Accurate Profiling of Microbial Communities from Massively Parallel Sequencing using Convex Optimization

We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using short sequence reads from Massively Parallel Sequencing (MPS) data obtained for specified genomic regions. We formulate the problem mathematically as a convex optimization problem and provide sufficient conditions for identifiability, namely the ability to reconstruct species identity and frequency correctly when the data size (number of reads) grows to infinity. We discuss different metrics for assessing the quality of the reconstructed solution, including a novel phylogenetically-aware metric based on the Mahalanobis distance, and give upper-bounds on the reconstruction error for a finite number of reads under different metrics. We propose a scalable divide-and-conquer algorithm for the problem using convex optimization, which enables us to handle large problems (with $\sim10^6$ species). We show using numerical simulations that for realistic scenarios, where the microbial communities are sparse, our algorithm gives solutions with high accuracy, both in terms of obtaining accurate frequency, and in terms of species phylogenetic resolution.Comment: To appear in SPIRE 1

Histochemical analysis of glycoconjugates in the domestic cat testis

The localization and characterization of oligosaccharide sequences in the cat testis was investigated using 12 lectins in combination with the ßelimination reaction, N-Glycosidase F and sialidase digestion. Leydig cells expressed O-linked glycans with terminal aGalNAc (HPA reactivity) and N-glycans with terminal/internal aMan (Con A affinity). The basement membrane showed terminal Neu5Aca2,6Gal/GalNAc, Galß1,3GalNAc, a/ßGalNAc, and GlcNAc (SNA, PNA, HPA, SBA, GSA II reactivity) in O-linked oligosaccharides, terminal Galß1,4GlcNAc (RCA120 staining) and aMan in N-linked oligosaccharides; in addition, terminal Neu5Aca2,3Galß1,4GlcNac, Forssman pentasaccharide, aGal, aL-Fuc and internal GlcNAc (MAL II, DBA, GSA I-B4, UEA I, KOH-sialidase-WGA affinity) formed both O- and N-linked oligosaccharides. The Sertoli cells cytoplasm contained terminal Neu5Ac- Galß1,4GlcNAc, Neu5Ac-ßGalNAc as well as internal GlcNAc in O-linked glycans, aMan in N-linked glycoproteins and terminal Neu5Aca2,6Gal/ GalNAc in both O- and N-linked oligosaccharides. Spermatogonia exhibited cytoplasmic N-linked glycoproteins with aMan residues. The spermatocytes cytoplasm expressed terminal Neu5Aca2,3Galß1,4 GlcNAc and Galß1,3GalNAc in O-linked oligosaccharides, terminal Galß1,4GlcNAc and a/ßGalNAc in N-linked glycoconjugates. The Golgi region showed terminal Neu5aca2,3Galß1,4GlcNac, Galß1,4GlcNAc, Forssman pentasaccharide, and aGalNAc in O-linked oligosaccharides, aMan and terminal ßGal in N-linked oligosaccharides. The acrosomes of Golgi-phase spermatids expressed terminal Galß1,3GalNAc, Galß1,4GlcNAc, Forssmann pentasaccharide, a/ßGalNAc, aGal and internal GlcNAc in O-linked oligosaccharides, terminal a/ßGalNAc, aGal and terminal/internal aMan in N-linked glycoproteins. The acrosomes of cap-phase spermatids lacked internal Forssman pentasaccharide and aGal, while having increased a/ßGalNAc. The acrosomes of elongated spermatids did not show terminal Galß1,3GalNAc, displayed terminal Galß1,4GlcNAc and a/ßGalNAc in N-glycans and Neu5Ac-Galß1,3GalNAc in O-linked oligosaccharides

Association energetics of cross-reactive and specific antibodies

HyHEL-8, HyHEL-10, and HyHEL-26 (HH8, HH10, and HH26, respectively) are murine monoclonal IgG1 antibodies which share over 90% variable-region amino acid sequence identity and recognize identical structurally characterized epitopes on hen egg white lysozyme (HEL). Previous immunochemical and surface plasmon resonance-based studies have shown that these antibodies differ widely in their tolerance of mutations in the epitope. While HH8 is the most cross-reactive, HH26 is rigidified by a more extensive network of intramolecular salt links and is highly specific, with both association and dissociation rates strongly affected by epitope mutations. HH10 is of intermediate specificity, and epitope mutations produce changes primarily in the dissociation rate. Calorimetric characterization of the association energetics of these three antibodies with the native antigen HEL and with Japanese quail egg white lysozyme (JQL), a naturally occurring avian variant, shows that the energetics of interaction correlate with cross-reactivity and specificity. These results suggest that the greater cross-reactivity of HH8 may be mediated by a combination of conformational flexibility and less specific intermolecular interactions. Thermodynamic calculations suggest that upon association HH8 incurs the largest configurational entropic penalty and also the smallest loss of enthalpic driving force with variant antigen. Much smaller structural perturbations are expected in the formation of the less flexible HH26 complex, and the large loss of enthalpic driving force observed with variant antigen reflects its specificity. The observed thermodynamic parameters correlate well with the observed functional behavior of the antibodies and illustrate fundamental differences in thermodynamic characteristics between cross-reactive and specific molecular recognition

Targeting angiogenesis in multiple myeloma by the VEGF and HGF blocking DARPin® protein MP0250: a preclinical study

The investigational drug MP0250 is a multi-specific DARPin® molecule that simultaneously binds and neutralizes VEGF and HGF with high specificity and affinity. Here we studied the antiangiogenic effects of the MP0250 in multiple myeloma (MM). In endothelial cells (EC) isolated from bone marrow (BM) of MM patients (MMEC) MP0250 reduces VEGFR2 and cMet phosphorylation and affects their downstream signaling cascades. MP0250 influences the secretory profile of MMEC and inhibits their in vitro angiogenic activities (spontaneous and chemotactic migration, adhesion, spreading and capillarogenesis). Compared to anti-VEGF or anti-HGF neutralizing mAbs, MP0250 strongly reduces capillary network formation and vessel-sprouting in a Matrigel angiogenesis assay. MP0250 potentiates the effect of bortezomib in the same in vitro setting. It significantly reduces the number of newly formed vessels in the choriollantoic membrane assay (CAM) and the Matrigel plug assay. In the syngeneic 5T33MM tumor model, MP0250 decreases the microvessel density (MVD) and the combination MP0250/bortezomib lowers the percentage of idiotype positive cells and the serum levels of M-protein. Overall results define MP0250 as a strong antiangiogenic agent with potential as a novel combination drug for treatment of MM patients

Worsening Glycemia increases the Odds of intermittent But Not Persistent Staphylococcus aureus Nasal Carriage in Two Cohorts of Mexican american adults

Numerous host and environmental factors contribute to persistent and intermittent nasal Staphylococcus aureus carriage in humans. The effects of worsening glycemia on the odds of S. aureus intermittent and persistent nasal carriage was established in two cohorts from an adult Mexican American population living in Starr County, Texas. The anterior nares were sampled at two time points and the presence of S. aureus determined by laboratory culture an

The herpetofauna of Veracruz, Mexico: composition, distribution, and conservation status

The herpetofauna of the state of Veracruz, Mexico, currently consists of 359 species, including 76 anurans, 45 caudates, one caecilian, one crocodylian, 217 squamates, and 19 turtles. The distribution of the herpetofaunal species are catalogued here among the four recognized physiographic regions in the state. The total number of species ranges from 179 in the Sierra de Los Tuxtlas to 236 in the Sierra Madre Oriental. The number of species shared among the four physiographic regions ranges from 100 between the Gulf Coastal Lowlands and the Transmexican Volcanic Belt, to 190 between the Sierra Madre Oriental and the Transmexican Volcanic Belt. A similarity dendrogram based on the Unweighted Pair Group Method with Arithmetic Averages (UPGMA) depicts two distinct clusters, one between the Sierra Madre Oriental and the Transmexican Volcanic Belt, and the other between the Gulf Coastal Lowlands and the Sierra de Los Tuxtlas. The former cluster refects two adjacent regions in highland environments that share a substantial number of herpetofaunal species, and the latter cluster shares a sizeable number of wide-ranging, generalist, lowland species found on the Atlantic and Pacifc versants of Mexico and Central America. The level of herpetofaunal endemism is relatively high, with 182 of 359 species either endemic to Mexico or to Veracruz. The distributional categorization of the total herpetofauna is as follows: 169 non-endemic species; 138 country endemic species; 44 state endemic species; and eight non-native species. The 169 non-endemic species are allocated to the following distributional categories: MXCA (89), MXSA (30), MXUS (29), USCA (11), USSA (four), and OCEA (fve). The principal environmental threats to the herpetofauna of Veracruz include deforestation, livestock, roads, water pollution, myths and other cultural factors, diseases, invasive species, and illegal commerce. The conservation status of each native species was evaluated using the SEMARNAT, IUCN, and EVS systems, of which the EVS system proved to be the most useful. The Relative Herpetofaunal Priority method was employed to determine the rank order signifcance of the four regions, and this identifed the Sierra Madre Oriental as the region of greatest importance. Only six protected areas exist in Veracruz, most of which are located in the Gulf Coastal Lowlands, the region of least conservation signifcance. The area of greatest signifcance, the Sierra Madre Oriental, does not contain any protected areas. A total of 265 species have been recorded within the six protected areas, of which 138 are non-endemics, 89 are country endemics, 31 are state endemics, and seven are non-natives. Finally, we provide a set of conclusions and recommendations to enhance the prospects for the future protection of the herpetofauna of Veracruz

Brain morphology and immunohistochemical localization of the gonadotropin-releasing hormone in the bluefin tuna, <i>Thunnus thynnus</i>

The present study was focused on the morphology of the diencephalic nuclei (likely involved in reproductive functions) as well as on the distribution of GnRH (gonadotropin-releasing hormone) in the rhinencephalon, telencephalon and the diencephalon of the brain of bluefin tuna (Thunnus thynnus) by means of immunohistochemistry. Bluefin tuna has an encephalization quotient (QE) similar to that of other large pelagic fish. Its brain exhibits well-developed optic tecta and corpus cerebelli. The diencephalic neuron cell bodies involved in reproductive functions are grouped in two main nuclei: the nucleus preopticus-periventricularis and the nucleus lateralis tuberis. The nucleus preopticus-periventricularis consists of the nucleus periventricularis and the nucleus preopticus consisting of a few sparse multipolar neurons in the rostral part and numerous cells closely packed and arranged in several layers in its aboral part. The nucleus lateralis tuberis is located in the ventral-lateral area of the diencephalon and is made up of a number of large multipolar neurones. Four different polyclonal primary antibodies against salmon (s)GnRH, chicken (c)GnRH-II (cGnRH-II 675, cGnRH-II 6) and sea bream (sb)GnRH were employed in the immunohistochemical experiments. No immunoreactive structures were found with anti sbGnRH serum. sGnRH and cGnRH-II antisera revealed immunoreactivity in the perikarya of the olfactory bulbs, preopticus-periventricular nucleus, oculomotor nucleus and midbrain tegmentum. The nucleus lateralis tuberis showed immunostaining only with anti-sGnRH serum. Nerve fibres immunoreactive to cGnRH and sGnRH sera were found in the olfactory bulbs, olfactory nerve and neurohypophysis. The significance of the distribution of the GnRHimmunoreactive neuronal structures is discussed

Language of CTO interventions – Focus on hardware

AbstractThe knowledge of variety of chronic total occlusion (CTO) hardware and the ability to use them represents the key to success of any CTO interventions. However, the multiplicity of CTO hardware and their physical character and the terminology used by experts create confusion in the mind of an average interventional cardiologist, particularly a beginner in this field. This knowledge is available but is scattered. We aim to classify and compare the currently used devices based on their properties focusing on how physical character of each device can be utilized in a specific situation, thus clarifying and simplifying the technical discourse

The effect of neuromuscular blockade on mask ventilation

Summary We wished to test the hypothesis that neuromuscular blockade facilitates mask ventilation. In order reliably and reproducibly to assess the efficiency of mask ventilation, we developed a novel grading scale (Warters scale), based on attempts to generate a standardised tidal volume. Following induction of general anaesthesia, a blinded anaesthesia provider assessed mask ventilation in 90 patients using our novel grading scale. The non-blinded anaesthesiologist then randomly administered rocuronium or normal saline. After 2 min, mask ventilation was reassessed by the blinded practitioner. Rocuronium significantly improved ventilation scores on the Warters scale (mean (SD) 2.3 (1.6) vs 1.2 (0.9), p &lt; 0.001). In a subgroup of patients with a baseline Warters scale value of &gt; 3 (i.e. difficult to mask ventilate; n = 14), the ventilation scores also showed significant improvement (4.2 (1.2) vs 1.9 (1.0), p = 0.0002). Saline administration had no effect on ventilation scores. Our data indicate that neuromuscular blockade facilitates mask ventilation. We discuss the implications of this finding for unexpected difficult airway management and for the practice of confirming adequate mask ventilation before the administration of neuromuscular blockade