Role of low-pressure negative pleural suction in patients with thoracic trauma - a randomized controlled trial.

BACKGROUND: Thoracic trauma frequently includes a pneumothorax, hemothorax, or hemopneumothorax, which may necessitate an Intercostal drainage (ICD) for air and fluid evacuation to improve breathing and circulatory function. It is a simple and life-saving procedure; nevertheless, it carries morbidity, even after its removal. Efforts have been made continuously to shorten the duration of ICD, but mostly in non-trauma patients. In this study, we evaluated the impact of negative pleural suction over the duration of ICD. METHODS: This study was a prospective randomized controlled interventional trial conducted at Level 1 Trauma Centre. Thoracic trauma patients with ICD, who met the inclusion criteria (sample size 70) were randomized into two groups, the first group with negative pleural suction up to -20 cm H2O, and the second group as conventional, i.e. ICD connected to underwater seal container only. The primary objective was to compare the duration of ICDs and the secondary objectives were the length of hospital stay and various complications of thoracic trauma. RESULTS: Duration of ICD was measured in median days with minimum & maximum days. For the negative suction group, it was 4 days (2-16 days); for the conventional group, it was also 4 days (2-17 days). There was also no significant difference among both groups in length of hospital stay. CONCLUSION: The beneficial effect of negative pleural suction to ICD could not be demonstrated over the duration of ICD and hospital stay. In both groups, there was no significant difference in complication rates like recurrent pneumothorax, retained hemothorax, persistent air leak, and empyema. LEVEL OF EVIDENCE: Therapeutic Study, Level II TRIAL REGISTRATION: This trial was registered with the Clinical Trial Registry of India (CTRI) with registration no. REF/2020/11/038403.

Role of cytokine in malignant T-cell metabolism and subsequent alternation in T-cell tumor microenvironment.

T cells are an important component of adaptive immunity and T-cell-derived lymphomas are very complex due to many functional sub-types and functional elasticity of T-cells. As with other tumors, tissues specific factors are crucial in the development of T-cell lymphomas. In addition to neoplastic cells, T- cell lymphomas consist of a tumor micro-environment composed of normal cells and stroma. Numerous studies established the qualitative and quantitative differences between the tumor microenvironment and normal cell surroundings. Interaction between the various component of the tumor microenvironment is crucial since tumor cells can change the microenvironment and vice versa. In normal T-cell development, T-cells must respond to various stimulants deferentially and during these courses of adaptation. T-cells undergo various metabolic alterations. From the stage of quiescence to attention of fully active form T-cells undergoes various stage in terms of metabolic activity. Predominantly quiescent T-cells have ATP-generating metabolism while during the proliferative stage, their metabolism tilted towards the growth-promoting pathways. In addition to this, a functionally different subset of T-cells requires to activate the different metabolic pathways, and consequently, this regulation of the metabolic pathway control activation and function of T-cells. So, it is obvious that dynamic, and well-regulated metabolic pathways are important for the normal functioning of T-cells and their interaction with the microenvironment. There are various cell signaling mechanisms of metabolism are involved in this regulation and more and more studies have suggested the involvement of additional signaling in the development of the overall metabolic phenotype of T cells. These important signaling mediators include cytokines and hormones. The impact and role of these mediators especially the cytokines on the interplay between T-cell metabolism and the interaction of T-cells with their micro-environments in the context of T-cells lymphomas are discussed in this review article.

An Autoinhibited Dimeric Form of BAX Regulates the BAX Activation Pathway.

Pro-apoptotic BAX is a cell fate regulator playing an important role in cellular homeostasis and pathological cell death. BAX is predominantly localized in the cytosol, where it has a quiescent monomer conformation. Following a pro-apoptotic trigger, cytosolic BAX is activated and translocates to the mitochondria to initiate mitochondrial dysfunction and apoptosis. Here, cellular, biochemical, and structural data unexpectedly demonstrate that cytosolic BAX also has an inactive dimer conformation that regulates its activation. The full-length crystal structure of the inactive BAX dimer revealed an asymmetric interaction consistent with inhibition of the N-terminal conformational change of one protomer and the displacement of the C-terminal helix α9 of the second protomer. This autoinhibited BAX dimer dissociates to BAX monomers before BAX can be activated. Our data support a model whereby the degree of apoptosis induction is regulated by the conformation of cytosolic BAX and identify an unprecedented mechanism of cytosolic BAX inhibition.

Crystallization and preliminary crystallographic analysis of the type III secretion translocator chaperone SicA from Salmonella enterica.

SicA is a member of the class II chaperones in type III secretion systems which bind to the pore-forming translocators in the bacterial cytoplasm and prevent them from premature association and degradation. In this study, SicA from Salmonella enterica serovar Typhimurium was overexpressed, purified and crystallized using PEG 8000 as the precipitant. X-ray diffraction data were collected using synchrotron radiation and processed at 3.5 Šresolution. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 180.4, b = 94.1, c = 131.8 Å, ß = 130.9°. There may be eight monomers in the crystallographic asymmetric unit, corresponding to a V(M) of 2.52 Å(3) Da(-1) and a solvent content of 51.1%. This suggests an oligomerization state that differs from those of previously reported type III secretion chaperones.

Structural insights into mouse anti-apoptotic Bcl-xl reveal affinity for Beclin 1 and gossypol.

This study reports the crystal structures of Bcl-xl wild type and three Bcl-xl mutants (Y101A, F105A, and R139A) with amino acid substitutions in the hydrophobic groove of the Bcl-xl BH3 domain. An additional 12 ordered residues were observed in a highly flexible loop between the alpha1 and alpha2 helices, and were recognized as an important deamidation site for the regulation of apoptosis. The autophagy-effector protein, Beclin 1, contains a novel BH3 domain (residues 101-125), which binds to the surface cleft of Bcl-xl, as confirmed by nuclear magnetic resonance (NMR) spectroscopy and analytical gel-filtration results. Gossypol, a potent inhibitor of Bcl-xl, had a K(d) value of 0.9 microM. In addition, the structural and biochemical analysis of five Bcl-xl substitution mutants will provide structural insights into the design and development of anti-cancer drugs.

Crystal structure of bacterioferritin from Rhodobacter sphaeroides.

Iron is essential for the survival of organisms, but either excess or deficient levels of iron induce oxidative stress, thereby causing cell damage. As a result, iron regulation is essential for proper cell growth and proliferation in most organisms. Bacterioferritin is a ferritin-like family protein that contains a heme molecule and a ferroxidase site at the di-iron center. This protein plays a primary role in intracellular iron storage for iron homeostasis, as well as in the maintenance of iron in a soluble and non-toxic form. Although several bacterioferritin structures have been determined, no structural studies have successfully elucidated the molecular function of the heme molecule and the ferroxidase center. Here, we report the crystal structure of bacterioferritin from Rhodobacter sphaeroides. This protein exists in a roughly spherical configuration via the assembly of 24 subunits. We describe the oligomeric arrangement, ferroxidase center and heme-binding site based on this structure. The protein contains a single iron-binding configuration in the ferroxidase center, which allows for the release of iron by His130 when the protein is in the intermediate state. The heme molecule in RsBfr is stabilized by shifting of the van der Waals interaction center between the porphyrin of the heme and Trp26. We anticipate that further structural analysis will provide a more complete understanding of the molecular mechanisms of members of the ferritin-like family.

Determination of heavy metals in fresh water fish species of the River Ravi, Pakistan compared to farmed fish varieties.

The untreated industrial and sewage wastes arising from industries and metropolitan activities make their passage to the River Ravi, Pakistan, where Balloki Headworks is one of the major sites of effluent concentration. This study was designed to evaluate the concentration of various toxic elements in fishes of that area compared to a nearby fish farm. The concentrations of heavy metals, such as As, Cd, Cu, Pb, Hg, and Zn, and electrolytes Ca, K, and Na were determined in different edible and non-edible fresh water fish varieties. Fish samples were collected from two selected sites and were analyzed for aforementioned elements. Higher levels of As (35.74-45.33 ppm), Cd (0.35-0.45 ppm), Pb (2.1-3.0 ppm), Hg (83.03-92.35 ppm) while normal levels of Zn (37.85-40.74 ppm) and Cu (1.39-2.93 ppm) were observed. Mercury, higher levels of which trigger cough, impairment of pulmonary function, and psychotic reactions, was significantly higher in all studied categories. At the sites under study, there has been observed alarming levels of toxic metals which are needed to be monitored regularly.

The crystal structure of an HSL-homolog EstE5 complex with PMSF reveals a unique configuration that inhibits the nucleophile Ser144 in catalytic triads.

The esterase/lipase family (EC 3.1.1.3/EC 3.1.1.1) represents a diverse group of hydrolases that catalyze the cleavage of ester bonds and are widely distributed in animals, plants and microorganisms. Among these enzymes, hormone-sensitive lipases, play a critical role in the regulation of rodent fat cell lipolysis and are regarded as adipose tissue-specific enzymes. Recently, we reported the structural and biological characterization of EstE5 from the metagenome library [K.H. Nam, M.Y. Kim, S.J. Kim, A. Priyadarshi, W.H. Lee, K.Y. Hwang, Structural and functional analysis of a novel EstE5 belonging to the subfamily of hormone-sensitive lipase, Biochem. Biophys. Res. Commun. 379 (2009) 553-556]. The structure of this protein revealed that it belongs to the HSL-family. Here, we report the inhibition of the activity of the HSL-homolog EstE5 protein as determined by the use of esterase/lipase inhibitors. Our results revealed that the EstE5 protein is significantly inhibited by PMSF. In addition, this is the first study to identify the crystal structures of EstE5-PMSF at 2.4 and 2.5A among the HSL-homolog structures. This structural configuration is similar to that adopted when serine proteases are inhibited by PMSF. The results presented here provide valuable information regarding the properties of the HSL-family.

Structural and functional analysis of Vitamin K2 synthesis protein MenD.

Here we describe in detail the crystal structures of the Vitamin K(2) synthesis protein MenD, from Escherichia coli, in complex with thiamine diphosphate (ThDP) and oxoglutarate, and the effects of cofactor and substrate on its structural stability. This is the first reported structure of MenD in complex with oxoglutarate. The residues Gly472 to Phe488 of the active site region are either disordered, or in an open conformation in the MenD oxoglutarate complex structure, but adopt a closed conformation in the MenD ThDP complex structure. Biospecific-interaction analysis using surface plasmon resonance (SPR) technology reveals an affinity for ThDP and oxoglutarate in the nanomolar range. Biochemical and structural analysis confirmed that MenD is highly dependent on ThDP for its structural stability. Our structural results combined with the biochemical assay reveal novel features of the enzyme that could be utilized in a program of rational structure-based drug design, as well as in helping to enhance our knowledge of the menaquinone synthesis pathway in greater detail.

Structural insights of the MenD from Escherichia coli reveal ThDP affinity.

MenD (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate) synthase belongs to the superfamily of thiamin diphosphate-dependent decarboxylases, which converts isochorismate and 2-oxoglutarate to SHCHC, pyruvate, and carbon dioxide. Here, we report the first crystal structure of apo-MenD from Escherichia coli determined in tetragonal crystal form. The subunit displays the typical three-domain structure observed for ThDP-dependent enzymes. Analytical gel filtration shows that EcMenD behaves as a dimer as well as a tetramer. Circular dichroism and isothermal calorimetry results confirm EcMenD dependency on ThDP, which concomitantly helps to stabilize with better configuration.

Structural insights into the alanine racemase from Enterococcus faecalis.

Alanine racemase (AlaR) is a bacterial enzyme that belongs to the fold-type III group of pyridoxal 5'-phosphate (PLP)-dependent enzymes. AlaR catalyzes the interconversion between L- and D-alanine, which is important for peptidoglycan biosynthesis. This enzyme is common in prokaryotes, but absent in eukaryotes, which makes it an attractive target for the design of new antibacterial drugs. Here, we report the crystal structures of both the apoenzyme and the d-cycloserine (DCS) complex of AlaR from the pathogenic bacterium Enterococcus faecalis v583, at a resolution of 2.5 A. DCS is a suicide inhibitor of AlaR and, as such, serves as an antimicrobial agent and has been used to treat tuberculosis and urinary tract infection-related diseases, and makes several hydrogen bonds with the conserved active site residues, Tyr44 and Ser207, respectively. The apoenzyme crystal structure of AlaR consists of three monomers in the asymmetric unit, including a polyethylene glycol molecule in the dimer interface that surrounds one of the His 293 residues and also sits close to one side of the His 293 residue in the opposite monomer. Our results provide structural insights into AlaR that may be used for the development of new antibiotics targeting the alanine racemase in pathogenic bacteria.

Structural and functional analysis of a novel EstE5 belonging to the subfamily of hormone-sensitive lipase.

Hormone-sensitive lipase (HSL) plays an important role in the regulation of rodent fat cell lipolysis. It is regarded as an adipose tissue-specific enzyme whose sole metabolic role is the catalysis of hormone-stimulated lipolysis in mammalian cells. In this report we describe the functional and structural analysis of an EstE5 protein from a soil metagenome library. Function analysis results indicated that EstE5 preferentially hydrolyzes short-chain ester compounds, and our kinetic studies revealed the optimal pH and temperature. Based on the structural analysis, we defined the active site and the binding pocket. Structurally, EstE5 belongs to the HSL family and these structural studies may have applications in the production of value-added products, including pharmaceuticals.

Crystallization and preliminary X-ray crystallographic analysis of the probable tRNA-modification GTPase (TrmE) from Staphylococcus aureus.

Probable tRNA-modification GTPase (TrmE) is a guanine nucleotide-binding protein that is conserved between bacteria and humans. GTPase hydrolyzes GTP and plays a pivotal role in signalling pathways. In this study, TrmE from Staphylococcus aureus was overexpressed in Escherichia coli. The enzyme was found to crystallize at 295 K when ammonium sulfate was used as a precipitant. X-ray diffraction data were collected to 2.9 A resolution from the crystallized enzyme using synchrotron radiation. The crystal was found to belong to the cubic space group I23, with unit-cell parameters a = b = c = 229.47 A, alpha = beta = gamma = 90 degrees . The crystal is likely to contain four monomers in the asymmetric unit, with a corresponding V(M) of 2.4 A(3) Da(-1) and a solvent content of 50%.

Overexpression, crystallization, and preliminary X-ray crystallographic analysis of the alanine racemase from Enterococcus faecalis v583.

Alanine racemase, a bacterial enzyme belonging to the fold-type III group of pyridoxal 5'-phosphate (PLP)-dependent enzymes, has been shown to catalyze the interconversion between L- and D-alanine. The alanine racemase from the pathogenic bacterium Enterococcus faecalis v583 has been overexpressed in E. coli and was shown to crystallize an enzyme at 295 K, using polyethylene glycol (PEG) 8000 as a precipitant. X-ray diffraction data to 2.5 A has been collected using synchrotron radiation. The crystal is a member of the orthorhombic space group, C222(1), with unit cell parameter of a=94.634, b=156.516, c=147.878 A, and alpha=beta;=gamma=90 degrees. Two or three monomers are likely to be present in the asymmetric unit, with a corresponding Vm of 3.38 A3 Da(-1) and 2.26 A Da(-1) and a solvent content of 63.7% and 45.5%, respectively.

Crystallization and preliminary X-ray crystallographic studies of fatty acid-CoA racemase from Mycobacterium tuberculosis H37Rv.

Fatty acid-CoA racemase plays an important role in the beta-oxidation of branched-chain fatty acids and fatty-acid derivatives as it catalyzes the conversion of several (2R)-branched-chain fatty acid-CoAs to their (2S)-stereoisomers. Fatty acid-CoA racemase from Mycobacterium tuberculosis H37Rv has been purified to homogeneity and crystallized by the hanging-drop vapour-diffusion method with polyethylene glycol 4000 as precipitant. The crystals belong to the trigonal space group P3(1) or P3(2), with unit-cell parameters a = b = 109.56, c = 147.97 A. The asymmetric unit contains six monomers, corresponding to a VM value of 2.15 A3 Da(-1). A complete native data set has been collected at 2.7 A resolution using a synchrotron-radiation source.