A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data.

Genetic and gene expression heterogeneity is an essential hallmark of many tumors, allowing the cancer to evolve and to develop resistance to treatment. Currently, the most commonly used data types for studying such heterogeneity are bulk tumor/normal whole-genome or whole-exome sequencing (WGS, WES); and single-cell RNA sequencing (scRNA-seq), respectively. However, tools are currently lacking to link genomic tumor subclonality with transcriptomic heterogeneity by integrating genomic and single-cell transcriptomic data collected from the same tumor. To address this gap, we developed scBayes, a Bayesian probabilistic framework that uses tumor subclonal structure inferred from bulk DNA sequencing data to determine the subclonal identity of cells from single-cell gene expression (scRNA-seq) measurements. Grouping together cells representing the same genetically defined tumor subclones allows comparison of gene expression across different subclones, or investigation of gene expression changes within the same subclone across time (i.e., progression, treatment response, or relapse) or space (i.e., at multiple metastatic sites and organs). We used simulated data sets, in silico synthetic data sets, as well as biological data sets generated from cancer samples to extensively characterize and validate the performance of our method, as well as to show improvements over existing methods. We show the validity and utility of our approach by applying it to published data sets and recapitulating the findings, as well as arriving at novel insights into cancer subclonal expression behavior in our own data sets. We further show that our method is applicable to a wide range of single-cell sequencing technologies including single-cell DNA sequencing as well as Smart-seq and 10x Genomics scRNA-seq protocols.

High-order superlattices by rolling up van der Waals heterostructures.

Two-dimensional (2D) materials1,2 and the associated van der Waals (vdW) heterostructures3-7 have provided great flexibility for integrating distinct atomic layers beyond the traditional limits of lattice-matching requirements, through layer-by-layer mechanical restacking or sequential synthesis. However, the 2D vdW heterostructures explored so far have been usually limited to relatively simple heterostructures with a small number of blocks8-18. The preparation of high-order vdW superlattices with larger number of alternating units is exponentially more difficult, owing to the limited yield and material damage associated with each sequential restacking or synthesis step8-29. Here we report a straightforward approach to realizing high-order vdW superlattices by rolling up vdW heterostructures. We show that a capillary-force-driven rolling-up process can be used to delaminate synthetic SnS2/WSe2 vdW heterostructures from the growth substrate and produce SnS2/WSe2 roll-ups with alternating monolayers of WSe2 and SnS2, thus forming high-order SnS2/WSe2 vdW superlattices. The formation of these superlattices modulates the electronic band structure and the dimensionality, resulting in a transition of the transport characteristics from semiconducting to metallic, from 2D to one-dimensional (1D), with an angle-dependent linear magnetoresistance. This strategy can be extended to create diverse 2D/2D vdW superlattices, more complex 2D/2D/2D vdW superlattices, and beyond-2D materials, including three-dimensional (3D) thin-film materials and 1D nanowires, to generate mixed-dimensional vdW superlattices, such as 3D/2D, 3D/2D/2D, 1D/2D and 1D/3D/2D vdW superlattices. This study demonstrates a general approach to producing high-order vdW superlattices with widely variable material compositions, dimensions, chirality and topology, and defines a rich material platform for both fundamental studies and technological applications.

Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data.

MOTIVATION: Multiple displacement amplification (MDA) has become the most commonly used method of whole genome amplification, generating a vast amount of DNA with higher molecular weight and greater genome coverage. Coupling with long-read sequencing, it is possible to sequence the amplicons of over 20 kb in length. However, the formation of chimeric sequences (chimeras, expressed as structural errors in sequencing data) in MDA seriously interferes with the bioinformatics analysis but its influence on long-read sequencing data is unknown. RESULTS: We sequenced the phi29 DNA polymerase-mediated MDA amplicons on the PacBio platform and analyzed chimeras within the generated data. The 3rd-ChimeraMiner has been constructed as a pipeline for recognizing and restoring chimeras into the original structures in long-read sequencing data, improving the efficiency of using TGS data. Five long-read datasets and one high-fidelity long-read dataset with various amplification folds were analyzed. The result reveals that the mis-priming events in amplification are more frequently occurring than widely perceived, and the propor tion gradually accumulates from 42% to over 78% as the amplification continues. In total, 99.92% of recognized chimeric sequences were demonstrated to be artifacts, whose structures were wrongly formed in MDA instead of existing in original genomes. By restoring chimeras to their original structures, the vast majority of supplementary alignments that introduce false-positive structural variants are recycled, removing 97% of inversions on average and contributing to the analysis of structural variation in MDA-amplified samples. The impact of chimeras in long-read sequencing data analysis should be emphasized, and the 3rd-ChimeraMiner can help to quantify and reduce the influence of chimeras. AVAILABILITY AND IMPLEMENTATION: The 3rd-ChimeraMiner is available on GitHub, https://github.com/dulunar/3rdChimeraMiner.

PGD: Shared gene linking polycystic ovary syndrome and endometrial cancer, influencing proliferation and migration through glycometabolism.

The relationship among polycystic ovary syndrome (PCOS), endometrial cancer (EC), and glycometabolism remains unclear. We explored shared genes between PCOS and EC, using bioinformatics to unveil their pathogenic connection and influence on EC prognosis. Gene Expression Omnibus datasets GSE226146 (PCOS) and GSE196033 (EC) were used. A protein-protein interaction (PPI) network was constructed to identify the central genes. Candidate markers were screened using dataset GSE54250. Differences in marker expression were confirmed in mouse PCOS and human EC tissues using RT-PCR and immunohistochemistry. The effect of PGD on EC proliferation and migration was explored using Ki-67 and Transwell assays. PGD's impact on the glycometabolic pathway within carbon metabolism was assessed by quantifying glucose content and lactic acid production. R software identified 31 common genes in GSE226146 and GSE196033. Gene Ontology functional classification revealed enrichment in the "purine nucleoside triphosphate metabolism process," with key Kyoto Encyclopedia of Genes and Genomes pathways related to "carbon metabolism." The PPI network identified 15 hub genes. HK2, NDUFS8, PHGDH, PGD, and SMAD3 were confirmed as candidate markers. The RT-PCR analysis validated distinct HK2 and PGD expression patterns in mouse PCOS ovarian tissue and human EC tissue, as well as in normal and EC cells. Transfection experiments with Ishikawa cells further confirmed PGD's influence on cell proliferation and migration. Suppression of PGD expression impeded glycometabolism within the carbon metabolism of EC cells, suggesting PGD as a significant PCOS risk factor impacting EC proliferation and migration through modulation of single carbon metabolism. These findings highlight PGD's pivotal role in EC onset and prognosis.

Arsenic: A Global Environmental Challenge.

Arsenic is a naturally occurring metalloid and one of the few metals that can be metabolized inside the human body. The pervasive presence of arsenic in nature and anthropogenic sources from agricultural and medical use have perpetuated human exposure to this toxic and carcinogenic element. Highly exposed individuals are susceptible to various illnesses, including skin disorders; cognitive impairment; and cancers of the lung, liver, and kidneys. In fact, across the globe, approximately 200 million people are exposed to potentially toxic levels of arsenic, which has prompted substantial research and mitigation efforts to combat this extensive public health issue. This review provides an up-to-date look at arsenic-related challenges facing the global community, including current sources of arsenic, global disease burden, arsenic resistance, and shortcomings of ongoing mitigation measures, and discusses potential next steps.

quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics.

MOTIVATION: In time-critical clinical settings, such as precision medicine, genomic data needs to be processed as fast as possible to arrive at data-informed treatment decisions in a timely fashion. While sequencing throughput has dramatically increased over the past decade, bioinformatics analysis throughput has not been able to keep up with the pace of computer hardware improvement, and consequently has now turned into the primary bottleneck. Modern computer hardware today is capable of much higher performance than current genomic informatics algorithms can typically utilize, therefore presenting opportunities for significant improvement of performance. Accessing the raw sequencing data from BAM files, e.g. is a necessary and time-consuming step in nearly all sequence analysis tools, however existing programming libraries for BAM access do not take full advantage of the parallel input/output capabilities of storage devices. RESULTS: In an effort to stimulate the development of a new generation of faster sequence analysis tools, we developed quickBAM, a software library to accelerate sequencing data access by exploiting the parallelism in commodity storage hardware currently widely available. We demonstrate that analysis software ported to quickBAM consistently outperforms their current versions, in some cases finishing an analysis in under 3 min while the original version took 1.5 h, using the same storage solution. AVAILABILITY AND IMPLEMENTATION: Open source and freely available at https://gitlab.com/yiq/quickbam/, we envision that quickBAM will enable a new generation of high-performance informatics tools, either directly boosting their performance if they are currently data-access bottlenecked, or allow data-access to keep up with further optimizations in algorithms and compute techniques.

Exact Solution of the Bose-Hubbard Model with Unidirectional Hopping.

A one-dimensional Bose-Hubbard model with unidirectional hopping is shown to be exactly solvable. Applying the algebraic Bethe ansatz method, we prove the integrability of the model and derive the Bethe ansatz equations. The exact eigenvalue spectrum can be obtained by solving these equations. The distribution of Bethe roots reveals the presence of a superfluid-Mott insulator transition at the ground state, and the critical point is determined. By adjusting the boundary parameter, we demonstrate the existence of a non-Hermitian skin effect even in the presence of interaction, but it is completely suppressed for the Mott insulator state in the thermodynamical limit. Our result represents a new class of exactly solvable non-Hermitian many-body systems, which has no Hermitian correspondence and can be used as a benchmark for various numerical techniques developed for non-Hermitian many-body systems.

Prevalent arbuscular mycorrhizae in roots and highly variable mycobiome in leaves of epiphytic subtropical fern Ophioderma pendulum.

PREMISE: Endophytic and mycorrhizal fungi are crucial in facilitating plant nutrition acquisition and stress tolerance. In epiphytic habitats, plants face nutrition and water stress, but their roots are mostly nonmycorrhizal and especially lacking in arbuscular mycorrhizal associations. Ophioderma pendulum is an epiphytic fern with a partially mycoheterotrophic lifestyle, likely heavily reliant on symbiotic fungi. To characterize fungal associations in the sporophyte of O. pendulum, we focused on leaves and roots of O. pendulum, seeking to reveal the fungal communities in these organs. METHODS: Roots and leaves from O. pendulum in a subtropical forest were examined microscopically to observe the morphology of fungal structures and determine the percentage of various fungal structures in host tissues. Fungal composition was profiled using metabarcoding techniques that targeted ITS2 of the nuclear ribosomal DNA. RESULTS: Roots were consistently colonized by arbuscular mycorrhizal fungi (Glomeromycota), especially Acaulospora. Unlike previous findings on epiphytic ferns, dark septate endophytes were rare in O. pendulum roots. Leaves were predominantly colonized by Ascomycota fungi, specifically the classes Dothideomycetes (46.88%), Eurotiomycetes (11.51%), Sordariomycetes (6.23%), and Leotiomycetes (6.14%). Across sampling sites, fungal community compositions were similar in the roots but differed significantly in the leaves. CONCLUSIONS: Ophioderma pendulum maintains stable, single-taxon-dominant communities in the roots, primarily featuring arbuscular mycorrhizal fungi, whereas the leaves may harbor opportunistic fungal colonizers. Our study underlines the significance of mycorrhizal fungi in the adaptation of epiphytic ferns.

Investigating the transcriptomic variances in two phases Ecytonucleospora hepatopenaei (EHP) in Litopenaeus vannamei.

This study explores the transcriptomic differences in two distinct phases of Ecytonucleospora hepatopenaei (EHP) in Litopenaeus vannamei, a crucial aspect in shrimp health management. We employed high-throughput sequencing to categorize samples into two phases, 'Phase A' and 'Phase B', defined by the differential expression of PTP2 and TPS1 genes. Our analysis identified 2057 genes, with 78 exhibiting significant variances, including 62 upregulated and 16 downregulated genes. Enrichment analyses via GO and KEGG pathways highlighted these genes' roles in cellular metabolism, signal transduction, and immune responses. Notably, genes like IQGAP2, Rhob, Pim1, and PCM1 emerged as potentially crucial in EHP's infection process and lifecycle. We hypothesize that these genes may influence trehalose metabolism and glucose provision, impacting the biological activities within EHP during different phases. Interestingly, a lower transcript count in 'Phase A' EHP suggests a reduction in biological activities, likely preparing for host cell invasion. This research provides a foundational understanding of EHP infection mechanisms, offering vital insights for future studies and therapeutic interventions.

Double-Level Knee Derotational Osteotomy Yields Better Postoperative Outcomes Than Tibial Tubercle Transfer Combined With Medial Patellofemoral Ligament Reconstruction in Patients With Recurrent Patellar Instability and Severe Malrotation.

PURPOSE: To assess the postoperative outcomes of double-level knee derotational osteotomy (KDRO) combined with medial patellofemoral ligament reconstruction (MPFLR) and to compare it with tibial tuber transfer (TTT) and MPFLR without derotational osteotomy in patients with recurrent patellar instability and a marked torsional deformity. METHODS: From March 2020 to December 2021, patients with torsion deformity (combined femoral torsion [FT] and tibial torsion [TTn] ≥30°) were retrospectively included. The minimum follow-up time was 18 months. Patients who received KDRO and MPFLR were categorized as the KDRO group and patients who received a combined TTT and MPFLR were categorized as the control group. Preoperative and postoperative clinical symptoms, patient-reported outcomes (Kujala, visual analog scale, Lysholm, International Knee Documentation Committee, Tegner, and Knee Injury and Osteoarthritis Outcome scores), and imaging parameters (FT, TTn, patellar height, femoral trochlear dysplasia, congruence angle, patellar tilt angle, lateral patellar angle, lateral patellar translation, and tibial tubercle-trochlear groove distance) were analyzed. RESULTS: In all, 36 patients were included with 18 in KDRO group and 18 in control group. The mean follow-up time was 30 (range 21-39) months. At the latest follow-up, no patient experienced redislocation in either group. Except for the FT and TTn in the control group, postoperative imaging parameters were significantly reduced to the normal range. KDRO group had a lower patellar tilt angle (P = .043, effect size 0.64). All clinical scores in both groups significantly improved postoperatively. The KDRO group had better functional scores than control group except the KOOS daily living activities subscore and the KOOS sports and recreation subscore. More patients in the KDRO group met the minimal clinically important difference for most patient-reported outcomes than the control group. Eight patients (44%) in the control group complained of postoperative anterior knee pain, compared with 1 patient (6%) in the KDRO group (P = .018). CONCLUSIONS: KDRO combined with MPFLR was associated with better postoperative outcomes than TTT combined with MPFLR in patients with recurrent patellar instability and a torsion deformity. LEVEL OF EVIDENCE: Level III, retrospective cohort study.

The Value of Minimal Clinically Important Difference, Substantial Clinical Benefit, and Patient-Acceptable Symptomatic State for Commonly Used Patient-Reported Outcomes in Recurrent Patellar Instability Patients After Medial Patellofemoral Ligament Reconstruction and Tibial Tubercle Transfer.

PURPOSE: To identify the minimal clinically important difference (MCID), substantial clinical benefit (SCB) and patient-acceptable symptomatic state (PASS) for commonly used patient-reported outcomes (PROs) in recurrent patellar instability patients after medial patellofemoral ligament reconstruction (MPFLR) and tibial tubercle transfer (TTT), and to determine the impact of potential prognostic factors on the likelihood of achieving these values. METHODS: From April 2015 to February 2021, patients who underwent MPFLR and TTT were retrospectively reviewed. PROs included Kujala, Knee Injury and Osteoarthritis Outcome (KOOS), Lysholm, International Knee Documentation Committee (IKDC), and Tegner score. Relevant anchor questions were provided. A distribution- or anchor-based method was adopted to determine the MCID, SCB, and PASS. Minimal detectable change (MDC) was included to confirm the validity. Univariate regression analyses were conducted to determine the potential prognostic factors. RESULTS: One hundred forty-two patients were included. The MCID were 9.1 (Kujala), 11.1 (Lysholm), 0.9 (Tegner), 9.9 (IKDC), 9.0 (KOOS-Pain), 10.8 (KOOS-Symptoms), 10.0 (KOOS-Activities of Daily Living [ADL]), 17.8 (KOOS-Sports and Recreation [Sports/Rec]), and 12.7 (KOOS-Quality of Life [QoL]). The SCB were 14.5 (Kujala), 12.5 (Lysholm), 1.5 (Tegner), 14.5 (IKDC), 13.9 (KOOS-Pain), 14.3 (KOOS-Symptoms), 18.4 (KOOS-ADL), 47.5 (KOOS-Sports/Rec), and 15.0 (KOOS-QoL). The PASSs were 85.5 (Kujala), 75.5 (Lysholm), 3.5 (Tegner), 73.2 (IKDC), 87.5 (KOOS-Pain), 73.2 (KOOS-Symptoms), 92.0 (KOOS-ADL), 77.5 (KOOS-Sports/Rec), and 53.1 (KOOS-QoL). All SCBs were valid except KOOS-QoL. All MCIDs were valid at the 95% confidence interval (CI) except KOOS scores, the majority of which were valid at the 90% CI. A younger age was an independent prognostic factor of reaching PASS for Lysholm, IKDC, Tegner, and KOOS-ADL score. A higher baseline score was a negative prognostic factor for achieving MCID or SCB but had a slightly positive influence on the achievement of PASS. CONCLUSIONS: This study established the MCID, SCB, and PASS for commonly used PROs and confirmed their validity in recurrent patellar instability patients after MPFLR and TTT. Younger age and lower baseline scores were prognostic factors of achieving MCID and SCB, whereas patients with higher baseline scores were more likely to report satisfaction. LEVEL OF EVIDENCE: Level III, retrospective comparative prognostic trial.

Application of Deferoxamine in Tissue Regeneration Attributed to Promoted Angiogenesis.

Deferoxamine, an iron chelator used to treat diseases caused by excess iron, has had a Food and Drug Administration-approved status for many years. A large number of studies have confirmed that deferoxamine can reduce inflammatory response and promote angiogenesis. Blood vessels play a crucial role in sustaining vital life by facilitating the delivery of immune cells, oxygen, and nutrients, as well as eliminating waste products generated during cellular metabolism. Dysfunction in blood vessels may contribute significantly to the development of life-threatening diseases. Anti-angiogenesis therapy and pro-angiogenesis/angiogenesis strategies have been frequently recommended for various diseases. Herein, we describe the mechanism by which deferoxamine promotes angiogenesis and summarize its application in chronic wounds, bone repair, and diseases of the respiratory system. Furthermore, we discuss the drug delivery system of deferoxamine for treating various diseases, providing constructive ideas and inspiration for the development of new treatment strategies.

Oral appliance therapy vs. positional therapy for managing positional obstructive sleep apnea; a systematic review and meta-analysis of randomized control trials.

AIM: To assess the efficacy of positional therapy and oral appliance therapy for the management of positional obstructive sleep apnea. METHODS: We searched PubMed, Web of Science, Cochrane, and SCOPUS for relevant clinical trials. Quality assessment of the included trials was evaluated according to Cochrane's risk of bias tool. We included the following outcomes: The apnea-hypopnea index (AHI), AHI non-supine, AHI supine, sleep efficiency, percentage of supine sleep, Adherence (≥ 4 h/night, ≥ 5 days/week), Oxygen desaturation Index, Arousal Index, Epworth Sleepiness Scale score (ESS), Mean SpO2, and Functional Outcomes of Sleep Questionnaire. RESULTS: The AHI non-supine and the ESS scores were significantly lower in the OAT cohort than in the PT cohort. The PT cohort was associated with a significantly decreased percentage of supine sleep than the OAT cohort (MD= -26.07 [-33.15, -19.00], P = 0.0001). There was no significant variation between PT cohort and OAT cohort regarding total AHI, AHI supine, ODI, sleep efficiency, arousal index, FOSQ, adherence, and mean SpO2. CONCLUSION: Both Positional Therapy and Oral Appliance Therapy effectively addressed Obstructive Sleep Apnea. However, Oral Appliance Therapy exhibited higher efficiency, leading to increased supine sleep percentage and more significant reductions in the Apnea Hypopnea Index during non-supine positions, as well as lower scores on the Epworth Sleepiness Scale.

The Green Box: Selenoviologen-Based Tetracationic Cyclophane for Electrochromism, Host-Guest Interactions, and Visible-Light Photocatalysis.

The novel selenoviologen-based tetracationic cyclophanes (green boxes 3 and 5) with rigid electron-deficient cavities are synthesized via SN2 reactions in two steps. The green boxes exhibit good redox properties, narrow energy gaps, and strong absorption in the visible range (370-470 nm), especially for the green box 5 containing two selenoviologen (SeV2+) units. Meanwhile, the femtosecond transient absorption (fs-TA) reveals that the green boxes have a stabilized dicationic biradical, high efficiency of intramolecular charge transfer (ICT), and long-lived charge separation state due to the formation of cyclophane structure. Based on the excellent photophysical and redox properties, the green boxes are applied to electrochromic devices (ECDs) and visible-light-driven hydrogen production with a high H2 generation rate (34 µmol/h), turnover number (203), and apparent quantum yield (5.33 × 10-2). In addition, the host-guest recognitions are demonstrated between the green boxes and electron-rich guests (e.g., G1:1-naphthol and G2:platinum(II)-tethered naphthalene) in MeCN through C-H···π and π···π interactions. As a one-component system, the host-guest complexes of green box⊃G2 are successfully applied to visible-light photocatalytic hydrogen production due to the intramolecular electron transfer (IET) between platinum(II) of G2 and SeV2+ of the green box, which provides a simplified system for solar energy conversion.

FAM3A Ameliorates Brain Impairment Induced by Hypoxia-Ischemia in Neonatal Rat.

Hypoxia-ischemia (HI) during crucial periods of brain formation can lead to changes in brain morphology, propagation of neuronal stimuli, and permanent neurodevelopmental impairment, which can have profound effects on cognitive function later in life. FAM3A, a subgroup of family with sequence similarity 3 (FAM3) gene family, is ubiquitously expressed in almost all cells. Overexpression of FAM3A has been evidenced to reduce hyperglycemia via the PI3K/Akt signaling pathway and protect mitochondrial function in neuronal HT22 cells. This study aims to evaluate the protective role of FAM3A in HI-induced brain impairment. Experimentally, maternal rats underwent uterine artery bilateral ligation to induce neonatal HI on day 14 of gestation. At 6 weeks of age, cognitive development assessments including NSS, wire grip, and water maze were carried out. The animals were then sacrificed to assess cerebral mitochondrial function as well as levels of FAM3A, TNF-α and IFN-γ. Results suggest that HI significantly reduced FAM3A expression in rat brain tissues, and that overexpression of FAM3A through lentiviral transduction effectively improved cognitive and motor functions in HI rats as reflected by improved NSS evaluation, cerebral water content, limb strength, as well as spatial learning and memory. At the molecular level, overexpression of FAM3A was able to promote ATP production, balance mitochondrial membrane potential, and reduce levels of pro-inflammatory cytokines TNF-α and IFN-γ. We conclude that FAM3A overexpression may have a protective effect on neuron morphology, cerebral mitochondrial as well as cognitive function. Created with Biorender.com.

A comparative transcriptome analysis of how shrimp endure and adapt to long-term symbiosis with Enterocytozoon hepatopenaei infection.

Enterocytozoon hepatopenaei (EHP) is a prevalent microsporidian pathogen responsible for hepatopancreatic microsporidiosis (HPM) in Litopenaeus vannamei. This infection not only leads to slowed growth in shrimp abut aslo inflicts substantial economic losses in the global aquaculture industry. However, the molecular mechanisms by which EHP influences the host during various infection stages remain unclear. This study employed comparative transcriptomics to examine the effects of EHP infection on Litopenaeus vannamei between early and late stage of infection groups. Utilizing transcriptomic approaches, we identified differentially expressed genes (DEGs) with notable biological significance through the COG, GO, KEGG, GSEA, and Mufzz time-series methodologies. The results reveal that EHP infection considerably influences host gene expression, with marked differences between early and late infection across distinct timeframes. Key processes such as detoxification, cell apoptosis, and lipid metabolism are pivotal during host-parasite interactions. Hexokinase and phosphatidic acid phosphatase emerge as key factors enabling invasion and sustained effects. Cytochrome P450 and glucose-6-phosphate dehydrogenase could facilitate infection progression. EHP significantly impacts growth, especially through ecdysteroids and 17ß-estradiol dehydrogenase. By delineating stage-specific effects, we gain insights into interaction between EHP and Litopenaeus vannamei, showing how intracellular pathogens reprogram host defenses into mechanisms enabling long-term persistence. This study provides a deeper understanding of host-pathogen dynamics, emphasizing the interplay between detoxification, metabolism, immunity, apoptosis and growth regulation over the course of long-term symbiosis.

Comparative transcriptome analysis of non-germinated and germinated spores of Enterocytozoon hepatopenaei (EHP) in vitro.

Enterocytozoon hepatopenaei (EHP), an obligate intracellular parasite classified as microsporidia, is an emerging pathogen with a significant impact on the global shrimp aquaculture industry. The understanding of how microsporidia germinate has been a key factor in exploring its infection process. However, the germination process of EHP was rarely reported. To gain insight into the germination process, we conducted a high-throughput sequencing analysis of purified EHP spores that had undergone in vitro germination treatment. This analysis revealed 137 differentially expressed genes, with 84 up-regulated and 53 down-regulated genes. While the functions of some of the genes remain unknown, this study provides important data on the transcriptomic changes before and after EHP germination, which can aid in further studies on the EHP infection mechanism.

Prevalence and a correlation analysis of discoid meniscus and femoral trochlear dysplasia.

BACKGROUND: Discoid meniscus (DM) and femoral trochlear dysplasia (FTD) are common knee disorders. Both as congenital malformation, whether there is a connection between them is unclear and the research on their prevalence in the general population is inadequate. This study aimed to investigate the prevalence of FTD and DM in the general population through a large sample size, and to explore the relationship between them. STUDY DESIGN: Retrospective study. METHODS: Patients undergoing knee magnetic resonance imaging (MRI) examinations at our outpatient clinic were screened and 1003 patients were enrolled in DM group with 989 patients in non-DM (NDM) group. The type of DM and FTD was classified with Watanabe classification and Dejour's classification, respectively. The prevalence of FTD and DM in the general population and the relationship between them were evaluated. RESULTS: The prevalence of DM and FTD was 10.0% and 14.5%, respectively. The overall percentage of FTD was higher in DM group (P < 0.001). The DM group has a higher percentage of all types of FTD except type D (P < 0.05), and a higher percentage of both low- and high-grade FTD (P < 0.001). There were 633 cases of type I DM and 370 cases of type II DM. The overall percentage of FTD was not significantly different between the two types (P = 0.106). No significant difference was detected for all types of FTD except type B (P < 0.05). The Type I DM group has a significant higher percentage of high-grade FTD than Type II group (P < 0.05). CONCLUSION: Patients with a DM are more likely to have FTD regardless of the type of DM, while those with a type I DM are more prone to have a high grade FTD.

Meniscal resection increases the risk of residual knee laxity even in patients undergoing anatomic double-bundle anterior cruciate ligament reconstruction with eight strands of hamstring autografts.

PURPOSE: To compare the midterm clinical outcomes of different meniscal surgeries in patients undergoing anatomic double-bundle anterior cruciate ligament reconstruction (DB-ACLR) with eight strands of hamstring (HT8) autografts and explore the potential predictive risk factors for residual knee laxity. METHODS: From 2010 to 2017, a total of 410 patients who underwent anatomic trans-tibial DB-ACLR with HT8 autografts (169 patients without meniscal surgery, 105 patients with meniscal repair, and 136 patients with meniscal resection) were included in this study. The equivalent graft diameter was introduced to make the total graft size of DB-ACLR comparable with that of single-bundle ACLR and calculated as the square root of the quadratic sum of the diameter for each bundle. Residual laxity was defined as excessive anterior tibial translation or residual pivot shift at any follow-up visit, while graft rupture was confirmed by second-look arthroscopy or magnetic resonance imaging. RESULTS: The mean follow-up period was 8.3 ± 2.2 years. The mean equivalent graft diameter was 9.9 ± 0.7 mm. Graft rupture was confirmed in 16 (3.9%) patients, while residual laxity was detected in 72 (17.6%) patients (34 [25.0%] in the meniscal resection group vs. 22 [13.0%] in the no meniscal surgery group, p = 0.021). In the multivariate logistic regression analysis, high-grade preoperative knee laxity (odds ratio OR 2.04, p = 0.020), equivalent graft diameter < 9 mm (OR 3.31 compared with 9-10 mm, p = 0.012; OR 3.28 compared with ≥ 10 mm, p = 0.019), and meniscal resection (OR 1.94 compared with no meniscal surgery, p = 0.045) were associated with residual laxity. CONCLUSION: During a midterm follow-up, meniscal resection increased the risk of residual knee laxity even in patients undergoing anatomic DB-ACLR with HT8 autografts. Increasing the hamstring graft diameter and preserving the menisci are important strategies for ACLR to restore knee stability. LEVEL OF EVIDENCE: Level III.

Dynamic Interplay of Metabolic and Transcriptional Responses in Shrimp during Early and Late Infection Stages of Enterocytozoon hepatopenaei (EHP).

Enterocytozoon hepatopenaei (EHP) is a microsporidian parasite that infects Litopenaeus vannamei, causing severe hepatopancreatic microsporidiosis (HPM) and resulting in significant economic losses. This study utilizes a combined analysis of transcriptomics and metabolomics to unveil the dynamic molecular interactions between EHP and its host, the Pacific white shrimp, during the early and late stages of infection. The results indicate distinct immunological, detoxification, and antioxidant responses in the early and late infection phases. During early EHP infection in shrimp, immune activation coincides with suppression of genes like Ftz-F1 and SEPs, potentially aiding parasitic evasion. In contrast, late infection shows a refined immune response with phagocytosis-enhancing down-regulation of Ftz-F1 and a resurgence in SEP expression. This phase is characterized by an up-regulated detoxification and antioxidant response, likely a defense against the accumulated effects of EHP, facilitating a stable host-pathogen relationship. In the later stages of infection, most immune responses return to baseline levels, while some immune genes remain active. The glutathione antioxidant system is suppressed early on but becomes activated in the later stages. This phenomenon could facilitate the early invasion of EHP while assisting the host in mitigating oxidative damage caused by late-stage infection. Notably, there are distinctive events in polyamine metabolism. Sustained up-regulation of spermidine synthase and concurrent reduction in spermine levels suggest a potential role of polyamines in EHP development. Throughout the infection process, significant differences in genes such as ATP synthase and hexokinase highlight the continuous influence on energy metabolism pathways. Additionally, growth-related pathways involving amino acids such as tryptophan, histidine, and taurine are disrupted early on, potentially contributing to the growth inhibition observed during the initial stages of infection. In summary, these findings elucidate the dynamic interplay between the host, Litopenaeus vannamei, and the parasite, EHP, during infection. Specific phase differences in immune responses, energy metabolism, and antioxidant processes underscore the intricate relationship between the host and the parasite. The disruption of polyamine metabolism offers a novel perspective in understanding the proliferation mechanisms of EHP. These discoveries significantly advance our comprehension of the pathogenic mechanisms of EHP and its interactions with the host.