Advancing our understanding of the connectivity, evolution and management of marine lobsters through genetics

The genomic revolution has provided powerful insights into the biology and ecology of many non-model organisms. Genetic tools have been increasingly applied to marine lobster research in recent years and have improved our understanding of species delimitation and population connectivity. High resolution genomic markers are just beginning to be applied to lobsters and are now starting to revolutionise our understanding of fine spatial and temporal scales of population connectivity and adaptation to environmental conditions. Lobsters play an important role in the ecosystem and many species are commercially exploited but many aspects of their biology is still largely unknown. Genetics is a powerful tool that can further contribute to our understanding of their ecology and evolution and assist management. Here we illustrate how recent genetic advancements are (1) leading to a step change in our understanding of evolution and adaptation, (2) elucidating factors driving connectivity and recruitment, (3) revealing insights into ecological processes and can (4) potentially revolutionise management of this commercially important group. We discuss how improvements in sequencing technologies and statistical methods for genetic data analyses combined with increased sampling efforts and careful sampling design have transformed our understanding of lobsters biology in recent years. We also highlight possible future directions in the application of genomic tools to lobster research that can aid management, in particular, the close-kin-mark-recapture method. Finally, we identify gaps and challenges in lobster research, such as the lack of any reference genomes and predictions on how lobsters will respond to future environmental conditions

The Type II supernovae 2006V and 2006au: two SN 1987A-like events

Supernova 1987A revealed that a blue supergiant (BSG) star can end its life as a core-collapse supernova (SN). SN 1987A and other similar objects exhibit properties that distinguish them from ordinary Type II Plateau (IIP) SNe, whose progenitors are believed to be red supergiants (RSGs). Similarities among 1987A-like events include a long rise to maximum, early luminosity fainter than that of normal Type IIP SNe, and radioactivity acting as the primary source powering the light curves. We present and analyze two SNe monitored by the Carnegie Supernova Project that are reminiscent of SN 1987A. Optical and near-infrared (NIR) light curves, and optical spectroscopy of SNe 2006V and 2006au are presented. These observations are compared to those of SN 1987A, and are used to estimate properties of their progenitors. Both objects exhibit a slow rise to maximum and light curve evolution similar to that of SN 1987A. At the earliest epochs, SN 2006au also displays an initial dip which we interpret as the signature of the adiabatic cooling phase that ensues shock break- out. SNe 2006V and 2006au are both found to be bluer, hotter and brighter than SN 1987A. Spectra of SNe 2006V and 2006au are similar to those of SN 1987A and other normal Type II objects, although both consistently exhibit expansion velocities higher than SN 1987A. Semi-analytic models are fit to the UVOIR light curve of each object from which physical properties of the progenitors are estimated. This yields ejecta mass estimates of about 20 solar masses, explosion energies of 2 - 3 x 10^51 erg, and progenitor radii of 75 - 100 solar radii for both SNe. The progenitors of SNe 2006V and 2006au were most likely BSGs with a larger explosion energy as compared to that of SN 1987A.Comment: 21 pages,15 figures, accepted for publication in A&A, 25 October 201

Development of a gas chromatography - mass spectrometry method for the determination of carbon disulfide in the atmosphere

[EN] Carbon disulfide (CS2), a relevant reduced sulfur compound in air, is well-known for its malodor and its significant effect on global atmospheric chemistry. Therefore, a reliable method for determining CS2 in atmospheric samples has been developed based on solid-phase sampling and gas chromatography-mass spectrometry (GC-MS). Two types of solid-phase sampling supports (Orbo-32 and SKC) and the elution with organic solvents - hexane and toluene - were evaluated for low-volume outdoor sampling. Recovery studies and the standard addition method were carried out to demonstrate the proper determination of CS2 in the absence of the influence of interferences such as ozone, hydrogen sulfide or water - important atmospheric pollutants. The proposed methodology was validated by performing experiments in a high-volume smog chamber and by comparison with two reference optical methods, Fourier Transform Infrared (FTIR) and Differential Optical Absorption Spectroscopy (DOAS) installed in these facilities. Satisfactory analytical parameters were reported: fast analysis, a correct repeatability of 6±1% and reproducibility of 14±3%, and low detection limits of 0.3-0.9pgm-3. Finally, the method was successfully applied to industrial samples near a pulp factory area, where a high correlation between industrial emissions and reported carbon disulfide concentrations were observed. © 2011 Elsevier B.V.The research leading to these results received funding from the Centro de Investigacion del Medio Ambiente (CIMA), Consejeria de Medio Ambiente, Gobierno de Cantabria. The Instituto Universitario CEAM-UMH is partly supported by Generalitat Valenciana, Fundacion Bancaja, and the projects GRACCIE (Consolider-Ingenio 2010) and FEEDBACKS (Prometeo - Generalitat Valenciana). We also acknowledged the European Community's Seventh Framework Program under the grant agreement no. 228335 (Eurochamp2), the Spanish Ministry of Science and Innovation, through INNPLANTA project: PCT-440000-2010-003 and the EUPHORE staff for their support in the chamber experiments. The authors also thank J.T.B. for his contribution.Borrás García, EM.; Ródenas, M.; Dieguez, J.; Pérez-García, M.; Lomba, R.; Lavin, J.; Tortajada-Genaro, LA. (2012). Development of a gas chromatography - mass spectrometry method for the determination of carbon disulfide in the atmosphere. Microchemical Journal. 101:37-42. https://doi.org/10.1016/j.microc.2011.10.002S374210

SN 1999ga: a low-luminosity linear type II supernova?

Type II-linear supernovae are thought to arise from progenitors that have lost most of their H envelope by the time of the explosion, and they are poorly understood because they are only occasionally discovered. It is possible that they are intrinsically rare, but selection effects due to their rapid luminosity evolution may also play an important role in limiting the number of detections. In this context, the discovery of a subluminous type II-linear event is even more interesting. We investigate the physical properties and characterise the explosion site of the type II SN 1999ga, which exploded in the nearby spiral galaxy NGC 2442. Spectroscopic and photometric observations of SN 1999ga allow us to constrain the energetics of the explosion and to estimate the mass of the ejected material, shedding light on the nature of the progenitor star in the final stages of its life. The study of the environment in the vicinity of the explosion site provides information on a possible relation between these unusual supernovae and the properties of the galaxies hosting them. Despite the lack of early-time observations, we provide reasonable evidence that SN 1999ga was probably a type II-linear supernova that ejected a few solar masses of material, with a very small amount of radioactive elements of the order of 0.01 solar masses.Comment: 11 pages, 9 figures. Accepted for publication in A&A (March 28, 2009

SN 2009E: a faint clone of SN 1987A

In this paper we investigate the properties of SN 2009E, which exploded in a relatively nearby spiral galaxy (NGC 4141) and that is probably the faintest 1987A-like supernova discovered so far. Spectroscopic observations which started about 2 months after the supernova explosion, highlight significant differences between SN 2009E and the prototypical SN 1987A. Modelling the data of SN 2009E allows us to constrain the explosion parameters and the properties of the progenitor star, and compare the inferred estimates with those available for the similar SNe 1987A and 1998A. The light curve of SN 2009E is less luminous than that of SN 1987A and the other members of this class, and the maximum light curve peak is reached at a slightly later epoch than in SN 1987A. Late-time photometric observations suggest that SN 2009E ejected about 0.04 solar masses of 56Ni, which is the smallest 56Ni mass in our sample of 1987A-like events. Modelling the observations with a radiation hydrodynamics code, we infer for SN 2009E a kinetic plus thermal energy of about 0.6 foe, an initial radius of ~7 x 10^12 cm and an ejected mass of ~19 solar masses. The photospheric spectra show a number of narrow (v~1800 km/s) metal lines, with unusually strong Ba II lines. The nebular spectrum displays narrow emission lines of H, Na I, [Ca II] and [O I], with the [O I] feature being relatively strong compared to the [Ca II] doublet. The overall spectroscopic evolution is reminiscent of that of the faint 56Ni-poor type II-plateau supernovae. This suggests that SN 2009E belongs to the low-luminosity, low 56Ni mass, low-energy tail in the distribution of the 1987A-like objects in the same manner as SN 1997D and similar events represent the faint tail in the distribution of physical properties for normal type II-plateau supernovae.Comment: 19 pages, 9 figures (+7 in appendix); accepted for publication in A&A on 3 November 201

Downregulation of metastasis suppressor 1(MTSS1) is associated with nodal metastasis and poor outcome in Chinese patients with gastric cancer

<p>Abstract</p> <p>Background</p> <p>The putative tumor metastasis suppressor 1(MTSS1) is an actin-binding scaffold protein that has been implicated to play an important role in carcinogenesis and cancer metastasis, yet its role in the development of gastric cancer has not been well illustrated. In this study, we detected MTSS1 expression and explored its clinical significance in gastric cancer.</p> <p>Methods</p> <p>Immunohistochemistry was performed using tissue microarrays containing gastric adenocarcinoma specimens from 1,072 Chinese patients with normal adjacent mucosa, primary gastric cancer and lymph node (LN) metastasis and specific antibody against MTSS1. MTSS1 mRNA and protein expression were detected by reverse transcription-polymerase chain reaction and Western blotting. The clinical follow-up was done in the 669 patients living in Shanghai that was chose from the 1072 cases.</p> <p>Results</p> <p>Complete loss of MTSS1 expression was observed in 751 cases (70.1%) of the 1,072 primary tumors and 103 (88%) of 117 nodal metastases; and loss of MTSS1 expression was significantly associated with poorly differentiated tumors, large tumor size, deep invasion level, the presence of nodal metastases and advanced disease stage. Moreover, multivariate analysis demonstrated that loss of MTSS1 expression correlated significantly with poor survival rates (RR = 0.194, 95% CI = 0.144-0.261, P < 0.001).</p> <p>Conclusions</p> <p>MTSS1 expression decreased significantly as gastric cancer progressed and metastasized, suggesting MTSS1 may serve as a useful biomarker for the prediction of outcome of gastric cancer.</p

An interlaboratory comparison of mid-infrared spectra acquisition: Instruments and procedures matter

Diffuse reflectance spectroscopy has been extensively employed to deliver timely and cost-effective predictions of a number of soil properties. However, although several soil spectral laboratories have been established worldwide, the distinct characteristics of instruments and operations still hamper further integration and interoperability across mid-infrared (MIR) soil spectral libraries. In this study, we conducted a large-scale ring trial experiment to understand the lab-to-lab variability of multiple MIR instruments. By developing a systematic evaluation of different mathematical treatments with modeling algorithms, including regular preprocessing and spectral standardization, we quantified and evaluated instruments' dissimilarity and how this impacts internal and shared model performance. We found that all instruments delivered good predictions when calibrated internally using the same instruments' characteristics and standard operating procedures by solely relying on regular spectral preprocessing that accounts for light scattering and multiplicative/additive effects, e.g., using standard normal variate (SNV). When performing model transfer from a large public library (the USDA NSSC-KSSL MIR library) to secondary instruments, good performance was also achieved by regular preprocessing (e.g., SNV) if both instruments shared the same manufacturer. However, significant differences between the KSSL MIR library and contrasting ring trial instruments responses were evident and confirmed by a semi-unsupervised spectral clustering. For heavily contrasting setups, spectral standardization was necessary before transferring prediction models. Non-linear model types like Cubist and memory-based learning delivered more precise estimates because they seemed to be less sensitive to spectral variations than global partial least square regression. In summary, the results from this study can assist new laboratories in building spectroscopy capacity utilizing existing MIR spectral libraries and support the recent global efforts to make soil spectroscopy universally accessible with centralized or shared operating procedures

Murine Missing in Metastasis (MIM) Mediates Cell Polarity and Regulates the Motility Response to Growth Factors

Missing in metastasis (MIM) is a member of the inverse BAR-domain protein family, and in vitro studies have implied MIM plays a role in deforming membrane curvature into filopodia-like protrusions and cell dynamics. Yet, the physiological role of the endogenous MIM in mammalian cells remains undefined.We have examined mouse embryonic fibroblasts (MEFs) derived from mice in which the MIM locus was targeted by a gene trapping vector. MIM(-/-) MEFs showed a less polarized architecture characterized by smooth edges and fewer cell protrusions as compared to wild type cells, although the formation of filopodia-like microprotrusions appeared to be normal. Immunofluorescent staining further revealed that MIM(-/-) cells were partially impaired in the assembly of stress fibers and focal adhesions but were enriched with transverse actin filaments at the periphery. Poor assembly of stress fibers was apparently correlated with attenuation of the activity of Rho GTPases and partially relieved upon overexpressing of Myc-RhoA(Q63L), a constitutively activated RhoA mutant. MIM(-/-) cells were also spread less effectively than wild type cells during attachment to dishes and substratum. Upon treatment with PDGF MIM(-/-) cells developed more prominent dorsal ruffles along with increased Rac1 activity. Compared to wild type cells, MIM(-/-) cells had a slower motility in the presence of a low percentage of serum-containing medium but migrated normally upon adding growth factors such as 10% serum, PDGF or EGF. MIM(-/-) cells were also partially impaired in the internalization of transferrin, fluorescent dyes, foreign DNAs and PDGF receptor alpha. On the other hand, the level of tyrosine phosphorylation of PDGF receptors was more elevated in MIM depleted cells than wild type cells upon PDGF treatment.Our data suggests that endogenous MIM protein regulates globally the cell architecture and endocytosis that ultimately influence a variety of cellular behaviors, including cell polarity, motility, receptor signaling and membrane ruffling

SN 1998A: Explosion of a Blue Supergiant

We present spectroscopic and photometric observations of the peculiar Type II supernova (SN) 1998A. The light curves and spectra closely resemble those of SN 1987A, suggesting that the SN 1998A progenitor exploded when it was a compact blue supergiant. However, the comparison with SN 1987A also highlights some important differences: SN 1998A is more luminous and the spectra show bluer continua and larger expansion velocities at all epochs. These observational properties indicate that the explosion of SN 1998A is more energetic than SN 1987A and more typical of SNe II. Comparing the observational data to simulations, we deduce that the progenitor of SN 1998A was a massive star (~ 25 Mo) with a small pre-supernova radius (< 6 x 10^{12} cm). The Ba II lines, unusually strong in SN 1987A and some faint II--P events, are almost normal in the case of SN 1998A, indicating that the temperature plays a key role in determining their strength.Comment: 15 pages, 16 figures, accepted for publication in MNRA