bluuebunny/crossref_metadata_2025 huggingface dataset:
Organohalide respiration potential in marine sediments from Aarhus Bay
Authors: Zhang Chen , Atashgahi Siavash , Bosma Tom N P , Peng Peng , Smidt Hauke
Published: June 2022

Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.
TwinEQTL: ultrafast and powerful association analysis for eQTL and GWAS in twin studies
Authors: Xia Kai , Shabalin Andrey A , Yin Zhaoyu , Chung Wonil , Sullivan Patrick F , Wright Fred A , Styner Martin , Gilmore John H , Santelli Rebecca C , Zou Fei
Published: June 2022

We develop a computationally efficient alternative, TwinEQTL, to a linear mixed-effects model for twin genome-wide association study data. Instead of analyzing all twin samples together with linear mixed-effects model, TwinEQTL first splits twin samples into 2 independent groups on which multiple linear regression analysis can be validly performed separately, followed by an appropriate meta-analysis-like approach to combine the 2 nonindependent test results. Through mathematical derivations, we prove the validity of TwinEQTL algorithm and show that the correlation between 2 dependent test statistics at each single-nucleotide polymorphism is independent of its minor allele frequency. Thus, the correlation is constant across all single-nucleotide polymorphisms. Through simulations, we show empirically that TwinEQTL has well controlled type I error with negligible power loss compared with the gold-standard linear mixed-effects models. To accommodate expression quantitative loci analysis with twin subjects, we further implement TwinEQTL into an R package with much improved computational efficiency. Our approaches provide a significant leap in terms of computing speed for genome-wide association study and expression quantitative loci analysis with twin samples.
Changes in Fall Rates From Before to During the COVID-19 Pandemic: Findings From the Prospective AMBROSIA Study
Authors: Bowling C Barrett , Wei Rong X , Qian Lei , Shimbo Daichi , Schwartz Joseph E , Muntner Paul , Cannavale Kimberly L , Harrison Teresa N , Reynolds Kristi
Published: June 2022

Background

Coronavirus disease 2019 (COVID-19) social distancing policies resulted in reductions in community movement, however, fall rates during this time have not been described.

Methods

This prospective study included adults ≥65 years old participating in the Ambulatory Blood Pressure in Older Adults (AMBROSIA) cohort and who completed ≥1 monthly falls calendar (August 2019–March 2021; n = 250). Months were grouped to correspond to the fall 2020 phased reopening (August–October) and the shelter-in-place policy during the winter 2020 surge (November–January) in Los Angeles, California and compared to the same months, 1 year earlier (ie, before the pandemic).

Results

Participants had a mean (standard deviation [SD]) age of 75.2 (6.1) years, 49.6% were White, and 53.2% were women. We obtained 2 795 falls calendars during follow-up. Overall, 110 (44.0%) participants reported a total of 421 falls (rate 15.1 per 100 calendar months). The highest monthly fall rate during the pandemic was 22.9 (95% confidence interval [CI] 16.4–31.1) per 100 calendar-months in August 2020. The lowest fall rate during the pandemic was 8.6 (95% CI 3.5–17.8) per 100 calendar-months in February 2021. During the pandemic, fall rates in August, September, and October 2020 were higher than the previous year (rate ratio 1.8 [95% CI 1.1–2.9]), and fall rates in November and December 2020 and January 2021 were lower than the previous year (rate ratio 0.5 [95% CI 0.4–0.8]).

Conclusion

As the pandemic continues and older adults resume community mobility after a shelter-in-place period, providers should pay attention to the risk of falls.
Muscle Fatigue in the Latch-Mediated Spring Actuated Mandibles of Trap-Jaw Ants
Authors: Larabee Fredrick J , Gibson Josh C , Rivera Michael D , Anderson Philip S L , Suarez Andrew V
Published: June 2022

Muscle fatigue can reduce performance potentially affecting an organism's fitness. However, some aspects of fatigue could be overcome by employing a latch-mediated spring actuated (LaMSA) system where muscle activity is decoupled from movement. We estimated the effects of muscle fatigue on different aspects of mandible performance in six species of ants, two whose mandibles are directly actuated by muscles and four that have LaMSA “trap-jaw” mandibles. We found evidence that the LaMSA system of trap-jaw ants may prevent some aspects of performance from declining with repeated use, including duration, acceleration, and peak velocity. However, inter-strike interval increased with repeated strikes suggesting that muscle fatigue still comes into play during the spring loading phase. In contrast, one species with directly actuated mandibles showed a decline in bite force over time. These results have implications for design principles aimed at minimizing the effects of fatigue on performance in spring and motor actuated systems.
Avoiding oversizing in sutureless valves leads to lower transvalvular gradients and less permanent pacemaker implants postoperatively
Authors: Szecel Delphine , Lamberigts Marie , Rega Filip , Verbrugghe Peter , Dubois Christophe , Meuris Bart
Published: June 2022

OBJECTIVES

The aim of this study was to evaluate the impact of changing the sizing strategy in aortic valve replacement using the Perceval sutureless prosthesis on haemodynamic outcomes and postoperative pacemaker implantation.

METHODS

Retrospective analysis of patients implanted with the Perceval valve between 2007 and 2019 was performed by comparing patients implanted before the modification of sizing strategy (OLD group) and after (NEW group). The outcome parameters evaluated were the implanted prosthesis size, haemodynamical profile and postoperative pacemaker implantation.

RESULTS

The entire patient cohort (784 patients) consisted of 52% female patients, with a mean age of 78.53 [standard deviation (SD): 5.8] years and a mean EuroSCORE II of 6.3 (range 0.7–76). In 55.5% of cases, surgery was combined. The NEW cohort had more male patients (54.6% vs 43.4%) (P = 0.002). Mean implanted valve size, corrected for body surface area, was significantly lower in the NEW cohort (13.1, SD: 1.4 vs 13.5, SD: 1.4 mm/m2, P < 0.001). The 30-day mortality was 3.4%. Peak and mean transvalvular gradients at discharge were significantly lower in the NEW versus OLD groups: 24.4 mmHg (SD: 9.2) versus 28.4 mmHg (SD: 10.3) (P < 0.001) and 13.6 mmHg (SD: 5.3) versus 15.5 mmHg (SD: 6.0) (P < 0.001). The mean effective opening area and the indexed effective opening area, respectively, increased from 1.5 cm2 (SD: 0.5) and 0.85 cm2/m2 (SD: 0.27) in the OLD group to 1.7 cm2 (SD: 0.5) and 0.93 cm2/m2 (SD: 0.30) in the NEW group (P < 0.001). No difference was found in paravalvular leakage ≥1/4. Centrovalvular leakage ≥1/4 significantly decreased from 18% to 7.9% (P < 0.001). With the new sizing, the new postoperative pacemaker implantation rate decreased significantly from 11% to 6.1% (P = 0.016).

CONCLUSIONS

Correct sizing of sutureless aortic valves is crucial to obtain the best possible haemodynamics and avoid complications.
Different ascending aortic phenotypes with similar mutations in 2 patients with Loeys-Dietz syndrome type 2
Authors: Heck Roland , Fischer-Zirnsak Björn , Photiadis Joachim , Horn Denise , Gehle Petra
Published: June 2022

Our goal was to present 2 infants with confirmed Loeys-Dietz syndrome. The missense mutations in exon 7 of the TGFBR2 gene are only 5 codons apart (c.1597T>C and c.1582C>G). Phenotypically, the aneurysms of the ascending aorta were restricted to different segments of the aorta: the suprajunctional segment in 1 patient and the aortic root in another. These cases highlight the complexity of signaling pathways and gene expression in the pathogenesis of aortic aneurysms.
An alpaca single-domain antibody (VHH) phage display library constructed by CDR shuffling provided high-affinity VHHs against desired protein antigens
Authors: Tsukahara Narutoshi , Murakami Akikazu , Motohashi Maiko , Nakayama Hiroshi , Kondo Yoshiro , Ito Yuji , Azuma Takachika , Kishimoto Hidehiro
Published: June 2022

Antigen-combining sites of the camelid heavy-chain antibody variable domain (VHH) are constructed by three complementarity-determining regions (CDR1, CDR2 and CDR3). We prepared cDNA using mRNA extracted from peripheral lymphocytes of alpacas that had been non-immunized or immunized with human serum albumin (HSA). The VHH gene fragments encoding the amino-terminal half-containing CDR1 as well as CDR2 and the carboxy-terminal half-containing CDR3 were amplified independently by PCR, and then full-length VHH gene fragments were generated by overlap extension PCR and cloned into the phagemid vector. This protocol, referred to as CDR shuffling, allowed us to construct an alpaca VHH phage display library possessing repertoires different from those naturally occurring in animals. We asked, first, whether this library was able to provide the functional VHH fragments against HSA, an immunized antigen, and obtained 29 anti-HSA VHH clones, 41% possessed KD values of lower than 10−8 M, 5 of which had KD values of 10−10 M. We also obtained VHH clones against non-immunized protein antigens such as cardiac troponin T and I, Ebola virus glycoprotein 1 and human immunoglobulin G by biopanning. We compared the amino acid sequences and affinities and found that 43% of VHHs had KD values of less than 10−8 M, although those having KD values of 10−10 M were unavailable. These results suggested that the CDR-shuffled VHH phage display library could potentially provide VHHs against non-immunized protein antigens with similar levels of affinities to those against immunized antigens.
The cellular and molecular basis of CD69 function in anti-tumor immunity
Authors: Koyama-Nasu Ryo , Wang Yangsong , Hasegawa Ichita , Endo Yukihiro , Nakayama Toshinori , Kimura Motoko Y
Published: June 2022

Cancer immunotherapy utilizes our immune system to attack cancer cells and is an extremely promising strategy for cancer treatment. Although immune-checkpoint blockade, such as anti-PD-1 (programmed cell death 1) antibody, has demonstrated significant enhancement of anti-tumor immunity and has induced notable clinical outcomes, its response rates remain low, and adverse effects are always a matter of concern; therefore, new targets for cancer immunotherapy are always desired. In this situation, new concepts are needed to fuel the investigation of new target molecules for cancer immunotherapy. We propose that CD69 is one such target molecule. CD69 is known to be an activation marker of leukocytes and is also considered a crucial regulator of various immune responses through its interacting proteins. CD69 promotes T-cell retention in lymphoid tissues via sphingosine-1-phosphate receptor 1 (S1P1) internalization and also plays roles in the pathogenesis of inflammatory disorders through interacting with its functional ligands Myl9/12 (myosin light chains 9, 12a and 12b). In anti-tumor immunity, CD69 is known to be expressed on T cells in the tumor microenvironment (TME) and tumor-draining lymph nodes (TDLNs). We revealed that CD69 negatively regulates the effector function of intratumoral T cells and importantly controls the ‘exhaustion’ of CD8 T cells. In addition, we and others showed that either CD69 deficiency or the administration of anti-CD69 monoclonal antibody enhances anti-tumor immunity. Thus, CD69 is an attractive target for cancer immunotherapy.
Effectiveness of clinical dashboards as audit and feedback or clinical decision support tools on medication use and test ordering: a systematic review of randomized controlled trials
Authors: Xie Charis Xuan , Chen Qiuzhe , Hincapié Cesar A , Hofstetter Léonie , Maher Chris G , Machado Gustavo C
Published: June 2022

Background

Clinical dashboards used as audit and feedback (A&F) or clinical decision support systems (CDSS) are increasingly adopted in healthcare. However, their effectiveness in changing the behavior of clinicians or patients is still unclear. This systematic review aims to investigate the effectiveness of clinical dashboards used as CDSS or A&F tools (as a standalone intervention or part of a multifaceted intervention) in primary care or hospital settings on medication prescription/adherence and test ordering.

Methods

Seven major databases were searched for relevant studies, from inception to August 2021. Two authors independently extracted data, assessed the risk of bias using the Cochrane RoB II scale, and evaluated the certainty of evidence using GRADE. Data on trial characteristics and intervention effect sizes were extracted. A narrative synthesis was performed to summarize the findings of the included trials.

Results

Eleven randomized trials were included. Eight trials evaluated clinical dashboards as standalone interventions and provided conflicting evidence on changes in antibiotic prescribing and no effects on statin prescribing compared to usual care. Dashboards increased medication adherence in patients with inflammatory arthritis but not in kidney transplant recipients. Three trials investigated dashboards as part of multicomponent interventions revealing decreased use of opioids for low back pain, increased proportion of patients receiving cardiovascular risk screening, and reduced antibiotic prescribing for upper respiratory tract infections.

Conclusion

There is limited evidence that dashboards integrated into electronic medical record systems and used as feedback or decision support tools may be associated with improvements in medication use and test ordering.
Lactose Concentration in Low-Lactose and Lactose-Free Milk, Milk Products, and Products Containing Dairy Ingredients by High Sensitivity Enzymatic Method (K-LOLAC), Collaborative Study: Final Action 2020.08
Authors: Ivory Ruth , Mangan David , McCleary Barry V
Published: June 2022

Background

The AOAC Stakeholder Panel on Strategic Food Analytical Methods issued a call for methods in 2018 for the measurement of lactose in low-lactose and lactose-free products under Standard Method Performance Requirement (SMPR®) 2018.009. Megazyme’s Lactose Assay Kit (K-LOLAC) was reviewed and accepted as a First Action Official MethodSM in 2020 (2020.08).

Objective

A collaborative study was conducted to evaluate the to evaluate the reproducibility of AOAC Official MethodSM2020.08 for the measurement of lactose concentration in low-lactose and lactose-free milk, milk products, and products containing dairy ingredients.

Method

Samples are deproteinated and clarified by treatment with Carrez reagents, and then free glucose is removed using a glucose oxidase and catalase treatment system. Quantification of lactose is based on the hydrolytic activity of β-galactosidase, which hydrolyses lactose to glucose and galactose. Any remaining free D-glucose is first measured using a hexokinase (HK)/glucose 6-phosphate dehydrogenase (G-6PDH)/6-phosphogluconate dehydrogenase (6-PGDH) based assay procedure, and then β-galactosidase is added to hydrolyze the lactose in the same reaction vessel with concurrent measurement of the released D-glucose. The samples analyzed included a number of lactose-free and low-lactose milk samples, lactose-free infant formula, lactose-free milkshake, lactose-free adult nutritional drink, lactose-free cream, and lactose-free cheese.

Results

All materials had repeatability relative standard deviations (RSDr) <7%. The reproducibility relative standard deviation (RSDR) varied from 3.8 to 14.9% with seven of the 10 test samples having an RSDR of <10%.

Conclusions

The Lactose Assay Kit (K-LOLAC) meets the requirements for reproducibility set out under SMPR 2018.009.

Highlights

The Lactose Assay (K-LOLAC) is a robust, simple, and reproducible method for analysis of lactose in foodstuffs and beverages.
Killer citiesandindustrious cities? New data and evidence on 250 years of urban growth
Authors: Gindelsky Marina , Jedwab Remi
Published: June 2022

In the historical literature, cities of the Industrial Revolution (IR) are portrayed as having a demographic penalty: killer cities with high death rates and industrious cities with low birth rates. To econometrically test this, we construct a novel data set of almost 2000 crude demographic rates for 142 large cities in 35 countries for 1700–1950. Mortality actually decreased faster than fertility during the IR era and rates of natural increase rose in the cities of industrializing countries, especially large cities. This implies a declining, not rising, demographic penalty thanks to the IR. To explain the puzzle, we posit that negative health and industriousness effects of industrial urbanization might have been outweighed by positive effects of increased income and life expectancy.
Lithology prediction method of coal-bearing reservoir based on stochastic seismic inversion and Bayesian classification: a case study on Ordos Basin
Authors: Liu Wei , Du Wenfeng , Guo Yinling , Li Dong
Published: June 2022

The Upper Palaeozoic coal measures in the Ordos Basin are rich in unconventional natural gas resources; however, the reservoir heterogeneity is relatively strong, which majorly restricts the accuracy of lithology prediction. Stochastic seismic inversion can synthesize the geological–geophysical information and establish high-resolution reservoir models based on geostatistical theory to obtain good inversion results; moreover, it can characterize reservoir lithology and fluid-bearing properties. The present study aimed to propose a high-precision lithology classification method for coal-bearing strata in the Ordos Basin, using Bayesian classification and stochastic seismic inversion. Initially, the reservoir geological model was established on the basis of the sequential Gaussian simulation algorithm, and stochastic seismic inversion was performed in combination with rock physics analysis, thereby obtaining a high-resolution elastic parameter data volume. Thereafter, the probability density function (PDF) and the probability density confusion matrix (PDF confusion matrix) were introduced to quantitatively analyse the ability of sensitive elastic parameters to distinguish lithology. Eventually, a logging lithology-fluid classification template was established based on the Bayesian classification technology; furthermore, a 3D lithology-fluid prediction was completed in combination with the inversion results. The prediction results are in good accordance with the logging data, which verifies the feasibility and effectiveness of the method.
Sequence Diversity and Differences at the Highly Duplicated MHC-I Gene Reflect Viral Susceptibility in Sympatric Pinniped Species
Authors: Gigliotti Alayna K , Bowen W Don , Hammill Michael O , Puryear Wendy B , Runstadler Jonathan , Wenzel Frederick W , Cammen Kristina M
Published: June 2022

Differences in disease susceptibility among species can result from rapid host–pathogen coevolution and differences in host species ecology that affect the strength and direction of natural selection. Among 2 sympatric pinniped species that differ in sociality and putative disease exposure, we investigate observed differences in susceptibility through an analysis of a highly variable, duplicated gene family involved in the vertebrate immune response. Using high-throughput amplicon sequencing, we characterize diversity at the 2 exons that encode the peptide binding region of the major histocompatibility complex class I (MHC-I) gene in harbor (N = 60) and gray (N = 90) seal populations from the Northwest Atlantic. Across species, we identified 106 full-length exon 2 and 103 exon 3 sequence variants and a minimum of 11 duplicated MHC-I loci. The sequence variants clustered in 15 supertypes defined by the physiochemical properties of the peptide binding region, including a putatively novel Northwest Atlantic MHC-I diversity sublineage. Trans-species polymorphisms, dN/dS ratios, and evidence of gene conversion among supertypes are consistent with balancing selection acting on this gene. High functional redundancy suggests particularly strong selection among gray seals at the novel Northwest Atlantic MHC-I diversity sublineage. At exon 2, harbor seals had a significantly greater number of variants per individual than gray seals, but fewer supertypes. Supertype richness and private supertypes are hypothesized to contribute to observed differences in disease resistance between species, as consistently, across the North Atlantic and many disease outbreaks, gray seals appear to be more resistant to respiratory viruses than harbor seals.
Quantile Spectral Beta: A Tale of Tail Risks, Investment Horizons, and Asset Prices
Authors: Baruník Jozef , Nevrla Matěj
Published: June 2022

This article investigates how two important sources of risk—market tail risk (TR) and extreme market volatility risk—are priced into the cross-section of asset returns across various investment horizons. To identify such risks, we propose a quantile spectral (QS) beta representation of risk based on the decomposition of covariance between indicator functions that capture fluctuations over various frequencies. We study the asymptotic behavior of the proposed estimators of such risk. Empirically, we find that TR is a short-term phenomenon, whereas extreme volatility risk is priced by investors in the long term when pricing a cross-section of individual stocks. In addition, we study popular industry, size and value, profit, investment, or book-to-market portfolios, as well as portfolios constructed from various asset classes, portfolios sorted on cash flow duration, and other strategies. These results reveal that tail-dependent and horizon-specific risks are priced heterogeneously across datasets and are important sources of risk for investors.
Small Area Estimation in Diverse Timber Types Using Multiple Sources of Auxiliary Data
Authors: Green P Corey , Hogg Dale W , Watson Brian , Burkhart Harold E
Published: June 2022

Informed forest management requires reliable information. As the demand for finer scale estimates has increased, so has the cost for obtaining them from design-based ground sampling. Small area estimation (SAE) is an estimation technique that leverages ancillary information to augment design-based samples with the goal of increasing estimate precision without increasing ground-based sample intensities. This work presents three case studies spanning an industrial timberland ownership in the United States making use of SAE techniques in operational forest inventories. Case studies include an inventory of pre-thin plantation loblolly pine (Pinus taeda L.) stands that had achieved crown closure in Alabama and Mississippi, a mixed pine–hardwood inventory in Alabama, and pre-thinning plantation Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) in Washington State. Using area-level SAE techniques, vegetation indices derived from 10 m Sentinel imagery were shown to reduce estimate uncertainty for common stand parameters. Additionally, when available, lidar and age were shown to offer additional improvements in estimate precision. The results of this study indicate the operational potential for using commonly available auxiliary data for producing forest parameter estimates with enhanced precision. The implications of these findings span multiple inventory objectives including, for example, commercial forest management, carbon accounting, and wildfire fuel assessments.

Study Implications: Forest management requires reliable quantitative information for informed decisions. Data from ground-based forest inventories are commonly used to construct design-unbiased direct estimates. Due to logistical and cost constraints, samples often do not provide estimates with sufficient precision for making confident decisions. The statistical estimation procedure, small area estimation, is able to leverage linearly related ancillary data across areas of interest to form composite estimates that have less uncertainty than direct estimates alone. This study shows how combining ground-based data with auxiliary data from remote sensing and stand records produced more precise estimates of forest stand parameters in three distinct timber types spanning a large ownership in the United States. Results indicate that significant inventory efficiency and confidence can be realized by incorporating commonly available auxiliary data into the estimation of forest characteristics.
The discovery of rubisco
Authors: Sharkey Thomas D
Published: June 2022

Rubisco is possibly the most important enzyme on Earth, certainly in terms of amount. This review describes the initial reports of ribulose 1,5-bisphosphate carboxylating activity. Discoveries of core concepts are described, including its quaternary structure, the requirement for post-translational modification, and its role as an oxygenase as well as a carboxylase. Finally, the requirement for numerous chaperonins for assembly of rubisco in plants is described.
Floral organ abscission in Arabidopsis requires the combined activities of three TALE homeodomain transcription factors
Authors: Crick Jennifer , Corrigan Laura , Belcram Katia , Khan Madiha , Dawson Jeff W , Adroher Bernard , Li Sibei , Hepworth Shelley R , Pautot Véronique
Published: June 2022

Floral organ abscission is a separation process in which sepals, petals, and stamens detach from the plant at abscission zones. Here, we investigated the collective role of three amino-acid-loop-extension (TALE) homeobox genes ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1), KNAT6 (for KNOTTED LIKE from Arabidopsis thaliana) and KNAT2, which form a module that patterns boundaries under the regulation of BLADE-ON-PETIOLE 1 and 2 (BOP1/2) co-activators. These TALE homeodomain transcription factors were shown to maintain boundaries in the flower, functioning as a unit to coordinate the growth, patterning, and activity of abscission zones. Together with BOP1 and BOP2, ATH1 and its partners KNAT6 and KNAT2 collectively contribute to the differentiation of lignified and separation layers of the abscission zone. The genetic interactions of BOP1/2 and ATH1 with INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) were also explored. We showed that BOP1/2 co-activators and ATH1 converge with the IDA signalling pathway to promote KNAT6 and KNAT2 expression in the abscission zone and cell separation. ATH1 acts as a central regulator in floral organ abscission as it controls the expression of other TALE genes in abscission zone cells.
A simple technology for plastid transformation with fragmented DNA
Authors: Ren Kang , Xu Wenbo , Ren Bailing , Fu Jinqiu , Jiang Chunmei , Zhang Jiang
Published: June 2022

Plastid engineering has several unique advantages such as high expression of transgenes due to high polyploidy of plastid genomes and environmental biosafety because of maternal inheritance of transgenes, and has become a promising tool for molecular farming, metabolic engineering, and genetic improvement. However, there are no standard vectors available for plastid transformation. Moreover, the construction of plastid transformation vectors containing long operons or genes encoding proteins that are toxic to Escherichia coli was tedious or difficult. Here, we developed a simple plastid transformation technology without the need for in vitro vector construction by using multiple linear DNA fragments which share homologous sequences (HSs) at their ends. The strategy is based on homologous recombination between HSs of DNA fragments via endogenous recombination machinery in plastids, which subsequently are integrated into the plastid genome. We found that HSs of 200 bp or longer were sufficient for mediating the integration into the plastid genome with at least similar efficiency to that of plasmid DNA-based plastid transformation. Furthermore, we successfully used this method to introduce a phage lysin-encoding gene and a long operon into a tobacco plastid genome. The establishment of this technology simplifies the plastid transformation procedure and provides a novel solution for expressing proteins, which are either toxic to the cloning host or large operons in plastids, without need of vector cloning.
Optical and X-ray GRB Fundamental Planes as cosmological distance indicators
Authors: Dainotti M G , Nielson V , Sarracino G , Rinaldi E , Nagataki S , Capozziello S , Gnedin O Y , Bargiacchi G
Published: June 2022

Gamma-ray bursts (GRBs), can be employed as standardized candles, extending the distance ladder beyond Type Ia supernovae (SNe Ia, z = 2.26). We standardize GRBs using the three-dimensional (3D) Fundamental Plane relation (the Dainotti relation) among the rest-frame end time of the X-ray plateau emission, its corresponding luminosity, and the peak prompt luminosity. Combining SNe Ia and GRBs, we constrain ΩM = 0.299 ± 0.009 assuming a flat Λ cold dark matter (ΛCDM) cosmology with and without correcting GRBs for selection biases and redshift evolution. Using a 3D optical Dainotti correlation, we find this sample is as efficacious in the determination of ΩM as the X-ray sample. We trimmed our GRB samples to achieve tighter planes to simulate additional GRBs. We determined how many GRBs are needed as stand-alone probes to achieve a comparable precision on ΩM to the one obtained by SNe Ia only. We reach the same error measurements derived using SNe Ia in 2011 and 2014 with 142 and 284 simulated optical GRBs, respectively, considering the error bars on the variables halved. These error limits will be reached in 2038 and in 2047, respectively. Using a doubled sample (obtained by future machine learning approaches allowing a light-curve reconstruction and the estimates of GRB redshifts when z is unknown) compared to the current sample, with error bars halved we will reach the same precision as SNe Ia in 2011 and 2014, now and in 2026, respectively. If we consider the current SNe precision, this will be reached with 390 optical GRBs by 2054.
WISDOM project – XI. Star formation efficiency in the bulge of the AGN-host Galaxy NGC 3169 with SITELLE and ALMA
Authors: Lu Anan , Boyce Hope , Haggard Daryl , Bureau Martin , Liang Fu-Heng , Liu Lijie , Choi Woorak , Cappellari Michele , Chemin Laurent , Chevance Mélanie , Davis Timothy A , Drissen Laurent , Elford Jacob S , Gensior Jindra , Kruijssen J M Diederik , Martin Thomas , Massé Etienne , Robert Carmelle , Ruffa Ilaria , Rousseau-Nepton Laurie , Sarzi Marc , Savard Gabriel , Williams Thomas G
Published: June 2022

The star formation efficiency (SFE) has been shown to vary across different environments, particularly within galactic starbursts and deep within the bulges of galaxies. Various quenching mechanisms may be responsible, ranging from galactic dynamics to feedback from active galactic nuclei (AGNs). Here, we use spatially resolved observations of warm ionized gas emission lines (Hβ, [O iii] λλ4959,5007, [N ii] λλ6548,6583, Hα and [S ii] λλ6716,6731) from the imaging Fourier transform spectrograph SITELLE at the Canada–France–Hawaii Telescope (CFHT) and cold molecular gas (12CO(2-1)) from the Atacama Large Millimeter/sub-millimeter Array (ALMA) to study the SFE in the bulge of the AGN-host galaxy NGC 3169. After distinguishing star-forming regions from AGN-ionized regions using emission-line ratio diagnostics, we measure spatially resolved molecular gas depletion times (τdep ≡1/SFE) with a spatial resolution of ≈100 pc within a galactocentric radius of 1.8 kpc. We identify a star-forming ring located at radii 1.25 ± 0.6 kpc with an average τdep of 0.3 Gyr. At radii <0.9 kpc, however, the molecular gas surface densities and depletion times increase with decreasing radius, the latter reaching approximately 2.3 Gyr at a radius ≈500 pc. Based on analyses of the gas kinematics and comparisons with simulations, we identify AGN feedback, bulge morphology and dynamics as the possible causes of the radial profile of SFE observed in the central region of NGC 3169.
Stringent limits on 28SiO maser emission from the recurrent nova T Coronae Borealis
Authors: Evans A , Pimpanuwat B , Richards A M S , Banerjee D P K , Munari U , Gray M D , Hutawarakorn Kramer B , Kraus A
Published: June 2022

There are indications that the third-known eruption of the recurrent nova T CrB is imminent, and multiwavelength observations prior to the eruption are important to characterize the system before it erupts. T CrB is known to display the SiO fundamental vibrational feature at 8 $\, \mu$m. When the anticipated eruption occurs, it is possible that the shock produced when the ejected material runs into the wind of the red giant in the system may be traced using SiO maser emission. We have used the 100 m Effelsberg Radio Telescope to search for 28SiO emission in the υ = 1, υ = 2, J = 1 → 0 transitions, at 43.122 GHz and 42.820 GHz, respectively, while the system is in quiescence. We find no evidence for such emission. We set stringent 3σ upper limits of 1.66 mJy on emission in the υ = 1, J = 1 → 0 transition, and 1.72 mJy in the υ = 2, J = 1 → 0 transition, respectively, for a noise bandwidth of 250 kHz. The corresponding limits for a 31.25 kHz bandwidth are 4.69 and 4.86 mJy, respectively. These upper limits improve on previous upper limits for this system by more than two orders of magnitude.
Noncanonical NF-κB factor p100/p52 regulates homologous recombination and modulates sensitivity to DNA-damaging therapy
Authors: Budke Brian , Zhong Alison , Sullivan Katherine , Park Chanyoung , Gittin David I , Kountz Timothy S , Connell Philip P
Published: June 2022

Homologous recombination (HR) serves multiple roles in DNA repair that are essential for maintaining genomic stability, including double-strand DNA break (DSB) repair. The central HR protein, RAD51, is frequently overexpressed in human malignancies, thereby elevating HR proficiency and promoting resistance to DNA-damaging therapies. Here, we find that the non-canonical NF-κB factors p100/52, but not RelB, control the expression of RAD51 in various human cancer subtypes. While p100/p52 depletion inhibits HR function in human tumor cells, it does not significantly influence the proficiency of non-homologous end joining, the other key mechanism of DSB repair. Clonogenic survival assays were performed using a pair DLD-1 cell lines that differ only in their expression of the key HR protein BRCA2. Targeted silencing of p100/p52 sensitizes the HR-competent cells to camptothecin, while sensitization is absent in HR-deficient control cells. These results suggest that p100/p52-dependent signaling specifically controls HR activity in cancer cells. Since non-canonical NF-κB signaling is known to be activated after various forms of genomic crisis, compensatory HR upregulation may represent a natural consequence of DNA damage. We propose that p100/p52-dependent signaling represents a promising oncologic target in combination with DNA-damaging treatments.
Insight into RNA–DNA primer length counting by human primosome
Authors: Baranovskiy Andrey G , Lisova Alisa E , Morstadt Lucia M , Babayeva Nigar D , Tahirov Tahir H
Published: June 2022

The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), synthesizes chimeric RNA–DNA primers of a limited length for DNA polymerases delta and epsilon to initiate DNA replication on both chromosome strands. Despite recent structural insights into the action of its two catalytic centers, the mechanism of DNA synthesis termination is still unclear. Here we report results of functional and structural studies revealing how the human primosome counts RNA–DNA primer length and timely terminates DNA elongation. Using a single-turnover primer extension assay, we defined two factors that determine a mature primer length (∼35-mer): (i) a tight interaction of the C-terminal domain of the DNA primase large subunit (p58C) with the primer 5′-end, and (ii) flexible tethering of p58C and the DNA polymerase alpha catalytic core domain (p180core) to the primosome platform domain by extended linkers. The obtained data allow us to conclude that p58C is a key regulator of all steps of RNA–DNA primer synthesis. The above-described findings provide a notable insight into the mechanism of DNA synthesis termination by a eukaryotic primosome, an important process for ensuring successful primer handover to replication DNA polymerases and for maintaining genome integrity.
Imaging in patients with glioblastoma: A national cohort study
Authors: Dumba Maureen , Fry Anna , Shelton Jon , Booth Thomas C , Jones Brynmor , Shuaib Haris , Williams Matt
Published: June 2022

Background

Glioblastoma is the most common malignant brain tumor in adults and has a poor prognosis. This cohort of patients is diverse and imaging is vital to formulate treatment plans. Despite this, there is relatively little data on patterns of use of imaging and imaging workload in routine practice.

Methods

We examined imaging patterns for all patients aged 15–99 years resident in England who were diagnosed with a glioblastoma between 1st January 2013 and 31st December 2014. Patients without imaging and death-certificate-only registrations were excluded.

Results

The analytical cohort contained 4,307 patients. There was no significant variation in pre- or postdiagnostic imaging practice by sex or deprivation quintile. Postdiagnostic imaging practice was varied. In the group of patients who were treated most aggressively (surgical debulking and chemoradiation) and were MRI compatible, only 51% had a postoperative MRI within 72 hours of surgery. In patients undergoing surgery who subsequently received radiotherapy, only 61% had a postsurgery and preradiotherapy MRI.

Conclusions

Prediagnostic imaging practice is uniform. Postdiagnostic imaging practice was variable. With increasing evidence and clearer recommendations regarding debulking surgery and planning radiotherapy imaging, the reason for this is unclear and will form the basis of further work.
Nicotine Delivery and Pharmacokinetics of an Electronic Cigarette Compared With Conventional Cigarettes in Chinese Adult Smokers: A Randomized Open-Label Crossover Clinical Study
Authors: Guo Yi , Li Shoufeng , Wang Zhi , Jiang Fulin , Guan Yanping , Huang Min , Zhong Guoping
Published: June 2022

Introduction

To evaluate the nicotine pharmacokinetics of a commercial electronic cigarette (e-cigarette) relative to conventional cigarettes in Chinese adult smokers.

Aims and Methods

A randomized, open-label, crossover clinical study was conducted on 23 healthy adult Chinese smokers. In two sessions, subjects used either the e-cigarettes with 30 mg/g nicotine in e-liquid or conventional cigarettes of a given brand, at one puff every 30 seconds for a total of 10 puffs. Blood samples were collected at specified time points for 4 hours after the first puff. Subjective effects on desire-to-smoke and physiological parameters such as heart rate and oxyhemoglobin saturation levels were also examined before and after using the two products.

Results

The baseline-adjusted maximum nicotine concentration (Cmax-BL), time-to-peak nicotine concentration (Tmax), and nicotine absorption rate (Cmax-BL divided by Tmax) were found to be similar for the e-cigarette versus those of conventional cigarettes (p > .05). Total nicotine exposure measured as the area-under-curve (AUC0-t-BL) was significantly lower for the e-cigarette relative to that of conventional cigarettes. In addition, the subjects found that e-cigarettes were well tolerated under controlled puffing conditions.

Conclusions

The test e-cigarettes achieved similar nicotine delivery and pharmacokinetic profiles to those of the comparator cigarettes, indicating that this e-cigarette could be a potential alternative to conventional cigarettes for those adult smokers.

Implications

There are no data in the published literature on the nicotine pharmacokinetics of e-cigarettes in Chinese smokers. To the best of our knowledge, this is the first study to evaluate the nicotine delivery and pharmacokinetic profile of a commercial e-cigarette brand compared with conventional cigarettes in Chinese adult smokers. After the use of test e-cigarettes, nicotine delivery and pharmacokinetic profile were similar to those of conventional cigarettes in Chinese adult smokers.
Perspectives of Zambian Clinical Oncology Trainees in the MD Anderson and Zambia Virtual Clinical Research Training Program (MOZART)
Authors: Diao Kevin , Kizub Darya A , Ausat Noveen , Mwaba Catherine K , Anakwenze Akinfenwa Chidinma P , Cameron Carrie A , Chiao Elizabeth Y , Lombe Dorothy C , Msadabwe Susan C , Lin Lilie L
Published: June 2022

Background

African countries are underrepresented in cancer research, partly because of a lack of structured curricula on clinical research during medical education. To address this need, the MD Anderson and Zambia Virtual Clinical Research Training Program (MOZART) was developed jointly by MD Anderson Cancer Center (MDA) and the Cancer Diseases Hospital in Zambia (CDH) for Zambian clinical oncology trainees. We explored participant perspectives to provide insight for implementation of similar efforts.

Materials and Methods

The MD Anderson and Zambia Virtual Clinical Research Training Program consisted of weekly virtual lectures and support of Zambian-led research protocols through longitudinal mentorship groups that included CDH faculty and MDA peer and faculty mentors. Participants were contacted via email to take part in semi-structured interviews, which were conducted via teleconference and audio-recorded, transcribed, and coded. Emergent themes were extracted and are presented with representative verbatim quotations.

Results

Thirteen of the 14 (93%) trainees were interviewed. Emergent themes included (1) participants having diverse educational backgrounds but limited exposure to clinical research, (2) importance of cancer research specific to a resource-constrained setting, (3) complementary roles of peer mentors and local and international faculty mentors, (4) positive impact on clinical research skills but importance of a longitudinal program and early exposure to clinical research, and (5) challenges with executing research protocols.

Conclusion

To our knowledge, this is the first qualitative study of African clinical oncology trainees participating in a virtual clinical research training program. The lessons learned from semi-structured interviews with participants in MOZART provided valuable insights that can inform the development of similar clinical research training efforts and scale-up.
Small EPIDERMAL PATTERNING FACTOR-LIKE2 peptides regulate awn development in rice
Authors: Xiong Luling , Huang Yingyong , Liu Zupei , Li Chen , Yu Hang , Shahid Muhammad Qasim , Lin Yanhui , Qiao Xiaoyi , Xiao Junyi , Gray Julie E , Jin Jing
Published: June 2022

The EPIDERMAL PATTERNING FACTOR (EPF) and EPF-LIKE (EPFL) family of small secreted peptides act to regulate many aspects of plant growth and development; however, their functions are not widely characterized in rice (Oryza sativa). Here, we used clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) technology to individually knockout each of 11 EPF/EPFL genes in the rice cultivar Kasalath. Loss of function of most OsEPF/EPFL genes generated no obvious phenotype alteration, while disruption of OsEPFL2 in Kasalath caused a short or no awn phenotype and reduced grain size. OsEPFL2 is strongly expressed in the young panicle, consistent with a role in regulating awn and grain development. Haplotype analysis indicated that OsEPFL2 can be classified into six major haplotypes. Nucleotide diversity and genetic differentiation analyses suggested that OsEPFL2 was positively selected during the domestication of rice. Our work to systematically investigate the function of EPF/EPFL peptides demonstrates that different members of the same gene family have been independently selected for their ability to regulate a similar biological function and provides perspective on rice domestication.
Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants
Authors: Weiss Trevor , Crisp Peter A , Rai Krishan M , Song Meredith , Springer Nathan M , Zhang Feng
Published: June 2022

CRISPR–Cas9-mediated genome editing has been widely adopted for basic and applied biological research in eukaryotic systems. While many studies consider DNA sequences of CRISPR target sites as the primary determinant for CRISPR mutagenesis efficiency and mutation profiles, increasing evidence reveals the substantial role of chromatin context. Nonetheless, most prior studies are limited by the lack of sufficient epigenetic resources and/or by only transiently expressing CRISPR–Cas9 in a short time window. In this study, we leveraged the wealth of high-resolution epigenomic resources in Arabidopsis (Arabidopsis thaliana) to address the impact of chromatin features on CRISPR–Cas9 mutagenesis using stable transgenic plants. Our results indicated that DNA methylation and chromatin features could lead to substantial variations in mutagenesis efficiency by up to 250-fold. Low mutagenesis efficiencies were mostly associated with repressive heterochromatic features. This repressive effect appeared to persist through cell divisions but could be alleviated through substantial reduction of DNA methylation at CRISPR target sites. Moreover, specific chromatin features, such as H3K4me1, H3.3, and H3.1, appear to be associated with significant variation in CRISPR–Cas9 mutation profiles mediated by the non-homologous end joining repair pathway. Our findings provide strong evidence that specific chromatin features could have substantial and lasting impacts on both CRISPR–Cas9 mutagenesis efficiency and DNA double-strand break repair outcomes.