Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events

Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis-regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis-regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression.

A region of suppressed recombination misleads neoavian phylogenomics

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.

Complexity of avian evolution revealed by family-level genomes

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)

BACKGROUND

Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary.

RESULTS

Here we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression.

CONCLUSIONS

Collectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.

[Epidemiological characteristics of a local cluster epidemic caused by the BA.2 evolutionary branch of Omicron variant]

Descriptive epidemiological methods were used to analyze the epidemiological characteristics of the local cluster of COVID-19 in the logistic park of Yuhang District in Hangzhou in March 2022. The cluster epidemic was detected by a case who actively visited the fever clinic. The epidemic lasted for 8 days, and a total of 58 cases (53 workers, 2 students, 1 farmer, 1 teacher and 1 unemployed) were found, including 40 males and 18 females. The age was (33.29±12.22) years. There cases were mainly in Yuhang District (48 cases, 82.77%) and Shangcheng District (7 cases, 12.07%) of Hangzhou. The real-time regeneration number peaked at 2.31 on March 10th and decreased to 0.37 on March 15th. The sequencing result of the indicated case was 100% homologous with the sequence uploaded from South Korea on March 4th, 2022.

[Clinical characteristics of epileptic seizure in neurofibromatosis type 1 in 15 cases]

Objective: To summarize the clinical characteristics of epileptic seizure associated with neurofibromatosis type 1 (NF1). Methods: From January 2017 to July 2023 at Children's Hospital Capital Institute of Pediatrics, medical records of patients with both NF1 and epileptic seizure were reviewed in this case series study. The clinical characteristics, treatment and prognosis were analyzed retrospectively. Results: A total of 15 patients(12 boys and 3 girls) were collected. Café-au-lait macules were observed in all 15 patients. There were 6 patients with neurodevelopmental disorders and the main manifestations were intellectual disability or developmental delay. The age at the first epileptic seizure was 2.5 (1.2, 5.5) years. There were various seizure types, including generalized tonic-clonic seizures in 8 patients, focal motor seizures in 6 patients, epileptic spasm in 4 patients, tonic seizures in 1 patient, absence in 1 patient, generalized myoclonic seizure in 1 patient and focal to bilateral tonic-clonic seizure in 1 patient. Among 14 patients whose brain magnetic resonance imaging results were available, there were abnormal signals in corpus callosum, basal ganglia, thalamus or cerebellum in 6 patients, dilated ventricles of different degrees in 3 patients, blurred gray and white matter boundary in 2 patients, agenesis of corpus callosum in 1 patient and no obvious abnormalities in the other patients. Among 13 epilepsy patients, 8 were seizure-free with 1 or 2 antiseizure medications(ASM), 1 with drug resistant epilepsy was seizure-free after left temporal lobectomy, and the other 4 patients who have received 2 to 9 ASM had persistent seizures. One patient with complex febrile convulsion achieved seizure freedom after oral administration of diazepam on demand. One patient had only 1 unprovoked epileptic seizure and did not have another seizure without taking any ASM. Conclusions: The first epileptic seizure in NF1 patients usually occurs in infancy and early childhood, with the main seizure type of generalized tonic-clonic seizure and focal motor seizure. Some patients have intellectual disability or developmental delay. Most epilepsy patients achieve seizure freedom with ASM.

Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction

High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.

Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data

The identification of microbial characteristics associated with diseases is crucial for disease diagnosis and therapy. However, the presence of heterogeneity, high dimensionality, and large amounts of microbial data presents tremendous challenges in discovering key microbial features. In this paper, we present IDAM, a novel computational method for inferring disease-associated gene modules from metagenomic and metatranscriptomic data. This method integrates gene context conservation (uber-operons) and regulatory mechanisms (gene co-expression patterns) within a mathematical graph model to explore gene modules associated with specific diseases. It alleviates reliance on prior meta-data. We applied IDAM to publicly available datasets from inflammatory bowel disease, melanoma, type 1 diabetes mellitus, and irritable bowel syndrome. The results demonstrated the superior performance of IDAM in inferring disease-associated characteristics compared to existing popular tools. Furthermore, we showcased the high reproducibility of the gene modules inferred by IDAM using independent cohorts with inflammatory bowel disease. We believe that IDAM can be a highly advantageous method for exploring disease-associated microbial characteristics. The source code of IDAM is freely available at https://github.com/OSU-BMBL/IDAM, and the web server can be accessed at https://bmblx.bmi.osumc.edu/idam/.

[A case of combined oxidative phosphorylation deficiency 32 caused by MRPS34 gene variation and literature review]

Objective: To investigate the clinical features and genetic features of combined oxidative phosphorylation deficiency 32 (COXPD32) caused by MRPS34 gene variation. Methods: The clinical data and genetic test of a child with COXPD32 hospitalized in the Department of Neurology, Children's Hospital, Capital Institute of Pediatrics in March 2021 were extracted and analyzed. A literature search was implemented using Wanfang, China biology medicine disc, China national knowledge infrastructure, ClinVar, human gene mutation database (HGMD) and Pubmed databases with the key words "MRPS34" "MRPS34 gene" and "combined oxidative phosphorylation deficiency 32" (up to February 2023). Clinical and genetic features of COXPD32 were summarized. Results: A boy aged 1 year and 9 months was admitted due to developmental delay. He showed mental and motor retardation, and was below the 3^rd percentile for height, weight, and head circumference of children of the same age and gender. He had poor eye contact, esotropia, flat nasal bridge, limbs hypotonia, holding instability and tremors. In addition, Grade Ⅲ/6 systolic murmur were heard at left sternal border. Arterial blood gases suggested that severe metabolic acidosis with lactic acidosis. Brain magnetic resonance imaging (MRI) showed multiple symmetrical abnormal signals in the bilateral thalamus, midbrain, pons and medulla oblongata. Echocardiography showed atrial septal defect. Genetic testing identified the patient as a compound heterozygous variation of MRPS34 gene, c.580C>T (p.Gln194Ter) and c.94C>T (p.Gln32Ter), with c.580C>T being the first report and a diagnosis of COXPD32. His parents carried a heterozygous variant, respectively. The child improved after treatment with energy support, acidosis correction, and "cocktail" therapy (vitaminB₁, vitaminB₂, vitaminB₆, vitaminC and coenzyme Q10). A total of 8 cases with COXPD32 were collected through 2 English literature reviews and this study. Among the 8 patients, 7 cases had onset during infancy and 1 was unknown, all had developmental delay or regression, 7 cases had feeding difficulty or dysphagia, followed by dystonia, lactic acidosis, ocular symptoms, microcephaly, constipation and dysmorphic facies(mild coarsening of facial features, small forehead, anterior hairline extending onto forehead,high and narrow palate, thick gums, short columella, and synophrys), 2 cases died of respiratory and circulatory failure, and 6 were still alive at the time of reporting, with an age range of 2 to 34 years. Blood and (or) cerebrospinal fluid lactate were elevated in all 8 patients. MRI in 7 cases manifested symmetrical abnormal signals in the brainstem, thalamus, and (or) basal ganglia. Urine organic acid test were all normal but 1 patient had alanine elevation. Five patients underwent respiratory chain enzyme activity testing, and all had varying degrees of enzyme activity reduction. Six variants were identified, 6 patients were homozygous variants, with c.322-10G>A was present in 4 patients from 2 families and 2 compound heterozygous variants. Conclusions: The clinical phenotype of COXPD32 is highly heterogenous and the severity of the disease varies from development delay, feeding difficulty, dystonia, high lactic acid, ocular symptoms and reduced mitochondrial respiratory chain enzyme activity in mild cases, which may survive into adulthood, to rapid death due to respiratory and circulatory failure in severe cases. COXPD32 needs to be considered in cases of unexplained acidosis, hyperlactatemia, feeding difficulties, development delay or regression, ocular symptoms, respiratory and circulatory failure, and symmetrical abnormal signals in the brainstem, thalamus, and (or) basal ganglia, and genetic testing can clarify the diagnosis.

Lineage-specific accelerated sequences underlying primate evolution

Understanding the mechanisms underlying phenotypic innovation is a key goal of comparative genomic studies. Here, we investigated the evolutionary landscape of lineage-specific accelerated regions (LinARs) across 49 primate species. Genomic comparison with dense taxa sampling of primate species significantly improved LinAR detection accuracy and revealed many novel human LinARs associated with brain development or disease. Our study also yielded detailed maps of LinARs in other primate lineages that may have influenced lineage-specific phenotypic innovation and adaptation. Functional experimentation identified gibbon LinARs, which could have participated in the developmental regulation of their unique limb structures, whereas some LinARs in the Colobinae were associated with metabolite detoxification which may have been adaptive in relation to their leaf-eating diet. Overall, our study broadens knowledge of the functional roles of LinARs in primate evolution.

Species-specific traits mediate avian demographic responses under past climate change

Anticipating species' responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking, and the traits that mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life history traits associated with changes in effective population size (N_e) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to ongoing climate warming.

Prediction of knee pain improvement over two years for knee osteoarthritis using a dynamic nomogram based on MRI-derived radiomics: a proof-of-concept study

OBJECTIVES

To develop and validate a nomogram to detect improved knee pain in osteoarthritis (OA) by integrating magnetic resonance imaging (MRI) radiomics signature of subchondral bone and clinical characteristics.

METHODS

Participants were selected from the Vitamin D Effects on Osteoarthritis (VIDEO) study. The primary outcome was 20% improvement of knee pain score over 2 years in participants administrated either vitamin D or placebo. Radiomics features of subchondral bone and clinical characteristics from 216 participants were extracted and analyzed. The participants were randomly split into the training and validation cohorts at a ratio of 8:2. Least absolute shrinkage and selection operator (LASSO) regression was used to select features and generate radiomics signatures. The optimal radiomics signature and clinical indicators were fitted into a nomogram using multivariable logistic regression model.

RESULTS

The nomogram showed favorable discrimination performance [AUC_training, 0.79 (95% CI: 0.72-0.79), AUC_validation, 0.83 (95% CI: 0.70-0.96)] as well as a good calibration. Additional contributing value of fusion radiomics signature to the nomogram was statistically significant (NRI, 0.23; IDI, 0.14, P < 0.001 in training cohort and NRI, 0.29; IDI, 0.18, P < 0.05 in validating cohort). Decision curve analysis confirmed the clinical usefulness of nomogram.

CONCLUSION

The radiomics-based nomogram comprising the MR radiomics signature and clinical variables achieves a favorable predictive efficacy and accuracy in differentiating improvement in knee pain among OA patients. This proof-of-concept study provides a promising way to predict clinically meaningful outcomes.

Polygamy and purifying selection in birds

Good genes theories of sexual selection predict that polygamy will be associated with more efficient removal of deleterious alleles (purifying selection), due to the alignment of sexual selection with natural selection. On the other hand, runaway selection theories expect no such alignment of natural and sexual selection, and may instead predict less efficient purifying selection in polygamous species due to higher reproductive variance. In an analysis of polymorphism data extracted from 150-bird genome assemblies, we show that polygamous species carry significantly fewer nonsynonymous polymorphisms, relative to synonymous polymorphisms, than monogamous bird species (p = .0005). We also show that this effect is independent of effective population size, consistent with the alignment of natural selection with sexual selection and "good genes" theories of sexual selection. Further analyses found no impact of polygamy on genetic diversity, while polygamy in females (polyandry) had a marginally significant impact (p = .045). We also recapitulate previous findings that smaller body mass and greater geographic range size are associated with more efficient purifying selection, more intense GC-biased gene conversion, and greater genetic diversity.

Draft genome assemblies of four manakins

Manakins are a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family has served as a good model for the study of sexual selection. Here we present genome assemblies of four manakin species, including Cryptopipo holochlora, Dixiphia pipra (also known as Pseudopipra pipra), Machaeropterus deliciosus and Masius chrysopterus, generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 29 Mb and contig N50 of 169 Kb. On average, 12,055 protein-coding genes were annotated in the genomes, and 9.79% of the genomes were annotated as repetitive elements. We further identified 75 Mb of Z-linked sequences in manakins, containing 585 to 751 genes and an ~600 Kb pseudoautosomal region (PAR). One notable finding from these Z-linked sequences is that a possible Z-to-autosome/PAR reversal could have occurred in M. chrysopterus. These de novo genomes will contribute to a deeper understanding of evolutionary history and sexual selection in manakins.

Measurement(s)	whole genome sequencing
Technology Type(s)	BGISEQ-500 Sequencing
Sample Characteristic - Organism	Pipridae

Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds

The rate of mutation accumulation in germline cells can be affected by cell replication and/or DNA damage, which are further related to life history traits such as generation time and body mass. Leveraging the existing datasets of 233 neoavian bird species, here, we investigated whether generation time and body mass contribute to the interspecific variation of orthologous microsatellite length, transposable element (TE) length, and deletion length and how these genomic attributes affect genome sizes. In nonpasserines, we found that generation time is correlated to both orthologous microsatellite length and TE length, and body mass is negatively correlated to DNA deletions. These patterns are less pronounced in passerines. In all species, we found that DNA deletions relate to genome size similarly as TE length, suggesting a role of body mass dynamics in genome evolution. Our results indicate that generation time and body mass shape the evolution of genomic attributes in neoavian birds.

Group B Streptococcus (GBS) colonisation is dynamic over time, whilst GBS capsular polysaccharides-specific antibody remains stable

Group B Streptococcus (GBS) is a leading cause of adverse pregnancy outcomes due to invasive infection. This study investigated longitudinal variation in GBS rectovaginal colonization, serum and vaginal GBS capsular polysaccharide (CPS)-specific antibody levels. Non-pregnant women were recruited in the UK and were sampled every 2 weeks over a 12-week period. GBS isolates were taken from recto-vaginal swabs and serotyped by polymerase chain reaction. Serum and vaginal immunoglobulin G (IgG) and nasal immunoglobulin A (IgA) specific to CPS were measured by Luminex, and total IgG/A by ELISA. Seventy women were enrolled, of median age 26. Out of the 66 participants who completed at least three visits: 14/47 (29.8%) women that were GBS negative at screening became positive in follow-up visits and 16/19 (84.2%) women who were GBS positive at screening became negative. There was 50% probability of becoming negative 36 days after the first positive swab. The rate of detectable GBS carriage fluctuated over time, although serum, vaginal, and nasal CPS-specific antibody levels remained constant. Levels of CPS-specific antibodies were higher in the serum of individuals colonized with GBS than in non-colonized, but similar in the vaginal and nasal mucosa. We found correlations between antibody levels in serum and the vaginal and nasal mucosa. Our study demonstrates the feasibility of elution methods to retrieve vaginal and nasal antibodies, and the optimization of immunoassays to measure GBS-CPS-specific antibodies. The difference between the dynamics of colonization and antibody response is interesting and further investigation is required for vaccine development.

Saturated hydraulic conductivity of compacted steel slag-bentonite mixtures--A potential hydraulic barrier material of landfill cover

The feasibility of using steel slag and bentonite mixtures to construct the hydraulic barrier of a landfill cover was explored in the present study. Fine-grained steel slag (SS; particle diameter < 1 mm) and sodium-activated calcium bentonite (SACB) were used to prepare compacted specimens, and the saturated hydraulic conductivity (k_s) was measured using a flexible-wall permeameter. Influential factors including SACB content (BC), SS gradation, water-washing treatment of SS and compaction water content (ω_comp) were investigated. The hydraulic conductivity results were interpreted in microscopic scale through mercury intrusion porosimetry (MIP) and scanning electron microscope (SEM). It was found that when BC was below 10%, the k_s value of the specimens prepared with well graded SS was about one order of magnitude lower than that of the specimens prepared with poorly graded SS. This was due to less macropores caused by better SS gradation. Yet, the effects of SS gradation on k_s diminished as BC further increased to 15%, suggesting the dominant role of BC on k_s at high BC. Water-washing treatment of SS helped reduce k_s significantly to 1.2 × 10^-10 m/s at BC of 10%, owing to less multivalent cations and hence lower osmotic swelling reduction caused by cations. Controlling ω_comp 1-2% wetter than the optimum water content (ω_opt) also helped reduce k_s significantly, owing to the reduction of macropores. Accordingly, it is suggested to use well-graded SS mixed with 10% SACB and then compact at ω_comp slightly wetter than ω_opt to the degree of compaction greater than 90% in engineering practice.

Incomplete lineage sorting and phenotypic evolution in marsupials

Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.

An improved ant colony algorithm based on artificial potential field and quantum evolution theory

The optimal evacuation route in emergency evacuation can further reduce casualties. Therefore, path planning is of great significance to emergency evacuation. Aiming at the blindness and relatively slow convergence speed of ant colony algorithm path planning search, an improved ant colony algorithm is proposed by combining artificial potential field and quantum evolution theory. On the one hand, the evacuation environment of pedestrians is modeled by the grid method. Use the potential field force in the artificial potential field, the influence coefficient of the potential field force heuristic information, and the distance between the person and the target position in the ant colony algorithm to construct comprehensive heuristic information. On the other hand, the introduction of quantum evolutionary theory. The pheromone is represented by quantum bits, and the pheromone is updated by quantum revolving door feedback control. In this way, it can not only reflect the high efficiency of quantum parallel computing, but also have the better optimization ability of ant colony algorithm. A large number of simulation experiments show that the improved ant colony algorithm has a faster convergence rate and is more effective in evacuation path planning.

A novel evacuation path planning method based on improved genetic algorithm

In order to solve the problem of finding the best evacuation route quickly and effectively, in the event of an accident, a novel evacuation route planning method is proposed based on Genetic Algorithm and Simulated Annealing algorithm in this paper. On the one hand, the simulated annealing algorithm is introduced and a simulated annealing genetic algorithm is proposed, which can effectively avoid the problem of the search process falling into the local optimal solution. On the other hand, an adaptive genetic operator is designed to achieve the purpose of maintaining population diversity. The adaptive genetic operator includes an adaptive crossover probability operator and an adaptive mutation probability operator. Finally, the path planning simulation verification is carried out for the genetic algorithm and the improved genetic algorithm. The simulation results show that the improved method has greatly improved the path planning distance and time compared with the traditional genetic algorithm.

[Clinical and prognostic study of anti-N-methyl-D-aspartate receptor encephalitis children with paroxysmal sympathetic hyperactivity syndrome]

The data of clinical characteristics, medical cost and prognosis of 22 anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis children from the Department of Neurology, Capital Institute of Pediatrics between May 2018 and January 2021 were analyzed, and 6 of them occurred paroxysmal sympathetic hyperactivity syndrome (PSH). It was found that the anti-NMDAR encephalitis children with PSH had severer consciousness disorder [median Glasgow Coma Scale (GCS) score at admission: 7.5], longer duration of consciousness disorder (median time: 53 days), higher hospitalization cost (median cost: 230 000 RMB), severer neurological injury at onset [median modified Rankin Scale (mRS) score at admission: 4], and longer recovery time of neurological function (median time of mRS score recovered to 0-2: 7 months), compared with those without PSH (all P<0.05). Therefore, more attention should be paid to sympathetic excited symptoms of anti NMDAR encephalitis, and thus identify and intervene early on PSH to reduce the neurological damage and economic burden.

Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos

The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.

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We generated two genomes from the likely extinct kouprey (Bos sauveli)

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Extensive mt and nuclear-genome-wide incomplete lineage sorting across wild Asian Bos

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Initial polytomic diversification of the wild Asian Bos—kouprey, banteng, and gaur

Comparable Number of Genes Having Experienced Positive Selection among Great Ape Species

Simple Summary

It is of great interest to quantify adaptive evolution in human lineage by studying genes under positive selection, since these genes could reveal insights into our own adaptive evolutionary history compared to our closely related species and often these genes are functionally important. We used the great apes as the subjects to detect gene-level adaptive evolution signals in all the great ape lineages and investigated the evolutionary patterns and functional relevance of these adaptive evolution signals. Even the differences in population size among these closely related great apes have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments, we found that they experienced comparable numbers of positive selection. Notably, we identified several genes that offer insights into great ape and human evolution. For example, SOD1, a gene associated with aging in humans, experienced positive selection in the common ancestor of the great ape and this positive selection may contribute to the aging evolution in great apes. Overall, an updated list of positively selected genes reported by this study not only informs us of adaptive evolution during great ape evolution, but is also helpful to the further study of non-human primate models for disease and other fields.

Abstract

Alleles that cause advantageous phenotypes with positive selection contribute to adaptive evolution. Investigations of positive selection in protein-coding genes rely on the accuracy of orthology, models, the quality of assemblies, and alignment. Here, based on the latest genome assemblies and gene annotations, we present a comparative analysis on positive selection in four great ape species and identify 211 high-confidence positively selected genes (PSGs). Even the differences in population size among these closely related great apes have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments, we found that they experienced comparable numbers of positive selection. We also uncovered that more than half of multigene families exhibited signals of positive selection, suggesting that imbalanced positive selection resulted in the functional divergence of duplicates. Moreover, at the expression level, although positive selection led to a more non-uniform pattern across tissues, the correlation between positive selection and expression patterns is diverse. Overall, this updated list of PSGs is of great significance for the further study of the phenotypic evolution in great apes.

Serum cholesterol efflux capacity is associated with coronary plaque progression in patients with coronary heart disease

Background

Coronary plaque progression is a major risk factor of adverse cardiac events in patients with coronary heart disease (CHD). Emerging evidence showed that attenuated high-density lipoprotein (HDL) function measured by cholesterol efflux capacity (CEC) was associated with development of atherosclerosis independent of HDL cholesterol level. In this study, we sought to investigate whether CEC is a predictor for coronary plaque progression in CHD patients.

Methods

We consecutively enrolled CHD patients from January 2017 to August 2019 in our Hospital who underwent elective percutaneous coronary intervention and had at least one non-target coronary lesion. Follow-up coronary angiography were performed at around 12 months. Fluorescence-labeled cholesterol and J774 macrophages were used to measure the CEC of ApoB-depleted serum sample from all patients. Quantitative coronary angiography (QCA) was performed both at baseline and follow-up to analyze the plaque progression.

Results

A total of 430 CHD patients with 586 non-target coronary lesions were included in the final analysis. During a mean follow-up time of 381.04±59.52 days, patients with decreased CEC presented more severe plaque progression (net luminal loss in highest to lowest CEC quartile: 0.22±0.42mm vs 0.20±0.41mm vs 0.13±0.36mm vs 0.11±0.34mm, p=0.035). In multivariate analysis, baseline CEC was independently associated with coronary plaque progression after adjustment for traditional risk factors including HDL cholesterol and ApoA-I, no matter treated as categorical variable (OR: 0.382 [95% CI 0.180–0.781] for highest to lowest quartile) or continuous variable (OR: 0.522 [95% CI 0.373–0.714] for per SD increase]. Furthermore, CEC demonstrated a better power in predicting coronary plaque progression compared with HDL cholesterol concentration (AUC=0.644 vs 0.514).

Conclusions

This study suggests that HDL function reflected by serum CEC is an independent predictor for coronary plaque progression in CHD patients.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Natural Science Foundation of China, Shanghai Municipal Commission of Health and Family Planning

[An optimized protocol of meniscus cell extraction for single-cell RNA sequencing]

OBJECTIVE

To optimize the protocol of meniscus cell extraction to enhance the efficiency of cell suspension preparation and maintain a high cell viability for single-cell RNA sequencing.

METHODS

We compared the efficiency of the routine cell extraction methods (short-time digestion and long-time digestion) and the optimized protocol for obtaining meniscus cell suspensions by evaluating the cell number obtained and the cell viability. Single-cell RNA sequencing datasets were analyzed to evaluate the stability of the cell suspension prepared using the optimized protocol. The reliability of the optimized protocol was assessed by comparing the single-cell RNA sequencing dataset obtained by the optimized protocol with published single-cell RNA sequencing datasets of the meniscus.

RESULTS

The optimized protocol harvested a greater number of cells (over 1×10⁵) than the routine protocols. The cell suspension prepared with the optimized protocol showed a cell viability higher than 80%, the highest among the 3 methods. Analysis of single-cell RNA sequencing datasets showed that the ratio of the mitochondrial genes was below 20% in over 80% of the cells. CD34⁺ cells, MCAM⁺ cells and COL1A1⁺ cells were identified in the datasets. Comparison with the publish datasets showed that the optimized protocol was capable of harvesting COL3A1⁺, COL1A1⁺, MYLK⁺, BMP2⁺, CD93⁺ and CDK1⁺ cells.

CONCLUSION

Single-cell suspension prepared from the meniscus can be stably obtained using the optimized protocol for single-cell RNA sequencing using the 10× Genomics platform.

Phylogeny and sex chromosome evolution of palaeognathae

Many paleognaths (ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes. We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of "evolutionary strata". Nine of the 15 studied species' sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate the "defeminization" of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females that evolved in their common ancestors.

Atmospheric Carbon and Transport - America (ACT-America) Data Sets: Description, Management, and Delivery

The ACT-America project is a NASA Earth Venture Suborbital-2 mission designed to study the transport and fluxes of greenhouse gases. The open and freely available ACT-America data sets provide airborne in situ measurements of atmospheric carbon dioxide, methane, trace gases, aerosols, clouds, and meteorological properties, airborne remote sensing measurements of aerosol backscatter, atmospheric boundary layer height and columnar content of atmospheric carbon dioxide, tower-based measurements, and modeled atmospheric mole fractions and regional carbon fluxes of greenhouse gases over the Central and Eastern United States. We conducted 121 research flights during five campaigns in four seasons during 2016-2019 over three regions of the US (Mid-Atlantic, Midwest and South) using two NASA research aircraft (B-200 and C-130). We performed three flight patterns (fair weather, frontal crossings, and OCO-2 underflights) and collected more than 1,140 h of airborne measurements via level-leg flights in the atmospheric boundary layer, lower, and upper free troposphere and vertical profiles spanning these altitudes. We also merged various airborne in situ measurements onto a common standard sampling interval, which brings coherence to the data, creates geolocated data products, and makes it much easier for the users to perform holistic analysis of the ACT-America data products. Here, we report on detailed information of data sets collected, the workflow for data sets including storage and processing of the quality controlled and quality assured harmonized observations, and their archival and formatting for users. Finally, we provide some important information on the dissemination of data products including metadata and highlights of applications of ACT-America data sets.

[Study on clinical symptoms and influencing factors of influenza-associated severe acute respiratory illness in children younger than 5 years old in Suzhou of China, 2011-2017]

Objective: To study the influencing factors of influenza-associated severe acute respiratory illness (SARI) in children younger than 5 years of old in Suzhou, and to provide evidence to support the improvement of prevention and control strategies for influenza in children. Methods: We conducted a prospective influenza surveillance for hospitalized SARI and outpatient influenza-like illness (ILI) at Children's Hospital of Soochow University from April 2011 to March 2017. We compared the clinical and other characteristics of influenza-positive patients with SARI to those with ILI to find the differences and to identify influencing factors of influenza-associated SARI, using χ² test and unconditional logistic regression. Results: We found 786 cases of influenza-associated ILI and 413 cases of influenza-associated SARI during the study period. Cough, runny nose, shortness of breath, asthma or wheezing were more common in influenza-associated SARI than in influenza-associated ILI (P<0.01). Univariate and multivariate logistic regression showed that the influencing factors which significantly associated with increased risk of influenza-associated SARI were as follows: younger age (<6 months OR=3.6, 6-23 months aOR=2.5), respiratory infection history within 3 months (aOR=4.5), chronic lung disease history (OR=3.4), fever above 39.0 ℃ (39.0-39.9 ℃ aOR=2.4, ≥40.0 ℃ aOR=6.0), and the presence of A/H1N1 (aOR=2.3), A/H3N2 (aOR=1.9). Conclusion: Children younger than 2 years old, with a history of chronic lung disease, a history of respiratory infection within 3 months, or with a fever peak above 39.0 ℃ should seek medical advice as soon as possible or receive annual influenza vaccination to reduce the incidence of influenza-associated serious outcomes.

POS0851 IDENTIFICATION OF HUB GENES AND PATHWAYS IN DERMATOMYOSITIS BY BIOINFORMATICS ANALYSIS

Background:

Dermatomyositis (DM) is a chronic systemic autoimmune disease characterized by inflammatory infiltrates in the skin and muscle1. The genes and pathways in the inflamed myopathies in patients with DM are poorly understood2.

Objectives:

To identify the key genes and pathways associated with DM and further discover its pathogenesis.

Methods:

Muscle tissue gene expression profile (GSE143323) were acquired from the GEO database, which included 39 DM samples and 20 normal samples. The differentially expressed genes (DEGs) in DM muscle tissue were screened by adopting the R software. Gene ontology (GO) and Kyoto Encyclopedia of Genome (KEGG) pathway enrichment analysis was performed by Metascape online analysis tool. A protein-protein interaction (PPI) network was then constructed by STRING software using the genes in significantly different pathways. Network of DEGs was analyzed by Cytoscape software. And degree of nodes was used to screen key genes.

Results:

Totally, 126 DEGs were obtained, which contained 122 up-regulated and 4 down-regulated. GO analysis revealed that most of the DEGs were significantly enriched in type I interferon signaling pathway, response to interferon-gamma, collagen-containing extracellular matrix, response to interferon-alpha and bacterium, positive regulation of cell death, leukocyte chemotaxis. KEGG pathway analysis showed that upregulated DEGs enhanced pathways associated with the hepatitis C, complement and coagulation cascades, p53 signaling pathway, RIG-I-like receptor signaling, Osteoclast differentiation, and AGE-RAGE signaling pathway. Ten hub genes were identified in DM, they were ISG15, IRF7, STAT1, MX1, OASL, OAS2, OAS1, OAS3, GBP1, and IRF9 according to the Cytoscape software and cytoHubba plugin.

Conclusion:

The findings from this bioinformatics network analysis study identified the key hub genes that might provide new molecular markers for its diagnosis and treatment.

References:

[1]Olazagasti JM, Niewold TB, Reed AM. Immunological biomarkers in dermatomyositis. Curr Rheumatol Rep 2015;17(11):68. doi: 10.1007/s11926-015-0543-y [published Online First: 2015/09/26].

[2]Chen LY, Cui ZL, Hua FC, et al. Bioinformatics analysis of gene expression profiles of dermatomyositis. Mol Med Rep 2016;14(4):3785-90. doi: 10.3892/mmr.2016.5703 [published Online First: 2016/09/08].

[3]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

POS0458 IDENTIFICATION OF HUB GENES AND MOLECULAR PATHWAYS IN PATIENTS WITH RHEUMATOID ARTHRITIS BY BIOINFORMATICS ANALYSIS

Background:

Rheumatoid arthritis (RA) is a chronic, inflammatory synovitis based systemic disease of unknown etiology1. The genes and pathways in the inflamed synovium of RA patients are poorly understood.

Objectives:

This study aims to identify differentially expressed genes (DEGs) associated with the progression of synovitis in RA using bioinformatics analysis and explore its pathogenesis2.

Methods:

RA expression profile microarray data GSE89408 were acquired from the public gene chip database (GEO), including 152 synovial tissue samples from RA and 28 healthy synovial tissue samples. The DEGs of RA synovial tissues were screened by adopting the R software. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. Protein-protein interaction (PPI) networks were assembled with Cytoscape software.

Results:

A total of 654 DEGs (268 up-regulated genes and 386 down-regulated genes) were obtained by the differential analysis. The GO enrichment results showed that the up-regulated genes were significantly enriched in the biological processes of myeloid leukocyte activation, cellular response to interferon-gamma and immune response-regulating signaling pathway, and the down-regulated genes were significantly enriched in the biological processes of extracellular matrix, retinoid metabolic process and regulation of lipid metabolic process. The KEGG annotation showed the up-regulated genes mainly participated in the staphylococcus aureus infection, chemokine signaling pathway, lysosome signaling pathway and the down-regulated genes mainly participated in the PPAR signaling pathway, AMPK signaling pathway, ECM-receptor interaction and so on. The 9 hub genes (PTPRC, TLR2, tyrobp, CTSS, CCL2, CCR5, B2M, fcgr1a and PPBP) were obtained based on the String database model by using the Cytoscape software and cytoHubba plugin3.

Conclusion:

The findings identified the molecular mechanisms and the key hub genes of pathogenesis and progression of RA.

References:

[1]Xiong Y, Mi BB, Liu MF, et al. Bioinformatics Analysis and Identification of Genes and Molecular Pathways Involved in Synovial Inflammation in Rheumatoid Arthritis. Med Sci Monit 2019;25:2246-56. doi: 10.12659/MSM.915451 [published Online First: 2019/03/28]

[2]Mun S, Lee J, Park A, et al. Proteomics Approach for the Discovery of Rheumatoid Arthritis Biomarkers Using Mass Spectrometry. Int J Mol Sci 2019;20(18) doi: 10.3390/ijms20184368 [published Online First: 2019/09/08]

[3]Zhu N, Hou J, Wu Y, et al. Identification of key genes in rheumatoid arthritis and osteoarthritis based on bioinformatics analysis. Medicine (Baltimore) 2018;97(22):e10997. doi: 10.1097/MD.0000000000010997 [published Online First: 2018/06/01]

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

AB0005 IDENTIFICATION OF KEY GENES AND PATHWAYS FOR PSORIASIS BASED ON GEO DATABASES BY BIOINFORMATICS ANALYSIS

Background:

Psoriasis is an immune-mediated, genetic disease manifesting in the skin or joints or both, and also has a strong genetic predisposition and autoimmune pathogenic traits1. The hallmark of psoriasis is sustained inflammation that leads to uncontrolled keratinocyte proliferation and dysfunctional differentiation. And it’s also a chronic relapsing disease, which often necessitates a long-term therapy2.

Objectives:

To investigate the molecular mechanisms of psoriasis and find the potential gene targets for diagnosis and treating psoriasis.

Methods:

Total 334 gene expression data of patients with psoriasis research (GSE13355 GSE14905 and GSE30999) were obtained from the Gene Expression Omnibus database. After data preprocessing and screening of differentially expressed genes (DEGs) by R software. Online toll Metascape3 was used to analyze Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs. Interactions of proteins encoded by DEGs were discovered by Protein-protein interaction network (PPI) using STRING online software. Cytoscape software was utilized to visualize PPI and the degree of each DEGs was obtained by analyzing the topological structure of the PPI network.

Results:

A total of 611 DEGs were found to be differentially expressed in psoriasis. GO analysis revealed that up-regulated DEGs were mostly associated with defense and response to external stimulus while down-regulated DEGs were mostly associated with metabolism and synthesis of lipids. KEGG enrichment analysis suggested they were mainly enriched in IL-17 signaling, Toll-like receptor signaling and PPAR signaling pathways, Cytokine-cytokine receptor interaction and lipid metabolism. In addition, top 9 key genes (CXCL10, OASL, IFIT1, IFIT3, RSAD2, MX1, OAS1, IFI44 and OAS2) were identified through Cytoscape.

Conclusion:

DEGs of psoriasis may play an essential role in disease development and may be potential pathogeneses of psoriasis.

References:

[1]Boehncke WH, Schon MP. Psoriasis. Lancet 2015;386(9997):983-94. doi: 10.1016/S0140-6736(14)61909-7 [published Online First: 2015/05/31].

[2]Zhang YJ, Sun YZ, Gao XH, et al. Integrated bioinformatic analysis of differentially expressed genes and signaling pathways in plaque psoriasis. Mol Med Rep 2019;20(1):225-35. doi: 10.3892/mmr.2019.10241 [published Online First: 2019/05/23].

[3]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

POS0742 SCREENING AND BIOINFORMATICS ANALYSIS OF HUB GENES AND PATHWAYS FOR PRIMARY SJÖGREN’S SYNDROME BASED ON GEO DATABASE

Background:

Primary Sjögren’s syndrome (pSS) is an autoimmune disease that featured as lymphoplasmacytic infiltration of the exocrine glands leading to sicca symptoms1. However, its underlying molecular mechanisms remain elusive.

Objectives:

This study aims to identify differentially expressed genes (DEGs) and pathways associated with the progression of pSS using bioinformatics analysis and explore its pathogenesis.

Methods:

The pSS-associated gene chip data set GSE66795 was obtained from the Gene Expression Omnibus (GEO) database, which included 131 cases of fully-phenotyped pSS patients’ whole blood samples and 29 cases of control samples. DEGs were screened Using R software. Online tool Metascape2 was used to make Gene Ontology (GO) and KEGG pathway enrichment. The PPI network was performed using String database. Hub genes were identified by Cytoscape.

Results:

A total of 108 DEGs were captured, including 101 up-regulated genes and 7 down-regulated genes. GO enrichment showed that these DEGs were primarily enriched in defense response to virus, response to interferon-gamma, regulation of innate immune response, response to interferon-beta, double-stranded RNA binding, response to interferon-alpha. KEGG pathway enrichment analysis showed these DEGs were principally enriched in Influenza A, RIG-I-like receptor signaling pathway, necroptosis, Staphylococcus aureus infection. Finally, 9 hub genes (STAT1, IRF7, OAS2, GBP1, OAS1, IFIT3, IFIH1, OAS3, DDX60) had highest degree value.

Conclusion:

The findings identified molecular mechanisms and the key hub genes that may involve in the occurrence and development of pSS.

References:

[1]Francois H, Mariette X. Renal involvement in primary Sjogren syndrome. Nat Rev Nephrol 2016;12(2):82-93. doi: 10.1038/nrneph.2015.174 [published Online First: 2015/11/17].

[2]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

POS0848 IDENTIFICATION OF POTENTIAL CRUCIAL GENES AND KEY PATHWAYS IN PULMONARY ARTERIAL HYPERTENSION WITH SYSTEMIC SCLEROSIS BY BIOINFORMATIC ANALYSIS

Background:

Pulmonary arterial hypertension with systemic sclerosis (SSc-PAH) is the main cause of death in patients with SSc. Early diagnosis and timely treatment are very important to reduce the mortality of patients with SSc-PAH1. At present, there are not many sensitive markers for the diagnosis of SSc-PAH. Therefore, it is necessary to mine more sensitive markers as more accurate and practical predictors, which is of great significance for the diagnosis and treatment of SSc-PAH.

Objectives:

To discover the differentially expressed genes (DEGs) and activated signaling pathways in SSc-PAH.

Methods:

Fifty-five samples (27 SSc-PAH v.s 28 normal controls) in GSE33463 chip data obtained from Gene Expression Omnibus (GEO) were included in this study. DEGs in SSc-PAH patients were screened by R, key pathways and hub genes were discoved by Metascape2, STRING3 and Cytoscape.

Results:

Total 431 genes with large differences were identified, including 238 up-regulated genes and 193 down-regulated genes, after standardizing the data (|logFC| > 1; P < 0.05). GO analysis showed that the upregulated genes were mainly involved in defense response to virus, hemoglobin complex, platelet alpha granule membrane and cytokine binding. The downregulated genes were mainly characterized by positive regulation of cell death, regulation of MAPK cascade, regulation of DNA-binding transcription factor activity and transcription factor AP-1 complex. Several significant enriched pathways obtained in the KEGG pathway analysis were Influenza A, Hepatitis C, IL-17 signaling pathway, MAPK signaling pathway, Toll-like receptor signaling pathway. Finally, after the selected differential genes were introduced into STRING online software, the data information of protein interaction network was derived, and 12 core genes in the network were identified, they were CXCL8, PPBP, LPAR1, FPR2, GNG11, CXCL10, LPAR5, JUN, C3AR1, CCR2, CCR3, IRF2.

Conclusion:

The genes and signal pathways related to SSc-PAH discovered by bioinformatics methods could not only provided new molecular markers for its diagnosis and treatment, but also provided new ideas for its related biological research.

References:

[1]Zheng JN, Li Y, Yan YM, et al. Identification and Validation of Key Genes Associated With Systemic Sclerosis-Related Pulmonary Hypertension. Front Genet 2020;11:816. doi: 10.3389/fgene.2020.00816 [published Online First: 2020/08/15].

[2]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].

[3]Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2019;47(D1):D607-D13. doi: 10.1093/nar/gky1131 [published Online First: 2018/11/27].

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

Prediction of spinal anesthesia-induced hypotension during elective cesarean section: a systematic review of prospective observational studies

BACKGROUND

Spinal anesthesia is the standard for elective cesarean section but spinal anesthesia-induced hypotension remains an important problem. Accurate prediction of hypotension could enhance clinical decision-making, alter management, and facilitate early intervention. We performed a systematic review of predictors of spinal anesthesia-induced hypotension and their predictive value during cesarean section.

METHODS

PubMed, Embase, Cochrane Library, Google Scholar and Web of Science databases were searched for prospective observational studies assessing the diagnostic accuracy of predictors of spinal anesthesia-induced hypotension in elective cesarean section. The quality of studies was assessed and predictors were grouped in domains based on the type of predictor.

RESULTS

Thirty-eight studies (n=3086 patients) were included. In most studies, patients received 500-1000 mL crystalloid preload or 500-2000 mL crystalloid coload. Vasopressors for post-spinal hypotension were boluses of ephedrine 5-15 mg and/or phenylephrine 25-100 µg in most studies. The hypotension rate varied from 29% to 80% based on the definition. For analysis, >30 predictors were classified into seven domains: demographic characteristics, baseline hemodynamic variables, baseline sympathovagal balance, postural stress testing, peripheral perfusion indices, blood volume and fluid responsiveness indices, and genetic polymorphism.

CONCLUSIONS

Environmental and individual factors increased outcome variability, which restricted the value of the autonomic nervous system and peripheral perfusion indices for prediction of spinal anesthesia-induced hypotension. Supine stress tests may reflect parturients' cardiovascular tolerance during hemodynamic fluctuations and may optimize the predictive value of static state predictors. Future research for predicting spinal anesthesia-induced hypotension should focus on composite and dynamic parameters during the supine stress tests.

Construction of an MnO2 nanosheet array 3D integrated electrode for sensitive enzyme-free glucose sensing

MnO₂ based electrochemical enzyme-free glucose sensors remain significantly limited by their low electronic conductivity and associated complex preparation. In this paper, an MnO₂ nanosheet array supported on nickel foam (MnO₂ NS/NF) was prepared using a simple hydrothermal synthesis and employed as a 3D integrated electrode for enzyme-free glucose detection. It was found that MnO₂ NS/NF shows high performance with a wide linear range from 1 μM to 1.13 mM, a high sensitivity of 6.45 mA mM^-1 cm^-2, and a low detection limit of 0.5 μM (S/N = 3). Besides, MnO₂ NS/NF shows high selectivity against common interferences and good reliability for glucose detection in human serum. This work demonstrates the promising role of MnO₂ NS/NF as an efficient integrated electrode in enzyme-free glucose detection with high performance.

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes

Emu and other ratites are more informative than any other birds in reconstructing the evolution of the ancestral avian or vertebrate karyotype because of their much slower rate of genome evolution. Here, we generated a new chromosome-level genome assembly of a female emu, and estimated the tempo of chromosome evolution across major avian phylogenetic branches, by comparing it to chromosome-level genome assemblies of 11 other bird and one turtle species. We found ratites exhibited the lowest numbers of intra- and inter-chromosomal changes among birds since their divergence with turtles. The small-sized and gene-rich emu microchromosomes have frequent inter-chromosomal contacts that are associated with housekeeping genes, which appears to be driven by clustering their centromeres in the nuclear interior, away from the macrochromosomes in the nuclear periphery. Unlike nonratite birds, only less than one-third of the emu W Chromosome regions have lost homologous recombination and diverged between the sexes. The emu W is demarcated into a highly heterochromatic region (WS0) and another recently evolved region (WS1) with only moderate sequence divergence with the Z Chromosome. WS1 has expanded its inactive chromatin compartment, increased chromatin contacts within the region, and decreased contacts with the nearby regions, possibly influenced by the spreading of heterochromatin from WS0. These patterns suggest that alteration of chromatin conformation comprises an important early step of sex chromosome evolution. Overall, our results provide novel insights into the evolution of avian genome structure and sex chromosomes in three-dimensional space.