Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression in the Star Mutation of Petunia ×hybrida Vilm

Gene silencing is one of the ways in which gene expression is controlled. The authors have developed a model system to study anthocyanin gene silencing using a recessive mutation in Petunia Juss. (Star mutation) and the ability of certain viruses to reverse the gene silencing mutation. In healthy plants, the star pattern was enhanced (increase in level of gene silencing) under high temperature or light growing conditions. Virus infection did not significantly influence the star pattern when plants were grown under either low-light or low-temperature conditions. Under high-light and -temperature conditions, virus infection reverses silencing, leading to a change in the star pattern. These changes in the star pattern corresponded to changes in gene expression. Viral infection had a greater affect on regulatory gene (Wd40, Myc, and Myb) expression than on structural gene expression (Chs and Ans). The Star mutation in Petunia ·hybrida results in flowers expressing a white star pattern on a pigmented background. This mutation was first described in 1838 as P. vittata Vilm. (Ewart, 1984). A major breakthrough in breeding occurred when A. Howard released the cultivar 'Howard's Star' in the late 1800s, which is in the genetic background of nearly every modern star cultivar. Anthocyanin biosynthetic gene expression within the white and colored tissues of the Star mutation has been extensively studied. There is an absence of chalcone synthase enzyme (CHS) activity in the white tissue compared with the colored tissue (Mol et al., 1983). A more complete analysis of structural gene expression in the Star mutant demonstrated that the level of expression of chalcone isomerase gene (Chi), flavanone 3-hydroxylase (F3H), dihydroflavonol reductase (Dfr), flavo- noid 3-glucosyltransferase (3Gt), and anthocyanin synthase (Ans) was similar in white and red tissues (Koseki et al., 2005).
BRCA1-Dependent Ubiquitination of γ-Tubulin Regulates Centrosome Number

ABSTRACT Proper centrosome duplication and spindle formation are crucial for prevention of chromosomal instability, and BRCA1 plays a role in this process. In this study, transient inhibition of BRCA1 function in cell lines derived from mammary tissue caused rapid amplification and fragmentation of centrosomes. Cell lines tested that were derived from nonmammary tissues did not amplify the centrosome number in this transient assay. We tested whether BRCA1 and its binding partner, BARD1, ubiquitinate centrosome proteins. Results showed that centrosome components, including γ-tubulin, are ubiquitinated by BRCA1/BARD1 in vitro. The in vitro ubiquitination of γ-tubulin was specific, and function of the carboxy terminus was necessary for this reaction; truncated BRCA1 did not ubiquitinate γ-tubulin. BRCA1/BARD1 ubiquitinated lysines 48 and 344 of γ-tubulin in vitro, and expression in cells of γ-tubulin K48R caused a marked amplification of centrosomes. This result supports the notion that the modification of these lysines in living cells is critical in the maintenance of centrosome number. One of the key problems in understanding the biology of BRCA1 has been the identification of a specific target of BRCA1/BARD1 ubiquitination and its effect on mammary cell biology. The results of this study identify a ubiquitination target and suggest a biological impact important in the etiology of breast cancer.
OBSERVATIONS ON THE MAINTENANCE MECHANISMS OF METAPOPULATIONS, WITH SPECIAL REFERENCE TO THE EARLY REPRODUCTIVE PROCESS OF THE MANILA CLAM RUDITAPES PHILIPPINARUM (ADAMS & REEVE) IN TOKYO BAY

Abstract To obtain basic ecological information on declining Tokyo Bay stocks of the Manila clam Ruditapes philippinarum, life history (including spawning, larval transport and settlement, and growth and survival of benthic clams) was investigated in local habitats, mainly in Sanbanse and Kisarazu. Spawning-stage adult clams were histologically detected from May to October at both sites, with two peak periods in summer and autumn. From May to November, between 13 and 23 larval cohorts appeared annually in each site, even during periods when spawning-stage adults were not detected. Spawning over many months plus larval transport from other habitats may contribute to the continuous appearance of larvae at both sites. This confirms the hypothesis that the clam population is maintained and supported by the reproduction of local populations. High density cohorts of newly settled clams, which later formed adult populations, may originate from larval cohorts spawned during peak spawning periods. A number of summer cohorts of benthic juveniles disappeared within 3–4 mo after settlement, whereas autumn cohorts maintained a relatively high density through the following spring, and subsequently they formed adult populations. Severe mortality resulting from extreme environmental factors may have affected the summer cohorts during summer and autumn. The recent decline of the adult stocks may be related to the unstable recruitment of summer cohorts, which was one of the two major seasonal components contributing to recruitment.
Short Title: Gsk3a is essential for male fertility

The signaling enzyme glycogen synthase kinase 3 exists as two isoforms – GSK3A and GSK3B. Protein phosphorylation by GSK3 has important signaling roles in several cells. In our past work we found that both isoforms of GSK3 are present in mouse sperm and that catalytic GSK3 activity correlates with motility of sperm from several species. Here we examined the role of Gsk3a in male fertility using a targeted gene knockout approach. The mutant mice are viable but have a male infertility phenotype, while female fertility is unaffected. Testis weights of Gsk3a (-/-) mice are normal and sperm are produced in normal numbers. Although spermatogenesis is apparently unimpaired, sperm motility parameters in vitro are impaired. In addition, the flagellar waveform appears abnormal characterized by low amplitude of flagellar beat. Sperm ATP levels were lower in Gsk3a (-/-) mice compared to wild type animals. Protein phosphatase PP1 gamma2 (PPP1CC2) protein levels were unaltered, but its catalytic activity was elevated in KO sperm. Remarkably, tyrosine phosphorylation of hexokinase and capacitation associated changes in tyrosine phosphorylation of proteins are absent or significantly lower in Gsk3a (-/-) sperm. The GSK3B isoform was present and unaltered in testis and sperm of Gsk3a (-/-) mice showing the inability of GSK3B to substitute for GSK3A in this context. Our studies show that sperm GSK3A is essential for male fertility. In addition, the GSK3A isoform with its highly conserved glycine rich N-terminus in mammals, may have an isoform-specific role in its requirement for normal sperm motility and
Bioconcentration of metals in the body muscle and gut of Clarias gariepinus exposed to sublethal concentrations of soap and detergent effluent.

The toxicity of Sublethal concentrations of effluents from a soap and detergent industry were investigated on African catfish Clarias gariepinus using a renewable static bioassay. The trend of bioconcentration of metals in the muscle and gut of the test organisms differs significantly (p muscle. The result revealed that the muscle had the least concentration of manganese at 0.1 x 10 -3 mg/kg and 10.7 x 10 -3 mg/kg recorded for zinc as the highest. While the highest iron concentration of 15.80 x 10 -3 mg/kg was recorded in the gut tissues of C. gariepinus, but mercury had the least concentration of 1.00 x 10 -3 mg/ kg. It was revealed that fish can bioaccumulate heavy metals from a polluted environment, which may result in impairment of natural population size; thus consumption of fish from such polluted environment should be discouraged.
SERIES ''AIRWAY REMODELLING: FROM BASIC SCIENCE TO CLINICAL PRACTICE'' Edited by L-P. Boulet and P.J. Sterk Number 3 in this Series Allergen-induced airway remodelling

Airway remodelling is associated with chronic asthma but it remains unclear whether it results from airway inflammation in response to allergens or immune-mediated events such as viral infections. Although the acute inflammation associated with asthma has been modelled extensively both in vitro and in vivo, the structural changes occurring in the lung have only recently been investigated. These in vitro, in vivo and in silico systems have been designed to examine the pathways leading to allergen-induced airway remodelling and have enabled investigators to draw conclusions about the participation of key cells and molecules in the development of allergen-induced airway remodelling. However, fundamental questions remain regarding the genesis of remodelling as well as the relationship between functional symptoms and pathological changes that occur. In this review the key questions relating allergen exposure to development of remodelling are discussed, as well as the steps that are being undertaken to investigate them.
ENVIRONMENTAL AND BIOMEDICAL SAMPLE ANALYSIS IN SUPPORT OF ALLEGATIONS OF USE OF CHEMICAL WARFARE AGENTS

In cases of allegations of use of chemical weapons, supporting evidence may be obtained from the analysis of environmental samples for chemical agents and their degradation products, and from the analysis of biomedical samples for metabolites and covalent adducts of agents with proteins and DNA. The concentrations of analytes may vary from parts per million or higher, down to sub-parts per billion, requiring a number of different mass spectral techniques. This paper provides an overview of the analysis of environmental and biomedical samples associated with the use of chemical warfare agents in the Iraq-Iran conflict, and against the Kurdish population in Iraq. It is based, in part, on a presentation to the International Symposium on NBC Terrorism Defence, held in the 10th anniversary year of the terrorist dissemination of sarin in the Tokyo subway, 20 March 1995.
Development, In Vitro Characterization, and In Vivo Toxicity Evaluation of Chitosan-Alginate Nanoporous Carriers Loaded with Cisplatin for Lung Cancer Treatment

Polysaccharide-based aerogels are promising drug carriers. Being nanoporous with a high specific surface area allows their use as a drug vehicle for various delivery routes. Intratracheal and intravenous administration of free cisplatin causes toxicity in the rat liver, lungs, and kidneys. In this work, microspherical particles based on alginate-chitosan without a traditional crosslinker were evaluated for targeted delivery of cisplatin by intratracheal administration. The aerogel particles were prepared using the emulsion gelation method, followed by supercritical carbon dioxide extraction. Loading of cisplatin on the prepared porous particles was performed by impregnation using supercritical fluid technology. The prepared carrier and the loaded drug were evaluated for drug content, release, and in vivo acute and subacute toxicity. Cisplatin was successfully loaded (percent drug loading > 76%) on the prepared carrier (particle size = 0.433 ± 0.091 μm) without chemically interacting with the carrier and without losing its crystal form. Sixty percent of cisplatin was released within 2 h, and the rest was loaded inside the polymer pores and had a sustained first-order release over 6 h. Loading cisplatin on the carrier developed herein reduced the cisplatin lung toxicity but increased the liver toxicity after intratracheal administration with nephrotoxicity being proportional to cisplatin dose in case of carrier-loaded cisplatin. Moreover, loading cisplatin on the carrier significantly reduced mortality rate and prevented weight loss in rats as compared to free cisplatin in subacute studies after intratracheal administration. Thus, the developed carrier showed high potential for targeted delivery of cisplatin for lung cancer treatment by inhalation. Graphical abstract Graphical abstract
Soil factors affecting the sustainability and productivity of perennial and annual pastures in the high rainfall zone of south-eastern Australia

A field study was carried out in the high rainfall zone (HRZ, >600 mm p.a.) of southern Australia from March 1994 to August 1997 to test the hypothesis that sown perennial grasses and liming could make the existing pastures more sustainable through better use of water and nitrogen. The site, on an acid duplex soil at Book Book near Wagga Wagga in southern New South Wales, was typical of much of the HRZ grazing country in southern New South Wales and north-east Victoria. The experiment consisted of 4 replicate paddocks (each 0.135 ha) of 4 treatments: annual pasture (mainly ryegrass Lolium rigidum, silver grass Vulpia spp., subterranean clover Trifolium subterraneum and broadleaf weeds) without lime, annual pasture with lime, perennial pasture (phalaris Phalaris aquatica, cocksfoot Dactylis glomerata and subterranean clover T. subterraneum) without lime, and perennial pasture with lime. Soil pH (0–10 cm) in the limed treatments was maintained at 5.5 (0.01 mol/L CaCl2), compared to 4.1 in the unlimed treatments. The pastures were rotationally grazed with Merino ewe or wether hoggets at a stocking rate which varied with the season, but was 10–25% higher on the limed pastures [14.8–17.3 dry sheep equivalent (dse)/ha] than the unlimed pastures. One replicate set of pasture treatments was intensively monitored for surface runoff, subsurface flow (at the top of the B horizon), water potential gradients and ammonium volatilisation. Other measurements of nitrogen inputs, transformations and losses were made on all paddocks. In a normal to wet year, surface runoff, subsurface flow and deep drainage (>180 cm depth) were about 40 mm less from the perennial than the annual pastures. The reduction in deep drainage under the perennials was about one-third to one-half (20–29 mm/year). The smaller loss of solution NO3– from the perennial pastures (up to 12 kg N/ha.year) suggested soil acidification under perennials was reduced by about 1 kmol H+/ha.year. Denitrification and volatilisation losses of N were small (1–12 kg N/ha.year). Nitrogen fixed by subterranean clover (above ground parts) ranged from 2–8 kg N/ha in the drought of 1994–95 to 128 kg N/ha in a normal year (1996). The soil-pasture nitrogen balance was positive for all treatments and averaged 76 kg N/ha.year over 2 years. The abundance of introduced and native earthworms increased from 85 to 250/m2 in the limed pastures between 1994 and 1997. Introduced species, such as Aporrectodea trapezoides, were especially responsive to lime. Animal production per hectare was 10–25% higher on pastures with lime. Critical gross margins per dse were lowest ($16/ha) for a long-lived perennial pasture (>15 years), and highest ($20/ha) for a short-lived perennial (5 years). Overall, there were substantial benefits in animal production, improved soil quality and water use from establishing perennial grass pastures with lime on these strongly acid soils.
Characterization of distinct bloom phenology regimes in the Southern Ocean

In this study, we document the regional variations of bloom phenology in the Southern Ocean, based on a 13-year product of ocean colour measurements co-located with observation-based estimates of the mixed-layer depth. One key aspect of our work is to discriminate between mixed-layer integrated blooms and surface blooms. By segregating blooms that occur before or after the winter solstice and blooms where integrated and surface biomass increase together or display a lag, we define three dominating Southern Ocean bloom regimes. While the regime definitions are solely based on bloom timing characteristics, the three regimes organize coherently in geographical space, and are associated with distinct dynamical regions of the Southern Ocean: the subtropics, the subantarctic, and the Antarctic Circumpolar Current region. All regimes have their mixed-layer integrated onset between autumn and winter, when the daylength is short and the mixed layer actively mixes and deepens. We discuss how these autumn–winter bloom onsets are controlled by either nutrient entrainment and/or reduction in prey-grazer encounter rate. In addition to the autumn–winter biomass increase, the subantarctic regime has a significant spring biomass growth associated with the shutdown of turbulence when air–sea heat flux switches from surface cooling to surface warming.
PRELIMINARY PHYTOCHEMICAL EVALUATION OF IN VIVO AND IN VITRO PLANT PARTS OF ADANSONIA DIGITATA L.: AN ENDANGERED MEDICINAL TREE

Adansonia digitata L. is a native deciduous tree of African savannas and belongs to the family Bombacaceae. The tree faces a crisis of survival and is enlisted as an endangered species in the Red Data book. Currently, fear has been expressed about its regeneration. Adansonia has immense medicinal value and possesses various pharmacological properties like anti-bacterial, anti-fungal, anti-malarial, anti-pyretic and almost all parts of the tree are used for healing purposes. To explore its pharmacological uses and isolation of bioactive compounds, phytochemical screening of in vivo and in vitro parts was carried out in Acetone, Methanol and Aqueous solvents. Results indicate the presence of phytochemicals like Alkaloids, Flavonoids, Saponins, Terpenoids and Tannins in almost all extracts. Fatty acid content was highest in methanol fruit pulp. Presence of phytochemicals may further contribute to anti-microbial activity and isolation of bioactive compounds using cell and suspension culture technology in near future. Looking into
Glutathione-dependent formaldehyde dehydrogenase from golden pothos (Epipremnum aureum) and the production of formaldehyde detoxifying plants

Glutathione-dependent formaldehyde dehydrogenase (FALDH) is an enzyme involved in formaldehyde metabolism in eukaryotes. FALDH cDNA was cloned from golden pothos, which is reported to effectively purify gaseous formaldehyde from enclosed room atmosphere. FALDH cDNAs from Arabidopsis, rice and golden pothos were overexpressed in transgenic Arabidopsis, and the enzyme activity was compared to determine the one most suitable for the molecular breeding of formaldehyde-detoxifying plants. The transgenic lines exhibited modified levels of the FALDH transcript, i.e. 10-800% compared to the endogenous transcript, due to either an overexpression or a cosuppression phenotype. The enzyme activity in the crude leaf extract was not proportionate, but did correlate with the transcription levels with certain exceptions. The FALDHs from the three plant species indicated similar enzymatic activity on average. The capacity to detoxify exogenous formaldehyde in the transformants with the FALDHs was determined at the whole plant level. Plants overexpressing FALDH from the three plant species displayed up to a 40% increase in their efficiency to take up exogenous formaldehyde as compared with the wild-type plants. On the other hand, no difference in the survival rate was observed among the transformants and wild type plants on formaldehyde-containing agar medium. These results show the FALDH from golden pothos to be similarly or more effective for detoxifying formaldehyde in transgenic plants compared with Arabidopsis and rice, and that this cDNA is applicable to the molecular breeding of formaldehyde detoxifying plants.
Ultrastructural Changes in the Midgut Epithelium of Acheta domesticus (Orthoptera: Gryllidae) During Degeneration and Regeneration

Abstract The midgut of Acheta domesticus L. (Orthoptera: Gryllidae) is composed of anterior and posterior parts. Midgut epithelium has columnar digestive cells and regenerative cells, the latter of which form regenerative crypts. Differences at the ultrastructural level between digestive and regenerative cells of the anterior and posterior midgut are described. Processes of degeneration and regeneration are more extensive in the posterior midgut, where entire groups of the digestive cells undergo necrosis, whereas only individual degenerating cells are observed in the anterior midgut. Regenerative cells, which occupy the basal regions of regenerative crypts, proliferate intensively, and they are the stem cells of the midgut epithelium. The cells situated in the apical part of the regenerative crypt assume an epithelial character and differentiate into epithelial cells. Those digestive cells that degenerate separate from the basal lamina and are lost. Regeneration in this species proceeds in a continuous manner.
Variability in the nutrients, antinutrients and other bioactive compounds in soybean [Glycine max (L.) Merrill] genotypes

One hundred forty soybean genotypes were evaluated for their physicochemical properties and biochemical diversity in contents of nutrients (total proteins, oil, total sugars and sucrose), antinutrients (trypsin inhibitor activity and phytic acid) and bioactive compounds (tannins, saponins, phenolics and tocopherols) with the aim to identify the improved genotypes having low antinutrient and high nutrient traits for human/livestock consumption. Physicochemical characterization indicated that exotic genotypes had highest mean values for water absorption, volume expansion, hydration capacity, swelling capacity and their indices. Soybean genotypes exhibited 38.4–46.5% protein, 20.8–23.6% oil, 1.3–13.9% total soluble sugars, 0.24–13.8% sucrose, 2.50–33.5 mg/g to copherol, 8.9–20.5 mg/g tannins and 11–38.3 mg/g phenols. Genotypes SL 1000, SL 716 and SL 990 recorded minimum trypsin inhibitor activity, phytate and tannin content, respectively. Soybean genotypes investigated differed in their nutritional and antinutritional characteristics. Such information will be useful for breeding purposes as well as in selecting soybean varieties to manufacture various soy food preparations.
Population Genetic Structure of the Twospotted Spider Mite (Acari: Tetranychidae) from China

Abstract The Chinese population genetic structure of the twospotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), was investigated by amplifying and sequencing a portion (453 bp) in the mitochondrial DNA gene coding for cytochrome oxidase I (COI). The study was aimed at checking genetic difference among the Chinese populations of the mite and analyzing its possible dispersal within China. Thirteen populations from east, west, northeast, northwest, and central parts of mainland China were sampled. In the comparisons of these sequences, 36 nucleotide positions (7.9% of the total length) were found polymorphic, of which 88.9% were silent substitutions. Intraspecific variation analysis showed that the Xinjiang (XJ) sample differed from the other samples by an average of 4.68% nucleotide divergence, which was represented two different phylogenetic lineages in the phylogenetic tree. Apart from the XJ sample, the other samples displayed little variation (nucleotide divergences below 1.77%) with each other and clustered in one of the lineages. We argue that the reasons for the remarkable distinction are probably geographical barriers and the use of different host plants.