Activation of a signaling pathway by the physical translocation of a chromosome

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The effects of the muscular contraction on the abdominal biomechanics: a numerical investigation

Abdominal wall biomechanics is strongly affected by muscular contraction and intra-abdominal pressure (IAP) which characterize different physiological functions and daily tasks. However, the active muscular behavior is generally not considered in current computational models of the abdominal wall. The aim of this study is to develop a numerical model mimicking muscular activation and IAP.

A three dimensional Finite Element model of a healthy abdominal wall is developed detailing the principal abdomen components reconstructed upon anatomical data and medical images. Fascial tissues, aponeuroses and linea alba are modelled as hyperelastic fiber-reinforced materials, while a three-element Hill’s model is assumed for muscles. Numerical analyses are performed increasing the IAP up to 100?mmHg and simultaneously activating the muscular structures.

The obtained abdominal behavior is compared to a similar model with same IAPs, but passive muscles conditions. Abdomen stiffness and strength are computed in regions in which hernias can potentially occur. A global stiffening of the abdominal wall is found corresponding to a low abdomen deformation and the membrane force on fascial structures is reduced by muscular contraction.

Representing active muscular contraction leads to advanced findings, otherwise membrane force results overestimated considering a purely passive behavior for the abdominal wall.     

Building a secreting nanomachine: a structural overview of the T3SS

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Chitin contributes to the formation of a feeding structure in a predatory nematode

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Diet leaves a genetic signature in a keystone member of the gut microbiota

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Validation of a protein panel for the noninvasive detection of recurrent non-muscle invasive bladder cancer

Context: About 50–70% of patients with non-muscle invasive bladder cancer (NMIBC) experience relapse of disease.

Objective: To establish a panel of protein biomarkers incorporated in a multiplexed microarray (BCa chip) and a classifier for diagnosing recurrent NMIBC.

Materials and methods: Urine samples from 45 patients were tested. Diagnostic performance was evaluated by receiver operating characteristic (ROC) analysis.

Results: A multi biomarker panel (ECadh, IL8, MMP9, EN2, VEGF, past recurrences, BCG therapies and stage at diagnosis) was identified yielding an area under the curve of 0.96.

Discussion and conclusion: This biomarker panel represents a potential diagnostic tool for noninvasive diagnosis of recurrent NMIBC.     

Deciphering the MHC-associated peptidome: a review of naturally processed ligand data

Introduction: The availability of big data sets (‘OMICS’) has greatly impacted fundamental and translational science. High-throughput analysis of HLA class I and II associated peptidomes by mass spectrometry (MS) has generated large datasets, with the last decade witnessing tremendous growth in the breadth and number of studies.

Areas covered: For this, we first analyzed naturally processed peptide (NP) data captured within the IEDB to survey and characterize the current state of NP data. We next asked to what extent the NP data overlap with existing T cell epitope and MHC binding data.

Expert commentary: The current collection of NP data represents a large and diverse set of class I/II peptides mostly derived from self-antigens. These data overlap only marginally with existing immunogenicity and binding data and it is thus difficult to ascertain the correspondence between the different assay methodologies. This highlights a need for unbiased studies benchmarking in model antigen systems how well MHC binding and NP data predicts immunogenicity. Going forward, efforts at generating an integrated process for capturing all NP, curating associated metadata and accessing NP data from an immunological viewpoint will be important for development of novel methods for identifying optimal target antigens and for class I and II epitope prediction.     

Apparent survival rates of a long-lived partial migrant: the Yellow-legged Gull Larus michahellis

Capsule: In Yellow-legged Gull Larus michahellis populations from the eastern Adriatic Sea, there are considerable differences in the ratio of migratory birds and apparent survival among the colonies. Survival was dependent on age, colony and area of dispersal.

Aims: To identify the ratio of migratory birds within populations of Yellow-legged Gulls, and to compare apparent survival of gulls during migration in central and northern Europe and around the Adriatic Sea.

Methods: We analysed 15 years of resighting data of Yellow-legged Gulls using a MARK multi-state model to calculate survival rates. The effects of age, natal colony and area of dispersal were examined.

Results: Almost 60% of Adriatic Yellow-legged Gulls were migratory but the ratio varied among colonies (10.3–78.3%). Survival was dependent on age, colony and area of dispersal, with average values per group ranging between 0.599 (se 0.093) and 0.684 (se 0.084).

Conclusion: The ratio of migratory and dispersive Yellow-legged Gulls from different Adriatic colonies might be affected by both inheritance and food availability.     

Habitat structure influences the song characteristics within a population of Great Tits Parus major

Capsule: The structure of Great Tit Parus major songs is shaped by the acoustic properties of the habitat within the breeding territory of individuals.

Aim: To test whether the structure of the habitat influences song structure within a population of Great Tits P. major.

Methods: We recorded Great Tit songs from 42 territories on two different days and measured the habitat structure in each territory. We also trapped the males and estimated the breeding density around each territory, so were able to control the analysis by date, breeding density and male characteristics.

Results: Song pause length was positively affected by the ground cover, while the song rate and the minimum frequency were negatively affected by the shrub cover. Male size negatively affected the peak frequency of the songs, whereas the age of the males affected the frequency range; older males sang with a broader bandwidth.

Conclusion: This study suggests that Great Tits are capable of adjusting their vocalizations in each territory, presumably to enhance transmission owing to vocal plasticity.     

Nocturnal bird migration in the Bay of Biscay as observed by a thermal-imaging camera

Capsule: Bird migration was recorded by an infrared device at three sites in the southeastern Bay of Biscay, indicating seasonal east–west differences in migration flow.

Aims: The main aims of this study were to quantify and describe nocturnal migration dynamics in proximity of a sea barrier, and to assess seasonal and geographical drivers of migration patterns.

Methods: A thermal-imaging camera was used at two coastal study sites (Punta Galea, Cape Higuer) in spring and three study sites (coast: Punta Galea, Cape Higuer; inland: Iregua Valley) in autumn for four hours from sunset over 90 nights in 2014 and 2015.

Results: Migration was strong at both coastal sites in early spring. Autumn migration was weak at the western coast, but strong at the eastern coast and inland. Tailwind had no significant effect on migration intensity, but migration ceased during strong cross- or headwinds despite clear skies. The majority of the targets were passerines.

Conclusions: The patterns observed suggest spring migration occurs on a broader front, potentially involving sea crossing further to the west, while autumn migration concentrates more eastwards over land. In both seasons, there was no significant response to wind conditions.     

Comparative analysis of the lipopolysaccharides of a rough and a smooth strain of Pseudomonas syringae pv. phaseolicola

The lipopolysaccharides (LPS) of a rough (R) and a smooth (S) strain of Pseudomonas syringae pv. phaseolicola were analysed. The S-LPS revealed markedly more rhamnose and fucose, but less glucose, than the R-LPS. The presence of 3-O-methyl-rhamnose (acofriose) in the S-LPS was confirmed by cochromatography with authentic acofriose. SDS polyacrylamide gel electrophoresis of the S-LPS demonstrated a cluster of regularly spaced high molecular weight fractions, which was almost lacking in the R-LPS. The main fatty acids of the lipid A of both LPS species were 3-OH-10:0,3-OH-12:0,2-OH-12:0, and 12:0. Two N-linked diesters were demonstrated: 3-O(12:0)-12:0 and 3-O(2-OH-12:0)-12:0. S-LPS was subjected to mild hydrolysis and the degraded polysaccharide separated into three fractions by gel permeation chromatography on a Fractogel TSK HW-50 column. Fraction I, representing nearly only the O-specific side chain, consisted of rhamnose and fucose in a molar ratio of 4:1, with 4% of the rhamnose being 3-O-methylated (acofriose). Fraction II, representing mostly core material, was composed of glucose, rhamnose, heptose, glucosamine, galactosamine, alanine, and a still unidentified amino compound, in an approximate molar ratio of 3:1:1:1:1:1:1, and KDO. Fraction III consisted of released monomers and salts. The LPS was highly phosphorylated (3.28% phosphorus in the core fraction). The thus characterized composition of the LPS O-chain seems to be unique for the pathovar phaseolicola of P. syringae, although many similarities exist to other pathovars as well as to other bacterial species.Abbreviations LPS lipopolysacchairdes - GC/MS combined gas liquid chromatography-mass spectrometry - HVE high voltage electrophoresis - KDO 2-keto-3-deoxyoctonic acid - PAGE polyacrylamide gel electrophoresis - SDS sodium dodecylsulfate P.s. pv. phaseolicola is termed P. phaseolicola in the text     

srb: a Bacillus subtilis Gene Encoding a Homologue of the {alpha}-Subunit of the Mammalian Signal Recognition Particle Receptor

We cloned a Bacillus subtilis gene (srb) encoding a homologueof the mammalian signal recognition particle receptor -subunit(SR). The gene is 987 bp in length and encodes a 329-amino acidprotein. The deduced amino acid sequence of the protein shared26.6, 36.2 and 49.7% identity with those of mammalian SR, archaebacterialDP and Escherichia coli FtsY, respectively. The protein containsthree conserved GTP-binding elements like the other three SRPreceptor proteins, though the N-terminal portion of the putativeB. subtilis protein was shorter than the others. Secondary structureprediction showed that an amphipathic -helix is positioned inthe N-terminal region. A defect in srb inhibited cell growthand protein translocation.     

Induction of Sexual Agglutinability by the Absorbed a Peptidyl Factor in a Mating Type Cells of Saccharomyces cerevisiae

The sexual agglutinability of inducible cells was induced byabsorbed pheromone in the absence of external a pheromone.The absorption needed no metabolic activity, but the inductiondid. This induction of sexual agglutinability by absorbed pheromonewas not accompanied or preceded by G1 arrest. The role of thebinding substance for pheromone in this induction is discussed. (Received November 13, 1980; Accepted December 19, 1980)     

Procellariiform remains and a new species from the latest Eocene of Antarctica

New remains from the La Meseta (Thanetian – Lutetian) and Submeseta (Lutetian – Rupelian) formations (Seymour Island, Antarctica) are tentatively assigned to Diomedeidae and Procellariidae (Procellariiformes). Based on the fossil record and several analyses that attempt to explain the evolutionary patterns of Diomedeidae, Notoleptos giglii gen. et sp. nov., based on a small tarsometatarsus, was an ancestral form that lived in Antarctica before the rise of large-sized albatrosses. Subsequent environmental cooling since the late Oligocene could have selected against small body size, to the detriment of small-sized albatrosses like Notoleptos, thus favoring large body size and setting the stage for the development of the specialized albatross flight.

ZooBank ID (LSID): urn:lsid:zoobank.org:pub:C8D9C862-1536-4EA3-8A76-70903AA75639     

Nitrate or ammonium: Influences of nitrogen source on the physiology of a green alga

In freshwaters, algal species are exposed to different inorganic nitrogen (N_i) sources whose incorporation varies in biochemical energy demand. We hypothesized that due to the lesser energy requirement of ammonium ()‐use, in contrast to nitrate ()‐use, more energy remains for other metabolic processes, especially under CO₂‐ and phosphorus (P_i) limiting conditions. Therefore, we tested differences in cell characteristics of the green alga Chlamydomonas acidophila grown on or under covariation of CO₂ and P_i‐supply in order to determine limitations, in a full‐factorial design. As expected, results revealed higher carbon fixation rates for ‐grown cells compared to growth with under low CO₂ conditions. ‐grown cells accumulated more of the nine analyzed amino acids, especially under P_i‐limited conditions, compared to cells provided with . This is probably due to a slower protein synthesis in cells provided with . In contrast to our expectations, compared to ‐grown cells ‐grown cells had higher photosynthetic efficiency under P_i‐limitation. In conclusion, growth on the N_i‐source did not result in a clearly enhanced C_i‐assimilation, as it was highly dependent on P_i and CO₂ conditions (replete or limited). Results are potentially connected to the fact that C. acidophila is able to use only CO₂ as its inorganic carbon (C_i) source.     

Fish-otoliths from the early Miocene of the Castillo Formation,Venezuela: a view into the proto-Caribbean teleostean assemblages

We describe the otolith assemblage from the early Miocene (Burdigalian) exposures of the Castillo Formation at the Cerro La Cruz locality (Falcón Basin, Lara State, northwestern Venezuela). The samples were obtained through surface and bulk sampling at distinct stratigraphic levels of the study area. The otolith assemblage from Cerro La Cruz includes 14 families, 25 genera and 30 taxa, of which 20 are reported for first time from the Castillo Formation. These include two new sciaenid taxa, Ctenosciaena angusticaudata nov. sp. and Pareques laraensis nov. sp. The Castillo Formation otolith assemblage represent fishes typical of shallow and near-shore and coral reef associated environments as characterized primarily by a high taxonomic diversity and abundance of Sciaenidae, and the lack of mesopelagic families (Myctophidae). The faunal composition of Cerro La Cruz is similar to other chronological equivalent sedimentary units along the proto-Caribbean area (Pirabas and Cantaure formations; Brazil and Venezuela respectively), though the Castillo Formation fish fauna shows lower taxonomic diversity, suggesting some heterogeneity of the coastal and near shore marine environments along the southern portion of the proto-Caribbean.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:B79F51B8-BC35-4119-8957-84544286868D