Result Of Biological Processes Research Articles

Characteristics of methanesulfonic acid, non-sea-salt sulfate and organic carbon aerosols over the Amundsen Sea, Antarctica

Abstract. To investigate the characteristics of particulate methanesulfonic acid (MSA(p)), non-sea-salt sulfate (nss SO42-) and organic carbon (OC) aerosols, aerosol and seawater samples were collected over the Southern Ocean (43–70∘ S) and the Amundsen Sea (70–75∘ S) during the ANA06B cruise conducted in the austral summer of 2016 aboard the Korean icebreaker IBR/V Araon. Over the Southern Ocean, the atmospheric MSA(p) concentration was low (0.10±0.002 µg m−3), whereas its concentration increased sharply up to 0.57 µg m−3 in the Amundsen Sea where Phaeocystis antarctica (P. antarctica), a producer of dimethylsulfide (DMS), was the dominant phytoplankton species. Unlike MSA(p), the mean nss SO42- concentration in the Amundsen Sea was comparable to that in the Southern Ocean. Water-soluble organic carbon (WSOC) concentrations over the Southern Ocean and the Amundsen Sea varied from 0.048 to 0.16 and 0.070 to 0.18 µgC m−3, with averages of 0.087±0.038 and 0.097±0.038 µgC m−3, respectively. For water-insoluble organic carbon (WIOC), its mean concentrations over the Southern Ocean and the Amundsen Sea were 0.25±0.13 and 0.26±0.10 µgC m−3, varying from 0.083 to 0.49 and 0.12 to 0.38 µgC m−3, respectively. WIOC was the dominant organic carbon species in both the Southern Ocean and the Amundsen Sea, accounting for 73 %–75 % of the total aerosol organic carbon. WSOC/Na+ and WIOC/Na+ ratios in the fine-mode aerosol particles were higher, especially in the Amundsen Sea where biological productivity was much higher than the Southern Ocean. The fluorescence properties of water-soluble organic aerosols investigated using a fluorescence excitation–emission matrix coupled with parallel factor analysis (EEM–PARAFAC) revealed that protein-like components were dominant in our marine aerosol samples, representing 69 %–91 % of the total intensity. Protein-like components also showed a significant positive relationship with the relative biomass of diatoms; however, they were negatively correlated with the relative biomass of P. antarctica. These results suggest that the protein-like component is most likely produced as a result of biological processes of diatoms in the Amundsen Sea.

Circulating tumour DNA (ctDNA) as a biomarker in metachronous melanoma and colorectal cancer- a case report

BackgroundCirculating tumour DNA (ctDNA) has emerged as a promising blood-based biomarker for monitoring disease status of patients with advanced cancers. The presence of ctDNA in the blood is a result of biological processes, namely tumour cell apoptosis and/or necrosis, and can be used to monitor different cancers by targeting cancer-specific mutation.Case presentationWe present the case of a 67 year old Caucasian male that was initially treated with BRAF inhibitors followed by anti-CTLA4 and then anti-PD1 immunotherapy for metastatic melanoma but later developed colorectal cancer. The kinetics of ctDNA derived from each cancer type were monitored targeting BRAF V600R (melanoma) and KRAS G13D (colon cancer), specifically reflected the status of the patient’s tumours. In fact, the discordant pattern of BRAF and KRAS ctDNA was significantly correlated with the clinical response of melanoma to pembrolizumab treatment and progression of colorectal cancer noted by PET and/or CT scan. Based on these results, ctDNA can be used to specifically clarify disease status of patients with metachronous cancers.ConclusionsUsing cancer-specific mutational targets, we report here for the first time the efficacy of ctDNA to accurately provide a comprehensive outlook of the tumour status of two different cancers within one patient. Thus, ctDNA analysis has a potential clinical utility to delineate clinical information in patients with multiple cancer types.

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Phylogenetic incongruence can be caused by analytical shortcomings or can be the result of biological processes, such as hybridization, incomplete lineage sorting and gene duplication. Differentiation between these causes of incongruence is essential to unravel complex speciation and diversification events. The phylogeny of the True Geese (tribe Anserini, Anatidae, Anseriformes) was, until now, contentious, i.e., the phylogenetic relationships and the timing of divergence between the different goose species could not be fully resolved. We sequenced nineteen goose genomes (representing seventeen species of which three subspecies of the Brent Goose, Branta bernicla) and used an exon-based phylogenomic approach (41,736 exons, representing 5887 genes) to unravel the evolutionary history of this bird group. We thereby provide general guidance on the combination of whole genome evolutionary analyses and analytical tools for such cases where previous attempts to resolve the phylogenetic history of several taxa could not be unravelled. Identical topologies were obtained using either a concatenation (based upon an alignment of 6,630,626 base pairs) or a coalescent-based consensus method. Two major lineages, corresponding to the genera Anser and Branta, were strongly supported. Within the Branta lineage, the White-cheeked Geese form a well-supported sub-lineage that is sister to the Red-breasted Goose (Branta ruficollis). In addition, two main clades of Anser species could be identified, the White Geese and the Grey Geese. The results from the consensus method suggest that the diversification of the genus Anser is heavily influenced by rapid speciation and by hybridization, which may explain the failure of previous studies to resolve the phylogenetic relationships within this genus. The majority of speciation events took place in the late Pliocene and early Pleistocene (between 4 and 2millionyears ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of temperate grasslands. Our approach will be a fruitful strategy for resolving many other complex evolutionary histories at the level of genera, species, and subspecies.

Mind the gap: non-biological processes contributing to soil CO2 efflux.

Widespread recognition of the importance of soil CO2 efflux as a major source of CO2 to the atmosphere has led to active research. A large soil respiration database and recent reviews have compiled data, methods, and current challenges. This study highlights some deficiencies for a proper understanding of soil CO2 efflux focusing on processes of soil CO2 production and transport that have not received enough attention in the current soil respiration literature. It has mostly been assumed that soil CO2 efflux is the result of biological processes (i.e. soil respiration), but recent studies demonstrate that pedochemical and geological processes, such as geothermal and volcanic CO2 degassing, are potentially important in some areas. Besides the microbial decomposition of litter, solar radiation is responsible for photodegradation or photochemical degradation of litter. Diffusion is considered to be the main mechanism of CO2 transport in the soil, but changes in atmospheric pressure and thermal convection may also be important mechanisms driving soil CO2 efflux greater than diffusion under certain conditions. Lateral fluxes of carbon as dissolved organic and inorganic carbon occur and may cause an underestimation of soil CO2 efflux. Traditionally soil CO2 efflux has been measured with accumulation chambers assuming that the main transport mechanism is diffusion. New techniques are available such as improved automated chambers, CO2 concentration profiles and isotopic techniques that may help to elucidate the sources of carbon from soils. We need to develop specific and standardized methods for different CO2 sources to quantify this flux on a global scale. Biogeochemical models should include biological and non-biological CO2 production processes before we can predict the response of soil CO2 efflux to climate change. Improving our understanding of the processes involved in soil CO2 efflux should be a research priority given the importance of this flux in the global carbon budget.

On the spatial and temporal dependence of CO2 emission on soil properties in sugarcane (Saccharum spp.) production

CO2 production in soil is the result of biological processes, such as the decomposition of organic matter and the respiration of roots and soil organisms. It also depends on the physical, chemical and biological properties and their interactions. Such properties exhibit variability in space and time, which provides a high degree of complexity on soil CO2 emission (FCO2). However few studies discuss the spatial and temporal component of FCO2, jointly. The objective of this study was to characterize the spatial and temporal variability of FCO2 and its relationship to the edaphoclimatic properties of the soil in sugarcane fields. The LI-8100 system, which monitors changes in CO2 concentrations within a portable chamber, was used to assess the FCO2. The CO2 flux measurements, soil temperature (0–20cm, thermometer of LI-8100) and soil water content (0–12cm, TDR device) were evaluated concomitantly. Overall, the mean values for FCO2, soil temperature and soil water content were 2.8μmolm−2s−1, 19.48°C and 17.20m3m−3, respectively. The FCO2 was positively correlated with the soil organic matter content (SOM) (r=0.67, p<0.001), the air-filled porosity (AFP) (r=0.71, p<0.001) and the available phosphorus (r=0.28, p<0.05) but negatively correlated with the soil C/N ratio (r=−0.75, p<0.001) and soil water content (r=−0.29, p<0.05). The air-filled porosity was the last property added to the multiple regression model and explained 77% of the spatial variability in soil CO2 emission. The largest temporal variations in CO2 emissions over the study period were explained by changes in soil water content, especially after rainfall. Spatially, the CO2 emission is modeled by chemical (organic matter and soil C/N ratio) and physical (air-filled porosity) soil properties which are associated to production and transport of CO2 in soil.

The Resurrection of Natural Law Theory

The job of legal scholars is to describe the structure and coherence of norms Many philosophers of law presume it is impossible to derive norms from facts. All that nature can offer is informatie, not prescription, it is said. However, such a rigourous divide will cause jurisprudence to cut itself off form new discoveries in empiric sciences. On what terms is a biological theory of law feasible? Could it meet the objections against natural law theory? Would it be possible to justify our deeds by referring to biological mechanisms? Aren't we actually doing it all the time? The author argues that biological mechanims can be morally obligatory, because not living by them is tantamount ot failure to live in a group, with the result that underlying genes will not spread. We feel we ought to live according to group moral and rules. 'Reason' and 'normative thinking' are the result of biological processes; there are no external sources.

Toxicant Exposure and Mental Health—Individual, Social, and Public Health Considerations

Thoughts and moods are the result of biological processes; disordered thoughts and moods may be the result of disordered biological processes. As brain dysfunction can manifest with emotional symptoms or behavioral signs, the etiology of some mental health afflictions and some abnormal conduct is pathophysiological rather than pathopsychological. Various studies confirm that some chemical toxicants which modify brain physiology have the potential to affect mood, cognitive function, and to provoke socially undesirable outcomes. With pervasive concern about myriad chemical agents in the environment and resultant toxicant bioaccumulation, human exposure assessment has become a clinically relevant area of medical investigation. Adverse exposure and toxicant body burden should routinely be explored as an etiological determinant in assorted health afflictions including disordered thinking, moods, and behavior. The impact of toxicant bioaccumulation in a patient with neuropsychiatric symptoms is presented for consideration as an example of the potential benefit of recognizing and implementing exposure assessment.

Biological Co-Adaptation of Morphological and Composition Traits Contributes to Mechanical Functionality and Skeletal Fragility

A path analysis was conducted to determine whether functional interactions exist among morphological, compositional, and microstructural traits for young adult human tibias. Data provided evidence that bone traits are co-adapted during ontogeny so that the sets of traits together satisfy physiological loading demands. However, certain sets of traits are expected to perform poorly under extreme load conditions. Previous data from inbred mouse strains suggested that biological processes within bone co-adapt morphological and compositional traits during ontogeny to satisfy physiological loading demands. Similar work in young adult humans showed that cortical tissue from slender tibias was stiffer, less ductile, and more susceptible to accumulating damage. Here we tested whether the relationships among morphology and tissue level mechanical properties were the result of biological processes that co-adapt physical traits, similar to those observed for the mouse skeleton. Cross-sectional morphology, bone slenderness (Tt.Ar/Le), and tissue level mechanical properties were measured from tibias from 14 female (22-46 yr old) and 17 male (17-46 yr old) donors. Physical bone traits measured included tissue density, ash content, water content, porosity, and the area fractions of osteonal, interstitial, and circumferential lamellar tissues. Bivariate relationships among traits were determined using linear regression analysis. A path analysis was conducted to test the hypothesis that Tt.Ar/Le is functionally related to mineralization (ash content) and the proportion of total area occupied by cortical bone. Ash content correlated negatively with several traits including Tt.Ar/Le and marrow area, indicating that slender bones were constructed of tissue with higher mineralization. Path analysis revealed that slender tibias were compensated by higher mineralization and a greater area fraction of bone. The results suggest that bone adapts by varying the relative amount of cortical bone within the diaphysis and by varying matrix composition. This co-adaptation is expected to lead to a particular set of traits that is sufficiently stiff and strong to support daily loads. However, increases in mineralization result in a more brittle and damageable material that would be expected to perform poorly under extreme load conditions. Therefore, focusing attention on sets of traits and the relationship among traits may advance our understanding of how genetic and environmental factors influence bone fragility.

A Look Inside

Standard neurobiology textbooks commonly do not contain a chapter on cancer, and the word might not even appear in the index. Its absence cannot be explained simply on the grounds that the subject falls more appropriately within the clinical realm, because you will find chapters devoted to various other nervous system diseases. Could this intellectual blind spot result from the fact that mature neurons, being post-mitotic, do not succumb to the disease? This absence in most texts is curious, considering the severe functional implications. The word is sometimes used metaphorically to connote an unstoppable process of destruction, and indeed some forms of brain cancer present the most dire prognosis of any cancer. But more importantly the neglect of this subject is curious, because on a molecular and cellular level, cancer is the result of biological processes that are at the forefront of modern neurobiological research. These include such current hot-topic areas as intraand inter-cellular signaling networks, regulation of gene transcription, control of cellular differentiation, regulation of cell motility, migration and cell death; the secretion and response to growth factors, and interactions with the vascular and immune systems. Finally, the current enthusiasm and promising research on the use of stem cells for therapeutic treatment of nervous system disease has brought us face-to-face with our ignorance in this area, as we find that many types of stem cells transplanted into the brain form tumors. This issue of Neuron Glia Biology contains a special collection of original research papers on cancer in the peripheral and central nervous system and a review on the subject. These papers are introduced below by Special Feature Editor, Philip Lee.

Taphonomy and palaeoecology of an assemblage of large mammals: Hyaenid activity in the Lower Pleistocene site at Venta Micena (Orce, Guadix-Baza Basin, Granada, Spain)

We report taphonomic and palaeoecologic data on the rich, diverse and well preserved assemblage of large mammals from lower Pleistocene deposits at Venta Micena (Orce, Granada, south-east Spain). The biostratinomic and diagenetic characteristics of the assemblage are congruous with the sedimentary context deduced from the study of the site, and both confirm that: (i) the assemblage represents an accumulated taphonomic stage, (ii) it was formed by demic, autochtonous palaeobiologic entities, which were preserved and recorded in situ, and (iii) it is the result of biological processes and agents. Interspecific analysis of size/abundance patterns in ungulates shows that the main taphonomic bias affecting the bones was produced by biological destruction before burial, and that the loss of information was greater for species of smaller body size. Factor correspondence analysis was used to compare the frequencies at which some groups of postcranial elements are represented in several recent and archaeological bone assemblages accumulated by carnivores, rodents and hominids. The results obtained strongly suggest that the bones from Venta Micena were collected mainly by hyaenids, which deposited them near shallow dens excavated around the ponds that surrounded the Pleistocene lake of Orce. An analysis of the abundance of major long bones has shown that differential fragmentation was produced by hyaenas as a function of their structural density and mean marrow content. All these data allow to formulate a descriptive-quantitative model for the characterization of bone assemblages generated from hyaenid activity, in which Venta Micena is an example of bone concentration and modification activities by Pachycrocuta brevirostris. Strong selection of prey by carnivores (which killed preferably juveniles, females and individuals with diminished locomotive capabilities among ungulate prey species of larger body size) is indicated by (i) the abundance of juvenile individuals with deciduous teeth in relation to the average weight estimated for adults in each ungulate species, by (ii) the U-shaped attritional mortality profiles deduced from crown heigth measurements, by (iii) the presence of many metapodials with different osteopathologies, and by (iv) a biased sexual ratio deduced from the metacarpals of large bovids. Comparison between the frequencies in which modern African carnivores kill and scavenge ungulates from different size classes and the abundance of these size categories in the assemblage suggests that the Venta Micena hyaena was a bone-cracking scavenger which fed largely on carcasses of ungulates preyed upon and partially consumed by flesh-eating carnivores such as saber-toothed felids and wild dogs.

Spatial variability and collector requirements for sampling throughfall volume and chemistry under a mixed-hardwood canopy

Throughfall was intensively sampled during five storms in August, September, and November 1988, July 1989, and January 1990. For each storm, 50 collector bottles with funnels were positioned at random on a 0.1-ha plot under a mixed-hardwood forest canopy in northern Virginia. Concentrations and net inputs of H+, NH4+, Na+, K+, Ca2+, Mg2+, Mn2+, Cl−, NO3−, and SO42− and throughfall volume were evaluated for spatial variability both within and among storms and were used to estimate the number of collectors necessary for throughfall collection. Ion concentrations were generally less variable within storms compared with net ion input data. Concentrations and net inputs of some ions were consistently less variable than others; for example, Ca2+, NO3−, and SO42− were less variable than NH4+ and K+. These patterns of variability were consistent in comparisons both within and among storms. The relatively low variability of NO3− and SO42− is probably due to dry deposition of these ions as anthropogenic pollutants, while the low variability of Ca2+ is the result of deposition in windblown soil particles. The high variability of NH4+ and K+ is probably the result of biological processes. Ammonium is strongly retained by the canopy, and K+ is readily leached from it. Retention by, and leaching from, the canopy can induce spatial variability as a result of spatial heterogeneity in the biota. Throughfall volume also displayed low variability within and among events, requiring an average of 11 collectors to estimate the mean within 10% at the 95% confidence level.

Perennial N2 supersaturation in an Antarctic lake.

The dry valleys of southern Victoria Land in Antarctica contain several closed basins in which perennially ice-covered lakes are found. One of the most unusual features of these lakes is the occurrence of high O2 concentrations in the water column; values ranging from slightly more than saturation to more than four times saturation have been reported. Recently, we considered a bulk O2 budget for Lake Hoare, Antarctica, which led us to suggest that biological processes alone were not sufficient to explain the observed elevated oxygen levels. Consequently, there must be a non-biological source of O2. We suggested that this source results from the exclusion of O2 during the freezing of aerated meltstream water at the bottom of the ice cover, and predicted that this physical mechanism should also enhance the other atmospheric gases. Here we report the results of a study which, for the first time, documents the supersaturation of N2 in a lake. Dissolved N2 levels of 145% and 163% were determined from samples taken just below the ice cover and at a depth of 12 m, respectively. The relatively importance of biological and abiological sources is reflected in the ratio of N2 concentration to O2 concentration. In Lake Hoare this ratio was 1.20 at ice/water interface and 1.05 at 12 m; considerably different from the ratio in equilibrium with air (approximately 1.8). Based on these results, we have determined that about half of the net O2 production in the lake is the result of biological processes.

Distribution and migration of dissolved silica in oceans

It is shown, among other things, that accessions of silica to the surface of oceanic aquatoria, positions of the zones of a particular abundance of phytoplankton where silica is accumulated by the organisms and is converted eventually into its suspended forms, and of the zones of enrichment of silica in oceanic sediments, are determined by hydrodynamic variables and not by positions of the original sources of silica in the hydrosphere, that enrichment of silica in oceanic sediments is the result of biological processes, and that chemogenic precipitation of solid amorphous silica is virtually impossible. -- IGR Staff.

BIOLOGICAL HOMOGENIZATION IN FOSSIL UNDERCLAYS AND SEAT ROCKS

Unbeddedness, or homogeneity, is the main characteristic of seat rocks and underclays, interpreted as fossil soils. Study of modern soils indicates that this homogeneity is a result of biological processes. Leaching and other chemical activities are for the most part related to roots, but the actual physical homogenization is due to the fauna of the soil.