Motivation Pairwise alignment of sequences is a fundamental method in modern molecular biology, implemented within multiple bioinformatics tools and libraries. Current advances in sequencing technologies press for the development of faster pairwise alignment algorithms that can scale with increasing read lengths and production yields. Results In this paper, we present the wavefront alignment algorithm (WFA), an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s2) memory. Furthermore, our algorithm exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code. We evaluate the performance of our algorithm, together with other state-of-the-art implementations. As a result, we demonstrate that the WFA runs 20-300x faster than other methods aligning short Illumina-like sequences, and 10-100x faster using long noisy reads like those produced by Oxford Nanopore Technologies. Availability The WFA algorithm is implemented within the wavefront-aligner library, and it is publicly available at https://github.com/smarco/WFA

In chickens, elevated environmental temperature reduces food intake. We have previously reported that, during heat stress, the intestinal mucosa has an increased capacity to take up sugars. To investigate whether the effects of warm environment on sugar uptake are an intestinal adaptation to lower energy intake or a response attributable to heat stress, we examined the glucose transport kinetics of apical and basolateral membranes of the jejunum and the mucosal morphology of broiler chickens maintained in climatic chambers for 2 wk. Experimental groups were 1) control ad libitum (CAL), fed ad libitum and in thermoneutral conditions (20 degrees C); 2) heat stress ad libitum (HSAL), fed ad libitum and kept in a heated environment (30 degrees C); and 3) control pair-fed (CPF), maintained in thermoneutral conditions and fed the same amount of food as that consumed by the HSAL group. Both the CPF and the HSAL groups showed reduced body weight gain, but only the HSAL chickens had lower plasma thyroid hormones and higher corticosterone than CAL and CPF groups. The fresh weight and length of the jejunum were only reduced in the HSAL group. The activity and expression of apical sodium-dependent glucose transporter 1 (SGLT-1) were increased by approximately 50% in the HSAL chickens, without effects in the CPF group. No changes in K(d) or in SGLT-1 and glucose transporter-2 K(m) were observed in the pair-fed and heated birds. These results support the view that increased intestinal hexose transport capacity is entirely dependent on adaptations of apical SGLT-1 expression to heat stress and is not due to reduced food intake.

In this study, we investigated intestinal barrier function during inflammation as well as the effects of dietary supplementation with porcine spray-dried animal plasma (SDAP) proteins and porcine immunoglobulin concentrate (IC). Wistar Lewis rats were fed from d 21 (weaning) until d 34 or 35 either a control diet or a diet containing SDAP or IC. On d 30 and d 33, rats received an intraperitoneal dose of Staphylococcus aureus enterotoxin B (SEB; 0.5 mg/kg body wt; groups SEB, SEB-SDAP, and SEB-IC). SEB reduced the potential difference across the jejunum by 60%, the short-circuit current by 70%, and Na-K-ATPase activity in intestinal mucosa (all P < 0.05). The fluxes of dextran flux (4 kDa) and horseradish peroxidase (HRP, 40 kDa) across the intestinal wall also increased in SEB-treated rats (P < 0.01, P = 0.068, respectively). SEB also increased HRP flux across the paracellular space (P < 0.05). Moreover, SEB-treated rats had a reduced expression of tight junction proteins, such as ZO-1 (10% reduction; P < 0.05) and beta-catenin (20% reduction; P < 0.05). Dietary supplementation with SDAP or IC prevented dextran (P < 0.05) and HRP (P < 0.05) paracellular flux across the intestinal epithelium. SDAP supplementation also prevented SEB effects on Na-K-ATPase activity (P < 0.05). In our model of SEB-induced intestinal inflammation, the increased permeability across the intestinal mucosa was due to the lower expression of tight junction proteins, an effect that can be prevented by both SDAP and IC supplementation.

The intestinal mucosa contributes to homeostasis by preventing the entrance of biological and chemical agents across the epithelium that could alter the stability of the system. This protective function is especially important at the time of weaning, when animals are exposed to infectious agents and to numerous stresses such as the change of environment and diet. Diets supplemented with spray-dried plasma or plasma protein fractions have been shown to improve growth performance of farm animals and have been proposed as an alternative to antibiotics. In this review, we summarize our findings on the mechanism of action of dietary plasma proteins using a rat model of intestinal inflammation, based on the administration of Staphylococcus aureus enterotoxin B (SEB). Staphylococcal enterotoxin B activates the gut-associated lymphoid tissue (GALT), increasing T-lymphocytes in Peyer's patches and the number of activated T lymphocytes in mesenteric lymph nodes (organized GALT). In the lamina propria SEB increased cytotoxic T gammadelta and natural killer cell populations of the diffuse GALT. Staphyloccocal enterotoxin B significantly increased proinflammatory cytokines in Peyer's patches and mucosa. Plasma protein supplements modulated the mucosal immune response in organized and diffuse GALT, protecting GALT from possible excessive activation by the SEB challenge. These effects are accompanied by a reduction of proinflammatory cytokine production, supporting the view that changes in cytokine production mediate the effects of dietary plasma proteins during intestinal inflammation. The increase in mucosal permeability and intestinal secretion induced by SEB was associated with decreased expression of mucosal tight-junction and adherent-junction proteins. Both plasma and plasma protein fractions prevented the effects of SEB on intestinal permeability, thus reducing the exposure of the host to microbial and food antigens across the interstitial space. These findings indicate that dietary plasma proteins modulate functional and structural properties of the intestinal mucosa.