Growth performance, carcass characteristics, fresh belly quality, and commercial bacon slicing yields of growing-finishing pigs from sire lines intended for different industry applications

The objective was to control intrinsic and extrinsic factors associated with the production and slaughter of pigs to determine effects of sire line (Pietrain vs. Duroc ancestry) on growth performance, carcass and belly characteristics, and commercial bacon yields of growing-finishing pigs. There were no differences in growth performance (P ≥ 0.08) or belly processing characteristics (P ≥ 0.09). Pietrain sired pigs had a greater lean yield (P ≤ 0.01). Duroc sired pigs had darker, more highly marbled loins (P ≤ 0.04) and thicker bellies (P < 0.001). Bacon from Pietrain sired pigs had a greater (P = 0.04) lean to fat ratio with 1.58% increase (P = 0.04) in average bacon slice lean. Barrows had more highly marbled loins (P ≤ 0.01) and thicker bellies (P < 0.001) than gilts. Bacon from barrows had a greater slice area (P < 0.001) while bacon from gilts had a greater lean to fat ratio (P = 0.04).

Relationships among early postmortem loin quality and aged loin and pork chop quality characteristics between barrows and gilts

Rapid assessment of pork quality by packers necessitates using early postmortem (∼1 d) traits as an indication of aged pork quality (∼14 d). Efforts have been made to develop a grading system based on color and marbling of the ventral side of boneless loins. In order for this system to be successful, there must be a correlation between early postmortem quality traits observed by packers and the same traits observed by consumers after aging. However, the strength and direction of those correlations are unclear. It is also unknown if the correlations between early and aged postmortem quality differ between barrows (B) and gilts (G). Therefore, the objectives were to determine correlations between early postmortem loin quality characteristics and aged loin quality characteristics, and determine if those correlations differed between barrows and gilts. Early postmortem (∼1 d) quality traits included: instrumental and subjective color, marbling and firmness, and loin pH on the ventral surface of the loin. Loins were aged until 14 d postmortem in vacuum packages. Aged quality traits included traits evaluated early as well as shear force and cook loss. Correlations were compared between barrows and gilts using a Fisher's z test. Overall, early subjective firmness scores of barrows were greater (P < 0.001) than those of gilts. No other early quality traits differed between sexes. Early pH was correlated with aged pH (r = 0.80 B; 0.75 G), ventral lightness (r = –0.57 B; –0.54 G), ventral yellowness (r = –0.55 B; –0.55 G), subjective ventral color (r = 0.55, B; 0.41 G), and subjective chop color (r = 0.42 B; 0.44 G). Correlations of early pH and aged quality did not differ between sexes. Early lightness was correlated with aged ventral pH (r = –0.56) and subjective color (r = –0.39) in barrows but not gilts (P ≤ 0.04). Early lightness was correlated with aged lightness (r = 0.60 B; 0.51 G) and yellowness (r = 0.49 B; 0.55 G), but was not correlated with to any aged chop quality traits. Early marbling was correlated with ventral color (r = 0.42) in barrows and ventral marbling (r = 0.67 B; 0.66 G) and chop marbling (r = 0.57 B; 0.59 G) in barrows and gilts. In summary, early pH and lightness were correlated with aged quality characteristics and correlations rarely differed between barrows and gilts. Sex does not need to be accounted for when relating early and aged quality characteristics.

Growth performance, carcass quality, fresh belly characteristics, and commercial bacon slicing yields of growing-finishing pigs fed a subtherapeutic dose of an antibiotic, a natural antimicrobial, or not fed an antibiotic or antimicrobial

The objective was to compare growth performance, belly characteristics, and bacon slicing yields of growing-finishing pigs fed a subtherapeutic dose of an antibiotic, a natural antimicrobial, or a diet containing no antibiotics or antimicrobials. Barrows and gilts (96 each, initial BW: 27.52±3.98kg) were housed in 48 pens (8 replications per treatment) in a 2×3 factorial randomized complete block design. Pens were assigned 1 of 3 diets: antibiotic free, oregano or tylosin phosphate. Pigs were slaughtered at an average BW of 127.31±10.18kg. There were no differences among dietary treatments for growth performance (P≥0.06), carcass cutability (P≥0.42), loin quality (P≥0.28), fresh belly dimensional characteristics (P≥0.11), IV (P≥0.87) or bacon processing characteristics (P≥0.07). Given the lack of differences in meat quality from pigs fed diets without antibiotics, the implementation of VFD in the United States should not result in changes in pork quality.

Effects of pelleting diets without or with distillers' dried grains with solubles on growth performance, carcass characteristics, and gastrointestinal weights of growing-finishing barrows and gilts

Pigs (192 total) were blocked by age and stratified by initial BW (25.75 ± 2.29 kg) into pens (2 barrows and 2 gilts per pen). Within blocks, pens were randomly allotted to treatments in a 2 × 2 factorial arrangement, with 2 diet forms (meal vs. pellet) and 2 distillers' dried grains with solubles (DDGS) inclusion levels (0 vs. 30%). Pigs were weighed at the beginning of the experiment and at the end of each feeding phase (d 35, 70, and 91) and daily feed allotments were recorded. Pigs were slaughtered at the end of the 91-d experiment, and full gastrointestinal (GI) tract and GI tract component weights were recorded immediately following evisceration. Carcass characteristics and meat quality were determined after a 24-h chill. Overall ADG was increased ( < 0.01) 3.2% when pigs were fed pelleted diets rather than meal diets, but there was no effect ( = 0.46) of DDGS inclusion on overall ADG. Overall ADFI of meal-fed pigs fed 30% DDGS was 4.7% greater ( < 0.01) than that of pigs fed 0% DDGS in meal form, but overall ADFI did not differ ( ≥ 0.19) between DDGS inclusion level in pellet-fed pigs (diet form × DDGS inclusion, < 0.01). When fed meal diets, pigs fed 0% DDGS had 2.7% greater ( = 0.02) overall G:F than pigs fed 30% DDGS; however, there was no difference ( = 0.42) in overall G:F between DDGS inclusion levels in pigs fed pelleted diets (diet form × DDGS inclusion, < 0.03). Pigs fed pelleted diets had 2.9% heavier HCW ( = 0.01), 10.4% greater 10th-rib back fat ( = 0.01), and 1.8 percentage units less estimated lean percentage ( = 0.04) than meal-fed pigs. Full GI tracts of pigs fed pelleted diets were 0.33 percentage units less ( = 0.03) of the ending live weight than that of meal-fed pigs due to decreased ( < 0.01) GI tract contents. Inclusion of DDGS increased ( = 0.03) full GI tract weight, large intestine weight ( < 0.01), and GI tract contents ( = 0.02). Severity of parakeratosis of the pars esophagea was greater ( < 0.01) in pellet-fed pigs than in meal-fed pigs, but the magnitude of the difference was likely not great enough to negatively affect drop credit of stomachs. In conclusion, feeding pelleted diets improved growth performance and increased carcass weight and fatness without causing the development of gastric lesions that would reduce the value of the stomach to packers. Furthermore, inclusion of DDGS in diets reduced HCW and dressing percent and increased GI tract and GI tract contents weight but had no effect on gastric lesion development or LM quality.

Effects of marketing group on the quality of fresh and cured hams sourced from a commercial processing facility

The objective was: 1) to characterize the effect of marketing group on fresh and cured ham quality, and 2) to determine which fresh ham traits correlated to cured ham quality traits. Pigs raised in 8 barns representing 2 seasons (hot and cold) and 2 production focuses (lean and quality) were used. Three groups were marketed from each barn. A total of 7,684 carcasses were used for data collection at the abattoir. Every tenth carcass was noted as a select carcass for in-depth ham quality analyses. Leg primal weight and instrumental color were measured on 100% of the population. On the select 10% of the population, hams were fabricated into sub-primal pieces, and 3-piece hams were manufactured to evaluate cured ham quality and processing yield. Data were analyzed as a split-plot design in the MIXED procedure of SAS with production focus as the whole-plot factor, and marketing group as the split-plot factor. Pearson correlation coefficients between fresh and cured ham traits were computed. There were no differences ( ≥ 0.15) in instrumental color or ultimate pH ( ≥ 0.14) among fresh ham muscles from any marketing group. The only exception was the semimembranosus of marketing group 2 was lighter than marketing group 1 ( = 0.03) and the dark portion of the semitendinosus muscle from group 1 was lighter than from group 3 ( = 0.01). There were no differences ( ≥ 0.33) in ultimate pH of fresh ham muscles between production focuses, but several muscles from quality focus pigs were lighter in color than ham muscles from lean focus pigs. The lack of differences in fresh ham quality lead to few differences in cured ham quality. Cured hams from the quality focus pigs had greater lipid content ( < 0.01) than hams from lean focus pigs. Cured lightness values of hams from marketing group 1 and 2 were 1.52 units lighter than hams from marketing group 3 ( 0.01). Overall, marketing group did not impact ham quality. Fresh ham quality was not strongly related to cured ham quality. Some correlations were present between fresh and cured ham traits, but those relationships were likely not strong enough to be used as a sorting tool for fresh hams to generate high quality cured hams.

Effects of feeding pelleted diets without or with distillers dried grains with solubles on fresh belly characteristics, fat quality, and commercial bacon slicing yields of finishing pigs

One hundred ninety-two pigs were blocked by age and stratified by initial BW (25.7 ± 2.3 kg) into pens (2 barrows and 2 gilts/pen), and within blocks, pens were assigned randomly to 1 of 4 treatments in a 2 × 2 factorial arrangement, with main effects of diet form (meal vs. pelleted) and distillers dried grains with solubles (DDGS) inclusion (0% vs. 30%). Pigs were slaughtered after a 91-d feeding trial, and carcasses were fabricated after a 24-h chilling period. Belly dimensions and flop distance were measured, and an adipose tissue sample from each belly was collected for fatty acid analysis. Bacon was manufactured at a commercial processing facility before being returned to the University of Illinois Meat Science Laboratory for further evaluation. Although bellies from pigs fed pelleted diets were 5.3% heavier ( < 0.01) than bellies from meal-fed pigs, belly weight as a percentage of chilled side weight ( = 0.55) and fresh belly dimensions ( ≥ 0.11) were not affected by diet form. Slab bacon weight and cooked yield were greater ( ≤ 0.01) for bellies from pellet-fed than meal-fed pigs. Despite pellet-fed pigs having a 3.1-unit greater iodine value (IV) than meal-fed pigs, there was no effect ( ≥ 0.16) of diet form on commercial bacon slicing yields. Bacon slabs from pellet-fed pigs produced more ( < 0.01) total bacon slices, but 3.1% fewer ( < 0.01) slices per kilogram than slabs from meal fed pigs. Inclusion of 30% DDGS reduced belly thickness ( < 0.001), flop distance ( < 0.001), and initial belly weight ( = 0.04) by 0.32 cm, 4.97 cm, and 2.85, respectively, and increased ( < 0.001) belly fat IV by 7.1 units compared with bellies from pigs fed 0% DDGS. Feeding 0% DDGS produced more ( < 0.01) total bacon slices than feeding 30% DDGS. Distillers dried grains with solubles inclusion had no effect on slice yields ( ≥ 0.14) or slices per kilogram ( = 0.08). Overall, bellies from pellet-fed pigs were heavier and had greater IV but did not differ in commercial slicing yields from meal-fed pigs. Feeding pigs 30% DDGS produced thinner, softer bellies with greater IV, but slicing yields were not different from bellies of pigs fed 0% DDGS. Thus, swine producers can feed pelleted diets, without or with 30% DDGS, without negatively affecting commercial bacon slicing yield.

Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei

Unusually for a eukaryote, genes transcribed by RNA polymerase II (pol II) in Trypanosoma brucei are arranged in polycistronic transcription units. With one exception, no pol II promoter motifs have been identified, and how transcription is initiated remains an enigma. T. brucei has four histone variants: H2AZ, H2BV, H3V, and H4V. Using chromatin immunoprecipitation (ChIP) and sequencing (ChIP-seq) to examine the genome-wide distribution of chromatin components, we show that histones H4K10ac, H2AZ, H2BV, and the bromodomain factor BDF3 are enriched up to 300-fold at probable pol II transcription start sites (TSSs). We also show that nucleosomes containing H2AZ and H2BV are less stable than canonical nucleosomes. Our analysis also identifies >60 unexpected TSS candidates and reveals the presence of long guanine runs at probable TSSs. Apparently unique to trypanosomes, additional histone variants H3V and H4V are enriched at probable pol II transcription termination sites. Our findings suggest that histone modifications and histone variants play crucial roles in transcription initiation and termination in trypanosomes and that destabilization of nucleosomes by histone variants is an evolutionarily ancient and general mechanism of transcription initiation, demonstrated in an organism in which general pol II transcription factors have been elusive.

Selective di- or trimethylation of histone H3 lysine 76 by two DOT1 homologs is important for cell cycle regulation in Trypanosoma brucei

DOT1 is an evolutionarily conserved histone H3 lysine 79 (H3K79) methyltransferase. K79 methylation is associated with transcriptional activation, meiotic checkpoint control, and DNA double-strand break (DSB) responses. Trypanosoma brucei has two homologs, DOT1A and DOT1B, which are responsible for dimethylation and trimethylation of H3K76, respectively (K76 in T. brucei is synonymous to K79 in other organisms). K76 dimethylation is only detectable during mitosis, whereas trimethylation occurs throughout the cell cycle. Deletion of DOT1B resulted in dimethylation of K76 throughout the cell cycle and caused subtle defects in cell cycle regulation and impaired differentiation. RNAi-mediated depletion of DOT1A appears to disrupt a mitotic checkpoint, resulting in premature progression through mitosis without DNA replication, generating a high proportion of cells with a haploid DNA content, an unprecedented state for trypanosomes. We propose that DOT1A and DOT1B influence the trypanosome cell cycle by regulating the degree of H3K76 methylation.

Histone H2AZ dimerizes with a novel variant H2B and is enriched at repetitive DNA in Trypanosoma brucei

H2AZ is a widely conserved histone variant that is implicated in protecting euchromatin from the spread of heterochromatin. H2AZ is incorporated into nucleosomes as a heterodimer with H2B, by the SWR1 ATP-dependent chromatin-remodeling complex. We have identified a homolog of H2AZ in the protozoan parasite Trypanosoma brucei, along with a novel variant of histone H2B (H2BV) that shares approximately 38% sequence identity with major H2B. Both H2AZ and H2BV are essential for viability. H2AZ localizes within the nucleus in a pattern that is distinct from canonical H2A and is largely absent from sites of transcription visualized by incorporation of 5-bromo-UTP (BrUTP). H2AZ and H2BV colocalize throughout the cell cycle and exhibit nearly identical genomic distribution patterns, as assessed by chromatin immunoprecipitation. H2AZ co-immunoprecipitates with H2BV but not with histones H2B or H2A nor with the variant H3V. These data strongly suggest that H2AZ and H2BV function together within a single nucleosome, marking the first time an H2AZ has been shown to associate with a non-canonical histone H2B.

A variant histone H3 is enriched at telomeres in Trypanosoma brucei

Variant histones play critical roles in transcriptional activation and repression, DNA repair and chromosome segregation. We have identified HTV, a single-copy gene in Trypanosoma brucei encoding a variant form of histone H3 (H3V). H3V is present at discrete nuclear foci that shift over the course of the cell cycle and associate with the mitotic spindle, a pattern of localization reminiscent of that described previously for both mini-chromosomes and telomeres. By combining fluorescence in situ hybridization with indirect immunofluorescence, we confirmed that the H3V foci overlap with a 177-bp repetitive sequence element found predominantly in mini-chromosomes, as well as with the TTAGGG repeats that compose telomeres. Chromatin immunoprecipitation studies, however, reveal that only the telomeric repeat DNA is substantially enriched with H3V. HTV is not essential for viability, mini-chromosome segregation, telomere maintenance or transcriptional silencing at the telomere-proximal expression sites from which bloodstream-form T. brucei controls antigenic variation. We propose that H3V represents a novel class of histone H3 variant, a finding that has evolutionary implications.

Telomerase-independent proliferation is influenced by cell type in Saccharomyces cerevisiae

Yeast strains harboring mutations in genes required for telomerase function (TLC1 and the EST genes) exhibit progressive shortening of telomeric DNA and replicative senescence. A minority of cells withstands loss of telomerase through RAD52-dependent amplification of telomeric and subtelomeric sequences; such survivors are now capable of long-term propagation with telomeres maintained by recombination rather than by telomerase. Here we report that simultaneous expression in haploid cells of both MATa and MATalpha information suppresses the senescence of telomerase-deficient mutants, with suppression occurring via the RAD52-dependent survivor pathway(s). Such suppression can be mimicked by deletion of SIR1-SIR4, genes that function in transcriptional silencing of several loci including the silent mating-type loci. Furthermore, telomerase-defective diploid strains that express only MATa or MATalpha information senesce at a faster rate than telomerase-defective diploids that are heterozygous at the MAT locus. This suggests that the RAD52-dependent pathway(s) for telomere maintenance respond to changes in the levels of recombination, a process regulated in part by the hierarchy of gene control that includes MAT regulation. We propose that cell-type-specific regulation of recombination at human telomeres may similarly contribute to the tissue-specific patterns of disease found in telomerase-deficient tumors.

Esa1p is an essential histone acetyltransferase required for cell cycle progression

Histones are dynamically modified during chromatin assembly, as specific transcriptional patterns are established, and during mitosis and development. Modifications include acetylation, phosphorylation, ubiquitination, methylation, and ADP-ribosylation, but the biological significance of each of these is not well understood. For example, distinct acetylation patterns correlate with nucleosome formation and with transcriptionally activated or silenced chromatin, yet mutations in genes encoding several yeast histone acetyltransferase (HAT) activities result in either no cellular phenotype or only modest growth defects. Here we report characterization of ESA1, an essential gene that is a member of the MYST family that includes two yeast silencing genes, human genes associated with leukemia and with the human immunodeficiency virus type 1 Tat protein, and Drosophila mof, a gene essential for male dosage compensation. Esa1p acetylates histones in a pattern distinct from those of other yeast enzymes, and temperature-sensitive mutant alleles abolish enzymatic activity in vitro and result in partial loss of an acetylated isoform of histone H4 in vivo. Strains carrying these mutations are also blocked in the cell cycle such that at restrictive temperatures, esa1 mutants succeed in replicating their DNA but fail to proceed normally through mitosis and cytokinesis. Recent studies show that Esa1p enhances transcription in vitro and thus may modulate expression of genes important for cell cycle control. These observations therefore link an essential HAT activity to cell cycle progression, potentially through discrete transcriptional regulatory events.

Telomere tales: chromatin, telomerase and telomere function in Saccharomyces cerevisiae

Unusual chromatin structures underlie epigenetic effects at the silent mating-type loci and telomeres in yeast. Many of the same genes appear to function in transcriptional silencing observed at both the silent mating-type loci and at telomeres. The observation that these loci are united by a requirement for shared factors suggests that the structure of chromatin at these regions is similar. Alteration of telomeric chromatin components affects regulation of transcription, telomeric length, recombination and chromosomal stability. Mutations in TLC1 and EST2, which both encode components of telomerase, cause identical phenotypes: progressive shortening of telomeric DNA, increased chromosome loss and eventually cell death. In this review, we examine the relationship between telomeric chromatin and telomere replication and discuss the possibility that telomerase itself is an integral part of telomeric chromatin structure.

3'-UTR-dependent deadenylation by the yeast poly(A) nuclease

Poly(A) tail removal is the first step in the degradation pathway for some mRNAs. The purified poly(A)-binding protein (PAB)-dependent poly(A) nuclease (PAN) from yeast removes mRNA poly(A) tails in vitro by a process similar to that observed in vivo. The exonucleolytic PAN degrades poly(A) and RNA bound by PAB, and can be activated by spermidine to degrade poly(A) in the absence of PAB. The shortening of the poly(A) tail down to 10-25 nucleotides and the terminal deadenylation of this short adenine tract are kinetically distinct reactions. Poly(A) shortening rates are stimulated by the yeast a-mating factor (MFA2) RNA 3' UTR sequence, and this occurs by switching PAN from a distributive to a more processive enzyme. Terminal deadenylation rates are also stimulated to different extents by various RNAs. Inversion of the MFA2 3' UTR sequence completely inhibits the terminal deadenylation reaction owing to the presence of an inhibitory element 70 nucleotides from the poly(A) tail. Other sequence elements inserted at a similar distance from the poly(A) tail also interfere with the reaction. These data suggest that the two phases of poly(A) degradation can be regulated by mRNA sequences, and they provide a mechanistic description of how this regulation could occur in vivo.