On the origins,rapid expansion and genetic diversity of native Americans from hunting‐gatherers to agriculturalists

Given the importance of Y‐chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y‐chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai‐Tai, Kungurtug, and Toora‐Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post‐migration population growth in the ubiquitous and diverse Y‐STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural‐ and trade‐based subsistence adopted during the Pre‐Classic, Classic and Post‐Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median‐joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y‐ STR average gene diversity indices. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales

The 16S rRNA gene has been used in the last decades as a gold standard for determining the phylogenetic position of bacteria and their taxonomy. It is a well conserved gene, with some variations, present in all bacteria and allows the reconstruction of genealogies of microorganisms. Nevertheless, this gene has its limitations when inferring phylogenetic relationships between closely related isolates. To overcome this problem, DNA–DNA hybridization appeared as a solution to clarify interspecies relationships when the sequence similarity of the 16S rRNA gene is above 97 %. However, this technique is time consuming, expensive and laborious and so, researchers developed other molecular markers such as sequencing of housekeeping or functional genes for accurate determination of bacterial phylogeny. One of these genes that have been used successfully, particularly in clinical microbiology, codes for the beta subunit of the RNA polymerase (rpoB). The rpoB gene is sufficiently conserved to be used as a molecular clock, it is present in all bacteria and it is a mono-copy gene. In this study, rpoB gene sequencing was applied to the phylum Planctomycetes. Based on the genomes of 19 planctomycetes it was possible to determine the correlation between the rpoB gene sequence and the phylogenetic position of the organisms at a 95–96 % sequence similarity threshold for a novel species. A 1200-bp fragment of the rpoB gene was amplified from several new planctomycetal isolates and their intra and inter-species relationships to other members of this group were determined based on a 96.3 % species border and 98.2 % for intraspecies resolution.     

Characterization of a planctomycete associated with the marine dinoflagellate Prorocentrum micans Her

During attempts to obtain axenic the cultures of the marine dinoflagellate Prorocentrum micans, a microorganism with peculiar features was isolated. This contaminant resisted the physical and antibiotic treatments performed. Subsequent characterization showed that in agar plates this microorganism develops round granular pink colonies. It is a salt-dependent mesophilic and chemoheterotrophic Gram negative bacterium with a rod to ovoid shape, presenting cell motility in young cultures. Cell division occurs by cell budding. The bacterium forms aggregates with a variable number of cells that are stacked by fibrillar glycoproteic material, the holdfast. A tuft of numerous short glycoproteic fimbriae emerges from one pole of the cell. Preeminent granular inclusions, also of glycoproteic nature, are present in the cytoplasm. Several structural and compositional aspects of the cell envelope and cytoplasm are provided. The production of fibrillar material and the existence of the polar appendages suggest that this microorganism should occur in aquatic environments bound to substrates and could be associated with P. micans in natural marine habitats. Based on the characteristics displayed, this microorganism is a member of the Planctomycetes, order Planctomycetales.     

Ascorbyl palmitate interaction with phospholipid monolayers: Electrostatic and rheological preponderancy

Ascorbyl palmitate (ASC₁₆) is an anionic amphiphilic molecule of pharmacological interest due to its antioxidant properties. We found that ASC₁₆ strongly interacted with model membranes. ASC₁₆ penetrated phospholipid monolayers, with a cutoff near the theoretical surface pressure limit. The presence of a lipid film at the interface favored ASC₁₆ insertion compared with a bare air/water surface. The adsorption and penetration time curves showed a biphasic behavior: the first rapid peak evidenced a fast adsorption of charged ASC₁₆ molecules to the interface that promoted a lowering of surface pH, thus partially neutralizing and compacting the film. The second rise represented an approach to the equilibrium between the ASC₁₆ molecules in the subphase and the surface monolayer, whose kinetics depended on the ionization state of the film. Based on the Langmuir dimiristoylphosphatidylcholine + ASC₁₆ monolayer data, we estimated an ASC₁₆ partition coefficient to dimiristoylphosphatidylcholine monolayers of 1.5 × 10⁵ and a ΔG_p = − 6.7 kcal·mol^− 1. The rheological properties of the host membrane were determinant for ASC₁₆ penetration kinetics: a fluid membrane, as provided by cholesterol, disrupted the liquid-condensed ASC₁₆-enriched domains and favored ASC₁₆ penetration. Subphase pH conditions affected ASC₁₆ aggregation in bulk: the smaller structures at acidic pHs showed a faster equilibrium with the surface film than large lamellar ones. Our results revealed that the ASC₁₆ interaction with model membranes has a highly complex regulation. The polymorphism in the ASC₁₆ bulk aggregation added complexity to the equilibrium between the surface and subphase form of ASC₁₆, whose understanding may shed light on the pharmacological function of this drug.     

Impact of DNA methyltransferases on the epigenetic regulation of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor expression in malignant melanoma

Aberrant promoter methylation and resultant silencing of TRAIL decoy receptors were reported in a variety of cancers, but to date little is known about the relevance of this epigenetic modification in melanoma. In this study, we examined the methylation and the expression status of TRAIL receptor genes in cutaneous and uveal melanoma cell lines and specimens and their interaction with DNA methyltransferases (DNMTs) DNMT1, DNMT3a, and DNMT3b. DR4 and DR5 methylation was not frequent in cutaneous melanoma but on the contrary it was very frequent in uveal melanoma. No correlation between methylation status of DR4 and DR5 and gene expression was found. DcR1 and DcR2 were hypermethylated with very high frequency in both cutaneous and uveal melanoma. The concordance between methylation and loss of gene expression ranged from 91% to 97%. Here we showed that DNMT1 was crucial for DcR2 hypermethylation and that DNMT1 and DNMT3a coregulate the methylation status of DcR1. Our work also revealed the critical relevance of DcR1 and DcR2 expression in cell growth and apoptosis either in cutaneous or uveal melanoma. In conclusion, the results presented here claim for a relevant impact of aberrant methylation of decoy receptors in melanoma and allow to understand how the silencing of DcR1 and DcR2 is related to melanomagenesis.     

FAM111A Mutations Result in Hypoparathyroidism and Impaired Skeletal Development

Kenny-Caffey syndrome (KCS) and the similar but more severe osteocraniostenosis (OCS) are genetic conditions characterized by impaired skeletal development with small and dense bones, short stature, and primary hypoparathyroidism with hypocalcemia. We studied five individuals with KCS and five with OCS and found that all of them had heterozygous mutations in FAM111A. One mutation was identified in four unrelated individuals with KCS, and another one was identified in two unrelated individuals with OCS; all occurred de novo. Thus, OCS and KCS are allelic disorders of different severity. FAM111A codes for a 611 amino acid protein with homology to trypsin-like peptidases. Although FAM111A has been found to bind to the large T-antigen of SV40 and restrict viral replication, its native function is unknown. Molecular modeling of FAM111A shows that residues affected by KCS and OCS mutations do not map close to the active site but are clustered on a segment of the protein and are at, or close to, its outer surface, suggesting that the pathogenesis involves the interaction with as yet unidentified partner proteins rather than impaired catalysis. FAM111A appears to be crucial to a pathway that governs parathyroid hormone production, calcium homeostasis, and skeletal development and growth.     

Functional properties of a manganese-activated exo-polygalacturonase produced by a thermotolerant fungus Aspergillus niveus

A thermotolerant fungus identified as Aspergillus niveus was isolated from decomposing materials and it has produced excellent levels of hydrolytic enzymes that degrade plant cell walls. A. niveus germinated faster at 40 °C, presenting protein levels almost twofold higher than at 25 °C. The crude extract of the A. niveus culture was purified by diethylaminoethyl (DEAE)-cellulose, followed by Biogel P-100 column. Polygalacturonase (PG) is a glycoprotein with 37.7 % carbohydrate, molecular mass of 102.6 kDa, and isoelectric point of 5.4. The optimum temperature and pH were 50 °C and 4.0–6.5, respectively. The enzyme was stable at pH 3.0 to 9.0 for 24 h. The DEAE-cellulose derivative was about sixfold more stable at 60 °C than the free enzyme. Moreover, the monoaminoethyl-N-aminoethyl-agarose derivative was tenfold more stable than the free enzyme. PG was 232 % activated by Mn²⁺. The hydrolysis product of sodium polypectate corresponded at monogalacturonic acid, which classifies the enzyme as an exo-PG. The K _m, V _max, K _cat, and K _cat/K _m values were 6.7 mg/ml, 230 U/mg, 393.3/s, and 58.7 mg/ml/s, respectively. The N-terminal amino acid sequence presented 80 % identity with PglB1, PglA2, and PglA3 putative exo-PG of Aspergillus fumigatus and an exo-PG Neosartorya fischeri.     

A new small mammal assemblage from the M013 Terre Rosse fissure filling (Gargano,South-Eastern Italy)

The taxonomic study of the small mammal assemblage from fissure M013, sampled by a team of the University of Torino during the 2005–2009 excavations in the Dell’Erba Quarry (Apricena, Foggia) is presented. The assemblage includes the Echinosoricinae Apulogalerix cf. pusillus and the Crocidosoricinae ?Lartetium cf. dehmi; the Myomiminae species Stertomys simplex and Stertomys lyrifer; a new genus and species of Cricetodontinae and a single specimen of Hattomys cf. nazarii. Muridae include Mikrotia cf. parva, Mikrotia sp. 1 and a new genus and species of Murinae, phylogenetically related to Mikrotia. The occurrence of the new Murinae, the new Cricetodontinae, the two species of glirids and the Crocidosoricinae, as well as the absence of Apodemus and Prolagus, indicates M013 as the oldest Gargano's faunal assemblage known to date, despite the occurrence of Hattomys cf. nazarii, Mikrotia cf. parva and Mikrotia sp. 1, which most probably results from infiltrations from younger fissure fillings. The M013 assemblage is an absolute novelty for the Abruzzo-Apulian Palaeobioprovince, opening new perspectives for the timing and mode of dispersal of the forerunners of the Gargano fauna.     

The endemic bovids from Sardinia and the Balearic Islands: State of the art

Bovids are not so common in endemic insular faunas and are mainly recorded in Southeast Asia, Japan and some Mediterranean islands. In the Western Mediterranean, endemic bovids have been recorded during the late Miocene in the Tusco-Sardinian palaeobioprovince (Baccinello-Cinigiano basin, South Tuscany, and Fiume Santo, north-western Sardinia). In the latest Neogene and Quaternary, bovids showing highly endemic features were restricted to the Balearic Islands and Sardinia, while Bovini only slightly reduced in size were present on Pianosa, Malta and Sicily. On Sardinia, the richest bovid sample comes from Monte Tuttavista (Orosei), where at least three species have been identified: Asoletragus genthry, Nesogoral aff. N. melonii, and Nesogoral sp. 2. On Mallorca (Balearic Islands) six chronospecies belonging to the Myotragus endemic phylogenetic lineage have been described, spreading in age from the Early Pliocene to the Holocene. For decades, a close phylogenetic relationship between Nesogoral and Myotragus has been widely accepted by scholars. Morphological and biometrical differences shown by Balearic and Sardinian bovids have generally been regarded as the result of the evolution into two different island ecological systems, characterized by different inter and intra-guild selection pressures. Indeed, the more diversified environment of Sardinia, as well as the presence of other large mammals (similar-sized competitors belonging to the same guild and a running predator), increased the interspecific competition, forcing Sardinian bovids to exploit different resources and to occupy different niches, while Myotragus exploited under a monopoly regime the supply of resources available for large herbivores on the Eastern Balearic Islands. Nonetheless, new data suggest that Nesogoral and Myotragus possibly originated from different taxa.