Adaptive functions of structural variants in human brain development

Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV map in a population of 562 rhesus macaques, verified by in-house benchmarks of eight macaque genomes with long-read sequencing and another one with genome assembly. This map indicates stronger selective constrains on inversions at regulatory regions, suggesting a strategy for prioritizing them with the most important functions. Accordingly, we identified 75 human-specific inversions and prioritized them. The top-ranked inversions have substantially shaped the human transcriptome, through their dual effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof of concept, we linked APCDD1, located on one of these inversions and down-regulated specifically in humans, to neuronal maturation and cognitive ability. We thus highlight inversions in shaping the human uniqueness in brain development.

[The trend of birth weight of full-term newborns and its association with parental reproductive age in Chongqing municipality from 2010 to 2022]

To analyze the trend of abnormal birth weight of full-term newborns and its correlation with parental reproductive age in Chongqing municipality from 2010 to 2022. Based on the Chongqing Birth Certificate System, full-term newborns born from January 2010 to December 2022 were selected. Parental information and birth weight were abstracted from the system. The joinpoint regression model was used to assess the trend of incidence of low birth weight (LBW) and macrosomia in the offspring from 2010 to 2022. The logistic regression model was utilized to analyze the association between parental reproduction age and birth weight of newborns. The average birth weight of 3 155 542 newborns was (3 305.8±410.5) g. The joinpoint regression model showed a decreasing trend for the incidence of LBW from 2010 to 2016 (APC=-4.26%, P<0.05), and an increasing trend from 2020 to 2022 (APC=8.99%, P<0.05). The incidence of macrosomia exhibited a decreasing trend from 2015 to 2022 (APC=-3.37%, P<0.05). The logistic regression model showed that, compared to the group with parents aged 20-34 years, the risk of LBW increased in other age groups. The risk of macrosomia decreased when either parent was aged<20 years, and increased when both parents were aged≥20 years. In conclusion, from 2010 to 2022, the incidence of LBW in full-term offspring in Chongqing municipality decreased first and then increased, and the incidence of macrosomia increased first and then decreased. Both young and advanced parental age were associated with an increased risk of LBW in offspring, and advanced parental age was also associated with an increased risk of macrosomia in offspring. Attention should be paid to the effects of advanced maternal and paternal age on offspring birth weight. Further efforts to control childbearing at a young age were needed.

6mA-Sniper: Quantifying 6mA sites in eukaryotes at single-nucleotide resolution

While N6-methyldeoxyadenine (6mA) modification is a fundamental regulation in prokaryotes, its prevalence and functions in eukaryotes are controversial. Here, we report 6mA-Sniper to quantify 6mA sites in eukaryotes at single-nucleotide resolution, and delineate a 6mA profile in Caenorhabditis elegans with 2034 sites. Twenty-six of 39 events with Mnl I restriction endonuclease sites were verified, demonstrating the feasibility of this method. The levels of 6mA sites pinpointed by 6mA-Sniper are generally increased after Pseudomonas aeruginosa infection, but decreased in strains with the removal of METL-9, the dominant 6mA methyltransferase. The enrichment of these sites on specific motif of [GC]GAG, the selective constrains on them, and their coordinated changes with METL-9 levels thus support an active shaping of the 6mA profile by methyltransferase. Moreover, for regions marked by 6mA sites that emerged after infection, an enrichment of up-regulated genes was detected, possibly mediated through a mutual exclusive cross-talk between 6mA and H3K27me3 modification. We thus highlight 6mA regulation as a previously neglected regulator in eukaryotes.

De novo genes with an lncRNA origin encode unique human brain developmental functionality

Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this all-or-nothing transition to functionality happens remains unclear. Here, in 74 human/hominoid-specific de novo genes, we identified distinctive U1 elements and RNA splice-related sequences accounting for RNA nuclear export, differentiating mRNAs from lncRNAs, and driving the origin of de novo genes from lncRNA loci. The polymorphic sites facilitating the lncRNA-mRNA conversion through regulating nuclear export are selectively constrained, maintaining a boundary that differentiates mRNAs from lncRNAs. The functional new genes actively passing through it thus showed a mode of pre-adaptive origin, in that they acquire functions along with the achievement of their coding potential. As a proof of concept, we verified the regulations of splicing and U1 recognition on the nuclear export efficiency of one of these genes, the ENSG00000205704, in human neural progenitor cells. Notably, knock-out or over-expression of this gene in human embryonic stem cells accelerates or delays the neuronal maturation of cortical organoids, respectively. The transgenic mice with ectopically expressed ENSG00000205704 showed enlarged brains with cortical expansion. We thus demonstrate the key roles of nuclear export in de novo gene origin. These newly originated genes should reflect the novel uniqueness of human brain development.

HTAADVar: Aggregation and fully automated clinical interpretation of genetic variants in heritable thoracic aortic aneurysm and dissection

PURPOSE

Early detection and pathogenicity interpretation of disease-associated variants are crucial but challenging in molecular diagnosis, especially for insidious and life-threatening diseases, such as heritable thoracic aortic aneurysm and dissection (HTAAD). In this study, we developed HTAADVar, an unbiased and fully automated system for the molecular diagnosis of HTAAD.

METHODS

We developed HTAADVar (http://htaadvar.fwgenetics.org) under the American College of Medical Genetics and Genomics/Association for Molecular Pathology framework, with optimizations based on disease- and gene-specific knowledge, expert panel recommendations, and variant observations. HTAADVar provides variant interpretation with a self-built database through the web server and the stand-alone programs.

RESULTS

We constructed an expert-reviewed database by integrating 4373 variants in HTAAD genes, with comprehensive metadata curated from 697 publications and an in-house study of 790 patients. We further developed an interpretation system to assess variants automatically. Notably, HTAADVar showed a multifold increase in performance compared with public tools, reaching a sensitivity of 92.64% and specificity of 70.83%. The molecular diagnostic yield of HTAADVar among 790 patients (42.03%) also matched the clinical data, independently demonstrating its good performance in clinical application.

CONCLUSION

HTAADVar represents the first fully automated system for accurate variant interpretation for HTAAD. The framework of HTAADVar could also be generalized for the molecular diagnosis of other genetic diseases.

CHDbase: A comprehensive knowledgebase for congenital heart disease-related genes and clinical manifestations

Congenital heart disease (CHD) is one of themost common causes of major birth defects, with a prevalence of 1%. Although an increasing number of studies reported the etiology of CHD, the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical practice. We therefore developed CHDbase, an evidence-based knowledgebase of CHD-related genes and clinical manifestations manually curated from 1114 publications, linking 1124susceptibility genes and 3591 variations to more than 300 CHD types and related syndromes. Metadata such as the information of each publication and the selected population and samples, the strategy of studies, and the major findings of studies were integrated with each item of the research record. We also integrated functional annotations through parsing ∼50 databases/tools to facilitate the interpretation of these genes and variations in disease pathogenicity. We further prioritized the significance of these CHD-related genes with a gene interaction network approach and extracted a core CHD sub-network with 163 genes. The clear genetic landscape of CHD enables the phenotype classification based on the shared genetic origin. Overall, CHDbase provides a comprehensive and freely available resource to study CHD susceptibility, supporting a wide range of users in the scientific and medical communities. CHDbase is accessible at http://chddb.fwgenetics.org.

[Preconception reproductive health and birth outcome cohort in Chongqing: the cohort profile]

Birth cohort is an important platform to study the effect of early-life exposure on health outcome, but large cohorts to investigate the effect of preconception exposure, especially paternal exposure, on reproductive health and birth outcome are limited. The Preconception Reproductive Health and Birth Outcome Cohort (PREBIC) is a prospective birth cohort study which pays equal attention to the contribution of environmental, psychological, behavioral as well as other factors to reproductive health and adverse birth outcomes in both men and women in Chongqing, China. PREBIC started in 2019 and plans to recruit 20 800 reproductive-age couples with child-bearing willingness. Followed up was conducted to understand the conception status of the women within two years. Women in pregnancy would be visited at first, second, third trimesters and after delivery. The offspring would be monitored until 2 years old to understand the incidences of preterm birth, low birth weight, birth defects, neurodevelopmental disorders and other outcomes. Related information and biospecimen collections (including semen, peripheral blood, urine, placenta, umbilical cord, cord blood and oral swab) were scheduled in each period. By January 2022, PREBIC had recruited 8 698 participants from all 38 districts in Chongqing. The goal of PREBIC is to establish one of the largest prospective preconception birth cohorts covering both men and women, which might provide a unique insight to understand the effects of the full reproductive cycle on reproductive health and adverse outcomes, with especial emphasis on preconception exposures.

Association of PLXND1 with a novel subtype of anomalous pulmonary venous return

Anomalous pulmonary venous return (APVR) is a potentially lethal congenital heart disease. Elucidating the genetic etiology is crucial for understanding its pathogenesis and improving clinical practice, while its genetic basis remains largely unknown due to complex genetic etiology. We thus performed whole-exome sequencing for 144 APVR patients and 1636 healthy controls and report a comprehensive atlas of APVR-related rare genetic variants. Novel singleton, loss-of-function and deleterious missense variants (DVars) were enriched in patients, particularly for genes highly-expressed in the developing human heart at the critical time point for pulmonary veins draining into the left atrium. Notably, PLXND1, encoding a receptor for semaphorins, represents a strong candidate gene of APVR (adjusted P = 1.1e-03, OR: 10.9-69.3), accounting for 4.17% of APVR. We further validated this finding in an independent cohort consisting of 82 case-control pairs. In these two cohorts, eight DVars were identified in different patients, which convergently disrupt the GTPase-activating protein-related domain of PLXND1. All variant carriers displayed strikingly similar clinical features, in that all anomalous drainage of pulmonary vein(s) occurred on the right side and incorrectly connected to the right atrium, may representing a novel subtype of APVR for molecular diagnosis. Studies in Plxnd1 knockout mice further revealed the effects of PLXND1 deficiency on severe heart and lung defects and cellular abnormalities related to APVR such as abnormal migration and vascular formation of vascular endothelial cells. These findings indicate the important role of PLXND1 in APVR pathogenesis, providing novel insights into the genetic etiology and molecular subtyping for APVR.

Directly quantified abdominal subcutaneous adipose tissue volume is negatively associated with subclinical coronary artery disease in men with psoriasis

Background

Psoriasis is a common chronic inflammatory condition associated with an increased risk of obesity and higher coronary atherosclerosis burden by coronary computed tomography angiography (CCTA). Prior studies have shown that the ability to expand subcutaneous adipose tissue (SAT) may serve to identify individuals at a lower risk of atherosclerotic cardiovascular disease. However, the relationship between abdominal SAT and high-risk subclinical coronary artery disease requires exploration.

Purpose

To characterize the relationship between abdominal SAT volume measured on low-dose computed tomography, and coronary artery disease assessed as noncalcified and lipid-rich necrotic core burden by CCTA in psoriasis.

Methods

We performed a cross-sectional study of 232 participants with psoriasis and without known cardiovascular disease. All participants underwent CCTA to characterize coronary artery disease burden and low dose abdominal computed tomography to quantify subcutaneous adipose tissue volumes. Fat depot volumes were first adjusted in a sex specific manner for each participant's body mass index in a linear regression model. The residual values from the sex stratified linear regression models were used for analyses. Coronary artery disease burden was quantified in the three main coronary arteries (QAngio, Medis, The Netherlands) and averaged. Analyses were performed with StataIC 16 (Stata Corp., College Station, TX, USA).

Results

Of the 232 participants, 92 (40%) were women and the average age was 50 years. In women, there was a positive correlation between abdominal SAT and systemic inflammation as assessed by hs-CRP (r=0.30; p=0.004) and GlycA (r=0.29; p=0.007) as well as total cholesterol (r=0.24; p=0.02) and LDL cholesterol (r=0.22; p=0.04). In men, abdominal SAT correlated with hs-CRP (r=0.18; p=0.04) and insulin resistance as assessed by the homeostatic model for insulin resistance (r=0.17; p=0.04). In models fully adjusted for traditional cardiovascular risk factors, abdominal SAT volume negatively associated with noncalcified and lipid-rich necrotic core burden in men (β=−0.17; p=0.03, β=−0.21; p=0.02, respectively), but not women (β=−0.04; p=0.72, β=0.05; p=0.68, respectively) with psoriasis (Table).

Conclusions

In psoriasis, for a given body mass index, abdominal SAT negatively associated with coronary atherosclerosis burden in men. The observed sex-specific effects on subclinical coronary artery disease warrant further study of abdominal SAT in states of chronic inflammation.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Heart, Lung and Blood Institute Intramural Research Program in Bethesda, Maryland

[The distribution of peripheral anterior synechiae in patients with primary angle-closure glaucoma]

Objective: To describe the distribution and characteristics of peripheral anterior synechiae (PAS) in patients with primary angle-closure glaucoma (PACG). Methods: Retrospective case study. A total of 285 PACG patients (406 eyes) diagnosed in the Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University from January 2017 to August 2019 were included. They were 102 males and 183 females, with a median age of 67 years old (range, 21 to 95 years old). The PAS range was detected by gonioscopy examination, and the frequency distribution of PAS at 12 clock points was counted by clockwise. The PAS distribution at the middle point of PAS with continuous distribution and ≤6 clock points was assessed. Results: In all cases, PAS of the right eye was concentrated at 11:00 to 4:00 regions [range, 62.0% (129/208) to 78.8% (164/208)]. PAS of the left eye was concentrated at 7:00 to 1:00 regions [range, 50.0% (99/198) to 75.8% (150/198)]. When the PAS range of the atrial angle was ≤6 clock regions, it was mainly at 12:00 to 3:00 [range, 58.3% (74/127) to 67.7% (86/127)] in the right eye and at 10:00 to 12:00 [range, 54.8% (68/124) to 66.1% (82/124)] in the left eye. Among 121 cases (242 eyes) with both eyes involved, the PAS region was at 11:00 to 5:00 [range, 52.1% (63/121) to 79.3% (96/121)] in the right eye and at 8:00 to 1:00 [range, 50.4% (61/121) to 76.9% (93/121)] in the left eye. When the PAS range of the atrial angle was ≤6 clock regions, it was mainly at 12:00 to 4:00 [range, 53.2% (41/77) to 71.4% (55/77)] in the right eye and at 10:00 to 12:00 [range, 50.6% (39/77) to 64.9% (50/77)] in the left eye. In all cases, there were 171 cases of right eyes and 175 cases of left eyes with continuous angle PAS. The central PAS clock position of the right eye was mainly at 11:00 to 3:00 [range, 15.2% (26/171) to 24.0% (41/171)], and that of the left eye was mainly at 8:00 to 12:00 [range, 15.4% (27/175) to 20.6% (36/175)]. Among cases with both eyes involved, there were 98 cases of right eyes and 104 cases of left eyes with continuous angle PAS. The clock distribution of the middle position of the right eye angle PAS was concentrated at 11:00 to 3:00 [range, 17.3% (17/98) to 26.5% (26/98)], and that of the left eye was concentrated at 8:00 to 12:00 [range, 13.5% (14/104) to 20.2% (21/104)]. Conclusions: The PAS of PACG patients is mainly located in the upper and nasal sides, and the closer to the temporal side, the smaller the PAS frequency, showing a gradual downward trend. The PAS distribution of binocular angles is of obvious mirror symmetry. (Chin J Ophthalmol, 2021, 57: 666-671).

Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure

Rhesus macaque is a unique nonhuman primate model for human evolutionary and translational study, but the error-prone gene models critically limit its applications. Here, we de novo defined full-length macaque gene models based on single molecule, long-read transcriptome sequencing in four macaque tissues (frontal cortex, cerebellum, heart and testis). Overall, 8 588 227 poly(A)-bearing complementary DNA reads with a mean length of 14 106 nt were generated to compile the backbone of macaque transcripts, with the fine-scale structures further refined by RNA sequencing and cap analysis gene expression sequencing data. In total, 51 605 macaque gene models were accurately defined, covering 89.7% of macaque or 75.7% of human orthologous genes. Based on the full-length gene models, we performed a human–macaque comparative analysis on polyadenylation (PA) regulation. Using macaque and mouse as outgroup species, we identified 79 distal PA events newly originated in humans and found that the strengthening of the distal PA sites, rather than the weakening of the proximal sites, predominantly contributes to the origination of these human-specific isoforms. Notably, these isoforms are selectively constrained in general and contribute to the temporospatially specific reduction of gene expression, through the tinkering of previously existed mechanisms of nuclear retention and microRNA (miRNA) regulation. Overall, the protocol and resource highlight the application of bioinformatics in integrating multilayer genomics data to provide an intact reference for model animal studies, and the isoform switching detected may constitute a hitherto underestimated regulatory layer in shaping the human-specific transcriptome and phenotypic changes.

Targeted resequencing of 358 candidate genes for autism spectrum disorder in a Chinese cohort reveals diagnostic potential and genotype-phenotype correlations

Autism spectrum disorder (ASD) is a childhood neuropsychiatric disorder with a complex genetic architecture. The diagnostic potential of a targeted panel of ASD genes has only been evaluated in small cohorts to date and is especially understudied in the Chinese population. Here, we designed a capture panel with 358 genes (111 syndromic and 247 nonsyndromic) for ASD and sequenced a Chinese cohort of 539 cases evaluated with the Autism Diagnostic Interview‐Revised (ADI‐R) and the Autism Diagnostic Observation Schedule (ADOS) as well as 512 controls. ASD cases were found to carry significantly more ultra‐rare functional variants than controls. A subset of 78 syndromic and 54 nonsyndromic genes was the most significantly associated and should be given high priority in the future screening of ASD patients. Pathogenic and likely pathogenic variants were detected in 9.5% of cases. Variants in SHANK3 and SHANK2 were the most frequent, especially in females, and occurred in 1.2% of cases. Duplications of 15q11–13 were detected in 0.8% of cases. Variants in CNTNAP2 and MEF2C were correlated with epilepsy/tics in cases. Our findings reveal the diagnostic potential of ASD genetic panel testing and new insights regarding the variant spectrum. Genotype–phenotype correlations may facilitate the diagnosis and management of ASD.

AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with strong genetic contributions. To provide a comprehensive resource for the genetic evidence of ASD, we have updated the Autism KnowledgeBase (AutismKB) to version 2.0. AutismKB 2.0 integrates multiscale genetic data on 1379 genes, 5420 copy number variations and structural variations, 11 669 single-nucleotide variations or small insertions/deletions (SNVs/indels) and 172 linkage regions. In particular, AutismKB 2.0 highlights 5669 de novo SNVs/indels due to their significant contribution to ASD genetics and includes 789 mosaic variants due to their recently discovered contributions to ASD pathogenesis. The genes and variants are annotated extensively with genetic evidence and clinical evidence. To help users fully understand the functional consequences of SNVs and small indels, we provided comprehensive predictions of pathogenicity with iFish, SIFT, Polyphen etc. To improve user experiences, the new version incorporates multiple query methods, including simple query, advanced query and batch query. It also functionally integrates two analytical tools to help users perform downstream analyses, including a gene ranking tool and an enrichment analysis tool, KOBAS. AutismKB 2.0 is freely available and can be a valuable resource for researchers.

Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates

While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts.

Although gene duplication has been believed as a predominant mechanism for creating new genes, recent reports suggested that new proteins could evolve “de novo” from non-coding DNA regions. These de novo genes are also named as “motherless” genes due to their lack of ancestral proteins as precursors, while recently we and others found that lncRNAs may represent an intermediate stage of their origination. To further elucidate this lncRNA-protein transition process, here we identified 64 hominoid-specific de novo genes and report a new mechanism for the origination of functional de novo proteins from ancestral non-coding transcripts: These non-coding “precursors” are generally not more selectively constrained than other lncRNA loci; and the existence of these de novo proteins is not beyond anticipation under neutral expectation; however, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution.

Statistical analysis of twenty years (1993 to 2012) of data from mainland China's first intervention center for children with autism spectrum disorder

BACKGROUND

Autism spectrum disorder (ASD) is characterized by persistent deficits in social communication and interaction, and restrictive and repetitive patterns of behavior, interests or activities. This study aimed to analyze trends in ASD diagnosis and intervention in 20 years of data from the Beijing Stars and Rain Education Institute for Autism (SR), the first autism intervention center in mainland China, and from a recent survey of members of the Heart Alliance, an industry association of autism intervention centers in China.

METHODS

We analyzed the registration data at the SR from 1993 to 2012 for a total of 2,222 children who had a parent-reported diagnosis of ASD and 612 of 'autistic tendencies'. Most of the children who were the primary focus of our analyses were age six and under. We also analyzed results of a survey we conducted in 2013 of 100 member centers of the Heart Alliance. Generalized Estimating Equations, multiple linear regression and the Mann-Whitney test were used for data analysis. Statistically significant findings are reported here.

RESULTS

The number of hospitals where SR children received their diagnosis increased from several in the early 1990s to 276 at present. The proportion of 'autistic tendencies' diagnosis increased 2.04-fold from 1998 to 2012 and was higher for children diagnosed at a younger age. The mean age at first diagnosis of ASD or 'autistic tendencies' decreased by 0.27 years every decade. A higher level of parental education was statistically significantly associated with an earlier diagnosis of the child. The mean parental age at childbirth increased by about 1.48 years per decade, and the mean maternal age was 1.40 and 2.10 years higher than that in the national population censuses of 2000 and 2010, respectively. At the time of the survey 3,957 children with ASD were being trained at the 100 autism intervention centers. Ninety-seven of these centers opened after the year 2000. Economically underdeveloped regions are still underserved.

CONCLUSIONS

This study revealed encouraging trends and remaining challenges in ASD diagnosis and intervention among children at the SR over the past 20 years and the 100 autism intervention centers in China at present.

Semiconducting quantum confined silicon-tin alloyed nanocrystals prepared by ns pulsed laser ablation in water

Here we demonstrate the material's synthetic feasibility for semiconducting alloyed silicon-tin nanocrystals (SiSn-NCs) with quantum confinement effects. An environmentally friendly synthesis is achieved by ns laser ablation of amorphous SiSn in water at ambient conditions. Plasmas generated in the liquid by laser pulses are characterized by spatial confinement with very high pressure (GPa), which allowed the growth of the SiSn-NCs via kinetic pathways. We further illustrate that surface engineering by a direct-current atmospheric pressure microplasma is capable of tailoring the SiSn-NCs surface properties without the need for lengthy surfactants, resulting in room temperature photoluminescence (PL); the PL peak wavelength is red-shifted by more than 250 nm with respect to the PL peak wavelengths observed for comparable elemental silicon nanocrystals.

Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs

Tinkering with pre-existing genes has long been known as a major way to create new genes. Recently, however, motherless protein-coding genes have been found to have emerged de novo from ancestral non-coding DNAs. How these genes originated is not well addressed to date. Here we identified 24 hominoid-specific de novo protein-coding genes with precise origination timing in vertebrate phylogeny. Strand-specific RNA–Seq analyses were performed in five rhesus macaque tissues (liver, prefrontal cortex, skeletal muscle, adipose, and testis), which were then integrated with public transcriptome data from human, chimpanzee, and rhesus macaque. On the basis of comparing the RNA expression profiles in the three species, we found that most of the hominoid-specific de novo protein-coding genes encoded polyadenylated non-coding RNAs in rhesus macaque or chimpanzee with a similar transcript structure and correlated tissue expression profile. According to the rule of parsimony, the majority of these hominoid-specific de novo protein-coding genes appear to have acquired a regulated transcript structure and expression profile before acquiring coding potential. Interestingly, although the expression profile was largely correlated, the coding genes in human often showed higher transcriptional abundance than their non-coding counterparts in rhesus macaque. The major findings we report in this manuscript are robust and insensitive to the parameters used in the identification and analysis of de novo genes. Our results suggest that at least a portion of long non-coding RNAs, especially those with active and regulated transcription, may serve as a birth pool for protein-coding genes, which are then further optimized at the transcriptional level.

Ever since the pre-genomic era, people believed that “mother gene”-based mechanisms such as gene duplication were the major means of creating new genes. Recently, we and others reported several “motherless” protein-coding genes in human, challenging the conventional idea in that some protein-coding genes might have emerged de novo from ancestral non-coding DNAs. However, how these interesting proteins originated is a question that remained unaddressed. The ancestral non-coding DNA must become transcribed and gain a translatable open reading frame before becoming a protein-coding gene, but either order of these two steps is possible. Here, we performed a comparative transcriptome study in human, chimpanzee, and rhesus macaque to address these fundamental questions. We found that most of the hominoid-specific de novo protein-coding genes encoded long non-coding RNAs in rhesus macaque or chimpanzee, with similar transcript structure and correlated tissue expression profile, but the protein-coding genes often had higher transcriptional abundance. According to the rule of parsimony, we conclude that at least a portion of long non-coding RNAs, especially those with active and regulated transcription, may serve as a birth pool for protein-coding genes that are then further optimized at the transcriptional level, a pattern insensitive to the parameters used in the identification and analysis of de novo genes.

RhesusBase: a knowledgebase for the monkey research community

Although the rhesus macaque is a unique model for the translational study of human diseases, currently its use in biomedical research is still in its infant stage due to error-prone gene structures and limited annotations. Here, we present RhesusBase for the monkey research community (http://www.rhesusbase.org). We performed strand-specific RNA-Seq studies in 10 macaque tissues and generated 1.2 billion 90-bp paired-end reads, covering >97.4% of the putative exon in macaque transcripts annotated by Ensembl. We found that at least 28.7% of the macaque transcripts were previously mis-annotated, mainly due to incorrect exon–intron boundaries, incomplete untranslated regions (UTRs) and missed exons. Compared with the previous gene models, the revised transcripts show clearer sequence motifs near splicing junctions and the end of UTRs, as well as cleaner patterns of exon–intron distribution for expression tags and cross-species conservation scores. Strikingly, 1292 exon–intron boundary revisions between coding exons corrected the previously mis-annotated open reading frames. The revised gene models were experimentally verified in randomly selected cases. We further integrated functional genomics annotations from >60 categories of public and in-house resources and developed an online accessible database. User-friendly interfaces were developed to update, retrieve, visualize and download the RhesusBase meta-data, providing a ‘one-stop’ resource for the monkey research community.

Meta-analysis and genome-wide interpretation of genetic susceptibility to drug addiction

Background

Classical genetic studies provide strong evidence for heritable contributions to susceptibility to developing dependence on addictive substances. Candidate gene and genome-wide association studies (GWAS) have sought genes, chromosomal regions and allelic variants likely to contribute to susceptibility to drug addiction.

Results

Here, we performed a meta-analysis of addiction candidate gene association studies and GWAS to investigate possible functional mechanisms associated with addiction susceptibility. From meta-data retrieved from 212 publications on candidate gene association studies and 5 GWAS reports, we linked a total of 843 haplotypes to addiction susceptibility. We mapped the SNPs in these haplotypes to functional and regulatory elements in the genome and estimated the magnitude of the contributions of different molecular mechanisms to their effects on addiction susceptibility. In addition to SNPs in coding regions, these data suggest that haplotypes in gene regulatory regions may also contribute to addiction susceptibility. When we compared the lists of genes identified by association studies and those identified by molecular biological studies of drug-regulated genes, we observed significantly higher participation in the same gene interaction networks than expected by chance, despite little overlap between the two gene lists.

Conclusions

These results appear to offer new insights into the genetic factors underlying drug addiction.

Enhancement of antibacterial activity of tilmicosin against Staphylococcus aureus by solid lipid nanoparticles in vitro and in vivo

This study aimed to enhance the antibacterial activity of tilmicosin by solid lipid nanoparticles (SLN). Tilmicosin-loaded hydrogenated castor oil (HCO)-SLN was prepared using a hot homogenisation and ultrasonication method. The physicochemical characteristics of SLN were investigated by scanning electron microscopy (SEM) and photon correlation spectroscopy (PCS). The antibacterial activity of tilmicosin-SLN against Staphylococcus aureus was evaluated by growth inhibition and colony-counting method. A therapeutic study of tilmicosin-SLN was conducted by subcutaneous injection in a mouse mastitis model infected with S. aureus by teat canal infusion. Therapeutic efficacy was assessed by physical appearance of the mammary gland and measurement of colony-forming units (CFU) per gland. The results showed that the diameter, polydispersivity index, zeta potential, encapsulation efficiency and loading capacity of the nanoparticles were 343±26 nm, 0.33±0.08, -7.9±0.4 mV, 60.4±3.3% and 11.2±0.47%, respectively. Tilmicosin-SLN showed a sustained-release effect and sustained and enhanced antibacterial activity in vitro. SLN significantly enhanced the therapeutic efficacy of tilmicosin determined by lower CFU counts and a decreased degree of inflammation. These results demonstrated that the HCO-SLN is an effective carrier to enhance the antibacterial activity of tilmicosin.

Prophylactic effect of glyceryl trinitrate on post-endoscopic retrograde cholangiopancreatography pancreatitis: A randomized placebo-controlled trial

AIM: To examine the prophylactic effect of glyceryl trinitrate on post-endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis and hyperamylasemia.

METHODS: Patients scheduled for ERCP were randomly divided into study group and placebo group. Patients in study group and placebo group were treated with 5 mg glyceryl trinitrate and 100 mg vitamin C, respectively, 5 min before endoscopic maneuvers.

RESULTS: A total of 74 patients were enrolled in the final analysis. Post-ERCP pancreatitis occurred in 3 patients (7.9%) of the study group and 9 patients (25%) in the placebo group (P = 0.012). Hyperamylasemia occurred in 8 patients of the study group (21.1%) and 13 patients (36.1%) of the placebo group (P = 0.037).

CONCLUSION: Glyceryl trinitrate before ERCP can effectively prevent post-ERCP and hyperamylasemia.

Flocculation behavior and mechanism of an exopolysaccharide from the deep-sea psychrophilic bacterium Pseudoalteromonas sp. SM9913

Flocculation behavior and mechanism of the exopolysaccharide secreted by Pseudoalteromonas sp. SM9913 (EPS SM9913), a psychrophilic bacterium isolated from 1855m deep-sea sediment, has been studied in this paper. EPS SM9913 showed a peak flocculating activity of 49.3 in 1g/L kaolin suspension with 4.55mmol/L CaCl2 and the optimum pH range of 5-8. It appears that the flocculating activity of EPS SM9913 was stimulated by Ca2+ and Fe2+. This study found that EPS SM9913 showed a better flocculation performance than Al2(SO4)3 at salinity of 5-100 per thousand or temperatures of 5-15 degrees C. In addition, this EPS was effective to flocculate several other suspended solids. The measured zeta-potentials, the size of flocs formed during the flocculation process and the surface profile of flocs revealed by scan electron micrograph suggest that bridging is the main flocculation mechanism of the studied EPS. Deacetylation of EPS SM9913 resulted in a significant decrease in its flocculating activity indicating that the large number of acetyl groups in EPS SM9913 played an important role in its flocculation performance.

Color removal from textile industry wastewater using composite flocculants

In this study, the decolorization of textile wastewater using composite flocculants was examined. It was composed of Fe(III) flocculants and polydimethyldiallylammonium chloride (PDMDAAC). The color removal efficiency of the composite flocculants was compared with that of individual flocculants, ferric chloride (FeCl3), polyferric chloride (PFC) and PDMDAAC, respectively. The results showed that the composite flocculants were more efficient than individual ones in color removal. The color removal efficiency of the composite flocculants was found to be related to the weight percentage of PDMDAAC (Wp), basicity (B) of PFC and molecular weight (MW) of PDMDAAC. The removal rate is higher at a larger Wp and MW value and lower B value. Chemical oxygen demand (COD) removal from textile wastewater was also investigated in this study. During color removal by the composite flocculants, only up to 20% COD could be removed from the textile wastewater. FeCl3 was then used to further remove the remaining COD from the decolorized wastewater. This two-step treatment of textile wastewater could achieve a 91.6% reduction in COD and an 88.9% reduction in color.

Formation mechanism of H2Ti3O7 nanotubes

Formation mechanism of H2Ti3O7 nanotubes by single-step reaction of crystalline TiO2 and NaOH has been investigated via transmission electron microscopy examinations of series specimens with different reaction times and extensive ab initio calculations. It was found that the growth mechanism includes several steps. Crystalline TiO2 reacts with NaOH, forming a highly disordered phase, which recrystallized into some H2Ti3O7 thin plates. H-deficiency on the top surface leads to an asymmetrical environment for the surface Ti3O2-7 layer. The calculations of the surface tension, elastic strain energy, interlayer coupling energy, and Coulomb force indicated that the asymmetrical environment is the principal driving force of the cleavage of the single sheets of H2Ti3O7 from the plates and the formation of the multiwall spiral nanotubes.

Enhancement of transgene expression by cotransfection of oriP plasmid with EBNA-1 expression vector

We have attempted to develop a system for specific enhancement of transgene expression, which has been one of the most important issues in human gene therapy. When an Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA-1) expression vector, pCMV-trEBNA-1, was cotransfected with an origin of latent viral DNA replication (oriP)-harboring plasmid, poriP-CMV-luciferase, luciferase gene expression was up to 20 times greater than in the absence of EBNA-1. This enhancement was regulated mainly at the transcriptional level and was dependent on the oriP sequence and the amount of EBNA-1. However, cointroduction of poriP-CMV-luciferase with purified recombinant EBNA-1 inhibited luciferase gene expression whereas no inhibition was observed when pCMV-luciferase was cointroduced with recombinant EBNA-1. We also introduced poriP-CMV-luciferase into mouse liver via the use of HVJ (hemagglutinating virus of Japan)-liposomes. By 10 days after transfer, luciferase gene expression was decreased to low levels. We then introduced pCMV-trEBNA-1 to mouse liver via HVJ-liposomes on day 10. Luciferase gene expression was reactivated, whereas no reactivation was detected by the injection of EBNA-1 expression plasmid into liver injected with pCMV-luciferase lacking the oriP sequence. Thus, cotransfection of oriP-harboring expression vector with EBNA-1 expression plasmid should be promising for human gene therapy, although the safety of the system must be investigated thoroughly.

RNA melanoma vaccine: induction of antitumor immunity by human glycoprotein 100 mRNA immunization

An RNA melanoma vaccine was investigated to induce protective immunity in a mouse-melanoma model. LacZ mRNA was synthesized in vitro by pSFV3 expression vector and introduced into the spleen of mice, using HVJ-liposomes. A high level of beta-galactosidase activity was detected for 10 days in mouse spleen. The human melanoma-associated antigen gp100 mRNA was synthesized in vitro by pSFV3 vector and encapsulated in HVJ-liposomes. Immunization by direct injection of the gp100 mRNA HVJ-liposomes into mouse spleen induced both anti-gp100 Ab and CTL responses against B16 melanoma. Immunization by administration of gp100 mRNA into the spleen delayed tumor growth and significantly prolonged survival compared with control treated mice. These preclinical studies demonstrate that an RNA tumor antigen vaccine strategy has potential application for human cancer treatment and prevention.

Protective immunization against melanoma by gp100 DNA-HVJ-liposome vaccine

DNA-based vaccine immunization effectively induces both humoral and cell-mediated immunity to antigens and can confer protection against numerous infectious diseases as well as some cancers. Human and mouse melanomas consistently express the tumor-associated antigen interacted with the melanogenesis pathway. Gp100 is immunogenic and has been shown to induce both antibody and cytotoxic T cell (CTL) responses in humans. To explore the potential use of DNA immunization to induce melanoma-specific immune responses, we assessed HVJ-AVE liposome incorporated with plasmid DNA encoding human gp100. The gp100 DNA vaccine was used in a mouse melanoma model to assess immunity against the B16 melanoma of C57BL/6 mice. Intramuscular injection of the DNA-HVJ-AVE liposomes induced both anti-gp100 antibody and CTL responses. Gp100 DNA-HVJ-AVE liposome immunization significantly delayed tumor development in mice challenged with B16 melanoma cells. Mice immunized with gp100 DNA-HVJ-AVE liposomes survived longer compared with control mice immunized with HVJ-AVE liposome alone. These results indicate that immunization with human gp100 DNA by HVJ-AVE liposomes can induce protective immunity against melanoma in this pre-clinical mouse model. This strategy may provide an effective approach for vaccine therapy with tumor-associated antigens against human melanoma.

[Efficacy and side effects following immunization with Salmonella typhi Vi capsular polysaccharide vaccine]

Efficacy and side effects following the immunization with Salmonella typhi Vi capsular polysaccharide vaccine (Vi) were assessed. The diluted solution (DS) of Vi was used as placebo. A total number of 777 children and adults were observed for side effect response. Mild and moderate fever appeared 16.93% and 0.05% in Vi group, 15.01% and 0.03% in DS group, respectively (statistically significant). Two cases with mild local reaction were observed in Vi group. A total number of 81,506 vaccinees were investigated on the efficacy of Vi vaccine, using positive blood culture of Salmonolla typhi as a diagnostic criterion. The protective rate and index of vaccine were 71.35% and 3.49% respectively. If 2 cases of positive Widal's test were included in, the protective rate would come up to 78.17% with a protective index 4.85. Clinical data showed that fever seen in the cases in Vi group was much lower than that of DS group. The systematic and local reaction of Vi vaccine were mild. The vaccine is safe and has high protective rate. It can also decrease the degree of fever with only one single dose as primary immunization. We believe Vi vaccine may serve as a vaccine of new generation to be promoted.

[Glomerulonephropathy associated with hepatitis B virus (HBV) infection]

Forty-seven renal biopsies of glomerulonephropathy with persistent Australian antigenaemia (HBsAg is mostly positive) were studied with light microscope, electron microscope and direct immunofluorescence. Immunohistochemical method (ABC method) was used to examine HBsAg, HBeAg and HBcAg deposits in renal tissue. In addition 20 cases of idiopathic membranous nephropathy (MN) were studied for comparison. These 47 cases included 19 children and 28 adults. The results indicated that Australian antigens diffusely deposited in glomeruli in 14 cases (29.7%), with HBsAg in 7 cases (50.0%), HBeAg in 13 cases (92.8%) and HBcAg in 2 cases (14.3%). The 14 positive cases included 11 children and 3 adults. The pathologic types were membranous nephropathy in 12 and membranoproliferative glomerulonephritis in 2 cases. The membranous type was characterized by irregular thickening of capillary wall and double contour, bubble-like appearance and spike formation of glomerular basement membrane (GBM); immune complexes and electron dense deposits may be present in different sites of glomeruli. Coarse granular deposits of IgG and C3 along GBM were the principal pattern, but IgA, IgM and C1q were often present. Among the 20 idiopathic MN, 2 were found to have HBeAg deposition along GBM, one was a child and the other an adult IgG, IgA, IgM, C3 and C1q with HBeAg deposits were present in glomeruli.