Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Method for Estimating Protein Stability: the Work of Nick Pace

Urea and Guanidine Hydrochloride Denaturation of Ribonuclease, Lysozyme, α-Chymotrypsin, and β-Lactoglobulin (Greene, R. F., Jr., and Pace, C. N. (1974) J. Biol. Chem. 249, 5388–5393) Carlos Nick Pace was born in Salt Lake City, Utah in 1940. He received his B.S. in chemistry from the University of Utah in 1962 and his Ph.D. in biochemistry from Duke University in 1966. For his Ph.D. research, Pace worked with Journal of Biological Chemistry (JBC) Classic author Charles Tanford (1), who was interested in protein denaturation and solubility in various solutions. After doing a postdoctoral fellowship from 1966 to 1968 with Gordon Hammes at Cornell University, Pace joined the faculty of the Department of Biochemistry and Biophysics at Texas A&M University. ​University. Figure 1 Nick Pace As an independent researcher, Pace used the ideas and techniques he learned in Tanford's laboratory to study protein folding and denaturation. The JBC Classic reprinted here describes a new method for estimating protein stability called the linear extrapolation method. The method is the most widely used method for measuring protein stability, and the paper has been cited more than 370 times. In the paper, Pace and Raymond F. Greene, Jr. used optical rotation measurements to follow the unfolding of ribonuclease, lysozyme, α-chymotrypsin, and goat β-lactoglobulin in urea and guanidine hydrochloride. By analyzing the proteins' denaturation curves, they were able to make linear plots of the free energy of unfolding (ΔG) versus denaturant concentration. The plot's intercept gave a measure of the protein's stability whereas the slope gave an “m value” that measured how strongly ΔG depended on urea concentration. Pace's follow-up paper on m values (2) is the third most cited paper in the history of Protein Science with about 800 citations. Today, Pace remains at Texas A&M where he is a distinguished professor at the Health Science Center. He has received many awards and honors for his contributions to science, including a Texas A&M University Association of Former Students Faculty Distinguished Achievement Award in Research (1999) and a Distinguished Achievement Award for Teaching (1990), a Texas A&M University System Health Science Center College of Medicine Senior Investigator Excellence in Research Award (1999), the Texas A&M University Regents Professor Service Award (2001), and the Sigma Xi Distinguished Scientist Award (2002).
What Do Real Population Dynamics Tell Us About Minimum Viable Population Sizes

There is no single "magic" population size that guarantees the persistence of animal populations (e.g., Shaffer 1981; Gilpin & Soule 1986; Soule and Simberloff 1986; Lande 1988; Simberloff 1988). This is partly because extinction is probabilistic and partly because each minimum viable population (MVP) must be estimated separately, after considering characteristics of the population and environment under scrutiny. MVP estimates are then used to design and manage reserves for focal species. This approach is exemplified by studies reported in the Special Section on Population Viability Analysis in the March 1990 issue of Conservation Biology. The papers by Murphy et al. (1990) and Menges (1990) emphasize aspects of the dynamic nature of the spatial distributions of populations, and they stress the need to conserve what could be termed Minimum Dynamic Areas, often in reserve networks. Yet in the few remote and relatively unmodified regions of the world where reserve design is still possible on a large scale (e.g., parts of Amazonia), many focal species (e.g., large forest eagles) are too poorly known to calculate their MVPs and Minimum Dynamic Areas. Land use decisions will be made before the detailed information necessary to calculate specific MVPs has been obtained and incorporated into appropriate models. It might, however, be feasible to estimate population densities of representative focal species, and measure their home ranges (Thiollay 1989). This less detailed information could then be used to make provisional conservation recommendations, sometimes decades before more accurate MVP and Minimum Dynamic Area estimates could become available. To do this requires MVP guidelines, if not
The 3′→5′ Exonucleases of DNA Polymerases δ and ɛ and the 5′→3′ Exonuclease Exo1 Have Major Roles in Postreplication Mutation Avoidance in Saccharomyces cerevisiae

ABSTRACT Replication fidelity is controlled by DNA polymerase proofreading and postreplication mismatch repair. We have genetically characterized the roles of the 5′→3′ Exo1 and the 3′→5′ DNA polymerase exonucleases in mismatch repair in the yeast Saccharomyces cerevisiae by using various genetic backgrounds and highly sensitive mutation detection systems that are based on long and short homonucleotide runs. Genetic interactions were examined among DNA polymerase ɛ (pol2-4) and δ (pol3-01) mutants defective in 3′→5′ proofreading exonuclease, mutants defective in the 5′→3′ exonuclease Exo1, and mismatch repair mutants (msh2, msh3, or msh6). These three exonucleases play an important role in mutation avoidance. Surprisingly, the mutation rate in an exo1 pol3-01 mutant was comparable to that in an msh2 pol3-01 mutant, suggesting that they participate directly in postreplication mismatch repair as well as in other DNA metabolic processes.
Carnosine content and antioxidant activity from poultry co-products, protein meal and stressed poultry tissues

The aim of the present research was (1) to extract carnosine from different poultry by-products and (2) to measure their antioxidant activities using different analytical methods. Poultry by-products such as head, liver, lungs, tail, gizzard, brain and heart were collected from a poultry processing facility. Carnosine was extracted using a hot water extraction and the content was analyzed using HPLC. Thiobarbituric Acid Reactive Species (TBARS) inhibition, metal chelating activity, free radical scavenging activity and Oxygen Radical Absorbing Capacity (ORAC) values were used as parameters to evaluate antioxidant activity of the extract. Carnosine was present in all the tissue samples investigated. Liver had the highest (102.29 mg/gm) and brain the lowest carnosine content (0.95 mg/gm) (p ≤ 0.05). Except for the brain, all tissue ultrafiltrates and reconstituted dry powders showed TBARS inhibition ranging from 20.87-39.57% and 5.66 -14.47%, respectively. Head ultrafiltrate and reconstituted dry powder had the maximum while gizzard exhibited the minimum metal chelating activity (p ≤ 0.05). Free radical scavenging activity of ultrafiltrate from all tissues samples ranged from 25.11 to 79.38%, while this activity was higher (29.76 to 84.05%) in the reconstituted dry powder of all tissue samples. ORAC values were highest in liver ultrafiltrate and lowest in heart (p ≤ 0.05), with a similar trend in reconstituted samples with liver the highest and head the lowest ORAC values (p ≤ 0.05).
Book Reviews

yin and yang), including love and revenge: “A partner who is too good to be nasty destroys the relationship” (p. 39). Revenge must always be proportional (maybe a little bit less) to what was received or it will only escalate the problem, but it must occur to maintain a healthy relationship. Having 22 chapters in 162 pages, the book covers a broad range of topics without fully discussing any single topic. In some ways this probably does a disservice to Hellinger and his ideas, because nothing receives full discussion and often leaves the reader with more questions than answers. Some of his ideas as presented would be abhorred by feminists. He opposes abortion and adoption, thinks that incest is not really that big of a problem for the victim, and believes that women have traditionally received priority in the family but not outside of the home. The book is written as a conversation between the two authors and has the feel of an informal discussion between two highly intelligent people. Although it is very easy to read, it does lack the thoroughness one needs to understand fully the work and philosophy of Hellinger. Perhaps the book best serves as an introduction, allowing individuals to become acquainted with Hellinger, and those who desire a more complete understanding of him may choose to do further study. To that end, Acknowledging What Is is recommended to those individuals who want to maintain an awareness of the various theoretical approaches of therapy.
Architecture of β‐barrel membrane proteins: Analysis of trimeric porins

We have analyzed the known three‐dimensional structures of trimeric porins from bacterial outer membranes. The distribution of surface‐exposed residues in a direction perpendicular to the membrane is similar to that in helical membrane proteins, with aliphatic residues concentrated in the central 20 Å of the bilayer. Outside these residues is a layer of aromatic residues, followed by polar and charged residues. Residues in the trimer interface are more conserved than residues not in the interface. By comparing the interface and noninterface residues, an interface preference scale has been derived that may be used as a basis for predicting interface surfaces in monomer models.
Effect of Carbon Dioxide Immobilization on the Bleeding of Chickens

ABSTRACT INTRODUCTION MANY processors believe that the improvement of the meat type birds through breeding and high carbohydrate and low protein feeding has resulted in slower and less complete bleeding of the birds at slaughter. This, coupled with accelerated processing procedures, has resulted in increased percentages of poorly bled and misbled carcasses. A number of investigators have worked for remedies. They studied the effects of various degrees of starving prior to sticking, Baker, Margolf and Callenbach (1950); the use of various sticking techniques, Newell and Shaffner (1950); Davis and Coe (1954); the injection of epinephrine into the veins, the treatment of birds with high concentrations of oxygen, Newell and Shaffner (1950a); the feeding of special rations to birds, Turner (1948); and the influence of electric shock, Mountney, Gardner and Gayvert (1956). Other researchers in working to improve slaughtering methods for use on mammals, reportedly have been successful in improving bleeding by .
Book Reviews: The Psychology of Today's Woman: New Psychoanalytic Visions. Edited by Toni Bernay and Dorothy W. Cantor. New York: Analytic Press, 1986, 388 pp., $39.95

birth ; it is clear from these letters that for most mothers, such advice was impossible to follow. Without electricity, running water, washing machines, modem stoves, and store-bought foods, it is hard to fathom how women with several small children managed it all. In spite of the acknowledged deep commitment of the famous women leaders of the Children’s Bureau, I found their responses to the letters disappointing and cold in tone; many responses to heart-wrenching problems were simply referrals to doctors. Yet, as Ladd-Taylor notes, &dquo;The Children’s Bureau correspondence documents the gap between the competent medical practice assumed in the [Bureau’s] bulletins and the care women actually received . Mothers’ letters document their horrible experiences with medical care. &dquo; The consistency of advice to see doctors thus seems particularly unhelpful.
Optimization of folate deposition in eggs through dietary supplementation of folic acid over the entire production cycle of Hy-Line W36, Hy-Line W98, and CV20 laying hens

SUMMARY Supplementing laying hen diets with folic acid at 4 mg/kg of diet for 3 wk led to the production of folate-enriched eggs with an approximately 3-fold increase in egg folate concentration relative to a regular commercial egg. However, because long-term consistency in folate deposition is important for successful folate enrichment of natural foods such as eggs, 2 studies were designed to determine the level of folic acid required to maximize egg folate content and consistency throughout the entire cycle of egg production. In study 1, Hy-Line W36 and W98 laying hens (n = 156/treatment) received a barley-based diet containing 0 and 4 mg/kg of folic acid, whereas in study 2, a total of 1,248 Hy-Line CV20 laying hens (n = 416/treatment) received a barley-based ration supplemented with folic acid at 0, 2, or 4 mg/kg of diet. Both studies lasted for eleven 28-d periods. Response criteria included production parameters, egg quality measurements, and measures of egg folate content. Results of both long-term production studies support the use of 4 mg of folic acid/kg of diet as the recommended level of folic acid supplementation in terms of maximizing egg folate concentration over time. This is supported by the higher egg folate content and more consistent egg folate deposition at 4 mg of folic acid/kg of diet as compared with 0 and 2 mg of folic acid/kg of diet. Hy-Line W98, a strain of hens selected for large egg mass, benefited more from increased dietary folic acid in terms of increased egg production than did Hy-Line W36 and CV20 hens, strains selected for better egg efficiency and livability. Sensitivity and responsiveness to increasing dietary folic acid concentration in terms of egg folate content were, however, similar for all strains. In conclusion, eggs of laying hens were consistently enriched with folate by dietary supplementation with 4 mg of folic acid/kg of diet throughout the production cycle.
Growth and Longevity of the „Living fossil” Congeria kusceri (Bivalvia: Dreissenidae) from the Subterranean Dinaric Karst of Croatia

ABSTRACT The present study analyzed growth and longevity of the endemic cave dwelling bivalve Congeria kusceri obtained from the pit Jama u Predolcu, Croatia. A water temperature of 13–14°C constituted the lower limit for shell growth of C. kusceri. Obtained data also indicated that enhanced calcium uptake by C. kusceri during its summer growth and reproductive phases coincided with a decrease in alkalinity of the pit water. An analysis of shell growth rings in C. kusceri has identified an impressive longevity of 53 years. Calculations of growth rate suggested maximum theoretical shell lengths (L∞) of 16.7 mm for males and 18.7 mm for females and a growth constant of 0.04 year-1 for both sexes. Congeria kusceri can, however, grow to a shell length of > 24 mm, suggesting that longevity of this species could be greater than that identified in this study. The obtained results add to our understanding of how colonisation and continued and successful occupation of a subterranean freshwater habitat has been achieved.
Egg production and hatching success in the calanoid copepods Calanus helgolandicus and Calanus finmarchicus in the North Sea from March to September 2001

Spatial and seasonal egg production rates (E r ) and egg hatching success in the copepods Calanus finmarchicus and Calanus helgolandicus were measured in the North Sea from March to September. Food availability was monitored by chlorophyll and protist concentrations and three size fractions of seston fatty acids. Seasonal and spatial distribution and production differed between the species. Calanus finmarchicus was found only offshore of the 50-m isobath, with decreasing E r (37-28 eggs female- day -1 ) from March to July. Calanus helgolandicus had two abundance peaks, in spring and autumn, with a low in May during which time the highest E r were observed (38 eggs female- day -1 ). At other times, E r in C. helgolandicus remained lower than in C. finmarchicus (∼20 eggs female -1 day -1 ). Normalized E r (E n ) in both C. finmarchicus and C. helgolandicus were positively related to ciliate biomass while only negative relationships were found for all other variables measured. Hatching success in both Calanus species combined was significantly correlated with the essential fatty acid ratio 22:6n3/20:5n3.
Determination of polyphenols in beer by an effective method based on solid-phase extraction and high performance liquid chromatography with diode-array detection

The determination of polyphenols by spectrophotometric detection is complicated due to their low concentrations in beer. The beer samples have to be pre-concentrated before using the spectrophotometric detection for their quantification. An analytical method based on solid-phase extraction (SPE) and followed by high performance liquid chromatographic separation with diode-array detection is used for the determination of free gallic, protocatechuic, caffeic, p-coumaric, ferulic and salicylic acids, of (+)-catechin, (-)-epicatechin, and quercetin. These phenolic compounds participate in colloidal and sensory stability of beer. Six different SPE cartridges were tested and three different types of elution with the most appropriate solvents (acetonitrile, acetone and methanol) were used. The performance of the HPLC method was assessed by the evaluation of parameters such as absolute recovery, relative standard deviation (RSD - lower than 10%), the limit of quantification (LOQ), and the limit of detection (LOD). The polyphenol content in various types of Czech beer is presented.
Fire History Reconstruction in the Black Oak (Quercus velutina) Savanna of High Park, Toronto

ABSTRACT: We employed tree-ring analysis to reconstruct the fire history of High Park, Toronto, Canada, in one of the largest remnants of black oak (Quercus velutina) savanna in Ontario. This heavily urbanized area has a long history of fire suppression, which has degraded the native savanna. Efforts to reintroduce fire would benefit from a fire history record. Ring width patterns were quantified for 38 black oak chronologies on 14 cross-sections and 10 cores using dendrochronology software that employs scanned (digital) ring sequences. Scar and sealing patterns and rapid growth responses following scarring were dated to indicate the timing of fire events. These dates were compared with the timing of regeneration pulses and the establishment of multistemmed individuals that would have sprouted in response to fire disturbance. Our records suggest that most of the mature black oak stems established synchronously, around 1865, following an apparently extensive fire event or set of events. We have evidence of four other fires in the century that followed. Dendrochronology in black oak savanna presents challenges due to this tree species' thick bark, and the low intensity savanna fires that do not breach all individuals in a stand. Further, the present black oak population has succumbed to disease and old age, leading to decay of the central stem and the loss of the oldest rings that were more likely to be scarred as they formed during the tree's youth. This is likely to be a limitation in other savanna communities in long-settled regions of North America. We suggest inclusion of corroborative evidence, such as that employed in the present study, including the use of multistemmed individuals as indicators of stem recruitment following fire, and demographic data for the population.
Market studies are important in order to find the price behaviour of the product, its market trends and to measure more exactly the effects of certain management measures on the species.

The Spanish market is the most important market for hake and hake has been for many years the demersal fish most captured in Spain. To the traditional product differentiation due to size, gear and presentation form (fresh, frozen and frozen fillets), a new differentiation can be performed regarding the hake species. Furthermore, from a commercial point of view the definition of hake seems less strict, resulting that not all the species named hake belong to the Merluccius genus. The aim of this paper is to verify the existence of these differentiations between products and the relationships between markets.
Genetic and physiological factors influencing feather pecking in chickens

Feather pecking is a major welfare problem in egg production. It may be caused by endogenous (genetic and physiological) and environmental (feeding, density and housing conditions) factors. Despite the number and variety of experiments performed over past years, it is still not possible to define a genetic background for this trait. A possible reason is the complex nature of feather pecking, but also the lack of a homogenous approach in the studies conducted. The present paper summarizes recent findings regarding genetic and physiological components of feather pecking. Furthermore, it emphasizes the need for complex study combining a selection experiment together with the power of molecular biology and bioinformatics.
Sexual reproduction of Abies amabilis

Pollen-cone and seed-cone buds which differentiated in the summer and fall of the year before pollination resumed development in early April after about 5 months of dormancy. The sporogenous cells present in the dormant pollen-cone bud divided and formed pollen mother cells which began meiosis by mid-April. Meiosis was completed by late April and mature five-celled pollen was formed by the 3rd week of May. Wind pollination occurred in late May.Each ovule developed a curved funnel-shaped integument tip with a shallowly notched flange-like lip to which pollen readily adhered. No pollination drop was observed. Pollen remained attached to the integument tip but did not germinate for about 1 month, during which time the nucellus grew out nearly to the micropyle and the lip of the integument folded slightly inward bringing the pollen close to the nucellar tip. Pollen tubes then developed rapidly and penetrated the nucellus during the 1st week of July.Each ovule contained a single large megaspore mother cell in .
Improved salt tolerance of jute plants expressing the katE gene from Escherichia coli

There is an urgent need for developing crops with greater tolerance to environmental stresses. This is even more important for fiber crops, which are being pushed to the marginal low-productive lands in order to make more room for food crops. Jute is the source of a highly versatile and environmentally friendly natural fiber, and is second only to cotton in terms of production and variety of uses. In this study, we used a tissue culture independent method for introducing a CMV 35S promoter driven katE gene from Escherichia coli K12 into a popular jute cultivar (Corchorus olitorius var O-72) in Bangladesh. Molecular analysis of the transgenic plants using PCR, reverse transcription PCR, and Southern blot confirmed the insertion of the katE gene into the jute genome and its successful expression. Salt stress regimens (150 mM NaCl) showed that transgenic plants were more tolerant as compared to wild plants.