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1.  Sauropod dinosaurs evolved moderately sized genomes unrelated to body size 
Sauropodomorph dinosaurs include the largest land animals to have ever lived, some reaching up to 10 times the mass of an African elephant. Despite their status defining the upper range for body size in land animals, it remains unknown whether sauropodomorphs evolved larger-sized genomes than non-avian theropods, their sister taxon, or whether a relationship exists between genome size and body size in dinosaurs, two questions critical for understanding broad patterns of genome evolution in dinosaurs. Here we report inferences of genome size for 10 sauropodomorph taxa. The estimates are derived from a Bayesian phylogenetic generalized least squares approach that generates posterior distributions of regression models relating genome size to osteocyte lacunae volume in extant tetrapods. We estimate that the average genome size of sauropodomorphs was 2.02 pg (range of species means: 1.77–2.21 pg), a value in the upper range of extant birds (mean = 1.42 pg, range: 0.97–2.16 pg) and near the average for extant non-avian reptiles (mean = 2.24 pg, range: 1.05–5.44 pg). The results suggest that the variation in size and architecture of genomes in extinct dinosaurs was lower than the variation found in mammals. A substantial difference in genome size separates the two major clades within dinosaurs, Ornithischia (large genomes) and Saurischia (moderate to small genomes). We find no relationship between body size and estimated genome size in extinct dinosaurs, which suggests that neutral forces did not dominate the evolution of genome size in this group.
doi:10.1098/rspb.2009.1343
PMCID: PMC2817110  PMID: 19793755
palaeogenomics; Dinosauria; genome size; genomics; Sauropodomorpha
2.  Palaeogenomics of pterosaurs and the evolution of small genome size in flying vertebrates 
Biology Letters  2008;5(1):47-50.
The two living groups of flying vertebrates, birds and bats, both have constricted genome sizes compared with their close relatives. But nothing is known about the genomic characteristics of pterosaurs, which took to the air over 70 Myr before birds and were the first group of vertebrates to evolve powered flight. Here, we estimate genome size for four species of pterosaurs and seven species of basal archosauromorphs using a Bayesian comparative approach. Our results suggest that small genomes commonly associated with flight in bats and birds also evolved in pterosaurs, and that the rate of genome-size evolution is proportional to genome size within amniotes, with the fastest rates occurring in lineages with the largest genomes. We examine the role that drift may have played in the evolution of genome size within tetrapods by testing for correlated evolution between genome size and body size, but find no support for this hypothesis. By contrast, we find evidence suggesting that a combination of adaptation and phylogenetic inertia best explains the correlated evolution of flight and genome-size contraction. These results suggest that small genome/cell size evolved prior to or concurrently with flight in pterosaurs. We predict that, similar to the pattern seen in theropod dinosaurs, genome-size contraction preceded flight in pterosaurs and bats.
doi:10.1098/rsbl.2008.0491
PMCID: PMC2657748  PMID: 18940771
genome size; palaeogenomics; pterosaurs
3.  Osteocytic osteolysis: time for a second look? 
BoneKEy Reports  2012;1:229.
Over 100 years ago it was suggested that osteocytes could remodel their surrounding environment by removing and replacing bone. In the 1960s and 1970s, many observations were made to suggest that osteocytes could resorb bone and increase the size of their lacunae. This concept became known as osteocytic osteolysis and studies suggested that it occurred in response to diverse stimuli such as parathyroid hormone, calcium restriction, hibernation and reproductive cycles. However, this concept fell out of favor in the late 1970s when it became clear that osteoclasts were the principal bone-resorbing cells in the skeleton. Over the past decade, we have increasingly appreciated that osteocytes are remarkably versatile cells and are involved in all aspects of skeletal biology, including the response to loading, the regulation of bone turnover and the control of mineral metabolism. Recent data have demonstrated that osteocytes remodel their perilacunar and canalicular matrix and participate in the liberation of skeletal calcium stores during lactation. In light of these new findings, it may be time to reassess the concept of osteocytic osteolysis and reconsider whether osteocyte lacunar and canalicular remodeling contributes more broadly to the maintenance of skeletal and mineral homeostasis.
doi:10.1038/bonekey.2012.229
PMCID: PMC3868715  PMID: 24363929
4.  Preliminary Analysis of Osteocyte Lacunar Density in Long Bones of Tetrapods: All Measures Are Bigger in Sauropod Dinosaurs 
PLoS ONE  2013;8(10):e77109.
Osteocytes harbour much potential for paleobiological studies. Synchrotron radiation and spectroscopic analyses are providing fascinating data on osteocyte density, size and orientation in fossil taxa. However, such studies may be costly and time consuming. Here we describe an uncomplicated and inexpensive method to measure osteocyte lacunar densities in bone thin sections. We report on cell lacunar densities in the long bones of various extant and extinct tetrapods, with a focus on sauropodomorph dinosaurs, and how lacunar densities can help us understand bone formation rates in the iconic sauropod dinosaurs. Ordinary least square and phylogenetic generalized least square regressions suggest that sauropodomorphs have lacunar densities higher than scaled up or comparably sized mammals. We also found normal mammalian-like osteocyte densities for the extinct bovid Myotragus, questioning its crocodilian-like physiology. When accounting for body mass effects and phylogeny, growth rates are a main factor determining the density of the lacunocanalicular network. However, functional aspects most likely play an important role as well. Observed differences in cell strategies between mammals and dinosaurs likely illustrate the convergent nature of fast growing bone tissues in these groups.
doi:10.1371/journal.pone.0077109
PMCID: PMC3812986  PMID: 24204748
5.  Changes in Intracortical Microporosities Induced by Pharmaceutical Treatment of Osteoporosis as Detected by High Resolution Micro-CT 
Bone  2011;50(3):596-604.
Bone’s microporosities play important biologic and mechanical roles. Here, we quantified 3D changes in cortical osteocyte-lacunae and other small porosities induced by estrogen withdrawal and two different osteoporosis treatments. Unlike 2D measurements, these data collected via synchrotron radiation-based μCT describe the size and 3D spatial distribution of a large number of porous structures. Six-month old female Sprague-Dawley rats were separated into four groups of age-matched controls, untreated OVX, OVX treated with PTH, and OVX treated with Alendronate (ALN). Intracortical microporosity of the medial quadrant of the femoral diaphysis was quantified at endosteal, intracortical, and periosteal regions of the samples, allowing the quantification of osteocyte lacunae that were formed primarily before versus after the start of treatment. Across the overall thickness of the medial cortex, lacunar volume fraction (Lc.V/TV) was significantly lower in ALN treated rats compared to PTH. In the endosteal region, average osteocyte lacunar volume () of untreated OVX rats was significantly lower than in age-matched controls, indicating a decrease in osteocyte lacunar size in bone formed on the endosteal surface after estrogen withdrawal. The effect of treatment (OVX, ALN, PTH) on the number of lacunae per tissue volume (Lc.N/TV) was dependent on the specific location within the cortex (endosteal, intracortical, periosteal). In both the endosteal and intracortical regions, Lc.N/TV was significantly lower in ALN than in untreated OVX, suggesting a site-specific effect in osteocyte lacuna density with ALN treatment. There also were a significantly greater number of small pores (5–100 μm3 in volume) in the endosteal region for PTH compared to ALN. The mechanical impact of this altered microporosity structure is unknown, but might serve to enhance, rather than deteriorate bone strength with PTH treatment, as smaller osteocyte lacunae may be better able to absorb shear forces than larger lacunae. Together, these data demonstrate that current treatments of osteoporosis can alter the number, size, and distribution of microporosities in cortical rat lamellar bone.
doi:10.1016/j.bone.2011.12.012
PMCID: PMC3278519  PMID: 22226688
PTH; Alendronate; OVX; osteocyte lacunae; synchrotron micro-CT; cortical bone porosity
6.  Evidence for the role of connexin 43-mediated intercellular communication in the process of intracortical bone resorption via osteocytic osteolysis 
Background
Connexin 43 (Cx43) is the predominant gap junction protein in bone. Mice with a bone-specific deletion of Cx43 (cKO) have an osteopenic cortical phenotype. In a recent study, we demonstrated that cKO mice are resistant to bone loss induced by hindlimb suspension (HLS), an animal model of skeletal unloading. This protective effect occurred primarily as a result of lower osteoclast-mediated bone resorption. Interestingly, we also documented a significant increase in cortical osteocyte apoptosis and reduced sclerostin production. In the present study, we investigated whether osteocytic osteolysis – bone resorption by osteocytes within lacunae – is induced by HLS and the potential effect of Cx43 deficiency on this process during unloading.
Methods
6-month-old male Cx43 cKO or wild-type (WT) mice were subjected to three weeks of HLS (Suspended) or normal loading conditions (Control) (n = 5/group). Lacunar morphology and tartrate-resistant acid phosphatase (TRACP) staining were assessed on sections of femur cortical bone. Experimental groups were compared via two-way ANOVA.
Results
Empty lacunae were 26% larger in cKO-Control vs. WT-Control (p < 0.05), while there was no difference in the size of empty lacunae between Control and Suspended within WT or cKO (p > 0.05). Similarly, there was a trend (p = 0.06) for 11% larger lacunae containing viable osteocytes for cKO-Control vs. WT-Control, with no apparent effect of loading condition. There was no difference in the proportion of TRACP + cells between WT-Control and cKO-Control (p > 0.05); however, WT-Suspended mice had 246% more TRACP + osteocytes compared WT-Control mice (p < 0.05). There was no difference in TRACP staining between cKO-Control and cKO-Suspended (p > 0.05).
Conclusions
Prior to undergoing apoptosis, osteocytes in cKO mice may be actively resorbing their respective lacunae via the process of osteocytic osteolysis. Interestingly, the proportion of TRACP + osteocytes increased dramatically following unloading of WT mice, an effect that was not observed in cKO mice subjected to HLS. The results of the present study provide initial evidence that osteocytic osteolysis is occurring in cortical bone in response to mechanical unloading. Furthermore, Cx43 deficiency appears to protect against osteocytic osteolysis in a manner similar to the inhibition of unloading-induced osteoclast activation that we have documented previously.
doi:10.1186/1471-2474-15-122
PMCID: PMC3984635  PMID: 24716486
Connexin 43; Osteocytic osteolysis; Hindlimb suspension; Unloading; Cortical bone; Porosity
7.  Comparison of climate space and phylogeny of Marmota (Mammalia: Rodentia) indicates a connection between evolutionary history and climate preference 
Palaeobiologists have investigated the evolutionary responses of extinct organisms to climate change, and have also used extinct organisms to reconstruct palaeoclimates. There is evidence of a disconnection between climate change and evolution that suggests that organisms may not be accurate palaeoclimate indicators. Here, marmots (Marmota sp.) are used as a case study to examine whether similarity of climate preferences is correlated with evolutionary relatedness of species. This study tests for a relationship between phylogenetic distance and `climate distance' of species within a clade. There should be a significant congruence between maximum likelihood distance and standardized Euclidian distance between climates if daughter species tend to stay in environments similar to parent species. Marmots make a good test case because there are many extant species, their phylogenies are well established and individual survival is linked to climatic factors. A Mantel test indicates a significant correlation between climate and phylogenetic distance matrices, but this relationship explains only a small fraction of the variance (regression R2=0.114). These results suggest that (i) closely related species of marmots tend to stay in similar environments; (ii) marmots may be more susceptible than many mammals to global climate change; and (iii) because of the considerable noise in this system, the correlation cannot be used for detailed palaeoclimate reconstruction.
doi:10.1098/rspb.2004.2979
PMCID: PMC1578709  PMID: 15799948
Marmota; climate and evolution; mammalian speciation; palaeoclimate reconstruction; geographic information system
8.  Effect of Raloxifene Treatment on Osteocyte Apoptosis in Postmenopausal Women 
Calcified Tissue International  2007;81(3):183-190.
Increased osteocyte apoptosis, as the result of estrogen deficiency, could play a role in the decrease of bone mass and bone strength seen in postmenopausal osteoporosis. We investigated whether treatment with raloxifene of postmenopausal women with osteoporosis affects osteocyte apoptosis. Transiliac bone biopsies were obtained from 26 osteoporotic women at baseline and after 2 years of treatment with placebo or raloxifene. Immunohistochemical detection of cleaved caspase-3 was performed on sections from nondecalcified bone biopsies to visualize apoptosis. In the trabecular bone total osteocytes, positively stained osteocytes and empty lacunae were counted and percent positive cells and percent empty lacunae determined. Statistical evaluation was performed by Wilcoxon’s paired t-test and Spearman’s rank correlations. There was no significant difference in percentage positive osteocytes between baseline and follow-up biopsies in both the placebo and the raloxifene groups. The percentage empty lacunae increased significantly in the placebo group (11.20 ± 1.43 vs. 9.00 ± 2.25, P = 0.014) but not in the raloxifene group. At baseline in both groups combined, there was a negative correlation between indices of bone remodeling and the percentage positive osteocytes (bone formation rate/bone volume r = −0.67, P = 0.001). We found no direct evidence for an effect of raloxifene treatment on osteocyte apoptosis, but small effects of raloxifene treatment cannot be excluded. The percent of apoptotic osteocytes was dependent on the level of bone remodeling in an individual.
doi:10.1007/s00223-007-9050-0
PMCID: PMC2039811  PMID: 17676256
Apoptosis; Histomorphometry; Osteocyte; Postmenopausal osteoporosis; Raloxifene
9.  Osteocyte and osteoblast apoptosis and excessive bone deposition accompany failure of collagenase cleavage of collagen 
Journal of Clinical Investigation  2000;106(8):941-949.
Mice carrying a targeted mutation (r) in Col1a1, encoding a collagenase-resistant form of type I collagen, have altered skeletal remodeling. In hematoxylin and eosin–stained paraffin sections, we detect empty lacunae in osteocytes in calvariae from Col1a1r/r mice at age 2 weeks, increasing through age 10–12 months. Empty lacunae appear to result from osteocyte apoptosis, since staining of osteocytes/periosteal osteoblasts with terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling is increased in Col1a1r/r relative to wild-type bones. Osteocyte perilacunar matrices stained with Ab that recognizes collagenase collagen α1(I) chain cleavage ends in wild-type but not Col1a1r/r calvariae. Increased calvarial periosteal and tibial/femoral endosteal bone deposition was found in Col1a1r/r mice from ages 3–12 months. Calcein labeling of calvarial surfaces was increased in Col1a1r/r relative to wild-type mice. Daily injections of synthetic parathyroid hormone for 30 days increased calcein-surface labeling in wild-type but caused no further increase in the already high calcein staining of Col1a1r/r bones. Thus, failure of collagenase cleavage of type I collagen in Col1a1r/r mice is associated with osteocyte/osteoblast death but increases bone deposition in a manner that mimics the parathyroid hormone–induced bone surface activation seen in wild-type mice.
PMCID: PMC314341  PMID: 11032854
10.  Out of Arabia: A Complex Biogeographic History of Multiple Vicariance and Dispersal Events in the Gecko Genus Hemidactylus (Reptilia: Gekkonidae) 
PLoS ONE  2013;8(5):e64018.
The geological history of the Arabian Peninsula has played a crucial role in shaping current diversity and distribution patterns of many Arabian and African faunal elements. The gecko genus Hemidactylus is not an exception. In this study, we provide an insight into the phylogeny and systematics of 45 recognized species of the so-called Arid clade of the genus Hemidactylus from Arabia, the Horn of Africa, the Levant and Iran. The material comprises 358 specimens sequenced for up to two mitochondrial (12S rRNA, cytochrome b) and four nuclear (mc1r, cmos, rag1, rag2) genes with 4766 bp of the concatenated alignment length. A robust calibrated phylogeny and reconstruction of historical biogeography are inferred. We link the history of this genus with major geological events that occurred in the region within the last 30 million years. Two basal divergences correspond with the break-ups of the Arabian and African landmasses and subsequent separation of Socotra from the Arabian mainland, respectively, segregating the genus by means of vicariance. Formation of the Red Sea led to isolation and subsequent radiation in the Arabian Peninsula, which was followed by multiple independent expansions: 13.1 Ma to Iran; 9.8 Ma to NE Africa; 8.2 to Socotra Archipelago; 7–7.3 Ma two colonizations to the Near East; 5.9 Ma to NE Africa; and 4.1 to Socotra. Moreover, using multiple genetic markers we detected cryptic diversity within the genus, particularly in south-western Arabia and the Ethiopian highlands, and confirmed the existence of at least seven new species in the area. These findings highlight the role of Arabia and the Horn of Africa as an important Hemidactylus diversity hotspot.
doi:10.1371/journal.pone.0064018
PMCID: PMC3664631  PMID: 23724016
11.  Tissue strain amplification at the osteocyte lacuna: A microstructural finite element analysis 
Journal of biomechanics  2007;40(10):2199-2206.
A parametric finite element model of an osteocyte lacuna was developed to predict the microstructural response of the lacuna to imposed macroscopic strains. The model is composed of an osteocyte lacuna, a region of perilacunar tissue, canaliculi, and the surrounding bone tissue. A total of 45 different simulations were modeled with varying canalicular diameters, perilacunar tissue material moduli, and perilacunar tissue thicknesses. Maximum strain increased with a decrease in perilacunar tissue modulus and decreased with an increase in perilacunar tissue modulus, regardless of the thickness of the perilacunar region. An increase in the predicted maximum strain was observed with an increase in canalicular diameter from 0.362 to 0.421 μm. In response to the macroscopic application of strain, canalicular diameters increased 0.8% to over 1.0% depending on the perilacunar tissue modulus. Strain magnification factors of over 3 were predicted. However, varying the size of the perilacunar tissue region had no effect on the predicted perilacunar tissue strain. These results indicate that the application of average macroscopic strains similar to strain levels measured in vivo can result in significantly greater perilacunar tissue strains and canaliculi deformations. A decrease in the perilacunar tissue modulus amplifies the perilacunar tissue strain and canaliculi deformation while an increase in the local perilacunar tissue modulus attenuates this effect.
doi:10.1016/j.jbiomech.2006.10.040
PMCID: PMC2094105  PMID: 17196968
Bone; Osteocyte; Lacuna; Tissue strain; Finite element model
12.  New Specimens of the Rare Taeniodont Wortmania (Mammalia: Eutheria) from the San Juan Basin of New Mexico and Comments on the Phylogeny and Functional Morphology of “Archaic” Mammals 
PLoS ONE  2013;8(9):e75886.
Background
Taeniodonta is a clade of Late Cretaceous – Paleogene mammals remarkable for their relatively extreme cranial, dental, and postcranial adaptations and notable for being among the first mammals to achieve relatively large size following the Cretaceous-Paleogene mass extinction. Previous workers have hypothesized that taeniodonts can be divided into two clades: Conoryctidae, a group of small-bodied taeniodonts with supposedly “generalized” postcranial skeletons, and Stylinodontidae, a group of large-bodied, robust animals with massive forelimbs and claws adapted for scratch-digging. However, many taeniodont taxa are poorly known and few are represented by postcranial material, leaving many details about their anatomy, biology, and evolution ambiguous.
Methodology/Principal Findings
In this paper, we describe three new specimens of the rare taxon Wortmaniaotariidens from the early Paleocene (Puercan) of New Mexico. Among these specimens is one that includes remarkably complete cranial and dental material, including associated upper and lower teeth, and another that consists of partial forelimbs. These specimens allow for an updated anatomical description of this unusual taxon, supply new data for phylogenetic analyses, and enable a more constrained discussion of taeniodont biology and functional morphology.
Conclusions/Significance
The new specimen of Wortmania that includes associated upper and lower teeth indicates that previous interpretations of the upper dentition of this taxon were not accurate and the taxon Robertschochiasullivani is a junior synonym of W. otariidens. New specimens that include partial forelimbs indicate that Wortmania is very similar to later, large-bodied taeniodonts, with marked and distinctive adaptations for scratch-digging. Comparisons with other taeniodont taxa that include postcranial material suggest that all taeniodonts may have had scratch-digging adaptations. A phylogenetic analysis shows that Schowalteria and Onychodectes are basal taeniodonts, Stylinodontidae (including Wortmania) is monophyletic, and a monophyletic Conoryctidae (but not including Onychodectes) is only recovered when certain characters are ordered.
doi:10.1371/journal.pone.0075886
PMCID: PMC3786969  PMID: 24098738
13.  Fluorescent Risedronate Analogues Reveal Bisphosphonate Uptake by Bone Marrow Monocytes and Localization Around Osteocytes In Vivo 
Bisphosphonates are effective antiresorptive agents owing to their bone-targeting property and ability to inhibit osteoclasts. It remains unclear, however, whether any non-osteoclast cells are directly affected by these drugs in vivo. Two fluorescent risedronate analogues, carboxyfluorescein-labeled risedronate (FAM-RIS) and Alexa Fluor 647–labeled risedronate (AF647-RIS), were used to address this question. Twenty-four hours after injection into 3-month-old mice, fluorescent risedronate analogues were bound to bone surfaces. More detailed analysis revealed labeling of vascular channel walls within cortical bone. Furthermore, fluorescent risedronate analogues were present in osteocytic lacunae in close proximity to vascular channels and localized to the lacunae of newly embedded osteocytes close to the bone surface. Following injection into newborn rabbits, intracellular uptake of fluorescently labeled risedronate was detected in osteoclasts, and the active analogue FAM-RIS caused accumulation of unprenylated Rap1A in these cells. In addition, CD14high bone marrow monocytes showed relatively high levels of uptake of fluorescently labeled risedronate, which correlated with selective accumulation of unprenylated Rap1A in CD14+ cells, as well as osteoclasts, following treatment with risedronate in vivo. Similar results were obtained when either rabbit or human bone marrow cells were treated with fluorescent risedronate analogues in vitro. These findings suggest that the capacity of different cell types to endocytose bisphosphonate is a major determinant for the degree of cellular drug uptake in vitro as well as in vivo. In conclusion, this study shows that in addition to bone-resorbing osteoclasts, bisphosphonates may exert direct effects on bone marrow monocytes in vivo. © 2010 American Society for Bone and Mineral Research
doi:10.1359/jbmr.091009
PMCID: PMC3153397  PMID: 20422624
bisphosphonates; fluorescent conjugates; cellular uptake; osteocytes; monocytes
14.  Parallel gigantism and complex colonization patterns in the Cape Verde scincid lizards Mabuya and Macroscincus (Reptilia: Scincidae) revealed by mitochondrial DNA sequences. 
The scincid lizards of the Cape Verde islands comprise the extinct endemic giant Macroscincus coctei and at least five species of Mabuya, one of which, Mabuya vaillanti, also had populations with large body size. Phylogenetic analysis based on DNA sequences derived from the mitochondrial cytochrome b, cytochrome oxidase I and 12S rRNA genes (711, 498 and 378 base pairs (bp), respectively) corroborates morphological evidence that these species constitute a clade and that Macroscincus is unrelated to very large skinks in other areas. The relationships are ((M. vaillanti and Mabuya delalandii) (Mabuya spinalis and Macroscincus coctei (Mabuya fogoensis nicolauensis (Mabuya fogoensis antaoensis and Mabuya stangeri)))). The Cape Verde archipelago was colonized from West Africa, probably in the Late Miocene or Early Pliocene period. The north-eastern islands were probably occupied first, after which the ancestor of M. vaillanti and M. delalandii may have originated on Boavista, the ancestor of the latter species arriving on Santiago or Fogo later. The M. fogoensis--M. stangeri clade colonized the islands of Branco, Razo, Santa Luzia and São Vicente from São Nicolau and reached Santo Antão after this. Colonization of these northeastern islands was slow, perhaps because the recipient islands had not developed earlier or because colonization cut across the path of the Canary Current and the Northeast Trade Winds, the main dispersing agents in the region. Rapid extension of range into the southwestern islands occurred later in M. spinalis and then in M. vaillanti and M. delalandii. The long apparent delay between the origin of these species and their southwestern dispersal may have been because there were earlier colonizations of the southern islands which excluded later ones until the earlier inhabitants were exterminated by volcanic or climatic events. The evolution of large size in Macroscincus occurred in the northwestern islands and was paralleled in the eastern and southern islands by populations of M. vaillanti. Both cases of size increase in Cape Verde skinks were accompanied by the development of herbivory.
doi:10.1098/rspb.2001.1699
PMCID: PMC1088783  PMID: 11487407
15.  Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2T, a cyanobacterium isolated from seawater of Chuuk lagoon 
Standards in Genomic Sciences  2013;9(1):197-204.
A photoautotrophic cyanobacterium, Rubidibacter lacunae was reported in 2008 for the first time. The type strain, KORDI 51-2T, was isolated from seawater of Chuuk lagoon located in a tropical area. Although it belonged to a clade exclusively comprised of extremely halotolerant strains by phylogenetic analyses, R. lacunae is known to be incapable of growth at high salt concentration over 10%. Here we report the main features of the genome of R. lacunae strain KORDI 51-2T. The genome of R. lacunae contains a gene cluster for phosphonate utilization encoding three transporters, one regulator and eight C-P lyase subunits.
doi:10.4056/sigs.4398180
PMCID: PMC3910548  PMID: 24501656
Cyanobacteria; phosphonate utilization; photoautotrophy; Rubidibacter lacunae; seawater
16.  Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics 
PLoS ONE  2011;6(8):e24161.
Background
Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks.
Methodology/Principals Findings
To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants.
Conclusions
We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5′ and 3′ ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.
doi:10.1371/journal.pone.0024161
PMCID: PMC3164143  PMID: 21904610
17.  Evidence of Spondyloarthropathy in the Spine of a Phytosaur (Reptilia: Archosauriformes) from the Late Triassic of Halberstadt, Germany 
PLoS ONE  2014;9(1):e85511.
Pathologies in the skeleton of phytosaurs, extinct archosauriform reptiles restricted to the Late Triassic, have only been rarely described. The only known postcranial pathologies of a phytosaur are two pairs of fused vertebrae of “Angistorhinopsis ruetimeyeri” from Halberstadt, Germany, as initially described by the paleontologist Friedrich von Huene. These pathologic vertebrae are redescribed in more detail in this study in the light of modern paleopathologic methods. Four different pathologic observations can be made in the vertebral column of this individual: 1) fusion of two thoracic vertebral bodies by new bone formation within the synovial membrane and articular capsule of the intervertebral joint; 2) fusion and conspicuous antero-posterior shortening of last presacral and first sacral vertebral bodies; 3) destruction and erosion of the anterior articular surface of the last presacral vertebra; and 4) a smooth depression on the ventral surface of the fused last presacral and first sacral vertebral bodies. Observations 1–3 can most plausibly and parsimoniously be attributed to one disease: spondyloarthropathy, an aseptic inflammatory process in which affected vertebrae show typical types of reactive new bone formation and erosion of subchondral bone. The kind of vertebral shortening present in the fused lumbosacral vertebrae suggests that the phytosaur acquired this disease in its early life. Observation 4, the smooth ventral depression in the fused lumbosacral vertebrae, is most probably not connected to the spondyloarthropathy, and can be regarded as a separate abnormality. It remains of uncertain origin, but may be the result of pressure, perhaps caused by a benign mass such as an aneurysm or cyst of unknown type. Reports of spondyloarthropathy in Paleozoic and Mesozoic reptiles are still exceptional, and our report of spondyloarthropathy in fossil material from Halberstadt is the first unequivocal occurrence of this disease in a Triassic tetrapod and in a phytosaur.
doi:10.1371/journal.pone.0085511
PMCID: PMC3893247  PMID: 24454880
18.  Cartilaginous Epiphyses in Extant Archosaurs and Their Implications for Reconstructing Limb Function in Dinosaurs 
PLoS ONE  2010;5(9):e13120.
Extinct archosaurs, including many non-avian dinosaurs, exhibit relatively simply shaped condylar regions in their appendicular bones, suggesting potentially large amounts of unpreserved epiphyseal (articular) cartilage. This “lost anatomy” is often underappreciated such that the ends of bones are typically considered to be the joint surfaces, potentially having a major impact on functional interpretation. Extant alligators and birds were used to establish an objective basis for inferences about cartilaginous articular structures in such extinct archosaur clades as non-avian dinosaurs. Limb elements of alligators, ostriches, and other birds were dissected, disarticulated, and defleshed. Lengths and condylar shapes of elements with intact epiphyses were measured. Limbs were subsequently completely skeletonized and the measurements repeated. Removal of cartilaginous condylar regions resulted in statistically significant changes in element length and condylar breadth. Moreover, there was marked loss of those cartilaginous structures responsible for joint architecture and congruence. Compared to alligators, birds showed less dramatic, but still significant changes. Condylar morphologies of dinosaur limb bones suggest that most non-coelurosaurian clades possessed large cartilaginous epiphyses that relied on the maintenance of vascular channels that are otherwise eliminated early in ontogeny in smaller-bodied tetrapods. A sensitivity analysis using cartilage correction factors (CCFs) obtained from extant taxa indicates that whereas the presence of cartilaginous epiphyses only moderately increases estimates of dinosaur height and speed, it has important implications for our ability to infer joint morphology, posture, and the complicated functional movements in the limbs of many extinct archosaurs. Evidence suggests that the sizes of sauropod epiphyseal cartilages surpassed those of alligators, which account for at least 10% of hindlimb length. These data suggest that large cartilaginous epiphyses were widely distributed among non-avian archosaurs and must be considered when making inferences about locomotor functional morphology in fossil taxa.
doi:10.1371/journal.pone.0013120
PMCID: PMC2948032  PMID: 20927347
19.  Cell autonomous requirement of connexin 43 for osteocyte survival: consequences for endocortical resorption and periosteal bone formation 
Connexin 43 (Cx43) mediates osteocyte communication with other cells and with the extracellular milieu and regulates osteoblastic cell signaling and gene expression. We now report that mice lacking Cx43 in osteoblasts/osteocytes or only in osteocytes (Cx43ΔOt mice) exhibit increased osteocyte apoptosis, endocortical resorption and periosteal bone formation, resulting in higher marrow cavity and total tissue areas measured at the femoral mid-diaphysis. Blockade of resorption reversed the increased marrow cavity but not total tissue area, demonstrating that endocortical resorption and periosteal apposition are independently regulated. Anatomical mapping of apoptotic osteocytes, osteocytic protein expression, and resorption and formation, suggests that Cx43 controls osteoclast and osteoblast activity by regulating osteoprotegerin and sclerostin levels, respectively, in osteocytes located in specific areas of the cortex. Whereas empty lacunae and living osteocytes lacking osteoprotegerin were distributed throughout cortical bone in Cx43ΔOt mice, apoptotic osteocytes were preferentially located in areas containing osteoclasts, suggesting that osteoclast recruitment requires active signaling from dying osteocytes. Furthermore, Cx43 deletion in cultured osteocytic cells resulted in increased apoptosis and decreased osteoprotegerin expression. Thus, Cx43 is essential in a cell-autonomous fashion in vivo and in vitro for osteocyte survival and for controlling the expression of osteocytic genes that affect osteoclast and osteoblast function.
doi:10.1002/jbmr.548
PMCID: PMC3271138  PMID: 22028311
connexin 43; apoptosis; osteocyte; osteoblast; bone resorption; osteoprotegerin; SOST/sclerostin; periosteal bone formation
20.  Brain Volume of the Newly-Discovered Species Rhynchocyon udzungwensis (Mammalia: Afrotheria: Macroscelidea): Implications for Encephalization in Sengis 
PLoS ONE  2013;8(3):e58667.
The Gray-faced Sengi (Rhynchocyon udzungwensis) is a newly-discovered species of sengi (elephant-shrew) and is the largest known extant representative of the order Macroscelidea. The discovery of R. udzungwensis provides an opportunity to investigate the scaling relationship between brain size and body size within Macroscelidea, and to compare this allometry among insectivorous species of Afrotheria and other eutherian insectivores. We performed a spin-echo magnetic resonance imaging (MRI) scan on a preserved adult specimen of R. udzungwensis using a 7-Tesla high-field MR imaging system. The brain was manually segmented and its volume was compiled into a dataset containing previously-published allometric data on 56 other species of insectivore-grade mammals including representatives of Afrotheria, Soricomorpha and Erinaceomorpha. Results of log-linear regression indicate that R. udzungwensis exhibits a brain size that is consistent with the allometric trend described by other members of its order. Inter-specific comparisons indicate that macroscelideans as a group have relatively large brains when compared with similarly-sized terrestrial mammals that also share a similar diet. This high degree of encephalization within sengis remains robust whether sengis are compared with closely-related insectivorous afrotheres, or with more-distantly-related insectivorous laurasiatheres.
doi:10.1371/journal.pone.0058667
PMCID: PMC3596274  PMID: 23516530
21.  Multilobular tumor of the mandible in a Pekingese dog 
Journal of Veterinary Science  2006;7(3):297-298.
Multilobular tumor of bone detected in a 2.5-year-old male Pekingese dog is reported. Grossly, the neoplasm consisted of multiple, variably sized, gritty, grayish-white to yellow nodules separated by thick collagenous septa. Histologically, these nodules contained multiple lobules of irregularly shaped and sized islands of well-differentiated osteoid and cartilage, separated by anastomosing fibrovascular septa. Chondrocytes and osteocytes were observed in the lacunae and in more osseous islands in the lobule, respectively. These lobules were surrounded by mesenchymal spindle cells. Mitotic figures were not evident. The neoplastic pattern was consistent with that of a multilobular bone tumor. Diagnosis was based on gross and light microscopic findings. The cause of this neoplasm was not determined.
doi:10.4142/jvs.2006.7.3.297
PMCID: PMC3242132  PMID: 16871027
dog; mandible; multilobular bone tumor; tumor
22.  Body Size Distribution of the Dinosaurs 
PLoS ONE  2012;7(12):e51925.
The distribution of species body size is critically important for determining resource use within a group or clade. It is widely known that non-avian dinosaurs were the largest creatures to roam the Earth. There is, however, little understanding of how maximum species body size was distributed among the dinosaurs. Do they share a similar distribution to modern day vertebrate groups in spite of their large size, or did they exhibit fundamentally different distributions due to unique evolutionary pressures and adaptations? Here, we address this question by comparing the distribution of maximum species body size for dinosaurs to an extensive set of extant and extinct vertebrate groups. We also examine the body size distribution of dinosaurs by various sub-groups, time periods and formations. We find that dinosaurs exhibit a strong skew towards larger species, in direct contrast to modern day vertebrates. This pattern is not solely an artefact of bias in the fossil record, as demonstrated by contrasting distributions in two major extinct groups and supports the hypothesis that dinosaurs exhibited a fundamentally different life history strategy to other terrestrial vertebrates. A disparity in the size distribution of the herbivorous Ornithischia and Sauropodomorpha and the largely carnivorous Theropoda suggests that this pattern may have been a product of a divergence in evolutionary strategies: herbivorous dinosaurs rapidly evolved large size to escape predation by carnivores and maximise digestive efficiency; carnivores had sufficient resources among juvenile dinosaurs and non-dinosaurian prey to achieve optimal success at smaller body size.
doi:10.1371/journal.pone.0051925
PMCID: PMC3526529  PMID: 23284818
23.  The evolution of fossoriality and the adaptive role of horns in the Mylagaulidae (Mammalia: Rodentia) 
Ceratogaulus, a member of the extinct fossorial rodent clade Mylagaulidae, is the only known rodent with horns and the smallest known horned mammal. The function of the large, dorsally projecting nasal horns on this burrowing animal has been the subject of wide speculation among palaeontologists; suggested uses range from sexual combat to burrowing. Mammals have evolved adaptations for digging repeatedly; horns and other cranial appendages have also evolved numerous times. These two adaptations co-occur in mammals extremely rarely: only two fossil genera (Ceratogaulus and the xenarthran Peltephilus) and no extant mammals are both horned and fossorial. Tracing the evolution of fossoriality in aplodontoid rodents (the larger clade to which Ceratogaulus belongs) reveals that Ceratogaulus descended from ancestors who dug by head-lifting. Whereas this suggests an obvious explanation for the horns of this rodent, evidence from functional morphology, anatomy, phylogeny and geologic context indicates that the horns in Ceratogaulus were used for defence, rather than digging, and evolved to offset increased predation costs associated with spending more time foraging above ground as body size increased.
doi:10.1098/rspb.2005.3171
PMCID: PMC1559849  PMID: 16087426
cranial appendages; adaptation; defence; predation; grasslands; Ceratogaulus
24.  Mouse Models for the Evaluation of Osteocyte Functions 
Journal of Bone Metabolism  2014;21(1):55-60.
Osteocytes establish an extensive intracellular and extracellular communication system via gap junction-coupled cell processes and canaliculi, through which cell processes pass throughout bone, and the communication system is extended to osteoblasts on the bone surface. To examine the osteocyte function, several mouse models were established. To ablate osteocytes, osteocytes death was induced by diphtheria toxin. However, any types of osteocyte death result in necrosis, because dying osteocytes are not phagocytosed by scavengers. After the rupture of cytoplasmic membrane, immunostimulatory molecules are released from lacunae to bone surface through canaliculi, and stimulate macrophages. The stimulated macrophages produce interleukin (IL)-1, IL-6, and tumor necrosis factor-alpha (TNF-α), which are the most important proinflammatory cytokines triggering inflammatory bone loss. Therefore, the osteocyte ablation results in necrosis-induced severe osteoporosis. In conditional knockout mice of gap junction protein alpha-1 (GJA1), which encodes connexin 43 in Gap junction, using dentin matrix protein 1 (DMP1) Cre transgenic mice, osteocyte apoptosis and enhanced bone resorption occur, because extracellular communication is intact. Overexpression of Bcl-2 in osteoblasts using 2.3 kb collagen type I alpha1 (COL1A1) promoter causes osteocyte apoptosis due to the severe reduction in the number of osteocyte processes, resulting in the disruption of both intracellular and extracellular communication systems. This mouse model unraveled osteocyte functions. Osteocytes negatively regulate bone mass by stimulating osteoclastogenesis and inhibiting osteoblast function in physiological condition. Osteocytes are responsible for bone loss in unloaded condition, and osteocytes augment their functions by further stimulating osteoclastogenesis and further inhibiting osteoblast function, at least partly, through the upregulation of receptor activator of nuclear factor-kappa B ligand (RANKL) in osteoblasts and Sost in osteocytes in unloaded condition.
doi:10.11005/jbm.2014.21.1.55
PMCID: PMC3970300
Bcl-2; Osteocyte; RANK ligand; Sost protein; Stress mechanical
25.  Relationships among magnetic resonance imaging, histological findings, and IGF-I in steroid-induced osteonecrosis of the femoral head in rabbits* §  
Objective: To study the relationships among magnetic resonance imaging (MRI), histological findings, and insulin-like growth factor-I (IGF-I) in steroid-induced osteonecrosis of the femoral head in rabbits. Methods: Thirty rabbits were randomly divided into experimental Group A (n=15) and control Group B (n=15). The 7.5 mg/kg (2 ml) of dexamethasone (DEX) and physiological saline (2 ml) were injected into the right gluteus medius muscle twice at one-week intervals in animals of Groups A and B, respectively. At 4, 8 and 16 weeks after obtaining an MRI, the rabbits were sacrificed and the femoral head from one side was removed for histological study of lacunae empty of osteocytes, subchondral vessels, and size of fat cells under microscopy, and the femoral head from the other side was removed for enzyme-linked immunoadsorbent assay (ELISA) for IGF-I. Results: At 4, 8 and 16 weeks after treatment, no necrotic lesions were detected in Group B, while they were detected in Group A. Light microscopy revealed that the fat cells of the marrow cavity were enlarged, subchondral vessels were evidently decreased, and empty bone lacunae were clearly increased. The IGF-I levels in Group A were significantly higher than those in Group B. At 8 weeks after the DEX injection, the MRI of all 20 femora showed an inhomogeneous, low signal intensity area in the femoral head, and at 16 weeks, the findings of all 10 femora showed a specific “line-like sign”. The MRI findings of all femora in Group B were normal. Conclusion: MRI is a highly sensitive means of diagnosing early experimental osteonecrosis of the femoral head. However, the abnormal marrow tissues appeared later than 4 weeks when the expression of IGF-I increased. This reparative factor has an early and important role in response to steroid-induced osteonecrosis of the femoral head, and provides a theoretical foundation for understanding the pathology and designing new therapies.
doi:10.1631/jzus.B0820127
PMCID: PMC2528890  PMID: 18837481
Dexamethasone (DEX); Insulin-like growth factor-I (IGF-I); Magnetic resonance imaging (MRI); Osteonecrosis of the femoral head; Pathology

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