The response of splanchnic tissue metabolism to different levels of metabolizable protein (MP) was measured in 6 catheterized multiparous lactating Holstein cows. Three diets, balanced to provide similar energy intakes and increasing amounts of MP (g/d)-1922 (low), 2264 (medium), and 2517 (high)-were fed during 21-d experimental periods according to a replicated Latin square. On d 18, 19, or 20, six hourly blood samples were collected simultaneously from the portal and hepatic veins plus an artery to determine net fluxes of nutrients across the portal-drained viscera and the liver. Yields of milk and protein increased, as did urinary N excretion with increasing MP. Portal absorption of essential amino acids (EAA) increased linearly with increasing MP supply, as did liver removal of His, Met, and Phe. In contrast, liver removal of the branched-chain AA (BCAA) and lysine was unaffected by diets. With increasing MP, the ratio of milk output to postliver supply of BCAA, Thr, and Lys decreased linearly, indicating oxidation of these AA in the peripheral tissues. Concomitant to a decreased catabolism of EAA in the liver (His, Met, Phe, and Thr) and/or in peripheral tissues (BCAA, Lys, and Thr), the efficiency of transfer of absorbed EAA into milk protein decreases markedly as protein supply increases. The efficiency of transfer of absorbed AA into milk also varies greatly between AA. These 2 important factors should be taken into account when building predictive schemes for milk protein output.

BackgroundTaxonomic classification is a corner stone for the characterisation and comparison of microbial communities. Currently, most existing methods are either slow, restricted to specific communities, highly sensitive to taxonomic inconsistencies, or limited to genus level classification. As crucial microbiota information is hinging on high-level resolution it is imperative to increase taxonomic resolution to species level wherever possible.ResultsIn response to this need we developed SPINGO, a flexible and stand-alone software dedicated to high-resolution assignment of sequences to species level using partial 16S rRNA gene sequences from any environment. SPINGO compares favourably to other methods in terms of classification accuracy, and is as fast or faster than those that have higher error rates. As a demonstration of its flexibility for other types of target genes we successfully applied SPINGO also on cpn60 amplicon sequences.ConclusionsSPINGO is an accurate, flexible and fast method for low-level taxonomic assignment. This combination is becoming increasingly important for rapid and accurate processing of amplicon data generated by newer next generation sequencing technologies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0747-1) contains supplementary material, which is available to authorized users.

BackgroundThe multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription initiation, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing.ResultsIn MCF-7 breast cancer cells, we find 2700 genes with interdependent alternative transcription initiation, splicing and polyadenylation events, both in proximal and distant parts of mRNA molecules, including examples of coupling between transcription start sites and polyadenylation sites. The analysis of three human primary tissues (brain, heart and liver) reveals similar patterns of interdependency between transcription initiation and mRNA processing events. We predict thousands of novel open reading frames from full-length mRNA sequences and obtained evidence for their translation by shotgun proteomics. The mapping database rescues 358 previously unassigned peptides and improves the assignment of others. By recognizing sample-specific amino-acid changes and novel splicing patterns, full-length mRNA sequencing improves proteogenomics analysis of MCF-7 cells.ConclusionsOur findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a basis to reveal largely unresolved mechanisms that coordinate transcription initiation and mRNA processing.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1418-0) contains supplementary material, which is available to authorized users.

Irradiance influences plant growth through photosynthetic activity and developmental responses. Our objectives were to determine the effect of irradiance on leaf anatomy and dry matter partitioning of tall rescue (Festuca arundinacea Schreb.). Plants were grown outdoors for 10 wk during summer 1986 and autumn 1987 with or without screencloth to give irradiances of 30% (low), 60% (medium), or full (high) sun. Data were similar for both years, although daily air temperatures averaged 25°C in 1986 and 12°C in 1987. Production of total plant dry matter was reduced at low irradiance, primarily due to fewer tillers per plant. Shoot/root ratio and leaf area ratio (leaf area per plant dry weight) were higher for plants grown at low irradiance than for those grown at high irradiance. Recently developed leaf blades on plants at low irradiance were 54 or 650/0 longer and had 56 or 77% more leaf area, but were 12% thinner and had 18 or 25% lower specific leaf weight than did those grown at high irradiance. Blade width was not affected. Total stomatal density at low irradiance was 17 or 24% lower than at high irradiance, with a larger reduction on the adaxial than on the abaxial epidermis. Proportional cross‐sectional areas of epidermis and bulliform cells, vascular bundle and fiber cap cells, and mesophyll cells were similar over treatments. Blades grown at low irradiance had ≈25% more air space than did those at high irradiance. At low irradiance, partitioning of dry matter among plant parts and developmental processes within the leaf blade were shifted to favor production of leaf blade area per unit of dry matter with no influence on forage quality.