Simian Primates Research Articles

Evolutionary dynamics of pro-inflammatory caspases in primates and rodents.

Caspase-1 and related proteases are key players in inflammation and innate immunity. Here, we characterize the evolutionary history of caspase-1 and its close relatives across 19 primates and 21 rodents, focusing on differences that may cause discrepancies between humans and animal studies. While caspase-1 has been retained in all these taxa, other members of the caspase-1 subfamily (caspase-4, -5, -11, -12, and CARD16, 17, and 18) each have unique evolutionary trajectories. Caspase-4 is found across simian primates, whereas we identified multiple pseudogenization and gene loss events in caspase-5, caspase-11, and the CARDs. Because caspases-4 and -11 are both key players in the non-canonical inflammasome pathway, we expected that these proteins would be likely to evolve rapidly. Instead, we found that these two proteins are largely conserved, whereas caspase-4's close paralog, caspase-5, showed significant indications of positive selection, as did primate caspase-1. Caspase-12 is a non-functional pseudogene in humans. We find this extends across most primates, although many rodents and some primates retain an intact, and likely functional, caspase-12. In mouse laboratory lines, we found that 50% of common strains carry non-synonymous variants that may impact the functions of caspase-11 and -12, and therefore recommend specific strains to be used (and avoided). Finally, unlike rodents, primate caspases have undergone repeated rounds of gene conversion, duplication, and loss leading to a highly dynamic pro-inflammatory caspase repertoire. Thus we uncovered many differences in the evolution of primate and rodent pro-inflammatory caspases, and discuss the potential implications of this history for caspase gene functions.

Evolutionary conservation of an ancient retroviral gagpol gene in Artiodactyla.

The genomes of mammals contain fingerprints of past infections by ancient retroviruses that invaded the germline of their ancestors. Most of these endogenous retroviruses (ERVs) contain only remnants of the original retrovirus; however, on rare occasions, ERV genes can be co-opted for a beneficial host function. While most studies of co-opted ERVs have focused on envelope genes, including the syncytins that function in placentation, there are examples of co-opted gag genes including one we recently discovered in simian primates. Here, we searched for other intact gag genes in non-primate mammalian lineages. We began by examining the genomes of extant camel species, which represent a basal lineage in the order Artiodactyla. This identified a gagpol gene with a large open reading frame (ORF) (>3,500 bp) in the same orthologous location in Artiodactyla species but that is absent in other mammals. Thus, this ERV was fixed in the common ancestor of all Artiodactyla at least 64 million years ago. The amino acid sequence of this gene, termed ARTgagpol, contains recognizable matrix, capsid, nucleocapsid, and reverse transcriptase domains in ruminants, with an RNase H domain in camels and pigs. Phylogenetic analysis and structural prediction of its reverse transcriptase and RNase H domains groups ARTgagpol with gammaretroviruses. Transcriptomic analysis shows ARTgagpol expression in multiple tissues suggestive of a co-opted host function. These findings identify the oldest and largest ERV-derived gagpol gene with an intact ORF in mammals, an intriguing milestone in the co-evolution of mammals and retroviruses. IMPORTANCE Retroviruses are unique among viruses that infect animals as they integrate their reverse-transcribed double-stranded DNA into host chromosomes. When this happens in a germline cell, such as sperm, egg, or their precursors, the integrated retroviral copies can be passed on to the next generation as endogenous retroviruses (ERVs). On rare occasions, the genes of these ERVs can be domesticated by the host. In this study we used computational similarity searches to identify an ancient ERV with an intact viral gagpol gene in the genomes of camels that is also found in the same genomic location in other even-toed ungulates suggesting that it is at least 64 million years old. Broad tissue expression and predicted preservation of the reverse transcriptase fold of this protein suggest that it may be domesticated for a host function. This is the oldest known intact gagpol gene of an ancient retrovirus in mammals.

Perception of color in primates: A conceptual color neurons hypothesis

Perception of color by humans and other primates is a complex problem, studied by neurophysiology, psychophysiology, psycholinguistics, and even philosophy. Being mostly trichromats, simian primates have three types of opsin proteins, expressed in cone neurons in the eye, which allow for the sensing of color as the physical wavelength of light. Further, in neural networks of the retina, the coding principle changes from three types of sensor proteins to two opponent channels: activity of one type of neuron encode the evolutionarily ancient blue-yellow axis of color stimuli, and another more recent evolutionary channel, encoding the axis of red-green color stimuli. Both color channels are distinctive in neural organization at all levels from the eye to the neocortex, where it is thought that the perception of color (as philosophical qualia) emerges from the activity of some neuron ensembles. Here, using data from neurophysiology as a starting point, we propose a hypothesis on how the perception of color can be encoded in the activity of certain neurons in the neocortex. These conceptual neurons, herein referred to as ‘color neurons’, code only the hue of the color of visual stimulus, similar to place cells and number neurons, already described in primate brains. A case study with preliminary, but direct, evidence for existing conceptual color neurons in the human brain was published in 2008. We predict that the upcoming studies in non-human primates will be more extensive and provide a more detailed description of conceptual color neurons.

Marmoset core visual object recognition behavior is comparable to that of macaques and humans

Among the smallest simian primates, the common marmoset offers promise as an experimentally tractable primate model for neuroscience with translational potential to humans. However, given its exceedingly small brain and body, the gap in perceptual and cognitive abilities between marmosets and humans requires study. Here, we performed a comparison of marmoset behavior to that of three other species in the domain of high-level vision. We first found that marmosets outperformed rats- a marmoset-sized rodent- on a simple recognition task, with marmosets robustly recognizing objects across views. On a more challenging invariant object recognition task used previously in humans, marmosets also achieved high performance. Notably, across hundreds of images, marmosets' image-by-image behavior was highly similar to that of humans- nearly as human-like as macaque behavior. Thus, core aspects of visual perception are conserved across monkeys and humans, and marmosets present salient behavioral advantages over other small model organisms for visual neuroscience.

Afferent Connections of Cytoarchitectural Area 6M and Surrounding Cortex in the Marmoset: Putative Homologues of the Supplementary and Pre-supplementary Motor Areas.

Cortical projections to the caudomedial frontal cortex were studied using retrograde tracers in marmosets. We tested the hypothesis that cytoarchitectural area 6M includes homologues of the supplementary and pre-supplementary motor areas (SMA and pre-SMA) of other primates. We found that, irrespective of the injection sites' location within 6M, over half of the labeled neurons were located in motor and premotor areas. Other connections originated in prefrontal area 8b, ventral anterior and posterior cingulate areas, somatosensory areas (3a and 1-2), and areas on the rostral aspect of the dorsal posterior parietal cortex. Although the origin of afferents was similar, injections in rostral 6M received higher percentages of prefrontal afferents, and fewer somatosensory afferents, compared to caudal injections, compatible with differentiation into SMA and pre-SMA. Injections rostral to 6M (area 8b) revealed a very different set of connections, with increased emphasis on prefrontal and posterior cingulate afferents, and fewer parietal afferents. The connections of 6M were also quantitatively different from those of the primary motor cortex, dorsal premotor areas, and cingulate motor area 24d. These results show that the cortical motor control circuit is conserved in simian primates, indicating that marmosets can be valuable models for studying movement planning and control.

Oral Administration of the LSD1 Inhibitor OG-S1335 Increases Fetal Hemoglobin in Humanized Transgenic Sickle Cell Disease Mice and in Baboons

Increased levels of fetal hemoglobin (HbF) lessen the severity of symptoms and increase the life span of patients with sickle cell disease (SCD). New and more effective strategies to increase HbF are needed because the current standard of care, hydroxyurea, is not effective in a significant proportion of patients. Although BM transplantation, gene therapy, and gene editing technologies offer the promise of a cure, it is unlikely that these methodologies can be implemented to treat the large numbers of patients projected worldwide, including those in developing nations that could most easily be treated with an effective, orally administered drug therapy that increased HbF. The lysine-specific demethylase 1A (KDM1A, also referred to as LSD1), is a component of co-repressor complexes that repress γ-globin gene expression and a therapeutic target for HbF reactivation (Shi et al, Nat Med 19:291, 2013). Our laboratory has shown that subcutaneous administration of RN-1, a pharmacological inhibitor of LSD1, increased γ-globin expression in SCD transgenic mice (Rivers et al, Exp Hematol 43:546, 2015; Cui et al, Blood 126:386, 2015) and in baboons (Rivers et al, Haematol 101:688, 2016), widely acknowledged as the best animal model to test the activity of HbF-inducing drugs due to conservation of structure and developmental regulation of the β-globin locus among simian primates. The objective of this investigation was to test whether oral administration of a new LSD1 inhibitor, OG-S1335, could increase HbF in SCD transgenic mice and baboons. Oral administration of varying doses (0.25, 0.5, 1.0mg/kg/d; 4d) of OG-S1335 to SCD mice (3 mice per dose) increased γ-globin expression and the percentage of circulating erythrocytes and reticulocytes positive for HbF (F cells and F retics; Table 1). In baboons, dose escalation was initially performed by administering the drug to a single animal in cycles of 3 days, followed by 1-2 weeks of observation to measure effects on blood parameters. Increased levels of F retics were initially observed at a dose of 100μg/kg/d and subsequently 4 additional baboons were treated with OG-S1335 (by oral gavage) at a dose of either 100 or 200μg/kg/d (7 separate experiments in total). The data presented are in the mean+SD format, with “post-dose” indicating the time point when the highest variation from baseline levels was reported. Increased F retics (pre=8.4+8.9%, post=43.0+27.9%; p<0.01), γ-globin chain synthesis (pre=0.05+0.05 γ/γ+β, post=0.28+0.18 γ/γ+β; p<0.01), and γ-globin mRNA (pre=0.02 +0.02 γ/γ+β, post=0.20+0.11 γ/γ+β) were observed with maximal levels achieved 7 days after administration of the first dose (d8). A decrease in the absolute number of reticulocytes (pre=72.8+17.8 X104/μL, post=35.4+17.8 X 104/μL; p<0.05; nadir on d6-8), neutrophils (pre=4634+994/μL, post=2655+1257/μL; p<0.02; nadir on d13-17), and platelets (pre=406+86 X103/μL, post=168+98 X103/μL; p<0.01; nadir on d8) was also reported, together with increased monocytes (pre=200+68/μL, post=541+213/μL; p<0.01; peak on d10-15). A negative correlation between decreased platelet counts and F retics (r= -0.55), γ-globin chain synthesis (r= -0.92), and γ-globin mRNA (r= -0.80) suggests that variability in drug exposure in addition to possible genetic factors regulating γ-globin expression may be responsible for the observed variability between animals. Additional experiments were performed in two phlebotomized anemic baboons to test the effect of the drug in a model with increased relevance to sickle cell disease. OG-S1335 (100μg/kg/d; 3d) induced high levels of F retics (PA8695, pre-dose=24%, post=66.8%; PA8698: pre-dose=13%, post=93.6%), γ-globin chain synthesis (PA8695: pre-dose=0.07 γ/γ+β, post=0.20 γ/γ+β; PA8698: pre-dose=0.02 γ/γ+β, post=0.44 γ/γ+β) and γ-globin mRNA (PA8695: pre-dose=0.06 γ/γ+β, post=0.18 γ/γ+β; PA8698: pre-dose=0.03 γ/γ+β, post=0.33 γ/γ+β) in each animal. We conclude that oral administration of the LSD1 inhibitor OG-S1335 significantly increased F retics, γ-globin chain synthesis, and γ-globin mRNA in SCD mice and in baboons, supporting further efforts toward the development of this drug for SCD therapy. [Display omitted] DisclosuresCiceri:Oryzon Genomics SA: Employment. Cavalcanti:Oryzon Genomics SA: Employment.

Combinatorial Administration of Pharmacological Inhibitors Targeting DNMT1 and KDM1A Produces Synergistic and Additive Increases in F Retiulocytes and γ-Globin Expression in Normal Baboons

Sickle cell disease (SCD) is an inherited blood disorder that severely impacts the quality of life and reduces the life expectancy of approximately 100,000 patients in the U.S. and millions worldwide. Elevated levels of Fetal Hemoglobin (HbF; α2γ2) reduce the severity of symptoms and lengthen the life span of patients with sickle cell disease by inhibiting deoxy HbS polymerization. Hydroxyurea (HU), the only FDA-approved drug shown to increase HbF, is not effective in a subset of patientsand importantly, in the refractory individuals the increased HbFis heterogeneously distributed within the erythrocyte population resulting in a large fraction of erythrocytes lacking protective levels. Simian primates such as the baboon are widely acknowledged as the best animal models for testing the ability of new drugs to increase γ-globin expression because results in baboons are predictive of effects in man due to conservation of the structure and developmental stage-specific regulation of the β-like globin genes in simian primates. Our previous studies in baboons have shown that the most powerful drugs for reactivation of HbF are DNMT1 and KDM1A inhibitors targeting enzymes located within the co-repressor complexes that act to establish and maintain repressive epigenetic modifications at the γ-globin promoter to repress γ-globin expression. Treatment of baboons with either decitabine, an inhibitor of DNMT1, or RN-1, an inhibitor of KDM1A, strongly stimulates HbF. Dose-limiting effects of these drugs include neutropenia, thrombocytopenia, and/or thrombophilia. In this investigation we have explored the hypothesis that a treatment regimen comprised of both decitabine and RN-1 could achieve additive or synergistic effects on HbF while minimizing adverse hematological side effects. Three baboons (PA8695, PA8697, PA8698) were treated with two courses of different doses of RN-1 (0.25 and 0.125mg/kg/d) administered subcutaneously for 3 days to select an optimal RN-1 dose for each animal. The response to RN-1 varied between individual animals and was associated with pretreatment levels of γ-globin expression. Higher pretreatment levels of γ-globin expression were observed in PA8697 (0.08 γ/γ+β) compared to PA8695 (0.014+0.005 γ/γ+β) and PA8698 (0.004+0.0007 γ/γ+β) and the effect on γ-globin expression in PA8697 (0.24+0.5 γ/γ+β) at the 0.125mg/kg/d dose was greater than the effect of 0.25 mg/kg/d dose in PA8695 (0.17+0.05 γ/γ+β) and PA8698 (0.121+0.006 γ/γ+β). For combinatorial studies with decitabine, an RN-1 dose of 0.125mg/kg/d was chosen for PA8697 and 0.25mg/kg/d for PA8695 and 8698. Decitabine (0.3mg/kg/d; 2d), administered as a single agent subcutaneously for two days increased F retics nearly 3 fold (23.6+12.5%; p&amp;lt;0.02) compared to pretreatment levels (8.26+9.90%) but changes in γ-globin expression (0.066+0.076 γ/γ+β) compared to the pretreatment levels (0.03+0.042 γ/γ+β) were not significant. For combinatorial experiments, decitabine (0.3mg/kg/d) was administered for 2 days followed by administration of RN-1 (0.25mg/kg/d PA8695 and 8698; 0.125mg/kg/d PA8697) for 3 days. This staggered dose schedule was used to avoid any possible effects of RN-1 on cell cycle kinetics that could potentially reduce incorporation of decitabine during S phase. The decitabine/RN-1 combination produced significantly higher increases in F retics (63.0+23.6%; p&amp;lt;0.002) than either RN-1 (29.9+27.1%) or decitabine (23.6+12.5%) alone. The effect of the decitabine/RN-1 combination on F retics was greater than additive (p&amp;lt;0.01; Figure 1A) in the two low HbF animals, PA8695 and 8698, and additive for the high HbF animal PA8697 (Figure 1B). Although increased levels of γ-globin expression produced by the decitabine/RN-1 combination (0.22+0.08 γ/γ+β) were not significantly different overall from those induced by RN-1 alone (0.178+0.06 γ/γ+β), individual analysis of PA8697 revealed an additive effect (Figure 1C). Plt and ANC remained with the normal range. In conclusion, targeting separate components of the γ-globin co-repressor complex by combinatorial administration of decitabine and RN-1 generated synergistic and additive increases in F retics and γ-globin expression in the absence of hematological toxicity. Future experiments will explore different doses, alternative schedules, and the effect of longer term treatment regimens. Disclosures Saunthararajah: EpiDestiny: Consultancy, Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees, Patents &amp; Royalties.

Retrotransposons spread potential cis-regulatory elements during mammary gland evolution.

Acquisition of cis-elements is a major driving force for rewiring a gene regulatory network. Several kinds of transposable elements (TEs), mostly retrotransposons that propagate via a copy-and-paste mechanism, are known to possess transcription factor binding motifs and have provided source sequences for enhancers/promoters. However, it remains largely unknown whether retrotransposons have spread the binding sites of master regulators of morphogenesis and accelerated cis-regulatory expansion involved in common mammalian morphological features during evolution. Here, I demonstrate that thousands of binding sites for estrogen receptor α (ERα) and three related pioneer factors (FoxA1, GATA3 and AP2γ) that are essential regulators of mammary gland development arose from a spreading of the binding motifs by retrotransposons. The TE-derived functional elements serve primarily as distal enhancers and are enriched around genes associated with mammary gland morphogenesis. The source TEs occurred via a two-phased expansion consisting of mainly L2/MIR in a eutherian ancestor and endogenous retrovirus 1 (ERV1) in simian primates and murines. Thus the build-up of potential sources for cis-elements by retrotransposons followed by their frequent utilization by the host (co-option/exaptation) may have a general accelerating effect on both establishing and diversifying a gene regulatory network, leading to morphological innovation.

The simian crease: Relationship to various genetic disorders.

The creases of the palm have been of interest for clinicians, anthropologists, and palmists for hundreds of years, but the variations in them have only been studied during the past 50 years. The simian crease, aptly named for its resemblance to the palmar creases of nonhuman simian primates, has received recognition clinically and anthropologically owing to its abnormal appearance and confounding cytogenetic etiology. Given the rarity of these palmar creases but also their usefulness in diagnosing congenital disorders, discussion of cases of those disorders could provide clinicians with further helpful diagnostic knowledge. This review of the literature focuses on the history, embryology, genetic and hereditary origins, and clinical significance of simian creases for the benefit of the diagnosing clinician. Clin. Anat. 32:1042-1047, 2019. © 2019 Wiley Periodicals, Inc.

Alpha satellite DNA-repeat OwlAlp1 forms centromeres in Azara's owl monkey.

Centromeres play crucial roles in faithful chromosome segregation and genome integrity. In simian primates, centromeres possess tandem array of alpha satellite DNA (also referred to as alphoid DNA). Average sizes of alpha satellite repeat units vary between species, for example, 171bp in human and 343-344bp in many platyrrhini species (New World monkeys). Interestingly, Azara's owl monkey (Aotus azarae), a platyrrhini species, possesses alpha satellite DNA of two distinct unit sizes, OwlAlp1 (185bp) and OwlAlp2 (344bp), both of which present as megasatellite DNAs in the genome. It is, however, unknown which repeat sequence is responsible for functional centromere formation. To investigate the localization of centromeres in vivo, we carried out chromatin immunoprecipitation (ChIP) assay using Azara's owl monkey cells. We found that CENP-A, a histone H3 variant essential for centromere formation, was enriched at OwlAlp1, but not at OwlAlp2. Moreover, CENP-A was detected only at constricted regions of chromosomes by immunofluorescent microscopy. In contrast, trimethylation of histone H3-K9 (H3K9me3), a marker of heterochromatin, was enriched at both OwlAlp1 and OwlAlp2. Our results show that the shorter alpha satellite repeat, OwlAlp1, is selectively used for centromere formation in this monkey.

The LSD1 Inhibitor RN-1 Increases γ-Globin Expression in Baboons By Targeting an Early Event Responsible for γ-Globin Repression

The HbF to HbA developmental globin switch is recapitulated during adult erythroid differentiation and involves the acquisition of repressive epigenetic marks at the γ-globin promoter catalyzed by “druggable” enzymes such as histone deacetylases (HDACs), DNA methyltransferase (DNMT1), LSD1 (KDM1A), and G9A (EHMT2) that are functional components of multiprotein co-repressors recruited to the γ-globin gene promoter by the trans-acting repressors TR2/TR4, BCL11A, and ZBTB7A. A logical approach to increase HbF that has been successfully pursued by our laboratory is to intervene with the epigenetic repression mechanism that executes the switch from HbF to HbA using pharmacological inhibitors of these enzymes. Simian primates such as the baboon are widely acknowledged as the best animal models for testing the ability of new drugs to increase γ-globin expression because results in baboons are predictive of effects in man due to conservation of the structure and developmental stage-specific regulation of the β-like globin genes in simian primates.Our laboratory has developed and utilized an in vivo baboon model for over thirty years to investigate globin gene regulation and the ability of pharmacological inhibitors of enzymes that catalyze repressive epigenetic modifications to increase HbF, generating results with DNMT inhibitors that were extended and confirmed in a number of clinical studies in patients with SCD and β-thalassemia. Following studies that identified LSD1 as an additional therapeutic target (Shi et al, Nat Med 19:291, 2013), we showed that the LSD1 inhibitor RN-1 dramatically increased HbF, F cells and F retics in baboons (Rivers et al, Haematol 101:698, 2015) and that these effects were sustained upon long-term treatment (>265d; Ibanez et al, Blood 129:260, 2017). ChIP analysis showed increased levels of Histone H3 di and tri-methyl K4 at the γ-globin gene, consistent with LSD1 inhibition. This current investigation seeks to identify the stage in the erythroid differentiation pathway targeted by LSD1 inhibitors to increase HbF and also to characterize additional effects of these drugs on erythroid differentiation that potentially impact mechanism of action. Subpopulations of bone marrow (BM) cells highly enriched in BFUe (CD105+CD34+CD117+bRBC-), CFUe (CD105+CD34+CD117+bRBC+), proerythroblasts (CD105+CD34-CD117+bRBC+) were purified from RN-1 treated (0.25mg/kg/d; 3d) and untreated baboons by immunomagnetic column separation combined with FACS. RT-PCR analysis of γ-globin expression within purified BM erythroid subpopulations showed that relative levels of γ-globin mRNA (γ/γ+β) in untreated baboons were 4 fold higher in BFUe than in CFUe and 11 fold higher in BFUe than in proerythroblasts consistent with repression of the γ-globin gene during the BFUe to CFUe transition. RN-1 treatment increased relative γ-globin expression (γ/γ+β) 4 fold in BFUe, 25 fold in CFUe, and >100 fold in proerythroblasts compared to untreated controls and thus partially prevented repression of the γ-globin expression at early stages of differentiation. Additional effects of the LSD1 inhibitor RN-1 on erythroid differentiation were measured by flow cytometry in baboon BM aspirates following RN-1 administration. RN-1 treatment (0.25mg/kg/d; 3d) increased the proportion of CD105+CD117+bRBC+BM cells (proerythroblasts) (24.2% pre-treatment; 48.4% post-treatment; p<0.02) and decreased the proportion of CD105+CD117-bRBC+ terminal erythroid BM cells (51.1% pre-treatment; 29.1% post-treatment; p<0.02). RNAseq analysis of CD105+CD34-CD117+bRBC+ FACS-purified BM cells (proerythroblasts) of untreated control (n=2) and RN-1 treated baboons (0.25mg/kg/d; 3d; n=4; 2 treated for 3d; 2 treated >265d) identified a common set of 41 genes whose expression was increased while the expression of 6 genes was decreased. RT-PCR assays confirmed increased expression of γ-globin, GATA-2, GFi-1B, DAP, IFI6, and Lyn in proerythroblasts of RN-1-treated baboons. We conclude that the LSD1 inhibitor RN-1 administered to baboons 1) restrains erythroid differentiation by modulating the expression of genes such as GATA-1 and GFi-1B that regulate erythroid differentiation, and 2) targets an early event responsible for γ-globin repression to increase γ-globin expression. DisclosuresSaunthararajah:Novo Nordisk, A/S: Patents & Royalties; EpiDestiny, LLC: Patents & Royalties. Lavelle:Global Blood therapeutics: Research Funding.

Cognitive Components of Vocal Communication: A Case Study.

Simple SummaryThe pygmy marmoset is the world’s smallest true monkey with a mean brain size of 4.5 g. I review the cognitive and pre-linguistic skills that these monkeys show in their vocal communication. Pygmy marmosets have several types of calls used to maintain contact with one another, and they use calls that are cryptic when they are close to group members, and calls that more easily detected when they are farther away. They take turns in contact calling. They modify their call structure when in a new social setting to match the structure of other group members or of mates. Infants display babbling behavior similar to human infants, and adult caretakers provide social reinforcement that lead infants to develop adult like calls. Thus, pygmy marmosets modify vocal structure and learn through social interactions. This contrasts sharply with the general view that most nonhuman primates do not display vocal learning or an ability to modify call structure. Pygmy marmosets signal other group members when they find food using specialized calls but inhibit these calls with living prey. These complex cognitive skills in communication indicate that brain size may not be a good predictor of cognitive ability.Communication among nonhuman animals is often presented as rigid and inflexible, reflecting emotional states rather than having any cognitive basis. Using the world’s smallest monkey, the pygmy marmoset (Cebuella pygmaea), with the smallest absolute brain size amongst simian primates as a case study, I review the role of cognition in the development and usage of vocalizations in pygmy marmosets and present new data on the instrumental use of babbling and of food associated vocalizations. Pygmy marmosets have several contact calls that differ in the psychoacoustic properties for sound localization as well as the distance at which they carry through the rainforest. Marmosets use these calls strategically based on distance from neighbors. Marmosets alter spectral and temporal aspects of call structure when exposed to new groups and when newly mated. They display population specific vocal dialects. Young pygmy marmosets engage in extensive babbling behavior rewarded by parents that helps the young develop adult vocal structures, but older monkeys also use babbling instrumentally in conflict situations. Specific food referential calls generally relate to food preferences, but food calls are suppressed in the presence of animate prey. Unmated animals systematically combine a long distance call with food calls as though advertising for mates. Taken together, these examples show that even small brained primates use their vocal signals flexibly and strategically in response to a variety of environmental and social conditions.

Cortical Afferents of Area 10 in Cebus Monkeys: Implications for the Evolution of the Frontal Pole.

Area 10, located in the frontal pole, is a unique specialization of the primate cortex. We studied the cortical connections of area 10 in the New World Cebus monkey, using injections of retrograde tracers in different parts of this area. We found that injections throughout area 10 labeled neurons in a consistent set of areas in the dorsolateral, ventrolateral, orbital, and medial parts of the frontal cortex, superior temporal association cortex, and posterior cingulate/retrosplenial region. However, sites on the midline surface of area 10 received more substantial projections from the temporal lobe, including clear auditory connections, whereas those in more lateral parts received >90% of their afferents from other frontal areas. This difference in anatomical connectivity reflects functional connectivity findings in the human brain. The pattern of connections in Cebus is very similar to that observed in the Old World macaque monkey, despite >40 million years of evolutionary separation, but lacks some of the connections reported in the more closely related but smaller marmoset monkey. These findings suggest that the clearer segregation observed in the human frontal pole reflects regional differences already present in early simian primates, and that overall brain mass influences the pattern of cortico-cortical connectivity.

Microbial translocation: translating simian immunodeficiency virus to HIV.

The article describes recent advances in understanding the causes and consequences of microbial translocation in HIV and simian immunodeficiency virus infections. Persistent microbial translocation contributes to aberrant immune activation in immunodeficiency lentiviral infections and thereby, pathogenesis and mortality. Efforts to delineate the circumstances surrounding translocation have benefited from use of simian immunodeficiency virus-infected nonhuman primates and highlight the overwhelming immunologic diversion caused by translocating microbes. The use of therapeutics aimed at reducing microbial translocation show promise and will benefit from continued research into the mechanisms that promote systemic microbial dissemination in treated and untreated infections. Insights into the source and identity of translocating microbes in lentiviral infections continue to enhance the development of adjunct therapeutics.

Evolutionary Origin of OwlRep, a Megasatellite DNA Associated with Adaptation of Owl Monkeys to Nocturnal Lifestyle.

Rod cells of many nocturnal mammals have a “non-standard” nuclear architecture, which is called the inverted nuclear architecture. Heterochromatin localizes to the central region of the nucleus. This leads to an efficient light transmission to the outer segments of photoreceptors. Rod cells of diurnal mammals have the conventional nuclear architecture. Owl monkeys (genus Aotus) are the only taxon of simian primates that has a nocturnal or cathemeral lifestyle, and this adaptation is widely thought to be secondary. Their rod cells were shown to exhibit an intermediate chromatin distribution: a spherical heterochromatin block was found in the central region of the nucleus although it was less complete than that of typical nocturnal mammals. We recently demonstrated that the primary DNA component of this heterochromatin block was OwlRep, a megasatellite DNA consisting of 187-bp-long repeat units. However, the origin of OwlRep was not known. Here we show that OwlRep was derived from HSAT6, a simple repeat sequence found in the centromere regions of human chromosomes. HSAT6 occurs widely in primates, suggesting that it was already present in the last common ancestor of extant primates. Notably, Strepsirrhini and Tarsiformes apparently carry a single HSAT6 copy, whereas many species of Simiiformes contain multiple copies. Comparison of nucleotide sequences of these copies revealed the entire process of the OwlRep formation. HSAT6, with or without flanking sequences, was segmentally duplicated in New World monkeys. Then, in the owl monkey linage after its divergence from other New World monkeys, a copy of HSAT6 was tandemly amplified, eventually forming a megasatellite DNA.

Temporal niche expansion in mammals from a nocturnal ancestor after dinosaur extinction.

Most modern mammals, including strictly diurnal species, exhibit sensory adaptations to nocturnal activity that are thought to be the result of a prolonged nocturnal phase or 'bottleneck' during early mammalian evolution. Nocturnality may have allowed mammals to avoid antagonistic interactions with diurnal dinosaurs during the Mesozoic. However, understanding the evolution of mammalian activity patterns is hindered by scant and ambiguous fossil evidence. While ancestral reconstructions of behavioural traits from extant species have the potential to elucidate these patterns, existing studies have been limited in taxonomic scope. Here, we use an extensive behavioural dataset for 2,415 species from all extant orders to reconstruct ancestral activity patterns across Mammalia. We find strong support for the nocturnal origin of mammals and the Cenozoic appearance of diurnality, although cathemerality (mixed diel periodicity) may have appeared in the late Cretaceous. Simian primates are among the earliest mammals to exhibit strict diurnal activity, some 52-33 million years ago. Our study is consistent with the hypothesis that temporal partitioning between early mammals and dinosaurs during the Mesozoic led to a mammalian nocturnal bottleneck, but also demonstrates the need for improved phylogenetic estimates for Mammalia.

Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara's Owl Monkey.

Owl monkeys (genus Aotus) are the only taxon in simian primates that consists of nocturnal or otherwise cathemeral species. Their night vision is superior to that of other monkeys, apes, and humans but not as good as that of typical nocturnal mammals. This incomplete night vision has been used to conclude that these monkeys only secondarily adapted to a nocturnal lifestyle, or to their cathemeral lifestyle that involves high night-time activity. It is known that the rod cells of many nocturnal mammals possess a unique nuclear architecture in which heterochromatin is centrally located. This “inverted nuclear architecture”, in contrast with “conventional nuclear architecture”, provides elevated night vision by passing light efficiently to the outer segments of photoreceptors. Owl monkey rod cells exhibit an intermediate chromatin distribution, which may provide them with less efficient night vision than other nocturnal mammals. Recently, we identified three megasatellite DNAs in the genome of Azara's owl monkey (Aotus azarae). In the present study, we show that one of the three megasatellite DNAs, OwlRep, serves as the primary component of the heterochromatin block located in the central space of the rod nucleus in A. azarae. This satellite DNA is likely to have emerged in the Aotus lineage after its divergence from those of other platyrrhini taxa and underwent a rapid expansion in the genome. Our results indicate that the heterochromatin core in the A. azarae rod nucleus was newly formed in A. azarae or its recent ancestor, and supports the hypothesis that A. azarae, and with all probability other Aotus species, secondarily acquired night vision.

Long-term simian research sites: significance for theory and conservation

Simian primates (monkeys and apes) are typically long-lived animals with slow life histories. They also have varying social organization and can slowly impact their environment by either being seed dispersers or by overbrowsing their food trees. As a result, short-term studies and those focusing on just 1 location only provide a snapshot of simian life under a specific set of ecological conditions that typically do not represent the complete spatial and temporal picture. Long-term field studies are needed to obtain a true understanding of their behavior, life history, ecology, and the selective pressures acting on them. Fortunately, there have been many long-term studies of simians, so a great deal is known about many species. Here, we consider examples of long-term studies that have operated continuously for approximately a decade or more. We review studies that deal with ecophysiology, social organization, population and community ecology, or conservation. The information emerging from these sites is particularly helpful in the construction of informed conservation plans, which are desperately needed given the severity of threats to simians and the fact that responses do not occur over the duration of a Ph.D. or granting cycle (typically 1–3 years).

Non-human Primate Schlafen11 Inhibits Production of Both Host and Viral Proteins

Schlafen11 (encoded by the SLFN11 gene) has been shown to inhibit the accumulation of HIV-1 proteins. We show that the SLFN11 gene is under positive selection in simian primates and is species-specific in its activity against HIV-1. The activity of human Schlafen11 is relatively weak compared to that of some other primate versions of this protein, with the versions encoded by chimpanzee, orangutan, gibbon, and marmoset being particularly potent inhibitors of HIV-1 protein production. Interestingly, we find that Schlafen11 is functional in the absence of infection and reduces protein production from certain non-viral (GFP) and even host (Vinculin and GAPDH) transcripts. This suggests that Schlafen11 may just generally block protein production from non-codon optimized transcripts. Because Schlafen11 is an interferon-stimulated gene with a broad ability to inhibit protein production from many host and viral transcripts, its role may be to create a general antiviral state in the cell. Interestingly, the strong inhibitors such as marmoset Schlafen11 consistently block protein production better than weak primate Schlafen11 proteins, regardless of the virus or host target being analyzed. Further, we show that the residues to which species-specific differences in Schlafen11 potency map are distinct from residues that have been targeted by positive selection. We speculate that the positive selection of SLFN11 could have been driven by a number of different factors, including interaction with one or more viral antagonists that have yet to be identified.

Vascular stiffness mechanoactivates YAP/TAZ-dependent glutaminolysis to drive pulmonary hypertension.

Dysregulation of vascular stiffness and cellular metabolism occurs early in pulmonary hypertension (PH). However, the mechanisms by which biophysical properties of the vascular extracellular matrix (ECM) relate to metabolic processes important in PH remain undefined. In this work, we examined cultured pulmonary vascular cells and various types of PH-diseased lung tissue and determined that ECM stiffening resulted in mechanoactivation of the transcriptional coactivators YAP and TAZ (WWTR1). YAP/TAZ activation modulated metabolic enzymes, including glutaminase (GLS1), to coordinate glutaminolysis and glycolysis. Glutaminolysis, an anaplerotic pathway, replenished aspartate for anabolic biosynthesis, which was critical for sustaining proliferation and migration within stiff ECM. In vitro, GLS1 inhibition blocked aspartate production and reprogrammed cellular proliferation pathways, while application of aspartate restored proliferation. In the monocrotaline rat model of PH, pharmacologic modulation of pulmonary vascular stiffness and YAP-dependent mechanotransduction altered glutaminolysis, pulmonary vascular proliferation, and manifestations of PH. Additionally, pharmacologic targeting of GLS1 in this model ameliorated disease progression. Notably, evaluation of simian immunodeficiency virus-infected nonhuman primates and HIV-infected subjects revealed a correlation between YAP/TAZ-GLS activation and PH. These results indicate that ECM stiffening sustains vascular cell growth and migration through YAP/TAZ-dependent glutaminolysis and anaplerosis, and thereby link mechanical stimuli to dysregulated vascular metabolism. Furthermore, this study identifies potential metabolic drug targets for therapeutic development in PH.