Very early life microbiome and metabolome correlates with primary vaccination variability in children

IMPORTANCE

We show that simultaneous study of stool and nasopharyngeal microbiome reveals divergent timing and patterns of maturation, suggesting that local mucosal factors may influence microbiome composition in the gut and respiratory system. Antibiotic exposure in early life as occurs commonly, may have an adverse effect on vaccine responsiveness. Abundance of gut and/or nasopharyngeal bacteria with the machinery to produce lipopolysaccharide-a toll-like receptor 4 agonist-may positively affect future vaccine protection, potentially by acting as a natural adjuvant. The increased levels of serum phenylpyruvic acid in infants with lower vaccine-induced antibody levels suggest an increased abundance of hydrogen peroxide, leading to more oxidative stress in low vaccine-responding infants.

High-resolution photocatalytic mapping of SARS-CoV-2 spike interactions on the cell surface

Identifying virus-host interactions on the cell surface can improve our understanding of viral entry and pathogenesis. SARS-CoV-2, the causative agent of the COVID-19 disease, uses ACE2 as a receptor to enter cells. Yet the full repertoire of cell surface proteins that contribute to viral entry is unknown. We developed a photocatalyst-based viral-host protein microenvironment mapping platform (ViraMap) to probe the molecular neighborhood of the SARS-CoV-2 spike protein on the human cell surface. Application of ViraMap to ACE2-expressing cells captured ACE2, the established co-receptor NRP1, and several novel cell surface proteins. We systematically analyzed the relevance of these candidate proteins to SARS-CoV-2 entry by knockdown and overexpression approaches in pseudovirus and authentic infection models and identified PTGFRN and EFNB1 as bona fide viral entry factors. Our results highlight additional host targets that participate in SARS-CoV-2 infection and showcase ViraMap as a powerful platform for defining viral interactions on the cell surface.

μMap Photoproximity Labeling Enables Small Molecule Binding Site Mapping

The characterization of ligand binding modes is a crucial step in the drug discovery process and is especially important in campaigns arising from phenotypic screening, where the protein target and binding mode are unknown at the outset. Elucidation of target binding regions is typically achieved by X-ray crystallography or photoaffinity labeling (PAL) approaches; yet, these methods present significant challenges. X-ray crystallography is a mainstay technique that has revolutionized drug discovery, but in many cases structural characterization is challenging or impossible. PAL has also enabled binding site mapping with peptide- and amino-acid-level resolution; however, the stoichiometric activation mode can lead to poor signal and coverage of the resident binding pocket. Additionally, each PAL probe can have its own fragmentation pattern, complicating the analysis by mass spectrometry. Here, we establish a robust and general photocatalytic approach toward the mapping of protein binding sites, which we define as identification of residues proximal to the ligand binding pocket. By utilizing a catalytic mode of activation, we obtain sets of labeled amino acids in the proximity of the target protein binding site. We use this methodology to map, in vitro, the binding sites of six protein targets, including several kinases and molecular glue targets, and furthermore to investigate the binding site of the STAT3 inhibitor MM-206, a ligand with no known crystal structure. Finally, we demonstrate the successful mapping of drug binding sites in live cells. These results establish μMap as a powerful method for the generation of amino-acid- and peptide-level target engagement data.

Proteomic mapping of intercellular synaptic environments via flavin-dependent photoredox catalysis

Receptor-ligand interactions play essential signaling roles within intercellular contact regions. This is particularly important within the context of the immune synapse where protein communication at the surface of physically interacting T cells and antigen-presenting cells regulate downstream immune signaling responses. To identify protein microenvironments within immunological synapses, we combined a flavin-dependent photocatalytic labeling strategy with quantitative mass spectrometry-based proteomics. Using α-PD-L1 or α-PD-1 single-domain antibody (VHH)-based photocatalyst targeting modalities, we profiled protein microenvironments within the intercellular region of an immune synapse-forming co-culture system. In addition to enrichment of both PD-L1 and PD-1 with either targeting modality, we also observed enrichment of both known immune synapse residing receptor-ligand pairs and surface proteins, as well as previously unknown synapse residing proteins.

Detection of cell-cell interactions via photocatalytic cell tagging

The growing appreciation of immune cell-cell interactions within disease environments has led to extensive efforts to develop immunotherapies. However, characterizing complex cell-cell interfaces in high resolution remains challenging. Thus, technologies leveraging therapeutic-based modalities to profile intercellular environments offer opportunities to study cell-cell interactions with molecular-level insight. We introduce photocatalytic cell tagging (PhoTag) for interrogating cell-cell interactions using single-domain antibodies (VHHs) conjugated to photoactivatable flavin-based cofactors. Following irradiation with visible light, the flavin photocatalyst generates phenoxy radical tags for targeted labeling. Using this technology, we demonstrate selective synaptic labeling across the PD-1/PD-L1 axis in antigen-presenting cell-T cell systems. In combination with multiomics single-cell sequencing, we monitored interactions between peripheral blood mononuclear cells and Raji PD-L1 B cells, revealing differences in transient interactions with specific T cell subtypes. The utility of PhoTag in capturing cell-cell interactions will enable detailed profiling of intercellular communication across different biological systems.

Placental uptake and metabolism of 25(OH)vitamin D determine its activity within the fetoplacental unit

Pregnancy 25-hydroxyvitamin D [25(OH)D] concentrations are associated with maternal and fetal health outcomes. Using physiological human placental perfusion and villous explants, we investigate the role of the placenta in regulating the relationships between maternal 25(OH)D and fetal physiology. We demonstrate active placental uptake of 25(OH)D₃ by endocytosis, placental metabolism of 25(OH)D₃ into 24,25-dihydroxyvitamin D₃ and active 1,25-dihydroxyvitamin D [1,25(OH)₂D₃], with subsequent release of these metabolites into both the maternal and fetal circulations. Active placental transport of 25(OH)D₃ and synthesis of 1,25(OH)₂D₃ demonstrate that fetal supply is dependent on placental function rather than simply the availability of maternal 25(OH)D₃. We demonstrate that 25(OH)D₃ exposure induces rapid effects on the placental transcriptome and proteome. These map to multiple pathways central to placental function and thereby fetal development, independent of vitamin D transfer. Our data suggest that the underlying epigenetic landscape helps dictate the transcriptional response to vitamin D treatment. This is the first quantitative study demonstrating vitamin D transfer and metabolism by the human placenta, with widespread effects on the placenta itself. These data demonstrate a complex interplay between vitamin D and the placenta and will inform future interventions using vitamin D to support fetal development and maternal adaptations to pregnancy.

Vaccine Hyporesponse Induced by Individual Antibiotic Treatment in Mice and Non-Human Primates Is Diminished upon Recovery of the Gut Microbiome

Emerging evidence demonstrates a connection between microbiome composition and suboptimal response to vaccines (vaccine hyporesponse). Harnessing the interaction between microbes and the immune system could provide novel therapeutic strategies for improving vaccine response. Currently we do not fully understand the mechanisms and dynamics by which the microbiome influences vaccine response. Using both mouse and non-human primate models, we report that short-term oral treatment with a single antibiotic (vancomycin) results in the disruption of the gut microbiome and this correlates with a decrease in systemic levels of antigen-specific IgG upon subsequent parenteral vaccination. We further show that recovery of microbial diversity before vaccination prevents antibiotic-induced vaccine hyporesponse, and that the antigen specific IgG response correlates with the recovery of microbiome diversity. RNA sequencing analysis of small intestine, spleen, whole blood, and secondary lymphoid organs from antibiotic treated mice revealed a dramatic impact on the immune system, and a muted inflammatory signature is correlated with loss of bacteria from Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. These results suggest that microbially modulated immune pathways may be leveraged to promote vaccine response and will inform future vaccine design and development strategies.

Assessing donor-to-donor variability in human intestinal organoid cultures

Donor-to-donor variability in primary human organoid cultures has not been well characterized. As these cultures contain multiple cell types, there is greater concern that variability could lead to increased noise. In this work we investigated donor-to-donor variability in human gut adult stem cell (ASC) organoids. We examined intestinal developmental pathways during culture differentiation in ileum- and colon-derived cultures established from multiple donors, showing that differentiation patterns were consistent among cultures. This finding indicates that donor-to-donor variability in this system remains at a manageable level. Intestinal metabolic activity was evaluated by targeted analysis of central carbon metabolites and by analyzing hormone production patterns. Both experiments demonstrated similar metabolic functions among donors. Importantly, this activity reflected intestinal biology, indicating that these ASC organoid cultures are appropriate for studying metabolic processes. This work establishes a framework for generating high-confidence data using human primary cultures through thorough characterization of variability.

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Developmental gene expression patterns were used to assess organoid variability

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Organoid differentiation patterns were consistent among independent donors

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Metabolic state of organoids was developmentally controlled

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Variability of hormone secretion and metabolic activity in organoids was minimal

Micro RNA Targets in HIV Latency: Insights into Novel Layers of Latency Control

Despite the considerable progress that has been made in identifying cellular factors and pathways that contribute to establishment and maintenance of the latent HIV reservoir, it remains the major obstacle to eradicating this virus. Most recently, noncoding genes have been implicated in regulation of HIV expression. In this study, small RNA sequencing was used to profile expression of microRNAs (miRNAs) in a primary CD4+ T cell in vitro model of HIV latency. Previously, we have shown that protein-coding genes dysregulated in this model were enriched for the p53 signaling pathway, which was confirmed experimentally. We further found a link between p53 signaling and dysregulated long noncoding RNAs. In this study, we hypothesized that miRNAs may provide an additional level of regulation of the p53 signaling pathway during HIV latency. Twenty-six miRNAs were identified to be dysregulated in our latency model. A subset of these miRNAs was validated by real-time quantitative polymerase chain reaction. Predicted messenger RNA (mRNA) targets and cellular pathways enriched for mRNA targets were identified using several analytical methods. Our analyses showed that many protein-coding genes and pathways targeted by dysregulated miRNAs have relevance to regulation of HIV expression or establishment of HIV latency. The p53 signaling pathway was found among pathways that were targeted by dysregulated miRNAs at a greater level than expected by chance. This study provides a mechanistic insight into regulation of the p53 pathway through miRNAs that may contribute to the establishment of latency.

Comprehensive plasma proteomic profiling reveals biomarkers for active tuberculosis

BACKGROUNDTuberculosis (TB) kills more people than any other infection, and new diagnostic tests to identify active cases are required. We aimed to discover and verify novel markers for TB in nondepleted plasma.METHODSWe applied an optimized quantitative proteomics discovery methodology based on multidimensional and orthogonal liquid chromatographic separation combined with high-resolution mass spectrometry to study nondepleted plasma of 11 patients with active TB compared with 10 healthy controls. Prioritized candidates were verified in independent UK (n = 118) and South African cohorts (n = 203).RESULTSWe generated the most comprehensive TB plasma proteome to date, profiling 5022 proteins spanning 11 orders-of-magnitude concentration range with diverse biochemical and molecular properties. We analyzed the predominantly low-molecular weight subproteome, identifying 46 proteins with significantly increased and 90 with decreased abundance (peptide FDR ≤ 1%, q ≤ 0.05). Verification was performed for novel candidate biomarkers (CFHR5, ILF2) in 2 independent cohorts. Receiver operating characteristics analyses using a 5-protein panel (CFHR5, LRG1, CRP, LBP, and SAA1) exhibited discriminatory power in distinguishing TB from other respiratory diseases (AUC = 0.81).CONCLUSIONWe report the most comprehensive TB plasma proteome to date, identifying novel markers with verification in 2 independent cohorts, leading to a 5-protein biosignature with potential to improve TB diagnosis. With further development, these biomarkers have potential as a diagnostic triage test.FUNDINGColciencias, Medical Research Council, Innovate UK, NIHR, Academy of Medical Sciences, Program for Advanced Research Capacities for AIDS, Wellcome Centre for Infectious Diseases Research.

Microenvironment mapping via Dexter energy transfer on immune cells

Many disease pathologies can be understood through the elucidation of localized biomolecular networks, or microenvironments. To this end, enzymatic proximity labeling platforms are broadly applied for mapping the wider spatial relationships in subcellular architectures. However, technologies that can map microenvironments with higher precision have long been sought. Here, we describe a microenvironment-mapping platform that exploits photocatalytic carbene generation to selectively identify protein-protein interactions on cell membranes, an approach we term MicroMap (μMap). By using a photocatalyst-antibody conjugate to spatially localize carbene generation, we demonstrate selective labeling of antibody binding targets and their microenvironment protein neighbors. This technique identified the constituent proteins of the programmed-death ligand 1 (PD-L1) microenvironment in live lymphocytes and selectively labeled within an immunosynaptic junction.

Long non-coding RNAs and latent HIV - A search for novel targets for latency reversal

The latent cellular reservoir of HIV is recognized as the major barrier to cure from HIV infection. Long non-coding RNAs (lncRNAs) are more tissue and cell type-specific than protein coding genes, and may represent targets of choice for HIV latency reversal. Using two in vitro primary T-cell models, we identified lncRNAs dysregulated in latency. PVT1 and RP11-347C18.3 were up-regulated in common between the two models, and RP11-539L10.2 was down-regulated. The major component of the latent HIV reservoir, memory CD4+ T-cells, had higher expression of these lncRNAs, compared to naïve T-cells. Guilt-by-association analysis demonstrated that lncRNAs dysregulated in latency were associated with several cellular pathways implicated in HIV latency establishment and maintenance: proteasome, spliceosome, p53 signaling, and mammalian target of rapamycin (MTOR). PVT1, RP11-347C18.3, and RP11-539L10.2 were down-regulated by latency reversing agents, suberoylanilide hydroxamic acid and Romidepsin, suggesting that modulation of lncRNAs is a possible secondary mechanism of action of these compounds. These results will facilitate prioritization of lncRNAs for evaluation as targets for HIV latency reversal. Importantly, our study provides insights into regulatory function of lncRNA during latent HIV infection.

Histone deacetylase inhibitors induce complex host responses that contribute to differential potencies of these compounds in HIV reactivation

Histone deacetylase (HDAC) inhibitors (HDACis) have been widely tested in clinical trials for their ability to reverse HIV latency but have yielded only limited success. One HDACi, suberoylanilide hydroxamic acid (SAHA), exhibits off-target effects on host gene expression predicted to interfere with induction of HIV transcription. Romidepsin (RMD) has higher potency and specificity for class I HDACs implicated in maintaining HIV provirus in the latent state. More robust HIV reactivation has indeed been achieved with RMD use ex vivo than with SAHA; however, reduction of viral reservoir size has not been observed in clinical trials. Therefore, using RNA-Seq, we sought to compare the effects of SAHA and RMD on gene expression in primary CD4+ T cells. Among the genes whose expression was modulated by both HDACi agents, we identified genes previously implicated in HIV latency. Two genes, SMARCB1 and PARP1, whose modulation by SAHA and RMD is predicted to inhibit HIV reactivation, were evaluated in the major maturation subsets of CD4+ T cells and were consistently either up- or down-regulated by both HDACi compounds. Our results indicate that despite having different potencies and HDAC specificities, SAHA and RMD modulate an overlapping set of genes, implicated in HIV latency regulation. Some of these genes merit exploration as additional targets to improve the therapeutic outcomes of "shock and kill" strategies. The overall complexity of HDACi-induced responses among host genes with predicted stimulatory or inhibitory effects on HIV expression likely contributes to differential HDACi potencies and dictates the outcome of HIV reactivation.

Quantitative proteomic profiling of primary cancer-associated fibroblasts in oesophageal adenocarcinoma

BACKGROUND

Cancer-associated fibroblasts (CAFs) form the major stromal component of the tumour microenvironment (TME). The present study aimed to examine the proteomic profiles of CAFs vs. normal fibroblasts (NOFs) from patients with oesophageal adenocarcinoma to gain insight into their pro-oncogenic phenotype.

METHODS

CAFs/NOFs from four patients were sub-cultured and analysed using quantitative proteomics. Differentially expressed proteins (DEPs) were subjected to bioinformatics and compared with published proteomics and transcriptomics  datasets.

RESULTS

Principal component analysis of all profiled proteins showed that CAFs had high heterogeneity and clustered separately from NOFs. Bioinformatics interrogation of the DEPs demonstrated inhibition of adhesion of epithelial cells, adhesion of connective tissue cells and cell death of fibroblast cell lines in CAFs vs. NOFs (p < 0.0001). KEGG pathway analysis showed a significant enrichment of the insulin-signalling pathway (p = 0.03). Gene ontology terms related with myofibroblast phenotype, metabolism, cell adhesion/migration, hypoxia/oxidative stress, angiogenesis, immune/inflammatory response were enriched in CAFs vs. NOFs. Nestin, a stem-cell marker up-regulated in CAFs vs. NOFs, was confirmed to be expressed in the TME with immunohistochemistry.

CONCLUSIONS

The identified pathways and participating proteins may provide novel insight on the tumour-promoting properties of CAFs and unravel novel adjuvant therapeutic targets in the TME.

Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment

The greatest obstacle to a cure for HIV is the provirus that integrates into the genome of the infected cell and persists despite antiretroviral therapy. A "shock and kill" approach has been proposed as a strategy for an HIV cure whereby drugs and compounds referred to as latency-reversing agents (LRAs) are used to "shock" the silent provirus into active replication to permit "killing" by virus-induced pathology or immune recognition. The LRA most utilized to date in clinical trials has been the histone deacetylase (HDAC) inhibitor-vorinostat. Potentially, pathological off-target effects of vorinostat may result from the activation of human endogenous retroviruses (HERVs), which share common ancestry with exogenous retroviruses including HIV. To explore the effects of HDAC inhibition on HERV transcription, an unbiased pharmacogenomics approach (total RNA-Seq) was used to evaluate HERV expression following the exposure of primary CD4+ T cells to a high dose of vorinostat. Over 2,000 individual HERV elements were found to be significantly modulated by vorinostat, whereby elements belonging to the ERVL family (e.g., LTR16C and LTR33) were predominantly downregulated, in contrast to LTR12 elements of the HERV-9 family, which exhibited the greatest signal, with the upregulation of 140 distinct elements. The modulation of three different LTR12 elements by vorinostat was confirmed by droplet digital PCR along a dose-response curve. The monitoring of LTR12 expression during clinical trials with vorinostat may be indicated to assess the impact of this HERV on the human genome and host immunity.

Increased circulating resistin levels in early-onset breast cancer patients of normal body mass index correlate with lymph node negative involvement and longer disease free survival: a multi-center POSH cohort serum proteomics study

BACKGROUND

Early-onset breast cancer (EOBC) affects about one in 300 women aged 40 years or younger and is associated with worse outcomes than later onset breast cancer. This study explored novel serum proteins as surrogate markers of prognosis in patients with EOBC.

METHODS

Serum samples from EOBC patients (stages 1-3) were analysed using agnostic high-precision quantitative proteomics. Patients received anthracycline-based chemotherapy. The discovery cohort (n = 399) either had more than 5-year disease-free survival (DFS) (good outcome group, n = 203) or DFS of less than 2 years (poor outcome group, n = 196). Expressed proteins were assessed for differential expression between the two groups. Bioinformatics pathway and network analysis in combination with literature research were used to determine clinically relevant proteins. ELISA analysis against an independent sample set from the Prospective study of Outcomes in Sporadic versus Hereditary breast cancer (POSH) cohort (n = 181) was used to validate expression levels of the selected target. Linear and generalized linear modelling was applied to determine the effect of target markers, body mass index (BMI), lymph node involvement (LN), oestrogen receptor (ER), progesterone receptor and human epidermal growth factor receptor 2 status on patients' outcome.

RESULTS

A total of 5346 unique proteins were analysed (peptide FDR p ≤ 0.05). Of these, 812 were differentially expressed in the good vs poor outcome groups and showed significant enrichment for the insulin signalling (p = 0.01) and the glycolysis/gluconeogenesis (p = 0.01) pathways. These proteins further correlated with interaction networks involving glucose and fatty acid metabolism. A consistent nodal protein to these metabolic networks was resistin (upregulated in the good outcome group, p = 0.009). ELISA validation demonstrated resistin to be upregulated in the good outcome group (p = 0.04), irrespective of BMI and ER status. LN involvement was the only covariate with a significant association with resistin measurements (p = 0.004). An ancillary in-silico observation was the induction of the inflammatory response, leucocyte infiltration, lymphocyte migration and recruitment of phagocytes (p < 0.0001, z-score > 2). Survival analysis showed that resistin overexpression was associated with improved DFS.

CONCLUSIONS

Higher circulating resistin correlated with node-negative patients and longer DFS independent of BMI and ER status in women with EOBC. Overexpression of serum resistin in EOBC may be a surrogate indicator of improved prognosis.

Lithium-responsive genes and gene networks in bipolar disorder patient-derived lymphoblastoid cell lines

Lithium (Li) is the mainstay mood stabilizer for the treatment of bipolar disorder (BD), although its mode of action is not yet fully understood nor is it effective in every patient. We sought to elucidate the mechanism of action of Li and to identify surrogate outcome markers that can be used to better understand its therapeutic effects in BD patients classified as good (responders) and poor responders (nonresponders) to Li treatment. To accomplish these goals, RNA-sequencing gene expression profiles of lymphoblastoid cell lines (LCLs) were compared between BD Li responders and nonresponders with healthy controls before and after treatment. Several Li-responsive gene coexpression networks were discovered indicating widespread effects of Li on diverse cellular signaling systems including apoptosis and defense response pathways, protein processing and response to endoplasmic reticulum stress. Individual gene markers were also identified, differing in response to Li between BD responders and nonresponders, involved in processes of cell cycle and nucleotide excision repair that may explain part of the heterogeneity in clinical response to treatment. Results further indicated a Li gene expression signature similar to that observed with clonidine treatment, an α2-adrenoceptor agonist. These findings provide a detailed mechanism of Li in LCLs and highlight putative surrogate outcome markers that may permit for advanced treatment decisions to be made and for facilitating recovery in BD patients.

Systems biology applications to study mechanisms of human immunodeficiency virus latency and reactivation

Eradication of human immunodeficiency virus (HIV) in infected individuals is currently not possible because of the presence of the persistent cellular reservoir of latent infection. The identification of HIV latency biomarkers and a better understanding of the molecular mechanisms contributing to regulation of HIV expression might provide essential tools to eliminate these latently infected cells. This review aims at summarizing gene expression profiling and systems biology applications to studies of HIV latency and eradication. Studies comparing gene expression in latently infected and uninfected cells identify candidate latency biomarkers and novel mechanisms of latency control. Studies that profiled gene expression changes induced by existing latency reversing agents (LRAs) highlight uniting themes driving HIV reactivation and novel mechanisms that contribute to regulation of HIV expression by different LRAs. Among the reviewed gene expression studies, the common approaches included identification of differentially expressed genes and gene functional category assessment. Integration of transcriptomic data with other biological data types is presently scarce, and the field would benefit from increased adoption of these methods in future studies. In addition, designing prospective studies that use the same methods of data acquisition and statistical analyses will facilitate a more reliable identification of latency biomarkers using different model systems and the comparison of the effects of different LRAs on host factors with a role in HIV reactivation. The results from such studies would have the potential to significantly impact the process by which candidate drugs are selected and combined for future evaluations and advancement to clinical trials.

Large-scale phenotyping of noise-induced hearing loss in 100 strains of mice

A cornerstone technique in the study of hearing is the Auditory Brainstem Response (ABR), an electrophysiologic technique that can be used as a quantitative measure of hearing function. Previous studies have published databases of baseline ABR thresholds for mouse strains, providing a valuable resource for the study of baseline hearing function and genetic mapping of hearing traits in mice. In this study, we further expand upon the existing literature by characterizing the baseline ABR characteristics of 100 inbred mouse strains, 47 of which are newly characterized for hearing function. We identify several distinct patterns of baseline hearing deficits and provide potential avenues for further investigation. Additionally, we characterize the sensitivity of the same 100 strains to noise exposure using permanent thresholds shifts, identifying several distinct patterns of noise-sensitivity. The resulting data provides a new resource for studying hearing loss and noise-sensitivity in mice.

Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency

Suberoylanilide hydroxamic acid (SAHA) has been assessed in clinical trials as part of a "shock and kill" strategy to cure HIV-infected patients. While it was effective at inducing expression of HIV RNA ("shock"), treatment with SAHA did not result in a reduction of reservoir size ("kill"). We therefore utilized a combined analysis of effects of SAHA on the host transcriptome and proteome to dissect its mechanisms of action that may explain its limited success in "shock and kill" strategies. CD4+ T cells from HIV seronegative donors were treated with 1μM SAHA or its solvent dimethyl sulfoxide (DMSO) for 24h. Protein expression and post-translational modifications were measured with iTRAQ proteomics using ultra high-precision two-dimensional liquid chromatography-tandem mass spectrometry. Gene expression was assessed by Illumina microarrays. Using limma package in the R computing environment, we identified 185 proteins, 18 phosphorylated forms, 4 acetylated forms and 2982 genes, whose expression was modulated by SAHA. A protein interaction network integrating these 4 data types identified the HIV transcriptional repressor HMGA1 to be upregulated by SAHA at the transcript, protein and acetylated protein levels. Further functional category assessment of proteins and genes modulated by SAHA identified gene ontology terms related to NFκB signaling, protein folding and autophagy, which are all relevant to HIV reactivation. In summary, SAHA modulated numerous host cell transcripts, proteins and post-translational modifications of proteins, which would be expected to have very mixed effects on the induction of HIV-specific transcription and protein function. Proteome profiling highlighted a number of potential counter-regulatory effects of SAHA with respect to viral induction, which transcriptome profiling alone would not have identified. These observations could lead to a more informed selection and design of other HDACi with a more refined targeting profile, and prioritization of latency reversing agents of other classes to be used in combination with SAHA to achieve more potent induction of HIV expression.

Replication competent virus as an important source of bias in HIV latency models utilizing single round viral constructs

The central memory T cell (TCM) model forms a unique HIV-1 latency model based on primary cells that closely resemble in vivo TCM. The virus employed in this model is based on an engineered vector incapable of replication after initial infection. We show that despite this strategy, replication competent viral particles are released into the culture medium due to recombination between overlapping sequences of the env deleted HIV genome that is co-transfected with intact env. This finding emphasizes the need for careful data analysis and interpretation if similar constructs are employed and urges for additional caution during laboratory work.

Differential gene expression in HIV-infected individuals following ART

Previous studies of the effect of ART on gene expression in HIV-infected individuals have identified small numbers of modulated genes. Since these studies were underpowered or cross-sectional in design, a paired analysis of peripheral blood mononuclear cells (PBMCs), isolated before and after ART, from a robust number of HIV-infected patients (N=32) was performed. Gene expression was assayed by microarray and 4157 differentially expressed genes (DEGs) were identified following ART using multivariate permutation tests. Pathways and gene ontology (GO) terms over-represented for DEGs reflected the transition from a period of active virus replication before ART to one of viral suppression (e.g., repression of JAK-STAT signaling) and possible prolonged drug exposure (e.g., oxidative phosphorylation pathway) following ART. CMYC was the DEG whose product made the greatest number of interactions at the protein level in protein interaction networks (PINs), which has implications for the increased incidence of Hodgkin's lymphoma (HL) in HIV-infected patients. The differential expression of multiple genes was confirmed by RT-qPCR including well-known drug metabolism genes (e.g., ALOX12 and CYP2S1). Targets not confirmed by RT-qPCR (i.e., GSTM2 and RPL5) were significantly confirmed by droplet digital (ddPCR), which may represent a superior method when confirming DEGs with low fold changes. In conclusion, a paired design revealed that the number of genes modulated following ART was an order of magnitude higher than previously recognized.

Therapeutic potential of HSP90 inhibition for neurofibromatosis type 2

PURPOSE

The growth and survival of neurofibromatosis type 2 (NF2)-deficient cells are enhanced by the activation of multiple signaling pathways including ErbBs/IGF-1R/Met, PI3K/Akt, and Ras/Raf/Mek/Erk1/2. The chaperone protein HSP90 is essential for the stabilization of these signaling molecules. The aim of the study was to characterize the effect of HSP90 inhibition in various NF2-deficient models.

EXPERIMENTAL DESIGN

We tested efficacy of the small-molecule NXD30001, which has been shown to be a potent HSP90 inhibitor. The antiproliferative activity of NXD30001 was tested in NF2-deficient cell lines and in human primary schwannoma and meningioma cultures in vitro. The antitumor efficacy of HSP90 inhibition in vivo was verified in two allograft models and in one NF2 transgenic model. The underlying molecular alteration was further characterized by a global transcriptome approach.

RESULTS

NXD30001 induced degradation of client proteins in and suppressed proliferation of NF2-deficient cells. Differential expression analysis identified subsets of genes implicated in cell proliferation, cell survival, vascularization, and Schwann cell differentiation whose expression was altered by NXD30001 treatment. The results showed that NXD30001 in NF2-deficient schwannoma suppressed multiple pathways necessary for tumorigenesis.

CONCLUSIONS

HSP90 inhibition showing significant antitumor activity against NF2-related tumor cells in vitro and in vivo represents a promising option for novel NF2 therapies.

A combined analysis of microarray gene expression studies of the human prefrontal cortex identifies genes implicated in schizophrenia

Small cohort sizes and modest levels of gene expression changes in brain tissue have plagued the statistical approaches employed in microarray studies investigating the mechanism of schizophrenia. To combat these problems a combined analysis of six prior microarray studies was performed to facilitate the robust statistical analysis of gene expression data from the dorsolateral prefrontal cortex of 107 patients with schizophrenia and 118 healthy subjects. Multivariate permutation tests identified 144 genes that were differentially expressed between schizophrenia and control groups. Seventy of these genes were identified as differentially expressed in at least one component microarray study but none of these individual studies had the power to identify the remaining 74 genes, demonstrating the utility of a combined approach. Gene ontology terms and biological pathways that were significantly enriched for differentially expressed genes were related to neuronal cell-cell signaling, mesenchymal induction, and mitogen-activated protein kinase signaling, which have all previously been associated with the etiopathogenesis of schizophrenia. The differential expression of BAG3, C4B, EGR1, MT1X, NEUROD6, SST and S100A8 was confirmed by real-time quantitative PCR in an independent cohort using postmortem human prefrontal cortex samples. Comparison of gene expression between schizophrenic subjects with and without detectable levels of antipsychotics in their blood suggests that the modulation of MT1X and S100A8 may be the result of drug exposure. In conclusion, this combined analysis has resulted in a statistically robust identification of genes whose dysregulation may contribute to the mechanism of schizophrenia.

Spyder proximal coronary vein graft patency over time: the SPPOT study

BACKGROUND

Clampless proximal anastomoses are associated with fewer strokes in coronary artery bypass (CAB) graft surgery, but lack of patency of proximal grafts has been an issue. The Spyder (Medtronic, Minneapolis, MN, USA) is an "exoconnector" device that deploys a nitinol clamping mechanism to attach a vein onto the aortotomy and create the proximal anastomosis.

METHODS

During a 22-month period we performed gated cardiac computed tomographic angiography on 38 patients who underwent off-pump CAB.

RESULTS

Of the 49 proximal anastomoses created with the Spyder, 44 (90%) remained patent at the time of study, with a mean follow-up period of 16.7 months.

CONCLUSIONS

The use of the Spyder exoconnector to create a clampless proximal anastomosis during off-pump CAB surgery is a reasonable strategy to improve graft patency.

An Investigation of the Use of the MicroFoss as an Indicator of the Shelf Life of Pasteurized Fluid Milk

The MicroFoss method was evaluated for its effectiveness as an indicator of fluid milk shelf life. Half-gallon, 2% fat fluid milk samples (n = 90) were obtained from a milk processing plant on 3 occasions postpasteurization and evaluated for shelf life. Sensory evaluation was performed by 3 judges experienced in the use of the American Dairy Science Association scorecard for milk. A score of 5 or less was considered to represent the end of the shelf life of the product. MicroFoss coupled with preliminary incubation (PI) was utilized to estimate the total viable (TVC) and gram-negative counts (GN) in the milk. The MicroFoss functions by using a pH indicator or CO2 production to detect changes in light reflection to estimate bacterial populations. Simple and multiple linear regression analyses were utilized to determine the relationship between MicroFoss (PI-GN and PI-TVC detection times) and product shelf life. It was concluded that using both PI-GN and PI-TVC in a combined algorithm is the optimal way of using MicroFoss as a shelf-life indicator. When PI-TVC was selected in the algorithm, a correlation coefficient of 0.89 existed between PI-TVC and shelf life; PI-GN was used in the algorithm in the place of PI-TVC when its detection time was within 6 h of the detection time of PI-TVC vials. The PI-GN detection times correlated well (r = 0.80) with shelf life, but more importantly, all but one PI-GN sample (n = 50) selected in the algorithm had a shelf life of less than 10 d. This indicates that the PI-GN measurement can be utilized along with PI-TVC detection time to indicate potential shelf-life problems.

Transmyocardial laser revascularization causes sustained VEGF secretion

Transmyocardial laser revascularization (TMR) using a carbon dioxide (CO(2)) laser has been shown to relieve angina, increase vascular density, and improve myocardial contraction. A study of 28 patients receiving TMR was conducted to monitor vascular endothelial growth factor (VEGF) levels with the goal of clarifying the relationship between TMR, the amelioration of angina, and vascular density. Serum VEGF levels were measured during four periods (preoperative, postoperative, convalescence, and late) in these 28 patients who received sole therapy TMR for un-revascularizable ischemic angina and the levels were compared with the control group consisting of 10 nonischemic thoracotomy patients. Twelve of the 28 patients had previous coronary artery bypass graft(s); 10 had unstable angina, and 1 had an ejection fraction less than 30%. Overall, angina class was reduced from 3.8 +/- 0.9 to 1.0 +/- 0.9 (P < 0.01) at the 1-year follow-up. There were no perioperative mortalities; however, there was one late mortality. The results show that VEGF levels were higher in the convalescence and late periods. Specifically in the late period, VEGF levels in TMR therapy patients surpassed those of the control group and normalized VEGF levels were three times higher in the late period than preoperatively. The sustained VEGF secretion observed in this study may help to explain why CO(2) TMR therapy causes locally increased vascular density and angina relief.

Clampless Anastomosis: Novel Device for Clampless Proximal Vein Anastomosis in OPCAB Surgery--The Initial Spyder Experience

The Spyder is a novel device that enables the attachment of a vein to the aorta by compliant, interrupted anastomosis; this minimizes aortic manipulation during off pump-coronary artery bypass (OPCAB) surgery. Its use may reduce transcranial Doppler signals recorded during CABG. We performed 250 anastomoses in 160 OPCAB cases in many centers and recorded efficiency and efficacy data. There were no adverse events noted during the operative period. In a subset of patients in one center, flow (n = 48) and transcranial Doppler signals (n = 22) were measured. We found the device to be a useful adjunct for minimally invasive CABG surgery.

A novel device for clampless proximal anastomosis in OPCAB surgery: the IPAD

The Coalescent IPAD (Coalescent Surgical, Sunnyvale, CA, USA) is a novel device that enables creation of a compliant proximal vein anastomosis to the aorta during off-pump coronary artery bypass (OPCAB) surgery while reducing the risk of cerebrovascular emboli and early stenosis. We performed IPAD-created anastomoses in 76 patients having standard OPCAB surgery. Following the procedures, no patients developed myocardial infarctions or reported angina, suggesting patency of the vein grafts to be of high quality. We found the device to be a useful adjunct for minimally invasive CAB graft surgery.

Influence of adjunct cultures on volatile free fatty acids in reduced-fat Edam cheeses

The effects of the adjunct cultures Lactococcus lactis ssp. diacetylactis, Brevibacterium linens BL2, Lactobacillus helveticus LH212, and Lactobacillus reuteri ATCC 23272 on volatile free fatty acid production in reduced-fat Edam cheese were studied. Lipase activity evaluation using p-nitrophenyl fatty acid ester substrates indicated that L. lactis ssp. diacetylactis showed the highest activity among the 4 adjunct cultures. Full-fat and 33% reduced-fat control cheeses (no adjunct) were made along with 5 treatments of reduced-fat cheeses, which included individual, and a mixture of the adjunct cultures. Volatile free fatty acids of cheeses were analyzed using static headspace analysis with 4-bromofluorobenzene as an internal standard. Changes in volatile free fatty acid concentrations were found in headspace gas of cheeses after 3-and 6-mo ripening. Acetic acid was the most abundant acid detected throughout ripening. Full-fat cheese had the highest relative amount of propionic acid among the cheeses. Certain adjunct cultures had a definite role in lipolysis at particular times. Reduced-fat cheese with L. lactis ssp. diacetylactis at 3-mo showed the highest levels of butyric, isovaleric, n-valeric, iso-caproic, and n-caproic acid. Reduced-fat cheese with Lactobacillus reuteri at 6 mo produced the highest relative concentration of isocaproic, n-caproic, and heptanoic, and the highest relative concentration of total acids.

Effect of Pressure and Fat Content on Particle Sizes in Microfluidized Milk

Average diameters and particle size distributions in fluid milks with different fat contents and subjected to various homogenization pressures with a "microfluidizer" were evaluated. Skim, 2%, and whole milks were microfluidized at 50, 100, 150, and 200 MPa. Cream containing 41% milk fat was microfluidized at 50, 100, and 150 MPa. Particle sizes were determined by laser light scattering. As microfluidization pressure was increased from 50 to 100 MPa, particle sizes in skim, 2%, and whole milks decreased. Microfluidization at pressures greater than 100 MPa had little additional effect on reducing the particle sizes in skim and 2% milks compared with microfluidization at 100 MPa, but the particle sizes in whole milk increased as the microfluidization pressure was increased from 100 to 200 MPa due to formation of homogenization clusters. The particle sizes in cream increased as the microfluidization pressure was increased from 50 to 150 MPa. When the microfluidization pressure was held constant, the particle sizes increased as the milk fat concentration was increased. The coefficients of variations of the volume-weighted particle size distributions for cream were higher than for skim, 2%, and whole milks. Larger "big" particles and smaller "small" particles were formed in whole milk after microfluidization at 200 MPa than at 100 MPa. Although microfluidization can be used to produce small particles in skim, 2%, and whole milks, a higher than optimum pressure (above 100 MPa) applied to whole milk will not lead to the minimum d(43) (volume-weighted average diameter) due to formation of clusters.

Interrupted distal anastomosis: the interrupted “porcupine” technique

The distal coronary artery bypass graft anastomosis created by an interrupted technique using nitinol clips is likely superior to that created with continuous suture because surgeons place clips with optimal visualization, and the anastomosis exhibits optimal compliance and cannot become a "purse-string" once constructed. Skillful use of the clips allows the surgeon to work in the ever more cramped quarters of the minithoracotomy or minimally invasive incision. Anastomosing vessels without knot tying is a valuable practice in the application of remote and robotic surgeries.

Properties of frozen dairy desserts processed by microfluidization of their mixes

Sensory properties and rate of meltdown of nonfat (0% fat) and low-fat (2% fat) vanilla ice creams processed either by conventional valve homogenization or microfluidization of their mixes were compared with each other and to ice cream (10% fat) processed by conventional valve homogenization. Mixes for frozen dairy desserts containing 0, 2, and 10% fat were manufactured. Some of the nonfat and low-fat ice cream mixes were processed by microfluidization at 50, 100, 150, and 200 MPa, and the remaining nonfat and low-fat ice cream mixes and all of the ice cream mix were processed by conventional valve homogenization at 13.8 MPa, first stage, and 3.4 MPa, second stage. The finished frozen and hardened products were evaluated at d 1 and 45 for meltdown rate and for flavor and body and texture by preference testing. Nonfat and low-fat ice creams that usually had a slower meltdown were produced when processing their mixes by microfluidization instead of by conventional valve homogenization. Sensory scores for the ice cream were significantly higher than sensory scores for the nonfat and low-fat ice creams, but the sensory scores for the conventional valve homogenized controls for the nonfat ice cream and low-fat ice cream were not significantly different from the sensory scores for the nonfat ice cream and low-fat ice cream processed by microfluidization of the mixes, respectively. Microfluidization produced nonfat and low-fat ice creams that usually had a slower meltdown without affecting sensory properties.

Influence of adjunct cultures on ripening of reduced fat Edam cheeses

The influence of four adjunct cultures [Brevibacterium linens (BL2), Lactococcus lactis ssp. diacetylactis, Lactobacillus helveticus (LH212), and Lactobacillus reuteri (ATCC 23272)] on chemical and sensory characteristics of reduced fat Edam cheese was studied. The aminopeptidase activity of Lactococcus lactis ssp. diacetylactis was higher than that of Lactobacillus helveticus, Lactobacillus reuteri, and Brevibacterium linens, respectively. Mean percent fat and moisture contents of reduced fat cheese were 20.85 +/- 0.69 and 42.95 +/- 0.43, respectively. Percentage of fat and moisture of full fat control cheese were 30.06 +/- 0.78 and 39.11 +/- 0.60. Titratable acidity increased in all cheese with aging while pH initially decreased but increased in cheese after 6 mo aging at 7 degrees C. Lactic acid bacteria counts were on average one log higher for reduced fat cheeses than for full fat control cheese and counts decreasing with aging. Free amino acids (FAA) in cheeses increased with aging, and were higher in reduced fat cheeses than in the full fat control cheese. Reduced fat cheeses containing L. helveticus exhibited the highest FAA content. Descriptive sensory panelists (n = 9) did not detect differences among cheeses after 3 and 6 mo ripening, but aged/developed flavors (fruity, nutty, brothy, sulfur, free fatty acid) and sweetness increased between 3 and 6 mo. Expert panelists (n = 6) detected differences in texture quality among the cheeses. Reduced fat control cheeses and reduced fat cheeses with L. helveticus and L. reuteri received the highest texture quality scores. Addition of L. helveticus and Lc. lactis ssp. diacetylactis, as adjunct cultures to reduced fat Edam cheeses increased proteolysis, while the addition of L. helveticus and L. reuteri increased texture quality of cheeses.

Formulations and processing of yogurt affect the microbial quality of carbonated yogurt

Carbonation, flavor, culture type, pH, and storage time were varied to investigate the effects of these variables and their interactions on the growth of both typical and nontypical yogurt cultures and some contaminating bacteria. Two types of yogurt cultures (YC-470 and YC-180) were used as the source of typical yogurt bacteria, Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus. In addition, Lactobacillus acidophilus (LA-K) and Bifidobacterium longum ATCC 15707 were added as nontypical yogurt cultures to make sweetened low fat (1%) Swiss-style plain, strawberry, and lemon yogurts. Samples were incubated at 43 degrees C until pH values of 5.0 or 4.2 were reached. Strawberry yogurts at low (4.2) and high (5.0) pHs were divided into three portions, which were separately inoculated with contaminating bacteria, Bacillus licheniformis ATCC 14580, Escherichia coli ATCC 11775, and Listeria monocytogenes Scott A. After incorporation of carbon dioxide (1.10 to 1.27 volume of CO2 gas dissolved in water), the yogurt was stored at 4 degrees C for a 90-d period. Carbon dioxide did not affect the growth of typical or nontypical yogurt bacteria. Also, CO2 did not inhibit the growth of undesirable microorganisms. In general, low levels of CO2 did not affect the bacterial population in yogurt. The microflora of yogurt were influenced by culture type, pH, flavor type, and storage time or their interactions.

Listeria monocytogenes, Yersinia enterocolitica, and Salmonella in dairy plant environments

In order to determine the presence of the three environmental pathogens in dairy plants, six milk and four ice cream plants in a three state area were sampled. A total of 353 environmental samples were taken over three replications. Bacterial counts were performed on the environmental samples for chi-square analysis. Salmonella spp. were not isolated from any of the environmental samples. Yersinia enterocolitica was isolated from 6.8% of the environmental samples. Listeria monocytogenes was isolated from 6.5% of the environmental samples. Listeria spp. other than L. monocytogenes were isolated from 9.3% of the environmental samples. The presence of Y. enterocolitica was significantly related to high bacterial counts for six microbiological tests. The presence of L. monocytogenes was not related to high bacterial counts.

Helping employees and families cope with breast cancer treatment

With respect to a lump in the breast, all findings can be considered significant until necessary evaluation is completed. Persons who have cancer often attribute all symptomatology to the disease; therefore, the nurse needs to allay fears about commonly occurring illnesses, while staying attuned to indications of metastasis. Keeping up-to-date with a rapidly changing field will be a challenge to nurses in the position to counsel and to have a positive effect on the lives of millions of women with or at risk for breast cancer. The occupational health nurse is in a strategic position to encourage prevention and surveillance, as well as to counsel employees during diagnosis, treatment, and rehabilitation.

Clinical experience with ciprofloxacin: analysis of a multi-practice study

In a multi-practice study of 113 patients treated with ciprofloxacin (mean daily dosage, 995 mg per day; mean duration of treatment, 9.6 days) for a variety of infections, 14 were microbiologically proven. Of these, bacteriologic cure and/or improvement resulted in 92.9% of cases. For all 113 infections, clinical cure and/or improvement resulted in 97.1% of cases. A total of 17 infections were classified as chronic. Therapy with ciprofloxacin was discontinued in three (2.6%) of 113 patients because of adverse effects. Overall, there were 5/113 (4.4%) adverse reactions (ADRs). Only one ADR was related definitely to ciprofloxacin therapy. Two ADRs were definitely not related; in two the relationship was uncertain. Two patients of the five (40%) elected to continue ciprofloxacin therapy despite mild side effects.

Assessment of Dairy Product Quality and Potential Shelf-Life - A Review

Over the years, many tests and assays have been developed to estimate the quality and potential shelf-life of dairy products. These have ranged from simple, standard bacterial enumerations to more complex metabolite detections. This paper is a review of the parameters that have been used to estimate, or indicate the inherent quality of dairy products.

Estimation of Potential Shelf Life of Cottage Cheese Utilizing Bacterial Numbers and Metabolites

A study was conducted to investigate the use of bacterial numbers and their metabolites as estimators of the potential shelf life of cottage cheese. Dry cottage cheese curd and cream dressing were obtained on the day of processing. Portions of the cream dressing were inoculated with Pseudomonas fluorescens P27 to result in approximate levels of 0, 1,000 and 100,000 bacteria per g in finished cottage cheese after combining the curd and cream. Samples, stored at 7°C, were sensorially evaluated on a daily basis and analyzed every 7 d for up to 35 d. On days of analysis each sample was subjected to preliminary incubation (PI) as follows: none, 21°C for 7 h, 21°C for 14 h, 13°C for 18 h and 18°C for 18 h. For each PI, samples were enumerated by aerobic plate count, modified psychrotrophic bacteria count and gram-negative (CVT) count. Samples were enumerated for the standard psychrotrophic bacteria count without PI. Samples were also exposed to 18°C for 18 h PI in plate count broth for impedance detection measurements. Endotoxin (lipopolysaccharide) concentration and proteolysis were determined by the Limulus amebocyte lysate assay and the o-phthaldialdehyde method, respectively. Bacterial enumerations proved to be of little estimative value as the highest correlation coefficient obtained was -0.61. Endotoxin, proteolysis and impedance detection methods resulted in high correlation coefficients as related to potential shelf life of cottage cheese, with values of -0.81, -0.87 and -0.90, respectively. A prediction equation was formulated from the data.

Estimation of Potential Shelf-life of Pasteurized Fluid Milk Utilizing Bacterial Numbers and Metabolites

A study was conducted on use of bacterial numbers and their metabolites, and any possible interaction thereof, as estimators of the potential shelf-life of pasteurized fluid milk. Whole and skim milk samples were obtained on the day of processing. Samples of each milk were inoculated in duplicate with 0, 1,000, or 100,000 bacteria/ml with a pure strain of Pseudomonas fluorescens P27. Samples, stored at 7°C, were analyzed for microbiological and bioichemical parameters every 5 d for up to 20 d, with organoleptic evaluations conducted on a daily basis. On days of analysis, each sample was subjected to various preliminary incubations. Bacterial enumerations conducted were psychrotrophic bacteria count, standard plate count, gram-negative bacteria count, and modified psychrotrophic bacteria count. Lipopolysaccharide (endotoxin) concentrations, degree of proteolysis and impedance detection were also determined. All bacterial enumerations and proteolysis were significantly related to potential shelf-life of pasteurized fluid milk (whole, skim, and combined) but were of little predictive value. Endotoxin concentration and impedance detection were highly significantly related to shelf-life, and provided predictive regression equations. Using combined data from whole and skim milk, impedance detection resulted in the preferred prediction equation suitable for pasteurized fluid milks.

Antibiotic Residue Detection in Milk - A Review

Methods for antibiotic residue detection in dairy products, especially raw milk, have greatly improved as to their rapidity, accuracy and sensitivity over the past 30 years. An assay requiring overnight coagulation was available in the mid-1950's, whereas now there is an immunologically-based test using monoclonal antibody technology requiring only 6 min. These advances have not come about without extensive research efforts. The following is an overview of the developments and their significance to the dairy industry.

Rapid Impedimetric Method for Determining the Potential Shelf-Life of Pasteurized Whole Milk

Potential shelf-life of 100 pasteurized whole milk samples, obtained from retail outlets and from dairy processors, was investigated. Parameters studied were: organoleptic evaluation, Standard Plate Count (SPC), psychrotrophic bacteria count (PBC), modified psychrotrophic bacteria count (mPBC), Moseley test (MSPC), and impedance detection time (IDT) at 18 and 21°C. Correlation coefficients were obtained for all possible data combinations in an attempt to detect significant relationships between the parameters studied and the true shelf-life of the product. None of the direct counts (SPC, PBC, and mPBC) correlated well enough with shelf-life to allow shelf-life prediction. Moseley test (MSPC) appeared to possess an adequate relationship to shelf-life with a correlation coefficient at -0.84. IDT 21°C and IDT 18°C proved to have the most significant relationships to shelf-life with correlation coefficients of 0.88 and 0.87, respectively. Therefore, the impedance method had three advantages over the Moseley test: (a) it was a better predictor of shelf-life, (b) it was less labor intensive, and (c) it required only 1-2 d, as opposed to 7-9 d to complete.

Preliminary Incubation Count as an Index of Raw Milk Microbiological Quality During Storage

During a 5-month period, 200 raw milk samples were collected from two Louisiana milk plants. Standard Plate Count (SPC), Psychrotrophic Bacteria Count (PBC), and Proteolytic Count (PC) of each sample were initially determined, then monitored daily during a 5-d storage period at 2.2°C. As hypothesized, all bacterial counts increased during the storage period. The magnitude of the increase in bacterial numbers during storage was further investigated by dividing the milk samples into bacteriologically acceptable and unacceptable groups based on SPC or Preliminary Incubation (PI) count. An SPC of 1.0 × 10⁵/ml and PI counts of 1.0 × 10⁵/ml, 1.5 × 10⁵/ml, 2.3 × 10⁵/ml, and 3.0 × 10⁵/ml were used to repeatedly dichotomize the 200 raw milk samples into two groups. Median SPC, PBC, and PC for each acceptable and unacceptable group were then calculated. Dichotomization based on PI counts yielded acceptable sample groups having consistently lower bacterial counts during storage than did the acceptable sample group, which resulted from the dichotomization based on a SPC of 1.0 × 10⁵/ml. The results of this study indicated that the PI count is of considerable value for raw milk quality control.