Glutamine is essential for overcoming the immunosuppressive microenvironment in malignant salivary gland tumors

Rationale: Immunosuppression in the tumor microenvironment (TME) is key to the pathogenesis of solid tumors. Tumor cell-intrinsic autophagy is critical for sustaining both tumor cell metabolism and survival. However, the role of autophagy in the host immune system that allows cancer cells to escape immune destruction remains poorly understood. Here, we determined if attenuated host autophagy is sufficient to induce tumor rejection through reinforced adaptive immunity. Furthermore, we determined whether dietary glutamine supplementation, mimicking attenuated host autophagy, is capable of promoting antitumor immunity. Methods: A syngeneic orthotopic tumor model in Atg5^+/+ and Atg5^flox/flox mice was established to determine the impact of host autophagy on the antitumor effects against mouse malignant salivary gland tumors (MSTs). Multiple cohorts of immunocompetent mice were used for oncoimmunology studies, including inflammatory cytokine levels, macrophage, CD4⁺, and CD8⁺ cells tumor infiltration at 14 days and 28 days after MST inoculation. In vitro differentiation and in vivo dietary glutamine supplementation were used to assess the effects of glutamine on Treg differentiation and tumor expansion. Results: We showed that mice deficient in the essential autophagy gene, Atg5, rejected orthotopic allografts of isogenic MST cells. An enhanced antitumor immune response evidenced by reduction of both M1 and M2 macrophages, increased infiltration of CD8⁺ T cells, elevated IFN-γ production, as well as decreased inhibitory Tregs within TME and spleens of tumor-bearing Atg5^flox/flox mice. Mechanistically, ATG5 deficiency increased glutamine level in tumors. We further demonstrated that dietary glutamine supplementation partially increased glutamine levels and restored potent antitumor responses in Atg5^+/+ mice. Conclusions: Dietary glutamine supplementation exposes a previously undefined difference in plasticity between cancer cells, cytotoxic CD8⁺ T cells and Tregs.

[Effects of methacrylic anhydride gelatin hydrogel loaded with silver and recombinant human basic fibroblast growth factor on deep partial-thickness burn wounds in rabbits]

Objective: To investigate the effects of methacrylic anhydride gelatin (GelMA) hydrogel loaded with silver and recombinant human basic fibroblast growth factor (rh-bFGF) on deep partial-thickness burn wounds in rabbits. Methods: The experimental research method was adopted. Low-concentration GelMA materials, medium-concentration GelMA materials and high-concentration GelMA materials containing different concentrations of methacrylic anhydride (MA) were prepared, after adding photoinitiator, low-concentration GelMA hydrogels, medium-concentration GelMA hydrogels, and high-concentration GelMA hydrogels were obtained, respectively. The nuclear magnetic resonance spectroscopy was performed to detect the hydrogen nuclear magnetic resonance spectra of the above-mentioned three concentrations of GelMA materials, and to calculate the degree of substitution according to the spectrum diagram. The three-dimensional microstructure and pore size of 3 types of above-mentioned GelMA hydrogels were detected by field emission scanning electron microscopy (FESEM), with 9 samples measured. According to the selected concentration of MA, ten kinds of solutions of GelMA with different concentration of silver (silver-containing GelMA) were synthesized, and the silver-containing GelMA solution of each concentration was divided into three parts, and then exposed to ultraviolet light lasting for 20, 25, and 35 s, respectively. After adding photoinitiator,the corresponding silver-containing GelMA hydrogels were obtained. The residual degradation rate of silver-containing GelMA hydrogel with different photocrosslinking times was detected by collagenase degradation method at degradation of 12, 24, 36, and 48 h; and the time required for complete degradation was detected, and the sample number was 5. The inhibition zone diameter of GelMA hydrogel under above screened photocrosslinking times containing 10 concentrations of silver against Staphylococcus aureus was measured to reflect its antibacterial ability, and the sample numbers were all 5. The silver-containing GelMA hydrogel with statistical significance compared with the antibacterial circle diameter of the silver-containing GelMA hydrogel containing the lowest concentration (no silver) was considered as having antibacterial activity. The three-dimensional microstructure and pore size of the silver-containing GelMA hydrogels with antibacterial activity and the lowest drug concentration selected were detected by FESEM, and the sample numbers were all 9. The freeze-dried alone GelMA hydrogel and the freeze-dried silver-containing GelMA hydrogel were soaked in phosphate buffer solution for 24 h, respectively, then the swelling rate of the two GelMA hydrogel were calculated and compared by weighing method, and the sample number was 5. GelMA hydrogel containing silver and rh-bFGF, namely compound hydrogel for short, was prepared according to the preliminary experiment and the above experimental results. The appearance of the composite hydrogel was observed in general, and its three-dimensional microstructure and pore size were detected by FESEM. The deep partial-thickness burn wound was made on the back of 30 rabbits (aged 4-6 months, female half and half). Meanwhile, with the rabbit head as the benchmark, the wounds on the left side of the spine were treated as composite hydrogel treatment group, and the wounds on the right side were treated as gauze control group, and which were treated accordingly. On post injury day (PID) 3, 7, 14, 21, and 28, the healing of wounds in the two groups was observed. On PID 7, 14, 21, and 28, the wound healing area was recorded and the healing rate was calculated, with a sample number of 30. Data were statistically analyzed with analysis of variance for repeated measurement, one-way analysis of variance, and independent sample t test. Results: The substitution degree among low-concentration GelMA materials, medium-concentration GelMA materials, and high-concentration GelMA materials was significantly different (F=1 628.00, P<0.01). The low-concentration GelMA hydrogel had a loose and irregular three-dimensional spatial network structure with a pore size of (60±17) μm; the medium-concentration GelMA hydrogel had a relatively uniform three-dimensional spatial network and pore size with a pore size of (45±13) μm; the high-concentration GelMA hydrogel had the dense and disordered three-dimensional spatial network with a pore size of (25±15) μm, the pore sizes of 3 types of GelMA hydrogels were significantly differences (F=12.20, P<0.01), and medium concentration of MA was selected for the concentration of subsequent materials. The degradability of silver-containing GelMA hydrogels with different concentrations of the same photocrosslinking time was basically same. The degradation residual rates of silver-containing GelMA hydrogels with 20, 25, and 35 s crosslinking time at 12 h were (74.2±1.7)%, (85.3±0.9)%, and (93.2±1.2)%, respectively; the residual rates of degradation at 24 h were (58.3±2.1)%, (65.2±1.8)%, and (81.4±2.6)%, respectively; the residual rates of degradation at 36 h were (22.4±1.9)%, (45.2±1.7)%, and (68.1±1.4)%, respectively; the residual rates of degradation at 48 h were (8.2±1.7)%, (32.4±1.3)%, and (54.3±2.2)%, respectively, and 20, 25, and 30 s photocrosslinking time required for complete degradation of silver-containing GelMA hydrogels were (50.2±2.4), (62.4±1.4), and (72.2±3.2) h, and the difference was statistically significant (F=182.40, P<0.01), 25 s were selected as the subsequent photocrosslinking time. The antibacterial diameters of 10 types of silver-containing GelMA hydrogels against Staphylococcus aureus from low to high concentrations were (2.6±0.4), (2.5±0.4), (3.2±0.4), (12.1±0.7), (14.8±0.7), (15.1±0.5), (16.2±0.6), (16.7±0.5), (16.7±0.4), and (16.7±0.6) mm, respectively, and which basically showed a concentration-dependent increasing trend, and the overall difference was statistically significant (F=428.70, P<0.01). Compared with the silver-containing GelMA hydrogel with the lowest concentration, the antibacterial circle diameters of other silver-containing GelMA hydrogels with antibacterial ability from low to high concentration were significantly increased (with t values of 26.35, 33.84, 43.65, 42.17, 49.24, 55.74, and 43.72, respectively, P<0.01). The silver-containing GelMA hydrogel with the antibacterial diameter of (12.1±0.7) mm had the lowest antibacterial activity against Staphylococcus aureus and the lowest drug loading concentration, and the concentration of silver was selected for the concentration of subsequent materials. The microscopic morphology of the silver-containing GelMA hydrogel containing silver element with a pore size of (45±13) μm had a regular and linear strip-like structure. After soaking for 24 h, the swelling ratio of silver-containing GelMA hydrogel was similar to that of alone GelMA hydrogel. The composite hydrogel was colorless, clear and transparent, and its three-dimensional microstructure was a regular and uniform grid, with a filament network structure inside, and the pore size of (40±21) μm. On PID 3, a large amount of necrotic tissue and exudate of rabbit wound in composite hydrogel group were observed, and scattered scabs, a small amount of necrotic tissue and exudate of rabbit wound in gauze control group were observed. On PID 7, the area of rabbit wound in composite hydrogel group was significantly reduced, and adhesion of rabbit wound and gauze in gauze control group was observed. On PID 14, In composite hydrogel group, the rabbit wound surface was ruddy, and the growth of granulation tissue was observed, and in gauze control group, the rabbit wound base was pale, and the blood supply was poor. On PID 21, the rabbit wounds in composite hydrogel group healed completely, and rabbit wound in gauze control group had healing trend. On PID 28, new hair could be seen on rabbit wound surface in composite hydrogel group; oval wound of rabbit in gauze control group still remained. On PID 7, 14, 21, and 28, the wound healing areas of rabbit in composite hydrogel group were significantly larger than those in gauze control group (with t values of 2.24, 4.43, 7.67, and 7.69, respectively, P<0.05 or P<0.01). Conclusions: The medium-concentration GelMA hydrogel has good physical and chemical properties in terms of swelling and degradability. The screened silver-containing GelMA hydrogels had the lowest antibacterial activity and the lowest drug loading concentration. Composite hydrogel can significantly shorten the healing time of deep partial-thickness burn wounds in rabbits.

A repeating fast radio burst source in a globular cluster

Fast radio bursts (FRBs) are flashes of unknown physical origin¹. The majority of FRBs have been seen only once, although some are known to generate multiple flashes^2,3. Many models invoke magnetically powered neutron stars (magnetars) as the source of the emission^4,5. Recently, the discovery⁶ of another repeater (FRB 20200120E) was announced, in the direction of the nearby galaxy M81, with four potential counterparts at other wavelengths⁶. Here we report observations that localized the FRB to a globular cluster associated with M81, where it is 2 parsecs away from the optical centre of the cluster. Globular clusters host old stellar populations, challenging FRB models that invoke young magnetars formed in a core-collapse supernova. We propose instead that FRB 20200120E originates from a highly magnetized neutron star formed either through the accretion-induced collapse of a white dwarf, or the merger of compact stars in a binary system⁷. Compact binaries are efficiently formed inside globular clusters, so a model invoking them could also be responsible for the observed bursts.

Effects of dietary supplementation with Taiwanese tea byproducts and probiotics on growth performance, lipid metabolism, and the immune response in red feather native chickens

Objective

This study compared the catechin composition of different tea byproducts and investigated the effects of dietary supplementation with green tea byproducts on the accumulation of abdominal fat, the modulation of lipid metabolism, and the inflammatory response in red feather native chickens.

Methods

Bioactive compounds were detected, and in vitro anti-obesity capacity analyzed via 3T3-L1 preadipocytes. In animal experiments, 320 one-day-old red feather native chickens were divided into 4 treatment groups: control, basal diet supplemented with 0.5% Jinxuan byproduct (JBP), basal diet supplemented with 1% JBP, or basal diet supplemented with 5×10⁶ colony-forming unit (CFU)/kg Bacillus amyloliquefaciens+5×10⁶ CFU/kg Saccharomyces cerevisiae (BA+SC). Growth performance, serum characteristics, carcass characteristics, and the mRNA expression of selected genes were measured.

Results

This study compared several cultivars of tea, but Jinxuan showed the highest levels of the anti-obesity compound epigallocatechin gallate. 3T3-L1 preadipocytes treated with Jinxuan extract significantly reduced lipid accumulation. There were no significant differences in growth performance, serum characteristics, or carcass characteristics among the groups. However, in the 0.5% JBP group, mRNA expression of fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC) were significantly decreased. In the 1% JBP group, FAS, ACC and peroxisome proliferator-activated receptor γ levels were significantly decreased. Moreover, inflammation-related mRNA expression levels were decreased by the addition of JBP.

Conclusion

JBP contained abundant catechins and related bioactive compounds, which reduced lipid accumulation in 3T3-L1 preadipocytes, however there was no significant reduction in abdominal fat. This may be due to a lack of active anti-obesity compounds or because the major changes in fat metabolism were not in the abdomen. Nonetheless, lipogenesis-related and inflammation-related mRNA expression were reduced in the 1% JBP group. In addition, dietary supplementation with tea byproducts could reduce the massive amount of byproducts created during tea production and modulate lipid metabolism and the inflammatory response in chickens.

Arginine starvation kills tumor cells through aspartate exhaustion and mitochondrial dysfunction

Defective arginine synthesis, due to the silencing of argininosuccinate synthase 1 (ASS1), is a common metabolic vulnerability in cancer, known as arginine auxotrophy. Understanding how arginine depletion kills arginine-auxotrophic cancer cells will facilitate the development of anti-cancer therapeutic strategies. Here we show that depletion of extracellular arginine in arginine-auxotrophic cancer cells causes mitochondrial distress and transcriptional reprogramming. Mechanistically, arginine starvation induces asparagine synthetase (ASNS), depleting these cancer cells of aspartate, and disrupting their malate-aspartate shuttle. Supplementation of aspartate, depletion of mitochondria, and knockdown of ASNS all protect the arginine-starved cells, establishing the causal effects of aspartate depletion and mitochondrial dysfunction on the arginine starvation-induced cell death. Furthermore, dietary arginine restriction reduced tumor growth in a xenograft model of ASS1-deficient breast cancer. Our data challenge the view that ASNS promotes homeostasis, arguing instead that ASNS-induced aspartate depletion promotes cytotoxicity, which can be exploited for anti-cancer therapies.

Autophagic reliance promotes metabolic reprogramming in oncogenic KRAS-driven tumorigenesis

Defects in basal autophagy limit the nutrient supply from recycling of intracellular constituents. Despite our understanding of the prosurvival role of macroautophagy/autophagy, how nutrient deprivation, caused by compromised autophagy, affects oncogenic KRAS-driven tumor progression is poorly understood. Here, we demonstrate that conditional impairment of the autophagy gene Atg5 (atg5-KO) extends the survival of KRASG12V-driven tumor-bearing mice by 38%. atg5-KO tumors spread more slowly during late tumorigenesis, despite a faster onset. atg5-KO tumor cells displayed reduced mitochondrial function and increased mitochondrial fragmentation. Metabolite profiles indicated a deficiency in the nonessential amino acid asparagine despite a compensatory overexpression of ASNS (asparagine synthetase), key enzyme for de novo asparagine synthesis. Inhibition of either autophagy or ASNS reduced KRASG12V-driven tumor cell proliferation, migration, and invasion, which was rescued by asparagine supplementation or knockdown of MFF (mitochondrial fission factor). Finally, these observations were reflected in human cancer-derived data, linking ASNS overexpression with poor clinical outcome in multiple cancers. Together, our data document a widespread yet specific asparagine homeostasis control by autophagy and ASNS, highlighting the previously unrecognized role of autophagy in suppressing the metabolic barriers of low asparagine and excessive mitochondrial fragmentation to permit malignant KRAS-driven tumor progression.

Identification of cis- and trans-acting factors regulating the expression of rat salivary-specific RP4 gene

The molecular basis of tissue-specific and cyclic AMP (cAMP)-inducible gene expression in salivary glands is not well understood. Previously, we cloned a salivary-specific proline-rich protein gene, RP4. To analyze the cis-regulatory element(s) that mediates the regulation of this rat salivary RP4 gene, chimeric pRP4CAT constructs containing up to 1.7 kb of the 5'-flanking region of RP4 fused to a reporter gene were transiently transfected into salivary cells. Deletion studies suggest that a 159 bp (-147/+12) fragment of the RP4 5'-flanking region is sufficient to confer salivary-specific induction by agents that can raise intracellular cAMP concentration. Further delineation of this essential sequence revealed that a segment from -136 to -109 is necessary and sufficient to confer cAMP responsiveness in a salivary-specific manner when linked to a heterologous promoter. However, this 28 bp fragment (-136/-109) does not contain an identical match to the consensus cAMP response element (CRE). DNA mobility shift binding assays establish that a sequence-specific DNA-protein complex is formed between this DNA fragment and nuclear proteins from salivary cells, but not with nuclear proteins from HeLa cells, which contain canonical CRE binding proteins (CREBs). Taken together, these data demonstrate that we have identified a 28 bp cis-regulatory element in the RP4 gene that mediates salivary-specific cAMP-inducible gene expression. We propose that the novel salivary-specific CRE binding protein (SCBP) is a key regulator for salivary cAMP-inducible gene expression.

A systematic review of prediction models for prevalent pulmonary tuberculosis in adults

A systematic review was conducted to describe the quality and characteristics of prediction models for prevalent pulmonary tuberculosis (PTB) in adults at routine TB care settings. A prediction model was defined as the combination of two or more clinical predictors designed to estimate the probability of having TB. Studies using culture-confirmed PTB as reference standard were included. Models for in-patients, children or specific patient populations were excluded. PubMed, Scopus and the Cochrane Library and abstracts from the International Union Against Tuberculosis and Lung Disease, American Thoracic Society and European Respiratory Society conferences were searched. The CHARMS (Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies) checklist was used for data extraction and quality assessment. From 13 671 identified records, six were included for data extraction; three assessed smear-negative, culture-positive PTB as outcome and three focused on human immunodeficiency virus infected individuals only. Reporting of model development, performance and evaluation was poor. In four studies, predictive performance was evaluated using the development data set (apparent performance), one study did an internal validation and one study did an external validation. Results were not pooled due to heterogeneity. Existing prediction models for estimating prevalent PTB in adults at primary care level are poorly reported and validated and are not useful for TB screening. The World Health Organization symptom screen is recommended.

Current State of Knowledge on Salivary Gland Cancers

Salivary gland cancers (SGCs), categorized as head and neck cancers (HNCs), constitute about 6% of head and neck cancer diagnoses based on estimate by American Head and Neck Society. Salivary gland tumors originate from different glandular cell types and are thus morphologically diverse. These tumors arise from any of the three major and various minor salivary glands. The incidence of SGCs has slowly increased during the last four decades. The etiology of SGCs is mostly unknown; however, specific gene mutations are associated with certain types of salivary tumors. Treatment options include surgical resection, radiation therapy (RT), chemotherapy, and multimodality therapy. HNC patients treated with RT often develop xerostomia and salivary hypofunction due to damaged salivary glands. In this review, we discuss etiology of SGCs, present findings on the role of autophagy in salivary tumorigenesis, review adverse effects of radiation treatment, and examine remedies for restoration of salivary function.

[Postoperative analgesia effect of different background volumes of ropivacaine in continuous tibial nerve block in patients with calcaneal surgery]

OBJECTIVE

To observe the clinical effect of different background volumes of ropivacaine in continuous tibial nerve block of postoperative analgesia after calcaneal surgery.

METHODS

This study was a prospective, randomized, controlled study. Sixty cases of calcaneal visual analogue scale (ASA) I or II undergoing elective surgery were selected and randomly assigned to two groups, thirty cases in each group. The patients received popliteal fossa posterior tibial nerve block using ultrasound guided. The continuous stimulation catheter was inserted after successful position and the 0.2% ropivacaine was injected. The background volumes of the A and B groups were 5 mL/h and 3.2 mL/h. The VAS score, the sensory block and motor block of tibial nerve and common peroneal nerve, and the satisfaction of the patients at h 12, h 24 and h 48 were recorded after catheter insertion.

RESULTS

The VAS scores at the three time points (h 12, h 24 and h 48) on the two groups of the patients were compared, and the difference was not statistically significant (P > 0.05). The difference of the sensory block and the motor block of the tibial nerve at the three time points (h 12, h 24 and h 48) on the two groups of the patients were also compared, and the difference was not statistically significant (P> 0.05). The difference of the sensory block and the motor block of common peroneal nerve at h 48 hs was statistically significant, group A was higher than the group B (P< 0.05). The difference of the patient satisfaction at the three time points (h 12, h 24 and h 48) on the two groups was not statistically significant (P> 0.05).

CONCLUSION

The use of 0.2% ropivacaine with the background volume of 3.2 mL/h in continuous tibial nerve block can provide good analgesia and reduce the incidence of the sensory block and motor block of the common peroneal nerve.

Palliative enteral feeding for patients with malignant esophageal obstruction: a retrospective study

BACKGROUND

Malignant esophageal obstruction leads to dysphagia, deterioration in quality of life, and malnutrition. Traditional bedside nasogastric (NG) tube placement is very difficult under these circumstances. However, endoscopically assisted NG tube placement under fluoroscopic guidance could be an alternative option for establishing palliative enteral nutrition. This study aimed to compare the clinical outcomes of enteral tube feeding and esophageal stenting for patients with malignant esophageal obstruction and a short life expectancy.

METHODS

Thirty-one patients were divided into 3 groups according to their treatment modality: NG tube (n = 12), esophageal stent group (n = 10), and supportive care with nil per os (NPO) (n = 9). Enteral nutrition, clinical outcomes, length of hospital stay, and median survival were evaluated.

RESULTS

There were no significant baseline differences among the groups, except in age. The tube and stent groups had significantly higher enteral calorie intake (p = 0.01), higher serum albumin (p < 0.01), shorter hospital stay (p = 0.01), and longer median survival (p < 0.01) than the NPO group. The incidence of dislodgement in the tube group was significantly higher than in the stent group (58% vs. 20%, respectively; p = 0.01). However, stenting costs more than NG tube placement.

CONCLUSIONS

Palliative enteral feeding by NG tube is safe, inexpensive, and has a low complication rate. Endoscopically assisted NG tube placement under fluoroscopic guidance could be a feasible palliative option for malignant esophageal obstruction for patients who have a short life expectancy.

The Role of Autophagy in Salivary Gland Homeostasis and Stress Responses

Autophagy is a catabolic process that has been shown to have a role in many cellular processes including the removal of excessive or damaged proteins and protein aggregates. The salivary glands play a critical role in oral health, and their secretory capacity may be critically intertwined with the autophagic process. This review describes the role of autophagy activation in normal salivary gland homeostasis and during the glandular stress responses of therapeutic radiation, ductal ligation, autoimmunity, and salivary gland adenoid cystic carcinoma.

Primary carcinoid tumor of the ovary arising in a mature cystic teratoma: a case report

Primary ovarian carcinoid tumors are rare entities, they may appear with other teratomatous components, and can be often being mistaken as part of mature cystic teratomas. Consistent with their rarity and low incidence, imaging clues that could have led to suspicion of this tumor are not well-documented. Herein, the authors present a rare case of primary ovarian carcinoid tumor in a mature cystic teratoma, who initially presented with complaints of abdominal distension for months. Contrast-enhanced computerized tomography (CT) demonstrated a multilobular mass with different density components including fat, soft tissue, and calcification materials, as well as rich vascular supply from the right ovarian vein. Serum tumor markers were within normal limits. Bilateral salpingo-oophorectomy was performed and the pathological diagnosis was mature cystic teratoma with coexisting primary ovarian carcinoid tumor, insular type. The patient has remained well with no residual disease for over one year of follow-up.

Improvements on a patient-specific dose estimation system in nuclear medicine examination

The purpose of this paper is to develop a patient-specific dose estimation system in nuclear medicine examination. A dose deposition routine to store the deposited energy of the photons during their flights was embedded in the widely used SimSET Monte Carlo code and a user-friendly interface for reading PET and CT images was developed. Dose calculated on ORNL phantom was used to validate the accuracy of this system. The ratios of S value for (99m)Tc, (18)F and (131)I computed by this system to those obtained with OLINDA for various organs were ranged from 0.93 to 1.18, which were comparable to that obtained from MCNPX2.6 code (0.88-1.22). Our system developed provides opportunity for tumor dose estimation which cannot be known from the MIRD. The radiation dose can provide useful information in the amount of radioisotopes to be administered in radioimmunotherapy.

Interferon-based therapy reduces risk of stroke in chronic hepatitis C patients: a population-based cohort study in Taiwan

BACKGROUND

Hepatitis C virus (HCV) infection has been linked to an increased risk of insulin resistance and carotid atherosclerosis.

AIM

To investigate the association between HCV infection and stroke, and the effect of interferon-based therapy (IBT) on stroke risk in chronic hepatitis C (CHC) patients.

METHODS

We conducted a retrospective cohort study that followed up 3113 subjects with a newly detected HCV infection and 12 452 age- and gender-matched subjects without HCV infection selected from a random sample of 10(6) beneficiaries from the Taiwan National Health Insurance Program up to 5 years. Use of IBT was defined as treatment with interferon alpha, pegylated interferon alpha-2a or pegylated interferon alpha-2b for at least 3 months. The hazard ratio (HR) for newly detected stroke was calculated for subjects with HCV compared to those without HCV, and for IBT-treated HCV patients compared to non-IBT-treated HCV patients while adjusting for possible confounding factors.

RESULTS

The overall person-years of follow-up were 8624.11 in patients with HCV, 54,533.69 in patients without HCV, 666.65 in IBT-treated patients, and 7886.49 in nontreated patients. The multivariable-adjusted hazard ratio (HR) for newly detected stroke was 1.23 for subjects with HCV compared to the age- and sex-matched subjects without HCV (adjusted HR = 1.23, 95% CI = 1.06-1.42, P = 0.008). Moreover, use of IBT significantly reduced the risk of stroke in HCV patients (adjusted HR = 0.39, 95% CI = 0.16-0.95, P = 0.039) after adjusting for known prognostic factors.

CONCLUSIONS

Interferon-based therapy may reduce the long-term risk of stroke in patients with chronic HCV infection.

Deletion of ATG5 shows a role of autophagy in salivary homeostatic control

Autophagy is a catabolic pathway utilized to maintain a balance among the synthesis, degradation, and recycling of cellular components, thereby playing a role in cell growth, development, and homeostasis. Previous studies revealed that a conditional knockout of essential member(s) of autophagy in a variety of tissues causes changes in structure and function of these tissues. Acinar cell-specific expression of knocked-in Cre recombinase through control of aquaporin 5 (Aqp5) promoter/enhancer (Aqp5-Cre) allows us to specifically inactivate Atg5, a protein necessary for autophagy, in salivary acinar cells of Atg5(f/f);Aqp5-Cre mice. There was no difference in apoptotic or proliferation levels in salivary glands of Atg5/Cre mice from each genotype. However, H&E staining and electron microscopy studies revealed modestly enlarged acinar cells and accumulated secretory granules in salivary glands of Atg5(f/f);Aqp5-Cre mice. Salivary flow rates and amylase contents of Atg5/Cre mice indicated that acinar-specific inactivation of ATG5 did not alter carbachol-evoked saliva and amylase secretion. Conversely, autophagy intersected with salivary morphological and secretory manifestations induced by isoproterenol administration. These results identified a role for autophagy as a homeostasis control in salivary glands. Collectively, Atg5(f/f);Aqp5-Cre mice would be a useful tool to enhance our understanding of autophagy in adaptive responses following targeted head and neck radiation or Sjögren syndrome.

An Internal Standard-Assisted Synthesis and Degradation Proteomic Approach Reveals the Potential Linkage between VPS4B Depletion and Activation of Fatty Acid β-Oxidation in Breast Cancer Cells

The endosomal/lysosomal system, in particular the endosomal sorting complexes required for transport (ESCRTs), plays an essential role in regulating the trafficking and destination of endocytosed receptors and their associated signaling molecules. Recently, we have shown that dysfunction and down-regulation of vacuolar protein sorting 4B (VPS4B), an ESCRT-III associated protein, under hypoxic conditions can lead to the abnormal accumulation of epidermal growth factor receptor (EGFR) and aberrant EGFR signaling in breast cancer. However, the pathophysiological consequences of VPS4B dysfunction remain largely elusive. In this study, we used an internal standard-assisted synthesis and degradation mass spectrometry (iSDMS) method, which permits the direct measurement of protein synthesis, degradation and protein dynamic expression, to address the effects of VPS4B dysfunction in altering EGF-mediated protein expression. Our initial results indicate that VPS4B down-regulation decreases the expression of many proteins involved in glycolytic pathways, while increased the expression of proteins with roles in mitochondrial fatty acid β-oxidation were up-regulated in VPS4B-depleted cells. This observation is also consistent with our previous finding that hypoxia can induce VPS4B down-regulated, suggesting that the adoption of fatty acid β-oxidation could potentially serve as an alternative energy source and survival mechanism for breast cancer cells in response to hypoxia-mediated VPS4B dysfunction.

Role of monokine induced by interferon-γ in liver injury induced by hepatitis B virus in mice

The chemokine monokine induced by interferon-γ (Mig) is involved in the recruitment of inflammatory cells and liver injury during hepatitis B virus (HBV) infection. HBV protein X contributes to Mig expression in vitro by activation of nuclear factor (NF)-κB; however, the molecular mechanisms by which HBV induces Mig expression in vivo are unknown. In this paper, we established a mouse model for HBV study by tail vein injection of HBV genome-containing adenovirus vectors. Host immune response to the secreted hepatitis B surface antigen and e antigen was detected and serum alanine aminotransferase (ALT) was elevated at different time points. We also demonstrated that peripheral and intrahepatic Mig expression was increased after Ad-HBV infection. This was followed by inflammatory cell migration and formation of inflammatory foci in the liver. In addition, NF-κB p65 subunit translocated from the cytoplasm to the nucleus, and phosphoinositide 3-kinase/Akt, extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) were to some extent phosphorylated after HBV injection. Following tail vein injection of Mig siRNA/in vivo-jetPEI-Gal complex, Mig expression was partially suppressed, inflammatory cell migration was inhibited, serum level of ALT were reduced. In conclusion, through NF-κB activation, HBV induced Mig expression in vivo, which recruited peripheral inflammatory cells to the liver and resulted in liver damage. Phosphorylation of phosphoinositide 3-kinase/Akt, ERK and JNK but not p38 might involved in the molecular mechanisms underlying HBV induced Mig expression in vivo.

Increasing insulin resistance is associated with increased severity and prevalence of gastro-oesophageal reflux disease

BACKGROUND

The diagnosis of gastro-oesophageal reflux disease (GERD) is based on reflux symptoms. Although metabolic syndrome has been linked to erosive oesophagitis (EO), the impact of insulin resistance, the core of the metabolic syndrome, on reflux symptoms remains to be elucidated.

AIM

To assess the effects of insulin resistance on GERD, including both endoscopic findings and symptoms.

METHODS

A total of 743 sonographic noncirrhotic adult subjects, who underwent an upper gastrointestinal endoscopic examination, completed a gastro-oesophageal reflux questionnaire and had available fasting insulin data were included. Endoscopic findings were classified according to the Los Angeles classification. Homeostatic model assessment-insulin resistance (HOMA-IR) index was used to evaluate the status of insulin resistance. Univariate and multivariate approaches were used to evaluate the associations between insulin resistance and GERD.

RESULTS

Older age, male gender, smoking and alcohol consumption increased the prevalence of EO, but not GERD symptoms. A large waist circumference, high fasting blood glucose levels and high number of metabolic syndrome components were associated with increased prevalence of both EO and GERD symptoms, while high blood pressure was associated with increased prevalence of EO only. Moreover, higher scores in the gastro-oesophageal reflux questionnaire were associated with higher HOMA-IR index, and higher HOMA-IR index was associated with increased prevalence of EO (adjusted odds ratio 1.14, 95% CI 1.03-1.26, P = 0.012).

CONCLUSIONS

Our findings demonstrate clear associations between insulin resistance, metabolic syndrome and GERD. Whether reducing insulin resistance may improve GERD symptoms or EO deserves prospective study.

Inserting the tunneller during an outside-in transobturator tape procedure by syringe-needle guidance

The objective of this study was to determine the feasibility of a novel syringe-needle guidance technique (SNG), and its impact on the perioperative variables and outcomes of patients undergoing an outside-in transobturator tape procedure (TOT). Between November 2006 and May 2008, 48 consecutive women who underwent TOT with SNG were included. Another 25 women without SNG between March 2004 and October 2006 were included as a historical control. There were no significant differences in hospital stays and complication rates between the two groups. However, the operating time was shorter (mean 23.0 vs 28.3 min, p=0.008) in the SNG group than in the control group. The presence of the SNG technique was the sole predictor of the operating time (p=0.003). In conclusion, the SNG technique is a feasible method to provide help in inserting the tunneller of TOT through the transobturator foramen, and did not compromise the outcome.

SUMOylation of the transcriptional co-repressor KAP1 is regulated by the serine and threonine phosphatase PP1

Krüppel-associated box (KRAB) domain-associated protein 1 [KAP1, also known as transcription intermediary factor-1beta (TIF1beta)] is a ubiquitous transcriptional co-repressor that is susceptible to phosphorylation at Ser(824) by ataxia-telangiectasia mutated (ATM) and to modification by small ubiquitin-like modifying (SUMO) proteins. Here, we found that, whereas the protein phosphatase 1alpha isoform (PP1alpha) directly interacted with KAP1 under basal conditions, PP1beta interacted with KAP1 only in response to genotoxic stress. Changes in the abundance of PP1alpha or PP1beta had differential effects on the phosphorylation and SUMOylation states of KAP1 under basal conditions and in response to DNA double-strand breaks (DSBs). Chromatin immunoprecipitation and re-immunoprecipitation experiments revealed that PP1alpha and PP1beta were recruited to KAP1 with different kinetics before and after the induction of DNA DSBs, which provided a mechanistic basis for the switch in the phosphorylation and SUMOylation states of KAP1. PP1beta-dependent SUMOylation of KAP1 occurred by mechanisms that were dependent and independent of the phosphorylation status of Ser(824). We posit a mechanism whereby the combined actions of PP1alpha and PP1beta cause dephosphorylation of KAP1 at Ser(824) and assure its SUMOylation to counter the effect of ATM, thereby regulating the transcription of KAP1 target genes in unstressed and stressed cells.

Suppression of nonhomologous end joining repair by overexpression of HMGA2

Understanding the molecular details associated with aberrant high mobility group A2 (HMGA2) gene expression is key to establishing the mechanism(s) underlying its oncogenic potential and effect on the development of therapeutic strategies. Here, we report the involvement of HMGA2 in impairing DNA-dependent protein kinase (DNA-PK) during the nonhomologous end joining (NHEJ) process. We showed that HMGA2-expressing cells displayed deficiency in overall and precise DNA end-joining repair and accumulated more endogenous DNA damage. Proper and timely activation of DNA-PK, consisting of Ku70, Ku80, and DNA-PKcs subunits, is essential for the repair of DNA double strand breaks (DSB) generated endogenously or by exposure to genotoxins. In cells overexpressing HMGA2, accumulation of histone 2A variant X phosphorylation at Ser-139 (gamma-H2AX) was associated with hyperphosphorylation of DNA-PKcs at Thr-2609 and Ser-2056 before and after the induction of DSBs. Also, the steady-state complex of Ku and DNA ends was altered by HMGA2. Microirradiation and real-time imaging in living cells revealed that HMGA2 delayed the release of DNA-PKcs from DSB sites, similar to observations found in DNA-PKcs mutants. Moreover, HMGA2 alone was sufficient to induce chromosomal aberrations, a hallmark of deficiency in NHEJ-mediated DNA repair. In summary, a novel role for HMGA2 to interfere with NHEJ processes was uncovered, implicating HMGA2 in the promotion of genome instability and tumorigenesis.

Risk factors for extra-pulmonary tuberculosis compared to pulmonary tuberculosis

BACKGROUND

Tuberculosis (TB) continues to be a major global health problem. Extra-pulmonary TB (EPTB) manifests with protean symptoms, and establishing a diagnosis is more difficult than pulmonary TB (PTB).

SETTING

A university-affiliated hospital in southern Taiwan.

OBJECTIVE

To analyse the risk factors for EPTB compared with PTB.

DESIGN

This retrospective study compared patients with EPTB and PTB in southern Taiwan by analysing their demographic data and clinical underlying diseases. Risk factors for EPTB were further analysed.

RESULTS

A total of 766 TB patients were enrolled in this study, with 102 (13.3%) EPTB and 664 (86.7%) PTB cases. Of the 766 patients, 3% of PTB patients had EPTB, while 19.6% of EPTB patients also had PTB. The most frequently involved EPTB site was the bone and joints (24.5%). The incidence of EPTB vs. PTB decreased significantly for each decade increase in patient age. Multivariate logistic regression analysis showed that being female, not being diabetic, having end-stage renal disease and not smoking were independent risk factors for EPTB.

CONCLUSION

This study defines the risk factors for EPTB compared with PTB. Awareness of these factors is essential for physicians to have a high index of suspicion for accurate and timely diagnosis.

PKC delta signaling: a dual role in regulating hypoxic stress-induced autophagy and apoptosis

The protein kinase C (PKC) family of serine/threonine kinases regulates diverse cellular function, including cell death, proliferation and survival. In particular, PKC delta governs the cellular homeostatic response against hypoxic stress. Autophagy, a lysosome-dependent degradative pathway, and apoptosis are two fundamental cellular pathways that respond to stress conditions, such as hypoxia, oxidative stress and nutrient starvation. Recently, we uncovered a novel role for PKC delta in the early stage of hypoxic response where PKC delta activates autophagy by promoting JNK1-mediated Bcl-2 phosphorylation and dissociation of the Bcl-2/Beclin 1 complex. Whereas acute hypoxic stress promotes autophagy, we have previously reported that prolonged hypoxic stress caused the cleavage of PKC delta by caspase-3, resulting in the nuclear translocation of a constitutively active catalytic fragment of PKC delta, PKC delta-CF. Moreover, PKC delta-CF also serves a feed-forward function for the reciprocal PKC delta and caspase-3 proteolytic activation. Here, we discussed the requirement for PKC delta and JNK1 for hypoxia-induced autophagy, and the kinetic relationship among Bcl-2/Beclin 1 interaction, caspase-3 activation and the steady-state level of Beclin 1 during hypoxic exposure. Based on these results, we propose a model for understanding the PKC delta-dependent crosstalk mechanisms between autophagy and apoptosis, both induced by hypoxic stress. These findings collectively support a pivotal role for PKC delta in regulating hypoxic stress with hitherto unappreciated significance.

SUMOylation of HMGA2: selective destabilization of promyelocytic leukemia protein via proteasome

The HMGA2 architectural protein functions in a variety of cellular processes, such as cell growth, transcription regulation, neoplastic transformation, and progression. Up-regulation of HMGA2 protein is observed in many tumors and is associated with advanced cancers with poor prognoses. Although the expression and biochemical properties of HMGA2 protein are regulated by microRNA and phosphorylation, it is unknown whether HMGA2 activity can also be regulated by SUMOylation, and that is what is investigated in this report. We identified HMGA2 as a SUMOylation target and showed that the expression of wild-type HMGA2, but not SUMOylation-defective HMGA2(2K/R), selectively lowered the steady-state level of PML protein. Consequently, the HMGA2-elicited PML down-regulation rendered a reduction in the average number of PML nuclear bodies per cell and the volume of PML assembled per PML nuclear body. Using small interfering RNA to suppress endogenous ubiquitin expression and proteasome inhibitor to repress ubiquitin-mediated protein degradation, we showed that HMGA2 confers PML down-regulation through ubiquitin-proteasome-dependent protein degradation. Importantly, arsenic trioxide treatment stimulated HMGA2 SUMOylation, leading to the formation of HMGA2 nuclear foci surrounding PML nuclear bodies and the stimulation of PML degradation. Collectively, our results unveil a previously unrecognized effect by HMGA2 on the modulation of PML protein level, providing a novel mechanism underlying HMGA2 function and underscoring the molecular basis for oncogenic progression by HMGA2.

Prediction of antibiotic resistance proteins from sequence-derived properties irrespective of sequence similarity

Increasing antibiotic resistance has become a worldwide challenge to the clinical treatment of infectious diseases. The identification of antibiotic resistance proteins (ARPs) would be helpful in the discovery of new therapeutic targets and the design of novel drugs to control the potential spread of antibiotic resistance. In this work, a support vector machine (SVM)-based ARP prediction system was developed using 1308 ARPs and 15587 non-ARPs. Its performance was evaluated using 313 ARPs and 7156 non-ARPs. The computed prediction accuracy was 88.5% for ARPs and 99.2% for non-ARPs. A potential application of this method is the identification of ARPs non-homologous to proteins of known function. Further genome screening found that ca. 3.5% and 3.2% of proteins in Escherichia coli and Staphylococcus aureus, respectively, are potential ARPs. These results suggest the usefulness of SVMs for facilitating the identification of ARPs. The software can be accessed at SARPI (Server for Antibiotic Resistance Protein Identification).

Homology-free prediction of functional class of proteins and peptides by support vector machines

Protein and peptide sequences contain clues for functional prediction. A challenge is to predict sequences that show low or no homology to proteins or peptides of known function. A machine learning method, support vector machines (SVM), has recently been explored for predicting functional class of proteins and peptides from sequence-derived properties irrespective of sequence similarity, which has shown impressive performance for predicting a wide range of protein and peptide classes including certain low- and non- homologous sequences. This method serves as a new and valuable addition to complement the extensively-used alignment-based, clustering-based, and structure-based functional prediction methods. This article evaluates the strategies, current progresses, reported prediction performances, available software tools, and underlying difficulties in using SVM for predicting the functional class of proteins and peptides.

A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor

Support vector machines (SVM) and other machine-learning (ML) methods have been explored as ligand-based virtual screening (VS) tools for facilitating lead discovery. While exhibiting good hit selection performance, in screening large compound libraries, these methods tend to produce lower hit-rate than those of the best performing VS tools, partly because their training-sets contain limited spectrum of inactive compounds. We tested whether the performance of SVM can be improved by using training-sets of diverse inactive compounds. In retrospective database screening of active compounds of single mechanism (HIV protease inhibitors, DHFR inhibitors, dopamine antagonists) and multiple mechanisms (CNS active agents) from large libraries of 2.986 million compounds, the yields, hit-rates, and enrichment factors of our SVM models are 52.4-78.0%, 4.7-73.8%, and 214-10,543, respectively, compared to those of 62-95%, 0.65-35%, and 20-1200 by structure-based VS and 55-81%, 0.2-0.7%, and 110-795 by other ligand-based VS tools in screening libraries of >or=1 million compounds. The hit-rates are comparable and the enrichment factors are substantially better than the best results of other VS tools. 24.3-87.6% of the predicted hits are outside the known hit families. SVM appears to be potentially useful for facilitating lead discovery in VS of large compound libraries.

Machine learning approaches for predicting compounds that interact with therapeutic and ADMET related proteins

Computational methods for predicting compounds of specific pharmacodynamic and ADMET (absorption, distribution, metabolism, excretion and toxicity) property are useful for facilitating drug discovery and evaluation. Recently, machine learning methods such as neural networks and support vector machines have been explored for predicting inhibitors, antagonists, blockers, agonists, activators and substrates of proteins related to specific therapeutic and ADMET property. These methods are particularly useful for compounds of diverse structures to complement QSAR methods, and for cases of unavailable receptor 3D structure to complement structure-based methods. A number of studies have demonstrated the potential of these methods for predicting such compounds as substrates of P-glycoprotein and cytochrome P450 CYP isoenzymes, inhibitors of protein kinases and CYP isoenzymes, and agonists of serotonin receptor and estrogen receptor. This article is intended to review the strategies, current progresses and underlying difficulties in using machine learning methods for predicting these protein binders and as potential virtual screening tools. Algorithms for proper representation of the structural and physicochemical properties of compounds are also evaluated.

Prediction of factor Xa inhibitors by machine learning methods

Factor Xa (FXa) inhibitors have been explored as anticoagulants for treatment and prevention of thrombotic diseases. Molecular docking, pharmacophore, quantitative structure-activity relationships, and support vector machines (SVM) have been used for computer prediction of FXa inhibitors. These methods achieve promising prediction accuracies of 69-80% for FXa inhibitors and 85-99% for non-inhibitors. Prediction performance, particularly for inhibitors, may be further improved by exploring methods applicable to more diverse range of compounds and by using more appropriate set of molecular descriptors. We tested the capability of several machine learning methods (C4.5 decision tree, k-nearest neighbor, probabilistic neural network, and support vector machine) by using a much more diverse set of 1098 compounds (360 inhibitors and 738 non-inhibitors) than those in other studies. A feature selection method was used for selecting molecular descriptors appropriate for distinguishing FXa inhibitors and non-inhibitors. The prediction accuracies of these methods are 89.1-97.5% for FXa inhibitors and 92.3-98.1% for non-inhibitors. In particular, compared to other studies, support vector machine gives a substantially improved accuracy of 94.6% for FXa non-inhibitors and maintains a comparable accuracy of 98.1% for inhibitors, based-on a more rigorous test with more diverse range of compounds. Our study suggests that machine learning methods such as SVM are useful for facilitating the prediction of FXa inhibitors.

The effect of activation treatments on the development of reconstructed bovine oocytes

The purpose of this study was to investigate the effect of different activation treatments on the development of IVM-derived and cloned bovine embryos. The effect of oocyte age (20h versus 24h after IVM) on the blastocyst rate was also investigated. No differences in the percentage of blastocyst development were observed between the oocytes matured for 20 and 24h (15% versus 27%, p>0.05). Reconstructed oocytes activated 4h after fusion (fusion before activation, FBA) had a higher blastocyst rate than those oocytes activated immediately after electrofusion (fusion and activation simultaneously, FAS) (26% versus 5%, p<0.01). Blastocyst rates were significantly greater (p<0.01) for the reconstructed oocytes activated by calcium ionophore (A23187) combined with 6-dimethylaminopurine (6-DMAP) (51.6%) than for those activated with cycloheximide (CHX) plus cytochalasin B (CB) treatment (1h, 8.2%; 5h, 14.3%). However, the blastocyst rates were similar among reconstructed oocytes activated by electric pulses and A23187 (30.5% versus 42.2%) or by A23187 and ionomycin (36.7% versus 33.3%) combined with 6-DMAP, respectively. Blastocysts that developed from reconstructed oocytes activated by A23187 and 6-DMAP resulted in three pregnancies (3/9) and one live birth from 18 embryos transferred to recipient cows. Genotypic analysis of six bovine microsatellite markers by polymerase chain reaction confirmed that the cloned calf was genetically identical to the nuclear donor. In conclusion, reconstructed oocytes that derived from oocytes exposed to activation treatment 4h after electrofusion are more likely to develop to the blastocyst stage. The best treatment to activate reconstructed bovine oocytes in this study was A23187 combined with 6-DMAP.

Transcriptional regulation by targeted expression of architectural transcription factor high mobility group A2 in salivary glands of transgenic mice

High mobility group A2 (HMGA2) protein is a non-histone architectural transcription factor. Numerous studies have demonstrated that HMGA2 is exclusively expressed in the nucleus of embryonic, but not of terminally differentiated, cells, and aberrant expression of HMGA2 is associated with various benign tumors, including pleomorphic salivary adenoma. Herein, we report the use of a 4.5-kb enhancer/promoter region of the aquaporin-5 (AQP-5) gene to target HMGA2 transgene expression in the mouse salivary acinar cells as a model to investigate the biochemical and biological role of ectopic HMGA2 expression. The expression pattern was analyzed by microarray analyses to profile HMGA2-dependent salivary gene regulation. By using quantitative reverse transcription-polymerase chain reaction (RT-PCR) assays, the expression of a cluster of genes involved in cytokine signaling, including Il7r, Il2rg, and Ptprc, was verified to be up-regulated in the salivary glands of AQP-5/HMGA2 mice. In concert, the expression of a cluster of genes, namely Ppara, Phyh, and Cidea, governing fatty acid and lipid metabolism, was confirmed to be down-regulated by HMGA2. Additionally, squamous carcinoma-like salivary tumors were observed in the AQP-5/HMGA2 transgenic mice, albeit at a low incidence. Our findings indicate that the AQP-5 promoter/enhancer-containing region is sufficient to target salivary-specific transgene expression and suggest novel roles for HMGA2 in salivary epithelial cells.

Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach

Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting metal-binding proteins irrespective of sequence similarity. This work explores support vector machines (SVM) as such a method. SVM prediction systems were developed by using 53,333 metal-binding and 147,347 non-metal-binding proteins, and evaluated by an independent set of 31,448 metal-binding and 79,051 non-metal-binding proteins. The computed prediction accuracy is 86.3%, 81.6%, 83.5%, 94.0%, 81.2%, 85.4%, 77.6%, 90.4%, 90.9%, 74.9% and 78.1% for calcium-binding, cobalt-binding, copper-binding, iron-binding, magnesium-binding, manganese-binding, nickel-binding, potassium-binding, sodium-binding, zinc-binding, and all metal-binding proteins respectively. The accuracy for the non-member proteins of each class is 88.2%, 99.9%, 98.1%, 91.4%, 87.9%, 94.5%, 99.2%, 99.9%, 99.9%, 98.0%, and 88.0% respectively. Comparable accuracies were obtained by using a different SVM kernel function. Our method predicts 67% of the 87 metal-binding proteins non-homologous to any protein in the Swissprot database and 85.3% of the 333 proteins of known metal-binding domains as metal-binding. These suggest the usefulness of SVM for facilitating the prediction of metal-binding proteins. Our software can be accessed at the SVMProt server http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi.

Modulation spectroscopy study of the effects of growth interruptions on the interfaces of GaAsSb/GaAs multiple quantum wells

The effects of growth interruption times combined with Sb exposure of GaAsSb/GaAs multiple quantum wells (MQWs) have been investigated by using phototransmittance (PT), contactless electroreflectance (CER) and wavelength modulated surface photovoltage spectroscopy (WMSPS). The features originated from different portions of the samples, including interband transitions of MQWs, interfaces and GaAs, are observed and identified through a detailed comparison of the obtained spectra and theoretical calculation. A red-shift of the interband transitions and a broader lineshape of the fundamental transition are observed from samples grown under Sb exposure compared to the reference sample grown without interruption. The results can be interpreted in terms of both increases in Sb content and mixing of Sb in the GaAs interface layers. An additional feature has been observed below the GaAs region in the samples with Sb treatment. The probable origin of this additional feature is discussed.

Prediction of MHC-binding peptides of flexible lengths from sequence-derived structural and physicochemical properties

Peptide binding to MHC is critical for antigen recognition by T-cells. To facilitate vaccine design, computational methods have been developed for predicting MHC-binding peptides, which achieve impressive prediction accuracies of 70-90% for binders and 40-80% for non-binders. These methods have been developed for peptides of fixed lengths, for a limited number of alleles, trained from small number of non-binders, and in some cases based straightforwardly on sequence. These limit prediction coverage and accuracy particularly for non-binders. It is desirable to explore methods that predict binders of flexible lengths from sequence-derived physicochemical properties and trained from diverse sets of non-binders. This work explores support vector machines (SVM) as such a method for developing prediction systems of 18 MHC class I and 12 class II alleles by using 4208-3252 binders and 234,333-168,793 non-binders, and evaluated by an independent set of 545-476 binders and 110,564-84,430 non-binders. Binder accuracies are 86-99% for 25 and 70-80% for 5 alleles, non-binder accuracies are 96-99% for 30 alleles. Binder accuracies are comparable and non-binder accuracies substantially improved against other results. Our method correctly predicts 73.3% of the 15 newly-published epitopes in the last 4 months of 2005. Of the 251 recently-published HLA-A*0201 non-epitopes predicted as binders by other methods, 63 are predicted as binders by our method. Screening of HIV-1 genome shows that, compared to other methods, a comparable percentage (75-100%) of its known epitopes is correctly predicted, while a lower percentage (0.01-5% for 24 and 5-8% for 6 alleles) of its constituent peptides are predicted as binders. Our software can be accessed at .

The effect of electrical field strength on activation and development of cloned caprine embryos

The activation procedure used in nuclear transfer (NT) is one of the critical factors affecting the efficiency of animal cloning. The purpose of this study was to compare the effect of two electrical field strengths (EFS) for activation on the developmental competence of caprine NT embryos reconstructed from ear skin fibroblasts of adult Alpine does. The NT embryos were obtained by transfer of the quiescent fibroblasts at the fourth passage into the enucleated metaphase II (M II) oocytes. Four to five hours after electrical fusion, the NT-embryos were activated by EFS either at 1.67 or at 2.33 kV/cm and immediately incubated in 6-DMAP (2 mM) for 4 h. The cleavage rate of the NT-embryos activated with 2.33 kV/cm was greater than that activated with 1.67 kV/cm after in vitro culture for 18 h (65.6% versus 19.6%, p < 0.001). No pregnancy was found in 14 recipient does after transferring 51 NT embryos at 1-2 cell stages activated with 1.67 kV/cm. In contrast, two of the seven recipients were pregnant and gave birth to three kids after transferring 61 NT embryos at 1-2 cell stages activated by 2.33 kV/cm. The birth weights of three cloned kids were within the normal range of Alpine goats. However, one kid died 1h after birth while the remaining two are still healthy. DNA analysis by polymerase chain reaction (single-strand conformation polymorphism, SSCP) confirmed that the three kids were genetically identical to the nuclear donor.

Prediction of the functional class of lipid binding proteins from sequence-derived properties irrespective of sequence similarity

Lipid binding proteins play important roles in signaling, regulation, membrane trafficking, immune response, lipid metabolism, and transport. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting lipid binding proteins irrespective of sequence similarity. This work explores the use of support vector machines (SVMs) as such a method. SVM prediction systems are developed using 14,776 lipid binding and 133,441 nonlipid binding proteins and are evaluated by an independent set of 6,768 lipid binding and 64,761 nonlipid binding proteins. The computed prediction accuracy is 78.9, 79.5, 82.2, 79.5, 84.4, 76.6, 90.6, 79.0, and 89.9% for lipid degradation, lipid metabolism, lipid synthesis, lipid transport, lipid binding, lipopolysaccharide biosynthesis, lipoprotein, lipoyl, and all lipid binding proteins, respectively. The accuracy for the nonmember proteins of each class is 99.9, 99.2, 99.6, 99.8, 99.9, 99.8, 98.5, 99.9, and 97.0%, respectively. Comparable accuracies are obtained when homologous proteins are considered as one, or by using a different SVM kernel function. Our method predicts 86.8% of the 76 lipid binding proteins nonhomologous to any protein in the Swiss-Prot database and 89.0% of the 73 known lipid binding domains as lipid binding. These findings suggest the usefulness of SVMs for facilitating the prediction of lipid binding proteins. Our software can be accessed at the SVMProt server (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi).

PEARLS: Program for Energetic Analysis of Receptor−Ligand System

Analysis of the energetics of small molecule ligand-protein, ligand-nucleic acid, and protein-nucleic acid interactions facilitates the quantitative understanding of molecular interactions that regulate the function and conformation of proteins. It has also been extensively used for ranking potential new ligands in virtual drug screening. We developed a Web-based software, PEARLS (Program for Energetic Analysis of Ligand-Receptor Systems), for computing interaction energies of ligand-protein, ligand-nucleic acid, protein-nucleic acid, and ligand-protein-nucleic acid complexes from their 3D structures. AMBER molecular force field, Morse potential, and empirical energy functions are used to compute the van der Waals, electrostatic, hydrogen bond, metal-ligand bonding, and water-mediated hydrogen bond energies between the binding molecules. The change in the solvation free energy of molecular binding is estimated by using an empirical solvation free energy model. Contribution from ligand conformational entropy change is also estimated by a simple model. The computed free energy for a number of PDB ligand-receptor complexes were studied and compared to experimental binding affinity. A substantial degree of correlation between the computed free energy and experimental binding affinity was found, which suggests that PEARLS may be useful in facilitating energetic analysis of ligand-protein, ligand-nucleic acid, and protein-nucleic acid interactions. PEARLS can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/rune.pl.

Prediction of transporter family from protein sequence by support vector machine approach

Transporters play key roles in cellular transport and metabolic processes, and in facilitating drug delivery and excretion. These proteins are classified into families based on the transporter classification (TC) system. Determination of the TC family of transporters facilitates the study of their cellular and pharmacological functions. Methods for predicting TC family without sequence alignments or clustering are particularly useful for studying novel transporters whose function cannot be determined by sequence similarity. This work explores the use of a machine learning method, support vector machines (SVMs), for predicting the family of transporters from their sequence without the use of sequence similarity. A total of 10,636 transporters in 13 TC subclasses, 1914 transporters in eight TC families, and 168,341 nontransporter proteins are used to train and test the SVM prediction system. Testing results by using a separate set of 4351 transporters and 83,151 nontransporter proteins show that the overall accuracy for predicting members of these TC subclasses and families is 83.4% and 88.0%, respectively, and that of nonmembers is 99.3% and 96.6%, respectively. The accuracies for predicting members and nonmembers of individual TC subclasses are in the range of 70.7-96.1% and 97.6-99.9%, respectively, and those of individual TC families are in the range of 60.6-97.1% and 91.5-99.4%, respectively. A further test by using 26,139 transmembrane proteins outside each of the 13 TC subclasses shows that 90.4-99.6% of these are correctly predicted. Our study suggests that the SVM is potentially useful for facilitating functional study of transporters irrespective of sequence similarity.

High mobility group A2 potentiates genotoxic stress in part through the modulation of basal and DNA damage-dependent phosphatidylinositol 3-kinase-related protein kinase activation

The high mobility group A2 (HMGA2) protein belongs to the architectural transcription factor HMGA family, playing a role in chromosomal organization and transcriptional regulation. We and others have previously reported that ectopic HMGA2 expression is associated with neoplastic transformation and anchorage-independent cell proliferation. Here, we reported a correlation between increased HMGA2 expression and enhanced chemosensitivity towards topoisomerase II inhibitor, doxorubicin, in breast cancer cells. Using cells exhibiting differential HMGA2 expression and small interfering RNA technique, we showed that HMGA2 expression modulates cellular response to the genotoxicity of DNA double-strand breaks. Notably, HMGA2 enhances doxorubicin-elicited cell cycle delay in sub-G1 and G2-M and augments cell cycle dysregulation on cotreatment of doxorubicin and caffeine. We further reported that HMGA2 induces a persistent Ser139 phosphorylation of histone 2A variant X, analogous to the activation by doxorubicin-mediated genotoxic stress. Moreover, this HMGA2-dependent enhancement of cytotoxicity is further extended to other double-strand breaks elicited by cisplatin and X-ray irradiation and is not restricted to one cell type. Together, we postulated that the enhanced cytotoxicity by double-strand breaks in HMGA2-expressing cells is mediated, at least in part, through the signaling pathway of which the physiologic function is to maintain genome integrity. These findings should contribute to a greater understanding of the role of HMGA2 in promoting tumorigenesis and conveying (chemo)sensitivity towards doxorubicin and other related double-strand breaks.

Prediction of functional class of novel plant proteins by a statistical learning method

In plant genomes, the function of a substantial percentage of the putative protein-coding open reading frames (ORFs) is unknown. These ORFs have no significant sequence similarity to known proteins, which complicates the task of functional study of these proteins. Efforts are being made to explore methods that are complementary to, or may be used in combination with, sequence alignment and clustering methods. A web-based protein functional class prediction software, SVMProt, has shown some capability for predicting functional class of distantly related proteins. Here the usefulness of SVMProt for functional study of novel plant proteins is evaluated. To test SVMProt, 49 plant proteins (without a sequence homolog in the Swiss-Prot protein database, not in the SVMProt training set, and with functional indications provided in the literature) were selected from a comprehensive search of MEDLINE abstracts and Swiss-Prot databases in 1999-2004. These represent unique proteins the function of which, at present, cannot be confidently predicted by sequence alignment and clustering methods. The predicted functional class of 31 proteins was consistent, and that of four other proteins was weakly consistent, with published functions. Overall, the functional class of 71.4% of these proteins was consistent, or weakly consistent, with functional indications described in the literature. SVMProt shows a certain level of ability to provide useful hints about the functions of novel plant proteins with no similarity to known proteins.