Liquid-liquid phase separation (LLPS) of some IDPs/IDRs can lead to the formation of the membraneless organelles in vitro and in vivo, which are essential for many biological processes in the cell. ...Here we select three different IDR segments of chaperon Swc5 and develop a polymeric slab model at the residue-level. By performing the molecular dynamics simulations, LLPS can be observed at low temperatures even without charge interactions and disappear at high temperatures. Both the sequence length and the charge pattern of the Swc5 segments can influence the critical temperature of LLPS. The results suggest that the effects of the electrostatic interactions on the LLPS behaviors can change significantly with the ratios and distributions of the charged residues, especially the sequence charge decoration (SCD) values. In addition, three different forms of swc conformation can be distinguished on the phase diagram, which is different from the conventional behavior of the free IDP/IDR. Both the packed form (the condensed-phase) and the dispersed form (the dilute-phase) of swc chains are found to be coexisted when LLPS occurs. They change to the fully-spread form at high temperatures. These findings will be helpful for the investigation of the IDP/IDR ensemble behaviors as well as the fundamental mechanism of the LLPS process in bio-systems.
East Asia has been hypothesized to be subdivided into two distinct northern and southern areas, separated by a band of dry climate that was far more severe in the early Tertiary but still exists ...today. However, this biogeographic hypothesis has rarely been tested using a molecular phylogeographic approach. We genotyped 70 populations throughout the distributional range of Asian butternuts (Juglans section Cardiocaryon) using eight chloroplast DNA regions, one single‐copy nuclear gene, and 17 nuclear microsatellite loci, supplemented with paleodistribution modeling of the major genetic clades. The genetic data consistently identified two clades, one northern, comprising Juglans mandshurica and Juglans ailantifolia, and one southern, comprising Juglans cathayensis. The two clades diverged through climate‐induced vicariance of an ancestral northern range during the mid‐Miocene and remained mostly separate thereafter, with geographical isolation of the Japanese Islands and refugial isolation or secondary contacts in the late Pleistocene producing further subdivision within the northern clade. But beyond all that, we also discovered a role of environmental adaptation in maintaining and/or reinforcing the north–south divergence. Asian butternuts offer a strong case for the existence of a biogeographic divide between the northern and southern parts of East Asia during the Neogene and into the Pleistocene.
In our recent publication, we have proposed a revised base excision repair pathway in which DNA polymerase β (Polβ) catalyzes Schiff base formation prior to the gap-filling DNA synthesis followed by ...β-elimination. In addition, the polymerase activity of Polβ employs the "three-metal ion mechanism" instead of the long-standing "two-metal ion mechanism" to catalyze phosphodiester bond formation based on the fact derived from time-resolved x-ray crystallography that a third Mg2+ was captured in the polymerase active site after the chemical reaction was initiated. In this study, we develop the models of the uncross-linked and cross-linked Polβ complexes and investigate the "three-metal ion mechanism" vs the "two-metal ion mechanism" by using the quantum mechanics/molecular mechanics molecular dynamics simulations. Our results suggest that the presence of the third Mg2+ ion stabilizes the reaction-state structures, strengthens correct nucleotide binding, and accelerates phosphodiester bond formation. The improved understanding of Polβ's catalytic mechanism provides valuable insights into DNA replication and damage repair.
The molecular mechanism controlling the dismantling of naive pluripotency is poorly understood. Here we show that microRNAs （miRNAs） have important roles during naive to primed pluripotency ...transition. Dgcr8-/- embryon- ic stem cells （ESCs） failed to completely silence the naive pluripotency program, as well as to establish the primed pluripotency program during differentiation, miRNA profiling revealed that expression levels of a large number of miRNAs changed dynamically and rapidly during naive to primed pluripotency transition. Furthermore, a miRNA screen identified numerous miRNAs promoting naive to primed pluripotency transition. Unexpectedly, multiple miR- NAs from miR-290 and miR-302 clusters, previously shown as pluripotency-promoting miRNAs, demonstrated the strongest effects in silencing naive pluripotency. Knockout of both miR-290 and miR-302 clusters but not either alone blocked the silencing of naive pluripotency program. Mechanistically, the miR-290/302 family of miRNAs may facili- tate the exit of naive pluripotency in part by promoting the activity of MEK pathway and through directly repressing Aktl. Our study reveals miRNAs as an important class of regulators potentiating ESCs to transition from naive to primed pluripotency, and uncovers context-dependent functions of the miR-290/302 family of miRNAs at different developmental stages.
ABSTRACT
We study the properties of magnetic fields in the circumgalactic medium (CGM) of z < 1 galaxies by correlating Faraday rotation measures (RMs) of ∼1000 high-redshift radio sources with the ...foreground galaxy number density estimated from the DESI Legacy Imaging Surveys. This method enables us to extract signals of RMs contributed by intervening gas around multiple galaxies. Our results show that there is no detectable correlation between the distribution of RMs and the number of foreground galaxies, contrary to several previous results. Utilizing the non-detection signals, we estimate 3σ upper limits to the RMs from the CGM of $\sim \!20 \rm \ rad\, m^{-2}$ within 50 kpc and $\sim \!10 \rm \ rad \, m^{-2}$ at separations of 100 kpc. By adopting a column density distribution of ionized gas obtained from absorption-line measurements, we further estimate the strengths of coherent magnetic fields parallel to the line of sight of $\lt \rm 2 \ \mu G$ in the CGM. We show that the estimated upper limits of RMs and magnetic field strengths are sufficient to constrain outputs of recent galaxy magnetohydrodynamic simulations. Finally, we discuss possible causes for the inconsistency between our results and previous works.
ZFP42 zinc finger protein (REX1), a pluripotency marker in mouse pluripotent stem cells, has been identified as a tumor suppressor in several human cancers. However, the function of REX1 in cervical ...cancer remains unknown. Both IHC and western blot assays demonstrated that the expression of REX1 protein in cervical cancer tissue was much higher than that in normal cervical tissue. A xenograft assay showed that REX1 overexpression in SiHa and HeLa cells facilitated distant metastasis but did not significantly affect tumor formation in vivo. In addition, in vitro cell migration and invasion capabilities were also promoted by REX1. Mechanistically, REX1 overexpression induced epithelial-to-mesenchymal transition (EMT) by upregulating VIMENTIN and downregulating E-CADHERIN. Furthermore, the JAK2/STAT3-signaling pathway was activated in REX1-overexpressing cells, which also exhibited increased levels of p-STAT3 and p-JAK2, as well as downregulated expression of SOCS1, which is an inhibitor of the JAK2/STAT3-signaling pathway, at both the transcriptional and translational levels. A dual-luciferase reporter assay and qChIP assays confirmed that REX1 trans-suppressed the expression of SOCS1 by binding to two specific regions of the SOCS1 promoter. Therefore, all our data suggest that REX1 overexpression could play a crucial role in the metastasis and invasion of cervical cancer by upregulating the activity of the JAK2/STAT3 pathway by trans-suppressing SOCS1 expression.
Trophic niche differentiation may explain coexistence and shape functional roles of species. In complex natural food webs, however, trophic niche parameters depicted by single and isolated methods ...may simplify the multidimensional nature of consumer trophic niches, which includes feeding processes such as food choice, ingestion, digestion, assimilation and retention.
Here we explore the correlation and complementarity of trophic niche parameters tackled by four complementary methodological approaches, that is, visual gut content, digestive enzyme, fatty acid and stable isotope analyses—each assessing one or few feeding processes, and demonstrate the power of method combination.
Focusing on soil ecosystems, where many omnivore species with cryptic feeding habits coexist, we chose Collembola as an example. We compiled 15 key trophic niche parameters for 125 species from 40 studies. We assessed correlations among trophic niche parameters and described variation of these parameters in different Collembola species, families and across life‐forms, which represent microhabitat specialisation.
Correlation between trophic niche parameters was weak in 45 out of 64 pairwise comparisons, pointing at complementarity of the four methods. Jointly, the results indicated that fungal‐ and plant‐feeding Collembola assimilate storage, rather than structural polysaccharides, and suggested bacterial feeding as a potential alternative feeding strategy. Gut content and fatty acid analyses suggested alignment between ingestion and assimilation/retention processes in fungal‐ and plant‐feeding Collembola. From the 15 trophic niche parameters, six were related to Collembola family identity, suggesting that not all trophic niche dimensions are phylogenetically structured. Only three parameters were related to the life‐forms, suggesting that species use various feeding strategies when living in the same microenvironments.
Consumers can meet their nutritional needs by varying their food choices, ingestion and digestion strategies, with the connection among different feeding processes being dependent on the consumed resource and consumer adaptations. Multiple methods reveal different dimensions, together drawing a comprehensive picture of the trophic niche. Future studies applying the multidimensional trophic niche approach will allow us to trace trophic complexity and reveal niche partitioning of omnivorous species and their functional roles, especially in cryptic environments such as soils, caves, deep ocean or benthic ecosystems.
The authors revealed the information provided by four complementary methods in trophic ecology, including visual gut content‐, digestive enzyme‐, fatty acid‐ and stable isotope analyses, thereby to demonstrate multidimensional nature of trophic niches in Collembola—one of the functionally diverse taxa with cryptic feeding habits in soil.
CircFNDC3B induced TIMP3 to suppress angiogenesis to inhibit CRC cell proliferation, migration and invasion by negatively targeting miR‐937‐5p. Also, circFNDC3B exosomes could repress CRC ...angiogenesis by decreasing VEGFR expression.
Circular RNA (circRNA) are single‐stranded RNA with covalently closed 3′ and 5′ ends, with many recognized to be involved in human diseases as gene regulators, typically by interacting with other RNA. CircFNDC3B is a circRNA formed by back‐splicing of exons 5 and 6 of the FNDC3B gene. CircFNDC3B was recently implicated in renal carcinoma, gastric and bladder cancer. However, the expression levels of circFNDC3B and its role in colorectal cancer (CRC) remain unclear. Expression of circFNDC3B and TIMP3 levels in CRC tissues and cell lines were found to be low, whereas microRNA (miR)‐937‐5p expression was high in CRC. MicroRNA‐937‐5p downregulated TIMP3, thereby promoting tumor cell proliferation, invasion, migration and angiogenesis. Moreover, CircFNDC3B was shown to bind to miR‐937‐5p. CircFNDC3B and circFNDC3B‐enriched exosomes inhibited tumorigenic, metastatic and angiogenic properties of CRC, and miR‐937‐5p overexpression or TIMP3 knockdown could reverse these effects. In vivo CRC tumor growth, angiogenesis and liver metastasis were suppressed by circFNDC3B overexpression, circFNDC3B‐enriched exosomes or miR‐937‐5p knockdown. In conclusion, our work reports a tumor‐suppressing role for the circFNDC3B–miR‐97‐5p–TIMP3 pathway and suggests that circFNDC3B‐enriched exosomes can inhibit angiogenesis and CRC progression.
With the coronavirus (COVID-19) outbreak in China, the Chinese government decided to ban any type of face-to-face teaching, disrupting classes and resulting in over 270 million students being unable ...to return to their universities/schools. Therefore, the Ministry of Education (MoE) launched an initiative titled ‘Ensuring learning undisrupted when classes are disrupted’ by reforming the entire educational system and including an online education component. However, this quick reform in this unexpected critical situation of widespread COVID-19 cases harbours several challenges, such as the lack of time and teacher/student isolation. This paper discusses the possibility of using open educational resources (OER) and open educational practices (OEP) as an effective educational solution to overcome these challenges. Particularly, this study presents a generic OEP framework built on existing open-practice definitions. It then presents, based on this framework and based on the challenges reported by several Chinese education specialists during two national online seminars, a set of guidelines for the effective use of OER and OEP for both teaching and learning. Finally, this study presents some recommendations for the better adoption of OER and OEP in the future. The findings of this study can help researchers and educators apply OER and OEP for better learning experiences and outcomes during the COVID-19 outbreak.
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