Population-based heteropolymer design to mimic protein mixtures.

Biological fluids, the most complex blends, have compositions that constantly vary and cannot be molecularly defined1. Despite these uncertainties, proteins fluctuate, fold, function and evolve as programmed2-4. We propose that in addition to the known monomeric sequence requirements, protein sequences encode multi-pair interactions at the segmental level to navigate random encounters5,6; synthetic heteropolymers capable of emulating such interactions can replicate how proteins behave in biological fluids individually and collectively. Here, we extracted the chemical characteristics and sequential arrangement along a protein chain at the segmental level from natural protein libraries and used the information to design heteropolymer ensembles as mixtures of disordered, partially folded and folded proteins. For each heteropolymer ensemble, the level of segmental similarity to that of natural proteins determines its ability to replicate many functions of biological fluids including assisting protein folding during translation, preserving the viability of fetal bovine serum without refrigeration, enhancing the thermal stability of proteins and behaving like synthetic cytosol under biologically relevant conditions. Molecular studies further translated protein sequence information at the segmental level into intermolecular interactions with a defined range, degree of diversity and temporal and spatial availability. This framework provides valuable guiding principles to synthetically realize protein properties, engineer bio/abiotic hybrid materials and, ultimately, realize matter-to-life transformations.

Monitoring the compaction of single DNA molecules in Xenopus egg extract in real time.

DNA compaction is required for the condensation and resolution of chromosomes during mitosis, but the relative contribution of individual chromatin factors to this process is poorly understood. We developed a physiological, cell-free system using high-speed Xenopus egg extracts and optical tweezers to investigate real-time mitotic chromatin fiber formation and force-induced disassembly on single DNA molecules. Compared to interphase extract, which compacted DNA by ~60%, metaphase extract reduced DNA length by over 90%, reflecting differences in whole-chromosome morphology under these two conditions. Depletion of the core histone chaperone ASF1, which inhibits nucleosome assembly, decreased the final degree of metaphase fiber compaction by 29%, while depletion of linker histone H1 had a greater effect, reducing total compaction by 40%. Compared to controls, both depletions reduced the rate of compaction, led to more short periods of decompaction, and increased the speed of force-induced fiber disassembly. In contrast, depletion of condensin from metaphase extract strongly inhibited fiber assembly, resulting in transient compaction events that were rapidly reversed under high force. Altogether, these findings support a speculative model in which condensin plays the predominant role in mitotic DNA compaction, while core and linker histones act to reduce slippage during loop extrusion and modulate the degree of DNA compaction.

Optimizing the administrated light dose during 5-ALA-mediated photodynamic therapy: Murine 4T1 breast cancer model.

Photodynamic therapy (PDT) is already used to treat many cancers, including breast cancer, the most common cancer in women worldwide. The destruction basis of this method is on produced singlet oxygen which is extremely reactive and is a major agent of tumor cell killing. The measurement of singlet oxygen produced within PDT is essential in predicting treatment outcomes and their optimization. This study aims to determine the optimal total light dose administered during PDT by calculating the singlet oxygen to facilitate the prediction of the treatment outcome in mice bearing 4T1 cell breast cancer. Monitoring the changes in photosensitizer fluorescence signals during PDT due to photobleaching can be one of the methods of determination of singlet oxygen generation in the PDT process. This study determined the oxygen singlet as a photodynamic dose from the three-dimensional Monte Carlo method and the photobleaching empirical dose constant. The photobleaching dose constant was established non-invasively by monitoring the in vivo protoporphyrin IX (PpIX) fluorescence and photobleaching during PDT. The photobleaching dose constant (ß) in J/cm2 was calculated using empirical fluorescence data. The in vivo photobleaching dose constant of aminolevulinic acid was found to be 11.6 J/cm2 and based on this value, the optimal treatment light dose was estimated at 120 J/cm2 in mice bearing 4T1 breast cancer. It is concluded that information can be obtained regarding optimal treatment parameters by monitoring the in vivo PpIX fluorescence and photobleaching during PDT.

Structural evidence for product stabilization by the ribosomal mRNA helicase.

Protein synthesis in all organisms proceeds by stepwise translocation of the ribosome along messenger RNAs (mRNAs), during which the helicase activity of the ribosome unwinds encountered structures in the mRNA. This activity is known to occur near the mRNA tunnel entrance, which is lined by ribosomal proteins uS3, uS4, and uS5. However, the mechanism(s) of mRNA unwinding by the ribosome and the possible role of these proteins in the helicase activity are not well understood. Here, we present a crystal structure of the Escherichia coli ribosome in which single-stranded mRNA is observed beyond the tunnel entrance, interacting in an extended conformation with a positively charged patch on ribosomal protein uS3 immediately outside the entrance. This apparent binding specificity for single-stranded mRNA ahead of the tunnel entrance suggests that product stabilization may play a role in the unwinding of structured mRNA by the ribosomal helicase.

Swimming exercise reduces oxidative stress and liver damage indices of male rats exposed to electromagnetic radiation.

OBJECTIVES: Hepatic damage caused by oxidative stress is one of the problems associated with the emission of electromagnetic radiation (EMR). In this study, the effects of swimming exercise (SE) on oxidative stress and liver cell damage caused by EMR emission in rats were investigated. METHODS: Thirty-two rats (8 weeks old) were randomly divided into four groups, including control (C), EMR, SE, and EMR + SE. During four weeks, the animals engaged in SE (30 min/session, 5session/week) and were also exposed to EMR (4 h/day, seven days/week) emission from a Wi-Fi 2.45GHZ router. The liver and blood samples were collected at 48 h after completing four weeks of SE to assess histopathological damage, oxidative stress, and liver enzymes. KEY FINDINGS: Tissue sections showed severe liver damage in the EMR group compared to the C group, while the SE attenuated the liver damage. In the EMR group, compared to the C, SE and EMR + SE groups, the activity of superoxide dismutase (SOD) and catalase (CAT) decreased significantly, and the concentration of malondialdehyde (MDA) and liver enzymes (AST, ALT, and ALP) increased significantly (P < 0.05). Swimming exercise in the SE and EMR + SE groups compared to EMR led to a significant increase in the activity of SOD and CAT and a significant decrease in the concentration of MDA and liver enzymes (P < 0.05). CONCLUSION: The study findings showed that the SE is beneficial in attenuating the harmful effects of RF-EMR emitted from the Wi-Fi on the liver.

Nanopore molecular trajectories of a eukaryotic reverse transcriptase reveal a long-range RNA structure sensing mechanism.

Eukaryotic reverse transcriptases (RTs) can have essential or deleterious roles in normal human physiology and disease. Compared to well-studied helicases, it remains unclear how RTs overcome the ubiquitous RNA structural barriers during reverse transcription. Herein, we describe the development of a Mycobacterium smegmatis porin A (MspA) nanopore technique to sequence RNA to quantify the single-molecule kinetics of an RT from Bombyx mori with single-nucleotide resolution. By establishing a quadromer map that correlates RNA sequence and MspA ion current, we were able to quantify the RT's dwell time at every single nucleotide step along its RNA template. By challenging the enzyme with various RNA structures, we found that during cDNA synthesis the RT can sense and actively destabilize RNA structures 11-12 nt downstream of its front boundary. The ability to sequence single molecules of RNA with nanopores paves the way to investigate the single-nucleotide activity of other processive RNA translocases.

A tandem active site model for the ribosomal helicase.

During protein synthesis, the messenger RNA (mRNA) helicase activity of the ribosome ensures that codons are made single stranded before decoding. Here, based on recent structural and functional findings, a quantitative model is presented for a tandem arrangement of two helicase active sites on the ribosome. A distal site encounters mRNA structures first, one elongation cycle earlier than a proximal site. Although unwinding of encountered mRNA structures past the proximal site is required for translocation, two routes exist for translocation past the distal site: sliding, which requires unwinding, and stick-slip, which does not. The model accounts in detail for a number of findings related to the ribosomal helicase and provides a testable framework to further study mRNA unwinding.

Factors influencing carbon dioxide emissions in Iran's provinces with emphasis on spatial linkages.

Current economic policy planning places much emphasis on balancing development and environmental protection. Hence, it is important to determine the drivers of environment pollution from the theoretical, scientific, and policymaking aspects in the context of continuous economic growth. This paper investigates the factors affecting per capita CO2 emissions in 30 provinces in Iran from 2009 to 2014 with emphasis on spatial spillover effects using the Spatial Durbin Model. The findings show that per capita CO2 emissions are positively and significantly affected by per capita GDP, industrialization, and urbanization but negatively affected by changes in population. The results of the spatial section of the model indicate that both the more and the less-polluted provinces tend to cluster together, indicating positive spatial dependence for CO2 emissions in the provinces. Also, the spatial spillover of per capita GDP and the growth of urbanization have a negative and significant effect on per capita CO2 emissions in the provinces, while the spatial effect of changes in population is significant but positive. In other words, the economic development and rise in urbanization in one province are the results of changes in pollution levels in neighboring provinces.

Oct4 cell-autonomously promotes primitive endoderm development in the mouse blastocyst.

In embryonic stem (ES) cells and in early mouse embryos, the transcription factor Oct4 is an essential regulator of pluripotency. Oct4 transcriptional targets have been described in ES cell lines; however, the molecular mechanisms by which Oct4 regulates establishment of pluripotency in the epiblast (EPI) have not been fully elucidated. Here, we show that neither maternal nor zygotic Oct4 is required for the formation of EPI cells in the blastocyst. Rather, Oct4 is first required for development of the primitive endoderm (PE), an extraembryonic lineage. EPI cells promote PE fate in neighboring cells by secreting Fgf4, and Oct4 is required for expression of Fgf4, but we show that Oct4 promotes PE development cell-autonomously, downstream of Fgf4 and Mapk. Finally, we show that Oct4 is required for the expression of multiple EPI and PE genes as well as multiple metabolic pathways essential for the continued growth of the preimplantation embryo.