Global Conformational Changes of Ribosome Observed by Normal Mode Fitting for 3D Cryo-EM Structures

SummaryMany three-dimensional density maps of 70S ribosome at various functional states are available now in the Electron Microscopy DataBank at EBI. We used our new flexible-fitting approach to systematically analyze these maps to reveal the global conformational differences between the EM structures. Large-scale ratchet-like deformations were observed in an EM structure of the initiation complex and in some EM structures bound with EFG, RF3, and RRF. In most of them, the L1 stalk, which interacts with the tRNA molecule at the E site of ribosome and is considered to be involved in the release of the tRNA, was in “the blocking state” for the E-tRNA. Furthermore, we found that the EM structures bound with EFG or RRF were aligned in the conformational space, suggesting that the large-scale conformational changes of the 70S ribosome bound with these factors occur along a specific pathway in a concerted manner

Correction to: ‘Violence in the prehistoric period of Japan: the spatio-temporal pattern of skeletal evidence for violence in the Jomon period’

Whether man is predisposed to lethal violence, ranging from homicide to warfare, and how that may have impacted human evolution, are among the most controversial topics of debate on human evolution. Although recent studies on the evolution of warfare have been based on various archaeological and ethnographic data, they have reported mixed results: it is unclear whether or notwarfare among prehistoric hunter–gathererswas common enough to be a component of human nature and a selective pressure for the evolution of human behaviour. This paper reports the mortality attributable to violence, and the spatio-temporal pattern of violence thus shown among ancient hunter–gatherers using skeletal evidence in prehistoric Japan (the Jomon period: 13 000 cal BC–800 cal BC). Our results suggest that the mortality due to violence was low and spatio-temporally highly restricted in the Jomon period, which implies that violence including warfare in prehistoric Japan was not common

Violence and warfare in prehistoric Japan

The origins and consequences of warfare or largescale intergroup violence have been subject of long debate. Based on exhaustive surveys of skeletal remains for prehistoric hunter-gatherers and agriculturists in Japan, the present study examines levels of inferred violence and their implications for two different evolutionary models, i.e., parochial altruism model and subsistence model. The former assumes that frequent warfare played an important role in the evolution of altruism and the latter sees warfare as promoted by social changes induced by agriculture. Our results are inconsistent with the parochial altruism model but consistent with the subsistence model, although the mortality values attributable to violence between hunter-gatherers and agriculturists were comparable

Physical properties of portland cement based concrete exposed at a depth of 3520 m in the Nankai Trough

Concrete is widely used in large-scale construction of submarine infrastructure because of its high strength, durability, and ease of handling. However, knowledge of its durability in deep seawater is lacking. In the deep sea, materials are exposed to high pressures and low temperatures, which may cause early deterioration of concrete over time. Concrete materials may also be affected by the chemical composition of seawater, which induces the leaching of calcium. In situ exposure tests are therefore important for understanding degradation processes in the deep sea. In this study, Portland cement based concrete specimens were placed at a depth of 3520 m on the northern edge of the Nankai Trough in 2018 and retrieved in 2019, in the deepest exposure testing conducted to date. Here we provide an outline of the tests, describe the physical properties of materials exposed to deep seawater, freshwater, and air, and discuss possible concrete degradation mechanisms

Longevity in Mice Is Promoted by Probiotic-Induced Suppression of Colonic Senescence Dependent on Upregulation of Gut Bacterial Polyamine Production

BACKGROUND: Chronic low-grade inflammation is recognized as an important factor contributing to senescence and age-related diseases. In mammals, levels of polyamines (PAs) decrease during the ageing process; PAs are known to decrease systemic inflammation by inhibiting inflammatory cytokine synthesis in macrophages. Reductions in intestinal luminal PAs levels have been associated with intestinal barrier dysfunction. The probiotic strain Bifidobacterium animalis subsp. lactis LKM512 is known to increase intestinal luminal PA concentrations. METHODOLOGY/PRINCIPAL FINDINGS: We supplemented the diet of 10-month-old Crj:CD-1 female mice with LKM512 for 11 months, while the controls received no supplementation. Survival rates were compared using Kaplan-Meier survival curves. LKM512-treated mice survived significantly longer than controls (P<0.001); moreover, skin ulcers and tumors were more common in the control mice. We then analyzed inflammatory and intestinal conditions by measuring several markers using HPLC, ELISA, reverse transcription-quantitative PCR, and histological slices. LKM512 mice showed altered 16S rRNA gene expression of several predominant intestinal bacterial groups. The fecal concentrations of PAs, but not of short-chain fatty acids, were significantly higher in LKM512-treated mice (P<0.05). Colonic mucosal function was also better in LKM512 mice, with increased mucus secretion and better maintenance of tight junctions. Changes in gene expression levels were evaluated using the NimbleGen mouse DNA microarray. LKM512 administration also downregulated the expression of ageing-associated and inflammation-associated genes and gene expression levels in 21-month-old LKM512-treated mice resembled those in 10-month-old untreated (younger) mice. CONCLUSION/SIGNIFICANCE: Our study demonstrated increased longevity in mice following probiotic treatment with LKM512, possibly due to the suppression of chronic low-grade inflammation in the colon induced by higher PA levels. This indicates that ingestion of specific probiotics may be an easy approach for improving intestinal health and increasing lifespan. Further studies are required to clarify its effectiveness in humans