Storing self-contained gel capillary cassettes for POC medical diagnostics

For effective clinical uptake of the lab on a chip/point of care technology (LOC-POC), in addition to cost advantages LOC-POC devices should offer multiple patient screening panels for related diseases as well as cold-chain transportation and storage abilities. We recently described a device that performs polymerase chain reaction (PCR) to simultaneously screen raw clinical samples from up to 16 patients for multiple infectious agents (Manage et al., Lab Chip, 2013, 13, 2576–2584). This cassette contains glass capillaries with desiccated semi-solid acrylamide gels that include all the reagents except for the sample, with integrated quality control. Here we report the development of protocols to store assembled PCR cassettes at room temperature, 4 uC or 220 uC as well as at +40 uC. We show that our cassettes are stable, with no loss of activity for at least 3 months at RT and at least 7 months at 4 uC and 220 uC. However, the activity of desiccated cassettes degrades when stored for more than 2 weeks at 40 uC, insufficient time for postmanufacture delivery and use of cassette PCR. To address this, we have evaluated two stage storage protocols. PCR cassettes can initially be stored at 4 uC and 220 uC for prolonged periods of time and removed for shorter term storage at RT, retaining activity for at least a month, which would facilitate transport to remote areas for testing. Effective use of cassette PCR in high temperature regions of the world, for experimental purposes defined here as 40 uC, appears to be feasible only after a first stage storage in the cold, followed by no more than 1 week at 40 uC. This should allow sufficient time for delivery by the manufacturer to a central area well served by power and refrigeration, for later ambient temperature transport and use in under-resourced areas that lack refrigeration

Evaluation of Groundwater Quality in Five Grama Divisions of Maharagama Urban Area Using Groundwater Quality Index (WQI)

Maharagama urban area is a heavily populated area in Colombo district. Groundwater in this area is having a great vulnerability for pollution by anthropogenic activities. The present study was carried out to monitor some important water quality parameters, to evaluate the quality of groundwater in the study area using a Water Quality Index (WQI) and to compare the water quality between Grama Niladari (GN) divisions in the study area. Five GN divisions (Jambugasmulla, Gangodawila south B, Wijerama, Navinna and Wattegedara) were selected for the study. 55 wells were sampled during the study. The resulted WQI values in groundwater ranged from 17.08 to 280.91. The results revealed that the water quality of the wells deviate from excellent to very poor quality. The nitrate concentration was high (>45mg/l) in some wells. Considering all the water quality parameters, the poorest water quality was recorded in Navinna GN division. It was observed that unregulated garbage dumping, uncontrolled application of organic and inorganic fertilizers, constructing toilet pits very close to wells and unregulated human settlements have been increasing in the study area. KEYWORDS: Ground water, nitrate, water quality, water quality inde

Invasive Aquatic Plants as Potential Sustainable Feedstocks for Biochar Production and as an Innovative Approach for Wastewater Treatment

Biochar (BC) is a well-established physical treatment method. The high-cost BC limits their use as adsorbents in wastewater. Thus, deriving BC from cheap and locally available waste materials is needed to develop a feasible waste removal technology. Nowadays, BC technology makes it possible to envision a new strategy to manage invasive plants by converting them into value-added products like BC. Hence, the present study was designed to evaluate the potential utilization of BC as an efficient filter medium made by invasive aquatic plants, Salvinia spp., and Eichhornia spp. A mass of 50 g of prepared activated and nonactivated BC was incorporated in a sand and gravel filter to treat rubber-manufactured wastewater. Wastewater was passed through the filter, and both raw and treated water samples were analyzed for pH, Total Suspended Solids (TSS), Biological Oxygen Demand (BOD5), Chemical Oxygen Demand (COD), Total Kjeldahl Nitrogen (TKN), Ammoniacal-Nitrogen (NH3-N), Electrical Conductivity (EC), Total Dissolved Solids (TDS), Total Phosphates (TP), Nitrate (NO3-N), turbidity and heavy metals (Zinc, Chromium). The control filter was developed only with sand and gravel, excluding BC. Fourier Transform-Infrared Spectroscopy (FT-IR) and Scanning electron microscopy (SEM) were used to analyze BC’s chemical and physical characteristics. A brine shrimp lethality assay was carried out for toxicological evaluation. OH stretching (3,550-3,200 cm−1), C=C aromatic stretching (1400-1660 cm−1), and Phenol-O-H bending (1,300-1,400 cm−1) were recorded in all BC samples that involved the adsorption mechanism. Observed images indicated differences in surface morphology of both activated and nonactivated BC were observed under SEM observation. The study concludes that the filter unit incorporated with activated Eichhornia spp. Gave the best treatment efficiency when compared to filter units incorporated with other activated and nonactivated BC. The toxicity assay revealed 100% mortality in the control setup and raw wastewater but only 60–70% in the nonactivated BC integrated filters. Activated BC-incorporated filters showed no mortalities. Hence, the study’s outcomes suggest a green approach using invasive aquatic plants for sustainable wastewater treatment

Formulation of Novel Microbial Consortia for Rapid Composting of Biodegradable Municipal Solid Waste: An Approach in the Circular Economy

Urbanization and rapid industrialization have led to the escalation of municipal solid waste generation and accumulation. Composting is widely recognized as a sustainable solution for solid waste management. However, its long-term investment is considered a disadvantage. The present research study discusses the rapid biotransformation of solid waste into valorized compost. Bacteria were isolated from soil, solid waste, and leachate samples from open dump sites. From the 18 different bacterial consortia created using potential isolates, the five most promising consortia were selected based on concurrent different enzyme production. These selected consortia were incorporated into typical compost bins with Municipal Solid Waste (MSW). Daily monitoring of enzymatic activity, pH, conductivity, bulk density, moisture, and temperature, along with other composting parameters, was conducted. The study’s results demonstrated that consortium No. 5, comprising Bacillus haynesii, Bacillus amyloliquefaciens, and Bacillus safensis, exhibited significant (p<0.05) enzyme activity of cellulase, amylase, lipase and proteinase enzymes during composting compared to the control and other treatment setups. Consortium No. 5 also facilitated rapid and successful composting, as evidenced by significant alterations of composting parameters by exhibiting a shorter average composting time, reducing it from 110±10 days to 20±3 days, showcasing the potential applicability of formulated bacterial consortium as a sustainable and greener approach to the global solid waste problem. The novelty of this study lies in the isolation of local bacterial strains from open dump sites soil, MSW, and MSW leachate samples, which were then utilized in the composting organic fraction of MSW, enhancing the potential for effective waste management

An enclosed in-gel PCR amplification cassette with multi-target, multi-sample detection for platform molecular diagnostics

This work describes a self-contained, simple, disposable, and inexpensive gel capillary cassette for DNA amplification in near point of care settings. The cassette avoids the need for pumps or valves during raw sample delivery or polymerase chain reaction (PCR) amplification steps. The cassette contains capillary reaction units that can be stored at room temperature for up to 3 months. The current cassette configuration format can simultaneously tests up to 16 patients for two or more targets, accommodates different sample types on the same cassette, has integrated positive and negative controls and allows flexibility for multiple geometries. PCR reagents in the cassette are desiccated to allow storage at room temperature with rehydration by raw sample at the time of testing. The sample is introduced to the cassette via a transfer pipette simply by capillary force. DNA amplification was carried out in a portable prototype instrument for PCR thermal cycling with fluorescence detection of amplified products by melt curve analysis. To demonstrate performance, raw genital swabs and urine were introduced to the same cassette to simultaneously detect four sexually transmitted infections. Herpes Simplex Viruses (HSV-1 and HSV-2) were detected from raw genital swabs. Ureaplasma Urealyticum (UU) and Mycoplasma Homonis (MH) were detected from raw urine. Results for multiple patients were obtained in as little as 50'. This platform allows multiparameter clinical testing with a pre-assembled cassette that requires only the introduction of raw sample. Modification of the prototype device to accommodate larger cassettes will ultimately provide high throughput simultaneous testing of even larger numbers of samples for many different targets, as is required for most clinical applications. Combinations of wax and/or polymer cassettes holding capillary reaction units are feasible. The components of the cassette are suited to mass production and robotic assembly to produce a readily manufactured disposable reaction cassette that can be configured for disease-specific testing panels. Rapid testing with a disposable reaction cassette on an inexpensive instrument will permit on the spot evaluation of patients in the clinic for faster medical decision-making and more informed therapeutic choices

Local spatial structure of forest biomass and its consequences for remote sensing of carbon stocks

Advances in forest carbon mapping have the potential to greatly reduce uncertainties in the global carbon budget and to facilitate effective emissions mitigation strategies such as REDD+. Though broad scale mapping is based primarily on remote sensing data, the accuracy of resulting forest carbon stock estimates depends critically on the quality of field measurements and calibration procedures. The mismatch in spatial scales between field inventory plots and larger pixels of current and planned remote sensing products for forest biomass mapping is of particular concern, as it has the potential to introduce errors, especially if forest biomass shows strong local spatial variation. Here, we used 30 large (8–50 ha) globally distributed permanent forest plots to quantify the spatial variability in aboveground biomass (AGB) at spatial grains ranging from 5 to 250m (0.025–6.25 ha), and we evaluate the implications of this variability for calibrating remote sensing products using simulated remote sensing footprints. We found that the spatial sampling error in AGB is large for standard plot sizes, averaging 46.3% for 0.1 ha subplots and 16.6% for 1 ha subplots. Topographically heterogeneous sites showed positive spatial autocorrelation in AGB at scales of 100m and above; at smaller scales, most study sites showed negative or nonexistent spatial autocorrelation in AGB. We further show that when field calibration plots are smaller than the remote sensing pixels, the high local spatial variability in AGB leads to a substantial “dilution” bias in calibration parameters, a bias that cannot be removed with current statistical methods. Overall, our results suggest that topography should be explicitly accounted for in future sampling strategies and that much care must be taken in designing calibration schemes if remote sensing of forest carbon is to achieve its promise

Population Dynamics and Diversity of Viruses, Bacteria and Phytoplankton in a Shallow Eutrophic Lake

We have studied the temporal variation in viral abundances and community assemblage in the eutrophic Lake Loosdrecht through epifluorescence microscopy and pulsed field gel electrophoresis (PFGE). The virioplankton community was a dynamic component of the aquatic community, with abundances ranging between 5.5 × 107 and 1.3 × 108 virus-like particles ml−1 and viral genome sizes ranging between 30 and 200 kb. Both viral abundances and community composition followed a distinct seasonal cycle, with high viral abundances observed during spring and summer. Due to the selective and parasitic nature of viral infection, it was expected that viral and host community dynamics would covary both in abundances and community composition. The temporal dynamics of the bacterial and cyanobacterial communities, as potential viral hosts, were studied in addition to a range of environmental parameters to relate these to viral community dynamics. Cyanobacterial and bacterial communities were studied applying epifluorescence microscopy, flow cytometry, and denaturing gradient gel electrophoresis (DGGE). Both bacterial and cyanobacterial communities followed a clear seasonal cycle. Contrary to expectations, viral abundances were neither correlated to abundances of the most dominant plankton groups in Lake Loosdrecht, the bacteria and the filamentous cyanobacteria, nor could we detect a correlation between the assemblage of viral and bacterial or cyanobacterial communities during the overall period. Only during short periods of strong fluctuations in microbial communities could we detect viral community assemblages to covary with cyanobacterial and bacterial communities. Methods with a higher specificity and resolution are probably needed to detect the more subtle virus–host interactions. Viral abundances did however relate to cyanobacterial community assemblage and showed a significant positive correlation to Chl-a as well as prochlorophytes, suggesting that a significant proportion of the viruses in Lake Loosdrecht may be phytoplankton and more specific cyanobacterial viruses. Temporal changes in bacterial abundances were significantly related to viral community assemblage, and vice versa, suggesting an interaction between viral and bacterial communities in Lake Loosdrecht

The global abundance of tree palms

Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests

The global abundance of tree palms

Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location Tropical and subtropical moist forests. Time period Current. Major taxa studied Palms (Arecaceae). Methods We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work. Conclusions Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests