Miracle-dz/UniFAR-FTUs huggingface dataset:
A Putative Role for the Vacuolar Calcium/Manganese Proton Antiporter AtCAX2 in Heavy Metal Detoxification

: Regulation of uptake and compartmentation of metal ions is important for the maintenance of metal ion homeostasis. To identify mechanisms involved in the protection of plants from Mn toxicity, wild-type yeast was transformed with an Arabidopsis cDNA library and transformants were screened on toxic Mn concentrations. Wild-type yeast could not grow in the presence of 30 mM MnSO4, while two transformants carrying variants of the same gene were able to grow. Database searches revealed that the isolated cDNAs correspond to AtCAX2, previously described as a vacuolar calcium-proton antiporter. Since no other genes could be identified, AtCAX2 might represent a major function permitting Mn detoxification in this suppressor screen. Furthermore, yeast transformed with the two AtCAX2 cDNAs showed increased sensitivity towards hydrogen peroxide, pointing to a limited availability of cytoplasmic Mn in the presence of AtCAX2 activity. The open reading frames of the cDNA encoded polypeptides that have a 42 and a 92 amino acids shorter N-terminal region relative to the predicted full-length coding region of AtCAX2. In contrast to both truncated cDNAs, the full-length clone was unable to confer Mn resistance to yeast, indicating that, similar to AtCAX1, AtCAX2 also carries an autoinhibitory N-terminal domain regulating the activity of AtCAX2.
Disruption of the actin cytoskeleton results in nuclear factor‐κB activation and inflammatory mediator production in cultured human intestinal epithelial cells

The cytoskeleton in eukaryotic cells is composed of two major filament systems, the microtubule system and the actin cytoskeleton. The microtubule system has recently emerged as an important regulator of NF‐κB function. However, the role that the actin microfilament system plays in controlling NF‐κB activation is incompletely understood. In this study, we examined the effect of actin cytoskeleton disruption on NF‐κB activation in human intestinal epithelial cells. Treatment of HT‐29 or Caco‐2 cells with the prototypic actin disrupting agents cytochalasin D or latrunculin B resulted in increased NF‐κB DNA binding and NF‐κB‐dependent transcriptional activity. This NF‐κB activation by cytochalasin D was secondary to an effect on IκB, because cytochalasin D‐induced IκB degradation and the cytochalasin D‐induced increase in NF‐κB‐dependent transcriptional activity was prevented by a dominant negative IκB mutant. Exposure of the cells to cytochalasins or latrunculin B increased gene expression and release of the NF‐κB‐dependent chemokines IL‐8 and GRO‐α. Cytochalasin D also activated p38 MAP kinase, which pathway contributed to the cytochalasin D‐induced increase in IL‐8 production. These results demonstrate that the actin cytoskeleton plays an important role in the regulation of NF‐κB activation and inflammatory events in intestinal epithelial cells. © 2004 Wiley‐Liss, Inc.
Callus induction and cell culture of castor (Ricinus communis L. CV. Shabje)

Context: Tissue culture is an important tool in plant biotechnology that allows for an increase in biomass or metabolite production by utilizing several techniques in callus or cell cultures. Ricin is a toxic protein that can be extracted from the castor bean as secondary metabolite. The ricin has been used experimentally in medicine to kill cancer cell. We developed callus and cell culture technique for the possible extraction of ricin from the cell suspension culture of Ricinus communis. Objectives: The present investigation aimed to develop the cell culture technique of R. communis L. cv. Shabje and tried to establish a protocol for cell suspension culture of castor for possible extraction of ricin from cell extract. Materials and Methods: The hypocotyl explants of R. communis L. cv. Shabje were used as experimental materials. Cultured on Murashige and Skoog medium supplemented with different concentrations and combinations of BAP, NAA, 2,4-D and IAA for callus induction. For cell culture, the media were used without agar with different concentrations and combinations of these hormones. Results: For callus induction the combination of BAP 2.0 mg/l + 0.5 mg/l NAA showed the best performance but in case of cell culture the combination of BAP 2.0 mg/l and 0.2 mg/l NAA showed the best result. Conclusion: The present investigation clearly established and demonstrated the method of obtaining cell suspension culture and important secondary metabolite ricin could be obtained from cell suspension culture of R. communis L. holding promises to explore cell culture industry for ricin production. DOI: http://dx.doi. org/10.3329/jbs.v20i0. 17738 J. bio-sci. 20: 161-169, 2012
Isolation of Geotrichum candidum pathogenic to tomato ( Solanum lycopersicum ) in Washington State

Geotrichum candidum was isolated from fruit of tomato ( Solanum lycopersicum ) in Washington state. Cultural and morphological features, and rDNA sequence data, are reported. Koch's postulates were completed on tomato fruit. This is the first report of this fungus causing disease of tomato in Washington state.
Over-expression of Gastrodia anti-fungal protein enhances Verticillium wilt resistance in coloured cotton

Currently there are no adequate control measures for the cotton fungal diseases Verticillium wilt and Fusarium wilt, which are important factors limiting yield under certain conditions. In this study the gene encoding a Gastrodia anti-fungal protein was introduced into three cultivars of coloured cotton using the method of pollen-tube pathway transformation, with the purpose of obtaining transgenic plants with improved resistance to wilt. Of the 121 herbicide-resistant cotton plants two, LB-5-8 and ZB-1-49, were scored as transgenic based on Southern blot, RT-PCR analysis and in vitro anti-fungal activity assay. Field analysis demonstrated that the transgenic lines LB-5-8 and ZB-1-49 possess an increased resistance to wilt. After 2 years of breeding, the progeny of LB-5-8 and ZB-1-49 lines still showed a stable and strong resistance to Verticillium wilt. Lines with high levels of resistance to Verticillium wilt obtained from the present study may be widely planted and help to reduce the future impact of cotton wilt on cotton production resulting in increased yields.
Regulation of Expression of D3-type Cyclins and ADP-Glucose Pyrophosphorylase Genes by Sugar, Cytokinin and ABA in Sweet Potato (Ipomoea batatas Lam.)

Abstract The productivity of sweet potato is governed by both the rate of cell division and sink activity of its tuberous root. The aim of this study was to reveal the mechanisms that regulate cell division activity and sink activity during tuberous root formation. As an indicator of the cell division activity, we used the transcript level of two D3-type cyclins, which regulate cell cycle progression through the formation of the regulatory subunit of the cyclin-dependent kinase complex. As an indicator of photosynthetic product sink activity, we used the gene expression of ADP-glucose pyrophosphorylase (AGPase), one of the key enzymes of starch synthesis. During tuberous root formation, the expression of D3 cyclin genes increased to the maximal levels and then decreased. In contrast, the expression of the AGPase gene increased continuously. Sucrose enhanced the expression of D3 cyclin and AGPase genes, but a high concentration of sucrose repressed the expression of a D3 cyclin gene. In the presence of sucrose, cytokinin increased the expression of D3 cyclins, but abscisic acid (ABA) did not. However, cytokinin and ABA repressed the induction of AGPase gene expression by sucrose. These results suggested that sugars, cytokinin and ABA regulate the cell division activity and the sink activity in sweet potato.
Reproductive success decreases with colony size in the European bee-eater

The evolution of coloniality is usually explained by a benefit/cost ratio greater than one. Alternatively, when costs exceed benefits, a clumped or restricted availability of limiting resources is used to explain coloniality. In this study we examine the relation between reproductive success and colony size in the European bee-eater (Merops apiaster). In our study population in Slovakia colony size varied from solitary breeding pairs up to 79 pairs per colony. We found no seasonal effects on reproductive success, however, there was a negative correlation between colony size and chick condition and survival. This relationship, although not significant, tended to be the same when examining only the earliest breeding pair of each colony site. There was no relation between reproductive parameters and age of parents and no indication for age related settlement or any effect of the nest hole position within a colony. Limitation of nesting sites and distribution of food are probably two important determinants for colonial breeding in this species. Different aspects, including the rare occurrence of helpers, are discussed as possible factors explaining the negative relationship between annual reproductive success and colony size.
Swedish nemerteans (phylum Nemertea), with description of a new hoplonemertean genus and species

A survey of the nemertean fauna along the Swedish west coast found specimens of 20 genera and 32 species, of which one genus and species is new to science (Tetraneuronemertes lovgreni gen. et sp. n.). The proportions of the three taxa Hoplonemertea, Heteronemertea, and Palaeonemertea are 34, 55, and 11%, respectively, with respect to specimen numbers, and the proportions for species within these taxa are 53, 31 and 16%, respectively. The most common species encountered during the survey were the heteronemerteans Lineus bilineatus, Micrura fasciolata, and Micrura purpurea, the hoplonemertean Nipponnemertes pulcher, and the palaeonemertean Cephalothrix rufifrons.
Rates of fermentation and short chain fatty acid and gas production of six starches by human faecal microbiota

Six starches (wheat, kidney bean, rice, corn, amylopectin and amylose) were fermented in vitro with mixed human faecal microbiota for 2, 4, 6, 8, 12 and 24 h to determine differences in rates of fermentation, and production of short chain fatty acid (SCF A) and gas. The starches differed significantly in rates of fermentation with wheat and rice starches being completely fermented by 12 h whereas all other starches had disappeared by 24 h. However, individual and total SCF A production g−1 starch fermented did not differ with starch source. Gas production was significantly correlated with SCF A production (P <0.0001). Although all starches were 100% fermentable by 24 h and produced similar types and quantities of SCF A, differences in the profiles, ie rates of gas and SCF A production, were observed.
Xp38γ/SAPK3 promotes meiotic G2/M transition in Xenopus oocytes and activates Cdc25C

We have studied the role of p38 mitogen‐activated protein kinases (MAPKs) in the meiotic maturation of Xenopus oocytes. Overexpression of a constitutively active mutant of the p38 activator MKK6 accelerates progesterone‐induced maturation. Immunoprecipit ation experiments indicate that p38γ/SAPK3 is the major p38 activated by MKK6 in the oocytes. We have cloned Xenopus p38γ (Xp38γ) and show that co‐expression of active MKK6 with Xp38γ induces oocyte maturation in the absence of progesterone. The maturation induced by Xp38γ requires neither protein synthesis nor activation of the p42 MAPK–p90Rsk pathway, but it is blocked by cAMP‐dependent protein kinase. A role for the endogenous Xp38γ in progesterone‐induced maturation is supported by the inhibitory effect of kinase‐dead mutants of MKK6 and Xp38γ. Furthermore, MKK6 can rescue the inhibition of oocyte maturation by anthrax lethal factor, a protease that inactivates MAPK kinases. We also show that Xp38γ can activate the phosphatase XCdc25C, and we identified Ser205 of XCdc25C as a major phosphorylation site for Xp38γ. Our results indicate that phosphorylation of XCdc25C by Xp38γ/SAPK3 is important for the meiotic G2/M progression of Xenopus oocytes.
The Effect of Median Lobe Presence on Oncologic and Functional Outcomes in Robot Assisted Radical Prostatectomy in the Learning Curve

Amac: Robot yardimli laparaskopik radikal prostatektomi (RALP), ogrenme egrisinde median lob (ML) varliginin, perioperatif , onkolojik ve fonksiyonel sonuclar uzerine etkisini arastirmayi amacladik. Meteryal Metod: Klinigimizde Temmuz 2017 ile Ekim 2019 tarihleri arasinda RALP uygulanan 38 ardisik hastayi analiz ettik. Hastalara ilk ogrenme egrisinde ki ayni cerrahi ekip tarafindan opere edildi. RARP sirasinda belirlenen bir ML varligina veya yokluguna gore iki grupta analiz edildi. Perioperatif, onkolojik ve fonksiyonel sonuclar gruplar arasinda karsilastirildi. Bulgular: Calismaya dahil edilen hastalarin 10 (% 26,3)’un da prostatik bir ML tespit edildi. Her iki grupta da prostat spesifik antijen (PSA), vucut kitle indeksi(BMI), hastanede kalis suresi , perioperatif ve postoperatif komplikasyon oranlari benzerdi(p<0,01). Cerrahi sinir pozitifligi orani ise ML grubunda %20 (2/10) iken ML’suz grupta %10,7 (3/28) olarak tespit edilidi. Gruplar arasi sayisal farklar istatistiksel acidan anlamli bulunmadi(p<0,01). Yine de, prostat volumu(p=0,008) ve tahmini kan kaybi(TKK) (p=0,001) median loblu bulunan hastalar lehine anlamli idi. Ortalama konsol suresi ML'lu hastalarda biraz daha fazla olmasina ragmen bu sayisal farklar istatistiksel acidan anlamli bulunmadi(p<0,01). Mesane boynu rekonstruksiyon oranlari ML grubunda %100 (%100) iken ML’suz grupta %14 (4/28) olarak olculdu(p=0,001). ML olan ve olmayan hastalar arasinda kontinans oranlari, kateter cikarilmasindan sonra 4. hafta da (% 20 - %35) , 12. hafta da (% 70 -% 64,2) ve 24. hafta da (% 90 -% 89,2) da benzer olup tum zamanlarda istatistiksel acidan anlamli fark gozlenmedi. Sonuc: Ilk ogrenme egrisinde RALP’nin yuksek cerrahi tecrubesi bulunmayan merkezlerde zorlu vakalarda da guvenli ve etkili bir sekilde uygulanabilecegini dusunmekteyiz. Bizim baslangic serimizde karsilastigimiz ML’lu vakalarin ML’suz hastalarla onkolojik, fonksiyonel sonuclari ve komplikasyon oranlari karsilastirildiginda literatur ile uyumlu sonuclar elde ettik.
Observations on Rhinomonas reticulata comb. nov. and R. reticulata var. eleniana var. nov. (Cryptophyceae), with comments on the genera Pyrenomonas and Rhodomonas

Seven marine red strains of Cryptophyceae were examined using scanning and transmission electron microscopy. Six of these, possessing a nucleomorph housed within the pyrenoid and a periplast with distinctly hexagonal periplast areas, are assigned to Rhinomonas reticulata comb. nov. Rhinomonas reticulata var. eleniana var. nov. is described on the basis of the smaller size of the periplast areas. In a strain of the genus Pyrenomonas, which Rhinomonas otherwise resembles, the periplast areas appear more or less rectangular. Since it is impossible to know with certainty which red marine forms fall within the original concept of the genus Rhodomonas, the name Pyrenomonas should be preferred to a recent emendation of Rhodomonas.
Age, growth, maturity, longevity and natural mortality of the shortfin mako shark (Isurus oxyrinchus) in New Zealand waters

Shortfin mako sharks were aged by counting growth bands in sectioned vertebrae (n = 256), and assuming annual band-pair deposition. No systematic ageing bias was present and count precision was high. 0+ juveniles were identified from length-frequency plots and assigned ages based on a theoretical birth date of 1 October and their date of capture. A Schnute generalised growth model fitted to the combined vertebral and 0+ data described the growth patterns best. Shortfin makos grow very rapidly initially, increasing by ∼39 cm fork length in their first year. Thereafter, males and females grow at similar but slower rates until about age 7 years, after which the relative growth of males declines. Longevity estimates were 29 and 28 years for males and females respectively. Natural mortality (M) is probably in the range of 0.10-0.15. Median ages at maturity were 7-9 years for males and 19-21 years for females. Comparisons of growth curves reported here and elsewhere suggest no regional differences in growth rates. The shortfin mako is a late-maturing species with moderate longevity and low natural mortality. With these life history characteristics and an unknown stock size and structure worldwide, management should be of a precautionary nature.
Fish assemblages in two sandy beaches in lower Purus river, Amazonas, Brazil

Fish assemblages from two sandy beaches in the lower Purus river (Amazonas, Brazil) were compared. Four sampling groups were represented by: day and night samples in sandy beach inside the Reserva Biologica de Abufari (biological reserve) and day and night samples in the Reserva de Desenvolvimento Sustentavel Piagacu-Purus (sustainable development reserve). Samples were collected during low water levels (November) in 2007. The fish were sampled by means of seines with mesh size of 5 mm between opposing knots, 11 m long and 6 m wide. A total of 112 fish species belonging to nine orders and 27 families was captured. The vast majority of the dominant forms consisted of small fishes (< 100 mm SL) or juveniles. Samples collected in Abufari at night presented more specimens (3,540), higher richness (84 spp.), larger total biomass (76,614 g) and higher diversity (H'= 2.57) than the other groups. The composition of fish assemblages was significantly different among all analyzed groups (ANOSIM, p < 0.0001, R= 0.71). NMDS analysis also clustered all species in four distinct groups according to species composition per period and site. SIMPER analyses showed that 80% of variation of species composition among the groups examined was due to 12 species. However, fish composition did not show any correlation with the abiotic factors examined. Different levels of use in both reserves may explain differences in fish composition.
Distribution of anionic sites on intracellular organelles: A study by labeling frozen thin-section with cationized ferritin.

The distribution of anionic sites on intracellular organelles were studied by labeling frozen thin-sections with the multivalent ligand, cationized ferritin, as a visual probe.Frozen thin-sections obtained from fixed rat cardiac muscles with 0.5% glutaraldehyde were incubated with cationized ferritin (50μg/l ml phosphate buffered saline, pH7.4) for 30min at room temperature.The ligands almost continuously labeled the surface of the sarcolemma and the junctional membrane forming the intermediate junction and desmosome, and the luminal surface of the T-tubules. In mitochondria, the ligand binding occurred to the outer surface of the outer mitochondrial membranes and to the matrix side of the inner mitochondrial membranes. High affinity for the ligand was seen on the cytoplasmic side of the gap junction. In addition, the sarcoplasmic reticulum and thick filaments showed moderately high affinity for cationized ferritin. The implications of our observations in the regulation or maintenance of cellular organization are discussed.
A Practical Polymerase Chain Reaction Laboratory for Introductory Biology Classes

The Polymerase Chain Reaction (PCR) is an in vitro method used to synthesize millions of copies of a specific DNA segment in a few hours. The process is extremely useful in singling out specific regions of the chromosome for study and in enabling investigation of DNA that is available in otherwise undetectable quantities. Since its introduction in 1985, PCR has revolutionized the field of DNA analysis. The PCR process is straightforward. It facilitates students' understanding of DNA structure and replication, and it teaches that Nobel Prize winning ideas do not need to be impossibly complicated. In this article we describe a PCR laboratory exercise that can be successfully performed by introductory biology students in one 45-55 minute dass period. Electrophoresis of the amplified DNA takes place during a subsequent class period. Thousands of Los Angeles area public high school students have successfully performed this lab over the past four years.
Modeling the Protonation States of the Catalytic Aspartates in β-Secretase

β-Secretase (BACE) is a critical enzyme in the production of β-amyloid, a protein that has been implicated as a potential cause of Alzheimer's disease (AD). There are two aspartic acid residues (Asp 32 and Asp 228) present in the catalytic region of BACE that can adopt multiple protonation states. The protonation state and precise location of the protons for these two residues, particularly in the presence of an inhibitor, are subjects of great interest since they have a direct bearing on the mechanism of aspartyl proteases and efforts to model β-secretase. We have carried out full liner-scaling quantum mechanical (QM) calculations that include Poisson−Boltzmann solvation in order to identify the preferred protonation state and proton location in the presence and absence of an inhibitor. These calculations favor the monoprotonated state in the presence of ligand, and di-deprotonated state in the absence of ligand. Further the proton in the monoprotonated state is located on the inner oxygen of Asp 228. Th.
A genetic analysis of seed and berry weight in grapevine

Fruit size and seedlessness are highly relevant traits in many fruit crop species, and both are primary targets of breeding programs for table grapes. In this work we performed a quantitative genetic analysis of size and seedlessness in an F1 segregating population derived from the cross between a classical seeded (Vitis vinifera L. 'Dominga') and a newly bred seedless ('Autumn Seedless') cultivar. Fruit size was scored as berry weight (BW), and for seedlessness we considered both seed fresh weight (SFW) and the number of seeds and seed traces (SN) per berry. Quantitative trait loci (QTL) analysis of BW detected 3 QTLs affecting this trait and accounting for up to 67% of the total phenotypic variance. QTL analysis for seedlessness detected 3 QTLs affecting SN (explaining up to 35% of total variance) and 6 affecting SFW (explaining up to 90% of total variance). Among them, a major effect QTL explained almost half of the phenotypic variation for SFW. Comparative analysis of QTLs for these traits reduced the number of grapevine genomic regions involved, one of them being a major effect QTL for seedlessness. Association analyses showed that microsatellite locus VMC7F2, closely linked to this QTL, is a useful marker for selection of seedlessnes.