Miracle-dz/UniFAR-FTUs huggingface dataset:
Transmembrane voltage potential controls embryonic eye patterning in Xenopus laevis

Uncovering the molecular mechanisms of eye development is crucial for understanding the embryonic morphogenesis of complex structures, as well as for the establishment of novel biomedical approaches to address birth defects and injuries of the visual system. Here, we characterize change in transmembrane voltage potential (V mem ) as a novel biophysical signal for eye induction in Xenopus laevis . During normal embryogenesis, a striking hyperpolarization demarcates a specific cluster of cells in the anterior neural field. Depolarizing the dorsal lineages in which these cells reside results in malformed eyes. Manipulating V mem of non-eye cells induces well-formed ectopic eyes that are morphologically and histologically similar to endogenous eyes. Remarkably, such ectopic eyes can be induced far outside the anterior neural field. A Ca 2+ channel-dependent pathway transduces the V mem signal and regulates patterning of eye field transcription factors. These data reveal a new, instructive role for membrane voltage during embryogenesis and demonstrate that V mem is a crucial upstream signal in eye development. Learning to control bioelectric initiators of organogenesis offers significant insight into birth defects that affect the eye and might have significant implications for regenerative approaches to ocular diseases. 2) of V mem of non-eye cells, such that their V mem now lies within the window of eye formation, results in the formation of ectopic eye tissue by these cells. Perturbation (depolarization, 3 and 4) of V mem in non-eye cells, such that their V mem still does not fall within the eye formation window, does not result in ectopic eye tissue formation from these cells.
Evaluation of Mg/Ca thermometry in foraminifera: Comparison of experimental results and measurements in nature

We studied Mg/Ca in high-Mg, shallow-water benthic foraminifera in culture and in samples from natural environments, in order to evaluate the expression of latitudinal and seasonal temperature variability in Mg/Ca in their tests. We cultured Planoglabratella opercularis (d'Orbigny) and Quinqueloculina yabei Asano under controlled temperature (10°–25°C) and salinity (30–38) conditions. Both species show a linear correlation between Mg/Ca and temperature, but they differ in temperature sensitivity. Salinity does not significantly influence Mg/Ca. In the samples collected in nature, Mg/Ca and seawater temperatures are positively correlated, but there are more complexities than in the records for cultured specimens due to such factors as seasonal fluctuations in temperature. We conclude that Mg/Ca ratios in monospecific benthic foraminiferal samples may be used as a reliable temperature proxy, if the lifetime of the species is taken into account.
Photosynthetic induction in wheat protoplasts and chloroplasts. Autocatalysis and light activation of enzymes

Abstract Unlike wheat chloroplasts, wheat protoplasts showed a pronounced restoration of the induction phase after a short period of darkness. This difference was used to investigate the relative roles of light-induced reductive activation of enzymes and the auto-catalytic increase in the level of substrates in the control of the rate of photosynthesis during induction. Light activation and dark inactivation of ribulose 5-phosphate kinase, fructose 1,6-biphosphatase and NADP+-specific glyceraldehydephosphate dehydrogenase were measured. In this respect there was no appreciable difference between protoplasts and chloroplasts. In contrast, the level of photosynthetic intermediates remained constant in darkened isolated chloroplasts, but declined rapidly in chloroplasts isolated from darkened protoplasts. When fructose 1,6-bisphosphatase was pre-activated by treating protoplasts with dithiothreitol the lag was only slightly shortened. These results are discussed in terms of control of the rate of the photosynthesis during the lag by substrates rather than limitation imposed by activity of any of the enzymes measured.
Structural Basis of Calcification Inhibition by α2-HS Glycoprotein/Fetuin-A

Genetic evidence from mutant mice suggests that α2-HS glycoprotein/fetuin-A (Ahsg) is a systemic inhibitor of precipitation of basic calcium phosphate preventing unwanted calcification. Using electron microscopy and dynamic light scattering, we demonstrate that precipitation inhibition by Ahsg is caused by the transient formation of soluble, colloidal spheres, containing Ahsg, calcium, and phosphate. These “calciprotein particles” of 30–150 nm in diameter are initially amorphous and soluble but turn progressively more crystalline and insoluble in a time- and temperature-dependent fashion. Solubilization in Ahsg-containing calciprotein particles provides a novel conceptual framework to explain how insoluble calcium precipitates may be transported and removed in the bodies of mammals. Mutational analysis showed that the basic calcium phosphate precipitation inhibition activity resides in the amino-terminal cystatin-like domain D1 of Ahsg. A structure-function analysis of wild type and mutant forms of cystatin-like domains from Ahsg, full-length fetuin-B, histidine-rich glycoprotein, and kininogen demonstrated that Ahsg domain D1 is most efficient in inhibiting basic calcium phosphate precipitation. The computer-modeled domain structures suggest that a dense array of acidic residues on an extended β-sheet of the cystatin-like domain Ahsg-D1 mediates efficient inhibition.
Molecular phylogeny of the specialized schizothoracine fishes (Teleostei: Cyprinidae), with their implications for the uplift of the Qinghai-Tibetan Plateau

Molecular phylogeny of three genera containing nine species and subspecies of the specialized schizothoracine fishes are investigated based on the complete nucleotide sequence of mitochondrial cytochromeb gene. Meantime relationships between the main cladogenetic events of the specialized schizothoracine fishes and the stepwise uplift of the Qinghai-Tibetan Plateau are also conducted using the molecular clock, which is calibrated by geological isolated events between the upper reaches of the Yellow River and the Qinghai Lake. Results indicated that the specialized schizothoracine fishes are not a monophyly. Five species and subspecies ofPtychobarbus form a monophyly. But three species ofGymnodiptychus do not form a monophyly.Gd. integrigymnatus is a sister taxon of the highly specialized schizothoracine fishes whileGd. pachycheilus has a close relation withGd. dybowskii, and both of them are as a sister group ofDiptychus maculatus. The specialized schizothoracines fishes might have originated during the Miocene (about 10 MaBP), and then the divergence of three genera happened during late Miocene (about 8 MaBP). Their main specialization occurred during the late Pliocene and Pleistocene (3.54-0.42 MaBP). The main cladogenetic events of the specialized schizothoracine fishes are mostly correlated with the geological tectonic events and intensive climate shift happened at 8, 3.6, 2.5 and 1.7 MaBP of the late Cenozoic. Molecular clock data do not support the hypothesis that the Qinghai-Tibetan Plateau uplifted to near present or even higher elevations during the Oligocene or Miocene, and neither in agreement with the view that the plateau uplifting reached only to an altitude of 2000 m during the late Pliocene (about 2.6 MaBP).
Progoniada and Goniadella (Annelida: Polychaeta: Goniadidae) from the outer continental shelf and slope off south-eastern Brazil

Species of the genera Progoniada and Goniadella are recorded from off the Brazilian coast, from depths of 93 to 808 m. The description of Progoniada regularis is complemented with new data on the number of chevrons and micrognaths. Goniadella revizee sp. nov. is described; it differs from the five known species of the genus mainly in having acicular chaetae above the dorsal cirrus, together with 20–21 uniramous chaetigers. The proboscideal papillae of both species are illustrated by scanning electron micrographs.
Modeling and Simulation of Molecular Mechanism of Action of Dietary Polyphenols on the Inhibition of Anti-Apoptotic PI3K/AKT Pathway

In recent years, the role of dietary phenolic compounds in the regulation of cellular metabolism in normal and pathological conditions has become increasingly important in cancer research. In most cases, the molecular mechanism of action related to the anticarcinogenic effect of phenolic compounds has been studied in vitro and in animal models, but these studies are still not complete. It is precisely here where in silico approaches can be an invaluable tool for complementing in vitro and in vivo research. In this paper, we adopt a tuple space-based modeling and simulation approach, and show how it can be applied to the simulation of complex interaction patterns of intracellular signaling pathways. Specifically, we are working to explore and to understand the molecular mechanism of action of dietary phenolic compounds on the inhibition of the PI3K/AKT anti-apoptotic pathway. As a first approximation, using the tuple spaces- based in silico approach, we model and simulate the anti-apoptotic PI3K/AKT pathway in the absence and presence of phenolic compounds, in order to determine the effectiveness of our platform, to employ it in future prediction of experimentally non visualized interactions between the pathway components and phenolic compounds.
Abstract

Simultaneous Salmonella typhimurium infection in birds, cats and people Tauni, M. A. & Österlund A. (2000) Outbreak of Salmonella typhimurium in cats and humans associated with infection in wild birds. Journal of Small Animal Practice 41, 339-341
The microtubule end-binding affinity of EB1 is enhanced by a dimeric organization that is susceptible to phosphorylation

ABSTRACT In cells, microtubule dynamics are regulated by plus-end tracking proteins (+TIPs). End-binding protein 1 (EB1, also known as MAPRE1) acts as a master regulator of +TIP networks by targeting the growing ends of microtubules and recruiting other factors. However, the molecular mechanism underlying high-affinity binding of EB1 to microtubule ends remains an open area of research. Using single-molecule imaging, we show that the end-binding kinetics of EB1 change when the polymerization and hydrolysis rates of tubulin dimers are altered, confirming that EB1 binds to GTP–tubulin and/or GDP–Pi–tubulin at microtubule growing ends. The affinity of wild-type EB1 to these sites is higher than that of monomeric EB1 mutants, suggesting that both calponin homology domains present in the EB1 dimer contribute to end binding. Introduction of phosphomimetic mutations into the EB1 linker domain weakens the end-binding affinity and confers a more curved conformation on the EB1 dimer without compromising dimerization, suggesting that the overall architecture of EB1 is important for its end-binding affinity. Taken together, our results provide insights into how the high-affinity end-binding of EB1 is achieved and how this activity may be regulated in cells. Summary: Phosphorylation of the linker domain causes EB1 to adopt a more curved structural conformation and disrupts the high-affinity binding of EB1 to microtubule growing ends.
Feeding habits of Calidris alpina L. and C. minuta Leisl. (Aves) in relation to the distribution of marine shore invertebrates.

During migration, various species of waders (Charadrii) frequently feed in mixed flocks. It is generally assumed that species foraging in the same habitats exploit different food sources (see Lack 1954: 148-49). The food relations of Calidris alpina L. and C. minuta Leisl. were studied in a marine shore-area in Saltviken (120 54'E, 550 44'N) on the Oresound in southern Sweden. The feeding of migrating waders in Sweden has previously been studied only by Norlin (1965). Ehlert (1964) studied the foraging behaviour and feeding of migrating waders of the genera Calidris and Crocethia in a tidal mudflat area on Mellum near Heligoland. In Scotland a similar study was started in 1963 (GossCustard 1965).
Somaclonal breeding of reed canarygrass (Phalaris arundinacea L.)

Tissue culture-induced variants (somaclones) of reed canarygrass (Phalaris arundinacea L.) were developed from callus cells of aseptic spikelet cultures. Molecular polymorphism of the populations of somaclones and spikelet-donor plants as natural vegetative clones were compared by the application of polymerase chain reaction (PCR)-based techniques of random amplified polymorphic DNA (RAPD)-, simple sequence repeat (SSR)-, and inter-simple sequence repeat (ISSR)-PCR to genomic DNA samples. The genetic diversity was higher in the somaclones compared with vegetative clones as measured by the maximum genetic distance (MaxGD) which increased from 0AE401 (vegetative clones) to 0AE498 (somaclones). Along with this change, the minimum genetic distance (MinGD) decreased from 0AE20 (control plants) to 0AE06 (somaclones) which demonstrated that genetic changes occurred not only in a positive (dissimilarity, MaxGD), but also in a negative (similarity, MinGD) direction. Structural carbohydrate analyses were also performed on the leaves to compare the somaclones with the donor vegetative clones. The mean neutral-detergent and acid-detergent fibre concentrations of the leaves of the somaclones were about 0AE20 lower than the donor vegetative clones suggesting that increases in the digestibility could be obtained from the somaclonal material.
Identification of Core α1,3-Fucosylated Glycans and Cloning of the Requisite Fucosyltransferase cDNA from Drosophila melanogaster

For many years, polyclonal antibodies raised against the plant glycoprotein horseradish peroxidase have been used to specifically stain the neural and male reproductive tissue ofDrosophila melanogaster. This epitope is considered to be of carbohydrate origin, but no glycan structure fromDrosophila has yet been isolated that could account for this cross-reactivity. Here we report that N-glycan core α1,3-linked fucose is, as judged by preabsorption experiments, indispensable for recognition of Drosophila embryonic nervous system by anti-horseradish peroxidase antibody. Further, we describe the identification by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry and high performance liquid chromatography of two Drosophila N-glycans that, as already detected in other insects, carry both α1,3- and α1,6-linked fucose residues on the proximal core GlcNAc. Moreover, we have isolated three cDNAs encoding α1,3-fucosyltransferase homologues from Drosophila. One of the cDNAs, when transformed into Pichia pastoris, was found to direct expression of core α1,3-fucosyltransferase activity. This recombinant enzyme preferred as substrate a biantennary core α1,6-fucosylated N-glycan carrying two non-reducingN-acetylglucosamine residues (GnGnF6;K m 11 μm) over the same structure lacking a core fucose residue (GnGn; K m 46 μm). The Drosophila core α1,3-fucosyltransferase enzyme was also shown to be able to fucosylate N-glycan structures of human transferrinin vitro, this modification correlating with the acquisition of binding to anti-horseradish peroxidase antibody.
Nuclear PCR-RFLP detects the brook chub, Squalius lucumonis (Leuciscinae: Cyprinidae), and related hybrids with other cyprinid species

Abstract The brook chub, Squalius lucumonis (Bianco, 1983), is an endemic endangered species inhabiting the rivers of Central Italy. Being subject to hybridizations with other cyprinids, particularly the congeneric S. squalus (Bonaparte, 1837), genetic overestimation can emerge when molecular markers are applied and mtDNA barcoding is not sufficient to ensure a correct attribution, due to its maternal inheritance. In this perspective, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach on rDNA is proposed to rapidly discriminate S. lucumonis from nine other cyprinids. For its capacity to identify hybrids of these species with S. lucumonis, this method should be considered as a fundamental tool to be applied prior to the application of other molecular markers in extensive genetic characterizations for phylogenetic, phylogeographic, population and management analyses.
Population Structure of Deep-Sea and Oceanic Phenotypes of Deepwater Redfish in the Irminger Sea and Icelandic Continental Slope: Are They Cryptic Species?

Abstract The deepwater redfish Sebastes mentella has a wide distribution in the North Atlantic Ocean. In the Irminger Sea, there is evidence for two phenotypes (deep-sea and oceanic) of deepwater redfish. The two phenotypes have overlapping geographic distributions but differ in depth preferences. There are two hypotheses on deepwater redfish stock structure in the Irminger Sea. One suggests that mature individuals of a single stock segregate according to size and age and therefore that the phenotypes represent different life stages of the same stock. The other hypothesis suggests that there are two different stocks and that these stocks segregate mainly according to depth. Additionally, it is not clear whether the fish of the deep-sea phenotype in the Irminger Sea and those on the Icelandic continental shelf represent one stock. Analysis of genetic variability at eight allozyme markers in 1,763 deepwater redfish from 26 samples collected at different depths in the Irminger Sea and the Icelandic continent.
β2 Adrenergic Receptor Activation

In many rhodopsin-like G-protein-coupled receptors, agonist binding to a cluster of aromatic residues in TM6 may promote receptor activation by altering the configuration of the TM6 Pro-kink and by the subsequent movement of the cytoplasmic end of TM6 away from TM3. We hypothesized that the highly conserved Cys6.47, in the vicinity of the conserved Pro6.50, modulates the configuration of the aromatic cluster and the TM6 Pro-kink through specific interactions in its different rotamer configurations. In the β2 adrenergic receptor, mutation of Cys6.47 to Thr, which in an α-helix has a different rotamer distribution from Cys and Ser, produced a constitutively active receptor, whereas the Ser mutant was similar to wild-type receptor. Use of the biased Monte Carlo technique of Conformational Memories showed that the rotamer changes among Cys/Ser/Thr6.47, Trp6.48, and Phe6.52 are highly correlated, representing a rotamer “toggle switch” that may modulate the TM6 Pro-kink. Differential modulation of the accessibility of Cys6.47 and an engineered Cys6.52 in wild type and a constitutively active background provides experimental support for the association of this rotamer switch with receptor activation.
Using climate downscaling to hypothesise impacts on apex predator marine ecosystem dynamics

Climate downscaling studies help to connect global predictions and projections with regional dynamics and generate a better understanding of past and future conditions. Adding ecological variables and trophic relationships into the climate equation is challenging since there are few clear connections. The present study is an exploratory data analysis to explain dusky dolphin (Lagenorhynchus obscurus) encounter rate patterns in Admiralty Bay, New Zealand. During 2001–2006, dolphin encounter rate in winter decreased from 6 to 0.8 groups/h and the proportion of dolphin groups observed feeding decreased from 80% to 38% in Inner Admiralty Bay. These trends generally corresponded to cooler and moderate El Niño Southern Oscillation years, lower sea surface height, southwesterly winds, increased surface mixing and decreased sea surface salinity. To fully grasp the significance of these relationships and potential impact(s) on dolphin population trends, directed long-term studies that synthesise dolphin, prey, water quality, anthropogenic pressures and climatic information into regional climate-ecosystem models are needed.
Poliovirus RNA-dependent RNA Polymerase (3Dpol)

We have analyzed the divalent cation specificity of poliovirus RNA-dependent RNA polymerase, 3Dpol. The following preference was observed: Mn2+ > Co2+ > Ni2+ > Fe2+ > Mg2+ > Ca2+ > Cu2+, and Zn2+ was incapable of supporting 3Dpol-catalyzed nucleotide incorporation. In the presence of Mn2+, 3Dpol activity was increased by greater than 10-fold relative to that in the presence of Mg2+. Steady-state kinetic analysis revealed that the increased activity observed in the presence of Mn2+ was due, primarily, to a reduction in the K M value for 3Dpol binding to primer/template, without any significant effect on the K M value for nucleotide. The ability of 3Dpol to catalyze RNA synthesis de novo was also stimulated approximately 10-fold by using Mn2+, and the enzyme was now capable of also utilizing a DNA template for primer-independent RNA synthesis. Interestingly, the use of Mn2+ as divalent cation permitted 3Dpolactivity to be monitored by following extension of 5′-32P-end-labeled, heteropolymeric RNA primer/templates. The kinetics of primer extension were biphasic because of the enzyme binding to primer/template in both possible orientations. When bound in the incorrect orientation, 3Dpol was capable of efficient addition of nucleotides to the blunt-ended duplex; this activity was also apparent in the presence of Mg2+. In the presence of Mn2+, 3Dpol efficiently utilized dNTPs, ddNTPs, and incorrect NTPs. On average, three incorrect nucleotides could be incorporated by 3Dpol. The ability of 3Dpol to incorporate the correct dNTP, but not the correct ddNTP, was also observed in the presence of Mg2+. Taken together, these results provide the first glimpse into the nucleotide specificity and fidelity of the poliovirus polymerase and suggest novel alternatives for the design of primer/templates to study the mechanism of 3Dpol-catalyzed nucleotide incorporation.
Guidelines for Field Triage of Injured Patients

The Centers for Disease Control and Prevention (CDC) has published significant data and trends related to the national public health burden associated with trauma and injury. In the United States (U.S.), injury is the leading cause of death for persons aged 1–44 years. In 2008, approximately 30 million injuries resulted in an emergency department (ED) evaluation; 5.4 million (18%) of these patients were transported by Emergency Medical Services (EMS). 1 EMS providers determine the severity of injury and begin initial management at the scene. The decisions to transport injured patients to the appropriate hospital are made through a process known as “field triage. ” Since 1986, the American College of Surgeons Committee on Trauma (ACS-COT) has provided guidance for the field triage process though its “Field Triage Decision Scheme. ” In 2005, the CDC, with financial support from the National Highway Traffic Safety Administration (NHTSA), collaborated with ASC-COT to convene the initial meeting of the National Expert Panel on Field Triage (the Panel) to revise the decision scheme. This revised version was published in 2006 by ASC-COT, and in 2009 the CDC published a detailed description of the scientific rational for revising the field triage criteria entitled, “Guidelines for Field Triage of Injured Patients. ”2–3 In 2011, the CDC reconvened the Panel to review the 2006 Guidelines and recommend any needed changes. We present the methodology, findings and updated guidelines from the Morbidity & Mortality Weekly Report (MMWR) from the 2011 Panel along with commentary on the burden of injury in the U.S., and the role emergency physicians have in impacting morbidity and mortality at the population level.