Spiral Tissue Microarrays as Next Evolutionary Step in the High-density Tissue Microarray Technology

Tissue microarray (TMA) is a well-established technique that connects basic research with clinical applications that allow the validation of many pathobiologic events from gene expression dysregulation to genomic aberrations. However, conventional TMAs have several limitations such as limited representation of tissue heterogeneity, destruction of donor tissue blocks due to coring and usage of particular specimens that have limited evaluable material (tissue from thin specimens or needle biopsies). We have developed a novel method, which we termed "Spiral TMA" that generates TMAs that allow for improved representation of the donor tissue while keeping the architectural details of the donor block intact. This technology is ideal for specimens with limited tissue without the need to punch holes into the original block and therefore preserving the tissue integrity. In this report, we describe the methodology of constructing Spiral TMA and demonstrate the validation of tumor representation and tissue heterogeneity by comparing Spiral TMA to conventional TMA using immunohistochemical staining to EGFR and CK7

Is “Common But Differentiated Responsibilities” principle applicable in biodiversity? – Towards approaches for shared responsibilities based on updated capabilities and data.

The application of the “Common But Differentiated Responsibilities (and Respective Capabilities)” (CBDR-RC) principle in the field of biodiversity received criticisms due to the lack of scientific evidence and/or outdated categories which in turn resulted in a knowledge gap in its applicability in policy-making. Reflecting on this research gap, we reviewed existing relevant publications by quantifying and evaluating the responsibility of different countries under various categories (i.e., low-, middle-, and high-income) for biodiversity loss. As concrete indicators, we used the five direct drivers of biodiversity loss by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) to examine and identify biodiversity-related footprints and challenges, whereby the applicability of the CBDR principle was considered. Data on the national impact and positive contributions to global biodiversity were also encompassed, considering all available data from older periods as possible. The results showed that low-, middle-, and high-income countries contributed to biodiversity loss, with high-income countries as the largest contributor, indicating relatively high responsibility by developed countries. Meanwhile, developing (middle- and low-income) countries contributed about 44% of biodiversity loss. The results further indicated that the shared responsibility was not clear enough to be sorted out by a simple dichotomy between developed and developing countries and immediately applying the CBDR principle. Besides, the impact of global trade should be fairly attributed to consumer countries (frequently developed countries) and producer countries (developing countries). Moreover, the upward move in the income category in many countries in the last decades has not been fully reflected in discussions under the Convention on Biological Diversity. This means that the respective capabilities have not been considered in a timely manner in policy-making. As such, we propose non-binary “Differentiated But Shared Responsibilities (and Updated Capabilities)” (DBSR-UC) as a new concept, highlighting the need for incentives and burdens based on scientific evidence

Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet

Although the origin and domestication process of foxtail millet (Setaria italica subsp. italica (L.) P. Beauv.) has been studied by several groups, the issue is still ambiguous. It is essential to resolve this issue by studying a large number of accessions with sufficient markers covering the entire genome. Genetic structures were analyzed by transposon display (TD) using 425 accessions of foxtail millet and 12 of the wild ancestor green foxtail (Setaria italica subsp. viridis (L.) P. Beauv.). We used three recently active transposons (TSI-1, TSI-7, and TSI-10) as genome-wide markers and succeeded in demonstrating geographical structures of the foxtail millet. A neighbor-joining dendrogram based on TD grouped the foxtail millet accessions into eight major clusters, each of which consisted of accessions collected from adjacent geographical areas. Eleven out of 12 green foxtail accessions were grouped separately from the clusters of foxtail millet. These results indicated strong regional differentiations and a long history of cultivation in each region. Furthermore, we discuss the relationship between foxtail millet and green foxtail and suggest a monophyletic origin of foxtail millet domestication

Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat

To evaluate the potential of genomic selection (GS), a selection experiment with GS and phenotypic selection (PS) was performed in an allogamous crop, common buckwheat (Fagopyrum esculentum Moench). To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598–50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding

Variation in floral scent compounds recognized by honeybees in Brassicaceae crop species

Floral scent attracts pollinators. We investigated the floral scent compounds recognized by pollinators in six Brassica crop species, including allogamous species with different genomes and autogamous species with two parental genomes and radish (Raphanus sativus). Biologically active compounds recognized by honeybees were screened from all floral compounds by combined gas chromatography–electroantennogram analysis and their profiles were determined by gas chromatography–mass spectrometry. Fourteen of the 52 compounds were active. All accessions had more than two active compounds, but the compounds greatly differed between the two genera. On the basis of similarities in whether active compounds were presence or absence, their amount and their composition ratio, we divided the Brassica accessions into three to five groups by cluster analyses. Most groups were composed of a mixture of allogamous and autogamous species sharing same genome, indicating that the variation depended on genome, not species. These results suggest that all species require pollinator visits for reproduction, despite their different reproductive systems. However, the inter-genus and intra-specific variations shown by the multiple groups within a species might cause different visitation frequencies by pollinators between genera and among accessions within a species, resulting in insufficient seed production in some accessions or species

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information

A Search for Infrared Emission from Core-Collapse Supernovae at the Transitional Phase

Most of the observational studies of supernova (SN) explosions are limited to early phases (< a few yr after the explosion) of extragalactic SNe and observations of SN remnants (> 100 yr) in our Galaxy or very nearby galaxies. SNe at the epoch between these two, which we call "transitional" phase, have not been explored in detail except for several extragalactic SNe including SN 1987A in the Large Magellanic Cloud. We present theoretical predictions for the infrared (IR) dust emissions by several mechanisms; emission from dust formed in the SN ejecta, light echo by circumstellar and interstellar dust, and emission from shocked circumstellar dust. We search for IR emission from 6 core-collapse SNe at the transitional phase in the nearby galaxies NGC 1313, NGC 6946, and M101 by using the data taken with the AKARI satellite and Spitzer. Among 6 targets, we detect the emission from SN 1978K in NGC 1313. SN 1978K is associated with 1.3 x 10^{-3} Msun of silicate dust. We show that, among several mechanisms, the shocked circumstellar dust is the most probable emission source to explain the IR emission observed for CSM-rich SN 1978K. IR emission from the other 5 objects is not detected. Our current observations are sensitive to IR luminosity of > 10^{38} erg s^{-1}, and the non-detection of SN 1962M excludes the existence of the shocked circumstellar dust for a high gas mass-loss rate of sim 10^{-4} Msun yr^{-1}. Observations of SNe at the transitional phase with future IR satellites will fill the gap of IR observations of SNe with the age of 10-100 years, and give a new opportunity to study the circumstellar and interstellar environments of the progenitor, and possibly dust formation in SNe.Comment: Accepted for publication in ApJ, 14 page

Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments

Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound from anthropogenic disturbances. An essential mechanism to adapt to environmental and social changes is the fluctuations in the host gut microbiome. Here we give a comprehensive description of anthropogenically induced microbiome alterations in Asian elephants (n = 30). We detected gut microbial changes due to overseas translocation, captivity and deworming. We found that microbes belonging to Planococcaceae had the highest contribution in the microbiome alterations after translocation, while Clostridiaceae, Spirochaetaceae and Bacteroidia were the most affected after captivity. However, deworming significantly changed the abundance of Flavobacteriaceae, Sphingobacteriaceae, Xanthomonadaceae, Weeksellaceae and Burkholderiaceae. These findings may provide fundamental ideas to help guide the preservation tactics and probiotic replacement therapies of a dysbiosed gut microbiome in Asian elephants. More generally, these results show the severity of anthropogenic activities at the level of gut microbiome, altering the adaptation processes to new environments and the subsequent capability to maintain normal physiological processes in animals