Miracle-dz/UniFAR-FTUs huggingface dataset:
A Phylogenetic Study of Sanicula sect. Sanicoria and S. sect. Sandwicenses (Apiaceae) Based on Nuclear rDNA and Morphological Data

Parsimony analysis of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences and morphological data provided a well-resolved set of phylogenetic hypotheses for Sanicula, with special emphasis on the western American species constituting sect. Sanicoria and the Hawaiian sect. Sandwicenses. A lineage that encompasses the western American sect. Sanicoria and the Hawaiian sect. Sandwicenses appears to comprise three major clades: Clade 1, a group of coastal North American and Hawaiian species; Clade 2, an ecologically diverse assemblage of continental taxa including maritime, marsh, chaparral, serpentine, and desert species; and Clade 3, a group of mostly narrowly-endemic species of interior habitats in western North America. Species of the largely Old World sect. Pseudopetagnia and sect. Sanicula fall outside the sect. Sanicoria + sect. Sandwicenses clade. The (weakly supported) phylogenetic patterns among species of sect. Pseudopetag- nia and sect. Sanicula are consistent with an Asian origin of Sanicula. As reported earlier, three primarily- Californian, coastal species of sect. Sanicoria (S. arctopoides, S. arguta, and S. laciniata) appear to be more closely related to the monophyletic Hawaiian group than to other members of sect. Sanicoria. Biogeographic recon- structions provide unequivocal support for dispersal of the Hawaiian ancestor from the California Floristic Province. Estimates of clade age from rate-constant ITS trees place the most recent common ancestor of the Hawaiian taxa at ? 0.9 ? 0.4 Ma, after the origin of Kaua'i, O'ahu, and West Maui, but indicate a divergence from the closest surviving American lineage at ? 8.9 + 1.5 Ma, i.e., possibly before the origin of the modern high islands. Our data confirm that the two South American species of sect. Sanicoria are conspecific with western North American S. crassicaulis and S. graveolens and originated from a minimum of two long-distance dispersal events < 2.5 Ma (since the late Pliocene). A suite of fruit characteristics that promote animal dispersal are common to the Hawaiian and South American species and their closest North American rela- tives. Dispersibility appears to have been lost multiple times in western North America, with limited diver-
Fucoid assemblages on the north coast of Spain: past and present (1977–2007)

Abstract Fucoid assemblages dominated by Pelvetia canaliculata, Fucus spiralis, F. vesiculosus, and Ascophyllum nodosum located at two sites on the central coast of Asturias (northern Spain) were sampled monthly in 1977. Repeating the same sampling methodology, a resurvey was done in 2007 to detect changes in the abundances of the species using the previous data as a baseline. Annual net primary production was lower for all the species in 2007, and there were differences in the timing of maximum biomass for P. canaliculata and F. vesiculosus, as well as a shortening of the growth period in 2007. Associated fauna also differed between dates. Higher abundances of Gibbula spp. occurred in 2007, whereas littorinid species densities in the upper intertidal were reduced in that year. As a result, the fucoid-grazers balance changed, with P. canaliculata and particularly F. vesiculosus, being the assemblages most sensitive to change. Observed modifications were not merely fluctuations in the biomass patterns of these species, but also responses to increases in air temperature and sea surface temperature and to a shift in the frequency and seasonality of upwelling episodes. Other long-term abiotic fluctuations not directly related to global warming should also be considered as possible drivers for these changes.
Seasonal Variation of Gonadal Development, Sexual Steroids, and Lipid Reserves in a Population of the Lizard Psammodromus algirus

We studied the seasonal variations of reproductive characteristics in a wild population of the lacertid lizard Psammodromus algirus by measuring gonadal weight, germinal epithelium height, sexual steroids (testosterone, estradiol, and progesterone), and lipid reserves (in fat bodies and liver) in three phases of the reproductive cycle: early breeding (late April), late breeding (mid-June), and post-breeding season (late July). In males, testis size, germinal epithelium, and testosterone plasma levels were high in the breeding season and decreased dramatically in July. However, spermatogenesis (maximum in June) was slightly delayed with respect to testosterone secretion (peak in April), suggesting that a previous increase in testosterone levels could be necessary to stimulate the initial stages of spermatogenesis
Molecular Mechanisms Underlying Profilin-1’s Regulation of Tumorigenic Potential of Breast Cancer Cells

A hallmark of oncogenic transformation is disruption of the actin cytoskeleton, which is partly attributed to altered expression and/or activity of proteins that bind to and regulate the state of polymerization of actin in cells. Profilin-1 (Pfn1) is a key regulator of actin polymerization that is downregulated in human breast cancer. Previous studies have also shown Pfn1 has a tumor-suppressive effect on triple-negative breast cancer (TNBC) cells with mesenchymal features, and Pfn1-induced growth suppression of TNBC cells is partly mediated by upregulation of cell-cycle inhibitor p27kip1 (p27). The aim of the first part of this dissertation was to elucidate the molecular mechanism of how Pfn1 elevation causes p27 accumulation in TNBC cells. It is demonstrated that Pfn1 overexpression leads to accumulation of p27 through promoting activation of AMP-activated kinase (AMPK) and AMPK-dependent phosphorylation of p27 on T198 residue (a post-translational modification that leads to increased protein stabilization of p27) secondary to a cadherin-mediated epithelial morphological reversion. These findings not only elucidate a potential mechanism of how Pfn1 may inhibit proliferation of mesenchymal TNBC cells, but also highlight a novel pathway of cadherin-mediated p27 induction and therefore cell-cycle control in cells. The aim of the second part of this dissertation was to investigate whether Pfn1 is a classic tumor-suppressive protein. Matrigel-based 3D-outgrowth assays that measure tumor-initiating capacity of breast cancer cells demonstrated that either depletion or elevation of Pfn1 expression impairs formation of filopodia-like structures (a feature that determines dormant vs proliferative phenotype) and outgrowth of TNBC cells suggesting that a balanced Pfn1 expression is most conducive for tumor-initiating capacity of TNBC cells. Furthermore, perturbing Pfn1 expression affects expression of stem cell-associated genes thereby impacting the overall stem-like phenotype of TNBC cells. Finally, the outgrowth-deficient phenotype of TNBC upon Pfn1-depletion can be rescued by modulating ECM component which suggests that alteration in cell-matrix adhesion and downstream signaling underlies the growth-related phenotypic changes induced by loss of Pfn1. Based on these results, we conclude that Pfn1 expression level is an important determinant for stemness and outgrowth potential of TNBC cells.
Genetic polymorphism of CYP1A1 (T6235C) Gene as a Risk Factor for Polycystic Ovary Syndrome

Objective: The aim of this study was to test the association of CYP1A1 gene T6235C polymorphism with Polycystic Ovary Syndrome (PCOS). Methods: In a case control study, 100 women with PCOS (Rotterdam criteria) and 100 age matched healthy controls were enrolled and compared with respect to CYP1A1 T6235C polymorphism. The clinical, biochemical and Sonographic parameters of wild type (TT), heterozygous (TC), and homozygous mutant (CC) genotypes in PCOS women were compared with that in controls. Results: The risk ratio of bearing TC genotype was 1.3327 (p=0.32), and CC genotype was 2.6084 (p=0.14) in women with PCOS on the whole. However in PCOS women with the Sonographic presence of polycystic ovaries (PCO), the risk ratio became significant for TC genotype (OR=1.872; p=0.04) but not for CC genotype (OR=4.05; p=0.08). There was also a significant association of TC and CC genotypes with ovarian volume (p=0.000) as well as with waist circumference (p=0.03). However, the Total Testosterone, Fasting Glucose: Insulin ratio, LH: FSH ratio and HDL were insignificantly altered. Conclusion: Both homozygous and heterozygous mutation of CYP1A1 confers an increased susceptibility to develop PCO. The abnormal folliculogenesis and hormone imbalance may be a result of CYP1A1 gene polymorphism due to toxin mediated endocrine disruption which along with other contributory factors may lead to full fledged polycystic ovary syndrome.
Ramophialophora, a new anamorphic genus of Sordariales

Ramophialophora vesiculosa gen. et sp. nov., a dematiaceous hyphomycete isolated from a soil sample in Spain, is described and illustrated. It is characterised by erect and branched conidiophores with branches ending in sterile vesicles, monoor polyphialidic, terminal and lateral conidiogenous cells with flared collarettes, and spherical, brown conidia with a protuberant basal hilum. ITS rDNA sequence analysis reveals its relationship with the Sordariales. Taxonomic novelties: Ramophialophora Calduch, Stchigel, Gene & Guarro gen. nov., Ramophialophora vesiculosa Calduch, Stchigel, Gene & Guarro sp. nov.
Effect of heating and probiotic fermentation on the phytochemical content and antioxidant potential of edible Irish brown seaweeds

Abstract Probiotic fermentation was conducted on two species of edible Irish brown seaweeds, Saccharina latissima and Laminaria digitata as a sole source of nutrition for the bacteria. Seaweeds were heat treated followed by fermentation with the probiotic Lactobacillus rhamnosus. Kinetics of cell growth, acid production, and sugar consumption were examined. The effects of heating and fermentation on the changes in total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity were also monitored. Lactobacillus rhamnosus grew well on both the seaweed species and reached nearly 10 log cfu ml-1 after 16–24 h of fermentation; however, the specific growth rate was 1.5 times higher on S. latissima. Lactic acid was the major product of the fermentation, followed by acetic acid. Heat treatment resulted in a 50–64.4% reduction in TPC and TFC for both the seaweeds concomitant with a leaching of phytochemicals into the water used for heating. Subsequently, fermentation resulted in 28% and 37.6% increases in the TPC and 1.18- and 2.04-fold increases in TFC for S. latissima and Lam. digitata, respectively, with a simultaneous increase in the antioxidant activity as well. Changes in the TPC and TFC were represented by zero-, first-, or second-order kinetic models. Fourier transform infrared analysis of the seaweeds as well as the broth revealed the presence of polyphenolic signals at different ranges.
Allele dependent silencing of collagen type I using small interfering RNAs targeting 3[prime]UTR indels [ndash] a novel therapeutic approach in osteogenesis imperfecta

Introduction: Osteogenesis imperfecta (OI) is a heterogenous disease of connective tissue, usually caused by dominant mutations in the genes encoding collagen I, COL1A1 and COL1A2 respectively. Severe forms are lethal, often due to thoracic fractures and intracerebral hemorrhaging. Bisphosphonates are generally the drug of choice, but the effect is neither sufficient nor satisfactory. A promising field is gene silencing through RNA interference, as silencing of the mutated allele would convert a severe OI to a mild OI type I in the case of a COL1A1 mutation and to a phenotypically normal patient in the case of a COL1A2 mutation. However, more than 800 different mutations have been described and creating unique small interfering RNAs (siRNAs), each targeting one mutation would be labour intensive. In this study allele preferential siRNAs were used to target two common 3′ untranslated region insertion/deletions (3′UTR indels) in COL1A1 and COL1A2 in a mutation independent approach. Method: Allele frequencies of the 3′UTR indels were determined in a cohort of 96 healthy individuals and in 96 patients with OI. Four siRNAs targeting each allele of the indels in COL1A1 and COL1A2 were designed and tested in various concentrations in cultures of primary bone derived cells using magnet-assisted transfection (MATRA). RNA was prepared 72 h post transfection and cDNA was created and sequenced. The software PeakPicker was used for calculations of insertion/non-insertion allele ratios. siRNA results were normalized to cell populations treated with negative control siRNAs. Quantitative PCR was used to determine the collagen type I mRNA abundances in treated and negative control treated cell populations. Results: Approximately 50% of individuals genotyped were heterozygous for each of the indels and thus potential candidates for therapy. Allele dependent silencing was observed, with the most promising results for siRNAs complementary to the insertion harbouring alleles. The allele ratio was shifted from 1 to 0.21 and 0.19 for COL1A1 and COL1A2 respectively at the highest concentration used. A slightly lower concentration rendered the ratios 0.21 and 0.34 and an appropriate reduction in mRNA abundance was subsequently demonstrated. This shift represents an increase in normal fibrils from 25 to 69% in COL1A1 and 50 to 75% in COL1A2. In conclusion allele dependent silencing of collagen type I utilizing indels is a promising mutation independent approach for OI.
Acetic Acid as a Causative Agent in Producing Stuck Fermentations

Sample lots of 1993 Chardonnay grape juice and Merlot must with skins were fermented in duplicate lots under controlled temperature using techniques common to commercial winemaking. At mid-fermentation, four levels of acetic acid were introduced to simulate fermentative acetic acid spoilage independent of other bacterial metabolism. Effects on fermentation rate are reported. An hypothesis for the mode of action of acetic acid toxicity is proposed.
A New Scincid Genus From Angola

A new genus Lubuya is described to accommodate the species Mabuya ivensii which differs significantly from all other members of that genus. It is tentatively suggested that 2 of the principal adaptations - the position of the nostrils on top of the snout and the restricted keeling of the dorsal scales - are functions of a semiaquatic way of life. * * *
Phenotypic and Molecular Characterization of Verticillium dahliae , the Causal Agent of Verticillium Wilt of Olive in Tunisia

Aims: During the last two decades, verticillium wilt of olive has spread to young olive orchards were it causes severe yield losses and death of olive trees in southern and central regions of Tunisia. Therefore, identification of the causal agent as well as the study of its pathogenicity will be useful for design the appropriate management program. Place and Duration of Study: This work was performed in the Laboratory of Phytopathology at the Olive Tree Institute (Sfax, Tunisia) between July 2014 and June 2015. Original Research Article Gharbi et al.; JALSI, 4(3): 1-8, 2016; Article no.JALSI. 23696 2 Methodology: This study was conducted using phenotypic and molecular methods to identify the causal agent of the decline and death of olive trees. The pathogen was recovered from infested tissues using a potato dextrose agar medium. Identity of the isolates was confirmed by ITS-RFLP and sequencing. Pathogenicity of the isolates was evaluated by infection bioassay on young olive plants. Results: All the fungal isolates were hyaline, flocculose and produced microsclerotia after 15 days of incubation at 25°C, which is in agreement with the identification key of Verticillium species. All the isolates were characterized by ITS-RFLP and sequencing of the internal transcribed spacer. All the isolates produced 470 bp using primers ITS1/ITS4. Digestion of the ITS product using EcoRI and HaeIII produced two fragment of 250 and 220 bp and three fragment of 300, 150, and 20 bp respectively. Pathogenicity was evaluated on two-year old olive plants using an artificial infection bioassay. After 15 days of inoculation, similar symptoms were produced as natural infection. Symptoms of wilt developed rapidly and caused the death of more than 50% of the inoculated plants. Conclusion: V. dahliae is present in almost all growing olive regions of Tunisia. However, local V. dahliae populations in Tunisia is predominated by a highly pathogenic clone which is able to overcome the resistance of the main olive cultivar.
Dynamics of Water-soluble Pectin during Unrefined Tea Processing: Content and Molecular Weight Distribution

We examined the dynamics of water-soluble pectin (WSP), specifically the content and molecular weight distribution, in tea leaves and tea infusions in relation to steaming time during unrefined tea processing. It was revealed that the fraction of higher-molecular weight (MW) WSP in tea leaves was infused at the beginning of unrefined tea processing at all steaming times, and lower-MW WSP was not infused during any processing steps. Moreover, by increasing steaming time, the increase of higher-MW WSP content in tea leaves was reflected by the increase in WSP content of corresponding size in the tea infusions.
Vinca Alkaloids: Anti-vascular Effects in a Murine Tumour

We have investigated the blood flow modifying effects of the vinca alkaloids, vincristine and vinblastine in the murine carcinoma CaNT. Vinblastine at doses of 7.5 or 10 mgkg induced profound and chronic reductions in tumour blood flow as measured by =RbCl extraction. Following the maximum tolerated dose of 10 mgkg, blood flow was reduced to 10% of pretreatment values after 2 h and remained below 20% of pretreatment values 24 h after drug administration. These findings are consistent with the early induction of necrosis by vinblastine and suggest that vascular-mediated cell death may account for a large part of the 11 day growth delay induced by this drug dose. In contrast to the large reductions in tumour blood flow, in skin, kidney, liver and muscle, blood flow reductions did not, at any time examined, exceed 40%. In all the normal tissues studied, blood flow had fully recovered by 6 h after vinblastine administration. Similar results, albeit less pronounced, have been obtained with vincristine at the maximum tolerated dose of 3 mgkg. The results clearly show that both vinblastine and vincristine can induce, with some selectivity, a dramatic and prolonged reduction in tumour blood flow and that this may contribute to the anti-turnout effects against the CaNT turnout.
A COMPARISON OF EGG SIZE, CAPSULE SIZE, AND DEVELOPMENT PATTERNS IN THE ORDER ASCOGLOSSA (SACOGLOSSA) (MOLLUSCA: OPISTHOBRANCHIA)

Data on egg size, capsule size, development type, and the presence and nature of albumen are summarized for 32 species of Ascoglossa, including new data on 23 species from Florida and the Caribbean. Lower limits of egg sizes for Ascoglossa with lecithotrophic and capsular development were substantially lower than limits reported for other opisthobranchs, probably because of the use of albumen as nutrient reserves in species with extended development. Capsule size is a more accurate predictor of development type than egg size. The use of albumen as a nutrient resource is associated with a relatively high plasticity of development.
Naturally occurring core internal deletion mutations of hepatitis B virus gene in chronic genotype B-infected adult

This study aimed to investigate the prevalence of the core internal deletion (CID) mutations in the genome of hepatitis B virus (HBV) from chronically HBV-infected adults in Nanchang city and to elucidate the location of the CID in the HBV genome. PCR was applied to amplify the DNA region containing the enhancer II and the core promoter and the pre-C/C gene from the sera of 205 patients with chronic hepatitis B. Eight patients (3.90%, 8/205) had two products including a smaller band and a band of the expected 840 bp. Only two patients (0.98%, 2/205) had a smaller band. The presence of the CID mutation was determined in all smaller products amplified from 10 patients (4.88%, 10/205) based on the sequence analysis. Seven patients had a single in-frame deletion whose size is various, covering codon 78–136 in the core gene. Three patients had two or three separated deletions in the core gene. The separated deletions, respectively, covering codons 95–98/94–110 and codons 106–126/122–132 in the core gene were identified from two patients of the three. Another patient of the three had separated deletions of nt2180–2203 and nt2255–2332 in the core gene. The deletion of nt2255–2332 was frameshift, resulting in the loss of codons 119–144, which overlaps the first eight codons (P, L, S, Y, Q, H, F, R) in the 5-terminus of the P gene. Immuno-epitope mapping showed that all CID sequences encompassed T-cell and B-cell epitopes in the core protein, which suggests that the CID may facilitate immune escape and contribute to chronic infection.
Flow regime effects on mature Populus fremontii (Fremont cottonwood) productivity on two contrasting dryland river floodplains

Abstract I compared riparian cottonwood (Populus fremontii) productivity-discharge relationships in a relictual stand along the highly regulated Green River and in a naturally functioning stand along the unregulated Yampa River in semiarid northwest Colorado. I used multiple regression to model flow effects on annual basal area increment (BAI) from 1982 to 2011, after removing any autocorrelation present. Each BAI series was developed from 20 trees whose mean size (67 cm diameter at breast height [DBH]) was equivalent in the two stands. BAI was larger in the Yampa River stand except in 2 y when defoliating leaf beetles were present there. I found no evidence for a Yampa flood-magnitude threshold above which BAI declined. Flow variables explained ∼45% of residual BAI variability, with most explained by current-year maximum 90-d discharge (QM90) in the Yampa River stand and by a measure of the year-to-year change in QM90 in the Green River stand. The latter reflects a management-imposed ceiling on flood magnitude—Flaming Gorge Dam power plant capacity—infrequently exceeded during the study period. BAI in the relictual stand began to trend upward in 1992 when flows started to mimic a natural flow regime. Mature Fremont cottonwoods appear to be ecologically resilient. Their productivity along regulated rivers might be optimized using multiyear environmental flow designs.
An ATM/Wip1-dependent timer controls the minimal duration of a DNA-damage mediated cell cycle arrest

After DNA damage, the cell cycle is arrested to avoid propagation of mutations. In G2 phase, the arrest is initiated by ATM/ATR-dependent signalling that blocks mitosis-promoting kinases as Plk1. Interestingly, Plk1 can counteract ATR-dependent signalling and is required for eventual resumption of the cell cycle. However, what determines when Plk1 activity can resume remains unclear. Here we use FRET-based reporters to show that a global spread of ATM activity on chromatin and phosphorylation of targets including Kap1 control Plk1 re-activation. These phosphorylations are rapidly counteracted by the chromatin-bound phosphatase Wip1, allowing a cell cycle restart despite persistent ATM activity present at DNA lesions. Combining experimental data and mathematical modelling we propose that the minimal duration of a cell cycle arrest is controlled by a timer. Our model shows how cell cycle re-start can occur before completion of DNA repair and suggests a mechanism for checkpoint adaptation in human cells.