Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the Genetic Region of Bacillus subtilis B3 Renders Bacillus subtilis 168 Biosynthesis of Lipopeptide Surfactin Positive

The 3642 base pairs genomic region of Bacillus subtilis B3, which converts B. subtilis 168 into a producer of surfactin, includes srfDB3 encoding thioesterase, aspB3 encoding aspartate aminotransferase, lpaB3 encoding phosphopantetheinyl transferase and yczEB3 encoding YczE-like protein. Deletion analysis and functionally complement results indicated that truncation of srfDB3, aspB3 and yczEB3 did not affect biosynthesis of surfactin in B. subtilis 168. The lpaB3 gene with its promoter and ribosome-binding site is essential, whereas its transcription terminator is not necessary for biosynthesis of surfactin in B. subtilis 168.
Liquid seal for compact micropiston actuation at the capillary tip

Liquid/gas surface tension seals a 3D printed pneumatic microactuator at the tip of a 140-μm flexible capillary. Actuators at the tip of a submillimetric catheter could facilitate in vivo interventional procedures at cellular scales by enabling tissue biopsy and manipulation or supporting active micro-optics. However, the dominance of frictional forces at this scale makes classical mechanism problematic. Here, we report the design of a microscale piston, with a maximum dimension of 150 μm, fabricated with two-photon lithography onto the tip of 140-μm-diameter capillaries. An oil drop method is used to create a seal between the piston and the cylinder that prevents any leakage below 185-mbar pressure difference while providing lubricated friction between moving parts. This piston generates forces that increase linearly with pressure up to 130 μN without breaking the liquid seal. The practical value of the design is demonstrated with its integration with a microgripper that can grasp, move, and release 50-μm microspheres. Such a mechanism opens the way to micrometer-size catheter actuation.
Association genetics reveal candidate gene SNPs affecting wood properties in Pinus radiata

Summary Association or linkage disequilibrium (LD) mapping is an emerging approach for identifying molecular markers linked to phenotypic variation. Forest trees are ideally suited to association mapping due to their low genomic LD which permits highresolution mapping of marker associations. Using this approach several single-nucleotide polymorphisms (SNPs) potentially influencing economically important wood traits (density, cellulose microfibril angle and modulus of elasticity) were identified in a Pinus radiata provenance trial. One hundred and forty-nine SNP markers from 44 cell wall candidate genes were examined. After accounting for population structure and multiple testing, 15 SNPs demonstrated significant associations at P < 0.05. We have demonstrated that linkage disequilibrium in the native populations of P. radiata decays within the length of a gene. Therefore, the identified associations may result from the SNP under examination, or at least a linked SNP within the same gene. Without accounting for multi-colinearity between markers, the proportion of trait variance attributed to individual SNPs ranged from 1.5% to 6.5%. SNP associations are presently undergoing validation in a second-generation Southern Tree Breeding Association progeny trial. The small proportion of total quantitative variation contributed by individual SNPs indicates molecular breeding strategies would achieve greatest gains using combinations of SNPs for marker-assisted selection. Establishing methods for efficient transfer of validated SNPs into breeding selection models is essential for the uptake of the marker technology identified here, and is the focus of ongoing research.
Differential regulation of LPS-induced IL-1β and EL-1 receptor antagonist mRNA by IFNα and IFNγ in murine peritoneal macrophages

IL-1 and its naturally occurring receptor antagonist, IL-1ra, are primarily synthesized by cells of the monocyte-macrophage lineage. The balance of the relative amounts of these secreted cytokines has major importance in the pathophysiology of various inflammatory disorders, especially bacterial sepsis and some autoimmune diseases. While both the agonist and the antagonist genes belong to the same family, IL-1β and IL-1ra are differentially regulated. In the present study, we examined the effects of macrophage activating factors, bacterial lipopolysaccharide (LPS), IFNα, and IFNγ, on the regulation of IL-1ra and IL-1β mRNA levels in thioglycollate-elicited mouse peritoneal macrophages. LPS-treatment of cultured macrophages resulted in a 3 to 4-fold increase in IL-1ra mRNA which peaked between 6-12 h, then started to decline but remained well above background levels at 24 h. In comparison to IL-1ra, the LPS-induced increase in IL-1β mRNA was larger, peaked earlier (at 2-4 h), and sharply decreased thereafter. In vivo analysis of mRNA from LPS-injected mice showed a similar temporal pattern of IL-1β and IL-1ra gene expression in bone marrow, spleen, and liver. In contrast to the effects of LPS, treatment with IFNα and IFNγ alone failed to affect the expression of either IL-1ra or IL-1β mRNA in vitro. However, in combination with LPS, IFNα and IFNγ had differential effects on the induction of these cytokines: IFNγ, but not IFNα, augmented the expression of LPS-induced IL-1ra. Conversely, both IFNα and IFNγ suppressed the induction of IL-1β mRNA by LPS. Thus, while IFNα only affects LPS-induced IL-1β gene expression, IFNγ exerts opposing effects on the LPS-induction of the agonist and antagonist, illustrating the complex role of interferons during the inflammatory process.
Properties, Potentials, and Prospects of Antifreeze Proteins

Antifreeze proteins (AFPs) are a group of proteins that protect organisms from deep freezing temperatures and are expressed in vertebrates, invertebrates, plants, bacteria, and fungi. The nuclear magnetic resonance, x-ray structure, and many spectroscopic studies with AFPs have been instrumental in determining the structure–function relationship. Mutational studies have indicated the importance of hydrophobic residues in ice binding. Various studies have pointed out that the mechanism of AFP action is through its adsorption on the ice surface, which leads to a curved surface, preventing further growth of ice by the “Kelvin effect. ” The AFPs have potential industrial, medical, and agricultural application in different fields, such as food technology, preservation of cell lines, organs, cryosurgery, and cold hardy transgenic plants and animals. However, the applications of AFPs are marred by high cost due to low yield. This review deals with the source and properties of AFPs from an angle of their application and their potential. The possibility of production using different molecular biological techniques, which will help increase the yield, is also dealt with.
Maximum Drawdown

A drawdown is defined as the accumulated percentage loss due to a sequence of drops in the price of an investment. It is collected over non-fixed time intervals and its duration is also a random variable. The maximum drawdown occurring over a fixed investment horizon is a flexible measure that provides a different perception of the risk and price flow of this investment. In this article a new modeling strategy for maximum drawdown that separates its duration and severity along with suggestions of a flexible distribution from the extreme value theory for modeling the losses is proposed. Applications for the fitted distribution, which include the computation of risk measures, classification and selection of investments, as well as its use in optimal portfolio allocation, are discussed. The properties of the model-based maximum drawdown-at-risk are then analyzed and a new risk measure, the conditional maximum drawdown-at-risk, is presented. Illustrations using stock market indexes as well as insights on the connection of the fluctuations of the maximum drawdown and the volatility of the underlying return series are provided. This methodology is applicable to various alternative investment strategies as well.
Phylogeny and generic concepts of the parasitoid wasp family Aulacidae (Hymenoptera: Evanioidea)

The results of the first phylogenetic investigation of members of the Aulacidae of the world are presented. The main objective was to test the monophyly of the currently recognised genera. In total, 79 morphological characters were scored for a substantial sample of the extant aulacid fauna, including 72 species, as well as 12 outgroup taxa belonging to Evaniidae, Gasteruptiidae, Megalyridae, Trigonalidae, Braconidae and Stephanidae. All zoogeographic regions were represented. The dataset was analysed under different conditions (ordered, unordered, equal and implied weighting). The results under different weighting conditions are not fully congruent and many relationships remain unresolved. However, the analyses demonstrate that the current generic classification of the Aulacidae is not a natural one. There is support for a very large, monophyletic clade which includes all Pristaulacus Kieffer spp. + Panaulix Benoit spp. This suggests a wider generic concept for Pristaulacus, which is redefined and rediagnosed here. As a consequence, Panaulix becomes a junior synonym of Pristaulacus (syn. nov.), and the two described species of Panaulix are transferred to Pristaulacus: Pristaulacus rex (Benoit, 1984), comb. nov., and Pristaulacus irenae (Madl, 1990), comb. nov. The genus Aulacus Jurine was consistently paraphyletic and is not valid as currently defined. Furthermore, we failed to retrieve a consistent topology among the different clades of Aulacus. A satisfactory reclassification of Aulacus, however, requires a much more comprehensive taxon sample and/or additional character data.
Description of Bacillus thermoaerophilus sp. nov., To Include Sugar Beet Isolates and Bacillus brevis ATCC 12990†

Isolates of thermophilic bacteria obtained from an Austrian beet sugar factory were screened by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and freeze-fracture electron microscopy for the presence of glycosylated crystalline cell surface layers (S-layers). On the basis of similarities in the protein band patterns on SDS-PAGE gels and the lattice geometry of the S-layers as revealed by electron micrographs, the 31 isolates which we studied were clustered into five groups (groups I to V) and several strains which exhibited no common characteristics (group 0). We found that the organisms belonging to groups I to III had glycosylated S-layer proteins, but the highest carbohydrate contents were observed in group III organisms. Partial sequencing of the 16S ribosomal DNAs of selected representative strains of each group revealed that the group I, II, IV, and V isolates and the few group 0 strains were different from the group III strains. The results of DNA-DNA hybridization experiments, SDS-PAGE, and an analysis of polar lipids demonstrated that group III isolates L419-91, L420-91T (T = type strain), and L438-91 belong to the same species. We chose the group III organism Bacillus sp. strain L420-91T for further analysis because of the high carbohydrate content of its S-layer protein. The taxonomic position of this isolate was determined by using a polyphasic approach. Phenotypic, chemotaxonomic, and genomic analyses revealed that strains L420-91T, L419-91, and L438-91 represent a new Bacillus species. We observed high levels of similarity between these strains and Bacillus brevis ATCC 12990, which also had a glycosylated S-layer protein. Our results show that strains L420-91T, L419-91, and L438-91 and B. brevis ATCC 12990 belong to the same species and that this species is a new Bacillus species, which we name Bacillus thermoaerophilus. The type strain of this species is strain L420-91 (= DSM 10154).
The interplay of facilitation and competition in plant communities

If plants cannot simultaneously acclimate to shade and drought because of physiological trade-offs, then plants are expected to be less tolerant to shading under drier conditions. One observation that, at first sight, seems incompatible with this idea is the fact that the establishment of new plants in dry areas is often restricted to shady sites under the canopy of other plants, called “nurse plants. ” We use a graphical model to resolve this paradox. The model visualizes how facilitative patterns can be understood from the simultaneous effects of plant canopies on microsite light and moisture, and the growth responses of establishing seedlings to those factors. The approach emphasizes the fact that positive and negative effects of plant canopies always occur simultaneously. In the presented light–water model, facilitation only occurs when the improvement of plant water relations under the canopy exceeds the costs caused by lower light levels. This may be true under dry conditions, whereas in less dry sit.
CORRECTIONS

APPLIED PHYSICAL SCIENCES, MEDICAL SCIENCES Correction for ‘‘Synchronization of chaotic early afterdepolarizations in the genesis of cardiac arrhythmias,’’ by Daisuke Sato, Lai-Hua Xie, Ali A. Sovari, Diana X. Tran, Norishige Morita, Fagen Xie, Hrayr Karagueuzian, Alan Garfinkel, James N. Weiss, and Zhilin Qu, which appeared in issue 9, March 3, 2009, of Proc Natl Acad Sci USA (106:2983–2988; first published February 13, 2009; 10.1073/pnas.0809148106). The authors note that the sentence starting on line 16 of the abstract appeared incorrectly. ‘This process creates multiple hat propagate ‘‘shifting’’ foci resembling polymorphic ventricular tachycardia’ should have appeared as ‘This process creates multiple premature ventricular complexes that propagate as ‘‘shifting’’ foci resembling polymorphic ventricular tachycardia. ’
Extracellular Domains of α-Neurexins Participate in Regulating Synaptic Transmission by Selectively Affecting N- and P/Q-Type Ca2+ Channels

Neurexins constitute a large family of highly variable cell-surface molecules that may function in synaptic transmission and/or synapse formation. Each of the three known neurexin genes encodes two major neurexin variants, α- and β-neurexins, that are composed of distinct extracellular domains linked to identical intracellular sequences. Deletions of one, two, or all three α-neurexins in mice recently demonstrated their essential role at synapses. In multiple α-neurexin knock-outs, neurotransmitter release from excitatory and inhibitory synapses was severely reduced, primarily probably because voltage-dependent Ca2+ channels were impaired. It remained unclear, however, which neurexin variants actually influence exocytosis and Ca2+ channels, which domain of neurexins is required for this function, and which Ca2+-channel subtypes are regulated. Here, we show by electrophysiological recordings that transgenic neurexin 1α rescues the release and Ca2+-current phenotypes, whereas transgenic neurexin 1β has no effect, indicating the importance of the extracellular sequences for the function of neurexins. Because neurexin 1α rescued the knock-out phenotype independent of the α-neurexin gene deleted, these data are consistent with a redundant function among different α-neurexins. In both knock-out and transgenically rescued mice, α-neurexins selectively affected the component of neurotransmitter release that depended on activation of N- and P/Q-type Ca2+ channels, but left L-type Ca2+ channels unscathed. Our findings indicate that α-neurexins represent organizer molecules in neurotransmission that regulate N- and P/Q-type Ca2+ channels, constituting an essential role at synapses that critically involves the extracellular domains of neurexins.
Horizontal migration of click beetle (Agriotes spp.) larvae depends on food availability

It is generally thought that soil animals face specific foraging conditions because movement through soil is highly energy consuming. The hypothesis tested here is that root‐feeding click beetle larvae (wireworms, Agriotes spp.; Coleoptera: Elateridae), to minimize energy loss, only migrate horizontally through soil when located in food‐depleted surroundings. Larvae were placed at either end of a root density gradient created by the grass Holcus lanatus L. (Poaceae), and their position in the gradient was recorded after 12 days of migration. Larval migration depended on the food situation at the starting point, with larvae moving from food‐depleted to food‐rich areas, but not leaving food‐rich areas. Larvae spread further around food‐rich areas when together with conspecifics than when being alone, presumably to avoid cannibalism. Food density‐dependent migration may have to be taken into account when using trap‐crops to control Agriotes larvae. Success may depend on the timing of trap‐crop establishment relative to the target crop to generate an effective food gradient.
BIOLOGY AND REARING OF THE SCARABAEID, SERICESTHIS GEMINATA (COLEOPTERA)

Last‐instar larvae of Sericesthis geminata (Boisduval) remain active in the field during the winter but development is depressed to a very low level by winter field temperatures. Therefore insects which overwinter in the field in the last‐instar, proceed to the pupal and adult stages at any time in the autumn and winter when kept at warm temperatures. At 21 ± 3°C (70 ± 5°F) the life cycle is completed in about 22 weeks. Caged adult S. geminata feed on young leaves of a number of eucalypt species. Viable eggs are produced by unfed beetles. Feeding on Eucalyptus blakelyi doubles the number of eggs produced.
Utility of storage lipid volumes in inferring recent trophic history of copepods

We were able to estimate lipid oil-sac volumes of Pseudocalanus spp. copepodids c3 to c5 on and around Western Bank, Scotian Shelf, during three cruises (October and November 1997 and January 1998) at stations on ( 60 m depth) the bank. We test the hypothesis that storage lipid volume was not significantly different between locations during these three months. Pseudocalanus spp. are an important prey for Atlantic cod (Gadus morhua) larvae that are spawned and persist on the bank. However, in contrast with the greater concentration of Pseudocalanus spp. on relative to off the bank, size-adjusted oil-sac volumes were on average larger and less variable at off-bank stations. We conclude that the greater copepod concentration on the bank does not result from enhanced and uniform nutrition on the bank. Lipid volumes averaged larger in winter than in the autumn, indicating that nutritional condition of Pseudocalanus spp. copepodids does not decline subsequent to the autumn bloom. Although .
Plio‐Pleistocene out‐of‐Australia dispersal in a camaenid land snail

Camaenidae are amongst the most diverse land snail groups in Southeast Asia and Australasia, but their phylogeny and biogeography are poorly understood. The monophyly and biogeographical origin of the Australian species has remained uncertain. Being reported from north‐western Australia as well as from the Lesser Sunda Islands, the genus Rhagada is crucial to our understanding of camaenid biogeography. By resolving the phylogeny of Rhagada, we aim to uncover spatial and temporal patterns of its diversification at the interface between Oriental and Australian biogeographical regions.
Caracterização biométrica e físico-química dos frutos de acessos de manga 'Ubá'

Este trabalho teve como objetivo avaliar a dissimilaridade genetica de acessos de manga 'Uba' na regiao leste de Minas Gerais, por meio da caracterizacao biometrica e fisico-quimica dos frutos, visando a identificar materiais de interesse industrial para futuros trabalhos de melhoramento. Frutos de 67 acessos de mangueira Uba provenientes do leste de Minas Gerais foram caracterizados, avaliando-se: massa da fruta, massa do endocarpo, relacao polpa/endocarpo, diâmetro longitudinal, diâmetro transversal, solidos soluveis totais, acidez total titulavel, relacao solidos soluveis total/acidez total titulavel e pH. Os resultados foram avaliados por estatistica descritiva, utilizando-se de medida de tendencia central (media) e de variabilidade de dados (desvio-padrao). Foram realizadas analises estatisticas, utilizando-se das tecnicas de agrupamento e medidas de dissimilaridade. Os frutos que apresentaram melhores caracteristicas para o processamento foram os provenientes dos acessos 10; 22; 23; 24; 35; 38; 40; 42; 52; 55 e 63. A analise de agrupamento mostrou a formacao de dois grupos de acessos com base nas caracteristicas biometricas e fisico-quimicas dos frutos, o que demonstra variabilidade genetica em mangueiras Uba, no leste de Minas Gerais.
Insights from a general model of herbivores and macroalgae on rocky shores

Many marine populations are recognized as intrinsically open in that the supply of juveniles is via planktonic dispersal from geographically separated populations (Booth and Brosnan 1995, Caley et al. 1996). Hence the recruitment of individuals to a site may be virtually independent of the number of adults at that site (Danilowicz 1997). For many marine populations, there may be no spatial scale at which a traditional closed model, such as the Lotka-Volterra, is appropriate (Roughgarden et al. 1994). Empirical studies of plant-herbivore interactions are well established in marine systems (Underwood 1980, Lubchenco and Gaines 1981, Hawkins and Hartnoll 1983, Lubchenco 1983, Chapman 1995). However, while models for open populations have been developed (e.g., Hughes 1984, Roughgarden et al. 1985, Bence and Nisbet 1989), appropriate models for species interactions in open systems are in their infancy (Gaines and Lafferty 1995). We have developed a general model for the interactions between macroalgae and herbivores on rocky shores. In such systems herbivores (often, but not exclusively, limpets and littorinids) graze the rock surface and thus remove algal spores. The use of fences to exclude grazers frequently leads to areas of rock covered by macroalgae (Hawkins and Hartnoll 1983, Chapman 1995). Grazers and macroalgae may occur together or may be mutually exclusive in these systems. Some interaction mechanisms have been proposed along gradients of shore exposure (Hawkins et al. 1992) or shore height (Underwood 1980). We show how these observations can be combined in a single mathematical framework which aids in the logical design and interpretation of experiments and generates new hypotheses about how the systems function.
Boomerang ecosystem fluxes: organic carbon inputs from land to lakes are returned to terrestrial food webs via aquatic insects

Many ecosystems are linked to their adjacent ecosystems by movements of organisms. For instance, aquatic and terrestrial ecosystems are linked via emerging aquatic insects that serve as prey for terrestrial consumers. However, the role of these organisms in returning recycled carbon to the ecosystem from which it originated is not well known. This is due to the fact that values of carbon isotope signatures from terrestrial leaves and aquatic resources are usually similar and hence results of isotope mixing models need to be considered with caution. We overcame this problem by adding isotopically distinct terrestrial particulate organic carbon (tPOC) as a tracer to the experimental sides of two lakes that were divided in two equal halves with plastic curtains. We focused on aquatic insect larvae (Chironomidae) that fed on maize Zea mays leaves experimentally added to the lakes, and subsequently became prey for terrestrial predators (spiders) after emergence. The carbon isotope values of Chironomidae and spiders were significantly elevated in the lake treatment sides as compared to reference sides, whereas the values of all autochthonous resources were not affected by maize additions. Estimates from stable isotope mixing models indicated a low but demonstrable contribution of maize leaves to the diet of Chironomidae. Overlap between the isotope values of alder leaves, the major natural tPOC source, and autochthonous resources prevented a reliable quantification of allochthony of Chironomidae. However, we qualitatively demonstrated the flow of terrestrial particulate organic carbon to lakes, as leaf fall, and back to terrestrial surroundings via emerging insects. This ‘boomerang’ carbon flux between land and lakes blurs the distinction between autochthonous and allochthonous carbon sources.