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Automated Drosophila Maintenance System

Drosophila spp., also known as fruit flies, are widely used in genetic research. Drosophila lines (e.g. flies with a particular mutation) can only be stored as live animals – they cannot be frozen and remain viable. So to maintain the stocks, the live flies are manually transferred from an old vial to a new vial on a regular basis (every 1-2 weeks). Some Drosophila labs maintain hundreds or even thousands of individual lines and so maintenance of these lines can be very time consuming. A UC Santa Cruz Drosophila researcher has developed a simpler and more efficient method of transferring the flies that requires significantly less hands-on work.

Nontoxic Alternatives to Phthalate Plasticizers for PVC

Phthalates are synthetic chemicals added to polyvinyl chloride (PVC) to make flexible plastics. Due to health concerns, phthalates have been banned from children's products in the United States and Europe, but they are still used in a wide range of consumer products, including food wrap, medical devices, automotive parts, and building materials., chemicals that interfere with the body's hormone systems. Effects on wildlife of phthalates in the environment are also a concern. Phthalates are readily absorbed by the body through inhalation, ingestion, or skin contact. Phthalate exposure has been associated with reproductive and developmental abnormalities in animal studies. Epidemiological studies in humans also suggest that exposure to phthalates may have adverse health effects, including reproductive abnormalities that can lead to infertility. Phthalates are metabolized by the body into compounds that are considered endocrine disruptors. Because phthalates are not chemically bound to the PVC polymer, they tend to migrate out of plastic products and into the environment. The same is true of alternative plasticizers currently on the market. Dr. Rebecca Braslau’s laboratory has developed an approach to use compounds to replace phthalates that can be chemically attached to the PVC polymer chain: “internal plasticizers.”    

Simple and Rapid Method for the Quantification of Haloginated Dissaccharides (i.e. Sucralose) in an Aqueous Media

Sucralose is widely used as an artificial sweetener because of its low caloric content and is sweeter than table sugar (sucrose). Due to its resistance to metabolic degradation, sucralose can also be used as a marker for noninvasively evaluating the gastrointestinal small digestive tract (intestine) or colonic permeability. This urinary marker is traditionally analyzed by time consuming and expensive methods, such as high performance liquid chromatography coupled to mass spectrometry (HPLC-MS) or evaporative light scatter as the detectors. UCSC researchers have developed an alternative method using a chemical-fluorescent technique for rapid analysis of halogenated disaccharides, such as sucralose.

Camera-Based Reader for Blurry and Low-Resolution 1D Barcodes

Virtually every item on the market today is labeled with at least one form of barcode, generally a flavor of either the EAN or the UPC standards. The success of barcode technology for identification, tracking, and inventory derives from its ability to encode information in a compact fashion with very low costs associated. Barcode reading via dedicated scanners is a mature technology. Commercial laser-based hand-held barcode scanners achieve robust readings. Recently, however, there has been growing interest in accessing barcodes with a regular cellphone, rather than with a dedicated device. Since cellphones are of universal use, this would enable a multitude of mobile applications. For example, several cellphone apps have appeared recently that provide access via barcode reading to the full characteristics of and user reviews for a product found at a store. Unfortunately, cellphone camera images are generated by low-grade lenses which produce blurred barcode images. Also, motion blur and noise can be expected with low ambient light. These factors, possibly combined with low image resolution, make barcode reading challenging in some situations.

Linear Lipopeptides as Treatments for Infectious Diseases

Leishmaniasis is a debilitating disease prevalent across many inter-tropical regions of the world. Caused by over twenty species of  parasite from the genus Leishmania and found in some species of sandflies, this disease can present itself in a number of different clinical manifestations including cutaneous, mucosal and visceral forms of the disease. Both the cutaneous and mucosal forms can cause severe disfigurements to patients including ulcerative skin lesions and the destruction of the mucous membranes of the nose, mouth and throat, leading to permanent disfigurement and frequent social ostracizing. Visceral forms can be more severe, with life-threatening symptoms such as fever, weight loss, and in some cases, enlargement of the liver and spleen. A shortfall of affordable and clinically effective treatments has led the World Health Organization to designate leishmaniasis as a Category 1 disease, signifying that it is an emerging and uncontrolled global health problem. Another infectious disease is Human African trypanosmiasis or sleeping sickness, a parasitic disease of people and animals caused by protozoa of the species Trypanosoma brucei,  transmitted by the tsetse fly. Symptoms of this disease occur in two stages: the first causes fever and joint pain, and the second stage confusion, tremors, muscle weakness, and even partial paralysis. It is estimated that 50,000 to 70,000 people are currently infected. The current standard treatment for first stage trypanosomiasis employs an administration of intravenous pentamidine (for Trypanosoma brucei gambiense) or intravenous suramin (for Trypanosoma brucei rhodesiense). Treatment for the second stage of this disease is nifurtimoz and eflornithine (for Trypanosoma brucei gambiense) and melarsopol (for Tryponosoma brucei rhodesiense). Melarsopol is problematic such that drug resistance can occur and death is a possible side effect.

Deep Tissue Optical Microscopy for Multi-Photon Microscope

Biological tissue is  rarely transparent, presenting major challenges for deep tissue optical microscopy. Due to its high-resolution and viewing of live organisms, optical microscopy has become an important tool for biological research and continues to open new avenues in its capabilities. In recent years, image resolution and speed has dramatically improved. However, the resolution and penetration depth is still in great need of improvement. The problem is caused by light being absorbed, refracted and scattered as it passes through biological tissue, limiting the resolution and depth of optical imaging. Overcoming these challenges will benefit a wide range of applications from basic biological research to clinical investigations.

Efficient Encoding of Genomic Data Using Deduplication

With today’s technology, storage of genome sequence data relies heavily on compression, using techniques such as Lempil, ziv and gziv, which are commonly stored in the file formats .bam or .sam forms. Current techniques use standard reference genomes, such as HG19, compiled from a variety of human genomes. The results of many small reads are aligned and stored along with their quality data stores. The impact of whole genome sequencing, particularly in clinical treatment of cancer, will rapidly consume available storage. In 2010, 13 million Americans had cancer; with the existing technology, a single whole genome sequence for each person would be 39 exabyte’s, equal to 39,000 petabytes, 39 million terabytes or 39 billion gigabytes. There simply isn't a storage system that large, as storage capacity only grows at a rate of less than 20% per year. 

Fast Frequency Estimator (FFE)

The problem of estimating and tracking the frequency of a weak sinusoidal signal occurs in many areas of signal processing. There are a variety of approaches to estimate the frequency of a harmonic signal. The most common approach is to directly measure the time difference between zero crossings and the number of cycles per second. However, this approach is very sensitive to signal noise. Solutions to overcome this problem have been proposed, such as the Fourier transform technique, correlation, the least square error technique, recursive algorithms, chirp Z transform (CZT), adaptive notch filters, and Kalman filtering that estimates instantaneous frequency of the signal. The Kalman filter is a recursive stochastic technique that gives an optimal estimation of state variables of given linear dynamic system from noisy measures. Moreover, the filter must always deal with the inherent nonlinearity and with extreme noise levels. Coincidentally, the Kalman filter also gives a time-varying gain, which is not amendable to frequency domain analysis.