Clinically relevant immune subtypes based on alternative splicing landscape of immune-related genes for lung cancer advanced PPPM approach.

Background: Alternative splicing (AS) occurs in the process of gene post-transcriptional process, which is very important for the correct synthesis and function of protein. The change of AS pattern may lead to the change of expression level or function of lung cancer-related genes, and then affect the occurrence and development of lung cancers. The specific AS pattern might be used as a biomarker for early warning and prognostic assessment of a cancer in the framework of predictive, preventive, and personalized medicine (PPPM; 3PM). AS events of immune-related genes (IRGs) were closely associated with tumor progression and immunotherapy. We hypothesize that IRG-AS events are significantly different in lung adenocarcinomas (LUADs) vs. controls or in lung squamous cell carcinomas (LUSCs) vs. controls. IRG-AS alteration profiling was identified to construct IRG-differentially expressed AS (IRG-DEAS) signature models. Study on the selective AS events of specific IRGs in lung cancer patients might be of great significance for further exploring the pathogenesis of lung cancer, realizing early detection and effective monitoring of lung cancer, finding new therapeutic targets, overcoming drug resistance, and developing more effective therapeutic strategies, and better used for the prediction, diagnosis, prevention, and personalized medicine of lung cancer. Methods: The transcriptomic, clinical, and AS data of LUADs and LUSCs were downloaded from TCGA and its SpliceSeq databases. IRG-DEAS events were identified in LUAD and LUSC, followed by their functional characteristics, and overall survival (OS) analyses. OS-related IRG-DEAS prognostic models were constructed for LUAD and LUSC with Lasso regression, which were used to classify LUADs and LUSCs into low- and high-risk score groups. Furthermore, the immune cell distribution, immune-related scores, drug sensitivity, mutation status, and GSEA/GSVA status were analyzed between low- and high-risk score groups. Also, low- and high-immunity clusters and AS factor (SF)-OS-related-AS co-expression network and verification of cell function of CELF6 were analyzed in LUAD and LUSC. Results: Comprehensive analysis of transcriptomic, clinical, and AS data of LUADs and LUSCs identified IRG-AS events in LUAD (n = 1607) and LUSC (n = 1656), including OS-related IRG-AS events in LUAD (n = 127) and LUSC (n = 105). A total of 66 IRG-DEAS events in LUAD and 89 IRG-DEAS events in LUSC were identified compared to controls. The overlapping analysis between IRG-DEASs and OS-related IRG-AS events revealed 14 OS-related IRG-DEAS events for LUAD and 16 OS-related IRG-DEAS events for LUSC, which were used to identify and optimize a 12-OS-related-IRG-DEAS signature prognostic model for LUAD and an 11-OS-related-IRG-DEAS signature prognostic model for LUSC. These two prognostic models effectively divided LUAD or LUSC samples into low- and high-risk score groups that were closely associated with OS, clinical characteristics, and tumor immune microenvironment, with significant gene sets and pathways enriched in the two groups. Moreover, weighted gene co-expression network (WGCNA) and nonnegative matrix factorization method (NMF) analyses identified four OS-relevant subtypes of LUAD and six OS-relevant subtypes of LUSC, and ssGSEA identified five immunity-relevant subtypes of LUAD and five immunity-relevant subtypes of LUSC. Interestingly, splicing factors-OS-related-AS network revealed hub molecule CELF6 was significantly related to the malignant phenotype in lung cancer cells. Conclusions: This study established two reliable IRG-DEAS signature prognostic models and constructed interesting splicing factor-splicing event networks in LUAD and LUSC, which can be used to construct clinically relevant immune subtypes, patient stratification, prognostic prediction, and personalized medical services in the PPPM practice. Supplementary Information: The online version contains supplementary material available at 10.1007/s13167-024-00366-4.

Demonstration of π-π Stacking at Interfaces: Synthesis of an Indole-Modified Monodisperse Silica Microsphere SiO2@IN.

In the present study, a novel silane coupling agent, designated INSi, was synthesized via a facile synthetic route, incorporating indole-functional moieties. This agent was further employed for the surface modification of homemade silica nanomicrospheres (SMPs). The ensuing nanomicrosphere composite, denoted as SiO2@IN, exemplified pronounced interfacial π-π interactions. Optimization of the reaction conditions was conducted using the response surface optimization technique. Subsequent validation of interfacial π-π interactions was accomplished through a synergistic approach, integrating theoretical calculations and comprehensive analyses of spectral and morphological attributes exhibited by the SiO2@IN.

Adjuvant therapy provides no additional recurrence-free benefit for esophageal squamous cell carcinoma patients after neoadjuvant chemoimmunotherapy and surgery: a multi-center propensity score match study.

Purpose: The need for adjuvant therapy (AT) following neoadjuvant chemoimmunotherapy (nICT) and surgery in esophageal squamous cell cancer (ESCC) remains uncertain. This study aims to investigate whether AT offers additional benefits in terms of recurrence-free survival (RFS) for ESCC patients after nICT and surgery. Methods: Retrospective analysis was conducted between January 2019 and December 2022 from three centers. Eligible patients were divided into two groups: the AT group and the non-AT group. Survival analyses comparing different modalities of AT (including adjuvant chemotherapy and adjuvant chemoimmunotherapy) with non-AT were performed. The primary endpoint was RFS. Propensity score matching(PSM) was used to mitigate inter-group patient heterogeneity. Kaplan-Meier survival curves and Cox regression analysis were employed for recurrence-free survival analysis. Results: A total of 155 nICT patients were included, with 26 patients experiencing recurrence. According to Cox analysis, receipt of adjuvant therapy emerged as an independent risk factor(HR:2.621, 95%CI:[1.089,6.310], P=0.032), and there was statistically significant difference in the Kaplan-Meier survival curves between non-AT and receipt of AT in matched pairs (p=0.026). Stratified analysis revealed AT bring no survival benefit to patients with pathological complete response(p= 0.149) and residual tumor cell(p=0.062). Subgroup analysis showed no significant difference in recurrence-free survival between non-AT and adjuvant chemoimmunotherapy patients(P=0.108). However, patients receiving adjuvant chemotherapy exhibited poorer recurrence survival compared to non-AT patients (p= 0.016). Conclusion: In terms of recurrence-free survival for ESCC patients after nICT and surgery, the necessity of adjuvant therapy especially the adjuvant chemotherapy, can be mitigated.

Whether Patients with Anterior Cruciate Ligament Reconstruction Walking at a Fast Speed Show more Kinematic Asymmetries?

OBJECTIVE: Knee kinematic asymmetries after anterior cruciate ligament reconstruction (ACLR) are correlated with poor clinical outcomes, such as the progression of knee cartilage degenerations or reinjuries. Fast walking in patients with knee conditions may exacerbate knee kinematic asymmetries, but its impact on ACLR patients is uncertain. The aim of this study is to investigate if fast walking induces more knee kinematic asymmetries in unilateral ACLR patients. METHODS: This cross-sectional study enrolled 55 patients with unilateral ACLR from January 2020 to July 2022. There were 48 males and seven females with an average age of 30.6 ± 6.4 years. Knee kinematic data were collected at three walking speeds: self-selected, fast (150% normal), and slow (50% normal). A 3D knee kinematic analysis system measured the data, and self-reported outcomes assessed comfort levels during walking. We used SPM1D for two-way repeated ANOVA and posthoc paired t-tests to analyze kinematic differences in groups. RESULTS: In fast walking, ACLR knees exhibited more transverse kinematic asymmetries than intact knees, including greater external rotation angle (1.8°, 38%-43%; gait cycle [GC], p < 0.05 & 1.8-2.7°, 50%-61% GC, p < 0.05) and increased proximal tibial translation (2.1-2.5 mm, 2%-6% GC, p < 0.05 & 2.5-3.2 mm, 92%-96% GC, p < 0.05). Additionally, ACLR knees showed greater posterior tibial translation than intact knees (3.6-3.7 mm, 7%-8% GC, p < 0.05) during fast walking. No posterior tibial translation asymmetries were observed in slow walking compared to normal walking levels. ACLR knees have the most comfortable feelings in slow walking speed, and the most uncomfortable feelings in fast walking speed levels (29%). CONCLUSIONS: Fast walking induces additional external tibial rotation and proximal and posterior tibial translation asymmetries in ACLR patients. This raises concerns about long-term safety and health during fast walking. Fast walking, not self-selected speed, is beneficial for identifying postoperative gait asymmetries in ACLR patients.

Aldehyde-free and bio-based durable coatings for cellulose fabrics with high flame retardancy, antibacteria and well wearing performance.

The bio-based coatings of cellulose fabrics (cotton) had attracted increasing attention for multifunction and sustainability but suffered from poor durability and low efficiency. Here, the aldehyde-free and durable coatings for cotton fabrics (CPZ@CF) with satisfactory flame retardancy, antibacteria as well as wearing performance were prepared through the interfacial coordination effect where the well-organized zinc phytate complex were in situ grew on the pre-treated surface of cotton fabrics with chitosan (CS) and Zn2+. The CZP@CF exhibited excellent antibacterial activity for Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) with 99.99 % antibacterial rates benefiting from the synergistic effect between Zn2+ and CS. Meanwhile, even the CPZ coatings loading was only 1.5 wt%, the fire safety of CZP@CF remarkably enhanced owing to the excellent synergistic catalytic charring and free radical capture. More importantly, the antibacterial rates of CZP@CF for S. aureus and E. coli still reached 99.99 % and 91.67 % after 50 washing cycles. Additionally, this treatment method did not deteriorate the fabrics properties, including mechanical and breathability as well as wearing performance, which provided the approach to fabricate the flame retardant and antibacterial textiles with well durability and wearing performance.

Intradural extramedullary spinal choristoma: A case report.

RATIONALE: A choristoma is a rare and benign neoplasm characterized by the presence of normal tissue in an anomalous anatomical location. In contrast, choristoma tend to occur in other body regions rather than within the spinal canal. Before our findings, only 4 cases of intraspinal choristoma had been recorded. Because its composition is complex and very rare, routine examinations, such as magnetic resonance imaging, are difficult to diagnose, and the possibility of its occurrence is often missed in clinical diagnosis. If there is no specificity in its components, such as in this case, even pathological examinations can only confirm the diagnosis as choristoma after eliminating other possibilities. Therefore, in clinical practice, when encountering patients with intraspinal tumors, it is essential to consider the possibility of choristoma. In this case, the choristoma lack of specific constituent composition sets it apart from previously reported intraspinal choristoma, significantly raising the diagnostic challenge, which offers valuable insights for clinical diagnosis. PATIENT CONCERNS: A female patient aged 48 years was admitted to our medical center due to experiencing persistent lower back pain accompanied by radiating pain in both legs for 5 months. Based on the findings from the neurological physical examination and magnetic resonance imaging, the patient was diagnosed with an intradural space-occupying lesion located at the level of the first lumbar vertebral body. We performed an enhanced magnetic resonance neurography examination to further determine the positional relationship between the occupation and nerves in preparation for surgery. Postoperative pathological biopsy showed that the mass was an intraspinal choristoma. DIAGNOSIS: Intradural extramedullary spinal choristoma. INTERVENTION: Occupied lesion is removed surgically. OUTCOMES: After surgery, all symptoms were significantly relieved, and when the patient was discharged, all symptoms disappeared completely. There was no sign of recurrence after 1 year of follow-up. LESSONS: Intraspinal choristomas are not specific and need to be diagnosed by pathologic examination. Early detection of and intervention for intraspinal tumors can mitigate nerve dysfunction.

A chromosome-scale assembly of the early-flowering Prunus campanulata and comparative genomics of cherries.

Prunus campanulata is an important flowering cherry germplasm of high ornamental value. Given its early-flowering phenotypes, P. campanulata could be used for molecular breeding of ornamental species and fruit crops belonging to the subgenus Cerasus. Here, we report a chromosome-scale assembly of P. campanulata with a genome size of 282.6 Mb and a contig N50 length of 12.04 Mb. The genome contained 24,861 protein-coding genes, of which 24,749 genes (99.5%) were functionally annotated, and 148.20 Mb (52.4%) of the assembled sequences are repetitive sequences. A combination of genomic and population genomic analyses revealed a number of genes under positive selection or accelerated molecular evolution in P. campanulata. Our study provides a reliable genome resource, and lays a solid foundation for genetic improvement of flowering cherry germplasm.

First description study on molecular characterization of Hemiclepsis khankiana (Hirudinea: Glossiphoniidae) in China.

BACKGROUND: Leeches are an integral component of aquatic biocenosis and can be found in a wide range of ecosystems such as freshwater, saltwater, flowing, and still-water ecosystems. It especially plays an important role in the freshwater benthic community and is an important part of the food web. In this study, a leech species was found in the mantle cavity of wild freshwater mussels in Zigong City, Sichuan Province, China, and its identity was determined through morphological analysis and molecular biological analysis. RESULTS: The leech is Hemiclepsis khankiana, a new species of Hemiclepsis that has been discovered in Russia in recent years. Through morphological analysis, the current survey observed that the morphological characteristics of Hemiclepsis khankiana eyespots were significantly different from the first reported description. The first pair of eyespots on the leech were separated and clear, while it had been reduced to unclear shadows in the previous report. The phylogenetic tree based on the COI gene showed that the COI gene sequence obtained in this study was in the same evolutionary branch as Hemiclepsis khankiana (MN295420, MN295421). Genetically, it was most closely related to Hemiclepsis kasmiana (mean COI p-distance = 3.98%). CONCLUSIONS: The current study reported on the new distribution range of Hemiclepsis khankiana, which was initially discovered in China. This study indicates that the distribution range of the leech species has expanded, laying a foundation for further studies in China.

ATGL promotes colorectal cancer growth by regulating autophagy process and SIRT1 expression.

CRC is a common malignant tumor in the gastrointestinal tract, and its incidence has increased significantly in recent years. Several studies revealed that lipid metabolism reprogramming contributed to tumorigenicity and malignancy by interfering with energy production, membrane formation, and signal transduction in cancers. ATGL is a kind of hydroxy fatty acid ester of fatty acid synthase, and its role in tumor remains controversial. We compared levels of adipose triglyceride lipase (ATGL) in human CRC specimens to adjacent specimens. To validate the effect of ATGL on the proliferation ability of CRC, CCK8 assay and clone formation assay were performed. To evaluate whether autophagy process takes part in the effect of ATGL on CRC proliferation, the value of LC3-II/LC3-I was detected by western blot and we blocked the SIRT1 to detect value of LC3-II/LC3-I and p62 via western blot. In the end, we detected the value of SIRT1 in CRC specimens. We found that ATGL showed high expression in CRC and positively correlated with clinical stage, indicating poor prognosis of CRC. Moreover, ATGL significantly promoted tumor cell proliferation in vitro. Mechanistically, ATGL promoted CRC cells proliferation by blocking mTOR signaling pathway and activating autophagy process. Further, ATGL regulated autophagy process through triggering SIRT1 expression. Our results reveal that ATGL promotes colorectal cancer growth by up regulating autophagy process and SIRT1 expression.

Hemalin vaccination modulates the host immune response and reproductive cycle of Haemaphysalis longicornis.

Haemaphysalis longicornis can transmit high varieties of tick-borne pathogens (TBPs), and a primary strategy for preventing the transmission of those TBPs is to control ticks. Hemalin, a thrombin inhibitor of the Kunitz-type family and a crucial component in H. longicornis feeding process has been isolated from parthenogentic ticks. This study aimed to evaluate the validity of a recombinant Hemalin (rHlHemalin) vaccination as an anti-tick vaccine against H. longicornis in rabbits to find a new candidate for an effective tick control. In this study, mouse splenocytes were isolated and used to investigate immune responses after rHlHemalin stimulation. The rabbits were vaccinated with the rHlHemalin protein. After tick challenges, body weight at engorgement, egg mass, and the reproductive cycle of H. longicornis were evaluated. To confirm the vaccination, the passive immunization tests of α-rHlHemalin sera were performed. The results showed that the rHlHemalin protein could stimulate cytokine production in mouse splenocytes. Vaccination assay revealed that the periods from tick infestations to egg-hatch in the vaccination group were significantly longer than those in the phosphate buffer saline (PBS) group (P = 0.0003). In addition, the tick body weight at engorgement (P = 0.0019) and egg mass at 10 days after oviposition (P = 0.0232) were higher than those in the PBS group. These findings were consistent with the current passive immunization results and suggest rHlHemalin vaccination extended the reproductive cycle in H. longicornis but did not decrease the body weight at engorgement or weight of egg mass. Therefore, it is debatable whether Hemalin vaccination is highly-effective anti-tick vaccine or not. However, due to the importance of thrombin inhibitors in tick blood feeding and blood digestion, additional inhibitor-based vaccines should be developed aiming to find an effective and environmentally friendly biological strategy to combat ticks.

Validation of low-cost mobile phone applications and comparison with professional imaging systems for three-dimensional facial imaging: A pilot study.

PURPOSE: The objective of this study was to investigate the accuracies of three-dimensional (3D) facial scanning mobile phone applications as compared to professional 3D facial imaging systems. MATERIALS AND METHODS: A manikin head model was used as the subject for comparing six 3D facial imaging systems which comprised three professional 3D scanners (3dMDface, Artec Eva and Vectra H2) and three mobile phone applications (Bellus3D, ScandyPro and Hedges). For each system, five scans were taken to analyse (1) linear accuracy using 9 measurements (2) global and (3) regional 3D accuracy of the scanned surface by root mean square (RMS) and colour map analysis. Another set of five scans was repeated by a second operator to evaluate the inter-operator reproducibility for each system. RESULTS: All the facial imaging systems had absolute errors lesser than 1.0 mm for the linear measurements. The technical error of measurement (TEM) for inter-examiner and intra-examiner linear measurements were within acceptable limits. Artec Eva, Vectra H2 and Scandy Pro had poor global 3D trueness (RMS > 1.0 mm) but good 3D regional trueness (RMS < 1.0 mm). 3dMDface, Bellus3D Face App and Heges had good global and regional 3D trueness. All the facial imaging systems had good global and regional 3D precision and reproducibility (RMS < 1.0 mm). CONCLUSION: This study demonstrated that mobile phone 3D scanning applications had comparable trueness, precision and reproducibility to professional systems. Colour map analysis supplemented the use of the RMS value to demonstrate facial regions of significant deviation. Clinicians should also consider the specific area or region of inaccuracies for each system to determine whether the chosen system is appropriate for the clinical condition or procedure. CLINICAL SIGNIFICANCE: Mobile phone 3D facial imaging applications may be as accurate as 3D professional facial scanning systems for craniomaxillofacial purposes. However, the choice of the system may vary depending on the specific area of interest.

The effect of conjugation degree of aromatic carboxylic acids on electronic and photo-responsive behaviors of naphthalenediimide-based coordination polymers.

Three novel naphthalenediimide-based (NDI-based) coordination polymers (CPs), namely [Cd(3-PMNDI)(2,2'-BPDC)] (1), [Cd2(3-PMNDI)1.5(4,4'-BPDC)2(H2O)3]·DMF (2) and [Cd(3-PMNDI)(4,4'-SDC)] (3) (2,2'-H2BPDC = 2,2'-biphenyldicarboxylic acid, 4,4'-H2BPDC = 4,4'-biphenyldicarboxylic acid, 4,4'-H2SDC = 4,4'-stilbenedicarboxylic acid, 3-PMNDI = N,N'-bis(3-pyridylmethyl)-1,4,5,8-naphthalenediimide, and DMF = N,N'-dimethylformamide), have been designed and synthesized here from electron-deficient PMNDI (electron acceptors, EAs) and electron-rich aromatic carboxylic acids (electron donors, EDs) in the presence of cadmium ions. The introduction of aromatic carboxylic acids with different sizes and conjugation degrees leads to the generation of a two-dimensional (2D) layer in 1, a two-fold interpenetrated three-dimensional (3D) network in 2 and an eight-fold interpenetrated 3D framework in 3. Furthermore, the use of distinct electron-donating aromatic carboxylic acids and the consequent different numbers and strengths of lone pair-π and π-π interactions in the interfacial contacts of EDs/EAs give rise to distinct intermolecular charge transfer (ICT) and initial colors of the three CPs, and consequently cause different photoinduced intermolecular electron transfer (PIET) and distinguishing photo-responsive behaviors (weak photochromic performance for 1, excellent photochromic properties for 2 and non-photochromism for 3). This study indicates that an appropriate ICT is beneficial for PIET, but too weak or too strong ICT is not conducive to PIET, which provides an effective strategy for the construction of functional CPs with distinguishing photo-responsive properties through the subtle balance of ICT and PIET.

Impact of minimally invasive total mesoesophageal excision and minimally invasive esophagectomy on failure patterns of locally advanced esophageal squamous cell carcinoma: a matched cohort study with long-term follow-up.

BACKGROUND: The effects of minimally invasive total mesoesophageal excision (MITME) on the long-term prognosis of locally advanced esophageal squamous cell carcinoma (ESCC) remain unknown. The objective of this study was to compare the static and dynamic failure patterns of MITME and minimally invasive esophagectomy (MIE) for locally advanced ESCC. METHODS: We use propensity score matching (PSM) method to analyze the postoperative failure patterns of the two groups. Cumulative event curves were analyzed for cumulative incidence of failure between different groups, and independent prognostic factors were assessed using time-dependent multivariate analyses. The risk of dynamic failure calculated at 12-month intervals was compared between the two groups using the lifetime table. RESULTS: A total of 366 ESCC patients were studied by 1:1 PSM for T stage and TNM stage (MITME group, n = 183; MIE group, n = 183). In the matched cohort, there was significant differences between the MITME and MIE groups in the failure pattern of regional lymph node recurrence (0.5 vs 3.8%, P = 0.032) and non-tumor death (10.9 vs 31.7%, P < 0.001). The cumulative event curve found that the 5-year cumulative failure rate was lower in the MITME group than in the MIE group (3.3 vs 17.1%, P = 0.026) after 5 years of survival. In addition, multivariate Cox regression analysis showed that MIE was an independent poor prognostic factor for a high cumulative failure rate in locally advanced ESCC patients at 5 years after surgery (HR:4.110; 95% CI 1.047-16.135; P = 0.043). The dynamic risk curve showed that the MITME group had a lower risk of failure within 5 years after surgery than the MIE group. CONCLUSION: Considering that MITME can significantly improve the postoperative failure pattern and the benefit lasts for at least 5 years, it is feasible to use MITME as a treatment for locally advanced ESCC.

The genetic structure and demographic history revealed by whole-genome resequencing provide insights into conservation of critically endangered Artocarpus nanchuanensis.

Introduction: Whole-genome resequencing technology covers almost all nucleotide variations in the genome, which makes it possible to carry out conservation genomics research on endangered species at the whole-genome level. Methods: In this study, based on the whole-genome resequencing data of 101 critically endangered Artocarpus nanchuanensis individuals, we evaluated the genetic diversity and population structure, inferred the demographic history and genetic load, predicted the potential distributions in the past, present and future, and classified conservation units to propose targeted suggestions for the conservation of this critically endangered species. Results: Whole-genome resequencing for A. nanchuanensis generated approximately 2 Tb of data. Based on abundant mutation sites (25,312,571 single nucleotide polymorphisms sites), we revealed that the average genetic diversity (nucleotide diversity, π) of different populations of A. nanchuanensis was relatively low compared with other trees that have been studied. And we also revealed that the NHZ and QJT populations harboured unique genetic backgrounds and were significantly separated from the other five populations. In addition, positive genetic selective signals, significantly enriched in biological processes related to terpene synthesis, were identified in the NHZ population. The analysis of demographic history of A. nanchuanensis revealed the existence of three genetic bottleneck events. Moreover, abundant genetic loads (48.56% protein-coding genes) were identified in Artocarpus nanchuanensis, especially in genes related to early development and immune function of plants. The predication analysis of suitable habitat areas indicated that the past suitable habitat areas shifted from the north to the south due to global temperature decline. However, in the future, the actual distribution area of A. nanchuanensis will still maintain high suitability. Discussion: Based on total analyses, we divided the populations of A. nanchuanensis into four conservation units and proposed a number of practical management suggestions for each conservation unit. Overall, our study provides meaningful guidance for the protection of A. nanchuanensis and important insight into conservation genomics research.

First description of Blastocystis sp. and Entamoeba sp. infecting zoo animals in the Qinghai-Tibetan plateau area, China.

Protozoan parasites are a well-known threat to human health, particularly for people working at or visiting zoos, and potentially cause zoonotic diseases in humans. Captive wildlife may be potential reservoirs for human infection with protozoan parasites. Therefore, focusing on zoonotic protozoan infections in zoo animals is critical. However, there is no report on this topic in the Qinghai-Tibetan Plateau region. In this study, a total of 167 and 103 fecal samples were collected from 12 animal species from Qinghai-Tibet Plateau Wildlife Park in winter and summer, respectively, to detection the prevalence of infections and subtype distribution with Entamoeba sp., Cryptosporidium sp., Giardia duodenalis, Enteromicrosporidia bieneusi sp., Blastocystis sp. by PCR assay. The results showed that a total of 21 fecal samples collected in winter, including from 2 white-lipped deer, 8 Sika deer, 6 blue sheep, 2 wolves and 3 bears, were positive for Entamoeba, with a 12.6% (21/167) positive rate. However, 4.9% (5/103) of animals in summer were positive for Entamoeba, including 1 snow leopard, 1 tiger, 1 Tibetan argali and 2 mouflon. Moreover, 1 white-lipped deer and 1 bear were found to be positive for Blastocystis sp., one zoonotic STs (ST10) was identified and found in white-lipped deer. We found no effect on season on Blastocystis sp. and Entamoeba sp. colonization. To the best of our knowledge, this study is the first description of Blastocystis sp. and Entamoeba sp. infecting zoo animals in the plateau area. The findings provide the latest data on Entamoeba sp. and Blastocystis sp. in zoo animals in China.

Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation.

Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene-Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.

Phylogenomics reveals widespread hybridization and polyploidization in Henckelia (Gesneriaceae).

BACKGROUND AND AIMS: Hybridization has long been recognized as an important process for plant evolution and is often accompanied by polyploidization, another prominent force in generating biodiversity. Despite its pivotal importance in evolution, the actual prevalence and distribution of hybridization across the tree of life remain unclear. METHODS: We used whole-genome shotgun (WGS) sequencing and cytological data to investigate the evolutionary history of Henckelia, a large genus in the family Gesneriaceae with a high frequency of suspected hybridization and polyploidization events. We generated WGS sequencing data at about 10× coverage for 26 Chinese Henckelia species plus one Sri Lankan species. To untangle the hybridization history, we separately extracted whole plastomes and thousands of single-copy nuclear genes from the sequencing data, and reconstructed phylogenies based on both nuclear and plastid data. We also explored sources of both genealogical and cytonuclear conflicts and identified signals of hybridization and introgression within our phylogenomic dataset using several statistical methods. Additionally, to test the polyploidization history, we evaluated chromosome counts for 45 populations of the 27 Henckelia species studied. KEY RESULTS: We obtained well-supported phylogenetic relationships using both concatenation- and coalescent-based methods. However, the nuclear phylogenies were highly inconsistent with the plastid phylogeny, and we observed intensive discordance among nuclear gene trees. Further analyses suggested that both incomplete lineage sorting and gene flow contributed to the observed cytonuclear and genealogical discordance. Our analyses of introgression and phylogenetic networks revealed a complex history of hybridization within the genus Henckelia. In addition, based on chromosome counts for 27 Henckelia species, we found independent polyploidization events occurred within Henckelia after different hybridization events. CONCLUSIONS: Our findings demonstrated that hybridization and polyploidization are common in Henckelia. Furthermore, our results revealed that H. oblongifolia is not a member of the redefined Henckelia and they suggested several other taxonomic treatments in this genus.

Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns.

Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.

Recombination Variation Shapes Phylogeny and Introgression in Wild Diploid Strawberries.

Introgressive hybridization is widespread in wild plants and has important consequences. However, frequent hybridization between species makes the estimation of the species' phylogeny challenging, and little is known about the genomic landscape of introgression as it results from complex interactions of multiple evolutionary processes. Here, we reconstructed the phylogeny of ten wild diploid strawberries with whole genome resequencing data and then investigated the influence of recombination rate variation on phylogeny and introgression. We found that genomic regions with low recombination showed reduced levels of incomplete lineage sorting and introgression, and concentrated phylogenetic signals, thus contributing to the most likely species tree of wild diploid strawberries. We revealed complex and widespread introgression across the genus Fragaria, with an average proportion of approximately 4.1% of the extant genome. Introgression tends to be retained in the regions with high recombination rates and low gene density. Furthermore, we identified four SLF genes under selective sweeps that may play potential roles in the possible regain of self-incompatibility by ancient introgression. Altogether, our study yielded novel insights into the evolutionary history and genomic characteristics of introgression in wild diploid strawberries and provides evidence for the role of introgression in plant mating system transitions.