Evolutionary analysis of the mTOR pathway provide insights into lifespan extension across mammals.

BACKGROUND: Lifespan extension has independently evolved several times during mammalian evolution, leading to the emergence of a group of long-lived animals. Though mammalian/mechanistic target of rapamycin (mTOR) signaling pathway is shown as a central regulator of lifespan and aging, the underlying influence of mTOR pathway on the evolution of lifespan in mammals is not well understood. RESULTS: Here, we performed evolution analyses of 72 genes involved in the mTOR network across 48 mammals to explore the underlying mechanism of lifespan extension. We identified a total of 20 genes with significant evolution signals unique to long-lived species, including 12 positively selected genes, four convergent evolution genes, and five longevity associated genes whose evolution rate related to the maximum lifespan (MLS). Of these genes, four positively selected genes, two convergent evolution genes and one longevity-associated gene were involved in the autophagy response and aging-related diseases, while eight genes were known as cancer genes, indicating the long-lived species might have evolved effective regulation mechanisms of autophagy and cancer to extend lifespan. CONCLUSION: Our study revealed genes with significant evolutionary signals unique to long-lived species, which provided new insight into the lifespan extension of mammals and might bring new strategies to extend human lifespan.

Evolutionary genetics of flipper forelimb and hindlimb loss from limb development-related genes in cetaceans.

BACKGROUND: Cetacean hindlimbs were lost and their forelimb changed into flippers characterized by webbed digits and hyperphalangy, thus allowing them to adapt to a completely aquatic environment. However, the underlying molecular mechanism behind cetacean limb development remains poorly understood. RESULTS: In the present study, we explored the evolution of 16 limb-related genes and their cis-regulatory elements in cetaceans and compared them with that of other mammals. TBX5, a forelimb specific expression gene, was identified to have been under accelerated evolution in the ancestral branches of cetaceans. In addition, 32 cetacean-specific changes were examined in the SHH signaling network (SHH, PTCH1, TBX5, BMPs and SMO), within which mutations could yield webbed digits or an additional phalange. These findings thus suggest that the SHH signaling network regulates cetacean flipper formation. By contrast, the regulatory activity of the SHH gene enhancer-ZRS in cetaceans-was significantly lower than in mice, which is consistent with the cessation of SHH gene expression in the hindlimb bud during cetacean embryonic development. It was suggested that the decreased SHH activity regulated by enhancer ZRS might be one of the reasons for hindlimb degeneration in cetaceans. Interestingly, a parallel / convergent site (D42G) and a rapidly evolving CNE were identified in marine mammals in FGF10 and GREM1, respectively, and shown to be essential to restrict limb bud size; this is molecular evidence explaining the convergence of flipper-forelimb and shortening or degeneration of hindlimbs in marine mammals. CONCLUSIONS: We did evolutionary analyses of 16 limb-related genes and their cis-regulatory elements in cetaceans and compared them with those of other mammals to provide novel insights into the molecular basis of flipper forelimb and hindlimb loss in cetaceans.

Experimental Study and Theoretical Analysis on the Compression-Shear Multiaxial Mechanical Properties of Recycled Concrete.

Recycled concrete, which is formed by replacing coarse aggregates in ordinary concrete with recycled aggregates (RA), is of great significance for the secondary utilization of waste building resources. In civil engineering, concrete structures are sometimes subjected to a compression-shear multiaxial stress state. Therefore, research on the compression-shear multiaxial mechanical properties of recycled concrete plays an important role in engineering practice. To explore the effect of RA replacement rate on the compression-shear properties of recycled concrete, an experimental study was carried out using a compression-shear testing machine and considering five RA replacement rates and five axial compression ratios. Consequently, the failure modes and mechanical property parameters under different working conditions were obtained and were used to analyze the effects of RA replacement rate and axial compression ratio on the shear stress of recycled concrete. Eventually, the following conclusions were reached: With the growth of axial compression ratio, the shear cracks exhibit a developing trend along the oblique direction, and the friction traces on the shear surface are gradually deepened. As the replacement rate increases, the number of shear cracks is gradually increased, accompanied by increasing broken fragments falling off from the shear interface. Since the action of the axial compression ratio can effectively improve the mechanical bite force and friction on the shear interface of recycled concrete, as the axial compression ratio increases, the shear stress is gradually increased. On the other hand, due to the initial damage of RA and its weak adhesion with cement mortar, the shear stress is gradually reduced with the increase of RA replacement rate. Meanwhile, the increase in shear stress shows a gradually decreasing trend with the growth of axial compression ratio. Specifically, for the RA replacement rates of 0% and 100%, the shear stress increased by 4.06 times and 3.21 times, respectively, under the influence of the axial compression ratio. Under different axial compression ratios, the shear stress was reduced by 43~46%, due to the increase of RA replacement rate. In addition, based on the octahedral stress space and the principal stress space, a compression-shear multiaxial failure criterion and shear stress calculation model for recycled concrete were proposed, by considering the effect of the RA replacement rate. The outcomes of this research are of great significance for engineering applications and the development of recycled concrete.

Research on Dynamic Compressive Performance and Failure Mechanism Analysis of Concrete after High Temperature and Rapid Cooling.

To investigate the dynamic compressive properties of concrete after high temperature and rapid cooling, an experimental study was carried out by considering five temperatures and four strain rates. The coupling effect of high temperature and strain rate on concrete damage morphology and mechanical parameters was comparatively analyzed. The main conclusions are as follows: the compressive damage morphology of concrete is affected by strain rate development trends of significant variability under different temperature conditions. As the strain rate increases, the compressive stress and elastic modulus of concrete are gradually increased. As the temperature increases, the increase in compressive stress is gradually reduced by the strain rate. For the temperatures of 20 °C and 800 °C, the increase in compressive stress by the strain rate is 38.69% and 7.78%, respectively. Meanwhile, SEM and CT scanning technology were applied to examine the mechanism of the effect of high temperature and strain rate on the mechanical properties of concrete from the microscopic perspective, and the corresponding constitutive model was proposed.

Regression of corpus luteum in cetaceans: A systematic review.

Functional and structural change of corpus luteum through the cascade of several genes in the ovary leads to ovulation and pregnancy. In most mammals, the absence of pregnancy leads to the disintegration of the corpus luteum. In the ovary of cetaceans, the regression of the corpus luteum gets delayed and persists on the surface as scars (corpus albicans). The database on luteolysis of mammals was collected and examined to know the mechanisms involved in the corpus luteum regression of cetaceans. Surprisingly, there existed no data on the concerned topic. Some past findings reported the persistence of ovarian scars through the entire life span, while few reported the regression. Also, those investigations were about the physiology and histology of corpus luteum regression. The pathways and the genes involved in the regression of the cetacean corpus luteum remain unexplored. This review is all about the regression of corpus luteum and recommends gene-based evolutionary studies in the future to resolve the existing theories on ovarian scar persistence in cetaceans.

Comparative analyses of aging-related genes in long-lived mammals provide insights into natural longevity.

Extreme longevity has evolved multiple times during the evolution of mammals, yet its underlying molecular mechanisms remain largely underexplored. Here, we compared the evolution of 115 aging-related genes in 11 long-lived species and 25 mammals with non-increased lifespan (control group) in the hopes of better understanding the common molecular mechanisms behind longevity. We identified 16 unique positively selected genes and 23 rapidly evolving genes in long-lived species, which included nine genes involved in regulating lifespan through the insulin/IGF-1 signaling (IIS) pathway and 11 genes highly enriched in immune-response-related pathways, suggesting that the IIS pathway and immune response play a particularly important role in exceptional mammalian longevity. Interestingly, 11 genes related to cancer progression, including four positively selected genes and seven genes with convergent amino acid changes, were shared by two or more long-lived lineages, indicating that long-lived mammals might have evolved convergent or similar mechanisms of cancer resistance that extended their lifespan. This suggestion was further corroborated by our identification of 12 robust candidates for longevity-related genes closely related to cancer.

Over-expression of the bottlenose dolphin Hoxd13 gene in zebrafish provides new insights into the cetacean flipper formation.

Cetaceans have evolved elongated soft-tissue flipper with digits made of hyperphalangy. Cetaceans were found to have 2-3 more alanine residues in Hoxd13 than other mammals, which were suggested to be related to their flipper. However, how Hoxd13 regulates other genes and induces hyperphalangy in cetaceans remain poorly understood. Here, we overexpressed the bottlenose dolphin Hoxd13 in zebrafish (Danio rerio). Combined with transcriptome data and evolutionary analyses, our results revealed that the Wingless/Integrated (Wnt) and Hedgehog signaling pathways and multiple genes might regulate hyperphalangy development in cetaceans. Meanwhile, the Notch and mitogen-activated protein kinase (Mapk) signaling pathways and Fibroblast growth factor receptor 1 (Fgfr1) are probably correlated with interdigital tissues retained in the cetacean flipper. In conclusion, this is the first study to use a transgenic zebrafish to explore the molecular evolution of Hoxd13 in cetaceans, and it provides new insights into cetacean flipper formation.

Uniaxial Dynamic Compressive Behaviors of Hydraulic Asphalt Concrete under the Coupling Effect between Temperature and Strain Rate.

To investigate the compressive dynamic properties of hydraulic asphalt concrete under various temperatures, four temperatures and four strain rates have been set to perform the uniaxial compression experiments using hydraulic servo machine in this paper. The influence of temperature and strain rate on the failure modes, stress-strain curves and mechanical characteristic parameters of hydraulic asphalt concrete is analyzed and the results reveal that the failure modes and stress-strain curves have significant temperature effect. When the temperature is between -20 °C and 0 °C, the failure mode is dominated by brittle failure of asphalt binder, and hydraulic asphalt concrete shows obvious strain softening. With the addition of temperature, the failure modes of specimens are transferred from brittle failure to ductile failure since the asphalt changes from elastic-brittleness to viscoelasticity. Influenced by temperature effect, the compressive stress-strain curves of hydraulic asphalt concrete show strain hardening while the peak stress of hydraulic asphalt concrete is obviously decreased, and the variation coefficient of peak stress has a power relation with temperature. With successive increases in strain rate, the stress-strain curves of hydraulic asphalt concrete gradually are transferred from strain hardening to strain softening. The peak stress and stiffness modulus of specimens under compression gradually increase, and the dynamic increase factor of peak stress is linearly related with the logarithm value of strain rate after dimensionless treatment. In terms of the quantitative analysis of the experimental data, two relationship models of the coupling effect between temperature and strain rate are proposed. The proposed models have good applicability to the quantitative analysis of the experimental results in the manuscript. This paper offers important insights into the application and development of hydraulic asphalt concrete in hydraulic engineering.

sRNA-Based Screening Chromosomal Gene Targets and Modular Designing Escherichia coli for High-Titer Production of Aglycosylated Immunoglobulin G.

The production of the aglycosylated immunoglobulin G (IgG) in Escherichia coli has received wide interest for its analytical and therapeutic applications. To enhance the production titer of IgG, we first used synthetic sRNAs to perform a systematical analysis of the gene expression in the translational level in the glycolytic pathway (module 1) and the tricarboxylic acid (TCA) cycle (module 2) to reveal the critical genes for the efficient IgG production. Second, to provide sufficient amino acid precursors for the protein biosynthesis, amino acid biosynthesis pathways (module 3) were enhanced to facilitate the IgG production. Upon integrated engineering of these genes in the three modules (module 1, aceF; module 2, gltA and acnA; module 3, serB) and optimization of fermentation conditions, the recombinant E. coli enabled a titer of the full-assembled IgG of 4.5 ± 0.6 mg/L in flask cultures and 184 ± 9.2 mg/L in the 5 L high cell density fed-batch fermenter, which is, as far as we know, the highest reported titer of IgG production in recombinant E. coli.

Shear Testing of the Interfacial Friction Between an HDPE Geomembrane and Solid Waste.

High-density polyethylene (HDPE) geomembrane is often used as an anti-seepage material in domestic and industrial solid waste landfills. To study the interfacial shear strength between the HDPE anti-seepage geomembrane and various solid wastes, we performed direct shear tests on the contact interface between nine types of industrial solid waste or soil (desulfurization gypsum, fly ash, red mud, mercury slag, lead-zinc slag, manganese slag, silica fume, clay and sand) and a geomembrane with a smooth or rough surface in Guizhou Province, China. Friction strength parameters like the interfacial friction angle and the apparent cohesion between the HDPE geomembrane and various solid wastes were measured to analyze the shear strength of the interface between a geomembrane with either a smooth or a rough surface and various solid wastes. The interfacial shear stress between the HDPE geomembrane and the industrial solid waste increased with shear displacement and the slope of the stress-displacement curve decreased gradually. When shear displacement increased to a certain range, the shear stress at the interface remained unchanged. The interfacial shear strength between the geomembrane with a rough surface and the solid waste was higher than for the geomembrane with a smooth surface. Consequentially, the interfacial friction angle for the geomembrane with a rough surface was larger. The geomembrane with a rough surface had a better shear resistance and the shear characteristics fully developed when it was in full contact with the solid waste.

Synthetic sRNA-Based Engineering of Escherichia coli for Enhanced Production of Full-Length Immunoglobulin G.

Production of monoclonal antibodies (mAbs) receives considerable attention in the pharmaceutical industry. There has been an increasing interest in the expression of mAbs in Escherichia coli for analytical and therapeutic applications in recent years. Here, a modular synthetic biology approach is developed to rationally engineer E. coli by designing three functional modules to facilitate high-titer production of immunoglobulin G (IgG). First, a bicistronic expression system is constructed and the expression of the key genes in the pyruvate metabolism is tuned by the technologies of synthetic sRNA translational repression and gene overexpression, thus enhancing the cellular material and energy metabolism of E. coli for IgG biosynthesis (module 1). Second, to prevent the IgG biodegradation by proteases, the expression of a number of key proteases is identified and inhibited via synthetic sRNAs (module 2). Third, molecular chaperones are co-expressed to promote the secretion and folding of IgG (module 3). Synergistic integration of the three modules into the resulting recombinant E. coli results in a yield of the full-length IgG ≈150 mg L-1 in a 5L fed-batch bioreactor. The modular synthetic biology approach could be of general use in the production of recombinant mAbs.

Accelerated evolution and diversifying selection drove the adaptation of cetacean bone microstructure.

BACKGROUND: The transition from land to sea by the ancestor of cetaceans approximately 50 million years ago was an incredible evolutionary event that led to a series of morphological, physiological, and behavioral adaptations. During this transition, bone microstructure evolved from the typical terrestrial form to the specialized structure found in modern cetaceans. While the bone microstructure of mammals has been documented before, investigations of its genetic basis lag behind. The increasing number of cetaceans with whole-genome sequences available may shed light on the mechanism underlying bone microstructure evolution as a result of land to water transitions. RESULTS: Cetacean bone microstructure is consistent with their diverse ecological behaviors. Molecular evolution was assessed by correlating bone microstructure and gene substitution rates in terrestrial and aquatic species, and by detecting genes under positive selection along ancestral branches of cetaceans. We found that: 1) Genes involved in osteoclast function are under accelerated evolution in cetaceans, suggestive of important roles in bone remodeling during the adaptation to an aquatic environment; 2) Genes in the Wnt pathway critical for bone development and homeostasis show evidence of divergent evolution in cetaceans; 3) Several genes encoding bone collagens are under selective pressure in cetaceans. CONCLUSIONS: Our results suggest that evolutionary pressures have shaped the bone microstructure of cetaceans, to facilitate life in diverse aquatic environments.

Molecular cloning and expression pattern of IGFBP-2a in black porgy (Acanthopagrus schlegelii) and evolutionary analysis of IGFBP-2s in the species of Perciformes.

Insulin-like growth factor-binding protein-2 (IGFBP-2) plays a key role in regulating growth and development by its affinity with insulin-like growth factors (IGFs). In this study, we cloned the coding sequence (CDS) of IGFBP-2a from the black porgy (Acanthopagrus schlegelii) muscle and identified that the full-length CDS of IGFBP-2a was 882 bp. Real-time quantitative PCR revealed that IGFBP-2a was most abundant in the liver of the black porgy and backcross breed (F1♀×black porgy♂) but remained lower in each tested tissue in self-cross breed (F1♀×F1♂). In addition, the IGFBP-2a expression in the liver of three breeds showed a negative correlation with their growth rates, indicating that the IGFBP-2a played a growth-inhibiting role in the three breeds. We further identified 810 bp IGFBP-2b gene from the draft genome of black porgy. Finally, we examined the IGFBP-2a and IGFBP-2b genes by scanning the genomes of the species of Perciformes and found the IGFBP-2 gene duplication took place earlier than the divergence of perciform species. Interestingly, six positively selected sites were detected in both Perciformes IGFBP-2 genes, although both genes were identified to be under purifying selection. Specially, these positively selected sites were located in the functional domains, suggesting these sites played key roles in the growth of Perciformes. Our study partially explains the molecular basis for the prepotency in black porgy hybrids, which will provide guidance for their cultivation in the future.

Divergent Evolution of TRC Genes in Mammalian Niche Adaptation.

Mammals inhabit a wide variety of ecological niches, which in turn can be affected by various ecological factors, especially in relation to immunity. The canonical TRC repertoire (TRAC, TRBC, TRGC, and TRDC) codes C regions of T cell receptor chains that form the primary antigen receptors involved in the activation of cellular immunity. At present, little is known about the correlation between the evolution of mammalian TRC genes and ecological factors. In this study, four types canonical of TRC genes were identified from 37 mammalian species. Phylogenetic comparative methods (phyANOVA and PGLS) and selective pressure analyses among different groups of ecological factors (habitat, diet, and sociality) were carried out. The results showed that habitat was the major ecological factor shaping mammalian TRC repertoires. Specifically, trade-off between TRGC numbers and positive selection of TRAC and the balanced evolutionary rates between TRAC and TRDC genes were speculated as two main mechanisms in adaption to habitat and sociality. Overall, our study suggested divergent mechanisms for the evolution of TRCs, prompting mammalian immunity adaptions within diverse niches.

Widespread positive selection on cetacean TLR extracellular domain.

Toll like receptors (TLRs), key members of innate immune system, can recognize a wide diversity of pathogens and initiate both innate and adaptive immune responses in vertebrate. Cetaceans must have faced new challenges of pathogens when their terrestrial relatives transitioned from the terrestrial to aquatic environment. Here, we sequenced the extracellular domain (ECD) of 10 TLRs in cetacean lineages because this region involved in the recognition of pathogens. A total of 148 sites ranging between 5-26 codons (0.01%-4.83%) were identified to be robust candidates of positive selection at the ECD of 10 TLRs. In addition, the majority (90.54%) of these positively selected codons were found to have radical amino acid changes, which strengthen the evidence of positive selection. Importantly, more radical amino acid changes in selected sites were enriched in the period of early evolutionary transition from land to semi-aquatic and from semi-aquatic to full-aquatic habitat, which might endow cetaceans with a faster adaptation to new pathogens as they transitioned into novel habitat. Interestingly, similar selective intensity was detected in both viral and non-viral TLRs in cetaceans, which was not in line with previous studies on primates and birds that reported stronger positive selection in non-viral TLRs than in viral TLRs. This result may be explained by the fact that cetaceans might have faced diversity of bacteria and viruses during its transitions from terrestrial to aquatic environment whereas both primates and birds probably being affected by only a restricted number of related viruses due to their homogeneous habitat.

Performance assessment of static lead-lag feedforward controllers for disturbance rejection in PID control loops.

This paper assesses the performance of feedforward controllers for disturbance rejection in univariate feedback plus feedforward control loops. The structures of feedback and feedforward controllers are confined to proportional-integral-derivative and static-lead-lag forms, respectively, and the effects of feedback controllers are not considered. The integral squared error (ISE) and total squared variation (TSV) are used as performance metrics. A performance index is formulated by comparing the current ISE and TSV metrics to their own lower bounds as performance benchmarks. A controller performance assessment (CPA) method is proposed to calculate the performance index from measurements. The proposed CPA method resolves two critical limitations in the existing CPA methods, in order to be consistent with industrial scenarios. Numerical and experimental examples illustrate the effectiveness of the obtained results.

Discovery and Synthesis of a Novel Series of Liver X Receptor Antagonists.

Fourteen novel compounds were prepared and their antagonistic activities against liver X receptors (LXR) α/ß were tested in vitro. Compound 26 had an IC50 value of 6.4 µM against LXRα and an IC50 value of 5.6 µM against LXRß. Docking studies and the results of structure-activity relationships support the further development of this chemical series as LXRα/ß antagonists.

Synthesis of substituted 6-amino-4-(2,4-dimethoxyphenyl)-[1,2]dithiolo[4,3-b]pyrrol-5-ones and their raising leukocyte count activities.

The design and synthesis of a series of substituted 6-amino-4-(2,4-dimethoxyphenyl)-[1,2]dithiolo[4,3-b]pyrrol-5-ones are described. All the synthesized compounds were evaluated for raising leukocyte count activities in normal mice. Four compounds (8a, b, d, h) exhibited raising leukocyte count activities close or higher than positive control recombinant human granulocyte colony stimulating factor (rhG-CSF), and some (8e-g, k, p, r) had a moderate effect. Among them, the most potent compound 8a was evaluated for its antileukopenia activity in cyclophosphamide (CTX) treated mice. Interestingly, 8a exhibited significant antileukopenia activity as compared to rhG-CSF. The results suggest that this kind of compounds might be utilized for the development of new candidate for treatment of leukocytopenia.