Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Resource Banks

B iological diversity is the key to maintaining life as we know it (Wilson 1992). However, rapidly growing human populations place extraordinary pressures on ecosystems, such as large-scale environmental destruction, habitat conversion, habitat fragmentation, and pollution. One reaction to these problems has been the emergence of conservation biology, an assemblage of scientific disciplines that are focused on sustaining biodiversity through a cooperative synthesis of ideas, information, and approaches. Virtually all conservation biologists agree that habitat preservation is the best way to conserve biodiversity. Setting aside large tracts of land so that they are free from human interference can protect many species, but this approach has also been charac-
A model for the temperature and density dependent reemergence of the bark beetle Ips typographus

A model is presented that describes the reemergence of parent spruce bark beetles, Ips typographus, based on breeding density and temperature conditions. Laboratory data obtained at one constant temperature provide the distribution of reemergence time and different combinations of threshold temperatures and degreedays (°D) at mean reemergence. Of these combinations, 167.71 °D above 7.5 °C gave the best correspondence between model prediction and field data obtained from densely infested standing trees. The model was in good agreement with the reemergence pattern found for two groups of infested logs under different temperature conditions when adjusted for the lower breeding density. The applicability of the model in the study of bark beetle reproductive biology and in forest management is discussed. The method used to construct the model should be useful in developing other models for poikilothermic processes.
Changes in Hemolymph Parameters in the Manila Clam Ruditapes philippinarum (Mollusca, Bivalvia) Following Bacterial Challenge

Abstract Manila clams, Ruditapes philippinarum, were experimentally challenged with a pathogenic bacterium, Vibrio P1, the causative agent of Brown Ring Disease. Changes in cellular and humoral hemolymph parameters were studied over a 7-week period. Hemocyte concentration increased to a maximum 2 weeks after exposure of the clams to the Vibrio and was considered as hemocytosis in response to the pathogenic stimulus. The hemocyte concentration decreased thereafter and low values were maintained up to 7 weeks. A significant rise of a peptidase activity was observed in the cellular fraction of hemolymph 3 days postchallenge. A peak of serum activity, 1 week postchallenge, probably reflected the release of this peptidase by hemocytes. However, the serum protein concentration in challenged clams did not show any significant variation. There was a conspicuous shift between the early enzymatic response in the cells and the rise of hemocyte concentration, which suggested that the cellular mobilization and the enzymatic responses are controlled by distinct mechanisms. Low peptidase activity levels in both hemocytes and serum were observed 2 weeks following challenge, whereas the number of clams exhibiting the symptoms of Brown Ring Disease increased, indicating the development of the disease. Indeed, both hemocyte concentrations and leucine-aminopeptidase-specific activity in infected clams decreased with increasing infection stages. The depletion of the hemolymph parameters in the late phase may be a consequence of physiological stress due to an harmful effect of Vibrio P1.
Reseating of ecological gradients. II. The effect of scale on symmetry of species response curves

Response curves are presented for 15 species of vascular plants, bryophytes, and lichens relative to the water-table gradient in a boreal Norwegian mire. The gradient is scaled in two ways; position of median water-table in cm below the surface of the bottom layer, and in units of compositional turnover (rescaled by DCA). The two scalings produce quite different curves above the maximum water-level, which corresponds to median water-level 10–14 cm below the surface of the bottom layer. The significant drop in compositional turnover above this level can be ascribed to vertical differences in water-table having a lesser effect on plants in aerated hummocks than on plants in temporarily water-logged hollows. Skewness of response curves was reduced by gradient rescaling, most strongly after removal of influence of other gradients. It is argued that response curves will generally be Gaussian if: (1) the response is with respect to a dominant ecological factor, (2) the range of variation along the gradient is sufficient, (3) the distribution of samples is adequate, and (4), the gradient is scaled in units of compositional turnover.
Polycation‐induced oligomerization and accelerated fibrillation of human α‐synuclein in vitro

The aggregation and fibrillation of α‐synuclein has been implicated as a causative factor in Parkinson's disease and several other neurodegenerative disorders known as synucleinopathies. The effect of different factors on the process of fibril formation has been intensively studied in vitro. We show here that α‐synuclein interacts with different unstructured polycations (spermine, polylysine, polyarginine, and polyethyleneimine) to form specific complexes. In addition, the polycations catalyze α‐synuclein oligomerization. The formation of α‐synuclein–polycation complexes was not accompanied by significant structural changes in α‐synuclein. However, α‐synuclein fibrillation was dramatically accelerated in the presence of polycations. The magnitude of the accelerating effect depended on the nature of the polymer, its length, and concentration. The results illustrate the potential critical role of electrostatic interactions in protein aggregation, and the potential role of naturally occurring polycations in modulating α‐synuclein aggregation.
Accelerated Cheddar cheese ripening with encapsulated proteinases

This work was undertaken to study the impact of bacterial and fungal proteinases encapsulated in liposomes on proteolysis and organoleptic properties of Cheddar cheese during ripening. Bacterial and fungal proteinases were encapsulated in liposomes with trapping efficiencies of 31.9 and 33.0%, respectively. The encapsulated bacterial proteinase was incorporated into Cheddar-cheese milk in order to reach enzyme concentrations of 5 x 10 -6 (B 1 ). 1 x 10 -5 (B 2 ) and 2 x 10 -5 (B 3 ) AU g -1 cheese curd, while encapsulated fungal proteinase was added in order to reach enzyme concentrations of 1 x 10 -6 (F 1 ), 2 x 10 -6 (F 2 ) and 4 x 10 -6 (F 3 ) AU g -1 cheese curd. Experimental cheeses showed slightly higher moisture content but lower protein content when compared to control cheeses. Rheological measurements revealed that experimental cheeses were slightly less firm but more brittle as compared to control cheeses. Proteolysis and texture development of experimental cheeses were faster than control cheeses. As observed by transmission-electron microscopy, liposome-treated cheeses exhibited less compact microstructure and liposomes were essentially located at the fat-casein interface. The elution patterns obtained from size-exclusion chromatography revealed that the accumulation of bitter and astringent peptides was higher in experimental cheeses than in control cheeses depending on the type and concentration of added enzyme. After 3 months ripening, the organoleptic properties of cheeses were markedly improved and no bitter off-flavour was detected among treatments except cheeses subjected to treatments B 3 and F 3 . The present study showed that micro-encapsulated enzymes can be successfully used to accelerate cheese ripening and to avoid drawbacks resulting from the use of free enzymes. It was also concluded that the addition of encapsulated bacterial proteinase (up to 1 x 10 -5 AU g -1 cheese curd) or encapsulated fungal proteinase (up to 2 x 10 -6 AU g -1 cheese curd) could be recommended to accelerate the flavour and texture development of Cheddar cheese.
Improved performance and small intestinal development of broiler chickens by dietary L-glutamine supplementation

An experiment was conducted to evaluate the effect of L-glutamine (Gln) supplementation on performance and intestinal morphology of broiler chickens. A total of 192 day-old male broilers (Ross 308) were used in a completely randomised design with four treatments and four replicates of 12 birds each. Four experimental diets were formulated to be isonitrogenous and isocaloric with different levels of Gln supplementation (0, 0.5, 1.0 and 1.5%) in control and treatment groups, respectively and were fed for the first 3 weeks of life. On days 21 and 42, one bird from each replicate was slaughtered and morphometric indices of the small intestine were evaluated. Results obtained on days 21 and 42 showed increased ADWG in the birds that consumed 1% Gln supplemented diet compared to the control birds fed a standard corn-SBM diet (P≤0.05). On day 21, birds fed diets supplemented with 1 or 1.5% Gln had a significantly heavier duodenum and jejunum relative weight compared to the control birds (P≤0.05). Morphological assays showed that villus height and villus surface area of the duodenum and jejunum were significantly increased at both 21 and 42 days of age, as 1 or 1.5% Gln was supplemented in broiler diets (P≤0.05). The results of this study indicated that addition of 1% Gln to the diet for 21 days improved growth performance and small intestinal development of broiler chickens at the end of the starter (day 21) and grower (day 42) period.
Development of microsatellite markers for the minute pirate bug Orius sauteri (Poppius), and their cross-species amplification in O. minutus (L.) and O. strigicollis (Poppius) (Heteroptera: Anthocoridae).

We developed 14 polymorphic microsatellite markers for the minute pirate bug Orius sauteri (Heteroptera: Anthocoridae), and tested them with five markers previously developed in O. strigicollis. Except at one locus from O. strigicollis, we obtained amplified fragments from a field population of O. sauteri. The number of alleles ranged from 2 to 14, and observed heterozygosity ranging from 0.000 to 0.900. The observed heterogeneity was negatively correlated with null allele frequencies. Linkage disequilibrium was detected in three pairs of loci. The 19 microsatellite loci were also tested for amplification and polymorphism in two congeneric species, O. minutus and O. strigicollis. Markers could be amplified at many loci, although null allele frequencies were higher in cross-species amplification than in intra-specific amplification. These microsatellite markers will be used in studies of genetic diversity in these species.
On the Problem of Discovering the Most Parsimonious Tree

The problem of discovering the most parsimonious tree is defined in terms of a set of linearly arrayed sequences. Simplifications are introduced to reduce the total amount of work including the elimination of uninformative positions and the recognition of equivalent positions. The procedure can be applied to any array of sequences, including amino acid. It is shown, however, that failure to convert such sequences, through the genetic code, into nucleotide sequences is very wasteful of pertinent information. Parsimony is shown as a procedure that minimizes discordancies (parallel and]or back substitutions). A procedure (a discordancy diagram) is given that enables one to recognize when two characters (nucleotide positions) will necessitate the acceptance of such discordancies and how many, at least, will be unavoidable. Subtraction of these unavoidable discordancies from a matrix of potential discordancies leads to a matrix of avoidable discordancies that generally give at least two pairs of taxa that are most closely related parsimoniously (i.e., zero avoidable discordancies) and may therefore be replaced by an ancestral form determined by the parsimony process. The parsimony process is also given. The process may be repetitively performed until the tree is completed. A method of determining a lower bound to the number of substitutions required is given that gives a much larger lower bound than previous estimates. A quick estimate of the upper bound is also provided. An alternative approach, using a Prim-Kruskal network (minimal spanning tree) on the avoidable discordancy distances, is given together with a procedure for interpreting such networks in terms of a phylogeny that appears more natural than the dendrograms usually employed in the interpretation of singlelinkage diagrams. The reduction of a strictly bifurcating tree to a Prim-Kruskal network is called compression and its reverse is called decompression with the original tree being recovered after a complete cycle of the two processes. There is a unique one-to-one correspondence between any phylogenetic tree and its compressed network form. The compressed form can be the basis for an unambiguous linear representation of a tree that is more compact than that of any other known method of representation.
Use of macroporous adsorption resin for simultaneous desalting and debittering of whey protein hydrolysates

Summary Whey protein isolate (WPI) was hydrolysed to whey protein hydrolysates (WPH) of degree of hydrolysis equal to 15% using Protease N ‘Amano’ G (IUB 3.4.24.28) in a batch reactor at 55 °C and pH 7.0 according to the pH-stat procedure. Ash was removed by adsorbing WPH onto macroporous adsorption resins (MAR). Following rinsing with deionised water, desorption was achieved by washing with 20%, 40% and 75% alcohol (v v−1) to obtain the three fractions HS20, HS40 and HS75. Ash reduced from 15.71% (WPH) to 4.38% (HS20), 2.02% (HS40) and 2.38% (HS75). Similarly, the protein content was enriched from a low of 64.89% (WPH) to 94.74% (HS20), 95.32% (HS40) and 92.00% (HS75). The fractions were analysed for surface hydrophobicity (SHo), angiotensin-I converting enzyme (ACE) inhibition, emulsifying activity index, total amino acids composition and molecular weight distribution. Fraction HS75 was objectionably bitter, showed superior ACE inhibition (lowest IC50), had the highest content of hydrophobic and essential amino acids and contained about 71% of <600 Da with no fractions exceeding 4142 Da. Desorption with alcohol weakened the hydrophobic interaction forces between the peptides and resins and hence eluted the peptides, with the bitter HS75 being extracted.
Double-stranded RNA-induced Inducible Nitric-oxide Synthase Expression and Interleukin-1 Release by Murine Macrophages Requires NF-κB Activation*

The effects of double-stranded RNA (synthetic polyinosinic-polycytidylic acid; poly(I-C)) on macrophage expression of inducible nitric-oxide synthase (iNOS), production of nitric oxide, and release of interleukin-1 (IL-1) were investigated. Individually, poly(I-C), interferon-γ (IFN-γ), and lipopolysaccharide (LPS) stimulate nitrite production and iNOS expression by RAW 264.7 cells. In combination, the effects of poly(I-C) + IFN-γ are additive, while poly(I-C) does not further potentiate LPS-induced nitrite production. These results suggest that poly(I-C) and LPS may stimulate iNOS expression by similar signaling pathways, which may be independent of pathways activated by IFN-γ. LPS-induced iNOS expression is associated with the activation of NF-κB. We show that inhibition of NF-κB by pyrrolidinedithiocarbamate prevents poly(I-C) + IFN-γ-, poly(I-C) + LPS-, and LPS-induced iNOS expression, nitrite production and IκB degradation by RAW 264.7 cells. The effects of poly(I-C) on iNOS expression appear to be cell-type specific. Poly(I-C), alone or in combination with IFN-γ, does not stimulate, nor does poly(I-C) potentiate, IL-1-induced nitrite production by rat insulinoma RINm5F cells. In addition, we show that the combination of poly(I-C) + IFN-γ stimulates iNOS expression, nitrite production, IκB degradation, and the release of IL-1 by primary mouse macrophages, and these effects are prevented by pyrrolidinedithiocarbamate. These findings indicate that double-stranded RNA, in the presence of IFN-γ, is a potent activator of macrophages, stimulating iNOS expression, nitrite production, and IL-1 release by a mechanism which requires the activation of NF-κB.
Multispectral bacterial identification

A multi spectral optical technique was developed to simultaneously classify individual bacterial cells within mixed populations. Multi spectral Bacterial Identification (mBID) combines innovations in microscopy with a software analysis program to measure and characterize the fluorescence signals from multiplexed 16S ribosomal RNA probes hybridized to populations of different bacteria. Software was developed to identify individual bacteria at the level of species within these mixed populations. TO test the feasibility of mBID, we examined the fluorescence emissions from a mixture of probes specific for individual species of known bacteria from the American Type Culture Collection. Currently, up to seven species can be detected simultaneously by fluorescence microscopy. An eighth signal was reserved for a universal probe to control for fluorescence intensity. mBID can also be used to identify uncultured microorganisms. We plan to couple this new multi spectral technology to existing identification technologies that utilize 16S rRNA sequence alignment. Using this integrated identification protocol, bacteria that may be associated with chronic conditions will be identified first by analyzing their 16S rDNA sequences and then by visualizing them with flourescent probes hybridized to their 16S rRNA in situ.
NMR characterization of lignins from transgenic poplars with suppressed caffeic acid O-methyltransferase activity

Perturbing the lignin biosynthetic pathway provides a tool for understanding the complex process of lignification. Caffeic acid O-methyltransferase (COMT) is required to produce syringyl units in lignins. Down-regulating the expression of its gene in poplar dramatically affects the lignin composition. 2D and 3D NMR investigations detail structural differences between lignins from a control and COMT-deficient poplars obtained by means of two independent transformation techniques. This first application of 3D NMR to natural abundance lignins reveals the full side-chain network and provides diagnostic evidence for the intimate incorporation of 5-hydroxyconiferyl alcohol into the lignins to form novel benzodioxanes as major structures. The flexibility of a plant to utilize novel monomers to produce functional lignins provides opportunities for engineering the structure and affecting the consequent properties of lignins.
Cloning and Expression of a Wheat (Triticum aestivumL.) Phosphatidylserine Synthase cDNA

We describe the cloning of a wheat cDNA (TaPSS1) that encodes a phosphatidylserine synthase (PSS) and provides the first strong evidence for the existence of this enzyme in a higher eukaryotic cell. The cDNA was isolated on its ability to confer increased resistance to aluminum toxicity when expressed in yeast. The sequence of the predicted protein encoded byTaPSS1 shows homology to PSS from both yeast and bacteria but is distinct from the animal PSS enzymes that catalyze base-exchange reactions. In wheat, Southern blot analysis identified the presence of a small family of genes that cross-hybridized to TaPSS1,and Northern blots showed that aluminum induced TaPSS1expression in root apices. Expression of TaPSS1complemented the yeast cho1 mutant that lacks PSS activity and altered the phospholipid composition of wild type yeast, with the most marked effect being increased abundance of phosphatidylserine (PS). Arabidopsis thaliana leaves overexpressingTaPSS1 showed a marked enhancement in PSS activity, which was associated with increased biosynthesis of PS at the expense of both phosphatidylinositol and phosphatidylglycerol. Unlike mammalian cells where PS accumulation is tightly regulated even when the capacity for PS biosynthesis is increased, plant cells accumulated large amounts of PS when TaPSS1 was overexpressed. High levels ofTaPSS1 expression in Arabidopsis and tobacco (Nicotiana tabacum) led to the appearance of necrotic lesions on leaves, which may have resulted from the excessive accumulation of PS. The cloning of TaPSS1 now provides evidence that the yeast pathway for PS synthesis exists in some plant tissues and provides a tool for understanding the pathways of phospholipid biosynthesis and their regulation in plants.
Banded phosphorus effects on alfalfa seedling growth and productivity after temporary waterlogging.

Phosphorus applied in a band below alfalfa (Medicago saliva L.) seed can increase seedling growth. A field study was conducted to evaluate the effect of banded-P and temporary flooding stress on alfalfa seedling growth in the autumn and subsequent productivity. Experiments were seeded in late August 1994 and 1995 at two locations in Ohio on soils having P levels typical for the region. Fertilizer treatments included no fertilizer P and 27 kg P ha -1 (62 kg P 2 O 5 ha - 1 ) banded under the seed. Flooded and unflooded treatments were imposed 21 to 26 d after seeding. Flooding was maintained for 11 to 18 d, then plots were allowed to drain naturally. Before flooding was imposed, banded-P increased seedling dry weight by an average of 60%. Flooding reduced seedling dry weight regardless of P treatment. At end of the flooding period, seedlings with banded-P were larger than the flooded, no-P controls at three of the four locations. In November, flooded seedlings with banded-P had greater root dry weight at two locations and greater shoot dry weight at one location compared with the flooded, no-P controls. Flooding in the autumn reduced dry matter yield the next year at two locations. In 1995, banded-P increased yield the year after seeding ∼15% in the unflooded treatment at one location and ∼15% in the flooded treatment at the other location. Although banded-P increased seedling growth in the autumn regardless of flooding treatment, its effect on stand density and yield the year after establishment was minimal.
Screening of endogenous antioxidants in some medicinal plants

The evaluation of antioxidant enzymes and antioxidant metabolites was done in leaf tissues of Azadirachta indica, Butea monosperma, Cassia fistula, Mangifera indica, and Syzygium cumini growing in the Thar Desert, Rajasthan, India. The plants are naturally exposed to drought stress and high temperatures during summer. Enzymatic reactive oxygen species (ROS) scavenging mechanisms in plants include superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase, catalase, and guaiacol peroxidase, and non-enzymatic antioxidants including the carotenoids, proline, and vitamin C were studied. The strategies to cope up with ROS under these extreme conditions are plant-specific. The highest activity of APX was found in M. indica (13.6 ± 2.4 units g−1 fresh wt.). A. indica exhibited maximum guaiacol peroxidase activity (0.024 ± 0.006 units min g−1 fresh wt.), while S. cumini showed maximum SOD (12.5 ± 2.3 units g−1 fresh wt.) and catalase activities (6.9 ± 2.2 units g−1 fresh wt.). M. indica and S. cumini have been found to be more potent antioxidant systems among the studied plants.