Seasonal variation of phytoplankton in My Thanh River, Mekong delta, Vietnam

A study on the seasonal variation of phytoplankton composition was conducted at the upper, middle, and lower parts of the My Thanh River, which supplies an important source of water for aquaculture. Qualitative and quantitative samples of phytoplankton were collected monthly at both high and low tide. The results showed that a total of 171 phytoplankton (algae) species were recorded, belonging to 59 genera and 5 phyla. Diatoms were the most abundant group with the highest species number, followed by green algae. The other phyla possessed a lower number of species. The species composition was more diverse in the rainy season and at high tide at most of the sampling sites. The mean density of algae varied from 30,900-43,521 ind.L^-1^. The density of diatoms was higher in the middle and lower parts. At the same time, euglenoids displayed the highest density in the upper part, showing a difference in the dominant algae group under the influence of salinity. Salinity was found to be significantly positively correlated (p<0.01) with diatoms, whereas it was negatively correlated (p<0.05) with blue-green algae and euglenoids. The algae composition was quite diverse, with the H' index ranging from 2.0-3.3, showing the water quality was slightly to moderately polluted

Variant mapping using mass spectrometry–based proteotyping as a diagnostic tool in von Willebrand disease

Background: von Willebrand disease (VWD) is the most common inherited bleeding disorder, characterized by either partial or complete von Willebrand factor (VWF) deficiency or by the occurrence of VWF proteoforms of altered functionality. The gene encoding VWF is highly polymorphic, giving rise to a variety of proteoforms with varying plasma concentrations and clinical significance. Objectives: To address this complexity, we translated genomic variation in VWF to corresponding VWF proteoforms circulating in blood. Methods: VWF was characterized in VWD patients (n = 64) participating in the Willebrand in the Netherlands study by conventional laboratory testing, DNA sequencing and complementary discovery, and targeted mass spectrometry–based plasma proteomic strategies. Results: Unbiased plasma profiling combined with immune enrichment of VWF verified VWF and its binding partner factor VIII as key determinants of VWD and revealed a remarkable heterogeneity in VWF amino acid sequence coverage among patients. Subsequent VWF proteotyping enabled identification of both polymorphisms (eg, p.Thr789Ala, p.Gln852Arg, and p.Thr1381Ala), as well as pathogenic variants (n = 16) along with their corresponding canonical sequences. Targeted proteomics using stable isotope–labeled peptides confirmed unbiased proteotyping for 5 selected variants and suggested differential proteoform quantities in plasma. The variant-to-wild-type peptide ratio was determined in 6 type 2B patients heterozygous for p.Arg1306Trp, confirming the relatively low proteoform concentration of the pathogenic variant. The elevated VWF propeptide/VWF ratio indicated increased clearance of specific VWF proteoforms. Conclusion: This study highlights how VWF proteotyping from plasma could be the first step to bridge the gap between genotyping and functional testing in VWD.</p

Studying the Physical Diversity of Late-M Dwarfs with Dynamical Masses

We present a systematic study of the physical properties of late-M dwarfs based on high-quality dynamical mass measurements and near-infrared (NIR) spectra. We use astrometry from Keck NGS and LGS AO imaging to determine orbits for late-M binaries. We find that LP 349-25 (M7.5+M8) is a pair of young brown dwarfs (Mtot = 0.120 Msun) for which Lyon and Tucson evolutionary models jointly predict an age of 140+/-30 Myr. This is consistent with the age of the Pleiades, but at least LP 349-25A defies the empirical Pleiades lithium depletion boundary, implying that the system is in fact older and that evolutionary models underpredict the component luminosities. We find that LHS 1901AB (M6.5+M6.5) is a pair of very low-mass stars (Mtot = 0.194 Msun) with model-derived ages consistent with limits from its lack of activity (> 6 Gyr). Our improved orbit for Gl 569Bab (M8.5+M9) results in a higher mass for this binary (Mtot = 0.140 Msun) compared to previous work (0.125 Msun). We use these masses along with our published results for 2MASS J2206-2047AB (M8+M8) to test four sets of ultracool model atmospheres currently in use. Fitting these models to our NIR integrated-light spectra provides temperature estimates warmer by ~250 K than those derived independently from Dusty evolutionary models given the measured masses and luminosities. We propose that model atmospheres are more likely to be the source of this discrepancy, as it would be difficult to explain a uniform temperature offset over such a wide range of masses, ages, and activity levels in the context of evolutionary models. Our results contrast those of Konopacky et al. as we find an opposite and smaller mass discrepancy from what they report when we adopt their model-testing approach since our Teff estimates from fitting spectra are ~650 K higher than from their fitting of broadband photometry alone.Comment: 53 pages, 12 figures, accepted to Ap

An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

An overview of the mid-infrared spectro-interferometer MATISSE: science, concept, and current status

MATISSE is the second-generation mid-infrared spectrograph and imager for the Very Large Telescope Interferometer (VLTI) at Paranal. This new interferometric instrument will allow significant advances by opening new avenues in various fundamental research fields: studying the planet-forming region of disks around young stellar objects, understanding the surface structures and mass loss phenomena affecting evolved stars, and probing the environments of black holes in active galactic nuclei. As a first breakthrough, MATISSE will enlarge the spectral domain of current optical interferometers by offering the L and M bands in addition to the N band. This will open a wide wavelength domain, ranging from 2.8 to 13 um, exploring angular scales as small as 3 mas (L band) / 10 mas (N band). As a second breakthrough, MATISSE will allow mid-infrared imaging - closure-phase aperture-synthesis imaging - with up to four Unit Telescopes (UT) or Auxiliary Telescopes (AT) of the VLTI. Moreover, MATISSE will offer a spectral resolution range from R ~ 30 to R ~ 5000. Here, we present one of the main science objectives, the study of protoplanetary disks, that has driven the instrument design and motivated several VLTI upgrades (GRA4MAT and NAOMI). We introduce the physical concept of MATISSE including a description of the signal on the detectors and an evaluation of the expected performances. We also discuss the current status of the MATISSE instrument, which is entering its testing phase, and the foreseen schedule for the next two years that will lead to the first light at Paranal.Comment: SPIE Astronomical Telescopes and Instrumentation conference, June 2016, 11 pages, 6 Figure

Genetic diversity and population structure of Ascochyta rabiei from the western Iranian Ilam and Kermanshah provinces using MAT and SSR markers

Knowledge of genetic diversity in A. rabiei provides different levels of information that are important in the management of crop germplasm resources. Gene flow on a regional level indicates a significant potential risk for the regional spread of novel alleles that might contribute to fungicide resistance or the breakdown of resistance genes. Simple sequence repeat (SSR) and mating type (MAT) markers were used to determine the genetic structure, and estimate genetic diversity and the prevalence of mating types in 103 Ascochyta rabiei isolates from seven counties in the Ilam and Kermanshah provinces of western Iran (Ilam, Aseman abad, Holaylan, Chardavol, Dareh shahr, Gilangharb, and Sarpul). A set of 3 microsatellite primer pairs revealed a total of 75 alleles; the number of alleles varied from 15 to 34 for each marker. A high level of genetic variability was observed among A. rabiei isolates in the region. Genetic diversity was high (He = 0.788) within populations with corresponding high average gene flow and low genetic distances between populations. The smallest genetic distance was observed between isolates from Ilam and Chardavol. Both mating types were present in all populations, with the majority of the isolates belonging to Mat1-1 (64%), but within populations the proportions of each mating type were not significantly different from 50%. Results from this study will be useful in breeding for Ascochyta blight-resistant cultivars and developing necessary control measures

First results from fringe tracking with the PRIMA fringe sensor unit

The fringe sensor unit (FSU) is the central element of the phase referenced imaging and micro-arcsecond astrometry (PRIMA) dual-feed facility for the Very Large Telescope interferometer (VLTI). It has been installed at the Paranal observatory in August 2008 and is undergoing commissioning and preparation for science operation. Commissioning observations began shortly after installation and first results include the demonstration of spatially encoded fringe sensing and the increase in VLTI limiting magnitude for fringe tracking. However, difficulties have been encountered because the FSU does not incorporate real-time photometric correction and its fringe encoding depends on polarisation. These factors affect the control signals, especially their linearity, and can disturb the tracking control loop. To account for this, additional calibration and characterisation efforts are required. We outline the instrument concept and give an overview of the commissioning results obtained so far. We describe the effects of photometric variations and beam-train polarisation on the instrument operation and propose possible solutions. Finally, we update on the current status in view of the start of astrometric science operation with PRIMA.Comment: 12 pages, 11 figures, SPIE 2010 conference proceeding

The UKIDSS-2MASS Proper Motion Survey I: Ultracool dwarfs from UKIDSS DR4

The UKIRT Infrared Deep Sky Survey (UKIDSS) is the first of a new generation of infrared surveys. Here we combine the data from two UKIDSS components, the Large Area Survey (LAS) and the Galactic Cluster Survey (GCS), with 2MASS data to produce an infrared proper motion survey for low mass stars and brown dwarfs. In total we detect 267 low mass stars and brown dwarfs with significant proper motions. We recover all ten known single L dwarfs and the one known T dwarf above the 2MASS detection limit in our LAS survey area and identify eight additional new candidate L dwarfs. We also find one new candidate L dwarf in our GCS sample. Our sample also contains objects from eleven potential common proper motion binaries. Finally we test our proper motions and find that while the LAS objects have proper motions consistent with absolute proper motions, the GCS stars may have proper motions which are significantly under-estimated. This is due possibly to the bulk motion of some of the local astrometric reference stars used in the proper motion determination.Comment: Accepted for publication in MNRA