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Peer Reviewe

A point mutation in the splice donor site of intron 7 in the as2-casein encoding gene of the Mediterranean River buffalo results in an allele-specific exon skipping

The CSN1S2 cDNA of 10 unrelated Mediterranean River Buffaloes reared in Southern Italy was amplified by RT-PCR, while the region from the 6th to the 8th exon of the CSN1S2 gene was amplified from genomic template. cDNA sequence comparisons showed that five individuals had a normal transcript only (named CSN1S2A), one had a deleted transcript only (named CSN1S2B), because of the splicing out of the 27-bp of exon 7, and the remaining four had a heterozygous pattern. Analysis of the genomic sequences revealed a FM865620: g.773G>C transversion that caused inactivation of the intron 7 splice donor site and, consequently, the allele-specific exon skipping characteristic of the CSN1S2B allele. The g.773G>C mutation creates a new AluI restriction site enabling a PCR– RFLP rapid genotyping assay. The cDNA sequences showed three additional exonic mutations forming an extended haplotype with the g.773G>C polymorphism: FM865618: c.459C>T, c.484A>T and c.568A>G homozygous and heterozygous respectively in the CSN1S2BB and CSN1S2AB buffaloes. The first is silent, while the remaining two are non-conservative (p.Ile162Phe and p.Thp200Ala respectively). The genotype frequencies (37 CSN1S2A/A, 15 CSN1S2A/B and one CSN1S2B/B) are in agreement with Hardy–Weinberg equilibrium, with the frequency of the deleted B allele being 0.16. The predicted bubaline as2B protein is 198 aa long instead of 207 aa and would also be characterized by the presence of Phe at position 147 and Ala at 185

Characterization of two new alleles at the goat CSN1S2 locus.

Two novel alleles at the goat CSN1S2 locus have been identified: CSN1S2(F) and CSN1S2(D). Sequence analyses revealed that the CSN1S2(F) allele is characterized by a G --> A transition at the 13th nucleotide in exon 3 changing the seventh amino acid of the mature protein from Val to Ile. The CSN1S2(D) allele, apparently associated with a decreased synthesis of alpha s2-casein, is characterized by a 106-bp deletion, involving the last 11 bp of the exon 11 and the first 95 bp of the following intron. Methods (PCR-RFLP and PCR) for identification of carriers of these alleles have been developed

Ricolinostat, a selective HDAC6 inhibitor, shows anti-lymphoma cell activity alone and in combination with bendamustine

Histone deacetylase inhibitors (HDACis) have emerged as a new class of anticancer agents, targeting the biological process including cell cycle and apoptosis. We investigated and explained the anticancer effects of an HDAC6 inhibitor, ricolinostat alone and in combination with bendamustine in lymphoma cell lines. Cell viability was measured by MTT assay. Apoptosis, reactive oxygen species (ROS) generation, Bcl-2 protein expression, cell cycle progression and tubuline expression were determined by flow cytometry. The effects of ricolinostat alone and in combination on the caspases, PI3K/Akt, Bcl-2 pathways, ER stress and UPR were assessed by immunoblotting. Ricolinostat shows anti lymphoma activity when used as single agent and its capability to induce apoptosis is synergistically potentiated by the bendamustine in lymphoma cell lines. Drug combination reduced the proportion of cells in the G0/G1and S phases and caused an increase of âsub-G0/G1â peak. The synergistic effect accompanied with the increased ROS, activation of caspase-8, -9, and -3, the cleavage of PARP and modulated by Bcl-2 proteins family. In addition, the exposure of ricolinostat induced the acetylation level of α-tubulin, the extend of which was not further modified by bendamustine. Finally, the apoptosis effect of ricolinostat/bendamustine may be mediated by a corresponding effect on microtubule stabilization. Our data suggest that ricolinostat in combination with bendamustine may be a novel combination with potential for use as an antitumor agent in lymphoma

Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs

Virtual screening is an early stage in the drug discovery process that selects the most promising candidates. In the urgent computing scenario, finding a solution in the shortest time frame is critical. Any improvement in the performance of a virtual screening application translates into an increase in the number of candidates evaluated, thereby raising the probability of finding a drug. In this paper, we show how we can improve application throughput using Out-of-kernel optimizations. They use input features, kernel requirements, and architectural features to rearrange the kernel inputs, executing them out of order, to improve the computation efficiency. These optimizations’ implementations are designed on an extreme-scale virtual screening application, named LiGen, that can hinge on CUDA and SYCL kernels to carry out the computation on modern supercomputer nodes. Even if they are tailored to a single application, they might also be of interest for applications that share a similar design pattern. The experimental results show how these optimizations can increase kernel performance by 2 X, respectively, up to 2.2X in CUDA and up to 1.9X, in SYCL. Moreover, the reported speedup can be achieved with the best-proposed parameterization, as shown by the data we collected and reported in this manuscript

Italian Mediterranean river buffalo CSN2 gene structure and promoter analysis

The nucleotide sequence of the whole buffalo β-casein encoding gene (CSN2) plus 1,476 nt at the 5' flanking region and 51 nt at the 3' flanking region was determined. The gene is spread over 10.2 kb and consists of 9 exons varying in length from 24 (exon 5) to 498 bp (exon 7) and 8 introns from 92 bp (intron 5) to 22 59 bp (intron 1). Furthermore, highly conserved sequences, mainly located in the 5' flanking region, were found between this gene and the β-casein encoding genes of other species. The comparison between the obtained promoter and exonic regions and buffalo sequences present in EMBL evidenced different polymorphic sites. Finally, 5 interspersed repeated elements (4 in the bovine CSN2 gene) were also identified at 3 different locations of the sequenced region: 5' untranscribed region, intron 1, and intron 4

The histone deacetylase inhibitor romidepsin synergizes with lenalidomide and enhances tumor cell death in T-cell lymphoma cell lines

We investigated the cytotoxic interactions of romidepsin, a histone deacetylase inhibitor, and lenalidomide, an immunomodulatory agent, in a T-cell lymphoma preclinical model. Hut-78 and Karpas-299 cells were treated with romidepsin and lenalidomide alone and in combination. The interaction between romidepsin and lenalidomide was evaluated by the Chou–Talalay method, and cell viability and clonogenicity were also evaluated. Apoptosis, reactive oxygen species (ROS) levels, and cell cycle distribution were determined by flow cytometry. ER stress, caspase activation, and the AKT, MAPK/ERK, and STAT-3 pathways were analyzed by Western blot. Combination treatment with romidepsin and lenalidomide had a synergistic effect in Hut-78 cells and an additive effect in Karpas-299 cells at 24 hours and did not decrease the viability of normal peripheral blood mononuclear cells. This drug combination induced apoptosis, increased ROS production, and activated caspase-8, −9, −3 and PARP. Apoptosis was associated with increased hallmarks of ER stress and activation of UPR sensors and was mediated by dephosphorylation of the AKT, MAPK/ERK, and STAT3 pathways.The combination of romidepsin and lenalidomide shows promise as a possible treatment for T-cell lymphoma. This work provides a basis for further studies

Use of multivariate factor analysis to characterize the fatty acid profile of buffalo milk

The suitability of multivariate factor analysis (MFA) to extract a small number of latent variables able to explain the correlation pattern among fatty acids (FA) in buffalo milk was evaluated. FA profile of milk samples from 214 Italian water buffaloes was analysed by gas chromatography. MFA, performed on the correlation matrix of 52 FA, was able to extract 10 latent factors with specific biological meaning related to a common metabolic origin for FA associated with the same factor. Scores of the factors were treated as new quantitative phenotypes to evaluate the effect of age, month of calving and lactation stage. MFA approach was effective in describing the FA profile of buffalo milk by using a low number of new latent variables that clustered FA having similar metabolic origin and function. The new variables were also useful to test the effect of environmental and individual animal factors on milk FA composition

Report of a rare case of colon cancer complicated by anomalies of intestinal rotation and fixation: a case report

Introduction: The Situs viscerum inversus associated with anomalies of intestinal rotation and fixation is an extremely rare condition. To the authors' knowledge, this is the first report of colon cancer associated with intestinal malrotation and mesenterium ileocolicum commune. Case presentation: A 34-year-old man with a 2-month history of diarrhea associated with abdominal pain and weight loss underwent abdominal ultrasonography, colonscopy with biopsies and abdominal computed tomography scan with intravenous contrast. A right colonic neoplasm was diagnosed, observed only at surgery, as neither computed tomography or ultrasonography showed the intestinal malrotation. Particularly, the third and the fourth part of the duodenum descended vertically, without Treitz's ligament in support to the duodeno-jejunal flexure. The small bowel and the colon were located in the right and left side of the abdominal cavity, respectively. Conclusion: The anomaly of situs viscerum inversus influenced the surgical strategy in this case because of the vascular and lymphatic anomalies. Lymphatic vessels were therefore marked with subserosal injection of patent blue in the proximity of the tumor. Subsequently, right colectomy was performed. Colectomy extended from the distal ileum to the descending colon, by ligature of the right colic artery and vein at the origin from the superior mesenteric vessels. Patent blue guided lymphadenectomy was also performed with curative intent. Finally, a mechanical ileo-colic anastomosis was carried out. After right colectomy and ileo-descending anastomosis, the Ladd's procedure for intestinal malrotation was unnecessary. The authors believe that this strategy, despite the anatomical difficulties, represents an effective procedure for the radical surgical treatment of the right colon cancer associated with anomalies of intestinal rotation and fixatio