Postreplicative formation of cohesion is required for repair and induced by a single DNA break

Sister-chromatid cohesion, established during replication by the protein complex cohesin, is essential for both chromosome segregation and double-strand break (DSB) repair. Normally, cohesion formation is strictly limited to the S phase of the cell cycle, but DSBs can trigger cohesion also after DNA replication has been completed. The function of this damage-induced cohesion remains unknown. In this investigation, we show that damage-induced cohesion is essential for repair in postreplicative cells in yeast. Furthermore, it is established genome-wide after induction of a single DSB, and it is controlled by the DNA damage response and cohesin-regulating factors. We thus define a cohesion establishment pathway that is independent of DNA duplication and acts together with cohesion formed during replication in sister chromatid-based DSB repair.     

Heterochromatin integrity affects chromosome reorganization after centromere dysfunction

The centromere is essential for the inheritance of genetic information on eukaryotic chromosomes. Epigenetic regulation of centromere identity has been implicated in genome stability, karyotype evolution, and speciation. However, little is known regarding the manner in which centromere dysfunction affects the chromosomal architectures. Here we show that in the fission yeast Schizosaccharomyces pombe, the conditional deletion of the centromere produces survivors that carry either a neocentromere-acquired chromosome at the subtelomeric region or an acentric chromosome rescued by intertelomere fusion with either of the remaining chromosomes. The ratio of neocentromere formation to telomere fusion is considerably decreased by the inactivation of genes involved in RNA interference-dependent heterochromatin formation. By affecting the modes of chromosomal reorganization, the genomic distribution of heterochromatin may influence the fate of karyotype evolution.     

Genetic variation of mitochondrial and nuclear genomes in carrots revealed by random amplified polymorphic DNA (RAPD)

Mitochondrial and nuclear genomic diversities of 8 carrot (Daucus carota ssp. sativus) varieties, including 6 pure lines and 2 cytoplasmic male sterile (cms) lines, were taxonomically identified using PCR with 19 RAPD primers. Dendrograms based on polymorphisms of both mitochondrial and nuclear genomes were constructed. According to the dendrogram of the mitochondrial genome revealed by RAPD, 4 differentiated clusters formed, in good accordance with the classification based on analyses with restriction enzyme digestion. Two cms lines were grouped into the same cluster, as genetically separated from the others. Thus, the cytoplasm donors of these male sterile lines were thought to be wild carrots. Conversely, RAPD analysis of the nuclear genome for these eight cultivars revealed no evident clusters although some cultivars were of a similar origin or place of cultivation. A correlation between nuclear and mitochondrial dendrograms was absent. RAPD has proved to be a useful tool for identifying mitochondrial and nuclear genomes. This technique will greatly aid in promoting efficient improvement of carrots. This revised version was published online in July 2006 with corrections to the Cover Date.     

Characteristics of burnt meat in cultured yellowtail <Emphasis Type="Italic">Seriola quinqueradiata</Emphasis>

ABSTRACT:   In order to understand the characteristics of burnt meat in cultured yellowtail Seriola quinqueradiata , fish were kept at two different temperatures (13 and 30°C) and slaughtered by either spinal cord destruction (SCD) or suffocation in air (SA). Early postmortem changes during storage at 32°C were analyzed by rheological, biochemical, and histological methods. The burnt meat (with lightness parameter, L* ≥ 55) was observed at 1-h storage in the SA 30°C group, at 2 h in SCD 30°C, and at 4 h in SA 13°C; meat was normal for the SCD 13°C group until 6 h of storage. Breaking strength scores were higher for the normal meat (200 g/cm²) than burnt meat (70 g/cm²) at 4 h of storage. Expressible water content was higher for the burnt meat than for the normal meat. Adenosine triphosphate concentrations for the SCD groups were higher than for the SA counterparts. Moreover, pH decrease was much faster in the 30°C groups, showing pH 5.6 at 2 h of storage. A negative correlation between the pH and lactic acid contents in muscle ( P  < 0.001) was found. Histological analysis evidenced a larger pericellular area (40%) in the burnt samples than in the normal samples (16%). It was confirmed that a higher fish-keeping water temperature and a stressful slaughter method (faster glycolytic process) were determinative factors that influence the occurrence of burnt muscle in yellowtail, and that the effect of the former is larger than the latter.     

Optimization of Hydrolysis Conditions for Production of Gelatin Hydrolysates from Shark Skin Byproduct and Evaluation of Their Antioxidant Activities

ABSTRACT

The effect of Alcalase hydrolysis conditions on antioxidant activities of shark skin gelatin hydrolysate (SSGH) byproduct was studied. Optimal hydrolysis condition for SSGH at 60°C, pH 7.5, and 2.70 AU kg^?1 gelatin protein was used for varied hydrolysis times (10–90 min). The IC₅₀ against DPPH radicals of SSGH hydrolyzed for 90 min (SSGH-90) was 27.39 mg ml^?1, which is greater than ascorbic acid. SSGH-90 was predominantly composed of 15–20 kDa protein fragments that regulated increases in peroxide value and thiobarbituric acid reactive substances values and suppressed decrease in DHA of a fish oil-in-water emulsion during storage at 30°C for 7 days.     

Growth model for the endangered cyprinid fish Tribolodon nakamurai based on otolith analyses

A growth model for the endangered cyprinid fish Tribolodon nakamurai was derived following otolith analyses of 16 wild and 53 reared specimens. The asteriscus was the most appropriate to measure size among three otolith elements, and its height OH  mm was used as size index of otolith. Standard length L  cm was best back-calculated using the Gompertz model, L  = 70.0·exp[–exp{−0.553 (OH   –  2.73)}]. Translucent zones on the lapilli, analyzed from 5-year-old-reared fish, were regarded as winter slow-growing zones. The ages of 10 wild specimens of 37.0–48.1 cm standard length were calculated as 7–10 years by counting the translucent zones on the lapilli. Age t was best back-calculated using the allometry model, t  = 1.33· OH ^1.37. The growth trajectory of T.   nakamurai followed a slender S curve, three typical growth models, von Bertalanffy, Logistic and Gompertz, and Richards' model, which is a general formula of the above three, being fitted using the maximum likelihood method. The Gompertz model, L_t  = 60.2·exp[–exp{−0.258( t  − 4.68)}], was found by Akaike's information criterion (AIC) to be the statistically most acceptable growth model.     

Effects of single and repeated heat stress on anxiety-like behavior and locomotor activity in medaka fish

In this study, we examined whether a single heat stress incident and long-term repeated heat stress could affect behavioral and neural responses in male medaka fish Oryzias latipes. By using the novel tank diving test, we found that 7-day repeated heat stress led to anxiety-like behaviors and suppressed locomotor activity, whereas fluoxetine treatment during repeated heat stress led to anxiolytic behaviors. Furthermore, a single heat stress incident increased hyper-locomotor activity. A single heat stress incident decreased mRNA expression of tryptophan hydroxylase 2 (tph2), a rate-limiting enzyme in serotonin biosynthesis, while a single heat stress increased mRNA expression of tyrosine hydroxylase 1 (th1) and tyrosine hydroxylase 2 (th2), catalyzing dopamine biosynthesis in the brain. Plasma cortisol concentration increased after a single stress, repeated stress, and fluoxetine treatment during repeated stress. These results suggest that medaka fish are a good model for assessing anxiety-like behavior induced by long-term repeated stress. Moreover, th1, th2, and tph2 in the brain would be key factors in the exploration of the central regulation of behavioral responses to a single and repeated stress in fish.

     

Use of GIS and machine learning to predict disease in shrimp farmed on the east coast of the Mekong Delta,Vietnam

Diseases in shrimp farms in the Mekong Delta of Vietnam cause significant crop losses and are therefore of great concern to producers. Once a pond becomes infected, it is difficult to prevent spread of the disease to nearby shrimp farming areas. Thus, predicting the occurrence of disease is an essential part of reducing the risk for shrimp farmers. In this study, we applied an integrated geographic information system and machine learning system to predict three serious diseases of shrimp, namely, acute hepatopancreatic necrosis, white spot syndrome disease, and Enterocytozoon hepatopenaei infection, based on data collected from shrimp farms in the Tra Vinh, Bac Lieu, Soc Trang, and Ca Mau provinces of Vietnam. We first constructed a map showing the distribution of these diseases using the locations of affected farms, and then we conducted spatial analysis to acquire the geographical features of the affected locations. This latter information was combined with environmental factors and clinical signs to form the set of independent variables affecting the outbreak of diseases. The neural network model outperformed the logistic regression, random forest, and gradient boosting methods in terms of predicting infection to estimate the probability of disease occurrence in farmed areas. Acute hepatopancreatic necrosis disease infected farms downstream of the Co Chien and Hau Rivers of Tra Vinh and west of Ca Mau. Enterocytozoon hepatopenaei infection is distributed in Soc Trang Province, while white spot syndrome virus has spread to the coastal districts of Soc Trang and Bac Lieu Provinces, where it is highly associated to water from a complex canal system.

     

A black soybean seed coat extract prevents obesity and glucose intolerance by up-regulating uncoupling proteins and down-regulating inflammatory cytokines in high-fat diet-fed mice

Black soybean seed coat extract (BE) is a polyphenol-rich food material consisting of 9.2% cyanidin 3-glucoside, 6.2% catechins, 39.8% procyanidins, and others. This study demonstrated that BE ameliorated obesity and glucose intolerance by up-regulating uncoupling proteins (UCPs) and down-regulating inflammatory cytokines in C57BL/6 mice fed a control or high-fat diet containing BE for 14 weeks. BE suppressed fat accumulation in mesenteric adipose tissue, reduced the plasma glucose level, and enhanced insulin sensitivity in the high-fat diet-fed mice. The gene and protein expression levels of UCP-1 in brown adipose tissue and UCP-2 in white adipose tissue were up-regulated by BE. Moreover, the gene expression levels of major inflammatory cytokines, tumor necrosis factor-α and monocyte chemoattractant protein-1 were remarkably decreased by BE in white adipose tissue. BE is a beneficial food material for the prevention of obesity and diabetes by enhancing energy expenditure and suppressing inflammation.