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Benjamin A Neely

Benjamin A Neely
National Institute of Standards and Technology, Charleston, South Carolina, United States · Marine Biochemical Sciences Group, Chemical Sciences Division

Ph.D.

About

57
Publications
4,041
Reads
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917
Citations
Additional affiliations
January 2012 - May 2016
Medical University of South Carolina
Position
  • Researcher
January 2010 - December 2012
Medical University of South Carolina
Position
  • Post Doctoral Scholar
June 2001 - August 2001
Vanderbilt University
Position
  • Summer Researcher

Publications

Publications (57)
Article
It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization...
Article
Full-text available
The apparent ability of bats to harbor many virulent viruses without showing disease is likely driven by distinct immune responses that coevolved with mammalian flight and the exceptional longevity of this order. Yet our understanding of the immune mechanisms of viral tolerance is restricted to a small number of bat–virus relationships and remains...
Preprint
The apparent ability of bats to harbor many virulent viruses without showing disease is likely driven by distinct immune responses that coevolved with mammalian flight and the exceptional longevity of this order. Yet our understanding of the immune mechanisms of viral tolerance is restricted to a small number of bat-virus relationships and remains...
Article
Full-text available
Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion...
Article
Full-text available
Many mammals use adaptive heterothermy (e.g. torpor, hibernation) to reduce metabolic demands of maintaining high body temperature (T b ). Torpor is typically characterized by coordinated declines in T b and metabolic rate (MR) followed by active rewarming. Most hibernators experience periods of euthermy between bouts of torpor during which homeost...
Article
Bats are increasingly studied as model systems for longevity and as natural hosts for some virulent viruses. Yet the ability to characterize immune mechanisms of viral tolerance and to quantify infection dynamics in wild bats is often limited by small sample volumes and few species-specific reagents. Here, we demonstrate how proteomics can overcome...
Preprint
Full-text available
Bats are increasingly studied as model systems for longevity and as natural hosts for some virulent viruses. Yet our ability to characterize immune mechanisms of viral tolerance and to quantify infection dynamics in wild bats is often limited by small sample volumes and few species-specific reagents. Here, we demonstrate how proteomics can overcome...
Preprint
Full-text available
Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample, as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in core facility settings has been slow. The Association of Biomolecular Resource Facilities conducted a large interlaboratory study to evaluat...
Article
Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, co-limitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in mari...
Article
Full-text available
Chronic rhinosinusitis with nasal polyps (CRSwNP) is an inflammatory disease with an unknown etiology. Recent studies have implicated the complement system as a potential modulator of disease immunopathology. We performed proteomic pathway enrichment analysis of differentially increased proteins, and found an enrichment of complement cascade pathwa...
Preprint
Full-text available
Urinary markers for the assessment of kidney diseases in wild animals are limited, in part, due to the lack of urinary proteome data, especially for marine mammals. One of the most prevalent kidney diseases in marine mammals is caused by Leptospira interrogans , which is the second most common etiology linked to stranding of California sea lions (...
Article
Hormonally Up-regulated Neu-associated Kinase (Hunk) is a protein kinase that was originally identified in the murine mammary gland and has been shown to be highly expressed in Human Epidermal Growth Factor Receptor 2 positive (HER2(+)/ErbB2(+)) breast cancer cell lines as well as MMTV-neu derived mammary tumor cell lines. However, the physiologica...
Article
Background: Serum proteomic biomarkers offer a promising approach for early detection of cancer. In this study, we aimed to identify proteomic profiles that could distinguish colon cancer cases from controls using serial pre-diagnostic serum samples. Methods: This was a nested case-control study of active duty military members. Cases consisted o...
Article
Full-text available
Renal cell carcinoma comprises 2 to 3% of malignancies in adults with the most prevalent subtype being clear-cell RCC (ccRCC). This type of cancer is well characterized at the genomic and transcriptomic level and is associated with a loss of VHL that results in stabilization of HIF1. The current study focused on evaluating ccRCC stage dependent cha...
Data
Positive and negative controls of immunohistochemical staining. (A-C) Controls for 6-phosphofructokinase (PFKP antibody): (A) Negative control on breast cancer tissue. (B) Positive control at 1:1000 and (C) 1:2000 on breast cancer tissue. (D-F) Controls for and pyruvate kinase (PKM2 antibody): (D) Negative control on normal lung tissue. (E) Positiv...
Data
Distribution of mRNA expression levels across all stages. Data from 94 arrays with 54,677 probes was RMA normalized and evaluated using a moderated t-test comparing all tumor normal-adjacent pairs. RMA normalized expression values were plotted against Benjamini-Hockberg (BH) adjusted p-values. Emphasized in red are probes with BH adjusted p < 0.001...
Data
Proteomic analysis of individual samples. Normalized spectral count values for the 783 proteins identified across 177 samples is given along with sample information and protein information. (XLSX)
Data
Replicate variability within pooled analysis. Variability between biological replicates in the pooled analysis was visualized using scatter plots of adjusted spectral counts for the 1551 proteins identified, and the Pearson's linear correlation coefficient (r) was calculated for each pair. There from four stage I tumor (t1_#), two stage I normal-ad...
Data
Comparison of proteomic results from pooled and individual samples. (A) Overlap between the proteins identified in the pooled and individual sample analysis. (B) Comparison of directionality agreement between the 663 overlapping proteins using log2 fold-change (tumor/normal-adjacent). There were 123 proteins changing in different directions but the...
Data
Predicted upstream effects. Using protein abundance data from all four stages, HIF1A, ESRRG, and ESRRA were predicted to be activated and WISP2, FOXA1, and MAPK1 were predicted to be inhibited. Bar graphs are four stage and all stage comparisons. Image generated with QIAGEN’s Ingenuity® Pathway Analysis. (TIF)
Data
Pathway enrichment analysis of previously published proteomic analyses of ccRCC. Differentially abundant proteins from this study (pooled and individual analyses) were compared to differentially abundant proteins identified in four other studies (granular proteomic results from Lebdai et al.[23] were not available): Perroud et al.[25] Supp. Table 3...
Data
Similarity of other shotgun proteomics studies with the current proteotranscriptomic study. Differentially abundant proteins and genes from this study (pooled, individual and 94 array) were compared to differentially abundant proteins identified in four other studies (granular proteomic results from Lebdai et al.[23] were not available): Perroud et...
Data
Proteomic analysis of pooled samples. Proteomic data from the pooled samples were evaluated by using the asp values for each protein to perform a Wilcoxon rank sum test using the exact method followed by a Benjamini-Hochberg (BH) procedure to correct for multiple hypothesis testing. Whether the sample is from pooled tumor tissues or normal-adjacent...
Data
Upstream regulator analysis of previously published proteomic analyses of ccRCC. Differentially abundant proteins from this study (pooled and individual analyses) were compared to differentially abundant proteins identified in four other studies (granular proteomic results from Lebdai et al.[23] were not available): Perroud et al.[25] Supp. Table 3...
Data
Data organization key. The tissues analyzed in this study were also part of two previous expression array studies. The proteomic data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD003271 and 10.6019/PXD003271. The PRIDE repository assigns assay numbers, but maintains mzIdentML f...
Data
Statistical analysis of fold-change protein differences between tumor and normal-adjacent pairs. For each of the 783 proteins identified in the individual analysis log2 fold-change is given as well as p-value (moderated t-test) and BH adjusted p-value for each stage and using all samples. (XLSX)
Article
Full-text available
Astrocytes and neurons form a highly specialized functional unit and the loss or gain of astrocytic functions can influence the initiation and progression of different neurodegenerative diseases. Neurons depend on the antioxidant protection provided by neighboring astrocytes. Glutathione (γ-l-glutamyl-l-cysteinyl-glycine) is a major component of th...
Article
Background: Patients with diabetes and chronic kidney disease (CKD) without proteinuria are often believed to have a cause of CKD other than diabetes. It was hypothesized that if this is true, the rate of renal function decline should be similar among nonproteinuric patients with and without diabetes. Methods: Patients seen in the nephrology, en...
Article
Proteomic studies including marine mammals are rare, largely due to the lack of fully sequenced genomes. This has hampered the application of these techniques toward biomarker discovery efforts for monitoring of health and disease in these animals. We conducted a pilot label-free LC-MS/MS study to profile and compare the cerebrospinal fluid from Ca...
Article
We have recently developed a MALDI imaging mass spectrometry (MALDI-IMS) method to spatially profile N-linked glycans in frozen and formalin-fixed paraffin-embedded (FFPE) tissue sections and tissue microarrays (TMAs). Tissues are incubated with peptide N-glycosidase, and released N-glycans are detected directly using MALDI-FTICR, linked directly w...
Article
Full-text available
Domoic acid toxicosis (DAT) in California sea lions (Zalophus californianus) is caused by exposure to the marine biotoxin domoic acid and has been linked to massive stranding events and mortality. Diagnosis is based on clinical signs in addition to the presence of domoic acid in body fluids. Chronic DAT further is characterized by reoccurring seizu...
Article
Full-text available
A recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) method to spatially profile the location and distribution of multiple N-linked glycan species in frozen tissues has been extended and improved for the direct analysis of glycans in clinically derived formalin-fixed paraffin-embedded (FFPE) tissues...
Article
Reducing the incidence and mortality rates for clear cell renal cell carcinoma (ccRCC) remains a significant clinical challenge with poor 5-year survival rates. A unique tissue cohort was assembled of matched ccRCC and distal non-tumor tissues (n=20) associated with moderate risk of disease progression, half of these from individuals who progressed...
Article
Full-text available
Similar to people with metabolic syndrome, bottlenose dolphins (Tursiops truncatus) can have a sustained postprandial hyperglycemia and hyperinsulinemia, dyslipidemia, and fatty liver disease. A panel of potential postprandial blood-based indicators of insulin resistance and metabolic syndrome were compared among 34 managed collection dolphins in S...
Article
Full-text available
High molecular weight (HMW) adiponectin levels are reduced in humans with type 2 diabetes and insulin resistance. Similar to humans with insulin resistance, managed bottlenose dolphins (Tursiops truncatus) diagnosed with hemochromatosis (iron overload) have higher levels of 2 h post-prandial plasma insulin than healthy controls. A parallel reaction...
Article
Full-text available
Prognostic biomarkers that predict the severity of AKI at an early time point are needed. Urinary angiotensinogen was recently identified as a prognostic AKI biomarker. The study hypothesis is that urinary renin could also predict AKI severity and that in combination angiotensinogen and renin would be a strong predictor of prognosis at the time of...
Article
Full-text available
Biomarkers for acute kidney injury (AKI) have been used to predict the progression of AKI, but a systematic comparison of the prognostic ability of each biomarker alone or in combination has not been performed. In order to assess this, we measured the concentration of 32 candidate biomarkers in the urine of 95 patients with AKIN stage 1 after cardi...
Article
Effectively identifying the proteins present in the cellular secretome is complicated due to the presence of cellular protein leakage and serum protein supplements in culture media. A metabolic labeling and click chemistry capture method is described that facilitates the detection of lower abundance glycoproteins in the secretome, even in the prese...
Article
Full-text available
Introduction Acute kidney injury (AKI) is commonly observed in the intensive care unit (ICU), where it can be caused by a variety of factors. The objective of this study was to evaluate the prognostic value of urinary angiotensinogen, a candidate prognostic AKI biomarker identified in post-cardiac surgery patients, in this heterogeneous population....
Article
Full-text available
Diabetic nephropathy is the leading cause of end-stage renal disease. The urinary albumin to creatinine ratio is used as a predictor for the development of nephropathy but it is neither sensitive nor specific. Here we used liquid chromatography/mass spectrometry on urine of eight normoalbuminuric patients with type 2 diabetes from the VA Diabetes T...
Article
Background: Biomarkers of AKI that can predict which patients will develop severe renal disease at the time of diagnosis will facilitate timely intervention in populations at risk of adverse outcomes. Design, setting, participants, & measurements: Liquid chromatography/tandem mass spectrometry was used to identify 30 potential prognostic urinary...
Article
Full-text available
Progression of hyperglycemia-induced renal injury is a contributing factor for diabetic nephropathy (DN)-induced end-stage renal disease (ESRD), and development of novel therapeutic strategies that act early to prevent progression of DN and ESRD are important. We examined the efficacy and mechanism(s) of suramin on hyperglycemia-induced renal injur...
Article
Full-text available
There are currently no reliable markers of acute domoic acid toxicosis (DAT) for California sea lions. We investigated whether patterns of serum peptides could diagnose acute DAT. Serum peptides were analyzed by MALDI-TOF mass spectrometry from 107 sea lions (acute DAT n = 34; non-DAT n = 73). Artificial neural networks (ANN) were trained using MAL...
Data
Table S4. Qualified performance of peak 3017 m/z using an independent test set. DAT is indicated by a '1' and non-DAT a '0'. Performance against training set is given for comparison. Table S5. Qualified performance of ANNs trained with Glu-Fib normalized data. Performance was qualified using an independent test set. DAT is indicated by a '1' and no...
Data
Table S1. Descriptive data of sea lions in the training dataset. Trauma included lacerations, bite wounds, broken bones, and anophthalmia. Pneumonia included verminous and/or parafilaroides. Table S2. Descriptive data of sea lions in the independent test set. Trauma was only to the flipper, and unknown was best described as lethargic. Pneumonia inc...
Data
Figure S1. Peak 1362 m/z spectra, ROC curve and performance. (A) 1362 m/z peak height was plotted between two groups. The dotted line corresponds to the threshold determined by ROC curve analysis. (B) An ROC curve was generated using 107 individuals in the training set and was used to determine the optimum threshold (OpT; indicated by arrow). (C) T...
Data
Full-text available
Figure S2. Unsupervised clustering of MALDI-TOF profiles of the training set. Data were standardized by each peak (n = 104; rows) and represented such that the mean is 0 and standard deviation is ± around this mean. Columns are individuals (n = 107), labeled at the top with red squares for acute-DAT and blue squares for non-DAT.
Article
Full-text available
Burkholderia vietnamiensis PR1(301) (PR1) exhibits pH-dependent nickel (Ni) tolerance, with lower Ni toxicity observed at pH 5 than at pH 7. The Ni tolerance mechanism in PR1 is currently unknown, and traditional mechanisms of Ni resistance do not appear to be present. Therefore, 2D gel electrophoresis was used to examine changes in protein express...
Article
The use of hydroxyapatite (HA) to sequester metals at mixed waste sites may reduce metal toxicity and facilitate microbial degradation of cocontaminant organics. The constitutive trichloroethylene (TCE) degrader, Burkholderia vietnamiensis PR1301, grew at 34.1 and 1.7 mM Ni at pH 5 and 7, respectively, with 0.01 g mL(-1) HA compared to 17 and 0.85...
Article
Full-text available
Evolutionary links between cytochrome P450 monooxygenases, a superfamily of extraordinarily divergent heme-thiolate proteins catalyzing a wide array of NADPH/NADH- and O2-dependent reactions, are becoming better understood because of availability of an increasing number of fully sequenced genomes. Among other reactions, P450s catalyze the site-spec...

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