Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution.

Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers, these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology's first digital revolution-online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a small proportion of the palaeontological data housed in museum collections. Although this issue has long been appreciated, the magnitude, and thus potential significance, of these so-called 'dark data' has been difficult to determine. Here, in the early phases of a second digital revolution in palaeontology--the digitization of museum collections-we provide an estimate of the magnitude of palaeontology's dark data. Digitization of our nine institutions' holdings of Cenozoic marine invertebrate collections from California, Oregon and Washington in the USA reveals that they represent 23 times the number of unique localities than are currently available in the PBDB. These data, and the vast quantity of similarly untapped dark data in other museum collections, will, when digitally mobilized, enhance palaeontologists' ability to make inferences about the patterns and processes of past evolutionary and ecological changes.

Cutting edge: control of Mycobacterium tuberculosis infection by a subset of lung parenchyma-homing CD4 T cells.

Th1 cells are critical for containment of Mycobacterium tuberculosis infection, but little else is known about the properties of protective CD4 T cell responses. In this study, we show that the pulmonary Th1 response against M. tuberculosis is composed of two populations that are either CXCR3(hi) and localize to lung parenchyma or are CX3CR1(hi)KLRG1(hi) and are retained within lung blood vasculature. M. tuberculosis-specific parenchymal CD4 T cells migrate rapidly back into the lung parenchyma upon adoptive transfer, whereas the intravascular effectors produce the highest levels of IFN-γ in vivo. Importantly, parenchymal T cells displayed greater control of infection compared with the intravascular counterparts upon transfer into susceptible T cell-deficient hosts. Thus, we identified a subset of naturally generated M. tuberculosis-specific CD4 T cells with enhanced protective capacity and showed that control of M. tuberculosis correlates with the ability of CD4 T cells to efficiently enter the lung parenchyma rather than produce high levels of IFN-γ.

Active multilayered capsules for in vivo bone formation.

Interest in the development of new sources of transplantable materials for the treatment of injury or disease has led to the convergence of tissue engineering with stem cell technology. Bone and joint disorders are expected to benefit from this new technology because of the low self-regenerating capacity of bone matrix secreting cells. Herein, the differentiation of stem cells to bone cells using active multilayered capsules is presented. The capsules are composed of poly-L-glutamic acid and poly-L-lysine with active growth factors embedded into the multilayered film. The bone induction from these active capsules incubated with embryonic stem cells was demonstrated in vitro. Herein, we report the unique demonstration of a multilayered capsule-based delivery system for inducing bone formation in vivo. This strategy is an alternative approach for in vivo bone formation. Strategies using simple chemistry to control complex biological processes would be particularly powerful, as they make production of therapeutic materials simpler and more easily controlled.

Lipid-based nanotherapeutics for siRNA delivery.

RNA interference (RNAi) is a specific gene-silencing mechanism triggered by small interfering RNA (siRNA). The application of RNAi in the clinic requires the development of safe and effective delivery systems. Inspired by progress with lipid-based systems in drug delivery, efforts have been dedicated to the development of liposomal siRNA delivery systems. Many of the lipid-based delivery vehicles self-assemble with siRNA through electrostatic interactions with charged amines, generating multi-lamellar lipoplexes with positively charged lipid bilayers separated from one another by sheets of negatively charged siRNA strands. Internalization of lipid-based siRNA delivery systems into cells typically occurs through endocytosis; accordingly, delivery requires materials that can facilitate endosomal escape. The size of the carrier is important as carriers <100 nm in diameter have been reported to have higher accumulation levels in tumours, hepatocytes and inflamed tissue, whereas larger particles tend to be taken up by Kupffer cells or other components of the reticuloendothelial system (RES). To reduce RES uptake and increase circulation time, carriers have been modified on the surface with hydrophilic materials, such as polyethyleneglycol. Herein, we review the molecular and structural parameters of lipid-based siRNA delivery systems.

Network approach identifies Pacer as an autophagy protein involved in ALS pathogenesis.

BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a multifactorial fatal motoneuron disease without a cure. Ten percent of ALS cases can be pointed to a clear genetic cause, while the remaining 90% is classified as sporadic. Our study was aimed to uncover new connections within the ALS network through a bioinformatic approach, by which we identified C13orf18, recently named Pacer, as a new component of the autophagic machinery and potentially involved in ALS pathogenesis. METHODS: Initially, we identified Pacer using a network-based bioinformatic analysis. Expression of Pacer was then investigated in vivo using spinal cord tissue from two ALS mouse models (SOD1G93A and TDP43A315T) and sporadic ALS patients. Mechanistic studies were performed in cell culture using the mouse motoneuron cell line NSC34. Loss of function of Pacer was achieved by knockdown using short-hairpin constructs. The effect of Pacer repression was investigated in the context of autophagy, SOD1 aggregation, and neuronal death. RESULTS: Using an unbiased network-based approach, we integrated all available ALS data to identify new functional interactions involved in ALS pathogenesis. We found that Pacer associates to an ALS-specific subnetwork composed of components of the autophagy pathway, one of the main cellular processes affected in the disease. Interestingly, we found that Pacer levels are significantly reduced in spinal cord tissue from sporadic ALS patients and in tissues from two ALS mouse models. In vitro, Pacer deficiency lead to impaired autophagy and accumulation of ALS-associated protein aggregates, which correlated with the induction of cell death. CONCLUSIONS: This study, therefore, identifies Pacer as a new regulator of proteostasis associated with ALS pathology.

Epigenetic regulation and nucleosome positioning in the human TATA-less IL-1 alpha promoter.

Interleukin-1 alpha (IL-1 alpha) is secreted by a variety of cell types and is a major player in immune and inflammatory processes. Genes involved in immunological processes are known to be strictly regulated; however, how epigenetic mechanisms contribute to this regulation in not understood. To gain insight into the epigenetic regulation of the human TATA-less IL-1A gene, we show that active and silent chromatin modifications characterize the regulatory regions of IL-1 alpha in expressing and non-expressing cells, respectively, and that the DNA methylation in the proximal promoter is associated with the expression status of the cells. Interestingly, although nucleosome depletion in active promoters is found in yeast and fly genes, now it has been reported in human promoters. We here show on the level of single DNA molecules that in expressing cells, a nucleosome is absent in about half of the proximal IL-1 alpha promoters. This observation might reflect a more subtle regulation of nucleosome positioning in TATA-less genes or human genes in general.

Ultrasound shear wave velocity in skeletal muscle: A reproducibility study.

PURPOSE: The purpose of the study was threefold: to assess the reliability of shear wave velocities (SWV) measurements in normal skeletal muscles; to evaluate intra- and inter-operator reproducibility of measurements for a specific site of the muscle and for the mean value in the whole muscle. MATERIALS AND METHODS: Two sets of measurements were performed at three weeks intervals of each other on 16 volunteers by two radiologists on medial gastrocnemius and tibialis anterior muscles. Each muscle was evaluated in 5 different sites, with three measurements for each site in the transverse and longitudinal planes. Reliability of SWV measurements was assessed by means of intraclass correlation coefficient (ICC). RESULTS: Reliability of the three independent SWV measurements was excellent, slightly better in the longitudinal plane. Inter/intra-operator reproducibility per site was fair to good in the longitudinal plane and poor to fair in the transverse plane. For global values of the whole muscle, ICC showed good agreement in the longitudinal plane and fair agreement in the transverse plane. CONCLUSION: Quantitative SWV measurements are reliable when performed in rigorous conditions. In conditions that mirror clinical practice, inter/intra-operator reproducibility is moderate, better for longitudinal compared to transverse plane.

[Competence approach in teaching-learning process]. / Abordagem por competências no processo ensino-aprendizagem.

The work relates the experience of the teaching-learning process based on the competence approach. The detail of that teaching process reveals the authors concern with the few occurrence of studies about the practical development of the competences theme in the Educational Practice and, point out to the need of more studies production in that dimension.

Erratic oscillatory characteristics of plasma insulin concentrations in patients with insulinoma: mechanism for unpredictable hypoglycemia.

Patients with insulin-producing tumors may have hypoglycemic symptoms at unpredictable times. This study evaluated whether plasma insulin oscillations, known to occur in normal individuals but not explored in patients with insulinomas, could be an underlying mechanism for such events. Nine normal subjects and five patients with proven insulinomas were studied in the fasting state. Serial sampling of arterialized blood over 80-100 min, at 2- or 3-min intervals was performed. In normal subjects, mean plasma glucose and insulin concentrations were 5.3 +/- 0.1 mmol/L and 58 +/- 9 pmol/L, respectively. Regular, low-amplitude plasma insulin oscillations were observed, with a period of 10-17 min. The subjects with insulinomas had lower mean plasma glucose and higher insulin concentrations than controls, 3.6 +/- 0.3 mmol/L (P = 0.01) and 150 +/- 42 pmol/L (P = 0.01), respectively. They also had insulin oscillations that appeared unstable as a result of variability in duration and amplitude compared with controls. The insulin pulses were irregular, and interpeak intervals varied between 4-54 min in different subjects; in some subjects, the amplitude was also variable, with sudden spontaneous pulses as high as 565 pmol/L, with an associated glucose decrement. We conclude that large spontaneous bursts of insulin secretion occur in patients with insulinomas as part of an erratic pattern of oscillatory insulin secretion, and these can account for unpredictable occurrences of hypoglycemia.

An overnight insulin infusion algorithm provides morning normoglycemia and can be used to predict insulin requirements in noninsulin-dependent diabetes mellitus.

Initial insulin requirements in noninsulin-dependent diabetes mellitus (NIDDM) are difficult to estimate because of individual variability in insulin sensitivity and secretion. We evaluated a simple, nurse-managed algorithm for overnight delivery of insulin, for its ability to provide morning near-normoglycemia and as a means to predict initial insulin requirements in NIDDM. Twenty-seven patients with poorly controlled NIDDM were studied on 30 occasions. A 12-h iv insulin infusion was begun at 2000 h, and bedside blood glucose concentrations were measured at hourly intervals. The rate of insulin infusion was adjusted according to blood glucose levels. We estimated the preprandial insulin dose requirement for the following day in 16 patients based on overnight insulin requirements to maintain normoglycemia. Preprandial insulin doses were adjusted for prevailing blood glucose concentrations. At 2000 h, the mean (+/-SEM) blood glucose concentration was 265.7 +/- 10.8; at 0300 h, it was 122.8 +/- 3.4; and at 0700 h, it was 123.8 +/- 5.1 mg/dL. On the next day, mean blood glucose levels (before and 2 h after a meal) were: breakfast, 102.5 +/- 5.9 and 177.3 +/- 19.2; lunch, 138.9 +/- 15.5 and 136.3 +/- 11.4; dinner, 105.7 +/- 7.2 and 178.1 +/- 15.7 mg/dL. There was no significant difference between mean calculated and administered total insulin dosage the next day (84.2 +/- 7.0 vs. 78.2 +/- 8.2 U). Thus, a weight-based algorithm for iv insulin infusion induced near-normoglycemia in NIDDM and successfully predicted the insulin dose requirement. We conclude that initiating insulin therapy in NIDDM patients can be achieved rapidly and efficiently based on a nurse-managed overnight insulin infusion.

A glucose reduction challenge in the differential diagnosis of fasting hypoglycemia: a two-center study.

Investigation of patients with suspected or proven hypoglycemia is often a time-consuming and expensive process. We describe a glucose reduction challenge test which may be useful as an out-patient screening procedure. Insulin is infused for 3 h at 40 mU/kg.h. Plasma glucose was monitored at the bedside during the test, and blood samples were collected for measurement of C-peptide. Responses were examined in 17 normal controls, and 6 patients with insulinomas. In normal subjects, mean plasma glucose fell to a plateau value of 3.2 +/- 0.2 mmol/L (57 +/- 2.6 mg/dL) and remained at that level with few symptoms. In contrast, five of six patients with insulinomas developed severe hypoglycemia, with plasma glucose levels between 1.9 (34 mg/dL) and 2.2 mmol/L (39 mg/dL). Plasma C-peptide concentrations were suppressed to 0.08 pmol/mL or less in normal subjects, but in insulinoma patients remained at 0.32-1.6 pmol/mL i.e. outside the normal range, and diagnostic of nonsuppressible insulin secretion. These data demonstrate that moderate reduction of serum glucose maintained for a prolonged period results in marked suppression of plasma C-peptide, permitting improved discrimination between normal subjects and patients with insulinomas. This glucose reduction challenge can, therefore, be used as a test of glucose-regulating ability, where failure (hypoglycemia) per se represents a measurable abnormality. C-Peptide measurements will determine whether the cause of hypoglycemia is due to hyperinsulinemia.

Synthesis of the tumorigenic 3,4-dihydrodiol metabolites of dibenz[a,j]anthracene and 7,14-dimethyldibenz[a,j]anthracene.

Syntheses are described of the trans-3,4-dihydrodiol derivatives (2a and 2b) of dibenz[a,j]anthracene and 7,14-dimethyldibenz[a,j]anthracene (1a and 1b), implicated as their proximate carcinogenic metabolites. Conversion of 2a to the bay region anti-diol epoxide derivative 3a, its putative ultimate carcinogenic metabolite, is also reported. The related diol epoxide derivative of 2b could not be prepared due to its chemical instability. Tumorigenicity assays confirm that 1b and 2b are potent carcinogens on mouse skin, while 1a and 2a are only relatively weakly active. The diol epoxide 3a exhibited significantly higher tumorigenicity than its dihydrodiol precursor 2a. These findings are consistent with the hypothesis that the bay region diol epoxide metabolites are the active carcinogenic forms of these hydrocarbons. They also support the generalization that methyl substitution in bay regions enhances the carcinogenic activity of polycyclic aromatic hydrocarbons.

Biologically active dihydrodiol metabolites of polycyclic aromatic hydrocarbons structurally related to the potent carcinogenic hydrocarbon 7,12-dimethylbenz[a]anthracene.

Syntheses of the trans-dihydrodiol derivatives implicated as the proximate carcinogenic metabolites of the polycyclic hydrocarbons cholanthrene, 6-methylcholanthrene, benz[a]anthracene, and 7- and 12-methylbenz[a]anthracene are described. These compounds are useful models for research to determine the molecular basis of the strong enhancement of carcinogenicity consequent upon methyl substitution in nonbenzo bay molecular sites and meso regions of polycyclic hydrocarbons. Synthesis of the bay region anti-diol epoxide derivative of cholanthrene, its putative ultimate carcinogenic metabolite, is also described. Tumorigenicity assays indicate that the 9,10-dihydrodiol derivatives of cholanthrene and its 3- and 6-methyl derivatives are all potent tumor initiators on mouse skin. The most active member of the series is the dihydrodiol derivative of 6-methylcholanthrene, which contains a bay region methyl group. The ability of the dihydrodiols 3a-c and the trans-3,4-dihydrodiol of 7,12-dimethylbenz[a]anthracene (3d) to induce chromosomal aberrations in rat bone marrow cells was also examined. The observed order of activity was 3d greater than 3c greater than 3b greater than 3a. These findings are consistent with the hypothesis that the diol epoxide metabolites of these dihydrodiols are the active carcinogenic forms of the parent hydrocarbons.

Quenching of the intrinsic fluorescence of bovine serum albumin by chlorpromazine and hemin.

The binding of chlorpromazine (CPZ) and hemin to bovine serum albumin was studied by the fluorescence quenching technique. CPZ is a widely used anti-psychotic drug that interacts with blood components, influences bioavailability, and affects function of several biomolecules. Hemin is an important ferric residue of hemoglobin that binds within the hydrophobic region of albumin with high specificity. Quenching of the intrinsic fluorescence of bovine serum albumin (BSA) was observed by selectively exciting tryptophan residues at 290 nm. Emission spectra were recorded in the range from 300 to 450 nm for each quencher addition. Stern-Volmer graphs were plotted, and the quenching constant estimated for BSA solution titrated with hemin at 25 masculine C was 1.44 (+/- 0.05) x 10(5) M(-1). Results showed that bovine albumin tryptophans are not equally accessible to CPZ, in agreement with the idea that polar or charged quenchers have more affinity for amino acid residues on the outer wall of the protein. Hemin added to albumin solution at a molar ratio of 1:1 quenched about 25% of their fluorescence. The quenching effect of CPZ on albumin-hemin solution was stronger than on pure BSA. This increase can be the result of combined conformational changes in the structure of albumin caused firstly by hemin and then by CPZ. Our results suggest that the primary binding site for hemin on bovine albumin may be located asymmetrically between the two tryptophans along the sequence formed by subdomains IB and IIA, closer to tryptophan residue 212.

A simple model for circadian timing by mammals.

Circadian timing is structured in such a way as to receive information from the external and internal environments, and its function is the timing organization of the physiological and behavioral processes in a circadian pattern. In mammals, the circadian timing system consists of a group of structures, which includes the suprachiasmatic nucleus (SCN), the intergeniculate leaflet and the pineal gland. Neuron groups working as a biological pacemaker are found in the SCN, forming a biological master clock. We present here a simple model for the circadian timing system of mammals, which is able to reproduce two fundamental characteristics of biological rhythms: the endogenous generation of pulses and synchronization with the light-dark cycle. In this model, the biological pacemaker of the SCN was modeled as a set of 1000 homogeneously distributed coupled oscillators with long-range coupling forming a spherical lattice. The characteristics of the oscillator set were defined taking into account the Kuramoto's oscillator dynamics, but we used a new method for estimating the equilibrium order parameter. Simultaneous activities of the excitatory and inhibitory synapses on the elements of the circadian timing circuit at each instant were modeled by specific equations for synaptic events. All simulation programs were written in Fortran 77, compiled and run on PC DOS computers. Our model exhibited responses in agreement with physiological patterns. The values of output frequency of the oscillator system (maximal value of 3.9 Hz) were of the order of magnitude of the firing frequencies recorded in suprachiasmatic neurons of rodents in vivo and in vitro (from 1.8 to 5.4 Hz).

K-region oxidized metabolites of 9-hydroxybenzo[a]pyrene.

Synthesis is described of the methyl ether of 9-hydroxybenzo[a]pyrene 4,5-oxide, previously implicated as a metabolite of benzo[a]pyrene which binds covalently to nucleic acids in vivo.

New synthetic approaches to polycyclic aromatic hydrocarbons and their carcinogenic oxidized metabolites: derivatives of benzo[s]picene, benzo[rst]pentaphene, and dibenzo[b,def]chrysene.

A new synthetic approach to polycyclic aromatic compounds is described that entails in the key steps double Suzuki coupling of PAH bisboronic acid derivatives with o-bromoaryl aldehydes to furnish aryl dialdehydes that are converted to larger polycyclic aromatic ring systems by either (a) conversion to diolefins by Wittig reaction followed by photocyclization or (b) reductive cyclization with triflic acid and 1,3-propanediol. This synthetic method provides convenient access to as many as three different polycyclic aromatic ring systems from a single Suzuki coupled intermediate. It was utilized to synthesize substituted derivatives of benzo[s]picene, benzo[rst]pentaphene, dibenzo[b,def]chrysene, and 13,14-dihydro-benz[g]indeno[2,1-a]fluorene, as well as the putative carcinogenic bisdihydrodiol metabolites of benzo[s]picene, benzo[rst]pentaphene, and dibenzo[b,def]chrysene.

Computer programs to assist in high resolution thermal denaturation and circular dichroism studies on nucleic acids.

Computer programs are described that direct the collection, processing, and graphical display of numerical data obtained from high resolution thermal denaturation (1-3) and circular dichroism (4) studies. Besides these specific applications, the programs may also be useful, either directly or as programming models, in other types of spectrophotometric studies employing computers, programming languages, or instruments similar to those described here (see Materials and Methods).

Covalent DNA adducts formed in mouse epidermis from dibenz[a,j]anthracene: evidence for the formation of polar adducts.

The formation of deoxyribonucleoside adducts in mouse epidermis has been examined following topical application of [3H]dibenz[a,j]anthracene (DB[a,j]A) or by 32P-postlabeling following topical application of unlabeled DB[a,j]A, DB[a,j]A trans-3,4-diol or the anti- or syn-3,4-diol 1,2-epoxides. A single topical application of [3H]DB[a,j]A at a dose of 400 nmol per mouse led to the formation of 11 detectable covalent DNA adducts. Seven of these DNA adducts were tentatively identified based on cochromatography with marker adducts using high-pressure liquid chromatography (HPLC). The presence of both deoxyguanosine (dGuo) as well as deoxyadenosine (dAdo) adducts formed from bay-region anti- and syn-3,4-diol 1,2-epoxides of DB[a,j]A was revealed. The major bay-region diol epoxide DNA adduct formed in mouse epidermis following topical application of [3H]DB[a,j]A was tentatively identified as the (4R,3S)-diol (2S,1R)-epoxide bound through trans addition of the exocyclic amino group of dGuo, although substantial amounts of the corresponding dAdo adduct were also detected. In addition, a K-region 5,6-oxide-dAdo adduct was tentatively identified in HPLC chromatograms based on cochromatography with an authentic marker adduct. 32P-Postlabeling analysis of DB[a,j]A-DNA adducts formed in mouse epidermis after topical application of unlabeled compound confirmed the presence of bay-region diol epoxide DNA adducts similar to those observed after application of [3H]DB[a,j]A. However, 32P-postlabeling analysis also revealed the presence of more polar covalent DNA adducts in epidermal DNA samples from DB[a,j]A-treated mice. These more polar DNA adducts represented a significant proportion of the 32P-labeled material recovered in HPLC chromatograms. While the exact nature of these adducts remains unknown at present, they had retention times identical to polar DNA adducts formed following topical application of DB[a,j]A trans-3,4-diol and may represent bis-dihydrodiol epoxide DNA adducts. The present results indicate that a rather broad spectrum of DNA adducts arises following topical application of DB[a,j]A to mouse epidermis.