Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of host’s immune responses and parasite load in Mastomys coucha immunized with recombinant mitochondrial HSP60 of human lymphatic filarial parasite Brugia malayi

Recently we have shown that mitochondrial HSP60 of Brugia malayi (mtHSP60bm) shows high degree of homology with Escherichia coli GroEL/ES and that the ATP binding pockets of HSP60 in humans, E. coli and B. malayi were structurally conserved. In the present study we investigated the immune responses to rmtHSP60bm in Mastomys coucha and the fate of infection in the immunized animals. The animals received 4 immunization doses of rmtHSP60bm and were subsequently exposed to B. malayi infection. Microfilaremia, adult worm status, nitric oxide (NO), Th1 (IFN-γ, IL-2) and Th2 (IL-4, IL-10 and TGF-β) cytokine release, cell proliferative response, levels of specific IgG and its subclasses, and the mast cell status in lymph nodes were assessed on day 135/136 post infection. Immunization with rmtHSP60bm and subsequent exposure to infection resulted in significantly high microfilaraemia but without any change in adult worm burden. Immunization with rmtHSP60bm increased IgG, IgG1 and IgG2b levels, and IL-2 and IFN-γ release and suppressed NO release and CMI responses, but without any change in IL-4 and IL-10 release. Exposure of immunized animals to infection enhanced the CMI responses and , NO and IL-10 release but decreased IgG1 levels and IL-2 and IL-4 release; however, IgG, IgG2a, IgG2b, and IFN-γ responses remained unaltered. Mast cells in the draining lymph nodes of immunized-infected animals showed significant degranulation but without any increase in cell count. However, no pathology was found in the lymph nodes. These findings indicate that mtHSP60bm may modulate and balance the host’s immune responses to favour parasite survival without inducing any pathology.
Plasmid Replicon Typing of Commensal and Pathogenic Types of Escherichia coli Isolates

Vol. 73, no. 6, p. 1976-1983, 2007. Page 1982, column 2: Acknowledgments should read as follows. This project was funded, in part, by The Alliance for the Prudent Use of Antibiotics (APUA; supported by NIH grant no. U24 AI 50139) and the Iowa State University Biotechnology Council, Provost's Office
Body shape analysis of Bosnian mountain horses using Procrustes statistics

Abstract Procrustes analysis was performed on 4 samples of horse populations (11 Bosniak horses from a private farm in Nevesinje, 2 Bosniak horses from a former state farm in Han Piesak, 12 Bosniak horses from the former state stud farm Borike and 18 purebred Arabian horses from Borike) in order to analyse the differences in body shape between the samples. The twodimensional shapes of the horses were presented as coordinates of 11 landmarks, which were constructed from measurements taken from living animals. Relative warp analysis revealed a separation between three of the samples. The private Bosniak horses are located between the Borike Bosniaks and purebred Arabian horses. Due to the similar shape of private Bosniaks and Arabian horses, which could be proven also by thin plate splines, we can conclude that the privat breeder selected Bosniak horses which were smaller than the Borike Bosniaks but more similar to the Arabian type of horse.
Phylogenetic Relationships of Gunnera based on Nuclear Ribosomal DNA ITS Region, rbcL and rps16 Intron Sequences

Abstract A previous analysis of two chloroplast gene regions, rbcL and the rps16 intron, showed a clear phylogenetic pattern in Gunnera. However, these regions were not informative enough to completely resolve the phylogeny. In this study the nuclear ITS region was sequenced for 24 specimens representing 22 species of Gunnera. 223 characters out of 819 were informative and supported the same monophyletic groups as the chloroplast gene regions. Because of its greater information content, the ITS region identified additional well-supported clades. In an analysis based on the three gene regions together, 272 characters out of 3154 were informative. The results show that the South American annual, G. herteri is sister to all other species. The African G. perpensa is well-supported as sister to the remaining species, which form two well-defined clades, one with the Malayan G. macrophylla as sister to subgenus Milligania from New Zealand and Tasmania. In the other clade, the South American subgenus Misandra is sister group to subgenus Panke from South America and Hawaii. Within Panke the two Hawaiian species form a sister group to the American species. The morphological classification of Schindler, together with some biogeographical and morphological features, is discussed. Communicating Editor: Paul Wilson
Colony dispersion and nesting habits of the ants, Dolichoderus thoracicus and Oecophylla smaragdina (Hymenoptera: Formicidae), in relation to their success as biological control agents on cocoa

In mixed cocoa-coconut palm plantations in Malaysia the palm spadices provide large, stable nesting sites for Dolichoderus thoracicus (Smith) in contrast to impermanent sites on cocoa and on the ground. D. thoracicus and the arboreal leaf-nesting Oecophylla smaragdina (Fabricius) both benefit from the mixed system which also provides a more stable food supply from honeydew-producing Homoptera. A scoring method showed that about 50–200 O. smaragdina or 200–2000 D. thoracicus on a cocoa tree can protect it effectively from Helopeltis theobromae Miller (Hemiptera: Miridae). The relatively greater efficiency of O. smaragdina as a biological control agent is associated with its actively dispersive predatory behaviour in contrast to the localized concentration of D. thoracicus workers at sites such as cocoa pods where it tends honeydew-producing Homoptera, and where it acts largely by deterring H. theobromae. Despite its biological control potential, the painfully biting O. smaragdina , unlike D. thoracicus , is normally considered unacceptable to plantation staff. Nevertheless it should be recognized as valuable in integrated pest management of cocoa pests especially where D. thoracicus is difficult to establish.
Determination of some quality properties of marinated sea bream (Sparus Aurata L., 1758) during cold storage

Majority of the fish obtained by means of fishing and farming in our country is consumed fresh; this is followed by frozen produce and processed food prepared with other processing techniques. Consumption of processed aquaculture products is beneficial for preservation and storage of the product; this also makes it possible to benefit from the products even further. For this reason, undertaking of studies required for obtaining the maximum yield from available natural resources, in addition to this, exploitation and preservation of the obtained products as best as possible, and presentation of the products to consumption of people have also become important in our country as is the case in other countries. “Ready to eat” term is used for products which are prepared by applying appropriate processing techniques and preservation methods; have a certain endurance time; are consumed either directly or by heating to eating temperature; and are consumed
Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Fusarium species, the causal agent associated with mulberry root rot disease in Northeastern Thailand

Thirty isolates of Fusarium species associated with mulberry root rot disease were characterized by using morphological, pathogenicity and molecular characteristics. All isolates were identified into eleven species including F. solani, F. oxysporum, F. phaseoli, F. culmorum, F. moniliforme, F. graminearum, F.scirpi, F. anthophilum, F. dlamini, F. dimerum and F. beomiforme. They were tested for their pathogenicity on mulberry cutting in plastic glass, 30 days after inoculation showed that F. solani was the most pathogenic, causing root rot at 90% disease incidence. The present study showed that all isolates can recovered from fibrous root, lateral root and basal of the cutting trees at 38 – 96%, 22 94 % and 16.04 – 48.02%, respectively. This has been the first pathogenic proven since 1954 that F. solani is the causal agent of mulberry root rot. Amplified Ribosomal DNA Restriction Analysis (ARDRA) was used to analyze the ITS1 5.8S rDNA ITS2 region, amplified with primer ITS1 and ITS4. The amplified products (590 bp) were digested with the restriction enzymes AluI, EcoRI, HaeIII, HinfI and MspI. The dendrograms generated by combination all five enzymes enabled the differentiation of F. solani the causal agent of mulberry root rot from other species.
Redescription of four Polish Endonura Cassagnau, 1979 (Collembola, Neanuridae, Neanurinae), with a nomenclature of the ventral chaetae of antennae

A new diagnosis of Endonura Cassagnau, 1979 is given. E. dudichi (Loksa, 1967) comb. nov., E. incolorata (Stach, 1951) comb. nov., E. lusatica (Dunger, 1966) comb. nov. and E. tatricola (Stach, 1951) are redescribed based on type and new material from Poland, Ukraine, Hungary and Slovakia. Lectotypes of E. incolorata and E. tatricola are designated. Endonura szeptyckii (Weiner, 1973) is synonymized with E. tatricola. Data of occurrence, ecological preferences, variability and morphology of the first instar of the species are provided. New morphological characters with associated nomenclature are proposed.
Morphological and molecular analysis of Colletotrichum acutatum sensu lato

The genetic relationships between several morphological groups recognized within Colletotrichum acutatum sensu lato were investigated using RAPD analysis and vegetative compatibility analysis. Isolates were examined from fruit rots originating in New Zealand and Australia, from Lupinus spp. in New Zealand, Canada, France and the U.K., and from Pinus radiata in New Zealand and Australia. The genetic distinctness of the groups recognized morphologically is confirmed. Two genetically distinct groups of C. acutatum-like pathogens are recognized from lupin, one comprising isolates from New Zealand and the U.K., the other isolates from Canada and France. C. acutatum f. sp. pineum isolates from New Zealand and Australia form two genetically distinct groups.
Short-term variability of intertidal microphytobenthic production using an oxygen microprofiling system.

Despite their high productivity and their key role in coastal processes, intertidal areas remain poorly documented because alternating conditions of sediment-water and sediment-air interfaces result in inaccurate temporal estimations of interfacial carbon exchanges. This study describes the short-term variability of microphytobenthic production in an estuarine mudflat (the Canche estuary of the English Channel) by using an autonomous acquisition system for oxygen microprofiles. More than 240 profiles were measured at low and high tide during three deployments performed within a 3-week period (April–May 2007). Additional measurements characterised the surficial sediments (granulometry, porosity, chlorophyll a, temperature, salinity) and incident light. Depth-integrated gross production values were correlated with light intensity and reached up to 146 mg C m–2 h–1, while the turbidity of the overlying water prevented any primary production during immersion. Photosynthesis–irradiance curves were highly variable between field campaigns. Indeed, we have recorded a drastic reduction in microphytobenthic production, which might result from a pulse input of polychaete juveniles (Lanice conchilega). Ephemeral structures, such as invertebrate tubes, are seldom considered as factors that may influence the variability of benthic primary production. Monitoring oxygen microprofiles may be a useful tool for understanding and quantifying the impact of short-term temporal changes on the budgets of microphytobenthic production.
Comprehensive Analysis of Plant Gene Expression in Soybean Root Nodules at Different Growth Stages

Gene expression profiles in early (12 d after sowing, DAS), mature (35 DAS) and senescent (77 DAS) soybean (Glycine max (L.) Merr. cv. Enrei) root nodules were analyzed using Lotus japonicus cDNA macroarray. The cDNA macroarray membranes contained 18,144 independent cDNAs of L. japonicus isolated from various organs. The membranes were hybridized to 33P-labeled single-strand cDNAs transcribed from mRNA extracted from the soybean root nodules at three different growth stages. The results showed that over 75% of the cDNA clones gave a relative signal intensity (RSI) lower than 300, irrespective of the soybean growth stage. cDNA with an RSI value over 5,000 accounted for 2.1, 1.2 and 0.5% of the total cDNA clones at 12, 35 and 77 DAS, respectively. The highest RSI value was detected in a clone hybridized to putative pectinesterase (MWM097c10_r) at 12 DAS, while the RSI value of lycopene β-cyclase (MWL025d06_r) was the highest at 35 and 77 DAS. At 77 DAS, the percentage of transferase gene cDNA clones accounted for 20.5% of the total cDNA clones showing an RSI value over 500, a value clearly lower than that at 12 and 35 DAS. On the other hand, the percentage of hydrolase gene cDNA clones accounted for 45.2% at 77 DAS, a value around 1.5 times higher than that at 12 and 35 DAS. The chronological RSI profiles of individual cDNA clones were classified into nine patterns, and the profiles of the cDNA clones belonging to 15 homologous gene groups encoding enzymes of nitrogen and carbon metabolism, nodule specific proteins, enzymes of RNA and protein hydrolysis, and synthesis of jasmonic acid precursor were compared within and between groups. As a result, significant variations both within- and between-groups were revealed.
Preliminary Phytochemical Screening and Anthelmintic Activity of Desmodium Triflorum (L.) DC Leaf and Root Extracts

The present day study is an attempt to know the anthelmintic activity of the leaves and roots of the Desmodium triflorum (L.) DC. For this work, the leaves and roots were extracted separately with cold water, Methanol and petroleum ether by following maceration method. Various doses of cold water, methanolic and combined (cold water, Methanol and petroleum ether) extracts were evaluated for their anthelmintic activity on adult Indian earthworms, Pheretima posthuma. All extracts were able to show anthelmintic activity of 10mg/mL concentration. All the doses of cold water, methanolic and combined extracts of Desmodium triflorum (L.) DC showed dose dependent anthelmintic activity in comparison to standard drugs.
Effects of Defaunation and Urea on Glutathione and Malondialdehyde Levels in Blood and Ruminal Fluid of Ramlıç Lambs

The objective of this study was to investigate ruminal fluid and whole blood oxidant-antioxidant status in normal and fauna-free small ruminants. Forty male Raml›c lambs, a local breed in the Afyon area, with an average body weight of 32-36 kg and approximately 210 days old were used. The lambs were divided equally into 4 groups (faunated (F), defaunated (D), faunated + urea (FU) and defaunated + urea (DU)). Malondialdehyde (MDA) and glutathione (GSH) concentrations in the ruminal fluid and blood were measured. In comparison with the controls, all parameters were significantly higher in the fauna-free animals. The ruminal fluid MDA concentration decreased and the GSH level increased when 2.9% urea was added to rations. The defaunation procedure causes MDA formation to increase in the blood and ruminal fluid. The presence of 2.9% urea in rations may lead to lower oxidative stress and an augmented GSH level in rumen of fauna-free animals. Therefore, urea can be an important local antioxidant for the rumen of ruminants. As a result, defaunation may make the animals more susceptible to oxidative stress. Urea supplementation appears to reduce oxidative stress status and to support the antioxidant defense system in the rumen. Urea supplementation may be of major importance for fauna-free ruminants, whose ruminal antioxidant status may not be sufficiently well prepared to enhance performance. Ozet: Bu cal›flma, defaunasyon ifllemi uygulanan ve rasyonlar›na ure kat›lan hayvanlarda kan ve rumen s›v›s›n›n oksidan-antioksidan statusunu araflt›rmak amac›yla, 32-36 kg a¤›rl›klar›nda ortalama 210 gunluk 40 erkek Raml›c kuzuda gerceklefltirildi. Raml›c ulkemizde gelifltirilmifl onemli bir koyun ›rk›d›r. Oksidan-antioksidan gostergeler ise bir canl› icin onemli yaflamsal parametreler olarak kabul edilmektedir. Araflt›rma, yemlerine 2,9 oran›nda ure kat›lm›fl kuzular (FU), defaunasyon uygulanan kuzular (D), hem defaunasyon uygulanm›fl hem de yemlerine 2,9 oran›nda ure kat›lm›fl kuzular (DU) ve faunal› normal beslenen kuzular (F) olmak uzere 4 grup oluflturularak gerceklefltirildi. Rumen s›v›s› ve kan orneklerinde lipid peroksidasyonu urunlerinden malondialdehit (MDA) ve glutatyon (GSH) duzeyleri araflt›r›ld›. Defaunasyon iflleminin hem rumen hem de kan MDA ve GSH duzeylerini yukselttii izlendi (P < 0,01). Ote yandan rasyona ure ilave edilen defaunal› hayvanlarda rumen s›v›s›nda MDA duzeyi azalm›fl; GSH konsantrasyonu ise, hem F hem de FU grubundan daha yuksek duzeye ulaflm›flt›r. DU grubunda rumen MDA duzeyi kan MDA duzeyinden kontrol grubuna oranla dufluktur. Bu veri, urenin rumende oksidatif strese karfl› antioksidan yap›y› guclendirerek peroksidasyonu azaltabilecek potansiyel bir antioksidan olabileceini gostermektedir. Sonuc olarak; defaunasyon iflleminin ruminantlarda oksidatif strese yol acabilecei, ancak rasyona kat›lan 2,9 oran›ndaki urenin hayvan›n verimlilik ve direncini azaltan oksidatif stresten korunmada etkili olabilecei kanaatine var›lm›flt›r.
The infusion of biology into physics demonstrations

This article traces the design and development of two engaging biology-infused demonstrations for year 11 and 12 (age 17-18) physics in Singapore, and the affective responses to these demonstrations of student participants (n = 133). The infusion of biology into physics demonstrations as a strategy to meet some of the goals of current educational initiatives within Singapore in the area of physics education, and the usefulness of demonstrations as a tool in the teaching and learning of physics are highlighted.
Estimation Problems in Complex Field Studies with Deep Interactions: Time-to-Event and Local Regression Models for Environmental Effects on Vital Rates

Estimation Problems in Complex Field Studies with Deep Interactions: Time-to-Event and Local Regression Models for Environmental Effects on Vital Rates September 2015 Krzysztof M. Sakrejda, B.A. Vassar College M.S. University of Oregon Ph.D. University of Massachusetts, Amherst Directed By: Dr. Benjamin H. Letcher Field studies that measure vital rates in context over extended time periods are a cornerstone of our understanding of population processes. These studies inform us about the relationship between biological process and environmental noise in an irreplaceable way. These data sets bring “big data” and “big model” challenges, which limit the application of standard software (e.g., BUGS). The environmental sensitivity of vital rates is also expected to exhibit interactions and non-linearity, which typically result in difficult model selection questions in large data sets. Finally, long-term ecological data sets often contain complex temporal structure. In commonly applied discrete-time models complex temporal structure forces the analyst to make many competing decisions about discretizing time, which add complexity to any analysis and confuse the interpretation of parameters. I tackle these problems in three ways: 1) I apply and improve current state of the art statistical algorithms and software (Hamiltonian Monte Carlo with the NUTS sampler implemented in Stan) to implement the estimation of vital rates from mark-recapture data in a large Atlantic salmon data set; 2) I extend continuous-time time-to-event models with continuous estimated rate functions to mark-recapture and emigration data; and 3) I apply simple local regression to the estimation of vital rates to turn the model-selection problem resulting from interactions and non-linearity into an estimation problem, which is solved by the estimation algorithm. For each model I present methods for visualizing the results in biologically meaningful terms and use these for model criticism.
GROWTH CHARACTERISTICS OF MARINE PHYTOPLANKTON DETERMINED BY CELL CYCLE PROTEINS: THE CELL CYCLE OF ETHMODISCUS REX (BACILLARIOPHYCEAE) IN THE SOUTHWESTERN NORTH ATLANTIC OCEAN AND CARIBBEAN SEA 1

Ethmodiscus spp. is an important contributor to oceanic tropical‐ooze sediments and thus might be an important transport vehicle of carbon from the ocean surface to sediments. The knowledge of its cell cycle and growth rate, which is still lacking, is necessary to evaluate the importance of Ethmodiscus in nutrient cycling and to solve the discrepancy between its high sedimentary abundance and rarity in the plankton. We used immunofluorescence of a cell cycle protein, prolqerating cell nuclear antigen (PCNA), and DNA‐specific staining to study the progression of the cell cycle and roughly estimate the growth rate for E. rex (Rattray) Wiseman and Hendey in the southwestern North Atlantic Ocean and Caribbean Sea in June 1994 and January 1995.
Spontaneous vegetation succession in human-disturbed habitats: A pattern across seres

Vegetation samples from 15 successional seres in various disturbed habitats in the western part of the Czech Republic were analysed to detect possible trends. For particular seres, data on species cover were available from the onset to 10- 76 yr of succession. All seres started on bare ground. Species which attained at least 1% cover in any sere in any year were used as input data for Canonical Correspondence Analysis, assessing the effect of time as the environmental variable, for Detrended Correspondence Analysis and TWINSPAN classifi- cation. Two distinct groups of seres were distinguished: 'ruderal', occurring in agricultural, industrial or urban landscapes altered by men, usually on fertile sites; and 'non-ruderal', occurring in less altered, mostly forested landscapes, usually on acid, nutri- ent-poor and wetter soils. The former type of succession starts with ruderal annuals, being followed by ruderal perennials. In the latter case non-ruderal clonal perennials prevail from the onset of succession. The landscape frame is emphasized, beside site environmental conditions, as influencing the type of succes- sion. The character of species attaining dominance in succes- sion, participation of dominant woody plants and the character of late successional stages, i.e. features important from the point of view of potential restoration of human-disturbed habitats, are discussed.
Modeling seed dispersal of black cherry, an invasive forest tree: how microsatellites may help?

We used empirical models and three dispersal functions (Weibull, lognormal and 2Dt) to model seed distributions derived from the black cherry (Prunus serotina Ehrh.) understorey of a pine-dominated stand. Two different approaches were used to disentangle the overlapping seed shadows: the traditional inverse modeling approach and the genetic approach that uses microsatellite markers to assign a dispersed seed to its maternal parent. The distinction was made between the seeds passively dispersed by gravity (fruits with mesocarp) and those dispersed by birds (fruits without mesocarp). Our main objectives were to compare the three dispersal functions and assess the differences between the two approaches used. The functions performed equally well, but the lognormal function often showed a better data correlation. The best dispersal curves obtained by both traditional and genetic approaches were quite similar for the seeds dispersed by gravity, and 95% of these seeds were predicted to fall 5 and 3 m away from the parent tree for the traditional and genetic approaches, respectively. Differences were more important for the seeds dispersed by birds. The traditional approach predicted a lower number of seeds near the parent plant and a higher dispersal distance. Microsatellites provided accurate information on individual dispersal events and led to a better insight into the dispersal process.