Miracle-dz/UniFAR-FTUs huggingface dataset:
Complex seasonality observed amongst diverse phytoplankton viruses in the Bay of Quinte, an embayment of Lake Ontario

Summary To initiate research on algal viruses (viruses that infect eukaryotic algae) and cyanophages (viruses that infect cyanobacteria) in the Bay of Quinte, a Lake Ontario embayment, samples of viruses free in the water (i.e. not associated with particulate material) were collected throughout 2011 with the goals of examining the diversity of phytoplankton viruses and monitoring their dynamics. PCR and sequencing of DNA polymerase (polB) and major capsid protein (MCP) genes from algal viruses, and sheath protein genes from cyanophages, revealed diverse phytoplankton viruses in the bay. Specifically, polB sequences from the bay were most closely related to sequences from viruses that infect prasinophyte algae, MCP sequences were related to sequences from viruses that infect prasinophytes and from Mimivirus-like viruses that infect prymnesiophytes and prasinophytes, whilst sheath protein sequences were related to sequences from the phage Ma-LMM01 that infects M. aeruginosa. The abundances of 10 distinct viral genes monitored using quantitative PCR ranged from exceptionally high values (e.g. 256 441 gene copies mL−1 for a putative M. aeruginosa phage) to values that were just above detection limits (e.g. a putative Prasinovirus never exceeded 20 gene copies mL−1). Patterns of abundance included genes that were seasonally sporadic or geographically patchy, as well as some that were stable throughout the bay over the entire year. Despite the heterogeneity of viral abundance across the bay, gene abundance clustered by sampling date and geographical location. Even for closely related viruses, seasonality and geographical distribution were distinct. By providing evidence for the complex seasonality of diverse phytoplankton viruses, this work highlighted significant gaps in knowledge of aquatic virus ecology that can be extrapolated from this one system to most aquatic environments.
Succession of bacterial communities during petroleum degradation in bark compost as detected by small subunit ribosomal RNA gene profiles

Bioremediation of crude oil was tested by hot bark composting, and the changes in microbial assemblages in the compost were monitored by polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis of small subunit ribosomal RNA gene (16S rDNA) sequences. Most of the analyzed 16S rDNA sequences were unrelated to any cultured and known uncultured microorganisms. Only two compost-derived 16S rDNA sequences from a total of 16 were related to known sequences at similarities higher than 97%, viz., a species-level criterion. One sequence related to an uncultured soil bacterium, which was affiliated with the Cytophaga-Flavobacterium-Bacteroides group, was found throughout petroleum degradation; and the other sequence related to Chryseobacterium indoltheticum, a Cytophaga-Flavobacterium-Bacteroides species, was only found in association with the petroleum degradation. Despite relatively low similarities (< 97%), the rest of the compost-derived 16S rDNA sequences were mostly ascribed to CFB and spore-forming Firmicutes. In particular, four 16S rDNA sequences (out of a total of five) specific to petroleum degradation were affiliated with the Cytophaga-Flavobacterium-Bacteroides group, with the other one related to an uncultured bacterium from a deep aquifer. Many species of the Cytophaga-Flavobacterium-Bacteroides group are known for their ability to degrade diverse refractory substrates. Therefore, isolation and characterization of these compost-derived bacteria may facilitate bioremediation of oil spill in soil as well as aquatic environments.
Phosphorus and Micronutrient Nutrition of Chickpea Genotypes in a Multi-Nutrient-Deficient Typic Ustochrept

ABSTRACT The chickpea breeding program in India has not yet considered the genotypic variation in phosphorus (P) efficiency, despite the fact that the largest proportion of chickpea-growing soils are P deficient. Since general P application to chickpea is at sub-optimum levels, efficient P-utilizing genotypes will perform better than others under P-deficient conditions. High levels of P application may induce zinc (Zn) deficiency in plants grown on Zn-deficient soils. Twenty chickpea genotypes were evaluated for their P efficiency at varied levels of added P, and the effect of P levels on Zn, iron (Fe), copper (Cu), and manganese (Mn) nutrition was studied in pot-culture experiments. Three criteria were used for evaluating P efficiency; shoot dry-matter yield without P, P-uptake efficiency (PUPE), and P-utilization efficiency (PUSE). Under P-deficiency conditions (control), the genotypes BG-256, HK-94-134, Phule-G-5, and Vikash produced the highest shoot biomass. However, genotypes that were found to be superior in the absence of P did not perform in a similar way under optimum P supply. Root dry weight showed a highly significant correlation with P uptake at all P levels. In the case of PUPE, genotypes KPG-59 and Pusa-209 were found to be superior to others. With increasing P levels, PUSE declined in all the genotypes. Increasing P up to 13.5 mg kg−1 soil increased Zn concentration, while further increase led to decreased concentration. Genotypes KPG-59, BG-256, RSG-888, and JG-315 showed Zn concentrations below the critical limit of 20 μg Zn g−1 dry weight (DW) at the high level of P application (27.0 mg kg−1). Iron concentration decreased with increasing P levels. Up to 13.5 mg kg−1 P application, Cu concentration increased and thereafter decreased. Manganese concentration gradually increased with the increasing P levels studied. Based on three criteria, BG-256 can be recommended for use in P-deficient conditions and can be good germplasm source material for chickpea-breeding programs for evolving P-efficient genotypes. Results also suggest that when selecting P-efficient genotypes of chickpea, it is essential to apply deficient micronutrients.
General Mechanisms for Solute Transport Across the Tonoplast of Plant Vacuoles: a Patch-Clamp Survey of Ion Channels and Proton Pumps

The electrical properties of the tonoplast from a large variety of plant materials such as mesophyll cells, storage cells, tumor cells, suspension cultured cells, guard cells, coleoptile cells, and liverwort cells have been investigated using the patch-clamp technique. Whole-vacuole recordings were employed to study the dynamics of an ATP-dependent proton pump by directly measuring the electrogenic currents. The addition of Mg-ATP induced an inwardly directed current which depolarized the tonoplast (the vacuole becoming positive inside). Furthermore, voltage-dependent passive ion fluxes were analyzed using whole vacuoles and isolated membrane patches. Whole-vacuolar currents and single-channel currents were induced at hyperpolarizing potentials, whereas currents decreased at positive trans-tonoplast potentials. The electrical properties of the tonoplast of vacuoles from various plant tissues were similar and it was concluded that ion fluxes across the tonoplast follow the same general mechanisms.
Subordinate male black howler monkey (Alouatta pigra) responses to loud calls: Experimental evidence for the effects of intra-group male relationships and age

When assessing a group's overall fighting ability, functional group size (i. e. the number of cooperative members willing to confront opponents) may be more important than actual group size. Despite obvious benefits, group members do not always act in a collective manner. For example, participation by subordinate male black howler monkeys (Alouatta pigra) in natural group-level contests is highly variable. Using playback experiments, we examined whether alpha-subordinate relationships, number of intruders, or age affected subordinate contest participation. Long-term census data were used to estimate the nature and duration of intra-group male associations. Some subordinate males had long-term relationships with the alpha that existed prior to residence in the current group or they were the alpha male's grown sons. Other subordinate males were in more recent associations with the alpha that formed under seemingly antagonistic circumstances (e. g. the deposed alpha or his grown sons). We found that subordinate males in long-term alpha-subordinate associations had stronger howling and approach responses than males in short-term associations. Younger long-term associates had the strongest reactions to simulated intruders, similarly aged shortterm associates rarely responded, and older males in both association categories responded at intermediate levels. We discuss the variable strategies of subordinate male black howlers and suggest that males who were more likely to participate in group-defence might be gaining direct or indirect fitness benefits by group living.
Geometric morphometrics shows differences and similarities in skull shape between the red and giant pandas

A morphometric analysis of the skull of the red or lesser panda, Aiulurus fulgens (Ailuridae), and the giant panda, Ailuropoda melanoleuca (Ursidae), was performed for evaluating the importance of natural selection and phylogenetic constraints in shaping the convergent morphological adaptations of these peculiar carnivores for feeding on bamboo. Principal components and discriminant analyses of landmark data was used in a comparative study across the families Procyonidae, Ursidae and Ailuridae. Skull morphospaces show that major patterns of morphological variation among these arctoid carnivorans correlate with differences in their feeding behavior. More specifically, this study has shown an extreme convergence in skull shape between the two bamboo specialists. Following the most recent molecular and morphological phylogenies, as well as the poor evidence from the fossil record, it seems highly improbable that homology could explain the shared morphology of the giant and red pandas, which lineages diverged ∼40 million years ago. On the contrary, most phylogenetic and paleontological data suggest that convergent or parallel evolution (homoplasy) would be the evolutionary process shaping the common morphological traits of these unusual carnivorans. Therefore, the overall resemblance in skull shape between the giant and red pandas was probably driven by extrinsic factors (natural selection and adaptation for feeding on bamboo) as well as by intrinsic ones (the shared developmental pathway of the carnivoran skull, which posed some biomechanical constraints on the direction of the evolution of pandas).
Changes with maturity in fibre composition and levels of extractable polyphenols in Greek browse: effects on in vitro gas production and in sacco dry matter degradation

Neutral and acid detergent fibre (NDF, ADF), lignin, crude protein (CP), total extractable phenols (TEPH), tannins (TETa), condensed tannins (vanillin assay TECTa; proanthocyanidins TEPAs) in the leaves of spring Phyllirea media (SPRG) or early summer (ESUM) and early autumn (EAUT) Carpinus duinensis, Quercus coccifera and Fraxinus ornus were studied. Gas production (in vitro) and dry matter (DM) degradation (in sacco) were also studied after incubation for up to 96 h. Concentrations of TEPH, TETa, TECTa, TEPAs and the fibre components were variable (P 0·05). Concentrations of phenolics were related negatively but more significantly to gas production than to DM degradation (in sacco). Therefore, the gas test was considered to be more efficient than the nylon bag technique for the identification of feeds with antinutritive factors. Based on their phenolic content and gas production or DM degradation, the nutritive value of P media = F ornus (ESUM and EAUT) > C duinensis = Q coccifera (ESUM) > C duinensis = Q coccifera (EAUT). It was concluded that the decline in CP with maturity could make nitrogen the factor limiting intake and digestibility. This would be accentuated with an increase in the concentration of phenolics, particularly tannins.
The effects of air‐borne nitrogen pollutants on species diversity in natural and semi‐natural European vegetation

The effects of increased atmospheric nitrogen inputs, from both NOy and NHx, on diversity in various semi‐natural and natural ecosystems are reviewed. The severity of these impacts depends on abiotic conditions (e.g. buffering capacity, soil nutrient status and soil factors that influence the nitrification potential and nitrogen immobilization rate) in the particular system. The sensitivity of fresh water ecosystems, wetlands and bogs, species‐rich grasslands, heathlands and field layer of forests, all of which have conservational value, are discussed in detail. The most important effects of nitrogen deposition are: (i) accumulation of nitrogenous compounds resulting in enhanced availability of nitrate or ammonium; (ii) soil‐mediated effects of acidification; and (iii) increased susceptibility to secondary stress factors. Long‐term nitrogen enrichment has gradually increased the availability of nitrogen in several vegetation types, leading to competitive exclusion of characteristic species by more nitrophilic plants, especially under oligo‐ to mesotrophic soil conditions. Soil acidification (with losses of buffering capacity and increased concentrations of toxic metals) is especially important after nitrification of ammonium in weakly buffered environments: acid‐resistant plant species then become dominant at the expense of the often rare plants typical of intermediate pH. The related change in the balance between ammonium and nitrate may also affect the performance of several species. The susceptibility of plant species to secondary stress factors (pathogens; frost and drought) may be affected by air‐borne nitrogen but data are only available for a few communities (e.g. dry heathlands). Most global biodiversity is contained within natural and semi‐natural vegetation. It is thus crucial to control emissions of nitrogenous compounds to the atmosphere, in order to reduce or prevent effects on diversity in these systems. Most research has focused on acidification in forestry stands and lakes and on the effects on trees. We highlight serious gaps in knowledge of other ecosystems.
Modulation of Esterase and Amidase Activity of Subtilisin Bacillus lentus by Chemical Modification of Cysteine Mutants

For synthetic applications of proteases, such as for peptide coupling, a combination of high esterase and low amidase activities is required. While achieving such specificity has been a long-standing goal, the decreases in amidase activity achieved to date have often also been accompanied by decreases in esterase activity. In the current study, a strategy of combined site-directed mutagenesis and chemical modification was applied to the serine protease subtilisin Bacillus lentus (SBL) to improve its esterase-over-amidase specificity. Using the crystal structure of SBL as a guide, the N62, L217, S166, and M222 active site residues were chosen for mutagenesis to cysteine and subsequent modification by alkyl methanethiosulfonate reagents. An initial rapid, combinatorial screen of the chemically modified mutant enzymes (CMMs) generated and, of their parent cysteine mutants, identified 25 promising candidates which were then subjected to detailed kinetic evaluations. Of these CMM and mutant enzymes, 20 exhibit.
ACCUMULATION OF β‐CAROTENE IN HALOTOLERANT ALGE: PURIFICATION AND CHARACTERIZATION OF β‐CAROTENE‐RICH GLOBULES FROM DUNALIELLA BARDAWIL (CHLOROPHYCEAE) 1

Dunaliella bardawil Ben‐Amotz & Avron, but not most other Dunaliella species, has a unique property of being able to accumulate, in addition to glycerol, large amounts of β‐carotene when cultivated under appropriate conditions. These include high light intensity, a high sodium chloride concentration, nitrate deficiency and extreme temperatures. Under conditions of maximal carotene accumulation D. bardawil contains at least 8% of its dry weight as β‐carotene while D. salina grown under similar conditions contains only about 0.3%. Electron micrographs of D. bardawil grown under conditions of high β‐carotene accumulation show many β‐carotene containing globules located in the interthylakoid spaces of the chloroplast. The same algae grown under conditions where β‐carotene does not accumulate, contain few to no β‐carotene globules. The β‐carotene‐rich globules were released from the algae into an aqueous medium by a two‐stage osmotic shock technique and further purified by centrifugal ion on 10% sucrose. The isolated purified globules were shown by electron microscopy to be free of significant contamination and composed of membrane‐free osmiophilic droplets with an average diameter of 150 nm. Reversed phase high performance liquid chromatography of a total pigment extract of the cells revealed the presence of β‐carotene as the major pigment, together with chlorophylls a and b, α‐carotene and the xanthophylls lutein, neoxauthin and zeaxanthin. β‐Carotene accounted for essentially all the pigment in the purified globules. Analysis of the algal and globule β‐carotene fractions by HPLC showed that the β‐carotene was composed of approximately equal amounts of all‐trans β‐carotene and of its 9‐cis isomer. Intact D. bardawil cells contained on a dry weight basis about 30% glycerol, 30% protein, 18% lipid, 11% carbohydrate, 9%β‐carotene and 1% chlorophyll. The β‐carotene globules were composed of practically only neutral lipids, more than half of which was β‐carotene. It is suggested that the β‐carotene globules may serve to protect D. bardawil against injury by the high intensity irradiation to which this alga is usually exposed in nature.
Evaluation of bacterial antagonists for the management of rhizome rot of cardamom (Elettaria cardamomum Maton).

Among the 90 rhizobacterial isolates screened against rhizome rot pathogens (Pythium vexans, Fusarium oxysporum and Rhizoctonia solani) of cardamom (Elettaria cardamomum) two bacterial strains viz., Pseudomonas fluorescens Pf 51 and Bacillus subtilis B45 were highly inhibitory. P. fluorescens Pf 51 exhibited highest inhibition (42.5%, 44.2% and 41.4% respectively) against P. vexans, F. oxysporum and R. solani. B. subtilis B45 also exhibited highest inhibition (43.2%, 41.2% and 42.4% respectively) against these three pathogens. P. fluorescens Pf51 was compatible with B. subtilis Bs 45. Peat formulation supported the survival of both the strains up to 270 days with a viable population of 4.3 × 107 cfu g-1 and 6.2 × 107 cfu g-1 respectively. Application of antagonists in combination with rhizome bacterization and soil application resulted in 54.0% reduction in rhizome rot over control as compared to single method such as rhizome bacterization (43.0%) or soil application (39.0%). Application of copper oxychloride and carbendazim resulted in 68.0% reduction of rhizome rot. Maximum height (167.21 cm) and number of tillers (30.14) were recorded due to the application of mixture of both the strains through rhizome bacterization and soil application.
Genetic studies of α-amylase isozymes in wheat VII. Variation in diploid ancestral species and phylogeny of tetraploid wheat

In order to investigate the phylogeny of polyploid wheat, the genetic variation of α-amylase isozymes in 127 strains of two diploid wheat species and five Aegilops species belonging to section Sitopsis was analyzed. Three types of zymogram were detected in 39 strains of Triticum monococcum and three other different types were detected in another diploid wheat, T. urartu. Two varieties of Ae. speltoides, var. ligustica and var. aucheri (subsection Truncata), were similar to each other and showed wide variation of zymograms. Sixteen strains of Ae. longissima and 13 strains of Ae. sharonensis were each grouped into four types. Ten strains of Ae. bicornis were grouped into three types, each including three or four strains. On the other hand, zymograms from five strains of Ae. searsii, which was formerly treated as a variety of Ae. longissima, were very different from those of Ae. longissima. In contrast to subsection Truncata, the zymogram types were rather simple and similar among species in subsection Emarginata (Ae. longissima, Ae. sharonensis, and Ae.bicornis) except for Ae. searsii. Finally, the phylogeny of tetraploid wheat was discussed on the basis of the results presented here along with those of the previous authors.
Leaf Analysis in Strawberries: Effects of Cultivar, Plant Age, and Sampling Time on Nutrient Levels

ABSTRACT In a four year survey, two control methods of nitrogen (N) supply in strawberry were combined. It was found that Nmin analysis could be used as a measurement of control from the beginning of the season, indicating the need of additional N supply. Leaf dry matter analysis, taken during beginning of flowering, could be used as an indicator thus making it possible to make corrections within the season, if needed. This study clearly showed variation in nutrient values among years and cultivars, whereas differences among plants of different age were not significant. It was concluded that the use of Nmin and leaf dry matter analyses combined might make corrections in nitrogen fertilization within the same year possible, and a new standard for leaf nutrient content, based on samples taken during beginning of flowering, was suggested.
Diel Littoral–Pelagic Movements by Juvenile Bluegills in a Small Lake

AbstractDiel littoral–pelagic migrations by juvenile fish have been suggested as a mechanism that optimizes the trade-off between predation risk and foraging return in open-water habitats. However, previous study designs have not been able to conclusively demonstrate this behavior in the field. We applied a horizontally oriented hydroacoustic transducer, set at the open-water edge of littoral vegetation, to observe diel fish behavior during two summers in Ridge Lake, Illinois, where the fish community is dominated by Largemouth Bass Micropterus salmoides and Bluegills Lepomis macrochirus. Based on acoustically tracked targets, most juvenile fish moved away from vegetated habitat at night and towards vegetation during the day. A greater number of predator-sized fish were observed in the open water during the day than at night and weak acoustic targets, most likely zooplankton, were more abundant in the open-water habitat at night. Therefore, it is likely that the reduced predator abundance and/or activity .
Molecular genetics of bacteria

Introduction Part I Genes: Replication and Expression Introduction to macromolecular synthesis: chromosome structure and replication Introduction to macromolecular synthesis: gene expression Part II Genes and Genetic Elements Mutations inbacteria Plasmids Conjugation Transformation Bacteriophages Transportation and nonhomologous recombination Part III Genes in Action Molecular basis of recombination DNA repair and mutagenesis Regulation of gene expression Global regulatory mechanisms Part IV: Genes in Practice Genetic analysis in phage Genetic Analysis in bacteria Recombinant DNA techniques and cloning bacterial genes Molecular genetic analysis and biotechnology