Miracle-dz/UniFAR-FTUs huggingface dataset:
Signaling Pathways to the Assembly of an Interferon-β Enhanceosome

Small molecules that modulate specific protein functions are valuable tools for dissecting complex signaling pathways. Here, we identified a small molecule that induces the assembly of the interferon-β (IFN-β) enhanceosome by stimulating all the enhancer-binding activator proteins: ATF2/c-JUN, IRF3, and p50/p65 of NF-κB. This compound stimulates mitogen-activated protein kinase kinase kinase 1 (MEKK1), which is a member of a family of proteins involved in stress-mediated signaling pathways. Consistent with this, MEKK1 activates IRF3 in addition to ATF2/c-JUN and NF-κB for the assembly of the IFN-β enhanceosome. MEKK1 activates IRF3 through the c-JUN amino-terminal kinase (JNK) pathway but not the p38 and IκB kinase (IKK) pathway. Taken together with previous observations, these results implicate that, for the assembly of an IFN-β enhanceosome, MEKK1 can induce IRF3 and ATF2/c-JUN through the JNK pathway, whereas it can induce NF-κB through the IKK pathway. Thus, specific MEKK family proteins may be able to integrate some of multiple signal transduction pathways leading to the specific activation of the IFN-β enhanceosome.
Biomass measurement of living Lumbriculus variegatus with impedance spectroscopy

Abstract Impedance spectroscopy is a useful tool for non-invasive and real time measurements of cell suspensions and a variety of biological tissues. The objective of this study was the investigation of the dielectric properties of living aquatic worms (Lumbriculus variegatus) using impedance spectroscopy in a frequency range between 100 Hz and 10 MHz. We demonstrate a linear relation between the worm biomass and the phase response of the signal thereby providing a quick and precise method to determine the biomass of aquatic worms in situ. Possible applications for non-destructive online biomass monitoring of aquatic worms and other aqueous organisms are discussed. Furthermore, we show that groups of worms fed different diets can be distinguished by the method presented. These results reveal a close relationship between the nutritional composition of the worms and the measured phase response. We also demonstrate that the phase response at 90 kHz does not depend on the worm size. In contrast, the response function for the signal at 440 Hz reveals a linear correlation of average individual worm size and phase. Therefore, we conclude that the measured phase response at 90 kHz qualifies as a measure of the total amount of worm biomass present in the measuring cell, whereas the phase measurement at 440 Hz can be used to estimate the average individual worm size.
Comparison of the phylogenetic performance of neodermatan mitochondrial protein‐coding genes

We examined the ability of all protein‐coding genes of 11 neodermatan mitochondrial genomes to recover the phylogeny of their combination. We subsampled randomly selected lengths (1–6000 bp) of contiguous sequence to consider the effect of length (100–6000 bp) on performance. All genes performed as well as randomly selected regions except ND2 (better) and ND5 (worse). All expected nodes were recovered (> 90% bootstrap) when 4.0 Kb had been sampled; 40 samples of 100 performed as well as four samples of 1000.
Impact of a fungal pathogen, Colletotrichum coccodes on growth and competitive ability of Abutilon theophrasti.

The combined effects of planting density and of different inoculation frequencies ofColletotrichum coccodes (Wallr.) Hughes on growth and competitive performance of Abutilon theophrasti Medik. were studied using a soybean-A. theophrasti target-neighbour design in a controlled environment. In both trials of the experiment, A. theophrasti inoculated at the highest planting density (four plants per ppt) suffered significantly greater reductions in height (41%) than did A. theophrasti at the lowest density (one plant per pot) (7%). Above-ground biomass and leaf area reductions, however were significantly greater at the highest density for only one of the trials. Soybean plants grown with inoculated A. theophrasti at the two highest planting densities had a significantly greater above-ground biomass (61%) and leaf area (68%) than did plants grown with uninoculated A. theophrasti at the same densities. By contrast, at the two lower densities, soybean above-ground biomass and leaf area were not increased significantly fallowing inoculation. Either one or two C. coccodes inoculations caused the greatest reductions in A. theophrasti growth compared with uninoculated plants. Conversely, three applications of the fungus generally resulted in less severe disease symptoms and resulted in the smallest decreases in A. theophrasti growth. Induced systemic resistance following two inoculations might have played an important role in limiting disease. However, the significantly greater biomass and height of A. theophrasti plants subjected to the triple C. caicudes treatment, compared with plants receiving either one or two inoculations in one of the trials, provides some evidence of a possible compensatory response in . 4. theophrasti. The relevance of these findings for biological weed control is examined.
Use of natural polymers as immobilizing agents and effects on the growth of Dunaliella salina and its glycerol production

Agar-agar, agarose, carrageenan and calcium alginate were used for the immobilization of Dunaliella salina cells. Out of the four, agar-agar was found to be the most effective and therefore the study was carried out on it using different pH values ranging from 6 to 10 and cell densities from 0.1 to 0.8 μg chlorophyll (chl, a) per bead to find which are is best suited for glycerol production. The maximum glycerol production of 9.2 μM/mg chl a was recorded in agar-agar immobilized algae and this was followed by 8.4 μM/mg chl a in calcium alginate. The maximum cell number 6.2 × 10 9 /ml and the specific growth rate (μ) of 0.80 1/day were reached at pH 8 in agar-agar immobilized algae. It was shown that the maximum amount of glycerol was produced when the cell density was 0.8 μg chl a/ block. Changing the medium after 24 hours affected the rate of glycerol production at different pH values. Using a cell density of 0.8 μg chl a/block at 16 W/m 2 light intensity increased the glycerol production in comparison with the use of free living cells.
Allozyme variation and genetic inter-relationships between seven flatfish species (Pleuronectiformes)

A total of 11 enzymes coded by 14 loci were assayed for each of 17 populations (from the north east Atlantic and Mediterranean) of seven flatfish species, including representatives of three of the four European families of the order Pleuronectiformes. Diagnostic alleles were observed for each species and there were fixed differences between the species at many loci. Thus all species were genetically distinct, although there were some common alleles. Hobs was higher than the average of a range of fish species and was also higher than that of vertebrate species as a whole. It seems that flatfish as a group may show higher levels of genetic variation than other fish. Values of genetic identity for all pairwise comparisons fell comfortably within the ranges expected. The data support the grouping of plaice and flounder into a single genus, Pleuronectes, but it is concluded that the retention of the dab in a separate genus, Limanda, is justified. A high level of genetic divergence was found between Dover and thickback soles. Genetic divergence data support the hypothesis that Pleuronectes flesus luscus in the Aegean Sea is a distinct subspecies of Pleuronectes flesus (flounder). The data show a clear separation of the Mediterranean Dover sole population from those in the Atlantic. Low genetic divergence was observed between the Aegean Sea and Atlantic brill populations. It is speculated that about 5 Mya the families Pleuronectidae and later Soleidae evolved from the ancestral Scophthalmidae.
RelB/p50 Dimers Are Differentially Regulated by Tumor Necrosis Factor-α and Lymphotoxin-β Receptor Activation

Tumor necrosis factor-α (TNF-α) and lymphotoxin-β receptor (LTβR) signaling both play important roles in inflammatory and immune responses through activation of NF-κB. Using various deficient mouse embryonic fibroblast cells, we have compared the signaling pathways leading to NF-κB induction in response to TNF-α and LTβR activation. We demonstrate that LTβR ligation induces not only RelA/p50 dimers but also RelB/p50 dimers, whereas TNF-α induces only RelA/p50 dimers. LTβR-induced binding of RelB/p50 requires processing of p100 that is mediated by IKKα but is independent of IKKβ, NEMO/IKKγ, and RelA. Moreover, we show that RelB, p50, and p100 can associate in the same complex and that TNF-α but not LTβ signaling increases the association of p100 with RelB/p50 dimers in the nucleus, leading to the specific inhibition of RelB DNA binding. These results suggest that the alternative NF-κB pathway based on p100 processing may account not only for the activation of RelB/p52 dimers but also for that of RelB/p50 dimers and that p100 regulates the binding activity of RelB/p50 dimers via at least two distinct mechanisms depending on the signaling pathway involved.
Effects of Epoxiconozale and Pyraclostrobin Fungicides in the Infection Process of Hemileia vastatrix on Coffee Leaves as Determined by Chlorophyll a Fluorescence Imaging

Coffee is the most traded commodity in the world, and Brazil is its largest producer. Coffee leaf rust, caused by the biotrophic fungus Hemileia vastatrix, is the most important coffee disease, reducing coffee yield by 35–50%. This study aimed to use the ratio of variable and maximum fluorescence of dark-adapted tissue (Fv/Fm) as a parameter to differentiate presymptomatic tissue from healthy tissue during disease development in plants sprayed with pyraclostrobin and epoxiconazole after 4 days postinoculation. Visual severity was considered as an indicative of apparent disease and true severity as an indicative of both apparent and non-apparent disease. There was a significant linear relationship between the areas of true severity and visual severity, and for each additional unit in the visual severity, there was an increase of 1.53 units on the true severity. For the epoxiconazole and pyraclostrobin treatments, coffee leaf rust symptoms decreased according to both visual and Fv/Fm images. Pustules on the leaves sprayed with epoxiconazole were smaller in size than those on the leaves of non-sprayed plants but bigger than those sprayed with pyraclostrobin. The reduction in Fv/Fm values at the pustule epicentres present on the leaves of plants sprayed with epoxiconazole, and pyraclostrobin was greater than those of the non-sprayed plants. This finding was expected and reflects the importance of these fungicides in prohibiting the progress of coffee leaf rust. The photosynthetic capacity of Coffea arabica was affected by H. vastatrix infection, and the Fv/Fm parameter was able to show this effect before the visual symptoms were noticed.
Lateral line deformities in wild and farmed sea bass (Dicentrarchus labrax, L.) and sea bream (Sparus aurata, L.)

Summary The lateral line of aquaculture fishes has rarely been studied although it is a very important anatomical organ that could serve as an inexpensive and easy tool to distinguish farmed from wild individuals. In the present study, lateral line deformities were examined in both wild and farmed sea bass (Dicentrarchus labrax) and sea bream (Sparus aurata) specimens to try to detail all possible differences between them. In order to do so, the morphology of the trunk lateral line in wild and farmed adults was examined whereby two major deformities were observed in both species: the ‘scale pocket’ deformity (14–40% incidence in all groups) where the specialized scales are missing but the canal underneath is present and the scale print is obvious, and the ‘somatic scales’ deformity (14–56% incidence in farmed individuals only) where the missing lateral line is covered with normal somatic scales. Histological examination confirmed the macroscopic observations in that the lateral line mechanism was present – although damaged – beneath the scale pocket deformity and completely absent beneath the somatic scales deformity. It is argued that the scale pocket deformity is a result of an accident during the life of the fish whereas the somatic scales deformity is an actual deformity in development.
Comparison of linseed (Linum usitatissimum L.) genotypes with respect to the content of polyunsaturated fatty acids

The aim of our work was to characterize linseed (Linum usitatissimum L.) genotypes divided into groups with high and low content of alpha-linolenic acid (ALA). Out of 32 linseed genotypes, 68.75 % represented high alpha-linolenic genotypes and 31.25 % were genotypes with low ALA content. Proportional representation of fatty acids was realized according to the norm (Czech Office for Standards, Metrology and Testing, 1994). Oil content was analyzed according to the internal methodology of Agritec Ltd., based on the norm (Czech Office for Standards, Metrology and Testing, 2011). The content of total fat ranged from 36.22 % to 46.35 %, that of ALA from 1.10 % to 65.20 %, and that of linoleic acid (LA) from 11.10 % to 75.00 % in the analyzed seed samples within all groups. The genotypes were divided also according to the seed color and a linear correlation between all three parameters within these groups was observed. Negative linear dependence was confirmed between parameters; ALA and LA content in the groups: high ALA brown seed (p < 0.0001; correlation coefficient (r) = −0.70), and high ALA yellow seed (p < 0.001; r = −0.36). Also, positive linear dependence between the total fat and the LA content in the groups: low ALA brown seed (p < 0.001; r = 0.34); low ALA yellow seed (p < 0.0001; r = 0.62), was found.
THE APPLICATION of ATP BIOLUMINESCENCE FOR the ASSESSMENT of MILK QUALITY and FACTORY HYGIENE

The speed of ATP bioluminescence assays makes them very useful for assessing product quality and efficiency of sanitation at food plants. the suitability of a new method for evaluating the quality of raw milk was compared with plate count. A good correlation was obtained between the ATP method and plate count for milks with counts above 1 × 104 cfu/ml. the combination of ATP bioluminescence with preincubation procedures was investigated for predicting the shelf-life of pasteurized milk. the best correlations were obtained when milks were preincubated at 15C for 25 h or at 21C for 25 h in the presence of an inhibitor system to prevent Gram-positive bacterial growth. Hygiene monitoring using bioluminescence gave a better indication of surface cleaniness than conventional swab counts. the reasons for the discrepancies in a small percentage of cases are discussed.
Do permit prices reflect the discounted value of fishing? Evidence from Alaska's commercial salmon fisheries

Nous prolongeons l'analyse de Karpoff (J.M. Karpoff. 1984. J. can. sci. halieut. aquat. 41: 1160-1166) qui montrait que les prix des permis de peche du saumon d'Alaska durant la periode 1975-1981 etaient lies au rendement de la peche conformement a la theorie des prix des elements d'actif. Nous avons elabore un modele semblable des prix des permis en utilisant les donnees sur les prix des permis et le rendement economique pour huit peches a la senne coulissante et au filet maillant au cours de la periode 1977-1990. Un examen des couts et des activites de peche pour 1979 nous a fourni des donnees permettant d'evaluer la relation transversale entre les couts de la peche, les caracteristiques des bateaux et les methodes de peche. On combine l'equation du cout transversal aux operations et aux caracteristiques des bateaux specifiques a la peche durant la periode 1977-1990, en vue de prevoir les couts a divers moments. Enfin, en calculant le rendement net en termes de la difference entre le revenu et le cout, nous estimons un modele d'anticipations adaptatives liant le rendement net aux prix des permis. En se fondant sur des essais de regroupement des deux types d'engins, nous sommes arrives a la conclusion que les peches a la senne coulissante et au filet maillant derivant devraient etre modelisees separement. Les estimations ainsi obtenues laissent supposer que le taux de rendement annuel reel est de 11 et de 6% pour la peche au filet derivant et a la senne coulissante, respectivement. A notre avis, ces resultats viennent confirmer que la limitation imposee par les permis permet de preserver les rentes economiques dans le domaine de la peche commerciale.
Separation of 24-Methylenecycloartanol from Cycloartenol Via a Chemical Method

A simple chemical method for the separation of 24-methylenecycloartanol [2] from a mixture of cycloartenol [1] and 2 has been developed. The method consists of five reaction steps: converting the 3-OH into 3-O-tetrahydropyran (3-OTHP), hydrocarboration of the double bond, mesylation, regeneration of the double bond, and removal of the protecting group. This approach is practical for large scale separation
Effect of High Lucerne (Medicago sativa L.) Sowing Rates on Establishment Year Yield, Stand Persistence and Forage Quality

The effect of very high sowing rates on establishment year dry matter (DM) yield and stand persistence of irrigated lucerne (Medicago sativa L.) was studied. Two cultivars (‘Peace’ and ‘Apollo II’) were sown in 1986 at two row spacings and six sowing rates from 5.6 to 50.4 kg ha−1. Established seedling density (Sd) increased linearly with sowing rate (R):Sd= 24.1R. Establishment year DM yield increased at sowing rates from 5.6 to 16.8 kg ha−1, levelled off as sowing rate increased to 33.6 ka ha−1, and then decreased as sowing rate increased further. Thus, there was a broad optimum sowing rate that gave a maximum sowing year DM yield. Percent plant survival to the third year (1988) decreased with increasing sowing rate so that plant densities became similar for sowing rates greater than 16.8 kg ha−1. Within the range 5.6 to 16.8 kg ha−1, increasing sowing rate increased stand persistence measured as 1988 plant density; however, a corresponding increase in DM yield was not obtained. For all full-production years, DM yield was independent of sowing rate. Sowing rate did not affect three chemical measures of forage quality.
Prospective Study of Type 1 and Type 2 Diabetes and Risk of Stroke Subtypes: the Nurses’ Health Study

W e thank Tuttolomondo et al. (1) for their interest in our study (2). In response, we would like to clarify several points. First, coding of strokes has been ongoing in the Nurses’ Health Study since 1976. We have not had funding to implement coding by TOAST (Trial of Org 10172 in Acute Stroke Treatment) classification (3) but hope to do so in the future. In an internal comparison of coding by Perth criteria (4) versus TOAST, the concordance rate for lacunar infarction was very high (91%); however, a percentage of large artery infarctions as classified by Perth coding criteria was classified as “unknown type” by TOAST criteria due to inconclusive carotid Doppler findings. Thus, it is possible that differences in stroke classification may have lead to slightly higher risk estimates for large artery infarction in our population. Second, our results are consistent with diabetes being a strong risk factor for lacunar infarction. As shown in Table 2 of the article, incidence rates for lacunar infarction were higher than for large artery infarction among women with type 2 diabetes (50 and 36 per 100,000 personyears, respectively), and risk estimates were also slightly higher for lacunar than large artery infarction (3.6 vs. 2.7 in ageadjusted analyses) compared with women without diabetes. Third, both fatal and nonfatal infarctions were included, but only first events were considered. Thus, our methods do differ from some hospital-based studies in that only first stroke events were included. As stated in the article, results were similar for confirmed (medical records) and probable (letter or telephone corroboration) cases, thus the combined results were presented (see p. 1731, column 2). Finally, as suggested by Tuttolomondo et al., it is possible that there are sex differences in the strength of association between diabetes and large artery infarction. Our results are limited to women, and we encourage further sex-specific evaluations of these associations.
Multiplication of Infectious Hematopoietic Necrosis Virus in Rainbow Trout following Immersion Infection: Whole-Body Assay and Immunohistochemistry

Abstract The sites of replication of infectious hematopoietic necrosis virus (IHNV) in infected tissues were detected in fingerling rainbow trout Oncorhynchus mykiss by in situ histologic techniques following immersion infection. Virus antigens in tissues were detected by a neutralizing mouse monoclonal antibody and a one-step anti-mouse biotin-streptavidin conjugated to horseradish peroxidase. The efficiency of infection and virulence of the virus determined by mortality rates showed high virulence of the selected IHNV isolates, and viral replication in individual fish showed that virus content of the fish increased rapidly from the second day to the seventh day postinfection. The earliest viral lesions following infection were detected in the epidermis of the pectoral fins, opercula, and ventral surface of the body. Virus lesions became evident in kidneys on the third day. By the fifth day, when there was a significant increase in virus titer, foci of viral replication were detected in gill tissue and i.
Importance of benthic production to fish populations in Lake Mead prior to the establishment of quagga mussels

Abstract Limnologists recently have developed an interest in quantifying benthic resource contributions to higher-level consumers. Much of this research focuses on natural lakes with very little research in reservoirs. In this study, we provide a contemporary snapshot of the food web structure of Lake Mead to evaluate the contribution of benthic resources to fish consumers. In addition, we document the available food to fishes on soft sediments and changes to the invertebrate community over 2 time periods. Benthic invertebrate food availability for fishes is greater in Las Vegas Bay than Overton Arm. Las Vegas Bay is dominated by oligochaetes, whose biomass increased with depth, while Overton Arm is dominated by chironomids, whose biomass did not change with depth. Diet and isotopic measurements indicate the fish community largely relies on benthic resources regardless of basin (Las Vegas Bay >80%; Overton Arm >92%); however, the threadfin shad likely contribute more to largemouth and striped bass production in Overton Arm versus Las Vegas Bay. A 2-time period analysis, pre and post quagga mussel establishment and during lake level declines, suggests there is no change in the density of benthic invertebrates in Boulder Basin, but there were greater abundances of select taxa in this basin by season and depth than in other basins. Given the potential of alterations as a result of the expansion of quagga mussel and the reliance of the fishery on benthic resources, future investigation of basin specific, benthic processes is recommended.
Overwintering Females and the Number of Generations of Typhlodromus (T.) pyri Scheuten (Acarina: Phytoseiidae) in Nova Scotia

Typhlodromus pyri Scheuten (= T. tiliae Oudms.) is the predominant species of predacious mite on apples in Nova Scotia. It feeds on a wide range of prey species (Herbert, 1959). Chant (1960) investigated the life-history and habits of this species in southeastern England and Herbert (1956) studied its life-history under controlled laboratory conditions. A knowledge of the life-histories of various components of the fauna is basic to an evaluation of predation; therefore, a study of the life-history and habits of T. pyri in the field was undertaken. This was supplemented by a laboratory study in which an attempt was made to duplicate field temperarures. The results of these studies are presented here.