Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth?

Here we describe recent breakthroughs in our understanding of microbial life in dry volcanic tephra (“soil”) that covers much of the surface area of the highest elevation volcanoes on Earth. Dry tephra above 6000 m.a.s.l. is perhaps the best Earth analog for the surface of Mars because these “soils” are acidic, extremely oligotrophic, exposed to a thin atmosphere, high UV fluxes, and extreme temperature fluctuations across the freezing point. The simple microbial communities found in these extreme sites have among the lowest alpha diversity of any known earthly ecosystem and contain bacteria and eukaryotes that are uniquely adapted to these extreme conditions. The most abundant eukaryotic organism across the highest elevation sites is a Naganishia species that is metabolically versatile, can withstand high levels of UV radiation and can grow at sub-zero temperatures, and during extreme diurnal freeze–thaw cycles (e.g. ??10 to +?30 °C). The most abundant bacterial phylotype at the highest dry sites sampled (6330 m.a.s.l. on Volcán Llullaillaco) belongs to the enigmatic B12-WMSP1 clade which is related to the Ktedonobacter/Thermosporothrix clade that includes versatile organisms with the largest known bacterial genomes. Close relatives of B12-WMSP1 are also found in fumarolic soils on Volcán Socompa and in oligotrophic, fumarolic caves on Mt. Erebus in Antarctica. In contrast to the extremely low diversity of dry tephra, fumaroles found at over 6000 m.a.s.l. on Volcán Socompa support very diverse microbial communities with alpha diversity levels rivalling those of low elevation temperate soils. Overall, the high-elevation biome of the Atacama region provides perhaps the best “natural experiment” in which to study microbial life in both its most extreme setting (dry tephra) and in one of its least extreme settings (fumarolic soils).     

Greenhouse gas fluxes of typical northern subtropical forest soils: Impacts of land use change and reduced precipitation北大核心CSCD

Aims: It is important to study the effects of land use change and reduced precipitation on greenhouse gas fluxes (CO2, CH4 and N2O) of forest soils. Methods: The fluxes of CO2, CH4 and N2O and their responses to environmental factors of primary forest soil, secondary forest soil and artificial forest soil under a reduced precipitation regime were explored using the static chamber and gas chromatography methods during the period from January to December in 2014. Important findings: Results indicate that CH4 uptake of primary forest soil ((-44.43 ± 8.73) μg C·m-2·h-1) was significantly higher than that of the secondary forest soil ((-21.64 ± 4.86) μg C·m-2·h-1) and the artificial forest soil ((-10.52 ± 2.11) μg C·m-2·h-1). CH4 uptake of the secondary forest soil ((-21.64 ± 4.86) μg C·m-2·h-1) was significantly higher than that of the artificial forest ((-10.52 ± 2.11) μg C·m-2·h-1). CO2 emissions of the artificial forest soil ((106.53 ± 19.33) μg C·m-2·h-1) were significantly higher than that of the primary forest soil ((49.50 ± 8.16) μg C·m-2·h-1) and the secondary forest soil ((63.50 ± 5.35) μg C·m-2·h-1) (p < 0.01). N2O emissions of the secondary forest soil ((1.91 ± 1.22) ug N·m-2·h-1) were higher than that of the primary forest soil ((1.40 ± 0.28) μg N·m-2·h-1) and the artificial forest soil ((1.01 ± 0.86) μg N·m-2·h-1). Reduced precipitation (-50%) had a significant inhibitory effect on CH4 uptake of the artificial forest soil, while it enhanced CO2 emissions of the primary forest soil and the secondary forest soil. Reduced precipitation had a significant inhibitory effect on CO2 emissions of the artificial forest soil and N2O emissions of the secondary forest (p < 0.01). Reduced precipitation promotes N2O emissions of the primary forest soil and the artificial forest soil. CH4 uptake of the primary forest and the secondary forest soil increased significantly with the increase of soil temperature under natural and reduced precipitation. CO2 and N2O emission fluxes of the primary forest soil, secondary forest soil and artificial forest soil were positively correlated with soil temperature (p < 0.05). Soil moisture inhibited CH4 uptake of the secondary forest soil and the artificial forest soil (p < 0.05). CO2 emissions of the primary forest soil were significantly positively correlated with soil moisture (p < 0.05). N2O emissions of primary forest soil and secondary forest soil were significantly correlated with the nitrate nitrogen content (p < 0.05). It was implied that reduced precipitation and land use change would have significant effects on greenhouse gas emissions of subtropical forest soils.     

Estimation of utilisable crude protein at the duodenum of dried distillers’ grains with solubles using a modified gas test

The objective of this study was to characterise the variation of utilisable crude protein at the duodenum (uCP) of dried distillers’ grains with solubles (DDGS) for ruminants using a modified gas test and to predict the uCP in DDGS based on chemical composition. Thirteen samples originating from wheat, maize, barley or blends of different substrates were studied. The in vitro uCP was estimated using the modified Hohenheim gas test (moHGT). Samples were incubated in rumen fluid for 8 h, 24 h and 48 h followed by ammonia distillation. The obtained values were compared to reference values of uCP (based on the contents of crude protein (CP), in situ undegraded CP and metabolisable energy). The reference and in vitro values of uCP were calculated according to passage rates of 2, 5 and 8%/h (i.e., uCP₂, uCP₅ and uCP₈, respectively). The in vitro uCP₈ ranged from 214 to 320 g/kg DM and reference values from 158 to 302 g/kg DM. The in vitro uCP₂ was on average lower (by 7 g/kg DM) and in vitro uCP₈ was higher (by 56 g/kg DM) than their respective reference values. The in vitro uCP₅ and uCP₈ were correlated with reference values and the correlations were improved with increasing passage rates. When the differences of uCP content between in vitro and reference values were related to CP fractions, they increased with increasing content of CP fraction A and decreasing content of CP fraction B3 for uCP₈. The prediction of uCP values from chemical composition was not reliable. It was concluded that uCP can be predicted on the basis of the moHGT method and CP fractions. The accuracy of prediction improved upon the inclusion of CP fractions and neutral-detergent insoluble nitrogen. The present study revealed a significant variation in the uCP content of DDGS, which should be considered when formulating rations for dairy cows.     

The study of the brain’s organization of creativity: I. Development of a psychological test

This article describes an original psychological test on verbal creative work comprising a number of tasks designed to study the organization of creative processes in human brain with the help of positron emission tomography (PET) and electroencephalography (EEG). When approved in a group of 30 healthy volunteers, the test revealed principal cognitive strategies of performing creative tasks which formed the basis for elaborating criteria for selecting subjects for physiological study. Empirical substantiation of the proposed test showed its validity for the use in the psychophysiological investigation of creative work.     

Astrocatalysis—Abiogenic synthesis and chemical evolution at pregeological stages of the Earth’s formation

The Earth’s biosphere appeared in a self-organization process along with the appearance of the Solar System. It is shown, based on the methods of self-organization examination and existing knowledge, that major stages of the chemical evolution in the early development of the biosphere include the “cold prehistory of life” in dense molecular nebulae, “pre-planetary chemocoenosis,” “RNA-world” in a circumsolar nebula, and primary biocoenoses of protocells (life) on the planetary bodies. Estimates for carbon in the primordial biosphere on the young Earth’s surface give 2.4 × 10¹⁹ kg. The decay of the primordial Earth’s biomass and biogeochemical cycles in 2.5 Myr led to the “planet of bacteria” with 2.0 × 10¹⁵ kg of biota in the Proterozoic (at the time of an oxygenated atmosphere). The main parameters (pressure, temperature, and state of catalytic solid phase) are estimated for these stages of the early evolution of life. It is shown that the abiogenic synthesis of the primordial matter was preformed in the Solar System on a grand scale with practically every atom in nanoparticles-catalysts participating. Selection among catalytically active nanoparticles worked towards the ability to synthesize high molecular compounds in a protoplanetary disk. Autocatalysts participated in the preplanetary chemical evolution, beginning from such simple substances as ethylene or glycolaldehyde. Primary synthesis of autocatalysts depended on external sources of energy, e.g., on ultraviolet radiation.     

Minimization of the Wilson’s Central Terminal voltage potential via a genetic algorithm

Objective

The Wilson Central Terminal (WCT) is an artificially constructed reference for surface electrocardiography, which is assumed to be near zero and steady during the cardiac cycle; namely it is the simple average of the three recorded limbs (right arm, left arm and left leg) composing the Einthoven triangle and considered to be electrically equidistant from the electrical center of the heart. This assumption has been challenged and disproved in 1954 with an experiment designed just to measure and minimize WCT. Minimization was attempted varying in real time the weight resistors connected to the limbs. Unfortunately, the experiment required a very cumbersome setup and showed that WCT amplitude could not be universally minimized, in other words, the weight resistors change for each person. Taking advantage of modern computation techniques as well as of a special ECG device that aside of the standard 12-lead Electrocardiogram (ECG) can measure WCT components, we propose a software minimization (genetic algorithm) method using data recorded from 72 volunteers.

Result

We show that while the WCT presents average amplitude relative to lead II of 58.85% (standard deviation of 30.84%), our minimization method yields an amplitude as small as 7.45% of lead II (standard deviation of 9.04%).

     

Experimental determination of the spatial scale of a prey patch from the predator’s perspective

Foraging theory predicts that predators should prefer foraging in habitat patches with higher prey densities. However, density depends on the spatial scale at which a “patch” is defined by an observer. Ecologists strive to measure prey densities at the same scale that predators do, but many natural landscapes lack obvious, well-defined prey patches. Thus one must determine the scale at which predators define patches of prey. We estimated the scale at which guppies, Poecilia reticulata, selected patches of zooplankton prey using a behavioral assay. Guppies could choose between two prey arrays, each manipulated to have a density that depended on the spatial scale at which density was calculated. We estimated the scale of guppy foraging by comparing guppy preferences across a series of trials in which we systematically varied the scale associated with “high” prey density. This approach enables the application of foraging theory to non-discrete habitats and prey landscapes.     

Can the use of natural biostimulants be a potential means of phytoremediating contaminated soils from goldmines in South Africa?

Biostimulants offer great potential in improving phytoremediation of contaminated soils. In the current greenhouse-based study, Brassica juncea seedlings grown on soils collected from Krugersdorp Goldmine and the adjourning areas (a Game Reserve and private farmland) were supplemented with different biostimulants (Kelpak® = KEL, vermicompost leachate = VCL, smoke-water = SW). Indole-3-butyric acid (IBA) was included in the study for comparative purposes because these biostimulants are known to enhance rooting. Prior to the pot trial, concentrations of elements in the three soil types were determined using Inductively Coupled Plasma-Optical Emission Spectroscopy. Plants were harvested after 105 days and the growth and concentrations of elements in the various plant organs were determined. TheB. juncea seedlings with and without biostimulants did not survive when growing in soil from the Krugersdorp Goldmine. The Game Reserve and private farmland soils supplemented with KEL produced the highest plant biomass and the lowest accumulation of metals in the organs of B. juncea. High concentrations (>13 000 mg kg^?1) of zinc and aluminium were quantified in the roots of IBA-supplemented soils from the Game Reserve. Generally, IBA and SW enhanced the phytoremediation of B. juncea due to elevated levels of elements that accumulated in their different organs.     

The Bryosphere: An Integral and Influential Component of the Earth’s Biosphere

A significant fraction of the Earth’s land surface is dominated by bryophytes. Research on carbon and nitrogen budgets of tundra, boreal, and peatland ecosystems has demonstrated the important role of mosses in understanding global change. Bryophytes are also habitat to a highly diverse microbiota that plays a key role in the function of these ecosystems. Here we define the term bryosphere to emphasize the combined role of mosses and their associated organisms in the functioning of ecosystems from local to global scales. In this minireview, we emphasize the value of the bryosphere as a spatially bounded, whole ecosystem that integrates aboveground and belowground processes, and we highlight the potential of the bryosphere as a natural model system (NMS) to assist in the study of environmental change on biodiversity and ecosystem functioning. We propose a formal definition of the bryosphere, attempt to summarize the current state of knowledge of the bryosphere, and discuss how the bryosphere can be a complex yet tractable system under an NMS framework. Recent use of the bryosphere as an NMS has shown how alterations in food web structure can affect ecosystem function in a manner that, although predicted by theory, has remained largely untested by experiment. An understanding of the biodiversity, ecosystem functioning, and adaptation of the bryosphere can be advanced by manipulative experiments coupled with a blend of techniques in molecular, physiological, community, and ecosystem ecology. Although studies described herein have demonstrated the utility of the bryosphere NMS for addressing ecological theory, the bryosphere is an underutilized system with exceptional promise.     

Masson’s tumor of the kidney: a case report

Background

Intravascular papillary endothelial hyperplasia (known also as Masson’s tumor) is a benign vascular lesion that commonly occurs in the skin and is rarely found in solid organs, especially in the kidney. In what follows, we will look into the first case of an unexpectedly diagnosed Masson’s tumor of the kidney presenting as a suspicious renal cyst.

Case presentation

A 61-year-old Arab man presented with a left renal cyst, incidentally revealed by ultrasonography. The laboratory values were unremarkable. Computed tomography and magnetic resonance imaging demonstrated a 38 mm left renal midportion Bosniak IV cyst. Our patient underwent a radical nephrectomy. Histopathology revealed the diagnosis of intravascular papillary endothelial hyperplasia. There was no recurrence detected after 9 years of follow-up.

Conclusions

Renal intravascular papillary endothelial hyperplasia is a rare benign tumor which can mimic a suspicious renal mass on radiological findings. Thus, this entity should be considered more often in the thick of the diagnostic possibilities in order to avoid unnecessary nephrectomies.

     

α-Glucosidase from a strain of deep-sea Geobacillus: a potential enzyme for the biosynthesis of complex carbohydrates

An α-glucosidase from Geobacillus sp. strain HTA-462, one of the deepest sea bacteria isolated from the sediment of the Mariana Trench, was purified to homogeneity and estimated to be a 65-kDa protein by SDS-PAGE. At low ion strength, the enzyme exists in the homodimeric form (130 kDa). It is a thermo- and alkaline-stable enzyme with a half-life of 13.4 h and a maximum hydrolytic activity at 60°C and pH 9.0 in 15 mM glycine–NaOH buffer. The enzyme exclusively hydrolyzed α-1,4-glycosidic linkages of oligosaccharides in an exo-type manner. The enzyme had an overwhelming transglycosylation activity and glycosylated various non-sugar molecules when maltose was used as a sugar donor. It converted maltose to isomaltose. The gene encoding the enzyme was cloned and sequenced. The recombinant enzyme could be extracellularly overproduced by Bacillus subtilis harboring its gene and preserved the primary properties of the native enzyme. Site-directed mutagenesis experiments showed that Asp98 is essential for the enzyme activity in addition to Asp199, Asp326, and Glu256.     

From bench to bed: the potential of stem cells for the treatment of Parkinson’s disease

Parkinson’s disease (PD) is the most common movement disorder. The neuropathology is characterized by the loss of dopamine neurons in the substantia nigra pars compacta. Transplants of fetal/embryonic midbrain tissue have exhibited some beneficial clinical effects in open-label trials. Neural grafting has, however, not become a standard treatment for several reasons. First, the supply of donor cells is limited, and therefore, surgery is accompanied by difficult logistics. Second, the extent of beneficial effects has varied in a partly unpredictable manner. Third, some patients have exhibited graft-related side effects in the form of involuntary movements. Fourth, in two major double-blind placebo-controlled trials, there was no effect of the transplants on the primary endpoints. Nevertheless, neural transplantation continues to receive a great deal of interest, and now, attention is shifting to the idea of using stem cells as starting donor material. In the context of stem cell therapy for PD, stem cells can be divided into three categories: neural stem cells, embryonic stem cells, and other tissue-specific types of stem cells, e.g., bone marrow stem cells. Each type of stem cell is associated with advantages and disadvantages. In this article, we review recent advances of stem cell research of direct relevance to clinical application in PD and highlight the pros and cons of the different sources of cells. We draw special attention to some key problems that face the translation of stem cell technology into the clinical arena.     

Time Evolution of the Macroscopic Characteristics of a Thin Current Sheet in the Course of Its Formation in the Earth’s Magnetotail

A numerical model is developed that allows tracing the time evolution of a current sheet from a relatively thick current configuration with isotropic distributions of the pressure and temperature in an extremely thin current sheet, which plays a key role in geomagnetic processes. Such a configuration is observed in the Earth’s magnetotail in the stage preceding a large-scale geomagnetic disturbance (substorm). Thin current sheets are reservoirs of the free energy released during geomagnetic disturbances. The time evolution of the components of the pressure tensor caused by changes in the structure of the current sheet is investigated. It is shown that the pressure tensor in the current sheet evolves in two stages. In the first stage, a current sheet with a thickness of eight to ten proton Larmor radii forms. This stage is characterized by the plasma drift toward the current sheet and the Earth and can be described in terms of the Chu–Goldberger–Low approximation. In the second stage, an extremely thin current sheet with an anisotropic plasma pressure tensor forms, due to which the system is maintained in an equilibrium state. Estimates of the characteristic time of the system evolution agree with available experimental data.     

Pattern and variation of C:N:P ratios in China’s soils: a synthesis of observational data

Inspired by previous studies that have indicated consistent or even well-constrained (relatively low variability) relations among carbon (C), nitrogen (N) and phosphorus (P) in soils, we have endeavored to explore general soil C:N:P ratios in China on a national scale, as well as the changing patterns of these ratios with soil depth, developmental stages and climate; we also attempted to determine if well-constrained C:N:P stoichiometrical ratios exist in China’s soil. Based on an inventory data set of 2,384 soil profiles, our analysis indicated that the mean C:N, C:P and N:P ratios for the entire soil depth (as deep as 250 cm for some soil profiles) in China were 11.9, 61 and 5.2, respectively, showing a C:N:P ratio of ~60:5:1. C:N ratios showed relatively small variation among different climatic zones, soil orders, soil depth and weathering stages, while C:P and N:P ratios showed a high spatial heterogeneity and large variations in different climatic zones, soil orders, soil depth and weathering stages. No well-constrained C:N:P ratios were found for the entire soil depth in China. However, for the 0–10 cm organic-rich soil, which has the most active organism–environment interaction, we found a well-constrained C:N ratio (14.4, molar ratio) and relatively consistent C:P (136) and N:P (9.3) ratios, with a general C:N:P ratio of 134:9:1. Finally, we suggested that soil C:N, C:P and N:P ratios in organic-rich topsoil could be a good indicator of soil nutrient status during soil development.     

Finding autophagy: It’s a question of how you look at it

To tell the truth, I find it difficult to work when flying, or even when sitting in an airport for an extended period of time. So, typically I take along a book to read. And when I truly cannot concentrate, for example when a flight is considerably delayed, I have even been known to resort to word puzzles. Depending on the type, they do not require much attention (that is, you can pick up right where you left off after you glance at the flight status screen for the twentieth or so time, even though you know nothing has changed), or effort (although you need to use a pen or pencil, not a keyboard), but nonetheless they can keep your mind somewhat occupied. I even rationalize doing them based on the assumption that they are sharpening my observational/pattern-finding skills. One type of word puzzle that is particularly mindless, but for that very reason I still enjoy in the above circumstances, is a word search; you are given a grid with letters and/or numbers, and a list of “hidden” terms, and you circle them within the grid, crossing them off the list as you go along. I do admit that the categories of terms used in the typical word searches can become rather mundane (breeds of dog, types of food, words that are followed by “stone,” words associated with a famous movie star, words from a particular television show, etc.). Therefore, on one of my last seminar trips I decided to generate my own word search, using the category of autophagy.     

Liebig’s law of the minimum applied to a greenhouse gas: alleviation of P-limitation reduces soil N2O emission

Background and aims

Emission of the greenhouse gas (GHG) nitrous oxide (N₂O) are strongly affected by nitrogen (N) fertilizer application rates. However, the role of other nutrients through stoichiometric relations with N has hardly been studied. We tested whether phosphorus (P) availability affects N₂O emission. We hypothesized that alleviation of plant P-limitation reduces N₂O emission through lowering soil mineral N concentrations.

Methods

We tested our hypothesis in a pot experiment with maize (Zea mays L.) growing on a P-limiting soil/sand mixture. Treatment factors included P and N fertilization and inoculation with Arbuscular Mycorrhizal Fungi (AMF; which can increase P uptake).

Results

Both N and P fertilization, as well as their interaction significantly (P?<?0.01) affected N₂O emission. Highest N₂O emissions (2.38 kg N₂O-N ha^?1) were measured at highest N application rates without P fertilization or AMF. At the highest N application rate, N₂O fluxes were lowest (0.71 kg N₂O-N ha^?1) with both P fertilization and AMF. The N₂O emission factors decreased with 50 % when P fertilization was applied.

Conclusions

Our results illustrate the importance of the judicious use of all nutrients to minimize N₂O emission, and thereby further underline the intimate link between sound agronomic practice and prudent soil GHG management.     

Going with the flow: a brief history of the study of the honeybee’s navigational ‘odometer’

Honeybees navigate to a food source using a sky-based compass to determine their travel direction, and an odometer to register how far they have travelled. The past 20 years have seen a renewed interest in understanding the nature of the odometer. Early work, pioneered by von Frisch and colleagues, hypothesized that travel distance is measured in terms of the energy that is consumed during the journey. More recent studies suggest that visual cues play a role as well. Specifically, bees appear to gauge travel distance by sensing the extent to which the image of the environment moves in the eye during the journey from the hive to the food source. Most of the evidence indicates that travel distance is measured during the outbound journey. Accumulation of odometric errors is restricted by resetting the odometer every time a prominent landmark is passed. When making detours around large obstacles, the odometer registers the total distance of the path that is flown to the destination, and not the “bee-line” distance. Finally, recent studies are revealing that bees can perform odometry in three dimensions.