[Correlation between preoperative MRI measurement of cross-sectional area of hamstring tendon and graft in anterior cruciate ligament reconstruction].

OBJECTIVE: To study the corretation between the cross-sectional area of hamstring tenden measured by MRI and gragt in anterior cruciate ligament rexonstruction. METHODS: MRI data of 50 patients who planned to undergo anterior cruciate ligament reconstruction from November 2021 to March 2022 were collected, including 32 males and 18 females, aged from 19 to 48 years old with an average of(31.1±8.7) years. Before the operation, the semitendinosus and gracilis tendons were measured and recorded by MRI, and then the anterior cruciate ligament was reconstructed under arthroscope. During the operation, gracilis and semitendinosus tendons were taken to prepare the final tendon to be transplanted, and the diameter of the prepared final graft was measured during the operation. Finally, the data were analyzed by statistical software. RESULTS: The cross sectional areas of semitendinosus tendon, gracilis tendon, semitendinosus tendon and gracilis tendon measured by MRI were significantly and positively correlated with the diameter of grafts required in anterior cruciate ligament surgery, the r values were 0.858, 0.728, 0.842(P<0.001), respectively. The area under curre (AUC), sensitivity, and specificity of the sum of the cross sectional areas of semitendinosus tendon and gracilis tendon were 0.925, 90.48%, and 85.71%, respectively. CONCLUSION: In patients undergoing anterior cruciate ligament reconstruction, preoperative MRI measurement has a strong statistical correlation with the diameter of hamstring muscle transplantation during operation. The sum of the cross sectional areas of semitendinosus tendon and gracilis tendon has a high predictive value for the diameter of grafts during anterior cruciate ligament reconstruction, and can predict the size of grafts during operation.

Chromosome-level de novo genome assembly and whole-genome resequencing of the threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot.

The Hengduan Mountains region is an important hotspot of alpine plant diversity and endemism. Acanthochlamys bracteata is a species of a threatened monotypic genus endemic to the Hengduan Mountains. In this study, we present a high-quality, chromosome-level reference genome for A. bracteata, constructed using long reads, short reads and Hi-C technology. We characterized its genetic diversity, population structure, demographic history and gene flow by resequencing individuals collected across its distribution. Comparative genomics analyses based on sequence information from single-copy orthologous genes revealed that A. bracteata and Dioscorea rotundata diverged ~104.5 million years ago. Whole-genome resequencing based on population genetic analysis revealed that the division of the 14 populations into 10 distinct clusters reflected geographical divergence, and three separate high levels of gene flow occurred sequentially between isolated populations of the Hengduan Mountains, a finding which is consistent with the turnover between ice ages and interglacial periods. Our findings indicate that Quaternary climatic changes played an important role in shaping the genetic structure and demographic trajectories of A. bracteata, and provide critical insights into the genetic status and evolutionary history of this poorly understood species, and possibly other alpine plants with a similar distribution. This study demonstrates the usefulness of population genomics for evaluating the effects of past climatic changes and identifying conservation units for the conservation and management of threatened species. Our high-quality genome represents a valuable resource for future studies of the underlying molecular mechanisms of adaptive evolution and provides insight for further comparative genomic analysis with other Velloziaceae species.

Effects of aging on gene expression in blood of captive Tibetan macaques ( Macaca thibetana) and comparisons with expression in humans.

Changes in gene expression occur as animals, including primates, age. Macaques have long been used as a model species for primate evolution and biomedical studies. Here, to study gene expression in Tibetan macaques (Macaca thibetana, TMs) and its differences to humans, we applied RNA-Seq to obtain the blood transcriptomes of 24 TMs. In total, 2 523 age-associated differentially expressed genes (DEGs) were identified. Several pathways and processes that regulate aging, including the FoxO signaling pathway, autophagy, and platelet activation, were significantly enriched in the up-regulated DEGs. Two significantly age-related modules were identified by weighted gene co-expression network analysis (WGCNA). The TMs and humans shared 279 common DEGs, including 111 up-regulated and 141 down-regulated genes with advancing age in the same expression direction. However, 27 age-related DEGs presented the opposite expression direction in TMs as that in humans. For example, INPPL1, with inhibitory effects on the B cell receptor signaling pathway, was up-regulated in humans but down-regulated in TMs. In general, our study suggests that aging is a critical factor affecting gene expression in the captive TM population. The similarities and differences in gene expression patterns between TMs and humans could provide new insights into primate evolution and benefit TM model development.

Reassessment of the taxonomic status of Craseomys and three controversial species of Myodes and Alticola (Rodentia: Arvicolinae).

The genera Myodes (red-backed voles) and Alticola (mountain voles) appear to be sister taxa based on morphological similarities, but molecular analyses fail to resolve them as monophyletic genera owing to the uncertain taxonomic status of Craseomys and Phaulomys. As a result of incomplete sampling of related specimens, ongoing controversies on the taxonomic positions of several generic and specific taxa necessitate further clarifications. Herein, we combined molecular, morphometric, and geometric morphometric approaches to analyze 217 specimens of 10 taxa of Myodes and Alticola systematically. We sequenced three genes (Cytb, COI, GHR) de novo from specimens with fresh tissues, and published sequences for M. shanseius and A. stoliczkanus for the first time. Based on this new molecular dataset, we produced phylogenetic trees using Bayesian inference, maximum likelihood, and maximum parsimony approaches. Our molecular and morphological analyses both identified three primary clades within Myodes and Alticola. The Craseomys-Phaulomys clade consistently separated from Myodes sensu stricto (s. str.) and Alticola s. str.-Platycranius. Our results support the resurrection of the genus Craseomys and the treatment of Phaulomys as its junior synonym. As Craseomys shanseius clustered with C. rufocanus in three gene phylogenies and this assessment was congruent with morphological results, we assigned C. shanseius to a subspecies of C. rufocanus. Specimens from one sampling site in Pulan County of Tibet possess M3 patterns typical of A. stoliczkanus and A. stracheyi, despite clustering together in matrilineal genealogy. Thus, we tentatively assigned A. stracheyi as a junior synonym of A. stoliczkanus. Our analyses confirmed the validity of A. semicanus and unambiguously distinguished it from A. argentatus by the ratio of tail length to head-body length, color of tail and feet, M3 pattern, and distribution.

Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes.

As the first examination of distribution, guanine-cytosine (GC) pattern, and variation analysis of microsatellites (SSRs) in different genomic regions of six bovid species, SSRs displayed nonrandomly distribution in different regions. SSR abundances are much higher in the introns, transposable elements (TEs), and intergenic regions compared to the 3'-untranslated regions (3'UTRs), 5'UTRs and coding regions. Trinucleotide perfect SSRs (P-SSRs) were the most frequent in the coding regions, whereas, mononucleotide P-SSRs were the most in the introns, 3'UTRs, TEs, and intergenic regions. Trifold P-SSRs had more GC-contents in the 5'UTRs and coding regions than that in the introns, 3'UTRs, TEs, and intergenic regions, whereas mononucleotide P-SSRs had the least GC-contents in all genomic regions. The repeat copy numbers (RCN) of the same mono- to hexanucleotide P-SSRs showed significantly different distributions in different regions (P < 0.01). Except for the coding regions, mononucleotide P-SSRs had the most RCNs, followed by the pattern: di- > tri- > tetra- > penta- > hexanucleotide P-SSRs in the same regions. The analysis of coefficient of variability (CV) of SSRs showed that the CV variations of RCN of the same mono- to hexanucleotide SSRs were relative higher in the intronic and intergenic regions, followed by the CV variation of RCN in the TEs, and the relative lower was in the 5'UTRs, 3'UTRs, and coding regions. Wide SSR analysis of different genomic regions has helped to reveal biological significances of their distributions.

Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes.

As the first systematic examination of simple sequence repeats (SSRs) and guanine-cytosine (GC) distribution in intragenic and intergenic regions of ten primates, our study showed that SSRs and GC displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation. Our results suggest that the majority of SSRs are distributed in non-coding regions, such as the introns, TEs, and intergenic regions. In these primates, trinucleotide perfect (P) SSRs were the most abundant repeats type in the 5'UTRs and CDSs, whereas, mononucleotide P-SSRs were the most in the intron, 3'UTRs, TEs, and intergenic regions. The GC-contents varied greatly among different intragenic and intergenic regions: 5'UTRs > CDSs > 3'UTRs > TEs > introns > intergenic regions, and high GC-content was frequently distributed in exon-rich regions. Our results also showed that in the same intragenic and intergenic regions, the distribution of GC-contents were great similarity in the different primates. Tri- and hexanucleotide P-SSRs had the most GC-contents in the 5'UTRs and CDSs, whereas mononucleotide P-SSRs had the least GC-contents in the six genomic regions of these primates. The most frequent motifs for different length varied obviously with the different genomic regions.