Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction of thalassemic mouse induced pluripotent stem cells for disease modeling

Induced pluripotent stem cells (iPSCs) have a great potential for disease modeling and therapeutic applications. One of the most common genetic diseases found in South East Asia is thalassemia. β-Thalassemia is an inherited single gene disorder caused by reduction or absence of β-globin chain production. The purpose of this study is to generate mouse iPSCs with β-thalassemia background. Mouse embryonic fibroblast (MEF) cells were obtained from transgenic β-thalassemic mouse, transduced with lentiviral vector carrying 4 transcription factors, Oct4, Klf4, Sox2 and c-Myc (OKSM), and cultured on a feeder layer. The embryonic stem (ES)-like colonies were manually picked up and expanded. The generated mouse iPSCs were similar to mouse embryonic stem cells (mESCs) in morphology, alkaline phosphatase activity and pattern of pluripotent gene expression and able to form teratoma containing tissues derived from all three germ layers. Therefore, we reported here an establishment of β-thalassemic mouse iPSCs which might be used for further disease modeling and therapeutic applications.
The White Amur as a Biological Control Agent of Aquatic Weeds in the Panama Canal.

Abstract The Panama Canal has been plagued with both floating and submerged aquatic weeds since its opening. Although more and more money has been spent on herbicides over the years, the weed problem has become more intense. In February 1978 the Panama Canal Company introduced the white amur fish as a biological tool to control the submerged macrophyte hydrilla to Gatun Lake, the large freshwater reservoir through which the majority of the length of the Canal passes. The first shipment of fish (125,000) did not successfully withstand the rapid change from cold Arkansas water temperatures to the warm tropical waters, with a resultant loss of about 50 percent. A series of tests was conducted to determine tempering rates of the fish with temperature, dissolved oxygen level, and time as the variables. Various experiments with chemical additives in the tempering water such as salt and quinaldine were also conducted. Based upon the tests, a tempering facility to acclimate a second fish shipment was constructed .
IMMUNOCYTOCHEMICAL LOCALIZATION OF α-ACTININ IN GAsTRIC PARIETAL CELLS OF THE RAT

Localization of α-actinin in the rat gastric parietal cell was studied using Lowicryl K4M embedding method as well as cryoultramicrotomy in combination with immunogold technique. These two methods gave similar results, but labeling efficiency was a little higher in cryoultrathin sections than in Lowicryl K4M sections.Labeling for α-actinin occurred in the cytoplasm adjacent to the zonula adherens, around the secretory canaliculus, in the microvillus, and along the basolateral infolding. Little labeling was seen around the tubulovesicle. Quantitative analysis of the distribution of gold particles in Lowicryl K4M sections revealed a significant decrease of α-actinin in the cytoplasm around the canaliculus in the secreting cell in comparison to the resting Cell.The present study showed that the gastric parietal cell is different from the intestinal epithelial cell in that it contains α-actinin in the microvilli. The decrease of α-acrinin around the intracellular canaliculus in the secretory state may be related to the morphological alteration of the parietal cell through reorganization of the actin filament meshwork.
Synthesis and evaluation of antioxidant activities of some indole-2,3-dione derivatives and analogs

In the present study, a series of novel Schiff bases of isatin were synthesized by condensation of imesatin with different aromatic aldehydes. The imesatins were synthesized by reaction of isatin with p-phenylenediamine. The chemical structures of the synthesized compounds were confirmed by means of IR, 1H-NMR, 13C-NMR, mass spectroscopy, and elemental analysis. These compounds were screened for antioxidant activity by DPPH, nitric oxide and hydrogen peroxide radical scavenging activity. In all the methods, the compound 3-(4-(3,4,5-trimethoxy benzylideneamino)phenylimino) indoline-2-one (5d) showed highest antioxidant activity because of the presence of electron donating groups and the compound 3-(4-(4-nitrobenzylideneamino)phenylimino) indoline-2-one (5f) showed the least activity because of the presence of an electron withdrawing group.
Parasitoses intestinais de indígenas da comunidade Mapuera (Oriximiná, Estado do Pará, Brasil): elevada prevalência de Blastocystis hominis e encontro de Cryptosporidium sp e Cyclospora cayetanensis

Occurrences of intestinal parasitosis in Indians of the Mapuera community (Oriximina, State of Para, Brazil) were evaluated. Within the context of group assessment, this study makes a contribution towards adequate knowledge of this subject, which is significant from a medical-sanitary point of view. Parasitological examination of feces from 83 individuals, performed using four different methods, could be considered to have reasonable amplitude for establishing diagnoses. Protozoan cysts and helminth eggs of many types were found, even with significant percentages. The frequent presence of Blastocystis hominis (57.8%), along with findings of Cryptosporidium sp (3.6%) and Cyclospora cayetanensis (10.8%), deserved highlighting with specific comments. The findings show that these Indians live in an environment in which poor hygiene conditions prevail. In particular, these facilitate the dissemination of protozoa and helminths through contact with the soil or through intake of contaminated water and food.
Haematology and Erythropoietic Response in the Catfish, Clarias albopunctatus (Lamonte and Nichole 1927), Exposed to Sublethal Concentrations of Gammalin 20 (Lindane)

Haematological changes in the fish Clarias albopunctatus (Lamonte and Nichole, 1927) subjected to sublethal concentrations (0, 0.25, 0.5, 0.75, and 1.0 µg/L) of Gammalin 20 for 21 days were studied in a static bioassay renewal system. Compared with the control, the erythocytic count haematocrit values and haemoglobin concentrations were significantly reduced (P > 0.05) in the treatment groups. These parameters also differed in the treatment groups. There was significant leucocytosis (P > 0.05) in the fish exposed to sublethal concentrations of Gammalin 20. The Gammalin-20-exposed fish suffered macrocytic anaemia. Key Words: Haematology, Erythropoietic, Catfish, Gammalin Bio-Research Vol.1(2) 2003: 61-68
Eastern Beringian biogeography: historical and spatial genetic structure of singing voles in Alaska

Aim Pleistocene climatic cycles have left marked signatures in the spatial and historical genetic structure of high‐latitude organisms. We examine the mitochondrial (cytochrome b) genetic structure of the singing vole, Microtus miurus (Rodentia: Cricetidae: Arvicolinae), a member of the Pleistocene Beringian fauna, and of the insular vole, Microtus abbreviatus, its putative sister species found only on the St Matthew Archipelago. We reconstruct the phylogenetic and phylogeographical structure of these taxa, characterize their geographical partitioning and date coalescent and cladogenetic events in these species. Finally, we compare the recovered results with the phylogenetic, coalescent and spatial genetic patterns of other eastern Beringian mammals and high‐latitude arvicoline rodents.
Appropriateness of Special Protection Areas for wide‐ranging species: the importance of scale and protecting foraging, not just nesting habitats

Effective conservation plans and design of Special Protection Areas (SPAs) for protected species should take into account ranging behaviour and foraging habitats, and this is particularly important for wide‐ranging species. Montagu's harriers Circus pygargus are ground‐nesting semi‐colonial raptors typical of agricultural habitats. We studied the foraging behaviour of 14 radio‐tracked male Montagu's harriers, in order to investigate the distance from nests of foraging birds, the extent to which foraging range overlapped with SPAs designated for this species, and foraging habitat selection within foraging ranges. Average foraging range size, estimated from either minimum convex polygon or kernel 90%, was larger than 100 km2. Only 19 ± 11% of the foraging ranges were within SPA limits. Cereal (the main habitat used for nesting) was slightly counterselected for foraging, and most prey (64%, n=117) captured in that habitat were insects. Hunting attempts occurred significantly more frequently than expected in alfalfa, where most prey captured were small mammals (70%, n=102). Use of this habitat for foraging increased throughout the season. Most prey captured in other habitats (mainly tree crops, shrubs or uncultivated land) were birds (83%, n=43). SPAs included a higher proportion of cereal, but a lower proportion of alfalfa than areas outside SPAs. Overall, our results show that breeding Montagu's harriers use an area for foraging much larger than current sizes of most SPAs for the species, that habitats selected for foraging differ from those used for nesting and that preferred foraging habitats were less common inside SPAs than outside. Conservation management for this species should aim to protect foraging habitats within a large radius of the colonies, probably requiring measures to be applied outside protected areas. More generally, SPAs designed without including information of ranging behaviour and foraging habitats may be ineffective.
Ultrastructure of the spermatozoid of Lycopodiella lateralis (Lycopodiaceae)

The spermatozoid of Lycopodiella lateralis (R. Br.) B. Ollgaard is ovoid and biflagellated and contains little cytoplasm. A large, rounded, condensed nucleus occupies the central region of the cell. At the rear of the cell is a cluster of starch-containing plastids associated with numerous elongated mitochondria and small pockets of remnant cytoplasm. The multilayered structure coils laterally around the cell anterior for just over one revolution. An anterior mitochondrion underlies the multilayered structure over its entire length and several smaller mitochondria line the inner anterior coil. Some 150 spline microtubules extend from the multilayered structure and coil posteriorly at approximately a 45° angle to the longitudinal axis of the cell. Microtubules progressively increase in length from the margins of the multilayered structure to the center and thus only a central core of approximately 30 microtubules encircles the organelles at the base of the cell. The two basal bodies are parallel and stagge.
Purification of β-Glucosidase from Saccharomyces lactis Strains Y-14 and Y-1057A

Two strains of Saccharomyces lactis (Y-14 and Y-1057A), medium (Bm) and low (B1) constitutive producers of β-glucosidase, were grown in enriched medium. β-Glucosidase was extracted by autolysis and purified by ammonium sulfate precipitation, gel filtration, and calcium phosphate gel adsorption-elution. The kinetics of release, purification, and stability of β-glucosidase from strains Y-14 and Y-1057A were compared with the enzyme from strain Y-123. The ability of glycerol, sorbitol, and mannitol to stabilize the β-glucosidases is presented. A lower molecular weight, labile form of the Y-14 enzyme is demonstrated. Differences in the initial specific activites of β-glucosidase among the three strains are discussed.
Research on Various Testing Procedures and Different Methods of Estimating Lactation Milk Yield in Dairy Cattle

This research was carried out to determine the effect of various milk sampling intervals and different methods on the accuracy of estimation of lactation milk yield in dairy cattle. Individual daily milk weights of 599 Holstein, Simmental and Brown Swiss lactations from the Aegean Agricultural Research Institute were used. It was assumed that test-day milk yields were obtained by regular and irregular intervals of 28 d and 56 d, with the irregular intervals having a standard deviation of 5 d. From test-day milk yields, 305 d milk yields were estimated by the Holland (Lactation yield = mean of test day yields x lactation duration (days)) and Test Interval methods. It was found that the bias of estimation increased significantly (P
78 CRYOPRESERVATION OF FROG (RANA PIPIENS) SPERM CELLS COLLECTED BY NON-LETHAL METHODS

There are few reported studies of cryopreservation of frog spermatoazoa. None have used non-lethal methods for collection, which involves a simple IP injection, followed by collection of sperm from the urine. Our study compared post-thaw survival of spermatozoa frozen using three different diluents: Salamon's ram semen diluent (SSD) (Evans and Maxwell 1987 Salamon's Artificial Insemination of Sheep and Goats, Sydney, Australia: Butterworths, pp. 122–141); our modification of Salamon's diluent (MSSD), containing an additional 5.9 mL glycerol and 6.6 g of sucrose per 100 mL; and a diluent reported to be currently the most successful for freezing frog sperm: Browne's frog diluent (BFD) (Browne et al. 2002 Cryobiology 44, 251–257). The 1 × SSD was composed of 2.9 g Tris, 0.4 g glucose, 3.2 g citric acid monohydrate, 12 mL egg yolk, and 4.5 mL glycerol per 100 mL. The composition of 1 × BFD was 10 g sucrose and 15 mL DMSO per 100 mL. Ten male frogs of unknown age were injected with 200 IU hCG (Chorulon; Intravet, Millsboro, DE, USA) in 500 µL PBS. Urine specimens were collected by cloacal lavage 30, 60, and 90 min post-injection. Specimenswere stored in a cold room at 8°C until all collections were finished. Diluents requiring addition of egg yolk were completed with that from a freshly laid chicken egg. Sperm cells were pooled and concentrations were measured using microscopy. Sperm cells were divided and combined with diluents in 1.5-mL microcentrifuge tubes. Tubes were suspended in a 500-mL beaker, which was placed in an ice bath to allow slow cooling to 2°C over 45 min. Aliquots of 100 µL were pipetted into indentations on dry ice and left to freeze for 3 min. Frozen pellets were plunged into liquid N2, and while under LN2, pellets were placed in microcentrifuge tubes, which were then stuffed with cotton wool. Upon thawing, pellets were removed from LN2 and dropped into 200 µL of thawing solution (0.9085 g Tris, 0.25 g fructose, and 0.45 g citric acid per 15 mL final volume) at 21°C while gently vortexing. Spermatozoa were assessed using live/dead cell stain (Molecular Probes, Eugene, OR, USA) and fluorescent microscopy. Percentages of live spermatozoa from the three treatments were 58.5%, 70.5%, and 44.1% in SSD, MSSD, and BFD, respectively. When considering the number of sperm cells lysed along with live/dead cell stain data, 40%, 55.2%, and 34.4% in SSD, MSSD, and BFD, respectively, survived post-thaw. All values were significantly different (P < 0.001). Superior results were observed with MSSD; use of SSD also resulted in better results than BFD. The most prevalent method for collection of frog sperm is to pith the frog and then macerate the testis. With frog populations dwindling worldwide, use of a technique that is virtually harmless such as used here in conjunction with cryopreservation of specimens could be useful for preserving genetic variation in endangered frog species.
An integrated metabonomics and microbiology analysis of host-microbiota metabolic interactions in rats with Coptis chinensis-induced diarrhea

Coptis chinensis Franch. , a bererine-containing traditional Chinese medicine (TCM), is often used to treat intestinal infections, diabetes and hyperlipidaemia, and often causes diarrhea. To clarify the potential mechanism of toxicity that induces diarrhea, Sprague-Dawley (SD) rats were treated with Coptis chinensis dosage of 5 g kg−1 for 14 consecutive days. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) was used to monitor the dynamic changes in the gut microbiota, while 1H NMR profiles were applied to reveal the metabolism of host and microflora. In the Coptis chinensis-treated group, decreased short chain fatty acids (SCFAs) and branched chain fatty acids (BCFAs) and increased branched chain amino acids (BCAAs) levels were detected in faeces, whereas increased BCFAs were present in the urine. This finding implied that Coptis chinensis triggered malabsorption and suppressed bacterial fermentation as well as protein degradation. Meanwhile, decreased levels of Bacteroides and Prevotella and elevated levels of Enterobacter and Veillonella in the treatment group were significantly correlated to the urinary and faecal metabolites. Using metabolite-set enrichment analysis (MSEA) and the correlation analysis between significant bacteria and metabolites, the results demonstrated that Coptis chinensis intervention suppressed glycine and serine metabolism which affected the growth of intestinal bacteria. Moreover, the perturbed microbiome consequently influenced the homeostasis of monosaccharides, amino acids, and choline, and energy metabolism of gut microbiota and host. These findings help to elucidate Coptis chinensis intervention and toxicity; simultaneously, this integrated strategy may provide an effective method for the systematic assessment of host responses to TCM or any other botanical-based nutraceuticals.
Rapid electroporation‐mediated plasmid transfer between Lactococcus lactis and Escherichia coli without the need for plasmid preparation

A simple and rapid method for the transfer of plasmids between the Gram‐positive species Lactococcus lactis and Escherichia coli without the need for plasmid preparation is described. The donor strain was subjected to an electroporation pulse which released plasmid DNA into the suspending buffer which was then centrifuged to remove cells and debris. The supernatant was mixed with the recipient strain and subjected to a second electroportion pulse, resulting in the transfer of plasmid from donor to recipient. In cases where a high transformation efficiency is not required, such as the transfer of a cloned construct from E. coli to Lactococcus or vice versa, this method has the advantages of convenience and rapidity.
Corrigendum: Correction of biomass estimates for heterotrophic micro‐organisms in Lake Tanganyika

In July 2005, the article ‘Abundance and biomass of heterotrophic micro-organisms in Lake Tanganyika was published in Freshwater Biology (Pirlot et al., 2005). Epifluorescence microscopy coupled with image analysis was used to estimate bacterial and protozoan biovolumes and then to calculate biomass adopting C:cell volume conversion factors found in the literature (Borsheim & Bratbak, 1987; Putt & Stoecker, 1989; Simon & Azam, 1989). Unfortunately, we discovered after publication that an error had been made programming the macro used to estimate the biovolume of heterotrophic micro-organisms by image analysis. This error produced globally small underestimations of bacterial biomass but more importantly, a systematic overestimation of protozoan biomasses. Recalculated values show that bacterial biomasses varied, in the mixed layer of Lake Tanganyika in 2002, between 17.6 and 48.7 mg C m)3, with an average of 26.8 mg C m)3. Fig. 1 presents the corrected biomass integrated on the 100 m water column. Averaged bacterial carbon content was 12.2 fg per cell in 2002. Flagellates biomass ranged between 5.1 and 10.8 mg C m)3, and ciliates biomass ranged between 0.7 and 3.0 mg C m)3. Averaged protozoan biomass was 9.0 mg C m)3 with 1.0 mg C m)3 attributed to the symbiotic green algae in Strombidium. The corrections presented above do not modify substantially our previous figures on bacterial biomass in Lake Tanganyika (Fig. 1) but, as flagellate and ciliate biomass was overestimated, bacteria were actually the most important heterotrophic compartment. Even if protozoan biomass is much lower than previously presented in Pirlot et al. (2005), these results confirm that heterotrophic micro-organisms are an important part of total planktonic biomass.
Mapping of quantitative trait loci controlling heading date among rice cultivars in the northernmost region of Japan

Heading date is the major factor in the regional and seasonal adaptation of rice cultivars. Although many genes controlling heading date have been identified using several mapping populations, it is not clear which previously identified genes contribute to the variation of heading date in particular regions. However, great effort is needed to identify quantitative trait loci (QTLs) among rice cultivars in rice breeding programs in a particular region because they are genetically closely related. In this study, we identified QTLs controlling heading date in 3 F2 populations among rice cultivars in Hokkaido, the northernmost region of Japan. The segregations of heading date were continuous in all populations. For QTL analysis in populations with genetically close relationships, we used SSR markers located near the known QTLs for the heading date. Three QTLs for the heading date, qDTH3, qDTH-6-1, and qDTH6-2, were detected on chromosomes 3 and 6. The relationships between the three QTLs identified in this study and the known QTLs are discussed.
Amylostereum orientale sp. nov. (Basidiomycota, Russulales) and first report of A. areolatum in China based on morphological and molecular characters

Amylostereum orientale S. H. He & Hai J. Li on Cunninghamia lanceolata is described from China as a new species, and A. areolatum is reported for the fi rst time from China. Amylostereum orientale is very similar to A. laevigatum in morphology, but the former has distinctly ellipsoid basidiospores and the host is a plant native in China. Representatives of the new taxon form a distinct clade in the phylogenetic tree inferred from the analysis of ITS rDNA sequences. A complete description with illustrations of the new species is provided.
Cytoplasmic Transfer of Chloramphenicol Resistance in Chinese Hamster Cells

Chloramphenicol resistance, a dominant marker, is readily transferred between Chinese hamster cells by fusing enucleated cytoplasts from resistant cells to a sensitive recipient strain. Isolation of cytohybrids depends on complementary selection for recessive characteristics present in recipient cells, e.g. resistance to bromodeoxyuridine. Sources of background variation in this system have been examined to determine the efficiency of cytoplasmic marker transfer. The frequency of mutants resistant to both chloramphenicol and bromodeoxyuridine was minimal in the parent strains used. Dual resistance was found to arise, however, by segregation within hybrids formed between nucleated cells present as contaminants in cytoplast fusion mixtures. Background variation may also simulate cytoplasmic transfer of nuclear markers from donor cells (e.g. resistance to ouabain). Cytohybrids resistant to both ouabain and chloramphenicol were in fact isolated from cytoplast fusion mixtures by selection with ouabain and bromodeoxyuridine. Such variants appeared to originate by mutation to ouabain resistance in recipient cells followed by cytoplasmic transfer of the chloramphenicol resistance marker.