Growth study on chrysene degraders isolated from polycyclic aromatic hydrocarbon polluted soils in Nigeria

Acinetobacter anitratus, Alcaligenes faecalis, Acinetobacter mallei and Micrococcus varians were isolated from polycyclic aromatic hydrocarbon polluted soils by enrichment culture using chrysene assole carbon and energy source. Physiochemical evaluation revealed that these isolates grew well at a temperature range of 20 - 40°C, pH 6.0-8.0 but less tolerable to various salt concentrations except Micrococcus varians which grew at 1.0 to 7.5% NaCl. These organisms utilized chrysene, anthracene, naphthalene, crude oil, kerosene, diesel and engine oil as sole carbon source. None could utilize benzene, hexane, xylene, phenol and toluene as carbon sources. Growth study of the isolates on 0.1%(w/v) chrysene resulted in highest cell density of 8.8x107, 7.9x107, 6.3x106, 6.3x106 cfu/ml for A. anitratus, Alc. faecalis, A. mallei and M. varians, respectively. There was statistical significant difference (P< 0.05) in the growth of these organisms on chrysene as sole carbon and energy source when compared with non-chrysene control. This study indicates the potential of these hitherto unreported tropical bacterial strains as chrysene degraders and their use in biodegradation processes involvingpetrochemical product

Mobile phones and wrong numbers: how Maasai agro-pastoralists form and use accidental social ties in East Africa

Mobile phones are recognized as important new tools for rural development in the Global South, but few studies have examined how phones can shape social networks. This study documents a new type of social tie, enabled by mobile phones, that to our knowledge has not previously been discussed in academic literature. In 2018, we discovered that Maasai pastoralists in northern Tanzania create new social ties through wrong numbers, a phenomenon with implications for theory on social networks and path dependency. We used a mixed ethnographic and survey-based design to examine the following: (1) the conditions under which wrong number connections (WNCs) are made; (2) the incidence of these connections in the study area; and (3) the association between WNCs and multiple livelihood strategies. Working in 10 rural communities in Tanzania, we conducted 16 group interviews with men about their phone use and found that WNCs are diverse and can provide households with important information, resources, and opportunities from an expansive geographic area. (Nine separate interviews with groups of women revealed that women do not create WNCs.) Based on early qualitative findings, we designed and conducted a standardized survey with 317 household heads. We found that 46% of respondents have had WNCs. Furthermore, multivariate regression models show a significant association between WNCs and the controversial practice of leasing land in one district. Taken together, our findings show that WNCs can be seen as innovations in social networking that reduce path dependency, increase the range of potential outcomes, and hold important implications for rural livelihoods in East Africa

A method for sensitivity analysis to assess the effects of measurement error in multiple exposure variables using external validation data

Measurement error in self-reported dietary intakes is known to bias the association between dietary intake and a health outcome of interest such as risk of a disease. The association can be distorted further by mismeasured confounders, leading to invalid results and conclusions. It is, however, difficult to adjust for the bias in the association when there is no internal validation data

Simulation, Experiment, and Evolution: Understanding Nucleation in Protein S6 Folding

In this study, we explore nucleation and the transition state ensemble of the ribosomal protein S6 using a Monte Carlo Go model in conjunction with restraints from experiment. The results are analyzed in the context of extensive experimental and evolutionary data. The roles of individual residues in the folding nucleus are identified and the order of events in the S6 folding mechanism is explored in detail. Interpretation of our results agrees with, and extends the utility of, experiments that shift f-values by modulating denaturant concentration and presents strong evidence for the realism of the mechanistic details in our Monte Carlo Go model and the structural interpretation of experimental f-values. We also observe plasticity in the contacts of the hydrophobic core that support the specific nucleus. For S6, which binds to RNA and protein after folding, this plasticity may result from the conformational flexibility required to achieve biological function. These results present a theoretical and conceptual picture that is relevant in understanding the mechanism of nucleation in protein folding.Comment: PNAS in pres

Simple models of protein folding and of non--conventional drug design

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of a protein whose sequence is known. Using insight obtained from simple model simulations of the folding of proteins, in particular of the fact that this phenomenon is essentially controlled by conserved (native) contacts among (few) strongly interacting ("hot"), as a rule hydrophobic, amino acids, which also stabilize local elementary structures (LES, hidden, incipient secondary structures like $\alpha$--helices and $\beta$--sheets) formed early in the folding process and leading to the postcritical folding nucleus (i.e., the minimum set of native contacts which bring the system pass beyond the highest free--energy barrier found in the whole folding process) it is possible to work out a succesful strategy for reading the native structure of designed proteins from the knowledge of only their amino acid sequence and of the contact energies among the amino acids. Because LES have undergone millions of years of evolution to selectively dock to their complementary structures, small peptides made out of the same amino acids as the LES are expected to selectively attach to the newly expressed (unfolded) protein and inhibit its folding, or to the native (fluctuating) native conformation and denaturate it. These peptides, or their mimetic molecules, can thus be used as effective non--conventional drugs to those already existing (and directed at neutralizing the active site of enzymes), displaying the advantage of not suffering from the uprise of resistance

Nucleation phenomena in protein folding: The modulating role of protein sequence

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation mechanism for protein folding whose basic premise is the idea that after completion of a specific set of contacts forming the so-called folding nucleus the native state is achieved promptly. Here we propose a methodology to identify folding nuclei in small lattice polymers and apply it to the study of protein molecules with chain length N=48. To investigate the extent to which protein topology is a robust determinant of the nucleation mechanism we compare the nucleation scenario of a native-centric model with that of a sequence specific model sharing the same native fold. To evaluate the impact of the sequence's finner details in the nucleation mechanism we consider the folding of two non- homologous sequences. We conclude that in a sequence-specific model the folding nucleus is, to some extent, formed by the most stable contacts in the protein and that the less stable linkages in the folding nucleus are solely determined by the fold's topology. We have also found that independently of protein sequence the folding nucleus performs the same `topological' function. This unifying feature of the nucleation mechanism results from the residues forming the folding nucleus being distributed along the protein chain in a similar and well-defined manner that is determined by the fold's topological features.Comment: 10 Figures. J. Physics: Condensed Matter (to appear

On the stability of renormalizable expansions in three-dimensional gravity

Preliminary investigations are made for the stability of the $1/N$ expansion in three-dimensional gravity coupled to various matter fields, which are power-counting renormalizable. For unitary matters, a tachyonic pole appears in the spin-2 part of the leading graviton propagator, which implies the unstable flat space-time, unless the higher-derivative terms are introduced. As another possibility to avoid this spin-2 tachyon, we propose Einstein gravity coupled to non-unitary matters. It turns out that a tachyon appears in the spin-0 or -1 part for any linear gauges in this case, but it can be removed if non-minimally coupled scalars are included. We suggest an interesting model which may be stable and possess an ultraviolet fixed point.Comment: 32 pages. (A further discussion to avoid tachyons is included. To be Published in Physical Review D.

RNA secondary structure formation: a solvable model of heteropolymer folding

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the transition between the native and molten phase of the RNA as a function of temperature. The transition is driven by a competition between the energy gained from the polymer's overlap with the native structure and the entropic gain of forming random contacts. A simplified Go-like model is proposed and solved exactly. The predicted critical behavior is verified via exact numerical enumeration of a large ensemble of similarly designed sequences.Comment: 4 pages including 2 figure

The Atrial Fibrillation Risk Score for Hyperthyroidism Patients

Thyrotoxicosis (TT) is associated with an increase in both total and cardiovascu-lar mortality. One of the main thyrotoxicosis risks is Atrial Fibrillation (AF). Right AF predicts help medical personal prescribe the correct medicaments and correct surgical or radioiodine therapy. The main goal of this study is creating a method for practical treatment and diagnostic AF. This study proposes a new method for assessing the risk of occurrence atrial fibrillation for patients with TT. This method considers both the features of the complication and the specifics of the chronic disease. A model is created based on case histories of patients with thyrotoxicosis. We used Machine Learning methods for creating several models. Each model has advantages and disadvantages depending on the diagnostic and medical purposes. The resulting models show high results in the different metrics of the prediction of AF. These models interpreted and simple for use. Therefore, models can be used as part of the support and decision-making system (DSS) by medical specialists in the treatment and diagnostic of AF

Statistical properties of contact vectors

We study the statistical properties of contact vectors, a construct to characterize a protein's structure. The contact vector of an N-residue protein is a list of N integers n_i, representing the number of residues in contact with residue i. We study analytically (at mean-field level) and numerically the amount of structural information contained in a contact vector. Analytical calculations reveal that a large variance in the contact numbers reduces the degeneracy of the mapping between contact vectors and structures. Exact enumeration for lengths up to N=16 on the three dimensional cubic lattice indicates that the growth rate of number of contact vectors as a function of N is only 3% less than that for contact maps. In particular, for compact structures we present numerical evidence that, practically, each contact vector corresponds to only a handful of structures. We discuss how this information can be used for better structure prediction.Comment: 20 pages, 6 figure