Miracle-dz/UniFAR-FTUs huggingface dataset:
The Vertical Distribution of Zooplankton in Relation to Habitat Zones in the Area of the Atlantis II Deep, Central Red Sea

The vertical distribution of mesozooplankton has been studied in the central Red Sea to determine its relationship to discrete habitat zones defined according to density, oxygen and nutrient concentrations, seston, and phytoplankton profiles. A disproportionately large amount of the 300 pm net plankton occurs both day and night in the epipelagic zone, which occupies the upper water layer above the abrupt thermohalocline at about lOOm In contrast, in the lower bathypelagic zone, a layer between 1,050 and 2 1,850 m, the numerical abundance and biomass of the zooplankton (0.2 specimens and 5 0 . 0 5 m g wet weight m-3) correspond to values encountered in other oligotrophic regions in tropical oceans below a depth of 4,000 to 6,000 m. The subsurface zooplankton maximum is situated in the core of the oxygen minimum layer, which is located in the mesopelagic zone (100 to 750m). Minimum oxygen values at ca. 400 m delimit the upper and lower interzonal (mesopelagic) assemblages. The unusual plankton distribution, the predominance of a few species and the ontogenetic segregation of the interzonal species are related to the abnormally high temperature (2 21.5") and salinity (240 .5% S) in the subsurface waters, coupled with a depleted oxygen content in the mesopelagic zone and lack of food in the bathypelagic zone. Vertical transport of organic matter is achieved by the 'ladder of migrations', involving a few interzonal species that descend into the upper bathypelagic zone but remain above ca 1,100m. Transport of organic debris below this depth by sinking is ineffective because its decay is too rapid.
Instantaneous benthic response to different organic matter quality: In situ experiments in the Benguela Upwelling System

Abstract The benthic community in continental slope and deep-sea sediments of the Benguela Upwelling System was supplied with 13C-labelled organic matter (OM) of two different qualities using a benthic chamber lander. Freeze-dried cultures of Skeletonema costatum served as ‘fresh’ OM. ‘Altered’ OM of the same material had been additionally dialysed to remove low-molecular weight compounds. In order to investigate the benthic response pattern, mineralization of labelled OM, uptake by macrofauna and incorporation into bacteria were followed over 18–36 h. Total oxygen uptake was not affected beyond natural variation by the OM addition. Mineralization dominated the 13C-labelled phytodetritus processing, constituting 71–95% of the total processed OM. Bacterial incorporation of phytodetrital carbon exceeded macrofaunal uptake at all stations. Stations situated in a major centre of OM deposition showed phytodetritus processing rates on average twice as high as outside the depocentre. Phytodetritus processing was 1.5, 2.5 and 4.3 times higher for fresh than for altered OM at 605, 1019 and 1335 m water depth, respectively. Our observations clearly indicate the importance of OM quality on mineralization rates.
Genetic structure in the species-pair Silene vulgaris and S. uniflora (Caryophyllaceae) on the Baltic island of Oland

Allozyme data were used to assess the genetic structure between 37 sympatric populations of the species-pair Silene vulgaris and S. uniflora ssp. petraea, and to infer levels of intra- and interspecific gene flow in the two species. Silene vulgaris is a g
Effect of forage matting on rate of grass drying, rate of silage fermentation, silage intake and digestibility of silage by sheep

The effects of forage matting on rate of grass drying and silage fermentation, digestibility, and intake were examined using perennial ryegrass swards. Treatments compared were: forage mats, where grass was processed through a laboratory scale macerator prior to matting and wilting to 228 g dry matter (DM) kg−1 (FM treatment); unconditioned grass which was direct ensiled at 163 g DM kg−1 (DE treatment); unconditioned grass which was wilted for the same period as FM to 213 g DM kg−1 (UC treatment); unconditioned grass which was wilted to 234 g DM kg−1 (UC25, treatment). All forages were dried on black plastic sheeting. For each treatment a total of approximately 80 kg grass DM was ensiled in seven 290 I plastic bins for 136 d prior to feeding to wether sheep. A further total of 14 kg grass DM from each treatment was ensiled in twenty-one plastic pipes (152 mm diameter, 762 mm long) to give a total of 84 pipes. Rate of silage fermentation was determined by destructively sampling pipes following 1, 2, 4, 6, 13, 20 and 50 d of ensilage. Over the mean wilting period of 6·9 h, grass from the FM treatment dried significantly faster (P < 0·001) and required less solar energy per unit of moisture loss than unconditioned grass. The rate of grass drying was highly correlated with solar radiation. The FM treatment did not influence the rate or extent of silage fermentation. The intakes and digestibilities of FM, UC and UC25 were not significantly (P < 0·05) different from each other but were higher than for the DE treatment (P < 0·05 for digestibility and NS for intake). In Northern Ireland it is unlikely that there will be sufficient solar radiation to allow forage mats to be made, wilted to a level to prevent effluent production and harvested within one working day. Further work is required to optimize mat-making technology for more rapid drying and to determine the effect of adverse weather on nutrient losses from mats.
Estimated Molecular Phylogenetic Relationships of Six Siphonostomatoid Families (Copepoda) Symbiotic on Elasmobranchs

Members of the Siphonostomatoida are associated with either invertebrates or vertebrates. Even though the interfamilial relationships within the Siphonostomatoida are unresolved, it has generally been assumed that those members parasitic on vertebrates form a derived and monophyletic group. Eleven of the families symbiotic on vertebrates have been reported from elasmobranchs. One nuclear genetic marker (18S rDNA) and two partial mitochondrial markers (16S rDNA and COI) were used to estimate the phylogenetic relationship among six families symbiotic on elasmobranchs. The estimated molecular topologies using maximum likelihood, parsimony (unweighted and weighted), and Bayesian analyses are mostly similar. The six families investigated grouped into two major clades, with Kroyeriidae, Caligidae, Pandaridae, and Dichelestiidae in one clade, and Eudactylinidae and Sphyriidae in the other. The molecular topologies are compared with the previous morphological topology and present some support for some of the proposed relationships and alternative hypotheses in the areas of conflict. Valuable information obtained from the study is the indication that the genes used are informative at this level of investigation and can therefore be used in more elaborate future studies.
Immunocytochemical localization of galactosyltransferase in HeLa cells: codistribution with thiamine pyrophosphatase in trans-Golgi cisternae

An affinity-purified, monospecific rabbit antibody against soluble human milk galactosyltransferase was used to localize the enzyme in HeLa cells by immunofluorescence and by the protein A-gold technique at the electron microscope level. Specific immunofluorescence was observed in a juxtanuclear cytoplasmic region which was identified, on immunostained thin sections of low-temperature Lowicryl K4M-embedded HeLa cells, as Golgi apparatus. Label by gold particles was limited to two to three trans cisternae of the Golgi apparatus, indicating a compartmentalization of galactosyltransferase in the cisternal stack. Combination of preembedding thiamine pyrophosphatase cytochemistry, with postembedding immunostaining for galactosyltransferase proved codistribution of the two enzymes. However, the acid phosphatase- positive, trans-most cisterna was negative for galactosyltransferase. The close topological association of both galactosyltransferase and thiamine pyrophosphatase (or nucleoside diphosphatase) suggests a concerted action of both enzymes in glycosylation.
Southern Benguela frontal region. I. Hydrology, phytoplankton and bacterioplankton

Physical and biological features of the shelf-break oceanic front of the southern Benguela upwelling region off the Cape Peninsula, South Africa, were studied in March 1983. The convergence front was situated between 90 and 110 km offshore, delineated by strong temperature and salinity gradients. Further inshore (45 km offshore), salinity sections revealed a shallow frontal feature between water masses of different upwelling origin. Recently upwelled water close inshore was slightly aged as indicated by some sun-warming to ca lS°C, the development of high chlorophyll a (up to 9 mg m-3) and reduced nitrate concentrations (< 11 pg-at N 1-l). These frontal regions were associated with elevated chlorophyll a concentrations and bacterial numbers. Although recently upwelled water was characterised by high chlorophyll a concentrations (5 to 8 mg m-3), bacterial biomass was relatively low (< 20 mg C m-3) w M e the converse was generally true for older offshore waters (< 2 mg chl a m-3; 20 to 40 mg bacterial C m-3). The overall positive relationship between chlorophyll a concentration and bacterial biomass was best described by a power curve as at high chlorophyll concentrations, bacterial blomass was proportionally reduced, probably due to predation. Close to the sediment water interface there was some evidence of nitrification. Indirect estimates of NHZ-N regeneration by the microplankton (< 200 pm), based on bacterial biomass, suggested that physical mixing processes at the shelf-break front ensure that 'new' nitrogen (NOT-N) can be entrained into the euphotic zone, while well-stratified oceanic waters rely mainly (65 %) on regenerated nitrogen.
Effects of benzoic acid, essential oils and Enterococcus faecium SF68 on growth performance, nutrient digestibility, blood profiles, faecal microbiota and faecal noxious gas emission in weanling pigs

A total of 150 weanling pigs (body weight of 8.86 ± 0.93 kg) were used in a 42-day trial to evaluate the efficacy of benzoic acid (BA), essential oils (EO) and Enterococcus faecium SF68. Pigs were randomly distributed into five treatments (six replicates and five pigs per pen): CON, control diet; B5E, CON + 0.5% BA + 0.01% EO; B5SF, CON + 0.5% BA + 7 × 108 CFU/kg E. faecium; B3E, CON + 0.3% BA + 0.01% EO; B3SF, CON + 0.3% BA + 7 × 108 CFU/kg E. faecium. During d 8–21 and overall, pigs fed B5E diets showed greater (P < 0.05) average daily gain and gain/feed ratio than CON. The dry matter digestibility in pigs fed B5E diet was increased (P < 0.05) compared with CON at d 21, while the nitrogen digestibility in B5E, B5SF and B3E was increased (P < 0.01) compared with CON. Faecal Lactobacillus counts were increased in B5E, whereas E. coli counts were decreased in B5E and B5SF (P < 0.01) compared with CON. All the supplementation treatments decreased (P < 0.05) the faecal NH3, total mercaptans and H2S emission. In conclusion, dietary inclusion of 0.5% BA plus 0.01% EO and 7 × 108 CFU E. faecium/kg of diet could improve growth performance, decrease faecal E. coli counts, while 0.3% BA combination with EO or E. faecium almost had no effect on the parameters except the decreased faecal noxious gas contents.
Delphi technique for generating criteria and indicators in monitoring ecotourism sustainability in Northern forests of Iran: Case study on Dohezar and Sehezar Watersheds

Ecotourism is widely accepted as the most effective type of sustainable development. For monitoring ecotourism sustainability in the Northern forest of Iran, a study was designed to help identifying criteria and indicators (C&I) with the principle goal to ensure the objectives of forest management, and at the same time – maintain processes in a sustainable manner. Indicators act as an instrument which can be used for monitoring sustainability. Hence indicators should be multidisciplinary, and cover all aspect of social, ecological, cultural, economic and institutional factors affecting sustainability of ecotourism. In this study, C&I were identified by using the Delphi approach through multidisciplinary panel team. Three rounds of meetings were held for discussions and dissemination of research to a panel of local experts. At the end of the second round we reached a consensus on 9 criteria and 61 indicators, which include 21 indicators related to ecological aspects, 8 to economic aspects, 21 to social aspects, 6 to cultural aspects and 5 to institutional aspects. The selected indicators would be applied by the Iranian Cultural, Heritage, Handicrafts and Tourism Organization for monitoring ecotourism sustainability in the Northern forest of Iran.
Coloring Carbohydrates: Investigation of Azulene Derivatives as Blue Protecting Groups

Coloring carbohydrate derivatives by a chromophore tag greatly facilitates all purification steps during a synthetic sequence, according to a methodology called “chromophore-supported purification” (CSP). Herein an Fmoc-analogous blue protective group for CSP is introduced, based on guaiazulene. Following a mechanistic rational, the synthesis and introduction of this new protecting group is shown, together with its removal under variable conditions and its application for the synthesis of glycoclusters of a glycopeptide and glycopeptoid type.
CHEMICAL CONTROL OF INSECTS ATTACKING ALFALFA IN SOUTHWESTERN ONTARIO

Surveys in southwestern Ontario in 1953 and 1954 showed that the initial small numbers of sucking insects found in alfalfa fields in early spring tended to increase rapidly as the season progressed. Each time the hay was cut the number of insects was reduced but the invading population soon built up, often to economic proportions. A spray of malathion, perthane, toxaphene, or heptachlor, applied in the spring of 1954, prevented the usual build-up of spittlebug nymphs. Each of the insecticides tested, except heptachlor, increased the yield of the first cutting of hay. An application after each of the first and second cuttings did not give adequate control of sucking insects present and did not increase either cutting of hay.
Evidence that reactive oxygen species do not mediate NF‐κB activation

It has been postulated that reactive oxygen species (ROS) may act as second messengers leading to nuclear factor (NF)‐κB activation. This hypothesis is mainly based on the findings that N‐acetyl‐L‐cysteine (NAC) and pyrrolidine dithiocarbamate (PDTC), compounds recognized as potential antioxidants, can inhibit NF‐κB activation in a wide variety of cell types. Here we reveal that both NAC and PDTC inhibit NF‐κB activation independently of antioxidative function. NAC selectively blocks tumor necrosis factor (TNF)‐induced signaling by lowering the affinity of receptor to TNF. PDTC inhibits the IκB–ubiquitin ligase activity in the cell‐free system where extracellular stimuli‐regulated ROS production does not occur. Furthermore, we present evidence that endogenous ROS produced through Rac/NADPH oxidase do not mediate NF‐κB signaling, but instead lower the magnitude of its activation.
A general and efficient route for chemical aminoacylation of transfer RNAs

The preparation of aminoacyl pdCpA in one step and in high yield by reaction of the cyanomethyl active esters of N-protected α-amino acids with pdCpA is detailed. The preparation and photodeprotection of aminoacyl pdCpA derivatives containing nitroveratryl (NVOC) N-protected amino acids is also studied. The utility of the above methods for preparing aminoacyl tRNA was confirmed by enzymatically ligating NVOC-phenylalanyl pdCpA to tRNA-C OH followed by photolysis to provide unprotected phenylalanyl tRNA. The phenylalanyl tRNA was shown to be competent in an in vitro protein biosynthesis system. These protocols greatly simplify the use of chemically misacylated tRNAs in the synthesis of proteins containing unnatural amino acids, as well as in studies of protein biosynthesis
Microbial 16.BETA.-hydroxylation of steroids with Aspergillus niger.

Microbial 16β-hydroxylation of some steroids with Wojnowicia graminis, Corticium centrifugum and Bacillus megaterium has been reported, but not 16β-hydroxylation of normal 17-oxo steroids with Aspergillus niger. This time, we tried microbial transformation of dehydroepiandrosterone with this fungus, and obtained 4-androstene-3,17-dione, 17β-hydroxy-4-androstene-3,16-dione, 16β,17β-dihydroxy-4-androsten-3-one and a new compound, 16β-hydroxy-4-androstene-3,17-dione. This new compound was also obtained by the fermentation of 4-androstene-3,17-dione and testosterone.
Molecular Marker Diversity and Yield of Isogenic 2x and 4x Single‐Crosses of Alfalfa

The positive correlation between level of heterozygosity and yield in autotetraploid alfalfa (Medicago sativa L.) suggests that genetic diversity between parents may be related to yield of their hybrid progeny. This was tested by comparing the levels of polymorphism among parental genotypes for restriction fragments homologous to 61 recombinant DNA clones with the yield of their single-cross progenies. Diploid (2x) genotypes were chromosome doubled to produce autotetraploids (4x), and these isogenic 2x and 4x genotypes were used as parents to generate progenies in 4×4 diallels [. ]
Green grafting: A useful technique for detecting grapevine viruses

A green grafting technique for indexing grapevines for viruses is described. It consists of joining actively growing stock and scion tissues with a slanting cut and then binding with a plastic or a rubber tie. The technique has some advantages over the more generally used dormant-chip-budding method, as it can be done for the greater part of the growing season, and very small stocks and scions can be grafted. It also provides a more rapid means of testing for GFLV than does chip-budding.
Improving the Precision of the Structure–Function Relationship by Considering Phylogenetic Context

Understanding the relationship between protein structure and function is one of the foremost challenges in post-genomic biology. Higher conservation of structure could, in principle, allow researchers to extend current limitations of annotation. However, despite significant research in the area, a precise and quantitative relationship between biochemical function and protein structure has been elusive. Attempts to draw an unambiguous link have often been complicated by pleiotropy, variable transcriptional control, and adaptations to genomic context, all of which adversely affect simple definitions of function. In this paper, I report that integrating genomic information can be used to clarify the link between protein structure and function. First, I present a novel measure of functional proximity between protein structures (F-score). Then, using F-score and other entirely automatic methods measuring structure and phylogenetic similarity, I present a three-dimensional landscape describing their inter-relationship. The result is a “well-shaped” landscape that demonstrates the added value of considering genomic context in inferring function from structural homology. A generalization of methodology presented in this paper can be used to improve the precision of annotation of genes in current and newly sequenced genomes.
The Relationship of Goα Subunit Deamidation to the
 
Tissue Distribution, Nucleotide Binding Properties, and βγ Dimer
 
Interactions of Goα Subunit Isoforms

Abstract : The distribution and properties in brain of the α subunits of the major bovine brain Go isoforms, GoA, GoB and GoC, were characterized. The αoA and αoB isoforms arise from alternative splicing of RNAs from a single αo gene, whereas αoC is a deamidated form of αoA. All three Go isoforms purify from brain with different populations of βγ dimers. This variable subunit composition of Go heterotrimers is likely a consequence of their functional differences. This study examined the biochemical properties of the αo isoforms to see if these properties explain the variable βγ composition of their heterotrimers. The brain distribution of αoB differed substantially from that of αoA and αoC, as did its guanine nucleotide binding properties. The unique subunit composition of GoB can be explained by its expression in different brain regions. The αoA and αoC showed slight differences in guanine nucleotide binding properties but no preference for particular βγ dimers when reassociated with a heterogeneous βγ pool. The αoC protein occurred in a constant ratio to αoA throughtout the brain, but was a much larger percent of total brain αo than previously thought, ~35%. These results suggest that αoA is a precursor of αoC and that the association of Goα subunits with different βγ dimers reflects the function of an adaptive, G‐protein signaling mechanism in brain.
Mucous Cells in the Gills of Snow Trout, Schizothorax curvifrons Heckel (Pisces, Cypriniformes, Cyprinidae)

The ultrastructural and histochemical characteristics of mucous cells and their functional significance in the gills of Schizothorax curvifrons were studied with the objectives that this study could serve as a basis for further studies in relation to histopathology, aquatic toxicology and stress conditions in aquaculture and natural or polluted environments. The electron microscopical analysis of the gills following fixation in Karnovsky's fluid and post fixation in osmium tetraoxide revealed that the mucous cells were covered by epithelial cells and their major part was occupied by firmly arranged large mucous globules of different electrodensities, displacing their nuclei towards the basal position. The cytoplasmic extensions and islets among the mucous globules and the cellular interdigitations between mucous cells and neighbouring cells were present and the release of mucin by exocytosis was also observed. Utilizing histochemical techniques that included methods of periodic acid Schiff (PAS) reaction and alcian blue method (AB pH 2.5) for localization of neutral and acid mucopolysaccharide secreting mucous cells showed that the gill epithelium was lined by mucous cells which were found to be PAS and AB positive, confirming the presence of both neutral mucous cells secreting hexose containing mucosubstances and acidic mucous cells secreting weakly acidic sulphated mucosubstances and sialomucins. The possible roles of the mucous cells and the products secreted by them have been discussed in this paper.
Changes in Whole-Tree Water Use Following Live-Crown Pruning in Young Plantation-Grown Eucalyptus pilularis and Eucalyptus cloeziana

Pruning of live branches is a management option to enhance wood quality in plantation trees. It may also alter whole-tree water use, but little is known about the extent and duration of changes in transpiration. In this study, sap flow sensors were used to measure transpiration for 14 days prior to, and 75 days following the removal, through pruning, of the lower 50% of the live-crown length of 10–11 m tall four-year old Eucalyptus pilularis Sm. and E. cloeziana F. Muell. trees. Pruning had no effect on stem growth, sapwood water content or radial pattern of sap velocity in either species. Pruning reduced mean daily water use by 39% in E. pilularis and 59% in E. cloeziana during the first eight days after pruning. Thirty six days after pruning there were no longer any significant differences in transpiration rates between pruned and unpruned trees in either species. Our results show that pruning of live branches had only a short-term effect on whole-tree transpiration in these sub-tropical eucalypt species.