GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes.

Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.

The ATF4-RPS19BP1 axis modulates ribosome biogenesis to promote erythropoiesis.

ABSTRACT: Hematopoietic differentiation is controlled by intrinsic regulators and the extrinsic hematopoietic niche. Activating transcription factor 4 (ATF4) plays a crucial role in the function of fetal and adult hematopoietic stem cell maintenance. However, the precise function of ATF4 in the bone marrow (BM) niche and the mechanism by which ATF4 regulates adult hematopoiesis remain largely unknown. Here, we used 4 cell-type-specific mouse Cre lines to achieve conditional knockout of Atf4 in Cdh5+ endothelial cells, Prx1+ BM stromal cells, Osx+ osteoprogenitor cells, and Mx1+ hematopoietic cells and uncovered the role of Atf4 in niche cells and hematopoiesis. Intriguingly, depletion of Atf4 in niche cells did not affect hematopoiesis; however, Atf4-deficient hematopoietic cells exhibited erythroid differentiation defects, leading to hypoplastic anemia. Mechanistically, ATF4 mediated direct regulation of Rps19bp1 transcription, which is, in turn, involved in 40 S ribosomal subunit assembly to coordinate ribosome biogenesis and promote erythropoiesis. Finally, we demonstrate that under conditions of 5-fluorouracil-induced stress, Atf4 depletion impedes the recovery of hematopoietic lineages, which requires efficient ribosome biogenesis. Taken together, our findings highlight the indispensable role of the ATF4-RPS19BP1 axis in the regulation of erythropoiesis.

Convergent molecular evolution of thermogenesis and circadian rhythm in Arctic ruminants.

The muskox and reindeer are the only ruminants that have evolved to survive in harsh Arctic environments. However, the genetic basis of this Arctic adaptation remains largely unclear. Here, we compared a de novo assembled muskox genome with reindeer and other ruminant genomes to identify convergent amino acid substitutions, rapidly evolving genes and positively selected genes among the two Arctic ruminants. We found these candidate genes were mainly involved in brown adipose tissue (BAT) thermogenesis and circadian rhythm. Furthermore, by integrating transcriptomic data from goat adipose tissues (white and brown), we demonstrated that muskox and reindeer may have evolved modulating mitochondrion, lipid metabolism and angiogenesis pathways to enhance BAT thermogenesis. In addition, results from co-immunoprecipitation experiments prove that convergent amino acid substitution of the angiogenesis-related gene hypoxia-inducible factor 2alpha (HIF2A), resulting in weakening of its interaction with prolyl hydroxylase domain-containing protein 2 (PHD2), may increase angiogenesis of BAT. Altogether, our work provides new insights into the molecular mechanisms involved in Arctic adaptation.

Clinical efficacy of photodynamic therapy on halitosis: a systematic review and meta-analysis.

Halitosis is a widespread health problem with complex factors, and therapeutic effects sometimes are unsatisfactory. Plenty of clinical trials have tried to prove the effectiveness of photodynamic therapy (PDT), but the results are indeterminate. This study aimed to evaluate the clinical efficacy of PDT on halitosis. We searched PubMed, Cochrane Library, Embase, Web of Science, and Scopus from inception to August 10, 2022, and only studies about the PDT on halitosis were included. The criteria for meta-analysis comprised randomized controlled trials (RCTs) comparing the treatment of PDT with tongue scraper (TS) immediately after the halitosis therapy and during a 7-, 14-, 30-, and 90-day follow-up. Eight eligible studies involving 345 patients were included in this study. It was shown that PDT (MD = - 34.49, 95% CI [- 66.34, - 2.64], P = 0.03) or PDT + TS (MD = - 67.72, 95% CI [- 101.17, - 34.28], P < 0.001) had better efficacy than TS on the H2S concentration reduction immediately after the halitosis therapy. No significant differences were observed in reducing the H2S among TS, PDT alone, and PDT + TS at the follow-up. Besides, no difference between PDT and TS was found in the reduction of CH3SCH3 and CH3SH. Based on the current evidence, PDT and PDT + TS demonstrate efficacy in the treatment of halitosis in the short term, and PDT was shown to be a beneficial and promising therapeutic method.

Direction-tunable enhanced emission from a subwavelength metallic double-nanoslit structure.

Controlling light emission out of subwavelength nanoslit/aperture structures is of great important for highly integrated photonic circuits. Here we propose a new method to achieve direction-tunable emission based on a compact metallic microcavity with double nanoslit. Our method combines the principles of Young's interference and surface plasmon polaritons interference. We show that the direction of the far-field beam can be controlled over a wide range of angles by manipulating the frequency and relative phase of light arriving at the two slits, which holds promise for applications in the ultracompact optoelectronic devices.

New flavanol and cycloartane glucosides from Landoltia punctata.

Chemical investigation on the constituents of Landoltia punctata led to the isolation and identification of 17 compounds, four of which were new and identified as (3b,24S)-9,19-cycloartane-3,22,24,25-tetraol 3-O-[b-D-glucopyranosyl-(1→2)]-[b-D-glucopyranosyl-(1→6)]-b-D-glucopyranoside (1), (3b,24S)-9,19-cycloartane-3,24,25-triol 3-O-[b-d-glucopyranosyl-(1→2)]-[b-D-glucopyranosyl-(1→6)]-b-D-glucopyranoside (2), 3,4'-dihydroxy-7,3'-dimethoxyflavan-5-O-b-D-glucopyranoside (3) and 3,4'-dihydroxy-4,7,3'-trimethoxyflavan-5-O-b-D-glucopyranoside (4). Their structures were elucidated by spectroscopic, chemical, and biochemical methods. Thus, cycloartane triterpenoids were discovered in the Lemnaceae family for the first time. Compound 3 showed antioxidant capacity in the positively charged 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radical (ABTS+•) and superoxide anion radical scavenging assays.

p21/Zbtb18 repress the expression of cKit to regulate the self-renewal of hematopoietic stem cells.

The maintenance of hematopoietic stem cells (HSCs) is a complex process involving numerous cell-extrinsic and -intrinsic regulators. The first member of the cyclin-dependent kinase family of inhibitors to be identified, p21, has been reported to perform a wide range of critical biological functions, including cell cycle regulation, transcription, differentiation, and so on. Given the previous inconsistent results regarding the functions of p21 in HSCs in a p21-knockout mouse model, we employed p21-tdTomato (tdT) mice to further elucidate its role in HSCs during homeostasis. The results showed that p21-tdT+ HSCs exhibited increased self-renewal capacity compared to p21-tdT- HSCs. Zbtb18, a transcriptional repressor, was upregulated in p21-tdT+ HSCs, and its knockdown significantly impaired the reconstitution capability of HSCs. Furthermore, p21 interacted with ZBTB18 to co-repress the expression of cKit in HSCs and thus regulated the self-renewal of HSCs. Our data provide novel insights into the physiological role and mechanisms of p21 in HSCs during homeostasis independent of its conventional role as a cell cycle inhibitor.

Multisite chronic pain as a causal risk factor for coronary artery disease: findings from Mendelian randomization.

ABSTRACT: The potential consequences of the number of chronic pain sites (referred to multisite chronic pain) on the risk of cardiovascular diseases (CVDs) remain unclear. We attempted to investigate the causality of multisite chronic pain with CVDs and its possible causal mediators. Using summary genome-wide association statistics, two-sample Mendelian randomization (MR) analyses were performed to assess whether multisite chronic pain has a causal effect on the 3 CVDs including coronary artery disease, atrial fibrillation, and stroke. We then conducted MR mediation analyses to establish whether body mass index (BMI), smoking, and depression causally mediate any association. Genetic liability to multisite chronic pain was associated with increased risk of coronary artery disease (odds ratio [OR] 1.52, 95% confidence interval [CI] 1.19-1.95 per one increase in the number of pain locations) but not with atrial fibrillation or stroke. We also found positive causal effects of multisite chronic pain on BMI, smoking, and depression and causal effects of BMI, smoking, and depression on coronary artery disease. In multivariable MR analyses, the excess risk of coronary artery disease was attenuated after adjusting for BMI (OR 1.43, 95% CI 1.05-1.93), smoking (OR 1.49, 95% CI 1.11-2.00), depression (OR 1.44, 95% CI 1.03-2.01), and 3 risk factors combined (OR 1.34, 95% CI 0.88-2.05). Our findings demonstrated that multisite chronic pain led to higher risk of coronary artery disease, which is partly mediated through BMI, smoking, and depression.

Chitosan-based therapeutic systems and their potentials in treatment of oral diseases.

The increasing morbidity of oral diseases, such as dental caries, periodontitis and oral cancer, has greatly compromised the life quality of humans. With the rapid development of biomaterials and nanotechnology, various biomaterials-based systems have been reported to treat oral diseases. As the biocompatible, biodegradable and bioadhesive polysaccharide biomaterials, chitosan and its derivatives have also been widely used for the oral disease therapy, either as the antibacterial agents, drug delivery carriers or tissue engineering scaffolds. It has been well demonstrated that chitosan can significantly enhance the therapy efficacy for various oral diseases, due to its intrinsic antibacterial activity and controlled drug release feature. Herein, we aim to provide a comprehensive understanding of the biological functions of chitosan, such as antimicrobial, anticancer and remineralization activity, and summarize the applications of chitosan-based therapeutic systems in treating the typical oral diseases, including dental caries, endodontic diseases, periodontal diseases, oral cancer, oral and maxillofacial surgery, and oral mucosal diseases. In addition, the concerns and possible solutions of the clinical use of chitosan are also discussed.

CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network.

The genetic information coded in DNA leads to trait innovation via a gene regulatory network (GRN) in development. Here, we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network (CNEReg) to investigate the ruminant multi-chambered stomach innovation. We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep, and revealed 1601 active ruminant-specific conserved non-coding elements (active-RSCNEs). To interpret the function of these active-RSCNEs, we defined toolkit transcription factors (TTFs) and modeled their regulation on rumen-specific genes via batteries of active-RSCNEs during development. Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules. Notably, 6 TTFs (OTX1, SOX21, HOXC8, SOX2, TP63, and PPARG), as well as 16 active-RSCNEs, functionally distinguished the rumen from the esophagus. Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.

[Research Advance of the Roles of N6-methyladenosine in the Regulation of Hematopoiesis--Review].

There are more than 150 types of chemical modifications in RNA, mainly methylation, which are widely distributed in all kinds of RNA, including messenger RNA, transfer RNA, ribosomal RNA, non-coding small RNA and long non-coding RNA. In recent years, the identification of RNA methylation modification enzymes and the development of high-throughput sequencing technology at transcriptome level laid a foundation for revealing the expression and function of genes regulated by chemical modification of RNA. In this review, the most recent advances of RNA methylation, especially N6-methyladenosine (m6a) in the blood system, including the regulation of RNA methyltransferases, RNA demethylases and RNA binding proteins on normal and malignant hematopoiesis through the regulation of RNA methylation level were summarized briefly.

Willingness to receive SARS-CoV-2 vaccine among healthcare workers in public institutions of Zhejiang Province, China.

This study aims to investigate healthcare workers' (HCWs) willingness to receive SARS-CoV-2 vaccine in Zhejiang and to discover the related influential factors. The survey was conducted in six regions of Zhejiang Province, China, and 13 hospitals and 12 Centers for Disease Control and Prevention (CDC) were incorporated into the survey research. Participants were healthcare workers and a total of 3726 questionnaires were collected online, of which 3634 (97.53%) were analyzed. The relationships between the factors and the willingness to get vaccinated against COVID-19 were computed as odds ratios (ORs) by means of multi-factor non-conditional logistic regression analysis. Of the 3634 participants, 2874 (79.09%) HCWs expressed their willingness to get vaccinated if the SARS-CoV-2 vaccine becomes available. Respondents who were younger than 50 years (OR = 1.502, 95% CI: 1.047-2.154), those who believed that they were somewhat likely (OR = 1.658, 95% CI: 1.297-2.120) or likely (OR = 1.893, 95% CI: 1.334-2.684) to get infected by SARS-COV-2 and those with a positive attitude toward the SARS-CoV-2 vaccine were more willing to get vaccinated. Furthermore, compared to doctors, nurses were more reluctant to get vaccinated. In addition, it was found that higher the education level, lower the willingness to get vaccinated. This study revealed that HCWs in Zhejiang Province had a high willingness to get vaccinated. Awareness about the vaccine's effectiveness and safety and the disease severity should be promoted among HCWs over 50 years of age and nurses to increase the willingness to get vaccinated.

Modes of genetic adaptations underlying functional innovations in the rumen.

The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We analyzed 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations. We identified genes with relatively high expression in the rumen, of which many appeared to be recruited from other tissues. These genes show functional enrichment in ketone body metabolism, regulation of microbial community, and epithelium absorption, which are the most prominent biological processes involved in rumen innovations. Several modes of genetic change underlying rumen functional innovations were uncovered, including coding mutations, genes newly evolved, and changes of regulatory elements. We validated that the key ketogenesis rate-limiting gene (HMGCS2) with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals. Two newly evolved genes (LYZ1 and DEFB1) are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium. Furthermore, we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment. These results greatly improve our understanding of rumen evolution and organ evo-devo in general.

Combinatorial search for iron/titanium-based ternary oxides with a visible-light response.

A combinatorial approach has been carried out to systematically investigate visible-light responsiveness of Fe-Ti-M (M: various metal elements) oxides for photoelectrochemical water splitting. Among the 25 elements tested, strontium was the most effective. A ternary metal oxide with the composition Fe(86.1)Ti(9.6)Sr(4.3)O(x) has been identified as a new lead structure for a visible-light responsive, n-type semiconductor. We have conducted various kinds of characterization of the Fe-Ti-Sr oxide semiconductor and discussed the reason why Sr in the Fe-Ti oxide gave the highest photocurrent.

Clinical characteristics and prognosis of idiopathic pulmonary hemosiderosis in pediatric patients.

OBJECTIVE: This study aimed to analyze the clinical characteristics and prognosis of pediatric idiopathic pulmonary hemosiderosis (IPH). METHODS: Pediatric IPH cases that were diagnosed at West China Second University Hospital, Sichuan University between 1996 and 2017 were reviewed. Follow-up data from 34 patients were collected. RESULTS: A total of 107 patients were included (42 boys and 65 girls). The median age was 6 years at diagnosis. The main manifestations of the patients were as follows: anemia (n = 100, 93.45%), cough (n = 68, 63.55%), hemoptysis (n = 61, 57%), fever (n = 23, 21.5%), and dyspnea (n = 23, 21.5%). There were relatively few pulmonary signs. The positive rates of hemosiderin-laden macrophages in sputum, gastric lavage fluid, and bronchoalveolar lavage fluid were 91.66%, 98.21%, and 100%, respectively. Seventy-nine patients were misdiagnosed. A total of 105 patients were initially treated with glucocorticoids, among whom 102 survived and three died. Among the followed up patients, two died and 32 survived, among whom 10 presented with recurrent episodes. CONCLUSIONS: The classic triad of pediatric IPH is not always present. The rates of misdiagnosis and recurrence of IPH are high. Early recognition and adequate immunosuppressive therapy are imperative for improving prognosis of IPH.

The long-non-coding RNA NEAT1 is a novel target for Alzheimer's disease progression via miR-124/BACE1 axis.

OBJECTIVES: Long-non-coding RNAs (lncRNAs) have been involved in central nervous system recently. A number of studies have reported that lncRNA NEAT1 exerts critical roles in neurodegenerative disorder. Beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) has been reported to exert function in the accumulation of amyloid-ß (Aß). Moreover, BACE1 acts as a target of miR-124 in the progression of AD. So far, the biological role and underlying mechanisms of NEAT1 and miR-124 in AD remains elusive. METHODS: The relative NEAT1 and miR-124 expression was examined by qRT-PCR in the tissues and cells line of AD. Cell apoptosis was examined by FACS. Luciferase reporter assay was performed to verify that miR-124 is a direct target of NEAT1, and BACE1 is a downstream target of miR-124. qRT-PCR and western blot analysis were also performed to determinate the BACE1 and the phosphorylation of tau protein. RESULTS: NEAT1 was notably up-regulated and miR-124 was remarkably down-regulated in AD mouse model. Knockdown of NEAT1 or overexpression of miR-124 showed the protective effects on cellular AD model induced by Aß. Moreover, miR-124 expression could be up- and down-regulated by suppression or overexpression of NEAT1, respectively. In addition, the expression of BACE1 was the potential functional target of miR-124. These findings suggested that NEAT1 might play a vital role in the development of AD by regulating miR-124/BACE1 axis. DISCUSSION: The present study showed that NEAT1 worked as a regulating factor to promote the development of AD via modulating miR-124/BACE1 axis, which might be considered as a novel target in AD treatment.

Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids.

Divergence of gene expression and alternative splicing is a crucial driving force in the evolution of species; to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expression (ASE) and allele-specific alternative splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interference of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horse×donkey (mule/hinny) and cattle×yak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, lncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptation. In conclusion, our study demonstrated that exploration of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.

Genetic basis of ruminant headgear and rapid antler regeneration.

Ruminants are the only extant mammalian group possessing bony (osseous) headgear. We obtained 221 transcriptomes from bovids and cervids and sequenced three genomes representing the only two pecoran lineages that convergently lack headgear. Comparative analyses reveal that bovid horns and cervid antlers share similar gene expression profiles and a common cellular basis developed from neural crest stem cells. The rapid regenerative properties of antler tissue involve exploitation of oncogenetic pathways, and at the same time some tumor suppressor genes are under strong selection in deer. These results provide insights into the evolutionary origin of ruminant headgear as well as mammalian organ regeneration and oncogenesis.

Clinicopathological features of pediatric renal biopsies in the plateau regions of China.

OBJECTIVE: This study aimed to analyze the clinicopathological features of pediatric renal biopsies from plateau regions of China. METHODS: Clinicopathological features of pediatric renal biopsies were compared between plateau and non-plateau regions in patients who were admitted to West China Second University Hospital, Sichuan University between April 2001 and March 2017. Patients were children younger than 18 years. RESULTS: The proportion of primary glomerular disease in the plateau group was lower than that in the non-plateau group (45.56% vs 62.09%, respectively). In the plateau group, IgA nephropathy (IgAN) was the major primary glomerulonephritis (GN) pathology. IgAN accounted for 36.54% and 21.63% of GN cases with nephrotic syndrome and hematuria, respectively. Henoch-Schönlein purpura nephritis was the most common secondary GN in both groups. The proportion of hepatitis B virus-associated GN was higher and that of lupus nephritis was lower in the plateau group than in the non-plateau group. CONCLUSIONS: There are differences in renal pathological types between children in plateau regions and those in non-plateau regions. Among children in plateau regions, IgAN and Henoch-Schönlein purpura nephritis were the most common kidney diseases.

Hydroxycinnamoylmalated flavone C-glycosides from Lemna japonica.

Three previously undescribed flavone C-glycosides (1-3), along with seven known ones (4-10), were isolated and characterized from the smallest flowering aquatic plant, Lemna japonica. On the basis of spectroscopic analysis and alkaline hydrolysis, compounds 1-3 were identified to be luteolin 6-C-(2″-O-trans-caffeoyl-d-malate)-ß-glucoside (1), apigenin 6-C-(2″-O-trans-caffeoyl-d-malate)-ß-glucoside (2), and luteolin 6-C-(2″-O-trans-coumaroyl-d-malate)-ß-glucoside (3). Compounds 1-3 are characteristic of a trans-coumaroyl-d-malate or trans-caffeoyl-d-malate linked to C-2″ of the glucose, which was reported for the first time. Compounds 1-3 exhibited weak cytotoxicity against HepG-2, SW-620, and A-549 cell lines, with IC50 values between 42.5 and 19.2µg/ml, and moderate antioxidant activity. Meanwhile compound 3 displayed moderate nematocidal activity with an EC50 value of 1.56mg/ml.