Procjena kvalitete i upravljanje onečišćenim sedimentima: potrebna kakvoća podataka – od molekularne razine do razine riječnih bazena

Management of environmental risks in river basins needs to address quality aspects of sediment – both because of its storage capacity for contaminants and due to its potential function as a secondary source of pollution. Assessment of sediment quality, however, is still prone to a number of uncertainties and insufficient information with regard to regulation, analytical methods, risk assessment and risk management. The European Water Framework Directive (WFD), e.g., has not come up with environmental quality standards for sediments. Lack of harmonization, representativeness and traceability of sediment data, not fully understood processes governing bioavailability of sediment-bound contaminants, all add up to the uncertainty that needs to be quantified. This paper details uncertainties ranging from the molecular to the basin scale level with regard to sediment quality assessment and its integration into management approaches, and it suggests ways of how to cope with a lack of data and insecure data while still developing an overview of basin wide risks.Upravljanje rizicima po okoliš u riječnim bazenima treba sadržavati i aspekt kvalitete sedimenata – zbog njihovog kapaciteta za pohranu onečišćivala, ali i zbog njihove potencijalne uloge kao sekundarnog izvora zagađenja. Međutim, procjena kvalitete sedimenata ograničena je nekim nepoznanicama i nedovoljnim brojem podataka koji se odnose na propise, analitičke metode, procjenu rizika i njegovo upravljanje. Europska direktiva za vode (European Water Framework Directive – WFD) nije još uvijek donijela standard za okolišnu kakvoću sedimenata. Nedostatak harmonizacije, reprezentativnosti i dostupnosti podataka za sedimente, kao i nedovoljno poznati procesi koji upravljaju biološkom dostupnošću onečišćivala sadržanih u sedimentu doprinose stupnju neizvjesnosti koji je potrebno kvantificirati. U radu su opisane neizvjesnosti, u rasponu od molekularne razine do razine riječnih bazena, s obzirom na postupak procjene kvalitete sedimenata i integriranje tog postupka u upravljačke sustave, uz predlaganje načina kako se usprkos nedostatku podataka ili njihovoj upitnosti mogu primijeniti metodologije procjene rizika na razini riječnih bazen

Autonomous capillary systems for life science research and medical diagnostics

In autonomous capillary systems (CS) minute amounts of liquid are transported owing to capillary forces. Such CSs are appealing due to their portability, flexibility, and the exceptional physical behavior of liquids in micrometer sized microchannels, in particular, capillarity and short diffusion times. CSs have shown to be a promising technology for miniaturized immunoassays in life science research and diagnostics. Building on existing experimental demonstrations of immunoassays in CSs, a theoretical model of such immunoassays is implemented, tools and CSs for performing immunoassays are developed, key functional elements of CSs such as capillary pumps and valves are explored experimentally, and a proof-of-concept of the ultimate goal of one-step immunoassays are given in this work. For the theoretical modeling of immunoassays in CSs a finite difference algorithm is applied to delineate the role of the transport of analyte molecules in the microchannel (convection and diffusion), the kinetics of binding between the analyte and the capture antibodies, and the surface density of the capture antibody on the assay. The model shows that assays can be greatly optimized by varying the flow velocity of the solution of analyte in the microchannels. The model also shows how much the analyte-antibody binding constant and the surface density of the capture antibodies influence the performance of the assay. We derive strategies to optimize assays toward maximal sensitivity, minimal sample volume requirement or fast performance. A method using evaporation for controlling the flow rate in CSs was developed for maximum flexibility for developing assays. The method allows to use small CSs that initially are filled by capillary forces and then provide a well defined area of the liquid-air interface from which liquid can evaporate. Temperature and humidity are continuously measured and Peltier-elements are used to adjust the temperatures in multiple areas of the CSs relative to the dew-point. Thereby flow rates in the range from ~1.2 nL s−1 to ~30 pL s−1 could be achieved in the microchannels. This method was then used for screening cells for surface receptors. CSs, that do not need any peripherals for controlling flow rates become even more appealing. We explored the filling behavior of such CSs having microchannels of various length and large capillary pumps. The capillary pumps comprise microstructures of various sizes and shapes, which are spaced to encode certain capillary pressures. The spacing and shape of the microstructures is also used to orient the filling front to obtain a reliable filling behavior and to minimize the risk of entrapping air. We show how two capillary pumps having different hydrodynamic properties can be connected to program a sequence of slow and fast flow rates in CSs. Liquid filling CSs can hardly be stopped, but in some cases it might be beneficial to do so. In a separate chapter we explore how microstructures need to be designed to use capillary forces to stop, time, or trigger liquids. Besides well-defined flow rates in CSs accurately patterned capture antibodies (cAbs) are key for performing high-sensitive surface immunoassays in CSs. We present a method compatible with mass fabrication for patterning cAbs in dense lines of up to 8 lines per millimeter. These cAbs are used with CSs that are optimized for convenient handling, pipetting of solutions, pumping of liquids such as human serum, and visualization of signals for fluorescence immunoassays to detect c-reactive protein (CRP) with a sensitivity of 0.9 ng mL−1 (7.8 pM) from 1 uL of CRP-spiked human serum, within 11 minutes, with 4 pipetting steps, and a total volume of sample and reagents of <1.5 uL. CSs for diagnostic applications have different requirements than CSs that are used as a research tool in life sciences, where a high flexibility and performance primes over the ease of use and portability of the CSs. We give a proof-of-concept for one-step immunoassays based on CSs which we think can be the base for developing portable diagnostics for point-of-care applications. All reagents are preloaded in the CSs. A sample loaded in the CSs redissolves and reconstitutes the detection antibodies (dAbs), analyte-dAb-complexes are formed and detected downstream in the CSs. A user only needs to load a sample and measure the result using a fluorescence microscope or scanner. C-reactive protein was detected in human serum at clinical concentrations within 10 minutes and using only 2 uL of sample

Разработка и исследование химических реагентов с повышенной эффективностью растворения в технологических жидкостях для строительства скважин

Объектами исследования являются системы промывочных жидкостей на водной основе. Цель работы – разработать методы модифицирования полимерных реагентов и исследовать эффективность их применения в промывочных жидкостях для строительства скважин. В результате исследования предложены три способа модифицирования полимерных реагентов (суспендирование, создание покрытий, частичное сшивание) для повышения их эффективности растворения в промывочных жидкостях для строительства скважин; выявлены ограничения предложенных способов повышения эффективности растворения полимерных реагентов; сформулированы рекомендации по целесообразности применения каждого из предложенных способов модифицирования. Область применения: промывочные жидкости для строительства скважин.Objects of study: water-based drilling fluids. The purpose of the work is to develop methods for modification of polymer reagents and to investigate an effectiveness of their use in drilling fluids for drilling wells. As a result of the study, three methods were proposed for modifying polymer reagents (suspension, coating, partial crosslinking) to increase their dissolution efficiency in drilling fluids; limitations of the proposed methods for increasing the dissolution efficiency of polymer reagents were identified; recommendations were made on the appropriateness of each of the proposed methods of modification. Scope: drilling fluids

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation

Background: Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters. Results: A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file. Conclusions: The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes