With the rapid development of genome sequencing technologies, a large amount of prokaryote genomes have been sequenced in recent years. To further investigate the models and functions of genomes, the algorithms for genome annotations based on the sequence and homology features have been widely implemented to newly sequenced genomes. However, gene annotations only using the genomic information are prone to errors, such as the incorrect N-terminals and pseudogenes. It is even harder to provide reasonable annotating results in the case of the poor genome sequencing results. The transcriptomics based on the technologies such as microarray and RNA-seq and the proteomics based on the MS/MS have been used widely to identify the gene products with high throughput and high sensitivity, providing the powerful tools for the verification and correction of annotated genome. Compared with transcriptomics, proteomics can generate the protein list for the expressed genes in the samples or cells without any confusion of the non-coding RNA, leading the proteogenomics an important basis for the genome annotations in prokaryotes. In this paper, we first described the traditional genome annotation algorithms and pointed out the shortcomings. Then we summarized the advantages of proteomics in the genome annotations and reviewed the progress of proteogenomics in prokaryotes. Finally we discussed the challenges and strategies in the data analyses and potential solutions for the developments of proteogenomics.
Genomics ; Molecular Sequence Annotation ; Prokaryotic Cells ; metabolism ; Proteomics ; Tandem Mass Spectrometry

Objective To investigate the role of serotonin transporter (SERT) in pathogenesis of abdominal pain in irritable bowel syndrome (IBS). Methods Neonatal SD rats were divided into control group and IBS abdominal pain model group which was established by colorectal distension.The colon, nucleus raphes dorsalis (NRD) and prefrontal cortex (FC) tissues were harvested when all rats grew into adults. Expressions of SERT and 5-HT were determined by real-time PCR and immunohistochemistry. Results The expression of SERT mRNA in colon, NRD and FC tissues in model and control group were 13.95±2.05 vs 8.65±1.33, 52.69±22.59 vs 13.82±5.71 and0.48±0.17 vs 0.17±0.14, respectively, with significant differences (all P values ＜0.05). The protein expression of SERT in colon and NRD,but not FC tissues,decreased in model group compared with control group (13.19±3.82 vs 21.35±4.49,2.47±0.44 vs 4.55±0.92, respectively, P＜0.05).Meanwhile, in comparison with control group, the expression of 5-HT in colon was significantly increased in model group (5.56±0.48 vs 2.68±0.22), but decreased in NRD and FC tissues (3.75±0.43 vs 7.46±0.72, 5.07 ± 0.80 vs 7.97 ±1.10, respectively, P＜0.05). Conclusions Low expression of SERT in brain and colon may attribute to the pathogenesis of abdominal pain in IBS.

Objective To study the clinical features of invasive pulmonary aspergillosis (IPA) with chronic obstructive pulmonary diseases (COPD),so as to provide evidence for early diagnosis and treatment.Methods A retrospective analysis was made upon clinical data,diagnosis,treatment and prognosis of 53 patients with IPA and COPD admitted between January 2005 and February 2011 collected in a respiratory unit of the Second Xiangya Hospital Affiliated Central South University.Results There were 53 cases of diagnosed as IPA with COPD,with history of using broad-spectrum antibiotics.And there were 43 cases using steroids more than 2 weeks,51 with obvious breathlessness,and 20 with fever.Early stage didn't present characteristical changes on CT scan.However,after disease progression,32 cases had maculas shadows and nonspecific consolidations in bilateral lung,14 with solitary or multiple nodules,4 with solitary or multiple air crescent sign,and 2 with halo sign.Four patients of COPD with IPA underwent bronchoscopy examination.In fungi pathogeny,sputum positive rate and galactomannan positive rate were 56.6％ and 52.8％,respectively.A total of 53 cases received antifungal treatment.Among 37 cases which underwent mechanical ventilation,24 received noninvasive ventilation and 13 received invasive ventilation.There were 33 cases which were improved and cured,and 20 cases which had no relief after half-a-month treatment or withdrew treatment.Among them,13 cases died because of multiple-organ failure (5/15) or acute renal failure (8/15).Conclusions Early suspected diagnosis,timely examination in allusion to IPA,actively searching for etiological and imaging evidences,early established diagnosis and antifungal treatment would improve prognosis of patients with COPD combined IPA who have history of high doses of cortieosteroids,obvious breathlessness and non-response to antibiotics.

Objective: This present study is to investigate the biochemical adaptations in the related brain regions of the mesolimbic dopamine system, such as the ventral tegrnental area (VTA), nucleus accumbens (Nac), amygdale (Amy), prefrontal cortex (PFC) , substantia nigra (SN) and caudateputamen (Cpu) in response to heroin self-administration in rats and observe the effect of electroacupuncture on them. Methods: 2hirty rats were trained by nose-poking response to establish stable intravenous heroin self-administration within 14 days, and then divided randomly into model group (group B) including 6 rats, withdrawal group which were withdrawn from heroin for 1 week (group C, n = 6) and for 2 weeks (group D, n= 6), during which time they only lived in their individual home cages,and electro-acupuncture group which were also withdrawn from heroin for 1 week (group E, n= 6) and for 2 weeks (group F, n= 6), during which time they were given electro-acupuncture treatment for 20 min daily and then returned to their individual home cages; in the meantime, another 6 rats were trained by nose-poking response with saline for 14 days as control (group A); Then the levels of tyrosine hydroxylase (TH) and glial fibrillary acidic protein (GFAP) in VTA, Nac, Amy, PFC, SN, Cpu were detected with immunohistochemistry method. Results: The leveks of TH and GFAP in VTA of the heroin self-administrating rats were obviously increased, and the levels of TH and GFAP in Nac were also decreased, and these changes were not found in SN, Cpu, Amy and PFC; Electro-acupuncture could promote the up-regulation of TH and GFAP in VTA and down-regulation of TH and GFAP in Nac to return to the normal level. Conclusions: The chronic heroin self-administration produced some biochemical adaptations in the rdated brain regions of the mesolimbic dopamine system and electroacupuncture could promote the repair of the injured DA neurons in VTA of heroin addicted rats and their functional recovery.

0.05).The addition of sIL-6R to group SFT6 restored UCB cells expansion to a higher extent than in group SFT,SFT6 and SFTs(P0.05).Conclusion:The IL-6/sIl-6R in combination with SCF,FL and TPO could enhance the expansion of cord blood CD34+ cells and their expression of CD49d,CD62L and CXCR4.

To observe the effect of electro-acupuncture on the relapse to heroin-seeking induced by heroin-related cues after withdrawal from heroin self-administration in rats.Methods:Sixty male Wistar rats were randomized into physiological saline group,withdrawal group A,withdrawal group B,electro-acupuncture(EA)treatment group A and EA treatment group B,with 12 rats in each group.The rats were trained by nose-poke response to self administer heroin (50 μg/kg/per infusion) or saline with one daily 4-h session for 14 consecutive days,the session ended after 25 infusions were eamed or 4 hours had passed,the reinforcement schedule was a progressive ratio.Then rats in withdrawal group A and withdrawal group B were withdrawn from heroin for 1 week and 2 weeks respectively,and then they were reintroduced to their training chambers for 4-h relapse testing which was induced by heroin-related environmental cues;And rats in EA treatment group A and EA treatment group B were also withdrawn from heroin for 1 week and 2 weeks respectively,during which they were given EA treatment for 20 min daily,then they received relapse testing;In the meantime,rats in saline group were trained with saline instead of heroin for 14 days as control.after 7 days of withdrawal from saline,they received relapse testing.Results:Following 7-8 days of drug training,the rats began to establish the stable intravenous heroin self-administration behavior;For the stable heroin self-administrating rats that received EA treatment,when they were reintroduced to their training chambers,their heroin-seeking behaviors were obviously inhibited,and this inhibitory effect related to the cumulativeness of EA stimulation.Conclusion:The results suggested that EA could prevent relapse to heroin-seeking to a certain extent.

Objective To explore the types and drug resistance of pathogens in patients with type Ⅰ incision surgical site infection in orthopedics department.Methods Patients with type Ⅰ incision surgical site infection in orthopedics department at Peking University Third Hospital from January 2005 to December 2013 were retrospectively collected.Clinical characteristics of patients,distribution and drug resistance of pathogens were analyzed.Results A total of 58.2 thousands patients with type Ⅰ incision surgical site were hospitalized from January 2005 to December 2013 in orthopedics department,and among them 442 patients had infection in the type Ⅰ incision surgical site.The infection rate was 0.8％.Infection was mainly observed in elderly patients.The most common diseases were lumbar canal stenosis (21.7％),cervical spondylosis (20.6％) and lumbar intervertebral disc herniation (14.0％).A total of 453 pathogenic strains were detected,of which 52.9％ were gram-positive bacteria,45.5％ were gramnegative bacteria and 1.6 ％ were fungi.The common pathogens were Staphylococcus aureus (25.2 ％),Staphylococcus epidermidis (14.1 ％),Escherichia coli (11.5 ％),Enterobacter cloacae (7.3 ％),Pseudomonas aeruginosa (6.2 ％) and Acinetobacter baumannii (6.0 ％).The percentage of Meticillinresistant Staphylococcus aureus (MRSA) was 23.7％ and the percentage of Meticillin-resistant Staphylococcus epidermidis (MRSE) was 43.8％.Vancomycin or linezolid-resistant Staphylococcus aureus or Staphylococcus epidermidis were not detected.Proportion of extended-spectrum beta-lactamases (ESBL) producing strains in Escherichia coli was 53.8％,and proportion of ESBL-producing strains in Klebesiella pneumonia was 50.0％.The resistance rates to impenem and meropenem of the three different species in Enterobacteriaceae,including Escherichia coli,Enterobacter cloacae and Klebsiella pneumonia,were 0.Resistance rates of Pseudomonas aeruginosa to cefoperazone-sulbactam,piperacillin-tazobactam were less than 10 ％.Resistance rate of Acinetobacter baumannii to minocyline was 11.1％ and resistance rates of it to other drugs were more than 20％.Conclusions The rate of type Ⅰ incision surgical site infection in orthopedics department is low.Gram-positive and gram-negative bacteria each account for half of the pathogens.The proportion of resistant pathogens is high and empirical treatment is needed to cover these pathogens.

OBJECTIVE:To comprehend the causes for adverse drug reactions (ADR)associated with the traditional Chinese medicine injections in order to improve therapeutic safety.METHODS:Through tracking visits and retrospective study of patient cases,100 control cases and 93 ADR cases are analyzed in terms of medicine,patient,prescribing and nursing,both by single-factor and multi-factor approach.RESULTS:The main causes of ADR associated with traditional Chinese medicine injections are:overdosing,combined administration of drugs,longer-than-required time gap between dispensing and transfusion,failure to do pre-dosing liver or kidney function checkup,irrelevance of indication,lack of detailed instruction about way of administration and dosing,and lack of remarks on pharmacological action.CONCLUSION:It’s vitally important to improve prescribing and nursing behaviors for the sake of enhanced safety of clinical use of drugs.

OBJECTIVE:To investigate the characteristics and the prevention of traditional Chinese medicine-induced death. METHODS: The traditional Chinese medicine-induced death cases from 1994 to 2006 collected by retrieving full-text data base of CHKD were analyzed statistically. RESULTS: Of the total traditional Chinese medicine-induced death cases, drugs were chiefly administered by intravenous drip and oral administration, and allergic shock was the chief death causes. CONCLUSION: Clinicians and pharmacists should attach great importance on the ADRs induced by traditional Chinese medicines to ensure safe and effective drug use.

The treatments for insomnia after stroke were various in recent years, including acupuncture with its distinguishing feature. It’s reviewed and summarized that experimental researches on Chinese and English databases about acupuncture treatment of insomnia after stroke in recent 10 years. Clinicians had chosen different acupuncture therapies for insomnia after stroke according to yinyang, zangfu, meridians, opening and closing of qi activity. Although those acupuncture therapies had achieved obvious clinical effects, they were deficient in experimental design and methodology.