Digging deeper into ancient skeletal proteomes through consecutive digestion with multiple proteases

An increasing number of studies utilise the recovery of ancient skeletal proteomes for phylogenetic and evolutionary analysis. Although these studies manage to extract and analyse ancient peptides, the recovered proteomes are generally small in size and with low protein sequence coverage. We expand on previous observations which have shown that the parallel digestion and analysis of Pleistocene skeletal proteomes increases overall proteome size and protein sequence coverage. Furthermore, we demonstrate that the consecutive digestion of a skeletal proteome using two proteases, particularly the combination of Glu-C or chymotrypsin followed by trypsin digestion, enables the recovery of alternative proteome components not reachable through trypsin digestion alone. The proteomes preserved in Pleistocene skeletal specimens are larger than previously anticipated, but unlocking this protein sequence information requires adaptation of extraction and protein digestion protocols. The sequential utilisation of several proteases is, in this regard, a promising avenue for the study of highly degraded but unique hominin proteomes for phylogenetic purposes. SIGNIFICANCE: Palaeoproteomic analysis of archaeological materials, such as hominin skeletal elements, show great promise in studying past organisms and evolutionary relationships. However, as most proteomic methods are inherently destructive, it is essential to aim to recover as much information as possible from every sample. Currently, digestion with trypsin is the standard approach in most palaeoproteomic studies. We find that parallel or consecutive digestion with multiple proteases can improve proteome size and coverage for both Holocene and Pleistocene bone specimens. This allows for recovery of more proteomic data from a sample and maximises the chance of recovering phylogenetically relevant information.

APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries

The recognition of peptides bound to class I major histocompatibility complex (MHC-I) receptors by T-cell receptors (TCRs) is a determinant of triggering the adaptive immune response. While the exact molecular features that drive the TCR recognition are still unknown, studies have suggested that the geometry of the joint peptide-MHC (pMHC) structure plays an important role. As such, there is a definite need for methods and tools that accurately predict the structure of the peptide bound to the MHC-I receptor. In the past few years, many pMHC structural modeling tools have emerged that provide high-quality modeled structures in the general case. However, there are numerous instances of non-canonical cases in the immunopeptidome that the majority of pMHC modeling tools do not attend to, most notably, peptides that exhibit non-standard amino acids and post-translational modifications (PTMs) or peptides that assume non-canonical geometries in the MHC binding cleft. Such chemical and structural properties have been shown to be present in neoantigens; therefore, accurate structural modeling of these instances can be vital for cancer immunotherapy. To this end, we have developed APE-Gen2.0, a tool that improves upon its predecessor and other pMHC modeling tools, both in terms of modeling accuracy and the available modeling range of non-canonical peptide cases. Some of the improvements include (i) the ability to model peptides that have different types of PTMs such as phosphorylation, nitration, and citrullination; (ii) a new and improved anchor identification routine in order to identify and model peptides that exhibit a non-canonical anchor conformation; and (iii) a web server that provides a platform for easy and accessible pMHC modeling. We further show that structures predicted by APE-Gen2.0 can be used to assess the effects that PTMs have in binding affinity in a more accurate manner than just using solely the sequence of the peptide. APE-Gen2.0 is freely available at https://apegen.kavrakilab.org.

Neurotoxicant effects of bisphenol A, nonylphenol, and tert‑butyl phenol in the Nile tilapia (Oreochromis niloticus)

Worldwide production of alkyl phenols and ethoxylated alkyl phenols is high due to their broad industrial uses. It has been widely documented that they are endocrine disruptors, and it has been suggested that they could exert neurotoxic effects. However, a lack of information about the neurotoxic effects of APs and APEs prevails. In this study, the bisphenol A (BPA), 4-nonylphenol (NP), and 3‑tert-butylphenol (tertBP) effects on brain and spinal cord of Nile tilapia exposed to environmental concentrations were evaluated by assessing acetylcholinesterase (AChE), butyrylcholinesterase (BuChE), and carboxylesterases (CES) activities, and γ-aminobutyric acid (GABA) levels and their effects were evaluated by molecular docking. BPA and NP, tertBP behave as agonists and antagonists of AChE, BuChE, CES, and GABA, with notable differences among organs. However, none of these compounds or their metabolites interact with the enzymes' catalytic triad, suggesting an indirect alteration of enzymatic activities. While inhibiting these enzymes stand out hydrophobic interactions with the peripheral anion site, contacts with the inner face of the active site and blocking the mouth of the gorge of the active site, and steric hindrance in the enzyme pocket of glutamate decarboxylase (GAD). In contrast, inductions probably are by homotropic pseudo-cooperative phenomenon, where APEs behave as anchors favoring the active site to remain open and interactions that confer a conservative stabilization of the regulatory domain. Although the results of this study are complex, with notable differences between organs and toxicants, they are some of the first evidence of the neurotoxicity of alkylphenols and their ethoxylated derivatives.

Diverse cytomegalovirus US11 antagonism and MHC-A evasion strategies reveal a tit-for-tat coevolutionary arms race in hominids

Recurrent, ancient arms races between viruses and hosts have shaped both host immunological defense strategies as well as viral countermeasures. One such battle is waged by the glycoprotein US11 encoded by the persisting human cytomegalovirus. US11 mediates degradation of major histocompatibility class I (MHC-I) molecules to prevent CD8+ T-cell activation. Here, we studied the consequences of the arms race between US11 and primate MHC-A proteins, leading us to uncover a tit-for-tat coevolution and its impact on MHC-A diversification. We found that US11 spurred MHC-A adaptation to evade viral antagonism: In an ancestor of great apes, the MHC-A A2 lineage acquired a Pro184Ala mutation, which confers resistance against the ancestral US11 targeting strategy. In response, US11 deployed a unique low-complexity region (LCR), which exploits the MHC-I peptide loading complex to target the MHC-A2 peptide-binding groove. In addition, the global spread of the human HLA-A*02 allelic family prompted US11 to employ a superior LCR strategy with an optimally fitting peptide mimetic that specifically antagonizes HLA-A*02. Thus, despite cytomegaloviruses low pathogenic potential, the increasing commitment of US11 to MHC-A has significantly promoted diversification of MHC-A in hominids.

Curcumin alleviates myocardial inflammation, apoptosis, and oxidative stress induced by acute pulmonary embolism by regulating microRNA-145-5P/insulin receptor substrate 1 axis

The treatment of patients with acute pulmonary embolism (APE) is extremely challenging due to the complex clinical presentation and prognosis of APE related to the patient's hemodynamic status and insufficient arterial blood flow and right ventricular overload. Protective efficacy against cardiovascular diseases of curcumin, a common natural polyphenolic compound, which has antithrombotic properties and reduces platelet accumulation in the circulation by inhibiting thromboxane synthesis has been demonstrated. However, the direct effect of curcumin on APE has rarely been studied. Therefore, the present study aimed to investigate the therapeutic potential of curcumin in APE and associated myocardial injury to provide new insights into curcumin as a promising competitive new target for the treatment of APE. A suspension of 12 mg/kg microspheres was injected intravenously into rats. An APE rat model was built. Before modeling, intragastric 100 mg/kg curcumin was given, and/or lentiviral plasmid vector targeting microRNA-145-5p or insulin receptor substrate 1 (IRS1) was injected. Pulmonary artery pressure was measured to assess right ventricular systolic pressure (RVSP). Hematoxylin and eosin (H&E) staining was performed on liver tissues and myocardial tissues of APE rats. TUNEL (terminal deoxynucleotidyl transferase biotin-dUTP nick end labeling) staining and immunohistochemical (IHC) staining were conducted to measure apoptosis and CyPA-CD147 expression in the myocardium, respectively. Inflammatory indices interleukin-1beta (IL-1β), interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) were measured by ELISA in cardiac tissues. RT-qPCR and Western blot were performed to determine the expression levels of related genes. In addition, by dual luciferase reporter assay and RIP assay, the relationship between microRNA-145-5p and insulin receptor substrate 1 (IRS1) was confirmed. In results: curcumin improved APE-induced myocardial injury, reduced myocardial tissue edema, and thrombus volume. It attenuated APE-induced myocardial inflammation and apoptosis, as well as reduced lung injury and pulmonary artery pressure. Curcumin promoted microRNA-145-5p expression in APE rat myocardium. MicroRNA-145-5p overexpression protected against APE-induced myocardial injury, and microRNA-145-5p silencing abolished the beneficial effects of curcumin in APE-induced myocardial injury. IRS1 was targeted by microRNA-145-5p. IRS1 silencing attenuated APE-induced myocardial injury, and enhanced therapeutic effect of curcumin on myocardial injury in APE rats. In conclusion, curcumin alleviates myocardial inflammation, apoptosis, and oxidative stress induced by APE by regulating microRNA-145-5p/IRS1 axis.

Phytochemical profiles, antioxidant activities, and synergistic antiproliferative effects of blueberry and apple peel extracts

BACKGROUND

Blueberries and apples exhibit favorable bioactivity and health benefits as a result of their rich phytochemicals. Natural phytochemicals exist in complex forms, but there are few reports on whether have additive, synergistic or antagonistic effects between different phytochemicals. The present study aimed to elucidate the synergistic effects of blueberry extract (BE) and apple peel extract (APE) together with respect to inhibiting the proliferation of HepG2 liver cancer cells. Meanwhile, phytochemical characterization of BE and APE was conducted by HPLC, and total antioxidant activity was determined via a cellular antioxidant activity assay, oxygen radical absorption capacity assay and peroxy radical scavenging capacity assay.

RESULTS

The results showed that BE and APE were rich in phytochemicals and had potent antioxidant activities, which synergistically inhibited cell proliferation. In the bilateral combination, the dose reduction index value increased by two-fold, and the combination index value at 95% inhibition was less than 1. Additionally, BE + APE supplementation could promote the expression levels of p53 and c-myc genes. In conclusion, the BE and APE had strong antioxidant activity and exhibited synergistic inhibition against proliferation of HepG2 cells.

CONCLUSION

The present study can provide a theoretical basis for the synergistic effect of different phytochemicals in health care. © 2023 Society of Chemical Industry.

Signatures of Co-evolution and Co-regulation in the CYP3A and CYP4F Genes in Humans

Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drug responses and metabolic functions. In this study, we investigate the genetic diversity of CYP450 genes. We found that two clusters, CYP3A and CYP4F, are notably differentiated across human populations with evidence for selective pressures acting on both clusters: we found signals of recent positive selection in CYP3A and CYP4F genes and signals of balancing selection in CYP4F genes. Furthermore, an extensive amount of unusual linkage disequilibrium is detected in this latter cluster, indicating co-evolution signatures among CYP4F genes. Several of the selective signals uncovered co-localize with expression quantitative trait loci (eQTL), which could suggest epistasis acting on co-regulation in these gene families. In particular, we detected a potential co-regulation event between CYP3A5 and CYP3A43, a gene whose function remains poorly characterized. We further identified a causal relationship between CYP3A5 expression and reticulocyte count through Mendelian randomization analyses, potentially involving a regulatory region displaying a selective signal specific to African populations. Our findings linking natural selection and gene expression in CYP3A and CYP4F subfamilies are of importance in understanding population differences in metabolism of nutrients and drugs.

Preventive Effects of Apple Polyphenol Extract on High-Fat-Diet-Induced Hepatic Steatosis Are Related to the Regulation of Hepatic Lipid Metabolism, Autophagy, and Gut Microbiota in Aged Mice

Our previous study confirmed that the ameliorated effects of an intervention with an apple polyphenol extract (APE) on hepatic steatosis induced by a high-fat diet (HFD) are dependent on SIRT1. Since SIRT1 expression decreases with age, it remains unclear whether APE intervention is effective against hepatic steatosis in aged mice. Thus, 12-month-old C57BL/6 male mice were fed with an HFD to establish an aging model of hepatic steatosis and treated with 500 mg/(kg·bw·d) APE for 12 weeks. Young mice (two months old) and baseline mice were used as controls to examine the effects of natural aging on hepatic steatosis. Compared with baseline mice, no obvious difference in hepatic histopathological assessment was observed for both young and aged mice on normal diets. Meanwhile, HFD induced much higher nonalcoholic fatty liver disease (NAFLD) activity scores in aged mice than in young mice. APE intervention ameliorated lipid and glucose metabolic disorders and liver injury in HFD-fed aged mice, improved hepatic steatosis, and reduced NAFLD activity scores. The upregulated expressions of SIRT1, HSL, ATG5, Ulk1, and Becn1 and downregulated expressions of HMGCR and FOXO1 suggested improved lipid metabolism and activated autophagy. APE intervention decreased the ratio of Firmicutes/Bacteroidetes and elevated the Akkermansia probiotics abundance. In summary, HFD showed a more significant effect on hepatic steatosis compared to the natural aging process in aged mice, and APE might be a promising dietary ingredient for alleviating hepatic steatosis.

Machine learning-based protein signatures for differentiating hypertensive disorders of pregnancy

Hypertensive disorders of pregnancy (HDP) result in major maternal and fetal complications. Our study aimed to find a panel of protein markers to identify HDP by applying machine-learning models. The study was conducted on a total of 133 samples, divided into four groups, healthy pregnancy (HP, n = 42), gestational hypertension (GH, n = 67), preeclampsia (PE, n = 9), and ante-partum eclampsia (APE, n = 15). Thirty circulatory protein markers were measured using Luminex multiplex immunoassay and ELISA. Significant markers were screened for potential predictive markers by both statistical and machine-learning approaches. Statistical analysis found seven markers such as sFlt-1, PlGF, endothelin-1(ET-1), basic-FGF, IL-4, eotaxin and RANTES to be altered significantly in disease groups compared to healthy pregnant. Support vector machine (SVM) learning model classified GH and HP with 11 markers (eotaxin, GM-CSF, IL-4, IL-6, IL-13, MCP-1, MIP-1α, MIP-1β, RANTES, ET-1, sFlt-1) and HDP with 13 markers (eotaxin, G-CSF, GM-CSF, IFN-gamma, IL-4, IL-5, IL-6, IL-13, MCP-1, MIP-1β, RANTES, ET-1, sFlt-1). While logistic regression (LR) model classified PE with 13 markers (basic FGF, IL-1β, IL-1ra, IL-7, IL-9, MIP-1β, RANTES, TNF-alpha, nitric oxide, superoxide dismutase, ET-1, PlGF, sFlt-1) and APE by 12 markers (eotaxin, basic-FGF, G-CSF, GM-CSF, IL-1β, IL-5, IL-8, IL-13, IL-17, PDGF-BB, RANTES, PlGF). These markers may be used to diagnose the progression of healthy pregnant to a hypertensive state. Future longitudinal studies with large number of samples are needed to validate these findings.

Wheat Germ-Derived Peptide Alleviates Dextran Sulfate Sodium-Induced Colitis in Mice

This study explores the protective properties and potential mechanisms of wheat-germ-derived peptide APEPEPAF (APE) against ulcerative colitis. Colitis mice induced by dextran sulfate sodium (DSS) were used as the animal model. The results showed that the APE peptide could alleviate colitis symptoms including weight loss, colon shortening, and histopathological changes. This peptide attenuated the generation of inflammatory cytokines by inhibiting the phosphorylation of protein kinase PKCζ (Thr410) and NF-κB transcriptional activity in DSS-induced mice, suggesting that APE ameliorates colitis inflammation by regulating the PKCζ/NF-κB signaling pathway. APE also preserved the barrier function of the colon by dose-dependently promoting the expression of tight junction proteins (claudin-1, zonula occluded-1, and occludin). In addition, APE significantly decreased the abundance of Bacteroides and increased the abundance of Dubosiella and Lachnospiraceae_UCG-006 to improve the intestinal flora imbalance in DSS-induced colitis mice. Therefore, wheat germ peptide APE can be used as a novel agent and dietary supplement to treat ulcerative colitis..

Apple Polyphenol Extract Ameliorates Atherosclerosis and Associated Cognitive Impairment through Alleviating Neuroinflammation by Weakening TLR4 Signaling and NLRP3 Inflammasome in High-Fat/Cholesterol Diet-Fed LDLR-/- Male Mice

Although studies have supported the beneficial effects of the ingredients of apple polyphenol extract (APE), a polyphenol mixture being extracted from whole fresh apples, on neurodegenerative diseases, the role of APE in atherosclerosis-related cognitive impairment remains unclear. To clarify the role of APE in regulating cognitive dysfunction in mice with atherosclerosis and the underlying mechanisms, high-fat/cholesterol diet-fed male LDLR-/- mice were gavaged with 125 or 500 mg/(kg·bw·d) APE solution or sterile double-distilled water for consecutive 8 weeks, and age-matched C57BL/6 male mice were employed as normal control. APE intervention increased the serum concentration of high-density apolipoprotein cholesterol, improved atherosclerosis, and ameliorated cognitive function of mice by inhibiting the phosphorylation of tau protein, supporting with significantly reduced platform latency and obviously increased swimming distance in the target quadrant according to the Morris water maze test. APE intervention alleviated neuroinflammation by attenuating the activation of microglia and astrocytes and inhibiting TLR4 signaling with reduced protein expression of NF-κB, MyD88, TRIF, and IKKβ. Meanwhile, APE intervention inactivated NLRP3 inflammasome with downregulated protein expression of caspase-1, IL-18, and IL-1β. Additionally, APE intervention improved the damaged brain barrier structure by upregulating the protein expression of ZO-1 and occludin. Therefore, our research supplemented new data, supporting the potential of APE as an effective dietary bioactive ingredient to improve atherosclerosis and associated cognitive impairment.

Sirtuin3 confers protection against acute pulmonary embolism through anti-inflammation, and anti-oxidative stress, and anti-apoptosis properties: participation of the AMP-activated protein kinase/mammalian target of rapamycin pathway

An increasing number of studies have suggested that oxidative stress and inflammation play momentous roles in acute pulmonary embolism (APE). Honokiol, a bioactive biphenolic phytochemical substance, is known for its strong anti-oxidative and anti-inflammatory effects, and it served as an activator of sirtuin3 (SIRT3) in the present study. The purposes of the study were to explore the effects of honokiol on APE rats and investigate whether the function of honokiol is mediated by SIRT3 activation. In the study, the rats received a right femoral vein injection of dextran gel G-50 particles (12 mg/kg) to establish the APE model and were subsequently administered honokiol and/or a selective SIRT3 inhibitor 3-(1H-1,2,3-triazol-4-yl)pyridine (3-TYP; 5 mg/kg) intraperitoneally. The results showed that SIRT3 activation by honokiol attenuated the loss in lung function, ameliorated the inflammatory response and oxidative damage, and inhibited apoptosis in lung tissues of the rats with APE but that this was reversed by 3-TYP. In addition, we found that the AMP-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) pathway might be activated by honokiol but restrained by 3-TYP. These results indicated that honokiol was capable of suppressing the adverse effects of APE and that this was diminished by SIRT3 suppression, implying that activation of SIRT3 might serve as a therapeutic method for APE.

Functional importance and divergence of plant apurinic/apyrimidinic endonucleases in somatic and meiotic DNA repair

Apurinic/apyrimidinic (AP) sites are one of the most abundant DNA lesions and are mainly repaired by AP endonucleases (APEs). While most eukaryotic genomes encode two APEs, plants usually possess three APEs, namely APE1L, APE2, and ARP. To date, the biological relevance and functional divergence of plant APEs are unclear. Here, we show that the three plant APEs have ancient origins, with the APE1L clade being plant-specific. In Arabidopsis thaliana, simultaneously mutating APE1L and APE2, but not ARP alone or in combination with either APE1L or APE2, results in clear developmental defects linked to genotoxic stress. Genetic analyses indicated that the three plant APEs have different substrate preferences in vivo. ARP is mainly responsible for AP site repair, while APE1L and APE2 prefer to repair 3'-blocked single-stranded DNA breaks. We further determined that APEs play an important role in DNA repair and the maintenance of genomic integrity in meiotic cells. The ape1l ape2 double mutant exhibited a greatly enhanced frequency of sporulation 1 (SPO11-1)-dependent and SPO11-1-independent double-stranded DNA breaks. The DNA damage response (DDR) was activated in ape1l ape2 to trigger pollen abortion. Our findings suggest functional divergence of plant APEs and reveal important roles of plant APEs during vegetative and reproductive development.

Discovery, classification, evolution and diversity of Siglecs

Immunoglobulin (Ig) superfamily proteins play diverse roles in vertebrates, including regulation of cellular responses by sensing endogenous or exogenous ligands. Siglecs are a family of glycan-recognizing proteins belonging to the Ig superfamily (i.e., I-type lectins). Siglecs are expressed on various leukocyte types and are involved in diverse aspects of immunity, including the regulation of inflammatory responses, leukocyte proliferation, host-microbe interaction, and cancer immunity. Sialoadhesin/Siglec-1, CD22/Siglec-2, and myelin-associated glycoprotein/Siglec-4 were among the first to be characterized as members of the Siglec family, and along with Siglec-15, they are relatively well-conserved among tetrapods. Conversely, CD33/Siglec-3-related Siglecs (CD33rSiglecs, so named as they show high sequence similarity with CD33/Siglec-3) are encoded in a gene cluster with many interspecies variations and even intraspecies variations within some lineages such as humans. The rapid evolution of CD33rSiglecs expressed on leukocytes involved in innate immunity likely reflects the selective pressure by pathogens that interact and possibly exploit these Siglecs. Human Siglecs have several additional unique and/or polymorphic properties as compared with closely related great apes, changes possibly related to the loss of the sialic acid Neu5Gc, another distinctly human event in sialobiology. Multiple changes in human CD33rSiglecs compared to great apes include many examples of human-specific expression in non-immune cells, coinciding with human-specific diseases involving such cell types. Some Siglec gene polymorphisms have dual consequences-beneficial in a situation but detrimental in another. The association of human Siglec gene polymorphisms with several infectious and non-infectious diseases likely reflects the ongoing competition between the host and microbial pathogens.

Transcutaneous vagus nerve stimulation attenuates autoantibody-mediated cardiovagal dysfunction and inflammation in a rabbit model of postural tachycardia syndrome

PURPOSE

Previous studies demonstrated M2 muscarinic acetylcholine receptor-activating autoantibodies (M2R-AAb) were present in some patients with postural tachycardia syndrome (POTS). This study examines how these autoantibodies might contribute to the pathophysiology of POTS, and whether low-level tragus stimulation (LLTS) can ameliorate autoantibody-mediated autonomic dysregulation in the rabbit.

METHODS

Five New Zealand white rabbits were immunized with a M2R second extracellular loop peptide to produce cholinomimetic M2R-AAb. Tilt test and infusion studies were performed on conscious rabbits before immunization, 6 weeks after immunization, and 8 weeks after immunization with 2-week daily LLTS treatment. Each rabbit served as its own control.

RESULTS

Compared to preimmune state, an enhanced heart rate increase and decreased parasympathetic activity upon tilting were observed in immunized rabbits. Furthermore, these rabbits demonstrated an attenuated heart rate-slowing response to infusion of the M2R orthosteric agonist arecaidine propargyl ester (APE), suggesting an inhibitory allosteric effect of M2R-AAb. There was also a significant increase in serum inflammatory cytokines in immunized rabbits. LLTS treatment suppressed the postural tachycardia, improved the sympathovagal balance with increased acetylcholine secretion, reduced the levels of inflammatory cytokines, and reversed the attenuated heart rate response to APE in immunized rabbits. No suppression of M2R-AAb expression by LLTS was found during this short-term study period. Receptor-modulating activity of M2R-AAb produced in immunized rabbits was confirmed with in vitro bioassay.

CONCLUSIONS

Autoantibody inhibition of cholinergic ligand activity may be involved in the development of cardiovagal dysfunction and inflammation associated with POTS, both of which can be improved by vagal stimulation.

Ancestral APOBEC3B Nuclear Localization Is Maintained in Humans and Apes and Altered in Most Other Old World Primate Species

APOBEC3B is an innate immune effector enzyme capable of introducing mutations in viral genomes through DNA cytosine-to-uracil editing. Recent studies have shown that gamma-herpesviruses, such as Epstein-Barr virus (EBV), have evolved a potent APOBEC3B neutralization mechanism to protect lytic viral DNA replication intermediates in the nuclear compartment. APOBEC3B is additionally unique as the only human DNA deaminase family member that is constitutively nuclear. Nuclear localization has therefore been inferred to be essential for innate antiviral function. Here, we combine evolutionary, molecular, and cell biology approaches to address whether nuclear localization is a conserved feature of APOBEC3B in primates. Despite the relatively recent emergence of APOBEC3B approximately 30 to 40 million years ago (MYA) in Old World primates by genetic recombination (after the split from the New World monkey lineage 40 to 50 MYA), we find that the hallmark nuclear localization of APOBEC3B shows variability. For instance, although human and several nonhuman primate APOBEC3B enzymes are predominantly nuclear, rhesus macaque and other Old World primate APOBEC3B proteins are clearly cytoplasmic or cell wide. A series of human/rhesus macaque chimeras and mutants combined to map localization determinants to the N-terminal half of the protein with residues 15, 19, and 24 proving critical. Ancestral APOBEC3B reconstructed from present-day primate species also shows strong nuclear localization. Together, these results indicate that the ancestral nuclear localization of APOBEC3B is maintained in present-day human and ape proteins, but nuclear localization is not conserved in all Old World monkey species despite a need for antiviral functions in the nuclear compartment. IMPORTANCE APOBEC3 enzymes are single-stranded DNA cytosine-to-uracil deaminases with beneficial roles in antiviral immunity and detrimental roles in cancer mutagenesis. Regarding viral infection, all seven human APOBEC3 enzymes have overlapping roles in restricting virus types that require DNA for replication, including EBV, HIV, human papillomavirus (HPV), and human T-cell leukemia virus (HTLV). Regarding cancer, at least two APOBEC3 enzymes, APOBEC3B and APOBEC3A, are prominent sources of mutation capable of influencing clinical outcomes. Here, we combine evolutionary, molecular, and cell biology approaches to characterize primate APOBEC3B enzymes. We show that nuclear localization is an ancestral property of APOBEC3B that is maintained in present-day human and ape enzymes, but not conserved in other nonhuman primates. This partial mechanistic conservation indicates that APOBEC3B is important for limiting the replication of DNA-based viruses in the nuclear compartment. Understanding these pathogen-host interactions may contribute to the development of future antiviral and antitumor therapies.

Human-specific ARHGAP11B ensures human-like basal progenitor levels in hominid cerebral organoids

The human-specific gene ARHGAP11B has been implicated in human neocortex expansion. However, the extent of ARHGAP11B's contribution to this expansion during hominid evolution is unknown. Here we address this issue by genetic manipulation of ARHGAP11B levels and function in chimpanzee and human cerebral organoids. ARHGAP11B expression in chimpanzee cerebral organoids doubles basal progenitor levels, the class of cortical progenitors with a key role in neocortex expansion. Conversely, interference with ARHGAP11B's function in human cerebral organoids decreases basal progenitors down to the chimpanzee level. Moreover, ARHGAP11A or ARHGAP11B rescue experiments in ARHGAP11A plus ARHGAP11B double-knockout human forebrain organoids indicate that lack of ARHGAP11B, but not of ARHGAP11A, decreases the abundance of basal radial glia-the basal progenitor type thought to be of particular relevance for neocortex expansion. Taken together, our findings demonstrate that ARHGAP11B is necessary and sufficient to ensure the elevated basal progenitor levels that characterize the fetal human neocortex, suggesting that this human-specific gene was a major contributor to neocortex expansion during human evolution.

Human-specific ARHGAP11B ensures human-like basal progenitor levels in hominid cerebral organoids

The human-specific gene ARHGAP11B has been implicated in human neocortex expansion. However, the extent of ARHGAP11B's contribution to this expansion during hominid evolution is unknown. Here we address this issue by genetic manipulation of ARHGAP11B levels and function in chimpanzee and human cerebral organoids. ARHGAP11B expression in chimpanzee cerebral organoids doubles basal progenitor levels, the class of cortical progenitors with a key role in neocortex expansion. Conversely, interference with ARHGAP11B's function in human cerebral organoids decreases basal progenitors down to the chimpanzee level. Moreover, ARHGAP11A or ARHGAP11B rescue experiments in ARHGAP11A plus ARHGAP11B double-knockout human forebrain organoids indicate that lack of ARHGAP11B, but not of ARHGAP11A, decreases the abundance of basal radial glia - the basal progenitor type thought to be of particular relevance for neocortex expansion. Taken together, our findings demonstrate that ARHGAP11B is necessary and sufficient to ensure the elevated basal progenitor levels that characterize the fetal human neocortex, suggesting that this human-specific gene was a major contributor to neocortex expansion during human evolution.

Calcium isotopic patterns in enamel reflect different nursing behaviors among South African early hominins

Nursing is pivotal in the social and biological evolution of hominins, but to date, early-life behavior among hominin lineages is a matter of debate. The calcium isotopic compositions (δ^44/42Ca) of tooth enamel can provide dietary information on this period. Here, we measure the δ^44/42Ca values in spatially located microsized regions in tooth enamel of 37 South African hominins to reconstruct early-life dietary-specific variability in Australopithecus africanus, Paranthropus robustus, and early Homo. Very low δ^44/42Ca values (<-1.4‰), indicative of milk consumption, are measured in early Homo but not in A. africanus and P. robustus. In these latter taxa, transitional or adult nonmilk foods must have been provided in substantial quantities relative to breast milk rapidly after birth. The results suggest that early Homo have continued a predominantly breast milk-based nursing period for longer than A. africanus and P. robustus and have consequently more prolonged interbirth interval.

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

BACKGROUND

The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively.

RESULTS

Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification.

CONCLUSIONS

The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized between moderately divergent proteomes, as indicated by almost complete recovery of informative positions in the search against the chimpanzee proteome (≈90%, 6-8 Ma). This provides a bioinformatic background to future phylogenetic and proteomic analysis of ancient hominin proteomes, including the future description of novel hominin amino acid sequences, but also has negative implications for the study of fast-evolving proteins in hominins, non-hominin animals, and ancient bacterial proteins in evolutionary contexts.

Incremental distribution of strontium and zinc in great ape and fossil hominin cementum using synchrotron X-ray fluorescence mapping

Cementum and the incremental markings it contains have been widely studied as a means of ageing animals and retrieving information about diet and nutrition. The distribution of trace elements in great ape and fossil hominin cementum has not been studied previously. Synchrotron X-ray fluorescence (SXRF) enables rapid scanning of large tissue areas with high resolution of elemental distributions. First, we used SXRF to map calcium, phosphorus, strontium and zinc distributions in great ape dentine and cementum. At higher resolution, we compared zinc and strontium distributions in cellular and acellular cementum in regions where clear incremental markings were expressed. We then mapped trace element distributions in fossil hominin dentine and cementum from the 1.55-1.65 million year old site of Koobi Fora, Kenya. Zinc, in particular, is a precise marker of cementum increments in great apes, and is retained in fossil hominin cementum, but does not correspond well with the more diffuse fluctuations observed in strontium distribution. Cementum is unusual among mineralized tissues in retaining so much zinc. This is known to reduce the acid solubility of hydroxyapatite and so may confer resistance to resorption by osteoclasts in the dynamic remodelling environment of the periodontal ligament and alveolar bone.

Lineage-Specific Changes in Biomarkers in Great Apes and Humans

Although human biomedical and physiological information is readily available, such information for great apes is limited. We analyzed clinical chemical biomarkers in serum samples from 277 wild- and captive-born great apes and from 312 healthy human volunteers as well as from 20 rhesus macaques. For each individual, we determined a maximum of 33 markers of heart, liver, kidney, thyroid and pancreas function, hemoglobin and lipid metabolism and one marker of inflammation. We identified biomarkers that show differences between humans and the great apes in their average level or activity. Using the rhesus macaques as an outgroup, we identified human-specific differences in the levels of bilirubin, cholinesterase and lactate dehydrogenase, and bonobo-specific differences in the level of apolipoprotein A-I. For the remaining twenty-nine biomarkers there was no evidence for lineage-specific differences. In fact, we find that many biomarkers show differences between individuals of the same species in different environments. Of the four lineage-specific biomarkers, only bilirubin showed no differences between wild- and captive-born great apes. We show that the major factor explaining the human-specific difference in bilirubin levels may be genetic. There are human-specific changes in the sequence of the promoter and the protein-coding sequence of uridine diphosphoglucuronosyltransferase 1 (UGT1A1), the enzyme that transforms bilirubin and toxic plant compounds into water-soluble, excretable metabolites. Experimental evidence that UGT1A1 is down-regulated in the human liver suggests that changes in the promoter may be responsible for the human-specific increase in bilirubin. We speculate that since cooking reduces toxic plant compounds, consumption of cooked foods, which is specific to humans, may have resulted in relaxed constraint on UGT1A1 which has in turn led to higher serum levels of bilirubin in humans.

Theodore E. Woodward award. The evolution of obesity: insights from the mid-Miocene

All humans are double knockouts. Humans lack the ability to synthesize vitamin C due to a mutation in L-gulono-lactone oxidase that occurred during the late Eocene, and humans have higher serum uric acid levels due to a mutation in uricase that occurred in the mid Miocene. In this paper we review the hypothesis that these mutations have in common the induction of oxidative stress that may have had prosurvival effects to enhance the effects of fructose to increase fat stores. Fructose was the primary nutrient in fruit which was the main staple of early primates, but this food likely became less available during the global cooling that occurred at the time of these mutations. However, in today's society, the intake of fructose, primarily in the form of added sugars, has skyrocketed, while the intake of natural fruits high in vitamin C has fallen. We suggest that it is the interaction of these genetic changes with diet that is responsible for the obesity epidemic today. Hence, we propose that Neel's thrifty gene hypothesis is supported by these new insights into the mechanisms regulating fructose metabolism.

Origin and evolution of ubiquitin-conjugating enzymes from Guillardia theta nucleomorph to hominoid

The origin of eukaryotic ubiquitin-conjugating enzymes (E2s) can be traced back to the Guillardia theta nucleomorph about 2500 million years ago (Mya). E2s are largely vertically inherited over eukaryotic evolution [Lespinet, O., Wolf, Y.I., Koonin, E.V., Aravind, L., 2002. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 1048-1059], while mammal E2s experienced evolution of multigene families by gene duplications which have been accompanied by the increase in the species complexity. Because of alternatively splicing, primate-specific expansions of E2s happened once again at a transcriptional level. Both of them resulted in increasing genomic complexity and diversity of primate E2 proteomic function. The evolutionary processes of human E2 gene structure during expansions were accompanied by exon duplication and exonization of intronic sequences. Exonizations of Transposable Elements (TEs) in UBE2D3, UBE2L3 and UBE2V1 genes from primates indicate that exaptation of TEs also plays important roles in the structural innovation of primate-specific E2s and may create alternative splicing isoforms at a transcriptional level. Estimates for the ratio of dN/dS suggest that a strong purifying selection had acted upon protein-coding sequences of their orthologous UBE2D2, UBE2A, UBE2N, UBE2I and Rbx1 genes from animals, plants and fungi. The similar rates of synonymous substitutions are in accordance with the neutral mutation-random drift hypothesis of molecular evolution. Systematic detection of the origin and evolution of E2s, analyzing the evolution of E2 multigene families by gene duplications and the evolutionary processes of E2s during expansions, and testing its evolutionary force using E2s from distant phylogenetic lineages may advance our distinguishing of ancestral E2s from created E2s, and reveal previously unknown relationships between E2s and metazoan complexity. Analysis of these conserved proteins provides strong support for a close relationship between social amoeba and eukaryote, choanoflagellate and metazoan, and for the central roles of social amoeba and choanoflagellate in the origin and evolution of eukaryote and metazoan. Retracing the different stages of primate E2 exonization by monitoring genomic events over 63 Myr of primate evolution will advance our understanding of how TEs dynamically modified primate transcriptome and proteome in the past, and continue to do so.

Mitochondrial targeting adaptation of the hominoid-specific glutamate dehydrogenase driven by positive Darwinian selection

Many new gene copies emerged by gene duplication in hominoids, but little is known with respect to their functional evolution. Glutamate dehydrogenase (GLUD) is an enzyme central to the glutamate and energy metabolism of the cell. In addition to the single, GLUD-encoding gene present in all mammals (GLUD1), humans and apes acquired a second GLUD gene (GLUD2) through retroduplication of GLUD1, which codes for an enzyme with unique, potentially brain-adapted properties. Here we show that whereas the GLUD1 parental protein localizes to mitochondria and the cytoplasm, GLUD2 is specifically targeted to mitochondria. Using evolutionary analysis and resurrected ancestral protein variants, we demonstrate that the enhanced mitochondrial targeting specificity of GLUD2 is due to a single positively selected glutamic acid-to-lysine substitution, which was fixed in the N-terminal mitochondrial targeting sequence (MTS) of GLUD2 soon after the duplication event in the hominoid ancestor ∼18–25 million years ago. This MTS substitution arose in parallel with two crucial adaptive amino acid changes in the enzyme and likely contributed to the functional adaptation of GLUD2 to the glutamate metabolism of the hominoid brain and other tissues. We suggest that rapid, selectively driven subcellular adaptation, as exemplified by GLUD2, represents a common route underlying the emergence of new gene functions.

Little is known about the functional evolution of new hominoid genes. In this study, we utilized a combination of evolutionary analyses and cell biology experiments to unveil a novel mode by which the human- and ape-specific glutamate dehydrogenase enzyme (GLUD2) functionally adapted. We find that whereas the GLUD1 parental protein (present in all mammals) localizes to mitochondria and also to the cytoplasm, GLUD2 is specifically targeted to mitochondria. Using resurrected ancestral proteins and site-directed mutagenesis, we show that the optimized mitochondrial targeting capacity of GLUD2 is due to a single positively selected amino acid substitution in its N-terminal targeting sequence, which occurred soon after the duplication event in the ape ancestor 18–25 million years ago. The specialization in mitochondrial localization is probably linked to the function of GLUD2 in the glutamate metabolism of the brain (recycling of glutamate in astrocytes), but is likely also of functional relevance in other tissues in which GLUD2 is expressed. We suggest that in addition to the traditionally considered modes of functional adaptation (changes in gene expression and/or the biochemical function of the protein), rapid and selectively driven subcellular adaptation to specific ancestral compartments may represent a common yet previously little-considered mechanism for the origin of new gene functions.

Effects of Brain Evolution on Human Nutrition and Metabolism

The evolution of large human brain size has had important implications for the nutritional biology of our species. Large brains are energetically expensive, and humans expend a larger proportion of their energy budget on brain metabolism than other primates. The high costs of large human brains are supported, in part, by our energy- and nutrient-rich diets. Among primates, relative brain size is positively correlated with dietary quality, and humans fall at the positive end of this relationship. Consistent with an adaptation to a high-quality diet, humans have relatively small gastrointestinal tracts. In addition, humans are relatively "undermuscled" and "over fat" compared with other primates, features that help to offset the high energy demands of our brains. Paleontological evidence indicates that rapid brain evolution occurred with the emergence of Homo erectus 1.8 million years ago and was associated with important changes in diet, body size, and foraging behavior.

A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids

Most new genes arise by duplication of existing gene structures, after which relaxed selection on the new copy frequently leads to mutational inactivation of the duplicate; only rarely will a new gene with modified function emerge. Here we describe a unique mechanism of gene creation, whereby new combinations of functional domains are assembled at the RNA level from distinct genes, and the resulting chimera is then reverse transcribed and integrated into the genome by the L1 retrotransposon. We characterized a novel gene, which we termed PIP5K1A and PSMD4-like (PIPSL), created by this mechanism from an intergenic transcript between the phosphatidylinositol-4-phosphate 5-kinase (PIP5K1A) and the 26S proteasome subunit (PSMD4) genes in a hominoid ancestor. PIPSL is transcribed specifically in the testis both in humans and chimpanzees, and is post-transcriptionally repressed by independent mechanisms in these primate lineages. The PIPSL gene encodes a chimeric protein combining the lipid kinase domain of PIP5K1A and the ubiquitin-binding motifs of PSMD4. Strong positive selection on PIPSL led to its rapid divergence from the parental genes PIP5K1A and PSMD4, forming a chimeric protein with a distinct cellular localization and minimal lipid kinase activity, but significant affinity for cellular ubiquitinated proteins. PIPSL is a tightly regulated, testis-specific novel ubiquitin-binding protein formed by an unusual exon-shuffling mechanism in hominoid primates and represents a key example of rapid evolution of a testis-specific gene.

Energetics in Homo erectus and other early hominins: The consequences of increased lower-limb length

Previous studies of daily energy expenditure (DEE) in hominin fossils have estimated locomotor costs using a formula that was based on six species, all 18 kg or less in mass, including no primates, and that has a number of other problems when applied in an ecological context. It is well established that the energetic cost of human walking is lower than that of representative mammals, particularly for individuals with long lower limbs. The current study reevaluates the daily energy expenditures of a variety of hominin species using more appropriate approaches to estimating locomotor costs. To estimate DEE for primates, I relied on published data on body mass, day range, and the percentage of time spent in various activities. Based on those data, I calculated a value for nonlocomotor DEE. I then used a variant of a method that I have suggested elsewhere to calculate the daily cost due to locomotion (DEEL) and summed the two to calculate total DEE. The more up-to-date methods for calculating the cost of travel result in lower estimates of this aspect of the energy budget than seen in previous studies. Values obtained here for DEE in various representatives of Australopithecus are lower than reported previously by around 200 kcal/day. Taking into account the greater economy of human walking, particularly the effect of the longer lower limbs found in many later Homo species, also results in lowered estimates of DEE. Elongation of the lower limbs in H. erectus reduced relative travel costs nearly 50% in comparison to A.L. 288-1 (A. afarensis). The present method for calculating DEE indicates that female H. erectus DEE was 84% greater than that of female Australopithecus; this disparity is even larger than that suggested by previous workers.

The testis-specific apoptosis related gene TTL.6 underwent adaptive evolution in the lineage leading to humans

The TTL.6 gene is a member of the tubulin-tyrosine ligase (TTL) family involved in apoptosis and preferentially expressed in the testis. We sequenced the coding region and part of the introns of TTL.6 in world wide human populations and five representative nonhuman primate species covering great apes, lesser ape and Old World monkey. The sequence substitution patterns of TTL.6 in primates demonstrated a sharp difference in evolutionary rates among different primate lineages. Our results indicated an accelerated evolution of TTL.6 in the human lineage, which was caused by Darwinian positive selection. Further analysis on sequence variations in human populations demonstrated an excess of derived common alleles, which was likely caused by genetic hitchhiking, an implication of recent positive selection on TTL.6 in human populations.

Intraspecies variation in BMR does not affect estimates of early hominin total daily energy expenditure

We conducted a meta-analysis of 45 studies reporting basal metabolic rate (BMR) data for Homo sapiens and Pan troglodytes to determine the effects of sex, age, and latitude (a proxy for climate, in humans only). BMR was normalized for body size using fat-free mass in humans and body mass in chimpanzees. We found no effect of sex in either species and no age effect in chimpanzees. In humans, juveniles differed significantly from adults (ANCOVA: P < 0.001), and senescent adults differed significantly from adults younger than 50 years (P < 0.001). Europeans differed significantly from tropical populations (P < 0.001). On the basis of these observations, we derived new equations describing the relationship between BMR and body size, and used them to predict total daily energy expenditure (TEE) in four early hominin species. Our predictions concur with previous TEE estimates (i.e. Leonard and Robertson: Am J Phys Anthropol 102 (1997) 265-281), and support the conclusion that TEE increased greatly with H. erectus. Our results show that intraspecific variation in BMR does not affect TEE estimates for interspecific comparisons. Comparisons of more closely related groups such as humans and Neandertals, however, may benefit from consideration of this variation.

Hominins, sedges, and termites: new carbon isotope data from the Sterkfontein valley and Kruger National Park

Stable carbon isotope analyses have shown that South African australopiths did not have exclusively frugivorous diets, but also consumed significant quantities of C4 foods such as grasses, sedges, or animals that ate these foods. Yet, these studies have had significant limitations. For example, hominin sample sizes were relatively small, leading some to question the veracity of the claim for australopith C4 consumption. In addition, it has been difficult to determine which C4 resources were actually utilized, which is at least partially due to a lack of stable isotope data on some purported australopith foods. Here we begin to address these lacunae by presenting carbon isotope data for 14 new hominin specimens, as well as for two potential C4 foods (termites and sedges). The new data confirm that non-C3 foods were heavily utilized by australopiths, making up about 40% and 35% of Australopithecus and Paranthropus diets respectively. Most termites in the savanna-woodland biome of the Kruger National Park, South Africa, have intermediate carbon isotope compositions indicating mixed C3/C4 diets. Only 28% of the sedges in Kruger were C4, and few if any had well-developed rhizomes and tubers that make some sedges attractive foods. We conclude that although termites and sedges might have contributed to the C4 signal in South African australopiths, other C4 foods were also important. Lastly, we suggest that the consumption of C4 foods is a fundamental hominin trait that, along with bipedalism, allowed australopiths to pioneer increasingly open and seasonal environments.

Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux

The enzyme glutamate dehydrogenase (GDH) is important for recycling the chief excitatory neurotransmitter, glutamate, during neurotransmission. Human GDH exists in housekeeping and brain-specific isotypes encoded by the genes GLUD1 and GLUD2, respectively. Here we show that GLUD2 originated by retroposition from GLUD1 in the hominoid ancestor less than 23 million years ago. The amino acid changes responsible for the unique brain-specific properties of the enzyme derived from GLUD2 occurred during a period of positive selection after the duplication event.

Can fat explain the human brain's big bang evolution?-Horrobin's leads for comparative and functional genomics

When David Horrobin suggested that phospholipid and fatty acid metabolism played a major role in human evolution, his 'fat utilization hypothesis' unified intriguing work from paleoanthropology, evolutionary biology, genetic and nervous system research in a novel and coherent lipid-related context. Interestingly, unlike most other evolutionary concepts, the hypothesis allows specific predictions which can be empirically tested in the near future. This paper summarizes some of Horrobin's intriguing propositions and suggests as to how approaches of comparative genomics published in Cell, Nature, Science and elsewhere since 1997 may be used to examine his evolutionary hypothesis. Indeed, systematic investigations of the genomic clock in the species' mitochondrial DNA, the Y and autosomal chromosomes as evidence of evolutionary relationships and distinctions can help to scrutinize associated predictions for their validity, namely that key mutations which differentiate us from Neanderthals and from great apes are in the genes coding for proteins which regulate fat metabolism, and particularly the phospholipid metabolism of the synapses of the brain. It is concluded that beyond clues to humans' relationships with living primates and to the Neanderthals' cognitive performance and their disappearance, the suggested molecular clock analyses may provide crucial insights into the biochemical evolution-and means of possible manipulation-of our brain.

Metabolic correlates of hominid brain evolution

Large brain sizes in humans have important metabolic consequences as humans expend a relatively larger proportion of their resting energy budget on brain metabolism than other primates or non-primate mammals. The high costs of large human brains are supported, in part, by diets that are relatively rich in energy and other nutrients. Among living primates, the relative proportion of metabolic energy allocated to the brain is positively correlated with dietary quality. Humans fall at the positive end of this relationship, having both a very high quality diet and a large brain size. Greater encephalization also appears to have consequences for aspects of body composition. Comparative primate data indicate that humans are 'under-muscled', having relatively lower levels of skeletal muscle than other primate species of similar size. Conversely, levels of body fatness are relatively high in humans, particularly in infancy. These greater levels of body fatness and reduced levels of muscle mass allow human infants to accommodate the growth of their large brains in two important ways: (1) by having a ready supply of stored energy to 'feed the brain', when intake is limited and (2) by reducing the total energy costs of the rest of the body. Paleontological evidence indicates that the rapid brain evolution observed with the emergence of Homo erectus at approximately 1.8 million years ago was likely associated with important changes in diet and body composition.

Evolution of dietary antioxidants

Oxygen is vital for most organisms but, paradoxically, damages key biological sites. Oxygenic threat is met by antioxidants that evolved in parallel with our oxygenic atmosphere. Plants employ antioxidants to defend their structures against reactive oxygen species (ROS; oxidants) produced during photosynthesis. The human body is exposed to these same oxidants, and we have also evolved an effective antioxidant system. However, this is not infallible. ROS breach defences, oxidative damage ensues, accumulates with age, and causes a variety of pathological changes. Plant-based, antioxidant-rich foods traditionally formed the major part of the human diet, and plant-based dietary antioxidants are hypothesized to have an important role in maintaining human health. This hypothesis is logical in evolutionary terms, especially when we consider the relatively hypoxic environment in which humans may have evolved. In this paper, the human diet is discussed briefly in terms of its evolutionary development, different strategies of antioxidant defence are outlined, and evolution of dietary antioxidants is discussed from the perspectives of plant need and our current dietary requirements. Finally, possibilities in regard to dietary antioxidants, evolution, and human health are presented, and an evolutionary cost-benefit analysis is presented in relation to why we lost the ability to make ascorbic acid (vitamin C) although we retained an absolute requirement for it.

Metabolic impact of body fat distribution

Many studies have shown that fat distribution influences metabolism independently of the effects of total body fat stores. The accumulation of fat in the abdominal area, particularly in the visceral fat compartment, seems to be associated with an increased risk to display complications such as insulin resistance, diabetes, dyslipidemias and atherosclerosis. As reviewed in this paper, the mechanisms explaining this impact of fat distribution is not clearly established, although evidence suggests that free-fatty acids, leptin, TNF-alpha, PPAR-gamma, and F are directly or indirectly involved in this process. Despite a lot of research has yet to be performed to mechanistically characterize the impact of visceral fat on the metabolic profile, there is enough consensus in the literature about its effect to justify its consideration in a clinical setting. In this regard, the use of waist circumference as a clinical marker of variations in visceral fat is highly relevant and should be encouraged. This review also presents an evolutionary perspective according to which body fat gain would have been and may still remain an adaptation that helps to deal with stress and inflammation.

Comparative and evolutionary dimensions of the energetics of human pregnancy and lactation

The purpose of this article is to compare the energetics of reproduction for human and other primates in order to evaluate the extent to which human reproductive energetics are distinct from other primates and other large-bodied placental mammals. The article also evaluates the energetics of human and primate gestation and lactation using data from a variety of different populations living under different environmental circumstances. Energetics refers to energy intake and expenditure, and changes in body fat stores. Human and nonhuman primates have longer periods of gestation and lactation and slower prenatal and postnatal growth than other mammals of similar size. This reduces daily maternal energy costs. The development of sizable fat stores is not unique to humans, but fat stores are typically greater in human females and may play a greater role in reproduction. The strategies used to meet the energy costs of pregnancy vary among populations of humans and nonhuman primates and among humans interindividual variability is high. In pregnancy, some increase energy intake but others apparently do not. Increases in metabolic efficiency are evident in some human populations, whereas decreases in physical activity occur, but are not seen in all human or primate populations. Lactation is more energetically costly on a daily basis among humans and nonhuman primates, but has not been as well studied. It appears that both nonhuman and human primates tend to increase energy intake to meet in part the cost of lactation. They also use other strategies such as relying on body tissue stores, reductions in physical activity, and/or increases in metabolic efficiency to meet the remainder of the cost. It is also clear that human females in different populations and different women in the same population use a different combination of strategies to meet the cost of lactation.

Energetic consequences of being a Homo erectus female

Body size is one of the most important characteristics of any animal because it affects a range of behavioral, ecological, and physiological traits including energy requirements, choice of food, reproductive strategies, predation risk, range size, and locomotor style. This article focuses on the implications of being large bodied for Homo erectus females, estimated to have been over 50% heavier than average australopithecine females. The energy requirements of these hominins are modeled using data on activity patterns, body mass, and life history from living primates. Particular attention is given to the inferred energetic costs of reproduction for Homo erectus females based on chimpanzee and human reproductive scheduling. Daily energy requirements during gestation and lactation would have been significantly higher for Homo erectus females, as would total energetic cost per offspring if the australopithecines and Homo erectus had similar reproductive schedules (gestation and lactation lengths and interbirth intervals). Shortening the interbirth interval could considerably reduce the costs per offspring to Homo erectus and have the added advantage of increasing reproductive output. The mother would, however, incur additional daily costs of caring for the dependent offspring. If Homo erectus females adopted this reproductive strategy, it would necessarily imply a revolution in the way in which females obtained and utilized energy to support their increased energetic requirements. This transformation is likely to have occurred on several levels involving cooperative economic division of labor, locomotor energetics, menopause, organ size, and other physiological mechanisms for reducing the energetic load on females.

Energetics and evolution: an emerging research domain

The study of energetics is important to human biology because the availability and utilization of food energy influence health, survival, and reproduction. Over the last decade, human biologists, biological anthropologists, and other evolutionary scientists have increasingly come to recognize the importance of energy dynamics in shaping evolutionary processes. Thus far, different lines of energetics research have been conducted largely in isolation from one another. This thematic collection examines topics of evolutionary energetics from several different perspectives, drawing together research from human paleontology, comparative primate and mammalian biology, human population biology, and mathematical modeling. It represents a starting point for further integrative research on human evolutionary energetics.

Comparative energetics of primate fetal growth

Among the primates, Homo sapiens has evolved a life history which includes long gestation, relatively slow growth to reproductive maturity, and large body size. While the slow growth rate may be linked to the energetic demands of having a large brain, there are other important morphological and physiological linkages that may be adaptive, including the development of significant fat stores with which to buffer against episodic and periodic energetic stress. In this comparative analysis of the energetic burden of pregnancy among primates (including humans), the daily energy investment in the development of neonatal tissue is modeled. During pregnancy, larger primates, notably the Hominidae, invest a smaller proportion of their maternal daily nonmaintenance energy budget in fetal tissue with increasing energy budget, allowing diverse adaptations, including foraging strategies which include folivory and mixed patterns of food getting, and meat consumption. Humans have a similar proportion of maternal daily nonmaintenance energy budget invested in fetal tissue with increasing energy budget to other apes and have a diet which is of much higher quality than predicted for body size and metabolic needs. The combination of high diet quality and low proportion of maternal daily nonmaintenance energy budget invested in fetal tissue allows greater brain size relative to body weight at birth compared with all other primates, apart from chimpanzees, and higher birthweight and body fatness at birth for a given body size than other primate species.

Neandertal cold adaptation: physiological and energetic factors

European Neandertals employed a complex set of physiological cold defenses, homologous to those seen in contemporary humans and nonhuman primates. While Neandertal morphological patterns, such as foreshortened extremities and low relative surface-area, may have explained some of the variance in cold resistance, it is suggested the adaptive package was strongly dependent on a rich array of physiological defenses. A summary of the environmental cold conditions in which the Neandertals lived is presented, and a comparative ethnographic model from Tierra del Fuego is used. Muscle and subcutaneous fat are excellent "passive" insulators. Neandertals were quite muscular, but it is unlikely that they could maintain enough superficial body fat to offer much cold protection. A major, high-energy metabolic adaptation facilitated by modest amounts of highly thermogenic brown adipose tissue (BAT) is proposed. In addition, Neandertals would have been protected by general mammalian cold defenses based on systemic vasoconstriction and intensified by acclimatization, aerobic fitness, and localized cold--induced vasodilation. However, these defenses are energetically expensive. Based on contemporary data from circumpolar peoples, it is estimated that Neandertals required 3,360 to 4,480 kcal per day to support strenuous winter foraging and cold resistance costs. Several specific genetic cold adaptations are also proposed--heat shock protein (actually, stress shock protein), an ACP*1 locus somatic growth factor, and a specialized calcium metabolism not as yet understood.

Sexual division of labor: energetic and evolutionary scenarios

This article examines comparative energetic data on hunter-gatherers in the context of evolutionary scenarios of the sexual division of labor, with respect to both specific task allocation and overall levels of daily physical activity. The division of labor between men and women, well marked in contemporary foraging societies, was once posited as the "true watershed" for the evolution of the genus Homo. Some research on brain-wiring even links sex differences in cognitive and spatial abilities to sex-specific foraging activities. Most recent evolutionary arguments posit that men focus on hunting and women on gathering activities to realize potentially conflicting mating and parenting goals. A range of cooperative strategies (male/female and female/female) for child provisioning is also under investigation. Attention to energetic and reproductive trade-offs has usefully challenged the proposition that women are excluded from big-game hunting due to constraints of foraging ecology and reproduction. Simplistic assumptions about gender roles are thus increasingly questioned in anthropology, as well as in archaeology. Current models in behavioral ecology explore ways in which foraging practices vary with ecological circumstances, aiming to derive testable hypotheses from fine-grained data on the behavior of contemporary hunter-gatherers. Data on overall physical activity levels (PAL) can also serve to evaluate relative male/female workloads in modern groups, reconstruct hominid energy requirements and activity profiles, and examine changes with subsistence intensification. Male/female PAL ratios show that a task-specific division of labor does not readily extrapolate to 24-hour energy expenditure and that male/female differences in workloads were not necessarily reduced with the transition to agriculture. With respect to gender roles and PAL, a shift away from facile stereotypes of human behavior is evident. The challenge is to incorporate a range of behavioral responses to ecological circumstances in reconstructions of our evolutionary past.

An unusual population of pyramidal neurons in the anterior cingulate cortex of hominids contains the calcium-binding protein calretinin

In the context of an on-going comparative analysis of primate neocortex evolution, we describe the occurrence and distribution of a previously unrecognized group of pyramidal neurons, restricted to the superficial part of layer V in the anterior cingulate cortex of hominids and characterized by immunoreactivity to the calcium-binding protein, calretinin. These neurons were rare in orangutans, more numerous in gorillas and common chimpanzees, while humans had the highest numbers. These calretinin-containing pyramidal cells were not observed in the cingulate cortex of any other primate or mammalian species. This finding, together with other recent observations on the hominoid cingulate cortex, is interesting when considering primate neocortical evolution, as it indicates possible adaptive and anatomical modifications in a cortical region critical for the integration of many aspects of autonomic function, vocalization, and cognitive processes.

Molecular diversity in the biosynthesis of GI tract glycoconjugates. A blood-group-related chart of microorganism receptors

This paper examines the potential of carbohydrate blood-group antigens present on mucosal surfaces in acting as receptors for microorganisms. Mucosal surfaces express significant amounts of carbohydrate blood-group antigens under the control of the Secretor, Lewis and ABO systems. The exact glycoconjugate profile an individual presents to the lumen is complex, and can only be correctly determined by a combination of serology and genotyping. We have isolated and structurally resolved the glycolipids expressed in the small intestine of group O individuals having various common or rare phenotypes. Using this information, we have been able to construct a biosynthetic pathway and propose that the type, size and glycotopes expressed, are controlled to a major extent by blood-group-related glycosyltransferases. Many of these glycotopes are potential receptors for microorganisms; some resemble tumour antigens, while others resemble the lipopolysaccharides of some pathogens. Although the origins of the blood-group glycosyltransferases remain uncertain, it is evident that they significantly diversify the mucosal glycotopes exposed to microbes; and therein may be found a potential explanation for their existence.