A New Ichnospecies of Arthrophycus from the Upper Cambrian-Lower Tremadocian of Northwest Argentina: Implications for the Arthrophycid Lineage and Potential in Ichnostratigraphy

A new ichnospecies of Arthrophycus Hall 1852, A. minimus , is described from Upper Cambrian-Lower Tremadocian, shallow-marine strata of northwest Argentina. This new ichnospecies consists of small, long, regularly annulated hypichnial elements displaying subcircular to squarish cross-section and a ventral median groove. Side branches are occasionally present, but palmate, fan-like structures and scribbling patterns are absent. We adopt a relatively narrow diagnosis of Arthrophycus , suggesting that roughly annulated, cylindrical structures should not be included in this ichnogenus, unless other diagnostic features (i.e., squarish cross-section, median groove, zipper-like annulations) are also present. Arthrophycus is a common ichnotaxon in Ordovician-Silurian shallow-marine siliciclastic environments. Post-Paleozoic occurrences are removed from Arthrophycus . Arthrophycus has been proposed as a biostratigraphic index fossil in Ordovician-Silurian rocks. The presence of A. minimus in the Santa Rosita Formation of northwest Argentina indicates that Arthrophycus ranges at least from the Upper Cambrian-Lower Tremadocian with probable representatives in the Lower Cambrian and, therefore, its biostratigraphic utility is extended. Arthrophycus minimus represents the first Cambrian occurrence exhibiting not only fine, diagnostic morphologic features, but also the classical Arthrophycus behavioral pattern in dense monoichnospecific assemblages. The exploratory behavioral pattern displayed by A. minimus is simpler than that of the younger ichnospecies, particularly A. brogniartii, A. alleghaniensis, and A. lateralis . This is consistent with the basal position of A. minimus within the arthrophycid lineage.     

Survival of Aeromonas hydrophila, Aeromonas caviae and Aeromonas sobria in soil

The survival of mesophilic Aeromonas spp. in soil in the presence or absence of indigenous microflora was evaluated in a laboratory study. Two cytotoxic ( Aer. hydrophila and Aer. caviae ) and one invasive ( Aer. sobria ) clinical isolate strains were selected for this study. After contamination of sterile or unsterilized soil with the three strains of Aeromonas , the number of living cells was determined over at least 5 months. For all strains the survival curves were characterized by an initial re-growth followed by a slow inactivation of bacteria, with significant differences due to the presence of indigenous microflora. The times necessary to achieve a 95% reduction of the initial population were > 140, 113 and 62 d in sterilized soil respectively for Aer. caviae, Aer. hydrophila and Aer. sobria , while the corresponding times in unsterilized soil were 42, 38 and 11 d. All strains preserved the virulence factors for the entire period of the study. These results suggest that the soil may be an important reservoir for Aeromonas spp. and, thus, may play an important role in the epidemiology of Aeromonas -associated human infections.     

exonsampler: a computer program for genome‐wide and candidate gene exon sampling for targeted next‐generation sequencing

The computer program exonsampler automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next‐generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User‐adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of exonsampler to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon‐capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16 000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection.     

Interleukin-2 induces the proliferation of mouse primordial germ cells in vitro

Primordial germ cells (PGCs) are the stem cell precursors of the germ line. Several growth factors contribute to enlarging the PGC population by acting as mitogens, survival factors or both. Interleukin-2 (IL-2) has a growth-promoting activity for T and B-lymphocytes, but its role in PGCs had not yet been studied. Here, we show that PGCs isolated from 10.5, 11.5 and 12.5 day postcoitum (dpc) mouse embryos constitutively express the three subunits (alpha, beta and gamma) of the IL-2 receptor (IL-2R). In contrast, IL-2 mRNA was not detected in these cells. However, the addition of recombinant IL-2 to the culture medium increased the number of PGCs in vitro via a mitogenic effect, as indicated by bromodeoxyuridine incorporation assays. Neutralization of the IL-2 receptor using anti-IL-2R subunit antibodies inhibited this IL-2-mediated proliferative effect on PGCs from 11.5 dpc embryos. Together, these data are indicative of a paracrine effect of IL-2 on PGC proliferation. In this regard, we also compared the effect of IL-2 with other compounds such as basic fibroblast growth factor (bFGF), steel factor, leukemia inhibitory factor and forskolin, and found that the degree of proliferation induced by IL-2 was similar to that induced by bFGF and forskolin. These observations support the notion that similar patterns of molecular signaling may underlie the developmental pathways of hematopoietic and germ stem cell precursors.     

A novel mode of bathing behavior of hummingbirds recorded in the Brazilian ruby Heliodoxa rubricauda and allies (Aves: Trochilidae)

acta ethologica - The Brazilian ruby, Heliodoxa rubricauda, is a forest species of hummingbird endemic to the Atlantic Forest. It belongs to an Andean clade of birds with robust and strong legs and...     

Analyzing the hydrodynamic and crowding evolution of aqueous hydroxyapatite‐gelatin networks: Digging deeper into bone scaffold design variables

The hydration of the polypeptide network is a determinant factor to be controlled on behalf of the design of precise functional tissue scaffolding. Here we present an exhaustive study of the hydrodynamic and crowding evolution of aqueous gelatin‐hydroxyapatite systems with the aim of increasing the knowledge about the biomimesis of collagen mineralization; and how it can be manipulated for the preparation of collagenous derived frameworks with specific morphological characteristics. The solution's density and viscosity evaluation measurements in combination with spectroscopic techniques revealed that there is a progressive association of protein chain that can be influenced by the amount of hydroxyapatite nanorods. Gelatin and additives’ concentration effect on the morphology of the gelatin scaffolds was investigated. Transverse and longitudinal sections of the obtained scaffolds were taken and analyzed using optical microscopy. It can be seen that the porous size and shape of gelatin assemblies can be easily adjusted by controlling the gelatin/HAp ratio in the solution used as template in agreement with our statement. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 393–405, 2015.     

Parvulin 17-catalyzed Tubulin Polymerization Is Regulated by Calmodulin in a Calcium-dependent Manner

Recently we have shown that the peptidyl-prolyl cis/trans isomerase parvulin 17 (Par17) interacts with tubulin in a GTP-dependent manner, thereby promoting the formation of microtubules. Microtubule assembly is regulated by Ca²⁺-loaded calmodulin (Ca²⁺/CaM) both in the intact cell and under in vitro conditions via direct interaction with microtubule-associated proteins. Here we provide the first evidence that Ca²⁺/CaM interacts also with Par17 in a physiologically relevant way, thus preventing Par17-promoted microtubule assembly. In contrast, parvulin 14 (Par14), which lacks only the first 25 N-terminal residues of the Par17 sequence, does not interact with Ca²⁺/CaM, indicating that this interaction is exclusive for Par17. Pulldown experiments and chemical shift perturbation analysis with ¹⁵N-labeled Par17 furthermore confirmed that calmodulin (CaM) interacts in a Ca²⁺-dependent manner with the Par17 N terminus. The reverse experiment with ¹⁵N-labeled Ca²⁺/CaM demonstrated that the N-terminal Par17 segment binds to both CaM lobes simultaneously, indicating that Ca²⁺/CaM undergoes a conformational change to form a binding channel between its two lobes, apparently similar to the structure of the CaM-smMLCK^796–815 complex. In vitro tubulin polymerization assays furthermore showed that Ca²⁺/CaM completely suppresses Par17-promoted microtubule assembly. The results imply that Ca²⁺/CaM binding to the N-terminal segment of Par17 causes steric hindrance of the Par17 active site, thus interfering with the Par17/tubulin interaction. This Ca²⁺/CaM-mediated control of Par17-assisted microtubule assembly may provide a mechanism that couples Ca²⁺ signaling with microtubule function.