A human-specific insertion promotes cell proliferation and migration by enhancing TBC1D8B expression

Human-specific insertions play important roles in human phenotypes and diseases. Here we reported a 446-bp insertion (Insert-446) in intron 11 of the TBC1D8B gene, located on chromosome X, and traced its origin to a portion of intron 6 of the EBF1 gene on chromosome 5. Interestingly, Insert-446 was present in the human Neanderthal and Denisovans genomes, and was fixed in humans after human-chimpanzee divergence. We have demonstrated that Insert-446 acts as an enhancer through binding transcript factors that promotes a higher expression of human TBC1D8B gene as compared with orthologs in macaques. In addition, over-expression TBC1D8B promoted cell proliferation and migration through "a dual finger" catalytic mechanism (Arg538 and Gln573) in the TBC domain in vitro and knockdown of TBC1D8B attenuated tumorigenesis in vivo. Knockout of Insert-446 prevented cell proliferation and migration in cancer and normal cells. Our results reveal that the human-specific Insert-446 promotes cell proliferation and migration by upregulating the expression of TBC1D8B gene. These findings provide a significant insight into the effects of human-specific insertions on evolution.

Divergent Evolutionary Rates of Primate Brain Regions as Revealed by Genomics and Transcriptomics

Although the primate brain contains numerous functionally distinct structures that have experienced diverse genetic changes during the course of evolution and development, these changes remain to be explored in detail. Here we utilize two classic metrics from evolutionary biology, the evolutionary rate index (ERI) and the transcriptome age index (TAI), to investigate the evolutionary alterations that have occurred in each area and developmental stage of the primate brain. We observed a higher evolutionary rate for those genes expressed in the non-cortical areas during primate evolution, particularly in human, with the highest rate of evolution being exhibited at brain developmental stages between late infancy and early childhood. Further, the transcriptome age of the non-cortical areas was lower than that of the cerebral cortex, with the youngest age apparent at brain developmental stages between late infancy and early childhood. Our exploration of the evolutionary patterns manifest in each brain area and developmental stage provides important reference points for further research into primate brain evolution.

Deciphering the Role of Rapidly Evolving Conserved Elements in Primate Brain Development and Exploring Their Potential Involvement in Alzheimer's Disease

Although previous studies have identified human-specific accelerated regions as playing a key role in the recent evolution of the human brain, the characteristics and cellular functions of rapidly evolving conserved elements (RECEs) in ancestral primate lineages remain largely unexplored. Here, based on large-scale primate genome assemblies, we identify 888 RECEs that have been highly conserved in primates that exhibit significantly accelerated substitution rates in the ancestor of the Simiiformes. This primate lineage exhibits remarkable morphological innovations, including an expanded brain mass. Integrative multiomic analyses reveal that RECEs harbor sequences with potential cis-regulatory functions that are activated in the adult human brain. Importantly, genes linked to RECEs exhibit pronounced expression trajectories in the adult brain relative to the fetal stage. Furthermore, we observed an increase in the chromatin accessibility of RECEs in oligodendrocytes from individuals with Alzheimer's disease (AD) compared to that of a control group, indicating that these RECEs may contribute to brain aging and AD. Our findings serve to expand our knowledge of the genetic underpinnings of brain function during primate evolution.

Integrative Omics Reveals Rapidly Evolving Regulatory Sequences Driving Primate Brain Evolution

Although the continual expansion of the brain during primate evolution accounts for our enhanced cognitive capabilities, the drivers of brain evolution have scarcely been explored in these ancestral nodes. Here, we performed large-scale comparative genomic, transcriptomic, and epigenomic analyses to investigate the evolutionary alterations acquired by brain genes and provide comprehensive listings of innovatory genetic elements along the evolutionary path from ancestral primates to human. The regulatory sequences associated with brain-expressed genes experienced rapid change, particularly in the ancestor of the Simiiformes. Extensive comparisons of single-cell and bulk transcriptomic data between primate and nonprimate brains revealed that these regulatory sequences may drive the high expression of certain genes in primate brains. Employing in utero electroporation into mouse embryonic cortex, we show that the primate-specific brain-biased gene BMP7 was recruited, probably in the ancestor of the Simiiformes, to regulate neuronal proliferation in the primate ventricular zone. Our study provides a comprehensive listing of genes and regulatory changes along the brain evolution lineage of ancestral primates leading to human. These data should be invaluable for future functional studies that will deepen our understanding not only of the genetic basis of human brain evolution but also of inherited disease.

Phylogenomic analyses provide insights into primate evolution

Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.

Genomic evidence for the nonpathogenic state in HIV-1-infected northern pig-tailed macaques

HIV-1 is a highly host-specific retrovirus that infects humans but not most nonhuman primates. Thus, the lack of a suitable primate model that can be directly infected with HIV-1 hinders HIV-1/AIDS research. In the previous study, we have found that the northern pig-tailed macaques (NPMs) are susceptible to HIV-1 infection but shows a nonpathogenic state. In this study, to understand this macaque-HIV-1 interaction, we assembled a de novo genome and longitudinal transcriptome for this species during the course of HIV-1 infection. Using comparative genomic analysis, a positively selected gene, Toll-like receptor 8 (TLR8), was identified with a weak ability to induce an inflammatory response in this macaque. In addition, an IFN-stimulated gene, interferon alpha inducible protein 27 (IFI27), was upregulated in acute HIV-1 infection and acquired an enhanced ability to inhibit HIV-1 replication compared with its human ortholog. These findings coincide with the observation of persistently downregulated immune activation and low viral replication, and can partially explain the AIDS-free state in this macaque following HIV-1 infection. This study identified a number of unexplored host genes that may hamper HIV-1 replication and pathogenicity in NPMs, and provided new insights into the host defense mechanisms in cross-species infection of HIV-1. This work will facilitate the adoption of NPM as a feasible animal model for HIV-1/AIDS research.

Genomic and Phenotypic Analyses Reveal Mechanisms Underlying Homing Ability in Pigeon

The homing pigeon was selectively bred from the domestic pigeon for a homing ability over long distances, a very fascinating but complex behavioral trait. Here, we generate a total of 95 whole genomes from diverse pigeon breeds. Comparing the genomes from the homing pigeon population with those from other breeds identifies candidate positively selected genes, including many genes involved in the central nervous system, particularly spatial learning and memory such as LRP8. Expression profiling reveals many neuronal genes displaying differential expression in the hippocampus, which is the key organ for memory and navigation and exhibits significantly larger size in the homing pigeon. In addition, we uncover a candidate gene GSR (encoding glutathione-disulfide reductase) experiencing positive selection in the homing pigeon. Expression profiling finds that GSR is highly expressed in the wattle and visual pigment cell layer, and displays increased expression levels in the homing pigeon. In vitro, a magnetic field stimulates increases in calcium ion concentration in cells expressing pigeon GSR. These findings support the importance of the hippocampus (functioning in spatial memory and navigation) for homing ability, and the potential involvement of GSR in pigeon magnetoreception.

Performance of the rapidly extracted auditory evoked potentials index to detect the recovery and loss of wakefulness in anesthetized and paralyzed patients

BACKGROUND

The rapidly extracted auditory evoked potentials index (A-lineTM ARX Index or AAI) has been proposed as a method to measure the depth of anesthesia. A prospective study was designed to assess the performance of AAI to detect the recovery and loss of wakefulness in anesthetized and paralyzed patients.

METHODS

Fourteen adult patients undergoing elective surgery were anesthetized with propofol 1.5 mg kg-1, vecuronium 0.1 mg kg-1 and further propofol 1.0 mg kg-1. Wakefulness was measured by the ability of the patient to respond to command using the isolated forearm technique (IFT). After the patient responded, propofol was infused at 10 mg kg-1. h-1 until wakefulness (responsiveness) was lost. The AAI was recorded continuously throughout the study and analyzed off-line.

RESULTS

The AAI showed a significant difference between the values registered during, 30 s before and 30 s after the recovery, and also between 30 s before and 30 s after the loss of wakefulness. The prediction probability (Pk) values for AAI were 0.786 and 0.864 during the transitions from unresponsiveness to responsiveness and from responsiveness to unresponsiveness. The area under the receiver operating characteristic curve for the responsive and unresponsive values was 0.926 (SE 0.002, 95% CI 0.922-0.931), and the AAI values of approximately 5%, 50% and 95% predicted probability of wakefulness were 19, 29 and 39, respectively.

CONCLUSION

The AAI may be a good predictor of recovery and loss of wakefulness for anesthetized and paralyzed patients.

Changes in the rapidly extracted auditory evoked potentials index and the bispectral index during sedation induced by propofol or midazolam under epidural block

BACKGROUND

The bispectral index (BIS) and the rapidly extracted auditory evoked potentials index (A-line ARX Index or AAI) have been proposed as methods to measure the depth of sedation. A prospective study was designed to assess the performance of both these methods for measuring the depth of sedation induced by propofol or midazolam under epidural block.

METHODS

Thirty-two ASA I and II adult patients undergoing elective gynaecological surgery under low-thoracolumbar epidural block were studied. Eighteen patients received propofol (Group P: 20 mg bolus every 3 min) and 14 received midazolam (Group M: 0.5 mg bolus every 5 min) until an observer's assessment of alertness/sedation (OAA/S) scale score of 1 was achieved. AAI and BIS were monitored for different OAA/S scores.

RESULTS

AAI and BIS decreased and increased following the changes on the patients' OAA/S scores and correlated with sedation significantly. During the onset phase, the coefficients of Spearman's rank correlation for AAI and BIS were respectively 0.958 and 0.898 (P < 0.001) for Group P, and 0.973 and 0.945 (P < 0.001) for Group M. During the recovery phase in Group P, the coefficients were respectively 0.946 and 0.702 (P < 0.001). Linear regression analysis showed that both AAI and BIS were linearly related to the OAA/S scores. The coefficients of Spearman's rank correlation and linear regression for AAI were all greater than those for BIS (P < 0.05).

CONCLUSIONS

Both AAI and BIS correlated well with the depth of sedation induced by propofol or midazolam under epidural block. AAI may be more valuable when monitoring depth of sedation.

Preparation of levoglucosan by pyrolysis of cellulose and its citric acid fermentation

Levoglucosan (LG), 1,6-anhydro-beta-D-glucopyranose, was produced by pyrolysis of cellulose. A response surface method was used to optimize the reaction parameters: X1, temperature; X2, time required for heating cellulose from room temperature to the designed pyrolysis temperature; and X3, vacuum, and a Box-Behnken design was employed for this purpose. The optimal temperature and time were found to be 388 degrees C and 26.2 min by fixing the vacuum at 1 mm Hg. The levoglucosan prepared was fermented to citric acid by Aspergillus niger CBX-209, which was a mutant derived by gamma-ray mutagenesis of the parent strain CBX-2. The mutant could produce increasing citric acid with increasing LG purity and had a citric acid yield of 87.5% when using purified levoglucosan as the sole carbon source in a 5 day fermentation period.

Effects of bupivacaine and ropivacaine on high-voltage-activated calcium currents of the dorsal horn neurons in newborn rats

BACKGROUND

Local anesthetics, such as bupivacaine, have been reported to block calcium currents in primary sensory neurons and to interfere with the release of neurotransmitters in central nervous system neurons. However, it is unknown whether local anesthetics affect the calcium current activity of central nervous system neurons.

METHODS

Using a traditional whole cell voltage clamp technique, effects of bupivacaine and ropivacaine on high-voltage-activated calcium currents (HVA-Ic(a)) were investigated in enzymatically dissociated dorsal horn neurons of neonatal rats. Calcium currents were evoked by testing pulses from a holding potential of -90 to 0 mV.

RESULTS

Bupivacaine significantly reduced HVA-Ic(a) in a dose-dependent manner. The peak HVA-Ic(a) decreased by 24.5+/-2.5, 32.0+/-6.8, 59.4+/-6.2, 88.3+/-1.5, and 91.6+/-1.1% in response to 10, 30, 50, 100 and 200 microM bupivacaine, respectively. Unlike bupivacaine, ropivacaine markedly increased HVA-Ic(a) at lower concentrations (< 50 microM) but decreased HVA-Ic(a) at higher concentrations (> or = 50 microM). The percent increases in peak HVA-Ic(a) induced by 10 and 30 microM ropivacaine were 95+/-19.1 and 41.6+/-8.3%, respectively. The percent decreases in response to 50, 100, and 200 microM ropivacaine were 21.1+/-2.1, 63.2+/-6.0 and 79.1+/-7.6%, respectively. Results indicate that the inhibitory potency of ropivacaine on HVA-Ic(a) was significantly lower than that of bupivacaine at the same concentrations.

CONCLUSIONS

The current study showed that bupivacaine inhibited HVA-Ic(a) recorded from dorsal horn neurons and that ropivacaine increased HVA-Ic(a) at lower concentrations but decreased HVA-Ic(a) at higher concentrations. The inhibitory potency of ropivacaine was lower than that of bupivacaine. Inhibition of calcium currents of central nervous system neurons may be related to the systemic neurotoxic effects of local anesthetics (e.g., convulsions, seizures).

The effects of ropivacaine on sodium currents in dorsal horn neurons of neonatal rats

We used a whole cell patch clamp technique to study the effects of ropivacaine on rat dorsal horn neurons. Under voltage clamp, ropivacaine (10-400 microM) produced a dose-dependent inhibition of sodium current. From a holding potential (V(h)) of -80 mV, sodium currents evoked by test pulses to 0 mV were inhibited by ropivacaine with a mean drug concentration required to produce 50% current inhibition (IC(50)) value of 117.3 microM, which was more than the value of the bupivacaine (IC(50) 53.7 microM). The inhibition effect of ropivacaine was also voltage-dependent. Current evoked from a V(h) of -60 mV was inhibited by ropivacaine with a mean IC(50) value of 74.3 microM, which was less than that obtained at the V(h) of -80 mV. The inhibition effect of ropivacaine on sodium current was use dependent. Repeated activation by a train of depolarizing pulses (5 Hz, 20 ms) increased the inhibitory effects of ropivacaine. The ratio amplitudes of the 20th to the first pulse were 91.2% and 71.1%, respectively, in the absence and presence of ropivacaine (50 microM). Ropivacaine also produced a significant hyperpolarizing shift of 11 mV in the steady-state inactivation curve of sodium current. The inhibition of ropivacaine on the sodium channel may contribute to the mechanism of action of local anesthetics during epidural and spinal anesthesia.

[Hemodynamic changes in normovolemic and hypovolemic canines during epidural block]

Hemodynamic changes were studied in normovolemic and hypovolemic canines during epidural block. In normovolemic canines after epidural block, stroke volume (SV) increased, heart rate (HR) slowed down and total peripheral resistance (TPR) and mean arterial pressure (MAP) decreased. In addition, hepatic vascular resistance (HVR) and renal vascular resistance (RVR) decreased but quantity of hepatic artery per beat (QHR/HR), quantity of hepatic artery per beat (QPV/HR) and quantity of renal artery per beat (QRA/HR) increased significantly. In hypovolemic canines, the hemodynamic changes after epidural block were similar in normovolemic ones but more abrupt. The increase of QHA/HR, QPV/HR and QRA/HR was not statistically significant, but minute hepatic blood volume quantity of hepatic artery (QHA), quantity of portal vein (QPV) and hepatic blood flow (HBF) decreased significantly. In hypovolemic canines during epidural block, ischemic injury of the liver should be alerted and abrupt hemodynamic changes should be well controlled.