Effects of genetics and environment on isoflavone content of soybean from different regions of Brazil

The effects of genetics and environmental factors on isoflavone content of soybean (Glycine max L.) cultivars grown in different locations in Brazil in 1993/94 were evaluated. Seeds of different cultivars were analised by high performance liquid chromatography (HPLC). In Rio Grande do Sul (RS), Paraná (PR), and Mato Grosso do Sul (MS) States, a significant difference in the isoflavone total content average of the cultivars IAS 5 and FT-Abyara (163.9, 116.4 and 79.5 mg/100 g, respectively) was observed. In general, IAS 5 contained higher isoflavone than FT-Abyara. Cultivars IAS 5 and FT-Abyara grown at Vacaria, RS (28°30' S latitude) with temperature average of 19°C, had the highest isoflavone concentrations (218.7 and 163.8 mg/100 g, respectively). In Palotina, PR (24°27' S latitude), where temperature average was 24°C, the isoflavone concentrations were 105.9 and 86.8 mg/100 g, respectively. The lowest isoflavone contents were observed for FT-Estrela and FT-Cristalina, (27.6 and 46.5 mg/100 g, repectively) at Rondonópolis, MT (16°20' S latitude), where the temperature was 27°C.

On stand by: host genetics of HIV control.

The impact of host genetic variation on determining the differential outcomes after HIV infection has been studied by two approaches: targeting of candidate genes and genome-wide association studies (GWASs). The overlap in genetic variants that has been identified by these two means has essentially been restricted to variants near to the human leukocyte antigen (HLA) class I genes, although variation in the CCR5 locus, which was first shown to have an effect on HIV outcomes using the candidate gene approach, does reach significance genome-wide when very large samples sizes (i.e. thousands) are used in GWAS. Overall, many of the variants identified by the candidate gene approach are likely to be spurious, as no additional variants apart from a novel variant near the HLA-C gene have been consistently identified by GWAS. Variants with low frequency and/or low impact on HIV outcomes are likely to exist in the genome and there could be many of them, but these are not identifiable, given current GWAS sample sizes. Several loci centrally involved in the immune response, including the immunoglobulin genes, T-cell receptor loci, or leukocyte receptor complex, are either poorly covered on the GWAS chips or difficult to interpret due to their repetitive nature and/or the presence of insertion/deletion polymorphisms in the region. These loci warrant further interrogation, but genetic characterization of these regions across a range of individuals will first be required. Finally, synergistic interactions between loci may affect outcome after infection, as suggested by associations of specific, functionally relevant HLA and killer cell immunoglobulin-like receptor variants with HIV disease outcomes, and these require further consideration as well.

Arbuscular mycorrhiza: the challenge to understand the genetics of the fungal partner.

Arbuscular mycorrhizal symbioses occur between fungi and the majority of plant species. They are important for plant nutrition, plant growth, protection from pathogens, plant diversity, nutrient cycling, and ecosystem processes. A key goal in research is to understand the molecular basis of the establishment, regulation, and functioning of the symbiosis. However, lack of knowledge on the genetics of the fungal side of this association has hindered progress. Here, we show how several key, recently discovered processes concerning the genetics of arbuscular mycorrhizal fungi could be essential for ultimately understanding the molecular genetics of this important symbiosis with plants.

NLRC5 exclusively transactivates MHC class I and related genes through a distinctive SXY module.

MHC class II (MHCII) genes are transactivated by the NOD-like receptor (NLR) family member CIITA, which is recruited to SXY enhancers of MHCII promoters via a DNA-binding "enhanceosome" complex. NLRC5, another NLR protein, was recently found to control transcription of MHC class I (MHCI) genes. However, detailed understanding of NLRC5's target gene specificity and mechanism of action remained lacking. We performed ChIP-sequencing experiments to gain comprehensive information on NLRC5-regulated genes. In addition to classical MHCI genes, we exclusively identified novel targets encoding non-classical MHCI molecules having important functions in immunity and tolerance. ChIP-sequencing performed with Rfx5(-/-) cells, which lack the pivotal enhanceosome factor RFX5, demonstrated its strict requirement for NLRC5 recruitment. Accordingly, Rfx5-knockout mice phenocopy Nlrc5 deficiency with respect to defective MHCI expression. Analysis of B cell lines lacking RFX5, RFXAP, or RFXANK further corroborated the importance of the enhanceosome for MHCI expression. Although recruited by common DNA-binding factors, CIITA and NLRC5 exhibit non-redundant functions, shown here using double-deficient Nlrc5(-/-)CIIta(-/-) mice. These paradoxical findings were resolved by using a "de novo" motif-discovery approach showing that the SXY consensus sequence occupied by NLRC5 in vivo diverges significantly from that occupied by CIITA. These sequence differences were sufficient to determine preferential occupation and transactivation by NLRC5 or CIITA, respectively, and the S box was found to be the essential feature conferring NLRC5 specificity. These results broaden our knowledge on the transcriptional activities of NLRC5 and CIITA, revealing their dependence on shared enhanceosome factors but their recruitment to distinct enhancer motifs in vivo. Furthermore, we demonstrated selectivity of NLRC5 for genes encoding MHCI or related proteins, rendering it an attractive target for therapeutic intervention. NLRC5 and CIITA thus emerge as paradigms for a novel class of transcriptional regulators dedicated for transactivating extremely few, phylogenetically related genes.

A knowledge based signal processing approach to tonic identification in indian classical music

In this paper, we describe several techniques for detecting tonic pitch value in Indian classical music. In Indian music, the raga is the basic melodic framework and it is built on the tonic. Tonic detection is therefore fundamental for any melodic analysis in Indian classical music. This workexplores detection of tonic by processing the pitch histograms of Indian classic music. Processing of pitch histograms using group delay functions and its ability to amplify certain traits of Indian music in the pitch histogram, is discussed. Three different strategies to detect tonic, namely, the concert method, the template matching and segmented histogram method are proposed. The concert method exploits the fact that the tonic is constant over a piece/concert.templatematchingmethod and segmented histogrammethodsuse the properties: (i) the tonic is always present in the background, (ii) some notes are less inflected and dominant, to detect the tonic of individual pieces. All the three methods yield good results for Carnatic music (90−100% accuracy), while for Hindustanimusic, the templatemethod works best, provided the v¯adi samv¯adi notes for a given piece are known (85%).

Width and serialization of classical planning problems

We introduce a width parameter that bounds the complexity of classical planning problems and domains, along with a simple but effective blind-search procedure that runs in time that is exponential in the problem width. We show that many benchmark domains have a bounded and small width provided thatgoals are restricted to single atoms, and hence that such problems are provably solvable in low polynomial time. We then focus on the practical value of these ideas over the existing benchmarks which feature conjunctive goals. We show that the blind-search procedure can be used for both serializing the goal into subgoals and for solving the resulting problems, resulting in a ‘blind’ planner that competes well with a best-first search planner guided by state-of-the-art heuristics. In addition, ideas like helpful actions and landmarks can be integrated as well, producing a planner with state-of-the-art performance.

Speciation genetics: reinforcement by shades and hues.

Mating with a member of another species can seriously reduce an organism's fitness, so mechanisms ought to evolve to prevent it where hybridizing species meet. This old idea of 'reinforcement' has found new support in an elegant pair of studies of the ecological genetics of flower colour in an annual herb.

Planning under partial observability by classical replanning: theory and experiments

Planning with partial observability can be formulated as a non-deterministic search problem in belief space. The problem is harder than classical planning as keeping track of beliefs is harder than keeping track of states, and searching for action policies is harder than searching for action sequences. In this work, we develop a framework for partial observability that avoids these limitations and leads to a planner that scales up to larger problems. For this, the class of problems is restricted to those in which 1) the non-unary clauses representing the uncertainty about the initial situation are nvariant, and 2) variables that are hidden in the initial situation do not appear in the body of conditional effects, which are all assumed to be deterministic. We show that such problems can be translated in linear time into equivalent fully observable non-deterministic planning problems, and that an slight extension of this translation renders the problem solvable by means of classical planners. The whole approach is sound and complete provided that in addition, the state-space is connected. Experiments are also reported.

ECIL-3 classical diagnostic procedures for the diagnosis of invasive fungal diseases in patients with leukaemia.

Invasive fungal diseases (IFDs) continue to cause considerable morbidity and mortality in patients with haematological malignancy. Diagnosis of IFD is difficult, with the sensitivity of the gold standard tests (culture and histopathology) often reported to be low, which may at least in part be due to sub-optimal sampling or subsequent handling in the routine microbiological laboratory. Therefore, a working group of the European Conference in Infections in Leukaemia was convened in 2009 with the task of reviewing the classical diagnostic procedures and providing recommendations for their optimal use. The recommendations were presented and approved at the ECIL-3 conference in September 2009. Although new serological and molecular tests are examined in separate papers, this review focuses on sample types, microscopy and culture procedures, antifungal susceptibility testing and imaging. The performance and limitations of these procedures are discussed and recommendations are provided on when and how to use them and how to interpret the results.

Classification of indian classical vocal styles from melodic contours

A prominent categorization of Indian classical music is the Hindustani and Carnatic traditions, the two styleshaving evolved under distinctly different historical andcultural influences. Both styles are grounded in the melodicand rhythmic framework of raga and tala. The styles differ along dimensions such as instrumentation,aesthetics and voice production. In particular, Carnatic music is perceived as being more ornamented. The hypothesisthat style distinctions are embedded in the melodic contour is validated via subjective classification tests. Melodic features representing the distinctive characteristicsare extracted from the audio. Previous work based on the extent of stable pitch regions is supported by measurements of musicians’ annotations of stable notes. Further, a new feature is introduced that captures thepresence of specific pitch modulations characteristic ofornamentation in Indian classical music. The combined features show high classification accuracy on a database of vocal music of prominent artistes. The misclassifications are seen to match actual listener confusions.

Detection of Raga-characteristic phrases from Hindustani Classical Music Audio

Melodic motifs form essential building blocks in Indian Classical music. The motifs, or key phrases, providestrong cues to the identity of the underlying raga in both Hindustani and Carnatic styles of Indian music. Automatic identification and clustering of similar motifs is relevant in this context. The inherent variations in various instances of a characteristic phrase in a bandish (composition)performance make it challenging to identify similar phrases in a performance. A nyas svara (long note)marks the ending of these phrases. The proposed method does segmentation of phrases through identification ofnyas and computes similarity with the reference characteristic phrase.

Quantitative genetics of learning ability and resistance to stress in Drosophila melanogaster.

Even though laboratory evolution experiments have demonstrated genetic variation for learning ability, we know little about the underlying genetic architecture and genetic relationships with other ecologically relevant traits. With a full diallel cross among twelve inbred lines of Drosophila melanogaster originating from a natural population (0.75 < F < 0.93), we investigated the genetic architecture of olfactory learning ability and compared it to that for another behavioral trait (unconditional preference for odors), as well as three traits quantifying the ability to deal with environmental challenges: egg-to-adult survival and developmental rate on a low-quality food, and resistance to a bacterial pathogen. Substantial additive genetic variation was detected for each trait, highlighting their potential to evolve. Genetic effects contributed more than nongenetic parental effects to variation in traits measured at the adult stage: learning, odorant perception, and resistance to infection. In contrast, the two traits quantifying larval tolerance to low-quality food were more strongly affected by parental effects. We found no evidence for genetic correlations between traits, suggesting that these traits could evolve at least to some degree independently of one another. Finally, inbreeding adversely affected all traits.