Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene order in human α‐globin locus is required for their temporal specific expressions

The human α‐globin cluster represents a unique model of transcriptional regulation and provides challenges to the current understanding of interactions between distal and proximal regulatory elements. Although the gene proximal regions are believed to possess almost all the necessary elements for temporal and spatial specificity of gene transcription, it is still not clear whether the relative distance of embryonic ζ‐ and fetal/adult α‐genes to their distal regulatory element α‐URE plays any role in transcriptional switching. To investigate the role of gene order in regulating temporal expression, we inverted the entire structure gene region of human α‐globin locus in a BAC clone bringing α‐genes closest to α‐URE and ζ‐gene the farthest away. Expression analysis of the reverted locus in transgenic mice showed that α‐globin genes, now relocated closer to α‐URE, maintained their expression levels through all developmental stages. However, the ζ‐globin gene suffered a total loss at both embryonic and fetal/adult stages. It indicates that proximal location of ζ‐globin gene to α‐URE is necessary for its normal embryonic expression and necessary to prevent embryonic expression of the α‐globin gene. We proved that, in the human α‐globin gene cluster, the normal order of structural genes relative to α‐URE plays a crucial role in the regulation of developmental switching.
G Protein Activation without Subunit Dissociation Depends on a Gαi-specific Region*

G proteins transmit a variety of extracellular signals into intracellular responses. The Gα and Gβγ subunits are both known to regulate effectors. Interestingly, the Gα subunit also determines subtype specificity of Gβγ effector interactions. However, in light of the common paradigm that Gα and Gβγ subunits dissociate during activation, a plausible mechanism of how this subtype specificity is generated was lacking. Using a fluorescence resonance energy transfer (FRET)-based assay developed to directly measure mammalian G protein activation in intact cells, we demonstrate that fluorescent Gαi1,2,3, Gαz, and Gβ1γ2 subunits do not dissociate during activation but rather undergo subunit rearrangement as indicated by an activation-induced increase in FRET. In contrast, fluorescent Gαo subunits exhibited an activation-induced decrease in FRET, reflecting subunit dissociation or, alternatively, a distinct subunit rearrangement. The αB/C-region within the α-helical domain, which is much more conserved within Gαi1,2,3 and Gαz as compared with that in Gαo, was found to be required for exhibition of an activation-induced increase in FRET between fluorescent Gα and Gβγ subunits. However, the αB/C-region of Gαil alone was not sufficient to transfer the activation pattern of Gαi to the Gαo subunit. Either residues in the first 91 amino acids or in the C-terminal remainder (amino acids 93–354) of Gαil together with the αB/C-helical region of Gαi1 were needed to transform the Gαo-activation pattern into a Gαi1-type of activation. The discovery of subtype-selective mechanisms of G protein activation illustrates that G protein subfamilies have specific mechanisms of activation that may provide a previously unknown basis for G protein signaling specificity.
Cloning and Characterization of the Caspase Family Member BmDronc from Bombyx mori (Lepidoptera: Bombycidae) Embryo Cells

ABSTRACT Caspases are a family of cysteinyl aspartate proteinases known for their essential roles in the regulation of apoptosis. To date, ≈20 caspases have been identified, although few have been cloned and characterized in Bombyx mori (L.). Two caspase-9 variants from the B. mori embryo cell line (BmE), designated BmDroncL and BmDroncS, were cloned. BmDroncL has three classic domains: a caspase recruitment domain and large and small subunits, and is a homologue of Drosophila Dronc, human caspase-9, Aedes Dronc, and fish caspase-9, whereas BmDroncS lacks the large subunit. Instantaneous expression of BmDroncL caused typical apoptosis in Sf-9 cells. Moreover, BmDronc gene expression increased markedly during the silkworm metamorphosis at the larva-pupa and pupa-moth stages, which suggested that BmDronc plays a crucial role during B. mori metamorphosis.
Acceleration of the Decay of Membrane Potential after Energization of Chloroplasts in Intact Zea mays Leaves

The relationship between dissipation of the flash-induced membrane potential across the thylakoid membrane and the high energy state was studied in Zea mays leaves. The dark decay of the flash-induced 515-nm absorbance change was accelerated by short preillumination of the leaf. No acceleration of the decay by preillumination was observed when leaves were incubated in argon or COa gas or treated with DCMU. These effects of preillumination and incubation were reversible. The delayed fluorescence from chlorophyll a was reversibly decreased by incubating leaves in argon or CO2 gas, though the modes of depression were somewhat different from each other. In leaves incubated in argon or CO2 gas, the phase of slow decrease of the intensity of prompt fluorescence during illumination reversibly disappeared. The results suggested that the dissipation of membrane potential generated by a flash was accelerated after the energization of chloroplasts in leaves, probably by increased H+ permeability of the thylakoid membrane. O2 was important in maintaining (in darkness) and forming (under illumination) the high energy state in chloroplasts in intact leaves.
PHYTOCHEMICAL SCREENING, GAS CHROMATOGRAPHY-MASS SPECTROMETRY (GC-MS) ANALYSIS OF PHYTOCHEMICAL CONSTITUENTS AND ANTIBACTERIAL ACTIVITY OF CORIANDRUM SATIVUM (L) SEEDS

Objective : The present study was carried out to evaluate the phytochemical screening, Gas Chromatography–Mass Spectrometry analysis of phyto-constituents and antibacterial activity of Coriandrum sativum (L.) seeds against the bacterial [Microbial Type Culture Collection (MTCC)] strains. Methods : Methanol, ethanol, ethyl acetate, acetone and water extracts of Coriandrum sativum (L) seeds were prepared using the Soxhlet apparatus. The antibacterial activity of various extracts of C. sativum seeds were identified by disc diffusion method against bacterial strains. The bioactive components of methanol and acetone fraction of C. sativum seeds were evaluated by Gas Chromatography-Mass Spectrometry (GC-MS) analysis. The minimal inhibitory concentration (MIC) values were obtained by the well diffusion method between the ranges of 1000µg/ml to 7. 8µg/ml. Results : The preliminary phytochemical screening of various extracts of C. sativum revealed the presence of different Phyto-constituents. Methanol extract of C. sativum showed the maximum inhibition zone (20 mm) against Staphylococcus aureus and followed by Klebsiella pneumoniae (17 mm). The MIC values of methanol extract were found to be 62. 5µg/ml against Staphylococcus aureus , Proteus mirabilis and Bacillus subtilis . In the GC-MS analysis of phyto-compounds, the methanol extracts showed fourteen bioactive fractions and eleven compounds from acetone extract. Conclusion : The methanol and acetone extracts of Coriandrum sativum seeds showed maximum inhibitory activity against the tested bacterial strains.
Carob pods (Ceratonia siliqua L.) inhibit human neutrophils myeloperoxidase and in vitro ROS-scavenging activity

Natural antioxidants such as phenolic compounds protect cells against the damaging effects of reactive oxygen species (ROS). In this study, we investigated the effect of carob pods aqueous extract (CPAE) on the reactive oxygen species (ROS) production by human neutrophils, myeloperoxidase (MPO) activity and expression as well as lactoferrin and NADPH oxidase phosphorylation. Neutrophils were isolated from whole human blood using the ficoll–dextran method and ROS generation was measured by luminol-amplified chemiluminescence. Superoxide anion generation was detected by chemiluminescence using the lucigenin method. H2O2 was detected by the chemiluminescence assay. MPO activity was measured by the tetramethylbenzidine oxidation method. Western blotting analysis was used to determine the MPO and lactoferrin as well as P47phox–Ser-328 phosphorylation. The use of HPLC technique revealed the identification of many phenolic compounds in carob pods with pyrogallol as the main compound in the pulp and tannic acid in the seeds. We also found that CPAE inhibits luminol-amplified chemiluminescence in human neutrophils stimulated by PMA and that it is able to scavenge superoxide anion and hydrogen peroxide. Carob extract significantly reduces MPO activity and expression. More importantly, CPAE inhibits PMA-induced p47phox phosphorylation on Ser328 as well as lactoferrin release by neutrophils in a concentration-dependent manner. The effects are generally more marked for the seeds compared to the pulp. In conclusion, we suggest in the present study that Carob pods (Ceratonia siliqua L.) inhibit human neutrophils myeloperoxidase and in vitro ROS production.
Taxonomic Revision of genus Macrophya Dahlbom (Hymenoptera, Symphyta, Tenthredinidae, Tenthredininae) from India

The genus Macrophya Dahlbom is revised from India, with an addition of 6 new species. Described as new are M. khasiana, M. manganensis, M. pseudoplanata, M. rufipodus, M. punctata, & M. ukhrulensis. With first record of M. pompilina Malaise and M. formosana Rohwer, this genus is nos represented by 14 species from India. M. metepimerata Singh et al. and M. concolor Saini et al. are synonymized with M. brancuccii Muche. Treatment of each species includes synonymy (if any), detailed description, collection data and the population variation (if any). For all the known species a dichotomous key is provided.
Different Lactations for Estimating Genetic Merit of Dairy Cows

Heritabilities for milk and fat production of Holstein cows were highest at . 35 and . 33 for first lactation and decreased to . 21 and . 20 for fifth lactation. Genetic correlations between consecutive lactations were above . 9, except for . 75 between first and second, and decreased as lactations were farther apart. Relationships between production by cows and their daughters tended to be higher when both animals were in the same herd than when they were in different herds. The cow lactation most valuable in predicting a daughter lactation was generally the one with the same number; this finding suggests that production in different lactations is controlled by some different genes. The third lactation of a cow was most highly related to lifetime production of the daughter. First lactation was not as useful in estimating genetic merit as is accepted generally. The results provide little support for weighting lactations differentially for sequence.
Estimation of Genetic Correlations and Selection Responses for Carcass Traits between Ultrasound and Real Carcass Measurements in Hanwoo Cows

ABSTRACT This study was conducted to determine genetic correlations among carcass traits measured by ultrasound and real carcass measurements and to estimate indirect selection responses for real carcass traits based on ultrasound measurements in Hanwoo cows. To accomplish this, 22,080 ultrasound measurement records from 17,926 cows collected from 2001 to 2012 and 11,907 carcass records obtained from fattened cattle from 2008 to 2012 were used. Genetic parameters were estimated based on eye muscle area (EMA), backfat thickness (BF) and marbling score (MS) measured by ultrasound-scanning of live cows and using the official technique on chilled bovine half-carcasses after slaughtering. Heritability and genetic correlation for carcass traits were estimated using a mixed model equation that consisted of environmental effects as fixed parameters and additive genetic effects and residual effects as random parameters, assuming that traits were different between ultrasound and carcass measurements. This statistical method was applied to the average information restricted maximum likelihood method. The heritability of EMA, BF and MS measured by ultrasound were 0.33, 0.61 and 0.46, respectively, while the heritability estimates of the corresponding traits based on carcass measurements were 0.29, 0.40 and 0.38, respectively and the genetic correlation between ultrasound and carcass traits for EMA, BF and MS were 0.41, 0.78 and 0.67, respectively. The genetic correlation between ultrasound and carcass traits was highly positive. Additionally, the selection response for marbling score was estimated to be 0.42 per generation if the cows were selected based on the ultrasound scan marbling score with an assumed selection intensity of 0.8. Overall, these results indicate that the ultrasound scan technique would be applicable to judging cow selection for genetically improved meat quality. (
Foraging ranges of solitary bees

Summary 1 Habitat requirements of solitary bees include nesting sites, food resources and nesting material. We used translocation experiments to establish foraging distances and measured foraging trip duration to analyse how solitary bees cope with the distance between nesting sites and suitable food plants in different habitat types. 2 Maximum foraging distance between nesting site and food patch was 150–600 m for the 16 bee species examined. Foraging distance was correlated positively with body length. Mean foraging trip duration, measured for seven bee species, ranged from 6 to 28 min and was also correlated with body length. In a study of the polylectic species Osmia rufa , we found a significant decrease in foraging trip duration with increasing number of plant species. Logistic regressions showed that the oligolectic Megachile lapponica nested in trap nests with a probability of 50% if the distance between trap nest and food patch was less than 250 m. The oligolectic Chelostoma rapunculi utilized trap nests when the distance to the nearest food patch was less than 300 m. 3 These experiments showed that solitary bees have a rather small foraging range so local habitat structure appears to be of more importance than large-scale landscape structure. All requirements for sustaining viable populations must be within this range. Therefore, it is necessary to maintain and restore a dense network of habitat patches in landscapes to ensure long-term sustainability of wild bee diversity and their ecological function as pollinators.
IMPROVING STORAGE ROOT PROTEIN CONTENT IN SWEET POTATO THROUGH OPEN-MATING POLLINATION

A field experiment was conducted at the Research Station of Brawijaya University from April to August 2009. An augmented randomized complete block design with seven blocks was utilized, seven parental clones as standard treatments and seven half-sib families as augmented treatments. Each block consisted of seven parental clones plus one randomly assigned family of half-sibs. In addition, the first block contained 29 accessions, the 2 nd block had 120, the 3 rd block had 194, the 4 th block had 45, the 5 th block had 28, the 6 th block had 186, and the 7 th block had 108. Ten cuttings of each parental was planted in each block, along with a single plant of each accession. There were five improved clones identified with high protein content and high yield, ranging from 6.00-8.21% dwb and 1.95 to 2.73 kg/plant, respectively. Broad-sense heritability and genetic advance of storage root weight, storage root number, percentage dry matter and protein content were high, whereas vegetative biomass and harvest index were low. The results showed that storage root weight, storage root number, percentage dry matter and protein content could be used as the basis for a crop improvement program in sweet potato.
Interactions of barley α-amylase isozymes with Ca2 + , substrates and proteinaceous inhibitors

α-Amylases are endo-acting retaining enzymes of glycoside hydrolase family 13 with a catalytic (β/α)8-domain containing an inserted loop referred to as domain B and a C-terminal anti-parallel β-sheet termed domain C. New insights integrate the roles of Ca2 + , different substrates, and proteinaceous inhibitors for α-amylases. Isozyme specific effects of Ca2 + on the 80% sequence identical barley α-amylases AMY1 and AMY2 are not obvious from the two crystal structures, containing three superimposable Ca2 + with identical ligands. A fully hydrated fourth Ca2 + at the interface of the AMY2/barley α-amylase/subtilisin inhibitor (BASI) complex interacts with catalytic groups in AMY2, and Ca2 + occupies an identical position in AMY1 with thiomaltotetraose bound at two surface sites. EDTA-treatment, DSC, and activity assays indicate that AMY1 has the highest affinity for Ca2 + . Subsite mapping has revealed that AMY1 has ten functional subsites which can be modified by means protein engineering to modulate the substrate specificity. Other mutational analyses show that surface carbohydrate binding sites are critical for interaction with polysaccharides. The conserved Tyr380 in the newly discovered ‘sugar tongs’ site in domain C of AMY1 is thus critical for binding to starch granules. Furthermore, mutations of binding sites mostly reduced the degree of multiple attack in amylose hydrolysis. AMY1 has higher substrate affinity than AMY2, but isozyme chimeras with AMY2 domain C and other regions from AMY1 have higher substrate affinity than both parent isozymes. The latest revelations addressing various structural and functional aspects that govern the mode of action of barley α-amylases are reported in this review.
Population Connectivity of Endangered Ozark Big-Eared Bats (Corynorhinus townsendii ingens)

The endangered Ozark big-eared bat (Corynorhinus townsendii ingens) is restricted to eastern Oklahoma and western and north-central Arkansas, where populations may be susceptible to losses of genetic variation due to patchy distribution of colonies and potentially small effective population sizes. We used mitochondrial D-loop DNA sequences and 15 nuclear microsatellite loci to determine population connectivity among Ozark big-eared bat caves. Assessment of 7 caves revealed a haplotype not detected in a previous study (2002–2003) and gene flow among colonies in eastern Oklahoma. Our data suggest genetic mixing of individuals, which may be occurring at nearby swarming sites in the autumn. Further evidence of limited gene flow between caves in Oklahoma with a cave in Arkansas highlights the importance of including samples from geographically widespread caves to fully understand gene flow in this subspecies. It appears autumn swarming sites and winter hibernacula play an important role in providing opportunities for mating; therefore, we suggest protection of these sites, maternity caves, and surrounding habitat to facilitate gene flow among populations of Ozark big-eared bats.
Underestimated effects of climate on plant species turnover in the Southwest Australian Floristic Region

Spatial turnover in plant species composition reflects the interplay between species’ environmental requirements and their dispersal dynamics. However, its origins are also historical, arising from speciation, extinction and past range dynamics. Here, we test the effects of current environmental gradients and geographical distance on regional species turnover. Using a new approach, we then interpret residual turnover patterns, unexplained by these factors.
Uncoupling Kapβ2 Substrate Dissociation and Ran Binding

Karyopherinbeta2 (Kapbeta2) imports a variety of mRNA binding proteins into the nucleus. Release of import substrates in the nucleus involves formation of a high-affinity Kapbeta2-RanGTP complex and concomitant dissociation of import substrates. The crystal structure of the Kapbeta2-RanGppNHp complex shows that Ran binds in the Kapbeta2 N-terminal arch and substrate most likely binds its C-terminal arch. The structure suggested a mechanism for Ran-mediated substrate dissociation where a long internal acidic loop in Kapbeta2 transmits structural information between the GTPase and substrate sites, leading to displacement of substrate by the loop when Ran is bound. To study the molecular mechanism of substrate dissociation, we have cleaved the acidic loop of Kapbeta2 proteolytically (cl-Kapbeta2) and also constructed a mutant of Kapbeta2 with a truncated loop (TL-Kapbeta2). Both modified Kapbeta2s are unable to undergo Ran-mediated substrate dissociation. We have also mapped the boundaries of the Kapbeta2 binding site of substrate mRNA binding protein A1 using a widely applicable method employing NMR spectroscopy. This has allowed design of reagents to quantitate the affinities of the Kapbeta2 proteins for Ran and substrate. cl-Kapbeta2, TL-Kapbeta2, and native Kapbeta2 have comparable affinities for both RanGppNHp and import substrates, indicating that perturbation of the loop has not altered the strength of binary Kapbeta2-Ran or Kapbeta2-substrate interactions. The TL-Kapbeta2 mutant also binds RanGppNHp and substrate simultaneously to form a ternary complex, indicating that in addition to the loss of coupling between Ran binding and substrate dissociation, the two ligand sites on Kapbeta2 are spatially distinct. The uncoupling of Ran binding and substrate dissociation in the TL-Kapbeta2 mutant is further evident in significant loss of Ran-mediated nuclear uptake of fluorescent substrate in digitonin-permeabilized HeLa cells. These results support our previously proposed GTPase-mediated Kapbeta2-substrate dissociation mechanism where the acidic loop of Kapbeta2 physically couples distinct Ran and substrate binding sites.
Macroalgas bentónicas de Puerto Real, Faro Santa Rosalía y Playa Preciosa, Campeche, México, con algunas consideraciones florísticas y ecológicas para el estado

Este estudio agrega 51 taxa algales (26 Rhodophyta, 19 Chlorophyta y 6 Phaeophyta), incluyendo 19 registros nuevos y dos localidades nuevas (Faro Santa Rosalia y Playa Preciosa) a la ficoflora del litoral continental del estado de Campeche. Se discute, con base en la informacion floristica disponible, la posible afinidad de las localidades continentales mejor documentadas con otras (incluyendo, ad hoc., algunas insulares), ubicadas en las regiones Carolineana (Atlantico Norte Templado –Golfo de Mexico-) y Tropical (incluyendo el Caribe mexicano). El coeficiente floristico de Cheney (R+C/P = 6.9) sugiere una afinidad tropical con escaso intercambio templado. La flora estuarina, inferida de la literatura, comprende 113 taxa (33 Chlorophyta, 8 Phaeophyta y 72 Rhodophyta). El elevado coeficiente de Cheney (13.1), es, sin embargo, coherente con aquel para otros estuarios en la region y, consecuentemente, con el aislamiento caracteristico para tales ambientes. La flora para las localidades continentales contempladas en este estudio (Isla Aguada, Sabancuy, Faro Santa Rosalia, Playa Preciosa y Playa Bonita) es de 84 taxa (31 Chlorophyta, 7 Phaeophyta y 46 Rhodophyta); el coeficiente correspondiente es de 6.57, indicando, en este caso, una mayor afinidad con el Caribe mexicano (47.7% de especies en comun con Isla Mujeres, Quintana Roo), que con la region Carolineana templada del Atlantico Este (apenas un 18% de especies en comun con Isla Verde, Veracruz).