Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, ...particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.
Bifunctional duocarmycin analogues are highly cytotoxic compounds that have been shown to be irreversible aldehyde dehydrogenase 1 inhibitors. Interestingly, cells with low aldehyde dehydrogenase 1 ...expression are also sensitive to bifunctional duocarmycin analogues, suggesting the existence of another target. Through in silico approaches, including principal component analysis, structure-similarity search, and docking calculations, protein tyrosine kinases, and especially the vascular endothelial growth factor receptor 2 (VEGFR-2), were predicted as targets of bifunctional duocarmycin analogues. Biochemical validation was performed in vitro, confirming the in silico results. Structural optimization was performed to mainly target VEGFR-2, but not aldehyde dehydrogenase 1. The optimized bifunctional duocarmycin analogue was synthesized. In vitro assays revealed this bifunctional duocarmycin analogue as a strong inhibitor of VEGFR-2, with low residual aldehyde dehydrogenase 1 activity. Altogether, studies revealed bifunctional duocarmycin analogues as a new class of naturally derived compounds that express a very high cytotoxicity to cancer cells overexpressing aldehyde dehydrogenase 1 as well as VEGFR-2.
The response of permafrost to marine submergence can vary between ice‐rich late Pleistocene deposits and the thermokarst basins that thawed out during the Holocene. We hypothesize that inundated ...Alases offshore thaw faster than submerged Yedoma. To test this hypothesis, we estimated depths to the top of ice‐bearing permafrost offshore of the Bykovsky Peninsula in northeastern Siberia using electrical resistivity surveys. The surveys traversed submerged lagoon deposits, drained and refrozen Alas deposits, and undisturbed Yedoma from the coastline to 373 m offshore. While the permafrost degradation rates of the submerged Yedoma were in the range of similar sites, the submerged Alas permafrost degradation rates were up to 170% faster. Remote sensing analyses suggest that 54% of lagoons wider than 500 m along northeast Siberian and northwest American coasts originated in thermokarst basins. Given the abundance of thermokarst basins and lakes along parts of the Arctic coastline, their effect on subsea permafrost degradation must be similarly prevalent.
Plain Language Summary
Permafrost is defined as any ground or rock colder than 0°C for two or more consecutive years. In unglaciated regions of Siberia during the last ice age, the ground froze 1 km deep. When the ice sheets and glaciers melted at the end of the last Ice Age, millions of square kilometers of this cold permafrost were inundated with seawater on shallow Arctic shelves, creating subsea permafrost. Even today, new permafrost is submerged because of coastal erosion. Once submerged, heat and salt flow thaw the permafrost. However, the rate of subsea permafrost thaw partially depends on its temperature, ice content, and sediment type. Some permafrost areas called Alases already experienced deep thaw and refreezing from Arctic lake formation and drainage. On the southern coastline of the Bykovsky Peninsula in Siberia, we carried out non‐invasive marine geophysical surveys parallel to the coastline to estimate how fast permafrost thaws beneath a submerged Alas next to a lagoon and permafrost areas without Alases. We discovered that subsea permafrost degradation was up to 170% faster beneath the submerged Alas nearshore. To highlight the broader relevance of these Alas‐lagoon landscapes along the Arctic coastline, we map out Arctic lagoons.
Key Points
Subsea permafrost degradation was up to 170% faster below submerged thermokarst basins compared to submerged Yedoma remnants nearshore
Re‐worked permafrost beneath thermokarst basins adjacent to lagoons induces rapid offshore thaw
Along the assessed Arctic coastline, 54% of lagoons originated in thermokarst basins
Introduction. Selecting the best available stem cell donor is crucial to optimize outcome after allogeneic hematopoietic cell transplantation (alloHCT). For several decades, matched sibling donors ...(MSD) were considered to be the best choice for all patients. Recently published data suggest that young unrelated donors (UD) may represent a favorable alternative. However, analyses in contemporary disease-specific registry cohorts are still rare. Therefore, we set out to investigate whether young UD provide a benefit for older patients with myeloid malignancies compared to MSD. Patients and Methods. We performed a retrospective study with data of the Deutsches Register Stammzelltransplantation (DRST) on patients 50 years and older who received a first alloHCT for AML, MDS, MDS/MPN or CMML between January 2010 and December 2020. We compared results of patients who were transplanted from MSD aged 50 years or older and young UD aged 35 years or younger who were HLA-compatible for HLA-A, -B, -C, and -DRB1. We evaluated the primary endpoint, event-free survival (EFS), and the secondary endpoints overall survival (OS), cumulative incidence of relapse/progression (CIR), non-relapse mortality (NRM), acute and chronic Graft-versus-Host Disease (GvHD) in multivariable Cox regression models. Results. In total, we analyzed data from 3460 patients. Median patient age was 63.5 years for 2225 patients with UD compared to 60.9 years for 1235 patients with MSD (p<.001). The median donor age was 27 years (range 18-35 years) for UD compared to 58 years (range 50-79 years) for MSD (p<.001). Overall, male donors accounted for 77.9% of UD compared to 49.3% of MSD (p<.001). Fewer male patients had female UD than female MSD (8.6% versus 30%, p<.001). Also, more cytomegalovirus (CMV) seronegative patients had CMV seronegative UD (34.9% versus 23%, p<.001). The percentage of alloHCT with UD increased in recent years, from 46% in 2010 to 72% in 2020 (p<.001). HLA-DQB1-mismatches were reported for 2.5% of UD. HLA-DPB1 matching information was available for 33.6% of UD. We found no differences with respect to the distribution of Karnofsky performance status, disease risk, reduced intensity conditioning (circa 80% of patients) and graft source (almost exclusively PBSC) between the two donor types. GVHD prophylaxis differed significantly, more patients with UD received ATG compared to patients with MSD (87.4% versus 52.9%, p<.001). In univariate comparisons, we observed a trend towards improved EFS (HR 0.91, p=.07; Figure Panel A) and improved OS (HR 0.88, p=.03) for UD compared to MSD transplants. CIR was lower with UD (HR 0.87, p=.04, Figure Panel B) and NRM was not statistically different (HR 0.96, p=.6). The 150-days cumulative incidence of aGVHD was 28.2% for UD versus 31.3% for MSD transplants (p=.09). Corresponding numbers for the 1-year cumulative incidence of cGVHD were 31.3% and 39.4% for UD versus MSD transplants (p=<.001). After multivariable adjustment for patient age, performance status, disease risk, conditioning type, stem cell source, and HLA-DQB1-mismatches, EFS and OS were significantly better for 10/10 UD compared to MSD transplantation with hazard ratios (HR) of 0.86 for EFS (p=.003) and 0.82 for OS (p<.001). After UD alloHCT we found a lower risk of relapse (HR 0.84, p=.018), less chronic GVHD (HR 0.7, p<.001) and a trend towards lower NRM (HR 0.87, p=.07). Conclusions. Selecting HLA-compatible UD over older MSD improves the chances of survival (both OS and EFS) after alloHCT for older patients with myeloid malignancies. This beneficial effect was mediated mainly by a reduced risk for relapse/progression suggesting more potent Graft-versus-Leukemia effects after UD transplantation despite less chronic GVHD.
OBJECTIVE:Lethal sepsis occurs when an excessive inflammatory response evolves that cannot be controlled by physiologic anti-inflammatory mechanisms, such as the recently described cholinergic ...anti-inflammatory pathway. Here we studied whether the cholinergic anti-inflammatory pathway can be activated by pharmacologic cholinesterase inhibition in vivo.
DESIGN:Prospective, randomized laboratory investigation that used an established murine sepsis model.
SETTING:Research laboratory in a university hospital.
SUBJECTS:Female C57BL/6 mice.
INTERVENTIONS:Sepsis in mice was induced by cecal ligation and puncture. Animals were treated immediately with intraperitoneal injections of nicotine (400 μg/kg), physostigmine (80 μg/kg), neostigmine (80 μg/kg), or solvent three times daily for 3 days.
MEASUREMENTS AND MAIN RESULTS:Treatment with physostigmine significantly reduced lethality (p ≤ .01) as efficiently as direct stimulation of the cholinergic anti-inflammatory pathway with nicotine (p ≤ .05). Administration of cholinesterase inhibitors significantly down-regulated the binding activity of nuclear factor-κB (p ≤ .05) and significantly reduced the concentration of circulating proinflammatory cytokines tumor necrosis factor-α, interleukin-1β, and interleukin-6 (p ≤ .001), and pulmonary neutrophil invasion (p ≤ .05). Animals treated with the peripheral cholinesterase inhibitor neostigmine showed no difference compared with physostigmine-treated animals.
CONCLUSIONS:Our results demonstrate that cholinesterase inhibitors can be used successfully in the treatment of sepsis in a murine model and may be of interest for clinical use.
Objective
To investigate posterior visual pathway damage in multiple sclerosis using ultrahigh-field magnetic resonance imaging (MRI) at 7 Tesla (7 T), and to determine its correlation with visual ...disability and retinal fibre layer (RNFL) damage detectable by optic coherence tomography (OCT).
Methods
We studied 7 T MRI, OCT, functional acuity contrast testing (FACT), and visually evoked potentials (VEP, n = 16) in 30 patients (including 26 relapsing-remitting MS and four clinically isolated syndrome patients) and 12 healthy controls to quantify RNFL thickness, optic radiation lesion volume, and optic radiation thickness.
Results
Optic radiation lesion volume was associated with thinning of the optic radiation (
p
< 0.001), delayed VEP (
p
= 0.031), and visual disability indicated by FACT (
p
= 0.020). Furthermore, we observed an inverse correlation between optic radiation lesion volume and RNFL thickness (
p
< 0.001), including patients without previous optic neuritis (
p
< 0.001).
Conclusions
Anterior visual pathway damage, but also (subclinical) optic radiation integrity loss detectable by 7 T MRI are common findings in MS that are mutually affected. Given the association between optic radiation damage, visual impairment, and increased VEP latency in this exploratory study of a limited sample size, clinicians should be aware of acute lesions within the optic radiation in patients with (bilateral) visual disturbances.
Key Points
•
Focal destruction of the optic radiation is detectable by 7 T MRI.
•
Focal optic radiation damage is common in MS.
•
Optic radiation damage is associated with RNFL thinning, detectable by OCT.
•
Optic radiation damage is associated with delayed VEP and visual dysfunction.
•
RNFL thickness in non-optic neuritis eyes correlates with optic radiation demyelination.
This study aims to investigate whether a Web-based tool will facilitate the adoption of feedback control over calorie balance in overweight individuals, thereby promoting an increase of physical ...activity and a reduction of body weight and cardiovascular risk factors. This is a prospective exercise intervention study, commencing with a minimum weekly 3 × 20-min requirement of high-intensity interval training and requirement for Web-based self-monitoring and self-reporting of exercise and body weight. Subjects of this study include 83 overweight, sedentary, otherwise healthy adults aged 26–68 years. Anthropometric parameters, body fat, peak oxygen consumption, self-reported physical activity, frequency of use of the Web-based tool are among the characters measured in this study. This 24-week intervention substantially increased time spent for exercise (mean and median of 135 and 170 min/week, respectively) among the 72 % of participants who had adopted cognitive feedback control vs. no increase in the remaining participants of nonadopters. Adopters witnessed significantly improved peak oxygen consumption of >1 metabolic equivalent vs. no improvement among nonadopters. Adopters also reduced body mass index, body weight, and body fat by 1.6 kg/m
2
, 4.8 kg, and 3.6 kg, respectively vs. 0.4 kg/m
2
, 1.4 kg, and 1.1 kg in the control group. The increase in physical activity came at virtually no intervention effort of the investigators. This study demonstrates for the first time that adoption of cognitive feedback control over energy balance is possible with the help of a simple Web-based tool and that overweight adopters self-regulate exercise volume to significantly reduce body weight and improve biomarkers of fitness and cardiovascular risk.
Reliable and high-resolution subsurface characterization beyond the field scale is of great interest for precision agriculture and agro-ecological modelling because the shallow soil (~1–2 m depth) is ...responsible for the storage of moisture and nutrients that are accessible to crops. This can potentially be achieved with a combination of direct sampling and Electromagnetic Induction (EMI) measurements, which have shown great potential for soil characterization due to their non-invasive nature and high mobility. However, only a few studies have used EMI beyond the field scale because of the challenges associated with a consistent interpretation of EMI data from multiple fields and acquisition days. In this study, we performed a detailed EMI survey of an area of 1 km2 divided in 51 agricultural fields where previous studies showed a clear connection between crop performance and soil properties. In total, nine apparent electrical conductivity (ECa) values were measured at each location with a depth of investigation ranging between 0–0.2 to 0–2.7 m. Based on the combination of ECa maps and available soil maps, an a priori interpretation was performed and four sub-areas with characteristic sediments and ECa were identified. Then, a supervised classification methodology was used to divide the ECa maps into areas with similar soil properties. In a next step, soil profile descriptions to a depth of 2 m were obtained at 100 sampling locations and 552 samples were analyzed for textural characteristics. The combination of the classified map and ground truth data resulted in a 1 m resolution soil map with eighteen units with a typical soil profile and texture information. It was found that the soil profile descriptions and texture of the EMI-based soil classes were significantly different when compared using a two-tailed t-test. Moreover, the high-resolution soil map corresponded well with patterns in crop health obtained from satellite imagery. It was concluded that this novel EMI data processing approach provides a reliable and cost-effective tool to obtain high-resolution soil maps to support precision agriculture and agro-ecological modelling.
•A large-scale multi-configuration EMI dataset was analyzed and interpreted.•Supervised image classification was used to classify EMI data.•A 1 m resolution soil map was produced from EMI classification and ancillary data.•Observed patterns in crop growth matched well with the high-resolution soil map.
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