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1.
Genes (Basel) ; 12(7)2021 06 24.
Article in English | MEDLINE | ID: mdl-34202821

ABSTRACT

The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul-i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level-by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000-4000 years ago (3-4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.


Subject(s)
Genetics, Population , Genome, Mitochondrial/genetics , Phylogeny , Phylogeography , Animals , Archaeology/history , Asia , Australia , Coleoptera/genetics , Female , Haplotypes/genetics , History, Ancient , Humans , Male , New Guinea , Oceania
2.
Adv Wound Care (New Rochelle) ; 9(7): 426-439, 2020 07.
Article in English | MEDLINE | ID: mdl-32520664

ABSTRACT

Significance: Toxic epidermal necrolysis (TEN) and Steven-Johnson syndrome (SJS) are potentially fatal acute mucocutaneous vesiculobullous disorders. Evidence to date suggests that outcomes for patients with both TEN and SJS are largely dependent on stopping the causative agent, followed by supportive care and appropriate wound management in a specialized burns unit. These are life-threatening conditions characterized by widespread full-thickness cutaneous and mucosal necrosis. This article outlines the approach to holistic management of such patients, in a specialized unit, highlighting various practical aspects of wound care to prevent complications such as infection, mucosal and adhesions, and ocular scaring. Recent Advances: There is improved understanding of pain and morbidity with regard to the type and frequency of dressing changes. More modern dressings, such as nanocrystalline, are currently favored as they may be kept in situ for longer periods. The most recent evidence on systemic agents, such as corticosteroids and cyclosporine, and novel treatments, are also discussed. Critical Issues: Following cessation of the culprit trigger, management in a specialized burns unit is the most important management step. It is now understood that a multidisciplinary team is essential in the care of these patients. Following admission of such patients, dermatology, ear, nose, and throat surgery, ophthalmology, urology, colorectal surgery, and gynecology should all be consulted to prevent disease sequelae. Future Directions: Looking forward, research is aimed at achieving prospective data on the efficacy of systemic immunomodulating agents and dressing types. Tertiary centers with burns units should develop policies for such patients to ensure that the relevant teams are consulted promptly to avoid mucocutaneous complications.


Subject(s)
Holistic Health , Nutritional Support/methods , Palliative Care/methods , Skin Transplantation/methods , Stevens-Johnson Syndrome/therapy , Adrenal Cortex Hormones/pharmacology , Adrenal Cortex Hormones/therapeutic use , Animals , Bandages , Burn Units/organization & administration , Cyclosporine/pharmacology , Cyclosporine/therapeutic use , Hospitalization , Humans , Immunoglobulins, Intravenous/pharmacology , Immunoglobulins, Intravenous/therapeutic use , Immunologic Factors/pharmacology , Immunologic Factors/therapeutic use , Length of Stay , Patient Care Team/organization & administration , Skin/drug effects , Skin/immunology , Stevens-Johnson Syndrome/epidemiology , Stevens-Johnson Syndrome/etiology , Swine , Tertiary Care Centers/organization & administration , Transplantation, Heterologous/methods , Treatment Outcome , Wound Healing/drug effects , Wound Healing/immunology
3.
JCI Insight ; 3(4)2018 02 22.
Article in English | MEDLINE | ID: mdl-29467321

ABSTRACT

BACKGROUND: Constitutive activation of ERK1/2 occurs in various cancers, and its reactivation is a well-described resistance mechanism to MAPK inhibitors. ERK inhibitors may overcome the limitations of MAPK inhibitor blockade. The dual mechanism inhibitor SCH772984 has shown promising preclinical activity across various BRAFV600/RAS-mutant cancer cell lines and human cancer xenografts. METHODS: We have developed an orally bioavailable ERK inhibitor, MK-8353; conducted preclinical studies to demonstrate activity, pharmacodynamic endpoints, dosing, and schedule; completed a study in healthy volunteers (P07652); and subsequently performed a phase I clinical trial in patients with advanced solid tumors (MK-8353-001). In the P07652 study, MK-8353 was administered as a single dose in 10- to 400-mg dose cohorts, whereas in the MK-8353-001 study, MK-8353 was administered in 100- to 800-mg dose cohorts orally twice daily. Safety, tolerability, pharmacokinetics, pharmacodynamics, and antitumor activity were analyzed. RESULTS: MK-8353 exhibited comparable potency with SCH772984 across various preclinical cancer models. Forty-eight patients were enrolled in the P07652 study, and twenty-six patients were enrolled in the MK-8353-001 study. Adverse events included diarrhea (44%), fatigue (40%), nausea (32%), and rash (28%). Dose-limiting toxicity was observed in the 400-mg and 800-mg dose cohorts. Sufficient exposure to MK-8353 was noted that correlated with biological activity in preclinical data. Three of fifteen patients evaluable for treatment response in the MK-8353-001 study had partial response, all with BRAFV600-mutant melanomas. CONCLUSION: MK-8353 was well tolerated up to 400 mg twice daily and exhibited antitumor activity in patients with BRAFV600-mutant melanoma. However, antitumor activity was not particularly correlated with pharmacodynamic parameters. TRIAL REGISTRATION: ClinicalTrials.gov NCT01358331. FUNDING: Merck Sharp & Dohme Corp., a subsidiary of Merck & Co. Inc., and NIH (P01 CA168585 and R35 CA197633).


Subject(s)
Indazoles/pharmacology , MAP Kinase Signaling System/drug effects , Neoplasms/drug therapy , Protein Kinase Inhibitors/pharmacology , Pyridines/pharmacology , Pyrrolidines/pharmacology , Triazoles/pharmacology , Administration, Oral , Adult , Animals , Biological Availability , Cell Line, Tumor , Diarrhea/chemically induced , Diarrhea/epidemiology , Dogs , Dose-Response Relationship, Drug , Drug Eruptions/epidemiology , Drug Eruptions/etiology , Drug Evaluation, Preclinical , Fatigue/chemically induced , Fatigue/epidemiology , Female , Humans , Indazoles/therapeutic use , Male , Maximum Tolerated Dose , Mice , Middle Aged , Mitogen-Activated Protein Kinase 1/antagonists & inhibitors , Mitogen-Activated Protein Kinase 1/metabolism , Mitogen-Activated Protein Kinase 3/antagonists & inhibitors , Mitogen-Activated Protein Kinase 3/metabolism , Nausea/chemically induced , Nausea/epidemiology , Neoplasm Staging , Neoplasms/genetics , Neoplasms/pathology , Protein Kinase Inhibitors/therapeutic use , Pyridines/therapeutic use , Pyrrolidines/therapeutic use , Rats , Triazoles/therapeutic use , Xenograft Model Antitumor Assays , Young Adult
4.
Nat Commun ; 8: 15425, 2017 06 09.
Article in English | MEDLINE | ID: mdl-28598412

ABSTRACT

Marine sediment records suggest that episodes of major atmospheric CO2 drawdown during the last glacial period were linked to iron (Fe) fertilization of subantarctic surface waters. The principal source of this Fe is thought to be dust transported from southern mid-latitude deserts. However, uncertainty exists over contributions to CO2 sequestration from complementary Fe sources, such as the Antarctic ice sheet, due to the difficulty of locating and interrogating suitable archives that have the potential to preserve such information. Here we present petrographic, geochemical and microbial DNA evidence preserved in precisely dated subglacial calcites from close to the East Antarctic Ice-Sheet margin, which together suggest that volcanically-induced drainage of Fe-rich waters during the Last Glacial Maximum could have reached the Southern Ocean. Our results support a significant contribution of Antarctic volcanism to subglacial transport and delivery of nutrients with implications on ocean productivity at peak glacial conditions.

5.
Nature ; 544(7650): 357-361, 2017 04 20.
Article in English | MEDLINE | ID: mdl-28273061

ABSTRACT

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.


Subject(s)
DNA, Ancient/analysis , Dental Calculus/chemistry , Diet/history , Food Preferences , Health/history , Neanderthals/microbiology , Neanderthals/psychology , Animals , Belgium , Carnivory , Caves , Enterocytozoon/genetics , Enterocytozoon/isolation & purification , Genome, Bacterial/genetics , History, Ancient , Humans , Intestines/microbiology , Meat/history , Methanobrevibacter/genetics , Methanobrevibacter/isolation & purification , Mouth/microbiology , Pan troglodytes/microbiology , Penicillium/chemistry , Perissodactyla , Sheep , Spain , Stomach/microbiology , Symbiosis , Time Factors , Vegetarians/history
6.
Nature ; 544(7649): 180-184, 2017 04 13.
Article in English | MEDLINE | ID: mdl-28273067

ABSTRACT

Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair samples, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49-45 ka. After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.


Subject(s)
Genome, Mitochondrial/genetics , Human Migration/history , Native Hawaiian or Other Pacific Islander/genetics , Phylogeography , Australia , Cultural Evolution , DNA, Mitochondrial/genetics , Haplotypes/genetics , History, Ancient , Humans , Phylogeny
7.
Med J Aust ; 206(1): 41-45, 2017 Jan 16.
Article in English | MEDLINE | ID: mdl-28076744

ABSTRACT

Acne is a chronic inflammatory disease of the pilosebaceous unit resulting from androgen-induced increased sebum production; altered keratinisation; bacterial colonisation of hair follicles on the face, neck, chest and back by Propionibacterium acnes; and an inflammatory response in the skin. The exact way these processes interact and the order in which they occur in the pathogenesis of acne are still unclear. Scarring that occurs from acne, particularly severe acne, can persist a lifetime and have long lasting psychosocial effects. Depression, social isolation and suicidal ideation are frequent comorbidities in acne. Despite the plethora of topical and systemic treatments available for acne, there is a relative lack of quality evidence for its application. Of the systemic treatments available, oral isotretinoin remains the most effective well established treatment for acne that targets all the aetiological factors. Current guidelines for the treatment of acne are based largely on expert consensus and advocate a combination of topical agents in mild to moderate cases and reserve the use of systemic therapies for moderate to severe or refractory cases of acne. However, given the psychosocial impacts of acne, there is a strong argument for early, effective treatment with systemic therapy when topical and general measures have failed.


Subject(s)
Acne Vulgaris/therapy , Acne Vulgaris/etiology , Administration, Oral , Administration, Topical , Androgen Antagonists/therapeutic use , Anti-Bacterial Agents/therapeutic use , Benzoyl Peroxide/therapeutic use , Cicatrix/etiology , Cicatrix/therapy , Contraceptives, Oral, Hormonal/therapeutic use , Dermatologic Agents/therapeutic use , Humans , Laser Therapy , Photochemotherapy , Phototherapy , Quality of Life , Retinoids/therapeutic use , Risk Factors , Skin Care , Spironolactone/therapeutic use
8.
Nature ; 528(7583): 499-503, 2015 Dec 24.
Article in English | MEDLINE | ID: mdl-26595274

ABSTRACT

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.


Subject(s)
Genome, Human/genetics , Selection, Genetic/genetics , Agriculture/history , Asia/ethnology , Body Height/genetics , Bone and Bones , DNA/genetics , DNA/isolation & purification , Diet/history , Europe/ethnology , Genetics, Population , Haplotypes/genetics , History, Ancient , Humans , Immunity/genetics , Male , Multifactorial Inheritance/genetics , Pigmentation/genetics , Sequence Analysis, DNA
9.
Nature ; 522(7555): 207-11, 2015 Jun 11.
Article in English | MEDLINE | ID: mdl-25731166

ABSTRACT

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian. By ∼6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.


Subject(s)
Cultural Evolution/history , Grassland , Human Migration/history , Language/history , Europe/ethnology , Genome, Human/genetics , History, Ancient , Humans , Male , Polymorphism, Genetic/genetics , Population Dynamics , Russia
10.
J Clin Pathol ; 67(11): 949-54, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25232128

ABSTRACT

AIMS: Extending work with brain tumours, the hypothesis that micronutrients may usefully augment anticancer regimens, chokeberry (Aronia melanocarpa) extract was tested to establish whether it has pro-apoptotic effects in AsPC-1, an established human pancreatic cell line, and whether it potentiates cytotoxicity in combination with gemcitabine. Pancreatic cancer was chosen as a target, as its prognosis remains dismal despite advances in therapy. METHODS: An MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide) assay was used to assess the growth of the single pancreatic cancer cell line AsPC-1, alone and in comparison or combination with gemcitabine. This was backed up by flow cytometric DRAQ7 cell viability analysis. TUNEL assays were also carried out to investigate pro-apoptotic properties as responsible for the effects of chokeberry extract. RESULTS: Chokeberry extract alone and its IC75 value (1 µg/mL) in combination with gemcitabine were used to assess the growth of the AsPC-1 cell line. Gemcitabine in combination with chokeberry extract was more effective than gemcitabine alone. TUNEL assays showed apoptosis to be a mechanism occurring at 1 µg/mL concentration of chokeberry, with apoptotic bodies detected by both colourimetric and fluorometric methods. CONCLUSIONS: The implication of this study, using single cancer cell line, is that chemotherapy (at least with gemcitabine) might be usefully augmented with the use of micronutrients such as chokeberry extract.


Subject(s)
Adenocarcinoma/pathology , Antineoplastic Agents, Phytogenic/pharmacology , Antineoplastic Combined Chemotherapy Protocols/pharmacology , Deoxycytidine/analogs & derivatives , Pancreatic Neoplasms/pathology , Photinia , Polyphenols/pharmacology , Antineoplastic Agents, Phytogenic/isolation & purification , Apoptosis/drug effects , Cell Survival/drug effects , Colorimetry , Deoxycytidine/pharmacology , Dose-Response Relationship, Drug , Drug Synergism , Flow Cytometry , Humans , In Situ Nick-End Labeling , Photinia/chemistry , Phytotherapy , Plants, Medicinal , Polyphenols/isolation & purification , Gemcitabine
11.
Int J Med Sci ; 11(9): 948-54, 2014.
Article in English | MEDLINE | ID: mdl-25076850

ABSTRACT

BACKGROUND: Consumption of lycopene through tomato products has been suggested to reduce the risk of prostate cancer. Cellular adhesion and migration are important features of cancer progression and therefore a potential target for cancer interception. In the present study we have examined the in vitro effect of lycopene on these processes. METHODS: Prostate cancer cell lines PC3, DU145 and immortalised normal prostate cell line PNT-2 were used. The adhesion assay consisted of seeding pre-treated cells onto Matrigel™, gently removing non-adherent cells and quantitating the adherent fraction using WST-1. Migratory potential was assessed using ibidi™ migration chamber inserts, in which a cell-free zone between two confluent areas was allowed to populate over time and the migration measured. RESULTS: 24 hour incubation of prostate cell lines with 1.15µmol/l lycopene showed a 40% reduction of cellular motility in case of PC3 cells, 58% in DU145 cells and no effect was observed for PNT2 cells. A dose related inhibition of cell adhesion to a basement membrane in the form of Matrigel™ was observed in all three cell lines and it reached statistical significance for PC3 and PNT2 cells at lycopene concentrations ≥1.15µmol/l. However, in case of DU145, only a concentration of 2.3µmol/l showed a significant reduction. CONCLUSION: This in vitro investigation indicates that lycopene can influence the cell adhesion and migration properties of cancer cells at a dose which is arguably achievable in patients. The results of our study expand our understanding of a chemo preventive role of lycopene in prostate cancer.


Subject(s)
Carotenoids/administration & dosage , Cell Adhesion/drug effects , Prostatic Neoplasms/diet therapy , Solanum lycopersicum , Apoptosis/drug effects , Cell Movement/drug effects , Humans , Lycopene , Male , Prostatic Neoplasms/pathology
12.
Science ; 342(6155): 257-61, 2013 Oct 11.
Article in English | MEDLINE | ID: mdl-24115443

ABSTRACT

The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.


Subject(s)
DNA, Mitochondrial/genetics , Genetic Drift , Genetic Variation , Population/genetics , Agriculture/history , Base Sequence , DNA, Mitochondrial/history , Europe , History, Ancient , Humans , Molecular Sequence Data , Transients and Migrants
13.
Conserv Biol ; 26(6): 1091-9, 2012 Dec.
Article in English | MEDLINE | ID: mdl-23025275

ABSTRACT

Late Quaternary extinctions and population fragmentations have severely disrupted animal-plant interactions globally. Detection of disrupted interactions often relies on anachronistic plant characteristics, such as spines in the absence of large herbivores or large fruit without dispersers. However, obvious anachronisms are relatively uncommon, and it can be difficult to prove a direct link between the anachronism and a particular faunal taxon. Analysis of coprolites (fossil feces) provides a novel way of exposing lost interactions between animals (depositors) and consumed organisms. We analyzed ancient DNA to show that a coprolite from the South Island of New Zealand was deposited by the rare and threatened kakapo (Strigops habroptilus), a large, nocturnal, flightless parrot. When we analyzed the pollen and spore content of the coprolite, we found pollen from the cryptic root-parasite Dactylanthus taylorii. The relatively high abundance (8.9% of total pollen and spores) of this zoophilous pollen type in the coprolite supports the hypothesis of a former direct feeding interaction between kakapo and D. taylorii. The ranges of both species have contracted substantially since human settlement, and their present distributions no longer overlap. Currently, the lesser short-tailed bat (Mystacina tuberculata) is the only known native pollinator of D. taylorii, but our finding raises the possibility that birds, and other small fauna, could have once fed on and pollinated the plant. If confirmed, through experimental work and observations, this finding may inform conservation of the plant. For example, it may be possible to translocate D. taylorii to predator-free offshore islands that lack bats but have thriving populations of endemic nectar-feeding birds. The study of coprolites of rare or extinct taxonomic groups provides a unique way forward to expand existing knowledge of lost plant and animal interactions and to identify pollination and dispersal syndromes. This approach of linking paleobiology with neoecology offers significant untapped potential to help inform conservation and restoration plans.


Subject(s)
Balanophoraceae/physiology , Conservation of Natural Resources , Endangered Species , Food Chain , Fossils , Parrots/physiology , Animals , DNA/analysis , Diet , Feces/chemistry , New Zealand , Plant Dispersal , Pollen/chemistry , Polymerase Chain Reaction
14.
PLoS One ; 7(6): e40025, 2012.
Article in English | MEDLINE | ID: mdl-22768206

ABSTRACT

Knowledge about the diet and ecology of extinct herbivores has important implications for understanding the evolution of plant defence structures, establishing the influences of herbivory on past plant community structure and composition, and identifying pollination and seed dispersal syndromes. The flightless ratite moa (Aves: Dinornithiformes) were New Zealand's largest herbivores prior to their extinction soon after initial human settlement. Here we contribute to the knowledge of moa diet and ecology by reporting the results of a multidisciplinary study of 35 coprolites from a subalpine cave (Euphrates Cave) on the South Island of New Zealand. Ancient DNA analysis and radiocarbon dating revealed the coprolites were deposited by the extinct upland moa (Megalapteryx didinus), and span from at least 6,368±31 until 694±30 (14)C years BP; the approximate time of their extinction. Using pollen, plant macrofossil, and ancient DNA analyses, we identified at least 67 plant taxa from the coprolites, including the first evidence that moa fed on the nectar-rich flowers of New Zealand flax (Phormium) and tree fuchsia (Fuchsia excorticata). The plant assemblage from the coprolites reflects a highly-generalist feeding ecology for upland moa, including browsing and grazing across the full range of locally available habitats (spanning southern beech (Nothofagus) forest to tussock (Chionochloa) grassland). Intact seeds in the coprolites indicate that upland moa may have been important dispersal agents for several plant taxa. Plant taxa with putative anti-browse adaptations were also identified in the coprolites. Clusters of coprolites (based on pollen assemblages, moa haplotypes, and radiocarbon dates), probably reflect specimens deposited at the same time by individual birds, and reveal the necessity of suitably large sample sizes in coprolite studies to overcome potential biases in diet interpretation.


Subject(s)
Ecosystem , Extinction, Biological , Fossils , Palaeognathae/classification , Animals , Caves , DNA, Plant/genetics , Humans , New Zealand , Palaeognathae/genetics , Plants/classification , Plants/genetics , Pollen/genetics , Radiometric Dating , Species Specificity
15.
Oncol Rep ; 28(4): 1435-42, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22842701

ABSTRACT

Malignant brain tumours are rare but are the most challenging types of cancers to treat. Despite conventional multimodality approaches available for their management, the outlook for most patients remains dismal due to the ability of the tumour cells to invade the normal brain. Attention has now focused on novel therapeutic interventions such as as the use of micronutrients. Both chokeberry extract (Aronia melanocarpa), which is rich in natural pigments such as anthocyanins and curcumin (diferuloylmethane) found in turmeric (Curcuma longa) have been reported to possess anticancer properties in other cancers. The aim of this study was to extend our previous research to evaluate the therapeutic potential of these two agents by testing their ability to induce apoptosis in an established glioblastoma cell line (U373). This was accomplished by treating the cells for 48 h with either chokeberry extract or curcumin, and using the Annexin-V assay. Gene profiles of 8 MMPs (2, 9, 14, 15, 16, 17, 24 and 25) and 4 TIMPs (1, 2, 3 and 4) were analysed for effects of mediators of invasion by quantitative real-time polymerase chain reaction (RT-PCR). The IC50 values determined for curcumin and chokeberry extract were 15 and 200 µg/ml, respectively. Our results also suggest that curcumin induces apoptosis but chokeberry extract is necrotic to this cell line. It is possible that chokeberry extract kills the cells by other non-apoptotic pathways. In addition, the RT-PCR results show downregulation of the gene expression of MMP-2, -14, -16 and -17 for both micronutrients. Taken together, the comparative data suggest that both curcumin and chokeberry extract may exhibit their anticancer potential by inducing apoptosis and inhibiting invasion by reducing MMP gene expression.


Subject(s)
Antineoplastic Agents, Phytogenic/pharmacology , Apoptosis/drug effects , Brain Neoplasms/drug therapy , Curcumin/pharmacology , Matrix Metalloproteinases, Secreted/genetics , Photinia/chemistry , Polyphenols/pharmacology , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Cell Death/drug effects , Cell Line, Tumor/drug effects , Drug Screening Assays, Antitumor , Gene Expression Regulation, Neoplastic/drug effects , Glioblastoma/drug therapy , Glioblastoma/genetics , Glioblastoma/pathology , Humans , Inhibitory Concentration 50 , Matrix Metalloproteinase 14/genetics , Matrix Metalloproteinase 16/genetics , Matrix Metalloproteinase 2/genetics , Matrix Metalloproteinases, Membrane-Associated/genetics , Plant Extracts/pharmacology
16.
Opt Express ; 20(28): 29378-85, 2012 Dec 31.
Article in English | MEDLINE | ID: mdl-23388765

ABSTRACT

We propose and experimentally demonstrate a new class of sensor for specific DNA sequences based on molecular beacons (MB) immobilized on the internal surfaces of suspended core optical fibers (SCF). MBs, a type of hairpin structured DNA probe, are attached on the surface of the SCF core using a fuzzy nanoassembly process used in conjunction with a biotin-streptavidin-biotin surface attachment strategy. The proposed DNA sensor detects complementary DNA sequences (cDNA) while discriminating sequences differing from the target by just one base. This enables the detection of DNA in unprecedentedly small sample volumes (nL scale) and is, to the best of our knowledge, the first specific DNA detection using a DNA probe immobilized within a microstructured optical fiber.


Subject(s)
DNA/analysis , Molecular Probe Techniques , Molecular Probes , Optical Fibers , Fluorescence , Microscopy, Electron, Scanning , Nucleic Acid Hybridization , Solutions
17.
Nature ; 479(7373): 359-64, 2011 Nov 02.
Article in English | MEDLINE | ID: mdl-22048313

ABSTRACT

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.


Subject(s)
Biota , Climate Change/history , Extinction, Biological , Human Activities/history , Mammals/physiology , Animals , Bayes Theorem , Bison , DNA, Mitochondrial/analysis , DNA, Mitochondrial/genetics , Europe , Fossils , Genetic Variation , Geography , History, Ancient , Horses , Humans , Mammals/genetics , Mammoths , Molecular Sequence Data , Population Dynamics , Reindeer , Siberia , Species Specificity , Time Factors
18.
Bioorg Med Chem Lett ; 19(22): 6331-6, 2009 Nov 15.
Article in English | MEDLINE | ID: mdl-19819138

ABSTRACT

The present paper describes a novel series of HCV RNA polymerase inhibitors based on a pyrazolo[1,5-a]pyrimidine scaffold bearing hydrophobic groups and an acidic functionality. Several compounds were optimized to low nanomolar potencies in a biochemical RdRp assay. SAR trends clearly reveal a stringent preference for a cyclohexyl group as one of the hydrophobes, and improved activities for carboxylic acid derivatives.


Subject(s)
DNA-Directed RNA Polymerases/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Hepatitis C/enzymology , Pyrazoles/pharmacology , Pyrimidines/pharmacology , RNA, Viral/drug effects , RNA-Dependent RNA Polymerase/antagonists & inhibitors , Drug Evaluation, Preclinical , Hepacivirus , Hepatitis C/virology , Inhibitory Concentration 50 , Molecular Weight , Small Molecule Libraries
19.
Proc Natl Acad Sci U S A ; 104(39): 15276-81, 2007 Sep 25.
Article in English | MEDLINE | ID: mdl-17855556

ABSTRACT

The Neolithic Revolution began 11,000 years ago in the Near East and preceded a westward migration into Europe of distinctive cultural groups and their agricultural economies, including domesticated animals and plants. Despite decades of research, no consensus has emerged about the extent of admixture between the indigenous and exotic populations or the degree to which the appearance of specific components of the "Neolithic cultural package" in Europe reflects truly independent development. Here, through the use of mitochondrial DNA from 323 modern and 221 ancient pig specimens sampled across western Eurasia, we demonstrate that domestic pigs of Near Eastern ancestry were definitely introduced into Europe during the Neolithic (potentially along two separate routes), reaching the Paris Basin by at least the early 4th millennium B.C. Local European wild boar were also domesticated by this time, possibly as a direct consequence of the introduction of Near Eastern domestic pigs. Once domesticated, European pigs rapidly replaced the introduced domestic pigs of Near Eastern origin throughout Europe. Domestic pigs formed a key component of the Neolithic Revolution, and this detailed genetic record of their origins reveals a complex set of interactions and processes during the spread of early farmers into Europe.


Subject(s)
DNA, Mitochondrial/genetics , Agriculture , Animals , Asia , Biometry , Europe , Geography , History, Ancient , Markov Chains , Molecular Sequence Data , Monte Carlo Method , Regression Analysis , Sequence Analysis, DNA , Sus scrofa , Swine
20.
BJU Int ; 99(6): 1456-60, 2007 Jun.
Article in English | MEDLINE | ID: mdl-17484766

ABSTRACT

OBJECTIVE: To investigate whether lycopene levels in blood and seminal plasma increase after dietary supplementation with a natural source of the compound, and whether any potential increase of lycopene levels in semen translates into increased free-radical trapping capacity in the seminal plasma. METHODS: Reactive oxygen species are detrimental to the health and function of spermatozoa. Semen contains enzymatic and non-enzymatic defence mechanisms to combat such species, and lycopene, a dietary antioxidant, forms part of the non-enzymatic arm. Immuno-infertile men have significantly lower levels of lycopene in their semen, and oral lycopene therapy can improve various seminal variables in idiopathic infertility. Whether this improvement is a direct consequence of increased lycopene levels in semen, resulting in an increased radical scavenging ability, remains unknown. Blood and seminal lycopene levels were measured in healthy volunteers, using high-performance liquid chromatography, before and after a period of dietary supplementation. The antioxidant capacity of seminal plasma was also assayed to determine if supplementation results in a measurable increase in seminal radical scavenging ability. RESULTS: There were statistically significant increases in blood and seminal plasma lycopene levels after dietary supplementation. The increase in seminal and blood lycopene levels showed a strong positive correlation (r = 0.84, P < 0.05). There was no measurable increase in the total radical scavenging capacity of semen. CONCLUSION: This study confirms the presence of lycopene in human semen, the levels of which can be significantly increased after dietary supplementation with a natural source of lycopene. Further studies to establish whether this would also be the case in infertile men, with possible associated improvements in their seminal quality, are warranted.


Subject(s)
Antioxidants/metabolism , Carotenoids/metabolism , Dietary Supplements , Infertility, Male/diet therapy , Semen/chemistry , Adult , Antioxidants/therapeutic use , Carotenoids/blood , Carotenoids/therapeutic use , Chromatography, High Pressure Liquid , Humans , Lycopene , Male , Reactive Oxygen Species/metabolism
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