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

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passed,the reinforcement schedule was a progressive ratio.Then rats in withdrawal group A and withdrawal group B were withdrawn from heroin for 1 week and 2 weeks respectively,and then they were reintroduced to their training chambers for 4-h relapse testing which was induced by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: 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.

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.

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.

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.

Purpose　The aim is to find out an effective preventing influenza immune preparation. Methods　Egg yolk immune solution of anti-influenza virus(FM1 stem) was prepared from egg of the hens that had been successfully immunized with influenza virus (FM1 stem). Its effects of anti-virus were observed through animal experiment.Results　When the mice of control group began to die the average daily drink quantity of the mice of normal saline control group, egg yolk immune solution control group, immediate preventive group was (3.06±0.86), (2.93±1.47) and (3.99±0.21)ml(P＜0.05)respectively. The average body weights of the mice of these three groups were (15.85±2.70),(14.58±1.92) and (18.27±1.71)g(P＜0.05)respectively. Their mortality was separately 53.84%,69.23% and 3.84%(P＜0.01). The antibody positive rate of survived mice′s serum (1∶10 diluted) was separately 100%, 100% and 0%(P＜0.01). Conclusion　The anti-virus effects of egg yolk immune solution of anti-influenza virus was powerful. The result of preventing mice′s influenza was remarkable.

Objective: This present study is to establish a rat model of intravenous heroin self-administration and observe the effect of electro-acupuncture on the heroin-seeking behavior of the heroin self-administrating rat. Methods: Six Male Wistar rats were surgically implanted with an intra-jugular intravenous catheters under sodium pentobarbital anesthesia,following a minimum recovery of 7 days, the rats were trained by nose-poke response with one daily 4-hour session for 14 consecutive days to self administer heroin (50 μg /kg / per injection), the session ended after 25 infusions were earned or 4 hours had passed, whichever came first, the reinforcement schedule was fixed ratio 1 (FR1) that the rat received a heroin injection for each nose poke response. And then the rats were given electro-acupuncture treatment daily 30min prior to each session and then were trained with one daily 4-h session for 7 consecutive days. Results: Stable intravenous heroin self-administration behavior of rats was established after 7-8 days' drug training, electro-acupuncture given to the stable heroin self-administrating rat 30 min prior to each session could reduce the drug self-administration behavior, namely the total heroin intake in each session was reduced, especially the 1st hour heroin intake, the initiation of first nose-poke response in each session was relayed, and the haste heroin-seeking behavior also became slower. Conclusions: The above results suggested that the electro-acupuncture had better detoxification effect.

Objective To compare the reproducibility and reliability of facial soft tissue landmarks using a direct and an indirect placement methods in facial three-dimensional (3D) soft tissue assessment.Methods 3D coordinates of 37 soft tissue landmarks were obtained respectively in 35 normal healthy volunteers from 3D optical capture system and Materialise's interactive medical image control system (Mimics).Landmarks were affixed on the cutaneous surface (direct method) and marked on the 3D reconstructed craniofacial model (indirect method).Intra-class correlation coefficients (ICCs) and paired t-tests were used to compare the reliability and reproducibility of facial landmarks between two placement methods.Results For the direct placement method,86.5 ％ landmarks had an ICC higher than 0.75.For the indirect placement method,75.7％ landmarks had an ICC higher than 0.75.The inter-observer variability using the direct placement method was (1.259±0.566) mm,which was significantly smaller (P＜0.05) than (1.420±0.638) mm obtained by the indirect placement method.Conclusions Compared with indirect method,direct method has higher reliability and reproducibility in evaluating facial soft tissue.

Objective To study the neurotrophic activity of Schwann cells derived neurotrophic factor (SDNF) on developing motoneurons Methods The right facial nerve of 14 neonatal SD rats was transected neonatal SD rats was transected. The rats were randomly divided into two groups. SDNF (10?g/d) was applied for 7 days in experimental group and PBS(loul) was received in contral group. The mounts and morphology of motoneurons were studied. Results The number and morphometry of experimental group was better than that of controlled group significantly. Conclusion SDNF could save facial motoneurons fron axotomy induced cell death in neonatal rats.