Convergent adaptation of the genomes of woody plants at the land-sea interface

Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies. While such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method (convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with P-true (probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid (AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence

Micropollutant rejection by nanofiltration membranes: a mini review dedicated to the critical factors and modelling prediction

Nanofiltration (NF) membranes, extensively used in advanced wastewater treatment, have broad application prospects for the removal of emerging trace organic micropollutants (MPs). The treatment performance is affected by several factors, such as the properties of NF membranes, characteristics of target MPs, and operating conditions of the NF system concerning MP rejection. However, quantitative studies on different contributors in this context are limited. To fill the knowledge gap, this study aims to assess critical impact factors controlling MP rejection and develop a feasible model for MP removal prediction. The mini-review firstly summarized membrane pore size, membrane zeta potential, and the normalized molecular size (λ = rs/rp), showeing better individual relationships with MP rejection by NF membranes. The Lindeman-Merenda-Gold model was used to quantitatively assess the relative importance of all summarized impact factors. The results showed that membrane pore size and operating pressure were the high impact factors with the highest relative contribution rates to MP rejection of 32.11% and 25.57%, respectively. Moderate impact factors included membrane zeta potential, solution pH, and molecular radius with relative contribution rates of 10.15%, 8.17%, and 7.83%, respectively. The remaining low impact factors, including MP charge, molecular weight, logKow, pKa and crossflow rate, comprised all the remaining contribution rates of 16.19% through the model calculation. Furthermore, based on the results and data availabilities from references, the machine learning-based random forest regression model was trained with a relatively low root mean squared error and mean absolute error of 12.22% and 6.92%, respectively. The developed model was then successfully applied to predict MPs’ rejections by NF membranes. These findings provide valuable insights that can be applied in the future to optimize NF membrane designs, operation, and prediction in terms of removing micropollutants

Global divergent trends of algal blooms detected by satellite during 1982–2018

Algal blooms (ABs) in inland lakes have caused adverse ecological effects, and health impairment of animals and humans. We used archived Landsat images to examine ABs in lakes (>1 km2) around the globe over a 37-year time span (1982–2018). Out of the 176032 lakes with area >1 km2 detected globally, 863 were impacted by ABs, 708 had sufficiently long records to define a trend, and 66% exhibited increasing trends in frequency ratio (FRQR, ratio of the number of ABs events observed in a year in a given lake to the number of available Landsat images for that lake) or area ratio (AR, ratio of annual maximum area covered by ABs observed in a lake to the surface area of that lake), while 34% showed a decreasing trend. Across North America, an intensification of ABs severity was observed for FRQR (p<.01) and AR (p <.01) before 1999, followed by a decrease in ABs FRQR (p <.01) and AR (p <.05) after the 2000s. The strongest intensification of ABs was observed in Asia, followed by South America, Africa, and Europe. No clear trend was detected for the Oceania. Across climatic zones, the contributions of anthropogenic factors to ABs intensification (16.5% for fertilizer, 19.4% for gross domestic product, and 18.7% for population) were slightly stronger than climatic drivers (10.1% for temperature, 11.7% for wind speed, 16.8% for pressure, and for 11.6% for rainfall). Collectively, these divergent trends indicate that consideration of anthropogenic factors as well as climate change should be at the forefront of management policies aimed at reducing the severity and frequency of ABs in inland waters

A two-step lineage reprogramming strategy to generate functionally competent human hepatocytes from fibroblasts

Terminally differentiated cells can be generated by lineage reprogramming, which is, however, hindered by incomplete conversion with residual initial cell identity and partial functionality. Here, we demonstrate a new reprogramming strategy by mimicking the natural regeneration route, which permits generating expandable hepatic progenitor cells and functionally competent human hepatocytes. Fibroblasts were first induced into human hepatic progenitor-like cells (hHPLCs), which could robustly expand in vitro and efficiently engraft in vivo. Moreover, hHPLCs could be efficiently induced into mature human hepatocytes (hiHeps) in vitro, whose molecular identity highly resembles primary human hepatocytes (PHHs). Most importantly, hiHeps could be generated in large quantity and were functionally competent to replace PHHs for drug-metabolism estimation, toxicity prediction and hepatitis B virus infection modeling. Our results highlight the advantages of the progenitor stage for successful lineage reprogramming. This strategy is promising for generating other mature human cell types by lineage reprogramming.</p

CMRxRecon: An open cardiac MRI dataset for the competition of accelerated image reconstruction

Cardiac magnetic resonance imaging (CMR) has emerged as a valuable diagnostic tool for cardiac diseases. However, a limitation of CMR is its slow imaging speed, which causes patient discomfort and introduces artifacts in the images. There has been growing interest in deep learning-based CMR imaging algorithms that can reconstruct high-quality images from highly under-sampled k-space data. However, the development of deep learning methods requires large training datasets, which have not been publicly available for CMR. To address this gap, we released a dataset that includes multi-contrast, multi-view, multi-slice and multi-coil CMR imaging data from 300 subjects. Imaging studies include cardiac cine and mapping sequences. Manual segmentations of the myocardium and chambers of all the subjects are also provided within the dataset. Scripts of state-of-the-art reconstruction algorithms were also provided as a point of reference. Our aim is to facilitate the advancement of state-of-the-art CMR image reconstruction by introducing standardized evaluation criteria and making the dataset freely accessible to the research community. Researchers can access the dataset at https://www.synapse.org/#!Synapse:syn51471091/wiki/.Comment: 14 pages, 8 figure

Hydrostatic pressure in combination with topographical cues affects the fate of bone marrow-derived human mesenchymal stem cells for bone tissue regeneration

Topographical and mechanical cues are vital for cell fate, tissue development in vivo, and to mimic the native cell growth environment in vitro. To date, the combinatory effect of mechanical and topographical cues as not been thoroughly investigated. This study investigates the effect of PCL nanofiber alignment and hydrostatic pressure on stem cell differentiation for bone tissue regeneration. Bone marrow-derived human mesenchymal stem cells were seeded onto standard tissue culture plastic and electrospun random and aligned nanofibers. These substrates were either cultured statically or subjected to intermittent hydrostatic pressure at 270 kPa, 1 Hz for 60 min daily over 21 days in osteogenic medium. Data revealed higher cell metabolic activities for all mechanically stimulated cell culture formats compared with non-stimulated controls; and random fibers compared with aligned fibers. Fiber orientation influenced cell morphology and patterns of calcium deposition. Significant up-regulation of Collagen-I, ALP, and Runx-2 were observed for random and aligned fibers following mechanical stimulation; highest levels of osteogenic markers were expressed when hydrostatic pressure was applied to random fibers. These results indicate that fiber alignment and hydrostatic pressure direct stem cell fate and are important stimulus for tissue regeneration

Solution processed graphene structures for perovskite solar cells

Organometallic trihalide perovskite light absorber based solar cells have drawn increasing attention because of their recent rapid increase in power conversion efficiency (PCE). These photovoltaic cells have relied significantly on transparent conducting oxide (TCO) electrodes which are costly and brittle. Herein, solution processed transparent conductive graphene films (TCGFs) are utilized, for the first time, as an alternative to traditional TCO electrodes at the electron collecting layer in perovskite solar cells (PSCs). By investigating and optimizing the trade-off between transparency and sheet resistance (Rs) of the graphene films, a PCE of 0.62% is achieved. This PCE is further improved to 0.81% by incorporating graphene structures into both compact and mesoporous TiO2 layers of the solar cell. We anticipate that the present study will lead to further work to develop graphene-based transparent conductive electrodes for future solar cell devices