Temporal dynamics of stress response in Halomonas elongata to NaCl shock: physiological, metabolomic, and transcriptomic insights.

BACKGROUND: The halophilic bacterium Halomonas elongata is an industrially important strain for ectoine production, with high value and intense research focus. While existing studies primarily delve into the adaptive mechanisms of this bacterium under fixed salt concentrations, there is a notable dearth of attention regarding its response to fluctuating saline environments. Consequently, the stress response of H. elongata to salt shock remains inadequately understood. RESULTS: This study investigated the stress response mechanism of H. elongata when exposed to NaCl shock at short- and long-time scales. Results showed that NaCl shock induced two major stresses, namely osmotic stress and oxidative stress. In response to the former, within the cell's tolerable range (1-8% NaCl shock), H. elongata urgently balanced the surging osmotic pressure by uptaking sodium and potassium ions and augmenting intracellular amino acid pools, particularly glutamate and glutamine. However, ectoine content started to increase until 20 min post-shock, rapidly becoming the dominant osmoprotectant, and reaching the maximum productivity (1450 ± 99 mg/L/h). Transcriptomic data also confirmed the delayed response in ectoine biosynthesis, and we speculate that this might be attributed to an intracellular energy crisis caused by NaCl shock. In response to oxidative stress, transcription factor cysB was significantly upregulated, positively regulating the sulfur metabolism and cysteine biosynthesis. Furthermore, the upregulation of the crucial peroxidase gene (HELO_RS18165) and the simultaneous enhancement of peroxidase (POD) and catalase (CAT) activities collectively constitute the antioxidant defense in H. elongata following shock. When exceeding the tolerance threshold of H. elongata (1-13% NaCl shock), the sustained compromised energy status, resulting from the pronounced inhibition of the respiratory chain and ATP synthase, may be a crucial factor leading to the stagnation of both cell growth and ectoine biosynthesis. CONCLUSIONS: This study conducted a comprehensive analysis of H. elongata's stress response to NaCl shock at multiple scales. It extends the understanding of stress response of halophilic bacteria to NaCl shock and provides promising theoretical insights to guide future improvements in optimizing industrial ectoine production.

Machine learning methods for predicting the key metabolic parameters of Halomonas elongata DSM 2581 T.

Ectoine is generally produced by the fermentation process of Halomonas elongata DSM 2581 T, which is one of the primary industrial ectoine production techniques. To effectively monitor and control the fermentation process, the important parameters require accurate real-time measurement. However, for ectoine fermentation, three critical parameters (cell optical density, glucose, and product concentration) cannot be measured conveniently in real-time due to time variation, strong coupling, and other constraints. As a result, our work effectively created a series of hybrid models to predict the values of these three parameters incorporating both fermentation kinetics and machine learning approaches. Compared with the traditional machine learning models, our models solve the problem of insufficient data which is common in fermentation. In addition, a simple kinetic modeling is only applicable to specific physical conditions, so different physical conditions require refitting the function, which is tedious to operate. However, our models also overcome this limitation. In this work, we compared different hybrid models based on 5 feature engineering methods, 11 machine-learning approaches, and 2 kinetic models. The best models for predicting three key parameters, respectively, are as follows: CORR-Ensemble (R2: 0.983 ± 0.0, RMSE: 0.086 ± 0.0, MAE: 0.07 ± 0.0), SBE-Ensemble (R2: 0.972 ± 0.0, RMSE: 0.127 ± 0.0, MAE: 0.078 ± 0.0), and SBE-Ensemble (R2:0.98 ± 0.0, RMSE: 0.023 ± 0.001, MAE: 0.018 ± 0.001). To verify the universality and stability of constructed models, we have done an experimental verification, and its results showed that our proposed models have excellent performance. KEY POINTS: • Using the kinetic models for producing simulated data • Through different feature engineering methods for dimension reduction • Creating a series of hybrid models to predict the values of three parameters in the fermentation process of Halomonas elongata DSM 2581 T.

Physiological metabolic topology analysis of Halomonas elongata DSM 2581T in response to sodium chloride stress.

The halophilic bacterium Halomonas elongata DSM 2581T generally adapts well to high level of salinity by biosynthesizing ectoine, which functions as an important compatible solute protecting the cell against external salinity environment. Halophilic bacteria have specific metabolic activities under high-salt conditions and are gradually applied in various industries. The present study focuses on investigating the physiological and metabolic mechanism of H. elongata DSM 2581T driven by the external salinity environment. The physiological metabolic dynamics under salt stress were investigated to evaluate the effect of NaCl stress on the metabolism of H. elongata. The obtained results demonstrated that ectoine biosynthesis transited from a nongrowth-related process to a growth-related process when the NaCl concentration varied from 1% to 13% (w/v). The maximum biomass (Xm = 41.37 g/L), and highest ectoine production (Pm = 12.91 g/L) were achieved under 8% NaCl. Moreover, the maximum biomass (Xm ) and the maximum specific growth rates (µm ) showed a first rising and then declining trend with the increased NaCl stress. Furthermore, the transcriptome analysis of H. elongata under different NaCl concentrations demonstrated that both 8% and 13% NaCl conditions resulted in increased expressions of genes involved in the pentose phosphate pathway, Entner-Doudoroff pathway, flagellar assembly pathway, and ectoine metabolism, but negatively affected the tricarboxylic acid cycle and fatty acid metabolism. At last, the proposed possible adaptation mechanism under the optimum NaCl concentration in H. elongata was described.

Multiscale engineering of microbial cell factories: A step forward towards sustainable natural products industry.

Microbial cell factories (bacteria and fungi) are the leading producers of beneficial natural products such as lycopene, carotene, herbal medicine, and biodiesel etc. These microorganisms are considered efficient due to their effective bioprocessing strategy (monoculture- and consortial-based approach) under distinct processing conditions. Meanwhile, the advancement in genetic and process optimization techniques leads to enhanced biosynthesis of natural products that are known functional ingredients with numerous applications in the food, cosmetic and medical industries. Natural consortia and monoculture thrive in nature in a small proportion, such as wastewater, food products, and soils. In similitude to natural consortia, it is possible to engineer artificial microbial consortia and program their behaviours via synthetic biology tools. Therefore, this review summarizes the optimization of genetic and physicochemical parameters of the microbial system for improved production of natural products. Also, this review presents a brief history of natural consortium and describes the functional properties of monocultures. This review focuses on synthetic biology tools that enable new approaches to design synthetic consortia; and highlights the syntropic interactions that determine the performance and stability of synthetic consortia. In particular, the effect of processing conditions and advanced genetic techniques to improve the productibility of both monoculture and consortial based systems have been greatly emphasized. In this context, possible strategies are also discussed to give an insight into microbial engineering for improved production of natural products in the future. In summary, it is concluded that the coupling of genomic modifications with optimum physicochemical factors would be promising for producing a robust microbial cell factory that shall contribute to the increased production of natural products.

Neuroprotective effect of leptin on a primate model of cerebral ischemia.

The purpose of this study was to evaluate the neuroprotective effect of leptin on a non-human primate model of cerebral ischemia. A total of 39 Guangxi macaques were used to establish the primate cerebral-ischemia model. HE staining was used to evaluated the pathological changes. Moreover, magnetic resonance imaging was used for the detection of embolic area. The measurements of behavior observation and cerebral infarction area were also performed. They all received autologous thrombus operation. Furthermore, western blot and RT-PCR were also used to detect the protein and mRNA expression levels of apoptosis-related factors. Our results showed that leptin could reduce the volume of cerebral infarction by about 35%. Behavioral defects can be significantly improved. In addition, mid-term and long-term behavioral deficiencies had been significantly improved by leptin. Moreover, leptin significantly decreased the expression levels of caspase-3 and Bax, and increased the expression levels of Bcl-2. In conclusion, leptin has neuroprotective effects on cerebral ischemia by effectively reducing the volume of cerebral infarction.

A Novel Post-Operative ALRI Model Accurately Predicts Clinical Outcomes of Resected Hepatocellular Carcinoma Patients.

BACKGROUND: Hepatocellular carcinoma (HCC) is one of the leading malignant tumors worldwide. Prognosis and long-term survival of HCC remain unsatisfactory, even after radical resection, and many non-invasive predictors have been explored for post-operative patients. Most prognostic prediction models were based on preoperative clinical characteristics and pathological findings. This study aimed to investigate the prognostic value of a newly constructed nomogram, which incorporated post-operative aspartate aminotransferase to lymphocyte ratio index (ALRI). METHODS: A total of 771 HCC patients underwent radical resection from three medical centers were enrolled and grouped into the training cohort (n = 416) and validation cohort (n = 355). Prognostic prediction potential of ALRI was assessed by receiver operating curve (ROC) analysis. The Cox regression model was used to identify independent prognostic factors. Nomograms for overall survival (OS) and disease-free survival (DFS) were constructed and further validated externally. RESULTS: The ROC analysis ranked ALRI as the most effective prediction marker for resected HCC patients, with the cut-off value determined at 22.6. Higher ALRI level positively correlated with larger tumor size, higher tumor node metastasis (TNM) stage, and inversely with lower albumin level and shorter OS and DFS. Nomograms for OS and DFS were capable of discriminating HCC patients into different risk-groups. CONCLUSIONS: Post-operative ALRI was of prediction value for HCC prognosis. This novel nomogram may categorize HCC patients into different risk groups, and offer individualized surveillance reference for post-operative patients.

A new model based on gamma-glutamyl transpeptidase to platelet ratio (GPR) predicts prognostic outcome after curative resection of solitary hepatocellular carcinoma.

BACKGROUND: This study intends to explore the potential clinical value of gamma-glutamyl transpeptidase to platelet ratio (GPR) and the new multi-factor scoring model for recurrence and prognosis prediction in solitary HCC patients who received radical resection. METHODS: This study retrospectively analyzed 295 HCC patients after curative resection. According to the Receiver Operating Characteristic (ROC) curve, the optimal cut-off value of GPR for predicting prognosis of HCC after resection was determined. The Kaplan Meier method and Cox regression analysis were performed to assess the important potential factors in the prognosis of HCC and determine the independent risk factors. Assign a value to each independent risk factor and establish a new scoring model. Then, using GPR and the new scoring model to evaluate overall survival (OS) and postoperative recurrence probability. RESULTS: When GPR's cut-off value was selected as 0.30, its predictive efficiency for postoperative prognosis was more favorable than those of other cut-off values (0.76, 0.84 and 0.94). GPR, tumor size, microvascular invasion and neutrophil to lymphocyte ratio (NLR) were identified as independent prognostic predictors. Using these variables, a novel prognostic scoring model was devised and established to identify different levels of risk: high, intermediate and low risk groups. We found that patients with high GPR level and of high risk group would have a poorer OS and a higher recurrence rate after radical resection. CONCLUSIONS: GPR may serve as a promising predictor for postoperative prognosis and recurrence probability of HCC, and the new prognostic scoring model may be available for postoperative management among HCC patients.

The Significance of Gamma-Glutamyl Transpeptidase to Lymphocyte Count Ratio in the Early Postoperative Recurrence Monitoring and Prognosis Prediction of AFP-Negative Hepatocellular Carcinoma.

BACKGROUND: Currently, there is still a lack of effective biomarkers for the recurrence monitoring and survival prognosis assessment of hepatocellular carcinoma (HCC) patients with alpha-fetoprotein (AFP)-negative (≤20 ng/mL) after radical resection. METHODS: The clinicopathological data of 606 patients (303 in the AFP-negative group and 303 in the AFP-positive group) who underwent radical resection of HCC were analyzed retrospectively. RESULTS: The gamma-glutamyl transpeptidase to lymphocyte count ratio (GLR) of patients in the AFP-negative group was lower than that in the AFP-positive group (p <0.001). The GLR level of the early-recurrence group was higher than that of the non-early-recurrence group (p =0.003). GLR had fair accuracy in predicting the early-recurrence of HCC patients [c-index=0.654 (95% CI=0.606-0.702); AUC=0.681 (95% CI=0.625-0.733)]. Univariate analysis showed that patients with tumor size <5 cm, no microvascular invasion, single tumor, no metastasis, BCLC stage 0-A, no recurrence, and GLR ≤45.0 had longer disease-free survival (DFS) and overall survival (OS) among AFP-negative HCC patients. In addition, multivariate Cox proportional hazards regression analysis showed that tumor size <5 cm (p =0.003), no recurrence (p <0.001), and GLR <45.0 (p <0.001) were independent predictors of longer OS. CONCLUSION: GLR may be a potential indicator for early recurrence monitoring and prognosis evaluation in HCC patients with AFP-negative after radical resection.

AGLR is a novel index for the prognosis of hepatocellular carcinoma patients: a retrospective study.

BACKGROUND: Most hepatocellular carcinoma (HCC) patients' liver function indexes are abnormal. We aimed to investigate the relationship between (alkaline phosphatase + gamma-glutamyl transpeptidase)/lymphocyte ratio (AGLR) and the progression as well as the prognosis of HCC. METHODS: A total of 495 HCC patients undergoing radical hepatectomy were retrospectively analyzed. We randomly divided these patients into the training cohort (n = 248) and the validation cohort (n = 247). In the training cohort, receiver operating characteristic (ROC) curve was used to determine the optimal cut-off value of AGLR for predicting postoperative survival of HCC patients, and the predictive value of AGLR was evaluated by concordance index (C-index). Further analysis of clinical and biochemical data of patients and the correlation analysis between AGLR and other clinicopathological factors were finished. Univariate and multivariate analyses were performed to identify prognostic factors for HCC patients. Survival curves were analyzed using the Kaplan-Meier method. RESULTS: According to the ROC curve analysis, the optimal predictive cut-off value of AGLR was 90. The C-index of AGLR was 0.637 in the training cohort and 0.654 in the validation cohort, respectively. Based on this value, the HCC patients were divided into the low-AGLR group (AGLR ≤ 90) and the high-AGLR group (AGLR > 90). Preoperative AGLR level was positively correlated with alpha-fetoprotein (AFP), tumor size, tumor-node-metastasis (TNM) stage, and microvascular invasion (MVI) (all p < 0.05). In the training and validation cohorts, patients with AGLR > 90 had significantly shorter OS than patients with AGLR ≤ 90 (p < 0.001). Univariate and multivariate analyses of the training cohort (HR, 1.79; 95% CI 1.21-2.69; p < 0.001) and validation cohort (HR, 1.82; 95% CI 1.35-2.57; p < 0.001) had identified AGLR as an independent prognostic factor. A new prognostic scoring model was established based on the independent predictors determined in multivariate analysis. CONCLUSIONS: The elevated preoperative AGLR level indicated poor prognosis for patients with HCC; the novel prognostic scoring model had favorable predictive capability for postoperative prognosis of HCC patients, which may bring convenience for clinical management.

Two-Component-System RspA1/A2-Dependent Regulation on Primary Metabolism in Streptomyces albus A30 Cultivated With Glutamate as the Sole Nitrogen Source.

In our previous study, a two-component-system (TCS) RspA1/A2 was identified and proven to play a positive role in the regulation of salinomycin (antibiotic) biosynthesis in Streptomyces albus. However, the regulatory mechanism of RspA1/A2 using a carbon source (glucose or acetate) for the cell growth of S. albus is still unclear till present research work. Therefore, in this work, the mechanistic pathway of RspA1/A2 on carbon source metabolism is unveiled. Firstly, this work reports that the response regulator RspA1 gene rspA1 knocked-out mutant ΔrspA1 exhibits lower biomass accumulation and lower glucose consumption rates as compared to the parental strain A30 when cultivated in a defined minimal medium (MM) complemented with 75 mM glutamate. Further, it is demonstrated that the regulation of TCS RspA1/A2 on the phosphoenolpyruvate-pyruvate-oxaloacetate node results in decreasing the intracellular acetyl-CoA pool in mutant ΔrspA1. Subsequently, it was verified that the RspA1 could not only directly interact with the promoter regions of key genes encoding AMP-forming acetyl-CoA synthase (ACS), citrate synthase (CS), and pyruvate dehydrogenase complex (PDH) but also bind promoter regions of the genes pyc, pck, and glpX in gluconeogenesis. In addition, the transcriptomic data analysis showed that pyruvate and glutamate transformations supported robust TCS RspA1/A2-dependent regulation of glucose metabolism, which led to a decreased flux of pyruvate into the TCA cycle and an increased flux of gluconeogenesis pathway in mutant ΔrspA1. Finally, a new transcriptional regulatory network of TCS RspA1/A2 on primary metabolism across central carbon metabolic pathways including the glycolysis pathway, TCA cycle, and gluconeogenesis pathway is proposed.

Deeply-Supervised Networks With Threshold Loss for Cancer Detection in Automated Breast Ultrasound.

ABUS, or Automated breast ultrasound, is an innovative and promising method of screening for breast examination. Comparing to common B-mode 2D ultrasound, ABUS attains operator-independent image acquisition and also provides 3D views of the whole breast. Nonetheless, reviewing ABUS images is particularly time-intensive and errors by oversight might occur. For this study, we offer an innovative 3D convolutional network, which is used for ABUS for automated cancer detection, in order to accelerate reviewing and meanwhile to obtain high detection sensitivity with low false positives (FPs). Specifically, we offer a densely deep supervision method in order to augment the detection sensitivity greatly by effectively using multi-layer features. Furthermore, we suggest a threshold loss in order to present voxel-level adaptive threshold for discerning cancer vs. non-cancer, which can attain high sensitivity with low false positives. The efficacy of our network is verified from a collected dataset of 219 patients with 614 ABUS volumes, including 745 cancer regions, and 144 healthy women with a total of 900 volumes, without abnormal findings. Extensive experiments demonstrate our method attains a sensitivity of 95% with 0.84 FP per volume. The proposed network provides an effective cancer detection scheme for breast examination using ABUS by sustaining high sensitivity with low false positives. The code is publicly available at https://github.com/nawang0226/abus_code.

Prognostic Value of Gamma-Glutamyl Transpeptidase to Lymphocyte Count Ratio in Patients With Single Tumor Size ≤ 5 cm Hepatocellular Carcinoma After Radical Resection.

Prediction of prognosis of hepatocellular carcinoma (HCC) has shown an important role in improving treatment outcomes and preventing disease progression, however, the prognostic indicator of HCC is still lacking. The purpose of this study is to investigate the predictive value of GLR (gamma-glutamyl transpeptidase to lymphocyte count ratio) in single HCC with a tumor size (TS) ≤ 5 cm. A retrospective analysis was performed on 272 patients with TS ≤ 5 cm who underwent radical resection. The Pearson χ2 test was applied to discuss the relationship between HCC and GLR, alpha-fetoprotein (AFP). Then univariate and multivariate analysis was utilized to predict the risk factors for survival prognosis in patients. In this study, GLR showed a positive relation with tumor size, tumor-node-metastasis (TNM) stage, microvascular invasion, early recurrence, and serum aspartate aminotransferase (AST) level, while the AFP value only correlated with drinking. Elevated GLR value had poor overall survival (OS) and progression-free survival (PFS) of TS ≤ 5 cm HCC patients, GLR level and tumor size were closely related to the prognosis of small HCC patients compared with AFP. GLR may serve as a prognostic marker for dynamic monitoring of HCC patients with single TS ≤ 5 cm after radical resection.

Preoperative prediction of hepatocellular carcinoma with portal vein tumor thrombus based on conventional data.

Hepatocellular carcinoma (HCC) has a high predilection with portal vein tumor thrombosis (PVTT). However, part of the PVTT type can be found only under the microscopy, which was namely as type I0. The objective of this study was to establish a simple and inexpensive non-invasive model to predict the presentation of PVTT at HCC patients. A total of 815 HCC patients were retrospectively evaluated and randomly assigned into 2 groups: the training group (n = 408) and validation group (n = 407). A new index model, namely WγAL, was built to predict the presence of PVTT in the training subjects and was further validated in the validation subjects. At the optimal cutoff of 8.90, WγAL identified patients with a hazard ratio (HR) of 7.139 for the presence of PVTT. The area under receiver operating characteristic (AUROC) of WγAL was 0.795 (sensitivity: 71.9%; specificity: 78.6%) for differentiation between PVTT and non-PVTT patients in the training group. The AUROC of WγAL in differentiating patients with PVTT type I0 from non-PVTT patients was 0.748 (sensitivity: 72.1%; specificity: 68.4%) with an HR of 5.355. In addition, WγAL > 8.90 was significantly associated with large tumors, multiple tumor numbers, TNM stage III-IV, metastasis, and overall survival in HCC patients. The novel predictive model represents a simple and inexpensive model that can identify the presence of PVTT in HCC patients with a high degree of accuracy, with important clinical significance in the future therapeutic management of HCC patients.

Upregulation of colonic and hepatic tumor overexpressed gene is significantly associated with the unfavorable prognosis marker of human hepatocellular carcinoma.

Colonic hepatic tumor overexpressed gene (ch-TOG), a member of the highly conserved XMAP215 family of microtubule-associated proteins (MAPs), plays a crucial role in bipolar mitotic spindle assembly. Here, we performed proof-of-principle studies targeting ch-TOG for the development of HCC and further compared its prognostic significance with the clinicopathologic features of HCC. Quantitative real-time PCR was used to measure the expression level of ch-TOG mRNA in 207 cases of paired HCC and adjacent noncancerous liver tissues (ANLT). Additionally, immunohistochemistry was employed to identify ch-TOG protein in 71 HCC tissues. All HCC patients were divided into two groups according to the expression level of ch-TOG. Cumulative progression-free survival (PFS) and overall survival (OS) curves were estimated using the Kaplan-Meier method, and the prognostic value of ch-TOG was further evaluated using the Cox proportional hazards regression model. Our studies suggested that ch-TOG is overexpressed in HCC tissues compared with ANLT. The ch-TOG level was correlated with other prognostic factors, including the hepatitis B surface antigen (HBsAg) (p = 0.030), median size (p = 0.008), clinical tumor-node-metastasis (TNM) stage (p = 0.002), and alpha-fetoprotein (AFP) level (p = 0.030). Kaplan-Meier survival analysis showed that increased ch-TOG was associated with reduced PFS (p = 0.002) and OS (p = 0.004). Multivariate Cox proportional hazards analysis identified ch-TOG as an independent prognostic factor for the PFS (hazard ratio [HR] = 1.479, 95% confidence interval [CI] = 1.028-2.127, p = 0.035) and OS (HR = 1.609, 95% CI = 1.114-2.325, p = 0.011) of the HCC patients. Increased ch-TOG represents a powerful marker for predicting poorer prognosis in the clinical management of HCC, and may serve as a potential molecular target for HCC therapies in the future.

Activation of spinal phosphatidylinositol 3-kinase/protein kinase B mediates pain behavior induced by plantar incision in mice.

The etiology of postoperative pain may be different from antigen-induced inflammatory pain and neuropathic pain. However, central neural plasticity plays a key role in incision pain. It is also known that phosphatidylinositol 3-kinase (PI3K) and protein kinase B/Akt (PKB/Akt) are widely expressed in laminae I-IV of the spinal horn and play a critical role in spinal central sensitization. In the present study, we explored the role of PI3K and Akt in incision pain behaviors. Plantar incision induced a time-dependent activation of spinal PI3K-p110γ and Akt, while activated Akt and PI3K-p110γ were localized in spinal neurons or microglias, but not in astrocytes. Pre-treatment with PI3K inhibitors, wortmannin or LY294002 prevented the activation of Akt brought on by plantar incision in a dose-dependent manner. In addition, inhibition of spinal PI3K signaling pathway prevented pain behaviors (dose-dependent) and spinal Fos protein expression caused by plantar incision. These data demonstrated that PI3K signaling mediated pain behaviors caused by plantar incision in mice.

[CT perfusion study of acute local cerebral infarction in rhesus monkeys].

OBJECTIVE: To explore the value of CT perfusion in early diagnosis and management of superacute local cerebral infarction in rhesus monkeys. METHOD: Acute local cerebral infarction was induced in the rhesus monkeys during digital subtraction angiography (DSA) by introduction of pale thrombus prepared from autologous blood into the M1 branch of the middle cerebral artery (MCA). Plain CT scan and CT perfusion scanning were performed at different time points before and after DSA operation, and the results were analyzed in conjunction with the pathologic changes. RESULTS: Ischemic lesions were displayed on CT perfusion images, which showed local hypoperfusion, reduced cerebral blood flow and volume, and mean transit time delay in the compromised area. Local hypointense infarct area was identified in plain CT scan 24 h after the DSA operation, and the results were in good agreement with pathological examination during autopsy. CONCLUSION: CT perfusion imaging of the brain can accurately capture the cerebral perfusion deficits in acute ischemic stroke before morphologic changes take place, and therefore provides good means for thrombolytic treatment evaluation of stroke.