Miracle-dz/UniFAR-FTUs huggingface dataset:
Economic importance and application options of some industrial sludge conditioned by different treatment methods

Industrial sludge was obtained from four industries: aluminium extrusion, brewery, pharmaceutical and textile processing factory and treated by aerobic, anaerobic, physicochemical, combined aerobic/physicochemical and combined anaerobic/physicochemical methods. The results showed that the final destination of the sludge would determine the type and degree of treatment required for the sludge. Physicochemical method generally increases the quantity of sludge solids, thus making the sludge suitable for land reclamation; also, the firmer and denser floc characteristics of the physicochemicallly treated sludge makes the methods a better alternative if conditioned sludge are to be used to reinforce cement for brick making. Biological treatment methods (aerobic and anaerobic) can be used to reduce the quantity of sludge before disposal. Solids destruction is closely related to biogas production. If using sludge as a source of fuel is the focus, the anaerobic biological system may be the best option. Aerobic biological method and the combined aerobic/physicochemical methods are good options for ammonia reduction. Anaerobic biological method is best for improving the nitrogen content and hence the protein content of sludge so as to use the waste sludge as feeds for poultry birds and livestock. Economic values, application and disposal options of the various sludge are discussed.
AFLP analysis of genetic diversity in three populations of ayu Plecoglossus altivelis

The genetic diversity among three populations of ayu was analyzed by using fluorescence-based AFLP. Eight fish were collected from each of three locations representing native populations of the am phidromous form (AM), the landlocked form (LL), and the subspecific population from the Kawauchi River on Amami-oshima Island (RK). A total of 745 DNA fragments were scored using 19 arbitrarily chosen primer combinations, based on the restriction enzymes Msel and EcoRI with three and two base pair extensions, respectively. The proportions of polymorphic genes and the average heterozygosity were, respectively, 0.550 and 0.107 for AM, 0.521 and 0.095 for LL, and 0.135 and 0.022 for RK. The band-sharing coefficients were 0.839 for AM, 0.853 for LL, and 0.970 for RK. Genetic variation in each population varied directly with population size. The RK population, which is considered in danger of extinction, showed very low polymorphism. Nei's genetic distance was 0.017 between AM and LL, 0.410 between AM and RK, and 0.414 between LL and RK. These results suggest that AFLP markers provide useful data for the evaluation of genetic variability and divergence in fish.
The discovery and importance of multiple islands of most

The set of most-parsimonious trees for a data matrix may include several distinct classes (islands) of trees. An island is defined as a collection of trees, all less than a specified length, each tree connected to every other tree in the island through a series of trees, and each one differing from the next by a single rearrangement of branches. One advantage of this method of defining classes of trees is that islands are easily found by tree-searching programs. Multiple islands can be discovered by conducting many searches using a tree-searching program, each search beginning with a different tree. Among 37 data matrices examined, all 8 data matrices with two or more islands have retention indices less than 0.67. Trees are generally more similar within islands than among islands, as judged by analysis of partition metric distances between trees. As a consequence, trees in different islands may have different implications for character evolution, and for this reason should be sought. (Parsimony; phylogeny; tree searching; opti- mization; multiple optima; islands of trees; character evolution.)
Fear No Weevil?

Biological control of pests can seem a safe, attractive alternative to pesticides. But the process can sometimes go alarmingly awry, as described in a report in this issue by [ Louda et al . ][1] on an introduced thistle and its control organism, a weevil. In his Perspective, Strong discusses the lessons we have learned from failed biological control measures, and how we can use this potentially important tool more effectively. [1]: http://www.sciencemag. org/cgi/content/short/277/5329/1088
Specific Antibodies to Detect Tamarillo leaf malformation virus (TaLMV) in Tamarillo

In Colombia, yields of tamarillo are seriously affected by a complex viral disease known as virosis. This pathology was first reported in 1991 in the north of Antioquia and currently affects all tamarillo growing regions in the country. Recent works have demonstrated the association of two potyviruses (potyviridae) with this disease: Potato virus Y (PVY) and Tamarillo leaf malformation virus (TaLMV, proposed species). Specific diagnostic tools are required for early asymptomatic detection of these viruses and tamarillo certification programs. In this study, we report the obtention of TaLMV specific antibodies using a 15 residues peptide mimicking the N-terminal coat protein. Specificity and sensitivity of the anti-TaLMV antibodies was determined by ELISA and dot-blot using recombinant protein and synthetic peptides as controls. The usefulness of these antibodies was validated from a preliminary trial of TaLMV detection in plant samples obtained from tamarillo crops in eastern Antioquia and results were compared with a TaMLV specific coat RT-PCR detection protocol.
Evolutionary dynamics of intergenic sites, pan-genomes, and introgression in bacteria

5 Chapter 1: ​Introduction 6 Chapter 2: ​Comparative analyses of selection operating on non-translated intergenic regions of diverse bacterial species 37 Chapter 3: ​Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria 62 Chapter 4: ​Variation in deleterious mutation load in ​H. pylori​ populations, and effect of selection on introgressed DNA in hpEurope 80 Chapter 5: ​Compensatory evolution is widespread in Rho-independent terminators in bacteria 95 Chapter 6: ​Discussion 108
Cross-Species Characterisation of Alternative Splicing Patterns

Alternative splicing is a common post-transcriptional process in eukaryote organisms by which a single gene can produce more than one distinct transcript. First discovered in the late 1970s, alternative splicing has been the focus of intense attention after the release of the human genome draft revealed a lower than expected gene number. Almost all human protein coding genes are now known to be alternatively spliced. However, how alternative splicing in humans and other well studied model organisms compares to other less characterised taxa such as protists and fungi or what is the functional role of alternative splicing remains poorly understood. Here I analyse alternative splicing in dozens of species using millions of partial transcript sequences ESTs. By applying a transcript normalisation method I showed that alternative splicing in protists and fungi is higher than previously reported and highly variable. I further observed that in representatives of both taxa, associations with translation are overrepresented among alternatively spliced genes. However, no evidence for a relationship between alternative splicing and complex phenotypes was found. Taking human lice as a model I explored the role of alternative splicing in the evolution of phenotypic variants. I found that, despite the fact that the transcriptome profiles of head and body lice are nearly identical, there are markedly differences in alternative splicing patterns. Development related functional associations were found to be enriched among genes with body lice specific alternative splicing events but not in head lice consistent with a scenario of differential patterns of alternative splicing contributing to the phenotypic innovations as human lice adapted to life in human clothing. I further explore the functional relevance of alternative splicing and its possible role in driving genomic innovations even preceding events of gene duplication. Together the work presented show that alternative splicing is widespread among previously understudied fungi and protist species and provide insights on its role in species adaptation to novel environments in using human lice as a model.
REACTIONS OF HEMOGLOBIN AND STEADY STATES IN THE HUMAN RESPIRATORY SYSTEM: AN INVESTIGATION USING MATHEMATICAL MODELS AND AN ELECTRONIC COMPUTER

Using thermodynamic principles relating to steady state processes, a detailed biophysicochemical model of the human external respiratory subsystem was constructed. Mathematical experiments performed with this model give good agreement with reported physiological data relating to the functioning of this subsystem under normal and some abnormal conditions. Because of the complexity of the model, experiments with it are conducted on a high-speed computer. The model was applied to the representation of the exchanges of respiratory gases and related chemical phenomena occurring between the venous and arterial sides of the total air-blood system. In addition, the model was used to explore the quantitative as well as qualitative significance of biochemical functions that are believed to be important in establishing the characteristics of the system. These functions include the Bohr effects of hemoglobin and various hypotheses of carbamino formation, as well as the dynamic steady-state gradients imposed by the erythrocyte metabolic pump and the disparate concentrations of nondiffusible species operating across the cell membranes. The capacity of mathematical models of this type to incorporate and rigorously interrelate a large number of detailed biochemical reactions so as to yield total subsystem effects that compare well with physiological reality suggest that such models should provide a useful tool for many biological investigations.
Oxidative and hydrolytic properties of β-amyloid

β-Amyloid protein is the major component of senile plaques found in the brains of Alzheimer's patients. Previously, a new biochemical property of amyloid, its ability to disrupt ester and peptide bonds, was described [Elbaum, D. , Brzyska, M. , Bacia, A. & Alkon, D. (2000) Biochem. Biophys. Res. Commun. 267, 733–738]. In the present work we compare the ability of β-amyloid to hydrolyse and oxidize model fluorescent derivatives of dichlorofluorescein [dichlorodihydrofluorescein (H2DCF) or dichlorofluorescein diacetate (DCF-DA), respectively] to the same final product (dichlorofluorescein). Although there is accumulating evidence of oxidative properties of β-amyloid, little is known about its hydrolytic abilities. Chemical modification studies revealed that hydrolytic properties are related to a His, Ser and Asp/Glu triad, while residues of His, Tyr and Met are involved in the oxidative activity of amyloid. Studies with the rat homologue of human β-amyloid (1–40), containing three amino-acid substitutions (Arg5Gly, Tyr10Phe and His13Arg) confirmed a role of His in the studied processes. Reduction of the hydrolysis product caused by inhibitors of Ser esterases (phenylmethylsulphonyl fluoride and eserine) suggests that β-amyloid-mediated hydrolysis is Ser sensitive. Antioxidants and metal chelators that reduced H2DCF oxidation did not change or increase DCF-DA hydrolysis. Solvent isotope effects suggest the involvement of hydrogen bonds in the hydrolysis reaction. Hydrolysis was inhibited by redox-active metal ions and was practically oxygen independent while the oxidation process was redox-active-metal enhanced [Cu(II) and Fe(II) primarily], and oxygen dependent. Product formation was significantly inhibited by catalase and superoxide dismutase as well as benzoquinone, a specific superoxide anion radical scavenger. Increase of fluorescence by oxidation was strongly inhibited by azide and His and enhanced in samples prepared with deuterated phosphate buffer, suggesting singlet oxygen intermediacy. Our data are consistent with superoxide-mediated singlet oxygen intermediate in this Fenton mechanism-driven reaction. These results indicate that hydrolytic and oxidative properties of β-amyloid are distinct features of this peptide and probably require different mechanisms to occur, but both of them may contribute to β-amyloid toxicity.
Dilute acid pretreatment of biomass at high solids concentrations

The dilute acid pretreatment of biomass (aspen wood and wheat straw) at high solids concentrations (up to 40 weight percent) has been investigated. It produces a concentrated monomeric soluble sugar stream (mainly xylose) with little degradation of the available sugars and a solid residue containing cellulose and lignin. The cellulose remaining in the residue from both aspen and straw pretreated at either 140 degrees or 160 degrees was highly digestible with commercial available enzymes. A somewhat higher acid consumption for wheat straw compared with that for aspen can be alleviated by a cation-removal step.
Case 3428 Palaemon rosenbergii De Man, 1879 (currently Macrobrachium rosenbergii; Crustacea, Decapoda): proposed conservation of usage by designation of a neotype

Abstract. The purpose of this application, under Article 75.6 of the Code, is to conserve the usage of the specific name of Macrobrachium rosenbergii (De Man, 1879) for a commercially important giant freshwater prawn from Southeast Asia by designating a neotype. Recent taxonomic reappraisals show that the two subspecies of this prawn, Macrobrachium rosenbergii rosenbergii (De Man, 1879) and M. rosenbergii dacqueti (Sunier, 1925) are in fact distinct species. The usage of the name M. rosenbergii for the species of prawn that is predominantly fished, cultured and studied by biologists is threatened, as its recently designated lectotype is M. dacqueti, while the holotype of M. rosenbergii is a different species, which has generated much less commercial and scientific interest. As substantial confusion will result if the names are changed, it is proposed that the existing holotype of Macrobrachium rosenbergii (De Man, 1879) be set aside and the lectotype of M. dacqueti (Sunier, 1925) be designated as neotype of Macrobrachium rosenbergii in its place. This action will allow biologists to retain the name M. rosenbergii for the commercially valuable species and will result in the less frequently used name M. dacqueti becoming a junior objective synonym of M. rosenbergii. For the species defined by the current holotype of M. rosenbergii, a new name Macrobrachium wallacei is proposed and a holotype is designated.
Molecular characterization and optimization of enzymes involved in glycosaminoglycan biosynthesis

Glycosaminoglycans are biological active polysaccharides composed of repeating disaccharides composed of a hexuronic acid and a hexosamine. They have various pharmaceutical applications and traditionally this type of molecule is isolated from animal tissue. Since extraction from animal derivatives has serious limitations for the production of a large variety of defined glycosaminoglycans, there is a general interest in developing alternative systems enabling a more tightly controlled synthesis. During this research project we explored alternative ways of controlled chemo-enzymatic synthesis ofmonodisperse and uniform glycosaminoglycans for pharmaceutical applications, with a main focus on heparin. Heparin is a highly sulfated and complex glycosaminoglycan which is worldwide used as an anticoagulant to prevent blood clotting during surgery.Upon closer investigation of the heparin biosynthesis the D-glucuronyl C5-epimerase was recognized as a key enzyme, as this is the only reaction that cannot be done chemically. Two alternative approaches were taken to get closer to an industrial applicable enzyme; improvement of the animal heparin sulfate D-glucuronyl C5-epimerase and identification and isolation of novel candidate C5-epimerases from prokaryotes. Both approaches gave functional production of C5-epimerases.
Histomorphological study on prenatal development of the lymphoid organs of native chickens of Bangladesh.

Native chickens (Gallus domesticus) of Bangladesh are scavenging in nature. Data regarding morphology of lymphoid organs in prenatal stages are lacking. H&E staining method was performed to study the development of the bursa of Fabricius, thymus, spleen and cecal tonsil from embryonic day (ED) 10 to 20. The budding of thymus was seen on ED 10. At ED 12, fiber network of thymus was formed to create a basement of cells of thymus and on ED 14 these cells began to organize to form cortex and medulla. But the cortex and medulla of thymus could not be differentiated before ED 20. The plicae of bursa Fabricius started to develop on ED 10. From ED 12 the plicae became shorter and wider to form bursal follicles and these follicles were clearly organized into cortex and medulla on ED 20. At ED 10, very thin capsule was seen in embryonic spleen. During ED 12, only a few white pulps were observed, while on ED 14, purple colored white pulp and pinkish red pulp were easily visible. At ED 20, the thickness of capsule was increased and pulps were more distinguishable. All the lymphoid organs showed major development during the later incubation period, indicating that the immune system in that period is being prepared to face the scavenging environment after hatching.
Evolving a Playful Brain: A Levels of Control Approach

Play is rare in the Animal Kingdom, but relatively common in the larger brained vertebrate taxa. Comparisons at the level of classes, orders, and, in some cases, families, suggest that larger brained taxa are more likely to contain playful species. However, at the species level, such relationships generally disappear. In some well documented mammalian taxa, such as Rodentia, it is clear that there are species which do not play at all, some where the play is quite complex and some showing all grades in between. Comparative methods are used here to supplement proximal analyses of the content of one particular form of play, play fighting, so as to identify the neurobehavioral mechanisms that are needed in rodents to evolve complex play from simpler antecedents. At least five independent neural mechanisms are shown to be necessary to produce the most complex example of play fighting in rodents. The identification of such levels of control provides a new method for systematizing the diversity of play present in mammals. Furthermore, this approach sets the stage for re-evaluating the relationship between brain size and play. That is, the issue can be reconceptualized in terms of whether species with larger brains are more likely to have a greater number of control mechanisms. It is not that larger brained species are more likely to play, but rather, that when they do play, the content of their play is more flexible. Suitable comparative data sets are needed to test these possibilities.
ANTIOXIDANT ACTIVITY OF HERBAL PLANTS: A RECENT REVIEW

Antioxidants or inhibitors of oxidation are compounds which retard or prevent the oxidation and in generalprolong the life of the oxidizable matter. Majority of the diseases/disorders are mainly linked to oxidative stressdue to free radicals. The free radicals (oxidants) are species with very short half-life, high reactivity and damagingactivity towards macromolecules like proteins, DNA and lipids. In general, the reactive oxygen species circulatingin the body tend to react with the electron of other molecules in the body and these also effect various enzymesystems and cause damage which may further contribute to conditions such as cancer, ischemia, aging, adultrespiratory distress syndromes, rheumatoid arthritis etc. A plant-based diet protects against chronic oxidativestress-related diseases. Dietary plants contain variable chemical families and amounts of antioxidants. It has beenhypothesized that plant antioxidants may contribute to the beneficial health effects of dietary plants. This reviewpresents some information about the antioxidant/antiradicals and their role in our body and also their presence inspices and herbs.Key words: Antioxidants, Free radicals, Herbal Plants
A new species of Trichogramma (Hymenoptera: Trichogrammatidae) parasitic on eggs of the alderfly Sialis melania (Neuroptera: Sialidae) from Japan, with comments on its phylogeny and male wing polymorphism

A new species of Trichogramma that parasitizes Sialis melania eggs is described as Trichogramma tajimaense Yashiro, Hirose and Honda, sp. nov. from Japan. Its phylogenetic position is based on a DNA‐based analysis, and data regarding its male wing polymorphism are also presented. The view that T. tajimaense is closely related to T. semblidis, another parasitoid of Sialis eggs, is supported by the results of a phylogenetic analysis, as well as by the biological and morphological similarities between both species. Trichogramma tajimaense is also similar in male wing polymorphism to T. kurosuae, a gregarious egg parasitoid of the lepidopteran Ivela auripes, as both Trichogramma species exhibit male wing trimorphism (fully alate, brachypterous and apterous forms) in contrast to the male wing dimorphism (fully alate and apterous forms) of T. semblidis. However, no phylogenetic analysis reveals a close relationship between T. tajimaense and T. kurosuae, and a difference exists between these two species in the mean percentage of flightless (brachypterous and apterous) males that emerge from a host egg mass; 96% of T. tajimaense males are incapable of flight, whereas about 50% of T. kurosuae males are flightless. Because all or almost all males of T. semblidis parasitizing Sialis eggs are apterous, T. tajimaense is more similar to T. semblidis than to T. kurosuae in the proportion of flightless males. In addition, male wing polymorphisms of Trichogramma in relation to mating systems could also show a similarity between T. tajimaense and T. semblidis when considering both species as quasi‐gregarious parasitoids of Sialis eggs.
High-Level Production of RecombinantGeotrichum candidumLipases in YeastPichia pastoris

Abstract We describe the heterologous high-level expression of the two Geotrichum candidum lipase (GCL) isoenzymes from strain ATCC 34614 in the methylotrophic yeast Pichia pastoris. The lipase cDNAs were placed under the control of the methanol-inducible alcohol oxidase promoter. The lipases expressed in P. pastoris were fused to the α-factor secretion signal peptide of Saccharomyces cerevisiae and were secreted into the culture medium. Cultures of P. pastoris expressing lipase accumulated active recombinant enzyme in the supernatant to levels of ∼60 mg/L virtually free from contaminating proteins. This yield exceeds that previously reported with S. cerevisiae by a factor of more than 60. Recombinant GCL I and GCL II had molecular masses of ∼63 and ∼66 kDa, respectively, as determined by SDS–PAGE. The result of endoglucosidase H digestion followed by Western blot analysis of the lipases suggested that the enzymes expressed in P. pastoris received N-linked high-mannose-type glycosylation to an extent, 6–8% (w/w), similar to that in G. candidum. The specific activities and substrate specificities of both recombinant lipases were determined and were found to agree with what has been reported for the enzymes isolated from the native source.