Paleogenomic and ancient DNA

Introduction The DNA is a nucleic acid that contains the genetic information necessary for RNA and protein biosynthesis. DNA extracted from past samples (teeth, bones, faeces, etc.) is defined ancient DNA (aDNA) and needs, to preserve, low level of oxygen, fast decrease in water content and, above all, according to the Arrhenius equation, low temperature. From 1985 (first aDNA extracted from a mummy) with the introduction of the Polymerase Chain Reaction (PCR) several studies of paleogenomic were born, but it is essential to identify some possible errors such as fragmentations, contaminations and post-mortal mutations [1]. The applications of the paleogenomic are: evolutionary biology, population studies, studies of the pathogens and microorganism. Materials and methods We report 3 cases studied by the Division of Paleopathology of Pisa: a) Ferrante I, king of Naples (1431-1494). The natural mummy showed round white formations of the pelvis infiltrating the abdominal wall ( 1a-b). b) Maria of Aragon (1503-1568). The well-preserved artificial mummy had a small peduncolate arborescence neoformation in the right inguinal region. c) Andean female mummy (so-called ‘Fi9’) dated 10th–11th century A.D by radiocarbonium analyses. The natural young mummy presented a marked megavisceral syndrome characterized by megacolon, megaoesophagus and cardiomegaly. It was possible to perform complete autopsies and collect tissue samples utilized for histological analyses and DNA extraction. Results a) Histology performed on the round formations confirmed the diagnosis of colorectal adenocarcinoma. Amplification of aDNA highlighted a point mutation of the codon 12 in K-Ras oncogene responsible for the cancer [2] (fig. 1c). b) Macroscopic and histological aspects seemed peculiar of condyloma acuminatum, a papillomavirus-induced squamous lesion also called “venereal wart”. Molecular study revealed the presence of HPV 18, a virus with high oncogenic potential. Automated sequencing of several clones revealed 100% similarity sequences of both HPV 18 and JC9813 DNA, a putative novel HPV with low oncogenic potential [3] (fig. 2c) c) Analysis of the gut microbiome (paleofeces, descending, transverse and ascending colon) underlined the massive presence of Clostridiceae. Sequences homologous to HPVs in the mummified gut (descending colon) was particularly surprising. It was detected also the Tripanosoma cruzi; by comparing a partial sequence homologous to the large ribosomal subunit alpha of the presumptive ancient T. cruzi with modern strains, we suggest that this pathogen may have a more remote origin than previously expected. We also found sequences associated with putative beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters [4] (fig. 3c). Conclusion a) The alimentary “environment” of the Neapolitan court of the XV century, with its abundance of natural alimentary alkylating agents (red smoked meat), well explains the acquired mutation of K-Ras. b) This represented the first molecular diagnosis of HPV in mummies. HPV is a very old virus that evolved together with man. c) Streptococcus, Staphylococcus, Bacillus and Pseudomonas sequences were identified in the mummified gut, opening the opportunity to investigate possible mechanisms by which these bacteria are preserved. The detection of sequences homologous to those of pathogens such as T. cruzi and HPV indicate their presence in the Americas prior to European colonization. The presence of antibiotic-resistance genes in an 11th century pre-Columbian Andean mummy is intriguing as antibiotics were introduced recently. The presence of beta-lactam antibiotic resistance is certainly not unexpected in any culture, as would be in the case of resistance to any natural rather than a semi- or completely synthetic antibiotic as a result of exposure to natural antibiotic-producing microbiota originating from the environment (e.g. soil); however, vancomycin, particularly, was discovered more than 50 years ago, and vancomycin-resistance genes have been mainly implicated with the increased use of this antibiotic. The presence of antibiotic-resistance genes in the ancient human gut microbiome clearly indicates that these genes pre-date therapeutical use of these compounds and that they are not necessarily associated to a selective pressure of antibiotics use. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses. References Willerslev E, Cooper A. Review paper. Ancient Dna. Proceedings of the Royal Society of London B: Biological Sciences. 2005; 272(1558):3– 16. Marchetti A, Pellegrini S, Bevilacqua G, Fornaciari G. K-RAS mutation in the tumour of Ferrante I of Aragon, King of Naples. The Lancet; 1996, May 4;347(9010):1272. Fornaciari G, Zavaglia K, Ciranni R. Human papillomavirus in a 16th century mummy. The Lancet; 2003, Oct 3, vol 362. Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Gut Microbiome of an 11th Century A.D. PreColumbian Andean Mummy. PLoS One, 2015 Sep 30;10(9)

Stomatal and non-stomatal limitations on leaf carbon assimilation in beech (Fagus sylvatica L.) seedlings enduring moderate water stress under natural conditions

Seasonal variation and the differential effect of drought on photosynthetic parameters involved in carbon assimilation in forest species have been poorly studied under natural conditions. Limitations to diffusion and biochemical factors affecting leaf carbon uptake were analyzed in young beech seedlings (Fagus sylvatica L.) growing in natural gaps of a beech-wood at the southern limit of the species. Half of the seedling received periodic watering in addition to natural rainfall to reduce the severity of the summer drought which is typical in the area. Plant water status was evaluated by measuring predawn water potential. Basic biochemical parameters were inferred from photosynthesis-CO2 curves (A-Cc) under saturating light and chlorophyll fluorescence. The curves were established on three dates during the summer months Main variables studied included: stomatal and mesophyll conductance to CO2 (gs and gm respectively), maximum velocity of carboxylation (Vcmax) and maximum electron transport capacity (Jmax). The gm was estimated by two methodologies: the curve-fitting and J constant methods. Seedlings withstood a moderate water stress as the leaf predawn water potential (Ψpd) measured during the study was within the range –0.2 to –0.5 MPa. A mild drought caused gs and gm to decrease only slightly in response to Ψpd. However both diffusional parameters explained most of the limitations to CO2 uptake. Furthermore, non-stomatal limitations were also important limiting net photosynthesis as water stress increased. In addition, it should be highlighted that the biochemical limitations, prompted by Vcmax and Jmax, were related mainly to ontogenic factors, without any clear relationship with drought under the moderate water stress experienced by beech seedlings through the study. The results may help to further understand of the functional mechanisms influencing carbon fixation capacity of beech seedlings. This capacity may influence the total carbon balance of beech seedlings, and feed forward to their growth and survival under drought-prone environments such as those in the south of Europe.Peer reviewe

Stomatal and non-stomatal limitations on leaf carbon assimilation in beech (Fagus sylvatica L.) seedlings under natural conditions

Limitations to diffusion and biochemical factors affecting leaf carbon uptake were analyzed in young beech seedlings (Fagus sylvtica L.) growing in natural gaps of a beech-wood at the southern limit of the species. Half of the seedlings received periodic watering in addition to natural rainfall to reduce the severity of the summer drought. Plant water status was evaluated by measuring predawn water potential. Basic biochemical parameters were inferred from chlorophyll fluorescence and photosynthesis-CO2 curves (A-Cc) under saturating light. The curves were established on three dates during the summer months. The main variables studied included: stomatal and mesophyll conductance to CO2 (gs and gm respectively), maximum velocity of carboxylation (Vcmax) and maximum electron transport capacity (Jmax). The gm was estimated by two methodologies: the curve-fitting and J constant methods. Seedlings withstood moderate water stress, as the leaf predawn water potential (Ψpd) measured during the study was within the range –0.2 to –0.5 MPa. Mild drought caused gs and gm to decrease only slightly in response to Ψpd. However both diffusional parameters explained most of the limitations to CO2 uptake. In addition, it should be highlighted that biochemical limitations, prompted by Vcmax and Jmax, were related mainly to ontogenic factors, without any clear relationship with drought under the moderate water stress experienced by beech seedlings through the study. The results may help to further understanding of the functional mechanisms influencing the carbon fixation capacity of beech seedlings under natural conditions.Peer reviewe

SSDSS IV MaNGA - Properties of AGN host galaxies

We present here the characterization of the main properties of a sample of 98 AGN host galaxies, both type-II and type-I, in comparison with those of about 2700 non-active galaxies observed by the MaNGA survey. We found that AGN hosts are morphologically early-type or early-spirals. For a given morphology AGN hosts are, in average, more massive, more compact, more central peaked and rather pressurethan rotational-supported systems. We confirm previous results indicating that AGN hosts are located in the intermediate/transition region between star-forming and non-star-forming galaxies (i.e., the so-called green valley), both in the ColorMagnitude and the star formation main sequence diagrams. Taking into account their relative distribution in terms of the stellar metallicity and oxygen gas abundance and a rough estimation of their molecular gas content, we consider that these galaxies are in the process of halting/quenching the star formation, in an actual transition between both groups. The analysis of the radial distributions of the starformation rate, specific star-formation rate, and molecular gas density shows that the quenching happens from inside-out involving both a decrease of the efficiency of the star formation and a deficit of molecular gas. All the intermediate data-products used to derive the results of our analysis are distributed in a database including the spatial distribution and average properties of the stellar populations and ionized gas, published as a Sloan Digital Sky Survey Value Added Catalog being part of the 14th Data Release: http://www.sdss.org/dr14/manga/manga-data/manga-pipe3d-value-added-catalog/Comment: 48 pages, 14 figures, in press in RMxA

Vanadium Inhalation in a Mouse Model for the Understanding of Air-Suspended Particle Systemic Repercussion

There is an increased concern about the health effects that air-suspended particles have on human health which have been dissected in animal models. Using CD-1 mouse, we explore the effects that vanadium inhalation produce in different tissues and organs. Our findings support the systemic effects of air pollution. In this paper, we describe our findings in different organs in our conditions and contrast our results with the literature

First-line single-agent regorafenib in frail patients with metastatic colorectal cancer: a pilot phase II study of the Spanish Cooperative Group for the Treatment of Digestive Tumours (TTD)

BackgroundTreatment of frail patients with advanced colorectal cancer (CRC) is controversial. This pilot phase II trial aimed to assess the efficacy and safety of regorafenib when administered in first-line to frail patients with advanced CRC.MethodsFrail patients without prior advanced colorectal cancer treatment were included in the study. Definition of frailty was defined per protocol based on dependency criteria, presence of chronic comorbid pathologies and/or geriatric features. Main objective: to assess progression-free survival (PFS) rate at 6months. Treatment consisted of 28-daycycles of orally administered regorafenib 160mg/day (3 weeks followed by 1 week rest).ResultsForty-seven patients were included in the study. Median age was 81years (range 63-89). Frailty criteria: dependency was observed in 26 patients (55%), comorbidities in 27 (57%) and geriatric features in 18 (38%). PFS rate at 6months was 45% (95% confidence interval [CI] 30-60]. Median PFS was 5.6months (95%CI 2.7-8.4). Median overall survival (OS) was 16months (95%CI 7.8-24). Complete response, partial response and stable disease were observed in one, two and 21 patients respectively (objective response rate 6.4%; disease control rate 51%). Thirty-nine patients (83%) experienced grade 3-4 adverse events (AEs). The most common grade 3-4 AEs were hypertension (15 patients; 32%), asthenia (14; 30%), hypophosphatemia (6; 13%); diarrhea (4; 8%), hand-foot-skin reaction (4; 8%). There were two toxic deaths (4.2%) (grade 5 rectal bleeding and death not further specified). Dose reduction was required in 26 patients (55%) and dose-delays in 13 patients (28%).ConclusionsThe study did not meet the pre-specified boundary of 55% PFS rate at 6months. Toxicity observed (83% patients experienced grade 3 and 4 AEs) preclude its current use in clinical practice on this setting. Disease control rate and overall survival results are interesting and might warrant further investigation to identify those who benefit from this approach.Trial registrationThis trial was prospectively registered at EudraCT (2013-000236-94). Date of trial registration: April 9th, 2013

Can integrated care help in meeting the challenges posed on our health care systems by COVID-19? Some preliminary lessons learned from the european VIGOUR project

The COVID-19 pandemic puts health and care systems under pressure globally. This current paper highlights challenges arising in the care for older and vulnerable populations in this context and reflects upon possible perspectives for different systems making use of nested integrated care approaches adapted during the work of the EU-funded project VIGOUR