Context.
The cosmic structure formed from baryon acoustic oscillations (BAO) in the early universe is imprinted in the galaxy distribution observable in large-scale surveys and is used as a standard ...ruler in contemporary cosmology. Typically, BAOs are detected as a preferential length scale in two-point statistics, which gives little information about the location of the BAO structures in real space.
Aims.
The aim of the algorithm described in this paper is to find probable centers of BAOs in the cosmic matter distribution.
Methods.
The algorithm convolves the three-dimensional distribution of matter density with a spherical shell kernel of variable radius placed at different locations. The locations that correspond to the highest values of the convolution correspond to the probable centers of BAOs. This method is realized in an open-source, computationally efficient algorithm.
Results.
We describe the algorithm and present the results of applying it to the SDSS DR9 CMASS survey and associated mock catalogs.
Conclusions.
A detailed performance study demonstrates the ability of the algorithm to locate BAO centers and in doing so presents a novel detection of the BAO scale in galaxy surveys.
During transition into a dormant state, Mycolicibacterium (Mycobacterium) smegmatis cells are able to accumulate free porphyrins that makes them sensitive to photodynamic inactivation (PDI). The ...formation of dormant cells in a liquid medium with an increased concentration of magnesium (up to 25 mM) and zinc (up to 62 µM) resulted in an increase in the total amount of endogenous porphyrins in dormant M. smegmatis cells and their photosensitivity, especially for bacteria phagocytosed by macrophages. To gain insight into possible targets for PDI in bacterial dormant mycobacterial cells, a proteomic profiling with SDS gel electrophoresis and mass spectrometry analysis were conducted. Illumination of dormant forms of M. smegmatis resulted in the disappearance of proteins in the separating SDS gel. Dormant cells obtained under an elevated concentration of metal ions were more sensitive to PDI. Differential analysis of proteins with their identification with MALDI-TOF revealed that 45.2% and 63.9% of individual proteins disappeared from the separating gel after illumination for 5 and 15 min, respectively. Light-sensitive proteins include enzymes belonging to the glycolytic pathway, TCA cycle, pentose phosphate pathway, oxidative phosphorylation and energy production. Several proteins involved in protecting against oxygen stress and protein aggregation were found to be sensitive to light. This makes dormant cells highly vulnerable to harmful factors during a long stay in a non-replicative state. PDI caused inhibition of the respiratory chain activity and destroyed enzymes involved in the synthesis of proteins and nucleic acids, the processes which are necessary for dormant cell reactivation and their transition to multiplying bacteria. Because of such multiple targeting, PDI action via endogenous porphyrins could be considered as an effective approach for killing dormant bacteria and a perspective to inactivate dormant mycobacteria and combat the latent form of mycobacteriosis, first of all, with surface localization.
Summary
The culturability of several actinobacteria is controlled by resuscitation‐promoting factors (Rpfs). These are proteins containing a c. 70‐residue domain that adopts a lysozyme‐like fold. The ...invariant catalytic glutamate residue found in lysozyme and various bacterial lytic transglycosylases is also conserved in the Rpf proteins. Rpf from Micrococcus luteus, the founder member of this protein family, is indeed a muralytic enzyme, as revealed by its activity in zymograms containing M. luteus cell walls and its ability to (i) cause lysis of Escherichia coli when expressed and secreted into the periplasm; (ii) release fluorescent material from fluorescamine‐labelled cell walls of M. luteus; and (iii) hydrolyse the artificial lysozyme substrate, 4‐methylumbelliferyl‐β‐d‐N,N′,N′′‐triacetylchitotrioside. Rpf activity was reduced but not completely abolished when the invariant glutamate residue was altered. Moreover, none of the other acidic residues in the Rpf domain was absolutely required for muralytic activity. Replacement of one or both of the cysteine residues that probably form a disulphide bridge within Rpf impaired but did not completely abolish muralytic activity. The muralytic activities of the Rpf mutants were correlated with their abilities to stimulate bacterial culturability and resuscitation, consistent with the view that the biological activity of Rpf results directly or indirectly from its ability to cleave bonds in bacterial peptidoglycan.
For adaptation to stressful conditions,
(
) is prone to transit to a dormant, non-replicative state, which is believed to be the basis of the latent form of tuberculosis infection. Dormant bacteria ...persist in the host for a long period without multiplication, cannot be detected from biological samples by microbiological methods, however, their "non-culturable" state is reversible. Mechanisms supporting very long capacity of mycobacteria for resuscitation and further multiplication after prolonged survival in a dormant phase remain unclear. Using methods of 2D electrophoresis and MALDI-TOF analysis, in this study we characterized changes in the proteomic profile of
stored for more than a year as dormant, non-replicating cells with a negligible metabolic activity, full resistance to antibiotics, and altered morphology (ovoid forms). Despite some protein degradation, the proteome of 1-year-old dormant mycobacteria retained numerous intact proteins. Their protein profile differed profoundly from that of metabolically active cells, but was similar to the proteome of the 4-month-old dormant bacteria. Such protein stability is likely to be due to the presence of a significant number of enzymes involved in the protection from oxidative stress (katG/Rv1908, sodA/Rv3846, sodC/Rv0432, bpoC/Rv0554), as well as chaperones (dnaJ1/Rv0352, htpG/Rv2299, groEL2/Rv0440, dnaK/Rv0350, groES/Rv3418, groEL1/Rv3417, HtpG/Rv2299c, hspX/Rv2031), and DNA-stabilizing proteins. In addition, dormant cells proteome contains enzymes involved in specific metabolic pathways (glycolytic reactions, shortened TCA cycle, degradative processes) potentially providing a low-level metabolism, or these proteins could be "frozen" for usage in the reactivation process before biosynthetic processes start. The observed stability of proteins in a dormant state could be a basis for the long-term preservation of
cell vitality and hence for latent tuberculosis.
Resuscitation promoting factors (Rpf) are a family of proteins secreted by actively growing actinobacteria, including Mycobacterium tuberculosis. Experimental evidence suggests that Rpfs play a ...distinct role in bacterial resuscitation and re-growth as well as reactivation of chronic tuberculosis in mice. The striking similarity of the Rpfs structure to cell wall hydrolysing enzymes has provided a basis for the development of novel low molecular weight inhibitors of Rpfs activity. In particular, recently characterised nitrophenylthiocyanate compounds could be considered as a promising scaffold for generation of therapeutic agents targeting reactivation of latent tuberculosis. This review describes recent progress in understanding of molecular mechanisms of Rpf biological activity.
Resuscitation promoting factors (RPF) are secreted proteins involved in reactivation of dormant actinobacteria, including Mycobacterium tuberculosis. They have been considered as prospective targets ...for the development of new anti-tuberculosis drugs preventing reactivation of dormant tubercle bacilli, generally associated with latent tuberculosis. However, no inhibitors of Rpf activity have been reported so far. The goal of this study was to find low molecular weight compounds inhibiting the enzymatic and biological activities of Rpfs.
Here we describe a novel class of 2-nitrophenylthiocyanates (NPT) compounds that inhibit muralytic activity of Rpfs with IC(50) 1-7 microg/ml. Fluorescence studies revealed interaction of active NPTs with the internal regions of the Rpf molecule. Candidate inhibitors of Rpf enzymatic activity showed a bacteriostatic effect on growth of Micrococcus luteus (in which Rpf is essential for growth protein) at concentrations close to IC(50). The candidate compounds suppressed resuscitation of dormant ("non-culturable") cells of M. smegmatis at 1 microg/ml or delayed resuscitation of dormant M. tuberculosis obtained in laboratory conditions at 10 microg/ml. However, they did not inhibit growth of active mycobacteria under these concentrations.
NPT are the first example of low molecular weight compounds that inhibit the enzymatic and biological activities of Rpf proteins.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Earlier we demonstrated that the adenylyl cyclase (AC) encoded by the
gene plays a key role in the resuscitation and growth of dormant
and that overexpression of this gene leads to an increase in ...intracellular cAMP concentration and prevents the transition of
from active growth to dormancy in an extended stationary phase accompanied by medium acidification. We surmised that the homologous
gene of
(
), the main cAMP producer, plays similar physiological roles by supporting, under these conditions, the active state and reactivation of dormant bacteria. To test this hypothesis, we established
strain overexpressing
and compared its
and
growth characteristics with a control strain.
, the AC-overexpressing pMind
strain demonstrated faster growth in a liquid medium, prolonged capacity to form CFUs and a significant delay or even prevention of transition toward dormancy. AC-overexpressing cells exhibited easier recovery from dormancy.
, AC-overexpressing bacteria demonstrated significantly higher growth rates (virulence) in the lungs and spleens of infected mice compared to the control strain, and, unlike the latter, killed mice in the TB-resistant strain before month 8 of infection. Even in the absence of selecting hygromycin B, all pMind
CFUs retained the
insert during
growth, strongly suggesting that AC overexpression is beneficial for bacteria. Taken together, our results indicate that cAMP supports the maintenance of
cells vitality under unfavorable conditions
and their virulence
.
Sensors fabricated from high resistivity, float zone, silicon material have been the basis of vertex detectors and trackers for the last 30 years. The areas of these devices have increased from a few ...square cm to >200m2 for the existing CMS tracker. High Luminosity Large Hadron Collider (HL-LHC), CMS and ATLAS tracker upgrades will each require more than 200 m2 of silicon and the CMS High Granularity Calorimeter (HGCAL) will require more than 600 m2. The cost and complexity of assembly of these devices is related to the area of each module, which in turn is set by the size of the silicon sensors. In addition to large area, the devices must be radiation hard, which requires the use of sensors thinned to 200 microns or less. The combination of wafer thinning and large wafer diameter is a significant technical challenge, and is the subject of this work. We describe work on development of thin sensors on 200 mm wafers using wafer bonding technology. Results of development runs with float zone, Silicon-on-Insulator and Silicon-Silicon bonded wafer technologies are reported.
Resuscitation promoting factors (Rpfs) are the proteins involved in the process of reactivation of the dormant cells of mycobacteria. Recently a new class of nitrophenylthiocyanates (NPTs), capable ...of inhibiting the biological and enzymatic activities of Rpfs has been discovered. In the current study the inhibitory properties of the compounds containing both nitro and thiocyanate groups alongside with the compounds with the modified number and different spatial location of the substituents are compared.
New benzoylphenyl thiocyanates alongside with nitrophenylthiocyanates were tested in the enzymatic assay of bacterial peptidoglycan hydrolysis as well as against strains of several actinobacteria (Mycobacterium smegmatis, Mycobacterium tuberculosis) on in-lab developed models of resuscitation of the dormant forms.
Introduction of the additional nitro and thiocyanate groups to the benzophenone scaffold did not influence the inhibitory activity of the compounds. Removal of the nitro groups analogously did not impair the functional properties of the molecules. Among the tested compounds two molecules without nitro group: 3-benzoylphenyl thiocyanate and 4-benzoylphenyl thiocyanate demonstrated the maximum activity in both enzymatic assay (inhibition of the Rpf-mediated peptidoglycan hydrolysis) and in the resuscitation assay of the dormant M. tuberculosis cells.
The current study demonstrates dispensability of the nitro group in the NPT's structure for inhibition of the enzymatic and biological activities of the Rpf protein molecules. These findings provide new prospects in anti-TB drug discovery especially in finding of molecular scaffolds effective for the latent infection treatment.
Context.
High order correlations in the cosmic matter density have become increasingly valuable in cosmological analyses. However, computing these correlation functions is computationally expensive.
...Aims.
We aim to circumvent these challenges by developing a new algorithm called ConKer for estimating correlation functions.
Methods.
This algorithm performs convolutions of matter distributions with spherical kernels using FFT. Since matter distributions and kernels are defined on a grid, it results in some loss of accuracy in the distance and angle definitions. We study the algorithm setting at which these limitations become critical and suggest ways to minimize them.
Results.
ConKer is applied to the CMASS sample of the SDSS DR12 galaxy survey and corresponding mock catalogs, and is used to compute the correlation functions up to correlation order
n
= 5. We compare the
n
= 2 and
n
= 3 cases to traditional algorithms to verify the accuracy of the new algorithm. We perform a timing study of the algorithm and find that three of the four distinct processes within the algorithm are nearly independent of the catalog size
N
, while one subdominant component scales as
O
(
N
). The dominant portion of the calculation has complexity of
O
(
N
c
4/3
log
N
c
), where
N
c
is the of cells in a three-dimensional grid corresponding to the matter density.
Conclusions.
We find ConKer to be a fast and accurate method of probing high order correlations in the cosmic matter density, then discuss its application to upcoming surveys of large-scale structure.
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