Chromosomal double-strand breaks (DSBs) are resected by 5′-nucleases to form 3′ single-strand DNA (ssDNA) substrates for binding by homologous recombination and DNA damage checkpoint proteins. Two redundant pathways of extensive resection were described both in cells 1-3 and in vitro 4-6, one relying on Exo1 exonuclease and the other on Sgs1 helicase and Dna2 nuclease. However, it remains unknown how resection proceeds within the context of chromatin where histones and histone-bound proteins represent barriers for resection enzymes. Here, we have identified the yeast nucleosome remodeling enzyme Fun30 as novel factor promoting DSB end resection. Fun30 is the major nucleosome remodeler promoting extensive Exo1- and Sgs1-dependent resection of DSBs while the RSC and INO80 chromatin remodeling complexes play redundant roles with Fun30 in resection adjacent to DSB ends. ATPase and helicase domains of Fun30, which are needed for nucleosome remodeling 7, are also required for resection. Fun30 is robustly recruited to DNA breaks and spreads around the DSB coincident with resection. Fun30 becomes less important for resection in the absence of the histone-bound Rad9 checkpoint adaptor protein known to block 5′ strand processing 8 and in the absence of either histone H3 K79 methylation or γ-H2A, which mediate recruitment of the Rad9 9, 10. Together these data suggest that Fun30 helps to overcome the inhibitory effect of Rad9 on DNA resection.

Comprehensive discovery of genetic mechanisms of drug resistance and identification of in vivo drug targets represent significant challenges. Here we present a functional variomics technology in the model organism Saccharomyces cerevisiae. This tool analyzes numerous genetic variants and effectively tackles both problems simultaneously. Using this tool, we discovered almost all genes that, due to mutations or modest overexpression, confer resistance to rapamycin, cycloheximide, and amphotericin B. Most significant among the resistance genes were drug targets, including multiple targets of a given drug. With amphotericin B, we discovered the highly conserved membrane protein Pmp3 as a potent resistance factor and a possible novel target. Widespread application of this tool should allow rapid identification of conserved resistance mechanisms and targets of many more compounds. New genes and alleles that confer resistance to other stresses can also be discovered. Similar tools in other systems such as human cell lines will also be useful.

:The study was conducted to examine the effects of partially replacing soybean meal (SBM) by solid-state fermented cottonseed meal (FCSM) on growth performance, serum biochemical parameters and immune function of broilers. After inoculated with Bacillus subtilis BJ-1 for 48 h, the content of free gossypol in cottonseed meal was decreased from 0.82 to 0.21 g/kg. A total of 600, dayold male yellow-feathered broilers were randomly divided into four groups with three replicates of 50 chicks each. A corn-SBM based control diet was formulated and the experimental diets included 4, 8 or 12% FCSM, replacing SBM. Throughout the experiment, broilers fed 8% FCSM had higher (p<0.05) body weight gain than those fed 0, 4 and 12% FCSM. The feed intake in 8% FCSM group was superior (p<0.05) to other treatments from d 21 to 42. On d 21, the concentration of serum immunoglobin M in the 4% and 8% FCSM groups, as well as the content of complements (C3, C4) in 8% FCSM group were greater (p<0.05) than those in the SBM group. Besides, birds fed 8% FCSM had increased (p<0.05) serum immunoglobin M, immunoglobulin G and complement C4 levels on d 42 compared with bird fed control diet. No differences (p>0.05) were found between treatments regarding the serum biochemical parameters and the relative weights of immune organs. In conclusion, FCSM can be used in broiler diets at up to 12% of the total diet and an appropriate replacement of SBM with FCSM may improve growth performance and immunity in broilers.

Two experiments were conducted to test the feeding value of fermented cottonseed meal (FCSM) in broilers. In experiment 1, 480 1-day-old male yellow-feathered broilers were allocated into 4 dietary treatments with 6 replicates (20 birds per replicate) to examine the effects of FCSM on the growth response of chickens. Experimental feeding was performed for 6 weeks in two phases (starter, days 0 to 21; finisher, days 22 to 42). FCSM was used at 0, 40, 80, and 120 g/kg levels to replace soybean meal in the basal diet. The dietary inclusion of 40 and 80 g/kg FCSM increased (quadratic (Q): p<0.01) the body weight gain of broilers in the starter and in the overall feeding periods. Experiment 2 determined the effect of FCSM on the cecal microbial populations, intestinal morphology, and digestive enzyme activity of broilers. The number of lactobacilli in the cecal digesta increased at day 21 (p<0.01) and day 42 (linear (L): p=0.01). Coliform bacteria counts decreased (L: p<0.05) with the increasing inclusion of FCSM at day 21. The inclusion of FCSM increased (L-Q: p<0.05) villus height in the duodenum and linearly elevated (p<0.05) villus height and the villus height to crypt depth ratio in the jejunum at day 21. Similar improvement (L: p<0.05) was noted in jejunal villus height at day 42. The inclusion of FCSM improved (p<0.05) the activities of amylase and protease at day 21, as well as protease at day 42. In conclusion, the appropriate inclusion of FCSM improves growth, cecal microflora, intestinal morphology, and digestive enzyme activity in yellow-feathered broilers.

The study was conducted to investigate the effects of dietary inclusion of fermented cottonseed meal (FCM) on the ileal and cecal bacterial microbiota of broiler chickens. A total of 300 newborn yellow-feathered broiler chickens were randomly divided into 2 treatments with 3 replicates each (50 birds per replicate): control and 80 g/kg of FCM group. The feeding trial lasted for 42 d. Ileal and cecal digesta samples were collected from 8 chicks per replicate at 21 and 42 d of age to determine the composition of bacterial microbiota using denaturing gradient gel electrophoresis, cloning, sequencing, and real-time quantitative PCR analysis. The results demonstrated that the microbial composition in the ileum and cecum were considerably affected by the diet. The similarity dendrogram of banding profiles showed a more rapid stabilization of intestinal bacterial microbiota in broilers fed diets supplemented with FCM, compared with that of the birds fed the control diet. No significant difference was observed in total number of bands and Shannon-Weaver index, indicating that FCM had no effects on bacterial diversity. However, enumeration of bacteria in the ileal and cecal contents by quantitative PCR showed an increased (P < 0.05) population of lactobacilli, as well as a decreased (P < 0.05) Escherichia coli number by the dietary inclusion of FCM. In summary, dietary inclusion of FCM did not affect the intestinal microbial diversity but shifted intestinal microbiota, with a more homogenous population and an increased colonization of lactobacilli. The results also support the concept that dietary FCM inclusion could promote the beneficial bacteria in the intestinal tract.

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By using PBD and CCD, we obtained the optimal composition for xylanase production by Aspergillus niger XY-1 in SSF, and the results of no additional expensive medium and shortened fermentation time for higher xylanase production show the potential for industrial utilization.

A feeding trial was performed for 28 days to evaluate the effects of replacement of fish meal (FM) with fermented cottonseed meal (FCM) on growth, body composition and haemolymph indexes of juvenile Litopenaeus vannamei. Four isonitrogenous and isoenergetic diets were formulated by using FCM (96.4, 206, 317 and 417 g kg À1 ) to substitute 25%, 50%, 75% and 100% of FM in a control diet respectively. Each diet was randomly allotted to four tanks with 20 shrimp per tank. The feeding trail was conducted in an indoor flow-through aquaculture system. Shrimp fed diets containing 317 and 417 g kg À1 of FCM obtained lower (P < 0.05) final weight, weight gain, specific growth ratio, protein efficiency ratio as well as a higher (P < 0.05) feed conversion ratio compared with shrimp fed the control diet. The body ash content decreased (P < 0.05) in shrimp fed the diet with complete replacement of FM than those in other treatments. Moreover, increasing the dietary inclusion of FCM linearly raised (P < 0.05) the concentrations of total gossypol, (À) and (+) gossypol enantiomers in the whole shrimp body. No difference (P > 0.05) was observed in haematological parameters among the treatments. The results suggest that up to 50% of FM can be replaced by FCM without adverse effects on growth and feed utilization of L. vannamei.