From Virus Research to Molecular Biology: Tobacco Mosaic Virus in Germany, 1936-1956

In 1937, a group of researchers in Nazi Germany began investigating tobacco mosaic virus (TMV) with the hope of using the virus as a model system for understanding gene behavior in higher organisms. They soon developed a creative and interdisciplinary work style and were able to continue their research in the postwar era, when they made significant contributions to the history of molecular biology. This group is significant for two major reasons. First, it provides an example of how researchers were able to produce excellent scientific research in the midst of dictatorship and war.Coupled with the group's ongoing success in postwar Germany, the German TMV investigators provide a dramatic example of how scientific communities deal with adversity as well as rapid political and social change. Second, since the researchers focused heavily (though no exclusively) on TMV, their story allows us to analyze how an experimental system other than phage contributed to the emergence of molecular biology.     

Solid cultures of thrips-pathogenic fungi Isaria javanica strains for enhanced conidial productivity and thermotolerance

Entomopathogenic fungi have great potential to control agricultural and horticultural insect pests, however optimizing conidial production systems to demonstrate high productivity and stability still needs additional efforts for successful field application and industrialization. Although many virulent entomopathogenic fungal isolates have been viewed as potential candidates in a laboratory environment, very few of the isolates are being used in practice for application in agricultural fields as commercial products. I. javanicus is an entomopathogenic fungus that is parasitic to various diverse coleopteran and lepidopteran insects and thought good candidate as biopesticdes. In this work, the basic characteristics of two entomopathogenic fungi, I. javanica FG340 and Pf04, were investigated in morphological examinations, genetic identification, and virulence against Thrips palmi, and then the feasibility of various grains substrates for conidial production was assessed, particularly focusing on conidial productivity and thermotolerance. Isaria javanica FG340 and Pf04 conidia were solid-cultured on 12 grains for 14?days in a Petri dish. Of the tested Italian millet, perilla seed, millet and barley-based cultures showed high conidial production. The four-grain media yielded >1?×?10⁹ conidia/g of I. javanica FG340 and Pf04. Pf04 strain had enhanced thermotolerance up to 45?°C when cultured on Italian millet. In application, it was easy to make a conidial suspension using the cultured grains, and several surfactants were tested to release the conidia. This work suggests several possible inexpensive grain substrates by which to promote conidial production combined with enhanced stability against exposure to high temperature.     

Non-invasive diagnosis of cutaneous leishmaniasis by the direct boil loop-mediated isothermal amplification method and MinION™ nanopore sequencing

Cutaneous leishmaniasis (CL) is gaining attention as a public health problem. We present two cases of CL imported from Syria and Venezuela in Japan. We diagnosed them as CL non-invasively by the direct boil loop-mediated isothermal amplification method and an innovative sequencing method using the MinION? sequencer. This report demonstrates that our procedure could be useful for the diagnosis of CL in both clinical and epidemiological settings.     

Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

若尔盖人-狼冲突现状与管理研究

大中型食肉动物肇事事件导致人类与野生动物关系恶化,给生物多样性保护工作带来巨大的挑战。若尔盖湿地是我国三大湿地之一,湿地、草原分布广泛,生物多样性丰富,畜牧业发达,但近年来狼(Canis lupus)捕杀牲畜的肇事事件时有发生。为了解若尔盖野生狼肇事件的空间分布以及牧民对人-狼冲突管理的看法,本研究于2022年对若尔盖县13个乡镇83个行政村进行走访调查。结果表明：(1)多数受访者(66.0%)认为在过去5年内,若尔盖县野生狼数量有所增加;(2)狼肇事事件具有明显的空间分异性,最严重的是包座乡。包座乡临近山区,该区域牧场面积广阔、牧民饲养牲畜数量多等原因导致该镇发生狼肇事事件较多;(3)对于狼肇事,绝大多数牧民(85.0%)更希望采取经济补偿或者驱赶措施,只有少数牧民(9.4%)希望采取捕杀的措施;(4)影响牧民对狼肇事管理措施的偏好因子中,受教育程度、年龄、民族以及被杀牲畜数量有显著影响。建议加强狼种群监测管理,采取措施减少狼捕杀牲畜,优化补偿机制,缓解当地牧民与狼之间的矛盾。本研究为当前若尔盖县野生动物保护和管理决策提供了依据,对其他地区大型食肉动物与当地居民冲突管理具有借鉴意义。     

Comparison of bioelectrical impedance and BMI in predicting obesity-related medical conditions

Objective : To determine the relative validity of specific bioelectrical impedance analysis (BIA) prediction equations and BMI as predictors of physiologically relevant general adiposity. Research Methods and Procedures : Subjects were >12, 000 men and women from the Third National Health and Nutrition Examination Survey population. We examined the correlations between BMI and percentage body fat based on 51 different predictive equations, blood pressure, and blood levels of glucose, high‐density lipoprotein cholesterol, and triglycerides, which are known to reflect adiposity, while controlling for other determinants of these physiological measures. Results : BMI consistently had one of the highest correlations across biological markers, and no BIA‐based measure was superior. Percent body fat estimated from BIA was minimally predictive of the physiological markers independent of BMI. Discussion : These results suggest that BIA is not superior to BMI as a predictor of overall adiposity in a general population.     

Citizen science and observer variability during American pika surveys

Within- and between-group observer variability can confound scientific discovery. If observer variability can be quantified and is addressed, data collected by participants with wide ranges of experience and training can yield more reliable inferences. The American pika (Ochotona princeps) is a mammalian sentinel of climate change that has received consideration for listing under the United States Endangered Species Act. As a result, numerous pika monitoring initiatives have been started throughout the mountains in western North America. Some initiatives employ research teams of biological science technicians (professionals), whereas many rely on networks of citizen scientists, or volunteers, for data collection. To date, few studies have quantified observer variability during pika surveys; none have explored the reliability of professional crews or volunteers. We conducted pika surveys in Glacier National Park, Montana, to quantify observer variability. We investigated observer variability 1) among a crew of professionals, 2) among volunteers, and 3) between professionals and volunteers. Professionals were more consistent at identifying pika signs and estimating potential home ranges and consistently found more pika signs than did the volunteers, with the exception of pika sightings. Estimates of pika occupancy were consistent at each site among volunteers conducting sitting surveys. We suggest that sitting surveys conducted by volunteers can reliably detect pika site occupancy. However, data on population dynamics of pikas (e.g., density) should be collected by professionals. Observer variability analyses of this nature should be common practice for wildlife-resource managers and scientists, especially with observers of varying levels of experience and motivation. © 2012 The Wildlife Society.     

Minority of mammalian orthologs can be regarded as physiologically closest genes

Orthologs are genes from different genomes that originate from a common ancestor gene by speciation event. They are most similar by the structure of encoded proteins and therefore should have a similar function. Here I apply the principle used for detection of structural orthology for a genome-wide analysis of gene expression. For this purpose, I determine the mutual similarity rank in all-by-all comparison of among-tissues expression patterns. The expression of most part of human–mouse orthologs in homologous tissues is poorly correlated (average mutual coexpression rank is only 4835 out of 18,092). Genes from evolutionarily labile gene families, which experience rapid turnover of family composition, are among those with the strongest expression change. However, the revealed phenomenon is not limited to them. There is no or very weak relationship between protein sequence divergence and mutual coexpression rank. Also, generally there is no relationship between the ratio of nonsynonymous to synonymous nucleotide substitutions and coexpression rank. This relationship is tangible only within evolutionarily labile gene families. These results indicate that despite of a similar biochemical function of orthologs reflected in the conserved protein sequence, the physiological (systemic) context of this function can be changed. Also, these results suggest that gene biochemical function and its physiological role in the organism can evolve independently.     

车八岭山地常绿阔叶林冰灾后林木受损的生态学评估

从植物生态学的角度对2008年初南方冻雨冰雪灾害对典型的亚热带山地常绿阔叶林造成的损害情况做了研究。对12个优势种和亚优势种的受灾情况做了对比分析, 对不同径级和不同地形因子下林木抵抗冻雨灾害的差异做了对比。统计检验结果显示林木受损程度存在显著的种间差异、径级差异和地形级差异。优势种米槠(Castanopsis carlesii)比多数亚优势种受害更严重; 各树种抗冻雨灾害能力以山茶科和樟科的种较强, 而壳斗科的多个种, 如米槠、栲(C. fargesii)受灾较为严重; 林木的受损比例随着胸径(diameter at breast height, DBH)增加而增大; 在未受灾的各级林木中, 超过70%的个体集中在最小一级径阶(1-5 cm)。χ²检验显示坡度、坡向、坡位等地形因子对林木受损状况有显著的影响, 随着坡位上升, 林木受损程度逐渐加重, 上坡位的林木受损比例最大, 下坡位最小, 这可能与随着坡位升高, 迎风面降温效果更迅速有关。对于坡向和坡度而言, 位于半阳坡的林木受灾比例显著高于半阴坡, 位于坡度级III (15°-25°)、IV (25°-35°)、V (35°-45°)上的林木受灾最严重。该研究结果对于亚热带常绿阔叶林的保育和应对未来可能再次发生的冰雪灾害有重要意义; 同时对于森林恢复和演替、乡土阔叶树种的选育及森林经营等方面的研究和应用也有重要的参考价值。     

The pathogenesis of atherosclerosis. An interpretive history of the cholesterol controversy, part IV: the 1984 coronary primary prevention trial ends it--almost

As of the early 1980s, despite the wealth of evidence from experimental animal models, the extensive epidemiologic evidence, the powerful genetic evidence, and the strongly suggestive clinical intervention trial results, most clinicians still remained unpersuaded regarding the relevance of the lipid hypothesis. What was needed was a well-designed, large-scale, long-term, double-blind study demonstrating a statistically significant impact of treatment on coronary heart disease events. The National Institutes of Health (NIH) had laid the groundwork for such a study as early as 1970, but the study was not completed and the results published until 1984. This study, the Coronary Primary Prevention Trial, showed that treatment with a bile acid binding resin reduced major coronary events in hypercholesterolemic men by 19%, with a P value of 0.05. The NIH followed this up with a national Consensus Development Conference on Lowering Blood Cholesterol to Prevent Heart Disease. For the first time, the NIH now went on record advocating screening for hypercholesterolemia and urging aggressive treatment for those at high risk. The Institute initiated a national cooperative program to that end, the National Cholesterol Education Program. For the first time, preventing coronary heart disease became a national public health goal.