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These findings are consistent with other research which has shown that junk food availability and consumption has been increasing in Nepal [ 79 — 84 ].
Also, as junk food becomes more affordable, there have been recent increases in vegetable prices, making healthy foods harder for poorer households in Nepal to afford [ 85 ]. Political environment The political environment had the potential to influence behaviour with government campaigns or policies and legislative moves. Here discrepancies were evident between the presence of and dissemination of campaigns to improve dietary behaviour. Evidently, political will is in place to bring about changes to improve the political environment surrounding patients in Nepal.
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However, this political will was not evidently translated into political action. Therefore, though potential existed to bring about positive change in policy, the opportunities for the political environment to influence dietary behaviour positively appeared limited.
The area of political change and policy warrants further research and this investigation has been started by the lead author who has analysed NCD policy in Nepal in more detail, and makes recommendations for policy-makers on how to improve dietary support for patients with NCDs, specifically diabetes.
The cultural consumption of certain foods was central to dietary behaviours. It was a commonly held cultural belief amongst participants that rice is a necessary part of every meal and it made them feel full. A meal without rice was seen as no meal at all.
Rice is a filling food and therefore made participants feel full after eating it. It was clear that rice is heavily laden with cultural significance in Nepal, and consumption of it is central to being part of Nepali culture. Patients found it difficult to break the cultural code of eating white rice and replace it with alternative carbohydrates such as roti.
White rice ranks very high in the glycemic index which means it can cause a spike in blood sugar levels and consumption of it has been linked to diabetes [ 86 ].
For these reasons patients with diabetes or HBGLs are warned against consuming large amounts of white rice. I try to eat roti instead. This allowed them to retain some of the cultural practice which was so central to their identity, whilst still maintaining a healthy diet. These findings are supported by the literature which has found that white rice is predominantly seen as the most filling and healthiest food to consume, an essential component to the Nepalese diet [ 83 , 87 ]. Meals without rice are often seen as incomplete and a large helping of rice is seen as essential for health and well-being.
Wholegrains like millet and buckwheat are not seen as good enough compared with rice [ 88 ]. The cultural significance of culturally appropriate foods such as rice and its complex meaning must be explored within the context of diabetes and healthy eating behaviour.
In addition to the importance of rice in Nepalese diets, in certain ethnic groups different eating practices were important due to varying ethnic and cultural traditions and rituals. Fasting for long periods is harmful to people with diabetes and HBGLs who need to eat regularly to regulate their blood sugar levels [ 89 ], however fasting can be a vitally important cultural practice in Nepal.
Eating practices around festival times were particularly challenging. One patient described a religious festival which was observed by Hindu women called Teej, in which she did not eat food to honour her husband.
Our patients reflected the rich diversity of ethnicities in Kathmandu. Patients from the ethnic groups Newari and Chettri, both of which follow the Hindu religion, demonstrated particularly distinct ethnic dietary traditions throughout the year, often linked to festivals.
Then we cook bara [spiced lentil patties], varieties of potato and black eye bean curry. The lentils are soaked in water a day before and the next day the covers are peeled off, the lentils are ground and breads are made out of them. On day 3 S.
As control S. Total RNA and cytosolic proteins were extracted after 48 h time point 1 and 72 h time point 2. All experiments were performed in triplicates. Figure 1 Overview of experimental setup and fungal VOC effect on bacterial growth. Schematic overview of the plate-within-a-plate system a.
Growth of S. Controls S. After scratching off the cells from the surface dilution series of each treatment were prepared in 10 mM phosphate buffer pH 6. Sample number n represents biological replicates. RNA Extraction S. The mixture was centrifuged at 14, rpm for 1. Differentially expressed genes DEGs were defined with a cutoff at log fold change of greater than 0.
Data were filtered with a p-value of 0.
Venn diagrams were produced using Venny Table 1 Primers used in qPCR. Standard curves were established for each cDNA sample to calculate the expression values Ct-value. Protein extraction and MS sample preparation S. Cytosolic proteins were extracted using a bead-beating protocol. Fractions were transferred into 2 ml Eppendorf tubes with 0. Eight rounds of 30 s lysis at 6. Reduction of disulfide bonds with TCEP, alkylation of thiolgroups with iodoacetamide and subsequent in-solution digestion of proteins using trypsin was performed as described by Muntel et al.
Desalting of peptides prior to mass spectrometry analysis using Stage tips was done according to the protocol by Rappsilber et al.
The data were searched against a randomized S. For the final analysis only identifications based on at least two peptides were considered. In total 9 MS-runs per time point were conducted 3 biological replicates with 3 technical replicates each.
This reduced the false discovery rate per sample to less than 0. Data were corrected for detector saturation effects by implementing a correction factor as recently described Statistical analysis was done using MeV v4.
Only proteins showing at least 1. Volatile trapping For the collection of volatiles produced during the interaction, partitioned glass Petri dishes with lids connected to a steel trap containing mg Tenax TA and mg Carbopack B Markes International Ltd. The insertion was confirmed by colony PCR and sequencing. All experiments were performed in duplicates. The traps were measured as described in the previous section with a split ratio set to Results Genomic features of S. After these transformations, the atomic coordinates of the original base are removed.
This type of procedure preserves the coordinates of all ribose rings and phosphates atoms, constituting the phosphosugar backbone, as well as the torsion angles of the glycosidic bonds. The Kabsch algorithm for least-squares superposition 31 is implemented to overlay 3D structure elements, based on common canonical base pair residues. Subsequently, all atom coordinates within the newly added fragment are removed to avoid the coordinate duplication.
After the addition of the last structure element, due to the graph representation, all residues are renumbered according to their sequence. In the first step, the atom coordinates are strictly converted to the CYANA program format and energy is minimized in the torsion angle space using the standard protocol conjugate gradient, iteration steps , as well as the distance restrains for hydrogen bonds.
The accuracy of the predicted full atomic structures relative to the respective RNA crystal structures is described using two measures. The global and local RNA structure all atoms r. The interaction network fidelity INF all measure 33 was used to check all the canonical and non-canonical base pairing and stacking. Base pair interactions and the base stacking network for the tertiary structures were obtained using RNAView 34 and MC-Annotate 35 programs, respectively.
In a similar fashion, we have calculated the parameter INF cbp to inspect the conservation of canonical base pairs. The architecture of the RNAComposer web server The architecture of the RNAComposer system comprises two components: a computational server and a web application server.
The computational server represents the back-end layer of the RNAComposer system and hosts the translation machine engine encoded in Java 1. The computational server is a 64 - bit Intel Xeon 2. The web application server is an Intel Pentium 4 3. It represents the front-end layer of the RNAComposer system and provides a simple, effective and user-friendly web interface implemented in C on a ASP.
The net platform, using a PostgreSQL 8. The transcripts were purified by denaturing gel electrophoresis 8 M urea , followed by elution and ethanol precipitation. The mixture was divided into equal parts, treated with 7.
Modified sites were detected by primer extension as described earlier 37 except that DTT and betaine were added to final concentrations of 5 mM and 1 M, respectively. Dideoxy sequencing markers were generated using unmodified RNA. It needs neither structural templates nor RNA sequence alignment, required for comparative methods. RNA 3D models are built in fully automated way comprised of four major steps depicted on the Figure 1 B and exemplified on the structure of mer RNA hairpin with an internal loop.
The secondary structure of this hairpin, described by a sequence and a secondary structure topology in the dot-bracket notation, is an input to our system.
In the first step, this structure is fragmented into four secondary structure elements, in accordance with its tree graph representation 39 : two stems Figure 1 B; Stems 1 and 2: 5 and 3 bp long, respectively , one internal loop Loop 1: 13 nt size, including two closing base pairs and one apical tetra-loop Loop 2: 6 nt size, including closing base pair. These fragments constitute input patterns for the search procedure in the dictionary.
The search returns a series of 3D elements for every input pattern: 11 results matching 5 bp stem, results for 3 bp stem, 0 elements matching the pattern of the internal loop and results for apical loop. Since the dictionary does not contain corresponding tertiary structure element for the internal loop, the system performs another search for 3D structures matching secondary structure topology only.
The latter run returns 74 elements of a given topology but with various sequences. Figure 1.
RNA secondary structure to tertiary structure machine translation. A The general principle. B Schematic of the basic steps of RNA structure machine translation.
View large Download slide RNA secondary structure to tertiary structure machine translation. The search results tertiary structure elements are next processed in the second, preparation step which encompasses multi-criteria selection of the 3D structure elements Supplementary Figure S1 and base replacement procedure in this case, for the internal loop.Volatile trapping For the collection of volatiles produced during the interaction, partitioned glass Petri dishes with lids connected to a steel trap containing mg Tenax TA and mg Carbopack B Markes International Ltd.
Data were filtered with a p-value of 0. This illustrates the importance of understanding the varied religious and ethnic cultures in Kathmandu and how they create, form and reinforce culture.
Fasting for long periods is harmful to people with diabetes and HBGLs who need to eat regularly to regulate their blood sugar levels [ 89 ], however fasting can be a vitally important cultural practice in Nepal. Figure 2 Changes in transcriptome of S. Nothing, however, has been accomplished in this country in the direction of carrying freight by electricity.
Ayrton and John Perry with those of Prof. The translation engine can generate a family of closely related 3D models.