Alexander Pozhitkov | University of Washington (original) (raw)

Papers by Alexander Pozhitkov

Multiplexed milliliter-scale chemostats are useful for measuring cell physiology under various de... more Multiplexed milliliter-scale chemostats are useful for measuring cell physiology under various degrees of nutrient limitation and for experimental evolution. In each chemostat, fresh medium containing a growth rate-limiting metabolite is pumped into the culturing chamber at a constant rate, while culture effluent exits at an equal rate. Although such devices have been developed by various labs, key parameters-the accuracy and precision of flow rate and the operational rangeare not explicitly characterized. Here we report the development of multiplexed milliliter-scale chemostats where flow rates for eight chambers can be independently controlled to vary within a wide range, corresponding to population doubling times of 3~ 13 hours. Importantly, flow rates are precise and accurate without the use of expensive feedback systems. Among the eight chambers, the maximal coefficient of variation in flow rate is less than 3%, and average flow rates are only slightly below targets, i.e., 3-6% for 13-hour and 0.6-1.0% for 3-hour doubling times. This deficit is largely due to evaporation and should be correctable. We experimentally demonstrate that our device allows accurate and precise quantification of population phenotypes.

Springer eBooks, 2003

The comparative study of the behavior of DsRed1, EYFP and ECFP under high pressure was carried ou... more The comparative study of the behavior of DsRed1, EYFP and ECFP under high pressure was carried out. We found that only chromophores of EYFP and ECFP were sensitive to pressure treatment. The result is interesting from the point of view of high structural similarity of DsRed1 and other studied proteins leading to the discovery of new properties in high pressure studies that wouldn’t show up otherwise.

Clinical Lymphoma Myeloma and Leukemia

Quantitative Biology, 2018

Background: Multiplexed milliliter-scale chemostats are useful for measuring cell physiology unde... more Background: Multiplexed milliliter-scale chemostats are useful for measuring cell physiology under various degrees of nutrient limitation and for carrying out evolution experiments. In each chemostat, fresh medium containing a growth rate-limiting metabolite is pumped into the culturing chamber at a constant rate, while culture effluent exits at an equal rate. Although such devices have been developed by various labs, key parametersthe accuracy, precision, and operational range of flow rateare not explicitly characterized. Methods: Here we re-purpose a published multiplexed culturing device to develop a multiplexed milliliter-scale chemostat. Flow rates for eight chambers can be independently controlled to a wide range, corresponding to population doubling times of 3~13 h, without the use of expensive feedback systems. Results: Flow rates are precise, with the maximal coefficient of variation among eight chambers being less than 3%. Flow rates are accurate, with average flow rates being only slightly below targets, i.e., 3%-6% for 13-h and 0.6%-1.0% for 3-h doubling times. This deficit is largely due to evaporation and should be correctable. We experimentally demonstrate that our device allows accurate and precise quantification of population phenotypes. Conclusions: We achieve precise control of cellular growth in a low-cost milliliter-scale chemostat array, and show that the achieved precision reduces the error when measuring biological processes.

JDR Clinical & Translational Research, 2019

Introduction: Epigenetic changes are associated with various inflammatory diseases and are influe... more Introduction: Epigenetic changes are associated with various inflammatory diseases and are influenced by environmental factors. Recent data support an association between titanium dissolution products and peri-implantitis. We hypothesize that site-specific changes in gene methylation, a form of epigenetic regulation, around dental implants may be influenced by local environmental factors, such as titanium dissolution particles. Objectives: The primary purpose of this study was to assess global methylation patterns related to the disease status of dental implants and the concentration of titanium particles. Methods: We assessed peri-implantitis cases defined according to established definitions from a cross-sectional study that had implants in function for at least 2 y. Controls were sampled from the same population and had healthy implants. Peri-implant crevicular fluid samples were collected and prepared for immunohistochemical analysis of 5-methylcytosine (5mC), and submucosal plaque samples were collected and subjected to inductively coupled plasma mass spectrometry (ICP-MS) for measuring titanium. Data were analyzed via generalized estimating equation models to account for multiple implants per participant.

Nucleic Acids Research, 2007

Microarray experiments typically involve washing steps that remove hybridized nonspecific targets... more Microarray experiments typically involve washing steps that remove hybridized nonspecific targets with the purpose of improving the signal-to-noise ratio. The quality of washing ultimately affects downstream analysis of the microarray and interpretation. The paucity of fundamental studies directed towards understanding the dissociation of mixed targets from microarrays makes the development of meaningful washing/dissociation protocols difficult. To fill the void, we examined activation energies and preexponential coefficients of 47 perfect match (PM) and double-mismatch (MM) duplex pairs to discover that there was no statistical difference between the kinetics of the PM and MM duplexes. Based on these findings, we evaluated the nonequilibrium thermal dissociation (NTD) approach, which has been used to identify specific microbial targets in mixed target samples. We found that the major premises for various washing protocols and the NTD approach might be seriously compromised because: (i) nonspecific duplexes do not always dissociate before specific ones, and (ii) the relationship between dissociation rates of the PM and MM duplexes depends on temperature and duplex sequence. Specifically for the NTD, we show that previously suggested use of reference curves, indices of curves and temperature ramps lead to erroneous conclusions.

Journal of Microbiological Methods, 2008

The nonequilibrium thermal dissociation (NTD) methodology has been proposed to provide a superior... more The nonequilibrium thermal dissociation (NTD) methodology has been proposed to provide a superior discrimination between specific and nonspecific hybridizations than the commonly used array techniques involving hybridization followed by a single stringent wash. Multiple studies have used this method on gelpad, planar, and nylon membrane arrays to identify specific microbial targets in complex target mixtures. A recent physicochemical study revealed several problems, particularly when the method was used to examine complex target samples. In the present study, we investigated the effect of target concentration on NTD of complex target samples obtained from an anaerobic bioreactor. Our purpose was to experimentally demonstrate that variation in the concentrations of both specific and nonspecific targets determines the course of dissociation, which was not evaluated in initial microbiological studies. We also present an approach for analyzing the dissociation curves that is less error prone compared to those used in the previous studies. Our results show that: (i) a specific target in a mixture, at a certain concentration, may have a higher dissociation temperature/time than that of the same pure target, and (ii) the concentration dependence of the dissociation precludes usage of reference curves for identifying a target. Contrary to the previous studies, an explicit calibration is required, which makes the NTD approach impractical for high throughput analysis.

Applied and Environmental Microbiology, 2005

Past studies have suggested that thermal dissociation analysis of nucleic acids hybridized to DNA... more Past studies have suggested that thermal dissociation analysis of nucleic acids hybridized to DNA microarrays would improve discrimination among duplex types by scanning through a broad range of stringency conditions. To more fully constrain the utility of this approach using a previously described gel-pad microarray format, artificial neural networks (NNs) were trained to recognize noisy or low-quality data, as might derive from nonspecific fluorescence, poor hybridization, or compromised data collection. The NNs were trained to classify dissociation profiles (melts) into groups based on selected characteristics (e.g., initial signal intensity, area under the curve) using a data set of 21,044 profiles derived from 186 probes hybridized to a study set of RNA extracted from 32 microbes common to the human oral cavity. Three melt profile groups were identified: one group consisted mostly of ideal melt profiles; another group consisted mostly of poor melt profiles; and, the remainder w...

Background. The American Society of Anesthesiologists (ASA) Physical Status Classification System... more Background. The American Society of Anesthesiologists (ASA) Physical Status Classification System defines peri-operative patient scores as 1 (healthy) thru 6 (brain dead). The scoring is used by the anesthesiologists to classify surgical patients based on co-morbidities and various clinical characteristics. The classification is always done by an anesthesiologist prior operation. There is a variability in scoring stemming from individual experiences / biases of the scoring anesthesiologists, which impacts prediction of operating times, length of stay in the hospital, necessity of blood transfusion, etc. In addition, the score affects anesthesia coding and billing. It is critical to remove subjectivity from the process to achieve reproducible generalizable scoring. Methods. A machine learning (ML) approach was used to associate assigned ASA scores with peri-operative patients' clinical characteristics. More than ten ML algorithms were simultaneously trained, validated, and tested...

Leukemia & Lymphoma

Multiple myeloma (MM) is a blood neoplasia characterized by abnormal proliferation of plasma cell... more Multiple myeloma (MM) is a blood neoplasia characterized by abnormal proliferation of plasma cells. Various treatments such as stem cell transplant (SCT), proteasome inhibitors, immune-modulating drugs, monoclonal antibodies and selective inhibitors of nuclear export have been routinely used to treat MM. However, relapse and treatment resistance are common problems in MM patients. Treatments are enhanced by Dexamethasone (Dex), a synthetic steroid that activates the glucocorticoid receptor (GR) which leads to apoptosis. To evaluate the potential impact of GR expression on overall survival, MM patient data from the CoMMpass study of 650 patients were analyzed. Multivariate modeling results show that increased GR expression at diagnosis is associated with a decreased risk of dying relative to those with lower levels of expression.

International Journal of Oncology

The post-translational modification of proteins by ubiquitinating enzymes plays a central role in... more The post-translational modification of proteins by ubiquitinating enzymes plays a central role in a number of cellular functions, such as cell proteolysis, DNA repair, and cell signaling and communication. Deubiquitinating enzymes (DUBs) disassemble ubiquitin chains and remove ubiquitin moieties from proteins. Targeting DUBs in cancer models has revealed an important role for these enzymes in tumorigenesis, and they therefore have emerged as attractive therapeutic targets. In the present study, the effects of three DUB inhibitors, PR-619, RA-9 and LDN-91946, on a non-small cell lung cancer cell line (A549) and a mesothelioma cell line (H2373) were investigated. PR-619 significantly inhibited cell adhesion and the proliferation of both cell lines. RA-9 exerted an inhibitory effect on the adhesion and proliferation of H2373 cells, whereas it had no effect on A549 cells. Notably, however, while PR-619 attenuated the proliferation of both cell lines, it exerted an opposite effect on cell motility; in the case of A549 cells, there was a significant increase in cell motility, while for the H2373 cells, there was a significant decrease. Furthermore, protein phosphorylation kinetic analyses revealed that the effects were cell line-specific. In H2373 cells, the phosphorylation of only one peptide corresponding to the P85A protein was significantly affected, and while LDN-91946 treatment increased phosphorylation, treatment with RA-9 or PR-619 decreased its phosphorylation compared to the DMSO control. By contrast, in the case of A549 cells, the phosphorylation of 21 peptides was significantly affected by the same compounds. In light of the potential for the negative side-effects of DUB inhibition, such as increased cancer cell motility, the data presented herein underscore the dire need for the development of specific DUB inhibitors and to elucidate the individual role of DUB family members in cancer biology before they can be specifically pharmacologically targeted.

The Biochemist

In life, most internal organs of a healthy adult vertebrate are essentially ‘microbial-cell-free’... more In life, most internal organs of a healthy adult vertebrate are essentially ‘microbial-cell-free’ – but in death, microorganisms invade and proliferate these internal organs and genes are expressed by the host presumably in response. We recently investigated how these two interconnected processes change with postmortem time and examined the feasibility of using this information to determine the postmortem interval, i.e. the elapsed-time-since-death. Although more research is needed, our findings suggest one of them has a significant potential to determine the length of time from the person dying until discovery of the body.

Blood Advances

Key Points Teriflunomide, the active metabolite of leflunomide, downregulates c-Myc expression th... more Key Points Teriflunomide, the active metabolite of leflunomide, downregulates c-Myc expression through inhibition of PIM kinases. Leflunomide together with lenalidomide significantly extended survival in an in vivo MM model.

ABSTRACTOur previous study found more than 500 transcripts significantly increased in abundance i... more ABSTRACTOur previous study found more than 500 transcripts significantly increased in abundance in the zebrafish and mouse several hours to days postmortem relative to live controls. The current literature suggests that most mRNAs are post-transcriptionally regulated in stressful conditions, we rationalized that the postmortem transcripts must contain sequence features (3 to 9 mers) that are unique from those in the rest of the transcriptome – specifically, binding sites for proteins and/or non-coding RNAs involved in regulation. Our new study identified 5117 and 2245 over-represented sequence features in the mouse and zebrafish, respectively. Some of these features were disproportionately distributed along the transcripts with high densities in the 3-UTR region of the zebrafish (0.3 mers/nt) and the ORFs of the mouse (0.6 mers/nt). Yet, the highest density (2.3 mers/nt) occurred in the ORFs of 11 mouse transcripts that lacked UTRs. Our results suggest that these transcripts might s...

Clinical Implant Dentistry and Related Research

BACKGROUND Recent data support the implication of accelerated titanium dissolution products in pe... more BACKGROUND Recent data support the implication of accelerated titanium dissolution products in peri-implantitis. It is unknown whether these dissolution products have an effect on the peri-implant microbiome, the target of existing peri-implantitis therapies. PURPOSE This study assessed the relationship between the peri-implant microbiome, dissolved titanium levels, and peri-implantitis. MATERIALS AND METHODS Clinical, microbiome, and titanium data were collected from a periodontal population having implants in function for 10 years. Clinical examinations were performed, and submucosal plaque samples were collected from the deepest site per implant. An aliquot of the sample was used for 16S rRNA gene sequencing, with the remainder analyzed for titanium quantity using mass spectrometry. Sequences were clustered into taxonomic units at 97% minimum sequence similarity using the QIIME pipeline approach. RESULTS Fifteen implants were assessed. According to established case definitions, six had a diagnosis of peri-implantitis; nine were healthy. The genera Streptococcus, Prevotella and Haemophilus characterized peri-implant health. Peri-implantitis was associated with a marked increase in Veillonella. Quantities of dissolved titanium were identified in 40% of sites. Titanium presence was associated with peri-implant disease status (P = .02) and correlated to the first principal component of the microbiome (rho = 0.552) and its alpha-diversity (rho = -0.496). Canonical correlation analyses found that titanium levels, but not health or disease status of the implant, were significantly associated with the microbiota composition (P = .045). CONCLUSIONS These findings suggest an association between titanium dissolution products and peri-implantitis and support a role for these products in modifying the peri-implant microbiome structure and diversity.

BMC genomics, Jan 14, 2018

Our previous study found that more than 500 transcripts significantly increased in abundance in t... more Our previous study found that more than 500 transcripts significantly increased in abundance in the zebrafish and mouse several hours to days postmortem relative to live controls. The current literature suggests that most mRNAs are post-transcriptionally regulated in stressful conditions. We rationalized that the postmortem transcripts must contain sequence features (3- to 9- mers) that are unique from those in the rest of the transcriptome and that these features putatively serve as binding sites for proteins and/or non-coding RNAs involved in post-transcriptional regulation. We identified 5117 and 2245 over-represented sequence features in the mouse and zebrafish, respectively, which represents less than 1.5% of all possible features. Some of these features were disproportionately distributed along the transcripts with high densities in the 3' untranslated regions of the zebrafish (0.3 mers/nt) and the open reading frames of the mouse (0.6 mers/nt). Yet, the highest density (2...

Communicative & Integrative Biology

We previously reported that thousands of transcripts in the mouse and zebrafish significantly inc... more We previously reported that thousands of transcripts in the mouse and zebrafish significantly increased in abundance in a time series spanning from life to several days after death. Transcript abundances were determined by: calibrating each microarray probe using a dilution series of pooled RNAs, fitting the probe-responses to adsorption models, and back-calculating abundances using the probe signal intensity of a sample and the best fitting model. The accuracy of the abundance measurements was not assessed in our previous study because individual transcript concentrations in the calibration pool were not known. Accurate transcript abundances are highly desired for modeling the dynamics of biological systems and investigating how systems respond to perturbations. In this study, we show that accurate transcript abundances can be determined by calibrating the probes using a calibration pool of transcripts with known concentrations. Instructions for determining accurate transcript abundances using the Gene Meter approach are provided.

BioEssays

After a vertebrate dies, many of its organ systems, tissues, and cells remain functional while it... more After a vertebrate dies, many of its organ systems, tissues, and cells remain functional while its body no longer works as a whole. We define this state as the &amp;amp;amp;amp;amp;amp;amp;quot;twilight of death&amp;amp;amp;amp;amp;amp;amp;quot; - the transition from a living body to a decomposed corpse. We claim that the study of the twilight of death is important to ethical, legal and medical science. We examined gene expression at the twilight of death in the zebrafish and mouse reaching the conclusion that apparently thousands of transcripts significantly increase in abundance from life to several hours/days postmortem relative to live controls. Transcript dynamics of different genes provided &amp;amp;amp;amp;amp;amp;amp;quot;proof-of-principle&amp;amp;amp;amp;amp;amp;amp;quot; that models accurately predict an individual&amp;amp;amp;amp;amp;amp;amp;#39;s elapsed-time-of-death (i.e. postmortem interval). While many transcripts were associated with survival and stress compensation, others were associated with epigenetic factors, developmental control, and cancer. Future studies are needed to determine whether the high incidence of cancer in transplant recipients is due to the postmortem processes in donor organs.

Open biology, 2017

In life, genetic and epigenetic networks precisely coordinate the expression of genes-but in deat... more In life, genetic and epigenetic networks precisely coordinate the expression of genes-but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became significantly more abundant after death of healthy adult animals in a time series spanning up to 96 h postmortem. Ordination plots revealed non-random patterns in the profiles by time. While most of these transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h postmortem. Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regula...

In life, genetic and epigenetic networks precisely coordinate the expression of genes—but in deat... more In life, genetic and epigenetic networks precisely coordinate the expression of genes—but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became significantly more abundant after death of healthy adult animals in a time series spanning up to 96 h postmortem. Ordination plots revealed non-random patterns in the profiles by time. While most of these transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h postmortem. Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regula...