Miracle-dz/UniFAR-FTUs huggingface dataset:
Hierarchical Phylogeographic Structure of Coho Salmon in California

AbstractEvaluation of population genetic structure and variation is an important part of planning for the recovery and management of protected species. Data from 18 polymorphic microsatellite DNA markers were used to analyze the phylogeographic structure of protected Coho Salmon Oncorhynchus kisutch from populations throughout California. Fish from 30 locations in two evolutionarily significant units (ESUs) representing most of the extant populations in the state were studied. Multiple analyses indicated a hierarchical pattern of population structure: the greatest divergence was found at the broadest geographic scale (ESU), followed by the divergences between basins and populations within basins. The populations of the large Klamath River basin were consistently identified as a distinct phylogenetic group, nearly as divergent from all other populations as the two ESUs were from each other. All populations in different basins were differentiated from each other and a pattern of isolation by distance was fo.
Nuclear alignment in myotubes requires centrosome proteins recruited by nesprin-1

ABSTRACT Myotubes are syncytial cells generated by fusion of myoblasts. Among the numerous nuclei in myotubes of skeletal muscle fibres, the majority are equidistantly positioned at the periphery, except for clusters of multiple nuclei underneath the motor endplate. The correct positioning of nuclei is thought to be important for muscle function and requires nesprin-1 (also known as SYNE1), a protein of the nuclear envelope. Consistent with this, mice lacking functional nesprin-1 show defective nuclear positioning and present aspects of Emery–Dreifuss muscular dystrophy. In this study, we perform small interfering RNA (siRNA) experiments in C2C12 myoblasts undergoing differentiation, demonstrating that the positioning of nuclei requires PCM-1, a protein of the centrosome that relocalizes to the nuclear envelope at the onset of differentiation in a manner that is dependent on the presence of nesprin-1. PCM-1 itself is required for recruiting proteins of the dynein–dynactin complex and of kinesin motor complexes. This suggests that microtubule motors that are attached to the nuclear envelope support the movement of nuclei along microtubules, to ensure their correct positioning in the myotube. Highlighted Article: Nuclear positioning in myotubes requires centrosome proteins recruited early in differentiation to the nuclear envelope in a nesprin-1-dependent manner. These contribute to the recruitment of microtubule motor proteins.
A new species of Corticium s. st. Studies in the genera Dendrocorticium and Dentocorticium (Basidiomycotina).

Une nouvelle espece Corticium malagasoroseum Duhem nov. sp. du complexe roseum, recoltee a Madagascar, est decrite et illustree. Ses differences avec C. lombardiae, espece la plus proche, sont discutees. Laeticorticium pilatii est transfere dans le genre Dentocorticium. Dendrocorticium piceinum Lemke 1977 est considere comme synonyme posterieur de Cerocorticium notabile (H.S. Jacks.) Julich et Stalpers 1980. Les auteurs proposent finalement une nouvelle cle des especes recensees dans le genre Corticium s. str.
Effect of ultraviolet-B radiation on biochemical composition of three Ulva species (Chlorophyta) from southeast coast of India

The young plants of Ulva fasciata, U. reticulata and U. lactuca were subjected to UV-B (320-280 nm) radiation for 30, 60, 90, 120, 150 and 180 min. The changes in chlorophylls, carotenoids, protein, nitrate contents and reductase activities were studied. Compared to control, in UV exposed plants both pigments and protein concentrations were significantly decreased. The magnitude of such decrease was higher in Ulva lactuca than in other two species. In contrast to this in vitro nitrate reductase activity was more severely affected in Ulva reticulata. The experiments clearly showed that the UV (A & B)-B radiation has a strong inhibitory effects on biochemical properties in all three Ulva species. However, the rate of inhibition is dependent on the duration of exposure of plants to UV (A & B)-B radiation.
The influence of pHand aluminium on the g rowth of filamentous algae in artificialstreams

Community structure of freshwater filamentous benthic algae can be statistically related to acidification, with taxa ranked in terms of the mode of their abundance with respect to pH. However, pH is closely correlated with other variables, and statistical procedures relating species abundance to environmental variables cannot discriminate between closely correlated variables as potential causes of the species distribution. To investigate the independent influences of pH, aluminium and silicon levels, we set up two series of experiments using filamentous algal isolates in recirculating artificial streams. The isolates belonged to the genera Draparnaldia, Geminella, Hormidium, Mougeotia, Oedogonium and Stigeoclonium. Growth rate was calculated from rate of increase of cell numbers in algal filaments attached to glass slides, and the accumulation of total biomass was also monitored. In experiment 1, pH was adjusted to values between 4 and 6, with other conditions fixed. Growth rates of all taxa changed with pH and all had a maximum within the range tested. Final biomass was lower at the extremes of pH. In experiment 2, pH was set to 5.5 and levels of dissolved aluminium and silica varied with reference to a control. In the enhanced Al treatment, the effect of 7.4 μmol/l of total aluminium was to cause a rapid decline in growth rate in most species, and a lower final biomass. These results are discussed in relation to field observations of the distribution of the genera tested.
The feminizing effect of metabolic heating in Green Turtle (Chelonia mydas) clutches in the eastern Mediterranean

Metabolic heating has been poorly investigated in eastern Mediterranean coastline of Turkey, which host some of the most important Green Turtle (Chelonia mydas) nesting sites in the Mediterranean. We studied the effects of clutch size and embryo numbers on nest temperature and discuss the feminizing effect of metabolic heating. Two test sites were conducted in Sugözü Beaches (Turkey). Data loggers were placed in eight nests with different clutch sizes. Nest temperature was strongly correlated with embryo numbers and metabolic heating produced by embryos was calculated to be 0.019°C per late stage embryo and 0.020°C per hatchling. Metabolic heating was calculated to be 0.6°C in the middle third of the incubation period during which sex is determined. It was estimated that metabolic heating increased 10.4% of female hatchlings. The heat produced by embryos should be taken into consideration while estimating sex ratios indirectly by nest and sand temperatures. Additionally, the metabolic heating value should be known for conservation measures, such as nest relocation, dividing the nest for controlling nest temperature, especially related to climate change.
Stem cells: promises and realities of cellular therapy

This paper aims to present to the reader aspects of the current debate about embryonic stem cells in our country. The text was developed based on a presentation showed at the XI Annual Scientific Meeting of the Butantan Institute, held on December 3, 2009 in Sao Paulo. The article shows the steps taken so far, given in order of the scientific integration and points to the need of expanding the generation of knowledge through the establishment of networks ́research Key – words: Research in biotechnology, Embryonic stem cells, Instituto Butantan
Organic selection may improve yield efficiency in spring wheat: a preliminary analysis

Abstract: Organic spring wheat (Triticum aestivum L.) breeding programs have been initiated, yet yield efficiency and N economy research is limited. We evaluated the performance of advanced lines selected from an organic breeding program initiated in 2003. Fourteen F8 and F9 lines in 2009 and 11 lines in 2010 were compared with commercial (check) cultivars. Field experiments were conducted under organic management at four site–years in Manitoba and Saskatchewan. Combined analysis showed no difference in biomass accumulation between organic lines and check cultivars; however, harvest index and grain yield were greater in organic lines compared with the checks. Organic lines were shorter than check cultivars, but yield efficiency, defined as kernel number per unit of crop biomass at anthesis, was higher (P < 0.05). Kernel mass was also greater for organic lines. Biomass N uptake was similar for organic lines and check cultivars, although total uptake of N into grain was greater for organic lines. The average grain protein content of organic lines was significantly lower than the check cultivars. This study demonstrated that improved yield under organic management was because of better assimilate partitioning, both at anthesis and crop maturity, for organically selected genotypes.
EFFECTS OF GROWTH REGULATING SUBSTANCES IN CEREAL SEED GERMINATION

The initiation of embryo growth and endosperm breakdown in cereal seeds is caused by a series of complex and interacting processes, some of which have been explored in considerable detail whereas others are still virtually unknown. There seems to be little doubt, however, that these processes are regulated and, to a large extent, controlled by the activities of various endogenous growth substances which are exerting either promoting
RETRACTED ARTICLE: Evaluation of carbon sources as positive selection agents for chrysanthemum (Dendranthema × grandiflorum) transformation

Abstract Fourteen different carbon sources were evaluated using thin cell layers to determine their suitability as positive selection agents for chrysanthemum (Dendranthema × grandiflorum) transformation. The choice of carbon source is an indispensable factor in the success of organogenic (callogenic, caulogenic, rhizogenic, and to a lesser extent, somatic embryogenic) programmes in in vitro micropropagation of chrysanthemum. Using flow cytometry, histological analyses, and confirmation of flowering normality, the impact of carbon source on the qualitative and quantitative outcome and response of thin cell layers when these were placed onto organogenic media was assessed. Threshold survival levels (TSLs) could not be obtained for sucrose, fructose, or glucose. TSLs together with organ differentiation were, however, obtained for mannose (60–80 g/litre), xylose and lactose (40 g/litre), and cellulose (60–80 g/litre), although abnormal shoot formation was observed in the first of these. Xylose, lactose, and .
Evolutionary history of the Persian Jird, Meriones persicus, based on genetics, species distribution modelling and morphometric data

The Persian Jird, Meriones persicus, is distributed from Eastern Anatolia to Afghanistan and western Pakistan. Six subspecies were described based on skull features and coat colours, but the validity of these subspecies is uncertain, and no molecular work has ever been conducted on this species. Iran appears to be a key geographical region in which to revise the systematic and evolutionary history of this species, because five of the six subspecies are present in this country. To evaluate the phylogeographical history and taxonomy of this species in Iran, we used a combination of genetic (cytochrome b gene sequences of 70 specimens) and geometric morphometric (2D landmarks on the ventral side of skull of 258 specimens) analyses. We also used ecological niche modelling to make inferences about the evolutionary history of these lineages. Our molecular data highlight the existence of four genetic lineages, but they only partly correspond to the previously described subspecies. Our molecular and morphometric data confirm the validity of M. p. rossicus and show that it has a wider geographical range than previously thought. M. p. gurganensis and M. p. baptistae are genetically very close. The skull of M. p. gurganensis is morphologically distinguishable from other subspecies. The subspecies M. p. persicus and M. p. baptistae are genetically distinct, but morphologically close. Meriones p. ambrosius is genetically close to M. p. persicus, and additional analyses with more specimens are needed to validate its subspecific status. The genetic structure observed in Iran seems to fit the topography and biogeography of the country and emphasize the role of the Abarkooh, Central and Lut deserts as barriers to gene flow. All intraspecific divergent events within the Persian Jird occurred during the last 1.4 My, suggesting that climatic changes probably trigger diversification within this species. Our genetic and species niche modelling results suggest that potential refugial areas persisted during glacial periods for this species in north-western Zagros Mountains, north-eastern Alborz Mountains and Kohrud Mountains.
Solid-phase synthesis of cell-penetrating γ-peptide/antimicrobial peptide conjugates and of cyclic lipodepsipeptides derived from fengycins

This thesis is focused on the development of synthetic approaches to obtain new bioactive peptides. The first part deals with the design of new antimicrobial peptide/cell-penetrating peptide conjugates as anticancer agents. Their conjugation enhanced the activity of the antimicrobial peptides against cancer cells while maintained their low toxicity. These compounds are interesting for the design of new anticancer agents. On the second part, a new versatile methodology for the synthesis of natural fengycin derivatives is described. Our strategy represents the first synthetic approach for the total solid-phase synthesis of these cyclic lipodepsipeptides and can be easily adapted to obtain a wide range of analogues. Aquesta tesi doctoral s’ha centrat en el desenvolupament d’estrategies sintetiques utils per a l’obtencio de nous peptids bioactius. Primerament, s’han dissenyat nous peptids conjugats antitumorals a traves de la unio d’un peptid antimicrobia i un cell-pentrating peptide. Aquesta conjugacio augmenta l’activitat antitumoral del peptid mantenint la toxicitat baixa. Aquests conjugats son interessants pel desenvolupament de nous agents antitumorals. A continuacio, s’ha desenvolupat una metodologia per a la preparacio de peptids ciclics derivats de les fengicines. Aquesta metodologia representa la primera estrategia sintetica descrita per a l’obtencio en fase solida d’aquesta familia de ciclolipodepsipeptids i pot ser facilment adaptada per a l’obtencio d’una amplia varietat d’analegs.
Serum cortisol concentration in cattle of different genetic groups slaughtered in confinement

The objective of this work was to compare the serum cortisol levels among four genetic cattle groups slaughtered in confinement. Thirty-two non-castrated male bovines from four genetic groups were analyzed: Nelore, Aberdeen Angus × Nelore, Caracu × Nelore, and Guzera × Nelore. The blood samples were collected on the day of weighing (every 28 days) and during the slaughter. Regarding the concentration of serum cortisol, no significant differences were found among the groups during the first, second, and fourth collections. However, during the third collection and at the day of slaughter, respectively, the Nelore group (3.15 ng/dL; 2.98 ng/dL) showed similarity to the Caracu × Nelore (2.02 ng/dL; 2.07ng/dL) and Guzera × Nelore (2.33 ng/dL; 2.40 ng/dL) groups. Nelore showed a significant difference compared with the Aberdeen Angus × Nelore group (1.21 ng/dL; 1.61 ng/dL). With respect to the overall collection averages, the Nelore group (2.85 ± 0.87 ng/dL) showed greater values than the Aberdeen Angus × Nelore group (1.61 ± 0.87 ng/dL). However, it showed similarities to the Caracu × Nelore (2.06 ± 1.31 ng/dL) and Guzera × Nelore (2.48 ± 1.16 ng/dL) groups. It was also observed that animals with low cortisol values gained more weight, as demonstrated by the correlation between ADG and the cortisol collection averages (-0.54; p 0.05, ns) showed that meat tenderness in the studied groups was not affected.
Determination of water potential on mango trees by pressure chamber

The determination of water potential in mango trees, using a leaf petiole in a pressure chamber has not correctly expressed plant water potential, so several authors use stomatal resistance in mango water relation studies. The main problem of the leaf petiole method is that when pressure is applied exudation of the sap from the phloem masks the exudation of the watery sap from the xylem, thus misleading the reading point for the determination of water potential. The use of a small branch rather than a leaf petiole for determination of plant water potential has been suggested to adequately relates plant water potential to soil water potential.
Interaction among Fusarium moniliforme, Tyrolichus casei, and mangiferin as related to malformation of Mangifera indica

Interaction among Fusarium moniliforme Sheld. , Tyrolichus casei Oudemans colonizing malformed mango (Mangifera indica cv. Banarasi Langra) panicles, and mangiferin (1, 3, 6, 7-tetrahydroxyxanthone-C 2 -β-D glucoside) a defensive metabolite of the host plant in relation to floral malformation, was investigated. The fungal and mite populations were initially positively related to the mangiferin content and the disease incidence. Further increase in mangiferin content reduced the fungal and mite populations; however, the increase in infection rate was not affected until the Fusarium population was too low. The fungal conidia remained adhered to the body surface of the mites inhabiting malformed panicles, and its plating on potato dextrose agar showed a trail of fungal colonies along the pathway of its movement. Tyrolichus casei facilitated the ingress of the fungus into the host cells while F. moniliforme served as the feed of T. casei and increased its multiplication.
Modular growth vessels for the cultivation of the cyanobacterium Synechococcus sp. PCC 7002

ABSTRACT Synechococcus sp. PCC 7002 is a euryhaline cyanobacterium that serves as a model organism for studies of photosynthesis and cellular metabolism. At high light intensity Synechococcus sp. PCC 7002 exhibits a fast growth rate and rapid biomass accumulation, making it an ideal candidate for the production of biofuels and commercially valuable secondary metabolites. To fully realise the production potential for this cyanobacterium a system is required to maintain axenic cultures under optimal growth conditions. We have designed and constructed two sizes of modular culture vessel systems, designed specifically to meet the abnormally high light penetration requirements of Synechococcus sp. PCC 7002. The smaller volume culture vessels are best suited to phenotype analysis, allowing multiple candidate strains to be screened simultaneously, whereas the larger vessels are designed to facilitate higher biomass production.
Sex Allocation and Colony Maintenance in Monogyne and Polygyne Colonies of Formica truncorum (Hymenoptera: Formicidae): The Impact of Kinship and Mating Structure

The aim of this article is to discriminate between genetic (worker-queen conflict) and ecological (mating structure, colony productivity) determinants of resource allocation in ants. Both the allocation to growth versus reproduction (reproductive allocation) and the allocation to males versus females (sex allocation) were analyzed as a function of colony kin structure, colony productivity, and mating structure in monogyne and polygyne populations of the ant species Formica truncorum. Colonies headed by single queens (monogyne colonies) were smaller and produced more sexuals per adult worker than those with multiple queens (polygyne colonies). Monogyne colonies with a high total production relative to colony size invested excess resources in reproduction, whereas the reproductive allocation did not change with increased productivity in polygyne colonies. The results suggest that workers control reproductive allocation. The population-level sex ratio was female biased in the monogyne population and male biased in the polygyne population. The colony-level variation in sex allocation in the monogyne colonies was best explained by variation in relatedness asymmetry (the relative relatedness of workers to males vs. females) among colonies, together with colony size and the percentage of sexuals in the brood (r2 = 0.77). In polygyne colonies male bias increased with increasing production of sexuals, which suggests that local resource competition was the main determinant of colony-level sex-allocation variation in these colonies.
Understanding two inhibitors of NF-κB: A20 and IκBβ

Inhibitors of NF-κB: A20 and IκBβ Arnab De While prompt activation of NF-κB is essential for optimal immune response, it is equally important to terminate the response to avoid tissue damage and perhaps even death resulting from organ failure. This thesis describes two inhibitors of NF-κB, A20 and IκBβ. A20 is an essential inhibitor of NF-κB mediated inflammation as mice lacking A20 die from multi-organ inflammation and cachexia. Multiple biochemical approaches have suggested that A20 functions as a deubiquitinase by disassembling K63-linked regulatory ubiquitin chains from upstream adapter molecules like RIP1. To determine the contribution of the deubiquitinase role of A20 in downregulating NF-κB, we generated and characterized a knock-in mouse lacking the deubiquitinase activity of A20. However, we find that these mice display normal NF-κB activation and show no signs of inflammation. Our results suggest that the deubiquitinase activity of A20 is dispensable for downregulating NF-κB. The second part of this thesis unravels a new biological pathway mediated by IκBβ. Unlike IκBα, which functions solely as an inhibitor of NF-κB, IκBβ can both inhibit and activate NF-κB depending on the physiological context. We hypothesized that this may be because IκBβ (unlike IκBα ) exists in two forms, a constitutively phosphorylated form and an unphosphorylated form. Prior work from our group has demonstrated that hypophosphorylated IκBβ complexes with p65:cRel and mediates the expression of certain inflammatory genes like TNFα . We report here that Glycogen Synthase Kinase 3β (GSK-3β ) interacts with and phosphorylates IκBβ at Serine-346. This phosphorylation masks the NLS of p65 in the phospho-IκBβ:p65:cRel complex, thereby sequestering the complex in the cytoplasm and mediating the anti-inflammatory role of IκBβ. We discovered a peptide that can inhibit this phosphorylation by abrogating the interaction between GSK-3β and IκBβ. Mice succumb to a sublethal dose of LPS when injected with this peptide because of increased production of TNFα (but not IL-6); thereby demonstrating the inflammatory role of unphosphorylated IκBβ in upregulating specific genes like TNFα. We propose a signaling model by which phosphorylation by GSK-3β can regulate the functions of IκBβ in response to LPS.
Reduced expression and hypermethylation of headpin, a serine proteinase inhibitor (serpin) , in human oral squamous cell carcinoma

SUMMARY Headpin, which is located at chromosome 18q21.3, belongs to serine proteinase inhibitor family （serpin） . One of the functions of this gene family is believed to inhibit hemangiogenesis, invasion, and metastasis of tumors. In this study, 30 clinical tissue specimens of oral squamous cell carcinoma （OSCC） and 9 OSCC-derived cell lines were examined for the down regulation of the gene expression. In addition, the restoration of headpin mRNA expression induced by 5-Aza-2’ -deox ycytidine （5-AzaC） treatment, a DNA demethylating agent, was evaluated in OSCC-derived cell lines. RT-PCR revealed the down-regulation of headpin gene expression in 17 （56.7%） of 30 primary OSCC samples and in 5 （55.6%） ; SAS, HSC-3, OK92, HO-1-N-1 and SCC4, of 9 OSCC-derived cell lines. Among those 5 cell lines, 5-AzaC treatment induced the restoration of headpin gene expression in 4 （80.0%） cell lines; SAS, HSC-3, OK92 and SCC4. These results suggested that the down-regulation of headpin ex pression contributes to the development of human OSCC and that DNA hypermethylation is one of the important mechanisms inactivating the headpin gene in oral carcinogenesis.