Delayed improvements in visual memory task performance among chronic schizophrenia patients after high-frequency repetitive transcranial magnetic stimulation.

BACKGROUND: Cognitive impairments are core characteristics of schizophrenia, but are largely resistant to current treatments. Several recent studies have shown that high-frequency repetitive transcranial magnetic stimulation (rTMS) of the left dor-solateral prefrontal cortex (DLPFC) can reduce negative symptoms and improve certain cognitive deficits in schizophrenia patients. However, results are inconsistent across studies. AIM: To examine if high-frequency rTMS of the DLPFC can improve visual memory deficits in patients with schizophrenia. METHODS: Forty-seven chronic schizophrenia patients with severe negative symptoms on stable treatment regimens were randomly assigned to receive active rTMS to the DLPFC (n = 25) or sham stimulation (n = 22) on weekdays for four consecutive weeks. Patients performed the pattern recognition memory (PRM) task from the Cambridge Neuropsychological Test Automated Battery at baseline, at the end of rTMS treatment (week 4), and 4 wk after rTMS treatment (week 8). Clinical symptoms were also measured at these same time points using the Scale for the Assessment of Negative Symptoms (SANS) and the Positive and Negative Syndrome Scale (PANSS). RESULTS: There were no significant differences in PRM performance metrics, SANS total score, SANS subscores, PANSS total score, and PANSS subscores between active and sham rTMS groups at the end of the 4-wk treatment period, but PRM performance metrics (percent correct and number correct) and changes in these metrics from baseline were significantly greater in the active rTMS group at week 8 compared to the sham group (all P < 0.05). Active rTMS treatment also significantly reduced SANS score at week 8 compared to sham treatment. Moreover, the improvement in visual memory was correlated with the reduction in negative symptoms at week 8. In contrast, there were no between-group differences in PANSS total score and subscale scores at either week 4 or week 8 (all P > 0.05). CONCLUSION: High-frequency transcranial magnetic stimulation improves visual memory and reduces negative symptoms in schizophrenia, but these effects are delayed, potentially due to the requirement for extensive neuroplastic changes within DLPFC networks.

A Simple Technique for Direct Immobilization of Target Enzymes from Cell Lysates Based on the SpyTag/SpyCatcher Spontaneous Reaction.

Many of the current methods for enzyme purification and immobilization suffer from several drawbacks, such as requiring tedious multistep procedures or long preparation, and being environmentally unfriendly, due to the chemicals and conditions involved. Thus, a simple technique for direct purification and immobilization of target enzymes from cell lysates was proposed. The elastin-like polypeptides (ELPs)-SpyCatcher chimera could mediate the formation of silica carriers within seconds and the target enzymes were then covalently immobilized on silica carriers via SpyCatcher/SpyTag spontaneous reaction. These tailor-made carriers were easily prepared, with precisely controlled morphology and size, as well as none-consuming surface modification needed, which could specifically immobilize the SpyTag-fused target enzymes from the cell lysate without pre-purification.

The type 2 diabetes mellitus susceptibility gene CDKAL1 polymorphism is associated with depressive symptom in first-episode drug-naive schizophrenic patients.

BACKGROUND: Patients with schizophrenia have an increased prevalence of type 2 diabetes mellitus that has shown a significant association with the rs7754840 polymorphism in the gene encoding the cyclin-dependent kinase 5 (CDK5) regulatory subunit-associated protein 1-like 1 (CDKAL1). OBJECTIVE: To examine whether this polymorphism was involved in the susceptibility in first-episode drug-naive schizophrenic patients (FDSP), and further influenced their clinical symptoms. METHODS: This polymorphism was genotyped in 239 FDSP and 368 healthy controls. The clinical symptoms in FDSP were assessed using the Positive and Negative Syndrome Scale (PANSS) five-factor models. RESULTS: There was no significant difference in the allelic and genotypic frequencies of this polymorphism between two groups (both p > 0.05) after adjusting for covariates. However, the PANSS depressive score significantly differed by genotype in FDSP after adjusting for covariates (F = 5.25, p = 0.006). This significant difference also persisted after Bonferroni correction (p < 0.05). FDSP with C/C genotype had significantly higher PANSS depressive score than those with C/G genotype (p = 0.007) and those with G/G genotype (p = 0.005). Moreover, further stepwise multivariate regression analysis showed the significant association between the rs7754840 polymorphism and PANSS depressive score in FDSP (ß = -1.07, t = -2.75, p = 0.007). CONCLUSIONS: Our findings demonstrated that although the CDKAL1 rs7754840 polymorphism did not contribute to the susceptibility to FDSP, it might be implicated in depressive symptoms in this patient group.

Sex Differences in the Prevalence and Clinical Features of Comorbid Depressive Symptoms in Never-Treated Chinese Patients With First-Episode Schizophrenia.

BACKGROUND: Many studies have indicated a sex-specific effect in many aspects of schizophrenia. The presence of depressive symptomatology exists in all phases of schizophrenia. The aim of this study is to investigate the sex differences in the proportion of comorbid depressive symptoms and sex-specific relationships between depressive symptoms and clinical correlates in never-treated Chinese patients with first-episode schizophrenia (NTFE patients), which have not been reported yet. METHODS: Via a cross-sectional design, 240 NTFE inpatients (male/female = 111/129) between ages 16 and 45 years and meeting DSM-IV-TR criteria of schizophrenia were recruited. The Positive and Negative Syndrome Scale (PANSS) was used for the psychopathology, and the 17-item Hamilton Depression Rating Scale (HDRS-17) for the comorbid depressive symptoms. This study was conducted from June 2013 to December 2015. RESULTS: The proportion of patients with depressive symptoms (total score on HDRS-17 ≥ 8) in men was significantly higher than in women (male: 62.2%, female: 48.1%; χ²1 = 4.28, P = .039). Male patients had significantly greater depressive symptoms as shown on the HDRS-17 than female patients (t1, 238 = 2.75, P = .006). Further, we found that age, the age at onset, smoking rate, and PANSS total and general psychopathology, negative symptoms, and cognitive factor subscores favored significant sex differences in female patients (all P < .05). Interestingly, we found sex differences in the correlation between the HDRS-17 score and clinical phenotype, showing that in male patients, the PANSS general psychopathology subscore (ß = 0.75, t = 7.72, P < .001) and total score (ß = 0.44, t = 4.81, P < .001) significantly predicted the HDRS-17 total score, while in female patients, the PANSS general psychopathology subscore (ß = 0.74, t = 8.45, P < .001), total score (ß = 0.47, t = 5.71, P < .001), and cognitive factor subscore (ß = 0.24, t = 2.60, P < .001) significantly predicted the HDRS-17 total score. CONCLUSIONS: Our results indicate sex differences in the frequency and severity of comorbid depressive symptoms and in associations between depressive symptoms and clinical correlates in NTFE patients.

Association between decreased serum TBIL concentration and immediate memory impairment in schizophrenia patients.

Cognitive impairment is a core feature of schizophrenia (SCH). In addition to the toxic effect of Bilirubin (BIL), it has antioxidant properties that were associated with the psychopathology and cognitive impairment of psychiatric disorders. The aim of this study was to examine the correlation of serum total BIL (TBIL) concentration with cognitive impairment in SCH patients. We recruited 34 SCH patients and 119 healthy controls (HCs) in this case-control design. Cognition was assessed using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). Serum TBIL concentration was measured using the immunoturbidimetric method. Serum TBIL concentration was significantly decreased in SCH patients compared to HCs after adjusting for age, gender, and education. Serum TBIL concentration in SCH patients was also positively correlated with the RBANS immediate memory score. Further stepwise multiple regression analysis confirmed the positive association between serum TBIL concentration and immediate memory score in SCH patients. Our findings supported that the decline in serum TBIL concentration was associated with the immediate memory impairment and psychopathology of SCH.

A Weighted Genetic Risk Score Using Known Susceptibility Variants to Predict Graves Disease Risk.

CONTEXT: Graves disease (GD) is a common thyroid-specific autoimmune disease and one of the most heritable diseases in the population. We present a risk-prediction model, including confirmed, known genetic variants associated with GD. DESIGN: To construct a stable-prediction model, we used known GD susceptibility single nucleotide polymorphisms (SNPs) as markers and trained and tested our model in a cohort of 4897 patients with GD and 5098 healthy controls. We weighted the contribution of each SNP to the disease to calculate the weighted genetic risk score (wGRS) for each individual. The efficiency of this model can be estimated by the area under the curve (AUC) receiver operator characteristic curve and the specificity and sensitivity of each wGRS. RESULTS: With the 20 confirmed GD risk-related SNPs, our wGRS-prediction model could predict patients with GD from the general population (AUC 0.70 [95% CI: 0.69 to 0.71]) and did especially well in predicting patients with GD with persisting thyroid-stimulating hormone receptor antibody positive [pTRAb+; AUC 0.74 (95% CI: 0.72 to 0.76)]. We also evaluated how the four pTRAb+ specific risk SNPs predicted patients with GD with pTRAb+ among all patients with GD [AUC 0.62 (95% CI: 0.61 to 0.63)]. For clinical use, we partitioned subjects in each set into different risk categories to generate the wGRS cutoff of high risk for reference. CONCLUSIONS: Our study provides an approach to predict GD risk in the general population by the calculation of the wGRS of 20 known GD susceptibility variants. The wGRS-prediction model was more stable and convenient, whereas the prediction performance was still modest.

π-π stacking interaction is a key factor for the stability of GH11 xylanases at low pH.

Acidic xylanases possess the unique features necessary for the tolerance of acidic environments, which may have great potentials for industrial purposes. However, factors controlling the pH-dependent stability of xylanases are only partially known. Here we proposed a residue interaction networks based method to analyze the differences of residue interactions between 6 pairs of experimentally verified acidic and neutral xylanases. They had very close numbers of aromatic amino acids, however extremely significant more (p < 0.001) π-π stacking interactions existed in acidic xylanases, which has not been reported before. Whereas the interactions between Tyrosine-Phenylalanine (Tyr-Phe) and Phenylalanine-Phenylalanine (Phe-Phe) were the main contributors. An equation quantitatively described the relationship between the optimal pH and the number of π-π stacking interactions was proposed. The predicted optimal pHs for three xylanases was 4.13, 6.7 and 6.1, while the experimental values of the optimum pHs were 4.6, 6.5 and 6.5, with an absolute error of 0.47, 0.2 and 0.4 pH unit, respectively. By counting the aromatic residue pairs forming π-π stacking in the 3D structure of an acidic (PDB ID: 1BK1, with an optimal pH of 2) and a neutral (PDB ID:1XXN, with an optimal pH of 6.5) xylanase, we found significant differences existed in the positions ranging from 145 to 166 in forming π-π stacking. Two phenylalanines at position 149 and 157 in the acidic xylanase, which involved in 7 π-π stacking interactions, played an important role in the stability of xylanase at low pH environment, which was further proved by a mutation experiment. A mutated xylanase with Phe149 → Ala149 and Phe157 → Ala157 was expressed and purified, resulting the optimal pH shifted from 2 to 4.5. The interaction networks based method paved a new way in underlying and engineering the acid-stability of xylanase, as well as the characteristics of other enzymes.

Characterization of a novel psychrophilic and halophilic ß-1, 3-xylanase from deep-sea bacterium, Flammeovirga pacifica strain WPAGA1.

ß-1, 3-Xylanase is one of the most important hydrolytic enzymes to prepare oligosaccharides as functional foods in seaweed industry. However, less than five ß-1, 3-xylanases have been experimentally expressed and characterized; moreover, none of them is psychrophilic and salt tolerant. Here, we mined a novel ß-1, 3-xylanase (Xyl512) from the genome of the deep-sea bacterium Flammeovirga pacifica strain WPAGA1 and biochemically characterized it in detail. The Xyl512 did not contain any carbohydrate-binding module; the catalytic domain of it belonged to the glycoside hydrolase family 26. The optimum temperature and pH of the purified ß-1, 3-xylanase was 20 °C and pH 7.0 in the condition of no NaCl. However, they shifted to 30 °C and 7.5 with 1.5 mol/L NaCl, respectively. In this condition (1.5 mol/L NaCl), the overall activity was 2-fold as high as that without NaCl. Based on the residue interactions and the electrostatic surfaces, we addressed the possible mechanism of its adaption to low temperature and relative high NaCl concentration. The Xyl512 showed significantly reduced numbers of hydrogen bonds leading to a more flexible structure, which is likely to be responsible for its cold adaptation. While the negatively charged surface may contribute to its salt tolerance. The ß-1, 3-xylanase we identified here was the first reported psychrophilic and halophilic one with functionally characterized. It could make new contributions to exploring and studying the ß-1, 3-xylanase for further associated investigations.

Association between PLA2G12A polymorphism and patients with schizophrenia in a southern Chinese Han population.

BACKGROUND: Elevated phospholipase A2 (PLA2) activity is reported to be involved in the development of schizophrenia. Further study revealed an association between PLA2 groups XIIA (PLA2G12A) polymorphism and patients with schizophrenia in a northeast Chinese Han population. OBJECTIVE: This study will further examine whether PLA2G12A rs3087494 polymorphism is associated with patients with schizophrenia in a southern Chinese Han population. METHODS: This polymorphism was genotyped in 438 patients with schizophrenia (diagnosed according to Diagnostic and Statistical Manual of Mental Disorders-IV) and 876 healthy controls using a case-control design. Demographic and clinical data were collected in all subjects. RESULTS: The allele and genotype frequencies of PLA2G12A rs3087494 polymorphism significantly differed between groups (both, p < .001). These differences still were significant by adjusting for sex and age. However, there was no difference in age at onset among 3 genotype groups in patients with schizophrenia by adjusting for the variables (F = 0.22, p = .80). Stepwise multivariate regression analysis showed that this polymorphism was not associated with age at onset in patients with schizophrenia (ß = .008, t = .07, p = .94). CONCLUSIONS: Our results indicated that even though PLA2G12A rs3087494 polymorphism did not influence age at onset in patients with schizophrenia, it may play an important role in the susceptibility to schizophrenia in a southern Chinese Han population.

SgRNA Expression of CRIPSR-Cas9 System Based on MiRNA Polycistrons as a Versatile Tool to Manipulate Multiple and Tissue-Specific Genome Editing.

CRISPR/Cas9-mediated genome editing is a next-generation strategy for genetic modifications. Typically, sgRNA is constitutively expressed relying on RNA polymerase III promoters. Polymerase II promoters initiate transcription in a flexible manner, but sgRNAs generated by RNA polymerase II promoter lost their nuclease activity. To express sgRNAs in a tissue-specific fashion and endow CRISPR with more versatile function, a novel system was established in a polycistron, where miRNAs (or shRNAs) and sgRNAs alternately emerged and co-expressed under the control of a single polymerase II promoter. Effective expression and further processing of functional miRNAs and sgRNAs were achieved. The redundant nucleotides adjacent to sgRNA were degraded, and 5'- cap structure was responsible for the compromised nuclease capacity of sgRNA: Cas9 complex. Furthermore, this strategy fulfilled conducting multiplex genome editing, as well as executing neural- specific genome editing and enhancing the proportion of homologous recombination via inhibiting NHEJ pathway by shRNA. In summary, we designed a new construction for efficient expression of sgRNAs with miRNAs (shRNAs) by virtue of RNA polymerase II promoters, which will spur the development of safer, more controllable/regulable and powerful CRISPR/Cas9 system-mediated genome editing in a wide variety of further biomedical applications.

Heat-resistant cytosolic malate dehydrogenases (cMDHs) of thermophilic intertidal snails (genus Echinolittorina): protein underpinnings of tolerance to body temperatures reaching 55°C.

Snails of the genus Echinolittorina are among the most heat-tolerant animals; they experience average body temperatures near 41-44°C in summer and withstand temperatures up to at least 55°C. Here, we demonstrate that heat stability of function (indexed by the Michaelis-Menten constant of the cofactor NADH, KMNADH) and structure (indexed by rate of denaturation) of cytosolic malate dehydrogenases (cMDHs) of two congeners (E. malaccana and E. radiata) exceeds values previously found for orthologs of this protein from less thermophilic species. The ortholog of E. malaccana is more heat stable than that of E. radiata, in keeping with the congeners' thermal environments. Only two inter-congener differences in amino acid sequence in these 332 residue proteins were identified. In both cases (positions 48 and 114), a glycine in the E. malaccana ortholog is replaced by a serine in the E. radiata protein. To explore the relationship between structure and function and to characterize how amino acid substitutions alter stability of different regions of the enzyme, we used molecular dynamics simulation methods. These computational methods allow determination of thermal effects on fine-scale movements of protein components, for example, by estimating the root mean square deviation in atom position over time and the root mean square fluctuation for individual residues. The minor changes in amino acid sequence favor temperature-adaptive change in flexibility of regions in and around the active sites. Interspecific differences in effects of temperature on fine-scale protein movements are consistent with the differences in thermal effects on binding and rates of heat denaturation.

Ufm1 inhibits LPS-induced endothelial cell inflammatory responses through the NF-κB signaling pathway.

Endothelial cell dysfunction and inflammatory responses are important early contributors to the occurrence and development of atherosclerosis (AS), which still remains to be decoded. Ubiquitin-fold modifier 1 (Ufm1) is a new member of the ubiquitin-like protein family, and its biological function remains largely unknown, particularly in endothelial cell injury and inflammatory responses. In the present study, we showed that Ufm1 was highly expressed in both the nucleus and cytoplasm of human umbilical vein endothelial cells (HUVECs). We also demonstrated that the Ufm1 expression level was increased following lipopolysaccharide (LPS)­induced inflammation in HUVECs. Moreover, overexpression of Ufm1 in HUVECs alleviated the inflammatory responses induced by LPS treatment. Additionally, we found that Ufm1 overexpression inhibited the nuclear translocation of nuclear factor-κB (NF-κB) after LPS treatment, suggesting its implication in the LPS/Toll-like receptor 4 (TLR4)/NF-κB pathway. Taken together, in addition to decoding its expression pattern in endothelial cells, we showed for the first time that Ufm1 is upregulated in LPS-induced inflammation and Ufm1 plays an inhibitory role in inflammatory responses by targeting NF-κB nuclear translocation. Thus, Ufm1 may be a novel gene that protects against inflammatory responses.

Follow-up of N400 in the Rehabilitation of First-episode Schizophrenia.

BACKGROUND: The N400 component of event-related potentials (ERP) has recently drawn widespread attention at home and abroad. This study was to explore the relationship between N400 changes and risperidone treatment and rehabilitation infirst-episode schizophrenia (FES). METHODS: ERP component N400 was recorded by Guangzhou Runjie WJ-1 ERP instruments, in 58 FES before and 6 months, 15 months after risperidone treatment, and in 62 normal controls. The patients' syndromes were assessed by Positive and Negative Syndrome Scale (PANSS). And the stimuli are Chinese sentences with matching (congruent) or mismatching (incongruent) ending words. RESULTS: N400 latencies were prolonged, and amplitudes were decreased in Cz, Pz, Fz, C3, C4, in FES compared with in NC, before treatment. The prolonged N400 latencies and decreased amplitudes were negatively correlated with the patients' positive scale and total scale of PANSS. There are significant differences of N400 amplitudes and latencies in 6 months and 15 months follow-up after treatment. Before treatment, 6 months and 15 months after treatment, N400 latencies are 446 ± 35 ms, 440 ± 37 ms, 414 ± 31 ms (F = 9.72, P < 0.01) in incongruent situation; N400 amplitudes are 5.2 ± 4.6 µV, 5.7 ± 4.8 µV, 7.3 ± 5.0 µV (F = 2.06, P > 0.05) in congruent situation, and 8.5 ± 5.9 µV, 10.1 ± 5.0 µV, 11.9 ± 7.0 µV (F = 3.697, P < 0.05) in incongruent situation. CONCLUSIONS: N400 could be used to predict the effects of treatment of schizophrenia to some degree. The linguistic and cognitive impairment in schizophrenia can be improved by antipsychotic drugs.

UFM1 Protects Macrophages from oxLDL-Induced Foam Cell Formation Through a Liver X Receptor α Dependent Pathway.

AIM: Macrophage foam cell formation is the most prominent characteristic of the early stages of atherosclerosis. Ubiquitin Fold Modifier 1 (UFM1) is a new member of the ubiquitin-like protein family, and its underlying mechanism of action in macrophage foam cell formation is poorly understood. Our current study focuses on UFM1 and investigates its role in macrophage foam cell formation. METHODS: Using real-time quantitative PCR (qRT-PCR) and western blot analysis, we first analyzed the UFM1 expression in mouse peritoneal macrophages (MPMs) from ApoE－/－ mice in vivo and in human macrophages treated with oxLDL in vitro. Subsequently, the effects of UFM1 on macrophages foam cell formation were determined by Nile Red staining and direct lipid analysis. We then examined whether UFM1 affects the process of lipid metabolism in macrophages. Lastly, with the method of small interfering RNA (siRNA), we delineated the mechanism of UFM1 to attenuate lipid accumulation in THP-1 macrophages. RESULTS: UFM1 is dramatically upregulated under atherosclerosis conditions both in vivo and in vitro. Moreover, UFM1 markedly decreased macrophage foam cell formation. Mechanistic studies revealed that UFM1 increased the macrophage cholesterol efflux, which was due to the increased expression of ATP-binding cassette transporters A1 (ABCA1) and G1 (ABCG1). Furthermore, the upregulation of ABCA1 and ABCG1 by UFM1 resulted from liver X receptor α (LXRα) activation, which was confirmed by the observation that LXRα siRNA prevented the expression of ABCA1 and ABCG1. Consistent with this, the UFM1-mediated attenuation of lipid accumulation was abolished by such inhibition. CONCLUSIONS: Taken together, our results showed that UFM1 could suppress foam cell formation via the LXRα-dependent pathway.

Enhancement predicting accuracy for elastin-like polypeptides temperature transition by back propagation neural network.

Elastin-like polypeptides (ELPs) have been widely used to promote the development of a variety of smart biomaterials. Transition temperature is a key attribute of ELPs central to ELPs researches. Therefore, it is essential to establish predictive models of transition temperature that are both computationally efficient and reliable by employing simple parameters. Back propagation neural network (BPNN), a powerful feed-forward algorithm designed to solve problems with overwhelming complexity, has been successfully used in non-linear predictor model. In this study, two pH-sensitive ELPs were expressed, purified and determined for temperature transition across a range of pH. The pH, concentration and molecular weight (MW) as well as isoelectric point (PI) and pseudo amino acid (PseAA) of these two ELPs were adopted as input parameters. Support vector machine (SVM) and back propagation neural network (BPNN) were performed respectively. We selected Lamda (λ) value by training set and evaluated predictor model by jackknife test that combined with Uniform Design (UD). According to the results of BPNN and SVM, whose mean absolute error (MAE) of BPNN model jackknife test were 4.80 and 4.95 respectively, the predictive ability of BPNN is a minor improvement over SVM. Applying Mackay's data, MAE of BPNN jackknife test was 2.02, while the MAE between experimental and predicted transition temperature was 2.30 in Mackay's predictor model. Compared with Mackay predictor model, the enhancement in the accuracy indicates that the proposed BPNN method could play a complementary role to predict ELPs transition temperature.

Psychosomatic conditions of the children and adolescents exposed to 5.12 Wenchuan earthquake.

BACKGROUND: A devastating earthquake registering 8.0 on the Richter Scale struck Wenchuan County in Northwest Sichuan Province in China on May 12, 2008, claiming over 69,200 lives, seriously wounding more than 374,600 people, and rendering more than 18,400 people missing. The epicenter was close to Yingxiu Township in Wenchuan County. PURPOSE: This study aimed to investigate the psychosomatic conditions of the children and adolescents exposed to the devastating earthquake and explore the risk factors for psychosomatic symptoms. METHOD: A total of 1,828 participants aged 6 to 16 years, of whom 842 from the affected area and 986 from non-affected area, were administered a Psychosomatic Conditions Scale. RESULTS: Each factor score, total somatic score, total psychological score, and total psychosomatic score of the experimental group were significantly higher than those of the control group (P < 0.001). Positive correlation was found between the psychological state and somatic symptoms in the experimental group(r = 0.157 ~ 0.489, P < 0.01). Respiratory system, cardiovascular system, nervous system, digestive system, urogenital system, emotion, behavior, and language, combined as a panel, were significantly differentiated between the two groups, accounting for 73.4% of the total difference. In the experimental group, the factor scores of anxiety, behavior, total psychological score, and total psychosomatic score of the girls were obviously higher than those of the boys (P < 0.01 ~ 0.05); most somatic factors and psychological factors, total somatic score, total psychological score, and total psychosomatic score of the elder adolescents were significantly higher than those of the younger children (P < 0.01 ~ 0.05). CONCLUSION: The children and adolescents exposed to 5.12 earthquake greatly suffered from terrible psychosomatic conditions, among whom the elder girls had more severe symptoms, particularly in terms of anxiety and behavior.

Predicting lipase types by improved Chou's pseudo-amino acid composition.

By proposing a improved Chou's pseudo amino acid composition approach to extract the features of the sequences, a powerful predictor based on k-nearest neighbor was introduced to identify the types of lipases according to their sequences. To avoid redundancy and bias, demonstrations were performed on a dataset where none of the proteins has > or =25% sequence identity to any other. The overall success rate thus obtained by the 10-fold cross-validation test was over 90%, indicating that the improved Chou's pseudo amino acid composition might be a useful tool for extracting the features of protein sequences, or at lease can play a complementary role to many of the other existing approaches.

Predicting the cofactors of oxidoreductases based on amino acid composition distribution and Chou's amphiphilic pseudo-amino acid composition.

Predicting the cofactors of oxidoreductases plays an important role in inferring their catalytic mechanism. Feature extraction is a critical part in the prediction systems, requiring raw sequence data to be transformed into appropriate numerical feature vectors while minimizing information loss. In this paper, we present an amino acid composition distribution method for extracting useful features from primary sequence, and the k-nearest neighbor was used as the classifier. The overall prediction accuracy evaluated by the 10-fold cross-validation reached 90.74%. Comparing our method with other eight feature extraction methods, the improvement of the overall prediction accuracy ranged from 3.49% to 15.74%. Our experimental results confirm that the method we proposed is very useful and may be used for other bioinformatical predictions. Interestingly, when features extracted by our method and Chou's amphiphilic pseudo-amino acid composition were combined, the overall accuracy could reach 92.53%.

[Molecular docking of Bacillus pumilus xylanase and xylan substrate using computer modeling].

Bacillus pumilus xylanase was cloned and sequenced. Based on the tertiary structure that originated from homology modeling, the potential active pocket was searched and ligand-protein docking was performed using relative softwares. The information extracted from the molecular docking is analyzed; several amino acid residues might play a vital role in the xylanase catalytic reaction are obtained to instruct the further modification of xylanase directed-evolution.

[A uniform design based PCA-SVM model for predicting optimum pH in chitinase].

The principal component analysis (PCA) was applied to the data processing in training sets, the new principal components were then used as input data for support vector machine model. A prediction model for optimum pH of chitinase was established based on uniform design. When The regularized constant C, epsilon and Gamma were 10, 0.7 and 0.5 respectively, the calculated pHs fitted the reported optimum pHs of chitinase very well and the MAPEs (Mean Absolute Percent Error) was 3.76%. At the same time, the predicted pHs fitted the reported optimum pHs well and the MAE (Mean Absolute Error) was 0.42 pH unit. It was superior in fittings and predictions compared to the model based on back propagation (BP) neural network.