History matching and prediction of a polymer flood pilot in heavy oil reservoir on Alaska North Slope

Thesis (M.S.) University of Alaska Fairbanks, 2021The first-ever polymer flood pilot to enhance heavy oil recovery on Alaska North Slope is ongoing. After more than 3 years of polymer injection, significant benefit has been observed from the decrease in water cut from 65% to less than 15% in the project producers. The primary objective of this study is to develop a robust history-matched reservoir simulation model capable of predicting future polymer flood performance. In this work, the reservoir simulation model has been developed based on the geological model and available reservoir and fluid data. In particular, four high transmissibility strips were introduced to connect the injector-producer well pairs, simulating short-circuiting flow behavior that can be explained by viscous fingering and reproducing the water cut history. The strip transmissibilities were manually tuned to improve the history matching results during the waterflooding and polymer flooding periods, respectively. It has been found that higher strip transmissibilities match the sharp water cut increase very well in the waterflooding period. Then the strip transmissibilities need to be reduced with time to match the significant water cut reduction. The viscous fingering effect in the reservoir during waterflooding and the restoration of injection conformance during polymer flooding have been effectively represented. Based on the validated simulation model, numerical simulation tests have been conducted to investigate the oil recovery performance under different development strategies, with consideration for sensitivity to polymer parameter uncertainties. The oil recovery factor with polymer flooding can reach about 39% in 30 years, twice as much as forecasted with continued waterflooding. Besides, the updated reservoir model has been successfully employed to forecast polymer utilization, a valuable parameter to evaluate the pilot test's economic efficiency. All the investigated development strategies indicate polymer utilization lower than 3.5 lbs/bbl in 30 years, which is less than that of the same polymer used in a polymer pilot in Argentina.U.S. Department of Energy Award Number DE-FE0031606, Hilcorp Alaska, LL

The SMC Condensin Complex Is Required for Origin Segregation in Bacillus subtilis

SummarySMC condensin complexes play a central role in organizing and compacting chromosomes in all domains of life [1, 2]. In the bacterium Bacillus subtilis, cells lacking SMC are viable only during slow growth and display decondensed chromosomes, suggesting that SMC complexes function throughout the genome [3, 4]. Here, we show that rapid inactivation of SMC or its partner protein ScpB during fast growth leads to a failure to resolve newly replicated origins and a complete block to chromosome segregation. Importantly, the loss of origin segregation is not due to an inability to unlink precatenated sister chromosomes by Topoisomerase IV. In support of the idea that ParB-mediated recruitment of SMC complexes to the origin is important for their segregation, cells with reduced levels of SMC that lack ParB are severely impaired in origin resolution. Finally, we demonstrate that origin segregation is a task shared by the condensin complex and the parABS partitioning system. We propose that origin-localized SMC constrains adjacent DNA segments along their lengths, drawing replicated origins in on themselves and away from each other. This SMC-mediated lengthwise condensation, bolstered by the parABS system, drives origin segregation

Bacillus Subtilis SMC Complexes Juxtapose Chromosome Arms as They Travel from Origin to Terminus

Structural maintenance of chromosomes (SMC) complexes play critical roles in chromosome dynamics in virtually all organisms, but how they function remains poorly understood. In the bacterium Bacillus subtilis, SMC-condensin complexes are topologically loaded at centromeric sites adjacent to the replication origin. Here we provide evidence that these ring-shaped assemblies tether the left and right chromosome arms together while traveling from the origin to the terminus (>2 megabases) at rates >50 kilobases per minute. Condensin movement scales linearly with time, providing evidence for an active transport mechanism. These data support a model in which SMC complexes function by processively enlarging DNA loops. Loop formation followed by processive enlargement provides a mechanism by which condensin complexes compact and resolve sister chromatids in mitosis and by which cohesin generates topologically associating domains during interphase. Keywords: SMC; ParB; condensin; cohesion; loop extrusion; TADNational Institutes of Health (U.S.) (Grant GM082899

Lysine-Cysteine-Lysine (KCK) tag changes ParB action in vitro but not in vivo

Due to the enhanced labeling capability of maleimide-based fluorescent probes in in vitro experiments, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. Here we show that, although no noticeable changes were detected from in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered DNA compaction rates by Bacillus subtilis ParB protein in in vitro single-molecule DNA flow-stretching experiments. Furthermore, our measurements and statistical analyses demonstrate that the KCK-tags also altered the ParB protein’s response to nucleotide (cytidine triphosphate CTP or its nonhydrolyzable analog CTPγS) binding and the presence of the specific DNA binding sequence (parS). Remarkably, the appended KCK-tags are capable of even reversing the trends of DNA compaction rates upon different experimental conditions. DNA flow-stretching experiments for both fluorescently-labeled ParB proteins and ParB proteins with an N-terminal glutamic acid-cysteine-glutamic acid (ECE) tag support the notion that electrostatic interactions between charges on the tags and the DNA backbone are an underlying cause of the protein’s property changes. While it is typically assumed that the short KCK-tag minimally perturbs protein function, our results demonstrate that this assumption must be carefully tested when using tags for protein labeling

Bypass of a protein roadblock by a replicative DNA helicase

Replicative DNA helicases generally unwind DNA as a single hexamer that encircles and translocates along one strand of the duplex while excluding the complementary strand (“steric exclusion”). In contrast, large T antigen (T-ag), the replicative DNA helicase of the Simian Virus 40 (SV40), is reported to function as a pair of stacked hexamers that pumps double-stranded DNA through its central channel while laterally extruding single-stranded DNA. Here, we use single-molecule and ensemble assays to show that T-ag assembled on the SV40 origin unwinds DNA efficiently as a single hexamer that translocates on single-stranded DNA in the 3′ to 5′ direction. Unexpectedly, T-ag unwinds DNA past a DNA-protein crosslink on the translocation strand, suggesting that the T-ag ring can open to bypass bulky adducts. Together, our data underscore the profound conservation among replicative helicase mechanisms while revealing a new level of plasticity in their interactions with DNA damage

Quantification of hypsarrhythmia in infantile spasmatic EEG:a large cohort study

Infantile spasms (IS) is a neurological disorder causing mental and/or developmental retardation in many infants. Hypsarrhythmia is a typical symptom in the electroencephalography (EEG) signals with IS. Long-Term EEG/video monitoring is most frequently employed in clinical practice for IS diagnosis, from which manual screening of hypsarrhythmia is time consuming and lack of sufficient reliability. This study aims to identify potential biomarkers for automatic IS diagnosis by quantitative analysis of the EEG signals. A large cohort of 101 IS patients and 155 healthy controls (HC) were involved. Typical hypsarrhythmia and non-hypsarrhythmia EEG signals were annotated, and normal EEG were randomly picked from the HC. Root mean square (RMS), teager energy (TE), mean frequency, sample entropy (SamEn), multi-channel SamEn, multi-scale SamEn, and nonlinear correlation coefficient were computed in each sub-band of the three EEG signals, and then compared using either a one-way ANOVA or a Kruskal-Wallis test (based on their distribution) and the receiver operating characteristic (ROC) curves. The effects of infant age on these features were also investigated. For most of the employed features, significant ({p} &lt; {0}.{05} ) differences were observed between hypsarrhythmia EEG and non-hypsarrhythmia EEG or HC, which seem to increase with increased infant age. RMS and TE produce the best classification in the delta and theta bands, while entropy features yields the best performance in the gamma band. Our study suggests RMS and TE (delta and theta bands) and entropy features (gamma band) to be promising biomarkers for automatic detection of hypsarrhythmia in long-Term EEG monitoring. The findings of our study indicate the feasibility of automated IS diagnosis using artificial intelligence.</p

Replication shapes chromosome organization and segregation in Escherichia coli

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Independent Segregation of the Two Arms of the Escherichia coli ori Region Requires neither RNA Synthesis nor MreB Dynamics ▿ § ‡

The mechanism of Escherichia coli chromosome segregation remains elusive. We present results on the simultaneous tracking of segregation of multiple loci in the ori region of the chromosome in cells growing under conditions in which a single round of replication is initiated and completed in the same generation. Loci segregated as expected for progressive replication-segregation from oriC, with markers placed symmetrically on either side of oriC segregating to opposite cell halves at the same time, showing that sister locus cohesion in the origin region is local rather than extensive. We were unable to observe any influence on segregation of the proposed centromeric site, migS, or indeed any other potential cis-acting element on either replication arm (replichore) in the AB1157 genetic background. Site-specific inhibition of replication close to oriC on one replichore did not prevent segregation of loci on the other replichore. Inhibition of RNA synthesis and inhibition of the dynamic polymerization of the actin homolog MreB did not affect ori and bulk chromosome segregation

An Entropy Model of Credit Risk Contagion in the CRT Market

This paper reports the effect of the change in the credit status of debtors on investors as a result of the banks&apos; transferring of credit risk to investors in the credit risk transfer (CRT) market. Thus, an entropy spatial model is introduced, in which the spatial distance and nonlinear coupling between the banks and the investors, the transfer ability of credit risk of banks, and investor appetite for risk in the CRT network are considered. The contagion effects of the credit default of debtor on the default rates of investors in the CRT market are investigated using numerical simulation and sensitivity analysis