Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of catchability equations for population estimation of marron, Cherax tenuimanus (Smith) (Decapoda : Parastacidae)

Marron in a 0 . 01-ha hatchery pond were sampled after sunset on 14 occasions over 2 years in a standardized manner using baited drop nets. An inventory of the total population was taken after each sampling by draining the pond. Variation in catchability. p, was analysed by linear logit models of p/(1 - p) using the likelihood ratio χ2- statistic G2 as a measure of goodness of fit. A reduction in G2 of 83% was produced by inclusion of water temperature. To (C); relative position of marron in the size distribution, S (rather than absolute size); and a between-years factor, Y. The following catchability equation was calculated: In[pI/(l-pI)] = -5.40 +0.523S-0.246S2 +0.220T+1.40Y. The catchability equation was then applied to drop-net catch numbers from stocks of marron of 2-2+ years old in 10 0.1-ha farm dams. Estimated cohort numbers were compared with 'true' values obtained by independent removal of the stocks by seining. Agreement was improved by adjusting these estimates for differences in Secchi disk values, D. between dams (because daytime sampling was pursued and illuminance markedly influences catch rates) and in coefficient of size variation, V, The latter was negatively correlated with catchability and appeared to reflect the intensity of size dominance in feeding competition. A catchability equation. including these additional factors, was calculated: In[pI/(l -pI)] = -0.081 +0.664S -0.214S2 +0,284T -0.668ln D - 19.5V. Compared with other methods of estimation in which equal catchability is assumed, this method takes into consideration variation in catchability, requires no marking of individuals, and needs only one sampling occasion to obtain an estimate of crayfish numbers. Because of dependence of catchability on size of marron, sample means over estimated mean individual body weight by 13-48%. The catchability equation was also used to correct for this bias.
Synergism between mutational meltdown and Red Queen in parthenogenetic biotypes of the freshwater planarian Schmidtea polychroa

Do parasites and accumulation of deleterious mutations act synergistically in balancing the costs of sex? We addressed this possibility in the freshwater planarian flatworm Schmidtea polychroa. Sexual and parthenogenetic forms of this species sometimes coexist but show no ecological separation. Previous studies indicate that in a mixed sexual/ parthenogenetic population in Lago di Caldonazzo (N. Italy) parthenogens get more frequently infected with parasites. At the same time, they suffer from higher embryo mortality, which has been interpreted as a sign of accumulation of deleterious mutations. In the present study, we test whether these two factors are correlated, by focusing on the differences among the clonal lineages of a predominantly parthenogenetic subpopulation. Our results suggest that, for two out of three parasite types found, the infections are positively associated with the indirect measure of host mutation load.
Response of a sulfonylurea (SU)-resistant biotype of Limnophila sessiliflora to selected SU and alternative herbicides

Abstract Sulfonylurea (SU) herbicides, known for their high herbicidal activity and low mammalian toxicity, were used since 1988 to control Limnophila sessiliflora and other broadleaf weeds on rice fields at Sennan Village, Akita Prefecture, Japan. Since 1996, control of L. sessiliflora with the SU herbicides was no longer satisfactory. Two greenhouse studies at Tohoku National Agricultural Experiment Station and one experiment in the rice fields at Sennan Village were conducted in 1997 to confirm L. sessiliflora resistance to SU herbicides and to compare herbicide treatments for control of SU-resistant L. sessiliflora . Greenhouse studies showed that the L. sessiliflora biotype from Sennan Village was cross-resistant to four SU herbicides, including bensulfuron-methyl (BSM), pyrazosulfuron-ethyl (PSE), imazosulfuron (IMS), and ethoxysulfuron (ETS). The resistant biotype was 300–900 times more resistant to SU herbicides than the susceptible biotype from Omagari, Akita based on GR 50 (50% growth reduction) values. Standard treatments of pretilachlor and pentoxazone or mixtures of simetryn + MCPA-thioethyl, ETS + pyrazolate + pretilachlor, BSM + cafenstrole + daimuron, and BSM + daimuron + cafenstrole + azimusulfuron applied postemergence controlled SU-resistant L. sessiliflora . In the field experiment, mixtures of IMS + cafenstrole + daimuron and BSM + mefenacet failed to control L. sessiliflora , but herbicide treatments controlling SU-resistant L. sessiliflora included postemergence applications of mixtures of esprocarb + dimethametryn + PSE + pretilachlor and BSM + thiobencarb + mefenacet and sequential applications of pretilachlor/thiobencarb + simetryn + MCPB, pretilachlor/bifenox + SAP, pretilachlor/MCPA-thioethyl + simetryn, and pretilachlor/BSM + thiobencarb + mefenacet. Our results suggest that the SU-resistant L. sessiliflora had not developed multiple resistances to herbicides with different modes of action. In particular, amide or phenoxy herbicides were effective control measures.
Hydroxyindole-O-methyltransferase, a Season-coding Enzyme for Melatonin Synthesis in the Pineal Gland of Rodents

The time giver hormone melatonin is secreted with both daily and seasonal rhythms in the mammalian pineal gland. We report here that the two main melatoninsynthesizing enzymes N-acetyltransferase (NAT) and hydroxyindole-O-methyltransferase (HIOMT) are differently involved in the regulation of the daily and photoperiodic rhythms of melatonin synthesis. The activity of the unstable NAT enzyme is stimulated acutely at night by norepinephrine via cAMP-dependent transcriptional mechanisms, indicating that it triggers the nocturnal increase in melatonin synthesis and drives its duration according to the night length. In contrast, the activity of the stable HIOMT enzyme is regulated chronically by a norepinephrine-induced, 2-fold increase in HIOMT mRNA that occurs every night. Such regulation leads to a photoperiodic variation in HIOMT activity which is positively related to duration of the night. Whether in vivo or in vitro, at high NAT activity, HIOMT activity appears to limit the amount of melatonin release. This suggests that HIOMT activity may tune the amplitude of the nocturnal increase in pineal melatonin secretion with photoperiodic variations.
The winter immunoenhancement hypothesis: associations among immunity, density, and survival in prairie vole (Microtus ochrogaster) populations

Seasonal variations in photoperiod, temperature, and population density have been shown to modulate immune responsiveness of animals in laboratory studies. To examine these associations under natural conditions, we monitored 3 populations of prairie voles (Microtus ochrogaster) for temporal variations in selected immunological parameters, population density, and survival rate from winter 1996 to spring 1997. Spontaneous and cytokine-stimulated T-cell proliferative responsiveness of prairie voles peaked in winter and declined in spring. Relative organ mass, hemolytic-complement activity, and in vivo hypersensitivity responses varied temporally but showed no clear seasonal trend. The population density and survival rate of all 3 prairie vole populations varied temporally and correlated with measures of immunity. Multiple regression analysis indicated that the model containing relative spleen mass, cytokine-stimulated T-cell proliferation, and in vivo hypersensitivity explained a significant amount of variab.
Accumulation of poly-β-hydroxybutyrate by Rhodobacter sphaeroides on various carbon and nitrogen substrates

Combinations of various carbon and nitrogen substrates were used to study poly-β-hydroxybutyrate accumulation and H2 evolution by Rhodobacter sphaeroides strain RV. The cells evolved hydrogen on lactate, pyruvate, or succinate under nitrogen-deprived conditions and on lactate-glutamate and pyruvate-glutamate media. Poly-β-hydroxybutyrate content under nitrogen-sufficient and nitrogen-deprived conditions was highest on acetate (up to ∼40% of cell dry weight). Transfer of the cells from ammonium to ammonium-free medium resulted in increases in the poly-β-hydroxybutyrate content on lactate and pyruvate of up to ∼15% and ∼20%, respectively. An increase in pH caused a decrease in H2 production and an increase in poly-β-hydroxybutyrate accumulation on lactate under nitrogen-deprived conditions.
Identification and discrimination of thiobacilli using ARDREA, RAPD and rep‐APD

A highly reliable procedure for fast identification and taxonomical categorization of thiobacilli is presented. The procedure includes RFLP analysis of PCR amplified 16S rDNA, 23S rDNA, and intergenic spacer rDNA between the 16S and the 23S rRNA‐genes (amplified ribosomal DNA restriction enzyme analysis – ARDREA), as well as genomic fingerprinting using random primers (RAPD) and repetitive primers (Rep‐APD). The taxonomic and discriminatory power of these three analytical approaches is compared. It is demonstrated that the RAPD and Rep‐APD methods provide taxonomic results which are in agreement with the classification based on the RFLP analysis of the highly conservative ribosomal RNA (rrn) operons of the strains studied. Moreover, both kinds of genomic PCR fingerprinting, due to the fact that they derive information from different parts of the whole bacterial genome which may possess different degrees of variability, are more informative than ARDREA. By them, a discrimination of closely related Thiobacillus strains is possible. In addition, they are easier to perform and faster than the ARDREA. Using the method described, it was found that one Thiobacillus isolate recovered from uranium waste heaps described in the literature as Thiobacillus ferrooxidans ATCC 33020 is taxonomically neither closely related to the type strain of the species, Thiobacillus ferrooxidans ATCC23270T, nor to any other strain of this species analysed in the present work.
Probiotics in aquaculture

Abstract Probiotics, which are micro-organisms or their products with health benefit to the host, have found use in aquaculture as a means of disease control, supplementing or even in some cases replacing the use of antimicrobial compounds. A wide range of microalgae (Tetraselmis), yeasts (Debaryomyces, Phaffia and Saccharomyces) and Gram-positive (Bacillus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Micrococcus, Streptococcus and Weissella) and Gram-negative bacteria (Aeromonas, Alteromonas, Photorhodobacterium, Pseudomonas and Vibrio) has been evaluated. However, the mode of action of the probiotics is rarely investigated, but possibilities include competitive exclusion, i.e. the probiotics actively inhibit the colonization of potential pathogens in the digestive tract by antibiosis or by competition for nutrients and/or space, alteration of microbial metabolism, and/or by the stimulation of host immunity. Probiotics may stimulate appetite and improve nutrition by the production of vitamins, detoxification of compounds in the diet, and by the breakdown of indigestible components. There is accumulating evidence that probiotics are effective at inhibiting a wide range of fish pathogens, but the reasons for the inhibitions are often unstated.
Recognition sequence of a highly conserved DNA binding protein RBP-Jx

DNA binding specificity of the RBP-J kappa protein was extensively examined. The mouse RBP-J kappa protein was originally isolated as a nuclear protein binding to the J kappa type V(D)J recombination signal sequence which consisted of the conserved heptamer (CACTGTG) and nonamer (GGTTTTTGT) sequences separated by a 23-base pair spacer. Electrophoretic mobility shift assay using DNA probes with mutations in various parts of the J kappa recombination signal sequence showed that the RBP-J kappa protein recognized the sequence outside the recombination signal in addition to the heptamer but did not recognize the nonamer sequence and the spacer length at all. Database search identified the best naturally occurring binding motif (CACTGTGGGAACGG) for the RBP-J kappa protein in the promoter region of the m8 gene in the Enhancer of split gene cluster of Drosophila. The binding assay with a series of m8 motif mutants indicated that the protein recognized mostly the GTGGGAA sequence and also interacted weakly with ACT and CG sequences flanking this hepta-nucleotide. Oligonucleotides binding to the RBP-J kappa protein were enriched from a pool of synthetic oligonucleotides containing 20-base random sequences by the repeated electrophoretic mobility shift assay. The enriched oligomer shared a common sequence of CGTGGGAA. All these data indicate that the RBP-J kappa protein recognizes a unique core sequence of CGTGGGAA and does not bind to the V(D)J recombination signal without the flanking sequence.
Effects ofα1-adrenergic Stimulation on L-type Ca2+Current in Rat Ventricular Myocytes ☆

The effect ofα1-adrenergic stimulation onl-type Ca2+current (ICa,L) in adult rat ventricular myocytes was investigated using three different methods of current recording. During conventional whole-cell recordings with 5 mm-BAPTA included in the pipette solution, phenylephrine (20μm) did not increase ICa,Lafter 10 min of application. With nystatin perforated-patch whole-cell recordings, phenylephrine potentiated ICa,L, although there were variations among myocytes. The most frequent response was a transient suppression of peak ICa,Lat 2 min of exposure followed by a sustained increase of current amplitude evident after 5–10 min exposure. The relative current amplitude 10 min after phenylephrine application was 1.08±0.05 compared to control (n=14 cells,P<0.05). During cell-attached single channel recordings, phenylephrine (1μm) increased thel-type Ca2+channel open probability (NPo) by 2.25±0.31-fold (n=21,P<0.01). It potentiated NPoby increasing the number of openings per sweep and also by promoting longer openings. These effects developed slowly in 10 min. Phenylephrine had no effect on unitary current amplitude. The potentiation was also elicited by methoxamine (5μm) and was blocked by prazosin (1μm), indicating that it was mediated byα1-adrenergic receptor stimulation. The increase in NPowas suppressed by chelerythrine, a protein kinase C inhibitor. Our results demonstrate that ICa,Lcan be enhanced byα1-adrenergic stimulation, and stress the importance of not disturbing the intracellular environment during studies of the modulation of cardiac ICa,Lbyα1-adrenergic stimulation.
Efficient Bacillus subtilis Cloning System using Bacteriophage Vector 01Q5J9

SUMMARY: An efficient system for cloning in Bacillus subtilis is described which uses a newly constructed bacteriophage vector, 01O5J9. The phage genome contains cloning sites for the enzymes BamHl, Xba and Sail, and can accommodate inserts of passenger DNA of at least 4 kbp. Recombinant phages, which can both plaque and lysogenize normally, are recovered after direct transfection of protoplasts in the presence of polyethylene glycol. Several fully functional sporulation genes and one biosynthetic gene from B. subtilis have been isolated from genomic libraries that were constructed with the new vector. The system may provide an alternative to some of the cloning methods currently available that use Escherichia coli as host.
Some observations on oxygen transport in conifer seedlings

Summary The diffusive flux of oxygen from the roots of intact conifer seedlings was measured by a polarographic technique. With an anaerobic solution bathing the roots maintained at 23° C and with their aerial parts in air, flux rates were appreciable from eight of the twenty-five seedlings tested. When the aerial parts were placed in oxygen, there was a large increase in flux from each pine seedling. While their general response was barely measurable, a significant but much smaller increase occurred from eight of the spruce. Oxygen transport through the plants appeared to be by diffusion chiefly in the gas phase and significant flux rates from the roots with aerial parts in air might indicate some capacity for wet soil tolerance in the seedlings concerned. When the external concentration of oxygen was increased five-fold there was a disproportionate increase in oxygen flux from pine roots indicating that respiration in the plants might be affecting the flux rates. By cooling the bathing medium to 30 C a further demonstration of the respiratory effect-a large increase in flux rate-was obtained. With respiration reduced by cooling, the flux rates from the pine seedlings increased approximately five-fold for a five-fold increase in the external oxygen concentration. Cooling did not induce any pronounced response from the spruce seedlings. Internal diffusional resistance and oxygen leakage from the sub-apical parts of the roots may account for the absence of high apical flux rates in the pines and the extremely low readings recorded for the spruce seedlings.
Mouse autoreactive γ/δ T cells I. Functional properties of autoreactive T cell hybridomas

A minor population of dendritic epidermal T cells (DETC) express the Vγ1. 1Cγ4Vδ6 T cell receptor and T cell clones and hybridomas derived from this subset constitutively secrete cytokines in culture secondary to recognition of an autoantigen. Activation of these autoreactive cells requires the use of the vitronection receptor (VNR) as an accessory molecule which interacts with the Arg‐Gly‐Asp‐Ser (RGDS) sequence of extracellular matrix (ECM) proteins. We have compared the functional properties of Cγ4+ hybridomas derived from newborn thymocytes and from adult spleen with the DETC hybridomas/lines in terms of their ability to secrete cytokines spontaneously and for the use of the VNR as an accessory molecule. Almost all of the Cγ4+ thymocyte hybridomas secreted cytokines spontaneously and in the majority of lines the most prominent cytokine secreted was granulocyte‐monocyte colony‐stimulating factor. In contrast, none of the four splenic Cγ4+ hybridomas secreted cytokines spontaneously although all were capable of cytokine production following activation via the T cell receptor. Although the thymocyte hybridomas did not grow as adherent cell lines in culture, constitutive cytokine production required engagement of the VNR by its ligand in ECM proteins. In all cases, cytokine production could be inhibited by an anti‐VNR monoclonal antibody as well as by soluble RGDS. The strong correlation of functional and molecular properties (see accompanying report) between thymocyte Cγ4+ hybridomas and Cγ4+ DETC suggests that the Cγ4+ DETC may be of thymic origin and that cells with potential for autoreactivity residing in the thymus at birth may populate other peripheral locations in the mouse. The data also support the concept that the VNR, and possibly other integrins, play a role as accessory elements for autoreactive cells and may be essential for the regulation of such activity.
SOLID-STATE PRODUCTION OF PHENOLIC ANTIOXIDANTS FROM CRANBERRY POMACE BY RHIZOPUS OLIGOSPORUS

ABSTRACT Cranberry pomace is a byproduct of the cranberry processing industry that can be targeted for production of value-added phenolic ingredients. Bio-processing of pomace by solid state fermentation (SSF) using food grade fungi provides unique strategies to improve nutraceutical properties and to produce functional phenolic ingredients. Several functional phenolic phytochemicals exist as glycosides or as other conjugated forms with reduced biological activity. We hypothesize that during SSF the fungal glycosidases mobilize some phenolic antioxidants in cranberry pomace and their activity by hydrolysis via β-glucosidase and releasing the aglycone. To develop this strategy we used food grade fungus Rhizopus oligosporus. Our goal was to target the release of simple phenolic aglycones and mobilized diphenyls. SSF of cranberry pomace was done for 16 days with nitrogen sources, ammonium nitrate (NH4NO3) and fish protein hydrolysate (FPH). The two nitrogen treatments increased water extractable phenolics by 15–26% by day 10 in the pomace. Antioxidant protection factor was highest on day 10 for both nitrogen treatments and was 20–25% higher than control for water extracts and 16.5–19.5% for ethanol extracts. The DPPH radical inhibition (DRI) capacity increased by 5% only for the NH4NO3 treatment and gradually decreased for FPH treatment in water extracts. There was no significant change in DRI of the ethanol extracts. The β-glucosidase activity increased by 60-fold for NH4NO3 treatment and by over 100-fold for FPH treatment and correlated well with the increase in the extractable phenolics and antioxidant activity. Changes in diphenyl profiles during the solid-state process analyzed using HPLC indicated that ellagic acid increased by 4–5 fold in water extracts for both the nitrogen treatments. This increase was between 15–27% in the ethanol extracts. We conclude that SSF of cranberry pomace increased the antioxidant activity concurrent with increased β-glucosidase activity. The HPLC profile showed ellagic acid, a compound with anti-carcinogenic properties was enriched. The antioxidant function has implications for prevention of major oxidation-linked diseases such as cancer and CVD. This value-added SSF strategy is an innovative approach to enhance nutraceutically-relevant functional phytochemicals for food and feed applications.
Lipolytic Starter Culture Effects on Production of Free Fatty Acids in Fermented Sausages

Fermented sausages, inoculated with lipolytic and non lipolytic starter cultures and a control containing glucono-δ-lactone (GDL) and an antibiotic mixture were prepared. The sausages were analyzed on the basis of color, pH, water activity, weight loss, moisture and fat contents. Microbiological analyses were performed to measure total viable counts, lactobacilli and, staphylococci and micrococci. The increase in total and individual free fatty acids, and lipid oxidation was monitored. Results showed no difference (p>0.05) in the level of free fatty acids between treatments, indicating that lipolysis was most likely due to endogenous meat enzymes.
Wood Microbiology: Decay and Its Prevention

Introductory text on the principles of decay and discoloration processes in wood, with emphasis on the major fungal damages which may develop during the growth, storage, and use of wood. The characteristics, detection, effects, and control of microbial attacks are stressed. Provides a synthesis of the current literature on wood microbiology, a rapidly expanding field of study. (Abstractor's note: This is an important resource for conservation researchers studying the decay of wood in art and architecture.) The following is a list of chapter headings: 1) Introduction to wood microbiology; 2) Wood deterioration agents; 3) Characteristics and classification of fungi and bacteria; 4) Factors affecting the growth and survival of fungi in wood (fungal ecology); 5) Fungal metabolism in relation to wood decay; 6) The decay setting: some structural, chemical, and moisture features of wood in relation to decay development; 7) General features, recognition, and anatomical aspects of wood decay; 8) Chemical changes in wood caused by decay fungi; 9) Ultrastructural features of wood decay; 10) Changes caused by decay fungi in the strength and physical properties of wood; 11) Colonization and microbial interactions in wood decay; 12) Decays originating in the stems of living trees; 13) Biodeterioration of stored wood and its control; 14) Wood stains and discolorations; 15) Decay problems associated with some major uses of wood products; 16) Detection of internal decay; 17) Paint mildew and related degradative problems; 18) Natural decay resistance (wood durability); 19) Chemical protection of wood (wood preservation); and 20) Some trends in wood microbiology research and a new emphasis (biotechnology). -- AATA