraints
- 2011
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Ingår i: Journal of Environmental Science and Health. Part A. - : Informa UK Limited. - 1093-4529 .- 1532-4117. ; 46:11, s. 1163-1176
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Tidskriftsartikel (refereegranskat)abstract
- Arsenic (As) enrichment in groundwater has become a major global environmental disaster. Groundwater samples were collected from 64 sites located in the districts of 24-Parganas (S), and Nadia in West Bengal, India (Bhagirathi sub-basin), and 51 sites located in the districts of Comilla, Noakhali, Magura, Brahman baria, Laxmipur, Munshiganj, Faridpur and Jhenaida in Bangladesh (Padma-Meghna sub-basin). Groundwater samples were also collected from two As-affected areas (Chianan and Lanyang plains) of Taiwan (n = 26). The concentrations of major solutes in groundwater of the Padma-Meghna sub-basin are more variable than the Bhagirathi sub-basin, suggesting variations in the depositional and hydrological settings. Arsenic concentrations in groundwaters of the studied areas showed large variations, with mean As concentrations of 125 mu g/L (range: 0.20 to 1,301 mu g/L) in Bhagirathi sub-basin, 145 mu g/L (range: 0.20 to 891 mu g/L) in Padma-Meghna sub-basin, 209 mu g/L (range: 1.3 to 575 mu g/L) in Chianan plain, and 102 mu g/L (range: 2.5 to 348 mu g/L) in Lanyang plain groundwater. The concentrations of Fe, and Mn are also highly variable, and are mostly above the WHO-recommended guideline values and local (Indian and Bangladeshi) drinking water standard. Piper plot shows that groundwaters of both Bhagirathi and Padma-Meghna sub-basins are of Ca-HCO(3) type. The Chianan plain groundwaters are of Na-Cl type, suggesting seawater intrusion, whereas Lanyang plain groundwaters are mostly of Na-HCO(3) type. The study shows that reductive dissolution of Fe(III)-oxyhydroxides is the dominant geochemical process releasing As from sediment to groundwater in all studied areas.
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7. |
- Maity, Jyoti Prakash, et al.
(författare)
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Arsenic-induced health crisis in peri-urban Moyna and Ardebok villages, West Bengal, India : an exposure assessment study
- 2012
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Ingår i: Environmental Geochemistry and Health. - : Springer Science and Business Media LLC. - 0269-4042 .- 1573-2983. ; 34:5, s. 563-574
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Tidskriftsartikel (refereegranskat)abstract
- Drinking of arsenic (As)-contaminated groundwater has adverse effects on health of millions of people worldwide. This study aimed to determine the degree of severity of As exposure from drinking water in peri-urban Moyna and Ardebok villages, West Bengal, India. Arsenic concentrations in hair, nail and urine samp les of the individuals were determined. Arsenical dermatosis, keratosis and melanosis were investigated through medical evaluation. We have evaluated the association between As exposure from drinking water, and keratosis and melanosis outcomes. The results showed that 82.7 % of the sampled tube wells contain As concentrations above 10 mu g/L, while 57.7 % contain As concentrations above 50 mu g/L. The hair, nail and urine As concentrations were positively correlated with As concentrations in drinking water. In our study population, we observed a strong association between As concentrations ranging 51-99 mu g/L and keratosis and melanosis outcomes, although the probability decreases at higher concentration ranges perhaps due to switching away from the use of As-contaminated tube wells for drinking and cooking purposes. High As concentrations in hair, nail and urine were observed to be associated with the age of the study population. The level of As concentrations in hair, nail and urine samples of the study population indicated the degree of severity of As exposure in the study region.
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8. |
- Maity, Jyoti Prakash, et al.
(författare)
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Biogeochemical characteristics of Kuan-Tzu-Ling, Chung-Lun and Bao-Lai hot springs in southern Taiwan
- 2011
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Ingår i: Journal of Environmental Science and Health. Part A. - : Informa UK Limited. - 1093-4529 .- 1532-4117. ; 46:11, s. 1207-1217
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Tidskriftsartikel (refereegranskat)abstract
- Hot springs are the important natural sources of geothermally heated groundwater from the Earth's crust. Kuan-Tzu-Ling (KTL), Chung-Lun (CL) and Bao-Lai (BL) are well-known hot springs in southern Taiwan. Fluid and mud (sediments) samples were collected from the eruption points of three hot springs for detailed biogeochemical characterization. The fluid sample displays relatively high concentrations of Na(+) and Cl(-) compared with K(+), Mg(2+), Ca(2+), NO(2)(-), and SO(4)(2-), suggesting a possible marine origin. The concentrations of Fe, Cr, Mn, Ni, V and Zn were significantly higher in the mud sediments compared with fluids, whereas high concentrations of As, Ba, Cu, Se, Sr and Rb were observed in the fluids. This suggests that electronegative elements were released during sediment-water interactions. High As concentration in the fluids was observed to be associated with low redox (Eh) conditions. The FTIR spectra of the humic acid fractions of the sediments showed the presence of possible functional groups of secondary amines, ureas, urethanesm (amide), and silicon. The sulfate-reducing deltaproteobacterium 99% similar to Desulfovibrio psychrotolerans (GU329907) were rich in the CL hot spring while mesophilic, proteolytic, thiosulfate-and sulfur-reducing bacterium that 99% similar to Clostridium sulfidigenes (GU329908) were rich in the BL hot spring.
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9. |
- Maity, Jyoti Prakash, et al.
(författare)
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The potential for reductive mobilization of arsenic [As(V) to As(III)] by OSBH(2) (Pseudomonas stutzeri) and OSBH(5) (Bacillus cereus) in an oil-contaminated site
- 2011
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Ingår i: Journal of Environmental Science and Health. Part A. - : Informa UK Limited. - 1093-4529 .- 1532-4117. ; 46:11, s. 1239-1246
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Tidskriftsartikel (refereegranskat)abstract
- Microbial reduction of arsenate [As(V)] plays an important role in arsenic (As) mobilization in aqueous environments. In this study, we investigated reduction of arsenate by different bacterial isolates such as OSBH(1) (GU329913), OSBH(2) (GU329914), OSBH(3) (GU329915), OSBH(4) (GU329916) and OSBH(5) (GU329917), isolated from the oil sludge of a sewage treatment plant operated by the China Petroleum Refinery Company in Kaohsiung, southern Taiwan. Bacterial strains of pure culture were identified by 16S rRNA analysis (>= 99 % nucleotide similarity). Morphological and 16S rRNA analysis show that the isolate OSBH(1) is similar to E. coli, OSBH(2) is similar to P. stutzeri, OSBH(3) is similar to P. putida, OSBH(4) is similar to P. aeruginosa, and OSBH(5) is similar to B. Cereus. The As(V) was transformed to As(III) in the presence of isolates OSBH(2) and OSBH(5) by a detoxification process. The potential reduction rates of As(V) were higher in the presence of isolate OSBH(5) compared to the isolate OSBH(2). The microbial growth (cell/mL) of isolate OSBH(5) was significantly higher in culture medium compared to OSBH(2). The bacterial isolates such as OSBH(1), OSBH(3) and OSBH(4) were found to be incapable of transforming the As(V). It is concluded that the activity of the oil-degrading bacterial isolates described in this work contributes to the mobilization of As in the more toxic As(III) form that affects biotic life.
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