Research Progress of Natural Product Photosensitizers in Photodynamic Therapy.

Photodynamic therapy is a noninvasive cancer treatment that utilizes photosensitizers to generate reactive oxygen species upon light exposure, leading to tumor cell apoptosis. Although photosensitizers have shown efficacy in clinical practice, they are associated with certain disadvantages, such as a certain degree of toxicity and limited availability. Recent studies have shown that natural product photosensitizers offer promising options due to their low toxicity and potential therapeutic effects. In this review, we provide a summary and evaluation of the current clinical photosensitizers that are commonly used and delve into the anticancer potential of natural product photosensitizers like psoralens, quinonoids, chlorophyll derivatives, curcumin, chrysophanol, doxorubicin, tetracyclines, Leguminosae extracts, and Lonicera japonica extract. The emphasis is on their phototoxicity, pharmacological benefits, and effectiveness against different types of diseases. Novel and more effective natural product photosensitizers for future clinical application are yet to be explored in further research. In conclusion, natural product photosensitizers have potential in photodynamic therapy and represent a promising area of research for cancer treatment.

Analysis of risk factors for postoperative deep vein thrombosis after craniotomy and nomogram model construction.

BACKGROUND: Deep vein thrombosis (DVT) of the lower extremity is one of the most common postoperative complications, especially after craniocerebral surgery. DVT may lead to pulmonary embolism, which has a devastating impact on patient prognosis. This study aimed to investigate the incidence and risk factors of DVT in the lower limbs following craniocerebral surgery. AIM: To identify independent risk factors for the development of postoperative DVT and to develop an effective risk prediction model. METHODS: The demographic and clinical data of 283 patients who underwent craniocerebral surgery between December 2021 and December 2022 were retrospectively analyzed. The independent risk factors for lower extremity DVT were identified by univariate and multivariate analyses. A nomogram was created to predict the likelihood of lower extremity DVT in patients who had undergone craniocerebral surgery. The efficacy of the prediction model was determined by receiver operating characteristic curve using the probability of lower extremity DVT for each sample. RESULTS: Among all patients included in the analysis, 47.7% developed lower extremity DVT following craniocerebral surgery. The risk of postoperative DVT was higher in those with a longer operative time, and patients with intraoperative intermittent pneumatic compression were less likely to develop postoperative DVT. CONCLUSION: The incidence of lower extremity DVT following craniocerebral surgery is significant, highlighting the importance of identifying independent risk factors. Interventions such as the use of intermittent pneumatic compression during surgery may prevent the formation of postoperative DVT.

Network pharmacology integrated with molecular docking technology to reveal the potential mechanism of Shuganfang against drug-induced liver injury.

This study aimed to investigate the active composition and mechanism of the Shuganfang (SGF) in treating drug-induced liver injury (DILI) using network pharmacology and molecular docking. The potential active ingredients and targets of SGF were obtained from the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) database. DILI-related targets were queried from various databases including GEO, GeneCards, OMIM, NCBI, and DisGeNET. The STRING database was used to establish a protein-protein interaction (PPI) network. DAVID was utilized for conducting gene ontology (GO) function enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses. The data visualization and analysis of herb-ingredient-target and disease-pathway-target-ingredient networks were conducted using Cytoscape software (version 3.7.2). PyMoL and AutoDock software was used to select the best binding target for molecular docking. A total of 177 active ingredients,126 targets and 10112 disease targets were obtained, including 122 intersection targets. The identified potential active ingredients consisted of quercetin, kaempferol, luteolin, tanshinone IIa, nobiletin, isorhamnetin, beta-sitosterol and naringenin. The core targets implicated in the study were IL6, estrogen receptor 1 (ESR1), hypoxia-inducible factor alpha subunit 1 (HIF1A), MYC and vascular endothelial growth factor A (VEGFA). KEGG analysis revealed that the treatment of DILI with SGF mainly acted through apoptosis, the PI3K-Akt signaling pathway, and the tumor necrosis factor (TNF) signaling pathway. Furthermore, the binding affinities between the potential ingredients and the core targets were subsequently confirmed through molecular docking experiments. The findings indicated that the docking outcomes remained consistent and demonstrated a favorable capacity for binding. SGF exerts a therapeutic effect on DILI through multiple active ingredients, multiple targets and multiple pathways. Our findings contribute to a positive investigation and establish a theoretical basis for further extensive exploration of SGF as a potential treatment for DILI in future research.

Non-overlapping epitopes on the gHgL-gp42 complex for the rational design of a triple-antibody cocktail against EBV infection.

Epstein-Barr virus (EBV) is closely associated with cancer, multiple sclerosis, and post-acute coronavirus disease 2019 (COVID-19) sequelae. There are currently no approved therapeutics or vaccines against EBV. It is noteworthy that combining multiple EBV glycoproteins can elicit potent neutralizing antibodies (nAbs) against viral infection, suggesting possible synergistic effects. Here, we characterize three nAbs (anti-gp42 5E3, anti-gHgL 6H2, and anti-gHgL 10E4) targeting different glycoproteins of the gHgL-gp42 complex. Two antibody cocktails synergistically neutralize infection in B cells (5E3+6H2+10E4) and epithelial cells (6H2+10E4) in vitro. Moreover, 5E3 alone and the 5E3+6H2+10E4 cocktail confer potent in vivo protection against lethal EBV challenge in humanized mice. The cryo-EM structure of a heptatomic gHgL-gp42 immune complex reveals non-overlapping epitopes of 5E3, 6H2, and 10E4 on the gHgL-gp42 complex. Structural and functional analyses highlight different neutralization mechanisms for each of the three nAbs. In summary, our results provide insight for the rational design of therapeutics or vaccines against EBV infection.

A feruloyl esterase/cellulase integrated biological system for high-efficiency and toxic-chemical free isolation of tobacco based cellulose nanofibers.

Tobacco based cellulose nanofiber (TCNF) is a novel nanocellulose that has recently been used to replace undesirable wood pulp fibers in the preparation of reconstructed tobacco sheets (RTS). However, given the strict requirements for controlling toxic chemical content in tobacco products, there is a global interest in developing a green, efficient, and toxic-chemical free approach to isolate TCNF from tobacco stem as a bioresource. In this study, we propose a creative and environmentally friendly method to efficiently and safely isolate TCNF from tobacco stem pulp, which involves integrated biological pretreatment followed by a facile mechanical defibrillation process. Feruloyl esterase is used to pretreat the stem pulp by disrupting the ether and ester bonds between lignin and polysaccharide carbohydrates within the fiber wall, which effectively facilitates cellulase hydrolysis and swelling of the stem pulp fiber, as well as the following mechanical shearing treatment for TCNF isolation. The results demonstrate that TCNF obtained by the comprehensive feruloyl esterase/cellulase/mechanical process exhibit uniform and well-dispersed nanofiber morphology, higher crystallinity, and stronger mechanical properties than those of the control. The addition of 0.5 % TCNF can replace wood pulp by 18 wt% ~ 25 wt% in the production of RTS samples while maintaining their reasonable strength properties.

Analysis of risk factors and treatment strategies for lumbar cistern blockage after craniocerebral surgery.

Objective: Lumbar cistern blockage is a common complication of continuous lumbar cistern drainage. This paper analyzes the risk factors for lumbar cistern blockage drainage due to various causes and proposes a series of prevention and intervention measures to reduce blockage or improve recanalization after blockage. Methods: The clinical data of 637 patients with various lesions who underwent lumbar cistern drainage in our hospital were retrospectively collected and analyzed. Perioperative clinical and imaging data were assessed. Variates were analyzed using univariate and multivariate logistic regression analyses. Results: A total of 13.7% (87/637) of patients had lumbar cistern blockage. Multivariate analysis revealed that drainage time (≥7 days), CSF volume <200 (mL/d), CSF leakage, and abnormal CSF properties were predictors of lumbar cistern blockage. Reducing the probability of lumbar cistern blockage can be achieved by repeatedly flushing, increasing the drainage flow and shortening the drainage time. The recanalization rate after blockage was 67.8% (59/87). After the drainage tube was removed, no complications related to the drainage tube occurred during the 1-week follow-up. Conclusion: Lumbar cistern blockage is the main reason for poor drainage. Prevention or early intervention can effectively reduce the probability of blockage and achieve the purpose of drainage of cerebrospinal fluid.

Early discontinuation and results reporting of robot-assisted surgery studies registered on ClinicalTrials.gov: a research on research study.

OBJECTIVES: In this study, we aimed to investigate the characteristics of robot-assisted surgery studies registered on ClinicalTrials.gov and identify factors associated with early trial discontinuation and timely results reporting. DESIGN: We searched ClinicalTrials.gov to identify interventional studies on robot-assisted surgery on 24 May 2021. All structured information of the potential studies was downloaded and reviewed. A descriptive analysis was performed. Logistic and Cox regression analyses were respectively performed to determine the significance of the association of study characteristics with results reporting and early discontinuation. RESULTS: A total of 529 interventional studies on robot-assisted surgery were included, with 45 studies reporting results and 54 studies being stopped early. Of the 289 due studies, only 45 (16%) had submitted their results, and only 6 (2%) had submitted their results within the 1-year deadline. Funding source was associated with results reporting: academic funded were 63% less likely than industry to report results (OR=0.37, 95% CI: 0.16 to 0.83, p=0.02). Studies related to device feasibility were associated with greater risk of early discontinuation compared to treatment-related studies (HR=2.30, 95% CI: 1.08 to 4.89, p=0.03). Surprisingly, National Institutes of Health-funded studies were at greater hazard of discontinuation compared to industry-funded studies (HR=3.30, 95% CI: 1.09 to 10.00, p=0.04). CONCLUSIONS: There was poor compliance with results reporting requirements for robot-assisted surgical studies. It is important that investigators remain informed about the regulatory requirements, and should be helped to develop a sense of responsibility for reporting results. Also, they need to ensure the careful design of the study protocol and adequate resources to reduce the risk of early discontinuation.

Risk factors influencing cerebral venous infarction after meningioma resection.

BACKGROUND: Cerebral venous infarction (CVI) is a serious complication after meningioma resection. The risk factors of postoperative cerebral venous infarction after surgical resection of meningioma can be determined through large samples and this study can add evidence to the literature. METHODS: The clinical and imaging data of 1127 patients with intracranial meningiomas who underwent resection in our hospital were retrospectively collected and analyzed. CVI was evaluated by postoperative imaging and clinical manifestations. Univariate and multivariate analyses were performed to identify risk factors associated with CVI. RESULTS: Overall, 4.7% (53/1127) of patients experienced CVI after meningioma resection. Multivariate analysis revealed superficial meningioma, moderate to severe peritumoral edema, peritumoral critical vein and WHO grade II-III as independent predictors of a postoperative CVI. After timely intervention, the symptoms were clearly alleviated in one month, and the prognosis was good, but injury to key veins could cause irreversible neurological disorders. CONCLUSIONS: Intraoperative protection of veins is the primary way to prevent CVI. The present study identified several significant and independent risk factors for postoperative venous infarction, thereby enabling the identification of high-risk patients who require special attention during clinical and surgical management.

Characterization of Insulin-like Peptide (ILP) and Its Potential Role in Ovarian Development of the Cuttlefish Sepiella japonica.

The insulin-like peptide (ILP) family is well known for regulating reproduction in invertebrates, while its role in mollusks remains largely unknown. In this study, we first isolated and characterized the ILP gene in the cuttlefish Sepiella japonica. The full-length SjILP cDNA obtained was 926 bp and encoded a precursor protein of 161 amino acids. The precursor protein consisted of a signal peptide, a B chain, a C-peptide, and an A chain. It possessed the typical features of ILP proteins, including two cleavage sites (KR) and eight conserved cysteines. To define the function of SjILP, the expression of SjILP in different tissues and ovarian development stages were analyzed using qRT-PCR. SjILP was mainly expressed in the ovary, and its gene expression correlated with ovarian development. Furthermore, silencing SjILP using RNA interference (RNAi) dramatically decreased the expression levels of four ovarian-development-related genes (vitellogenin1, vitellogenin2, cathepsin L1-like, and follistatin). These data suggest the critical role of SjILP in the regulation of ovarian development in S. japonica.

Evaluation of Pembrolizumab Monotherapy Efficacy in Advanced Non-Small-Cell Lung Cancer by Serial Monitoring of Circulating Tumor DNA Using Next-Generation Sequencing.

INTRODUCTION: Pembrolizumab is widely used in advanced non-small-cell lung cancer (NSCLC) patients with positive programmed death-ligand 1 (PD-L1). However, efficacy evaluation along treatment by serial monitoring of circulating tumor DNA (ctDNA) using next-generation sequencing remained to be well studied. METHODS: Nine PD-L1 positive advanced NSCLC patients were prospectively enrolled and received pembrolizumab monotherapy. Pretreatment tissue and/or plasma samples were collected as baseline reference. Serial plasma samples were collected after 3 and 6 weeks of treatment as well as at disease progression. All samples underwent targeted next-generation sequencing. RESULTS: The median progression-free survival (mPFS) and median overall survival (mOS) were 4.43 and 25.53 months, respectively. In total, 3 patients achieved partial response (PR) or stable disease (SD) for more than 6 months and were thus classified into the durable clinical benefit (DCB) group, whereas the rest 6 were grouped as nondurable benefit (NDB) patients. Molecular profiling of baseline samples revealed that TP53 and APC were the 2 most frequently mutated genes in all patients, whereas POT1 and SETD2 mutations were enriched in DCB and NDB groups, respectively. Higher tumor mutational burden (TMB) was observed in DCB patients than NDB group. During serial ctDNA monitoring, 2 DCB patients showed a dramatic ctDNA reduction while 75% of NDB patients' ctDNA concentration increased at week 6. Several acquired mutations might contribute to the pembrolizumab resistance, including CDKN2A frameshift and MITF nonsense mutations. CONCLUSIONS: Genomic profiling of peripheral blood samples can be applied to dynamically monitor disease progression. The reduction in ctDNA concentration during treatment implied DCBs.

Engineering for an HPV 9-valent vaccine candidate using genomic constitutive over-expression and low lipopolysaccharide levels in Escherichia coli cells.

BACKGROUND: The various advantages associated with the growth properties of Escherichia coli have justified their use in the production of genetically engineered vaccines. However, endotoxin contamination, plasmid vector instability, and the requirement for antibiotic supplementation are frequent bottlenecks in the successful production of recombinant proteins that are safe for industrial-scaled applications. To overcome these drawbacks, we focused on interrupting the expression of several key genes involved in the synthesis of lipopolysaccharide (LPS), an endotoxin frequently responsible for toxicity in recombinant proteins, to eliminate endotoxin contamination and produce better recombinant proteins with E. coli. RESULTS: Of 8 potential target genes associated with LPS synthesis, we successfully constructed 7 LPS biosynthesis-defective recombinant strains to reduce the production of LPS. The endotoxin residue in the protein products from these modified E. coli strains were about two orders of magnitude lower than that produced by the wild-type strain. Further, we found that 6 loci-lpxM, lpxP, lpxL, eptA, gutQ and kdsD-were suitable for chromosomal integrated expression of HPV L1 protein. We found that a single copy of the expression cassette conferred stable expression during long-term antibiotic-free cultivation as compared with the more variable protein production from plasmid-based expression. In large-scale fermentation, we found that recombinant strains bearing 3 to 5 copies of the expression cassette had 1.5- to 2-fold higher overall expression along with lower endotoxin levels as compared with the parental ER2566 strain. Finally, we engineered and constructed 9 recombinant E. coli strains for the later production of an HPV 9-valent capsid protein with desirable purity, VLP morphology, and antigenicity. CONCLUSIONS: Reengineering the LPS synthesis loci in the E. coli ER2566 strain through chromosomal integration of expression cassettes has potential uses for the production of a 9-valent HPV vaccine candidate, with markedly reduced residual endotoxin levels. Our results offer a new strategy for recombinant E. coli strain construction, engineering, and the development of suitable recombinant protein drugs.

The Effect of Hippocampal Avoidance Whole Brain Radiotherapy on the Preservation of Long-Term Neurocognitive Function in Non-Small Cell Lung Cancer Patients With Brain Metastasis.

Whole-brain radiotherapy (WBRT) is the mainstay of therapy in treating cancer patients with brain metastases, but unfortunately, it might also lead to decline in neurocognitive function. This study aims to investigate the preservation of long-term neurocognitive function in patients after hippocampal avoidance whole-brain radiotherapy (HA-WBRT). Retrospectively, 47 patients diagnosed with brain metastases of non-small cell lung cancer (NSCLC) between 2015-01-01 and 2017-12-31 at the Department of Oncology, XXX Hospital were selected and divided into 2 groups. Group A (n = 27) received HA-WBRT, whereas group B (n = 20) received WBRT. Neurocognitive function was analyzed at baseline and at 3, 6, 9, 12 and 24 months after radiotherapy, using Mine-Mental State Examination (MMSE) scales and Montreal Cognitive Assessment (MoCA) scales. The OS, PFS and tumor recurrence sites were also analyzed. When evaluated at 12 and 24 months after radiotherapy, the cognitive function scores of the hippocampal avoidance group were significantly higher than those of the non-hippocampal avoidance group (P < 0.001). In terms of patient survival, there was no significant difference in OS (P = 0.2) and PFS (P = 0.18) between these 2 groups. Fourteen patients in group A and 12 patients in group B had brain tumor recurrence after radiation, only one patient in group A occurred within 5 mm from the edge of the hippocampus (P > 0.05). In conclusion, HA-WBRT might have a protective effect on long-term neurocognitive function and did not affect patient survival.

C3 glomerulonephritis associated with ANCA positivity: a case report.

BACKGROUND: C3 glomerulopathy (C3G) is a recent disease classification that is characterized by the presence of glomerular deposits (composed of C3) in the absence of significant amounts of immunoglobulin and comprises dense deposit disease and C3 glomerulonephritis (C3GN). Most C3GN manifests as membranoproliferative, mesangial proliferative glomerulonephritis patterns via light microscopy. Pure membranous nephropathy (MN)-like glomerular lesions are rare manifestations of C3GN. Anti-neutrophil cytoplasmic antibodies (ANCAs) are also seldomly reported to be positive in C3GN. Herein, we report the case of a C3GN patient presenting with an MN-like glomerular pattern with ANCA positivity. CASE PRESENTATION: A 68-year-old woman was admitted to a local hospital with elevated serum creatinine for two weeks. Laboratory tests showed a hemoglobin level of 85 g/L. Urinalysis was positive for 2 + protein and 360 RBCs/HPF. Blood biochemistry analysis revealed the following concentrations: albumin, 30.3 g/L; globulin, 46.2 g/L; blood urea nitrogen, 19.9 mmol/L; and serum creatinine, 234 µmol/L. The serum C3 level was 0.4950 g/L, and the serum C4 level was 0.1050 g/L. The direct Coombs test was positive. Serologic testing for ANCA revealed the presence of p-ANCA (1:10) by indirect immunofluorescence microscopy assay, as well as the presence of PR3 1.2 (normal range < 1) and MPO 3.5 (normal range < 1) by enzyme immunoassay. Renal biopsy sample pathology showed 2/6 cellular crescents and thickened glomerular basement membranes. Immunofluorescence testing revealed only diffuse, finely granular depositions of C3 along the glomerular capillary walls in frozen and paraffin-embedded tissue sections. Electron microscopy demonstrated the presence of subepithelial electron-dense deposits, similar to those that are observed in membranous nephropathy. Corticosteroid and cyclophosphamide were administered, with a subsequent improvement in renal function. CONCLUSIONS: We present the rare case of a patient with MN-like C3GN with ANCA positivity. C3GN with ANCA positivity may be represented by more crescents, severe renal dysfunction and more extrarenal manifestations. More cases are needed to elucidate the clinicopathologic features and optimal treatments of these patients.

Large-scale sequencing of flatfish genomes provides insights into the polyphyletic origin of their specialized body plan.

The evolutionary and genetic origins of the specialized body plan of flatfish are largely unclear. We analyzed the genomes of 11 flatfish species representing 9 of the 14 Pleuronectiforme families and conclude that Pleuronectoidei and Psettodoidei do not form a monophyletic group, suggesting independent origins from different percoid ancestors. Genomic and transcriptomic data indicate that genes related to WNT and retinoic acid pathways, hampered musculature and reduced lipids might have functioned in the evolution of the specialized body plan of Pleuronectoidei. Evolution of Psettodoidei involved similar but not identical genes. Our work provides valuable resources and insights for understanding the genetic origins of the unusual body plan of flatfishes.

Isolation and utilization of tobacco-based cellulose nanofiber (TCNF) for high performance reconstructed tobacco sheet (RTS).

Nowadays, wood pulp addition (such as softwood, hardwood, etc.) into manufacture reconstructed tobacco sheet (RTS) via a paper-making process is a feasible and sustainable technology. However, the addition of wood pulp in RTS would weaken the tobacco fragrance of cigarette by bring wood gas when smoking. In this study, a practical and feasible pretreatment by hot water/cooking process combined with cationic modification/homogenization treatment was proposed to directly isolate desirable cellulose nanofibers from tobacco stem, named TCNF. The obtained TCNF was applied in the preparation of RTS to improve its physical properties but with a reduced wood pulp proportion (from 25 wt% decreased to 16 wt%). Results showed that TCNF exhibit a similar morphology with wood based nanocellulose, and that the addition of TCNF (0.5 wt% based dried tobacco pulp) can substitute 9 % of wood pulp compared with that of the control at the similar physical properties.

The lipid platform increases the activity of STING agonists to synergize checkpoint blockade therapy against melanoma.

The response rate to PD-1/PD-L1 immune checkpoint inhibition (ICI) therapy in melanoma remains low due to the immunosuppressive tumor microenvironment. Novel strategies synergizing ICI treatment are urgently sought after. Activation of the stimulator of interferon genes (STING) has recently emerged as a critical pathway to overcome immunosuppression. Herein, 2'3' cyclic guanosine monophosphate-adenosine monophosphate (cGAMP), a universal STING agonist, was encapsulated into lipid nanoparticles conjugated with mannose (LP-cGAMP) for dendritic cell (DC)-specific cytosolic delivery. LP-cGAMP induced STING-related pro-inflammatory and intratumoral injections of LP-cGAMP increased DC maturation and CD8+ T cell infiltration more efficiently compared to free cGAMP. Given the upregulation of PD-L1 on tumor cells in response to STING activation, we further tested the combination therapy of LP-cGAMP and anti-PD-L1 and observed a superior antitumor effect in B16F10 and BRAF-mutated murine melanoma models. Our findings prove that targeted delivery of cGAMP can synergize PD-L1 blockade therapy in melanoma and the combinational immune therapy has a great potential to produce a long-lasting anti-tumor effect.

Gene rearrangements in the mitochondrial genome of Chiromantes eulimene (Brachyura: Sesarmidae) and phylogenetic implications for Brachyura.

Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Here we determined the complete mitogenome sequence of Chiromantes eulimene (Brachyura: Sesarmidae) for the first time. The total length is 15,894 bp and includes 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, as well as a putative control region. The genome composition is highly A + T biased (75.5%), and exhibits a negative AT-skew (-0.017) and GC-skew (-0.206). All of the 13 PCGs are initiated by the start codon ATN, with an exception (GTG) in ND1. The typical stop codon (TAA or TAG) is detected in ten PCGs, whereas the remaining three PCGs (COI, COII and Cyt b) terminate by an incomplete T. The gene order in C. eulimene mitogenome was rearranged compared with that of the ancestor of Decapoda. The gene order of F-ND5-H changed to H-F-ND5. Like other sesarmid crabs, the I-Q-M gene cluster in the pancrustacean ground pattern became Q-I-M order in C. eulimene genome. Tandem duplication-random loss model and slipped-strand mispairing mechanism are determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis places all Sesarmidae species into one group. Almost all families except Xanthidae, Gecarcinidae and Homolidae form a monophyletic clade and the polyphyly of Eriphioidea, Ocypodoidea and Grapsoidea is well supported. These results will help to better understand the gene rearrangements and evolutionary position of C. eulimene and lay a foundation for further phylogenetic studies of Brachyura.

Genome re-sequencing and reannotation of the Escherichia coli ER2566 strain and transcriptome sequencing under overexpression conditions.

BACKGROUND: The Escherichia coli ER2566 strain (NC_CP014268.2) was developed as a BL21 (DE3) derivative strain and had been widely used in recombinant protein expression. However, like many other current RefSeq annotations, the annotation of the ER2566 strain was incomplete, with missing gene names and miscellaneous RNAs, as well as uncorrected annotations of some pseudogenes. Here, we performed a systematic reannotation of the ER2566 genome by combining multiple annotation tools with manual revision to provide a comprehensive understanding of the E. coli ER2566 strain, and used high-throughput sequencing to explore how the strain adapted under external pressure. RESULTS: The reannotation included noteworthy corrections to all protein-coding genes, led to the exclusion of 190 hypothetical genes or pseudogenes, and resulted in the addition of 237 coding sequences and 230 miscellaneous noncoding RNAs and 2 tRNAs. In addition, we further manually examined all 194 pseudogenes in the Ref-seq annotation and directly identified 123 (63%) as coding genes. We then used whole-genome sequencing and high-throughput RNA sequencing to assess mutational adaptations under consecutive subculture or overexpression burden. Whereas no mutations were detected in response to consecutive subculture, overexpression of the human papillomavirus 16 type capsid led to the identification of a mutation (position 1,094,824 within the 3' non-coding region) positioned 19-bp away from the lacI gene in the transcribed RNA, which was not detected at the genomic level by Sanger sequencing. CONCLUSION: The ER2566 strain was used by both the general scientific community and the biotechnology industry. Reannotation of the E. coli ER2566 strain not only improved the RefSeq data but uncovered a key site that might be involved in the transcription and translation of genes encoding the lactose operon repressor. We proposed that our pipeline might offer a universal method for the reannotation of other bacterial genomes with high speed and accuracy. This study might facilitate a better understanding of gene function for the ER2566 strain under external burden and provided more clues to engineer bacteria for biotechnological applications.

The complete mitochondrial genome of Calappa bilineata: The first representative from the family Calappidae and its phylogenetic position within Brachyura.

In this study, we determined the complete mitogenome sequence of Calappa bilineata, which is the first mitogenome of Calappidae up to now. The total length is 15,606 bp and includes 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and one control region. The genome composition is highly A + T biased (68.7%), and exhibits a negative AT-skew (-0.010) and GC-skew (-0.267). As with other invertebrate mitogenomes, the PCGs start with the standard ATN and stop with the standard TAN codons or incomplete T. Phylogenetic analysis showed that C. bilineata was most closely related to Matuta planipes (Matutidae), and these two species formed a sister clade, constituting a Calappoidea group and forming a sister clade with part of Eriphioidea. The existence of the polyphyletic families raised doubts over the traditional classification system. These results will help to better understand the features of the C. bilineata mitogenome and lay foundation for further evolutionary relationships within Brachyura.

Novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura.

The complete mitochondrial genomes (mitogenomes) can indicate phylogenetic relationships among organisms, as well as useful information about the process of molecular evolution and gene rearrangement mechanisms. However, knowledge on the complete mitogenome of Coenobitidae (Decapoda: Anomura) is quite scarce. Here, we describe in detail the complete mitogenome of Coenobita brevimanus, which is 16,393 bp in length, and contains 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region. The genome composition shows a moderate A + T bias (65.0%), and exhibited a negative AT-skew (-0.148) and a positive GC-skew (0.183). Five gene clusters (or genes) involving eleven tRNAs and two PCGs were found to have rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination models were determined as most likely to explain the observed large-scale gene rearrangements. Phylogenetic analysis placed all Coenobitidae species into one clade. The polyphyly of Paguroidea was well supported, whereas the non-monophyly of Galatheoidea was inconsistence with previous findings on Anomura. Taken together, our results help to better understand gene rearrangement process and the evolutionary status of C. brevimanus and lay a foundation for further phylogenetic studies of Anomura.