bluuebunny/crossref_metadata_2025 huggingface dataset:
Highly accurate long reads are crucial for realizing the potential of biodiversity genomics
Authors: Hotaling Scott , Wilcox Edward R. , Heckenhauer Jacqueline , Stewart Russell J. , Frandsen Paul B.
Published: March 2023

Background

Generating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in genome science. With the rise of long-read sequencing, assembly challenges have shifted from merely increasing contiguity to correctly assembling complex, repetitive regions of interest, ideally in a phased manner. At present, researchers largely choose between two types of long read data: longer, but less accurate sequences, or highly accurate, but shorter reads (i.e., >Q20 or 99% accurate). To better understand how these types of long-read data as well as scale of data (i.e., mean length and sequencing depth) influence genome assembly outcomes, we compared genome assemblies for a caddisfly, Hesperophylax magnus, generated with longer, but less accurate, Oxford Nanopore (ONT) R9.4.1 and highly accurate PacBio HiFi (HiFi) data. Next, we expanded this comparison to consider the influence of highly accurate long-read sequence data on genome assemblies across 6750 plant and animal genomes. For this broader comparison, we used HiFi data as a surrogate for highly accurate long-reads broadly as we could identify when they were used from GenBank metadata.

Results

HiFi reads outperformed ONT reads in all assembly metrics tested for the caddisfly data set and allowed for accurate assembly of the repetitive ~ 20 Kb H-fibroin gene. Across plants and animals, genome assemblies that incorporated HiFi reads were also more contiguous. For plants, the average HiFi assembly was 501% more contiguous (mean contig N50 = 20.5 Mb) than those generated with any other long-read data (mean contig N50 = 4.1 Mb). For animals, HiFi assemblies were 226% more contiguous (mean contig N50 = 20.9 Mb) versus other long-read assemblies (mean contig N50 = 9.3 Mb). In plants, we also found limited evidence that HiFi may offer a unique solution for overcoming genomic complexity that scales with assembly size.

Conclusions

Highly accurate long-reads generated with HiFi or analogous technologies represent a key tool for maximizing genome assembly quality for a wide swath of plants and animals. This finding is particularly important when resources only allow for one type of sequencing data to be generated. Ultimately, to realize the promise of biodiversity genomics, we call for greater uptake of highly accurate long-reads in future studies.
Associations of genome-wide and regional autozygosity with 96 complex traits in old order Amish
Authors: Lynch Megan T. , Maloney Kristin A. , Xu Huichun , Perry James A. , Center Regeneron Genetics , Shuldiner Alan R. , Mitchell Braxton D.
Published: March 2023

Background: Autozygosity, the proportion of the genome that is homozygous by descent, has been associated with variation in multiple health-related traits impacting evolutionary fitness. Autozygosity (FROH) is typically measured from runs of homozygosity (ROHs) that arise when identical-by-descent (IBD) haplotypes are inherited from each parent. Population isolates with a small set of common founders have elevated autozygosity relative to outbred populations. Methods: In this study, we examined whether degree of autozygosity was associated with variation in 96 cardiometabolic traits among 7221 Old Order Amish individuals residing in Lancaster County, PA. We estimated the average length of an ROH segment to be 6350 KB, with each individual having on average 17.2 segments 1.5 KB or larger. Measurements of genome-wide and regional FROH were used as the primary predictors of trait variation in association analysis. Results: In genome-wide FROH analysis, we did not identify any associations that withstood Bonferroni-correction (p = 0.0005). However, on regional FROH analysis, we identified associations exceeding genome-wide thresholds for two traits: serum bilirubin levels, which were significantly associated with a region on chromosome 2 localized to a region surrounding UGT1A10 (p = 1 × 10− 43), and HbA1c levels, which were significantly associated with a region on chromosome 8 localized near CHRNB3 (p = 8 × 10− 10). Conclusions: These analyses highlight the potential value of autozygosity mapping in founder populations.
No association of a Vascular endothelial growth factor A (VEGFA) gene polymorphism with pre-eclampsia among pregnant women in Uganda
Authors: Nabweyambo Sheila , Kanyerezi Stephen , Petterson John H.-O. , Katabazi Fred Ashaba , Ssekagiri Alfred , Mwesigwa Savannah , Mboowa Gerald , Nakazzi Faith , Keesiga Annette , Adroma Moses , Bwanga Freddie , McGovern Naomi , Sande Obondo James , Nakimuli Annettee
Published: March 2023

Background

Vascular endothelial growth factor A (VEGFA) is a major angiogenic factor that plays an important role in the formation of blood vessels during embryonic development. VEGFA has been implicated in the pathophysiology of pre-eclampsia (PE), since pre-eclamptic women present with reduced levels of free circulating VEGFA. The 3’ untranslated region (3’-UTR) of the VEGFA gene consists of elements that regulate the transcription and hence expression of the VEGFA protein in circulation. Hence it is suggested that variations thereof could underlie the reduced VEGFA levels observed in pre-eclamptic women. The purpose of this study was to investigate presence of the + 936C/T polymorphism, a common single nucleotide polymorphism (SNP) in the 3’-UTR of the VEGFA gene, and determine its association with PE among pregnant women in Uganda.

Results

There was no significant difference observed in the allele and genotype frequencies of the + 936C/T 3’ UTR-VEGFA polymorphism between pre-eclamptic and normotensive pregnant women (P > 0.05). Additionally, there was no significant difference in the median plasma levels of free VEGFA among women with the wild type, CT and TT genotypes of the + 936C/T VEGFA polymorphism (median = 0.84 pg/mL (IQR = 0.39–1.41) Vs 1.05 (0.61–1.18) Vs 1.05 (1.05–1.05) respectively, p-value = 0.7161).

Conclusions

These study findings indicate that the + 936C/T 3’ UTR-VEGFA polymorphism had no significant association with increased susceptibility to PE among women in Uganda. Further studies with a larger sample size are recommended.
Transcriptomic profiles of the ruminal wall in Italian Mediterranean dairy buffaloes fed green forage
Authors: Salzano Angela , Fioriniello Salvatore , D’Onofrio Nunzia , Balestrieri Maria Luisa , Aiese Cigliano Riccardo , Neglia Gianluca , Della Ragione Floriana , Campanile Giuseppe
Published: March 2023

Background

Green feed diet in ruminants exerts a beneficial effect on rumen metabolism and enhances the content of milk nutraceutical quality. At present, a comprehensive analysis focused on the identification of genes, and therefore, biological processes modulated by the green feed in buffalo rumen has never been reported. We performed RNA-sequencing in the rumen of buffaloes fed a total mixed ration (TMR) + the inclusion of 30% of ryegrass green feed (treated) or TMR (control), and identified differentially expressed genes (DEGs) using EdgeR and NOISeq tools.

Results

We found 155 DEGs using EdgeR (p-values < 0.05) and 61 DEGs using NOISeq (prob ≥0.8), 30 of which are shared. The rt-qPCR validation suggested a higher reliability of EdgeR results as compared with NOISeq data, in our biological context.

Gene Ontology analysis of DEGs identified using EdgeR revealed that green feed modulates biological processes relevant for the rumen physiology and, then, health and well-being of buffaloes, such as lipid metabolism, response to the oxidative stress, immune response, and muscle structure and function. Accordingly, we found: (i) up-regulation of HSD17B13, LOC102410803 (or PSAT1) and HYKK, and down-regulation of CDO1, SELENBP1 and PEMT, encoding factors involved in energy, lipid and amino acid metabolism; (ii) enhanced expression of SIM2 and TRIM14, whose products are implicated in the immune response and defense against infections, and reduced expression of LOC112585166 (or SAAL1), ROR2, SMOC2, and S100A11, encoding pro-inflammatory factors; (iii) up-regulation of NUDT18, DNAJA4 and HSF4, whose products counteract stressful conditions, and down-regulation of LOC102396388 (or UGT1A9) and LOC102413340 (or MRP4/ABCC4), encoding detoxifying factors; (iv) increased expression of KCNK10, CACNG4, and ATP2B4, encoding proteins modulating Ca2+ homeostasis, and reduced expression of the cytoskeleton-related MYH11 and DES.

Conclusion

Although statistically unpowered, this study suggests that green feed modulates the expression of genes involved in biological processes relevant for rumen functionality and physiology, and thus, for welfare and quality production in Italian Mediterranean dairy buffaloes.

These findings, that need to be further confirmed through the validation of additional DEGs, allow to speculate a role of green feed in the production of nutraceutical molecules, whose levels might be enhanced also in milk.
Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanut
Authors: Liu Xing , Su Liangchen , Li Limei , Zhang Zhi , Li Xiaoyun , Liang Qingjian , Li Ling
Published: March 2023

Background

HR (hairy root) has emerged as a valuable tissue for the rapid characterization of plant gene function and enzyme activity in vivo. AhGLK1 (Arachis hypogaea L. golden2-like 1) is known to play a role in post-drought recovery. However, it is unclear (a) whether HR has properties that are distinct from those of PR (primary root); and (b) which gene networks are regulated by AhGLK1 in response to drought stress and recovery in peanut.

Results

We found that cells of the root tip cortex were larger in HR than in PR, while a total of 850 differentially expressed genes (DEGs) were identified in HR compared to PR. Eighty-eight of these DEGs, relating to chlorophyll and photosynthesis, were upregulated in HR. In addition, AhGLK1-OX (AhGLK1-overexpressing) HR showed a green phenotype, and had a higher relative water content than 35 S::eGFP (control) HR during drought stress. RNA-seq analysis showed that 74 DEGs involved both in the drought response and the post-drought recovery process were significantly enriched in the galactose metabolism pathway. GO terms enrichment analysis revealed that 59.19%, 29.79% and 17.02% of the DEGs mapped to the ‘biological process’ (BP), ‘molecular function’ (MF) and ‘cellular component’ (CC) domains, respectively. Furthermore, 20 DEGs involved in post-drought recovery were uniquely expressed in AhGLK1-OX HR and were significantly enriched in the porphyrin metabolism pathway. GO analysis showed that 42.42%, 30.30% and 27.28% of DEGs could be assigned to the BP, MF and CC domains, respectively. Transcription factors including bHLH and MYB family members may play a key role during drought stress and recovery.

Conclusion

Our data reveal that HR has some of the characteristics of leaves, indicating that HR is suitable for studying genes that are mainly expressed in leaves. The RNA-seq results are consistent with previous studies that show chlorophyll synthesis and photosynthesis to be critical for the role of AhGLK1 in improving post-drought recovery growth in peanut. These findings provide in-depth insights that will be of great utility for the exploration of candidate gene functions in relation to drought tolerance and/or post-drought recovery ability in peanut.
Proteomics and transcriptomics profiling reveals distinct aspects of kidney stone related genes in calculi rats
Authors: Zhu Wang , Qiong Deng , Yanli Gu , Min Li , Ying Zhang , Qiyi Hu , Shenping Zhang , Xisheng Wang , Hui Liang
Published: March 2023

Backgrounds

Kidney stone also known as urolithiasis or nephrolithiasis, is one of the oldest diseases known to medicine, however, the gene expression changes and related kidney injury remains unclear.

Methods

A calculi rat model was developed via ethylene glycol– and ammonium chloride–induction. Integrated proteomic and transcriptomic analysis was performed to characterize the distinct gene expression profiles in the kidney of calculi rat. Differential expressed genes (DEGs) were sub-clustered into distinct groups according to the consistency of transcriptome and proteome. Gene Ontology and KEGG pathway enrichment was performed to analyze the functions of each sub-group of DEGs. Immunohistochemistry was performed to validated the expression of identified proteins.

Results

Five thousand eight hundred ninety-seven genes were quantified at both transcriptome and proteome levels, and six distinct gene clusters were identified, of which 14 genes were consistently dysregulated. Functional enrichment analysis showed that the calculi rat kidney was increased expression of injured & apoptotic markers and immune-molecules, and decreased expression of solute carriers & transporters and many metabolic related factors.

Conclusions

The present proteotranscriptomic study provided a data resource and new insights for better understanding of the pathogenesis of nephrolithiasis, will hopefully facilitate the future development of new strategies for the recurrence prevention and treatment in patients with kidney stone disease.
dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations
Authors: Lv Kangqi , Chen Dayang , Xiong Dan , Tang Huamei , Ou Tong , Kan Lijuan , Zhang Xiuming
Published: March 2023

Background

Copy number variation (CNV) is a type of structural variation, which is a gain or loss event with abnormal changes in copy number. Methods to predict the pathogenicity of CNVs are required to realize the relationship between these variants and clinical phenotypes. ClassifyCNV, X-CNV, StrVCTVRE, etc. have been trained to predict the pathogenicity of CNVs, but few studies have been reported based on the deleterious significance of features.

Results

From single nucleotide polymorphism (SNP), gene and region dimensions, we collected 79 informative features that quantitatively describe the characteristics of CNV, such as CNV length, the number of protein genes, the number of three prime untranslated region. Then, according to the deleterious significance, we formulated quantitative methods for features, which fall into two categories: the first is variable type, including maximum, minimum and mean; the second is attribute type, which is measured by numerical sum. We used Gradient Boosted Trees (GBT) algorithm to construct dbCNV, which can be used to predict pathogenicity for five-tier classification and binary classification of CNVs. We demonstrated that the distribution of most feature values was consistent with the deleterious significance. The five-tier classification model accuracy for 0.85 and 0.79 in loss and gain CNVs, which proved that it has high discrimination power in predicting the pathogenicity of five-tier classification CNVs. The binary model achieved area under curve (AUC) values of 0.96 and 0.81 in the validation set, respectively, in gain and loss CNVs.

Conclusion

The performance of the dbCNV suggest that functional deleteriousness-based model of CNV is a promising approach to support the classification prediction and to further understand the pathogenic mechanism.
Genetic variation and demographic history of Sudan desert sheep reveal two diversified lineages
Authors: Salim Bashir , Alasmari Saeed , Mohamed Nouh Saad , Ahmed Mohamed-Khair A. , Nakao Ryo , Hanotte Olivier
Published: March 2023

More than 400 million sheep are raised on the African continent, the majority of which are indigenous and are primarily reared for sustenance. They have effectively adapted to various climatic and production environments, surviving and flourishing. The genetic relationships among these sheep populations remain understudied. Herein, we sequenced the entire mitochondrial DNA control region of 120 animals from Hamary and Kabashi and their crossbreed (Hamary x Kabashi) of Sudan desert sheep (SDS) to understand their maternal-inherited genetic variation and demographic history profiles and relate those to the history of sheep pastoralism on the African continent. The results show a diversified and predominant D- loop haplogroup B (n = 102, 85%), with all other sequences belonging to haplogroup A. Most of the maternal genetic variation was partitioned between haplogroup (76.3%) while within haplogroup accounted for 23.7% of the variation. However, little genetic differentiation was observed among the two breeds and their crosses, with our results supporting a Hamari maternal origin for the crossbreed. Bayesian coalescent-based analysis reveals distinct demographic history between the two haplogroups, two breeds and their crosses. Comparison of the two haplogroup showed that haplogroup B experienced an earlier expansion than haplogroup A. Unlike the breed-based comparison, the expansion of the two breeds started roughly at the same time, around 6500 years ago, with Kabashi having a slightly greater effective population size. The maternal ancestors of SDS may have diverged before their introduction to the African continent. This study provides novel insights into the early history of these two main breeds of Sudan desert sheep and their crosses.
Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets
Authors: Panzer Jonathan J. , Romero Roberto , Greenberg Jonathan M. , Winters Andrew D. , Galaz Jose , Gomez-Lopez Nardhy , Theis Kevin R.
Published: March 2023

The existence of a placental microbiota is debated. The human placenta has historically been considered sterile and microbial colonization was associated with adverse pregnancy outcomes. Yet, recent DNA sequencing investigations reported a microbiota in typical human term placentas. However, this detected microbiota could represent background DNA or delivery-associated contamination. Using fifteen publicly available 16S rRNA gene datasets, existing data were uniformly re-analyzed with DADA2 to maximize comparability. While Amplicon Sequence Variants (ASVs) identified as Lactobacillus, a typical vaginal bacterium, were highly abundant and prevalent across studies, this prevalence disappeared after applying likely  DNA contaminant removal to placentas from term cesarean deliveries. A six-study sub-analysis targeting the 16S rRNA gene V4 hypervariable region demonstrated that bacterial profiles of placental samples and technical controls share principal bacterial ASVs and that placental samples clustered primarily by study origin and mode of delivery. Contemporary DNA-based evidence does not support the existence of a placental microbiota.

Importance

Early-gestational microbial influences on human development are unclear. By applying DNA sequencing technologies to placental tissue, bacterial DNA signals were observed, leading some to conclude that a live bacterial placental microbiome exists in typical term pregnancy. However, the low-biomass nature of the proposed microbiome and high sensitivity of current DNA sequencing technologies indicate that the signal may alternatively derive from environmental or delivery-associated bacterial DNA contamination. Here we address these alternatives with a re-analysis of 16S rRNA gene sequencing data from 15 publicly available placental datasets. After identical DADA2 pipeline processing of the raw data, subanalyses were performed to control for mode of delivery and environmental DNA contamination. Both environment and mode of delivery profoundly influenced the bacterial DNA signal from term-delivered placentas. Aside from these contamination-associated signals, consistency was lacking across studies. Thus, placentas delivered at term are unlikely to be the original source of observed bacterial DNA signals.
Gut microbiota characteristics of Mongolian and Han populations in anti-tuberculosis drug-induced liver injury: a population-based case–control study
Authors: Hao Jinqi , Li Yuhong , Yu Yanqin , Zheng Limin , Feng Fumin
Published: March 2023

Background

The pathogenesis of anti-tuberculosis (TB) drug-induced liver injury (ADLI) is complicated and remains unclear. We aimed to analyse the relationship between the characteristics of gut microbiota and ADLI in Mongolian and Han patients with pulmonary TB and identify the most notable bacteria related to the occurrence of liver injury in those populations.

Methods

Patients with concurrent liver injury (LI) and no liver injury (ULI) before receiving first-line anti-TB drug treatment (T1) from the Han population in Tangshan and the Mongolian population in Inner Mongolia were selected as research subjects. At the time of liver injury (T2), stool samples were measured by bacterial 16S rRNA gene high-throughput sequencing to analyse and compare the differences in the gut microbiota of the LI and ULI Mongolian and Han patients at T1 and T2 and identify the differences between those patients.

Results

A total of 45 Mongolian and 37 Han patients were enrolled in our study. A dynamic comparison from T1 to T2 showed that the microbiota of the LI and ULI groups changed significantly from T1 to T2 in both the Mongolian and Han populations. However, there were commonalities and personality changes in the microbiota of the two ethnic groups.

Conclusion

Differences in gut microbes in ADLI were found among the Han and Mongolian patients in our study. Ekmania and Stenotrophomonas were related to the occurrence of ADLI in Mongolian patients, while Ekmania and Ruminococcus__gnavus_group were related to the occurrence of ADLI in the Han population.
Surfactant nanovesicles for augmented antibacterial activity against carbapenemase resistant enterobacteriaceae and extended spectrum beta-lactamases producing bacteria: in vitro and in vivo evaluation
Authors: Abo Kamer Amal M. , Amer Noha M. , Abdelmegeed Ahmed A. , El Maghraby Gamal M. , Gamaleldin Noha M.
Published: March 2023

The ubiquitous emergence of bacterial resistance is a challenging problem in infectious diseases treatment. Recently, new research lines employed nano-drug delivery systems to enhance antibacterial activity of the existing antibiotics. Accordingly, the objective of this study is to optimize surfactant nanovesicles to improve the antimicrobial effect of meropenem, ertapenem and tigecycline against Carbapenemase Resistant Enterobacteriaceae (CRE) and extended spectrum beta-lactamases producing bacteria (ESBL). Klebsiella pneumoniae and Escherichia coli were used as the test organisms. In vivo and in vitro evaluations were conducted to prove the efficacy of niosome-encapsulated drugs formulations. The results revealed that surfactant vesicles were able to reduce the MIC values of the tested drugs by nine-fold change compared to their free forms. Scanning Electron Microscope (SEM) showed possible adhesion/fusion of the vesicles encapsulated drugs on the bacterial cells compared to its solution. In vivo investigations using animal skin model confirmed the superiority of nanovesicles drug encapsulation regarding both wound size and histopathological examination. Wound surface area was reduced from 24.6mm2 in absence of drug to reach 13.9, and 6.2mm2 in presence of ertapenem solution or niosomes, respectively. Nanovesicular formulations can be considered as effective drug delivery systems that can diminish bacterial resistance against β-lactams antibiotics.
Brain magnetic resonance imaging in the DE50-MD dog model of Duchenne muscular dystrophy reveals regional reductions in cerebral gray matter
Authors: Crawford Abbe H. , Hornby Natasha L. , de la Fuente Alerie G. , Piercy Richard J.
Published: March 2023

Background

Duchenne muscular dystrophy is a X-linked disease characterized by severe and progressive muscle weakness, alongside cognitive impairment and a range of neurobehavioral disorders secondary to brain dystrophin deficiency. Duchenne muscular dystrophy patients have reduced cerebral gray matter and altered white matter ultrastructure (detected by magnetic resonance imaging) compared to age-matched controls.

Methods

We studied the DE50-MD canine model of Duchenne muscular dystrophy, which is deficient in full length brain dystrophin (Dp427) isoforms and has a neurocognitive phenotype. Eight DE50-MD and 6 age-matched littermate wild type male dogs underwent serial brain magnetic resonance imaging from 14 to 33 months of age.

Results

Reduced regional gray matter was detected in DE50-MD dogs compared with wildtype, including the piriform lobe, hippocampus and cingulate gyrus. Lateral ventricle volume was larger in DE50-MD dogs. Differences did not progress over time. White matter volume did not differ between DE50-MD and wildtype dogs. There was no difference in brain nor cranial vault volume between DE50-MD and wildtype dogs.

Conclusion

Dystrophin deficiency in the canine brain results in structural changes that likely contribute to the neurocognitive phenotype.
Overexpression of OsERF106MZ promotes parental root growth in rice seedlings by relieving the ABA-mediated inhibition of root growth under salinity stress conditions
Authors: Chen Hung-Chi , Huang Shi-Cheng , Chen Yen-Fu , Kuo Che-Wei , Chen Ying-Hsuan , Chang Men-Chi
Published: March 2023

Background

Roots are essential for plant growth and have a variety of functions, such as anchoring the plant to the ground, absorbing water and nutrients from the soil, and sensing abiotic stresses, among others. OsERF106MZ is a salinity-induced gene that is expressed in germinating seeds and rice seedling roots. However, the roles of OsERF106MZ in root growth remain poorly understood.

Results

Histochemical staining to examine β-glucuronidase (GUS) activity in transgenic rice seedlings harboring OsERF106MZp::GUS indicated that OsERF106MZ is mainly expressed in the root exodermis, sclerenchyma layer, and vascular system. OsERF106MZ overexpression in rice seedlings leads to an increase in primary root (PR) length. The phytohormone abscisic acid (ABA) is thought to act as a hidden architect of root system structure. The expression of the ABA biosynthetic gene OsAO3 is downregulated in OsERF106MZ-overexpressing roots under normal conditions, while the expression of OsNPC3, an AtNPC4 homolog involved in ABA sensitivity, is reduced in OsERF106MZ-overexpressing roots under both normal and NaCl-treated conditions. Under normal conditions, OsERF106MZ-overexpressing roots show a significantly reduced ABA level; moreover, exogenous application of 1.0 µM ABA can suppress OsERF106MZ-mediated root growth promotion. Additionally, OsERF106MZ-overexpressing roots display less sensitivity to ABA-mediated root growth inhibition when treated with 5.0 µM ABA under normal conditions or exposed to NaCl-treated conditions. Furthermore, chromatin immunoprecipitation (ChIP)-qPCR and luciferase (LUC) reporter assays showed that OsERF106MZ can bind directly to the sequence containing the GCC box in the promoter region of the OsAO3 gene and repress the expression of OsAO3.

Conclusions

OsERF106MZ may play a role in maintaining root growth for resource uptake when rice seeds germinate under salinity stress by alleviating ABA-mediated root growth inhibition.
Genome-wide identification of the TIFY family reveals JAZ subfamily function in response to hormone treatment in Betula platyphylla
Authors: Lv Guanbin , Han Rui , Shi Jingjing , Chen Kun , Liu Guifeng , Yu Qibin , Yang Chuanping , Jiang Jing
Published: March 2023

Background

The TIFY family is a plant-specific gene family and plays an important role in plant growth and development. But few reports have been reported on the phylogenetic analysis and gene expression profiling of TIFY family genes in birch (Betula platyphylla).

Results

In this study, we characterized TIFY family and identified 12 TIFY genes and using phylogeny and chromosome mapping analysis in birch. TIFY family members were divided into JAZ, ZML, PPD and TIFY subfamilies. Phylogenetic analysis revealed that 12 TIFY genes were clustered into six evolutionary branches. The chromosome distribution showed that 12 TIFY genes were unevenly distributed on 5 chromosomes. Some TIFY family members were derived from gene duplication in birch. We found that six JAZ genes from JAZ subfamily played essential roles in response to Methyl jasmonate (MeJA), the JAZ genes were correlated with COI1 under MeJA. Co-expression and GO enrichment analysis further revealed that JAZ genes were related to hormone. JAZ proteins involved in the ABA and SA pathways. Subcellular localization experiments confirmed that the JAZ proteins were localized in the nucleus. Yeast two-hybrid assay showed that the JAZ proteins may form homologous or heterodimers to regulate hormones.

Conclusion

Our results provided novel insights into biological function of TIFY family and JAZ subfamily in birch. It provides the theoretical reference for in-depth analysis of plant hormone and molecular breeding design for resistance.
Silencing of the calcium-dependent protein kinase TaCDPK27 improves wheat resistance to powdery mildew
Authors: Yue Jie-yu , Jiao Jin-lan , Wang Wen-wen , Jie Xin-rui , Wang Hua-zhong
Published: March 2023

Background

Calcium ions (Ca2+), secondary messengers, are crucial for the signal transduction process of the interaction between plants and pathogens. Ca2+ signaling also regulates autophagy. As plant calcium signal-decoding proteins, calcium-dependent protein kinases (CDPKs) have been found to be involved in biotic and abiotic stress responses. However, information on their functions in response to powdery mildew attack in wheat crops is limited.

Result

In the present study, the expression levels of TaCDPK27, four essential autophagy-related genes (ATGs) (TaATG5, TaATG7, TaATG8, and TaATG10), and two major metacaspase genes, namely, TaMCA1 and TaMCA9, were increased by powdery mildew (Blumeria graminis f. sp. tritici, Bgt) infection in wheat seedling leaves. Silencing TaCDPK27 improves wheat seedling resistance to powdery mildew, with fewer Bgt hyphae occurring on TaCDPK27-silenced wheat seedling leaves than on normal seedlings. In wheat seedling leaves under powdery mildew infection, silencing TaCDPK27 induced excess contents of reactive oxygen species (ROS); decreased the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT); and led to an increase in programmed cell death (PCD). Silencing TaCDPK27 also inhibited autophagy in wheat seedling leaves, and silencing TaATG7 also enhanced wheat seedling resistance to powdery mildew infection. TaCDPK27-mCherry and GFP-TaATG8h colocalized in wheat protoplasts. Overexpressed TaCDPK27-mCherry fusions required enhanced autophagy activity in wheat protoplast under carbon starvation.

Conclusion

These results suggested that TaCDPK27 negatively regulates wheat resistance to PW infection, and functionally links with autophagy in wheat.
Genetic and ecophysiological evidence that hybridization facilitated lineage diversification in yellow Camellia (Theaceae) species: a case study of natural hybridization between C. micrantha and C. flavida
Authors: Wei Sujuan , Zhang Qiwei , Tang Shaoqing , Liao Wenbo
Published: March 2023

Background

Hybridization is generally considered an important creative evolutionary force, yet this evolutionary process is still poorly characterized in karst plants. In this study, we focus on natural hybridization in yellowCamelliaspecies, a group of habitat specialists confined to karst/non-karst habitats in southwestern China.

Results

Based on population genome data obtain from double digest restriction-site associated DNA (ddRAD) sequencing, we found evidence for natural hybridization and introgression betweenC. micranthaandC. flavida, and specifically confirmed their hybrid population,C. “ptilosperma”. Ecophysiological results suggested that extreme hydraulic traits were fixed inC. “ptilosperma”, these being consistent with its distinct ecological niche, which lies outside its parental ranges.

Conclusion

The identified hybridization event is expected to have played a role in generating novel variation during, in which the hybrid population displays different phenological characteristics and novel ecophysiological traits associated with the colonization of a new niche in limestone karst.
Development of prediction models to estimate extubation time and midterm recovery time of ophthalmic patients undergoing general anesthesia: a cross-sectional study
Authors: Huang Xuan , Tan Ronghui , Lin Jian-Wei , Li Gonghui , Xie Jianying
Published: March 2023

Background

To develop prediction models for extubation time and midterm recovery time estimation in ophthalmic patients who underwent general anesthesia.

Methods

Totally 1824 ophthalmic patients who received general anesthesia at Joint Shantou International Eye Center were included. They were divided into a training dataset of 1276 samples, a validation dataset of 274 samples and a check dataset of 274 samples. Up to 85 to 87 related factors were collected for extubation time and midterm recovery time analysis, respectively, including patient factors, anesthetic factors, surgery factors and laboratory examination results. First, multiple linear regression was used for predictor selection. Second, different methods were used to develop predictive models for extubation time and midterm recovery time respectively. Finally, the models’ generalization abilities were evaluated using a same check dataset with MSE, RMSE, MAE, MAPE, R-Squared and CCC.

Results

The fuzzy neural network achieved the highest R-Squared of 0.956 for extubation time prediction and 0.885 for midterm recovery time, and the RMSE value was 6.637 and 9.285, respectively.

Conclusion

The fuzzy neural network developed in this study had good generalization performance in predicting both extubation time and midterm recovery time of ophthalmic patients undergoing general anesthesia.

Trial registration

This study is prospectively registered in the Chinese Clinical Trial Registry, registration number: CHiCRT2000036416, registration date: August 23, 2020.
The Minimum Effective Concentration (MEC95) of different volumes of ropivacaine for ultrasound-guided caudal epidural block: a dose-finding study
Authors: Ma Dongmei , Chen Yan , Chen Ping , Xu Jianhong , Guo Jian , Peng Lijia
Published: March 2023

Background

Caudal epidural block (CEB) may be beneficial in anorectal surgery because its use may extend postoperative analgesia. This dose-finding study aimed to estimate the minimum effective anesthetic concentrations for 95% patients(MEC95) of 20 ml or 25 ml of ropivacaine in with CEB.

Patients and methods

In this double-blind, prospective study, the concentration of ropivacaine administered in 20 ml and 25 ml for ultrasound-guided CEB were determined using the sample up-and-down sequential allocation study design of binary response variables. The first participant was given 0.5% ropivacaine. Depending on whether a block was successful or unsuccessful, the concentration of local anesthesia was decreased or increased by 0.025% in the next patient. Every five minutes for 30 min, the sensory blockade using a pin-prick sensation at S3 dermatome compared to at T6 dermatome were evaluated every 5 min within 30 min. An effective CEB was defined as a a reduction of sensation at S3 dermatome and the existence of flaccid anal sphincter. Anesthesia was considered successful if the surgeon could perform the surgery without additional anesthesia. We determined the MEC50 using the Dixon and Massey up-and-down method and estimated the MEC95 using probit regression.

Results

The concentration of ropivacaine administered in 20 ml for CEB ranged from 0.2% to 0.5%. Probit regression with a bias-corrected Morris 95% CI derived by bootstrapping showed an MEC50 and MEC 50 of ropivacaine for anorectal surgical anesthesia were 0.27% (95% CI, 0.24 to 0.31) and 0.36%(95% CI, 0.32 to 0.61). The concentration of ropivacaine administered in 25 ml for CEB ranged from 0.175 to 0.5. Probit regression with a bias-corrected Morris 95% CI derived by bootstrapping showed an MEC50 and MEC95 for CEB were 0.24% (95% CI, 0.19 to 0.27) and 0.32% (95% CI, 0.28 to 0.54).

Conclusion

With ultrasound-guided CEB, the MEC95 of 0.36% ropivacaine at 20 ml and 0.32% ropivacaine at 25 ml provide adequate surgical anesthesia/analgesia 95% of patients undergoing anorectoal surgery.

Trial registration

Clinicaltrails.gov: Retrospectively registered (ChiCTR2100042954; Registration date:1/2, 2021).
Comparison of the effectiveness of ultrasound-guided versus fluoroscopy-guided medial lumbar bundle branch block on pain related to lumbar facet joints: a multicenter randomized controlled non-inferiority study
Authors: Nisolle Marie-Laure , Ghoundiwal Djamal , Engelman Edgard , El Founas Walid , Gouwy Jonathan , Guntz Emmanuel , Kapessidou Panayota , Tuna Turgay
Published: March 2023

Background

The aim of this multicenter randomized interventional prospective study was to compare the ultrasound (US)-guided lumbar medial branch block (LMBB) with the fluoroscopy (FS)-guided LMBB in terms of analgesic efficacy and disability in the setting of the treatment of pain arising from the lumbar facet joints (LFJ).

Methods

Fifty adults with a “LFJ” syndrome were randomized into two groups: in group FS, fluoroscopic-guidance was used to block the medial branch at three lumbar levels (L3-L4, L4-L5 and L5-S1); in group US, same blocks were performed under ultrasound. Needle transverse approach was used with both techniques. Effects of these procedures were assessed with a Visual Analogue Pain Scale (VAPS), the Oswestry Disability Index (ODI) and the Duke’s Activity Status Index (DASI) scale, before the treatment, 1 week and 1 month after. Hospital Anxiety and Depression Scale (HADS) score was also collected before the procedure. Analysis of variance, one (for non-inferiority) and two-sided Mann-Whitney tests and Chi-square tests were performed.

Results

LMBB under US-guidance was not inferior to FS-guidance (P = 0.047) in terms of VAPS, ODI and DASI at 1 week and 1 month. Duration of techniques and HADS were similar between groups (=0.34; p = 0.59).

Conclusions

The medial lumbar bundle branch block under ultrasound-guidance is not inferior to the fluoroscopy-guidance procedure in effectively alleviating pain arising from the facet joints. Considering that this ultrasound technique has the benefit of an irradiation-free, real-time procedure, it can be considered as an effective alternative to the fluoroscopy-guided technique.
Trajectory of worst pain within the first two weeks following pelvic and sacral tumor surgery and long-term outcome: a pilot observational prospective cohort study
Authors: Zhang Qingfen , Wu Yaqing , Hong Shenda , Feng Yi
Published: March 2023

Background

Pain management after pelvic and sacral tumor surgery is challenging and requires a multidisciplinary and multimodal approach. Few data on postoperative pain trajectories have been reported after pelvic and sacral tumor surgery. The aim of this pilot study was to determine pain trajectories within the first 2 weeks after surgery and explore the impact on long-term pain outcomes.

Methods

Patients scheduled for pelvic and sacral tumor surgery were prospectively recruited. Worst/average pain scores were evaluated postoperatively using questions adapted from the Revised American Pain Society Patient Outcome Questionnaire (APS-POQ-R) until pain resolution was reached or up to 6 months after surgery. Pain trajectories over the first 2 weeks were compared using the k-means clustering algorithm. Whether pain trajectories were associated with long-term pain resolution and opioid cessation was assessed using Cox regression analysis.

Results

A total of 59 patients were included. Two distinct groups of trajectories for worst and average pain scores over the first 2 weeks were generated. The median pain duration in the high vs low pain group was 120.0 (95% CI [25.0, 215.0]) days vs 60.0 (95% CI [38.6, 81.4]) days (log rank p = 0.037). The median time to opioid cessation in the high vs low pain group was 60.0 (95% CI [30.0, 90.0]) days vs 7.0 (95% CI [4.7, 9.3]) days (log rank p < 0.001). After adjusting for patient and surgical factors, the high pain group was independently associated with prolonged opioid cessation (hazard ratio [HR] 2.423, 95% CI [1.254, 4.681], p = 0.008) but not pain resolution (HR 1.557, 95% CI [0.748, 3.243], p = 0.237).

Conclusions

Postoperative pain is a significant problem among patients undergoing pelvic and sacral tumor surgery. High pain trajectories during the first 2 weeks after surgery were associated with delayed opioid cessation. Research is needed to explore interventions targeting pain trajectories and long-term pain outcomes.

Trial registration

The trial was registered at ClinicalTrials.gov (NCT03926858, 25/04/2019).
Association between serum HMGB1 elevation and early pediatric acute respiratory distress syndrome: a retrospective study of pediatric living donor liver transplant recipients with biliary atresia in China
Authors: Cao Yimei , Zhi Jiahao , Ren Hengchang , Sheng Mingwei , Jia Lili , Weng Yiqi , Du Hongyin , Yu Wenli
Published: March 2023

Background

High mobility group box 1 (HMGB1) protein is one of the main risk factors for pediatric acute respiratory distress syndrome (PARDS) after living donor liver transplantation (LDLT). However, studies of the relationship between HMGB1 and PARDS are lacking. We evaluated the link between anomalies of intraoperative serum HMGB1 and PARDS in pediatric LDLT recipients with biliary atresia during the first week after transplant.

Methods

Data for 210 pediatric patients with biliary atresia who underwent LDLT between January 2018 and December 2021 were reviewed retrospectively. The main measure was serum HMGB1 levels 30 min after reperfusion, while the outcome was early PARDS after LDLT. Data including pretransplant conditions, laboratory indexes, variables of intraoperation, clinical complications, and outcomes after LDLT were analyzed for each patient. Univariate analysis of PARDS and multivariate logistic regression analyses of serum HMGB1 levels at 30 min in the neohepatic phase in the presence of PARDS were conducted to examine the potential associations. Subgroup interaction analyses and linear relationships between intraoperative serum HMGB1 levels and PARDS were also performed.

Results

Among the participants, 55 had PARDS during 7 days after LDLT, including four in the first HMGB1 tertile (4.3–8.1 pg/mL), 18 in the second tertile (8.2–10.6 pg/mL), and 33 in the third tertile (10.6–18.8 pg/mL). The nonadjusted association between intraoperative HMGB1 levels and PARDS was positive (odds ratio 1.41, 95% confidence intervals 1.24–1.61, P < 0.0001). The association remained unchanged after adjustment for age, weight, pretransplant total bilirubin, albumin, graft cold ischemia time, and intraoperative blood loss volume (odds ratio 1.28, 95% confidence interval 1.10–1.49, P = 0.0017). After controlling for potential confounders, the association between intraoperative HMGB1 levels and PARDS remained positive, as well as in the subgroup analyses.

Conclusions

Serum HMGB1 levels at 30 min after reperfusion were positively associated with early PARDS among pediatric patients with biliary atresia who had undergone LDLT. Identifying such patients early may increase the efficacy of perioperative respiratory management.
Effective dose of remimazolam co-administered with remifentanil to facilitate I-gel insertion without neuromuscular blocking agents: an up-and-down sequential allocation trial
Authors: Oh Juyeon , Park Sung Yong , Lee Ga Yun , Park Ji Hyun , Joe Han Bum
Published: March 2023

Background

Remimazolam is a new anesthetic drug developed and is an ultra-short-acting agent with rapid onset and offset. The pharmacology of this drug seems to be ideal for short surgeries eligible for I-gel insertion. Therefore, this study aimed to determine the optimal bolus dose of remimazolam for I-gel insertion when co-administered with remifentanil without neuromuscular blocking agents (NMBAs).

Methods

Patients aged 19–65 years with American Society of Anesthesiologists physical status I or II scheduled for general anesthesia were enrolled. The first dose of remimazolam was 0.15 mg/kg and remifentanil was co-administered at an effect-site concentration (Ce) of 3.0 ng/mL. The dose of remimazolam for the following patient was decreased or increased by 0.05 mg/kg depending on the success or failure of I-gel insertion in the previous patient.

Results

The remimazolam bolus dose required for successful I-gel insertion in 50% of adult patients using modified Dixon’s up-and-down method with remifentanil Ce 3.0 ng/mL and no NMBAs was 0.280 ± 0.048 mg/kg. Isotonic regression analysis showed that the 50% and 95% effective doses were 0.244 (83% confidence interval [CI] 0.213–0.313) mg/kg and 0.444 (95% CI 0.436–0.448) mg/kg, respectively. The mean time to loss of consciousness (Modified Observer’s Assessment of Alertness/Sedation score < 2) was 52.2 s. Three patients (12.0%) showed a reduction in systolic blood pressure of more than 30% from baseline.

Conclusions

Selecting the appropriate dose of remimazolam/remifentanil without NMBAs makes it feasible to insert the I-gel.

Trial registration

This study protocol was registered at http://cris.nih.go.kr (KCT0007801, 12th, October, 2022).
Ultrasound-guided transversalis fascia plane block versus lateral quadratus lumborum plane block for analgesia after inguinal herniotomy in children: a randomized controlled non-inferiority study
Authors: Abdelbaser Ibrahim , Salah Doaa Mahmoud , Ateyya Amer Abdullah , Abdo Marwa Ibrahim
Published: March 2023

Background

Surgical repair of inguinal hernia is one of the most common day case surgeries in the pediatric population. This study compared the postoperative analgesic effects of transversalis fascia plane block (TFB) versus quadratus lumborum block (QLB) in children scheduled for open unilateral inguinal herniotomy.

Methods

In this prospective, randomized, double-blind, controlled non-inferiority study, 76 eligible patients were recruited. Patients were randomly allocated to either the TFB or QLB group. The primary outcome measure was the proportion of patients who needed rescue analgesia during the first postoperative 12 h. The secondary outcomes were, the time needed to perform the block, the postoperative FLACC score, intraoperative heart rate (HR) and mean arterial pressure (MAP).

Results

The proportion of patients who required a rescue analgesic was comparable (p = 1.000) between the TFB group (7/34, 20.5%) and the QLB group (6/34, 17.6%). The median [Q1-Q3] time needed to perform the block (min) was significantly longer (p < 0.001) in the QLB group (5[5]) compared with the TFB group. The postoperative FLACC pain scale was comparable between the two groups at all-time points of assessment. There is no difference regarding the heart rate and mean arterial blood pressure values at the time points that the values were recorded. (P > 0.005).

Conclusions

Both TFB and QLB similarly provide good postoperative analgesia by reducing the proportion of patients who required rescue analgesia, pain scores and analgesic consumption. Moreover, TFB is technically easier than QLB.