Michael Black

California Polytechnic State University, San Luis Obispo | Cal Poly · Department of Biological Sciences

Microbial Source Tracking (MST) aims to classify the source host-species of biological matter, typically fecal matter, using strains of fecal indicator bacteria, often E. coli. This paper continues addressing the MST problem using analysis of a library of bacterial fingerprints started in [9]. The Cal Poly Library of Pyroprints (CPLOP) is a collect...

Contamination of fluid and processed milk products with endospore-forming bacteria, such as Bacillaceae, affect milk quality and longevity. Contaminants come from a variety of sources, including the dairy farm environment, transportation equipment, or milk processing machinery. Tracking the origin of bacterial contamination to allow specifically ta...

The primary goal of this project was to identify the biological sources of fecal contamination within and around the Mission tunnel of SLO Creek. Fecal coliform bacteria are used as an indication of fecal contamination that may include disease‐causing bacteria and viruses. Using a library‐based approach, we were able to track the possible sources o...

We have developed a novel genotypic fingerprinting method for typing Escherichia coli strains via simultaneous, multi‐locus pyrosequencing of the internal transcribed spacer (ITS) regions in ribosomal RNA operons. The data generated, called pyroprints, are unique to the polymorphic ITS alleles and their relative frequency among the seven rRNA opero...

Pyroprinting is a novel library-based microbial source tracking method developed by the Biology department at Cal Poly, San Luis Obispo. Biologists conducting research using pyroprinting rely on methods for partitioning collected bacterial isolates into bacterial strains. Clustering algorithms are often used for bacterial strain analysis of organis...

To date, microbial source tracking (MST), i.e. determining the source of microbial contamination based on the specific strains observed in environment, is done using methods that are time-consuming, expensive and not always reliable. The biology department at Cal Poly, San Luis Obispo has developed a new method for MST called pyroprinting. Pyroprin...

Microbial Source Tracking (MST) is a field in which microbial strains are identified and associated with a specific host source (e.g., human, canine, avian, etc). Identifying the hosts of microbial strains lies at the heart of many studies of bacterial contamination in the environment. Being able to determine which host species is responsible, e.g....

Hierarchical clustering is used in computational biology as a method of comparing sequenced bacterial strain DNA and determining bacterial isolates that belong to the same strain. However, the results of the hierarchical clustering are, at times, difficult to read and interpret. This paper is a case study for the use of a modified hierarchical clus...

From bottlenose dolphins, to walruses, to sea otters, the parasitic protozoan Toxoplasma gondii is infecting marine mammals around the world. Whereas the terrestrial transmission pathways of T. gondii are well-described, the transmission pathway by which marine mammals are being infected is unknown. We hypothesize that migratory filter feeders, spe...

The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the classroom...

The endocytic pathway in yeast leads to the vacuole, but resident proteins of the late Golgi, and some endocytosed proteins such as the exocytic SNARE Snc1p, are retrieved specifically to the Golgi. Retrieval can occur from both a late pre-vacuolar compartment and early or 'post-Golgi' endosomes. We show that the endosomal SNARE Pep12p, and a mutan...

The AP-1 adaptor complex has been cast as the major player in clathrin coat formation for vesicular transport from the trans-Golgi to the endocytic pathway. But new results on 'GGA' proteins have raised doubts about this paradigm and suggest both a new sorting mechanism and an unexpected complexity in the roles of clathrin.

Membrane proteins transported to the yeast vacuole can have two fates. Some reach the outer vacuolar membrane, whereas others enter internal vesicles, which form in late endosomes, and are ultimately degraded. The vacuolar SNAREs Nyv1p and Vam3p avoid this fate by using the AP-3-dependent pathway, which bypasses late endosomes, but the endosomal SN...

Pep12p is a yeast syntaxin located primarily in late endosomes. Using mutagenesis of a green fluorescent protein chimera we have identified a sorting signal FSDSPEF, which is required for transport of Pep12p from the exocytic pathway to late endosomes, from which it can, when overexpressed, reach the vacuole. When this signal is mutated, Pep12p ins...

This chapter describes methodologies for both forward genetics—(i.e., conventional and transmission genetics) and reverse genetics (transfection/transformation). The study of parasitic protozoa has benefited relatively little from the application of genetics. In part, this is because most of the organisms that have been models for biochemical and m...

This report describes the use of restriction enzyme-mediated integration (REMI) to increase the transformation frequency and allow co-transfection of several unselected constructs under the selection of a single selectable marker. We found that while BamHI (the enzyme used to originally demonstrate REMI (Schiestl, R.H. and Petes, T.D. (1991) Integr...