Evaluation of methods for extraction of bacteria from soil

Abstract Several methods for dispersion of soil were tested for possible use in procedures for extraction of bacteria. Physical cell damage on cells and efficiency in extraction of indigenous cells from soil, were investigated. Cell damage by the dispersion methods was investigated by measuring the physical cell integrity and viability of pure cultures of Escherichia coli and Bacillus subtilis , as well as soil bacteria extracted from soil, when dispersed in slurries of γ-sterilized soil. Separation of bacteria and soil particles on the basis of buoyant density was conducted with the nonionic density gradient medium Nycodenz. When slurries of γ-sterilized soil with added pure cultured cells were centrifuged (10000 × g ) over cushions of Nycodenz (1.3 g ml⁻¹), practically all the added cells were recovered in a layer on top of the cushion. This proves that a reversible attachment and cosedimentation is not an important phenomenon in this procedure. The efficiency of the different dispersion methods for the extraction of indigenous soil bacteria, was assessed after separation of dislodged and attached soil bacteria. This separation was done either on the basis of sedimentation rate by low speed centrifugation, or buoyant density by Nycodenz density gradient centrifugation. The physical dispersion by ultrasonic treatment and chemical dispersion by the use of a chelating agent together with a detergent, were inferior to physical dispersion either by Waring blender (for large volumes) or a rotating rubber pestle treatment (for smaller volumes). The physical dispersion did not appear to be destructive to the cells tested.     

Blockage errors in studies of the effect of wind on thermoregulatory responses

1. 1.The presence of an animal in a wind tunnel increases the effective wind velocity, and so increases heat transfer rates.

2. 2.Potentially significant errors in thermal conductance and thermoregulatory metabolism measurements may result.

3. 3.In a given wind tunnel metabolism chamber, these errors are size dependent and thus may lead to invalid allometric or adaptive interpretations of data.

4. 4.The errors are also sensitive to the shape, orientation, and characteristics of the fur or feather insulation of the animal. Thus, only approximate guidelines can be given for choosing correction factors.

NO and N2O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains

Fungal denitrification is claimed to produce non-negligible amounts of N₂O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with . Enzymatic reduction of (NIR) and NO (NOR) was assessed by correcting measured NO- and N₂O-kinetics for abiotic NO- and N₂O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N₂O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N₂O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N₂O as a response to an abiotic NO production from the medium.     

Letter: Notes on "heat loss from a Newtonian animal"

Parker, Baker &; Smith (1972) have demonstrated mathematically that given the evolution of sexual reproduction, disruptive selection for the production of either many small gametes or a few large gametes may occur, resulting in a stable polymorphism of “sperm” and “egg” producers. Their model for the evolution of anisogamy requires only that zygote fitness (F) increase steeply with increases in zygote volume (V) (for Foc∝ V^x, x must be greater than 1·5) and that a sufficiently broad range of zygote productivity-size variants exist in the population (the higher the value of x, the broader the range needed). They suggest that anisogamy is almost universal in multicellular organisms but relatively rare in unicellular organisms because only for the former is an investment in extra gametic reserves at the expense of the number of gametes produced likely to be worthwhile in terms of increasing the survival probability of the zygote. In this note a graphical analysis and evidence from the anisogamous Protista will be presented concerning this hypothesis.     

Nitrous Oxide Production and Methane Oxidation by Different Ammonia-Oxidizing Bacteria

Ammonia-oxidizing bacteria (AOB) are thought to contribute significantly to N₂O production and methane oxidation in soils. Most of our knowledge derives from experiments with Nitrosomonas europaea, which appears to be of minor importance in most soils compared to Nitrosospira spp. We have conducted a comparative study of levels of aerobic N₂O production in six phylogenetically different Nitrosospira strains newly isolated from soils and in two N. europaea and Nitrosospira multiformis type strains. The fraction of oxidized ammonium released as N₂O during aerobic growth was remarkably constant (0.07 to 0.1%) for all the Nitrosospira strains, irrespective of the substrate supply (urea versus ammonium), the pH, or substrate limitation. N. europaea and Nitrosospira multiformis released similar fractions of N₂O when they were supplied with ample amounts of substrates, but the fractions rose sharply (to 1 to 5%) when they were restricted by a low pH or substrate limitation. Phosphate buffer (versus HEPES) doubled the N₂O release for all types of AOB. No detectable oxidation of atmospheric methane was detected. Calculations based on detection limits as well as data in the literature on CH₄ oxidation by AOB bacteria prove that none of the tested strains contribute significantly to the oxidation of atmospheric CH₄ in soils.     

Records of ocean sunfish Mola mola along the Norwegian coast spanning two centuries, 1801–2015

Records of the ocean sunfish Mola mola along the Norwegian coast were compiled from all possible sources: literature, media, databases and museums. A total of 216 records were found between 1801 and 2015. They were distributed along the whole coast, except for the most north‐eastern part. Nearly all years with more than five records were after 2000, with 1985 as the only exception and with a maximum of 23 records in 2014. Most, 92·4%, were from July to December. Records from before 1979 were more incidental and random and no sunfish were recorded in 54 separate years between 1879 and 2015. The northernmost record was from 70° 44′ N in December 1881. No relationship between year and latitude was found. Forty‐four per cent of the records were of sunfish caught in fishing gear, 27% were found stranded and 30% were observed alive at sea. A trend of a decrease in numbers of observations of living individuals and an increase in numbers of strandings as dead individuals as autumn progressed was found. Geographical differences in the three categories of observation were also found. Among the specimens whose size was recorded, most were small, <30 kg and 70 cm in total length. Only 10 were heavier than 100 kg, all these were from before 1960. Annual numbers correlated weakly with sea temperatures. This was supported by a weak negative correlation with the North Atlantic Oscillation (NAO) index, because the majority of years since 2000 had a negative NAO.     

Cell type discovery and representation in the era of high-content single cell phenotyping

Background

A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and therapeutic/vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting from the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology.

Results

In this paper, we provide examples of state-of-the-art cellular biomarker characterization using high-content cytometry and single cell RNA sequencing, and present strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies, including “context annotations” in the form of standardized experiment metadata about the specimen source analyzed and marker genes that serve as the most useful features in machine learning-based cell type classification models. We also propose a statistical strategy for comparing new experiment data to these standardized cell type representations.

Conclusion

The advent of high-throughput/high-content single cell technologies is leading to an explosion in the number of distinct cell types being identified. It will be critical for the bioinformatics community to develop and adopt data standard conventions that will be compatible with these new technologies and support the data representation needs of the research community. The proposals enumerated here will serve as a useful starting point to address these challenges.

     

The Kaposi's sarcoma-associated herpesvirus G protein-coupled receptor contains an immunoreceptor tyrosine-based inhibitory motif that activates Shp2

The Kaposi's sarcoma-associated herpesvirus (KSHV) G protein-coupled receptor (vGPCR) is a constitutively active, highly angiogenic homologue of the interleukin-8 (IL-8) receptors that signals in part via the cytoplasmic protein tyrosine phosphatase Shp2. We show that vGPCR contains a bona fide immunoreceptor tyrosine-based inhibitory motif (ITIM) that binds and constitutively activates Shp2.     

Uracil-DNA glycosylase in base excision repair and adaptive immunity: species differences between man and mouse

Genomic uracil is a DNA lesion but also an essential key intermediate in adaptive immunity. In B cells, activation-induced cytidine deaminase deaminates cytosine to uracil (U:G mispairs) in Ig genes to initiate antibody maturation. Uracil-DNA glycosylases (UDGs) such as uracil N-glycosylase (UNG), single strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1), and thymine-DNA glycosylase remove uracil from DNA. Gene-targeted mouse models are extensively used to investigate the role of these enzymes in DNA repair and Ig diversification. However, possible species differences in uracil processing in humans and mice are yet not established. To address this, we analyzed UDG activities and quantities in human and mouse cell lines and in splenic B cells from Ung(+/+) and Ung(-/-) backcrossed mice. Interestingly, human cells displayed ～15-fold higher total uracil excision capacity due to higher levels of UNG. In contrast, SMUG1 activity was ～8-fold higher in mouse cells, constituting ～50% of the total U:G excision activity compared with less than 1% in human cells. In activated B cells, both UNG and SMUG1 activities were at levels comparable with those measured for mouse cell lines. Moreover, SMUG1 activity per cell was not down-regulated after activation. We therefore suggest that SMUG1 may work as a weak backup activity for UNG2 during class switch recombination in Ung(-/-) mice. Our results reveal significant species differences in genomic uracil processing. These findings should be taken into account when mouse models are used in studies of uracil DNA repair and adaptive immunity.