Intermediates Stabilized by Tryptophan Pairs Exist in Trpzip Beta-Hairpins

Transitions of protein secondary structures, such as alpha-helices and beta-hairpins, are often too small and too fast to follow by many single-molecular approaches. Here we describe new population deconvolution methods to investigate the mechanical unfolding/refolding events in Trpzip β-hairpins that are tethered between two optically trapped polystyrene particles through click chemistry. The application of force to the Trpzip peptides shifted population distribution, which allowed us to identify intermediates from regular force–extension curves of the peptides after population deconvolution analysis. Comparison of the intermediates between the Trpzip2 and Trpzip4 peptides suggests the intermediates are likely stabilized by the tryptophan pair stacking. We anticipate the method of population deconvolution described here can offer a unique capability to investigate fast transitions in small biological structures

Quantification of Topological Coupling between DNA Superhelicity and G‑quadruplex Formation

It has been proposed that new transcription modulations can be achieved via topological coupling between duplex DNA and DNA secondary structures, such as G-quadruplexes, in gene promoters through superhelicity effects. Limited by available methodologies, however, such a coupling has not been quantified directly. In this work, using novel magneto-optical tweezers that combine the nanometer resolution of optical tweezers and the easy manipulation of magnetic tweezers, we found that the flexibility of DNA increases with positive superhelicity (σ). More interestingly, we found that the population of G-quadruplex increases linearly from 2.4% at σ = 0.1 to 12% at σ = −0.03. The population then rapidly increases to a plateau of 23% at σ < −0.05. The rapid increase coincides with the melting of double-stranded DNA, suggesting that G-quadruplex formation is correlated with DNA melting. Our results provide evidence for topology-mediated transcription modulation at the molecular level. We anticipate that these high-resolution magneto-optical tweezers will be instrumental in studying the interplay between the topology and activity of biological macromolecules from a mechanochemical perspective

Effects of macrobenthic bioturbation on the abundance and community composition of ammonia-oxidizing prokaryotes under different temperatures

<p>In order to investigate the effects of macrobenthos on the abundance and community composition of ammonia-oxidizing prokaryotes under different temperature conditions, laboratory microcosms containing two kinds of macrobenthos (<i>Corbicula fluminea</i> and <i>Tubificid</i> worms) were constructed. Real-time polymerase chain reaction (PCR) and clone libraries were applied to analyze the ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities in the surface sediments. The lowest abundances of the archaeal and bacterial <i>amoA</i> gene were found in the samples cultured under 28 °C (archaeal <i>amoA</i> gene abundance, 2.71 × 10⁶ copies/g dry sediment; bacterial <i>amoA</i> gene abundance, 1.17 × 10⁷ copies/g dry sediment) of the <i>C. fluminea</i> group. However, there was no significant difference in terms of the abundance of archaeal <i>amoA</i> gene in all <i>Tubificid</i> worms treatment groups. Compared to the community composition of AOB, greater variations in the community composition of AOA were observed among the three different temperature groups.</p

Image_3_Increasing evapotranspiration decouples the positive correlation between vegetation cover and warming in the Tibetan plateau.TIF

Plant growth generally responds positively to an increase in ambient temperature. Hence, most Earth system models project a continuous increase in vegetation cover in the future due to elevated temperatures. Over the last 40 years, a considerable warming trend has affected the alpine ecosystem across the Tibetan Plateau. However, we found vegetation growth in the moderately vegetated areas of the plateau were negatively related to the warming temperatures, thus resulting in a significant degradation of the vegetative cover (LAI: slope = −0.0026 per year, p < 0.05). The underlying mechanisms that caused the decoupling of the relationship between vegetation growth and warming in the region were elaborated with the analysis of water and energy variables in the ecosystem. Results indicate that high temperatures stimulated evapotranspiration and increased the water consumption of the ecosystem (with an influence coefficient of 0.34) in these degrading areas, significantly reducing water availability (with an influence coefficient of −0.68) and limiting vegetation growth. Moreover, the negative warming effect on vegetation was only observed in the moderately vegetated areas, as evapotranspiration there predominantly occupied a larger proportion of available water (compared to the wet and highly vegetated areas) and resulted in a greater increase in total water consumption in a warmer condition (compared to dry areas with lower levels of vegetation cover). These findings highlight the risk of vegetation degradation in semi-arid areas, with the degree of vulnerability depending on the level of vegetation cover. Furthermore, results demonstrate the central role of evapotranspiration in regulating water stress intensity on vegetation under elevated temperatures.</p

Image_1_Increasing evapotranspiration decouples the positive correlation between vegetation cover and warming in the Tibetan plateau.TIF

Plant growth generally responds positively to an increase in ambient temperature. Hence, most Earth system models project a continuous increase in vegetation cover in the future due to elevated temperatures. Over the last 40 years, a considerable warming trend has affected the alpine ecosystem across the Tibetan Plateau. However, we found vegetation growth in the moderately vegetated areas of the plateau were negatively related to the warming temperatures, thus resulting in a significant degradation of the vegetative cover (LAI: slope = −0.0026 per year, p < 0.05). The underlying mechanisms that caused the decoupling of the relationship between vegetation growth and warming in the region were elaborated with the analysis of water and energy variables in the ecosystem. Results indicate that high temperatures stimulated evapotranspiration and increased the water consumption of the ecosystem (with an influence coefficient of 0.34) in these degrading areas, significantly reducing water availability (with an influence coefficient of −0.68) and limiting vegetation growth. Moreover, the negative warming effect on vegetation was only observed in the moderately vegetated areas, as evapotranspiration there predominantly occupied a larger proportion of available water (compared to the wet and highly vegetated areas) and resulted in a greater increase in total water consumption in a warmer condition (compared to dry areas with lower levels of vegetation cover). These findings highlight the risk of vegetation degradation in semi-arid areas, with the degree of vulnerability depending on the level of vegetation cover. Furthermore, results demonstrate the central role of evapotranspiration in regulating water stress intensity on vegetation under elevated temperatures.</p

Image_2_Increasing evapotranspiration decouples the positive correlation between vegetation cover and warming in the Tibetan plateau.TIF

Plant growth generally responds positively to an increase in ambient temperature. Hence, most Earth system models project a continuous increase in vegetation cover in the future due to elevated temperatures. Over the last 40 years, a considerable warming trend has affected the alpine ecosystem across the Tibetan Plateau. However, we found vegetation growth in the moderately vegetated areas of the plateau were negatively related to the warming temperatures, thus resulting in a significant degradation of the vegetative cover (LAI: slope = −0.0026 per year, p < 0.05). The underlying mechanisms that caused the decoupling of the relationship between vegetation growth and warming in the region were elaborated with the analysis of water and energy variables in the ecosystem. Results indicate that high temperatures stimulated evapotranspiration and increased the water consumption of the ecosystem (with an influence coefficient of 0.34) in these degrading areas, significantly reducing water availability (with an influence coefficient of −0.68) and limiting vegetation growth. Moreover, the negative warming effect on vegetation was only observed in the moderately vegetated areas, as evapotranspiration there predominantly occupied a larger proportion of available water (compared to the wet and highly vegetated areas) and resulted in a greater increase in total water consumption in a warmer condition (compared to dry areas with lower levels of vegetation cover). These findings highlight the risk of vegetation degradation in semi-arid areas, with the degree of vulnerability depending on the level of vegetation cover. Furthermore, results demonstrate the central role of evapotranspiration in regulating water stress intensity on vegetation under elevated temperatures.</p

Temperature Responses of Ammonia-Oxidizing Prokaryotes in Freshwater Sediment Microcosms

<div><p>In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial <i>amoA</i> gene. The elevated temperature increased the abundance of archaeal <i>amoA</i> gene, whereas the abundance of bacterial <i>amoA</i> gene decreased. The highest diversity of bacterial <i>amoA</i> gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal <i>amoA</i> gene. Most of the archaeal <i>amoA</i> sequences obtained in this study affiliated with the <i>Nitrosopumilus</i> cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the <i>Nitrosotalea</i> cluster. <i>N. oligotropha</i> lineage was the most dominant bacterial <i>amoA</i> gene group. Several sequences affiliated to <i>Nitrosospira</i> and undefined <i>N. europaea/NC. mobilis</i> like lineage were found in the pre-incubation and 25°C treatment groups.</p></div

Phylogenetic trees of the archaeal (A) and bacterial (B) <i>amoA</i> gene sequences.

<p>Sequences obtained in this study were written in bold and colors, which represent different clone libraries (Red: 0 d; pink: 15°C treatment; blue: 25°C treatment; green: 35°C treatment). One representative sequence from each OTU is shown in the phylogenetic trees. Numbers in parentheses indicate the number of sequences affiliated to the same OTU. Bootstrap numbers >50% are shown.</p

CD experiments of ILPR-I3 at different pH and temperature in a 10 mM sodium phosphate buffer with 100 mM KCl and 5 µM DNA concentration.

<p>(A) CD spectra of the ILPR-I3 in pH 4.5–8.0. (B) Peak wavelength <i>vs</i> pH for the ILPR-I3 (obtained from (A)) and ILPR-I4 (obtained from the CD spectra of the ILPR-I4 at pH 4.5–8.0, data not shown). (C) CD spectra acquired at 23–68°C (pH 5.5). (D) Peak wavelength <i>vs</i> temperature (obtained from (C)). The transition points in B) and D) are determined by sigmoidal fitting (solid curves).</p

Formation of an intermolecular i-motif.

<p>(A) Schematic of the formation of an intermolecular i-motif. The proposed structure in the ILPR-I3 is shown on the left. Each C:CH⁺ pair is represented by two opposite rectangles. (B) PAGE gel image of the Br₂ footprinting experiment. Lane 1, the ILPR-I3/ILPR-I1 (I₃+I₁) mixture at pH 7.0. Lane 2, the I₃+I₁ sample at pH 5.5. Lane 3, the ILPR-I3 (I₃) at pH 5.5. Lane 4, the ILPR-I4 (I₄) at pH 5.5. The band intensity for lane 2 is shown to the left of the gel. The fold protection for the I₃+I₁ sample at pH 5.5 is shown to the right. The dotted vertical lines indicate the average fold protection for each C4 tract. The blue arrows indicate the loop cytosines. Error bar represents the standard deviation of three independent experiments. The blue arrows indicate the cytosines in the ACA section of each fragment. Note that the fold protection for adenines at 3'-end (indicated by asterisk *) is not accurate since they are close to the uncut oligo. (C) Normalized rupture force histogram for the I₃+I₁ sample at pH 5.5. The solid black curve represents a two-peak Gaussian function. The dotted curve is the Gaussian fit for the rupture force histogram of the ILPR-I3 at pH 5.5.</p