Nature Precedings
Not a member yet
3446 research outputs found
Sort by
Changes in enzyme activities and in the functional diversity of actinomycetes due to long term agricultural management
No full textLong-term agricultural management alters soil organic matter, nutrient status, and potentially the decomposer community. We measured the abundance and activity of cellulose, chitin, and protease degrading bacteria, and total soil extra-cellular enzyme activity for cellulose (β-glucosidase), chitinase (N-acetyl-glucosaminidase), xylosidase, and phosphatase activity. By combining these methods, we could determine how bacterial decomposer abundance and function were altered by long-term management, and how the bacterial decomposer community relates to overall soil enzyme activity. We also measured microbial total fungal and bacterial biomass, soil organic carbon pools, and extractable nitrogen for supplementary comparisons. Soil samples were taken in June of 2010 from the Bad Lauchstädt field station’s Static Fertilization Experiment, under treatment for 108 years. Treatments include mineral (NPK) fertilizer (none or added at 140, 60, and 230 kg ha-1 yr-1) and manure addition (none, 20 T ha-1 2yr-1, and 30 T ha-1 2yr-1) in a full factorial experiment. We found that total cellulase activity and the abundance of cellulase degrading bacteria were higher in plots with manure addition. We observed the same pattern for total phosphatase activity, total chitinase activity, and the abundance of chitin degrading bacteria, although the trend was not statistically significant for total chitinase activity. These results suggest that long-term management does alter decomposition and that total soil enzyme activity reflects the abundance of decomposer bacteria
Deterministic Separation of Cancer Cells from Blood at 10 mL/min
Full text linkCirculating tumor cells (CTCs) and circulating clusters of cancer and stromal cells have been identified in the blood of patients with malignant cancer and can be used as a diagnostic for disease severity, assess the efficacy of different treatment strategies and possibly determine the eventual location of metastatic invasions for possible treatment. There is thus a critical need to isolate, propagate and characterize viable CTCs and clusters. Here, we present a microfluidic device for mL/min flow rate, continuous-flow capture of viable CTCs from blood using deterministic lateral displacement arrays. We show here that a deterministic bump array can be designed such that it will isolate with efficiency greater than 85% CTCs over a large range in sizes from millimeter volume clinical blood samples in minutes, with no effect on cell vitality so that further culturing and analysis of the cells can be carried out
A quantitative model for efficient construction of lentiviral vectors with a unique clone site
Full text linkLentiviral vectors (LVs) were a powerful tool for transgene expression in vivo and in vitro. However, the construction of LVs is of low efficiency, due to the large sizes and lack of proper clone sites. Therefore, it is critical to develop efficient strategies for cloning LVs. Here, we reported a combinatorial strategy to efficiently construct LVs using EGFP, hPlk2 wild type (WT) and mutant genes as inserts. Firstly, site-directed mutagenesis (SDM) was performed to create BamH I site for the inserts; secondly, pWPI LV was dephosphorylated after BamH I digestion; finally, the amounts and ratios of the insert and vector DNA were optimized to increase monomeric ligation. Our results showed that the total percentage of positive clones was approximately 51.3%±15.2%. Using this model, almost all the vectors could be constructed through two or three minipreps, therefore, our study provided an efficient quantitative model for constructing large-size vectors.

This paper has since been published in Scientific Reports: Zhang, G. & Tandon, A. Quantitative assessment on the cloning efficiencies of lentiviral transfer vectors with a unique clone site. Sci. Rep. 2, 415;
DOI:10.1038/srep00415 (2012
Mining PubMed for Biomarker-Disease Associations to Guide Discovery
Full text linkBiomedical knowledge is growing exponentially; however, meta-knowledge around the data is often lacking. PubMed is a database comprising more than 21 million citations for biomedical literature from MEDLINE and additional life science journals dating back to the 1950s. To explore the use and frequency of biomarkers across human disease, we mined PubMed for biomarker-disease associations. We then ranked the top 100 linked diseases by relevance and mapped them to medical subject headings (MeSH) and, subsequently, to the Disease Ontology. To identify biomarkers for each disease, we queried Covance BioPathways, an online data resource that maps commercial biomarker assays to biological and disease pathways. We then integrated pathways-based information to describe both known and potential biomarkers as well as disease-associated genes/proteins for select diseases. This approach identifies therapeutic areas with candidate or validated biomarkers, and highlights those areas where a paucity of biomarkers exists
The persistent impact of incidental experience
Full text linkAs we perform daily activities-- driving to work, unlocking the office door, grabbing a coffee cup-- our actions seem automatic and preprogrammed. Nonetheless, routine, well-practiced behavior is continually modulated by incidental experience: in repetitive experimental tasks, recent (~4) trials reliably influence performance and action choice. Psychological theories downplay the significance of sequential effects, explaining them as rapidly decaying perturbations of behavior with no long-term consequences. We challenge this traditional perspective in two studies designed to probe the impact of more distant experience, finding evidence for effects spanning up to a thousand intermediate events. We present a normative theory in which these persistent effects reflect optimal adaptation to a dynamic environment exhibiting varying rates of change. The theory predicts a heavy-tailed decaying influence of past experience, consistent with our data, and suggests that individual incidental experiences are catalogued in a temporally extended memory utilized to optimize subsequent behavior
Climate Change and Disease Simulation
Full text linkClimate change has manifested differential impacts on various components of the earth system. The impact of climate change is not merely limited to the climatic variable. Climate change has resulted in complex, unforeseen consequences in the biosphere of earth. The silent but gradual changes arise out of varied responses of disease-causing organism to the combination of the disease-conducive environmental variables. The change is the same for both the target hosts plant as well as the animal kingdom. There is an urgent need to look into the changing disease dynamics and the disease pathogen genome sensitivity to the changes in climatic variables. The long memory of genetic makeup of disease pathogen to capture, inherit and evolve or mutate the changed or impacted gene due to climate change in generation after generation may invite a cascading effect on the next generation of biosphere. These silent but gradual changes in the genome of disease organism are rarely investigated or included in simulation models. This also enhances the risk of quantification of uncertainties of various disease simulation models. Thus, chances and lists of black swan events in life and food insecurity are on the rise
Quantum probabilities in competing lizard communities
Full text linkDespite predictive success, population dynamics and evolutionary game theory still pose fundamental problems. Violation of the competitive exclusion principle in plankton communities provides an example. A promising solution of this ‘paradox of the plankton’ comes from theories involving cyclic competition, an evolutionary analogue of the classical rock-paper-scissors (RPS) game. However, modeling probabilistic RPS structures, one encounters a fundamental difficulty: the pairs rock-scissors, scissors-paper, and paper-rock possess representations in separate Kolmogorovian probability spaces, but a single global probability space for entire triplets does not exist. Populations that take part in cyclic competition should therefore involve probabilistic incompatibilities, analogous to those occurring in quantum mechanics. Here, using experimental data collected from 1990 to 2011 on the RPS cycles of lizards, we show that the incompatibilities are indeed unavoidable, and the data cannot be reconstructed from a single Kolmogorovian probability space. We then prove that the effect is genuinely quantum probabilistic, i.e. all the probabilities can be formulated in terms of a single density matrix and a set of non-commuting projectors. This formal quantum structure is dormant in games where probabilities of strategies do not entangle with probabilities of payoffs, and thus could be overlooked. In more realistic scenarios, involving games ‘with ace in a sleeve’, the non-Kolmogorovian structure can be activated. Surprisingly, lizards occasionally do play such games. In consequence, the formalism of evolutionary games, similarly to quantum mechanics, should begin with density matrix equations. Implications of our finding extend beyond lizard communities, given that RPS games are common in nature and higher dimensional RPS games may be even more common in ecosystems
Effect Of Pre-freeze Addition Of Cysteine Hydrochloride And Reduced Glutathione On Post-thaw Sperm Parameters And Field Fertility In Jersey Crossbred Bull Semen
Full text linkThe present study was aimed to assess the effect of pre-freeze addition of cysteine hydrochloride and glutathione (GSH) on post-thaw sperm functional parameters and field fertility. The experimental bulls aged 4 to 6 years were used for the present study. A total of 36 ejaculates, 6 ejaculates from each bull (n=6) were collected and divided in to three groups, group I (control), group II (5mM cysteine hydrochloride) and group III (5mM GSH). The extended semen samples were added with @5mM additives, filled in mini straw using automatic filling and sealing machine (IMV, France) and cryopreserved in liquid nitrogen. Post-freeze seminal traits were also recorded after thawing at 37oC for 30 seconds. Post thaw livability was significantly (p< 0.01) higher in GSH group as compared to cysteine and control groups. The loss of acrosomal integrity was significantly (p< 0.01) lower in GSH group than cysteine and control groups. Analysis of variance for post thaw motility parameters (Forward progressive and Total motility) has revealed that significant difference (p< 0.05) between the good and poor freezer in the group II and there was no difference in the group I and III under study at 0 and 1 hr incubation period and at 2 hrs the group III and at 4 hrs group I has revealed significance difference (p< 0.05).The curvilinear velocity (VCL) and amplitude of lateral head displacement (ALH) values were significantly (P<0.05) higher in GSH than the cysteine and control groups. The Mitochondrial membrane potential (per cent) had no significance difference between the treatment groups. The present study indicates that the addition of cysteine and GSH suggestive of reducing lipid peroxide levels. The conception rate (%) in glutathione (68) added semen was significantly (p>0.05) higher than cysteine (58) and control (49) groups. The post-thaw sperm progressive forward motility (r=0.4) had moderate but, no significant correlation with conception rate. However post-thaw VSL (r=0.7), loss of acrosomal integrity (r=-0.8) and mitochondrial membrane potential (r=0.9) had significant (p< 0.05) correlation with field fertility. The present study indicates that the use of glutathione as semen additives may be recommended for improving semen quality and overall augmentation of pregnancy in cows. The present study suggests that pre-freeze addition of glutathione was found to be better than cysteine in improving sperm fertility
Can bacteria adapt to starvation-free environment?
Full text linkBacteria will experience starvation-free environment if infinite nutrition is supplied continuously for a long period. In this study, an evolutionary experiment was performed for 118 days where bacteria adapted to starvation-free environment and reduced their doubling time. It is anticipated that this finding will help to select bacterial strains that can grow more rapidly in rich media
Aetiology and treatment of epidermal depigmentory disorder in humans
Full text linkThe epidermal depigmentary trigger in humans at post-natal level may occur with the toxification of skin organ with the endogenously produced melanocytotoxic hydrogen peroxide and subsequent formation of hydrogen peroxide- melanolipoprotein conjugate involving the hydrogen bonding of complementary hydroxyl and carbonyl molecular surfaces of these biosignitures respectively. The condition is multifactorial but reversible. The structural and functional degeneration of melanocytes under the acquired condition never occur. The molecular conjugation theory on the aetiology and line of treatment of the epidermal depigmentary disorder (recoined as hepato-epidermal syndrome HES) has been proposed. The inherent sulfoxides of Allium cepa have been found as the renaturant of HES condition with the capacity to dislodge the denaturant hydrogen peroxide forming stronger hydrogen bonding with hydrogen peroxide than that of carbonyl molecular surface of melanolipoprotein, the epidermal colour determinant. The orally and topically defined plant based combined therapy advances the recovery time of HES condition