Self-assembly of minimal peptoid sequences

Peptoids are biofunctional N-substituted glycine peptidomimics. Their self-assembly is of fundamental interest because they demonstrate alternatives to conventional peptide structures based on backbone chirality and beta-sheet hydrogen bonding. The search for self-assembling, water-soluble “minimal” sequences, be they peptide or peptidomimic, is a further challenge. Such sequences are highly desired for their compatibility with biomacromolecules and convenient synthesis for broader application. We report the self-assembly of a set of trimeric, water-soluble α-peptoids that exhibit a relatively low critical aggregation concentration (CAC ∼ 0.3 wt %). Cryo-EM and angle-resolved DLS show different sequence-dependent morphologies, namely uniform ca. 6 nm wide nanofibers, sheets, and clusters of globular assemblies. Absorbance and fluorescence spectroscopies indicate unique phenyl environments for π-interactions in the highly ordered nanofibers. Assembly of our peptoids takes place when the sequences are fully ionized, representing a departure from superficially similar amyloid-type hydrogen-bonded peptide nanostructures and expanding the horizons of assembly for sequence-specific bio- and biomimetic macromolecules

Correction to "self-assembly of minimal peptoid sequences"

It has come to our attention that some of our cryo-electron microscopy (cryo-EM) images actually show ice contamination, (1) instead of the soft matter aggregates originally indicated in our publication. The images only relate to counterexample peptoid sequences that did not properly assemble (originally Figures 3D–K and S5E–G, I–M, and P). As such, our main finding of an ultrashort water-soluble tripeptoid assembling into ordered nanofibers is not changed. Our overall conclusions based on complementary cryo-EM, DLS, CAC, and fluorescence spectroscopy measurements are also unaffected. Nonetheless, the figures indicated and associated text require correction. In re-examining our cryo-EM data set, we found micrographs showing additional structures that are unlikely to be contaminants, which we previously took as less representative. Like the artifacts, the structures now identified are also irregular and consist of an ensemble of sizes centered around a mean. Incidentally, the mean sizes of these structures (50–250 nm in diameter, depending on sequence) fit better with our complementary DLS results—no agglomeration effect of individual 5–20 nm ice artifacts is needed anymore to reconcile the sizes measured by EM and DLS

Soil bacterial community structure, metabolic adaptations, and their functional interactions to abiotic factors in Antarctica

Antarctica features one of the most ancient, largest glacier reserves and the most pristine environment left on the earth. However, in the last few decades disturbances due to industrialization and release of greenhouse gases have led to serious consequences such asmelting of polar ice sheets, changing atmospheric chemistry and ozone depletion. Here, we use high-throughput sequencing to understand the impact of subtle changes in environmental parameters on bacterial communities. We observed dominance of Cyanobacteria (41.93%) followed by Bacteroidetes (14.8%), Acidobacteria (13.35%), Proteobacteria (9.67%), Actinobacteria (7.79%), Firmicutes (3.46%) among all the samples collected every alternate day for 20 days. Additionally, metagenomic imputations revealed a higher abundance of gene families associated with DNA repair and carotenoid biosynthesis enabling bacterial communities to resist and function under the high UV radiations. We further observed bacterial communities are dependent on the single carbon metabolism as a strategy for nutrient uptake in such nutrient deprived conditions

Heat transfer and friction losses in rapid rotating electrical machinery

How cooling fluid pumped axially through a rapidly rotating Taylor-Couette system affects both the heat transport as well as the friction losses inside an electric machine is investigated in this work. The influence of liquid coolants and multiphase sprays affecting the friction losses of the rotating machine is addressed. Methods to increase the heat transport and prevent high friction losses are designed and tested

Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India

Abstract Marcha and thiat are traditionally prepared amylolytic starters use for production of various ethnic alcoholic beverages in Sikkim and Meghalaya states in India. In the present study we have tried to investigate the bacterial and fungal community composition of marcha and thiat by using high throughput sequencing. Characterization of bacterial community depicts phylum Proteobacteria is the most dominant in both marcha (91.4%) and thiat (53.8%), followed by Firmicutes, and Actinobacteria. Estimates of fungal community composition showed Ascomycota as the dominant phylum. Presence of Zygomycota in marcha distinguishes it from the thiat. The results of NGS analysis revealed dominance of yeasts in marcha whereas molds out numbers in case of thiat. This is the first report on microbial communities of traditionally prepared amylolytic starters of India using high throughput sequencing

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity

Phylum level bacterial richness at various depths.

<p>The X-axis represents the number of phyla (sum of the values given for presence/absence (binary values) of the particular phylum at respective depth), while Y axis represents the samples.</p

Phylum level bacterial diversity across various depths.

<p>The diagram depicts the distribution of the first 15 dominant phyla identified across the samples. The Y-axis represents the percent relative abundance of each phylum. A break is introduced on Y-axis at 0.89 to resolve the Y-axis within the range of 0.9–1.0.</p