Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteriophage proteins as affinity molecules for the detection of Salmonella, Cronobacter and Bacillus

Bacteriophage derived proteins have many possible applications in industry, and bacteriophage receptor binding proteins in particular have potential as affinity molecules. The aim of this project was to identify bacteriophages infecting Cronobacter species, which feature receptor binding proteins suitable for efficient binding of the pathogen. These are intended for further development as affinity molecules for detection of C. sakazakii in food. A library of novel bacteriophages specific for Cronobacter was isolated and their host range measured on a large collection of Cronobacter spp. and other Enterobacteriaceae species. Electron microscopy of six selected phages revealed they were Myoviruses. Two of these were sequenced and genomic analysis of vB_CsaM_A12 and vB_CsaM_B7 identified a close and syntenous genome wide relationship with Cronobacter phage vB_CsaM_GAP132,andE. coli phages RB16 and RB43. These E.coli phages are type pseudo T-even phages. The two novel Cronobacter phages have highly distinct host ranges, yet are virtually identical on a genomic level, with one notable exception of a point mutation in the receptor binding protein gp38. PCR screening identified a further ten similar phages from the original isolate collection, as well as the sequences of the respective receptor binding proteins. Multiple sequence alignments identified five unique receptor binding protein sequence types. Of these selected phages, vB_CsaM_A12 showed the broadest and most specific adsorption to bacterial cells, and was selected for further research towards the development of an affinity molecule from the receptor binding proteins. The data presented here offers interesting insight into an under researched field of phage-host interaction and the evolution of this infrequently studied phage population.
The first observation of Euphydryas aurinia (Lepidoptera, Nymphalidae) developing on Gentiana cruciata in Lithuania

A population of the endangered butterfly Marsh Fritillary Euphydryas aurinia, using exclusively Gentiana cruciata as a larval food plant, was recorded for the first time in the valley of the Dksta river (Vilnius administrative district) in Lithuania . Caterpillars were observed both in summer when they lived gregariously in numerous webs spun on gentians, and in spring when they were feeding on new shoots or basking in the sun. The butterfly is considered as dependent on Suc- cissa pratensis in Central and Northern Europe, therefore our finding is unexpected. Other plants including other Gentiana species are reported as locally used only in Southern Germany, Switzer- land and Spain. Phengaris'rebeli ' a well known butterfly related to G. cruciata occured sympatri- cally with E. aurinia at the Lithuanian site.
Novel metalloprotease–disintegrin, meltrin ϵ (ADAM35), expressed in epithelial tissues during chick embryogenesis

Members of the ADAM (a disintegrin and metalloprotease) family are involved in fertilization, morphogenesis, and pathogenesis. Their metalloprotease domains mediate limited proteolysis, including ectodomain shedding of membrane‐anchored growth factors and intercellular‐signaling proteins, and their disintegrin domains play regulatory roles in cell adhesion and migration. In screening for cDNAs encoding chicken ADAM proteins expressed during muscle development, we identified Meltrin ϵ as a novel member of this family. To elucidate its functions, we investigated its expression during development by using antibodies raised against its protease domain. In the somites, Meltrin ϵ protein was specifically expressed in the myotomal cells, which delaminate from the dermomyotome to form epithelial sheets. It was also found in the surface ectoderm, lens placodes, otic vesicles, and the gut epithelia. Basolateral localization of Meltrin ϵ in these epithelial cells suggests its unique roles in the organization of the epithelial tissues and development of the sensory organs and the gut. Developmental Dynamics 230:557–568, 2004. © 2004 Wiley‐Liss, Inc.
Co-Occurrence of the Invasive Banded and European Elm Bark Beetles (Coleoptera: Scolytidae) in North America

ABSTRACT The invasive European elm bark beetle, Scolytus multistriatus (Marsham), was detected in Massachusetts a century ago, and it now occurs throughout the continental United States and southern Canada. The Asian banded elm bark beetle, Scolytus schevyrewi Semenov, was discovered in the United States in 2003, and now occurs in 28 states and the province of Alberta, Canada. Although the indigenous populations of these two species are allopatric, the invasive populations are now sympatric in North America where they co-colonize elm (Ulmus spp.) trees. A large-scale survey of these two Scolytus species was conducted with baited funnel traps, Plexiglas panel traps, and Ulmus pumila L. trap logs. Sites (four per locality) were monitored around Sacramento, CA; Reno, NV; Ogden, UT; Newcastle, WY; and Fort Collins, CO (2006–2007), and Manhattan, KS, and Columbia, MO (both only in 2007). Trap catches of S. schevrewyi relative to both Scolytus species captured from all three trapping methods at each survey site were 90 and 89% in Colorado, 90 and 83% in Wyoming, 60 and 68% in Utah, 43 and 68% in Nevada, and 11 and 13% in California (all in 2006 and 2007, respectively), and 3.3% in Kansas and 2.7% in Missouri (both only in 2007). Elevated abundances of S. schevyrewi at survey sites in Colorado and Wyoming could be the result of competitive displacement of S. multistriatus by S. schevyrewi, whose occurrence and mechanism require further study. General seasonal trends from all sites indicated peak flight in July and August for S. schevyrewi and two peaks (May-June and July-August) for S. multistriatus. Funnel traps baited with Multilure and 2-methyl-3-buten-2-ol were highly attractive to S. multistriatus, and mildly attractive to S. schevyrewi, whereas panel traps caught few beetles. The U. pumila trap logs were a more sensitive monitoring tool for detecting the presence of S. schevyrewi.
Aphis craccivora Koch on wheat in Pakistan

Aphids are important insect pest of wheat (Triticum aestivum L.) which affect crop directly through feeding and indirectly by transmitting different viral diseases. Various aphids are reported in Pakistan and their population intensity on wheat crop is observed increasing over the last few years. An aphid specie on wheat was observed during 2009 which has consistent natural occurrence and association with the crop during the subsequent years (i.e. 2010-13) at the Nuclear Institute for Food and Agriculture (NIFA), Peshawar, Pakistan. Morph-taxonomic analyses of 2009 aphid collections were carried out and the aphid was identified as Aphis craccivora Koch commonly called cowpea aphid. This is the first report of Aphis craccivora Koch occurring on wheat in Pakistan. Further studies are needed to confirm this aphid as wheat pest and to explore its potential role as vector of barley yellow dwarf virus (BYDV's) the cause of barley yellow dwarf disease in cereals.
EVALUATION OF ANTIMICROBIAL ACTIVITY OF AN ENDOPHYTIC ASPERGILLUS SP. ISOLATED FROM AZADIRACHTA INDICA AGAINST PLANT AND HUMAN PATHOGENS.

ABSTACT Medicinal plants like neem which have been shown to contain bioactive compounds that exhibit multiple health benefits and are therefore, regarded as potential sources of new and improved therapeutic drugs. The present study aims to evaluate the antibacterial and antifungal activity of an endophytic Aspergillus sp. isolated from Azadirachta indica against ten selected plant and human pathogens. Out of the ten test pathogens, the Aspergillus sp. ’showed antimicrobial activity against eight pathogens. The endophytic Aspergillus sp. isolated from Azadirachta indica was found to exhibit the antibacterial activity against Gram-positive bacteria, Bacillus subtilis, and Gramnegative bacteria Escherichia coli (MTCC 40) and Pseudomonas fluorescens (MTCC 1748). The crude extract of Aspergillus sp. isolate inhibited the growth of opportunistic fungal pathogens, Candida albicans (MTCC 227) and Candida glabrata (MTCC 3814) which could not be inhibited by even the standard antifungal drug, Fluconazol. The Aspergillus sp. also showed zone of inhibition against phytopathogenic fungi Fusarium graminearum (MTCC 2089).
Regulation of shoot development in maize via brassinosteroid signaling

Brassinosteroids (BRs) are plant hormones involved in various growth and developmental processes. The BR signaling system is well established in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) but poorly understood in maize (Zea mays). BRI1is a BR receptor and database searches and additional genomic sequencing identified 5 maize homologs including duplicate copies of BRI1 itself. RNA interference (RNAi) using the extracellular coding region of a maize zmbri1 cDNA knocked down expression of all 5 homologs. Decreased response to exogenously applied brassinolide (BL), and altered BR marker
Effect of diet supplementation with Toyocerin® (Bacillus cereus var. toyoi) on performance and health of growing rabbits.

Two trials were performed to evaluate the effect of a dietary supplementation with Bacillus cereus var. toyoi on performance and health of growing rabbits. The studies were conducted in two commercial farms using the same experimental diets. In the first trial, 216 rabbits were controlled from 35 d (weaning) until 70 d of age. In the second trial, 180 rabbits were controlled from 37 until 79 d of age. At weaning, rabbits were put into bicellular cages, divided into three groups and fed the experimental diets: diet C, diet T1 and diet T2 supplemented with 0, 200 ppm (2x105 spores/g diet) and 1000 ppm (1x106 spores/g diet) of Toyocerin® (concentration: 1x109 B. cereus var. toyoi spores/g), respectively. The diets did not contain antibiotics or growth promoters and presented similar chemical composition (CP: 17.4% DM, NDF: 40.8% DM; ADL: 5.2% DM, starch: 16.5% DM). The differences in growth performance between the two trials depended mainly on the different final age of rabbits. Weight gain (42.0 vs 36.5 g/d) was lower and feed conversion (3.12 vs 3.96) higher in the second trial. Mortality (13.0% vs 21.7%) and morbidity (2.8% vs 25.0%) were significantly higher in the second trial. The probiotic supplementation (diet C vs diets T1+T2) significantly increased final live weight (2,517 vs 2,580 g; P=0.02) and daily weight gain (38.2 vs 39.8 g/d; P=0.01) and improved feed conversion (3.63 vs 3.50; P=0.01). Morbidity was significantly lower with supplemented diets (18.2 vs 10.3%; P=0.03), while mortality and sanitary risk were not affected by dietary treatment. No effect of probiotic inclusion rate (diet T1 vs diet T2) and no significant interaction between dietary treatment and trial were measured. In conclusion, the supplementation of Bacillus cereus var. toyoi improved growth performance and reduced morbidity of rabbits reared in farms with or without severe health problems. Increasing probiotic inclusion rate from 2x105 to 1x106 spores/g diet did not improve rabbit growth performance and health.
Evaluation of the genetic diversity of an Afghan wheat collection based on morphological variation, HMW glutenin subunit polymorphisms, and AFLP.

To reveal the genetic properties of an Afghan wheat collection maintained in Kyoto University, variations in morphological character and HMW glutenin subunit composition were investigated in 410 Afghan wheat accessions together with 65 accessions of Iranian and Pakistani wheat. The majority of the samples had primitive morphological characteristics, namely, tall plant height and lax spikes with a spelt head. The most frequent combination of HMW glutenin subunit was Glu-A1c (encoding subunit null), Glu-B1b (7 + 8), and Glu-D1a (2 + 12). Alleles preferable for modern breeding such as Glu-B1c and Glu-D1d were rare in our samples. Consequently, we concluded that the Afghan wheat accessions investigated in this study have genetic characteristics typical of landraces. As for their genetic diversity, the level of variation in the HMW glutenin subunit in Afghanistan was found to be equal to or lower than that in the neighboring countries. The largest variation was observed in Western Iran and Pakistan. AFLP analysis using 91 representative accessions also showed a comparatively low level of diversity in Afghanistan. These results suggest that a decrease in genetic diversity has occurred in Afghanistan. A novel HMW glutenin subunit (2.8) was found in this study, indicating the potential usefulness of Afghan landraces for wheat breeding.
Ochratoxin A is degraded by Yarrowia lipolytica and generates non-toxic degradation products

The mycotoxin ochratoxin A (OTA) is a common contaminant of various plant-derived foods and feeds. However, methods for complete decontamination remain to be established. Recently, biological approaches for mycotoxin removal using various species of yeast have been explored. In the present study, we investigated the efficacy of OTA degradation by the yeast Yarrowia lipolytica under various conditions, altering yeast concentration, temperature, pH, and concentration of OTA in order to determine the optimal requirements of this species. At a yeast concentration of 108 cells/ml, the degradation rate was higher than that observed at any other concentration and, after 24 h, the OTA concentration was reduced to almost half of the initial level introduced to the culture. Further, Y. lipolytica cultured at 28 °C showed the highest level of OTA degradation. Similarly, the culture performed optimally at a pH of 4. The initial concentration of OTA also affected the ability of the yeast to degrade OTA, with the level.
An SEM study of Acanthogyrus (Acanthosentis) tilapiae (Acanthocephala: Quadrigyridae) from Africa documenting previously unreported features and host parasite interface

Acanthogyrus (Acanthopsentis) tilapiae (Baylis, 1948) is the most widely distributed species of Acanthogyrus in many countries associated with the Nile River in Africa. It has been described by various authors but much of its external morphological features remained unknown until recently explored by SEM in our present study from specimens collected from cichlid fishes in Lake Malawi, Africa. Newly observed features include the proboscis armature and sensory pores, epidermal micropores, and trunk spines. Attachment and interface between worm and host intestinal lining are also reported for the first time.
Hazardous duty pay and the foraging cost of predation

We review the concepts and research associated with measuring fear and its consequences for foraging. When foraging, animals should and do demand hazardous duty pay. They assess a foraging cost of predation to compensate for the risk of predation or the risk of catastrophic injury. Similarly, in weighing foraging options, animals tradeoff food and safety. The foraging cost of predation can be modelled, and it can be quantitatively and qualitatively measured using risk titrations. Giving-up densities (GUDs) in depletable food patches and the distribution of foragers across safe and risky feeding opportunities are two frequent experimental tools for titrating food and safety. A growing body of literature shows that: (i) the cost of predation can be big and comprise the forager’s largest foraging cost, (ii) seemingly small changes in habitat or microhabitat characteristics can lead to large changes in the cost of predation, and (iii) a forager’s cost of predation rises with risk of mortality, the forager’s energy state and a decrease in its marginal value of energy. In titrating for the cost of predation, researchers have investigated spatial and temporal variation in risk, scale-dependent variation in risk, and the role of predation risk in a forager’s ecology. A risk titration from a feeding animal often provides a more accurate behavioural indicator of predation risk than direct observations of predator-inflicted mortality. Titrating for fear responses in foragers has some well-established applications and holds promise for novel methodologies, concepts and applications. Future directions for expanding conceptual and empirical tools include: what are the consequences of foraging costs arising from interference behaviours and other sources of catastrophic loss? Are there alternative routes by which organisms can respond to tradeoffs of food and safety? What does an animal’s landscape of fear look like as a spatially explicit map, and how do various environmental factors affect it? Behavioural titrations will help to illuminate these issues and more.
Benomyl inhibits phosphorus transport but not fungal alkaline phosphatase activity in a Glomus-cucumber symbiosis.

Short-term effects of benomyl on the arbuscular mycorrhizal fungus Glomus caledonium (Nicol. & Gerd.) Trappe and Gerdeman associated with Cucumis sativus L. were studied by measuring effects on fungal P transport and on fungal alkaline phosphatase activity. Mycorrhizal plants were grown in three compartment systems where nylon mesh was used to separate n root-free hyphal compartment (HC) and a root + hyphal compartment(RHC) from The main root compartment (RC). Non-mycorrhizal control plants were grown in similar growth units. After 6 wk benomyl was applied to the plants in three ways: as soil drenches to RHC or HC, or as u spray to the leaves. Benomyl was added in three concentrations. Equal amounts of 32 P and 33 P were added to the HC and to the RHC respectively, immediately after the application of benomyl. Plants were harvested 4-6 d later. Hyphal transport of 32 P from the HC was inhibited when benomyl was applied to the HC at 10 μg g-1 soil, whereas the uptake of 32 P from RHC I roots + hyphae) was reduced only at the highest dose of application to the RHC (100 μ g g-1 soil). In contrast to the marked reduction of benomyl on fungal P transport, the activity of fungal alkaline phosphatase inside the roots was unaffected by benomyl.
Computer-generated Keys to the Flora of Egypt. 2. The Chenopodiaceae

o overcome the well-known difficulties inherent in the identification of 77 species belonging to the 20 genera which represent the Chenopodiaceae in the flora of Egypt, two non-indented keys were constructed using the DELTA key-generating programs. One key was based on 46 morphological characters requiring no more than a hand-lens for use in identifying the plants in the field. Ten characters of stem anatomy were added to the dataset and used to construct the second key which serves the dual function of identifying specimens in the laboratory and confirming results obtained by the first key. While specimens of only 74 of the species were found in the four major herbaria (ALEX, CAI, CAID and CAIM), a re-run of the programs can easily bridge the gap in the two keys upon discovery of specimens of the three missing species.
Effects of chlorinated dioxins and furans on avian species : insights from in Ovo studies

In birds, activation of the aryl hydrocarbon receptor (AhR) by some polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) results in induction of cytochrome P4501A (CYP1A) expression. This response has been useful for predicting relative avian sensitivity to DLCs. To further investigate speciessensitivity to dioxins and DLCs induction of cytochrome P450 1A4 and 1A5 (CYP1A4 and CYP1A5) mRNA and ethoxyresorufin-O-deethylase (EROD) activity were quantified in liver of post-hatch White-leghorn chicken, Common pheasant and Japanese quail exposed to 2,3,7,8-tetrachlorodibenzo-p-doxin (TCDD), 2,3,4,7,8pentachlorodibenzofuran (PeCDF) or 2,3,7,8-tetrachlorodibenzofuran (TCDF) via air cell injection. The rank-order of sensitivity of TCDDand TCDF-exposed birds, based on CYP1A, was chicken > pheasant > quail. Based on CYP1A5 mRNA expression and EROD induction, the order of sensitivity of PeCDF exposed birds was identical to that for TCDD and TCDF. However, based on CYP1A4 mRNA expression the rank-order was pheasant > chicken > quail. When comparing the potency of the three compounds in each species, based on CYP1A4 mRNA expression, TCDD was the most potent compound in chicken. However, PeCDF was equally potent to TCDD in Japanese quail
Economic Analysis of Alternative Herbicide Regimes on Roundup Ready Soybeans

Roundup (glyphosate) is a nonresidual herbicide that controls grasses and dicot weeds but is injurious to soybeans. The development of Roundup-resistant soybeans [Glycine max (L.) Merr. ] (Roundup Ready soybeans) by Monsanto could allow farmers to substitute Roundup for all other herbicides to reduce production costs and weed control risk. Field trials at the University of Tennessee Milan Experiment Station from 1995 through 1997 were used to compare 1997 returns above variable costs for Roundup and 11 other herbicide systems on conventionally tilled, Roundup Ready soybeans. Although yields of only four herbicide systems on Roundup Ready soybeans were significantly lower than the yield of Roundup on Roundup Ready soybeans, net returns of nine systems were significantly lower. The significantly lower net returns resulted mostly from higher herbicide costs. Chemical companies would have to reduce the costs of most non-Roundup herbicide systems to unreasonably low levels (close to or less than zero) before farmers would have an economic incentive to use them instead of Roundup on Roundup Ready soybeans. Budgeted production costs for Roundup on Roundup Ready soybeans (Roundup Ready seed at $26/50 lb bag) were also compared with budgeted production costs for the non-Roundup herbicide systems on conventional soybean varieties (public-domain seed at $10.50/50 lb bag). Seven of the 11 non-Roundup herbicide systems on conventional varieties had costs that were greater than Roundup on Roundup Ready soybeans, suggesting that lower seed costs for the non-Roundup systems were more than offset by higher herbicide costs. Yields required to cover the cost differences between the non-Roundup herbicide systems and Roundup on Roundup Ready soybeans were calculated. These yield differences were added to the experimental yield obtained with Roundup on Roundup Ready soybeans to arrive at a break-even yield. A decision criterion for profit-maximizing farmers was developed from these break-even yields; if a profit-maximizing farmer expects to receive a yield from his/her highest-yielding conventional variety that is less than the break-even yield, the farmer should consider planting Roundup Ready soybeans to obtain a higher expected profit. If the decision criterion suggests staying with the conventional variety, the farmer should consider the nonbudgeted benefits of Roundup Ready soybeans, such as improved timeliness of planting and reduced weed control risk, before making the decision. To obtain more conclusive evidence about the relative profitability of Roundup Ready soybeans, future research should include side-by-side variety trials, more years of data, and no-tillage production methods.
Bioinformatics studies on induced pluripotent stem cell

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