mtPrimer3: PCR primer design for mtDNA

Due to their usefulness in tracking the evolution of man and the discovery that they cause many different diseases, the scientific community has become extremely interested in mitochondrial DNA (mtDNA) mutations. PCR is a key component in nearly all genotyping methods, but using it can be problematic for mtDNA since mtDNA\u27s highly polymorphic nature makes it difficult to design adequate primers. This is because polymorphisms can easily obscure the source sequence, preventing primers from annealing properly. For this reason, we modified a popular online primer design program, Primer3, to create mtPrimer3, a primer design program specially designed to create primers for mtDNA. mtPrimer3 creates primers that avoid highly polymorphic areas, to greatly increase the chances that the primers will properly anneal, and include areas that are unique to mtDNA only, so that false positive results are not generated by accidental annealing to nuclear DNA. This is accomplished by 1) checking the stretch of sequence that a primer anneals to against a database of known mitochondrial polymorphisms, and 2) by submitting the primers to BLAST to see if there is significant homology with human genomic DNA. If a primer pair has too many polymorphisms, then it is disqualified from being a good primer pair. The primer pairs that have been submitted to BLAST are scored based on a custom-designed scoring system, a harmonic mean that negatively penalizes primers with low expect values. The primer pairs are then ordered from greatest to least and the top scoring primer pairs are emailed to the user. In this way, mtPrimer3 creates primers that are suited for working with mtDNA

Strategy for Youth Empowerment and Entrepreneurship: An assessment of WOW Outreach, Flint, MI

This project will develop an outline for youth entrepreneurship in the North Side of Flint, Michigan with the help of WOW Outreach of Flint. The report will further WOW Outreach’s goals of reducing violence through positive opportunities and increasing economic opportunities through the use of Flint’s Community Capitals Framework. Through this research WOW Outreach will be able to address critical development needs, specifically focusing on youth empowerment, and allow youth entrepreneurship to grow and prosper in the North Side of Flint

Comparative Analysis of Colorfastness of Extracted Pigment from Kangkong (Ipomoea aquatica) with Varied Alcohol Solutions

Inorganic pigments are the most preferred pigments to be produced due to their greater resistance to fade, efficiency in the application, and how it is overall easier and faster to produce. However, natural water is polluted, and close vegetation is damaged because of the affected water channels that have been damaged due to improper disposal by the manufacturing industry. This paper reviews a comparative analysis of the colorfastness of extracted pigment from kangkong with varied alcohol solutions. A total of 7 varying ethyl alcohol solutions with concentrations ranging from 10% to 70% were obtained using the dilution equation. Kangkong leaves were then utilized for the extraction of chlorophyll due to its high leaf yield rate. The Brightness levels and Saturation levels had an inverse and direct correlation to the alcohol concentration, respectively. This suggests that a greater alcohol concentration is more effective and efficient in the extraction of chlorophyll because the samples had a better expression of colors. After observing the color value before and after administering the colorfastness test, the alcohol concentration in the extraction of chlorophyll has an inverse relationship with the colorfastness of the pigment on textile material

Monomeric C-Reactive Protein Localized in the Cerebral Tissue of Damaged Vascular Brain Regions Is Associated With Neuro-Inflammation and Neurodegeneration-An Immunohistochemical Study

Monomeric C-reactive protein (mCRP) is now accepted as having a key role in modulating inflammation and in particular, has been strongly associated with atherosclerotic arterial plaque progression and instability and neuroinflammation after stroke where a build-up of the mCRP protein within the brain parenchyma appears to be connected to vascular damage, neurodegenerative pathophysiology and possibly Alzheimer's Disease (AD) and dementia. Here, using immunohistochemical analysis, we wanted to confirm mCRP localization and overall distribution within a cohort of AD patients showing evidence of previous infarction and then focus on its co-localization with inflammatory active regions in order to provide further evidence of its functional and direct impact. We showed that mCRP was particularly seen in large amounts within brain vessels of all sizes and that the immediate micro-environment surrounding these had become laden with mCRP positive cells and extra cellular matrix. This suggested possible leakage and transport into the local tissue. The mCRP-positive regions were almost always associated with neurodegenerative, damaged tissue as hallmarked by co-positivity with pTau and β-amyloid staining. Where this occurred, cells with the morphology of neurons, macrophages and glia, as well as smaller microvessels became mCRP-positive in regions staining for the inflammatory markers CD68 (macrophage), interleukin-1 beta (IL-1β) and nuclear factor kappa B (NFκB), showing evidence of a perpetuation of inflammation. Positive staining for mCRP was seen even in distant hypothalamic regions. In conclusion, brain injury or inflammatory neurodegenerative processes are strongly associated with mCRP localization within the tissue and given our knowledge of its biological properties, it is likely that this protein plays a direct role in promoting tissue damage and supporting progression of AD after injury.The authors extend their appreciations to the deputyship for Research & Innovation, Ministry of Education in Saudi Arabia for funding this research work through the project number (lFP-2020-36). The authors would also like to thank Deanship of Scientific Research at Majmaah University, Al Majmaah-11952, Saudi Arabia for supporting this work. This work was supported from a grant from the Competitiveness Operational programme 2014–2020: C-reactive protein therapy for stroke-associated dementia: ID_P_37_674, My SMIS code:103432 contract 51/05.09.2016

Low-dose hydroxycarbamide therapy may offer similar benefit as maximum tolerated dose for children and young adults with sickle cell disease in low-middle-income settings [version 1; referees: 2 approved]

The multiple clinical benefits of hydroxycarbamide in sickle cell disease are supported by a large body of evidence. The maximum tolerated dose (MTD) is the regimen recommended by guidelines from a panel of National Heart, Lung, and Blood Institute (NHLBI) experts, but other dosage regimens have been used in babies (BABY-HUG) 9 to 18 months old (20 mg/kg per day) and developing countries such as India (10 mg/kg per day); however, there has been no direct comparison of the efficacy, effectiveness, or cost-effectiveness of these different regimens. The purpose of this review was to investigate the current situation with various hydroxycarbamide regimens with particular relevance to low-middle-income countries. In regard to methodology, a literature review was undertaken by using multiple databases in PubMed and Google and the search terms included sickle cell disease, hydroxyurea, hydroxycarbamide, sickle cell anaemia, low-middle-income countries, Sub-Saharan Africa, and India. Although MTD regimens have been widely used in research, especially within North America, clinical trials elsewhere tend to use fixed-dose regimens. In a survey of haematologists across Europe and Africa, 60% (75% response rate) did not use the MTD regimen for hydroxycarbamide treatment of sickle cell disease. The recommendations are (1) for practical purposes to commence using fixed-dose hydroxycarbamide in line with BABY-HUG recommendations and then (2) to consider or propose a trial comparing MTD escalation with various fixed doses and to include as end points health-related quality of life, haemoglobin F levels, adherence, and cost-effectiveness

The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework

Comparisons of stem cell experiments at both molecular and semantic levels remain challenging due to inconsistencies in results, data formats, and descriptions among biomedical research discoveries. The Harvard Stem Cell Institute (HSCI) has created the Stem Cell Commons (stemcellcommons.org), an open, community-based approach to data sharing. Experimental information is integrated using the Investigation-Study-Assay tabular format (ISA-Tab) used by over 30 organizations (ISA Commons, isacommons.org). The early adoption of this format permitted the novel integration of three independent systems to facilitate stem cell data storage, exchange and analysis: the Blood Genomics Repository, the Stem Cell Discovery Engine, and the new Refinery platform that links the Galaxy analytical engine to data repositories

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies

INVESTIGATION OF THE IMPACT OF HYPERGLYCEMIA ON THE IMMUNE SYSTEM IN TYPE 2 DIABETES

Ph.D

Monitoring of microplastic concentrations in 132 Iowa lakes in relation to abiotic, biotic, and anthropogenic factors

Global annual plastic production rate is approaching 400 million metric tons, with substantial amounts invading aquatic environments yearly. Numerous studies have been conducted monitoring marine environment plastic litter. An understanding of plastic litter’s magnitude in freshwater ecosystems is lagging, particularly for microplastics (MP(s) 100 nm to 5 mm in length/diameter). Their ubiquitous presence and small sizes are concerning, since MP effects remain inadequately understood. Our objective was to document MP concentration in lake surface waters, and investigate how abiotic, biotic, and anthropogenic elements explain MP concentration variability among lakes. We sampled MPs in 132 Iowa lakes, collected throughout the water column using a Wisconsin net (63µm mesh size). A fully automated custom-built Bruker LUMOS-II Fourier-transform infrared (FTIR) spectro-microscope was employed to identify MPs. Average MP concentration across lakes was 5.2 particles/L, with dimensions averaging 139 µm in length and 77 µm in width. Predominant MP polymers collected were polyvinyl chloride (46% of all MPs), polyester (30%), and polyethylene (11%). Two variance partitioning analysis models were created to explore variability in MP concentration. The first classical model explained 7.5% of data variability based on: roads; developed medium, and high intensity land cover; sewage plants; and thermocline. The second model, based on Louvain Groups, explained 8.3% of data variability based on: lake area; maximum lake depth; zooplankton tow depth; Secchi depth; lake perimeter; lake shoreline development factor; evergreen forest cover; and thermocline. Roads and developed intensity cover were positively correlated with MP concentrations, alongside household visits standardized to the lake area. Maximum lake depth, zooplankton tow depth, Secchi depth and thermocline presence were negatively correlated with MP concentration. In nine instances, MP concentrations exceeded 50% of the modeled hazardous concentration affecting 5% of aquatic species