Fabio Verginelli

The Analysis of Variation of mtDNA Hypervariable Region 1 Suggests That Eastern and Western Pygmies Diverged before the Bantu Expansion

The Eastern Pygmies from Zaire and Western Pygmies from Cameroon, Congo, and the Central African Republic represent the two principal groups of African Pygmies. In the “recent divergence” hypothesis in which Western Pygmies are thought to be the result of hybridization between the ancestors of Eastern Pygmies and Bantu farmers who penetrated the equatorial belt and came into contact with Pygmies around 2–3 kiloyears ago. On the basis of recent archaeological research in the tropical rain forest, we propose a “pre‐Bantu divergence” hypothesis, which posits the separation between the ancestors of Eastern and Western Pygmies earlier than 18 kiloyears ago. In order to test the two hypotheses, we analyzed the variation of the hypervariable region 1 of the mitochondrial DNA in the Mbenzele, Western Pygmies of the Central African Republic, and compared our results with those of previous mtDNA and Y chromosome studies. Distribution, sequence variation, and age of haplogroups along with genetic distances among populations, estimates of divergence times, and simulations based on the coalescent approach were found to be congruent with the pre‐Bantu divergence but failed to support the recent divergence hypothesis.

Phenotypic and genotypic characterization of Stenotrophomonas maltophilia isolates from patients with cystic fibrosis: Genome diversity, biofilm formation, and virulence

BackgroundStenotrophomonas maltophilia is emerging as one of the most frequently found bacteria in cystic fibrosis (CF) patients. In the present study, phenotypic and genotypic traits of a set of 98 isolates of S. maltophilia obtained from clinical (CF and non-CF patients) and environmental sources were comparatively evaluated.ResultsS. maltophilia exhibited a high level of genomic diversity in both CF and non-CF group, thus possibly allowing this bacterium to expand its pathogenic potentials. Strains sharing the same pulsotype infected different patients, thus likely indicating the occurrence of clonal spread or acquisition by a common source. CF isolates differed greatly in some phenotypic traits among each other and also when compared with non-CF isolates, demonstrating increased mean generation time and susceptibility to oxidative stress, but reduced ability in forming biofilm. Furthermore, in CF isolates flagella- and type IV pili-based motilities were critical for biofilm development, although not required for its initiation. Sequential isogenic strains isolated from the same CF patient displayed heterogeneity in biofilm and other phenotypic traits during the course of chronic infection. CF and non-CF isolates showed comparable virulence in a mouse model of lung infection.ConclusionsOverall, the phenotypic differences observed between CF and non-CF isolates may imply different selective conditions and persistence (adaptation) mechanisms in a hostile and heterogeneous environment such as CF lung. Molecular elucidation of these mechanisms will be essential to better understand the selective adaptation in CF airways in order to design improved strategies useful to counteract and eradicate S. maltophilia infection.

Cobalt nano-particles modulate cytokine in vitro release by human mononuclear cells mimicking autoimmune disease

: The use of particles from micro to nanoscale provides benefits to diverse scientific fields, but because a large percentage of their atoms lie on the surface, nanomaterials could be highly reactive and pose potential risks to humans. Due to their wide range of application, Cobalt nano-particles are of great interest both in industry and in life-science. To date, there are few studies on Co nano-particle toxicology. In this respect, this study aims at evaluating in vitro the potential interference of Co nano-particles on the production of several cytokines (IL-2, IL-4, IL-6, IL-10, IFNgamma and TNFalpha) by PBMCs, comparing their effects to those of Co micro-particles and Co solution (CoCl2). Cells were cultured in Opticell flasks with escalating concentrations (10-5, 10-6 and 10-7 M), of Co nano and micro-particles and CoCl2 or without metal. Cytokines were quantified in the supernatants using a human Th1/Th2 cytokine cytometric bead array. Co micro-particles showed a greater inhibitory effect compared to other Co forms. Its inhibitory activity was detected at all concentrations and towards all cytokines, whereas Co solutions selectively inhibited IL-2, IL-10 and TNF-alpha at maximal concentration. Co nano-particles induced an increase of TNF-alpha and IFN-gamma release and an inhibition of IL-10 and IL-2: a cytokine pattern similar to that detected in the experimental and clinical autoimmunity. On the basis of the obtained data, immune endpoints should be sought in the next series of studies both in vitro and in vivo in subjects exposed to cobalt nano-particles.The mainstay of therapy for patients with advanced prostate cancer still remains androgen deprivation, although response to this is invariably temporary. Most of the patients develop hormone-refractory disease resulting in progressive clinical deterioration and, ultimately, death. Until recently there has been no standard chemotherapeutic approach for hormone refractory prostate cancer (HRPC), the major benefits of chemotherapy being only palliative. The studies combining mitoxantrone plus a corticosteroid demonstrated that chemotherapy could be given to men with symptomatic HRPC with minimal toxicity and a significant palliation could be provided. Recently, results from 2 phase III randomized clinical trials demonstrating that a combination of docetaxel plus prednisone can improve survival in men with HRPC have propelled docetaxel-based therapy into the forefront of treatment options for these patients as the new standard of care. There is a promising activity of new drug combinations such as taxanes plus vinca alkaloids; bisphosphonates are assuming a prominent role in prostate therapy through their ability to prevent skeletal morbidity. Combinations of classic chemotherapeutic agents and biological drugs began to be tested in phase II-III trials and the first results appear interesting. This article focuses on combinations recently evaluated or under clinical development for the treatment of HRPC.

J1-M267 Y lineage marks climate-driven pre-historical human displacements.

The present day distribution of Y chromosomes bearing the haplogroup J1 M267*G variant has been associated with different episodes of human demographic history, the main one being the diffusion of Islam since the Early Middle Ages. To better understand the modes and timing of J1 dispersals, we reconstructed the genealogical relationships among 282 M267*G chromosomes from 29 populations typed at 20 YSTRs and 6 SNPs. Phylogenetic analyses depicted a new genetic background consistent with climate-driven demographic dynamics occurring during two key phases of human pre-history: (1) the spatial expansion of hunter gatherers in response to the end of the late Pleistocene cooling phases and (2) the displacement of groups of foragers/herders following the mid-Holocene rainfall retreats across the Sahara and Arabia. Furthermore, J1 STR motifs previously used to trace Arab or Jewish ancestries were shown unsuitable as diagnostic markers for ethnicity.

P53 mutations in colorectal cancer from northern Iran: Relationships with site of tumor origin, microsatellite instability and K-ras mutations†

CRC‐associated P53 mutations have not been studied extensively in non‐Western countries at relatively low CRC risk. We examined, for the first time, 196 paraffin‐embedded CRC cases from Northern Iran for mutations in P53 exons 5–8 using PCR‐direct sequencing. P53 status and mutation site/type were correlated with nuclear protein accumulation, clinicopathologic variables and data on K‐ras mutations and high‐level microsatellite instability (MSI‐H). We detected 96 P53 mutations in 87 (44.4%) cases and protein accumulation in 84 cases (42.8%). P53 mutations correlated directly with stage and inversely with MSI‐H. Distal CRCs were more frequently mutated at major CpG hotspot codons [248 (8/66, 12.1%), 175 (7/66, 10.6%), and 245 (7/66, 10.6%)], while in proximal tumors codon 213, emerged as most frequently mutated (5/28, 17.9% vs. 3/66, 4.5%, P = 0.048). Transitions at CpGs, the most common mutation type, were more frequent in non‐mucinous (25% vs. 10.4% in mucinous, P = 0.032), and distal CRC (27% vs. 12.5% in proximal, P = 0.02), and correlated with K‐ras transversions. Transitions at non‐CpGs, second most common P53 mutation, were more frequent in proximal tumors (15.6% vs. 4.7% in distal, P = 0.01), and correlated with K‐ras transitions and MSI‐H. Overall frequency and types of mutations and correlations with P53 accumulation, stage and MSI‐H were as reported for non‐Iranian patients. However P53 mutation site/type and correlations between P53 and K‐ras mutation types differed between proximal and distal CRC. The codon 213 P53 mutation that recurred in proximal CRC was previously reported as frequent in esophageal cancer from Northern Iran. J. Cell. Physiol. 216: 543–550, 2008.

Allele-specific loss and transcription of the miR-15a/16-1 cluster in chronic lymphocytic leukemia

Deregulation of the miR-15a/16-1 cluster has a key role in the pathogenesis of chronic lymphocytic leukemia (CLL), a clinically heterogeneous disease with indolent and aggressive forms. The miR-15a/16-1 locus is located at 13q14, the most frequently deleted region in CLL. Starting from functional investigations of a rare SNP upstream the miR cluster, we identified a novel allele-specific mechanism that exploits a cryptic activator region to recruit the RNA polymerase III for miR-15a/16-1 transcription. This regulation of the miR-15a/16- locus is independent of the DLEU2 host gene, which is often transcribed monoallellically by RPII. We found that normally one allele of miR-15a/16-1 is transcribed by RNAPII, the other one by RNAPIII. In our subset of CLL patients harboring 13q14 deletions, exclusive RNA polymerase III (RPIII)-driven transcription of the miR-15a/16-1 was the consequence of loss of the RPII-regulated allele and correlated with high expression of the poor prognostic marker ZAP70 (P=0.019). Thus, our findings point to a novel biological process, characterized by double allele-specific transcriptional regulation of the miR-15a/16-1 locus by alternative mechanisms. Differential usage of these mechanisms may distinguish at onset aggressive from indolent forms of CLL. This provides a basis for the clinical heterogeneity of the CLL patients carrying 13q14 deletions.

Cooperative pathogenicity in cystic fibrosis: Stenotrophomonas maltophilia modulates Pseudomonas aeruginosa virulence in mixed biofilm.

The present study was undertaken in order to understand more about the interaction occurring between S. maltophilia and P. aeruginosa, which are frequently co-isolated from CF airways. For this purpose, S. maltophilia RR7 and P. aeruginosa RR8 strains, co-isolated from the lung of a chronically infected CF patient during a pulmonary exacerbation episode, were evaluated for reciprocal effect during planktonic growth, adhesion and biofilm formation onto both polystyrene and CF bronchial cell monolayer, motility, as well as for gene expression in mixed biofilms. P. aeruginosa significantly affected S. maltophilia growth in both planktonic and biofilm cultures, due to an inhibitory activity probably requiring direct contact. Conversely, no effect was observed on P. aeruginosa by S. maltophilia. Compared with monocultures, the adhesiveness of P. aeruginosa on CFBE41o- cells was significantly reduced by S. maltophilia, which probably acts by reducing P. aeruginosas swimming motility. An opposite trend was observed for biofilm formation, confirming the findings obtained using polystyrene. When grown in mixed biofilm with S. maltophilia, P. aeruginosa significantly over-expressed aprA, and algD—codifying for protease and alginate, respectively—while the quorum sensing related rhlR and lasI genes were down-regulated. The induced alginate expression by P. aeruginosa might be responsible for the protection of S. maltophilia against tobramycin activity we observed in mixed biofilms. Taken together, our results suggest that the existence of reciprocal interference of S. maltophilia and P. aeruginosa in CF lung is plausible. In particular, S. maltophilia might confer some selective “fitness advantage” to P. aeruginosa under the specific conditions of chronic infection or, alternatively, increase the virulence of P. aeruginosa thus leading to pulmonary exacerbation.

Low AMY1 Gene Copy Number Is Associated with Increased Body Mass Index in Prepubertal Boys.

Background Genome-wide association studies have identified more than 60 single nucleotide polymorphisms associated with Body Mass Index (BMI). Additional genetic variants, such as copy number variations (CNV), have also been investigated in relation to BMI. Recently, the highly polymorphic CNV in the salivary amylase (AMY1) gene, encoding an enzyme implicated in the first step of starch digestion, has been associated with obesity in adults and children. We assessed the potential association between AMY1 copy number and a wide range of BMI in a population of Italian school-children. Methods 744 children (354 boys, 390 girls, mean age (±SD): 8.4±1.4years) underwent anthropometric assessments (height, weight) and collection of saliva samples for DNA extraction. AMY1 copies were evaluated by quantitative PCR. Results A significant increase of BMI z-score by decreasing AMY1 copy number was observed in boys (β: -0.117, p = 0.033), but not in girls. Similarly, waist circumference (β: -0.155, p = 0.003, adjusted for age) was negatively influenced by AMY1 copy number in boys. Boys with 8 or more AMY1 copy numbers presented a significant lower BMI z-score (p = 0.04) and waist circumference (p = 0.01) when compared to boys with less than 8 copy numbers. Conclusions In this pediatric-only, population-based study, a lower AMY1 copy number emerged to be associated with increased BMI in boys. These data confirm previous findings from adult studies and support a potential role of a higher copy number of the salivary AMY1 gene in protecting from excess weight gain.

Nutrigenetics in the light of human evolution.

Bio-cultural adaptations to new foods played a key role in human evolution. The fossil record and sequence differences between human and chimpanzee genes point to a major dietary shift at the stem of human evolution. The earliest representatives of the human lineage diverged from the ancestors of chimpanzees because of their better adaptation to hard and abrasive foods. Bipedalism and modifications of the hand, which allowed tool manufacture and use, impacted on dietary flexibility, facilitating access to foods of animal origin. This promoted major anatomic, physiologic and metabolic adaptations. Encephalization, which requires high-quality diet, characterizes the evolutionary sequence that, through the Homo ergaster/erectus stages, led to our species, Homo sapiens, which originated in Africa about 200,000 years ago. At the end of the Ice Age, climatic changes and human impact determined a major food crisis, which triggered the agricultural revolution. This affected nutrition and health, with rapid evolutionary adaptations through the selection of genetic variants that allowed better utilization of new foods, different in relation to geography and culture. Today population growth, globalization and economic pressure powerfully affect diets worldwide. We must take into account our evolutionary past to meet the present nutritional challenges.

Use of a multiplex polymerase chain reaction assay in the sex typing of DNA extracted from archaeological bone

We developed an original method that allows the simultaneous molecular amplification and analysis of human chromosome X- and Y-specific sequences from cortical compact bone using the polymerase chain reaction (PCR). The strategy is based on sequential amplification using external and internal primers. The targeted loci are SRY for chromosome Y and DXZ4 for chromosome X. Internal and external primer pairs for both loci were selected in order to allow the simultaneous amplification of short sequences of distinct molecular weight in the same reaction. Ethidium bromide stained PCR products were analysed on 2 per cent agarose gels. The presence of two distinct amplification bands permitted the fast and unequivocal identification of male bones, whereas female bones were identified by the presence of a single band. The technique was validated by comparative analysis of modern human DNAs of known sex and of DNAs from medieval bone samples whose sex could be determined using conventional anthropological methods. We then analysed bone samples from 40 burials found under the Church of St Maria Aprutiensis in Teramo, Abruzzo. These burials were dated to AD 800–1200 by 14C accelerated mass spectrometry radiometric analysis. Molecular analysis allowed the unambiguous identification of sex in all the samples studied. These results indicate that molecular techniques represent useful and often critical additions to anthropological studies of ancient human remains.