In vitro and in vivo methodologies for studying the Sigma 54-dependent transcription

Here we describe approaches and methods to assaying in vitro the major variant bacterial sigma factor, Sigma 54 (σ(54)), in a purified system. We include the complete transcription system, binding interactions between σ54 and its activators, as well as the self-assembly and the critical ATPase activity of the cognate activators which serve to remodel the closed promoter complexes. We also present in vivo methodologies that are used to study the impact of physiological processes, metabolic states, global signalling networks, and cellular architecture on the control of σ(54)-dependent gene expression.

Interplay among Pseudomonas syringae HrpR, HrpS and HrpV proteins for regulation of the type III secretion system

Pseudomonas syringae pv. tomato DC3000, a plant pathogenic gram-negative bacterium, employs the type III secretion system (T3SS) to cause disease in tomato and Arabidopsis and to induce the hypersensitive response in nonhost plants. The expression of T3SS is regulated by the HrpL extracytoplasmic sigma factor. Expression of HrpL is controlled by transcriptional activators HrpR and HrpS and negative regulator HrpV. In this study, we analysed the organization of HrpRS and HrpV regulatory proteins and interplay between them. We identified one key residue I26 in HrpS required for repression by HrpV. Substitution of I26 in HrpS abolishes its interaction with HrpV and impairs interactions between HrpS and HrpR and the self-association of HrpS. We show that HrpS self-associates and can associate simultaneously with HrpR and HrpV. We now propose that HrpS has a central role in the assembly of the regulatory HrpRSV complex. Deletion analysis of HrpR and HrpS proteins showed that C-terminal parts of HrpR and HrpS confer determinants indispensable for their self-assembly.

Intermittent or continuous occlusion of hepatic inflow

THE AIM OF THE STUDY

The aim was to compare the effects of intermittent and continuous inflow occlusion on liver I/R injury in an experimental model.

METHOD

The experiment was done using the Wistar rats that underwent continuous and intermittent inflow liver vascular occlusion. Blood and liver tissue samples were taken and parameters of hepatic ischemia/reperfusion injury were analyzed and compared.

RESULTS

Serum activities of ALT, AST and LDH were significantly higher and ALP activity and albumin concentration were markedly lower in rats with continuous liver ischemia. Also, histopathological examination revealed more severe changes in animals with continuous liver vascular occlusion.

CONCLUSION

The results of biochemical assay and histopathological examination were concurrent, both indicating more serious parenchymatous damage caused by continuous hepatic pedicle clamping. Study results clearly demonstrated a better tolerance of the liver to intermittent Pringle maneuver (Tab. 1, Fig. 5, Ref. 9).

Advantages of isolated application of fibrin glue over suture in preservation of second-grade spleen lesion

OBJECTIVES

The aim of this procedure was to assess the safety and efficiency of glue application in the treatment of lienal second-degree lesions, compared with traditional suture method of treatment.

BACKGROUND

The spleen is the most frequently injured intra-abdominal structure regardless of injury mechanisms. Fibrin glue is a useful bio-adhesive for safe and efficient treatment of diffuse parenchymatous spleen haemorrhages.

METHODS

Seventy dogs under intravenous anaesthesia were subdued to spleen incision in length of 5 cm and depth of 2 cm. Forty animals from the experimental group were treated with fibrin glue preservation, and 30 animals from the control group were treated with suture. Removed spleens were histologically analyzed. No animal was sacrificed.

RESULTS

The application of fibrin glue allowed reparation to be accomplished in all cases. The effectiveness of primary repair was registered in 95 %, with only 5 % of cases requiring an application of fibrin omentoplasty. Secondary bleeding was registered only in 1 (2.5 %) case. Preservation with suture is primarily effective only in 40 %, requires additional repair in 23 %, and even 37 % of cases are not feasible. This method is characterized by mortality of 21 %, secondary haemorrhage (32 %), appearance of focal necrosis (42 %) and abscess (11 %).

CONCLUSIONS

Application of FG is a method of choice in cases of second-degree transcapsular spleen lesions and it has a considerable advantage over suture (Tab. 4, Fig. 6, Ref. 24).

Prognostic value of survivin expression in Wilms tumor

PURPOSE

To determine survivin expression patterns in Wilms tumor (WT) and compare it with the expression in normal renal tissue. Also, to analyse cytoplasmic and nuclear survivin expression in relation to histological type, prognostic group and tumor stage.

METHODS

Immunohistochemical expression of survivin was analysed in 59 cases of primary WT and in 10 normal kidney specimens, taken from the same patients, but distant from the tumor.

RESULTS

51 out of 59 cases of WT (86.44%) showed decreased cytoplasmic survivin expression and 4 out of 59 cases of WT (6.78%) showed nuclear overexpression of survivin. There was statistically significant difference in the frequency of decreased cytoplasmic expression of survivin in individual components of WT (p=0.005). Decreased cytoplasmic expression of survivin in epithelial, blastemal and stromal component was found significantly more often in low stage WT compared to high stage WT (Fisher exact test, p=0.0002, p=0.002, p=0.002, respectively). There was no statistically significant difference in the frequency of survivin nuclear overexpression between different stages of WT (Fisher exact test, p=0.564), histological types (Fisher exact test, p=0.915), or between different prognostic groups (Fisher exact test, p=1).

CONCLUSION

Decreased survivin cytoplasmic expression or nuclear overexpression may be related to favorable prognosis of WT.

Can the official soccer game be considered the most important contribution to player's physical fitness level?

AIM

During competitive soccer match play, elite players are subdued to vigorous physical and psychological strains. Thus, some changes in overall physical fitness can be expected. The objective of this paper was to determine whether official games influence physical fitness in soccer players.

METHODS

The participants were divided according to the number of minutes spent in the game as well as according to some additional criteria into starters (STA; N.=33, >1000 minutes spent in the official game) and non-starters (NON; N.=31, <1000 minutes spent in the official game). Both groups participated in the initial (end of pre-season) and in the final testing procedures (one week after the end of the competition period). The total of 24 variables covered players' power performance, kicking the ball, aerobic capacity, agility and flexibility.

RESULTS

The STA group showed positive significant differences (P<0.05) from the NON group in 21 out of 24 variables. The most significant findings of this study point to the fact that official games help in maintaining and improving agility parameters (6 out of 7 tests) as well as in maintaining and improving overall power performance of soccer players which includes sprinting, jumping and kicking the ball.

CONCLUSION

Due to specific physiological and psychological factors, official matches make it possible for the starters to develop the mentioned aspects to a higher level when compared to the non-starting team colleagues.

Diagnostic value of the nuclear matrix protein 22 test and urine cytology in upper tract urothelial tumors

OBJECTIVE

To investigate the diagnostic value of the nuclear matrix protein 22 (NMP22) test in comparison to urine cytology for the detection of upper tract urothelial carcinoma.

PATIENTS AND METHODS

Patients with transitional cell carcinoma of the upper urinary tract (n = 34) and patients with renal calculosis (n = 25) were included in this study. Voided urine samples and separated catheter urine specimens were assayed for NMP22 and cytological examination.

RESULTS

The sensitivity of the NMP22 test in separated and voided urine was 73.2 and 70.5%, respectively, compared to 64.7 and 58.8% of urine cytology. The specificity of the NMP22 test in separated and voided urine was 88 and 92%, respectively, compared to 96 and 96% of urine cytology. The combination of separated and voided urine is the best method because the sensitivity is 79.41% and specificity 88%. There is a high agreement of the NMP22 test in voided and separated urine (kappa = 0.795, p < 0.01), indicating that the voided urine is adequate for diagnosis.

CONCLUSIONS

The NMP22 test has higher sensitivity but lower specificity than cytology. The combination of these two tests could be a very useful diagnostic method for detection of upper urothelial tumors.

Activity map of the Escherichia coli RNA polymerase bridge helix

Transcription, the synthesis of RNA from a DNA template, is performed by multisubunit RNA polymerases (RNAPs) in all cellular organisms. The bridge helix (BH) is a distinct feature of all multisubunit RNAPs and makes direct interactions with several active site-associated mobile features implicated in the nucleotide addition cycle and RNA and DNA binding. Because the BH has been captured in both kinked and straight conformations in different crystals structures of RNAP, recently supported by molecular dynamics studies, it has been proposed that cycling between these conformations is an integral part of the nucleotide addition cycle. To further evaluate the role of the BH, we conducted systematic alanine scanning mutagenesis of the Escherichia coli RNAP BH to determine its contributions to activities required for transcription. Combining our data with an atomic model of E. coli RNAP, we suggest that alterations in the interactions between the BH and (i) the trigger loop, (ii) fork loop 2, and (iii) switch 2 can help explain the observed changes in RNAP functionality associated with some of the BH variants. Additionally, we show that extensive defects in E. coli RNAP functionality depend upon a single previously not studied lysine residue (Lys-781) that is strictly conserved in all bacteria. It appears that direct interactions made by the BH with other conserved features of RNAP are lost in some of the E. coli alanine substitution variants, which we infer results in conformational changes in RNAP that modify RNAP functionality.

Regulation of the co-evolved HrpR and HrpS AAA+ proteins required for Pseudomonas syringae pathogenicity

The bacterial AAA+ enhancer-binding proteins (EBPs) HrpR and HrpS (HrpRS) of Pseudomonas syringae (Ps) activate σ⁵⁴-dependent transcription at the hrpL promoter; triggering type-three secretion system-mediated pathogenicity. In contrast with singly acting EBPs, the evolution of the strictly co-operative HrpRS pair raises questions of potential benefits and mechanistic differences this transcription control system offers. Here, we show distinct properties of HrpR and HrpS variants, indicating functional specialization of these non-redundant, tandemly arranged paralogues. Activities of HrpR, HrpS and their control proteins HrpV and HrpG from Ps pv. tomato DC3000 in vitro establish that HrpRS forms a transcriptionally active hetero-hexamer, that there is a direct negative regulatory role for HrpV through specific binding to HrpS and that HrpG suppresses HrpV. The distinct HrpR and HrpS functionalities suggest how partial paralogue degeneration has potentially led to a novel control mechanism for EBPs and indicate subunit-specific roles for EBPs in σ⁵⁴-RNA polymerase activation.

HrpR and HrpS enhancer-binding proteins of Pseudomonas syringae activate σ⁵⁴-dependent transcription of the HrpL promoter and are required for type-three secretion pathogenicity. Here, the authors demonstrate that, despite being co-regulated, HrpR and HrpS each have distinct functions for activating σ⁵⁴.