Indonesian Tapé Ketan Fermentation

Indonesian tapé ketan is a fermentation in which a mold, Amylomyces rouxii Calmette (Chlamydomucor oryzae Went and Prinsen Geerligs), in combination with one or more yeasts such as Endomycopsis burtonii converts steamed rice to a sweet-sour, slightly alcoholic paste. A study was made to determine the biochemical changes that occur in the substrate during fermentation. It was found that the product was ready for consumption after fermentation at 30°C for 36 to 48 h. A. rouxii used about 30% of the total rice solids, resulting in a crude protein of 12% in 96 h, whereas the combination of the mold with E. burtonii reduced total solids by 50% in 192 h, causing crude protein to increase to 16.5%. Soluble solids increased from 5 to about 67% in 36 h and decreased to 12% at 192 h with A. rouxii alone, whereas soluble solids fell to about 8% at 192 h in the fermentation with both the mold and the yeast. The mold, by itself, reduced the starch content of the rice from 78 to 10% in 48 h and to less than 2% in 144 h. The mold plus yeast reduced the starch content to about 18% in 48 h; however the “starch” content did not fall below 6% even at 192 h, presumably because the yeast was producing glycogen, which was determined along with the residual starch. With both the mold and the mold plus yeast fermentations, reducing sugars increased from less than 1% to approximately 5% in 24 h and reached maximum concentration, 16 to 17%, between 36 and 48 h. A. rouxii by itself produced a maximum of about 5.6% (vol/vol) ethanol at 96 h. The highest concentration of ethanol (8%, vol/vol) was produced by the mold plus E. burtonii at 144 h. The mold by itself reduced the starting pH from 6.3 to about 4.0 in 48 h. The combination of the mold and yeast reduced the pH to 4.1 in 144 h. The mold increased total acidity to approximately 6.2 meq of H⁺ per 100 ml, and the combination of the mold and yeast increased the total acidity to 7.8 meq of H⁺ per 100 ml in 192 h. At 48 h there was practically no difference in the volatile acidity (0.20) for the combined fermentation compared with 0.26 meq of H⁺ per 100 ml for the mold fermentation. The mold and at least one species of yeast were required to develop the rich aroma and flavor of typical Indonesian tapé.     

Aspects of sexual failure in the reproductive processes of a rare bulbiliferous plant,<Emphasis Type="Italic"> Titanotrichum oldhamii</Emphasis> (Gesneriaceae), in subtropical Asia

Titanotrichum oldhamii produces both flowers and asexual bulbils on its inflorescences. However, field observations and herbarium collections indicate that seed set is infrequent and that most reproduction is from vegetative bulbils. We have investigated the failure of sexual reproduction and identified four major causes: (1) in the wild, the seed:ovule ratio for open pollination was only 1.9%, in contrast to 10.1% for artificial cross-pollination, implying poor pollinator services. (2) The overall reproductive success was 5–10 times greater in glasshouse pollination treatments compared to field treatments. This suggests suboptimal environmental conditions for seed set in natural habitats, which may eliminate natural seed set completely. (3) Pollination experiments showed that outcrossed populations set significantly more seed and had higher germination rates than intra-populational and self crosses, in both field and glasshouse experiments. T. oldhamii thus appears to benefit from wide outcrossing. Pollen transfer between populations, however, seems to be infrequent because of the rarity and scattered distribution of Titanotrichum populations. (4) Flowers near the apex of the inflorescence are less likely to set seed, especially late in the season when inflorescences convert to bulbil production. In these late flowers, pollen tubes showed poor guidance as they approach the micropyle of the ovules. Even under optimal glasshouse conditions, the average outcrossing success was only 0.229. Almost one-half of the ovules remained undeveloped and 13.5% of ovules aborted after pollination, indicating a strong shift of resource allocation toward vegetative bulbils and rhizome development. Efficient reproduction from asexual bulbils may thus have released Titanotrichum from strong selection for efficient sexual reproduction. However, occasional seed set observed in the wild may be very important for maintaining some genetic diversity in populations, and promoting overall fitness.     

Plant eco-devo: the potential of poplar as a model organism

Ecological developmental genetics is the study of how ecologically significant traits originate in the genome and how the allelic combinations responsible are maintained in populations and species. Plant development involves a continuous feedback between growth and environment and the success of individual genotype x environment interactions determines the passage of alleles to the next generation: the adaptive recursion. Outbreeding plants contain a large amount of genetic variation, mostly in the form of single nucleotide polymorphisms (SNPs). One of the challenges of eco-devo is to distinguish neutral SNPs from those with ecological consequences. The complete genome sequence of Populus trichocarpa Torr. & A. Gray will be a significant aid in this endeavour. Occurring from California to Alaska, this is the first ecologically 'keystone' species to be sequenced. It has a rich natural history and is an obligate outbreeder. The individual sequenced, Nisqually-1, appears to be heterozygous on average about every 100 bp over the c. 500 million bp of the genome. Overlaid on this within-individual variation is some ecologically based between-individual genotypic variation evident across the distribution of the species. The synthesis of information from genomics and ecology is now in prospect. This 'ecomolecular synthesis' is likely to provide a rich insight into the genomic basis of plant adaptation.     

Evolution and alignment of the hypervariable arm 1 of Aeschynanthus (Gesneriaceae) ITS2 nuclear ribosomal DNA

Comparative ITS2 sequencing in the plant genus Aeschynanthus(Gesneriaceae) reveals an insertion/deletion (indel) hot spot in the ITS2 sequences that is difficult to align. Examination of other Gesneriaceae sequences shows that this is a widespread phenomenon in this plant family. Minimum free-energy secondary structure analyses localize the hot spot to the terminal part of arm 1. Arm 1 is twice as long in Gesneriaceae than in other asterids. In addition, the pattern of indels is consistent with this secondary structure model. The high variability of the extended terminal part of arm 1 in Gesneriaceae and the fact that it can be deleted altogether imply that it is functionally superfluous. In contrast, the base of arm 1 is relatively conserved and may function as an exonuclease recognition site. This study illustrates how comparative secondary structure analyses can be helpful in fine-scale alignment. Alignment based on secondary structure conflicts with our initial manual alignment and, to a lesser extent, with a CLUSTAL X alignment with default parameters.     

aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data

Background

Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a single library of paired-end reads: aTRAM, automated Target Restricted Assembly Method. The aTRAM pipeline uses a reference sequence, BLAST, and an iterative approach to target and locally assemble the genes of interest.

Results

Our results demonstrate that aTRAM rapidly assembles genes across distantly related taxa. In comparative tests with a closely related taxon, aTRAM assembled the same sequence as reference-based and de novo approaches taking on average < 1 min per gene. As a test case with divergent sequences, we assembled >1,000 genes from six taxa ranging from 25 – 110 million years divergent from the reference taxon. The gene recovery was between 97 – 99% from each taxon.

Conclusions

aTRAM can quickly assemble genes across distantly-related taxa, obviating the need for draft genome assembly of all taxa of interest. Because aTRAM uses a targeted approach, loci can be assembled in minutes depending on the size of the target. Our results suggest that this software will be useful in rapidly assembling genes for phylogenomic projects covering a wide taxonomic range, as well as other applications. The software is freely available http://www.github.com/juliema/aTRAM.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0515-2) contains supplementary material, which is available to authorized users.     

Identification of radiation-induced expression changes in nonimmortalized human T cells

In the event of a radiation accident or attack, it will be imperative to quickly assess the amount of radiation exposure to accurately triage victims for appropriate care. RNA-based radiation dosimetry assays offer the potential to rapidly screen thousands of individuals in an efficient and cost-effective manner. However, prior to the development of these assays, it will be critical to identify those genes that will be most useful to delineate different radiation doses. Using global expression profiling, we examined expression changes in nonimmortalized T cells across a wide range of doses (0.15-12 Gy). Because many radiation responses are highly dependent on time, expression changes were examined at three different times (3, 8, and 24 h). Analyses identified 61, 512 and 1310 genes with significant linear dose-dependent expression changes at 3, 8 and 24 h, respectively. Using a stepwise regression procedure, a model was developed to estimate in vitro radiation exposures using the expression of three genes (CDKN1A, PSRC1 and TNFSF4) and validated in an independent test set with 86% accuracy. These findings suggest that RNA-based expression assays for a small subset of genes can be employed to develop clinical biodosimetry assays to be used in assessments of radiation exposure and toxicity.     

In the eye (and ears) of the beholder: Receiver psychology and human signal design

Although the study of signals has been part of human behavioral ecology since the field's inception,¹ only recently has signaling theory become important to the evolutionary study of human behavior and culture.² Signaling theory's rise to prominence has been propelled mainly by applications of costly signaling theory,³ which has shed light on a wide variety of human behaviors ranging from hunting⁴ to religion.^5,6 Costly signaling rests on the idea that wasteful but highly visible traits and behaviors can be explained as honest indicators of underlying qualities that are otherwise difficult to detect. For example, a laborious hunting technique may serve as a display of skill on the part of the hunter, who may then be favorably perceived by potential mates and allies.⁴ The costs of the activity ensure that the signal is honest, since unskilled hunters will not be able to perform as well. Despite the usefulness of this perspective, many such studies begin by documenting a costly behavior that is then explained with reference to costly signaling theory. Because such behaviors are easy to detect, they may be overemphasized in the literature.⁷ Moreover, costly signaling theory by itself can explain neither all signals nor all aspects of signal design. In this review, we argue that a focus on the role that the psychology of the intended receiver plays in signal design can expand the scope of signaling theory as a promising avenue to explain human behavior.