Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipid raft abnormalities and subsequent protein trafficking effects in Niemann‐Pick type C1 (LB158)

Many proteins and lipid components are organized within membrane microdomains, known as lipid rafts (LR). LR are cholesterol‐ and sphingolipid‐rich membranes resistant to non‐ionic detergents. In Niemann‐Pick type C1 (NPC1), a neurovisceral lysosomal storage disease, entrapment of cholesterol and sphingolipids occurs and may lead to alterations in LR composition. We investigate the LR status in fibroblasts derived from a patient with NPC1 and analyze the trafficking profiles of a typical LR‐associated membrane protein, dipeptidylpeptidase IV (DPPIV).
Pharmacological actions of Radix Rehmanniae and its active components: research advances.

Water extraction of Radix Rehmanniae can protect gastric mucosa,restrain pulmonary fibrosis,and also has activities of improving hematopoiesis,anti-inflammation,antitumor,lowering blood sugar,and promoting the proliferation of vascular endothelial cells.Oligosaccharides,the main chemical components of Radix Rehmanniae,can enhance the proliferation of skeletal myoblasts,protect and induce differentiation of adipose tissue-derived mesenchymal stromal cells and bone marrow mesenchymal stem cells.Both oligosaccharides and catalpol possess the effect of reducing blood sugar and boosting up learning and memory.Polysaccharides extracting from Radix Rehmanniae are able to accelerate hematopoiesis function,protect adipose tissue-derived mesenchymal stromal cells,induce differentiation of bone marrow mesenchymal stem cells into nerve cells,and restrain the central nervous system.This article summarizes research advances in pharmacological actions of water extraction,oligosaccharides,polysaccharides and catalpol.
Epithelial-Mesenchymal Transition and Cancer Stem Cells

The epithelial to mesenchymal transition (EMT) is a highly coordinated process and a multistep event during which epithelial cells lose numerous epithelial characteristics and assume properties that are typical of mesenchymal cells, which requires complex changes in cell architecture and behavior. The conversion of epithelial cells to mesenchymal cells is critical for the formation of the body plan and in the differentiation of multiple tissues and organs during embryonic development and involves profound phenotypic changes such as the loss of cell-cell adhesion, the loss of cell polarity, and the acquisition of migratory and invasive properties (Thiery et al. 2009). EMT is also involved in the physiological response to injury and in the pathological processes such as organ fibrosis. Accumulating evidence suggests that aberrant activation of the EMT developmental program contributes to tumor initiation invasion, metastatic dissemination and acquisition of therapeutic resistance (Yang, et al., 2004; Yang and Weinberg, 2008; Thiery et al., 2009; Singh and Settleman, 2010; Acloque et al., 2009; Kalluri and Weinberg, 2009). EMT induction can participate in cancer initiation to promote the clonal expansion of premalignant epithelial cells (Tellez et al., 2011). Cancer cells undergoing EMT acquire the capacity to migrate, invade the stroma and metastasise. During the process of metastasis, the EMT program enables these cancer cells to disseminate from a primary tumor and also promotes their self-renewal capability to ensure generation of the critical tumor mass required for progression from microto macro-metastases (Ruan et al., 2009a; Ruan et al., 2009c; Ouyang et al., 2010). EMT-inducing signalling pathways, such as TGF-┚, Wnt, Notch and Hedgehog (Hh), along with other tumor microenvironmental cues, induce well-differentiated epithelial cells to convert into motile mesenchymal cells via the activation of multiple EMT transcription factors, including Twist1, Twist2, Snai1, Slug, ZEB1 and ZEB2. Similarities between developmental and oncogenic EMT have led to the identification of common contributing pathways, suggesting that the reactivation of developmental pathways in cancers contributes to tumor progression. For example, developmental EMT regulators including Twist1, Twist2, Snail, Slug and Six1, and Cripto, along with developmental signaling pathways including TGF-┚ and Wnt/┚-catenin, are misexpressed in breast cancer and correlate with poor clinical outcomes.
Targeting SUMO conjugates for degradation: The human RING finger RNF4 as a specialized ubiquitin ligase

Ubiquitin and the small ubiquitin related modifier (SUMO) belong to a group of small proteins that can be covalently attached to lysine side chains of other proteins, thereby changing their function, localization, interaction partners or stability. The conjugation reactions are mediated by an enzymatic cascade of specific activating, conjugating and ligating enzymes. A ubiquitin chain of at least four K48-linked ubiquitin molecules target substrate proteins for degradation by the proteasome. Several interconnections exist between the ubiquitin and SUMO system, with the latest discoveries made in yeast by identifying E3 ubiquitin ligases that target SUMO conjugates for ubiquitylation and subsequent degradation by the proteasome. These ubiquitin ligases for SUMO conjugates (ULS) recognize especially high molecular weight SUMO conjugates, probably modified with SUMO chains. In mammals, out of the three conjugatable SUMO paralogs, only SUMO-2/3 are able to form chains. Upon stress induction, the free pool of SUMO-2/3 is rapidly conjugated to cellular target proteins. These conjugates are under proteasomal control, implicating that the ULS pathway is conserved in humans. This work identified the RING finger protein RNF4 as a human ULS protein, confirming previous observations in which RNF4 complemented yeast ULS deletion phenotypes. RNF4 comprises a RING domain which is present in many E3 ligases and a stretch of up to four SUMO interaction motifs (SIMs) that confer binding to SUMO. In order to demonstrate ULS activity for RNF4, an in vitro ubiquitylation assay for SUMO conjugates has been developed. For that purpose, SUMOylated proteins were generated and purified as in vitro substrates from E. coli. RNF4 efficiently in vitro ubiquitylated SUMO modified PML while unmodified PML was not recognized as a substrate. This result is in line with recent studies in cells demonstrating that RNF4 targets PML in a SUMO-dependent manner after arsenic trioxide treatment, a drug which is applied in acute promyelocytic leukemia (APL). By investigating the SUMO binding properties of the RNF4 SIM domain, it became apparent that the interaction was especially enhanced by the presence of SUMO chains of more than two SUMOs. In addition, a SIM type specific recognition was noticed for different SUMO paralogs, which emphasizes the idea that there is also a SUMO paralogs specific regulation. Finally, in an attempt to find other ULS regulated cellular proteins, an RNF4 SIM domain construct was used to isolate poly- or multi-SUMOylated proteins from cells subjected to diverse cell stresses.
Producción estacional de materia seca de gramíneas y leguminosas forrajeras con cortes en el estado de quintana roo

The objective of this study was to evaluate grass and legume species in the Dry, Rainy and Windy seasons in Quintana Roo, Mexico for two years. Treatments consisted of harvests every 3, 6, 9 and 12 wk of regrowth. Species reached their highest dry matter (DM) yield and development in the rainy season. The highest forage yield was obtained at 12 wk regrowth (4.1 and 1.8 t DM ha-1 for grasses and legumes, respectively) and was different (P<0.05) from other regrowth ages. Plant height and sward cover increased with time. Interactions season by species, regrowth age by species and season by regrowth age were significant (P<0.05) for annual DM yields, height and sward cover variables. The highest (P<0.05) DM yield was observed in Brachiaria sp. (18 t DM ha-1.) followed by Paspalum atratum (17 t), while Panicum maximum cv. likoni showed the lowest DM yields, 13 t. Cratylia argentea and Crotalaria juncea were the more productive legumes, 9.2 and 9.4 t DM ha-1, respectively. It can be concluded that season and regrowth age affects dry matter yield in all evaluated species.
Evaluation of HIV-1 evolution and its role in development of antiretroviral drug resistance in Nairobi Cohort

The treatment of HIV-1 infection with antiretroviral drugs has greatly improved the survival of those who are infected. However, HIV-1 diversity and drug resistance are major challenges in patient management, disease control and surveillance especially in resource-poor countries.In this study, 188 blood samples were collected from Nairobi cohort and peripheral mononuclear cells (PBMCs) separated. Total proviral DNA was used in nested polymerase chain reaction to amplify 450bp HIV env C2V3, 288bp Integrase and env gp41 regions and directly sequenced . Generated sequences were aligned and phylogenetically analysed using known reference subtypes sequences and drug resistance mutations and substitutions determined.Phylogenetic analysis based on env C2V3 region revealed A1 (59.6%), C (18.1%), D (10.6%), B (2.1%), G (2.1%), CRF02_AG (3.2%) and the rest of 6.9% were CRFs. In HIV-1 co-receptor switch showed R5 tropism (69.6%) while X4 (30.4%). In addition, 2.4% T97A that is associated with reduced susceptibility to Raltegravir and 26.2% had secondary mutations associated with resistance to intergrase inhibitors. In fusion inhibitors, the following mutations were detected; A316T/I323V (2.6%) combination, A316T (63%), I323V (1.1%) for Maraviroc, (10%) K305R, (3.2%) G321E, (35.1%) R315Q, (4.5%) K305R/R315Q, (62.8%) T320R for Vicriviroc and (1.6%) A316T+ K305R+ R315Q, (12.7%) A316T+R315Q, (3.2%) R3I5Q+A316T+I323V, (0.5%) R315+A316T+G321E for Maraviroc and Vicriviroc combinations. In addition, 4.2% intermediate resistance associated to Enfuvirtide was detected. The point mutations at;N42S was detected in 16.7% of all the samples, while N42D was detected in 4.2%, S138L /T 3.1%, L44M 2.1% and 1% each for in the following mutations; N43I and L45V drug resistance mutations. In evolutionary rate; 12.5% had dNdS ration 1>, 88.5% dNdS ration < 1 and in those with dNdS ration ≠1.The results indicate that HIV-1 subtypes in Nairobi cohort like the rest of the country, is predominated by HIV-1 subtype A1, though there could be possibity of an increase proportion of HIV-1 subtype C prevalences. Existence of diverse HIV-1 recombinants indicated viral mixing among the population, possibly as a result of dual infections. Evolutionary rate of the virus showed natural selection with high proportions of R5 strains suggestive of feasibility of use of maraviroc (CCR5 antagonists) in Kenya. However, multiple drug resistance mutations observed in the newly classes of drug-prior to their introduction, there is a need for constant monitoring of HIV-1 genetic diversity and drug resistance. Drug resistance seen to common drugs was minimal (2 %), indicating that we need to continue to prescribe the current used drugs. In addition, the new classes of entry, fusion and integrase inhibitors are feasible as firstline and thirdline drugs respectively. In addition, it was realised that it is not necessary to carry out resistance testing at baseline unless there is strong evidence of virological failure.
Aportaciones al cálculo del índice de valor biológico (Sanders, 1960)

The usefulness of combining the spatio-temporal constancy and abundances of the species as tools to describe the species structure in marine communities is discussed, with special emphasis on benthos. A detailed guide of the algorithm for the calculation of the Biological Value Index or BVI (Sanders, 1960) is also presented. The BVI indicates the overall dominance per species, based on ranks and points. The procedure of working with ties in the ranking of abundances and the influente of the sampling dominance pattem on the determination of the maximum score is explained. For the fiist time a formula of the BVI is presented and the use of 95% of the individuals per sample is recommended to elirninate data which lack relevant information. 97 http://dx.doi. org/10.7773/cm.v16i2. 688
Respon anatomi struktur sekretori getah kuning, morfologi, dan fisiologi buah manggis (garcinia mangostana l.) Terhadap aplikasi kalsium secara eksternal

YAHMI IRA SETYANINGRUM. Structure Anatomy of Yellow Latex Secretory Duct, Morphology and Physiology on Mangosteen Fruit (Garcinia mangostana L.) Response on External Calcium Application. Under supervision of HAMIM and DORLY. Yellow latex (gamboges) in mangosteen (Garcinia mangostana L.) resulted from the damage of epithelium wall secretory duct in the pericarp is presumably caused by deficiency of calcium. The application of Ca to the soil in previous experiment didn’t increase calcium content on the fruit’s pericarp sufficiently. Therefore, the alternative method may need to be tried to improve Ca content. The objective of this research was to study the effect of calcium spraying to the growing mangosteen fruit on the anatomical structure of yellow latex secretory duct, morphological and physiological response. The Randomized Block Design with three replications was applied on fruit surface of ±30 years old mangosteen trees in Leuwiliang sub district. The treatments were CaCl2 0.25 M, CaCl2 0.5 M, CaCl2 1 M, Ca(OH)2 0.25 M, Ca(OH)2 0.5 M, and Ca(OH)2 1 M that was performed at the 2 nd , 4 th , 6 th , 8 th weeks after anthesis (WAA). The parameters analyzed were the thickness, length and wide of epithelium secretory duct cell wall, yellow latex score, physical and chemical characteristics, calcium content and. The result showed that Ca application was generally able to decrease yellow latex score on the skin as well as in the aril, but there was different respond between CaCl2 and Ca(OH)2 treatment. The reduction of yellow latex score on skin was highest on Ca(OH)2 1M treatment (26%) while on the aril it was CaCl2 0.5 M treatment (28%). The physiology respond showed that the increase Ca pectat was in accordance to the reduction of yellow latex score on the skin fruit. The application of Ca didn’t influence physical and chemical characteristics of the fruit neither total Ca content of the pericarp significantly.
AFLP analysis on genetic diversity and population structure of small yellow croaker Larimichthys polyactis

The population genetic structure and diversity of small yellow croaker Larimichthys polyactis in the Bohai Bay, Yellow Sea and East China Sea were analyzed using amplified fragment length polymorphism (AFLP). Ninety-one individuals were collected from six locations representing three stocks of small yellow croaker. A total of 218 putative loci were detected by 3 primer combinations, 148 of which were polymorphic (67.89%). The proportion of polymorphic loci and Nei’s genetic diversity for six populations ranged from 55.34 - 60.09%, and from 0.1244 - 0.1378. AMOVA analysis and pairwise FST revealed significant genetic differentiation among the three groups based on the breeding migration routes and over-wintering grounds, supporting separate stocks in this species. The result shows the migratory behavior might be an important factor which influences the genetic structure of this species. The UPGMA tree also revealed the significant geographic structure in this species. Pattern of isolation by distance was observed in this species, indicating that significant genetic differentiation among localities of small yellow croaker might be due to the geographic distance.
EQUAÇÕES PARA ESTIMAR O PESO DE CARBONO FIXADO EM ÁRVORES DE Mimosa scabrella Bentham (BRACATINGA) EM POVOAMENTOS NATIVOS

This research aimed to generate equations for estimating fixed carbon weight of Mimosa scabrella Bentham of native stands from the Curitiba metropolitan region. The data for the development of this research came from 194 Mimosa scabrella trees distributed in stands with ages ranging from five to eighteen years located in several counties of the Curitiba metropolitan region. Every sample tree was felled down and divided in the following components: stem, thick branches (diameter 4 cm), thin branches (diameter < 4 cm), foliage, and dead branches. The green weight of each tree component was weighted in the field. Small sub samples of each tree green component were also weighted in the field and brought to the laboratory for oven drying until reaching unchanged weight. Thus, it was obtained the dry weight of the whole component of the 194 trees by extrapolation of the sample weights. Small samples of each component from 55 trees were triturated for carbon content determination. DBH, total height and stem height were the main independent variables used for modeling carbon weights equations for the components firewood, stem and total. The adjusted equations for estimating carbon weight of the leaves and of the branches presented high standard errors and low determination coefficients.
ZNAČENJE LABORATORIJSKIH PODATAKA U NADZORU NAD TUBERKULOZOM U MEĐIMURSKOJ ŽUPANIJI

Mikrobiološka dijagnostika tuberkuloze temeljna je točka svakog nacionalnog programa za kontrolu tuberkuloze. U Međimurskoj županiji je godišnja incidencija na razini prosjeka Hrvatske, osim u 2009. godini kada je u Međimurskoj županiji iznosila 23/100.000 naspram 19/100.000 u Hrvatskoj. Cilj ovoga rada bio je analizirati laboratorijske rezultate (po dobi, spolu, osjetljivosti, genotipu) u kontroli tuberkuloze u Međimurskoj županiji. Na Odjelu za dijagnostiku tuberkuloze Hrvatskog zavoda za javno zdravstvo – na nacionalnoj razini provodi se prospektivna studija genotipizacije izolata Mycobacterium tuberculosis. Kao molekularna metoda za genotipizaciju članova M. tuberculosis kompleksa koristi se metoda MIRU-VNTR (engl. Mycobacterial Interspersed Repetitive Units, MIRU; Variable Number of Tandem Repeats, VNTR). U razdoblju od 2007. do 2009. godine tipizirano je ukupno 59 sojeva bolesnika iz Međimurske županije, od kojih je 27 (45,8%) jedinstvenog genotipa, a 32 (54,2%) je raspodijeljeno u ukupno 22 klastera (2 ili više sojeva identičnog genotipa) s brojem pripadajućih sojeva od 2 do 22. Od ukupno 22, dva klastera čine sojevi izolirani isključivo u Međimurskoj županiji. Osim što su ti sojevi karakteristični za Županiju, bolesnici u kojih su izolirani najvjerojatnije pripadaju istim putevima prijenosa. Ostalih 25 sojeva u klasterima je raspodijeljeno u ukupno 20 klastera, pri čemu su ostali sojevi izolirani u bolesnika koji dolaze iz drugih županija. Relativno visoki postotak sojeva jedinstvenog genotipa ukazuje da je stupanj nedavnog prijenosa bolesti relativno nizak. Rezultati molekularne epidemiologije ukazuju na učinkovitost protuepidemijskih mjera otkrivanjem neočekivanih puteva prijenosa, identificiranjem sojeva koji su prisutni u određenoj zajednici i imaju veću mogućnost izazivanja bolesti.
Central nervous system pathology contributes to respiratory deficits in Glycogen Storage Disease Type II (GSDII)

GSDII is caused by deficiency of the enzyme acid α‐glucosidase (GAA) and results in systemic glycogen accumulation. Respiratory deficits that accompany GSDII have been attributed to diaphragmatic muscle weakness. However, case reports suggest that motoneuron pathology is present in GSDII. Thus, we hypothesized that respiratory neural control is impaired in mice lacking GAA (Gaa−/−). Using plethysmography, breathing was quantified in Gaa−/− mice and age/gender matched controls (B6/129; Gaa−/−background strain). During quiet breathing, minute ventilation (mL/min) was attenuated (n=8/group, p<0.001) in Gaa−/− (43±4) vs. control mice (60±6). Phrenic motor output was assessed via nerve recordings in anesthetized, paralyzed, ventilated mice. Preliminary data suggest that phrenic inspiratory burst amplitude is lower (p<0.001) in Gaa−/− (0.2 ± 0.0 mV, PaCO2 = 51.5 ± 1.4 mmHg, n=3) vs. controls (15.4 ± 4.9 mV, PaCO2 = 54.5 ± 1.5 mmHg, n=2). Glycogen accumulation was quantified in the spinal segments containing phrenic motoneurons (C3‐C5) via the acid hydrolysis method. Glycogen (μg/mg wet wt) was elevated (n=6/group, p<0.001) in Gaa−/− (37.6±2.4) vs. control (17.4±0.5). We conclude: 1) Gaa−/− mice recapitulate clinical GSDII respiratory deficits, 2) spinal glycogen accumulation may impair motor output, and 3) respiratory neural control may be impaired in GSDII.
The Functional Role of Chloride Channels in Cardiac Pacemaker Activity

Chloride (Cl-) channels are transmembrane proteins in biological membranes, which form functional pores and allow the diffusion of negatively-charged Clions along the electrochemical gradients. These channels can also conduct other anions including I-, Br-, NO3-, aspartate, glutamate, etc. They are conventionally called Clchannels because Clis the most abundant and physiological anions in organisms. While cation (K+, Na+, and Ca2+) channels have received most of attentions in the past 50 years, the role of Clchannels in the pacemaker activity of the heart has been largely ignored and understudied (Duan, 2009). The possible contribution of Clcurrents to spontaneous cardiac action potentials was first described in multicellular preparations of Purkinje fibers by Carmeliet (Carmeliet, 1961) and Hutter & Noble in 1961 (Hutter & Noble, 1961). Later, investigators from several laboratories observed the Cldependence of the diastolic depolarization and action potential duration. They characterized a hyperpolarizationactivated Clcurrent in multicellular preparations of rabbit sinoatrial node (SAN) (De Mello, 1963;Noma & Irisawa, 1976;Seyama, 1979). Unfortunately, studies in the late 1970s raised serious doubts about the existence and functional role of any type of Clchannels in the heart. The potential functional role of the hyperpolarization-activated Clcurrents in cardiac pacemaker activity has therefore been completely disputed (Hume et al., 2000;Duan et al., 2005). Recent studies have characterized the functional and molecular expression of several Clchannels in cardiac SAN cells from different species (Duan, 2009). These include 1) a hyperpolarizationand cell swelling-activated inwardly rectifying Clcurrent (ICl.ir)(Duan et al., 2000), which may be encoded by ClC-2, a member of the ClC voltage-gated Clchannel gene superfamily (Thiemann et al., 1992;Britton et al., 2000;Duan et al., 2000;Britton et al., 2005;Huang et al., 2009); 2) a volume-regulated outwardly-rectifying Clcurrent (ICl,vol)(Hagiwara et al., 1992), which may be encoded by another member of the ClC superfamily, ClC-3 (Duan et al., 1997b;Duan et al., 1999a;Britton et al., 2000); and 3) a Ca2+activated Clcurrent (ICl.Ca) (Verkerk et al., 2002), which may be encoded by TEME16A (or Ano1) (Schroeder et al., 2008;Caputo et al., 2008;Yang et al., 2008;Hartzell et al., 2009). Therefore, experimental evidence are merging to support the potential role of Clchannels in
Does herbivory really suppress mycorrhiza? A meta‐analysis

1. aged and natural ecosystems, herbivory can have a major impact on plant growth. Defoliation and shoot removal reduce the photosynthetic capacity of plants and are also thought to reduce allocation of carbon to roots and mycorrhizal fungi. However, evidence supporting this assumption remains equivocal.