Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversification In African Cichlid Fishes: From Speciation To Macroevolutionary Patterns

The cichlid fishes of Lake Tanganyika in Eastern Africa are a celebrated example of both ecological and species diversification. Because population subdivision is likely to play an important role in the speciation process, understanding how habitat features interact with species’ demographic, behavioral and ecological attributes to influence gene flow and population divergence may help explain the causes of high species richness in this and other systems. Here, we test the roles of isolation-by-habitat and isolation-by-distance in generating fine-scale population genetic structure in three sympatric species of habitat-restricted cichlids in Lake Tanganyika. Using multi-locus microsatellite genotypes, we contrast patterns of population differentiation in these habitat specialists along a mosaic coastline of both favorable and unfavorable habitat. Despite their close phylogenetic relationship and shared habitat affinity, these species show striking differences in their pattern of genetic subdivision within the same geographical region, suggesting substantially different patterns of gene flow. In particular, two trophically specialized species exhibit much more restricted gene flow over sandy habitat than a trophically opportunistic species. This result suggests that ecological and behavioral traits have a strong influence on the scale and degree of population subdivision, a finding which has 1 1 This chapter has been published as Wagner, C. E. , and A. R. McCune. 2009. Contrasting patterns of spatial genetic structure in sympatric rock-dwelling cichlid fishes. Evolution 63:1312-1326,; it is reprinted here with permission. potentially important implications for understanding differential propensities for diversification among lineages and phylogenetic patterns of diversity.
Cis-GPRA synthesis by enzymatic removal of a p-methoxybenzyl protecting group from p-methoxybenzyl-7-phenylacetylamino-3-propenyl-3-cephem-4-carboxylate

Abstract Twelve typical commercial hydrolases and crude cell extract of Bacillus subtilis ATCC6633 were tested for their activity to synthesize cis-7-phenylacetamido-3-propenyl-cephalosporanic acid (cis-GPRA) by enzymatic removal of a p-methoxybenzyl protecting group from p-methoxybenzyl-7-phenylacetylamino-3-propenyl-3-cephem-4-carboxylate (GPRE) in aqueous– organic solvents. No activity was detected for 12 commercial enzymes. However, the crude cell extract showed significant activity for removing the p-methoxybenzyl protecting group from GPRE to produce cis-GPRA. The yield of cis-GPRA reached 73% with the initial reaction rate of 10.2 μM h−1 under the optimized reaction conditions.
Chromatographic isolation of antioxidants guided by a methyl linoleate assay

A convenient and fast method for establishing the relative antioxidant activity of chromatographically purified fractions of plant extracts has been developed. The assay electrochemically determines the myoglobin-catalyzed oxygen consumption following addition of the fractions to methyl linoleate. Since the oxygen consumption rate decreases with increasing antioxidant activity, the method can be used for systematic screening of naturally occurring antioxidants. Applying this method to extracts of Satureja hortensis led to isolation of rosmarinic acid.
Comparative Analysis of Osmolyte Accumulation in three Juncus Species, in Response to Abiotic Stress

Accumulation of compatible solutes or ‘osmolytes’ is a general response of plants to abiotic stress conditions, but we still have very limited knowledge on the relevance of this response for stress tolerance mechanisms of a given tolerant species. We have determined the levels of common osmolytes (proline, glycine betaine and total soluble sugars) in three Juncus species, two salt tolerant (J. acutus and J. maritimus) and one salt-sensitive (J. articulatus), subjected to salt or water stress treatments. Correlation of the patterns of osmolyte accumulation with salt tolerance of the three taxa, indicated that biosynthesis of Pro (but not the increase of glycine betaine or sugar contents) plays a relevant role in the stress tolerance of the analysed Juncus species.
Changes in needle retention associated with the spread and establishment of Phaeocryptopus gaeumannii in planted Douglas fir

The needle-infecting fungus Phaeocryptopus gaeumannii (Rohde) Petrak spread to stands of Douglas fir [Psendotsuga menziesii (Mirb.) Franco] in most parts of New Zealand following its first detection in the central North Island in 1959. At Hanmer Forest in the South Island, the percentage of infected needles rose more rapidly in a provenance from northern inland California than in one from Kaingaroa Forest in the North Island. Increase in infection was accompanied by a significant decrease in the proportion of needles retained on shoots of certain age classes, the reduction in the Californian seedlot being greater than in that from Kaingaroa. More older foliage was retained in the Kaingaroa provenance at Hanmer Forest, when infection averaged under 30 %, than at two other locations where mean infection exceeded 90 %. It is suggested that heavily infected production stands of Douglas fir suffer some premature casting of older needles, even when crowns appear healthy.
Limiting processes for perennial plant reintroduction to restore dry grasslands

In restored grasslands of southern Europe, perennial plants remain highly underrepresented compared with the reference ecosystems. We tested various treatments to reintroduce common perennial plant species (Brachypodium retusum, Poaceae, and Thymus vulgaris, Lamiaceae), which are usually not or poorly reintroduced via soil and hay transfer. Treatments included microenvironmental manipulations (rock cover and plant interactions) and two grazing intensities. Target perennial species were transplanted in 2002 in the reference grassland ecosystem (intact grassland area used as a control) and in two abandoned fields. Survival was assessed in June 2003 and June 2004. Target species shoot and root biomass were measured in June 2004. Grazing greatly reduced the survival and biomass of both target species and its effects were reinforced by summer drought: plants that did not establish well enough during the autumn and spring did not survive summer. The restored rock cover had a mild positive effect, particularly on B. retusum. There were no negative or positive plant neighbor interactions in the steppe, while there was competition in both abandoned fields. Competition was particularly intense in the abandoned melon field, composed of a dense sward of annual grasses (Bromus sp.). In order to reintroduce perennial species to dry grasslands, the ideal combination of treatments is to exclude or reduce grazing during the first year to allow seedlings to establish and to recreate adequate microenvironmental conditions. Reducing competition from arable weeds may help but is not essential in such dry grasslands.
Oocyte-Specific Expression of Granulin Precursor (Acrogranin) in Rat Ovary

Growth factors synthesized by ovarian somatic cells directly affect oocyte growth and function, but it is unclear whether oocyte-secreted factors play a reciprocal role in modulating somatic cell functions in vivo. Granulin (grn) and its precursor are polypeptides that possess growth-regulatory activities principally toward epithelial cells. To determine the localization of grn in rat ovary, we produced rabbit polyclonal antibodies that identified grn precursor protein using synthetic peptides. Four kinds of peptide on the basis of rat grn precursor protein were synthesized and immunized with a total of eight rabbits. All eight antisera were found to bind the original synthetic peptides in solid phase by ELISA method using synthetic peptide. Based on Western analysis of ovarian extracts using one antiserum raised against the synthetic peptides, an immunoreactive band at 67 kDa was detected. Immunohistochemical analysis in both neonatal and adult ovaries indicated that grn-like signals were obtained exclusively in oocytes and not granulosa or theca cells, suggesting the involvement of grn in regulating follicular functions.
Phenological growth stages of edible asparagus (Asparagus officinalis): codification and description according to the BBCH scale

BBCH [Biologische Bundesanstalt (Julius Kuhn-Institut), Bundessortenamt, CHemische Industrie] scales are used in applied natural sciences for the description of phenological growth stages of plants and are available for many crops today. Currently, a specific BBCH scale for Asparagus officinalis, a perennial vegetable plant of worldwide interest, does not exist. In this study, an extended BBCH scale was developed, describing precisely the growth stages of A. officinalis. Nine principal growth stages were defined and subdivided into several secondary growth stages resulting in a two-digit decimal code. Detailed descriptions of the particular stages and illustrations were included to clarify the application of the code system. The scale is proposed to specify and harmonise research activities as well as to enhance comparability of crop management practices for growers of asparagus.
Transcriptomic analysis of Sporisorium reilianum in response to the strigolactone analogue GR24

A suppression subtractive hybridization (SSH) approach was used to generate cDNA libraries representing genes differentially expressed in the haploid cells of the maize head smut pathogen Sporisorium reilianum exposed to GR24, a strigolactone analogue. Strigolactones are present in root exudates and have been known to trigger germination of parasitic plant seeds and signal mycorrhizal fungi to connect to root systems forming mutualistic relationships. Cell respiration increased within 1 h after GR24 addition, but decreased after 5 and 8 h. All induced cells were used to construct a cDNA library, which contained 1440 clones. The cDNA ESTs were deposited on macro-array membranes and hybridized with P32 cDNA probes obtained from mRNA isolated from S. reilianum yeast cultures exposed or not to 100 nM GR24 for three time intervals. A total of 678 ESTs were identified as differentially expressed during three time-courses in response to GR24. A set of 36 candidate genes were analyzed by qRT-PCR that presented an induction of the genes at 1 h, confirming the hybridization data. Induced genes mostly affect catalysis functions (45%) like cell respiration (27%), and cell signaling (26%). Although the biological significance of this perception remains hypothetical, these results indicate that strigolactones could have a wider biological influence in the rhizosphere than previously recognized.
The Wildlife Picture Index: monitoring top trophic levels

Although recent biodiversity loss has been compared with cataclysmic mass extinctions, we still possess few indicators that can assess the extent or location of biodiversity loss on a global scale. The Convention on Biological Diversity (CBD) has mandated development of indicators that can meet the needs of monitoring biodiversity by 2010. To date, many indicators rely on unwarranted assumptions, secondary data, expert opinion and retrospective time series. We present a new biodiversity indicator, the Wildlife Picture Index (WPI) that targets medium and large‐sized terrestrial birds and mammals in forested and savannah ecosystems that. The WPI is a composite indicator based on the geometric mean of relative occupancy estimates derived from camera trap sampling at a landscape scale. It has been designed to meet the needs of a CBD indicator while avoiding many of the pitfalls that characterize some CBD indicators. We present an example using 8 years of camera trap data from Bukit Barisan Selatan National Park, Indonesia to show that the WPI is capable of detecting changes in the rate of loss of biodiversity, a key requirement of a CBD indicator. We conclude that the WPI should be effective at monitoring top trophic levels in forest and savannah ecosystems using primary data and can fill the gap in knowledge about trends in tropical biodiversity.
A theoretical basis for understanding and managing biological populations with particular reference to the spruce bark beetle

The applicability of qualitative analysis and modelling is discussed with reference to the population dynamics of the spruce bark beetle Ips typographus. On the basis of a set of assumptions and postulates, the structure of the population dynamical interactions is discussed. Dynamic analysis suggest that the Scandinavian spruce bark beetle population is a stable system which may be triggered into “boom and bust” dynamics. We suggest that qualitative analysis should proceed, explicitly, through four steps: (1) An explicit statement of the biological assumptions and postulates. (2) A structural analysis, wherein the critical interaction network of the system is defined. (3) An equilibrium analysis, wherein the potential equilibrium points of the key organism (e.g., the pest species) are deduced. (4) A dynamic analysis, wherein the multispecies equilibrium points are found and their sensitivity to pertuberation analyzed. This formal approach should expose many and varied population systems to the interpretive and explanatory powers of qualitative analysis.
Spawning of the Temperate Sea Cucumber, Australostichopus mollis (Levin)

The spawning of sea cucumbers is related to the interaction of environmental cues and reproductive maturity. Groups of Australostichopus mollis were collected every 2 wk during the summer reproductive season from mid-October to early February. They were observed for spawning in the hatchery during heat-shock trials conducted 3–5 C above ambient seawater temperature. Lunar periodicity existed with spawning being most prominent in the week following a full moon. In the week prior to a spawning event, there was also a decrease in ambient incoming seawater temperature. More than 75% individuals spawned during most trials in which spawning occurred. In total, 40% of the 270 individuals spawned during the reproductive season. Reliable spawners were females with a yellow gonad color and large numbers of vitellogenic oocytes, and males with large numbers of spermatocytes and an absence of motile spermatozoa. Furthermore, the percentage germinal vesicle breakdown of oocytes exposed to starfish radial nerve extract compared to seawater was greater for the more orange-colored gonad of nonspawners. Gonad color is useful in determining the likelihood of spawning over a 2-wk period in the presence of a cue. Sea cucumbers held for short periods in the hatchery during the reproductive season maintain a natural rhythm of spawning that can be monitored using visual indices and augmented using heat shock.
Functional Modeling of Genes Upregulated in Chronic Myeloid Leukemia

Chronic myeloid leukemia (CML) is caused by the transformation of a primitive hematopoietic cell by the BCR/ABL1 fusion gene that is formed through the chromosomal translocation t(9;22). CML is currently successfully treated with tyrosine kinase inhibitors targeting the ABL1 kinase domain. However, the CML stem cells are insensitive to this drug and a large fraction of patients will have relapse following discontinuation of the drug. Thus, improved therapeutic strategies are needed towards the ultimate goal of curing CML. In Article I, the functional role of supressor of cytokine signaling 2 (SOCS2) in CML and in normal hematopoiesis was investigated. Mice deficient for the Socs2 gene displayed normal steady-state hematopoiesis and hematopoietic stem cell (HSC) function. Transduction of bone marrow (BM) cells from Socs2-deficient mice with BCR/ABL1 and subsequent transplantation resulted in a CML-like disease indistuingishable from the disease in control mice, suggesting that SOCS2 is dispensible for normal hematopoiesis and CML pathogenesis. In Article II, global gene expression analysis and subsequent flow cytometric analysis of normal and CML BM cells showed that interleukin-1 receptor acessory protein (IL1RAP) was highly upregulated on the cell surface of CML cells, allowing prospective separation of candidate CML stem cells from normal hematopoietic stem cells. The use of a polyclonal IL1RAP antibody enabled antibody-dependent cellular cytotoxicity (ADCC) of CD34+CD38- CML cells in vitro. In Article III, the function of IL1RAP in normal hematopoeisis and in CML was investigated. Mice lacking Il1rap displayed lower myeloid steady-state cell counts. Overexpression of IL1RAP in cord blood cells, followed by transplantation into immunodeficient mice, resulted in increased levels of myelopoeisis. Finally, CD34+CD38- CML cells were found to respond strongly to IL1B stimulation in vitro. Together, the results suggest that IL1RAP is a promising target for novel therapeutic approaches in CML. (Less)
A Treat towards an Artist‘s Psyche: A Psychoanalytical Reading of ̳Red’ by John Logan

The essence of human psyche as a primary subject of psychoanalytical discussions was in the center of attentions throughout the nineteenth and twentieth centuries. Thereupon, the investigations of various human psyche lead to the understanding of the relation between the conscious and the unconscious. In other words, what people do is done instinctively as a reaction toward their unconscious. On the contrary, human beings were not cognizant of unconscious‘ complexity; the directory of individual lives is interrelated to choices that are made in an out-of-reach aspect of mind, which does not always make a sense. Psychoanalysis, as a nonmedical observation of human mind, zooms in on various ways of interpretation of an individual‘s psyche. For instance, a famous play by John Logan entitled Red, written in 2009, appears to picture different aspects of an artist out of its characters‘ psyche while distinctively make conversation within the play. This paper‘s intention is to provide a reading Rothko, protagonist of Red, with having eye on the features discussed by the theories of psychoanalysis. The analysis illustrates the complexions of individuals‘ psyche interlocked with different circumstances and
Bottlenecks, isolation, and life at the northern range limit: Peary caribou on Ellesmere Island, Canada

Abstract During his expeditions to the North Pole Robert Peary harvested at least 233 Peary caribou (Rangifer tarandus pearyi) from the northeast (NE) portion of Ellesmere Island, Nunavut, Canada. To assess the impact of this intensive local harvest we compared historic and contemporary samples. We explored 2 models of repopulation for this region. In the recovery model animals not hunted by Peary were the source of the current population. In the recolonization model animals from adjacent regions contributed to the current population. A genetic assessment of mitochondrial DNA (mtDNA) diversity comparing historic specimens (n = 12) to contemporary samples from the same region (n = 22) indicates the loss of 1 major mtDNA haplogroup. In this region historic and contemporary samples were significantly differentiated from one another. Combined mtDNA (n = 121) and 9 nuclear DNA loci (n = 151) indicate that the contemporary NE animals are most similar to those in adjacent regions to the south. We interpret this as supporting our recolonization model and suggest that, following Peary, animals dispersed north from central Ellesmere. Animals from the region to the west (NW) of NE showed the greatest differentiation from all other regions, suggesting that although proximate in distance, movement between the NW and NE might always have been limited. The NW region was unique in that it contained 1 predominant mtDNA haplotype at high frequency (0.88), the lowest observed heterozygosity (HO = 0.50), and the highest mean relatedness (R = 0.063). Our combined results highlight the sensitivity of populations at the range limit to stochastic events and the potential limits to recovery following significant perturbations.
The Conserved Pch2 Gene Acts To Regulate Dna Doublestrand Break Repair In Saccharomyces Cerevisiae Meiosis

29 Author’s Summary 29 Introduction 30 Results 34 Discussion 79 Materials and Methods 86 Acknowledgements 88 References 89 CHAPTER 3. Zanders and Alani (2010) Pch2 regulates interhomolog and intersister double-strand break repair in budding yeast meiosis. (submitted) 96 Abstract 97 Author’s Summary 97 Introduction 9897 Author’s Summary 97 Introduction 98
VIRGIN-MALE MATING ADVANTAGE IN SAGEBRUSH CRICKETS: DIFFERENTIAL MALE COMPETITIVENESS OR NON-INDEPENDENT FEMALE MATE CHOICE?

Female sagebrush crickets (Cyphoderris strepitans) feed on males' fleshy hind wings during copulation and ingest haemolymph oozing from the wounds they inflict. The wounds are not fatal and usually only a portion of the hind wings are eaten at any one mating, so that mated males are not precluded from mating again. However, based on their relative abundance in the population, virgin males have a higher mating success than non-virgin males. One explanation for this virgin-male mating advantage is that non-virgin males, having been depleted of their energy reserves through the wing-feeding behaviour of their mates, are unable to sustain the same level of acoustic signalling they produce prior to copulation. Previous assays of male signalling behaviour have provided some support to this hypothesis. However, an alternative explanation is that females actively seek out virgin males as mates because of the greater material resources they offer. If the acoustic structure of males' signals were systematically altered by the loss of hind-wing material underlying the sound-producing tegmina, females could potentially discriminate against mated males through reduced phonotaxis to their calls. We tested this hypothesis by experimentally removing one hind wing from virgin males, thereby simulating the non-virgin condition without the attendant costs of copulation. We compared the mating success of these 'asymmetrical' males with that of sham-operated virgin males when competing under natural conditions. In a companion laboratory study, we used time-lapse video recording to examine the possibility that female preferences are exerted only after pair formation has occurred. There was no significant difference in male mating success across treatments in either study. We conclude, therefore, that the virgin-male mating advantage does not stem from an acoustically mediated, non-independent female mating preference, but rather, from the differential competitiveness of males.
Plot direction and spacing effects on interplot interference in spring wheat cultivar trials.

Interplot interference can distort treatment estimates when genotypes differ for height. Two field arrangements were examined to determine if interplot interference could be reduced. One arrangement compared north-south vs. east-west row direction at Saskatoon in 1995 and 1996. The other experiment investigated the effects of separating plots with a row of spring-planted winter wheat (Triticum aestivum L.) at Regina and Swift Current in 1995 and 1996. Interplot interference was evaluated with two spring wheat cultivars differing for height, Oslo (short) and Glenlea (tall). Interplot interference caused a 12% yield reduction in Oslo in the north-south rows, which was significantly greater than the 7% yield reduction in the east-west rows, The 7% yield reduction when spring-planted winter wheat separated the plots was significantly less than the 18% yield reduction when plots were adjacent. This study was conducted at fairly high latitudes and the conclusions should be restricted to higher latitudes. We conclude that spring wheat field trials with plots (tillering for height may have less interplot interference if rows are oriented eastwest and separated with winter wheat.