After six, at forty.

This is a nonfiction memoir detailing my journey as an African immigrant. The focus is two pronged: it describes my deeper religious understanding as I went through a journey of barrenness to childbirth while simultaneously narrating the comparison between Kenyan and contemporary American cultures as I emigrate and settle in the United States to pursue further education

Sample prep for proteomics of breast cancer: proteomics and gene ontology reveal dramatic differences in protein solubilization preferences of radioimmunoprecipitation assay and urea lysis buffers

<p>Abstract</p> <p>Background</p> <p>An important step in the proteomics of solid tumors, including breast cancer, consists of efficiently extracting most of proteins in the tumor specimen. For this purpose, Radio-Immunoprecipitation Assay (RIPA) buffer is widely employed. RIPA buffer's rapid and highly efficient cell lysis and good solubilization of a wide range of proteins is further augmented by its compatibility with protease and phosphatase inhibitors, ability to minimize non-specific protein binding leading to a lower background in immunoprecipitation, and its suitability for protein quantitation.</p> <p>Results</p> <p>In this work, the insoluble matter left after RIPA buffer extraction of proteins from breast tumors are subjected to another extraction step, using a urea-based buffer. It is shown that RIPA and urea lysis buffers fractionate breast tissue proteins primarily on the basis of molecular weights. The average molecular weight of proteins that dissolve exclusively in urea buffer is up to 60% higher than in RIPA.</p> <p>Gene Ontology (GO) and Directed Acyclic Graphs (DAG) are used to map the collective biological and biophysical attributes of the RIPA and urea proteomes. The Cellular Component and Molecular Function annotations reveal protein solubilization preferences of the buffers, especially the compartmentalization and functional distributions.</p> <p>It is shown that nearly all extracellular matrix proteins (ECM) in the breast tumors and matched normal tissues are found, nearly exclusively, in the urea fraction, while they are mostly insoluble in RIPA buffer. Additionally, it is demonstrated that cytoskeletal and extracellular region proteins are more soluble in urea than in RIPA, whereas for nuclear, cytoplasmic and mitochondrial proteins, RIPA buffer is preferred.</p> <p>Extracellular matrix proteins are highly implicated in cancer, including their proteinase-mediated degradation and remodelling, tumor development, progression, adhesion and metastasis. Thus, if they are not efficiently extracted by RIPA buffer, important information may be missed in cancer research.</p> <p>Conclusion</p> <p>For proteomics of solid tumors, a two-step extraction process is recommended. First, proteins in the tumor specimen should be extracted with RIPA buffer. Second, the RIPA-insoluble material should be extracted with the urea-based buffer employed in this work.</p

Dramatic down-regulation of oxidoreductases in human hepatocellular carcinoma hepG2 cells: proteomics and gene ontology unveiling new frontiers in cancer enzymology

<p>Abstract</p> <p>Background</p> <p>Oxidoreductases are enzymes that catalyze many redox reactions in normal and neoplastic cells. Their actions include catalysis of the transformation of free, neutral oxygen gas into oxygen free radicals, superoxide, hydroperoxide, singlet oxygen and hydrogen peroxide. These activated forms of oxygen contribute to oxidative stress that modifies lipids, proteins, DNA and carbohydrates. On the other hand, oxidoreductases constitute one of the most important free radical scavenger systems typified by catalase, superoxide dismutase and glutathione peroxidase.</p> <p>In this work, proteomics, Gene Ontology mapping and Directed Acyclic Graphs (DAG) are employed to detect and quantify differential oxidoreductase enzyme expressions between HepG2 cells and normal human liver tissues.</p> <p>Results</p> <p>For the set of bioinformatics calculations whose BLAST searches are performed using the BLAST program <b>BLASTP 2.2.13 [Nov-27-2005]</b>, DAG of the Gene Ontology's Molecular Function annotations show that oxidoreductase activity parent node of the liver proteome contains 331 annotated protein sequences, 7 child nodes and an annotation score of 188.9, whereas that of HepG2 cells has 188 annotated protein sequences, 3 child nodes and an annotation score of only 91.9. Overwhelming preponderance of oxidoreductases in the liver is additionally supported by the isomerase DAGs: nearly all the reactions described in the normal liver isomerase DAG are oxidoreductase isomerization reactions, whereas only one of the three child nodes in the HepG2 isomerase DAG is oxidoreductase. Upon normalization of the annotation scores to the parent Molecular Function nodes, oxidoreductases are down-regulated in HepG2 cells by 58%.</p> <p>Similarly, for the set of bioinformatics calculations whose BLAST searches are carried out using <b>BLASTP 2.2.15 [Oct-15-2006</b>], oxidoreductases are down-regulated in HepG2 cells by 56%.</p> <p>Conclusion</p> <p>Proteomics and Gene Ontology reveal, for the first time, differential enzyme activities between HepG2 cells and normal human liver tissues, which may be a promising new prognostic marker of Hepatocellular carcinoma.</p> <p>Two independent sets of bioinformatics calculations that employ two BLAST program versions, and searched different databases, arrived at essentially the same conclusion: oxidoreductases are down-regulated in HepG2 cells by approximately 57%, when compared to normal human liver tissues. Down-regulation of oxidoreductases in hepatoma is additionally supported by Gene Ontology analysis of isomerises.</p

Multistep tandem mass spectrometry for sequencing cyclic peptides in an ion-trap mass spectrometer

AbstractCollisionally activated decomposition (CAD) of a protonated cyclic peptide produces a superposition spectrum consisting of fragments produced following random ring opening of the cyclic peptide to give a set of acylium ions (or isomeric equivalents) of the same m/z. Assignment of the correct sequence is often difficult owing to lack of selectivity in the ring opening. A method is presented that utilizes multiple stages of CAD experiments in an electrospray ion-trap mass spectrometer to sequence cyclic peptides. A primary acylium ion is selected from the primary product-ion spectrum and subjected to several stages of CAD. Amino-acid residues are sequentially removed, one at each stage of the CAD, from the C-terminus, until a b2 ion is reached. Results are presented for seven cyclic peptides, ranging in sizes from four to eight amino-acid residues. This method of sequencing cyclic peptides eliminates ambiguities encountered with other MS/MS approaches. The power of the strategy lies in the capability to execute several stages of CAD upon a precursor ion and its decomposition products, allowing the cyclic peptide to be sequenced in an unambiguous, stepwise manner

The Influence of Microcredits Initiatives in Eliminating Poaching in Communities Around National Parks and Game Reserves in Tanzania.

The study assessed the influence of microcredit initiatives in eliminating poaching in communities around national parks and game reserves in Tanzania. Explanatory design was used through causal relationship testing between study variables in the process of knowledge generation. Three predictor variables were identified for testing on poaching elimination as the dependent variable including promotion of entrepreneurship, women empowerment and engagement in legitimate activities. Data were collected from community members as beneficiaries of the micro credits from the sample of 100 respondents through structured questionnaire. The collected results were computed in SPSS data sheet to produce statistical tests to present the findings. Descriptive statistics were used to present the results on profile of the respondents. Also, correlation and multiple regression analysis described the relationship between study variables. Findings showed that all three predicting variables tested namely promotion of entrepreneurship, women empowerment and engagement in legitimate activities were found positive with significant effect statistically on poaching elimination (p<0.05). The implication of the results is that poaching elimination through microcredit measures in communities living around national parks and game reserves is influenced with promotion of entrepreneurship, women empowerment and engagement in legitimate activities. Keywords: Microcredits, Poaching, Game Reserve, National Parks

Use of Sleeve Nets to Improve Survival of the Boisduval Silkworm, Anaphe panda, in the Kakamega Forest of Western Kenya

Prospects for development of a wild silk industry in Africa would be improved if silkworm survival during mass production could be improved. A study on the survival of the Boisduval silkworm, Anaphe panda (Boisduval) (Lepidoptera: Thaumetopoeidae) was conducted with and without protection by net sleeves in two different forest habitats (natural and modified) in the Kakamega forest of western Kenya. Overall, cohort survival was significantly higher (P < 0.001) in the natural than in the modified forest, but larval survival was improved over three-fold by protection with net sleeves in both habitat types. In the modified forest, only 16.8% of unprotected larvae survived to the pupal stage and formed cocoons, whereas 62.3% survived in the same environment when they were protected with net sleeves. In the natural forest, 20.4% of unprotected larvae survived, whereas 67.7% survived in net sleeves. There was also a significant effect of season; cohorts of larvae that eclosed in the wet season had significantly lower survival than those eclosing in the dry season (P = 0.02). Sources of mortality appeared to be natural enemies (parasites, predators and diseases) and climatic factors

Overnight interbank markets and the determination of the interbank rate: a selective survey

Overnight interbank markets provide critical facilities for the banking system to manage, pool and redistribute its cash reserves. We provide a selective survey of the literature on overnight interbank markets. We outline the typical structure of overnight markets, including the networking relationships involved, as an indispensable prerequisite for a clear understanding of the workings of these markets. We review the theoretical and empirical studies on the determination of the overnight rate, and in that context discuss the implications of the 2007–08 financial crisis. We summarise key issues for further research

Somatic evolution and global expansion of an ancient transmissible cancer lineage

The canine transmissible venereal tumour (CTVT) is a cancer lineage that arose several millennia ago and survives by ‘metastasising’ between hosts via cell transfer. The somatic mutations in this cancer record its phylogeography and evolutionary history. We constructed a time-resolved phylogeny from 546 CTVT exomes and describe the lineage’s worldwide expansion. Examining variation in mutational exposure, we identify a highly context-specific mutational process that operated early but subsequently vanished, correlate ultraviolet-light mutagenesis with tumour latitude, and describe tumours with heritable hyperactivity of an endogenous mutational process. CTVT displays little evidence of ongoing positive selection, and negative selection is detectable only in essential genes. We illustrate how long-lived clonal organisms capture changing mutagenic environments, and reveal that neutral drift is the dominant feature of long-term cancer evolution