Antagonistic circuits mediating infanticide and maternal care in female mice.

In many species, including mice, female animals show markedly different pup-directed behaviours based on their reproductive state1,2. Naive wild female mice often kill pups, while lactating female mice are dedicated to pup caring3,4. The neural mechanisms that mediate infanticide and its switch to maternal behaviours during motherhood remain unclear. Here, on the basis of the hypothesis that maternal and infanticidal behaviours are supported by distinct and competing neural circuits5,6, we use the medial preoptic area (MPOA), a key site for maternal behaviours7-11, as a starting point and identify three MPOA-connected brain regions that drive differential negative pup-directed behaviours. Functional manipulation and in vivo recording reveal that oestrogen receptor α (ESR1)-expressing cells in the principal nucleus of the bed nucleus of stria terminalis (BNSTprESR1) are necessary, sufficient and naturally activated during infanticide in female mice. MPOAESR1 and BNSTprESR1 neurons form reciprocal inhibition to control the balance between positive and negative infant-directed behaviours. During motherhood, MPOAESR1 and BNSTprESR1 cells change their excitability in opposite directions, supporting a marked switch of female behaviours towards the young.

Expression, purification, and characterization of transmembrane protein homogentisate solanesyltransferase.

Homogentisate solanesyltransferase (HST) is a crucial enzyme in the plastoquinone biosynthetic pathway and has recently emerged as a promising target for herbicides. In this study, we successfully expressed and purified a stable and highly pure form of seven times transmembrane protein Chlamydomonas reinhardtii HST (CrHST). The final yield of CrHST protein obtained was 12.2 mg per liter of M9 medium. We evaluated the inhibitory effect on CrHST using Des-Morpholinocarbony Cyclopyrimorate (DMC) and found its IC50 value to be 3.63 ± 0.53 µM, indicating significant inhibitory potential. Additionally, we investigated the substrate affinity of CrHST with two substrates, determining the Km values as 22.76 ± 1.70 µM for FPP and 48.54 ± 3.89 µM for HGA. Through sequence alignment analyses and three-dimensional structure predictions, we identified conserved amino acid residues forming the active cavity in the enzyme. The results from molecular docking and binding energy calculations indicate that DMC has a greater binding affinity with HST compared to HGA. These findings represent substantial progress in understanding CrHST's properties and potential for herbicide development. KEY POINTS: • First high-yield transmembrane CrHST protein via E. coli system • Preliminarily identified active cavity composition via activity testing • Determined substrate and inhibitor modes via molecular docking.

HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study.

Protein-nucleic acid interactions play essential roles in many biological processes, such as transcription, replication and translation. In protein-nucleic acid interfaces, hotspot residues contribute the majority of binding affinity toward molecular recognition. Hotspot residues are commonly regarded as potential binding sites for compound molecules in drug design projects. The dynamic property is a considerable factor that affects the binding of ligands. Computational approaches have been developed to expedite the prediction of hotspot residues on protein-nucleic acid interfaces. However, existing approaches overlook hotspot dynamics, despite their essential role in protein function. Here, we report a web server named Hotspots In silico Scanning on Nucleic Acid and Protein Interface (HISNAPI) to analyze hotspot residue dynamics by integrating molecular dynamics simulation and one-step free energy perturbation. HISNAPI is capable of not only predicting the hotspot residues in protein-nucleic acid interfaces but also providing insights into their intensity and correlation of dynamic motion. Protein dynamics have been recognized as a vital factor that has an effect on the interaction specificity and affinity of the binding partners. We applied HISNAPI to the case of SARS-CoV-2 RNA-dependent RNA polymerase, a vital target of the antiviral drug for the treatment of coronavirus disease 2019. We identified the hotspot residues and characterized their dynamic behaviors, which might provide insight into the target site for antiviral drug design. The web server is freely available via a user-friendly web interface at http://chemyang.ccnu.edu.cn/ccb/server/HISNAPI/ and http://agroda.gzu.edu.cn:9999/ccb/server/HISNAPI/.

Bioinformatics toolbox for exploring protein phosphorylation network.

A clear systematic delineation of the interactions between phosphorylation sites on substrates and their effector kinases plays a fundamental role in revealing cellular activities, understanding signaling modulation mechanisms and proposing novel hypotheses. The emergence of bioinformatics tools contributes to studying phosphorylation network. Some of them feature the visualization of network, enabling more effective trace of the underlying biological problems in a clear and succinct way. In this review, we aimed to provide a toolbox for exploring phosphorylation network. We first systematically surveyed 19 tools that are available for exploring phosphorylation networks, and subsequently comparatively analyzed and summarized these tools to guide tool selection in terms of functionality, data sources, performance, network visualization and implementation, and finally briefly discussed the application cases of these tools. In different scenarios, the conclusion on the suitability of a tool for a specific user may vary. Nevertheless, easily accessible bioinformatics tools are proved to facilitate biological findings. Hopefully, this work might also assist non-specialists, students, as well as computational scientists who aim at developing novel tools in the field of phosphorylation modification.

Multienzyme-Targeted Fluorescent Probe as a Biosensing Platform for Broad Detection of Pesticide Residues.

Pesticide residues, significantly hampering the overall environmental and human health, have become an increasingly severe issue. Thus, developing rapid, cost-effective, and sensitive tools for monitoring the pesticide residues in food and water is extremely important. Compared to the conventional and chromatographic techniques, enzyme inhibition-based biosensors conjugated with the fluorogenic probes provide effective alternative methods for detecting pesticide residues due to the inherent advantages including high selectivity and sensitivity, simple operation, and capability of providing in situ and real-time information. However, the detection efficiency of a single enzyme-targeted biosensor in practical samples is strongly impeded by the structural diversity of pesticides and their distinct targets. In this work, we developed a strategy of multienzyme-targeted fluorescent probe design and accordingly obtained a novel fluorescent probe (named as 3CP) for detecting the presence of wide variety of pesticides. The designed probe 3CP, targeting cholinesterases, carboxylesterases, and chymotrypsin simultaneously, yielded intense fluorescence in the solid state upon the enzyme-catalyzed hydrolysis. It showed excellent sensitivity against organophosphorus and carbamate pesticides, and the detection limit for dichlorvos achieved 1.14 pg/L. Moreover, it allowed for the diffusion-resistant in situ visualization of pesticides in live cells and zebrafish and the sensitive measurement of organophosphorus pesticides in fresh vegetables, demonstrating the promising potential for tracking the pesticide residues in environment and biological systems.

PIIMS Server: A Web Server for Mutation Hotspot Scanning at the Protein-Protein Interface.

Protein-protein interactions (PPIs) play vital roles in regulating biological processes, such as cellular and signaling pathways. Hotspots are certain residues located at protein-protein interfaces that contribute more in protein-protein binding than other residues. Research on the mutational effects of hotspots is important for understanding basic aspects of protein association. Hence, various computational tools have been developed to explore the impact of mutation hotspots, which will allow a better understanding of the forces that drive PPIs. However, tools that may provide comprehensive substitutions at hotspots are still rare. Hence, there is a strong need for a new free web server to explore mutational effects of hotspots. Herein we introduce a web server named PIIMS that integrates molecular dynamics simulation and one-step free energy perturbation. It contains two main computational functions: (1) computational alanine scanning analysis to identify hotspots and (2) full mutation scanning analysis to evaluate the effects of hotspot mutations. We rigidly validated its ability to predict binding free energy changes by using large and diverse datasets including 1,341 mutations from 50 PPIs with the correlation coefficient R = 0.75. The difference from the existing tools is that PIIMS can perform further evaluation of hotspot residues with regard to their different mutations. The PIIMS web server (accessible at http://chemyang.ccnu.edu.cn/ccb/server/PIIMS/index.php) is free and open to all users without login requirements.

Long-term in vivo recording of circadian rhythms in brains of freely moving mice.

Endogenous circadian clocks control 24-h physiological and behavioral rhythms in mammals. Here, we report a real-time in vivo fluorescence recording system that enables long-term monitoring of circadian rhythms in the brains of freely moving mice. With a designed reporter of circadian clock gene expression, we tracked robust Cry1 transcription reporter rhythms in the suprachiasmatic nucleus (SCN) of WT, Cry1-/- , and Cry2-/- mice in LD (12 h light, 12 h dark) and DD (constant darkness) conditions and verified that signals remained stable for over 6 mo. Further, we recorded Cry1 transcriptional rhythms in the subparaventricular zone (SPZ) and hippocampal CA1/2 regions of WT mice housed under LD and DD conditions. By using a Cre-loxP system, we recorded Per2 and Cry1 transcription rhythms specifically in vasoactive intestinal peptide (VIP) neurons of the SCN. Finally, we demonstrated the dynamics of Per2 and Cry1 transcriptional rhythms in SCN VIP neurons following an 8-h phase advance in the light/dark cycle.

Do alterations in plasma albumin and prealbumin after minimally invasive esophagectomy for squamous cell carcinoma influence the incidence of cervical anastomotic leak?

BACKGROUND: Anastomotic leak (AL) remains a challenging and bothersome complication of minimally invasive esophagectomy (MIE). In this retrospective study, we measured the perioperative albumin (ALB) and prealbumin (PA) of patients who underwent MIE, and investigated the relationship between the occurrence of AL and the altering levels of ALB/PA. PATIENTS AND METHODS: Sixty patients underwent video-assisted thoracoscopic-laparoscopic esophagectomy between September 2013 and August 2014. The preoperative and postoperative levels of ALB and PA were detected, and the baseline of altering levels for ALB and PA were established. According to the decreasing values of postoperative ALB, patients were divided into Group A1 (decreased value of ALB over the average level) and Group A2 (decreased value of ALB not reach the average level). Similarly, patients were also divided into Group P1 and Group P2 according to the average decreasing values of postoperative PA. The incidence of AL and non-anastomotic-relative complications between different groups were calculated and analyzed. RESULTS: One postoperative death occurred (1/60, 1.7 %). Eighteen complications were observed (18/60, 30 %), including seven cases of cervical AL (7/60, 11.7 %). There was no significant difference in background or clinicopathologic factors between different groups. The levels of ALB and PA descended significantly after MIE (p = 0.0000, p = 0.0000, respectively). No correlation between deficient levels of ALB and PA was observed (p = 0.1874, r = 0.0298). There was a significant higher AL incidence in Group P1 than in Group P2 (p = 0.0322). However, the incidence of AL did not exhibit significant difference between Group A1 and Group A2 (p = 0.9252). CONCLUSIONS: MIE appears to be a procedure of obvious influence on the nutrient metabolism of patients. The results demonstrated that patients with severely deficient level of PA had higher risk of AL after MIE.

Should stage T2 esophageal squamous cell carcinoma be subclassified?

BACKGROUND: In patients with esophageal squamous cell carcinoma (ESCC), pathologic examination allows T2 tumors to be further subclassified according to whether the circular or longitudinal muscle layers are invaded. Therefore, we aimed to investigate whether subclassifying the T2 stages can aid in determining the prognosis for patients with ESCC. METHODS: The clinical and pathologic characteristics of 85 ESCC patients with T2 tumors who underwent thoracoscopic esophagectomy between 2008 and 2013 were retrospectively analyzed. Univariate and multivariate analyses were performed to identify prognostic factors. The Kaplan-Meier method was used to compare survival differences with respect to each prognostic factor. RESULTS: Thirty-nine patients had tumors invading the circular muscle layer and were designated as having T2a disease. The remaining 46 patients had T2b disease, with tumors invading the longitudinal muscle layer. The overall 1-, 3-, and 5-year survival rates were 96.1, 53.8, and 36.4 %, respectively, with a median survival of 39.0 months. Univariate analysis indicated that sex, smoking history, grade, location, and tumor length did not significantly influence on survival. Only T stage (P = 0.017) and N stage (P = 0.003) were associated with survival. The results of multivariate Cox proportional hazard regression analysis showed that T stage (P = 0.045) and N stage (P = 0.003) were independent prognostic factors. CONCLUSIONS: N stage and subclassified T stage are independent prognostic factors in patients with T2 tumors. Therefore, we concluded that T2 tumors can be subclassified further into T2a and T2b stages, and patients with different T2 stages may have different prognoses.

Genetic diversity and tissue and host specificity of Grapevine vein clearing virus.

Grapevine vein clearing virus (GVCV) is a new badnavirus in the family Caulimoviridae that is closely associated with an emerging vein-clearing and vine decline disease in the Midwest region of the United States. It has a circular, double-stranded DNA genome of 7,753 bp that is predicted to encode three open reading frames (ORFs) on the plus-strand DNA. The largest ORF encodes a polyprotein that contains domains for a reverse transcriptase (RT), an RNase H, and a DNA-binding zinc-finger protein (ZF). In this study, two genomic regions, a 570-bp region of the RT domain and a 540-bp region of the ZF domain were used for an analysis of the genetic diversity of GVCV populations. In total, 39 recombinant plasmids were sequenced. These plasmids consisted of three individual clones from each of 13 isolates sampled from five grape varieties in three states. The sequence variants of GVCV could not be phylogenetically grouped into clades according to geographical location and grape variety. Codons of RT or ZF regions are subject to purifying selection pressure. Quantitative polymerase chain reaction assays indicated that GVCV accumulates abundantly in the petioles and least in the root tip tissue. Upon grafting of GVCV-infected buds onto four major grape cultivars, GVCV was not detected in the grafted 'Chambourcin' vine but was present in the grafted 'Vidal Blanc', 'Cayuga White', and 'Traminette' vines, suggesting that Chambourcin is resistant to GVCV. Furthermore, seven nucleotides were changed in the sequenced RT and ZF regions of GVCV from a grafted Traminette vine and one in the sequenced regions of GVCV from grafted Cayuga White but no changes were found in the sequenced regions of GVCV in the grafted Vidal Blanc. The results provide a genetic snapshot of GVCV populations, which will yield knowledge important for monitoring GVCV epidemics and for preventing the loss of grape production that is associated with GVCV.

Serum TNF-α level and probing depth as a combined indicator for peri-implant disease.

Peri-implant disease (PID) is a general term for inflammatory diseases of soft and hard tissues that occur around implants, including peri-implant mucositis and peri-implantitis. Cytokines are a class of small molecule proteins, which have various functions such as regulating innate immunity, adaptive immunity, and repairing damaged tissues. In order to explore the characteristics and clinical significance of tumor necrosis factor (TNF)-α, interleukin (IL)-6, IL-10, and tumor growth factor (TGF)-ß1 expression levels in serum of patients with peri-implant disease, 31 patients with PID and 31 patients without PID were enrolled. The modified plaque index (mPLI), modified sulcus bleeding index (mSBI), and peri-implant probing depth (PD) were recorded. The levels of serum TNF-α, IL-6, IL-10, and TGF-ß1 were detected by ELISA. TNF-α, mPLI, mSBI, and PD levels were significantly higher in the PID group. TGF-ß1 levels were significantly higher in the control group. There was a significant positive correlation between TNF-α and mPLI, mSBI, and PD. TGF-ß1 was negatively associated with TNF-α, mPLI, mSBI, and PD. Multiple logistic regression analysis showed that TNF-α and PD were risk factors for the severity of PID. The receiver operating curve analysis showed that high TNF-α levels (cut-off value of 140 pg/mL) and greater PD values (cut-off value of 4 mm) were good predictors of PID severity with an area under the curve of 0.922. These results indicated that TNF-α and PD can be used as a biological indicator for diagnosing the occurrence and progression of PID.

Intraperitoneal recombinant human endostatin combined with chemotherapy for refractory malignant ascites due to gastrointestinal cancer: a pilot study.

BACKGROUND/AIMS: To evaluate the efficacy, safety and consequent impact on quality of life of a combined-modality using intraperitoneal recombinant human endostatin, Endostar and chemotherapy in patients with refractory malignant ascites caused by gastrointestinal cancer. METHODOLOGY: Patients received combined intraperitoneal therapy repeated 3 weeks, which consisted of 5-fluorouracil 600 mg/m2 and cisplatin 30 mg/m2 on day 1-3 followed by Endostar 60 mg on day 4. RESULTS: A total of 18 patients were treated. The overall response rate was 55.6%, with a complete remission rate of 22.2%. The malignant ascites controlled rate was 77.8%. The median time to progression and overall survival was 2.6 and 4.9 months, respectively. Therapy-associated toxicities were generally mild to moderate treatment-related deaths. The mean Karnofsky performance status score was significantly improved from 59.4±2.49 at enrollment to 69.4±3.18 at 2 weeks after the first cycle of therapy (p=0.001). The mean score for overall ascites-associated symptoms was improved from 5.3±0.35 to 4.0±0.23 (p=0.004). Significant improvements of 6 individual symptoms were also observed. CONCLUSIONS: The combined-modality using intraperitoneal Endostar and chemotherapy is effective and safe in selected patients with refractory malignant ascites due to gastrointestinal cancer and significantly improves patient's quality of life with encouraging survival, which merits further investigation.

Mechanism and efficacy of mobilization of granulocyte colony-stimulating factor in the treatment of chronic hepatic failure.

BACKGROUND/AIMS: To explore the efficacy of G-CSF mobilization in the treatment of chronic liver failure (CLF) and the mechanism of its action. METHODOLOGY: The proportions of cluster-of-differentiation (CD)-34+ cells and their receptor-CXCR4 were detected by flow cytometry in patients with different types of chronic HBV infection. The levels of chemokines and cytokines were measured by enzyme-linked immunosorbent assay. RESULTS: The proportion of CD34+ cells in patients with cirrhosis was significantly increased compared with the healthy controls (p<0.05) and was increased obviously after treatment by G-CSF mobilization (p<0.01). The expression levels of SDF-1, SCF and MMP-9 were significantly elevated in patients with chronic hepatitis B and liver cirrhosis (p<0.01). The expression levels of SCF and MMP-9 were significantly elevated after treatment with G-CSF (p<0.05). No significant differences were found in the levels of total bilirubin, albumin and prothrombin time between the treated and control groups; furthermore, no significant differences were observed in the cure and improvement rates between the two groups. CONCLUSIONS: The basal levels of stem cell mobilization in patients with liver cirrhosis might be associated with the repair of liver injury. G-CSF could promote hematopoietic stem cell mobilization through regulation of the expression levels of stem-cell-mobilization-related factors in patients with liver cirrhosis. No apparent effects of G-CSF therapy on both liver function and short-term prognosis in patients with liver cirrhosis were confirmed.

Hypothalamic control of innate social behaviors.

Sexual, parental, and aggressive behaviors are central to the reproductive success of individuals and species survival and thus are supported by hardwired neural circuits. The reproductive behavior control column (RBCC), which comprises the medial preoptic nucleus (MPN), the ventrolateral part of the ventromedial hypothalamus (VMHvl), and the ventral premammillary nucleus (PMv), is essential for all social behaviors. The RBCC integrates diverse hormonal and metabolic cues and adjusts an animal's physical activity, hence the chance of social encounters. The RBCC further engages the mesolimbic dopamine system to maintain social interest and reinforces cues and actions that are time-locked with social behaviors. We propose that the RBCC and brainstem form a dual-control system for generating moment-to-moment social actions. This Review summarizes recent progress regarding the identities of RBCC cells and their pathways that drive different aspects of social behaviors.

Thermodynamic database supports deciphering protein-nucleic acid interactions.

The thermodynamics of protein-nucleic acid interactions (PNIs) is crucial for elucidating the mechanisms of molecular recognition and pathological consequences. The Protein-Nucleic Acid Thermodynamics Database (PNATDB) is a database containing experimentally determined thermodynamic parameters along with sequence, structural, and function data, which is available free online.

Protein-nucleic acid thermodynamic databases for specific uses.

In response to Gromiha and Harini, we review the currently available thermodynamic databases for protein-nucleic acid interactions. These databases are designed for particular uses. We give general comments on them to facilitate browsing and exploration.

Risk monitoring and pharmacovigilance of programmed cell death protein 1 / programmed cell death 1 ligand 1 in cancer patients after solid organ transplantation.

INTRODUCTION: Several medications are available for the treatment of cancer, and monoclonal antibodies that target PD-1 and PD-L1 represent first-line options for cancer. PD-1 promotes the ability of the immune system to recognize and attack cancer cells by activating T cells. PD-1 also activates the autoimmune system. This activation causes healthy cells in the body to be attacked by the immune system, resulting in immune-related adverse events (irAE). The objective of this study was to comprehensively evaluate the adverse events of rejection reactions in real-world solid organ transplant patients using monoclonal antibodies that target PD-1/PD-L1. METHODS: Data from 2016-2021 were extracted from the U.S. Food and Drug Administration(FDA) Adverse Reporting System (FAERS) to describe the rejection reaction in patients with solid organ transplantation cases after using PD-1/PD-L1 inhibitors approved by the FDA. The reporting odds ratio (ROR) with 95% confidence interval (CI) for rejection reaction was calculated for each PD-1/PD-L1 inhibitor. A disproportionality signal was defined when the lower limit of 95% CI>1. RESULTS: The FAERS database recorded 11,935 adverse events related to solid organ transplantation. Among these reports, 117 showed that various PD-1/PD-L1 inhibitors exhibited a strong correlation with solid organ transplantation rejection. The 3 medicines with the incidence of rejection reaction include avelumab (1), nivolumab (79) and pembrolizumab (37). The average time of solid organ transplantation rejection associated with PD1 / PD-L1 inhibitors was 40.64 days. Of those patients who experienced solid organ transplant rejection, a total of 24.79% died. CONCLUSION: This study found that PD-1/PD-L1 inhibitor use in patients with solid organ transplantation was associated with donor organ rejection. This information serves as a pharmacovigilance signal that we need to continue to track in the real world.

Robot-assisted thymectomy in large anterior mediastinal tumors: A comparative study with video-assisted thymectomy and open surgery.

BACKGROUND: The aim of this study was to evaluate the safety and effectiveness of robot-assisted thymectomy (RAT) in large anterior mediastinal tumors (AMTs) (size ≥6 cm) compared with video-assisted thymectomy (VAT) and open surgery. METHODS: A total of 132 patients with large AMTs who underwent surgical resection from January 2016 to June 2022 were included in this study. A total of 61 patients underwent RAT, 36 patients underwent VAT and 35 patients underwent open surgery. Perioperative outcomes were compared. RESULTS: There were no significant differences in tumor size (p = 0.141), or pathological types (p = 0.903). Compared with the open group, the RAT and VAT groups were associated with a shorter operation time (115.00 vs. 160.00, p = 0.012; 122.50 vs. 160.00, p = 0.071), and less blood loss (50.00 vs. 200.00, p < 0.001; 50.00 vs. 200.00, p < 0.001), respectively. The rate of conversion in the RAT group was similar to that in the VAT group (6.56% vs. 13.89%, p = 0.229). Concomitant resection was less frequently performed in the VAT group than in the RAT and open groups (5.56% vs. 31.15%, p = 0.040; 5.56% vs. 31.43%, p = 0.006). VAT patients had a lower drainage volume (365.00 vs. 700.00 and 910.00 mL, p < 0.001), shorter duration of chest tube (2.00 vs. 3.00 and 4.00, p < 0.001), and shorter hospital stay (5.00 vs. 6.00 and 7.00, p < 0.001) than the RAT and open groups. There was no 30-day mortality in any group. No difference was seen in R0 resection rates (p = 0.846). The postoperative complication rates were similar among the three groups (p = 0.309). Total in-hospital costs (66493.90 vs. 33581.05 and 42876.40, p < 0.001) were significantly higher in the RAT group. CONCLUSIONS: RAT is safe and effective for the resection of large AMTs compared to VAT and open surgery. Vascular resection in RAT is technically feasible. A long-term follow-up is required.