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.

MicroRNA-135b alleviates MPP+-mediated Parkinson's disease in in vitro model through suppressing FoxO1-induced NLRP3 inflammasome and pyroptosis

The present study focused on the novel roles and the underlying mechanisms of miR-135b in pyroptosis of MPP⁺-induced Parkinson's disease (PD). We established an in vitro PD model induced by MPP⁺. Our results demonstrated miR-135b was lower while FoxO1 was inversely higher in MPP⁺-treated SH-SY5Y and PC-12 cells. Luciferase reporter assay showed FoxO1 was a downstream target of miR-135b. MiR-135b mimics suppressed MPP⁺-induced pyroptosis and the upregulation of TXNIP, NLRP3, Caspase-1, ASC, GSDMD^Nterm and IL-1β. Moreover, FoxO1 overexpression had no effect on miR-135b but reversed its own downregulation caused by miR-135b mimics. Meanwhile, overexpression of FoxO1 abolished the inhibitory effects of miR-135b on pyroptosis and reversed the downregulation of pyroptotic genes and LDH release. In summary, miR-135b played a protective role in Parkinson's disease via inhibiting pyroptosis by targeting FoxO1. MiR-135b might serve as a potential therapeutic target in the treatment of Parkinson's disease.

Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing

The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat.

[Transmission cluster and network of HIV-1 CRF01_AE strain in China, 1996-2014]

Objective: To understand the transmission patterns and risk factors of HIV-1 strain CRF01_AE subtypes in China, and to provide guidance for the implementation of precise intervention. Methods: A total of 2 094 CRF01_AE pol sequences were collected in 19 provinces in China between 1996 and 2014. Phylogenetic tree was constructed by PhyML 3.0 software to select the transmission clusters. Transmission network was constructed by Cytoscape 3.6.0, which was further used for exploring of the major risk factors. Results: Of the 2 094 sequences, 12.18% (255/2 094) were in clusters. A total of 82 transmission clusters were identified. The numbers of clusters and contained sequences in intra-provincial transmission (61, 173) were significantly more than those in inter-provincial transmission (21, 82). The ratio of transmission clustering in MSM increased over time from 2.41% (2/83) during 1996-2008 to 23.61% (72/305) during 2013-2014, showing a significant upward trend (χ(2)=27.800, df=1, P=0.000). The proportion of MSM with inter-provincial transmission clusters were higher than those with intra-provincial transmission clusters, which increased from 0.67% (2/297) during 1996-2008 to 6.36%(30/472) during 2013-2014, showing a significant upward trend (χ(2)=20.276, df=1, P=0.000). The transmission rate in homosexuals of the inter-transmission clusters (86.59%, 71/82) was higher than that of intra-provincial transmission clusters (56.65%, 98/173), and the difference was statistically significant (χ(2)=22.792, P=0.000). The proportion of inter-provincial transmission clusters with more than 2 transmission routes (33.33%, 7/21) was higher than that of intra-provincial clusters (13.11%, 8/61), and the difference was statistically significant (χ(2)=4.273, P=0.039). Results from the transmission network analysis indicated that the proportion of high risk population (degree≥4) with inter-provincial transmission clusters (51.22%, 42/82) was significantly higher than that with intra-provincial transmission clusters (26.59%, 46/173), and the difference was statistically significant (χ(2)=14.932, P=0.000). Inter-provincial clusters were mainly detected in and and MSM. Conclusions: Complex transmission networks were found for HIV-1 CRF01_AE strains in the mainland of China. Inter-provincial transmission clusters increased rapidly, MSM played an important role in the wide spread of the strain. More researches in transmission networks are needed to guide the precision intervention.

[Effect of a novel cold atmospheric plasma jet treatment with different temperatures on resin-dentin bonding]

OBJECTIVE

To investigate the effect of different treatment temperatures of a novel cold atmospheric plasma jet treatment on the resin-dentin bonding.

METHODS

(1) Fifty-two freshly extracted, non-carious and intact third molars were collected. The occlusal one-third of the crown was removed by means of a water-cooled low-speed Isomet saw. One dentin disc [(900 ±100) μm] was prepared for each tooth. The fifty-two dentin discs were randomly divided into control group and experimental groups, of which four were in control group, and forty-eight were divided into four experimental groups according to the different treatment temperatures (4 °C, 10 °C, 20 °C and 30 °C) of the novel radio-frequency atmospheric-pressure glow discharge (RF-APGD) plasma jet, twelve in each group. Each experimental group was divided into three subgroups according to different treatment time (10 s, 20 s and 30 s), with four in each subgroup. The occlusal one-third of the crown was removed by means of a water-cooled low-speed Isomet saw. The morphology of demineralized dentin surfaces was analyzed using field emission scanning electron microscopy. (2) Twenty unerupted, non-carious and intact third molars were randomly divided into five groups, four in each group: control group, untreated; 4 °C, 10 °C, 20 °C and 30 °C experimental groups, each group was treated with the RF-APGD plasma jet for 20 s. The micro-tensile resin dentin bond strength was tested after 20 s RF-APGD plasma jet treatment with different temperatures, using a universal mechanical machine.

RESULTS

(1) The field emission scanning electron microscopy results indicated that when compared with the control group, a 10 s RF-APGD plasma jet treatment with 30 °C and 20 °C collapsed the collagen scaffold. Collagen fibrils maintained an uncollapsed three-dimensional structure after the 4 °C RF-APGD plasma jet treatment for even 30 s treatment. (2) The microtensile resin dentin bond strength results of the 4 °C RF-APGD plasma jet treatment group (57.8±0.7) MPa were significantly higher than that of the control group [(47.4±0.5) MPa] and 10 s, 20 s and 30 s RF-APGD plasma treatment group [(51.9±0.7) MPa,(29.7±1.0) MPa and (22.2±1.5) MPa] with statistically significant difference (P<0.05). Compared with the control group, the micro-tensile bond strength increased about 21.9% and 9.5% after 4 °C and 10 °C RF-APGD plasma jet treatment, respectively.

CONCLUSION

Compared with other treatment temperatures, this novel RF-APGD plasma jet treatment with the temperature of 4 °C can preserve the three-dimensional morphology of demineralized dentin better, and can improve the resin-dentin bonding.

Differential expression of mRNA-miRNAs related to intramuscular fat content in the longissimus dorsi in Xinjiang brown cattle

In this study, we examined the role of mRNAs and miRNAs in variations in intramuscular fat content in the longissimus dorsi muscle in Xinjiang brown cattle. Two groups of Xinjiang brown cattle with extremely different intramuscular fat content in the longissimus dorsi were selected for combined of miRNA and mRNA analysis using an RNA-Seq. In total, 296 mRNAs and 362 miRNAs were significantly differentially expressed, including 155 newly predicted miRNAs, 275 significantly upregulated genes, 252 significantly upregulated miRNAs, 21 significantly downregulated genes and 110 significantly downregulated miRNAs. The combined miRNA and mRNA analysis identified 96 differentially expressed miRNAs and 27 differentially expressed mRNAs. In all, 47 upregulated miRNAs had a regulatory effect on 14 differentially downregulated target genes, and 49 downregulated miRNAs had a regulatory effect on 13 upregulated target genes. To verify the sequencing results, 10 differentially expressed genes (DEGs) and 10 differentially expressed miRNAs were selected for qRT-PCR. The qRT-PCR results confirmed the sequencing results. The results of this study shed light on the molecular regulation of bovine adipose tissue, which might help with the development of new strategies for improving meat quality and animal productivity in beef cattle to provide healthier meat products for consumers.

Rapid Evolution of Genes Involved in Learning and Energy Metabolism for Domestication of the Laboratory Rat

The laboratory rat, widely used in biomedical research, is domesticated from wild brown rat. The origin and genetic mechanism underlying domestication of the laboratory rat remain largely elusive. In the present study, large scale genomes supported a single origin for the laboratory rat, possibly from a sister group to wild rats from Europe/Africa/Middle East. Genomic and transcriptomic analyses uncovered many artificially selected genes (e.g., FOXP2, B3GAT1, and CLOCK) involved in the nervous system. These genes associate with learning ability and regulation of circadian rhythm, which likely enabled the successful domestication of the laboratory rat. Particularly, many genes, including mitochondrial genes responsible for energy metabolism, displayed a substantially increased expression in the brain of laboratory rats compared with wild rats. Our findings demystify the origin and evolution of this model animal, and provide insight into the process of its domestication.

Expression of UCA1 and MALAT1 long-chain non-coding RNAs in esophageal squamous cell carcinoma tissues is predictive of patient prognosis

INTRODUCTION

The long non-coding RNAs (lncRNAs) urothelial cancer associated 1 (UCA1) and metastasis associated lung adenocarcinoma transcript 1 (MALAT1) are known to impact cancer cell regulation. The aim of the present study was to determine the relationship between the expression of these lncRNAs in esophageal squamous cell carcinoma (ESCC) tissues and disease prognosis.

MATERIAL AND METHODS

The expression of UCA1 and MALAT1 lncRNAs was assessed in ESCC and adjacent carcinoma tissues (5 cm away from the tumor) and evaluated in relation to overall survival (OS) and disease-free survival (DFS) of patients. This prospective study included 100 ESCC patients who were admitted to the First Hospital of Yulin City between January 2007 and January 2014.

RESULTS

The expression levels of UCA1 and MALAT1 lncRNAs in ESCC tissues were significantly higher than those in adjacent carcinoma tissues, and there were statistically significant differences in TNM staging between the patients with high lncRNA expression and low lncRNA expression. The OS and DFS of patients with high UCA1 and MALAT1 lncRNA expression levels were significantly shorter than those with low expression levels. Furthermore, the OS and DFS of ESCC patients appeared to be correlated with TNM staging.

CONCLUSIONS

These results imply that the up-regulation of UCA1 and MALAT1 lncRNAs in ESCC tissues can impact the degree of tumor progression and is predictive of postoperative survival. Therefore, the expression levels of these lncRNAs can be used as measurement indexes to determine the prognosis of ESCC patients.

Development and Standardization of a New Cognitive Assessment Test Battery for Chinese Aphasic Patients: A Preliminary Study

Background:

Nonlinguistic cognitive impairment has become an important issue for aphasic patients, but currently there are few neuropsychological cognitive assessment tests for it. To get more information on cognitive impairment of aphasic patients, this study aimed to develop a new cognitive assessment test battery for aphasic patients, the Non-language-based Cognitive Assessment (NLCA), and evaluate its utility in Chinese-speaking patients with aphasia.

Methods:

The NLCA consists of five nonverbal tests, which could assess five nonlinguistic cognitive domains such as visuospatial functions, attention test, memory, reasoning, and executive functions of aphasic patients. All tests are modified from the nonverbal items of the current existed tests with some changes to the characteristics of Chinese culture. The NLCA was tested in 157 participants (including 57 aphasic patients, 50 mild cognitive impairment (MCI) patients, and 50 normal controls), and was compared with other well-established relative neuropsychological tests on the reliability, validity, and utility.

Results:

The NLCA was fully applicable in the MCI patients and the normal controls, almost working in the aphasic patients (57/62 patients, 91.9%). The NLCA scores were 66.70 ± 6.30, 48.67 ± 15.04, and 77.58 ± 2.56 for the MCI group, the aphasic group, and the control group, respectively, and a significant difference was found among three groups (F = 118.446, P < 0.001). The Cronbach's alpha of the NLCA as an index of internal consistency was 0.805, and the test-retest and interrater reliability was adequate (r=0.977 and r= 0.970, respectively). The correlations of the cognitive subtests and their validation instruments were between 0.540 and 0.670 (all P < 0.05). Spearman's correlation analysis indicated that the coefficient of internal consistency of each subtest itself was higher than other subtests. When choosing the Montreal Cognitive Assessment score of <26 as the diagnostic criteria of cognitive impairment, the area under the curve for all participants in the control and MCI groups was 0.942 (95% confidence interval: 0.895–0.989), and an optimal cutoff point of 75.00 seemed to provide the best balance between sensitivity and specificity. Age (r = −0.406, P < 0.001) was the main influence factor for the NLCA.

Conclusions:

The NLCA could efficiently differentiate the cognitive impairment patients from the normal controls and is a reliable and valid cognitive assessment test battery to specially find nonlinguistic cognitive function for aphasic patients.

Influence of Working Temperature on The Formation of Electrospun Polymer Nanofibers

Temperature is an important parameter during electrospinning, and virtually, all solution electrospinning processes are conducted at ambient temperature. Nanofiber diameters presumably decrease with the elevation of working fluid temperature. The present study investigated the influence of temperature variations on the formation of polymeric nanofibers during single-fluid electrospinning. The surface tension and viscosity of the fluid decreased with increasing working temperature, which led to the formation of high-quality nanofibers. However, the increase in temperature accelerated the evaporation of the solvent and thus terminated the drawing processes prematurely. A balance can be found between the positive and negative influences of temperature elevation. With polyacrylonitrile (PAN, with N,N-dimethylacetamide as the solvent) and polyvinylpyrrolidone (PVP, with ethanol as the solvent) as the polymeric models, relationships between the working temperature (T, K) and nanofiber diameter (D, nm) were established, with D = 12598.6 - 72.9T + 0.11T ² (R = 0.9988) for PAN fibers and D = 107003.4 - 682.4T + 1.1T ² (R = 0.9997) for PVP nanofibers. Given the fact that numerous polymers are sensitive to temperature and numerous functional ingredients exhibit temperature-dependent solubility, the present work serves as a valuable reference for creating novel functional nanoproducts by using the elevated temperature electrospinning process.

Genetic variation in glia-neuron signalling modulates ageing rate

The rate of behavioural decline in the ageing population is remarkably variable among individuals. Despite the considerable interest in studying natural variation in ageing rate to identify factors that control healthy ageing, no such factor has yet been found. Here we report a genetic basis for variation in ageing rates in Caenorhabditis elegans. We find that C. elegans isolates show diverse lifespan and age-related declines in virility, pharyngeal pumping, and locomotion. DNA polymorphisms in a novel peptide-coding gene, named regulatory-gene-for-behavioural-ageing-1 (rgba-1), and the neuropeptide receptor gene npr-28 influence the rate of age-related decline of worm mating behaviour; these two genes might have been subjected to recent selective sweeps. Glia-derived RGBA-1 activates NPR-28 signalling, which acts in serotonergic and dopaminergic neurons to accelerate behavioural deterioration. This signalling involves the SIR-2.1-dependent activation of the mitochondrial unfolded protein response, a pathway that modulates ageing. Thus, natural variation in neuropeptide-mediated glia-neuron signalling modulates the rate of ageing in C. elegans.

A Normalization-Free and Nonparametric Method Sharpens Large-Scale Transcriptome Analysis and Reveals Common Gene Alteration Patterns in Cancers

Heterogeneity in transcriptional data hampers the identification of differentially expressed genes (DEGs) and understanding of cancer, essentially because current methods rely on cross-sample normalization and/or distribution assumption—both sensitive to heterogeneous values. Here, we developed a new method, Cross-Value Association Analysis (CVAA), which overcomes the limitation and is more robust to heterogeneous data than the other methods. Applying CVAA to a more complex pan-cancer dataset containing 5,540 transcriptomes discovered numerous new DEGs and many previously rarely explored pathways/processes; some of them were validated, both in vitro and in vivo, to be crucial in tumorigenesis, e.g., alcohol metabolism (ADH1B), chromosome remodeling (NCAPH) and complement system (Adipsin). Together, we present a sharper tool to navigate large-scale expression data and gain new mechanistic insights into tumorigenesis.

Red blood cell distribution width and ischaemic stroke

The red blood cell distribution width (RDW) is a measure of red blood cell (RBC) size heterogeneity, which is easily calculated by dividing the SD of erythrocyte volumes for the mean corpuscular volume. Recent reporter suggested that, besides haematological diseases and anaemia, many human disorders may be closely associated with the elevated RDW. A literature review has revealed the RDW may be closely related to the development of ischaemic stroke, carotid artery atherosclerosis and cerebral embolism. Higher RDW could independently predict adverse outcomes in patients in these conditions.

An integrated method for the identification of novel genes related to oral cancer

Cancer is a significant public health problem worldwide. Complete identification of genes related to one type of cancer facilitates earlier diagnosis and effective treatments. In this study, two widely used algorithms, the random walk with restart algorithm and the shortest path algorithm, were adopted to construct two parameterized computational methods, namely, an RWR-based method and an SP-based method; based on these methods, an integrated method was constructed for identifying novel disease genes. To validate the utility of the integrated method, data for oral cancer were used, on which the RWR-based and SP-based methods were trained, thereby building two optimal methods. The integrated method combining these optimal methods was further adopted to identify the novel genes of oral cancer. As a result, 85 novel genes were inferred, among which eleven genes (e.g., MYD88, FGFR2, NF-κBIA) were identified by both the RWR-based and SP-based methods, 70 genes (e.g., BMP4, IFNG, KITLG) were discovered only by the RWR-based method and four genes (L1R1, MCM6, NOG and CXCR3) were predicted only by the SP-based method. Extensive analyses indicate that several novel genes have strong associations with cancers, indicating the effectiveness of the integrated method for identifying disease genes.

Theoretical study of the spectroscopic and nonlinear optical properties of trans- and cis-4-hydroxyazobenzene

We investigate the molecular structure, vibrational and electronic absorption spectra, and electronic hyperpolarizabilities of trans and cis isomers of 4-hydroxyazobenzene (HOAB) via density functional theory. Results show that the azo dye exhibits a high third-order nonlinear optical response and good optical transparency. Both the basis set and the functional are important influences on the results obtained when calculating the absorption spectrum and NLO response. We also study the effect of the solvent on the electronic absorption spectrum to assess the ability of the functional to reproduce the experimental spectrum in combination with a suitable solvent model. Our calculations show that the SMD model of Truhlar et al. handles the electrostatic and the non-electrostatic effects of hydrogen-bonding solvents on the absorption spectrum better than the traditional polarizable continuum model does. In addition, our results indicate that the dye trans-HOAB exhibits a high second hyperpolarizability and excellent optical transparency. Also, although the second hyperpolarizability of cis-HOAB is much lower than that of trans-HOAB, it is non-negligible when calculating the optical nonlinearity of HOAB under an optical pump. We also examine the effect of frequency dispersion on second harmonic generation. This study provides the basis for further research on the spectroscopic and nonlinear optical properties of novel azo dyes and other π-conjugated compounds.

Insights Into the Evolution of Chemoreceptor Genes Superfamily in Tyrophagus putrescentiae (Acari: Acaridae)

All living organisms, including animals, plants, fungi, and bacteria, use the olfactory system to recognize chemicals or pheromone from their environment. Insects detect a volatile substance using odorant receptors (ORs) or gustatory receptors (GRs) and ionotropic receptors (IRs). The gene families of the olfactory system in Acari are still not clear. In this study, we identified seven ORs, one GR, and five IRs from the transcriptome of the storage mite, Tyrophagus putrescentiae Schrank. No olfactory coreceptor was found in this transcriptome. Phylogenetic analysis of these gene families with other Arthropoda species revealed the conservation of carbon dioxide receptors in all tested flying insects and T. putrescentiae Most of these ORs and GRs were unique to three mosquitoes (Anopheles gambiae Giles, Culex quinquefasciatus Say, and Aedes aegypti L.), Ixodes scapularis Say and Pediculus humanus L., indicating their involvement in specific aspects of both gustatory and olfactory perception. Some clades contained receptors obtained from all tested insect vector species, indicating a degree of conservation among some vector-dependent OR lineages. IRs family was a highly dynamic and independent original of the chemoreceptor genes subfamily. Our findings would make it possible for future research on the chemosensory recognition mechanism in Acari.

Dynamical control on helicity of electromagnetic waves by tunable metasurfaces

Manipulating the polarization states of electromagnetic (EM) waves, a fundamental issue in optics, attracted intensive attention recently. However, most of the devices realized so far are either too bulky in size, and/or are passive with only specific functionalities. Here we combine theory and experiment to demonstrate that, a tunable metasurface incorporating diodes as active elements can dynamically control the reflection phase of EM waves, and thus exhibits unprecedented capabilities to manipulate the helicity of incident circular-polarized (CP) EM wave. By controlling the bias voltages imparted on the embedded diodes, we demonstrate that the device can work in two distinct states. Whereas in the “On” state, the metasurface functions as a helicity convertor and a helicity hybridizer within two separate frequency bands, it behaves as a helicity keeper within an ultra-wide frequency band in the “Off” state. Our findings pave the way to realize functionality-switchable devices related to phase control, such as frequency-tunable subwavelength cavities, anomalous reflectors and even holograms.