Genetics web sites

Human Genome Project Information http://www.ornl.gov/TechResources/Human_Genome/home.html

Access Excellence http://www.accessexcellence.org/

Genetics Science Learning Centre at the Eccles Institute of Human Genetics, University of Utah http://gslc.genetics.utah.edu/

Blazing a Genetic Trial http://www.hhmi.org/GeneticTrail/

A Hypermedia Glossary of Genetic Terms prepared and presented by Birgid Schlindwein http://www.weihenstephan.de/~schlind/genglos.html

Virtual Flylab http://vcourseware5.calstatela.edu/VirtualFlyLab/IntroVflyLab.html

Web watch topics coming up…     

Web Watch

Plant biology - with an emphasis on photosynthesis

The Great Plant Escape http://www.urbanext.uiuc.edu/gpe/gpe.html

The Power of Green.http://researchmag.asu.edu/stories/power.html

Photosynthesis http://biology.ck.uc.edu/courses/biol04/photosyn.htm

An Introduction to Photosynthesis and its Applicationhttp://photoscience.la.asu.edu/photosyn/education/photointro.html

Aliens Explorers - Photosynthesis http://www.alienexplorer.com/ecology/topic3.html

The Photosynthesis Processhttp://www.ifmt.nf.ca/mi-net/enviro/photo3.htm     

Structural insights into the unique inhibitory mechanism of Kunitz type trypsin inhibitor from Cicer arietinum L.

Kunitz-type trypsin inhibitors bind to the active pocket of trypsin causing its inhibition. Plant Kunitz-type inhibitors are thought to be important in defense, especially against insect pests. From sequence analysis of various Kunitz-type inhibitors from plants, we identified CaTI2 from chickpea as a unique variant lacking the functionally important arginine residue corresponding to the soybean trypsin inhibitor (STI) and having a distinct and unique inhibitory loop organization. To further explore the implications of these sequence variations, we obtained the crystal structure of recombinant CaTI2 at 2.8Å resolution. It is evident from the structure that the variations in the inhibitory loop facilitates non-substrate like binding of CaTI2 to trypsin, while the canonical inhibitor STI binds to trypsin in substrate like manner. Our results establish the unique mechanism of trypsin inhibition by CaTI2, which warrant further research into its substrate spectrum. Abbreviations BApNA Nα-Benzoyl-L-arginine 4-nitroanilide

BPT bovine pancreatic trypsin

CaTI2 Cicer arietinum L trypsin inhibitor 2

DrTI Delonix regia Trypsin inhibitor

EcTI Enterolobium contortisiliquum trypsin inhibitor

ETI Erythrina caffra trypsin inhibitor

KTI Kunitz type inhibitor

STI soybean trypsin inhibitor

TKI Tamarindus indica Kunitz inhibitor

Communicated By Ramaswamy H. Sarma     

Erratum to: An S/MAR-based L1 retrotransposition cassette mediates sustained levels of insertional mutagenesis without suffering from epigenetic silencing of DNA methylation

This is an erratum to:

An S/MAR-based L1 retrotransposition cassette mediates sustained levels of insertional mutagenesis without suffering from epigenetic silencing of DNA methylation

DOI: 10.4161/epi.5.7.12647

Danny Rangasamy

Volume 5, Issue 7

Pages 601 - 611     

Autophagy and inflammation in chronic respiratory disease

Persistent inflammation within the respiratory tract underlies the pathogenesis of numerous chronic pulmonary diseases including chronic obstructive pulmonary disease, asthma and pulmonary fibrosis. Chronic inflammation in the lung may arise from a combination of genetic susceptibility and environmental influences, including exposure to microbes, particles from the atmosphere, irritants, pollutants, allergens, and toxic molecules. To this end, an immediate, strong, and highly regulated inflammatory defense mechanism is needed for the successful maintenance of homeostasis within the respiratory system. Macroautophagy/autophagy plays an essential role in the inflammatory response of the lung to infection and stress. At baseline, autophagy may be critical for inhibiting spontaneous pulmonary inflammation and fundamental for the response of pulmonary leukocytes to infection; however, when not regulated, persistent or inefficient autophagy may be detrimental to lung epithelial cells, promoting lung injury. This perspective will discuss the role of autophagy in driving and regulating inflammatory responses of the lung in chronic lung diseases with a focus on potential avenues for therapeutic targeting.

Abbreviations AR allergic rhinitis

AM alveolar macrophage

ATG autophagy-related

CF cystic fibrosis

CFTR cystic fibrosis transmembrane conductance regulator

COPD chronic obstructive pulmonary disease

CS cigarette smoke

CSE cigarette smoke extract

DC dendritic cell

IH intermittent hypoxia

IPF idiopathic pulmonary fibrosis

ILD interstitial lung disease

MAP1LC3B microtubule associated protein 1 light chain 3 beta

MTB Mycobacterium tuberculosis

MTOR mechanistic target of rapamycin kinase

NET neutrophil extracellular traps

OSA obstructive sleep apnea

PAH pulmonary arterial hypertension

PH pulmonary hypertension

ROS reactive oxygen species

TGFB1 transforming growth factor beta 1

TNF tumor necrosis factor

     

Evolution

BBC Education Evolution http://www.bbc.co.uk/education/darwin/index.shtml

Evolution theory and science

Eukaryotic Cells — the next evolutionary step

Evolution and the Nature of Science Institutes

Biology lessons: how do populations change over time?     

Progress in the search for circulating biomarkers of nonalcoholic fatty liver disease

Abstract

Context: The definitive standard for the diagnosis of nonalcoholic fatty liver disease (NAFLD) is clinico-pathological correlation, but frequently the only laboratory abnormality is an elevation of serum aminotransferases.

Objective: This has resulted in the search for more specific laboratory biomarkers.

Methods: The literature was searched for novel plasma/serum markers of NAFLD.

Results: Studies reviewed here included histologically-confirmed patients presenting some stage of NAFLD and monitored one or more novel serum/plasma biomarkers.

Conclusion: The most promising application of some of these novel biomarkers for the detection and quantification of NAFLD and particularly NASH appears to be in the combination of several into diagnostic panels.     

Web watch

Teachers' websites

Webwise Spinneret Biology websitehttp://web.ukonline.co.uk/webwise/spinnere:

Lesson Planet www.lessonplanet.com

Gourmet Curriculum Press www.gourmetcurriculumpress.com

Learn.co.ukwww.learn.co.uk

Just for Teacherswww.justforteachers.co.uk     

Early Miocene rodents of Gökler (Kazan Basin,Central Anatolia,Turkey)

Abstract

The rich and relatively diverse fossil mammalian assemblage from Gökler is of special importance for understanding of faunal evolution in Central Anatolia. Large mammals were not recovered, but insectivores and rodents are abundant. The assemblage of rodents is studied in detail and comprises mainly diversified cricetids. Dormice are abundant, but are represented by only one species. Squirrels are represented only by few specimens and also beaver remains were identified. Spanocricetodon sinuosus is referred to a new genus Latocricetodon nov. gen that is tentatively assigned to the Pseudocricetodontinae. Newly named species are Cricetodon goklerensis sp. nov., Democricetodon haltmari sp. nov., Eumyarion lukasi sp. nov. and Glirudinus matusi sp. nov. The rodent assemblage is assigned to local zone C which is correlated to the European biounit MN2 (early Miocene). Our biochronological assessment is supported by radiometric dating from two volcanic ash layers.

Latocricetodon

LSID http://zoobank.org/urn:lsid:zoobank.org:act:3414DB1E-0C5E-4154-BE5E-02A9ED183B1A

Cricetodon goklerensis

LSID http://zoobank.org/urn:lsid:zoobank.org:act:1B658872-6C10-4355-B87C-3E6277AF4EDA

Democricetodon haltmari

LSID http://zoobank.org/urn:lsid:zoobank.org:act:9B13F956-7F8C-406A-9970-1F5E999E54C6

Eumyarion lukasi

LSID http://zoobank.org/urn:lsid:zoobank.org:act:34DED87E-855F-4969-AB84-10BED5C572BF

Glirudinus matusi

LSID http://zoobank.org/urn:lsid:zoobank.org:act:798ECB9A-E3B5-4C38-B5B3-FEB17AF734FE     

Serum tumor markers in bile duct cancer – a review

Abstract

Context: Bile duct cancer (BDC) is a disease with a very grave prognosis, often diagnosed too late.

Objective: The aim of this review is to evaluate available literature on tumor markers in serum from patients with BDC.

Methods: Using the search words “serum markers”, “bile duct cancer”, “cholangiocarcinoma”, “biomarker” and “tumor marker”, a search was carried out.

Results: Seventy-five studies were included in the review.

Conclusion: CA19-9 is by far the most studied and most promising diagnostic and/or prognostic marker in BDC. But also the different mucins are interesting as new markers of BDC in serum.     

Neutrophil gelatinase-associated lipocalin after off pump versus on pump coronary artery surgery

Abstract

Context: Cardiac surgery.

Objective: To compare plasma and urinary neutrophil gelatinase-associated lipocalin (P-/U-NGAL) in on-pump (n?=?43) versus off-pump (n?=?40) surgery.

Materials and methods: We obtained perioperative P-/U-NGAL and outcome data.

Results: P-/U-NGAL increased after surgery. P-NGAL was higher post-surgery in on pump patients (139 versus 67?µg L^?1; p?<?0.001), but not at 24?h. There were no differences in U-NGAL. Correlation between P-/U-NGAL and plasma creatinine was weak.

Discussion: P-NGAL acts like a neutrophil activation biomarker and U-NGAL like a tubular injury marker.

Conclusion: On-pump patients had greater neutrophil activation. On- versus off-pump surgery had similar impact on tubular cells.     

The effects of simvastatin treatment on plasma lipid-related biomarkers in men with dyslipidaemia

Background: Lipidomic biomarkers will facilitate the development of novel anti-atherosclerotic therapies.

Objective: To evaluate the responses of circulating biomarkers to simvastatin treatment.

Methods: A randomized, cross-over study in men with mixed dyslipidaemia was used to compare effects of simvastatin 40?mg/day with placebo.

Results: Plasma concentrations of nine fatty acids (FA; of 33 evaluated) were reduced significantly by simvastatin. No changes in the rates of FA synthesis or in hepatic lipase or lipoprotein lipase activities were apparent. Circulating proprotein convertase subtilisin/kexin type 9 (PCSK9) levels increased.

Conclusion: We identified lipidomic biomarkers of simvastatin treatment effect that are consistent with statin inhibition of 3-hydroxy-3-methyl-glutaryl coenzyme A (HMG-CoA) reductase.

Trial registration: ClinicalTrials.gov identifier: NCT00935259.     

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data

Background

DNA methylation is a crucial epigenomic mechanism in various biological processes. Using whole-genome bisulfite sequencing (WGBS) technology, methylated cytosine sites can be revealed at the single nucleotide level. However, the WGBS data analysis process is usually complicated and challenging.

Results

To alleviate the associated difficulties, we integrated the WGBS data processing steps and downstream analysis into a two-phase approach. First, we set up the required tools in Galaxy and developed workflows to calculate the methylation level from raw WGBS data and generate a methylation status summary, the mtable. This computation environment is wrapped into the Docker container image DocMethyl, which allows users to rapidly deploy an executable environment without tedious software installation and library dependency problems. Next, the mtable files were uploaded to the web server EpiMOLAS_web to link with the gene annotation databases that enable rapid data retrieval and analyses.

Conclusion

To our knowledge, the EpiMOLAS framework, consisting of DocMethyl and EpiMOLAS_web, is the first approach to include containerization technology and a web-based system for WGBS data analysis from raw data processing to downstream analysis. EpiMOLAS will help users cope with their WGBS data and also conduct reproducible analyses of publicly available data, thereby gaining insights into the mechanisms underlying complex biological phenomenon. The Galaxy Docker image DocMethyl is available at https://hub.docker.com/r/lsbnb/docmethyl/.

EpiMOLAS_web is publicly accessible at http://symbiosis.iis.sinica.edu.tw/epimolas/.

     

Deregulated systemic IL-10/IL-12 balance in advanced and poor prognosis paediatric soft tissue sarcomas

Abstract

Context: The roles of interleukin 10 (IL-10) and IL-12 in regulation of cancer growth and Th1/Th2 immune responses towards cancer are unclear.

Objective: To establish the prognostic significance of serum IL-10 and IL-12 in paediatric soft tissue sarcomas (STS).

Materials and methods: ELISA determinations of cytokines were performed as pre-treatment in 59 children with STS and 30 healthy controls.

Results: Elevated IL-10 and decreased IL-12 serum levels correlated with advanced disease, poor response to chemotherapy and poor outcome. IL-10?≥?9.5?pg/ml, IL-12?≤?65?pg/ml and lymph nodes involvement independently predicted poor overall survival (OS) in multivariate Cox analysis.

Conclusion: Serum IL-10/IL-12 balance determination may facilitate to assess risk groups and prognosis in childhood STS.     

Circulating liver-specific microRNAs as noninvasive diagnostic biomarkers of hepatic diseases in human

Context: Hepatitis is an endemic disease worldwide leading to chronic and debilitating cancers. The viral agents and hepatotoxic substances lead to damage of hepatocytes and release of damage associated molecules in circulation. The lack of timely and rapid diagnosis of hepatitis results in chronic disease.

Objective: The present review aimed to describe regulation, release and functions of microRNAs (miR) during human liver pathology and insights into their promising use as noninvasive biomarkers of hepatitis.

Methods: Comprehensive data were collected from PubMed, ScienceDirect and the Web of Science databases utilizing the keywords “biomarkers”, “microRNAs” and “hepatic diseases”.

Results: The miRs are readily released in the body fluids and blood during HBV/HCV associated hepatitis as well as metabolic, alcoholic, drug induced and autoimmune hepatitis. The liver-specific microRNAs including miR-122, miR-130, miR-183, miR-196, miR-209 and miR-96 are potential indicators of liver injury (mainly via apoptosis, necrosis and necroptosis) or hepatitis with their varied expression during acute/fulminant, chronic, liver fibrosis/cirrhosis and hepato-cellular carcinoma.

Conclusions: The liver-specific miRs can be used as rapid and noninvasive biomarkers of hepatitis to discern different stages of hepatitis. Blocking or stimulating pathways associated with miR regulation in liver could unveil novel therapeutic strategies in the management of liver diseases.

• Clinical significance

• Liver specific microRNAs interact with cellular proteins and signaling molecules to regulate the expression of various genes controlling biological processes.

• The circulatory level of liver specific microRNAs is indicator of severity of HBV and HCV infections as well as prognostic and therapeutic candidates.

• The expression of liver specific microRNAs is strongly associated with infectious, drug-induced, hepatotoxic, nonalcoholic steatohepatitis and nonalcoholic fatty liver diseases.

     

Dynamic changes in serum angiopoietin-1, angiopoietin-2, and angiopoietin-2/angiopoietin-1 ratio in acute myocardial infarction patients treated with primary percutaneous coronary intervention

Context: Angiopoietin-1 (Ang-1) and angiopoietin-2 (Ang-2) play divergent roles in myocardial ischemia and reperfusion injury.

Objective: To investigate serum Ang-1 and Ang-2 levels in ST-segment elevation myocardial infarction (STEMI) patients treated with primary percutaneous coronary intervention (PCI).

Methods: Serum Ang-1 and Ang-2 were measured in 85 STEMI patients in the first week after PCI.

Results: Ang-1, Ang-2 and Ang-2/Ang-1 ratio (Ang-2/1) were all increased at admission, and had dynamic changes after PCI. Ang-2 and Ang-2/1 at admission and 2 h after PCI were positively correlated with peak cardiac troponin T levels.

Conclusion: The extent of myocardial damage may be linked to circulating Ang-2 and Ang-2/1.