High-quality binary protein interaction map of the yeast interactome network

Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering approximately 20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy.     

中日实学的交流:新井白石与朱之瑜

新井白石曾求学于儒学学者木下顺庵,而木下顺庵与浙江余姚的朱之瑜有交流,新井白石因顺庵举荐,曾出仕德川纲丰的甲府藩,白石一生著述甚丰,其语言学著作有<东雅>、<同文通考>、<东音谱>等书,<东雅>是一部关于古语名词语源的辞典.白石不仅关注一种语言内部的诸种变化,更注意到了多种语言间的相互影响.白石的研究语言的方法,一方面是木下顺庵那种广泛涉猎文献的实证学风的继承,另一方面也是吸收中国明代学术成果的结晶.朱之瑜在日本住了23年,白石著作中多处引用了朱之瑜的话,新     

Structural insights into the assembly of the type III secretion needle complex

Type III secretion systems (TTSSs) mediate translocation of virulence factors into host cells. We report the 17-angstrom resolution structures of a central component of Salmonella typhimurium TTSS, the needle complex, and its assembly precursor, the bacterial envelope-anchored base. Both the base and the fully assembled needle complex adopted multiple oligomeric states in vivo, and needle assembly was accompanied by recruitment of the protein PrgJ as a structural component of the base. Moreover, conformational changes during needle assembly created scaffolds for anchoring both PrgJ and the needle substructure and may provide the basis for substrate-specificity switching during type III secretion.     

An attempt at estrus detection in cattle by continuous measurements of ventral tail base surface temperature with supervised machine learning

We aimed to determine the effectiveness of estrus detection based on continuous measurements of the ventral tail base surface temperature (ST) with supervised machine learning in cattle. ST data were obtained through 51 estrus cycles on 11 female cattle (six Holsteins and five Japanese Blacks) using the tail-attached sensor. Three estrus detection models were constructed with the training data (n = 17) using machine learning techniques (random forest, artificial neural network, and support vector machine) based on 13 features extracted from sensing data (indicative of estrus-associated ST changes). Estrus detection abilities of the three models on test data (n = 34) were not statistically different among models in terms of sensitivity and precision (range 50.0% to 58.8% and 60.6% to 73.1%, respectively). The relatively poor performance of the models might indicate the difficulty of separating estrus-associated ST changes from estrus-independent fluctuations in ST.     

Histopathological changes in the pancreas due to decreased pancreatic blood flow in a canine tachycardia-induced cardiomyopathy model

In dogs, pancreatic acinar cell injury is thought to be caused by decreased pancreatic blood flow due to heart failure. In previous our report, it demonstrated that decreased heart function causes a significant decrease in pancreatic blood flow in heart failure dog model caused by rapid ventricular pacing (RVP). However, the types of histopathological changes remain unclear. We aimed to verify the types of histopathological changes occurring in the pancreatic tissue due to decreased heart function. After RVP for 4 weeks, atrophy of pancreatic acinar cells, characterized by a decrease in zymogen granules, was observed in all areas of the pancreas. In conclusion, the result of this study suggests that attention should be paid to ischemia/hypoperfusion injury in the pancreas.     

Rhizosphere pH Profile of Rice Plant Influenced by Al Treatment

To study the mechanisms of Al tolerance in rice, we focused on the change of rhizosphere pH. The 4-d seedlings were treated with Al solution (0, 10, 50 mM) for 24 h. Then each sample was put on an agarose gel including bromocresol green, so that the color of the gel indicated pH change. During 2-h contact, the pH of rhizosphere was decreased gradually, especially for Al-treated samples, showing the specific pH profiles along the root axis. Pretreatment of sample plants with a decoupling reagent 2,4-dinitrophenol (DNP) or a plasma membrane H⁺-ATPase inhibitor Na₃VO₄ did not decrease rhizosphere pH. Therefore, it was suggested that the H⁺ secretion activity was involved with Al-tolerant mechanisms of rice.     

Production of interspecific hybrids between Alstroemeria pelegrina L. var. rosea and A. magenta Bayer by ovule culture

Interspecific hybrids were efficiently produced in the cross-incompatible combination between Alstroemeria pelegrina L. var. rosea and A. magenta Bayer by culturing immature ovules with placenta 7–14 days after pollination on 2 g/l Gelrite-solidified MS medium containing 3% (w/v)sucrose. The plants showed intermediate characteristics between the parents and their hybridity was confirmed by karyotype and DNA analyses. The mean number of chromosome association per PMC at metaphase I was 2.60I+6.70II, pollen stainability was20.8%, and they produced viable seeds after self-pollination. Furthermore, mature plants were obtained when the hybrids were backcrossed as male parents with both the parents. The backcross-progeny from A. pelegrina var. rosea × hybrids exhibited 3.8 to 79.7% pollen stainability and that from A. magenta × hybrids 78.8 to 98.3%. Almost all of these plants produced viable seeds after self-pollination, which implies that they can beutilized for breeding of novel cultivars of Alstroemeria. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effects of ear corn silage supplementation on milk production and milk fatty acid profiles in grazing dairy farms

This study investigated the effects of substituting ear corn silage (ECS) for commercial formula feed on milk production and milk fatty acid profiles in grazing dairy farms during the summer season. A field survey was conducted on five grazing dairy farms in every summer month of 2017, 2018, and 2019. Three of the five farms substituted fresh ECS for the commercial formula feed at a ratio of 2:1 from July of each year (ECS farms). Other farms maintained the same feeding management as before (non‐ECS farms). An interview survey was conducted on each farm to calculate feed intake and milk yield per cow. Feed and milk samples were collected in each survey. Milk compositions and milk fatty acid profiles were determined. The substitution of ECS for the commercial formula feed did not affect milk yield or milk composition, but ECS farms maintained low levels of milk urea compared with non‐ECS farms (p < .01). The ECS substitution also influenced some of the milk fatty acid proportions; C16:0 and C16:1 increased, and trans‐11 C18:1, cis‐9,trans‐11 C18:2, and the sum of polyunsaturated fatty acids decreased, while these fatty acid proportions were maintained in non‐ECS farms throughout the summer season (p < .05).