About

John Clark is a Chicago-based designer and educator, working in spatial design, object design, fabrication, project management, planning, computation, photography, design research, and writing. He has taught design and fabrication courses in AIADO (Architecture, Interior Architecture, and Designed Objects) at the School of the Art Institute of Chicago and at the School of Architecture at the University of Illinois at Chicago. He holds degrees in architecture from the University of Illinois at Urbana-Champaign (BSArch 2007) and the University of Illinois at Chicago (MArch 2011), and he has practiced with international and local teams on projects ranging from large-scale design and consultancy to hands-on design and manufacture of custom furniture and art products.

Research topics

• Animal science
• Biology
• Endocrinology
• Food science
• Chemistry
• Biochemistry

Selected publications

• Functional properties of cream from dairy cows with experimentally altered milk fat composition

  Journal of Dairy Science · 2022 · 11 citations

  • Food science
  • Chemistry
  • Biochemistry

  Modification of milk fat composition might be a desirable method to alter manufacturing characteristics or produce dairy products low in saturated fat that more closely meet consumer dietary preferences. The aim of this research was to evaluate functional properties of cream obtained from milks with fat composition modified by altering the profile of long-chain fatty acids (FA) absorbed from the intestine. A control and 5 mixtures of long-chain free FA were infused into the abomasum of lactating dairy cows in a 6 × 6 Latin square design with 21-d periods. Treatments were as follows: (1) control (no FA infused), (2) mostly saturated FA (C16:C18 = 0.74), (3) low linoleic palm FA (C16:C18 = 0.73), (4) palm FA (C16:C18 = 0.73), (5) soy FA (C16:C18 = 0.10), and (6) high palmitic soy FA (C16:C18 = 0.73). All treatments included meat solubles and Tween 80 as emulsifiers. Viscosity, overrun, whipping time, foam firmness, and foam stability were evaluated in creams (33% fat). Cream from cows infused with soy FA (treatment 5) had the longest whipping time and lowest overrun, foam stability, viscosity, melting point, firmness, and solid fat content at 5 and 20°C because the fat had the highest unsaturated FA content. Increasing palmitic acid content of soy FA (treatment 6) improved functional variables in cream relative to soy FA alone. Differences among treatments 1 to 4 were less pronounced because of the effect of C18:1 trans in treatments 3 and 4 on milk fat yield and composition. Milk fat from cows infused with palm FA (treatment 4) exhibited comparable or better functionality than control cream. Increased polyunsaturated FA in milk fat resulted in increased amounts of triglyceride (TG) fractions with 28, 30, 38, and 40 carbon numbers, increased oleic acid resulted in increased 50-carbon TG, and higher palmitic and myristic acids resulted in greater 44, 46, and 48 carbon number TG. These TG groups consistently correlated with functional properties of creams from different treatments. Our results indicated that optimal functionality of cream is dependent more on its content of palmitic acid than on unsaturated FA. However, an optimal composition of milk fat for cream functional characteristics might be obtained through nutritional manipulation of diets for dairy cows to deliver an optimal profile of FA.

  PublisherOA PDFDOI

• Production, metabolism, and follicular dynamics in multiparous dairy cows fed diets providing different amounts of metabolizable protein prepartum and postpartum

  Journal of Dairy Science · 2022 · 5 citations

  • Animal science
  • Biology
  • Endocrinology

  Our objectives were (1) to determine whether increasing metabolizable protein (MP) supply above requirements in late-gestation cows would benefit health, milk production, and reproduction; (2) to determine whether an increased supply of MP postpartum affects production; and (3) to determine whether supply of MP prepartum interacts with MP supply postpartum. Pregnant nonlactating cows (n = 60) blocked by expected parturition date were assigned to 1 of 3 prepartum diets from 21 d prepartum to parturition: 12% crude protein (CP) soybean meal (SBM) supplement (LSB); 15% CP SBM supplement (HSB); and 15% CP SBM plus animal-marine protein supplement (HMP). Diets were formulated to supply an estimated 924, 988, and 1,111 g/d of MP, respectively, at 11.5 kg of dry matter intake (DMI). After parturition, cows received diets containing 18% CP, either from SBM (SB) or SBM plus animal-marine protein (AMP) supplements, that provided 2,056 (SB) or 2,293 g/d (AMP) of MP at 21 kg of DMI; thus, treatments were in a 3 × 2 factorial arrangement. Milk production and DMI were recorded for 63 d postpartum. Prepartum DMI was lower at wk -3 for cows fed LSB compared with those fed HSB or HMP. Postpartum DMI did not differ significantly between cows fed SB and those fed AMP (20.8 vs. 19.6 kg/d). Milk production did not differ due to prepartum diets or postpartum diets. Milk fat and protein percentages were not affected by prepartum or postpartum diets. Cows fed AMP postpartum tended to produce more milk fat, but 4% fat-corrected milk (FCM) did not differ from SB-supplemented cows (33.6 kg/d vs. 32.2 kg/d). Gross feed efficiency (FCM/DMI) was greater for cows fed AMP postpartum (1.82 vs. 1.68). Prepartum concentrations of urea N in plasma were lower for LSB than for HSB and HMP, and HSB was greater than HMP. Postpartum concentrations of nonesterified fatty acids and β-hydroxybutyrate were greater for cows fed AMP postpartum than for those fed SB. Postpartum urea N was higher for SB than for AMP (14.4 vs. 12.5 mg/dL). Concentration of total protein in plasma was greater postpartum for cows fed HSB or HMP prepartum than for those fed LSB, and was greater postpartum for cows fed AMP than for those fed SB. Hepatic concentrations of total lipids and triglyceride did not differ among treatments. Hepatic glycogen was greater postpartum for cows fed SB postpartum. Feeding HSB or HMP increased the number of follicles 6 to 9 mm in diameter compared with LSB. The size of the largest follicle was increased by HMP compared with HSB. In conclusion, increasing the amount of MP fed to cows during the last 21 d prepartum did not affect milk production or BCS but increased plasma total protein concentration. Follicular dynamics were improved by increasing the amount of MP prepartum. Feeding HMP prepartum improved follicular dynamics prepartum and increased milk fat yield in wk 1. Feeding AMP postpartum increased efficiency of FCM production and plasma total protein. We found few interactions between prepartum and postpartum MP supply.

  PublisherOA PDFDOI

• Design, Synthesis, and Evaluation of Homochiral Peptides Containing Arginine and Histidine as Molecular Transporters

  Molecules · 2018-06-29 · 22 citations

  articleOpen access

  Linear (HR)n and cyclic [HR]n peptides (n = 4,5) containing alternate arginine and histidine residues were synthesized. The peptides showed 0–15% cytotoxicity at 5–100 µM in human ovarian adenocarcinoma (SK-OV-3) cells while they exhibited 0–12% toxicity in human leukemia cancer cell line (CCRF-CEM). Among all peptides, cyclic [HR]4 peptide was able to improve the delivery of a cell impermeable fluorescence-labeled phosphopeptide by two-fold. Fatty acids of different alkyl chain length were attached at the N-terminal of the linear peptide (HR)4 to improve the molecular transporter property. Addition of fatty acyl chains was expected to help with the permeation of the peptides through the cell membrane. Thus, we synthesized seven fatty acyl derivatives of the linear (HR)4 peptide. The peptides were synthesized using Fmoc/tBu solid phase peptide chemistry, purified by reverse-phase high-performance liquid chromatography (RP-HPLC) and characterized by matrix-assisted laser desorption/ionization (MALDI) spectrometry. The fatty acyl peptides containing C8, C12, C14, and C18 alkyl chain did not show cytotoxicity on SK-OV-3 or CCRF-CEM cell lines up to 50 µM concentration; however, at higher concentration (100 µM), they showed mild cytotoxicity. For example, C16-(HR)4 was also found to reduce the proliferation of SK-OV-3 cells by 11% at 50 µM and C20-(HR)4 showed mild toxicity at 10 µM, reducing the proliferation of SK-OV-3 cells by 21%. Increase in the length of alkyl chain showed cytotoxicity to the cell lines. C20-(HR)4 peptide showed better efficiency in translocation of F′-GpYEEI to SK-OV-3 than the phosphopeptide alone. Further investigation of C20-(HR)4 peptide efficacy showed that the peptide could deliver doxorubicin and epirubicin into SK-OV-3 and also improved the drug antiproliferative ability. These studies provided insights into understanding the structural requirements for optimal cellular delivery of the fatty acyl-(HR)4 peptide conjugates.

  PublisherOA PDFDOI

• A Meta-analysis of Ruminal Outflow of Nitrogen Fractions in Dairy Cows

  Advances in Dairy Research · 2015-01-01 · 11 citations

  articleOpen accessSenior author

  et al., This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data from the scientific literature and statistical methods were used to estimate the magnitude and significance of the effects of the amount and source of dietary crude protein (CP) supplements on the supply of N fractions passing to the small intestine of lactating dairy cows. The passage of total N and nonammonia N from the rumen was influenced by the source of CP in the control diet and only marginally by the source of ruminally un-degradable protein (RUP) in the dietary treatment. Even though NH3N did not appear to limit growth of the microbes, overall flow of microbial N from the rumen was depressed when RUP partially replaced other sources of CP in the diet. This response tended to be affected by the source of RUP in the dietary treatment. The passage of nonammonia, nonmicrobial N to the duodenum increased when cows consumed diets that contained RUP supplements. The magnitude of this response, however, was distinctly altered by the source of CP in the control diet with which the RUP treatment was compared. In addition, the proportion and source of total CP supplied by RUP in the treatment diet tended to modulate the response. Feeding RUP resulted in a significant increase in the ruminal outflow of total and essential amino acids but the magnitude of this response depended on the source of RUP. Feeding some RUP

  PublisherOA PDFDOI

• A comparative review of the flow of nitrogen fractions at the omasal canal and duodenum of dairy cows

  Jukuri (Natural Resources Institute Finland (Luke)) · 2013-03-19

  other
  Publisher

• Effects of sodium sesquicarbonate on dry matter intake and production of milk and milk components by Holstein cows

  Journal of Dairy Science · 2009-06-15 · 21 citations

  articleOpen access1st authorCorresponding

  Forty-six multiparous Holstein cows were used to investigate the effects of sodium sesquicarbonate on dry matter intake, body weight, and production and composition of milk during a 308-d lactation. Diets contained alfalfa silage, corn silage, and concentrate. Composition of diets was changed twice during the 308-d lactation experiment. Diets fed during d 1 to 175 and d 176 to 245 were formulated to contain more rumen-undegradable protein and fat, and less forage than that fed during d 246 to 308. Sodium sesquicarbonate did not affect yields of milk, 4% fat-corrected milk, and components in milk, or percentages of components in milk during the complete 308-d lactation or during d 1 to 175 or d 176 to 245. However, from d 246 to 308, cows fed sodium sesquicarbonate produced more milk, 4% fat-corrected milk, fat, protein, and solids-not-fat than did control cows. Milk composition was not altered. These data suggest that composition of the diet has a significant effect on the response to dietary buffers by lactating dairy cows.

  PublisherOA PDFDOI

• Methods for assessing DNA hybridization of peptide nucleic acid–titanium dioxide nanoconjugates

  Analytical Biochemistry · 2008-09-09 · 36 citations

  articleOpen access
  PublisherOA PDFDOI

• Omasal Flow of Soluble Proteins, Peptides, and Free Amino Acids in Dairy Cows Fed Diets Supplemented with Proteins of Varying Ruminal Degradabilities

  Journal of Dairy Science · 2007-03-21 · 72 citations

  articleOpen accessSenior author

  Three ruminally and duodenally cannulated cows were assigned to an incomplete 4 4 Latin square with four 14-d periods and were fed diets supplemented with urea, solvent soybean meal, xylosetreated soybean meal (XSBM), or corn gluten meal to study the effects of crude protein source on omasal canal flows of soluble AA. Soluble AA in omasal digesta were fractionated by ultrafiltration into soluble proteins greater than 10 kDa (10K), oligopeptides between 3 and 10 kDa (3-10K), peptides smaller than 3 kDa (small peptides), and free AA (FAA). Omasal flow of total soluble AA ranged from 254 to 377 g/d and accounted for 9.2 to 15.9% of total AA flow. Averaged across diets, flows of AA in 10K, 3-10K, small peptides, and FAA were 29, 217, 50, and 5 g/d, respectively, and accounted for 10.3, 71.0, 17.5, and 1.6% of the total soluble AA flow. Cows with diets supplemented with solvent soybean meal had higher flows of Met, Val, and total AA associated with small peptides than those whose diets were supplemented with XSBM, whereas supplementation with corn gluten meal resulted in higher total small peptide-AA flows than did XSBM. Averaged across diets, 27, 75, and 93% of soluble AA in 10K, 3-10K, and peptides plus FAA flowing out of the rumen were of dietary origin. On average, 10% of

  PublisherOA PDFDOI

• A Comparison of Sampling Sites, Digesta and Microbial Markers, and Microbial References for Assessing the Postruminal Supply of Nutrients in Dairy Cows

  Journal of Dairy Science · 2007-03-21 · 41 citations

  articleOpen accessSenior author

  This study evaluated the impact of some methodological factors on the flows of nutrients at the omasal canal and duodenum of dairy cows fed corn-based diets. Three ruminally and duodenally cannulated cows were assigned to an incomplete 4 x 4 Latin square with four 14-d periods and fed diets formulated to contain different amounts and ruminal degradabilities of crude protein. Samples from the omasal canal and duodenum were obtained and processed according to methodologies routinely used in our laboratories and elsewhere. Methodological factors that were evaluated included microbial references and markers, digesta markers, and sampling sites (techniques). Considerable variation was found for the compositions of microbial references and their impact on the intestinal supply of microbial nonammonia nitrogen. Likewise, it appears that variation in measuring the ruminal outflow of nitrogen fractions of microbial and dietary origin could be reduced by using 15N rather than purines as microbial markers. Sampling from the omasum and duodenum resulted in differences for ruminal outflow and site of digestion as well as digestibility of some nutrients, particularly nitrogen fractions and starch. A sizable portion of this variation was associated with deviations from the assumed ideal behavior of digesta markers and collection of samples that were unrepresentative of true digesta. Collectively, outcomes from this study indicate that more research will be required to determine the accuracy of nutrient flows and the agreement between measurements at the omasal canal and duodenum when dairy cows are fed a variety of diets under different feeding systems. Therefore, caution is recommended when extrapolating or interpreting the underlying biology of published results as well as the results of their application (e.g., model parameters and predictions).

  PublisherOA PDFDOI

• NutriDense Corn Grain and Corn Silage for Dairy Cows

  Journal of Dairy Science · 2006-05-01 · 14 citations

  articleOpen accessSenior author

  Twenty multiparous Holstein cows, 4 of them surgically fitted with ruminal cannulas, were used in a replicated 4 x 4 Latin square to compare the effects of whole-plant silage and grain produced from NutriDense (ND), leafy NutriDense (LND), or a conventional yellow dent (YD) hybrid on ruminal fermentation, total tract nutrient digestibility, and performance of lactating dairy cows. On a DM basis, diets contained 30.6% corn silage and 27.7% corn grain provided from the 3 hybrids according to the following combinations: 1) YD grain and YD silage, 2) YD grain and LND silage, 3) ND grain and YD silage, and 4) ND grain and LND silage. The average concentrations of crude protein, neutral and acid detergent fiber, and ether extract of LND silage and ND grain were higher, but the contents of nonfibrous carbohydrates and starch were lower than those of their YD counterparts. Although DM intake was similar among treatments, feeding ND grain, LND silage, or both reduced the intakes of nonfibrous carbohydrates and starch but increased the intake of ether extract. Apparent digestibility of starch in the total tract was highest for the diet that contained LND silage and YD grain, whereas the amount and percentage of ether extract that were apparently digested in the total tract was increased and tended to be increased, respectively, by the addition of ND grain, LND silage, or both to the diets. Ruminal fermentation parameters were unaffected by treatments except for the concentration of ammonia nitrogen in the ruminal fluid, which tended to be increased by the feeding of ND grain, LND silage, or both. Production of milk, crude and true protein, fat, lactose, and total solids did not differ among diets. Concentration of milk urea nitrogen increased when the ND grain, LND silage, or both were fed to the cows. Results indicate that ND grain and LND silage were similar to the conventional grain and silage for the feeding of lactating dairy cows.

  PublisherOA PDFDOI

Frequent coauthors

• J.L. Firkins

  The Ohio State University

  99 shared

• G.A. Varga

  98 shared

• S.B. Peirce-Sandner

  Virginia Tech

  89 shared

• C.J. Sniffen

  85 shared

• C.E. Polan

  Virginia Tech

  85 shared

• T.V. Muscato

  Agricultural Research Service

  85 shared

• D.R. Nelson

  Urbana University

  80 shared

• T.R. Overton

  New York State College of Agriculture & Life Sciences

  80 shared