Endothelial dysfunction in vascular complications of diabetes: a comprehensive review of mechanisms and implications.

Diabetic vascular complications are prevalent and severe among diabetic patients, profoundly affecting both their quality of life and long-term prospects. These complications can be classified into macrovascular and microvascular complications. Under the impact of risk factors such as elevated blood glucose, blood pressure, and cholesterol lipids, the vascular endothelium undergoes endothelial dysfunction, characterized by increased inflammation and oxidative stress, decreased NO biosynthesis, endothelial-mesenchymal transition, senescence, and even cell death. These processes will ultimately lead to macrovascular and microvascular diseases, with macrovascular diseases mainly characterized by atherosclerosis (AS) and microvascular diseases mainly characterized by thickening of the basement membrane. It further indicates a primary contributor to the elevated morbidity and mortality observed in individuals with diabetes. In this review, we will delve into the intricate mechanisms that drive endothelial dysfunction during diabetes progression and its associated vascular complications. Furthermore, we will outline various pharmacotherapies targeting diabetic endothelial dysfunction in the hope of accelerating effective therapeutic drug discovery for early control of diabetes and its vascular complications.

Achyranthes bidentata polysaccharides improve cyclophosphamide-induced adverse reactions by regulating the balance of cytokines in helper T cells.

The manuscript aimed to study the immune function maintenance effect of Achyranthes bidentata polysaccharides (ABPs). The mice were divided into the control group, cyclophosphamide-induced (CTX) group, and ABPs-treated (ABP) group. The results showed that, compared with the CTX group, ABPs could significantly improve the spleen index and alleviate the pathological changes in immune organs. Ex vivo study of whole spleen cells, the levels of interleukin-2 (IL-2), interleukin-6 (IL-6), interferon-γ (IFN-γ), and tumor necrosis factor-α (TNF-α) were increased. The proliferation of lymphocytes and the proportion of CD3+CD4+ Th cells in peripheral blood mononuclear cells were increased. The transcription of GATA-3, Foxp3, and ROR γ t were decreased, while the transcription of T-bet was increased. The transcriptome sequencing analysis showed that the differentially expressed genes (DEGs) caused by ABPs-treated were mostly downregulated in CTX-induced mice. The Th2-related genes were significantly enriched in DEGs, with representative genes, including Il4, II13, Il9, etc., while increasing the expression of immune effector genes simultaneously, including Ccl3, Ccr5, and Il12rb2. It was suggested that ABPs possibly regulated the balance of cytokines in helper T cells to ameliorate the immune function of CTX-induced mice.

The Research Progress in Transforming Growth Factor-ß2.

Transforming growth factor-beta 2 (TGF-ß2), an important member of the TGF-ß family, is a secreted protein that is involved in many biological processes, such as cell growth, proliferation, migration, and differentiation. TGF-ß2 had been thought to be functionally identical to TGF-ß1; however, an increasing number of recent studies uncovered the distinctive features of TGF-ß2 in terms of its expression, activation, and biological functions. Mice deficient in TGF-ß2 showed remarkable developmental abnormalities in multiple organs, especially the cardiovascular system. Dysregulation of TGF-ß2 signalling was associated with tumorigenesis, eye diseases, cardiovascular diseases, immune disorders, as well as motor system diseases. Here, we provide a comprehensive review of the research progress in TGF-ß2 to support further research on TGF-ß2.

Identification of a Bacillus thuringiensis Q1 compound with algicidal activity.

Bacillus thuringiensis Q1, isolated from the eutrophic waters of the Haihe River in Tianjin, possesses remarkable algae dissolving character. We determined the lytic effect of B. thuringiensis Q1 fermentation broth, and it proved to be pH- and temperature-stable. Then, we investigated the structure of the algicidal compound by high performance liquid chromatography, gas chromatography tandem quadrupole mass spectrometry and fourier transform infrared spectroscopy, and identified as purine-derived C12H15O5N5. To further understand B. thuringiensis Q1, we performed genome sequencing and analysis. The genome was 5341610 bp, with 35.31% GC content. Some elements involved in algicidal activity, such as quorum sensing pathway and ABC transporter were predicted. Our results reveal that B. thuringiensis Q1 can be used for biological control of harmful algal blooms.

KV Channel-Interacting Proteins in the Neurological and Cardiovascular Systems: An Updated Review.

KV channel-interacting proteins (KChIP1-4) belong to a family of Ca2+-binding EF-hand proteins that are able to bind to the N-terminus of the KV4 channel α-subunits. KChIPs are predominantly expressed in the brain and heart, where they contribute to the maintenance of the excitability of neurons and cardiomyocytes by modulating the fast inactivating-KV4 currents. As the auxiliary subunit, KChIPs are critically involved in regulating the surface protein expression and gating properties of KV4 channels. Mechanistically, KChIP1, KChIP2, and KChIP3 promote the translocation of KV4 channels to the cell membrane, accelerate voltage-dependent activation, and slow the recovery rate of inactivation, which increases KV4 currents. By contrast, KChIP4 suppresses KV4 trafficking and eliminates the fast inactivation of KV4 currents. In the heart, IKs, ICa,L, and INa can also be regulated by KChIPs. ICa,L and INa are positively regulated by KChIP2, whereas IKs is negatively regulated by KChIP2. Interestingly, KChIP3 is also known as downstream regulatory element antagonist modulator (DREAM) because it can bind directly to the downstream regulatory element (DRE) on the promoters of target genes that are implicated in the regulation of pain, memory, endocrine, immune, and inflammatory reactions. In addition, all the KChIPs can act as transcription factors to repress the expression of genes involved in circadian regulation. Altered expression of KChIPs has been implicated in the pathogenesis of several neurological and cardiovascular diseases. For example, KChIP2 is decreased in failing hearts, while loss of KChIP2 leads to increased susceptibility to arrhythmias. KChIP3 is increased in Alzheimer's disease and amyotrophic lateral sclerosis, but decreased in epilepsy and Huntington's disease. In the present review, we summarize the progress of recent studies regarding the structural properties, physiological functions, and pathological roles of KChIPs in both health and disease. We also summarize the small-molecule compounds that regulate the function of KChIPs. This review will provide an overview and update of the regulatory mechanism of the KChIP family and the progress of targeted drug research as a reference for researchers in related fields.

Hologenomic insights into mammalian adaptations to myrmecophagy.

Highly specialized myrmecophagy (ant- and termite-eating) has independently evolved multiple times in species of various mammalian orders and represents a textbook example of phenotypic evolutionary convergence. We explored the mechanisms involved in this unique dietary adaptation and convergence through multi-omic analyses, including analyses of host genomes and transcriptomes, as well as gut metagenomes, in combination with validating assays of key enzymes' activities, in the species of three mammalian orders (anteaters, echidnas and pangolins of the orders Xenarthra, Monotremata and Pholidota, respectively) and their relatives. We demonstrate the complex and diverse interactions between hosts and their symbiotic microbiota that have provided adaptive solutions for nutritional and detoxification challenges associated with high levels of protein and lipid metabolisms, trehalose degradation, and toxic substance detoxification. Interestingly, we also reveal their spatially complementary cooperation involved in degradation of ants' and termites' chitin exoskeletons. This study contributes new insights into the dietary evolution of mammals and the mechanisms involved in the coordination of physiological functions by animal hosts and their gut commensals.

SOX4 is a novel phenotypic regulator of endothelial cells in atherosclerosis revealed by single-cell analysis.

INTRODUCTION: Atherosclerotic complications represent the leading cause of cardiovascular mortality globally. Dysfunction of endothelial cells (ECs) often initiates the pathological events in atherosclerosis. OBJECTIVES: In this study, we sought to investigate the transcriptional profile of atherosclerotic aortae, identify novel regulator in dysfunctional ECs and hence provide mechanistic insights into atherosclerotic progression. METHODS: We applied single-cell RNA sequencing (scRNA-seq) on aortic cells from Western diet-fed apolipoprotein E-deficient (ApoE-/-) mice to explore the transcriptional landscape and heterogeneity of dysfunctional ECs. In vivo validation of SOX4 upregulation in ECs were performed in atherosclerotic tissues, including mouse aortic tissues, human coronary arteries, and human renal arteries. Single-cell analysis on human aortic aneurysmal tissue was also performed. Downstream vascular abnormalities induced by EC-specific SOX4 overexpression, and upstream modulators of SOX4 were revealed by biochemical assays, immunostaining, and wire myography. Effects of shear stress on endothelial SOX4 expression was investigated by in vitro hemodynamic study. RESULTS: Among the compendium of aortic cells, mesenchymal markers in ECs were significantly enriched. Two EC subsets were subsequently distinguished, as the 'endothelial-like' and 'mesenchymal-like' subsets. Conventional assays consistently identified SOX4 as a novel atherosclerotic marker in mouse and different human arteries, additional to a cancer marker. EC-specific SOX4 overexpression promoted atherogenesis and endothelial-to-mesenchymal transition (EndoMT). Importantly, hyperlipidemia-associated cytokines and oscillatory blood flow upregulated, whereas the anti-diabetic drug metformin pharmacologically suppressed SOX4 level in ECs. CONCLUSION: Our study unravels SOX4 as a novel phenotypic regulator during endothelial dysfunction, which exacerbates atherogenesis. Our study also pinpoints hyperlipidemia-associated cytokines and oscillatory blood flow as endogenous SOX4 inducers, providing more therapeutic insights against atherosclerotic diseases.

A U-Shaped Dual-Frequency-Reconfigurable Monopole Antenna Based on Liquid Metal.

This study presents a U-shaped dual-frequency-reconfigurable liquid-metal monopole antenna. Eutectic Gallium-Indium (EGaIn) was used as a conductive fluid and filled in the two branches of the U-shaped glass tube. A precision syringe pump was connected to one of the branches of the U-shaped tube by a silicone tube to drive EGaIn, forming a height difference between the two liquid levels. When the height of liquid metal in the two branches met the initial condition of L1 = L2 = 10 mm, and L1 increased from 10 mm to 18 mm, the two branches obtained two working bandwidths of 2.27-4.98 GHz and 2.71-8.58 GHz, respectively. The maximum peak gain was 4.00 dBi. The initial amount of EGaIn also affected the available operating bandwidth. When the liquid metal was perfused according to the initial condition: L1 = L2 = 12 mm, and L1 was adjusted within the range of 12-20 mm, the two branches had the corresponding working bandwidths of 2.18-4.32 GHz and 2.57-9.09 GHz, and the measured maximum peak gain was 3.72 dBi. The simulation and measurement data corresponded well. A series of dual-frequency-reconfigurable antennas can be obtained by changing the initial amount of EGaIn. This series of antennas may have broad application prospects in fields such as base stations and navigation.

Restoration of Autophagic Flux Improves Endothelial Function in Diabetes Through Lowering Mitochondrial ROS-Mediated eNOS Monomerization.

Endothelial nitric oxide synthase (eNOS) monomerization and uncoupling play crucial roles in mediating vascular dysfunction in diabetes, although the underlying mechanisms are still incompletely understood. Increasing evidence indicates that autophagic dysregulation is involved in the pathogenesis of diabetic endothelial dysfunction; however, whether autophagy regulates eNOS activity through controlling eNOS monomerization or dimerization remains elusive. In this study, autophagic flux was impaired in the endothelium of diabetic db/db mice and in human endothelial cells exposed to advanced glycation end products or oxidized low-density lipoprotein. Inhibition of autophagic flux by chloroquine or bafilomycin A1 were sufficient to induce eNOS monomerization and lower nitric oxide bioavailability by increasing mitochondrial reactive oxygen species (mtROS). Restoration of autophagic flux by overexpressing transcription factor EB (TFEB), a master regulator of autophagy and lysosomal biogenesis, decreased endothelial cell oxidative stress, increased eNOS dimerization, and improved endothelium-dependent relaxations (EDRs) in db/db mouse aortas. Inhibition of mammalian target of rapamycin kinase (mTOR) increased TFEB nuclear localization, reduced mtROS accumulation, facilitated eNOS dimerization, and enhanced EDR in db/db mice. Moreover, calorie restriction also increased TFEB expression, improved autophagic flux, and restored EDR in the aortas of db/db mice. Taken together, the findings of this study reveal that mtROS-induced eNOS monomerization is closely associated with the impaired TFEB-autophagic flux axis leading to endothelial dysfunction in diabetic mice.

Endothelial shear stress signal transduction and atherogenesis: From mechanisms to therapeutics.

Atherosclerotic vascular disease and its complications are among the top causes of mortality worldwide. In the vascular lumen, atherosclerotic plaques are not randomly distributed. Instead, they are preferentially localized at the curvature and bifurcations along the arterial tree, where shear stress is low or disturbed. Numerous studies demonstrate that endothelial cell phenotypic change (e.g., inflammation, oxidative stress, endoplasmic reticulum stress, apoptosis, autophagy, endothelial-mesenchymal transition, endothelial permeability, epigenetic regulation, and endothelial metabolic adaptation) induced by oscillatory shear force play a fundamental role in the initiation and progression of atherosclerosis. Mechano-sensors, adaptor proteins, kinases, and transcriptional factors work closely at different layers to transduce the shear stress force from the plasma membrane to the nucleus in endothelial cells, thereby controlling the expression of genes that determine cell fate and phenotype. An in-depth understanding of these mechano-sensitive signaling cascades shall provide new translational strategies for therapeutic intervention of atherosclerotic vascular disease. This review updates the recent advances in endothelial mechano-transduction and its role in the pathogenesis of atherosclerosis, and highlights the perspective of new anti-atherosclerosis therapies through targeting these mechano-regulated signaling molecules.

Long-Read Genome Sequencing Provides Molecular Insights into Scavenging and Societal Complexity in Spotted Hyena Crocuta crocuta.

The spotted hyena (Crocuta crocuta) is a large and unique terrestrial carnivore. It is a particularly fascinating species due to its distinct phenotypic traits, especially its complex social structure and scavenging lifestyle, with associated high dietary exposure to microbial pathogens. However, the underlying molecular mechanisms related to these phenotypes remain elusive. Here, we sequenced and assembled a high-quality long-read genome of the spotted hyena, with a contig N50 length of ∼13.75 Mb. Based on comparative genomics, immunoglobulin family members (e.g., IGKV4-1) showed significant adaptive duplications in the spotted hyena and striped hyena. Furthermore, immune-related genes (e.g., CD8A, LAG3, and TLR3) experienced species-specific positive selection in the spotted hyena lineage. These results suggest that immune tolerance between the spotted hyena and closely related striped hyena has undergone adaptive divergence to cope with prolonged dietary exposure to microbial pathogens from scavenging. Furthermore, we provided the potential genetic insights underlying social complexity, hinting at social behavior and cognition. Specifically, the RECNE-associated genes (e.g., UGP2 and ACTR2) in the spotted hyena genome are involved in regulation of social communication. Taken together, our genomic analyses provide molecular insights into the scavenging lifestyle and societal complexity of spotted hyenas.

Effects of enhanced external counterpulsation on exercise capacity and quality of life in patients with chronic heart failure: A meta-analysis.

BACKGROUND: This meta-analysis aimed to synthesize randomized controlled trials to evaluate the effects of enhanced external counterpulsation (EECP) on exercise capacity and quality of life in patients with chronic heart failure (CHF). METHODS: Both English and Chinese databases were searched from their inception to June 30, 2020 (PubMed, EMBASE, Cochrane Library, CINAHL (EBSCO), Web of Science for English publications and Chinese Biomedical Database, China National Knowledge Infrastructure, Wanfang Data for Chinese publication). Titles, abstracts, and full-text articles were screened against study inclusion criteria: randomized controlled trials studying EECP intervention for patients with CHF. The meta-analysis was conducted with Revman 5.3 or STATA 16.0. RESULTS: Eight randomized controlled trials were included. EECP induced significant improvement in 6-min walking distance (WMD=84.79 m; 95% CI, 47.64 to 121.95; P < .00001). Moreover, EECP was beneficial for left ventricular ejection fraction (SMD = 0.64; 95% CI,0.29 to 1.00; P = .0004), and N-terminal pro brain natriuretic peptide (SMD = -0.61; 95%CI, -1.20 to -0.01; P = 0.04).However, compared with the control groups, EECP did not significantly reduce the Minnesota Living with Heart Failure Questionnaire scores(WMD, -9.28; 95% CI, -19.30 to 0.75; P = 0.07). CONCLUSIONS: Despite heterogeneity and risk of bias, this meta-analysis confirms that EECP can improve exercise capacity in CHF patients, especially the elderly. However, the evidence that EECP improves the quality of life in patients with CHF is still insufficient. More and larger well-designed randomized controlled trials are still warranted. REGISTRATION INFORMATION: PROSPERO registration no. CRD 42020188848.

KLF2 Mediates the Suppressive Effect of Laminar Flow on Vascular Calcification by Inhibiting Endothelial BMP/SMAD1/5 Signaling.

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Interplay Between Oxidative Stress, Cyclooxygenases, and Prostanoids in Cardiovascular Diseases.

Significance: Endothelial cells lining the lumen of blood vessels play an important role in the regulation of cardiovascular functions through releasing both vasoconstricting and vasodilating factors. The production and function of vasoconstricting factors are largely elevated in hypertension, diabetes, atherosclerosis, and ischemia/reperfusion injuries. Cyclooxygenases (COXs) are the major enzymes producing five different prostanoids that act as either contracting or relaxing substances. Under conditions of increased oxidative stress, the expressions and activities of COX isoforms are altered, resulting in changes in production of various prostanoids and thus affecting vascular tone. This review briefly summarizes the relationship between oxidative stress, COXs, and prostanoids, thereby providing new insights into the pathophysiological mechanisms of cardiovascular diseases (CVDs). Recent Advances: Many new drugs targeting oxidative stress, COX-2, and prostanoids against common CVDs have been evaluated in recent years and they are summarized in this review. Critical Issues: Comprehensive understanding of the complex interplay between oxidative stress, COXs, and prostanoids in CVDs helps develop more effective measures against cardiovascular pathogenesis. Future Directions: Apart from minimizing the undesired effects of harmful prostanoids, future studies shall investigate the restoration of vasoprotective prostanoids as a means to combat CVDs. Antioxid. Redox Signal. 34, 784-799.

CTRP15 derived from cardiac myocytes attenuates TGFß1-induced fibrotic response in cardiac fibroblasts.

PURPOSE: Cardiac fibrosis is characterized by net accumulation of extracellular matrix (ECM) components in the  myocardium and facilitates the development of heart failure. C1q/tumor necrosis factor-related protein 15 (CTRP15) is a novel member of the CTRP family, and its gene expression is detected in adult mouse hearts. The present study was performed to determine the effect of CTRP15 on pressure overload-induced fibrotic remodeling. METHODS: Mice were subjected to transverse aortic constriction (TAC) surgery, and adeno-associated virus serotype 9 (AAV9)-carrying mouse CTRP15 gene was injected into mice to achieve CTRP15 overexpression in the myocardium. Adenovirus carrying the gene encoding CTRP15 or small interfering RNA (siRNA) of interest was infected into cultured neonatal mouse ventricular cardiomyocytes (NMVCs) or cardiac fibroblasts (CFs). Gene expression was measured by quantitative real-time PCR, and protein expression and distribution were determined by Western blotting, immunocytochemistry, and immunofluorescence staining. RESULTS: CTRP15 was predominantly produced by cardiac myocytes. CTRP15 expression in the left ventricles was downregulated in mice that underwent TAC. AAV9-mediated CTRP15 overexpression alleviated ventricular remodeling and dysfunction in the pressure-overloaded mice. Treatment of CFs with recombinant CTRP15 or the conditioned medium containing CTRP15 inhibited transforming growth factor (TGF)-ß1-induced Smad3 activation and myofibroblast differentiation. CTRP15 increased phosphorylation of insulin receptor (IR), insulin receptor substrate-1 (IRS-1), and Akt. Blockade of IR/IRS-1/Akt pathway reversed the inhibitory effect of CTRP15 on TGF-ß1-induced Smad3 activation. CONCLUSION: CTRP15 exerts an anti-fibrotic effect on pressure overload-induced cardiac remodeling. The activation of IR/IRS-1/Akt pathway contributes to the anti-fibrotic effect of CTRP15 through targeting Smad3.

Peroxisome Proliferator-Activated Receptor-γ Coactivator-1α Inhibits Vascular Calcification Through Sirtuin 3-Mediated Reduction of Mitochondrial Oxidative Stress.

Aims: Vascular calcification is associated with cardiovascular death in patients with chronic kidney disease (CKD). Peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) plays an important role in various cardiovascular diseases. However, its role in vascular calcification remains unknown. Results: Adenine-induced rat CKD model was used to induce arterial medial calcification. The level of PGC-1α decreased in abdominal aorta of CKD rats. Overexpression of PGC-1α significantly ameliorated calcium deposition in rat abdominal aorta, isolated carotid rings, and cultured vascular smooth muscle cells (VSMCs). Mitochondrial reactive oxygen species (mtROS) increased in calcifying aorta and VSMCs. Upregulation of PGC-1α inhibited, whereas PGC-1α depletion promoted ß-glycerophosphate-induced mtROS production and calcium deposition. Moreover, PGC-1α increased superoxide dismutase 1 (SOD1) and SOD2 contents in vivo and in vitro, whereas SOD2 deletion eliminated PGC-1α-mediated mtROS change and promoted calcium deposition. Mechanistically, sirtuin 3 (SIRT3) expression declined in calcifying aorta and VSMCs, while PGC-1α overexpression restored SIRT3 expression. Inhibition of SIRT3 by 3-TYP or siRNA (small interfering RNA) reduced PGC-1α-induced upregulation of SOD1 and SOD2, and abolished the protective effect of PGC-1α on calcification of VSMCs. Importantly, PGC-1α was reduced in calcified femoral arteries in CKD patients. In phosphate-induced human umbilical arterial calcification, upregulation of PGC-1α attenuated calcium nodule formation, while this protective effect was abolished by SIRT3 inhibitor. Innovation: We showed for the first time that PGC-1α is an important endogenous regulator against vascular calcification. Induction of PGC-1α could be a potential strategy to treat vascular calcification in CKD patients. Conclusions: PGC-1α protected against vascular calcification by SIRT3-mediated mtROS reduction.

Endothelial TFEB (Transcription Factor EB) Restrains IKK (IκB Kinase)-p65 Pathway to Attenuate Vascular Inflammation in Diabetic db/db Mice.

Objective- TFEB (transcription factor EB) was recently reported to be induced by atheroprotective laminar flow and play an anti-atherosclerotic role by inhibiting inflammation in endothelial cells (ECs). This study aims to investigate whether TFEB regulates endothelial inflammation in diabetic db/db mice and the molecular mechanisms involved. Approach and Results- Endothelial denudation shows that TFEB is mainly expressed in ECs in mouse aortas. Western blotting shows TFEB total protein level decreases whereas the p-TFEB S142 (phosphorylated form of TFEB) increases in db/db mouse aortas, suggesting a decreased TFEB activity. Adenoviral TFEB overexpression reduces endothelial inflammation as evidenced by decreased expression of vascular inflammatory markers in db/db mouse aortas, and reduced expression of a wide range of adhesion molecules and chemokines in human umbilical vein ECs. Monocyte attachment assay shows TFEB suppresses monocyte adhesion to human umbilical vein ECs. RNA sequencing of TFEB-overexpressed human umbilical vein ECs suggested TFEB inhibits NF-κB (nuclear factor-kappa B) signaling. Indeed, luciferase assay shows TFEB suppresses NF-κB transcriptional activity. Mechanistically, TFEB suppresses IKK (IκB kinase) activity to protect IκB-α from degradation, leading to reduced p65 nuclear translocation. Inhibition of IKK by PS-1145 abolished TFEB silencing-induced inflammation in human umbilical vein ECs. Lastly, we identified KLF2 (Krüppel-like factor 2) upregulates TFEB expression and promoter activity. Laminar flow experiment showed that KLF2 is required for TFEB induction by laminar flow and TFEB is an anti-inflammatory effector downstream of laminar flow-KLF2 signaling in ECs. Conclusions- These findings suggest that TFEB exerts anti-inflammatory effects in diabetic mice and such function in ECs is achieved by inhibiting IKK activity and increasing IκBα level to suppress NF-κB activity. KLF2 mediates TFEB upregulation in response to laminar flow.

Genetic diversity and structure of Elymus tangutorum accessions from western China as unraveled by AFLP markers.

BACKGROUND: Understanding genetic diversity of wild plant germplasm and the relationships between ecogeographic and genetic characteristics may provide insights for better utilizing and conserving genetic resources. Elymus tangutorum (Nevski) Hand.-Mazz, a cool-season hexaploid perennial, is an important pasture bunchgrass species used for forages and grassland restoration in Qinghai-Tibet Plateau and northwest China. In this study, 27 E. tangutorum accessions from diverse origins of western China were evaluated using AFLP markers in an effort to delve into the genetic relationships among them. The effects of eco-environmental factors and geographical isolation on the genetic diversity and population structure were also elucidated. RESULTS: On account of 554 polymorphic fragments amplified with 14 primer combinations, the mean values of some marker parameters including polymorphic information content, resolving power and marker index were 0.2504, 14.10 and 23.07, respectively, validating the high efficiency and reliability of the markers selected. Genetic dissimilarity index values among accessions ranged from 0.1024 to 0.7137 with a mean of 0.2773. STRUCTURE, UPGMA clustering and PCoA analyses showed that all accessions could be divided into the three main clusters; however, this results do not exactly coincide with geographic groups. We found medium differentiation (F ST = 0.162) between Qinghai-Tibet Plateau (QTP) and Xinjiang (XJC), and high differentiation (F ST = 0.188) among three Bayesian subgroups. A significant correlation (r = 0.312) between genetic and geographical distance was observed by Mantel test in the species level, while the weak correlation was detected between genetic and environmental distance for all accessions and most of geographical groups. In addition, a significant ecological influence of average annual precipitation on genetic distance was revealed in XJC group and the Bayesian subgroup A. CONCLUSION: This study indicates that AFLP technique are a useful tool to measure genetic diversity in E. tangutorum, showing that geographical and environmental factors (especially precipitation) together, play a crucial role in genetic differentiation patterns. These findings underline the importance of local adaptation in shaping patterns of genetic variability and population structure in E. tangutorum germplasm collected in Western China.

Revisiting avian 'missing' genes from de novo assembled transcripts.

BACKGROUND: Argument remains as to whether birds have lost genes compared with mammals and non-avian vertebrates during speciation. High quality-reference gene sets are necessary for precisely evaluating gene gain and loss. It is essential to explore new reference transcripts from large-scale de novo assembled transcriptomes to recover the potential hidden genes in avian genomes. RESULTS: We explored 196 high quality transcriptomic datasets from five bird species to reconstruct transcripts for the purpose of discovering potential hidden genes in the avian genomes. We constructed a relatively complete and high-quality bird transcript database (1,623,045 transcripts after quality control in five birds) from a large amount of avian transcriptomic data, and found most of the presumed missing genes (83.2%) could be recovered in at least one bird species. Most of these genes have been identified for the first time in birds. Our results demonstrate that 67.94% genes have GC content over 50%, while 2.91% genes are AT-rich (AT% > 60%). In our results, 239 (53.59%) genes had a tissue-specific expression index of more than 0.9 in chicken. The missing genes also have lower Ka/Ks values than average (genome-wide: Ka/Ks = 0.99; missing gene: Ka/Ks = 0.90; t-test = 1.25E-14). Among all presumed missing genes, there were 135 for which we did not find any meaningful orthologues in any of the 5 species studied. CONCLUSION: Insufficient reference genome quality is the major reason for wrongly inferring missing genes in birds. Those presumably missing genes often have a very strong tissue-specific expression pattern. We show multi-tissue transcriptomic data from various species are necessary for inferring gene family evolution for species with only draft reference genomes.

The Origin and Population History of the Endangered Golden Snub-Nosed Monkey (Rhinopithecus roxellana).

The origin and population history of the endangered golden snub-nosed monkey (Rhinopithecus roxellana) remain largely unavailable and/or controversial. We here integrate analyses of multiple genomic markers, including mitochondrial (mt) genomes, Y-chromosomes, and autosomes of 54 golden monkey individuals from all three geographic populations (SG, QL, and SNJ). Our results reveal contrasting population structures. Mt analyses suggest a division of golden monkeys into five lineages: one in SNJ, two in SG, and two in QL. One of the SG lineages (a mixed SG/QL lineage) is basal to all other lineages. In contrast, autosomal analyses place SNJ as the most basal lineage and identify one QL and three SG lineages. Notably, Y-chromosome analyses bear features similar to mt analyses in placing the SG/QL-mixed lineage as the first diverging lineage and dividing SG into two lineages, while resembling autosomal analyses in identifying one QL lineage. We further find bidirectional gene flow among all three populations at autosomal loci, while asymmetric gene flow is suggested at mt genomes and Y-chromosomes. We propose that different population structures and gene flow scenarios are the result of sex-linked differences in the dispersal pattern of R. roxellana. Moreover, our demographic simulation analyses support an origin hypothesis suggesting that the ancestral R. roxellana population was once widespread and then divided into SNJ and non-SNJ (SG and QL) populations. This differs from previous mt-based "mono-origin (SG is the source population)" and "multiorigin (SG is a fusion of QL and SNJ)" hypotheses. We provide a detailed and refined scenario for the origin and population history of this endangered primate species, which has a broader significance for Chinese biogeography. In addition, this study highlights the importance to investigate multiple genomic markers with different modes of inheritance to trace the complete evolutionary history of a species, especially for those exhibiting differential or mixed patterns of sex dispersal.