Low Degree Metabolites Explain Essential Reactions and Enhance Modularity in Biological Networks

Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational and systems biology is to go beyond identification towards an explanation of specific modules and essential genes and reactions in terms of specific structural or evolutionary constraints. In the metabolic networks of E. coli, S. cerevisiae and S. aureus, we identified metabolites with a low degree of connectivity, particularly those that are produced and/or consumed in just a single reaction. Using FBA we also determined reactions essential for growth in these metabolic networks. We find that most reactions identified as essential in these networks turn out to be those involving the production or consumption of low degree metabolites. Applying graph theoretic methods to these metabolic networks, we identified connected clusters of these low degree metabolites. The genes involved in several operons in E. coli are correctly predicted as those of enzymes catalyzing the reactions of these clusters. We independently identified clusters of reactions whose fluxes are perfectly correlated. We find that the composition of the latter `functional clusters' is also largely explained in terms of clusters of low degree metabolites in each of these organisms. Our findings mean that most metabolic reactions that are essential can be tagged by one or more low degree metabolites. Those reactions are essential because they are the only ways of producing or consuming their respective tagged metabolites. Furthermore, reactions whose fluxes are strongly correlated can be thought of as `glued together' by these low degree metabolites.Comment: 12 pages main text with 2 figures and 2 tables. 16 pages of Supplementary material. Revised version has title changed and contains study of 3 organisms instead of 1 earlie

Boundary Shear Stress Distribution in Smooth and Rough Open Channel Flow

Boundary shear distribution in open channel flow is a crucial issue for river engineer and researchers working in this area.An experimental investigation has been carried out to measure the boundary shear stress distribution along the wetted perimeter of the smooth and rough channel using piston tube technique the accuracy of the method has been compared and checked with another convention method,NDM, VDM,MPM,Velocity Profile Method and energy gradient approach.The boundary shear along the bed and wall of the channel are different for different flow depth and for different roughness conditions.The percentage of boundary shear carried by the wall and bed has been analysed and found to depends on upon non-dimensional geometry and hydraulic parameters such as Aspect ratio,Reynolds number and Froude’s number.A multi linear regression model has been applied to predict the boundary shear distribution for bed.The equation is useful to calculate the roughness coefficient (friction factor) of the wall and bed of the channel separately,which further determines the composite roughness of the open channel flow accuracy.The methodology has been applied successfully to calculate the stage discharge relationship of the open channel flow.The methodology has been validated against other experimental data, other researcher’s models and Natural Rive

Exploring Foundations of Time-Independent Density Functional Theory for Excited-States

Based on the work of Gorling and that of Levy and Nagy, density-functional formalism for many Fermionic excited-states is explored through a careful and rigorous analysis of the excited-state density to external potential mapping. It is shown that the knowledge of the ground-state density is a must to fix the mapping from an excited-state density to the external potential. This is the excited-state counterpart of the Hohenberg-Kohn theorem, where instead of the ground-state density the density of the excited-state gives the true many-body wavefunctions of the system. Further, the excited-state Kohn-Sham system is defined by comparing it's non-interacting kinetic energy with the true kinetic energy. The theory is demonstrated by studying a large number of atomic systems.Comment: submitted to J. Chem. Phy

W40 region in the Gould Belt : An embedded cluster and H II region at the junction of filaments

We present a multiwavelength study of W40 star-forming region using IR observations in UKIRT JHK bands, Spitzer IRAC bands & Herschel PACS bands; 2.12 micron H2 narrow-band imaging; & radio observations from GMRT (610 & 1280 MHz), in a FoV of ~34'x40'. Spitzer observations along with NIR observations are used to identify 1162 Class II/III & 40 Class I sources in the FoV. The NN stellar surface density analysis shows that majority of these YSOs constitute the embedded cluster centered on the source IRS1A South. Some YSOs, predominantly younger population, are distributed along & trace the filamentary structures at lower stellar surface density. The cluster radius is obtained as 0.44pc - matching well with the extent of radio emission - with a peak density of 650pc^-2. The JHK data is used to map the extinction which is subsequently used to compute the cloud mass. It has resulted in 126 Msun & 71 Msun for the central cluster & the northern IRS5 region, respectively. H2 narrow-band imaging displays significant emission, which prominently resembles fluorescent emission arising at the borders of dense regions. Radio analysis shows this region as having blister morphology, with the radio peak coinciding with a protostellar source. Free-free emission SED analysis is used to obtain physical parameters of the overall region & the IRS5 sub-region. This multiwavelength scenario is suggestive of star formation having resulted from merging of multiple filaments to form a hub. Star formation seems to have taken place in two successive epochs, with the first epoch traced by the central cluster & the high-mass star(s) - followed by a second epoch which is spreading into the filaments as uncovered by the Class I sources & even younger protostellar sources along the filaments. The IRS5 HII region displays indications of swept-up material which has possibly led to the formation of protostars.Comment: 17 pages, 12 figures, 2 tables. Accepted for publication in The Astrophysical Journa

Young stellar population and ongoing star formation in the HII complex Sh2-252

In this paper an extensive survey of the star forming complex Sh2-252 has been undertaken with an aim to explore its hidden young stellar population as well as to understand the structure and star formation history. This complex is composed of five embedded clusters associated with the sub-regions A, C, E, NGC 2175s and Teu 136. Using 2MASS-NIR and Spitzer-IRAC, MIPS photometry we identified 577 young stellar objects (YSOs), of which, 163 are Class I, 400 are Class II and 14 are transition disk YSOs. Spatial distribution of the candidate YSOs shows that they are mostly clustered around the sub-regions in the western half of the complex, suggesting enhanced star formation activity towards its west. Using the spectral energy distribution and optical colour-magnitude diagram based age analyses, we derived probable evolutionary status of the sub-regions of Sh2-252. Our analysis shows that the region A is the youngest (~ 0.5 Myr), the regions B, C and E are of similar evolutionary stage (~ 1-2 Myr) and the clusters NGC 2175s and Teu 136 are slightly evolved (~ 2-3 Myr). Morphology of the region in the 1.1 mm map shows a semi-circular shaped molecular shell composed of several clumps and YSOs bordering the western ionization front of Sh2-252. Our analyses suggest that next generation star formation is currently under way along this border and that possibly fragmentation of the matter collected during the expansion of the HII region as one of the major processes responsible for such stars. We observed the densest concentration of YSOs (mostly Class I, ~ 0.5 Myr) at the western outskirts of the complex, within a molecular clump associated with water and methanol masers and we suggest that it is indeed a site of cluster formation at a very early evolutionary stage, sandwiched between the two relatively evolved CHII regions A and B.Comment: 19 pages, 13 figures, Accepted for publication in MNRA

Star Formation and Young Population of the HII Complex Sh2-294

The Sh2-294 HII region ionized by a single B0V star features several infrared excess sources, a photodissociation region, and also a group of reddened stars at its border. The star formation scenario in the region seems to be quite complex. In this paper, we present follow-up results of Sh2-294 HII region at 3.6, 4.5, 5.8, and 8.0 microns observed with the Spitzer Space Telescope Infrared Array Camera (IRAC), coupled with H2 (2.12 microns) observation, to characterize the young population of the region and to understand its star formation history. We identified 36 young stellar object (YSO, Class I, Class II and Class I/II) candidates using IRAC color-color diagrams. It is found that Class I sources are preferentially located at the outskirts of the HII region and associated with enhanced H2 emission; none of them are located near the central cluster. Combining the optical to mid-infrared (MIR) photometry of the YSO candidates and using the spectral energy distribution fitting models, we constrained stellar parameters and the evolutionary status of 33 YSO candidates. Most of them are interpreted by the model as low-mass (< 4 solar masses) YSOs; however, we also detected a massive YSO (~9 solar masses) of Class I nature, embedded in a cloud of visual extinction of ~24 mag. Present analysis suggests that the Class I sources are indeed younger population of the region relative to Class II sources (age ~ 4.5 x 10^6 yr). We suggest that the majority of the Class I sources, including the massive YSOs, are second-generation stars of the region whose formation is possibly induced by the expansion of the HII region powered by a ~ 4 x 10^6 yr B0 main-sequence star.Comment: 12 pages, 7 figures, 2 tables. Accepted for publication in The Astrophysical Journa

Effect of chronic administration of nicorandil (a potassium channel activator) on body weight of two different experimental animal species

Background: Potassium channel openers (Nicorandil being the prototype) are a distinct class of drugs, used in the management of chronic stable angina pectoris. Obesity is a frequent co-morbid condition and also a risk factor for angina pectoris. Anti-obesity drugs are used more frequently these days than ever before. Therefore, it is more likely that physician would be prescribing at least 2 or more drugs while treating such comorbid conditions. This generates a need for the development of a new drug which would work against both angina and obesity. The resultant effect would be a reduction in the cost burden, incidences of side effects and possible drug- drug interactions as compared to multidrug therapy. The purpose of this study is evaluating the chronic effect of Nicorandil (graded doses) on the body weight in 2 different species of animals i.e. rabbits and mice.Methods: In this study, 30 experimental animals of each species were selected. Pretreatment weight (Mean body weight±SEM) of each group were recorded and compared with the post-treatment values of the respective group in every week up to a period of 4 weeks. The route of administration was an intraperitoneal injection.Results: Chronic administration of nicorandil causes a significant reduction in body weight at moderate to high doses in both species of the study group. (p <0.05).Conclusions: Body weight reducing, an effect of nicorandil in animals, if established in human, could enhance its acceptability in obesity with various ischemic heart diseases including angina

Deep optical survey of the stellar content of Sh2-311 region

The stellar content in and around Sh2-311 region have been studied using the deep optical observations as well as near-infrared (NIR) data from 2MASS. The region contains three clusters, viz. NGC 2467, Haffner 18 and Haffner 19. We have made an attempt to distinguish the stellar content of these individual regions as well as to re-determine their fundamental parameters such as distance, reddening, age, onto the basis of a new and more extended optical and infrared photometric data set. NGC 2467 and Haffner 19 are found to be located in the Perseus arm at the distances of 5.0 $\pm$ 0.4 kpc and 5.7 $\pm$ 0.4 kpc, respectively, whereas Haffner 18 is located at the distance of 11.2 $\pm$ 1.0 kpc. The clusters NGC 2467 and Haffner 19 might have formed from the same molecular cloud, whereas the cluster Haffner 18 is located in the outer galactic arm, i.e. the Norma-Cygnus arm. We identify 8 class II young stellar objects (YSOs) using the NIR $(J - H)/(H - K)$ two colour diagram. We have estimated the age and mass of the YSOs identified in the present work and those by Snider et al. (2009) using the $V/(V - I)$ colour-magnitude diagram. The estimated ages and mass range of the majority of the YSOs are $\lesssim$1 Myr and $\sim$0.4 - 3.5 \msun, respectively, indicating that these sources could be T-Tauri stars or their siblings. Spatial distribution of the YSOs shows that some of the YSOs are distributed around the H II region Sh2-311, suggesting a triggered star formation at its periphery.Comment: 19 pages, 13 figures, 9 table; Accepted for publication in New Astronom

Optical and Near-infrared survey of the stellar contents associated with the star-forming Complex Sh2-252

We present the analyses of the stellar contents associated with the HII region Sh2-252 using UBVRI photometry, slit and slitless spectroscopy along with the NIR data from 2MASS for an area ~1 degree x 1 degree. We studied the sub-regions of Sh2-252 which includes four compact-HII (CHII) regions, namely A, B, C and E and two clusters NGC 2175s and Teutsch 136 (Teu 136). Of the fifteen spectroscopically observed bright stars, eight have been identified as massive members of spectral class earlier than B3. From the spectro-photometric analyses, we derived the average distance of the region as 2.4+/-0.2 kpc and the reddening of the massive members is found to vary between 0.35 to 2.1 mag. We found that NGC 2175s and Teu 136, located towards the eastern edge of the complex are the sub-clusters of Sh2-252. The stellar surface density distribution in K-band shows clustering associated with the regions A, C, E, NGC 2175s and Teu 136. We have also identified the candidate ionizing sources of the CHII regions. 61 H_alpha emission sources are identified using slitless spectroscopy. The distribution of the H_alpha emission sources and candidate YSOs with IR excess on the V/(V-I) CMD shows that a majority of them have approximate ages between 0.1 - 5 Myr and masses in the range of 0.3 - 2.5 M_sun. The CMDs of the candidate YSOs in the individual regions also show an age spread of 0.1 - 5 Myr for each of them. We calculated the KLFs for the sub-regions A, C, E, NGC 2175s and Teu 136. Within errors, the KLFs for all the sub-regions are found to be similar and comparable to that of young clusters of age < 5 Myr. We also estimated the mass functions (MFs) of the PMS sample of the individual regions in the mass range of 0.3 - 2.5 M_sun. In general, the slopes of the MFs of all the sub-regions are found comparable to the Salpeter value.Comment: published in MNRA