Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages

Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.

Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer

Pancreatic ductal adenocarcinoma is a lethal disease with limited treatment options and poor survival. We studied 83 spatial samples from 31 patients (11 treatment-naïve and 20 treated) using single-cell/nucleus RNA sequencing, bulk-proteogenomics, spatial transcriptomics and cellular imaging. Subpopulations of tumor cells exhibited signatures of proliferation, KRAS signaling, cell stress and epithelial-to-mesenchymal transition. Mapping mutations and copy number events distinguished tumor populations from normal and transitional cells, including acinar-to-ductal metaplasia and pancreatic intraepithelial neoplasia. Pathology-assisted deconvolution of spatial transcriptomic data identified tumor and transitional subpopulations with distinct histological features. We showed coordinated expression of TIGIT in exhausted and regulatory T cells and Nectin in tumor cells. Chemo-resistant samples contain a threefold enrichment of inflammatory cancer-associated fibroblasts that upregulate metallothioneins. Our study reveals a deeper understanding of the intricate substructure of pancreatic ductal adenocarcinoma tumors that could help improve therapy for patients with this disease.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

The origin and evolution of mutations in acute myeloid leukemia

Most mutations in cancer genomes are thought to be acquired after the initiating event, which may cause genomic instability and drive clonal evolution. However, for acute myeloid leukemia (AML), normal karyotypes are common, and genomic instability is unusual. To better understand clonal evolution in AML, we sequenced the genomes of M3-AML samples with a known initiating event (PML-RARA) versus the genomes of normal karyotype M1-AML samples and the exomes of hematopoietic stem/progenitor cells (HSPCs) from healthy people. Collectively, the data suggest that most of the mutations found in AML genomes are actually random events that occurred in HSPCs before they acquired the initiating mutation; the mutational history of that cell is "captured" as the clone expands. In many cases, only one or two additional, cooperating mutations are needed to generate the malignant founding clone. Cells from the founding clone can acquire additional cooperating mutations, yielding subclones that can contribute to disease progression and/or relapse.

DNMT3A mutations in acute myeloid leukemia

BACKGROUND

The genetic alterations responsible for an adverse outcome in most patients with acute myeloid leukemia (AML) are unknown.

METHODS

Using massively parallel DNA sequencing, we identified a somatic mutation in DNMT3A, encoding a DNA methyltransferase, in the genome of cells from a patient with AML with a normal karyotype. We sequenced the exons of DNMT3A in 280 additional patients with de novo AML to define recurring mutations.

RESULTS

A total of 62 of 281 patients (22.1%) had mutations in DNMT3A that were predicted to affect translation. We identified 18 different missense mutations, the most common of which was predicted to affect amino acid R882 (in 37 patients). We also identified six frameshift, six nonsense, and three splice-site mutations and a 1.5-Mbp deletion encompassing DNMT3A. These mutations were highly enriched in the group of patients with an intermediate-risk cytogenetic profile (56 of 166 patients, or 33.7%) but were absent in all 79 patients with a favorable-risk cytogenetic profile (P<0.001 for both comparisons). The median overall survival among patients with DNMT3A mutations was significantly shorter than that among patients without such mutations (12.3 months vs. 41.1 months, P<0.001). DNMT3A mutations were associated with adverse outcomes among patients with an intermediate-risk cytogenetic profile or FLT3 mutations, regardless of age, and were independently associated with a poor outcome in Cox proportional-hazards analysis.

CONCLUSIONS

DNMT3A mutations are highly recurrent in patients with de novo AML with an intermediate-risk cytogenetic profile and are independently associated with a poor outcome. (Funded by the National Institutes of Health and others.).

Detailed analysis of a contiguous 22-Mb region of the maize genome

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.

Recurring mutations found by sequencing an acute myeloid leukemia genome

BACKGROUND

The full complement of DNA mutations that are responsible for the pathogenesis of acute myeloid leukemia (AML) is not yet known.

METHODS

We used massively parallel DNA sequencing to obtain a very high level of coverage (approximately 98%) of a primary, cytogenetically normal, de novo genome for AML with minimal maturation (AML-M1) and a matched normal skin genome.

RESULTS

We identified 12 acquired (somatic) mutations within the coding sequences of genes and 52 somatic point mutations in conserved or regulatory portions of the genome. All mutations appeared to be heterozygous and present in nearly all cells in the tumor sample. Four of the 64 mutations occurred in at least 1 additional AML sample in 188 samples that were tested. Mutations in NRAS and NPM1 had been identified previously in patients with AML, but two other mutations had not been identified. One of these mutations, in the IDH1 gene, was present in 15 of 187 additional AML genomes tested and was strongly associated with normal cytogenetic status; it was present in 13 of 80 cytogenetically normal samples (16%). The other was a nongenic mutation in a genomic region with regulatory potential and conservation in higher mammals; we detected it in one additional AML tumor. The AML genome that we sequenced contains approximately 750 point mutations, of which only a small fraction are likely to be relevant to pathogenesis.

CONCLUSIONS

By comparing the sequences of tumor and skin genomes of a patient with AML-M1, we have identified recurring mutations that may be relevant for pathogenesis.

Basic Surgical Training in the Era of the European Working Time Directive: What are the Problems and Solutions?

Background and Aims

Imposed reductions in working hours will impact significantly on the ability of surgical trainees to achieve competency. The objective of this study was to obtain the opinions of Scottish surgical trainees concerning the training they receive, in order to inform and guide the development of future, high-standard training programmes.

Methods

An anonymous questionnaire was sent to basic surgical trainees on the Edinburgh, Aberdeen and Dundee Basic Surgical Rotations commencing after August 2002.

Results

Thirty six questionnaire responses were analysed. Very few of the returned comments were complimentary to the existing training structure; indeed, most comments demonstrated significant trainee disappointment. Despite “regular” exposure to operative sessions, training tutorials and named consultant trainers, the most common concern was a perceived lack of high-quality, structured, operative exposure and responsibility. Textbooks and journals remain the most frequently utilised learning tools, with high-tech systems such as teleconferencing, videos, CD-ROMS, and DVDs being poorly exploited.

Conclusions

Current surgical training is not meeting the expectation of the majority of its trainees. To solve this problem will require extensive revision of attitudes and current educational format. A greater emphasis on the integration of 21st century learning tools in the training programme may help bridge this gap.

Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny

To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism-based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80-110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently.

Evolution of symbiotic bacteria in the distal human intestine

The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes.

The total number of microbes that colonize the surfaces of our adult bodies is thought to be ten times greater than the total number of our human cells. Our microbial partners provide us with certain features that we have not had to evolve on our own. In this sense, we should consider ourselves to be a supraorganism whose genetic landscape includes both our own genome as well as the genomes of our resident microbes, and whose physiologic features are a synthesis of human and microbial metabolic traits. The largest collection of microbes resides in our gut, which harbors trillions of bacteria, representing hundreds of species, most falling into two groups—the Bacteroidetes and the Firmicutes. We have sequenced the genomes of two human gut-dwelling Bacteroidetes, and compared their genomes to the genomes of other bacteria that live both inside and outside of our bodies. Our results illustrate that adaptation to the gut habitat is a dynamic process that includes acquisition of genes from other microorganisms. These findings emphasize the importance of including the evolution of “our” microbial genomes when considering the evolution of humans.

Human microbiome evolution was explored by comparing human gut Bacteroidete genomic sequences to available data; common modes of evolution were revealed that have enabled these gut-dwelling microbes to adapt to their environments.

Evolutionary and biomedical insights from the rhesus macaque genome

The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.

The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression

Helicobacter pylori produces acute superficial gastritis in nearly all of its human hosts. However, a subset of individuals develops chronic atrophic gastritis (ChAG), a condition characterized in part by diminished numbers of acid-producing parietal cells and increased risk for development of gastric adenocarcinoma. Previously, we used a gnotobiotic transgenic mouse model with an engineered ablation of parietal cells to show that loss of parietal cells provides an opportunity for a H. pylori isolate from a patient with ChAG (HPAG1) to bind to, enter, and persist within gastric stem cells. This finding raises the question of how ChAG influences H. pylori genome evolution, physiology, and tumorigenesis. Here we describe the 1,596,366-bp HPAG1 genome. Custom HPAG1 Affymetrix GeneChips, representing 99.6% of its predicted ORFs, were used for whole-genome genotyping of additional H. pylori ChAG isolates obtained from Swedish patients enrolled in a case-control study of gastric cancer, as well as ChAG- and cancer-associated isolates from an individual who progressed from ChAG to gastric adenocarcinoma. The results reveal a shared gene signature among ChAG strains, as well as genes that may have been lost or gained during progression to adenocarcinoma. Whole-genome transcriptional profiling of HPAG1's response to acid during in vitro growth indicates that genes encoding components of metal uptake and utilization pathways, outer membrane proteins, and virulence factors are among those associated with H. pylori's adaptation to ChAG.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.

With the Caenorhabditis briggsae genome now in hand, C. elegans biologists have a powerful new research tool to refine their knowledge of gene function in C. elegans and to study the path of genome evolution

The DNA sequence of human chromosome 7

Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.

Initial sequencing and comparative analysis of the mouse genome

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

The use of a Giardia vaccine as an immunotherapeutic agent in dogs

Dogs (n = 13), which had failed to be cured of giardiosis following chemotherapeutic measures, were treated with a Giardia vaccine (2-3 injections). Clinical signs resolved between 16 and 42 days postvaccination and cessation of fecal cyst shedding was between 21 and 70 days. Vaccination is a potential method of treating giardiosis in dogs.

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Variation in distances among teats of Holstein cows: implications for automated milking

Distances among teats were measured immediately prior to and immediately following milking in 912 lactations of 506 Holstein cows to assess variation due to age (parity), stage of lactation, year, and observer. Data were used to simulate success or failure to attach by the Gascoigne Melotte robotic milker. Distance between front teats premilking was nearly twice that for rear teats. When attachment of the cluster to an udder with a particular set of teat distances was simulated, excessive distance between front teats was the most frequent cause of attachment failure for third and later parities. For first parity, extremely narrow distance between rear teats was the most frequent cause of predicted attachment failure. Reduction in teat distances because of milking was proportionately much greater for distance between rear teats (45 to 50%) than for other teat distances (25 to 29%). In a study of 10 Holstein cows measured at milking and at 0, 6, 8, and 12 h after milking, distances among teats increased linearly with time elapsed postmilking. Electronic storage of a profile of a cow for teat distance and adjustments for milking interval and stage of lactation can increase chances for successful cluster attachment.

Variation in milk somatic cells of heifers at first calving

To evaluate variation in milk somatic cells, 24 primiparous cows (paired by calving date) were sampled during the first 75 d of lactation. Milk somatic cell counts were lowest at 9 to 10 wk. For differential cell counts in milk, only percentage of macrophages changed significantly during first 75 d (33% at 1 wk, 25% at 6 wk, and 34% at 11 wk). Epithelial cells were identified and ranged from 11 to 20% of total. For milk somatic cell count, variation between cows within pairs sampled contemporaneously was small (3 to 24%). However, variation between cows was much greater for the differential cell counts (46% of total for lymphocytes and 34% for epithelial cells). Of 1021 quarter foremilk samples, 26 were positive for major pathogens, but 326 were positive for various species. Prevalence of bacteria was significantly higher during first 10 d after calving. Rear quarters had significantly higher bacterial presence: 47% for left rear versus 21% for left front and 37% for right rear versus 24% for right front. Total milk somatic cell count after first calving appears to depend primarily on differences in temporary factors and is not a stable characteristic of individual cows. Proportions of the different somatic cell types in milk may vary consistently by cow in early first lactation.

Relationship between immunoglobulin concentrations in milk and phagocytosis by bovine neutrophils

Using bovine neutrophils and radio-labelled Staphylococcus aureus, skim milk samples taken at 4 stages of lactation from the 4 mammary quarters of 48 cows were used in an in vitro phagocytosis assay. Immunoglobulin (Ig) isotype concentrations in the milk samples were estimated by use of an ELISA procedure. To determine associations of Ig concentrations with phagocytosis, correlations, simple regressions, and partial regressions were calculated. Simple correlations were computed between each Ig isotype and phagocytosis percentage for each lactation number stage of lactation category. Ranges of these correlations for IgM, IgG1, IgG2, and IgA were 0.33 to 0.60; -0.16 to 0.43; 0.04 to 0.46; and -0.30 to 0.36, respectively. Correlations for concentrations of IgG2 and IgM with percentage of phagocytosis tended to be slightly higher for samples from older cows, in contrast to the correlations calculated for IgA and IgG1. Multiple regression of percentage of phagocytosis calculated simultaneously on concentrations of the 4 Ig isotypes in the sample indicated that IgM, followed by IgG2 and IgA, was most closely associated with phagocytosis. Partial regression calculated on concentration of IgG1 was not significant. Addition of bacteriologic status of the quarter and somatic cell concentration in the milk sample did not increase accuracy of predicting percentage of phagocytosis, compared with use of Ig concentrations alone. These results supported the attribution of unique modes of action to IgM and IgG2 in promoting phagocytosis by neutrophils.

Comparison of single- and multiple-trait selected sires--response of heifer growth

Body weights and linear body measurements were on 386 heifers whose sires were selected according to two criteria: 1) Yield, selection only on milk yield Predicted Difference from daughters' first lactations; 2) Merit, selection on a combination of milk yield Predicted Difference (all daughters), udder type, and percentage of daughters leaving herd in first lactation. No significant differences existed between Yield and Merit heifers for body weights at various ages through first calving or in heart girth or withers height through 18 mo of age. Heifers born to dams first parity were lighter at birth but were not significantly different from other parties of dam for weight, withers height, or heart girth at later ages. Differential selection for milk yield as in this study did not change body weight of heifers.

Comparison of single and multiple-trait selected sires. Response in mastitis traits

Estimated somatic cell counts and incidence mastitis were measured on 163 daughters of two groups of bulls selected by two alternative criteria. Yield bulls were selected solely on progeny test for milk in first lactation; Merit bulls were selected by independent culling levels on fat-corrected milk yield, percent daughters culled in first lactation, and udder type conformation of daughters. Daughters of Yield sires exceeded daughters of Merit sires by 685 kg milk in first lactation. Groups did not differ significantly in measures of clinical mastitis or in measures of estimated cell counts of milk. Also, groups did not differ in kilograms milk discarded because of antibiotic treatment for mastitis, in spite of the large difference in total milk yield. Mean milk discarded per lactation completed was 171 kg, representing 64,243, and 207 g for parities one, two, and three.

Three times a day milking during the first half of lactation

Three milking frequency treatments were compared: twice daily milking; thrice daily milking until milk dropped below 24 kg; thrice daily milking until milk dropped below 31 kg. Three time milking was at least 45 days but no more than 150 days. Cows (12 to 14 per group) were managed alike except for milking frequency. In early lactation, increased milking had little effect. With time the superiority in yields increased such that cows on three times for 150 days were outproducing two time cows by 20%. Cumulative milk yields were greater for the thrice groups than for the twice group by 5% at 56 days, 11 and 8% at 154 days, 11 and 9% at 182 days, and 10% at 280 days. Fat percentage, adjusted for previous lactation fat percentage, averaged .2 to .3% lower for the cows milked three times until 24 kig but only .1% lower for cows milked thrice until 31 kg. Increased yield was primarily from prolonged peak yield and less subsequent decline. Switching from three to two milkings decreased yield 6 to 8% in the 1st wk. However, three time milking had a positive carryover, apparently due to higher starting yield at the point at which they were switched.

Genetic parameters of several measures of milk flow rate and milking time

Heritabilities and genetic correlations of milking rate, time, and yield were estimated by intrasire regression of daughter on dam for 252 Holstein pairs. Heritabilities were: lactation yield, .51 +/- .11; peak rate, .47 +/- .11; bucket milk yield, .38 +/- .10; average rate, .37 +/- .12; milk yield to .45 kg/min, .19 +/- .12; total time, .17 +/- .12; duration of peak rate, .10 +/- .10; strip time, .08 +/- .15; yield during peak rate, .07 +/- .11; and strip yield, .01 +/- .17. The genetic correlation of peak rate with lactation milk yield was .69 +/- .08, indicating substantial genetic improvement in milking rate by selecting for milk production. The genetic correlation between total milking time and lactation milk yield was .50 +/- .20, indicating an increase in total milking time due to selection for milk. Direct selection for peak rate would provide an opportunity to reduce total milking time.