Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection.

Niemann-Pick disease type C (NPC) is associated with mutations in NPC1 and NPC2, whose gene products are key players in the endosomal/lysosomal egress of low-density lipoprotein-derived cholesterol. NPC1 is also the intracellular receptor for Ebola virus (EBOV). Here, we present a 4.4 Å structure of full-length human NPC1 and a low-resolution reconstruction of NPC1 in complex with the cleaved glycoprotein (GPcl) of EBOV, both determined by single-particle electron cryomicroscopy. NPC1 contains 13 transmembrane segments (TMs) and three distinct lumenal domains A (also designated NTD), C, and I. TMs 2-13 exhibit a typical resistance-nodulation-cell division fold, among which TMs 3-7 constitute the sterol-sensing domain conserved in several proteins involved in cholesterol metabolism and signaling. A trimeric EBOV-GPcl binds to one NPC1 monomer through the domain C. Our structural and biochemical characterizations provide an important framework for mechanistic understanding of NPC1-mediated intracellular cholesterol trafficking and Ebola virus infection.

The rise of baobab trees in Madagascar.

The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight extant baobab species and argue that Madagascar should be considered the centre of origin for the extant lineages, a key issue in their evolutionary history2,3. Integrated genomic and ecological analyses revealed the reticulate evolution of baobabs, which eventually led to the species diversity seen today. Past population dynamics of Malagasy baobabs may have been influenced by both interspecific competition and the geological history of the island, especially changes in local sea levels. We propose that further attention should be paid to the conservation status of Malagasy baobabs, especially of Adansonia suarezensis and Adansonia grandidieri, and that intensive monitoring of populations of Adansonia za is required, given its propensity for negatively impacting the critically endangered Adansonia perrieri.

Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis.

WhiB7 represents a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, a unique group of iron-sulfur (4Fe-4S] cluster-containing proteins exclusive to the phylum of Actinobacteria. In Mycobacterium tuberculosis (Mtb), WhiB7 interacts with domain 4 of the primary sigma factor (σA4) in the RNA polymerase holoenzyme and activates genes involved in multiple drug resistance and redox homeostasis. Here, we report crystal structures of the WhiB7:σA4 complex alone and bound to its target promoter DNA at 1.55-Å and 2.6-Å resolution, respectively. These structures show how WhiB7 regulates gene expression by interacting with both σA4 and the AT-rich sequence upstream of the -35 promoter DNA via its C-terminal DNA-binding motif, the AT-hook. By combining comparative structural analysis of the two high-resolution σA4-bound Wbl structures with molecular and biochemical approaches, we identify the structural basis of the functional divergence between the two distinct subclasses of Wbl proteins in Mtb.

CUNet3+: A Multiscale Connected UNet for the Segmentation of Lung Cancer Cells in Pathology Sections Stained Using Rapid On-Site Cytopathological Evaluation.

Lung cancer is an increasingly serious health problem worldwide, and early detection and diagnosis are crucial for successful treatment. With the development of artificial intelligence and the growth of data volume, machine learning techniques can play a significant role in improving the accuracy of early detection in lung cancer. This study proposes a deep learning-based segmentation algorithm for rapid on-site cytopathological evaluation (ROSE) to enhance the diagnostic efficiency of endobronchial ultrasound-guided transbronchial needle aspiration biopsy (EBUS-TBNA) during surgery. By utilizing the CUNet3+ network model, cell clusters, including cancer cell clusters, can be accurately segmented in ROSE-stained pathological sections. The model demonstrated high accuracy, with an F1-score of 0.9604, recall of 0.9609, precision of 0.9654, and accuracy of 0.9834 on the internal testing data set. It also achieved an area under the receiver-operating characteristic curve of 0.9972 for cancer identification. The proposed algorithm provides time savings for on-site diagnosis, improves EBUS-TBNA efficiency, and outperforms classical segmentation algorithms in accurately identifying lung cancer cell clusters in ROSE-stained images. It effectively reduces over-segmentation, decreases network parameters, and enhances computational efficiency, making it suitable for real-time patient evaluation during surgical procedures.

Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb) WhiB3 is an iron-sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (σA4) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with σA4 to bind DNA and regulate transcription is unclear. Here we determined crystal structures of the WhiB3:σA4 complex without and with DNA at 1.5 Å and 2.45 Å, respectively, to elucidate how WhiB3 interacts with DNA to regulate gene expression. These structures reveal that the WhiB3:σA4 complex shares a molecular interface similar to other structurally characterized Wbl proteins and also possesses a subclass-specific Arg-rich DNA-binding motif. We demonstrate that this newly defined Arg-rich motif is required for WhiB3 binding to DNA in vitro and transcriptional regulation in Mycobacterium smegmatis. Together, our study provides empirical evidence of how WhiB3 regulates gene expression in Mtb by partnering with σA4 and engaging with DNA via the subclass-specific structural motif, distinct from the modes of DNA interaction by WhiB1 and WhiB7.

Results of a Pilot External Quality Assessment Scheme for Genetic Testing of Newborns with Spinal Muscular Atrophy.

BACKGROUND: This study aims to evaluate the ability of laboratories to perform spinal muscular atrophy (SMA) genetic testing in newborns based on dried blood spot (DBS) samples, and to provide reference data and advance preparation for establishing the pilot external quality assessment (EQA) scheme for SMA genetic testing of newborns in China. METHODS: The pilot EQA scheme contents and evaluation principles of this project were designed by National Center for Clinical Laboratories (NCCL), National Health Commission. Two surveys were carried out in 2022, and 5 batches of blood spots were submitted to the participating laboratory each time. All participating laboratories conducted testing upon receiving samples, and test results were submitted to NCCL within the specified date. RESULTS: The return rates were 75.0% (21/28) and 95.2% (20/21) in the first and second surveys, respectively. The total return rate of the two examinations was 83.7% (41/49). Nineteen laboratories (19/21, 90.5%) had a full score passing on the first survey, while in the second survey twenty laboratories (20/20, 100%) scored full. CONCLUSIONS: This pilot EQA survey provides a preliminary understanding of the capability of SMA genetic testing for newborns across laboratories in China. A few laboratories had technical or operational problems in testing. It is, therefore, of importance to strengthen laboratory management and to improve testing capacity for the establishment of a national EQA scheme for newborn SMA genetic testing.

High-Performance Flexible Graphene Oxide-Based Moisture-Enabled Nanogenerator via Multilayer Heterojunction Engineering and Power Management System.

Recently, there has been a surge of interest in nanogenerators within the scientific community because their immense potential for extracting energy from the surrounding environment. A promising approach involves utilizing ambient moisture as an energy source for portable devices. In this study, moisture-enabled nanogenerators (MENGs) are devised by integrating heterojunctions of graphene oxide (GO) and reduced graphene oxide (rGO). Benefiting from the unique structure, a larger ion concentration gradient is achieved as well as a lower resistance, which leads to enhanced electricity generation. The resulting MENG generates a desirable open-circuit voltage of 0.76 V and a short-circuit current density of 73 µA cm-2 with a maximum power density of 15.8 µW cm-2 . Notably, the designed device exhibits a high voltage retention of more than 90% after 3000 bending cycles, suggesting a high potential for flexible applications. Moreover, a large-scale integrated MENG array is developed by incorporating flexible printed circuit technology and connecting it to a power management system. This integrated system can provide ample energy to operate an electronic ink display and drive a heart rate sensor for health monitoring. The outcomes of this research present a novel framework for advancing next-generation self-powered flexible devices, thereby demonstrating significant promise for future wearable electronics.

Efficacy of treatment based on TKIs in combination with PD-1 inhibitors for unresectable recurrent hepatocellular carcinoma.

BACKGROUND AND OBJECTIVE: The recurrence occurs within 5 years in up to 70% of hepatocellular carcinoma (HCC) patients who received radical liver resection, and most patients are no longer suitable for repeat surgery. There are limited treatment options for unresectable recurrent HCC. This study aimed to explore the potential efficacy of treatment based on TKIs in combination with PD-1 inhibitors for unresectable recurrent HCC. METHODS: Forty-four patients with unresectable recurrent HCC after radical surgery between January 2017 and November 2022 were retrospectively collected and screened. All patients received the combination therapy of tyrosine kinase inhibitors (TKIs) and programmed cell death protein 1 (PD-1) inhibitors, and 18 of these patients received trans-arterial chemoembolization (TACE) or TACE combined with radiofrequency ablation (RFA). Two patients who received TKIs in combination with PD-1 inhibitors eventually obtained repeat surgery, with one patient undergoing a repeat hepatectomy and one patient receiving a liver transplant. RESULTS: The median survival for these patients was 27.0 months (95% confidence interval [CI] 21.2, 32.8), with a 1-year overall survival (OS) rate of 83.6% (95% CI 77.9%, 89.3%). Median progression-free survival (PFS) was 15.0 months (95.0% CI 12.1, 17.9), with a 1-year PFS rate of 77.0% (95% CI 70.6%, 83.4%). The two patients who underwent repeat surgery had a survival time of 34 and 37 months after the combined treatment with no recurrence, respectively, as of November 2022. CONCLUSION: The combination of TKIs and PD-1 inhibitors for unresectable recurrent HCC is effective and can prolong the survival of patients in this group.

Near-infrared optogenetic engineering of photothermal nanoCRISPR for programmable genome editing.

We herein report an optogenetically activatable CRISPR-Cas9 nanosystem for programmable genome editing in the second near-infrared (NIR-II) optical window. The nanosystem, termed nanoCRISPR, is composed of a cationic polymer-coated Au nanorod (APC) and Cas9 plasmid driven by a heat-inducible promoter. The APC not only serves as a carrier for intracellular plasmid delivery but also can harvest external NIR-II photonic energy and convert it into local heat to induce the gene expression of the Cas9 endonuclease. Due to high transfection activity, the APC shows strong ability to induce a significant level of disruption in different genomic loci upon optogenetic activation. Moreover, the precise control of genome-editing activity can be simply programmed by finely tuning exposure time and irradiation time in vitro and in vivo and also enables editing at multiple time points, thus proving the sensitivity and inducibility of such an editing modality. The NIR-II optical feature of nanoCRISPR enables therapeutic genome editing at deep tissue, by which treatment of deep tumor and rescue of fulminant hepatic failure are demonstrated as proof-of-concept therapeutic examples. Importantly, this modality of optogenetic genome editing can significantly minimize the off-target effect of CRISPR-Cas9 in most potential off-target sites. The optogenetically activatable CRISPR-Cas9 nanosystem we have developed offers a useful tool to expand the current applications of CRISPR-Cas9, and also defines a programmable genome-editing strategy toward high precision and spatial specificity.

Long-term survival and portal vein patency with novel PVTT surgery approach in advanced HCC patients with Vp3/4 PVTT following combination therapy of TKIs and PD-1 inhibitors.

BACKGROUND: It is controversial whether patients with hepatocellular carcinoma (HCC) with portal vein tumor thrombus (PVTT) should undergo salvage surgery following the combination therapy of tyrosine kinase inhibitors (TKIs) and programmed cell death protein 1 (PD-1) inhibitors. This study aimed to elucidate the efficiency and safety of salvage surgery following combination therapy, while also summarizing a novel surgical approach for Vp3/4 PVTT. METHODS: Between April 2019 and December 2022, a consecutive series of unresectable HCC patients with PVTT who received salvage surgery following combination therapy were enrolled. Evaluation included perioperative and long-term follow-up outcomes. The complete removal of Vp3/4 PVTT was achieved using a novel surgical approach characterized by "longitudinal incision and transverse suturing" and "angle-to-straight conversion". RESULTS: Forty patients including 22 patients with Vp3 and 18 patients with Vp4 were included. Long-term follow-up showed similar rates of portal vein patency (Vp3: 95.5%, Vp4:94.4%, p = 0.900), and 3-year portal vein patency rates were 95.0%. There were no significant differences observed in combination therapy-related adverse events (p = 0.253) and perioperative complications (p = 0.613) between the Vp3 and Vp4 groups. The recurrence patterns were similar between the two groups (p = 0.131). There were no significant differences in overall survival (OS) and recurrence-free (RFS) survival between the Vp3 and Vp4 groups (OS p = 0.457, RFS p = 0.985). Patients who achieved a pathological complete response had significantly better RFS (p = 0.011). CONCLUSION: Salvage surgery after combination therapy demonstrated favorable efficacy and safety. The novel surgical approach for PVTT can effectively achieve complete removal of PVTT and ensured long-term portal vein patency.

Comparison of survival benefit between salvage surgery after conversion therapy versus surgery alone for hepatocellular carcinoma with portal vein tumor thrombosis: a propensity score analysis.

BACKGROUND: Salvage surgery after conversion therapy with a combination of tyrosine kinase inhibitor and anti-programmed death-1 antibody has shown improved survival benefits in patients with hepatocellular carcinoma (HCC) with portal vein tumor thrombosis (PVTT). We aimed to compare the survival benefits in a retrospective cohort of patients with HCC with PVTT who underwent salvage surgery after conversion therapy and surgery alone. METHODS: From January 2015 to October 2021, we selected patients diagnosed with HCC with PVTT who underwent liver resection at Chinese PLA General Hospital. The primary endpoint in the comparison of survival benefits between conversion therapy and surgery-alone groups was recurrence-free survival. Propensity score matching was applied to reduce any potential bias in the study. RESULTS: The 6-, 12-, and 24-month recurrence-free survival rates in the conversion and surgery alone groups were 80.3% vs 36.5%, 65.4% vs 29.4%, and 56% vs 21%, respectively. On multivariable Cox regression analyses, conversion therapy significantly reduced HCC-related mortality and HCC recurrence rates compared with surgery alone. CONCLUSIONS: For patients with HCC with PVTT, surgery after conversion therapy is in relationship with increased survival in comparison with surgery alone.

Recent Development of Moisture-Enabled-Electric Nanogenerators.

Power generation by converting energy from the ambient environment has been considered a promising strategy for developing decentralized electrification systems to complement the electricity supply for daily use. Wet gases, such as water evaporation or moisture in the atmosphere, can be utilized as a tremendous source of electricity by emerging power generation devices, that is, moisture-enabled-electric nanogenerators (MEENGs). As a promising technology, MEENGs provided a novel manner to generate electricity by harvesting energy from moisture, originating from the interactions between water molecules and hydrophilic functional groups. Though the remarkable progress of MEENGs has been achieved, a systematic review in this specific area is urgently needed to summarize previous works and provide sharp points to further develop low-cost and high-performing MEENGs through overcoming current limitations. Herein, the working mechanisms of MEENGs reported so far are comprehensively compared. Subsequently, a systematic summary of the materials selection and fabrication methods for currently reported MEENG construction is presented. Then, the improvement strategies and development directions of MEENG are provided. At last, the demonstrations of the applications assembled with MEENGs are extracted. This work aims to pave the way for the further MEENGs to break through the performance limitations and promote the popularization of future micron electronic self-powered equipment.

Radiomic Features on Multiparametric MRI for Preoperative Evaluation of Pituitary Macroadenomas Consistency: Preliminary Findings.

BACKGROUND: Preoperative assessment of the consistency of pituitary macroadenomas (PMA) might be needed for surgical planning. PURPOSE: To investigate the diagnostic performance of radiomics models based on multiparametric magnetic resonance imaging (mpMRI) for preoperatively evaluating the tumor consistency of PMA. STUDY TYPE: Retrospective. POPULATION: One hundred and fifty-six PMA patients (soft consistency, N = 104 vs. hard consistency, N = 52), divided into training (N = 108) and test (N = 48) cohorts. The tumor consistency was determined on surgical findings. FIELD STRENGTH/SEQUENCE: T1-weighted imaging (T1WI), contrast-enhanced T1WI (T1CE), and T2-weighted imaging (T2WI) using spin-echo sequences with a 3.0-T scanner. ASSESSMENT: An automated three-dimensional (3D) segmentation was performed to generate the volume of interest (VOI) on T2WI, then T1WI/T1CE were coregistered to T2WI. A total of 388 radiomic features were extracted on each VOI of mpMRI. The top-discriminative features were identified using the minimum-redundancy maximum-relevance method and 0.632+ bootstrapping. The radiomics models based on each sequence and their combinations were established via the random forest (RF) and support vector machine (SVM), and independently evaluated for their ability in distinguishing PMA consistency. STATISTICAL TESTS: Mann-Whitney U-test and Chi-square test were used for comparison analysis. The area under the receiver operating characteristic curve (AUC), accuracy (ACC), sensitivity (SEN), specificity (SPE), and relative standard deviation (RSD) were calculated to evaluate each model's performance. ACC with P-value<0.05 was considered statistically significant. RESULTS: Eleven mpMRI-based features exhibited statistically significant differences between soft and hard PMA in the training cohort. The radiomics model built on combined T1WI/T1CE/T2WI demonstrated the best performance among all the radiomics models with an AUC of 0.90 (95% confidence interval [CI]: 0.87-0.92), ACC of 0.87 (CI: 0.84-0.89), SEN of 0.83 (CI: 0.81-0.85), and SPE of 0.87 (CI: 0.85-0.99) in the test cohort. DATA CONCLUSION: Radiomic features based on mpMRI have good performance in the presurgical evaluation of PMA consistency. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY: Stage 2.

High sensitivity detection of tumor cells in biological samples using a multivalent aptamer strand displacement strategy.

Monitoring the cell surface-expressed nucleolin facilitates early cancer diagnosis. Herein, we developed a multivalent aptamer displacement strand duplex strategy on cell membranes using a multi-receptor co-recognition design for improving the sensitivity and specificity of cancer cell recognition with an ultra-low background. The AS1411 aptamer labeled with the FAM fluorophore can be quenched using a partial complementary sequence modified with a BHQ1 tag which is partially hybridized with the AS1411 aptamer to create a receptor-activating aptamer. The multi-AS1411 activable probe based on the strand displacement strategy was constructed using multiple copies of the structure-switching AS1411 aptamer (bearing a short poly-A tail) linked together using the poly-T long chain (as a scaffold) which was synthesized by Terminal Deoxynucleotidyl Transferase (TDT)-mediated extension. We demonstrated the promising efficacy and sensitivity of our method in recognizing tumor cells in both cell mixtures and clinical cytology specimens. Due to its simple and fast operation with excellent cell recognition sensitivity and accuracy, it is expected to achieve the detection of low abundance target cells. Our approach will have broad application in clinical rapid detection and personalized medicine.

Re-Stickable Yarn Supercapacitors with Vaper Phase Polymerized Multi-Layered Polypyrrole Electrodes for Smart Garments.

Yarn supercapacitors have attracted significant attention for wearable energy storage due to their ability to be directly integrated with garments. Conducting polymer polypyrrole (PPy) based yarn supercapacitors show limited cycling stability because of the huge volume changes during the charge-discharge processes. In addition, laundering may cause damage to such yarn supercapacitors. Here, the fabrication of PPy-based re-stickable yarn supercapacitors is reported with good cycling stability by employing vapor phase polymerization (VPP) and water-soluble polyethylene oxide (PEO) film as the adhesive layer. VPP duration and cycle are controlled to achieve multi-layered PPy electrodes. The assembled yarn supercapacitors show a good cycling stability with capacitance retention of 79.1% after 5000 charge-discharge cycles. The energy stored in the yarn supercapacitor is sufficient to power a photodetector. After gluing the yarn supercapacitors onto a PEO film, the devices can be stunk on and peeled off the garment to avoid the mechanical stresses during the washing process. Three yarn supercapacitors connected in parallel on PEO film show negative changes in electrochemical performance after 5 sticking-peeling cycles. This work provides a facile way to fabricate PPy-based re-stickable energy storage devices with high cycling stability for smart garments.

The healing response of LAMax LAAC™ left atrial appendage occluder in a canine model: the potential influence of the implantation technique on the healing response.

BACKGROUND: Device-associated thrombus are potential causes for thromboembolic events post left atrial appendage closure (LAAC), and correlated with the complete endothelialization of the device surface. Our aim was to evaluate the endothelialization of LAMax LAAC™ occluder surface and analyze the potential influence of the implantation technique on the healing response. METHODS: A total of 29 healthy dogs (28.0 ± 3.7 kg) were implanted with the devices successfully after ensuring COVER signs was met (Concavity of the disc, Oversizing by 20-50%, Verifying position, Ensuring stability, Residual flow < 5 mm by transesophageal echocardiographic (TEE) examination), and sacrificed at < 24 h, 1-, 2-, 3-, and 6-months. Gross examinations were conducted to evaluate healing response. RESULTS: The mean diameters of LAA orifice measured by angiography and TEE were 19.0 ± 2.9 mm and 16.6 ± 2.9 mm (P < 0.05), respectively. TEE found that the discs in 18 dogs (62.1%) were completely pulled into the LAA with concavity and in 11 dogs incompletely pulled into the LAA with suboptimally concavity, while 5 of them had residual flow. Gross examinations showed that the complete endothelialization on the device surface with concaved disc was found at 1-month after LAAC. Microscopic examinations confirmed complete healing on the device with optimal closure effect. CONCLUSIONS: The good healing response and the optimal closure effect were observed using the LAMax device in a canine model by following the COVER implantation technique.

Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis.

WhiB1 is a monomeric iron-sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress in M. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 Å-resolution crystal structure of the [4Fe-4S] cluster-bound (holo-) WhiB1 in complex with the C-terminal domain of the σ70-family primary sigma factor σA of M. tuberculosis containing the conserved region 4 (σA4). Region 4 of the σ70-family primary sigma factors is commonly used by transcription factors for gene activation, and holo-WhiB1 has been proposed to activate gene expression via binding to σA4. The complex structure, however, unexpectedly reveals that the interaction between WhiB1 and σA4 is dominated by hydrophobic residues in the [4Fe-4S] cluster binding pocket, distinct from previously characterized canonical σ704-bound transcription activators. Furthermore, we show that holo-WhiB1 represses transcription by interaction with σA4in vitro and that WhiB1 must interact with σA4 to perform its essential role in supporting cell growth in vivo. Together, these results demonstrate that holo-WhiB1 regulates gene expression by a non-canonical mechanism relative to well-characterized σA4-dependent transcription activators.

A Duplex CRISPR-Cas9 Ribonucleoprotein Nanomedicine for Colorectal Cancer Gene Therapy.

Based on the high frequency of concurrent adenomatous polyposis coli (APC) and KRAS mutations and their strong cooperative interaction in human colorectal cancer (CRC) promotion, we herein develop a CRISPR-Cas9-based genome-editing nanomedicine to target both APC and KRAS mutations for the treatment of CRC. To this end, a hyaluronic acid (HA)-decorated phenylboronic dendrimer (HAPD) was designed for the targeted delivery of Cas9 ribonucleoprotein (RNP), by which both APC and KRAS genetic mutations harboring in CRC cells can be synergistically disrupted. Systemic administration of Cas9 RNP targeting APC and KRAS enabled by HAPD significantly inhibits tumor growth on xenografted and orthotopic CRC mouse models and also greatly prevents CRC-induced liver metastasis and lung metastasis. Thus, this duplex genome-editing system provides a promising gene therapy strategy for the treatment of human CRC and can be extended to other types of cancers with activated Wnt/ß-catenin and RAS/extracellular signal-regulated kinase (ERK) pathways.

A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms.

Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms.

Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species.

The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.