bluuebunny/crossref_metadata_2025 huggingface dataset:
Widespread Mitochondrial Disease in North American Bison
Authors: Pringle Thomas
Published: July 2019

North American bison have rebounded from near-extinction in the nineteenth century but from such small inbred founding populations that once-rare deleterious nuclear gene alleles and mitochondrial haplotypes are now at high frequencies. The initial bottleneck was compounded by decades of unnatural selection affecting bison conservation genomics and undercutting restoration initiatives. The genomics era began in late 2010 for bison and sister species yak with the release of 102 whole mitochondrial genomes, displacing earlier control region and microsatellite data not extending to coding regions. This allows detection of both sporadic and sub-clade level mutations in mitochondrially encoded proteins and tRNAs by comparative genomics methods: deleterious mutations in both cytochrome b (V98A) and ATP6 (I60N) occur within a single common bison haplotype. Since similar mutations in human and dog cause clinical impairment of mitochondrial oxidative phosphorylation, these bison are predicted to be significantly impaired in aerobic capacity, disrupting highly evolved cold tolerance, winter feeding behaviors, escape from predators and competition for breeding. Because Yellowstone National Park bison are subjected to genetically uninformed culls and surplus animals used to seed new conservation herds, mutational status has significant implications. Continuing take of the remaining bison with wildtype mitochondria may recapitulate errors of nineteenth century bison stewardship bringing bison conservation to the point of no return.
Molecular Bio-imprinting of Biocatalysts
Authors: Khan Israr , Akhtar Muhammad Waheed
Published: July 2019

Energy conservation is the cry of the day. Attempts are made all over the world to occupy and use energy reserves. Increased industrialization and mechanization has led to the depletion of natural energy reserves. Its unavoidable to search for renewable sources of energy, which may be not used now but can be used by future generations. We are using the expertise of our ancestors. Thus exploiting the nature and newer techniques in this area would yield the best results. Bio-imprinting is one of those techniques whereby chemical modification is done in order to achieve highly expressed protein which can be stored in its highly active form in the specific solvent.
Why not "do simple things in a simple way": Use of the Pap test as the first step in screening genetic stability for human cultured stem cell therapy?
Authors: Carvalho Katherine Athayde Teixeira de , Irioda Ana Carolina , Zocche Larissa , Souza Carolina Maria Costa de Oliveira , Ferreira Reginaldo J. , Aliprandini Eduardo , Cunha Ricardo C , Francisco Julio C , Guarita-Souza Luiz Cesar , Malvezzi Mariester , Beltrame Miriam , Mesquita Lismary , Kuczera Diogo , Vargas Rafael
Published: July 2019

The aim of this study was to analyze adipose tissue-derived mesenchymal stem cells (AT-MSCs) using the Pap test as a first screening step to evaluate genetic stability. Human adipose tissue from six healthy female donors was obtained from elective liposuction procedures. The cells were isolated, cultivated at P2/P3, characterized by flow cytometric analysis, and differentiation induced. The AT-MSCs were stained by Papanicolaou staining and analyzed according to the Bethesda classification, and viability-apoptosis relationships were evaluated. The results of the Pap test for Sample I indicated high-grade alterations consistent with genetic instability; for Samples II-V, atypical cells of undetermined significance; and for Sample VI, normal cells. These results demonstrate the potential of using the Pap test as an initial screening step to evaluate the genetic stability of cultured AT-MSCs and also suggest its use for other adherent cells such as embryonic stem cells or induced pluripotent stem cells.
Biodiversity Conservation Of The Irtysh River
Authors: Kulikov Yevgeniy , Kirichenko Olga
Published: July 2019

One of the basic principles of environmental protection is the conservation of biological diversity of natural objects. In addressing this issue plays an important role the Red Book of Kazakh-stan, which is one of the main effective instruments for the preservation and restoration of rare and declining in numbers and endangered species. Red Books are the main weapon of environmental education tool for the inventory of rare and endangered species, scientifically sound foundation for their protection. Studies of fish that are listed and recommended for inclusion in the Red Book, is a priority and is evidenced not only on the state of study of the securities and small fish species, but also to demonstrate the quality of protection and conservation of biodiversity. Prioritize the conservation of genetic resources for sustainable development is enshrined in the Convention on Biological Diversity. Government of the Republic of Kazakhstan in 2001 approved a national program "Conservation and sustainable use of rare and valuable species of farm animals", under which the task to preserve the gene pool of valuable species and breeds of fish.
`The frozen accident' as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms
Authors: Glazebrook James , Wallace Rodrick
Published: July 2019

We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks. The approach to most of these questions involves using elements of Shannon's rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure in proteins. This leads to the suggestion that the frozen accident may have been a type of evolutionary adaptation.
Archon Genomics X PRIZE Validation Protocol
Authors: Kedes Larry , Sutton Granger , Liu Edison , Jongeneel Victor
Published: July 2019

This document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies that emerge even after 2012.
Longitudinal Metagenomic Analysis of the Water and Soil from Gulf of Mexico Beaches Affected by the Deep Water Horizon Oil Spill
Authors: Widger William , Golovko Georgiy , Martinez Antonio , Ballesteros Efren , Howard Jesse , Xu Zhenkang , Pandya Utpal , Fofanov Viacheslav , Rojas Mark , Bradburne Christopher , Hadfield Ted , Olson Nels , Santarpia Joshua , Fofanov Yuriy
Published: July 2019

Estimates of 7x105 cubic meters of crude oil were released into the Gulf of Mexico as a consequence of the April 20th, 2010 Deep Water Horizon drilling rig explosion, leaving thousands of square miles of earth's surface covered in crude oil. Dispersants were used on large slicks and injected at the well head, resulting in oil being suspended throughout the water column. Starting in June 2010, oil reached hundreds of miles of Louisiana, Alabama, Mississippi, and Florida shoreline disturbing the ecological balance and economic stability of the region. While visible damages are evident in the wildlife populations and marine estuaries, the most significant affect may be on the most basic level of the ecosystems: the bacterial and plankton populations.We present results from high throughput DNA sequencing of close-to-shore water and beach soil samples before and during the appearance of oil in Louisiana and Mississippi. Sixteen samples were taken over a two month period at approximately two week intervals from Grand Isle, LA and Gulfport, MS and were sequenced using the Illumina GAIIx platform. Significant genomic-based population fluctuations were observed in the soil and water samples. These included large spikes in the human pathogen Vibrio cholera, a sharp increase in Rickettsiales sp., and decrease of Synechococus sp. in water samples. Analysis of the contiguous de-novo assembled DNAs (contigs) from the samples also suggested the loss of biodiversity in water samples by the time oil appeared at the shores in both locations. Our observations lead us to the conclusion that oil strongly influenced microbial population dynamics, had a striking impact on the phytoplankton and other flora present prior to the appearance of oil, and that the microbial community had not recovered to pre-spill conditions by the end of our observational period.
In-vitro Antifungal Activity of Some 1,3,5-triazine Derivatives
Authors: Singh Udaya Pratap , Gahtori Prashant , Singh Ramendra K.
Published: July 2019

A series of substituted phenylthiazolyl 1,3,5-triazine derivatives were screened for their in-vitro antifungal activity (MIC and MFC) against four fungi viz. Candida species (C. albicans NCIM-3102, C. glabrata NCIM-3266), Cryptococcus neoformans NCIM-3542, and Aspergillus niger NCIM-620 using modified broth microdilution method recommended by CLSI, with reference to fluconazole and amphotericin B.
Bacteria have transient influences on marine corrosion of steel
Authors: Melchers Robert , Jeffrey Robert
Published: July 2019

The contribution of bacteria to the corrosion mass loss and to pitting of mild steel was observed over 2.5 years using parallel streams of unpolluted natural (biotic) and nominally sterilized (abiotic) Pacific Ocean coastal seawater. As also observed by others, in artificial laboratory exposures, corrosion mass loss within the first few days of exposure was much greater in the biotic stream. However, after only about 10 days the difference in mass losses were gradually reduced and were very similar up to about one year of exposure. Thereafter, the corrosion loss in the biotic stream again became more severe. Pitting corrosion in the biotic stream was more severe from the very first exposure throughout the 2.5 years. Corrosion in both seawater streams exhibited three distinct but transient time-dependent phases. Of these only the first and third obviously involve bacteria. Similar longer-term observations in real seawaters have not been described previously but are generally consistent with some long-term field data. The results show that longer-term corrosion behavior and possible microbial influences cannot be predicted from short-term laboratory observations, even if natural seawater is used.
Insights from the Structure of Estrogen Receptor into the Evolution of Estrogens: Implications for Endocrine Disruption
Authors: Baker Michael
Published: July 2019

In the last decade, there has been important progress in understanding the origins and evolution of receptors for adrenal steroids (aldosterone, cortisol) and sex steroids (estradiol, progesterone, testosterone) due to the sequencing of genomes from animals that are at key sites in vertebrate evolution. Although the estrogen receptor [ER] appears to be the ancestral vertebrate steroid receptor and estradiol [E2] is the physiological ligand for vertebrate ERs, the identity of the ancestral ligand(s) for the ER remains unknown. Here, using an analysis of crystal structures of human ER[alpha] with E2 and other chemicals and 3D models of human ER[alpha] with 27-hydroxycholesterol and 5-androsten-3[beta],17[beta]-diol, we propose that one or more [DELTA]5 steroids were the ancestral ligands for the ER, with E2 evolving later as the canonical estrogen. The evidence that chemicals with a [beta]-hydroxy at C3 in a saturated A ring can act as estrogens and the conformational flexibility of the vertebrate ER can explain the diversity of synthetic chemicals that disrupt estrogen responses by binding to vertebrate ERs.
p53 independent epigenetic-differentiation treatment in xenotransplant models of acute myeloid leukemia
Authors: Saunthararajah Yogen , Ebrahem Quteba , Negrotto Soledad , Mahfouz Reda , Link Kevin , Hu Zhenbo , Gu Xiaorong , Advani Anjali , Kalaycio Matt , Sobecks Ronald , Sekeres Mikkael , Copelan Edward , Radivoyevitch Tomas , Maciejewski Jaroslaw , Mulloy James C. , Ng Kwok-Peng
Published: July 2019

Suppression of apoptosis by TP53 mutation contributes to resistance of acute myeloid leukemia (AML) to conventional cytotoxic treatment. Using differentiation to induce irreversible cell cycle exit in AML cells could be a p53-independent treatment alternative, however, this possibility requires evaluation. In vitro and in vivo regimens of the cytosine analogue decitabine that deplete the chromatin modifying enzyme DNA methyl-transferase 1 (DNMT1) without phosphorylating p53 or inducing early apoptosis were determined. These decitabine regimens but not equimolar DNA-damaging cytarabine up regulated the key late differentiation factors CEBP&x03B5; and p27/CDKN1B, induced cellular differentiation, and terminated AML cell-cycle, even in cytarabine-resistant p53- and p16/CDKN2A-null AML cells. Leukemia initiation by xeno-transplanted AML cells was abrogated but normal hematopoietic stem cell (HSC) engraftment was preserved. In vivo, the low toxicity allowed frequent drug administration to increase exposure, an important consideration for S-phase specific decitabine therapy. In xeno-transplant models of p53-null and relapsed/refractory AML, the non-cytotoxic regimen significantly extended survival compared to conventional cytotoxic cytarabine. Modifying in vivo dose and schedule to emphasize this pathway of decitabine action can bypass a mechanism of resistance to standard therapy.
Molecular modelling and Function Prediction of hABH7, human homologue of E. coli ALKB7
Authors: Shankaracharya Mr. , Das Saibal , Vidyarthi Ambarish Sharan
Published: July 2019

Human homologues of ALKB protein have shown the prime role in DNA damaging drugs, used for cancer therapy. Little is known about structure and function of hABH7, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeller 9v7 to predict the 3D structure of the hABH7 protein. The tertiary structure model of hABH7, ALKBH7.B99990002.pdb was predicted and evaluated. Validation results showed 97.8% residues in favored and additional allowed regions of Ramachandran plots. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, presence of a Phe120-Gly121-Gly122 conserved pattern in the functional domain was detected. In the predicted structural model of hABH7, amino acid residues, Arginine at 57, 58, 59 and 60 along with tyrosine at 61 were predicted in RNA binding sites of the model. The predicted and validated model of human homologue hABH7 resulting from this study may unveil the mechanism of DNA damage repair in humans and accelerate the research on designing appropriate inhibitors aiding in chemotherapy and cancer related diseases.
Herd Immunity/Herd Infection: Cultural Artifacts of Marginalization and the Dynamics of AIDS
Authors: Wallace Rodrick
Published: July 2019

We examine conditions under which high prevalence of infectious disease can become endemic within a community, in effect constituting a state of 'herd infection' inverse to epidemiological herd immunity. For something like AIDS, under such circumstances, a single behavioral lapse or adverse accident will probably be a death sentence.
Anthropogenic Renourishment Feedback on Shorebirds: a Multispecies Bayesian Perspective
Authors: Convertino Matteo , Donoghue Joseph , Chu-Agor Ma Librada , Kiker Gregory , Munoz-Carpena Rafael , Fischer Richard , Linkov Igor
Published: July 2019

In this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some possible geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping Plover (PP) (Charadrius melodus ) and Red Knot (RK) (Calidris canutus ). Additionally, we investigated the potential differences between the SP breeding and wintering distributions using only regional-scale physiognomic variables and the recorded occur- rences. To quantify the relationship between past renourishment projects and shorebird species we used a Monte Carlo procedure to sample from the posterior distribution of the binomial probabilities that a region is not a nesting or a wintering ground conditional on the occurrence of a beach replenishment intervention in the same and the previous year. The results indicate that it was 2.3, 3.1, and 0.8 times more likely that a region was not a wintering ground following a year with a renourishment intervention for the SP, PP and RK respectively. For the SP it was 2.5. times more likely that a region was not a breeding ground after a renourishment event. Through a maximum entropy principle model we observed small differences in the habitat use of the SP during the breeding and the wintering season. However the habitats where RK was observed appeared quite different. While ecological niche models at the macro-scale are useful for determining habitat suitability ranges, the characterization of the species’ local niche is fundamentally important for adopting concrete multi-species management scenarios. Maintaining and creating optimal suitable habitats for SP characterized by sparse low vegetation in the foredunes areas, and uneven/low-slope beach surfaces, is the proposed conservation scenario to convert anthropic beach restorations and SP populations into a positive feedback without impacting other threatened shorebird species.
Replacement and late formation of atmospheric N2 on undifferentiated Titan by impacts
Authors: Sekine Yasuhito , Genda Hidenori , Sugita Seiji , Kadono Toshihiko , Matsui Takafumi
Published: July 2019

Saturn’s moon, Titan, has remarkable surface features—a massive N2 atmosphere and hydrological cycle of CH4—that are often compared with that of Earth^1^. However, the origin and evolution of Titan’s atmosphere remains largely unknown. The proposed formation mechanisms for Titan’s N2 require a prolonged, warm proto-atmosphere during accretion^2-4^. These mechanisms accordingly would not have worked efficiently if Titan stayed cold, as indicated by the incompletely differentiated interior observed by Cassini^5^. Because formation of a massive secondary atmosphere on a planetary body would associate with a major differentiation of its sold body during accretion^6–8^, the presence of such an atmosphere on undifferentiated cold Titan poses a serious dilemma on our view of how planetary bodies develop atmospheres. Here we propose a new mechanism for the post-accretion formation of Titan’s N2 to resolve this problem: conversion and replenishment of N2 from NH3 contained in Titan by impacts during the late heavy bombardment (LHB)^9^. Our results show that Titan, regardless of its thermal history, would acquire sufficient N2 to account for the current atmosphere during the LHB and that most of the pre-LHB atmosphere would have replaced by impact-induced N2. This is the first scenario capable of generating a N2-rich and nearly primordial Ar-free atmosphere on undifferentiated cold Titan. We also suggest that Titan’s N2 was delivered from a different source in the solar nebula compared with Earth and that the origins of N2 on Titan and Triton are fundamentally different with that of N2 on Pluto.
Microarray Analysis of PBMC after Plasmodium falciparum Infection: Molecular Insights into Disease Pathogenesis
Authors: Hu Wan-Chung , Scott Alan , Wolfe Nathan , Singh Sher , Jedlicka Anne , Bourgeois August Louis
Published: July 2019

Our laboratory’s previous microarray analysis of subjects with Plasmodium falciparum revealed up-regulation of Toll-like receptor, NF-kB, TNF-α, IFN-γ, IL-1β, p38 MAPK, and MHC molecules. We performed further time-course microarray analysis focusing on malaria pathogenesis by using peripheral leukocytes as a cellular model. We found up-regulation of coagulation-related genes (SERPINB2, thrombomodulin, thrombospondin), heat shock proteins, glycolytic enzymes, glucose transporters, and vacuolar H+-ATPases in acute febrile malaria. In early malaria, prior to detectable parasitemia, CD36 and ICAM1 were up-regulated. During acute malaria, a correlation was observed between IL-1ß and heat shock proteins, suggesting heat shock protein response may be in the febrile response induced by IL-1ß. CD163, a hemoglobin scavenger receptor, was up-regulated in acute malaria to potentially facilitate free hemoglobin up-take by peripheral leukocytes. In acute malaria, high MafB gene expression was negatively correlated with down-regulation of hemoglobin and platelet counts. Consistent with a down-regulation of hemoglobin expression, peripheral RBC counts tended to increase during the acute malaria. In our model, up-regulations of RBC and/or leucocyte binding mediators like CD36, ICAM1, thrombospondin, and thrombomodulin may contribute to the pathogenesis of cerebral malaria. Similarly, up-regulation of genes coding for glycolytic enzymes, glucose transporter and H+-ATPases may contribute to the hypoglycemia and metabolic acidosis frequently observed in seriously ill malaria patients. Overall gender effects on gene expression profiles between male and female subjects were not apparent, except that some hemoglobins were significantly down-regulated in male versus female; suggesting males may be more prone to the development of malaria associate anemia.
Extending Tlusty's method to the glycome: Tuning the repertoire of glycan determinants
Authors: Wallace Rodrick , Wallace Deborah
Published: July 2019

We apply Tlusty's information-theoretic analysis of the genetic code to the glycome, using a cognitive paradigm in which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The resulting dynamic model suggests the possibility of observing spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity. These effects may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition.
Convergence of atmospheric and North Atlantic CO2 trends on multidecadal timescales
Authors: McKinley Galen , Fay Amanda , Takahashi Taro , Metzl Nicolas
Published: July 2019

The oceans’ carbon uptake substantially reduces the rate of anthropogenic carbon accumulation in the atmosphere1, and thus slows global climate change. Some diagnoses of trends in ocean carbon uptake have suggested a significant weakening in recent years2-8, while others conclude that decadal variability confounds detection of long-term trends9-11. Here, we study trends in observed surface ocean partial pressure of CO2 (pCO2) in three gyre-scale biomes of the North Atlantic, considering decadal to multidecadal timescales between 1981 and 2009. Trends on decadal timescales are of variable magnitudes and depend sensitively on the precise choice of years. As more years are considered, oceanic pCO2 trends begin to converge to the trend in atmospheric pCO2. North of 30oN, it takes 25 years for the influence of decadal-timescale climate variability to be overcome by a long-term trend that is consistent with the accumulation of anthropogenic carbon. In the permanently stratified subtropical gyre, warming has recently become a significant contributor to the observed increase in oceanic pCO2. This warming, previously attributed to both a multidecadal climate oscillation and anthropogenic climate forcing12,13, is beginning to reduce ocean carbon uptake.
Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
Authors: Fusi Nicolo , Stegle Oliver , Lawrence Neil
Published: July 2019

Expression quantitative trait loci (eQTL) studies are an integral tool to investigate the genetic component of gene expression variation. A major challenge in the analysis of such studies are hidden confounding factors, such as unobserved covariates or unknown environmental influences. These factors can induce a pronounced artifactual correlation structure in the expression profiles, which may create spurious false associations or mask real genetic association signals.Here, we report PANAMA (Probabilistic ANAlysis of genoMic dAta), a novel probabilistic model to account for confounding factors within an eQTL analysis. In contrast to previous methods, PANAMA learns hidden factors jointly with the effect of prominent genetic regulators. As a result, PANAMA can more accurately distinguish between true genetic association signals and confounding variation.We applied our model and compared it to existing methods on a variety of datasets and biological systems. PANAMA consistently performs better than alternative methods, and finds in particular substantially more trans regulators. Importantly, PANAMA not only identified a greater number of associations, but also yields hits that are biologically more plausible and can be better reproduced between independent studies.
Toxicological Assessment of Herbal Medicine in Rats
Authors: Perumal Samy Ramar , TK Chow Vincent
Published: July 2019

Protein profiles analysis of liver, kidney and spleen by SDS-PAGE in aqueous leaf extract of Tragia involucrata L. (Euphorbiaceae) was injected intraperitoneally in albino rats for 30 days. The variation of protein changes was recorded. In liver, the aqueous leaf extracts treated (1500 mg/kg body/weight) group did not exhibit a marked increase in any of the polypeptides over control. But in the case of other treatments (250, 500, 1000 and 2000 mg/kg body weight doses) the profile showed significant increases in the accumulation of all polypeptides that were quantified using densitometry. This concludes that the aqueous leaf extract influenced the accumulation of polypeptide in higher concentration. Extra polypeptides may be responsible for the protective action.
In vitro Evolution and Engineering for Improved Ribozyme Polymerase Production
Authors: Khan Israr , Akktar Muhammad Waheed , Khan Ayaz Ali
Published: July 2019

According to the "RNA World Hypothesis" the first self replicating molecule formed from the prebiotic chemicals is the ribozyme. A model compartmentalized self replicating system for ribozyme polymerases is designed and used to improve activity, fidelity and generality of the enzyme.
The universal "shape" of human languages: spectral analysis beyond speech
Authors: Moscoso del Prado Fermin
Published: July 2019

A common recommendation for linguists is that, when analyzing language, they should take a "man-from-mars", know-nothing, perspective to describe the structures that they observe, if possible limiting themselves to the mechanical application of a set of well-defined techniques and criteria. Unfortunately, the complex nature of linguistic structures makes it difficult to adopt such a detached perspective. A language, as represented by a corpus of text, can be described macroscopically by the symbolic periodogram of the corpus, analogous to the spectrograms commonly used for describing speech. Here, I show that the periodogram exhibits a universal "shape" from human languages, and this shape originates in known properties of the human mind. Despite the universality of the overall pattern, subtle differences also reveal particularities of individual languages. These differences demonstrate the long-held --but unproven-- hypothesis that human languages balance the amount of structure contained in different levels of description so that the total amount of linguistic structure remains fairly constant across languages. The universal pattern found in the periodograms illustrates how the biological properties of the mind constrain the structure of human languages.
Proteomics in the Light of Integral Value Transformations
Authors: Hassan Sk. S. , Choudhury P. Pal
Published: July 2019

In this paper, Proteomics have been studied in the light of Integral Value Transformations (IVTs) which was introduced by Sk. S. Hassan et al in 2010. For case study, a Human olfactory receptor OR1D2 protein sequence has been taken and then different IVTs have been used to evolve OR1D2 into some other proteomic like sequences. It has been observed that some of the generated sequences have been mapped to another olfactory receptor in Human or in some other species. Also it has been corroborated through fractal dimension that some of the fundamental protein properties have been nearly intact, even after the mapping. This study will help to comprehend the proteomic evolutionary network with the help of IVTs.
Cancer and the social induction of aging
Authors: Wallace Rodrick , Wallace Deborah
Published: July 2019

Age has long been known as the primary population 'risk factor' for cancer. We suggest that the observed disparities in hormonal cancers by ethnicity, gender, and other indices of social structure and power relationships, imply a differential aging by psychosocial and environmental exposures, in the context of cross-generational epigenetic heritage. A relatively simple model of malignancy regulation illuminates the cellular root of induced aging, and explains the decline in cancer rate with extreme old age via telomere shortening. We find that the multifactorial determinants of the disorder cannot be effectively addressed by 'small molecule' interventions at the individual level, but must involve comprehensive prevention strategies that lessen exposures to policies and cultural practices that accelerate senescence in vulnerable or targeted populations.
Conservation Pakage for Modal Ecorace
Authors: Sinha Ajit Kumar
Published: July 2019

Conserving biodiversity is about genetic variety, species, habitats and ecosystems. All are important, but it is often most appropriate, practical and effective to focus on species. With modern conservation awareness, there is a welcome and popular commitment to maintaining the diversity of species in India. Nevertheless, over the last 50 years, we have witnessed the severe decline of many once widespread and familiar species, such as tropical Tasar silkworm Antherea mylitta D. Conservation is not just about avoiding extinctions, but about restoring or recovering species populations to secure levels and preventing other species from reaching such a perilous situation in the first place. Species, by their very nature, have specific ecological requirements. They may appear to share the same habitat with many others but each has a different, specific niche. It is what sets them apart, and makes them what they are. Habitat loss has historically been a factor in species decline. However, the way existing habitats are managed is also important.
The effect of noise correlations in populations of diversely tuned neurons
Authors: Ecker Alexander , Berens Philipp , Tolias Andreas , Bethge Matthias
Published: July 2019

The amount of information encoded by networks of neurons critically depends on the correlation structure of their activity. Neurons with similar stimulus preferences tend to have higher noise correlations than others. In homogeneous populations of neurons this limited range correlation structure is highly detrimental to the accuracy of a population code. Therefore, reduced spike count correlations under attention, after adaptation or after learning have been interpreted as evidence for a more efficient population code. Here we analyze the role of limited range correlations in more realistic, heterogeneous population models. We use Fisher information and maximum likelihood decoding to show that reduced correlations do not necessarily improve encoding accuracy. In fact, in populations with more than a few hundred neurons, increasing the level of limited range correlations can substantially improve encoding accuracy. We found that this improvement results from a decrease in noise entropy that is associated with increasing correlations if the marginal distributions are unchanged. Surprisingly, for constant noise entropy and in the limit of large populations the encoding accuracy is independent of both structure and magnitude of noise correlations.
A novel alveolar Krebs cycle-triggered CO2 sensing mechanism regulates regional pulmonary ventilation.
Authors: Schulte-Uentrop Leoni , Goetz Alwin , Kiefmann Rainer , Keller Paula , Tritt Oliver , Heckel Kai , Tank Sascha , Kiefmann Martina
Published: July 2019

Pulmonary perfusion disorders provoke atelectasis in order to minimize ventilation/perfusion mismatch. However, the underlying mechanisms remain unknown. Because intraalveolar CO2 concentration ([CO2]iA) declines as a consequence of poor pulmonary perfusion we postulated the existence a novel alveolar CO2-sensing mechanism which adapts the ventilation to perfusion. Real-time fluorescence imaging of rat lungs revealed that low [CO2]iA decreased cytosolic and increased mitochondrial Ca2+ in alveolar epithelial cells (AEC), leading to reduction of surfactant secretion and alveolar ventilation. Mitochondrial inhibition by ruthenium red or rotenone blocked the hypocapnia-induced responses. In cultured Type 2 AEC hypocapnia decreased cytosolic Ca2+ independently from pH and increased the NADH production, the mitochondrial transmembrane potential, and subsequently the mitochondrial Ca2+ uptake. All responses were completely blocked by the gene knockdown of the NADH producing Krebs cycle enzyme isocitrate dehydrogenase. Furthermore, ligature of the pulmonary artery of rabbits decreased alveolar ventilation, surfactant secretion, and lung compliance. Addition of 5% CO2 to the inspiratory gas inhibited all responses. Accordingly, we provide evidence for a novel CO2-sensing mechanism of AEC regulated by the Krebs cycle activity in terms of a negative feedback loop adapting surfactant secretion and thus regional ventilation to pulmonary perfusion.
Screening of certain Ayurvedic plants extracts against E. turcicum
Authors: Bhati Kaushal Kumar , Prasad R. , Singh Rajesh
Published: July 2019

The use of chemicals against pathogens is environmentally dangerous, so use of natural inhibitors for disease management is needed. In this work we screen botanical extracts from ayurvedic plants for their antifungal properties against economically important plant fungal pathogen. As a test fungal pathogen, we select E. turcicum, a potent fungal pathogen responsible for Northern leaf corn blight of Maize. This fungal pathogen was challenged by the leaf extract prepared from certain Ayurvedic plants and these observations have shown a promising future in biocontrol of fungus by using such environmentally friendly antifungal agents.
Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models
Authors: Baianu I.
Published: July 2019

Operational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable 'next-state functions' is extended to a Łukasiewicz Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis.
Single Cancer Cell Detection by Near Infrared Microspectroscopy, Infrared Chemical Imaging and Fluorescence Microspectroscopy
Authors: Baianu I. , Korban Schuyler , Costescu Doina
Published: July 2019

Novel techniques are currently being developed and established for the accurate chemical analysis and detection of single cancer cells, single embryos and single seeds by Fourier Transform Near Infrared (FT-NIR) Microspectroscopy, Fourier Transform Infrared (FT-IR), Fluorescence and High-Resolution NMR (HR-NMR). The first FT-NIR chemical images of biological systems approaching 1micron resolution are here reported. 400 and 500 MHz, H-1 NMR analyses were carried out that allowed the selection of mutagenized embryos. Detailed chemical analyses are being demonstrated to be also possible by FT-NIR Chemical Imaging/ Microspectroscopy of single cancer cells. FT-NIR Microspectroscopy and Chemical Imaging are also shown to be potentially important in Functional Genomics and Proteomics research through the rapid and accurate detection of high-content microarrays (HCMA). Multi-photon (MP), pulsed femtosecond laser NIR Fluorescence Excitation techniques were shown to be capable of Single Molecule Detection (SMD. Thus, MP NIR excitation for Fluorescence Correlation Spectroscopy (FCS) allowed not only single molecule detection, but also molecular dynamics observations and high resolution, submicron imaging of sub-femtoliter volumes inside living cells with 0.25 micron spatial resolution, in both normal and cancer cells, as well as neoplastic tissues. These novel, ultra-sensitive and rapid FT-NIR/FCS analyses have, therefore, substantial potential for numerous applications in important research areas, such as: medicine, medical/cancer research, pharmacology, agricultural biotechnology, food safety, as well as clinical diagnosis of viral diseases and cancers.
RAB family gene expression in breast cancer cells under influence of paclitaxel
Authors: Rzymowska Jolanta , Malewski Tadeusz , Maj Piotr , Wilkolaski Andrzej
Published: July 2019

The aim of this study was to investigate the role of paclitaxel on RAB family of genes in primary breast cancer cell lines. The cancer breast cells obtained from 40 women during mastectomy were used to address this issue. The group included patients with intraductal breast cancer - lesions in I or II advancement level by TNM classification and G1-G2 by Bloom classification. (tumor dimensions up to 2.0 cm without metastases to lymph nodes). Cytostatic drugs before surgery were not administered to these patients. The cultures were conducted in 25 cm^2^ plastic containers at RPMI medium with addiction of 10% fetal bovine serum (FBS) at the standard conditions. After reaching concentration levels of 10 000/ml of the cells, the cultures were treated with 60 ng/ml and 300 ng/ml doses of paclitaxel. The concentrations were calculated in relation to therapeutic doses of paclitaxel, applied in polytherapy in patients with breast cancer. The cell cultures untreated for cytostatic were used as a control group. Analysis was conducted for RAB family of genes: RAB3D, RAB5B, RAB5C, RAB7, RAB7L1, RAB9P1, RAB10. RAB11A, RAB311B, RAB13, RAB18, RAB22A, RAB23, RAB26, RAB27A, RAB27B, RAB28, RAB30, RAB31, RAB33A, RAB3D6, RAB 38, RABL2B Total RNA was extracted from the harvest control group and the treated cells, and this was followed by cDNA synthesis, which was used for hybridization assays using arrays. A lower dose of paclitaxel (60 ng/ml) treatment resulted in an increase (2-4 fold- statistically significant), whereas a higher dose (300 ng/ml) caused a decrease (2-fold - statistically insignificant) in expression of examined oncogenes, compared to that of the control group.In summary, this data indicates that 60 ng/ml paclitaxel dose induced the RAB gene expression in an up-regulated pathway. A higher concentration of cytostatic (300 ng/ml) is a toxic dose for primary breast cells in vitro.
Identification Of Mitotically Competent SOX2+ Cells In White Matter Of Normal Human Adult Brain
Authors: Oliver-De la Cruz Jorge , Carrion-Navarro Josefa , Gutierrez-Martin Antonio , Escobedo-Lucea Carmen , Garcia-Verdugo Jose Manuel , Ayuso-Sacido Angel
Published: July 2019

SOX2 expression is linked to the undifferentiated state of stem cells in mammalian neurogenic niches. While its expression has been reported in the adult human subventricular zone (SVZ), to date it has not been detected in adult human white matter. Here we describe a population of SOX2+ cells from the white matter of the adult human temporal lobe, which proliferate and express glial markers in vitro.
Peduncle inheritance behavior in Antheraea mylitta. D. - An interesting observation
Authors: Rama Rao Mazumdar , Tiwari Santosh Kumar
Published: July 2019

In eco-racial hybridization of Antheraea mylitta D.( Raily X Daba ) the occurrence of long peduncle with two and more rings were found to be an interesting observation against Daba cultivar. Preliminary studies indicate to incorporate the peduncle structure in breeding programs apart from investigating its impact on physiological behavior of the insect.
Inositol-Related Gene Knockouts Mimic Lithium's Effect on Mitochondrial Function
Authors: Toker Lilach , Berry Gerard , Agam Galila , Belmaker RH , Moechars Dieder , Chalifa-Caspi Vered , Bersudsky Yuly , Plaschkes Inbar
Published: July 2019

Bipolar-disorder, characterized by switches between depressive and manic mood, is treated by mood-stabilizers, lithium being one of them. Among hypotheses suggested, the inositol-depletion hypothesis proposes that lithium attenuates hyperactivation of phosphatidylinositol signaling linked to neurotransmission-related receptors.Available for us are knockout-mice of two genes (IMPA1 or Slc5a3) each encoding for a protein related to inositol metabolism. We previously characterized these mice as exhibiting lithium-like neurochemical and behavioral phenotype. We performed a DNA-microarray study searching for pathways commonly affected by chronic lithium treatment and by the knockout of each of the genes. Here we show up-regulation of mitochondrial function in the three paradigms studied. To verify this result, the interrelationship between treatment with lithium and rotenone, an inhibitor of mitochondrial function, was studied behaviorally. Lithium and rotenone counteracted each other's effects in two bipolar-related models. The results support the inositol-depletion hypothesis and suggest amelioration of aberrant mitochondrial function consequent to inositol-depletion.
Paraoxonase 1 Polymorphism p.Q192R in Patients With Dementia
Authors: Krzywkowski Tomasz
Published: July 2019

PON1 PCR-RFLP polymorphism frequency and enzyme activity were determined in 223 patients with dementia (94 with AD, 55 with VaD and 74 with MD) and in 100 age and sex matched controls without dementia. I found no statistical significance of genotype frequencies between analyzed groups.Paraoxonase 1 activity was lower in patients carrying the R allele in locus 192 as compared with the R allele non-carriers. The results showed statistically significant association between PON1 polymorphism and enzyme activity and thus can suggest an important relationship between different isoforms of PON1, enzyme activity and dementia.
High-order chromatin architecture determines the landscape of chromosomal alterations in cancer
Authors: Fudenberg Geoffrey , Getz Gad , Meyerson Matthew , Mirny Leonid
Published: July 2019

The rapid growth of cancer genome structural information provides an opportunity for a better understanding of the mutational mechanisms of genomic alterations in cancer and the forces of selection that act upon them. Here we test the evidence for two major forces, spatial chromosome structure and purifying (or negative) selection, that shape the landscape of somatic copy-number alterations (SCNAs) in cancer. Using a maximum likelihood framework we compare SCNA maps and three-dimensional genome architecture as determined by genome-wide chromosome conformation capture (HiC) and described by the proposed fractal-globule (FG) model. This analysis provides evidence that the distribution of chromosomal alterations in cancer is spatially related to three-dimensional genomic architecture and additionally suggests that purifying selection as well as positive selection shapes the landscape of SCNAs during somatic evolution of cancer cells.
The Proteomics World is Flat: Dependence of Regulation upon Abundance
Authors: Good David , Zubarev Roman
Published: July 2019

The long-standing assumption that proteins divide into house-keeping and cell-specific groups was recently struck down after discovering that the vast majority of expressed proteins are shared across cell lines. Here, we tested a related hypothesis that abundant proteins are less regulated than low-abundance ones. Meta-analysis of published data revealed that protein regulation is only weakly dependent upon the protein abundance, thus providing support to cell characterization by the "top" proteome.
Large scale expansion of mobile elements in specific hotspot regions of the German outbreak _Escherichia coli_ O104:H4
Authors: Crossman Lisa
Published: July 2019

The outbreak strain of _E. coli_ O104:H4 has been sequenced by several groups and made available publicly for CrowdSourcing purposes. Genome comparisons of the complete finished sequence of TY2482 (BGI), have been made with the draft assemblies of c22711 (PacBio) and an historical outbreak strain from 2001 (U. Münster & Life Technologies). A plasmid, pTY2, carrying the _agg_ operon specifying the genes for aggregative adherence fimbriae reveals a frameshift in a gene, _aggB_, that may result in altered binding _in vivo_ compared to the unframeshifted state. Comparisons additionally reveal the presence of genomic islands specific to the outbreak strain relative to other sequenced _E. coli_ strains. These regions, and islands shared with the closest previously sequenced relative _E. coli_ 55989 have been analyzed for insertion sequences and transposable elements. Several islands found in the above strains that are not present in other sequenced _E. coli_ are found to harbor a large-scale expansion of mobile elements that are by and large confined to these hotspot or permissive areas of the chromosome. The implication is that these regions are in genomic flux and may represent specific areas of future concern due to the possibility of mobilisation of the associated genomic features likely responsible for the pathogenic features and antibiotic resistance seen in these strains.