Comparative transcriptomics analysis reveals a calcineurin B-like gene to positively regulate constitutive and acclimated freezing tolerance in potato.

Freezing stress is a major limiting factor in crop production. To increase frost-hardiness of crops via breeding, deciphering the genes conferring freezing-tolerance is vital. Potato cultivars (Solanum tuberosum) are generally freezing-sensitive, but some potato wild species are freezing-tolerant, including Solanum commersonii, Solanum malmeanum and Solanum acaule. However, the underlying molecular mechanisms conferring the freezing-tolerance to the wild species remain to be deciphered. In this study, five representative genotypes of the above-mentioned species with distinct freezing-tolerance were investigated. Comparative transcriptomics analysis showed that SaCBL1-like (calcineurin B-like protein) was upregulated substantially in all of the freezing-tolerant genotypes. Transgenic overexpression and known-down lines of SaCBL1-like were examined. SaCBL1-like was shown to confer freezing-tolerance without significantly impacting main agricultural traits. A functional mechanism analysis showed that SaCBL1-like increases the expression of the C-repeat binding factor-regulon as well as causes a prolonged higher expression of CBF1 after exposure to cold conditions. Furthermore, SaCBL1-like was found to only interact with SaCIPK3-1 (CBL-interacting protein kinase) among all apparent cold-responsive SaCIPKs. Our study identifies SaCBL1-like to play a vital role in conferring freezing tolerance in potato, which may provide a basis for a targeted potato breeding for frost-hardiness.

Genome-Wide Approach to Identify Quantitative Trait Loci for Drought Tolerance in Tetraploid Potato (Solanum tuberosum L.).

Drought represents a major abiotic stress factor negatively affecting growth, yield and tuber quality of potatoes. Quantitative trait locus (QTL) analyses were performed in cultivated potatoes for drought tolerance index DRYM (deviation of relative starch yield from the experimental median), tuber starch content, tuber starch yield, tuber fresh weight, selected transcripts and metabolites under control and drought stress conditions. Eight genomic regions of major interest for drought tolerance were identified, three representing standalone DRYM QTL. Candidate genes, e.g., from signaling pathways for ethylene, abscisic acid and brassinosteroids, and genes encoding cell wall remodeling enzymes were identified within DRYM QTL. Co-localizations of DRYM QTL and QTL for tuber starch content, tuber starch yield and tuber fresh weight with underlying genes of the carbohydrate metabolism were observed. Overlaps of DRYM QTL with metabolite QTL for ribitol or galactinol may indicate trade-offs between starch and compatible solute biosynthesis. Expression QTL confirmed the drought stress relevance of selected transcripts by overlaps with DRYM QTL. Bulked segregant analyses combined with next-generation sequencing (BSAseq) were used to identify mutations in genes under the DRYM QTL on linkage group 3. Future analyses of identified genes for drought tolerance will give a better insight into drought tolerance in potatoes.

Neural Representations in the Prefrontal Cortex Are Task Dependent for Scene Attributes But Not for Scene Categories.

Natural scenes deliver rich sensory information about the world. Decades of research has shown that the scene-selective network in the visual cortex represents various aspects of scenes. However, less is known about how such complex scene information is processed beyond the visual cortex, such as in the prefrontal cortex. It is also unknown how task context impacts the process of scene perception, modulating which scene content is represented in the brain. In this study, we investigate these questions using scene images from four natural scene categories, which also depict two types of scene attributes, temperature (warm or cold), and sound level (noisy or quiet). A group of healthy human subjects from both sexes participated in the present study using fMRI. In the study, participants viewed scene images under two different task conditions: temperature judgment and sound-level judgment. We analyzed how these scene attributes and categories are represented across the brain under these task conditions. Our findings show that scene attributes (temperature and sound level) are only represented in the brain when they are task relevant. However, scene categories are represented in the brain, in both the parahippocampal place area and the prefrontal cortex, regardless of task context. These findings suggest that the prefrontal cortex selectively represents scene content according to task demands, but this task selectivity depends on the types of scene content: task modulates neural representations of scene attributes but not of scene categories.SIGNIFICANCE STATEMENT Research has shown that visual scene information is processed in scene-selective regions in the occipital and temporal cortices. Here, we ask how scene content is processed and represented beyond the visual brain, in the prefrontal cortex (PFC). We show that both scene categories and scene attributes are represented in PFC, with interesting differences in task dependency: scene attributes are only represented in PFC when they are task relevant, but scene categories are represented in PFC regardless of the task context. Together, our work shows that scene information is processed beyond the visual cortex, and scene representation in PFC reflects how adaptively our minds extract relevant information from a scene.

Metabolomic markers and physiological adaptations for high phosphate utilization efficiency in rice.

Utilizing phosphate more efficiently is crucial for sustainable crop production. Highly efficient rice (Oryza sativa) cultivars have been identified and this study aims to identify metabolic markers associated with P utilization efficiency (PUE). P deficiency generally reduced leaf P concentrations and CO2 assimilation rates but efficient cultivars were reducing leaf P concentrations further than inefficient ones while maintaining similar CO2 assimilation rates. Adaptive changes in carbon metabolism were detected but equally in efficient and inefficient cultivar groups. Groups furthermore did not differ with respect to partial substitutions of phospholipids by sulfo- and galactolipids. Metabolites significantly more abundant in the efficient group, such as sinapate, benzoate and glucoronate, were related to antioxidant defence and may help alleviating oxidative stress caused by P deficiency. Sugar alcohols ribitol and threitol were another marker metabolite for higher phosphate efficiency as were several amino acids, especially threonine. Since these metabolites are not known to be associated with P deficiency, they may provide novel clues for the selection of more P efficient genotypes. In conclusion, metabolite signatures detected here were not related to phosphate metabolism but rather helped P efficient lines to keep vital processes functional under the adverse conditions of P starvation.

Modality-Independent Coding of Scene Categories in Prefrontal Cortex.

Natural environments convey information through multiple sensory modalities, all of which contribute to people's percepts. Although it has been shown that visual or auditory content of scene categories can be decoded from brain activity, it remains unclear how humans represent scene information beyond a specific sensory modality domain. To address this question, we investigated how categories of scene images and sounds are represented in several brain regions. A group of healthy human subjects (both sexes) participated in the present study, where their brain activity was measured with fMRI while viewing images or listening to sounds of different real-world environments. We found that both visual and auditory scene categories can be decoded not only from modality-specific areas, but also from several brain regions in the temporal, parietal, and prefrontal cortex (PFC). Intriguingly, only in the PFC, but not in any other regions, categories of scene images and sounds appear to be represented in similar activation patterns, suggesting that scene representations in PFC are modality-independent. Furthermore, the error patterns of neural decoders indicate that category-specific neural activity patterns in the middle and superior frontal gyri are tightly linked to categorization behavior. Our findings demonstrate that complex scene information is represented at an abstract level in the PFC, regardless of the sensory modality of the stimulus.SIGNIFICANCE STATEMENT Our experience in daily life includes multiple sensory inputs, such as images, sounds, or scents from the surroundings, which all contribute to our understanding of the environment. Here, for the first time, we investigated where and how in the brain information about the natural environment from multiple senses is merged to form modality-independent representations of scene categories. We show direct decoding of scene categories across sensory modalities from patterns of neural activity in the prefrontal cortex (PFC). We also conclusively tie these neural representations to human categorization behavior by comparing patterns of errors between a neural decoder and behavior. Our findings suggest that PFC is a central hub for integrating sensory information and computing modality-independent representations of scene categories.

Metabolite and transcript markers for the prediction of potato drought tolerance.

Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker-assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT-PCR and GC-MS profiling, respectively. Transcript marker candidates were selected from a published RNA-Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6% and 9%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions.

The drought response of potato reference cultivars with contrasting tolerance.

Systems responses to drought stress of four potato reference cultivars with differential drought tolerance (Solanum tuberosum L.) were investigated by metabolome profiling and RNA sequencing. Systems analysis was based on independent field and greenhouse trials. Robust differential drought responses across all cultivars under both conditions comprised changes of proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid and 102 transcript levels. The encoded genes contained a high proportion of heat shock proteins and proteins with signalling or regulatory functions, for example, a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant compared with the sensitive cultivars included arbutin, octopamine, ribitol and 248 transcripts. The gene products of many of these transcripts were pathogen response related, such as receptor kinases, or regulatory proteins, for example, a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply heat stress as a major acclimation component of potato leaves to long-term drought stress. Enhanced heat stress during drought can be caused by loss of transpiration cooling. This effect and CO2 limitation are the main consequences of drought-induced or abscisic acid-induced stomatal closure. Constitutive differences in metabolite and transcript levels between tolerant and sensitive cultivars indicate interactions of drought tolerance and pathogen resistance in potato.

Accurate quantification of more than 4000 mouse tissue proteins reveals minimal proteome changes during aging.

The biological process of aging is believed to be the result of an accumulation of cellular damage to biomolecules. Although there are numerous studies addressing mutation frequencies, morphological or transcriptional changes in aging mammalian tissues, few have measured global changes at the protein level. Here, we present an in depth proteomic analysis of three brain regions as well as heart and kidney in mice aged 5 or 26 months, using stable isotope labeling of whole animals (SILAC mouse) and high resolution mass spectrometry. In the frontal cortex and hippocampal regions of the brain, more than 4200 proteins were quantitatively compared between age groups. Proteome differences between individual mice were observable within and between age groups. However, mean protein abundance changes of more than twofold between young and old mice were detected in less than 1% of all proteins and very few of these were statistically significant. Similar outcomes were obtained when comparing cerebellum, heart, and kidney between age groups. Thus, unexpectedly, our results indicate that aging-related effects on the tissue proteome composition at the bulk level are only minor and that protein homeostasis remains functional up to a relatively high age.

Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing.

Comprehensive expression profiles of Arabidopsis (Arabidopsis thaliana) MIRNA genes and mature microRNAs (miRs) are currently not available. We established a quantitative real-time polymerase chain reaction platform that allows rapid and sensitive quantification of 177 Arabidopsis primary miR transcripts (pri-miRs). The platform was used to detect phosphorus (P) or nitrogen (N) status-responsive pri-miR species. Several pri-miR169 species as well as pri-miR398a were found to be repressed during N limitation, whereas during P limitation, pri-miR778, pri-miR827, and pri-miR399 species were induced and pri-miR398a was repressed. The corresponding responses of the biologically active, mature miRs were confirmed using specific stem-loop reverse transcription primer quantitative polymerase chain reaction assays and small RNA sequencing. Interestingly, the latter approach also revealed high abundance of some miR star strands. Bioinformatic analysis of small RNA sequences with a modified miRDeep algorithm led to the identification of the novel P limitation-induced miR2111, which is encoded by two loci in the Arabidopsis genome. Furthermore, miR2111, miR169, a miR827-like sequence, and the abundances of several miR star strands were found to be strongly dependent on P or N status in rapeseed (Brassica napus) phloem sap, flagging them as candidate systemic signals. Taken together, these results reveal the existence of complex small RNA-based regulatory networks mediating plant adaptation to mineral nutrient availability.

Heavy metals from the River Adayar, India: infiltration into the adjacent groundwater aquifer.

In the Adayar riverbed and its estuary 5 undisturbed sediment cores were drilled using a petrol-driven hammer. Cores of a depth of 4-5 m were sampled in 0.5 m steps. The distribution of heavy metals (Cr, Mn, Ni, Cu, Zn, Cd and Pb) in the top layers of fluvial and estuarine sediments indicates recent anthropogenic input: Revealing that the river acts as a sink for drainage from the residential and industrial zones. In this study, the mobilization of heavy metals into greater depths and their probable effects on the groundwater body are discussed. The high concentration of heavy metals and the influent character of the river Adayar allow the mobilization of metal ions and their transport into the deeper layers of the sediment. A changing environment due to effects such as saltwater intrusion and monsoon floods is the driving force for this phenomenon.