Phylogenomics of the leafhopper genus Neoaliturus Distant, 1918 (Hemiptera: Cicadellidae: Deltocephalinae) reveals genetically divergent lineages in the invasive beet leafhopper.

Phylogenomic analysis based on nucleotide sequences of 398 nuclear gene loci for 67 representatives of the leafhopper genus Neoaliturus yielded well-resolved estimates of relationships among species of the genus. Subgenus Neoaliturus (Neoaliturus) is consistently paraphyletic with respect to Neoaliturus (Circulifer). The analysis revealed the presence of at least ten genetically divergent clades among specimens consistent with the previous morphology-based definition of the leafhopper genus "Circulifer" which includes three previously recognized "species complexes." Specimens of the American beet leafhopper, N. tenellus (Baker), collected from the southwestern USA consistently group with one of these clades, comprising specimens from the eastern Mediterranean. Some of the remaining lineages are consistent with ecological differences previously observed among eastern Mediterranean populations and suggest that N. tenellus, as previously defined, comprises multiple monophyletic species, distinguishable by slight morphological differences.

Comprehensive multi-omics analysis of resectable locally advanced gastric cancer: Assessing response to neoadjuvant camrelizumab and chemotherapy in a single-center, open-label, single-arm phase II trial.

BACKGROUND: The current standard of care for locally advanced gastric cancer (GC) involves neoadjuvant chemotherapy followed by radical surgery. Recently, neoadjuvant treatment for this condition has involved the exploration of immunotherapy plus chemotherapy as a potential approach. However, the efficacy remains uncertain. METHODS: A single-arm, phase 2 study was conducted to evaluate the efficacy and tolerability of neoadjuvant camrelizumab combined with mFOLFOX6 and identify potential biomarkers of response through multi-omics analysis in patients with resectable locally advanced GC. The primary endpoint was the pathological complete response (pCR) rate. Secondary endpoints included the R0 rate, near pCR rate, progression-free survival (PFS), disease-free survival (DFS), and overall survival (OS). Multi-omics analysis was assessed by whole-exome sequencing, transcriptome sequencing, and multiplex immunofluorescence (mIF) using biopsies pre- and post-neoadjuvant therapy. RESULTS: This study involved 60 patients, of which 55 underwent gastrectomy. Among these, five (9.1%) attained a pathological complete response (pCR), and 11 (20.0%) reached near pCR. No unexpected treatment-emergent adverse events or perioperative mortality were observed, and the regimen presented a manageable safety profile. Molecular changes identified through multi-omics analysis correlated with treatment response, highlighting associations between HER2-positive and CTNNB1 mutations with treatment sensitivity and a favourable prognosis. This finding was further supported by immune cell infiltration analysis and mIF. Expression data uncovered a risk model with four genes (RALYL, SCGN, CCKBR, NTS) linked to poor response. Additionally, post-treatment infiltration of CD8+ T lymphocytes positively correlates with pathological response. CONCLUSION: The findings suggest the combination of PD-1-inhibitor and mFOLFOX6 showed efficacy and acceptable toxicity for locally advanced GC. Extended follow-up is required to determine the duration of the response. This study lays essential groundwork for developing precise neoadjuvant regimens.

The "quadrant-sandwich" method in clockwise modular D2 lymph node dissection in laparoscopic total gastrectomy: a retrospective cohort study.

Background: For patients who need laparoscopic radical gastrectomy, lymph node dissection (LND) and optimization of surgical procedures are particularly important. This study introduces the "quadrant-sandwich" method in clockwise modular D2 LND and evaluates the advantages and safety of this method. Methods: The clinical data of 108 laparoscopic total gastrectomy patients admitted to the Affiliated Cancer Hospital of Zhengzhou University from January 2019 to January 2022 were retrospectively analyzed. Based on the different LND processes, 55 patients were allocated to the observation group, which underwent clockwise modular LND using the "quadrant-sandwich method", and 53 patients were allocated to the control group, which underwent traditional LND. The effectiveness and safety of the approach in terms of operation time, blood loss, lymph node yield, postoperative recovery and postoperative complications were observed in the two groups. Results: There was no statistical difference between the baseline data of the two groups. In relation to the surgery, the observation group had an operation time of 227.0±48.5 minutes, and intraoperative bleeding of 100.0 mL [inter-quartile range (IQR), 30.0-200.0 mL], while the control group had an operation time of 247±41.5 minutes, and intraoperative bleeding of 180.0 mL (IQR, 130.0-245.0 mL). There were statistically significant differences between the two groups in terms of the operation time and intraoperative bleeding (P=0.001, P=0.020). In relation to the LND, there were no statistically significant differences between the two groups in terms of the total number of lymph nodes in each division, and the number of positive lymph nodes. In relation to the post-operative results, there were no statistically significant differences between the two groups in terms of the post-operative pathological stage, first postoperative oral feeding, post-operative hospitalization time, and post-operative complications. Conclusions: Clockwise modular D2 LND using the "quadrant-sandwich method" is potentially safe and feasible in laparoscopic total gastrectomy. It not only ensures the thoroughness of the LND, but also ensures and efficient and fast surgical process, shortens the operation time, and reduces the amount of intraoperative bleeding.

Postoperative superior anastomotic leakage classification and treatment strategy for postoperative esophagogastric junction cancer.

Background: At present, anastomotic fistula cannot be avoided after adenocarcinoma of the esophagogastric junction (AEG). Once the anastomotic leakage occurs, the posterior mediastinum and the left thoracic cavity are often seriously infected, which further impairs respiratory and circulatory function, heightening the danger of the disease course. The aim of this study was to identify the characteristics of superior anastomotic leakage after surgery for AEG and recommend corresponding treatment strategies to improve the diagnosis and treatment of superior anastomotic leakage after surgery for AEG. Methods: The clinical data of 57 patients with superior anastomotic leakage after surgery for AEG in the Affiliated Cancer Hospital of Zhengzhou University from January 2017 to March 2019 were retrospectively analyzed, including 27 cases referred from external hospitals and 30 cases at the Affiliated Cancer Hospital of Zhengzhou University. According to the diameter and risk level of anastomotic leakage, the high anastomotic leakage is divided into types I, II, III, and IV. Results: Patients with preoperative comorbidities or those treated with the transabdominal approach or laparoscopic surgery often had type I and type II anastomotic leakage; meanwhile, patients with preoperative comorbidities and sacral perforation or those treated with a thoracic and abdominal approach or open surgery often had type III and IV fistula. The difference between types I-II and types III-IV was statistically significant (P<0.05). The mortality rate of patients with type III and type IV leakage was 14.8% within 90 days after operation, while no deaths occurred among patients with type I and type II leakage, and the difference in mortality between the two groups was statistically significant (P<0.05). Conclusions: After surgery for AEG, suitable treatment measures should be adopted according to the type of superior anastomotic leakage that occurs. Types III and IV superior anastomotic leakages are associated with higher mortality and require greater attention from surgeons.

Clinicopathological features and prognoses in younger and older patients with mismatch repair defects colorectal cancer: a retrospective comparative cohort study.

Background: Microsatellite instability-high (MSI-H) is an important biomarker for predicting the effects of immune checkpoint inhibitors (ICIs) in colorectal cancer (CRC) patients. However, due to the low mutation rate of MSI-H/deficient mismatch repair (dMMR) in the overall population, some doctors are of the view that testing this indicator increases the burden on patients, and consequently some patients fail to receive the most beneficial treatment methods. In order to provide testing criteria for younger patients with a higher proportion of MSI-H, we designed this retrospective controlled study. Methods: A retrospective analysis was conducted of 1,901 patients who were admitted to the Affiliated Cancer Hospital of Zhengzhou University from January 2017 to December 2019 and underwent CRC-related gene testing. For this analysis, 100 patients aged 40 or younger are defined as the young group, and 305 patients aged 71 and older but younger than 80 are defined as the elderly group. We included patients who met the following criteria: (I) underwent preoperative colonoscopy or gastroscopy and were diagnosed with CRC; (II) received perioperative adjuvant therapy; (III) underwent curative surgery for CRC. Each patient was followed up from the time of surgery until April 30, 2023, or death, with follow-up visits scheduled every 3 months for the first 2 years after surgery, and every 6 months thereafter. Clinical characteristics such as age, gender, body mass index (BMI), tumor depth (T), number of metastatic lymph nodes (N), distant metastasis (M), tumor, node, metastasis (TNM) stage, extent of surgical resection, tumor size, tumor location, differentiation grade, and carcinoembryonic antigen (CEA) levels were collected. The microsatellite instability (MSI) status was analyzed using fluorescence in situ hybridization (FISH). Results: In young CRC patients, the proportion of MSI-H is higher than in elderly CRC patients (33% vs. 10.16%, P<0.001). The proportion of poorly differentiated tumors is also higher in young CRC patients compared to elderly CRC patients (53% vs. 31.15%, P<0.001). However, there were no significant differences in clinical characteristics between young and elderly CRC patients. In terms of prognosis, survival analysis of the young group showed that MSI status [hazard ratio (HR) =0.26, 95% confidence interval (CI): 0.08-0.88, P=0.03], TNM staging (HR =3.84, 95% CI: 1.38-10.71, P=0.010) were associated with the prognosis of CRC patients. Conclusions: The mutation rate of MSI-H is higher in young CRC patients compared to older. Our study further confirms that MSI-H can serve as a favorable prognostic marker for CRC patients. This finding may provide valuable guidance for clinicians in terms of prognosis assessment and treatment selection. If feasible, we hope that MSI testing can be performed for all CRC patients to enable targeted testing, with particular attention to monitoring the MSI status in young patients. This will aid clinicians in selecting appropriate treatment strategies for these patients.

Behavioral and genomic divergence between a generalist and a specialist fly.

The evolution of feeding habits leads to speciation in insects. Bactrocera true fruit flies display diverse feeding habits across species. We combine behavioral and functional genomic studies to probe the divergence between the specialist B. minax and the generalist B. dorsalis. We find that both vision and olfaction contribute to their respective host preferences, with a dominant effect of vision over the olfaction in short range. Correspondingly, host location-related genes are significantly enriched in the phototransduction pathway, of which the long-wavelength rhodopsin confers the color preference in both species and has been subject to selection in the specialist. We also find a massive expansion of olfactory receptors in the generalist, along with signatures of conditional expression and positive selection. The phylogenetic context suggests an ancestrally important role of vision in the host location of Bactrocera, as well as the increased performance and plasticity of olfaction alongside the arising of generalism.

Comparison of Traditional and Next-Generation Approaches for Uncovering Phytoplasma Diversity, with Discovery of New Groups, Subgroups and Potential Vectors.

Despite several decades' effort to detect and identify phytoplasmas (Mollicutes) using PCR and Sanger sequencing focusing on diseased plants, knowledge of phytoplasma biodiversity and vector associations remains highly incomplete. To improve protocols for documenting phytoplasma diversity and ecology, we used DNA extracted from phloem-feeding insects and compared traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas. Among 22 of 180 leafhopper samples that initially tested positive for phytoplasmas using qPCR, AHE yielded phytoplasma 16Sr sequences for 20 (19 complete and 1 partial sequence) while Sanger sequencing yielded sequences for 16 (11 complete and 5 partial). AHE yielded phytoplasma sequences for an additional 7 samples (3 complete and 4 partial) that did not meet the qPCR threshold for phytoplasma positivity or yielded non-phytoplasma sequences using Sanger sequencing. This suggests that AHE is more efficient for obtaining phytoplasma sequences. Twenty-three samples with sufficient data were classified into eight 16Sr subgroups (16SrI-B, I-F, I-AO, III-U, V-C, IX-J, XI-C, XXXVII-A), three new subgroups (designated as 16SrVI-L, XV-D, XI-G) and three possible new groups. Our results suggest that screening phloem-feeding insects using qPCR and AHE sequencing may be the most efficient method for discovering new phytoplasmas.

Selection of Digestive Tract Reconstruction After Partial Gastric Sparing Surgery in Patients With Adenocarcinoma of the Esophagogastric Junction of cT2-T3 Stage.

Objective: To investigate the appropriate reconstruction method of the digestive tract after partial gastric sparing surgery for adenocarcinoma of the esophagogastric junction of stage cT2-T3. Methods: A retrospective analysis of the clinical data of patients with adenocarcinoma of the esophagogastric junction from January 2015 to January 2019 in the General Surgery Department of Zhengzhou University Affiliated Tumor Hospital was performed. Patients with intraoperative double tract anastomosis composed the double tract reconstruction (DTR) group, and patients with intraoperative oesophagogastrostomy with a narrow gastric conduit group composed the oesophagogastrostomy by a narrow gastric conduit (ENGC) group. We analysed and compared the short-term postoperative complications and long-term postoperative nutritional status of the two groups of patients. Result: There were no statistically significant differences between the two groups of patients in terms of age, sex, preoperative haemoglobin level, albumin level, cT, cN, neoadjuvant therapy or not, pathological type and Siewert type. In terms of BMI and body weight, the ENGC group was higher than the DTR group, but the difference was not statistically significant (p = 0.099, p = 0.201). There was no significant difference between the two groups of patients in terms of upper resection margin, operation time, blood loss, tumor diameter, pT, pN and postoperative hospital stay. The gastric resection volume of the DTR group was much larger than that of the ENGC group, and there was a significant difference between the two (p = 0.000). The length of the lower resection margin of the DTR group was also significantly greater than that of the ENGC group (p = 0.000). In terms of surgical approach, the proportion of the DTR group with the abdominal approach was significantly higher than that of the ENGC group, and the difference between the two was statistically significant (p = 0.003). The postoperative exhaust time in the ENGC group was significantly shorter than that in the DTR group (p = 0.013). However, there was no statistically significant difference between the two groups in terms of anastomotic leakage, anastomotic bleeding, intestinal obstruction, abdominal infection, pneumonia, pancreatic leakage, lymphatic leakage,death within 30 days after surgery, or overall complications. In terms of anastomotic stenosis, the incidence in the ENGC group was higher than in the DTR group, and the difference was statistically significant (p = 0.001). There was no significant difference in oral PPI, haemoglobin or albumin levels in patients at 3 months, 6 months, or 12 months after surgery. Comparing reflux/heartburn symptoms at 3 months and 6 months after surgery, we found no statistically significant difference between the two, while in terms of reflux/heartburn symptoms at 12 months after surgery, the findings of the ENGC group were higher than those of the DTR group, and the difference was statistically significant (p = 0.045). In terms of poor swallowing, the ENGC group was always higher than the DTR group, and the difference between the two groups was statistically significant (p < 0.05). There was no statistically significant difference in body weight between the two groups at 3 months or 6 months after surgery. At 12 months after surgery, the body weight of the patients in ENGC group was significantly higher than that in the DTR group, and the difference between the two groups was statistically significant (p = 0.039). Conclusions: For patients with cT2-T3 stage oesophagogastric junction adenocarcinoma with tumours less than 4 cm in diameter, ENGC anastomosis is recommended for patients with a high tumour upper boundary, with obesity, short mesentery, or disordered vascular arch, and for routine patients, DTR anastomosis is recommended.

Landscape Composition Affects Elements of Metacommunity Structure for Culicidae Across South-Eastern Illinois.

The interplay among invasive alien vectors and the species assemblage of native potential vectors in areas of range expansion may affect the dynamics of pathogen transmission. In this study we investigate how Aedes albopictus, an invasive mosquito of considerable public health concern fits within mosquito communities at the edge of its range of distribution. This was addressed using a 2-year field survey of mosquitoes in south-eastern Illinois. We found that Ae. albopictus was more broadly distributed in this region than previously realized, with new occurrence records for nine counties. Abundance of this species varied strongly and peaked in locations of low-intermediate overall mosquito species richness. This differed from overall mosquito abundance, as well as abundance of another important vector, Cx. pipiens, for which the abundance-richness relationships were best described with power functions. Metacommunity analyses revealed that mosquito communities showed a non-random distribution with a Clementsian gradient, which suggests a pattern whereby distinct species assemblages are associated with specific habitats or environmental conditions. Land use was a significant underlying factor shaping mosquito community structure and species assemblages. Multivariate analyses showed that while Ae. canadensis and Cx. pipiens complex mosquitoes were associated with high and low proportions of wetlands in the environment, respectively, Ae. albopictus was most strongly associated with urban settlements. This work sheds light on landscape-level processes, such as niche differentiation driven by urban and agricultural development, structuring mosquito communities. We suggest that mosquito community assessments across habitats be incorporated as part of a One Health vector surveillance approach to aid in the goal of prediction and prevention of new and (re-)emerging vector-borne diseases.

Tunnel versus medial approach in laparoscopic radical right hemicolectomy for right colon cancer: a retrospective cohort study.

PURPOSE: This study aimed to explore the feasibility and safety of the tunnel approach in laparoscopic radical right hemicolectomy for colon cancer. METHODS: From July 2016 to October 2018, a total of 106 consecutive patients with colon cancer who underwent laparoscopic radical right hemicolectomy at the Affiliated Cancer Hospital of Zhengzhou University were enrolled. The patients were stratified into either a tunnel approach (TA) (n = 56) group or traditional medial approach (MA) (n = 50) group according to the surgical technique performed. The baseline demographics, perioperative outcomes and oncologic outcomes were compared between the two groups. RESULTS: The baseline characteristics did not differ between groups. The TA group had significantly less blood loss [20.0 (10.0-40.0) vs. 100 (100.0-150.0) ml, p < 0.001] and a shorter operation time [128.4 ± 16.7 vs. 145.6 ± 20.3 min, p < 0.001] than the MA group. The time to first flatus and postoperative hospital stay were similar [3.0 (2.0-4.0) vs. 3.0 (3-4.0) days, p = 0.329; 10.4 ± 2.6 vs. 10.7 ± 3.0 days, p = 0.506] between the two groups. The conversion to laparotomy and complication rates were similar between groups (0 vs. 6.0%, p = 0.203; 14.3% vs. 18.0%, p = 0.603, respectively). No treatment-related deaths occurred in either group. The TA group did not have significantly better survival outcomes than the MA group (p = 0.372). CONCLUSIONS: The TA seems to allow for more favourable results in terms of blood loss and operative time than the MA, with similar results regarding time to first flatus, hospital stay, postoperative complication rate, conversion rate and oncologic outcomes; moreover, the TA is easier for beginners to master.

Phylogenomics of flavobacterial insect nutritional endosymbionts with implications for Auchenorrhyncha phylogeny.

"Candidatus Sulcia muelleri" (Sulcia) is a diverse lineage of intracellular nutritional endosymbiotic bacteria strictly associated with auchenorrhynchous hemipteran insects. Sulcia has undergone long-term codiversification with its insect hosts but the phylogeny of these endosymbionts, their relationships to other bacteria, and the extent of their occurrence within various groups of Auchenorrhyncha remain inadequately explored. Comprehensive phylogenetic analyses of Sulcia and related bacteria were performed to elucidate its position relative to other members of Phylum Bacteroidetes and the degree of congruence to the phylogeny of its auchenorrhynchous hosts. Maximum likelihood (ML) and maximum parsimony (MP) analyses of Flavobacteriales based on genomic data from 182 bacterial strains recover a monophyletic Sulcia within a larger clade of flavobacterial insect endosymbionts, closely related to Weeksellaceae. Molecular divergence time analysis of Sulcia dates the origin of Sulcia at approximately 339.95 million years ago (Myr) and the initial divergence within Sulcia at approximately 256.91 Myr but these are considered underestimates due to the tendency for endosymbionts to evolve at higher rates compared to their free-living relatives. Screening of 96 recently sequenced hemipteran transcriptomes revealed that 73 of these species, all Auchenorrhyncha, harbored Sulcia. Phylogenetic analysis of 131 orthologous genes plus 16S rRNA for 101 Sulcia strains, representing six fulgoroid families and all the families of Cicadomorpha except Tettigarctidae, recover largely congruent phylogenies between Sulcia and Auchenorrhyncha. The phylogeny of Sulcia strongly supports the superfamily relationships Fulgoroidea + (Cicadoidea + (Cercopoidea + Membracoidea)). Relationships within individual superfamilies are also largely concordant, with the few areas of apparent incongruence between Sulcia and insect genes attributable to low branch support in one or both datasets. These results suggest that analysis of Sulcia phylogeny may contribute to resolution of contentious aspects of Auchenorrhyncha phylogeny.

Identification of Potential Host Plants of Sap-Sucking Insects (Hemiptera: Cicadellidae) Using Anchored Hybrid By-Catch Data.

Reliable host plant records are available for only a small fraction of herbivorous insect species, despite their potential agricultural importance. Most available data on insect-plant associations have been obtained through field observations of occurrences of insects on particular plants. Molecular methods have more recently been used to identify potential host plants using DNA extracted from insects, but most prior studies using these methods have focused on chewing insects that ingest tissues expected to contain large quantities of plant DNA. Screening of Illumina data obtained from sap feeders of the hemipteran family Cicadellidae (leafhoppers) using anchored hybrid enrichment indicates that, despite feeding on plant fluids, these insects often contain detectable quantities of plant DNA. Although inclusion of probes for bacterial 16S in the original anchored hybrid probe kit yielded relatively high detection rates for chloroplast 16S, the Illumina short reads also, in some cases, included DNA for various plant barcode genes as "by-catch". Detection rates were generally only slightly higher for Typhlocybinae, which feed preferentially on parenchyma cell contents, compared to other groups of leafhoppers that feed preferentially on phloem or xylem. These results indicate that next-generation sequencing provides a powerful tool to investigate the specific association between individual insect and plant species.

The genome of the black cutworm Agrotis ipsilon.

The black cutworm (BCW), Agrotis ipsilon, is a worldwide polyphagous and underground pest that causes a high level of economic loss to a wide range of crops through the damage of roots. This species performs non-directed migration throughout East and Southeast Asia seasonally. Lack of a genome information has limited further studies on its unique biology and the development of novel management approaches. In this study, we present a 476 Mb de novo assembly of BCW, along with a consensus gene set of 14,801 protein-coding gene models. Quality controls show that both genome assembly and annotations are high-quality and mostly complete. We focus manual annotation and comparative genomics on gene families that related to the unique attributes of this species, such as nocturnality, long-distance migration, and host adaptation. We find that the BCW genome encodes a similar gene repertoire in various migration-related gene families to the diural migratory butterfly Danaus plexiipus, with additional copies of long wavelength opsin and two eye development-related genes. On the other hand, we find that the genomes of BCW and many other polyphagous lepidopterans encode many more gustatory receptor genes, particularly the lineage-specific expanded bitter receptor genes, than the mono- or oligo-phagous species, suggesting a common role of gustatory receptors (GRs) expansion in host range expansion. The availability of a BCW genome provides valuable resources to study the molecular mechanisms of non-directed migration in lepidopteran pests and to develop novel strategies to control migratory nocturnal pests.

A multi-gene phylogenetic analysis of the leafhopper subfamily Typhlocybinae (Hemiptera: Cicadellidae) challenges the traditional view of the evolution of wing venation.

Genera of the diverse leafhopper subfamily Typhlocybinae have traditionally been classified into tribes primarily based on characters of the wing venation and an intuitive phylogeny of this group was previously proposed based on the hypothetical pattern of wing vein evolution. Some recent authors suggested that wing vein characters are not always reliable but few attempts have been made to examine the status and relationships of typhlocybine tribes using rigorous phylogenetic analyses. Phylogenetic analysis of a dataset comprising DNA sequences from five gene regions (H3, H2A, 28S rDNA D2, 16S rDNA, and COI with a total length of 2413 bps) and 61 species representing six previously recognized tribes of Typhlocybinae provides strong support for the monophyly of the subfamily and five of the previously recognized tribes. Most branches received moderate to strong maximum likelihood bootstrap support. The following intertribal relationships were recovered: (Alebrini + Empoascini) + ((Dikraneurini + Erythroneurini) + Typhlocybini). Maximum likelihood analysis recovered Zyginellini (treated as a separate tribe by some authors) as sister to Typhlocybini with low branch support, but the former tribe was derived from within the latter in Bayesian analysis of the same dataset and relationships within Typhlocybini (sensu lato) were generally poorly resolved in both analyses. The relationship of Typhlocybini to other tribes is also unstable, suggesting that more data are needed to resolve the position of this tribe with confidence. Parts of the phylogeny receiving strong support in both analyses contradict the traditional view that Alebrini, the only tribe retaining an appendix in the forewing, is the earliest diverging lineage and possibly gave rise to the other tribes. Ancestral state reconstructions indicate that characters of the wing venation traditionally used for diagnosing typhlocybine tribes are generally conservative but exhibit some homoplasy and may not, by themselves, be reliable for recognizing monophyletic groups within this subfamily.

The draft genome of the Asian corn borer yields insights into ecological adaptation of a devastating maize pest.

The Asian corn borer (ACB) is the most devastating pest on maize in the western Pacific region of Asia. Despite broad interests in insecticide resistance, seasonal adaptation, and larval color mimicry regarding the ACB system, lacking of reference genomic information and a powerful gene editing approach have hindered the in-depth studies of these aspects. Here we present a 455.7 Mb draft genome of ACB with 98.4% completeness. Comparative genomics analysis showed an evident expansion in gene families of gustatory receptors (105), which is related to polyphagous characteristics. Based on the comparative transcriptome analysis of resistant and susceptible ACB against Bt Cry1Ab toxin, we identified 26 genes related to Cry1Ab resistance. Additionally, transcriptomics of insects exposed to conditions of low temperature and diapause (LT) vs. room temperature and diapause (RT) provided insights into the genetic mechanisms of cold adaptation. We also successfully developed an efficient CRISPR/Cas9-based genome editing system and applied it to explore the role of color pattern genes in the ecological adaptation of ACB. Taken together, our study provides a fully annotated high-quality reference genome and efficient gene editing system to realize the potential of ACB as a study system to address important biological questions such as insecticide resistance, seasonal adaptation, and coloration. These valuable genomic resources will also benefit the development of novel strategies for maize pest management.

A risk signature with inflammatory and immune cells infiltration predicts survival and efficiency of chemotherapy in gastric cancer.

OBJECTIVE: Tumor immune microenvironment biomarkers might add predictive value for outcomes. This study aimed to construct a risk signature with tumor infiltration immune and inflammatory cells to improve the prediction of survival. METHODS: A risk signature model in combination with CD66b + neutrophils, CD3+ T, CD8+ T lymphocytes, and FOXP3 + regulatory T cells was developed in a training cohort of 327 GC patients undergoing surgical resection between 2011 and 2012, and validated in a validation cohort of 285 patients from 2012 to 2013. RESULTS: The high CD66b expression predicted the poor disease special survival (DSS) and inversely correlated with the CD8 (P < 0.05) and FOXP3 expression (P < 0.05) in the training cohort. This was comparable to the disease-free survival (DFS) findings observed in the validation cohort. Furthermore, a risk stratification was developed from the integration of CD66b + neutrophils and T immune cells. For DFS and DSS, both demonstrated the worse prognosis in the high-risk group, when compared to the low-risk group in both the training cohort and validation cohort (all P < 0.05). In addition, the high-risk group was associated with post-operative relapses, and this risk signature model increased the predictive accuracy and efficiency for post-operative relapses. Moreover, the high-risk group identified a subgroup of GC patients who tended not to benefit from the adjuvant chemotherapy. CONCLUSIONS: The incorporation of neutrophils into T lymphocytes could provide more accurate prognostic information in GC and this risk stratification has potential for identifying the subgroup of GC patients who could benefit from adjuvant chemotherapy.

Chromosome-level genome reference and genome editing of the tea geometrid.

The tea geometrid is a destructive insect pest on tea plants, which seriously affects tea production in terms of both yield and quality and causes severe economic losses. The tea geometrid also provides an important study system to address the ecological adaptive mechanisms underlying its unique host plant adaptation and protective resemblance. In this study, we fully sequenced and de novo assembled the reference genome of the tea geometrid, Ectropis grisescens, using long sequencing reads. We presented a highly continuous, near-complete genome reference (787.4 Mb; scaffold N50: 26.9 Mb), along with the annotation of 18,746 protein-coding genes and 53.3% repeat contents. Importantly, we successfully placed 97.8% of the assembly in 31 chromosomes based on Hi-C interactions and characterized the sex chromosome based on sex-biased sequencing coverage. Multiple quality-control assays and chromosome-scale synteny with the model species all supported the high quality of the presented genome reference. We focused biological annotations on gene families related to the host plant adaptation and camouflage in the tea geometrid and performed comparisons with other representative lepidopteran species. Important findings include the E. grisescens-specific expansion of CYP6 P450 genes that might be involved in metabolism of tea defensive chemicals and unexpected massive expansion of gustatory receptor gene families that suggests potential polyphagy for this tea pest. Furthermore, we developed an efficient genome editing system based on CRISPR/Cas9 technology and successfully implement mutagenesis of a Hox gene in the tea geometrid. Our study provides key genomic resources both for exploring unique mechanisms underlying the ecological adaptation of tea geometrids and for developing environment-friendly strategies for tea pest management.

Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera.

Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.