Probing biomolecular interaction forces using an anharmonic acoustic technique for selective detection of bacterial spores.

Receptor-based detection of pathogens often suffers from non-specific interactions, and as most detection techniques cannot distinguish between affinities of interactions, false positive responses remain a plaguing reality. Here, we report an anharmonic acoustic based method of detection that addresses the inherent weakness of current ligand dependant assays. Spores of Bacillus subtilis (Bacillus anthracis simulant) were immobilized on a thickness-shear mode AT-cut quartz crystal functionalized with anti-spore antibody and the sensor was driven by a pure sinusoidal oscillation at increasing amplitude. Biomolecular interaction forces between the coupled spores and the accelerating surface caused a nonlinear modulation of the acoustic response of the crystal. In particular, the deviation in the third harmonic of the transduced electrical response versus oscillation amplitude of the sensor (signal) was found to be significant. Signals from the specifically-bound spores were clearly distinguishable in shape from those of the physisorbed streptavidin-coated polystyrene microbeads. The analytical model presented here enables estimation of the biomolecular interaction forces from the measured response. Thus, probing biomolecular interaction forces using the described technique can quantitatively detect pathogens and distinguish specific from non-specific interactions, with potential applicability to rapid point-of-care detection. This also serves as a potential tool for rapid force-spectroscopy, affinity-based biomolecular screening and mapping of molecular interaction networks.

非特异性相互作用的断裂力与寿命测量

目的探讨量化非特异性相互作用在特异性选择素．配体分子相互作用中的贡献。方法利用光镊技术，对牛血清白蛋白（Bovine serum albumin，BSA）封闭的玻璃小球间的非特异性作用进行了系统测量，得出不同加载率下的断裂力以及不同外力作用下的寿命分布。结果实验结果表明，非特异性作用同样表现出断裂力随加载率增加而增大的趋势。在较低加载率下，非特异性断裂力与选择素-配体特异性断裂力大小、增大趋势基本一致；随着加载率增加，二者的差别逐渐显著，前者的断裂力增加速率远低于后者。同样外力作用下，非特异性作用的寿命平均值比特异性作用要小；不同外力作用下，非特异性作用的寿命随外力增大仅略有下降，与特异性作用中逆锁键-滑移键转化现象有明显不同。结论该研究结果将为正确评估非特异性相互作用对选择素-配体特异性相互作用实验结果的影响提供基础。

New methods for generating populations in Markov network based EDAs: Decimation strategies and model-based template recombination

Methods for generating a new population are a fundamental component of estimation of distribution algorithms (EDAs). They serve to transfer the information contained in the probabilistic model to the new generated population. In EDAs based on Markov networks, methods for generating new populations usually discard information contained in the model to gain in efficiency. Other methods like Gibbs sampling use information about all interactions in the model but are computationally very costly. In this paper we propose new methods for generating new solutions in EDAs based on Markov networks. We introduce approaches based on inference methods for computing the most probable configurations and model-based template recombination. We show that the application of different variants of inference methods can increase the EDAs’ convergence rate and reduce the number of function evaluations needed to find the optimum of binary and non-binary discrete functions.

Physical investigations of small particles : (I) aerosol particle charging and flux enhancement and (II) whispering gallery mode sensing

Part I

Particles are a key feature of planetary atmospheres. On Earth they represent the greatest source of uncertainty in the global energy budget. This uncertainty can be addressed by making more measurement, by improving the theoretical analysis of measurements, and by better modeling basic particle nucleation and initial particle growth within an atmosphere. This work will focus on the latter two methods of improvement.

Uncertainty in measurements is largely due to particle charging. Accurate descriptions of particle charging are challenging because one deals with particles in a gas as opposed to a vacuum, so different length scales come into play. Previous studies have considered the effects of transition between the continuum and kinetic regime and the effects of two and three body interactions within the kinetic regime. These studies, however, use questionable assumptions about the charging process which resulted in skewed observations, and bias in the proposed dynamics of aerosol particles. These assumptions affect both the ions and particles in the system. Ions are assumed to be point monopoles that have a single characteristic speed rather than follow a distribution. Particles are assumed to be perfect conductors that have up to five elementary charges on them. The effects of three body interaction, ion-molecule-particle, are also overestimated. By revising this theory so that the basic physical attributes of both ions and particles and their interactions are better represented, we are able to make more accurate predictions of particle charging in both the kinetic and continuum regimes.

The same revised theory that was used above to model ion charging can also be applied to the flux of neutral vapor phase molecules to a particle or initial cluster. Using these results we can model the vapor flux to a neutral or charged particle due to diffusion and electromagnetic interactions. In many classical theories currently applied to these models, the finite size of the molecule and the electromagnetic interaction between the molecule and particle, especially for the neutral particle case, are completely ignored, or, as is often the case for a permanent dipole vapor species, strongly underestimated. Comparing our model to these classical models we determine an “enhancement factor” to characterize how important the addition of these physical parameters and processes is to the understanding of particle nucleation and growth.

Part II

Whispering gallery mode (WGM) optical biosensors are capable of extraordinarily sensitive specific and non-specific detection of species suspended in a gas or fluid. Recent experimental results suggest that these devices may attain single-molecule sensitivity to protein solutions in the form of stepwise shifts in their resonance wavelength, \lambda_{R}, but present sensor models predict much smaller steps than were reported. This study examines the physical interaction between a WGM sensor and a molecule adsorbed to its surface, exploring assumptions made in previous efforts to model WGM sensor behavior, and describing computational schemes that model the experiments for which single protein sensitivity was reported. The resulting model is used to simulate sensor performance, within constraints imposed by the limited material property data. On this basis, we conclude that nonlinear optical effects would be needed to attain the reported sensitivity, and that, in the experiments for which extreme sensitivity was reported, a bound protein experiences optical energy fluxes too high for such effects to be ignored.

Characterizing the regulation of mitochondrial nucleoids

Mitochondria contain a 16.6 kb circular genome encoding 13 proteins as well as mitochondrial tRNAs and rRNAs. Copies of the genome are organized into nucleoids containing both DNA and proteins, including the machinery required for mtDNA replication and transcription. Although mtDNA integrity is essential for cellular and organismal viability, regulation of proliferation of the mitochondrial genome is poorly understood. To elucidate the mechanisms behind this, we chose to study the interplay between mtDNA copy number and the proteins involved in mitochondrial fusion, another required function in cells. Strikingly, we found that mouse embryonic fibroblasts lacking fusion also had a mtDNA copy number deficit. To understand this phenomenon further, we analyzed the binding of mitochondrial transcription factor A, whose role in transcription, replication, and packaging of the genome is well-established and crucial for cellular maintenance. Using ChIP-seq, we were able to detect largely uniform, non-specific binding across the genome, with no occupancy in the known specific binding sites in the regulatory region. We did detect a single binding site directly upstream of a known origin of replication, suggesting that TFAM may play a direct role in replication. Finally, although TFAM has been previously shown to localize to the nuclear genome, we found no evidence for such binding sites in our system.

To further understand the regulation of mtDNA by other proteins, we analyzed publicly available ChIP-seq datasets from ENCODE, modENCODE, and mouseENCODE for evidence of nuclear transcription factor binding to the mitochondrial genome. We identified eight human transcription factors and three mouse transcription factors that demonstrated binding events with the classical strand asymmetrical morphology of classical binding sites. ChIP-seq is a powerful tool for understanding the interactions between proteins and the mitochondrial genome, and future studies promise to further the understanding of how mtDNA is regulated within the nucleoid.

Sustainable IT and IT for sustainability

Energy and sustainability have become one of the most critical issues of our generation. While the abundant potential of renewable energy such as solar and wind provides a real opportunity for sustainability, their intermittency and uncertainty present a daunting operating challenge. This thesis aims to develop analytical models, deployable algorithms, and real systems to enable efficient integration of renewable energy into complex distributed systems with limited information.

The first thrust of the thesis is to make IT systems more sustainable by facilitating the integration of renewable energy into these systems. IT represents the fastest growing sectors in energy usage and greenhouse gas pollution. Over the last decade there are dramatic improvements in the energy efficiency of IT systems, but the efficiency improvements do not necessarily lead to reduction in energy consumption because more servers are demanded. Further, little effort has been put in making IT more sustainable, and most of the improvements are from improved "engineering" rather than improved "algorithms". In contrast, my work focuses on developing algorithms with rigorous theoretical analysis that improve the sustainability of IT. In particular, this thesis seeks to exploit the flexibilities of cloud workloads both (i) in time by scheduling delay-tolerant workloads and (ii) in space by routing requests to geographically diverse data centers. These opportunities allow data centers to adaptively respond to renewable availability, varying cooling efficiency, and fluctuating energy prices, while still meeting performance requirements. The design of the enabling algorithms is however very challenging because of limited information, non-smooth objective functions and the need for distributed control. Novel distributed algorithms are developed with theoretically provable guarantees to enable the "follow the renewables" routing. Moving from theory to practice, I helped HP design and implement industry's first Net-zero Energy Data Center.

The second thrust of this thesis is to use IT systems to improve the sustainability and efficiency of our energy infrastructure through data center demand response. The main challenges as we integrate more renewable sources to the existing power grid come from the fluctuation and unpredictability of renewable generation. Although energy storage and reserves can potentially solve the issues, they are very costly. One promising alternative is to make the cloud data centers demand responsive. The potential of such an approach is huge.

To realize this potential, we need adaptive and distributed control of cloud data centers and new electricity market designs for distributed electricity resources. My work is progressing in both directions. In particular, I have designed online algorithms with theoretically guaranteed performance for data center operators to deal with uncertainties under popular demand response programs. Based on local control rules of customers, I have further designed new pricing schemes for demand response to align the interests of customers, utility companies, and the society to improve social welfare.

On a method of determination of chlorophyll in cells of algae collected on a membrane filter. [Translation from: Trudy Instituta Biologii Vnutrennykh Vodnany 11(14), 198-202, 1966.]

The original method, proposed by Yentsch (1957), of determination of chlorophyll directly in the cells, attracts attention by its simplicity. In order to measure the content of chlorophyll by this method, a determined volume of suspension of algae is filtered through a membrane filter. The latter is dried a little, clarified by immersion oil, clamped between two glasses, and spectrophotometrized. Extinction is read off at , wavelengths equal to 670 millimicrons (around the maximum absorption of chlorophyll a in the cell) and 750 millimicrons (correction for non- specific absorption and dispersion of light by particles of the preparation). The method of Yentsch was employed by the authors for determination of chlorophyll-a in samples of phytoplankton. They conclude that in spite of the simplicity and convenience of determination the method must be applied sufficiently carefully. It is more suitable for analysis of cultures of algae, where, non-specific absorption of light is insignificant.

Validação do processo de limpeza de tanque multiuso utilizado para formulação de vacinas

A validação de limpeza de equipamentos é requisito regulatório para assegurar que os procedimentos de limpeza removem os resíduos de produto e agente de limpeza existentes até um nível de aceitação pré-determinado, garantindo que não haja contaminação cruzada. A metodologia analítica escolhida para monitorar a ocorrência de contaminação cruzada foi a determinação de carbono orgânico total (TOC) por ser uma técnica não específica permitindo assim quantificar os resíduos antes e após o procedimento de limpeza. Para execução desta validação foi selecionado o pior caso em relação ao contaminante. A vacina Hib foi escolhida como pior caso, pois possui maior aderência ao aço inox 316L, apresentando uma menor percentagem de recuperação, quando comparada à vacina Meningite A e C, sendo respectivamente de 93,0% e 98,4% para o tempo de extração de 30 segundos e 67,8% e 72,6% para o tempo de extração de 10 segundos. O resíduo aceitável de produto em água de rinsagem foi de 0,0007 g/mL de polissacarídeo (0,49 g/mL de TOC) e em swab foi de 0,006 g/mL de polissacarídeo (3,49 g/mL de TOC). As amostras retiradas para determinação de resíduo de produto foram analisadas e corrigidas pelo fator de recuperação deste resíduo para amostras de água de rinsagem que é de 98,5% e para amostras em swab que é de 98,4%. Já o resíduo aceitável para agente de limpeza (NaOH) foi de 3,5 g/mL que fornece um pH de 9,94, porém não existem evidências que a concentração calculada de resíduo de NaOH não interferirá quimicamente ao entrar em contato com a vacina. Assim o critério adotado foi o mesmo da água para injetáveis, segundo USP que é pH entre 5 e 7. As amostras retiradas para determinação de resíduo de agente de limpeza não foram corrigidas pelo fator de recuperação uma vez que o critério utilizado é muito mais crítico que o calculado. Todas as análises realizadas apresentaram resultados dentro dos parâmetros aceitáveis permitindo a conclusão de que o procedimento de limpeza para tanque de aço inox 316L é eficiente removendo os resíduos até níveis aceitáveis, evitando assim uma contaminação cruzada

Studies of dinucleoside monophosphates and monomer-polynucleotide interactions by proton magnetic resonance

The nature of the intra- and intermolecular base-stacking interactions involving several dinucleoside monophosphates in aqueous solution have been investigated by proton magnetic resonance spectrosocopy, and this method has been applied to a study of the interaction of polyuridylic acid with purine and adenosine monomers.

The pmr spectra of adenylyl (3' → 5') cytidine (ApC) and cytidylyl (3' → 5') adenosine (CpA) have been studied as a function of concentration and temperature. The results of these studies indicate that the intramolecular base-stacking interactions between the adenine and cytosine bases of these dinucleoside monophosphates are rather strong, and that the stacking tendencies are comparable for the two sequence isomers. The chemical shifts of the cytosine H₅ and adenine H₂ protons, and their variations with temperature, were shown to be consistent with stacked conformations in which both bases of the dinucleoside monophosphates are preferentially oriented in the anti conformation as in similar dApdC, and dCpdA (dA = deoxyadenosine; dC = deoxycytidine) segments in double helical DNA. The intramolecular stacking interaction was found to have a pronounced effect on the conformations of the ribose moieties, and these conformational changes are discussed. The concentration studies indicate extensive self-association of these dinucleoside monophosphates, and analysis of the concentration data facilitated determination of the dimerization constant for the association process as well as the nature of the intermolecular complexes.

The dependence of the ribose conformation upon the extent of intramolecular base-stacking was used to demonstrate that the base-base interaction in cytidylyl (3' → 5') cytidine (CpC) is rather strong, while there appears to be little interaction between the two uracil bases of uridylyl (3' → 5') uridine (UpU).

Studies of the binding of purine to several ribose and deoxyribose dinucleoside monophosphates show that the mode of interaction is base-stacking, and evidence for the formation of a purine-dinucleoside monophosphate intercalated complex is presented. The purine proton resonances are markedly broadened in this complex, and estimates of the purine linewidths in the complex and the equilibrium constant for purine intercalation are obtained.

A study of the interaction of unsubstitued purine with polyuridylic acid at 29°C by pmr indicated that purine binds to the uracil bases of the polymer by base-stacking. The severe broadening of the purine proton resonances observed provides strong evidence for the intercalation of purine between adjacent uracil bases of poly U. This interaction does not result in a more rigid or ordered structure for the polymer.

Investigation of the interaction between adenosine and polyuridylic acid revealed two modes of interaction between the monomer and the polymer, depending on the temperature. At temperatures above 26°C or so, monomeric adenosine binds to poly U by noncooperative A-U base stacking. Below this temperature, a rigid triple-stranded 1A:2U complex is formed, presumably via cooperative hydrogen-bonding as has previously been reported.

These results clearly illustrate the importance of base-stacking in non-specific interactions between bases, nucleosides and nucleotides, and also reveal the important role of the base-stacking interactions in cooperatively for med structures involving specific base-pairing where both types of interaction are possible.

Estruturas Discursivas: o Encapsulamento Anafórico em redações de pré-vestibulandos

O presente trabalho conta com cinquenta redações de alunos do curso Pré - vestibular do Sintuperj, que já concluíram o Ensino Médio e, agora, se preparam para fazer o exame de acesso ao ensino superior - vestibular. A abordagem proposta se baseia na análise da referenciação, forma de organização coesiva do texto, especificamente, o encapsulamento anafórico. Para verificar a função discursiva desse fenômeno argumentativo nas redações, a análise foi dividida em duas perspectivas: por um lado, foram investigados os tipos de cadeias de referenciação, designadas como específica, rotulando e contribuindo para a progressão referencial no texto; ou como não específica, simplesmente, retomando e resumindo o conteúdo antecedente, evitando repetições. De outro lado, ampliou-se a análise para os elementos que constituem essas cadeias, verificando como foi realizada a menção ao referente através da manutenção temática. Além disso, foi possível notar como essa manutenção dos dados no texto possibilita a coesão textual e enriquece a argumentação que o aluno faz para defender a sua tese. Portanto, pode-se afirmar que a principal contribuição que esse trabalho oferece para o ensino de língua materna concerne na abordagem do texto a partir de uma perspectiva dos processamentos cognitivos, revelando como os elementos vão sendo construídos nas redações, a partir de componentes culturais e conhecimentos diversos dos alunos, que proporcionam a progressão referencial

Associação entre estado nutricional e infecção assintomática por Leishmania infantum em moradores de áreas endêmicas para leishmaniose visceral no município de Teresina, Piauí

INTRODUÇÃO: A leishmaniose visceral (LV) é uma doença negligenciada de grande importância no cenário brasileiro, particularmente devido à sua gravidade, sua expansão geográfica e a associação com condições de pobreza. Nesta perspectiva, as condições nutricionais emergem como elementos a serem considerados na compreensão de sua situação epidemiológica, sejam como potenciais fatores de risco para o estabelecimento da doença após infecção ou como fatores associados ao prognóstico. OBJETIVO: Avaliar a associação entre estado nutricional e infecção por Leishmania infantum em moradores de áreas endêmicas para LV no município de Teresina, Piauí. MÉTODOS: Trata-se de um estudo seccional realizado em bairros de alta endemicidade para a doença, envolvendo 198 indivíduos com idade entre 2 e 65 anos. Peso e estatura foram aferidos no domicílio por profissionais treinados. Para a avaliação de adultos foi utilizado o índice de massa corporal (IMC). Para crianças e adolescentes foram avaliados os índices antropométricos (peso / idade, estatura / idade, peso / estatura e IMC / idade). A infecção por L. infantum foi avaliada a partir da intradermorreação de Montenegro (IDRM). Para a análise foi utilizada regressão logística multivariada, estimando-se razões de chances (OR) como medidas de associação e seus respectivos intervalos de confiança (95%). RESULTADOS: A prevalência de infecção assintomática foi de 32,6%. A prevalência de excesso de peso foi de 52% entre adultos (IMC ? 25 kg/m) e de 23,9% entre crianças e jovens (escore-z de IMC / idade > 1). Indivíduos com sobrepeso, tanto adultos como aqueles de até 19 anos, apresentaram chance de infecção cerca de 70% maior quando comparados aos eutróficos (p>0,05 para ambos). CONCLUSÃO: Ainda que não estatisticamente significante, a associação entre infecção assintomática por L. infantum e sobrepeso sugere que estes indivíduos possam estar sob maior risco de infecção por apresentarem déficits de micronutrientes relevantes para a resposta imune específica. Para investigar esta hipótese, são necessários estudos longitudinais que investiguem o papel do consumo alimentar e do perfil de micronutrientes desta população no risco de infecção por L. infantum.

Ontogenetic patterns and temperature-dependent growth rates in early life stages of Pacific cod (Gadus macrocephalus)

Pacific cod (Gadus macrocephalus) is an important component of fisheries and food webs in the North Pacific Ocean and Bering Sea. However, vital rates of early life stages of this species have yet to be described in detail. We determined the thermal sensitivity of growth rates of embryos, preflexion and postflexion larvae, and postsettlement juveniles. Growth rates (length and mass) at each ontogenetic stage were measured in three replicate tanks at four to five temperatures. Nonlinear regression was used to obtain parameters for independent stage-specific growth functions and a unified size- and temperature-dependent growth function. Specific growth rates increased with temperature at all stages and generally decreased with increases in body size. However, these analyses revealed a departure from a strict size-based allometry in growth patterns, as reduced growth rates were observed among preflexion larvae: the reduction in specific growth rate between embryos and free-swimming larvae was greater than expected based on body size differences. Growth reductions in the preflexion larvae appear to be associated with increased metabolic rates and the transition from endogenous to exogenous feeding. In future studies, experiments should be integrated across life transitions to more clearly define intrinsic ontogenetic and size-dependent growth patterns because these are critical for evaluations of spatial and temporal variation in habitat quality.

Avaliação da eficiência de wetland construído como unidade de polimento de efluente de tratamento secundário de lixiviado por lodos ativados

Uma das dificuldades a ser enfrentada na implantação de aterros sanitários é o tratamento adequado do lixiviado gerado e seu lançamento no meio ambiente dentro dos padrões estabelecidos pela legislação. O potencial poluidor do lixiviado está ligado principalmente aos altos valores de carga orgânica que promove a redução do oxigênio disponível (utilizado na degradação da matéria orgânica) em cursos dágua, prejudicando a fauna e a flora nesses meios. O objetivo do presente trabalho foi avaliar o sistema de tratamento por wetland construído como unidade de polimento do efluente secundário de uma estação de tratamento de lixiviado de aterro de resíduos sólidos urbanos na Região Metropolitana do Rio de Janeiro. Além dos parâmetros coletivos específicos e não específicos, também foram empregados o fracionamento pelo processo de separação por membranas e ensaios de toxicidade aguda. Os resultados mostram que o wetland tem uma ação positiva como unidade de polimento refletida na redução dos parâmetros turbidez (84%), DQO (19%), amônia (30%) e sólidos totais (3%) reduzindo, assim, os impactos ambientais do lançamento do lixiviado. Contudo, a qualidade do efluente final encontra-se acima dos parâmetros de referência de controle ambiental e mostra a necessidade de um efluente secundário de melhor qualidade. Os resultados mostraram também que altos valores de DQO inerte tanto no afluente (85% em média) quanto no efluente (93,5% em média) do wetland indicam que esses lixiviados apresentam natureza refratária confirmada pelos baixos valores de biodegradabilidade no afluente (20,5% em média) e no efluente (5% em média) do wetland. O fracionamento com membranas mostrou que o afluente e o efluente do wetland possuem maiores contribuições de moléculas na fração >1 kDa. Os ensaios de toxicidade com Aliivibrio fischeri mostraram que o afluente e o efluente do wetland possuem toxicidade aguda, sendo a mesma menor na faixa com moléculas menores.

Alterações da expressão da proteína PHEX na Hanseníase

A hanseníase é uma doença infecciosa causada pelo Mycobacteruim leprae, um bacilo intracelular obrigatório, que prolifera principalmente na pele e nos nervos periféricos no interior de células como macrófagos e células de Schwann. A transmissão ocorre por meio das mucosas das vias respiratórias, provavelmente por aerossóis expelidos por indivíduos infectados. O homem é o seu hospedeiro natural sendo a multiplicação do bacilo muito lenta, com um período de geração estimado de 14 dias. Apesar da mínima variação no genoma do M. leprae, a doença é caracterizada por um espectro de formas clínicas bem definido, decorrente da capacidade de resposta imune do hospedeiro. Em pacientes classificados como multibacilares (MB) a doença é disseminada, com inúmeras lesões de pele e proliferação bacilar considerável. Nesses indivíduos ocorre hiporresponsividade celular ao M. leprae. Nas formas paucibacilares (PB), os pacientes apresentam uma ou poucas lesões, a carga bacilar é pequena e, às vezes não observada por meio da baciloscopia tradicional e ocorre resposta imune patógeno-específica. As incapacidades físicas nos pacientes decorrem da neuropatia e osteopatia e podem ser irreversíveis. Essas deformidades podem avançar mesmo após a diminuição da carga bacilar com o final do tratamento poliquimioterápico. A presente tese teve por objetivo estudar as implicações da proteína PHEX nas alterações fisiopatológicas da hanseníase, em especial as alterações ósseas. A proteína PHEX (Phosphate-regulating gene with Homologies to Endopeptidase on the X chromosome) é expressa em várias células humanas e, no primeiro artigo que compõe essa tese, demonstramos que o M.leprae leva à diminuição da expressão de PHEX em linhagens de células de Schwann e osteoblastos humanos. Este efeito foi igualmente causado por outras espécies de micobactérias. No segundo manuscrito ora submetido, observamos que em leucócitos sanguíneos de pacientes hansenianos também ocorreu modulação negativa de PHEX. Este efeito não se relacionou com a capacidade de produção de citocinas inflamatórias frente ao M. leprae in vitro ou com alterações bioquímicas. O efeito inibidor da mineralização ocasionado pela modulação negativa de PHEX talvez contribua para a doença óssea da hanseníase, auxiliando a explicar a capacidade do M. leprae de penetrar e sobreviver no osso.

Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006-2007

We assess the application of the second-generation Environmental Sample Processor (ESP) for the detection of harmful algal bloom (HAB) species in field and laboratory settings using two molecular probe techniques: a sandwich hybridization assay (SHA) and fluorescent in situ hybridization (FISH). During spring 2006, the first time this new instrument was deployed, the ESP successfully automated application of DNA probe arrays for various HAB species and other planktonic taxa, but non-specific background binding on the SHA probe array support made results interpretation problematic. Following 2006, the DNA array support membrane that we were using was replaced with a different membrane, and the SHA chemistry was adjusted. The sensitivity and dynamic range of these modifications were assessed using 96-well plate and ESP array SHA formats for several HAB species found commonly in Monterey Bay over a range of concentrations; responses were significantly correlated (p < 0.01). Modified arrays were deployed in 2007. Compared to 2006, probe arrays showed improved signal:noise, and remote detection of various HAB species was demonstrated. We confirmed that the ESP and affiliated assays can detect HAB populations at levels below those posing human health concerns, and results can be related to prevailing environmental conditions in near real-time.