CRISPR-based strategies for studying regulatory elements and chromatin structure in mammalian gene control

Mammalian Genome - The development of high-throughput methods has enabled the genome-wide identification of putative regulatory elements in a wide variety of mammalian cells at an unprecedented...     

Geographic variability of agriculture requires sector-specific uncertainty characterization

Purpose

Regionalization in life cycle assessment (LCA) has focused on spatially differentiated environmental variables for regional impact assessment models. Relatively less attention has been paid to spatial disparities in intermediate flows for life cycle inventory (LCI).

Methods

First, we compiled state-specific LCIs for four major crops in the USA and evaluated their geographic variability in the characterized results due to the differences in intermediate inputs. Second, we evaluated the consequence of choosing average or region-specific LCIs in understanding the life cycle environmental implications of land use change from cotton to corn or soybean. Finally, we analyzed the implications of our findings in characterizing the uncertainties associated with geographic variability under the conventional pedigree approach.

Results and discussion

Our results show that spatial disparities in LCI alone lead to two to fourfold differences in characterized results for most impact categories. The differences, however, increase to over an order of magnitude for freshwater ecotoxicity and human health non-cancer. Among the crops analyzed, winter wheat shows higher variability partly due to a larger difference in yield. As a result, the use of national average data derived from top corn and soybean producing states significantly underestimates the characterized impacts of corn and soybean in the states where land conversion from cotton to corn or soybean actually took place. The results also show that the conventional pedigree approach to uncertainty characterization in LCA substantially underestimates uncertainties arising from geographic variability of agriculture. Compared to the highest geometric standard deviation (GSD) value of 1.11 under the pedigree approach, the GSDs that we derived are as high as 7.1, with the median around 1.9.

Conclusions

The results highlight the importance of building regional life cycle inventory for understanding the environmental impacts of crops at the regional level. The high geographic variability of crops also indicates the need for sector-specific approaches to uncertainty characterization. Our results also suggest that the uncertainty values in the existing LCI databases might have been signficantly underestimated especially for those products with high geographic variability, demanding a cautious interpretation of the results derived from them. 

     

Optimization of three-dimensional modeling for geometric precision and efficiency for healthy and diseased aortas

The study purpose is to optimize modeling parameters, specifically segmentation spacing and centerline extraction, to efficiently construct accurate 3D aortic models. Models are constructed by centerline extraction and orthogonal 2D segmentations. We examine the effect of segmentation interval spacing (2, 1, 0.5, 0.25 cm) and orthogonal segmentation and centerline extraction iteration (one, two, three iterations) for constructing models of Healthy, Tortuous, Aneurysmal, and Dissected human thoracic aortas. Aortic arclength, curvature, and cross-sectional axis ratio were computed to compare variations in modeling parameters. Centerline arclength is precisely characterized for all aortas with a single iteration of centerline extraction (≤1% deviation), however, complex anatomies required 1 cm segmentation intervals whereas the Healthy aorta only required 2 cm intervals. Centerline curvature is more sensitive to modeling methods, requiring 1 cm intervals for ≤5% deviation in peak curvature for the three diseased anatomies, and two iterations of segmentation and centerline extraction for the Aneurysmal and Dissected aortas. Accurate lumen cross-sectional characterization required 1 or 0.5 cm segmentation intervals, and two or three segmentation and centerline iterations, with greater refinement needed for more complex geometries. Depending on the geometric characteristic and complexity of anatomy and pathology, different levels of segmentation interval refinement and iterations of segmentation and centerline extraction are required.     

Phylogeny and species delineation in the marine diatom Pseudo‐nitzschia (Bacillariophyta) using cox1, LSU,and ITS2 rRNA genes: A perspective in character evolution

Analyses of the mitochondrial cox1, the nuclear‐encoded large subunit (LSU), and the internal transcribed spacer 2 (ITS2) RNA coding region of Pseudo‐nitzschia revealed that the P. pseudodelicatissima complex can be phylogenetically grouped into three distinct clades (Groups I–III), while the P. delicatissima complex forms another distinct clade (Group IV) in both the LSU and ITS2 phylogenetic trees. It was elucidated that comprehensive taxon sampling (sampling of sequences), selection of appropriate target genes and outgroup, and alignment strategies influenced the phylogenetic accuracy. Based on the genetic divergence, ITS2 resulted in the most resolved trees, followed by cox1 and LSU. The morphological characters available for Pseudo‐nitzschia, although limited in number, were overall in agreement with the phylogenies when mapped onto the ITS2 tree. Information on the presence/absence of a central nodule, number of rows of poroids in each stria, and of sectors dividing the poroids mapped onto the ITS2 tree revealed the evolution of the recently diverged species. The morphologically based species complexes showed evolutionary relevance in agreement with molecular phylogeny inferred from ITS2 sequence–structure data. The data set of the hypervariable region of ITS2 improved the phylogenetic inference compared to the cox1 and LSU data sets. The taxonomic status of P. cuspidata and P. pseudodelicatissima requires further elucidation.     

First finding of a quarantine pest,Atherigona (Acritochaeta) orientalis Schiner (Diptera: Muscidae), in Korea

The invasive quarantine pest fly, Atherigona (Acritochaeta) orientalis Schiner, is observed for the first time in tomato greenhouses in Gyeongsangbuk‐do, Korea. The genus Atherigona Rondani is also newly added to Korean fauna. Allium tuberosum is listed as a new host crop for this species. Some morphological characteristics for accurate identification and host lists are given to provide plant quarantine information for pest management.     

Prognostic Value of Lactate and Central Venous Oxygen Saturation after Early Resuscitation in Sepsis Patients

The objective of this study was to evaluate the prognostic value of static and dynamic variables of central venous oxygen saturation (ScvO₂) and lactate in patients with severe sepsis or septic shock who underwent early quantitative resuscitation. We also investigated whether ScvO₂ measured after initial resuscitation could provide additive prognostic value to that of lactate. We analyzed the sepsis registry for patients presenting to the emergency department and included patients with simultaneous measurements of lactate and ScvO₂ at the time of presentation (H0) and 6 hours (H6) after resuscitation. The primary outcome was 28-day mortality and multivariable logistic analysis was used to adjust for confounders. A total of 363 patients were included, and the overall 28-day mortality was 18%. The area under the receiver operator characteristic curve for predicting 28-day mortality was as follows: lactate (H6), 0.81; lactate (H0), 0.73; relative lactate change, 0.67; ScvO₂ (H6), 0.65; relative ScvO₂ change 0.59; ScvO₂ (H0), 0.58. Patients with lactate normalization showed significantly lower 28-day mortality compared to patients without lactate normalization (3% vs. 28%, P<0.01). However, in those who achieved ScvO₂ (H6) ≥70%, there was a significant difference in 28-mortality only in patients without lactate normalization (21% vs. 39%, P<0.01) but no difference in those with lactate normalization (4% vs. 3%, P = 0.71). In multivariable analysis, lactate normalization was significantly associated with 28-day mortality (adjusted odds ratio [OR] for 28-day mortality, 0.20; 95% confidence interval [CI], 0.07–0.54; P <0.01), but ScvO₂ (H6) ≥70% showed only a marginal association (the adjusted OR for 28-day mortality, 0.51; 95% CI, 0.26–1.01; P = 0.05). ScvO₂ (H6) ≥70% was associated with 28-day mortality only in cases without lactate normalization in subgroup analysis (adjusted OR 0.37, 95% CI, 0.18–0.79; P = 0.01). Six-hour lactate was the strongest predictor of 28-day mortality in patients with severe sepsis or septic shock. Six-hour ScvO₂ provided additional prognostic value only in cases where lactate values were not normalized after resuscitation.     

Automated Entire Thrombus Density Measurements for Robust and Comprehensive Thrombus Characterization in Patients with Acute Ischemic Stroke

Background and Purpose

In acute ischemic stroke (AIS) management, CT-based thrombus density has been associated with treatment success. However, currently used thrombus measurements are prone to inter-observer variability and oversimplify the heterogeneous thrombus composition. Our aim was first to introduce an automated method to assess the entire thrombus density and then to compare the measured entire thrombus density with respect to current standard manual measurements.

Materials and Method

In 135 AIS patients, the density distribution of the entire thrombus was determined. Density distributions were described using medians, interquartile ranges (IQR), kurtosis, and skewedness. Differences between the median of entire thrombus measurements and commonly applied manual measurements using 3 regions of interest were determined using linear regression.

Results

Density distributions varied considerably with medians ranging from 20.0 to 62.8 HU and IQRs ranging from 9.3 to 55.8 HU. The average median of the thrombus density distributions (43.5 ± 10.2 HU) was lower than the manual assessment (49.6 ± 8.0 HU) (p<0.05). The difference between manual measurements and median density of entire thrombus decreased with increasing density (r = 0.64; p<0.05), revealing relatively higher manual measurements for low density thrombi such that manual density measurement tend overestimates the real thrombus density.

Conclusions

Automatic measurements of the full thrombus expose a wide variety of thrombi density distribution, which is not grasped with currently used manual measurement. Furthermore, discrimination of low and high density thrombi is improved with the automated method.     

PpASCL,the Physcomitrella patens Anther-Specific Chalcone Synthase-Like Enzyme Implicated in Sporopollenin Biosynthesis,Is Needed for Integrity of the Moss Spore Wall and Spore Viability

Sporopollenin is the main constituent of the exine layer of spore and pollen walls. The anther-specific chalcone synthase-like (ASCL) enzyme of Physcomitrella patens, PpASCL, has previously been implicated in the biosynthesis of sporopollenin, the main constituent of exine and perine, the two outermost layers of the moss spore cell wall. We made targeted knockouts of the corresponding gene, PpASCL, and phenotypically characterized ascl sporophytes and spores at different developmental stages. Ascl plants developed normally until late in sporophytic development, when the spores produced were structurally aberrant and inviable. The development of the ascl spore cell wall appeared to be arrested early in microspore development, resulting in small, collapsed spores with altered surface morphology. The typical stratification of the spore cell wall was absent with only an abnormal perine recognisable above an amorphous layer possibly representing remnants of compromised intine and/or exine. Equivalent resistance of the spore walls of ascl mutants and the control strain to acetolysis suggests the presence of chemically inert, defective sporopollenin in the mutants. Anatomical abnormalities of late-stage ascl sporophytes include a persistent large columella and an air space incompletely filled with spores. Our results indicate that the evolutionarily conserved PpASCL gene is needed for proper construction of the spore wall and for normal maturation and viability of moss spores.     

Prognostic Impact of IPSS-R and Chromosomal Translocations in 751 Korean Patients with Primary Myelodysplastic Syndrome

Chromosomal translocations are rare in myelodysplastic syndrome (MDS) and their impact on overall survival (OS) and response to hypomethylating agents (HMA) is unknown. The prognostic impact of the revised International Prognostic Scoring System (IPSS-R) and for chromosomal translocations was assessed in 751 patients from the Korea MDS Registry. IPSS-R effectively discriminated patients according to leukaemia evolution risk and OS. We identified 40 patients (5.3%) carrying translocations, 30 (75%) of whom also fulfilled complex karyotype criteria. Translocation presence was associated with a shorter OS (median, 12.0 versus 79.7 months, P < 0.01). Multivariate analysis demonstrated that translocations (hazard ratio [HR] 1.64 [1.06–2.63]; P = 0.03) as well as age, sex, IPSS-R, and CK were independent predictors of OS. In the IPSS-R high and very high risk subgroup (n = 260), translocations remained independently associated with OS (HR 1.68 [1.06–2.69], P = 0.03) whereas HMA treatment was not associated with improved survival (median OS, 20.9 versus 21.2 months, P = 0.43). However, translocation carriers exhibited enhanced survival following HMA treatment (median 2.1 versus 12.4 months, P = 0.03). Our data suggest that chromosomal translocation is an independent predictor of adverse outcome and has an additional prognostic value in discriminating patients with MDS having higher risk IPSS-R who could benefit from HMA treatment.