Can plastid genome sequencing be used for species identification in the Lauraceae?

Using DNA barcoding for species identification remains challenging for many plant groups. New sequencing approaches such as complete plastid genome sequencing may provide some increased power and practical benefits for species identification beyond standard plant DNA barcodes. We undertook a case study comparing standard DNA barcoding to plastid genome sequencing for species discrimination in the ecologically and economically important family Lauraceae, using 191 plastid genomes for 131 species from 25 genera, representing the largest plastome data set for Lauraceae to date. We found that the plastome sequences were useful in correcting some identification errors and for finding new and cryptic species. However, plastome data overall were only able to discriminate c. 60% of the species in our sample, with this representing a modest improvement from 40 to 50% discrimination success with the standard plant DNA barcodes. Beyond species discrimination, the plastid genome sequences revealed complex relationships in the family, with 12/25 genera being non-monophyletic and with extensive incongruence relative to nuclear ribosomal DNA. These results highlight that although useful for improving phylogenetic resolution in the family and providing some species-level insights, plastome sequences only partially improve species discrimination, and this reinforces the need for large-scale nuclear data to improve discrimination among closely related species

Association of inpatient use of angiotensin converting enzyme inhibitors and angiotensin II receptor blockers with mortality among patients with hypertension hospitalized with COVID-19

Rationale: Use of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II receptor blockers (ARBs) is a major concern for clinicians treating coronavirus disease 2019 (COVID-19) in patients with hypertension. Objective: To determine the association between in-hospital use of ACEI/ARB and all-cause mortality in COVID-19 patients with hypertension. Methods and Results: This retrospective, multi-center study included 1128 adult patients with hypertension diagnosed with COVID-19, including 188 taking ACEI/ARB (ACEI/ARB group; median age 64 [IQR 55-68] years; 53.2% men) and 940 without using ACEI/ARB (non-ACEI/ARB group; median age 64 [IQR 57-69]; 53.5% men), who were admitted to nine hospitals in Hubei Province, China from December 31, 2019 to February 20, 2020. Unadjusted mortality rate was lower in the ACEI/ARB group versus the non-ACEI/ARB group (3.7% vs. 9.8%; P = 0.01). In mixed-effect Cox model treating site as a random effect, after adjusting for age, gender, comorbidities, and in-hospital medications, the detected risk for all-cause mortality was lower in the ACEI/ARB group versus the non-ACEI/ARB group (adjusted HR, 0.42; 95% CI, 0.19-0.92; P =0.03). In a propensity score-matched analysis followed by adjusting imbalanced variables in mixed-effect Cox model, the results consistently demonstrated lower risk of COVID-19 mortality in patients who received ACEI/ARB versus those who did not receive ACEI/ARB (adjusted HR, 0.37; 95% CI, 0.15-0.89; P = 0.03). Further subgroup propensity score-matched analysis indicated that, compared to use of other antihypertensive drugs, ACEI/ARB was also associated with decreased mortality (adjusted HR, 0.30; 95%CI, 0.12-0.70; P = 0.01) in COVID-19 patients with hypertension. Conclusions: Among hospitalized COVID-19 patients with hypertension, inpatient use of ACEI/ARB was associated with lower risk of all-cause mortality compared with ACEI/ARB non-users. While study interpretation needs to consider the potential for residual confounders, it is unlikely that in-hospital use of ACEI/ARB was associated with an increased mortality risk

Monitoring the Amery Ice Shelf front during 2004−2012 using ENVISAT ASAR data

The Amery Ice Shelf is the largest ice shelf in East Antarctica. It drains continental ice from an area of more than one million square kilometres through a section of coastline that represents approximately 2% of the total circumference of the Antarctic continent. In this study, we used a time series of ENVISAT ASAR images from 2004–2012 and flow lines derived from surface velocity data to monitor the changes in 12 tributaries of the Amery Ice Shelf front. The results show that the Amery Ice Shelf has been expanding and that the rates of expansion differ across the shelf. The highest average annual rate of advance from 2004–2012 was 3.36 m∙d-1 and the lowest rate was 1.65 m∙d-1. The rates in 2009 and 2010 were generally lower than those in other years. There was a low correlation between the rate of expansion and the atmospheric temperature recorded at a nearby research station, however the mechanism of the relationship was complex. This study shows that the expansion of the Amery Ice Shelf is slowing down, reflecting a changing trend in climate and ice conditions in East Antarctica

Tp47 induces cell death involving autophagy and mTOR in human microglial HMO6 cells

Abstract(#br)Background(#br)Tp47 can induce immune cells to produce numerous inflammatory factors, some of which can trigger autophagy. Increased autophagy has a dual effect on cell survival. However, whether Tp47 induces autophagy in microglia is unknown.(#br)Objective(#br)To evaluate the potential role of Tp47 in microglia.(#br)Methods(#br)After treatment with Tp47, autophagy-related proteins were assessed in HMO6 human microglial cells by flow cytometry, Western blotting and immunofluorescence. Cell death was assessed by flow cytometry and trypan blue staining. Changes in mTOR pathway proteins were explored by using Western blotting.(#br)Results(#br)After treatment with Tp47, a gradual increase in total LC3 expression was observed as a dose- and time-dependent accumulation of its active form, LC3-II ( P < 0.05), but P62 expression was downregulated ( P < 0.05). Moreover, microglial mortality gradually increased in a dose- and time-dependent manner. 3-Methyladenine (3-MA), a specific inhibitor of PI3KC3, reversed autophagy and cell death. The mortality rate of HMO6 microglial cells treated with Tp47 was approximately 13.7 ± 2%, and the basal expression of p-mTOR, p-p70s6k and p-S6 in these cells was significantly downregulated by Tp47. Moreover, the mortality rate of microglia was significantly reduced after mTOR agonist intervention.(#br)Conclusion(#br)In human microglial HMO6 cells, Tp47 induces autophagy- and mTOR pathway-dependent cell death

Analysis of gut microbiotal diversity in healthy young adults in Sunan County, Gansu Province, China

ObjectiveTo examine gut microbiotal diversity in the Han Chinese and Yugur populations of Sunan County, Gansu Province, living in the same environmental conditions, and to analyze possible causes of differences in diversity.MethodsWe selected 28 people, ages 18–45 years old, all of whom were third-generation pure Yugur or Han Chinese from Sunan County. Fresh fecal samples were collected, and total bacterial deoxyribonucleic acid (DNA) was extracted. We performed 16S ribosomal ribonucleic acid (16S rRNA) high-throughput sequencing (HTS) and bioinformatics to study the relationships among between gut microbiota structure, genetics, and dietary habits in Yugur and Han Chinese subjects.ResultsWe found 350 differential operational taxonomic units (OTUs) in Han Chinese and Yugur gut microbiota, proving that gut microbiota differed between the two populations. That were less abundant among Yugurs than Han Chinese were Prevotella_9 and Alloprevotella. That were more abundant among Yugurs than Han Chinese were Anaerostipes and Christensenellaceae_R-7_group. And they were significantly associated with a high-calorie diet In addition. we found differences in predicted gut microbiota structural functions (The main functions were metabolic and genetic information) between the two populations.ConclusionYugur subjects demonstrated differences in gut microbiotal structure from Han Chinese subjects, and this difference influenced by dietary and may be influenced by genetic influences. This finding will provide a fundamental basis for further study of the relationships among gut microbiota, dietary factors, and disease in Sunan County

Dense infraspecific sampling reveals cryptic differentiation in the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae)

Species delimitation remains a challenge worldwide, especially in highly diverse tropical and subtropical regions. Here, we use an integrative approach that combines morphology, phylogenomics, and species distribution modeling (SDM) to clarify the cryptic differentiation within the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae) in China and adjacent regions. We generated complete plastid genomes and nuclear ribosomal sequences for diverse samples from across the species range and compared results with previously published plastid data, recovering two well-supported monophyletic clades. Further, the analysis revealed significant differences in two morphological characters and SDM, indicating distinct environmental factors influencing their distributions. Fossil-calibrated analyses to estimate the origins and diversification patterns for the cryptic species gave divergence age estimates corresponding to the Oligo-Miocene; a period of new ecological opportunities associated with the prevailing East Asian monsoon. Multivariate analyses support the conclusion that southern China and adjacent regions have a different, previously unknown, cryptic lineage of C. filiformis. Our study highlights the importance of using multivariate approach to characterize plant species, as well as the significant role that past climatic changes have played in driving speciation in parasitic plants in tropical and subtropical zones.</p

Mapping blue-ice areas in Antarctica using ETM+ and MODIS data

AbstractBlue-ice areas (BIAs) and their geographical distribution in Antarctica were mapped using Landsat-7 ETM+ images with 15 m spatial resolution obtained during the 1999–2003 austral summers and covering the area north of 82.5° S, and a snow grain-size image of the MODIS-based Mosaic of Antarctica (MOA) dataset with 125 m grid spacing acquired during the 2003/04 austral summer from 82.5°S to the South Pole. A map of BIAs was created with algorithms of thresholds based on band ratio and reflectance for ETM+ data and thresholds based on snow grain size for the MOA dataset. The underlying principle is that blue ice can be separated from snow or rock by their spectral discrepancies and by different grain sizes of snow and ice. We estimate the total area of BIAs in Antarctica during the data acquisition period is 234 549 km2, or 1.67% of the area of the continent. Blue ice is scattered widely over the continent but is generally located in coastal or mountainous regions. The BIA dataset presented in this study is the first map covering the entire Antarctic continent sourced solely from ETM+ and MODIS data. This dataset can potentially benefit other studies in glaciology, meteorology, climatology and paleoclimate, meteorite collection and airstrip site selection.</jats:p

Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility

Nucleoid-associated proteins are bacterial proteins that are responsible for chromosomal DNA compaction and global gene regulation. One such protein is Escherichia coli Histone-like nucleoid structuring protein (H-NS) which functions as a global gene silencer. Whereas the DNA-binding mechanism of H-NS is well-characterized, its paralogue, StpA which is also able to silence genes is less understood. Here we show that StpA is similar to H-NS in that it is able to form a rigid filament along DNA. In contrast to H-NS, the StpA filament interacts with a naked DNA segment to cause DNA bridging which results in simultaneous stiffening and bridging of DNA. DNA accessibility is effectively blocked after the formation of StpA filament on DNA, suggesting rigid filament formation is the important step in promoting gene silencing. We also show that >1 mM magnesium promotes higher order DNA condensation, suggesting StpA may also play a role in chromosomal DNA packaging