Age and Depositional Environment of Whale-Bearing Sedimentary Succession from the Lower Pliocene of Tuscany (Italy): Insights from Palaeomagnetism, Calcareous Microfossils and Facies Analyses

A c. 31 m thick section straddling the fossil find of an Early Pliocene baleen whale (“Brunella”, hereafter), made in 2007 in the sedimentary fill of the Middle Ombrone Basin of Tuscany, is investigated for depositional age and environment combining palaeomagnetic, micropalaeontological (Foraminifera and calcareous nannofossils) and sedimentary facies analyses. Resting unconformably onto Late Miocene continental deposits, the Early Pliocene marine deposits include, from bottom to top, a coarse-grained wave-winnowing lag, the few metres-thick fossiliferous sandstone bedset from which Brunella was unearthed, and several metres of clays. The stratigraphic organisation of these deposits indicate deposition in a deepening upward inner shelf environment. Successful isolation of characteristic remanent magnetisation and calcareous nannofossil content indicate the investigated marine section was deposited during the interval of polarity Chron C3n.2n corresponding to the basal part of the Mediterranean nannofossil zone MNN13 (between Helicosphaera sellii Base common and the Amaurolithus primus Top) and allow estimating the depositional age of Brunella to c. 4.6 Ma. Sedimentary facies, benthic Foraminifera association and anisotropy of magnetic susceptibility characterising the deposits that embedded Brunella suggest deposition above the fair-weather base level.

Human occupation continuity in southern Italy towards the end of the Middle Palaeolithic: a palaeoenvironmental perspective from Apulia

After the last interglacial [Marine Isotope Stage (MIS) 5e] Europe was affected by several harsh climatic oscillations. In this context southern Italy acted, like the rest of peninsular Mediterranean Europe, as a 'glacial refugium', allowing the survival of various species, and was involved in the spread of 'cold taxa' (e.g. woolly mammoth and woolly rhino) only during the coldest phases (MIS 4 and MIS 2). Both late Mousterian and early Upper Palaeolithic sites testify to a human occupation continuity in southern Italy and especially in Apulia in this time span. Here we present a focus on three key Apulian Palaeolithic sequences (Grotta di Santa Croce, Riparo L'Oscurusciuto and Grotta del Cavallo - layers F-E) jointly spanning from the late MIS 4 to the demise of Neanderthals around 43 ka. Novel chronological, sedimentological and zooarchaeological data are discussed for the first time in the light of the palaeoenvironmental information provided by recent analyses carried out on a speleothem from Pozzo Cucù cave (Bari) and the results of the magnetic susceptibility analysis from Riparo L'Oscurusciuto. This integrated reading allows a better understanding of the role played by the Apulian region as both a refugium for late Neaderthals and a suitable habitat for the early settling of modern humans.

The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect

The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.

Human Immunodeficiency Virus Localization in Human Papillomavirus-Related, High-Grade Squamous Intraepithelial Lesions of the Cervix in Women with HIV Infection: Microdissection and Molecular Analysis on Formalin-Fixed and Paraffin-Embedded Specimens

OBJECTIVES

To evaluate a possible mechanism of human immunodeficiency virus (HIV) and human papillomavirus (HPV) interaction, we have identified the cervical tissue compartments that harbor HIV.

MATERIALS AND METHODS

We studied 39 paraffin-embedded, cervical conization specimens with high-grade cervical intraepithelial neoplasia (CIN3) occurring in HIV-infected women. From selected intraepithelial HPV-positive nonulcerated specimens (confirmed by in situ hybridization), we obtained serial 4- to 5-μm-thick sections that were stained with hematoxylin and eosin, anti-S100 protein, and anti-CD4. The presence of intramucosal Langerhans' cells or dendritic cells or CD4-positive cells was recorded. Three consecutive, nonmicrodissected, full-thickness sections of the same specimens were used for polymerase chain reaction (PCR) analysis (group A). Three other uncovered, consecutive sections from the same blocks were examined with an inverted microscope, and full-thickness specimens of mucosa were dissected from the underlying cervical stroma, were gently removed, and were used for PCR (group B). The quality of DNA was checked by HLA-DQa amplification; then a nested PCR for HIV proviral DNA was performed.

RESULTS

Of group A, 5 of 39 cases (12.8%) were positive, whereas HIV was not detected in the microdissected sections of group B, with or without intraepithelial Langerhans' or CD4 cells.

CONCLUSIONS

HIV does not affect cervical epithelium. The absence of infected Langerhans' or dendritic cells (or both) indicates a migration to the proximal lymph nodes of the in ….

Urinary JCV-DNA testing during natalizumab treatment may increase accuracy of PML risk stratification

The risk of progressive multifocal leukoencephalopathy (PML) in patients treated with natalizumab for multiple sclerosis (MS) is a serious concern. The presence of anti-JC virus antibodies is a risk factor for PML development, but 2.5 % of the patients result falsely-negative, while the prognostic relevance of testing JCV-DNA in biological fluids of treated patients is debated. Aim of this work was to evaluate the utility of testing JCV-DNA, together with anti-JCV antibodies, in biological samples of treated patients as a tool for PML risk stratification. 126 subjects from 5 MS Centers in Italy were included in the study. We performed a cross-sectional study in 63 patients testing JCV-DNA in blood, peripheral blood cells and urine. We longitudinally assessed the presence of JCV-DNA in a cohort of 33 subjects, one of which developed PML. We could test retrospectively serum samples from another PML case occurred during natalizumab therapy. Anti-JCV antibodies and urinary JCV-DNA were both tested in 73 patients. No changes in JCV-DNA status occurred during natalizumab treatment. The subject who developed PML in the longitudinal cohort had detectable JCV-DNA in urine at all time-points while serum or blood from both PML patients were always negative before the onset of disease and, in one case, after. Four subjects with JCV-DNA in urine and undetectable anti-JCV antibodies were retested for anti-JCV antibodies and three out of four resulted positive. In conclusion, testing JCV-DNA in urine is complementary to testing anti-JCV antibodies in identifying patients at risk of PML.

Parameters underlying successful protection with live attenuated mutants in experimental shigellosis

Because the use of live attenuated mutants of Shigella spp. represents a promising approach to protection against bacillary dysentery (M. E. Etherridge, A. T. M. Shamsul Hoque, and D. A. Sack, Lab. Anim. Sci. 46:61-66, 1996), it becomes essential to rationalize this approach in animal models in order to optimize attenuation of virulence in the vaccine candidates, as well as their route and mode of administration, and to define the correlates of protection. In this study, we have compared three strains of Shigella flexneri 5--the wild-type M90T, an aroC mutant, and a double purE aroC mutant--for their pathogenicity, immunogenicity, and protective capacity. Protection against keratoconjunctivitis, induced by wild-type M90T, was used as the protection read out in guinea pigs that were inoculated either intranasally or intragastrically. Following intranasal immunization, the aroC mutant elicited weak nasal tissue destruction compared to M90T and achieved protection correlated with high levels of local anti-lipopolysaccharide immunoglobulin A (IgA), whereas the purE aroC double mutant, which also elicited weak tissue destruction, was not protective and elicited a low IgA response. Conversely, following intragastric immunization, only the M90T purE aroC double mutant elicited protection compared to both the aroC mutant and the wild-type strain. This mutant caused mild inflammatory destruction, particularly at the level of Peyer's patches, but it persisted much longer within the tissues. This could represent an essential parameter of the protective response that, in this case, did not clearly correlate with high anti-lipopolysaccharide IgA titers.

Neuronal glycolytic pathway impairment induced by HIV envelope glycoprotein gp120

Neurological impairment is a common feature of Acquired Immunodeficiency Syndrome (AIDS); functional alterations have been reported both in central and peripheral nervous system and the Human Immunodeficiency Virus (HIV) envelope glycoprotein gp120 has been proposed as a neurotoxin acting through a calcium-dependent mechanism. On the other hand it has been reported that gp120 treatment also induce about a 20% decrease in the cerebral glucose utilization and in the cellular ATP levels. The reported observations were performed on experimental system where also non-neuronal cells where present; in order to evaluate whether a direct interaction between HIV proteins and neuronal cells takes place, we used a neuroblastoma cultures where only neuronal cells are present. We analysed the effects of gp120 on the N18TG2 neuroblastoma clone. Treatments were performed both on growing and confluent cultures. Short time treatment with gp120 of confluent cultures causes a 25% reduction in the level of neuron-specific enolase, resulting in a similar decrease of oxygen consumption. Long time exposure of growing cells also causes a reduction in cell survival. Furthermore, using a membrane-specific fluorescent probe we observed that gp120 produces an increase of membrane trafficking. These observations suggest a direct interaction between the viral envelope protein and neuronal cells, which results in an alteration of glycolytic metabolism. This alteration may be related to the neurologic impairments observed in AIDS patients.

The Lotus japonicus LjSym4 gene is required for the successful symbiotic infection of root epidermal cells

The role of the Lotus japonicus LjSym4 gene during the symbiotic interaction with Mesorhizobium loti and arbuscular mycorrhizal (AM) fungi was analyzed with two mutant alleles conferring phenotypes of different strength. Ljsym4-1 and Ljsym4-2 mutants do not form nodules with M. loti. Normal root hair curling and infection threads are not observed, while a nodC-dependent deformation of root hair tips indicates that nodulation factors are still perceived by Ljsym4 mutants. Fungal infection attempts on the mutants generally abort within the epidermis, but Ljsym4-1 mutants allow rare, successful, infection events, leading to delayed arbuscule formation. On roots of mutants homozygous for the Ljsym4-2 allele, arbuscule formation was never observed upon inoculation with either of the two AM fungi, Glomus intraradices or Gigaspora margarita. The strategy of epidermal penetration by G. margarita was identical for Ljsym4-2 mutants and the parental line, with appressoria, hyphae growing between two epidermal cells, penetration of epidermal cells through their anticlinal wall. These observations define a novel, genetically controlled step in AM colonization. Although rhizobia penetrate the tip of root hairs and AM fungi access an entry site near the base of epidermal cells, the LjSym4 gene is necessary for the appropriate response of this cell type to both microsymbionts. We propose that LjSym4 is required for the initiation or coordinated expression of the host plant cell's accommodation program, allowing the passage of both microsymbionts through the epidermis layer.

ArchAIDS connects a clinical department and a virological laboratory to automatize the follow up of AIDS patients

A communication system for the automation of the follow up of AIDS patients set up by DIST at the Molecular Virology Unit in the Advanced Biotechnology Centre of Genova and at the Department of Internal Medicine of the Medical School of Genova is presented. This system includes a distributed database to store both clinical and virological data and a set of procedures to transfer patient data with a complete respect of requirements about completeness and privacy.

Level of human immunodeficiency virus DNA in peripheral blood mononuclear cells correlates with efficacy of antiretroviral therapy

A novel colorimetric assay was developed and validated for accurate quantitation of human immunodeficiency virus (HIV) DNA in peripheral blood mononuclear cells (PBMCs). We tested 318 sequential samples from 56 subjects, 53 of whom were undergoing dual or triple therapy. Patients were considered responders when viremia levels were below 5, 000 HIV RNA copies/ml. The mean DNA copy numbers for untreated and responder subjects were similar (72 and 75, respectively), while it was 4.54-fold higher for nonresponders (339). This report provides strong evidence that HIV DNA levels in PBMCs correlate with therapeutic efficacy and suggests that DNA quantitation is a useful tool to monitor the decay of the HIV reservoir toward disease remission, especially when viremia is undetectable.

A novel and innovative quantitative kinetic software for virological colorimetric assays

This study addresses the limited range of quantification with colorimetric assays (ELISA) starting from the analysis of color production in a reference external curve. An automatic ELISA management software, designated Quanti-Kin Detection System (QKDS) is described, which retains the sensitivity of the end-point reading and extends the dynamic range up to five logarithms with mathematical interpretation of color production. The QKDS software is a generic system suitable for different types of ELISA with substrate incubation at room temperature, does not require dedicated instruments, performs accurate quantification (including assay quality control) and has a user friendly interface. Specific applications were developed for three types of analytes: antibodies, viral antigens and nucleic acids. Data are presented on three representative QKDS applications to HIV antibodies, p24 antigen and proviral DNA kits. The precision of quantification is strictly correlated with the precision of the kit; however, for almost all samples with known analyte amount, the error percentage was below 10%, only for two cases in quantification of HIV proviral DNA the error percentage was around 25%. The necessity for a wide quantification range has been demonstrated by measuring clinical samples, which showed a distribution in all possible quantification ranges for all kits.

Effects of erythropoietin administration on blood pressure and urinary albumin excretion in rats

The effects of recombinant human erythropoietin (rHuEPO) administration on blood pressure and urinary albumin excretion were studied in normotensive Wistar-Kyoto rats (WKY), in spontaneously hypertensive rats (SHR), and in SHR rats treated with an angiotensin converting enzyme inhibitor (SHR-ACEi). Rats were housed in metabolic cages and treated with rHuEPO (150 U/kg body weight [bw] three times a week) for 6 weeks. Control animals received the vehicle only (0.25 mL of physiological saline). An angiotensin converting enzyme inhibitor was administered in the drinking water for 6 weeks (spirapril 5 mg/kg bw). Systolic blood pressure (SBP), and 24 h urinary albumin excretion (UAE) were measured once a week. No significant differences in SBP were observed between rHuEPO and vehicle-treated normotensive animals at the end of the treatment (171.9 +/- 4.9 v 172.1 +/- 5.6 mm Hg, respectively). After 6 weeks, SBP was significantly higher in SHR and SHR-ACEi groups treated with rHuEPO than in control groups (239.8 +/- 7.3 and 243.0 +/- 7.3 mm Hg v 218.1 +/- 6.0 and 187.9 +/- 4.6 mm Hg, respectively); UAE was significantly higher in groups treated with rHuEPO than in control groups (WKY: 265.9 +/- 19.5 v 127.0 +/- 12.3 microg/100 g bw, SHR: 1668.4 +/- 564.6 v 234.8 +/- 22.9 microg/100 g bw, and SHR-ACEi: 1522.7 +/- 448.3 v 143.0 +/- 18.9 microg/100 g bw, respectively). We concluded that erythropoietin treatment causes an increase in arterial pressure in SHR only, and an increase in UAE in both normotensive and hypertensive rats. The albuminuric effect was not entirely dependent on increased blood pressure. The treatment with an angiotensin converting enzyme inhibitor did not modify either the proteinuric or the pressor effects.

Overexpression, one-step purification and characterization of UDP-glucose dehydrogenase and UDP-N-acetylglucosamine pyrophosphorylase

Two enzymes of the Leloir pathway, UDP-GlcNAc pyrophosphorylase and UDP-Glc dehydrogenase, which are involved in the synthesis of activated sugar nucleotides have been cloned, overexpressed in Escherichia coli, and purified to homogeneity in only one step by chelation-affinity chromatography. The gene KfaC of E. coli K5 was thus demonstrated to encode UDP-Glc DH. Some properties of the cloned enzymes, such as stability, pH dependence, and substrate kinetics, were studied in order to facilitate the use of these enzymes in carbohydrate synthesis, especially in the synthesis of hyaluronic acid.

Molecular mechanisms and genetics of hyaluronan biosynthesis

Hyaluronan is an extremely important polysaccharide from both the biological and commercial points of view. This review summarizes the present state of the art concerning the polymer and our understanding of the molecular mechanisms of its synthesis with emphasis on the implications of this understanding for polysaccharide engineering of hyaluronan.

Hyaluronate synthase: cloning and sequencing of the gene from Streptococcus sp

The complete nucleotide sequence of hyaluronate synthase from Streptococcus sp. and its flanking regions is presented. The gene locus was designated has. Southern-blotting results suggested that the gene was conserved in hyaluronate-producing streptococci. A putative translation-initiation codon was identified and the open reading frame consists of 1566 bp, specifying a protein of 56 kDa. Sequences resembling the promoter and ribosome-binding site of Gram-positive organisms are found upstream of the synthase. The predicted amino-acid sequence reveals the presence of a 35-residue signal peptide. The sequence has some similarity to bacterial peptide-binding proteins.

[Radioimmunoscintigraphy of colorectal tumors with 99m-Tc marked CEA antibodies. Indications and clinical value]

In Germany, radioimmunoscintigraphy (RIS) (scintigraphic, specific imaging of benign and malignant diseases by radioactively labelled monoclonal antibodies) has been employed since 1985 in clinical trials involving patients with colorectal cancer. After proving successful for identifying primary tumors, RIS is now increasingly being used for the early diagnosis of recurrent and metastatic lesions. In this prospective study involving 75 patients with colorectal tumors confirmed by endoscopy and biopsy, it was shown that RIS using the SPECT technique with 99m-Tc-labelled monoclonal CEA antibodies has a sensitivity of 78% in the detection of local recurrent disease in cases in which diagnostic work-up has been inconclusive.

Synthesis of the biologically active beta-subunit of human nerve growth factor in Escherichia coli

The gene (NGFB) encoding the beta subunit of mature human nerve growth factor (hNGFB) was subcloned into the pJLA503 expression vector under the control of bacteriophage promoters PR and PL, and expressed in Escherichia coli. The recombinant protein represented approximately 3% of the total cellular protein. Biologically active hNGFB was solubilized (0.2% total NGFB) and purified by cation-exchange chromatography and it yielded two bands on polyacrylamide-gel electrophoresis under nonreducing conditions, corresponding to the monomeric (14 kDa) and homodimeric (26.5 kDa) forms of the molecule. Both hNGFB forms were immunopositive on Western blots with rabbit anti-NGFB antibodies; however, following additional purification, only the species corresponding to the hNGFB homodimer was biologically active on cultured chicken dorsal root ganglion neurons. These results demonstrate the feasibility of synthesizing the biologically active form of hNGFB in E. coli.

Cloning and expression of human ciliary neurotrophic factor

Ciliary neurotrophic factor (CNTF) is a survival factor for avian ciliary ganglion neurons and a variety of other neuronal cell types in vitro. We report here the cloning of the entire genomic sequence encoding human CNTF and its primary structure. Biologically active CNTF has been expressed in Chinese hamster ovary cells from a human genomic DNA clone. Human CNTF has no significant sequence similarity to any previously reported protein, although approximately 84% similarity exists compared with rat and rabbit CNTF. The lack of both an N-terminal signal sequence and consensus sequences for glycosylation or hydrophobic regions, and the fact that active CNTF is expressed but not released into the culture medium of transfected cells, argue in favour of human CNTF as a cytosolic protein. These data provide a basis for understanding the role of CNTF in nervous system physiology and pathology.

Synthesis, purification, and characterization of human ciliary neuronotrophic factor from E. coli

The cDNA for human ciliary neuronotrophic factor (CNTF) has been cloned into an expression vector under the control of the T7 promoter. The BL21 strain of E. coli was transformed with this vector. Human CNTF accounted for about 30% of the total bacterial protein after induction with isopropyl-B-D-thiogalactopyranoside. This human CNTF was purified to homogeneity from inclusion bodies by a combination of ion exchange chromatography and reverse-phase high performance liquid chromatography. The amino-terminal amino acid sequence of the purified protein was identical to the deduced amino acid sequence; however, the methionyl residue has been removed. On SDS-PAGE gels, human CNTF displayed a molecular weight of about 24 kDa, in accord with its deduced molecular mass; a pI of 5.8 indicates the acidic nature of the molecule. A proposed structure for human CNTF includes major alpha helical regions. The ED50 of purified human CNTF was approximately 30 pM, using cultured embryonic day 10 chicken dorsal root ganglion neurons; no activity was observed with neurons from embryonic day 8 ganglia. Polyclonal antibodies prepared against both a synthetic peptide of CNTF and the entire human CNTF protein recognized a single 24 kDa band on Western blots, corresponding to human CNTF. However, only the antibodies against intact CNTF blocked its biological activity. This represents the first molecular expression and purification of human CNTF.