Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary thinking as a tool in pharmaceutical development

The rapidly expanding technologies involving chemical synthesis and screening, genomics, and bioinformatics are leading to the point where every gene product can be modulated as a therapeutic target. Thus, pharmaceuticals increasingly offer the potential to control disease processes. While great strides in understanding disease processes can come from this mechanistic approach (addressing “how? ” questions), complete understanding is impossible without addressing the ultimate causation of disease processes. By addressing ultimate (“why? ”) questions, evolutionary thinking provides a firm theoretical framework for all biological processes, including those relating to disease. Of practical relevance for pharmaceutical development is an increased awareness of evolved responses and potential consequences of bypassing these defenses. Examples involving reproductive medicine, components of the acute phase response, apoptosis, and axonal regeneration are discussed. Drug Dev. Res. 52:439–445, 2001. © 2001 Wiley‐Liss, Inc.
A new marine ammonium-oxidizing bacterium, Nitrosomonas cryotolerans sp. nov.

An ammonium-oxidizing chemolithotroph has been isolated from Alaskan waters that is different from any of the previously described species. The cells are 2.0–4.0 μm long and 1.2–2.2 μm wide. The cells contain flattened peripheral membranes that often expand, forming spherical structures near the ends of the cells. The cytomembrane structure is significantly different from any described species. The organism is an obligate halophile. The mol% G + C is 45.8, and DNA–DNA hybridization results indicate that the isolate is a new species; the name Nitrosomonas cryotolerans is proposed.
Recognition of the Anticodon Loop of tRNAIle 1 by Isoleucyl-tRNA Synthetase from Escherichia coli

Abstract For Escherichia coli tRNAIle 1 having anticodon G34-A35-U36, two variants with substitution and/or insertion in the anticodon loop were prepared by in vitro recombinant RNA method. A variant with replacement of the N-((9-β-D-ribofuranosyl-purine-6-yl)carbamoyl)threonine (t6A) residue at position 37 with an unmodified adeno-sine exhibited a drastic reduction in isoleucine-accepting activity. This shows that t6A37 plays a crucial role in the recognition by isoleucyl-tRNA synthetase (IleRS). Into this A37 variant, unmodified A was further inserted at position 36 so that a sequence of GAAUA was created. This insertion did not show further reduction in isoleucine-accepting activity, indicating that IleRS recognizes the three anticodon residues, which have already been found to be identity elements, individually but not as a whole.
Presence of long-lived invertebrate taxa and hydrologic permanence

The presence of long-lived invertebrate taxa has been used as a criterion for determining hydrologic status in streams based on the assumption that water is present for a sufficient period of time to allow the organisms to complete their life cycle. However, analysis of life-history strategies and age distribution of several long-lived taxa (Anchytarsus bicolor, Oulimnius latiusculus, Ameletus, Tipula, and Cambaridae) from headwater streams in West Virginia suggest that the presence of long-lived taxa is an insufficient indicator of hydrologic status. Anchytarsus bicolor, O. latiusculus, and Ameletus exhibited distinct cohort differences between ephemeral and perennial locations. These three taxa do not have life-history strategies for remaining on-site when the stream dries, suggesting that their presence in ephemeral sites was due to recent colonization. Tipula and Cambaridae did not show different size ranges between ephemeral and intermittent locations, possibly because of their ability to burrow into the substrate. The upper reaches of these headwaters can provide short-term habitat for opportunistic colonizers and relatively long-term habitat for invertebrates with specialized life-history strategies, such as burrowing. Life-history strategies and age distribution should be carefully considered before using the mere presence of long-lived taxa as an indicator of hydrologic permanence.
The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia

Kim, S. , Park, M. ‐H. , Jung, J.‐H. , Ahn, D. ‐H. , Sultana, T. , Kim, S. , Park, J.‐K. , Choi, H. ‐G. & Min, G. ‐S. (2012). The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia. —Zoologica Scripta, 41, 281–292.
Studies on Novel Pili from Shigella flexneri

Pili were detected using electron microscopy in clinical isolates of Shigella flexneri which had been continuously subcultivated in liquid media. Morphologically, the pili appeared as thin, flexible, cylindrical structures of up to 2–5 μm in length and about 3–5 nm in diameter. Two strains showed mannose‐resistant (MR) hemagglutination to fresh fowl erythrocytes (type 4), and one to tannic acid‐treated horse erythrocyte (type 3) pili. These pili are novel and different from the mannose‐sensitive (MS) type 1 pili described by Duguid and Gillies.
Lack of protective immunity against reinfection with hepatitis C virus

Some individuals infected with hepatitis C virus (HCV) experience multiple episodes of acute hepatitis. It is unclear whether these episodes are due to reinfection with HCV or to reactivation of the original virus infection. Markers of viral replication and host immunity were studied in five chimpanzees sequentially inoculated over a period of 3 years with different HCV strains of proven infectivity. Each rechallenge of a convalescent chimpanzee with the same or a different HCV strain resulted in the reappearance of viremia, which was due to infection with the subsequent challenge virus. The evidence indicates that HCV infection does not elicit protective immunity against reinfection with homologous or heterologous strains, which raises concerns for the development of effective vaccines against HCV.
The novel depot of buprenorphine propionate has a long‐acting effect on physical dependence on morphine

Buprenorphine is a promising drug for the treatment of physical dependence on opioids. The aim of the present study was to evaluate the efficacy and duration of action of a novel depot form of a buprenorphine prodrug, buprenorphine propionate, on physical dependence on morphine. Following intramuscular injection in morphine‐dependent mice, the efficacy and duration of action of buprenorphine propionate in sesame oil were evaluated. Two other dosage forms of buprenorphine were used as controls. Intramuscular injection of buprenorphine HCl (0.1 µmol/kg in saline) attenuated the severity of morphine dependence (P<0.05) with a 9‐h duration of action. However, a further increase in dose up to 60‐fold could not further increase its duration of action. On the other hand, buprenorphine base and propionate when prepared in sesame oil produced longer durations of action than did buprenorphine HCl in saline under an equimolar basis of 6 µmol/kg (P<0.05, for each comparison). Among dosage forms, buprenorphine propionate in sesame oil produced the longest duration of action, 11.3‐fold longer than that of buprenorphine HCl in saline and 2‐fold longer than buprenorphine base in oil. In conclusion, the novel depot of buprenorphine propionate produced a dose‐related long‐acting effect on physical dependence on morphine in mice. Drug Dev. Res. 67:462–469, 2006. © 2006 Wiley‐Liss, Inc.
Physiological and biochemical responses in Beetal goats during summer season.

The effect of summer heat stress on physiological responses and some of the biochemical constituents (lipid peroxidation, superoxide dismutase and glucose-6-phosphte dehydrogenase) of blood was studied during pre-summer and summer months in Beetal goats. A significant rise was observed in the heart rate, respiration rate and rectal temperature of the goats during summer compared to pre-summer months. Similar rise was observed in blood biochemical parameters viz lipid peroxidation, superoxide dismutase and glucose-6-phosphte dehydrogenase during summer as compared to the pre-summer period.
The Immunoglobulins: Structure and Function

Preface. Structural Aspects: General Characteristics of Immunoglobulin Molecules: Immunoglobulin Classes. Heterogeneity of Immunoglobulins. Detection and Isolation of Immunoglobulins. Proteolytic and Chemical Fragments of Immunoglobulins. Immunoglobulin Peptide Chains. Additional Peptide Chains. Immunoglobulin Fold (Domain). Fab Portion. Fc Portion. Immunoglobulin Molecules. Carbohydrate Components of Immunoglobulins. Animal and Human Immunoglobulins: Low Vertebrates. Birds. Mammals. Human Immunoglobulins. Origin of Antibody Diversity in Mice and Humans. Evolutionary Aspects. Engineering Antibody Molecules: Problems of Serum Immunotherapy. Chimeric Antibody Molecules and Humanization. Minimal Antibody Fragment (Fv). Production of Human Monoclonal Antibodies By Page-Display and Transgene Technologies. Engineering of Immunoglobulins with Novel Properties. Polymerization of Igg Molecules and Their Fragments. Bispecific Antibodies. Functional Aspects: Antigen-Combining Site: General Characteristics. Conformational Changes Linked with Antigen Binding. Complex of VH of Camelid Heavy Chain Antibodies with Antigen. Interaction of an Autoantibody (Rheumatoid Factor) with Fc. Structural Aspects of Antibody Specificity. Modeling Antibody-Combining Sites. Structural Aspects of Catalytic Antibody Activity. Antigen-Recognizing Molecules Other Than Antibodies: T-Cell Antigen Receptor. Proteins of Major Histocompatibility Complex. Complexes of T-Cell Receptor and Peptide-MHC. CDI Molecules. Natural Killer Cell Inhibitory Receptors. Comparison of Antigen Binding By Various Antigen-Recognizing Molecules. Interactions Outside the Antigen-Combining Site: Fc Receptor-Binding Sites. Complement-Binding Sites. Proteins Reacting with the Fc Portion. Proteins Reacting with the Fab Portion. Lectins. Molecular Chaperones. Bacterial Immunoglobulin-Binding Proteins. Segmental Movements of Immunoglobulin Molecules: General Aspects. Functional Aspects of Segmental Flexibility.
Diminishing return on investment for biodiversity data in conservation planning

It is generally assumed that gathering more data is a good investment for conservation planning. However, the benefits of additional data have seldom been evaluated by analyzing the return on investment. If there are diminishing returns in terms of improved planning, then resources might be better directed toward other actions, depending on their relative costs and benefits. Our aim was to determine the return on investment from spending different amounts on survey data before undertaking a program of implementing new protected areas. We estimated how much protea data is obtained as a function of dollars invested in surveying. We then simulated incremental protection and loss of habitat to determine the benefit of investment in that data on the protection of proteas. We found that, after an investment of only US$100,000 (∼780,000 South Africa Rand [ZAR]), there was little increase in the effectiveness of conservation prioritizations, despite the full data set costing at least 25 times that amount.
Secondary poisoning of stoats (Mustela erminea) at low mouse (Mus musculus) abundance in a New Zealand Nothofagus forest

Two different brodifacoum (Talon 20 P™) poisoning regimes effectively killed 100% of resident radio-tagged stoats (Mustela erminea) by secondary poisoning in a New Zealand Nothofagus forest when mice (Mus musculus) were scarce. Resident possums (Trichosurus vulpecula) and ship rats (Rattus rattus) were also killed. The relative importance of different prey species as sources of poison for stoats has not been clearly identified but availability of poisoned prey will determine the efficacy of secondary poisoning in years of low prey abundance. Tracking tunnels did not accurately measure the decline in the stoat population and were probably influenced by immigrant stoats that were kill-trapped and contained high levels of poison. This study corroborates the findings of several other similar studies that secondary poisoning using brodifacoum effectively kills stoats.
Energy landscapes, self-assembly and viruses

Phenomena such as protein folding, crystallisation, self-assembly, and the observation of magic number clusters in molecular beams are all the result of non-random searches. Analysis of the underlying potential energy surface may provide a unifying framework to explain how such events occur as the result of a guided exploration of the landscape. In particular, icosahedral shells composed of 12 pentagonal pyramids are found to be thermodynamically favourable and kinetically accessible when the pyramids are not too spiky and not too flat. Hence, viruses with icosahedral capsids not only minimise the genetic material required to encode the repeated subunits, but may also utilise the favourable properties of a potential energy surface that effectively directs self-assembly.
Harbour porpoise (Phocoena phocoena) foraging strategy at a high energy, near-shore site in south-west Wales, UK

Harbour porpoises (Phocoena phocoena) visit Ramsey Sound at specific states of tide to feed. The preferred foraging location is high-energy habitat in South Ramsey Sound where a tide race, overfalls and upwelling zones form during the ebb phase. Seabed topography and tidal currents combine to create a foraging resource exploited by harbour porpoises at regular and predictable intervals. Porpoises are observed surfacing repeatedly directly into the tidal stream above and adjacent to, a steep-sided trench on the seabed. Tidal currents and the steep walls of the trench are believed to concentrate prey which is funnelled towards the waiting porpoises. Schools with calves prefer areas on the periphery of the fastest flowing water, where current speeds are lower. The presence of harbour porpoises is restricted almost entirely to the ebb tidal phase, but porpoises regularly occupy this site for the entire ebb phase. Harbour porpoise foraging in a tide race habitat is widely reported from the geographical range of the harbour porpoise and raises issues regarding foraging strategy and the net energetic value of hunting prey in high-energy environments.
Tetrahymena cell model exhibiting Ca-dependent behavior

Using Tetrahymena pyriformis, strain w, and Tetrahymena thermophila, B-1868, we prepared cell models that showed ciliary reversal with change in Ca-ion concentration, as was also noted for the Paramecium cell model. No differences could be found between these two strains in the reactivation state, and their response to environmental conditions was essentially the same. The reactivation rate was 90% or more. Swimming velocity of the cell model was found to be 200 ± 49 μm/sec at 25.0°C ± 0.5°C, while the velocity for the living cells was 527 ± 101 μm/sec. Swimming velocity with change in environmental conditions, such as pH, Mg-ATP, and Ca-ion concentrations, was studied. Compared to the cell model of Paramecium, the Tetrahymena cell model had higher sensitivity toward Ca-ion in the reactivation medium. The effects of chlorpromazine, and inhibitor of calmodulin, on the swimming behavior of the cell models were studied.
Biotinylation of histones in human cells

An enzymatic mechanism has been proposed by which biotinidase may catalyze biotinylation of histones. Here, human cells were found to covalently bind biotin to histones H1, H2A, H2B, H3, and H4. Cells respond to proliferation with increased biotinylation of histones; biotinylation increases early in the cell cycle and remains increased during the cycle. Notwithstanding the catalytic role of biotinidase in biotinylation of histones, mRNA encoding biotinidase and biotinidase activity did not parallel the increased biotinylation of histones in proliferating cells. Biotinylation of histones might be regulated by enzymes other than biotinidase or by the rate of histone debiotinylation.
Changes in the Tissue and Volume of the Stomachs of Calves Following the Removal of Dry Feed or Consumption of Inert Bulk

Summary Twelve Holstein heifer calves at 16 and 38 wk. of age were sacrificed after a growth study in which six had voluntarily consumed a high-concentrate diet and six a high-roughage diet. Ratios of hay to concentrate were 9:1 and 1:9. Four bull calves, two fed only milk and two fed milk while consuming shavings, also were studied. The objectives were to observe the effects of continuous consumption of a high-roughage, a high-concentrate, and an inert bulk diet on stomach muscle, mucosa, and volume, and to test the effect on stomach anatomy of reversing 16-wk. -old calves from the above ratios of hay to concentrate back to milk. Rumen papillae disappeared in the calves reversed to milk diets. The rumen collapsed around less fill, but maintained the same potential (water-filled) volume after 18 wk. of milk feeding, as had existed in calves of the same age on dry feed slaughtered at the beginning of the reversal period. This observation was interpreted as indicating a stasis, and not retrogression of reticulo-rumen volume. The amount of muscular tissue (fat-free dry) was less in the reversal calves, but the effect was not statistically significant. A stasis in omasal tissue growth occurred, and the abomasum continued to grow at the same rate as body size. Mucosal and muscular growth were independent. This was evidenced in three ways. (1) Reticulo-rumen mucosa retrogressed at a more rapid rate than muscle. (2) Muscular development was extensive in the absence of mucosal development in the calves consuming shavings. (3) Compared to muscle, well-developed mucosa contained lower nitrogen percentages when expressed on a fat-free dry matter basis (13.3 and 15.1%, respectively). Rumen papillae length was greater in the faster-gaining (high-concentrate) calves. Apparently, both rapid growth and papillary development were due to the higher energy levels consumed by these animals.
Utilization of Natural Enemies of Chilo spp. for Management in Africa

Knowledge on the natural enemies of graminaceous stem borers is outlined, with special reference to mortality of Chilo spp. as crop pests in Africa. The quantitative scanty information available suggests that over 90% mortality of eggs and larvae takes place before the larvae become established as borers in the crop and that mortality of the older larvae and pupae is much lower. Possible manipulations of natural enemies to increase mortality further are reviewed. In view of the largely negative results of past classical biological control introductions the prospects do not appear very promising. However, the results do indicate some possibilities which should be investigated, notably trials with Apanteles spp. (Braconidae) and intra-continental redistribution of important species with restricted distributions. For short-term biological control, development of microbial biopesticides seems a more promising strategy than augmentation of insect parasitoids by breeding and release, particularly on small farms. A third possibility, enhancement of the action of native natural enemies by environmental manipulation, merits more attention as part of an integrated crop production approach to the improvement of the quantity and reliability of yields for the small farmer. RésuméLa connaissance des ennemis naturels des foreurs des graminées cultivées est delimitée par reférence particulière à la mortalité de Chilo spp. comme ravageurs des plantes cultivées en Afrique. Les renseignements quantitatifs sont maigres, mais ils indicent que plus de 90% mortalité des oeufs et larves s’arrive avant de leurs établissement comme les foreurs dans la plantation, et que la mortalité des larves plus vieux et des imagos est beaucoup plus basse. Les manipulations possibles des ennemis naturels pour augmenter la mortalité sont examinées. En considération des résultats, en grande partie negatif, des introductions d’autrefois pour la lutte biologique, l’avenir ne s’annonce pas bien. Cependant, les résultats indicent des possibilités ceux qui on doit investiger, notamment les essais avec Apanteles spp. (Braconidae) et rédistribution intercontinentale des espèces importantes ayant les distributions limitées. Pour la lutte biologique à court terme la développement des biopesticides microbiales serais une strategie qui promet beaucoup que l’augmentation des insectes parasitoides par l’élevage et la libération, particulièrement dans les fermes plus petites. Une possibilité troisième, l’enchérissement de l’action des ennemis naturels indigènes par la manipulation de l’environment se merite plus d’attention comme une partie d’une rapprochement integrée au production des plantes cultivées à l’amélioration de la quantité et la reliabilité des rendements pour le cultivateur de la petite ferme.
Effect of temperature on the behaviour of the endeavour prawns Metapenaeus endeavouri (Schmitt) and Metapenaeus ensis (De Haan) (Decapoda : Penaeidae)

The effect of water temperature on the duration of emergence and speed of movement of adult endeavour prawns, Metapenaeus endeavouri and M. ensis, was investigated in the laboratory under controlled conditions from 20˚ to 32˚C. The behaviour of 50 prawns was recorded on videotape over 48 h at five temperatures (20˚, 23˚, 26˚, 29˚ and 32˚C). In general, both species emerged from the substratum during dusk and remained on the substratum until dawn or just before dawn when they buried again. At 32˚C, however, some M. endeavouri emerged for much less time and started to bury shortly after midnight. The mean daily duration of emergence for M. endeavouri varied with temperature and was higher at 26˚ and 29˚C (653 40 min per day) than at other temperatures. In contrast, the mean duration of emergence for M. ensis was not significantly affected by temperature (range of times 663 45 to 693 9 min). The pattern of the mean hourly speed of movement for M. endeavouri varied with temperature, whereas that for M. ensis was bimodal at most temperatures: they were more active during dusk (1700 to 1800 hours) and dawn (0400 to 0500 hours) than at other times.