Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and Characterization of Galactosyltransferases and Fucosyltransferases Involved in Arabinogalactan-Protein Glycosylation

LIANG, YAN, Ph.D., August 2012, Molecular and Cellular Biology Identification and Characterization of Galactosyltransferases and Fucosyltransferases Involved in Arabinogalactan-Protein Glycosylation Director of Dissertation: (Allan M. Showalter) Arabinogalactan-proteins (AGPs) are highly glycosylated hydroxyproline-rich glycoproteins (HRGPs) that are frequently characterized by the presence of the repetitive dipeptide motifs [Ala-Hyp] or [Hyp-Ala]. Hydroxyproline (Hyp) residues in the dipeptide motifs are sites for the attachment of arabinogalactan (AG) sugar side chains. Fucose residues are found in some dicot AGPs, and AGP fucosylation is developmentally regulated. AGP galactosyltransferase (GalT) and fucosyltransferase (FUT) activities were investigated in three ways in this study. First, an in vitro AGP GalT assay was developed, which used permeabilized microsomal membranes from tobacco (Nicotiana tobacum) or Arabidopsis (Arabidopsis thaliana) suspension-cultured cells as the enzyme source and UDP-[C] Gal as the sugar donor. Two model AGP peptides, [Ala-Hyp]7 or [AO]7 and deglycosylated [Ala-Hyp]51 or d[AO]51, were used as substrate acceptors. Product analysis indicated that the [AO]7:GalT assay and the d[AO]51:GalT assay mainly detected GalT activities that added the first and the second Gal residues in the Hyp-AG side chain. Examination of the Hyp:GalT activity using various acceptor substrates, including two extensin sequences and a [AP]7 peptide, indicated this activity was specific for Hyp dipeptide motifs in AGPs. The [AO]7:GalT and d[AO]51:GalT activities were localized to the endomembrane system of Arabidopsis suspension cultured cells following sucrose 4 density gradient centrifugation. Second, five candidate AGP GALT genes (GALT1: At1g26810; GALT3: At3g06440; GALT4: At1g27120; GALT5: At1g74800; GALT6: At5g62620) were expressed in Pichia pastoris and tobacco suspension-cultured cells and tested for AGP GalT activity using the [AO]7:GalT and d[AO]51:GalT assay systems. Preliminary results indicate that heterologously expressed GalT3, GalT5 and GalT6 have AGP GalT activities. Furthermore, GalT3 was shown to be Golgi localized in a tobacco leaf expression system. Third, functions of the FUT4 and FUT6 genes were investigated using Arabidopsis fut4, fut6 and fut4/fut6 mutant plants. Biochemical analysis indicated that FUT4 was required for fucosylation of leaf AGPs, while both FUT4 and FUT6 contributed to fucosylation of root AGPs. In addition, glycome profiling indicated that fucosylated AGPs may regulate intermolecular interactions between AGPs and other wall components. Finally, a model of HRGP biosynthesis is proposed which highlights the glycosyltransferases involved in this process. Approved: _____________________________________________________________
Kemp's Ridley Sea Turtle Saga and Setback: Novel Analyses of Cumulative Hatchlings Released and Time-Lagged Annual Nests in Tamaulipas, Mexico

Abstract Kemp's ridley (Lepidochelys kempii) is the most endangered of the sea turtles. Its female population in the Gulf of Mexico suffered a major setback sometime between the ends of nesting seasons in 2009 and 2010. Prior to that, annual nests (i.e., clutches laid by multiple year-classes of nesters) at the female population's index beach in Tamaulipas, Mexico were increasing exponentially, the result of more than 4 decades of cumulative conservation efforts on land and at sea. Annual nests dropped 35.4% in 2010 and remained well below predicted levels through 2014, and annual hatchlings released (both sexes combined) also were lower in 2010–2014 compared with those in 2009. We conducted novel analyses of an available 1966–2014 time series of annual nests and annual hatchlings released on the index beach. We examined 1) the relationship between time-lagged annual nests during years 1986–2014 and cumulative hatchlings released by years 1976–2004, respectively, assuming female minimum age at maturity of 10 yrs, and 2) the time-series of time-lagged annual nests during 1986–2014 divided by cumulative hatchlings released by 1976–2004, respectively, under the same assumption. Both metrics showed extraordinary downward departures in 2010–2014, instead of expected increases. Although causes of the population's setback have not been determined with certainty, we suggest that the most expedient way to restore this population's growth would be to translocate more clutches to protective corrals, leaving fewer in situ where their survival is reduced. It could take at least 10 yrs before results of such a change in conservation practice become evident.
The dynamics of hummingbird dominance and foraging strategies during the winter season in a highland community in Western Mexico

Coexistence between ecologically similar species can promote competition for resources. Hummingbirds (Aves: Trochilidae) are nectarivorous birds that usually coexist in sympatry, and visit flowers using different foraging behaviors and levels of aggressiveness as a strategy to diminish resource competition. Here, we describe the dynamics in territorial and dominance behaviors in a hummingbird community inhabiting a highland during winter in Western Mexico. We explored in natural conditions how foraging strategies and dominance status of the hummingbirds was influenced by community species composition, sex, age and size of the individuals, floral abundance, and nectar resource availability. The community studied was composed of 11 species (four residents, three altitudinal migrants, three latitudinal migrants), and all possible combinations of dominance and territoriality were found. Differences in the dominance status and foraging behavior were related to the species, sex, age and body size of the individuals, as well as the number of flowers in the patches, and the abundance of the migratory species over time. The aggressive and territorial species preferred the places with more flowers, and started the majority of the interactions attacking even birds that did not visited the flowers. The subordinate non-territorial hummingbirds visited floral patches of different sizes, did not start aggressive interactions and when they were involved in one, this occurred during their visits to the territorial hummingbird's flowers. Hummingbird dominance changed during the winter and at the end of the season, when the latitudinal migrant species left our study site, the resident species were more abundant, dominant and territorial. Dominance status and foraging behavior, together with floral preferences and the spatial distribution of nectar resources, acted as mechanisms organizing this hummingbird community.
Effects of electroacupuncture on postoperative acute lung injury in patients with acute abdomen complicated with abdominal infection

Objective To evaluate the effects of electroacupuncture(EA) on postoperative acute lung injury(ALI) in patients with acute abdomen complicated with abdominal infection. Methods Ninety patients of both sexes with acute abdomen complicated with abdominal infection, with body mass index of 18-30 kg/m2, aged 35-64 yr, of American Society of Anesthesiologists physical status Ⅰor Ⅱ, scheduled for elective abdominal surgery with general anesthesia, were divided into 3 groups(n=30 each) using a random number table method: control group(group C), EA at acupoint group(group E) and EA at non-acupoint group(group N). Anesthesia was induced with midazolam, propofol, cis-atracurium and sufentanil.The patients were mechanically ventilated after tracheal intubation.Anesthesia was maintained with inhalation of sevoflurane, IV infusion of propofol and cis-atracurium and intermittent IV boluses of sufentanil.At 15 min of anesthesia induction, 2 h after skin incision and 2, 12 and 24 h after tracheal intubation, Hegu, Zusanli and Neiguan acupoints were stimulated for 15 min every time in group E, and the points 1 cm lateral to the acupoints of Hegu, Zusanli and Neiguan were stimulated for 15 min every time in group N, with disperse-dense waves, frequency 2/15 Hz, wave length 0.2-0.6 ms, at a voltage of 1-2 mA.Arterial blood samples were collected at 15 min before induction(T1) and 24 and 48 h after operation(T2 and T3) for blood gas analysis, oxygenation index was calculated, and the development of ALI(oxygenation index<300 mmHg) was recorded at T2 and T3.The concentrations of club cell protein 16(CC16), surfactant protein D(SP-D), soluble receptor for advanced glycation end products(sRAGE), interleukin-1(IL-1), IL-10, and tumor necrosis factor-alpha(TNF-α) in serum were detected by enzyme-linked immunosorbent assay. Results Compared with the baseline at T1, the serum concentrations of CC16, SP-D, sRAGE, IL-1 and TNF-α were significantly increased, and the serum IL-10 concentrations were decreased at T2 in C, E and N groups(P 0.05). Conclusion Although EA does not decrease the occurrence of ALI, it mitigates the degree of ALI to some extent in the patients with acute abdomen complicated with abdominal infection. Key words: Elactroacupuncture; Abdomen, acute; Intraabdominal infections; Respiratory distress syndrome, adult
The Undivided City

Two billion people are set to flood into the already crowded cities of the developing world over the next twenty-five years, mainly to live in the squalid surroundings of a slum or a shanty town and to endure the consequent effects of social injustice and division. James Wolfensohn, President of the World Bank, addresses the problem of urban poverty and describes initiatives for change that build upon a new recognition throughout the developing world that the urban poor have rights, and an essential part to play in building the cities of tomorrow.
Prolonged response to pemetrexed-based chemotherapy in a patient with peritoneal mesothelioma: a case report and review of the literature

Abstract Peritoneal mesothelioma is a rare tumor typically presenting with ascites and associated with occupational asbestos exposure with a latency period of 20–40 years. Intensive multi-modality approach combining cytoreductive surgery, intraperitoneal chemotherapy and possibly radiotherapy can be considered, but otherwise the prognosis is rather poor. Palliative chemotherapy may be an option in these rare cases. However, no approved systemic treatment exists for peritoneal mesothelioma. We present here a patient with peritoneal mesothelioma who was treated with the combination of pemetrexed with cisplatin shortly after the failure of hyperthermic intraperitoneal chemotherapy. The patient experienced durable partial response to the treatment, resolution of ascites, and returned to his normal daily life activities. With the exception of palliative chemotherapy in case of patients in good condition, therapeutic options in patients with peritoneal mesothelioma are currently very limited. The combination of pemetrexed and cisplatin can lead to long-term control in selected patients.
Faculty Opinions recommendation of Arabidopsis inositol polyphosphate 6-/3-kinase is a nuclear protein that complements a yeast mutant lacking a functional ArgR-Mcm1 transcription complex.

Inositol 1,4,5-trisphosphate 3-kinase, and more generally inositol polyphosphate kinases (Ipk), play important roles in signal transduction in animal cells; however, their functions in plant cells remain to be elucidated. Here, we report the molecular cloning of a cDNA ( AtIpk2 (cid:2) ) from a higher plant, Arabidopsis. Arabidopsis AtIpk2 (cid:2) is a 33-kD protein that exhibits weak homology ( (cid:2) 25% identical amino acids) with Ipk proteins from animals and yeast and lacks a calmodulin binding site, as revealed by sequence analysis and calmodulin binding assays. However, recombinant AtIpk2 (cid:2) phosphorylates inositol 1,4,5-trisphosphate to inositol 1,4,5,6-tetrakisphosphate and also converts it to inositol 1,3,4,5,6-pentakisphosphate [Ins(1,3,4,5,6)P 5 ]. AtIpk2 (cid:2) also phosphorylates inositol 1,3,4,5-tetrakisphosphate to Ins(1,3,4,5,6)P 5 . Thus, the enzyme is a D3/D6 dual-specificity inositol phosphate kinase. AtIpk2 (cid:2) complements a yeast ARG82/IPK2 mutant lacking a functional ArgR-Mcm1 transcription complex. This complex is involved in regulating Arg metabolism– related gene expression and requires inositol polyphosphate kinase activity to function. AtIpk2 (cid:2) was found to be located predominantly in the nucleus of plant cells, as demonstrated by immunolocalization and fusion to green fluorescent protein. RNA gel blot analysis and promoter– (cid:2) -glucuronidase reporter gene studies demonstrated AtIpk2 (cid:2) gene expression in various organs tested. These data suggest a role for AtIpk2 (cid:2) as a transcriptional control mediator in plants.
Evaluation of Spermatozoal Rna Extraction Methods

The study was aimed to compare different RNA isolation methods from sperm and testicular tissue. A suitable sperm purification technique is required as sperm RNA yield is strongly correlated with the number of sperms. Goat (Capra hircus) semen was purified by swim-up method. Motile sperm were selected for the process of RNA isolation. Four different RNA isolation methods namely cold Trizol, Gunidinium thiocyanate method and SDS lysis method and silica column based spin column method were used to isolate total RNA from sperm and testicular tissue. The hot Trizol method yielded good amount of RNA with less contamination of DNA and proteins. The modification of heating the sample in Trizol and an additional chloroform phase separation step increased the yield of total RNA. The modified method yielded highest amount of RNA for both tissue and sperm samples which was 139.5 ng/μL and 38.6 ng/μL respectively. The RNA integrity was high as was defined by a sharp 28S and 18S rRNA band in the agarose gel. The A260/A280 ratio was 2.1 and 1.923 for tissue and sperm samples which signifies purity of RNA. The mRNA was also reverse transcribed and GAPDH amplified. A modified Trizol method was developed which resulted in increased yield (38.60 ng/μL) and purity (A260/A280: 1.923).
Evaluation of Bioactive Plant Products for Ecofriendly and Effective Management of Cercospora Leaf Spot of Rauwolfia serpentina (L.) Benth Ex Kurz (Sarpagandha)

A B S T R A C T Rauwolfia serpentina (Indian snakeroot) is rich source of alkaloids, utilized for their medicinal properties. Diseases caused by foliar pathogens are major constraint in the economic production of the alkaloids from the dry roots of the plant. Among these diseases leaf spot caused by Cercospora rauwolfiae is of major importance, for its destructive nature resulting in huge economic losses. Management of the disease is achieved by use of chemical fungicides resulting in environment degradation and residual effect on the crop. Therefore in this study an attempt was made to evaluate the efficacy of commonly available essential oils and plant extracts for management of this destructive disease. Results of this study suggest that among the essential oils, mentha and peppermint oils at concentrations of 8 µL LG 1 result in complete (100%) growth inhibition of the C. rauwolfiae while palmarosa oil was least effective in inhibiting in vitro growth (41.17%) of the fungus. In case of plant extracts garlic bulb extract was found to be most effective resulting in complete (100%) growth inhibition of the pathogen followed by neem, eucalyptus and turmeric respectively while leaf extract of the Ocimum gave minimum (17.25%) growth inhibition of the test fungus. Results of this study indicate that ecofriendly and effective management of Cercospora leaf spot of Rauwolfia serpentina can be achieved by using the metabolites (crude extract and essential oil) of plant origin.
Variability in nest density, occupancy, and home range size of western bluebirds after forest treatments

Complex land use and fuels management histories have resulted in significant changes in composition, structure, and function of southwestern forests and subsequent changes in the extent and quality of wildlife habitats. We evaluated how several currently used fuel reduction treatments (e.g., mechanical thinning and prescribed fire alone and in combination) affect nest attributes, nest density, nest tree occupancy, and home range size of Western Bluebirds (Sialia mexicana) in ponderosa pine (Pinus ponderosa)-dominated forests of northern Arizona. Nest attributes, such as number of eggs or nestlings, varied among treatments, but did not differ statistically. Western Bluebird nest density was significantly influenced by treatment, with densities higher in treated areas, even though snag density was lower in treated areas than in control areas. The average (± SE) area of the 50% contour, across all treatment units, was 0.42 ± 0.07 ha, and the average area of the 90% contour was 2.36 ± 0.30 ha. Home range sizes for both probability contours evaluated were 1.5 times larger in the thin-only treatments than in the control units. Conversely, home range area in thin-and-burn treatments was approximately 30% smaller than in control units. The largest home ranges occurred in the burn-only treatments. Our results suggest that forest treatments, such as thinning and prescribed fire are, in general, beneficial to Western Bluebirds, but that low snag retention may be problematic in areas receiving prescribed fire as part of their treatment action.
Comparative Molecular Similarity Index Analysis on 2-(indol-5-yl)thiazolederivatives as Xanthine Oxidase(XO)inhibitors

Xanthine Oxidase is an enzyme, which oxidizes hypoxanthine to xanthine, and xanthine to uric acid. It is widely distributed throughout various organsincluding the liver, gut, lung, kidney, heart, brain and plasma. It is involved in gout pathogenesis. In this study, we have performed Comparative Molecular Field Analysis (CoMSIA) on a series of 2-(indol-5-yl) thiazole derivatives as xanthine oxidase (XO) inhibitors to identify the structural variations with their inhibitory activities. Ligand based CoMSIA models were generated based on atom-by-atom matching alignment. In atom-by-atom matching, the bioactive conformation of highly active molecule 11 was generated using systematic search. Compounds were aligned using the bioactive conformation and it is used for model generation. Different CoMSIA models were generated using different alignments and the best model yielded across-validated q 2 of 0.698 with five components and non-cross-validated correlation coefficient (r 2 ) of 0.992 with Fisher value as 236.431, and an estimated standard error of 0.068. The predictive ability of the best CoMSIA models was found to be r 2pred 0.653. The study revealed the important structural features required for the biological activity of the inhibitors and could provide useful for the designing of novel and potent drugs for the inhibition of Xanthine oxidase. (more bulk favored) and yellow (less bulk favored). The electrostatic field contours are displayed in red (elec-tronegative substitutions favored) and blue (electropos-itive substitutions favored) colors. The hydrophobic field contours are displayed in yellow (hydrophobic substitutions are favourable) and white (hydrophobic substitutions are unfavourable) colors. The H-bond donor field contours are displayed in cyan (hydrogen bond donor substitutions enhance activity) and purple (hydrogen bond donor substitutions reduce activity) colors. The H-bond acceptor field contours are displayed in magenta (hydrogen bond acceptor group enhance activity) and red (hydrogen bond acceptor group reduce activity) colors.
Interspecific relationships of Alocasia revealed by AFLP analysis

Summary This study analysed genetic relationships of 23 Alocasia cultivars across 17 species using amplified fragment length polymorphism (AFLP) markers. Six primer sets, selected from an initial screening of 48, generated a total of 578 scorable AFLP fragments of which 334 (58.4%) were polymorphic. All cultivars were clearly detected by their AFLP fingerprints. A dendrogram was constructed using the unweighted pair-group method of arithmetic averages (UPGMA). Principal coordinated analysis (PCOA) was carried out to show multiple dimensional distributions of cultivars. Both UPGMA and PCOA analyses separated the 23 cultivars into three clusters. Cluster I comprises 16 cultivars, mainly derived from A. crassifolia, A. cuprea, A. longiloba, A. grandis, A. guttata, A. plumbea, A. macrorrhiza, A. micholitziana, and A. villeneuvei or hybrids of A. lowii A. sanderiana and A. cuprea A. veitchii. Jaccard’s similarity coefficients for these species ranged from 0.43 to 0.77. Cluster II contains six cultivars, which include A. cadieri, A. cucullata, A. gageana, A. odora, and A. portei. Jaccard’s similarity coefficients varied from 0.52 to 0.83. There is only one cultivar, ‘Hilo Beauty’ in the cluster III, whose low similarity (0.21) with the rest of the Alocasia species may suggest that it could actually belong to another genus of Araceae. Based on documented interspecific hybrids, it appears that hybrids were developed from species exclusively within the identified clusters. This may suggest that Alocasia species sharing high Jaccard’s similarity coefficients are more likely to be intercrossable. The interspecific relationships detected by the AFLP analysis could provide the genetic basis for selecting parents for future hybrid development.
Isolation frequency and epidemiological characterization of yeast-like fungi and co-infected bacteria isolated from clinical patient

Pathogenic yeast-like fungi and bacteria are found all over the world, and are a frequent cause of invasive disease in immunocompromised hosts. However, there is a paucity of data on pathogenic yeast-like fungi in Korea. In this study, the characterization of pathogenic yeast-like fungi and co-infected bacteria isolated from 715 patients (ranging in age from 29 days to 99 years, with a mean age of 49 years) that were collected from general hospitals (from April 2011 to March 2013) in Busan were investigated. A total of 744 pathogenic yeast-like fungi and 170 six bacterial strains were isolated from clinical samples. The majority of isolates from sputum and urine samples were obtained from patients. The isolation frequency by sex was similar in females (48.6%) and males (51.4%). It was higher in individuals over 60 years of age (67.5%) than in younger individuals. The Candida species most frequently isolated from clinical samples was Candida albicans (64.0%), followed by Candida tropicalis (18.1%), Candida glabrata (8.6%), Candida parapsilosis (5.0%), Candida krusei (0.7%), and other Candida species (1.9%). The non-Candida species isolated most frequently from clinical samples was the Trichosporon species (1.2%). Although C. albicans was the most common species in almost clinical samples, C. tropicalis (47.6%) was most common species in urine samples. Staphylococcus aureus (15.3%) and Klebsiella pneumoniae (10.2%) were commonly isolated from patients infected with C. albicans. Although the epidemiology of pathogenic yeast-like fungal infection has been reported, these results are the first on the distribution of yeast-like fungi and co-infected bacteria from patients in Korea. Key words: Pathogenic yeast-like fungus, co-infected bacteria, infectious disease, epidemiology, Korea.