Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep (Ovis aries).

Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Asikli Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Asikli Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Asikli Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.

The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge.

Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.

Limited historical admixture between European wildcats and domestic cats.

Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities.

Dire wolves were the last of an ancient New World canid lineage.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

Origins and genetic legacy of prehistoric dogs.

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Human Endogenous Retrovirus-K HML-2 integration within RASGRF2 is associated with intravenous drug abuse and modulates transcription in a cell-line model.

HERV-K HML-2 (HK2) has been proliferating in the germ line of humans at least as recently as 250,000 years ago, with some integrations that remain polymorphic in the modern human population. One of the solitary HK2 LTR polymorphic integrations lies between exons 17 and 18 of RASGRF2, a gene that affects dopaminergic activity and is thus related to addiction. Here we show that this antisense HK2 integration (namely RASGRF2-int) is found more frequently in persons who inject drugs compared with the general population. In a Greek HIV-1-positive population (n = 202), we found RASGRF2-int 2.5 times (14 versus 6%) more frequently in patients infected through i.v. drug use compared with other transmission route controls (P = 0.03). Independently, in a United Kingdom-based hepatitis C virus-positive population (n = 184), we found RASGRF2-int 3.6 times (34 versus 9.5%) more frequently in patients infected during chronic drug abuse compared with controls (P < 0.001). We then tested whether RASGRF2-int could be mechanistically responsible for this association by modulating transcription of RASGRF2 We show that the CRISPR/Cas9-mediated insertion of HK2 in HEK293 cells in the exact RASGRF2 intronic position found in the population resulted in significant transcriptional and phenotypic changes. We also explored mechanistic features of other intronic HK2 integrations and show that HK2 LTRs can be responsible for generation of cis-natural antisense transcripts, which could interfere with the transcription of nearby genes. Our findings suggest that RASGRF2-int is a strong candidate for dopaminergic manipulation, and emphasize the importance of accurate mapping of neglected HERV polymorphisms in human genomic studies.

Relationship of axonal voltage-gated sodium channel 1.8 (NaV1.8) mRNA accumulation to sciatic nerve injury-induced painful neuropathy in rats.

Painful peripheral neuropathy is a significant clinical problem; however, its pathological mechanism and effective treatments remain elusive. Increased peripheral expression of tetrodotoxin-resistant voltage-gated sodium channel 1.8 (NaV1.8) has been shown to associate with chronic pain symptoms in humans and experimental animals. Sciatic nerve entrapment (SNE) injury was used to develop neuropathic pain symptoms in rats, resulting in increased NaV1.8 mRNA in the injured nerve but not in dorsal root ganglia (DRG). To study the role of NaV1.8 mRNA in the pathogenesis of SNE-induced painful neuropathy, NaV1.8 shRNA vector was delivered by subcutaneous injection of cationized gelatin/plasmid DNA polyplex into the rat hindpaw and its subsequent retrograde transport via sciatic nerve to DRG. This in vivo NaV1.8 shRNA treatment reversibly and repeatedly attenuated the SNE-induced pain symptoms, an effect that became apparent following a distinct lag period of 3-4 days and lasted for 4-6 days before returning to pretreatment levels. Surprisingly, apparent knockdown of NaV1.8 mRNA occurred only in the injured nerve, not in the DRG, during the pain alleviation period. Levels of heteronuclear NaV1.8 RNA were unaffected by SNE or shRNA treatments, suggesting that transcription of the Scn10a gene encoding NaV1.8 was unchanged. Based on these data, we postulate that increased axonal mRNA transport results in accumulation of functional NaV1.8 protein in the injured nerve and the development of painful neuropathy symptoms. Thus, targeted delivery of agents that interfere with axonal NaV1.8 mRNA may represent effective neuropathic pain treatments.

A genetic association study of single nucleotide polymorphisms in FGFR1OP2/wit3.0 and long-term atrophy of edentulous mandible.

BACKGROUND: After dental extraction, the external surface of alveolar bone undergoes resorption at various rates, and a group of patients develop excessive jawbone atrophy. Oral mucosa overlying the atrophied jawbone is unusually thin; therefore, we have hypothesized that excessive jawbone atrophy may be associated with abnormal oral mucosa contraction. FGFR1OP2/wit3.0, a cytoskeleton molecule initially identified in oral wound fibroblasts, has been shown to induce oral mucosa contraction after dental extraction. This study examined the genetic association between single nucleotide polymorphisms (SNPs) of FGFR1OP2/wit3.0 and excessive atrophy of edentulous mandible. METHODS AND FINDINGS: First, the expression of FGFR1OP2/wit3.0 was determined in gingival tissues of 8 subjects before and after dental extraction. In situ hybridization revealed that all subject increased FGFR1OP2/wit3.0 expression in the post-operative oral mucosa tissues; however, significantly high levels of FGFR1OP2/wit3.0 were observed in 3 out of 8 subjects. In a separate study, 20 long-term edentulous subjects (66.4 ± 9.4 years) were recruited. Tag-SNPs in the FGFR1OP2/wit3.0 allele were determined by Taqman-based polymerase chain reaction. The mandibular bone height was determined following the American College of Prosthodontists (ACP) protocol. Subjects with minor allele of rs840869 or rs859024 were found in the highly atrophied group by the ACP classification (Chi square test, p = 0.0384 and p = 0.0565, respectively; Fisher's Exact, p= 0.0515 and p = 0.2604, respectively). The linear regression analysis indicated a suggestive association between rs859024 and the decreased bone heights (Mann-Whitney, p = 0.06). The average bone height of the subjects with rs840869 or rs859024 minor alleles (10.6 ± 3.2 mm and 9.6 ± 3.2 mm, respectively) was significantly smaller than that of those subjects with the major alleles (14.2 ± 4.5 mm, p<0.05). CONCLUSIONS: The patients with the minor allele of rs840869 or rs859024 were associated with excessive atrophy of edentulous mandible. This study may provide the basis for a genetic marker identifying susceptible individuals to develop jawbone atrophy after dental extraction.

Wound closure and wound management: A new therapeutic molecular target.

Wound closure and infection control are the primary goal of wound management. A variety of disinfectants and antimicrobial agents are widely available today and routinely achieve infection control. On the contrary, wound closure still remains a challenging goal. Cell adhesion, migration and contraction play significant roles in creating contractile force of patent wound margins and in contributing to wound closure. Modulations of these cellular behaviors have been investigated in the context of wound contraction; however, therapeutic strategy to achieve wound closure has not been established. Recently, we have reported that a previously unknown cytoskeleton molecule, wound inducible transcript-3.0 (wit3.0) also known as fibroblast growth factor receptor 1 oncogene partner 2 (FGFR1OP2), can significantly modulate fibroblast-driven wound closure in vitro and in vivo. The dynamic role of cytoskeleton in different experimental models may provide a novel platform for designing the therapeutic target of wound management.

Small cytoskeleton-associated molecule, fibroblast growth factor receptor 1 oncogene partner 2/wound inducible transcript-3.0 (FGFR1OP2/wit3.0), facilitates fibroblast-driven wound closure.

Wounds created in the oral cavity heal rapidly and leave minimal scarring. We have examined a role of a previously isolated cDNA from oral wounds encoding wound inducible transcript-3.0 (wit3.0), also known as fibroblast growth factor receptor 1 oncogene partner 2 (FGFR1OP2). FGFR1OP2/wit3.0 was highly expressed in oral wound fibroblasts without noticeable up-regulation of alpha-smooth muscle actin. In silico analyses, denaturing and nondenaturing gel Western blot, and immunocytology together demonstrated that FGFR1OP2/wit3.0 were able to dimerize and oligomerize through coiled-coil structures and appeared to associate with cytoskeleton networks in oral wound fibroblasts. Overexpression of FGFR1OP2/wit3.0 increased the floating collagen gel contraction of naïve oral fibroblasts to the level of oral wound fibroblasts, which was in turn attenuated by small-interfering RNA knockdown. The FGFR1OP2/wit3.0 synthesis did not affect the expression of collagen I as well as procontractile peptides such as alpha-smooth muscle actin, and transforming growth factor-beta1 had no effect on FGFR1OP2/wit3.0 expression. Fibroblastic cells derived from embryonic stem cells carrying FGFR1OP2/wit3.0 (+/-) mutation showed significant retardation in cell migration. Thus, we postulate that FGFR1OP2/wit3.0 may regulate cell motility and stimulate wound closure. FGFR1OP2/wit3.0 was not up-regulated during skin wound healing; however, when treated with FGFR1OP2/wit3.0 -expression vector, the skin wound closure was significantly accelerated, resulting in the limited granulation tissue formation. Our data suggest that FGFR1OP2/wit3.0 may possess a therapeutic potential for wound management.

The role of titanium implant surface modification with hydroxyapatite nanoparticles in progressive early bone-implant fixation in vivo.

PURPOSE: This study evaluated the biologic effect in vivo of hydroxyapatite (HA) nanoparticle surface modification on commercially pure titanium or titanium alloy (Ti-6Al-4V) implants. MATERIALS AND METHODS: Miniature cylindric titanium and Ti-6Al-4V implants were pretreated with dual acid etching (DAE), and a subset was further modified with HA nanoparticles using discrete crystalline deposition (DCD). The resultant implant surface topography was characterized by interferometry and scanning electron microscopy. Miniature implants of DAE titanium, DAE Ti-6Al-4V, DCD titanium, and DCD Ti-6Al-4V were surgically placed in the femora of rats. After 4 days, 1 week, and 2 weeks of healing, osseointegration was evaluated by implant push-in tests or microcomputed tomography (microCT). Ti-6Al-4V samples were harvested at week 2 and prepared for nondecalcified histology and subjected to bone-to-implant contact (BIC) measurement. RESULTS: DCD treatment generated a complex surface morphology via the bonded HA nanoparticles. However, the amplitude and spatial, hybrid, and functional surface roughness parameters measured at the micron and submicron levels did not depict topographic differences between the DAE and the DCD-modified implants. DAE titanium and DAE Ti-6Al-4V implants showed a sharp increase in push-in values at week 1, followed by a plateau at week 2. DCD titanium and DCD Ti-6Al-4V implants showed similar sharp increases at week 1, but the push-in values continued to increase at week 2. The surrounding bone architecture evaluated by microCT and the BIC ratio did not correlate with the biomechanical implant osseointegration measurement. CONCLUSIONS: DCD-derived surface modification with HA nanoparticles on titanium and Ti-6Al-4V implants resulted in progressive osseointegration profiles that were distinctively different from those of DAE controls. Surrogate measurements such as surface roughness parameters and BIC did not predict the biologic effect of the DCD treatment. The data indicate that early osseointegration may be more sensitively regulated by nanoscale surface characteristics.

Vitamin D and bone physiology: demonstration of vitamin D deficiency in an implant osseointegration rat model.

PURPOSE: The patient population varies in nutritional deficiencies, which may confound the host response to biomaterials. The objective of this study was to evaluate the effect of a common deficiency of vitamin D on implant osseointegration in the rat model. MATERIALS AND METHODS: Male Sprague-Dawley rats were maintained under the cessation of vitamin D intake and UV exposure. The serum levels of 1,25(OH)(2)D(3), 25 OHD(3), Ca, and P were determined. Miniature cylindrical Ti6Al4V implants (2-mm long, 1-mm diameter) were fabricated with double acid-etched (DAE) surface or modified DAE with discrete crystalline deposition (DCD) of hydroxyapatite nanoparticles. DAE and DCD implants were placed in the femurs of vitamin D-insufficient and control rats. After 14 days of healing, the femur-implant samples were subjected to implant push-in test and nondecalcified histology. The surfaces of recovered implant specimens after the push-in test were further evaluated by scanning electron microscopy (SEM). RESULTS: The decreased serum level of 25 OHD(3) demonstrated the establishment of vitamin D insufficiency in this model. The implant push-in test revealed that DAE and DCD implants in the vitamin D-insufficient group (15.94 +/- 8.20 N, n = 7; 15.63 +/- 3.96 N, n = 7, respectively) were significantly lower than those of the control group (24.99 +/- 7.92 N, n = 7, p < 0.05; 37.48 +/- 17.58 N, n = 7, p < 0.01, respectively). The transcortical bone-to-implant contact ratio (BIC) was also significantly decreased in the vitamin D-insufficient group. SEM analyses further suggested that the calcified tissues remaining next to the implant surface after push-in test appeared unusually fragmented. CONCLUSIONS: The effect of vitamin D insufficiency significantly impairing the establishment of Ti6Al4V implant osseointegration in vivo was unexpectedly profound. The outcome of Ti-based endosseous implants may be confounded by the increasing prevalence of vitamin D insufficiency in our patient population.

Increased peripheral nerve excitability and local NaV1.8 mRNA up-regulation in painful neuropathy.

BACKGROUND: Neuropathic pain caused by peripheral nerve injury is a chronic disorder that represents a significant clinical challenge because the pathological mechanisms have not been fully elucidated. Several studies have suggested the involvement of various sodium channels, including tetrodotoxin-resistant NaV1.8, in affected dorsal root ganglion (DRG) neurons. We have hypothesized that altered local expression of NaV1.8 in the peripheral axons of DRG neurons could facilitate nociceptive signal generation and propagation after neuropathic injury. RESULTS: After unilateral sciatic nerve entrapment injury in rats, compound action potential amplitudes were increased in both myelinated and unmyelinated fibers of the ipsilateral sciatic nerve. Tetrodotoxin resistance of both fiber populations and sciatic nerve NaV1.8 immunoreactivity were also increased. Further analysis of NaV1.8 distribution revealed that immunoreactivity and mRNA levels were decreased and unaffected, respectively, in the ipsilateral L4 and L5 DRG; however sciatic nerve NaV1.8 mRNA showed nearly an 11-fold ipsilateral increase. Nav1.8 mRNA observed in the sciatic nerve was likely of axonal origin since it was not detected in non-neuronal cells cultured from nerve tissue. Absence of changes in NaV1.8 mRNA polyadenylation suggests that increased mRNA stability was not responsible for the selective peripheral mRNA increase. Furthermore, mRNA levels of NaV1.3, NaV1.5, NaV1.6, NaV1.7, and NaV1.9 were not significantly different between ipsilateral and contralateral nerves. We therefore propose that selective NaV1.8 mRNA axonal transport and local up-regulation could contribute to the hyperexcitability of peripheral nerves in some neuropathic pain states. CONCLUSION: Cuff entrapment injury resulted in significantly elevated axonal excitability and increased NaV1.8 immunoreactivity in rat sciatic nerves. The concomitant axonal accumulation of NaV1.8 mRNA may play a role in the pathogenesis of this model of neuropathic pain.

Oral fibroblast expression of wound-inducible transcript 3.0 (wit3.0) accelerates the collagen gel contraction in vitro.

Wounds of the oral mucosa show faster closure with less scar formation than skin wounds in other areas. A differentially expressed cDNA, wound-inducible transcript 3.0 (wit3.0), was isolated from oral mucosal wound in rats (Sukotjo, C., Abanmy, A. A., Ogawa, T., and Nishimura, I. (2002) J. Dent. Res. 81, 229-235). The purpose of this study was to characterize the wit3.0 gene structure and the function of its deduced peptide. Human and rat genome databases revealed that the gene for wit3.0 was located in human chromosome 12p11.23 and rat chromosome 4q44. Its human and rat gene structures were well conserved, composed of 7 exons spread over 20 kb. Exon 5 was alternatively spliced generating two transcripts encoding deduced peptides of 215 and 253 amino acids (wit3.0 alpha and wit3.0 beta, respectively). The protein families data base of alignments (Pfam) analysis suggested the wit3.0 peptide sequence shared similarity with a portion of the myosin II coiled-coil domain consensus sequence. Fibroblasts isolated from the rat oral wound up-regulated wit3.0 expression and exhibited greater ability to contract collagen gel in vitro than fibroblasts isolated from untreated oral mucosa/gingiva. NIH3T3 and rat oral fibroblasts transfected with expression vector containing the coding sequences of wit3.0 alpha or wit3.0 beta increased in vitro collagen gel contraction. When treated with TGF beta-1, NIH3T3 fibroblast expression of wit3.0 showed no significant change, whereas alpha smooth muscle actin was increased in a dose-dependent manner. These data suggest that there may be a novel wound healing pathway involving wit3.0 underlying the favorable early wound closure characteristics of oral mucosa.