bluuebunny/crossref_metadata_2025_split huggingface dataset:
MOLECULAR IDENTIFICATION OF PpHDAC1, THE FIRST HISTONE DEACETYLASE FROM THE SLIME MOLD PHYSARUM POLYCEPHALUM
Authors: Brandtner Eva‐Maria , Lechner Thomas , Loidl Peter , Lusser Alexandra 
Published: October 2002

AbstractThe dynamic state of post‐translational acetylation of eukaryotic histones is maintained by histone acetyltransferases (HATs) and histone deacetylases (HDACs). HATs and HDACs have been shown to be components of various regulatory protein complexes in the cell. Their enzymatic activities, intracellular localization and substrate specificities are regulated in a complex, cell cycle related manner. In the myxomycete Physarum polycephalum multiple HATs and HDACs can be distinguished in biochemical terms and they exhibit dynamic activity patterns depending on the cell cycle stage. Here we report on the cloning of the first P. polycephalum HDAC (PpHDAC1) related to the S. cerevisiae Rpd3 protein. The expression pattern of PpHDAC1 mRNA was analysed at different time points of the cell cycle and found to be largely constant. Treatment of macroplasmodia with the HDAC inhibitor trichostatin A at several cell cycle stages resulted in a significant delay in entry into mitosis of treated versus untreated plasmodia. No effect of TSA treatment could be observed on PpHDAC1 expression itself.
Pollen Evidence of Changing Holocene Monsoon Climate in Sichuan Province, China
Authors: Jarvis Devra I. 
Published: October 2002

AbstractPollen evidence from Lake Shayema, Mianning County, was obtained to examine postglacial vegetation and climatic change in southwestern Sichuan, China. The sclerophyllous character of the region's warm temperate vegetation today is a reflection of extreme drought in spring before the onset of the Asian monsoons. The pollen record displays several changes in the vegetation over the last 11,000 yr. From 11,000 to 9100 yr B.P., cold-tolerant species, such as Abies , Betula, and deciduous oaks, dominated the vegetation. Between 9100 and 7800 yr B.P., the abundance of deciduous oaks decreased and evergreen oaks increased, as did Tsuga and mesic deciduous species. This change suggests a warming climate with increased precipitation. From 7800 to 4000 yr B.P., sclerophyllous species increased at the expense of mesic deciduous species, an indication that precipitation was becoming more seasonal. Except for increased disturbance starting ca. 1000 yr B.P., the predominance of sclerophyllous vegetation continued until today. The pollen results are compatible with proposed global circulation hypotheses of a strengthened monsoon system during the early to mid Holocene.
Holocene Deglaciation, Sea-Level Change, and the Emergence of the Windmill Islands, Budd Coast, Antarctica
Authors: Goodwin Ian D. 
Published: October 2002

AbstractA Holocene deglaciation sequence for the Windmill Islands was determined from the 14C age of raised marine shorelines, lakebottom sediments, and Adelie penguin remains found in abandoned rookeries. A north-south gradient in the elevation of the upper marine limit was observed, with the highest marine limit (31-32 m) observed on Browning Peninsula and Hull Island at the southern edge of the islands. Correspondingly, the southern islands were found to have been deglaciated by 8000 (corr.) yr B.P. while the northern islands were deglaciated by 5500 (corr.) yr B.P. Isostatic uplift rates were calculated as 0.5 to 0.6 m/100 yr, with an estimated total uplift of around 53 m which indicates late Pleistocene ice sheet thicknesses of 200 and 400 m over the islands and adjacent Petersen Bank, respectively. The margin of the Late Pleistocene grounded ice sheet extended an estimated 8-15 km offshore which coincides with the location of the 200 m isobath.
Lake Levels and Sequence Stratigraphy of Lake Lisan, the Late Pleistocene Precursor of the Dead Sea
Authors: Bartov Yuval , Stein Mordechai , Enzel Yehouda , Agnon Amotz , Reches Ze'ev 
Published: October 2002

AbstractLake Lisan, the late Pleistocene precursor of the Dead Sea, existed from ∼70,000 to 15,000 yr B.P. It evolved through frequent water-level fluctuations, which reflected the regional hydrological and climatic conditions. We determined the water level of the lake for the time interval ∼55,000–15,000 cal yr B.P. by mapping offshore, nearshore, and fan-delta sediments; by application of sequence stratigraphy methods; and by dating with radiocarbon and U-series methods. During the studied time interval the lake-level fluctuated between ∼340 and 160 m below mean sea level (msl). Between 55,000 and 30,000 cal yr B.P. the lake evolved through short-term fluctuations around 280–290 m below msl, punctuated (at 48,000–43,000 cal yr B.P.) by a drop event to at least 340 m below msl. At ∼27,000 cal yr B.P. the lake began to rise sharply, reaching its maximum elevation of about 164 m below msl between 26,000 and 23,000 cal yr B.P., then it began dropping and reached 300 m below msl at ∼15,000 cal yr B.P. During the Holocene the lake, corresponding to the present Dead Sea, stabilized at ca. 400 m below msl with minor fluctuations. The hypsometric curve of the basin indicates that large changes in lake area are expected at above 403 and 385 m below msl. At these elevations the lake level is buffered. Lake Lisan was always higher than 380 m below msl, indicating a significantly large water contribution to the basin. The long and repetitious periods of stabilization at 280–290 m below msl during Lake Lisan time indicate hydrological control combined with the existence of a physical sill at this elevation. Crossing this sill could not have been achieved without a dramatic increase in the total water input to the lake, as occurred during the fast and intense lake rise from ∼280 to 160 m below msl at ∼27,000 cal yr B.P.
Effect of the use of vital dye, lymphoscintigraphy, or a combination for axillary lymphatic mapping and sentinel node biopsy in breast cancer
Authors: d’Eredita Giovanni , Serio Gabriella , Mele Marino , Giardina Carmela , Martellotta Martino , Ferrarese Filippo 
Published: October 2002

AbstractAxillary dissection in patients with breast cancer is associated with significant morbidity. Because 85% of the patients with a cancer ≤1 cm have negative axillary nodal status, axillary dissection in these patients is only a staging procedure. A study of the sentinel lymph node (SLN) biopsy has been developed to determine axillary nodal status by means of a minimally invasive procedure. The aim of our study was to estimate the degree of reliability for identifying the SLN using a vital dye or lymphoscintigraphy, or a combination of the two. From January 1999 to May 2000 a series of 60 patients with breast cancer were evaluated for enrollment in the study. For the mapping procedure, lymphoscintigraphy in combination with injection of vital blue dye was performed in 24 patients, and vital dye alone was utilized in 36. Complete axillary dissection was performed in all patients after SLN biopsy. The mapping procedure was possible in 59 cases (98.3%). The SLNs were positive in 19 patients (32.2%) and negative in 40; in 38 of the 40 patients all axillary nodes were negative. There was concordance in 57 of 59 cases (96.6%). The false‐negative rate was 5% (2/40). The overall sensitivity of the SLN biopsy was 90.4% (19/21), with a negative predictive value of 95% (38/40). Our results indicate that SLN biopsy guided by a gamma probe in combination with vital dye can identify a negative axilla with high accuracy. We conclude that the use of both techniques produces an optimal result, as they are complementanry.
Feeding standards for lactating riverine buffaloes in tropical conditions
Authors: PAUL SHYAM S. , MANDAL ASIT B. , PATHAK NITYA N. 
Published: September 2002

Data from 33 feeding trials, conducted on lactating riverine buffaloes from different institutes across India, were subjected to multiple regression analysis to derive nutritional requirements for dry matter (DM), total digestible nutrients (TDN), crude protein (CP) and digestible crude protein (DCP) for maintenance, milk production and body weight gain. Maintenance requirements for DM, TDN, CP and DCP were 59.9, 35.3, 5.43 and 3.14 g/kgW0.75, respectively; corresponding requirements for producing 1 kg 6% FCM were 688, 406, 90.3 and 55.2 g and for 1 g gain in body weight were 3.37, 1.97, 0.327 and 0.23 g. Regression equations had high R2 values (0.61, 0.66, 0.84 and 0.68 for prediction of DM, TDN, CP and DCP, respectively) and the equations (F-value) as well as coefficients were highly significant (P<0.001). Regressed values were used to derive feeding standards. Derived values matched well with the actual intake versus performance of animals under diverse feeding conditions. New standards predicted requirements and intake of nutrients for different production levels better than existing feeding standards. Because they are based on a more thorough analysis of data, the new feeding standards will be appropriate for use widely in India.
Microbial composition, including the incidence of pathogens, of goat milk from the Bergamo region of Italy during a lactation year
Authors: FOSCHINO ROBERTO , INVERNIZZI ALESSANDRO , BARUCCO ROBERTO , STRADIOTTO KATIA 
Published: September 2002

Sixty samples of raw goat milk intended for Caprino cheese-making were collected from ten farms in the Bergamo area over a 6-month period. Analyses of main microbial groups, somatic cell count (SCC) and pH were performed to determine the effect of origin (farm) and lactation period (April – September) on microbial composition and the incidence of pathogens in milk. Overall mean values were: standard plate count (SPC), 5.0×104 cfu/ml; yeasts, 2.5×102 cfu/ml; coliforms, 9.1×102 cfu/ml; Escherichia coli, 2.9 cells/ml; enterococci, 1.1×102 cfu/ml; lactococci, 3.4×103 cfu/ml; lactobacilli, 3.0×103 cfu/ml; halotolerant bacteria, 8.2×103 cfu/ml; spores of mesophilic aerobic bacteria, 11 cfu/ml; SSC, 9.9×105 cells/ml; pH, 6.63. Moulds and spores of sulphite-reducing clostridia were found intermittently. Neither Salmonella spp. nor Listeria monocytogenes was detected, while Esch. coli O157[ratio ]H7 was isolated from one milk sample (an incidence of 1.7%). Staphylococcus aureus was discovered at a level >102 cfu/ml in 26 samples (43%) with an overall mean of 1.2×103 cfu/ml, whereas coagulase-negative staphylococci were found in 54 samples (90%) with an overall mean of 1.3×103 cfu/ml. Of Staph. aureus strains, 23% proved to be enterotoxinogenic with a prevalence of enterotoxin C producers. Staph. caprae was the coagulase-negative species most frequently isolated; none of the coagulase-negative staphylococci strains synthesized any of the enterotoxins tested for.Sample source was the major factor affecting the microbial composition of goat milk: significant differences (P<0.01) were observed among samples from different farms for SPC, coliforms, lactococci, lactobacilli and halotolerant bacteria. Period of lactation had a significant effect (P<0.025) on SCC and pH. SPC correlated well with coliforms, lactococci and lactobacilli; SSC did not reveal positive interactions with any microbial groups or pH.
Manothermosonication of heat-resistant lipase and protease from Pseudomonas fluorescens: effect of pH and sonication parameters
Authors: VERCET ANTONIO , BURGOS JUSTINO , LOPEZ-BUESA PASCUAL 
Published: September 2002

The effect of different parameters (pH, ultrasonic amplitude and pressure) on the resistance to heat and manothermosonication (MTS) treatments of heat resistant lipase and protease produced by Pseudomonas fluorescens B52 and NCDO 2085, respectively, were studied. Lipase B52 thermoresistance decreases with an increase of pH. However, inactivation by MTS seems to be pH independent. There were only slight increases in the MTS efficiency when increasing pressure at UHT temperatures and the effect of amplitude was different depending on treatment temperature. Protease NCDO 2085, which was very resistant to MTS at 30 °C, was very sensitive to MTS at 76 °C. Increases in applied pressure had no effect on MTS efficiency at 140 °C and its inactivation by MTS was almost temperature independent between 76–109 °C. Data obtained are compared with previous published data and inactivation mechanisms are discussed.
Thermal inactivation of chymosin during cheese manufacture
Authors: HAYES MAURICE G. , OLIVEIRA JORGE C. , McSWEENEY PAUL L. H. , KELLY ALAN L. 
Published: September 2002

The aspartic proteinase, chymosin (EC 3.4.23.4) is the principal milk clotting enzyme used in cheese production and is one of the principal proteolytic agents involved in cheese ripening. Varietal differences in chymosin activity, due to factors such as cheese cooking temperature, fundamentally influence cheese characteristics. Furthermore, much chymosin is lost in whey, and further processing of this by-product may require efficient inactivation of this enzyme, with minimal effects on whey proteins. In the first part of this study, the thermal inactivation kinetics of Maxiren 15 (a recombinant chymosin preparation) were studied in skim milk ultrafiltration permeate, whole milk whey and skim milk whey. Inactivation of chymosin in these systems (at pH 6.64) followed first order kinetics with a D45.5 value of 100±21 min and a z-value of 5.9±0.3 °C. D-Values increased linearly with decreasing pH from 6.64 to 6.2, while z-values decreased as pH decreased from 6.64 to 6.4, but were similar at pH 6.4 and 6.2. Subsequent determination of chymosin activity during manufacture of Cheddar and Swiss-type cheese showed good correlations between predicted and experimental values for thermal inactivation of chymosin in whey. However, both types of cheese curd exhibited relatively constant residual chymosin activity throughout manufacture, despite the higher cooking temperature applied in the manufacture of Swiss cheese. Electrophoretic analysis of slurries made from Cheddar and Swiss cheese indicated decreased proteolysis due to chymosin activity during storage of the Swiss cheese slurry, but hydrolysis of sodium caseinate by coagulant extracted from both cheese types indicated similar levels of residual chymosin activity. This may suggest that some form of conformational change other than irreversible thermal denaturation of chymisin takes place in cheese curd during cooking, or that some other physico-chemical difference between Swiss and Cheddar cheese controls the activity of chymosin during ripening.
Expression of urokinase plasminogen activator receptor in resting and activated bovine neutrophils
Authors: POLITIS IOANNIS , ZAVIZION BORIS , CHELI FEDERICA , BALDI ANTONELLA 
Published: September 2002

Changes in urokinase-plasminogen activator (u-PA) and u-PA receptor (u-PAR) expression at the protein and mRNA level in resting neutrophils and in neutrophils activated by phorbol myristate acetate (PMA) were examined. Low amounts of u-PA were found intracellularly or membrane-bound in resting neutrophils. However, incubation of resting neutrophils with purified exogenous u-PA (10 IU/ml) revealed extensive binding of u-PA to cell membranes. Excess amino-terminal fragment of the u-PA molecule, a proteolytically inactive fragment of u-PA (amino acids 1–135) blocked binding of exogenous u-PA to the cell membrane. These results, collectively, indicate that the binding of u-PA is specific and that resting neutrophils have unoccupied u-PA receptors on their cell membrane. Addition of PMA led to an increase (P<0.01) in total cell-associated, membrane-bound u-PA activity and u-PA mRNA expression by bovine neutrophils. In contrast, PMA increased u-PAR mRNA levels but this was accompanied by a decrease (2.5-fold; P<0.01) in free, unoccupied u-PA binding sites. No significant effects on total cell-associated or membrane-bound u-PA were found when neutrophils were treated with 4-phorbol 12,13 didecanoate, a phorbol ester that does not activate protein kinase C (PKC). Furthermore, addition of 1-(5-isoquinolinesylphonyl)-2-methylpiperazine dihydrochloride (H-7), a potent PKC inhibitor, blocked the effect of PMA on total cell-associated u-PA activity. Thus, PKC plays a role in the modulation of u-PA and u-PAR by PMA in bovine neutrophils.
Lactobacillus reuteri DSM 20016: purification and characterization of a cystathionine γ-lyase and use as adjunct starter in cheesemaking
Authors: DE ANGELIS MARIA , CURTIN ÁINE C. , McSWEENEY PAUL L. H. , FACCIA MICHELE , GOBBETTI MARCO 
Published: September 2002

A homo-tetrameric ∼160-kDa cystathionine γ-lyase was purified to homogeneity from Lactobacillus reuteri DSM 20016 by four chromatographic steps. The activity was pyridoxal-5′-phosphate dependent and the enzyme catalyzed the α,γ-elimination reaction of L-cystathionine, producing L-cysteine, ammonia and α-ketobutyrate. The enzyme was active towards a range of amino acids and amino acid derivatives, including methionine. The pH and temperature optima were found to be 8.0 and 35 °C, respectively. Isoelectric pH (pI) was ∼5.0 as determined by two-dimensional electrophoresis. Sensitivity to chemical inhibitors was typical of lactococcal cystathionine γ- and β-lyases, except it was inhibited by sulphydryl reagents. The N-terminal sequence was MKFNTQLIHGGNSED, which had 100% homology with cystathionine β-lyase of Lb. reuteri 104R (Accession Number CAC05298). Lb. reuteri DSM 20016, together with 10 other strains of non-starter lactic acid bacteria, was used as adjunct starter in the production of miniature Canestrato Pugliese-like cheeses. After 40 d ripening, the water-soluble extract of the cheeses with added Lactobacillus fermentum DT41 and Lb. reuteri DSM 20016 contained the highest enzyme activities on cystathionine and methionine substrates. Determinations of methanethiol, dimethyl sulphide, dimethyl disulphide and dimethyl trisulphide in the miniature cheeses confirmed the findings of enzyme activities.
The weakly nonlinear interfacial stability of a
core–annular flow in a corrugated tube
Authors: WEI HSIEN-HUNG , RUMSCHITZKI DAVID S. 
Published: September 2002

A core–annular flow, the concurrent axial flow of two immiscible fluids in a circular
tube or pore with one fluid in the core and the other in the wetting annular region,
is frequently used to model technologically important flows, e.g. in liquid–liquid displacements in secondary oil recovery. Most of the existing literature assumes that the
pores in which such flows occur are uniform circular cylinders, and examine the interfacial stability of such systems as a function of fluid and interfacial properties. Since
real rock pores possess a more complex geometry, the companion paper examined the
linear stability of core–annular flows in axisymmetric, corrugated pores in the limit
of asymptotically weak corrugation. It found that short-wave disturbances that were
stable in straight tubes could couple to the wall's periodicity to excite unstable long
waves. In this paper, we follow the evolution of the axisymmetric, linearly unstable
waves for fluids of equal densities in a corrugated tube into the weakly nonlinear
regime. Here, we ask whether this continual generation of new disturbances by the
coupling to the wall's periodicity can overcome the nonlinear saturation mechanism
that relies on the nonlinear (kinematic-condition-derived) wave steepening of the
Kuramoto–Sivashinsky (KS) equation. If it cannot, and the unstable waves still saturate, then do these additional excited waves make the KS solutions more likely
to be chaotic, or does the dispersion introduced into the growth rate correction by
capillarity serve to regularize otherwise chaotic motions?We find that in the usual strong surface tension limit, the saturation mechanism of
the KS mechanism remains able to saturate all disturbances. Moreover, an additional
capillary-derived nonlinear term seems to favour regular travelling waves over chaos,
and corrugation adds a temporal periodicity to the waves associated with their
periodical traversing of the wall's crests and troughs. For even larger surface tensions,
capillarity dominates over convection and a weakly nonlinear version of Hammond's
no-flow equation results; this equation, with or without corrugation, suggests further
growth. Finally, for a weaker surface tension, the leading-order base flow interface
follows the wall's shape. The corrugation-derived excited waves appear able to push
an otherwise regular travelling wave solution to KS to become chaotic, whereas
its dispersive properties in this limit seem insufficiently strong to regularize chaotic
motions.
Understanding protein folding with energy landscape theory Part I: Basic concepts
Authors: Plotkin Steven S. , Onuchic José N. 
Published: September 2002

1. Introduction 1112. Levinthal's paradox and energy landscapes 1152.1 Including randomness in the energy function 1212.2 Some effects of energetic correlations between structurally similar states 1263. Resolution of problems by funnel theory 1283.1 Physical origin of free-energy barriers 1334. Generic mechanisms in folding 1384.1 Collapse, generic and specific 1394.2 Helix formation 1394.3 Nematic ordering 1414.4 Microphase separation 1425. Signatures of a funneled energy landscape 1456. Statistical Hamiltonians and self-averaging 1527. Conclusions and future prospects 1568. Acknowledgments 1579. Appendix: Glossary of terms 15710. References 158The current explosion of research in molecular biology was made possible by the profound
discovery that hereditary information is stored and passed on in the simple, one-dimensional
(1D) sequence of DNA base pairs (Watson & Crick, 1953). The connection between heredity
and biological function is made through the transmission of this 1D information, through
RNA, to the protein sequence of amino acids. The information contained in this sequence is
now known to be sufficient to completely determine a protein's geometrical 3D structure, at
least for simpler proteins which are observed to reliably refold when denatured in vitro, i.e.
without the aid of any cellular machinery such as chaperones or steric (geometrical)
constraints due to the presence of a ribosomal surface (for example Anfinsen, 1973) (see
Fig. 1). Folding to a specific structure is typically a prerequisite for a protein to function,
and structural and functional probes are both often used in the laboratory to test for the
in vitro yield of folded proteins in an experiment.
A review of DNA sequencing techniques
Authors: França Lilian T. C. , Carrilho Emanuel , Kist Tarso B. L. 
Published: September 2002

1. Summary 1692. Introduction 1703. Sanger's method and other enzymic methods 1703.1 Random approach 1713.2 Direct approach 1713.3 Enzyme technology 1753.4 Sample preparation 1753.5 Labels and DNA labelling 1763.5.1 Radioisotopes 1763.5.2 Chemiluminescent detection 1763.5.3 Fluorescent dyes 1773.6 Fragment separation and analysis 1803.6.1 Electrophoresis 1803.6.2 Mass spectrometry – an alternative 1824. Maxam & Gilbert and other chemical methods 1835. Pyrosequencing – DNA sequencing in real time by the detection of released PPi 1876. Single molecule sequencing with exonuclease 1907. Conclusion 1928. Acknowledgements 1929. References 193The four best known DNA sequencing techniques are reviewed. Important practical issues
covered are read-length, speed, accuracy, throughput, cost, as well as the automation of
sample handling and preparation. The methods reviewed are: (i) the Sanger method and its
most important variants (enzymic methods); (ii) the Maxam & Gilbert method and other
chemical methods; (iii) the PyrosequencingTM method – DNA sequencing in real time by the
detection of released pyrophosphate (PPi); and (iv) single molecule sequencing with
exonuclease (exonuclease digestion of a single molecule composed of a single strand of
fluorescently labelled deoxynucleotides). Each method is briefly described, the current
literature is covered, advantages, disadvantages, and the most suitable applications of each
method are discussed.