Splicing and alternative splicing in rice and humans

Rice is a monocot gramineous crop, and one of the most important staple foods. Rice is considered a model species for most gramineous crops. Extensive research on rice has provided critical guidance for other crops, such as maize and wheat. In recent years, climate change and exacerbated soil degradation have resulted in a variety of abiotic stresses, such as greenhouse effects, lower temperatures, drought, floods, soil salinization and heavy metal pollution. As such, there is an extremely high demand for additional research, in order to address these negative factors. Studies have shown that the alternative splicing of many genes in rice is affected by stress conditions, suggesting that manipulation of the alternative splicing of specific genes may be an effective approach for rice to adapt to abiotic stress. With the advancement of microarrays, and more recently, next generation sequencing technology, several studies have shown that more than half of the genes in the rice genome undergo alternative splicing. This mini-review summarizes the latest progress in the research of splicing and alternative splicing in rice, compared to splicing in humans. Furthermore, we discuss how additional studies may change the landscape of investigation of rice functional genomics and genetically improved rice. [BMB Reports 2013; 46(9): 439-447]     

Vicariance and endemism in a Neotropical savanna hotspot: distribution patterns of Cerrado squamate reptiles

Aim To test predictions of the vicariance model, to define basic biogeographical units for Cerrado squamates, and to discuss previous biogeographical hypotheses. Location Cerrado; South American savannas south of the Amazon, extending across central Brazil, with marginal areas in Bolivia and Paraguay and isolated relictual enclaves in adjacent regions. Methods We compiled species occurrence records via field sampling and revision of museum specimens and taxonomic literature. All species were mapped according to georeferenced locality records, and classified as (1) endemic or non‐endemic, (2) typical of plateaus or depressions, and (3) typical of open or forested habitats. We tested predictions of the vicariance model using biotic element analysis, searching for non‐random clusters of species ranges. Spatial congruence of biotic elements was compared with putative areas of endemism revealed by sympatric restricted‐range species. Effects of topographical and vegetational mosaics on distribution patterns were studied according to species composition in biotic elements and areas of endemism. Results We recorded 267 Cerrado squamates, of which 103 (39%) are endemics, including 20 amphisbaenians (61% endemism), 32 lizards (42%) and 51 snakes (32%). Distribution patterns corroborated predictions of the vicariance model, revealing groups of species with significantly clustered ranges. An analysis of endemic species recovered seven biotic elements, corroborating results including non‐endemics. Sympatric restricted‐range taxa delimited 10 putative areas of endemism, largely coincident with core areas of biotic elements detected with endemic taxa. Distribution patterns were associated with major topographical and vegetational divisions of the Cerrado. Endemism prevailed in open, elevated plateaus, whereas faunal interchange, mostly associated with forest habitats, was more common in peripheral depressions. Main conclusions Our results indicate that vicariant speciation has strongly shaped Cerrado squamate diversity, in contrast to earlier studies emphasizing faunal interchange and low endemism in the Cerrado vertebrate fauna. Levels of squamate endemism are higher than in any other Cerrado vertebrate group. The high number of recovered endemics revealed previously undetected areas of evolutionary relevance, indicating that biogeographical patterns in the Cerrado were poorly represented in previous analyses. Although still largely undocumented, effects of vicariant speciation may be prevalent in a large fraction of Cerrado and Neotropical biodiversity.     

Trace elements in children with autism spectrum disorder: A meta-analysis based on case-control studies

Autism spectrum disorder (ASD) is a common childhood neurodevelopmental disorder that may be related to trace elements. However, reports on the relationship between them are still inconsistent. In this article, we conducted a meta-analysis on this issue. We searched the PubMed, EMBASE, and Cochrane databases as of November 15, 2019. A random-effects model was used, and subgroups of studies were analyzed using samples of different measurements. Twenty-two original articles were identified (18 trace elements, including a total of 1014 children with ASD and 999 healthy controls). In autistic children, the overall levels of barium (Ba), mercury (Hg), lithium (Li), and lead (Pb) were higher. There were significant differences in the levels of copper (Cu) in the hair and serum between autistic children and the control group. The levels of Hg, Li, Pb and selenium (Se) in the hair of autistic children were higher than those of healthy children, while the levels of zinc (Zn) in the blood were lower. Excessive exposure to toxic heavy metals and inadequate intake of essential metal elements may be associated with ASD. Preventing excessive exposure to toxic metals and correcting poor dietary behaviors may be beneficial for the prevention and treatment of the disease.     

Trace elements under the spotlight: A powerful nutritional tool in cancer

Cancer is the second leading cause of death worldwide. Research on the relationships between trace elements (TE) and the development of cancer or its prevention is a field that is gaining increasing relevance. This review provides an evaluation of the effects of TE (As, Al, B, Cd, Cr, Cu, F, I, Pb, Li, Mn, Hg, Mo, Ni, Se, Si, Sn, V and Zn) intake and supplementation in cancer risk and prevention, as well as their interactions with oncology treatments. Advancements in the knowledge of TE, their dietary interactions and their main food sources can provide patients with choices that will help them to improve their quality of life and therapy outcomes. This approach could open new opportunities for treatments based on the integration of conventional therapies (chemotherapy, radiotherapy, and immunotherapy) and dietary interventions that provide advanced personalized treatments.     

Recombination of repeat elements generates somatic complexity in human genomes

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A structured analysis of risk to important wildlife elements in three Australian Wildlife Conservancy sanctuaries

Where data and information are lacking, structured expert risk assessments can provide a powerful tool to progress natural resource planning. In many situations, practitioners make informal assessments of risk within small groups that typically constitute employees. In this study, we report on three small (in terms of experts) structured expert‐based risk assessment case studies conducted by expert employees of a not‐for‐profit organisation (Australian Wildlife Conservancy) to demonstrate the utility of the approach. The case studies were carried out for three wildlife sanctuaries managed by AWC: Faure Island, Karakamia and Paruna. The likelihood that a set of direct risk factors would cause management failure for sets of important wildlife elements in the three sanctuaries was elicited from the small group of ecological experts. The analysis was couched in terms of a management aim to not lose species from each wildlife element over the management period of 25 years with current management. The experts believed, in particular, that increasing temperature and decreasing water availability associated with climate change were likely to impact significantly upon the vegetation elements and water‐reliant fauna associated with the sanctuaries. Some vegetation elements were also thought likely to be at risk of over‐grazing, unsuitable fire regimes and, in some cases, disease. In addition to predation by exotic predators at one sanctuary, the experts identified additional direct risk factors for various fauna elements associated with expected changes to the vegetation elements, including reduction in food availability, nesting habitat, and generally important life media. From the risk analyses, a preliminary conceptual model was developed to underpin monitoring and to indicate areas for possible management intervention and research. The case studies demonstrate that even in a small workplace team, structured risk assessments can be efficiently accomplished and can provide expedient and transparent information that effectively captures and aggregates the views of the experts.     

Bacterial isolates harboring antibiotics and heavy-metal resistance genes co-existing with mobile genetic elements in natural aquatic water bodies

The rise in antibiotic-resistant bacteria and contamination of water bodies is a serious issue that demands immense attention of scientific acumen. Here, we examined the pervasiveness of ESBL producing bacteria in Dal Lake and Wular Lake of Kashmir valley, India. Isolates were screened for antibiotic, heavy metal resistant elements, and their coexistence with mobile genetic elements. Out of two hundred one isolates screened, thirty-eight were found positive for ESBL production. Antibiotic profiling of ESBL positive isolates with 16 different drugs representing β-lactam or -non-β-lactam, exhibited multidrug resistance phenotype among 55% isolates. Molecular characterization revealed the occurrence of drug resistance determinants blaTEM, AmpC, qnrS, and heavy metal resistance genes (MRGs) merB, merP, merT, silE, silP, silS, and arsC. Furthermore, mobile genetic elements IntI, SulI, ISecp1, TN3, TN21 were also detected. Conjugation assay confirmed the transfer of different ARGs, HMRGs, and mobile elements in recipient Escherichia coli J53 AZ^R strain. Plasmid incompatibility studies showed blaTEM to be associated with Inc groups B/O, HI1, HI2, I1, N, FIA, and FIB. Co-occurrence of blaTEM, HMRGs, and mobile elements from the aquatic milieu of Kashmir, India has not been reported so far. From this study, the detection of the blaTEM gene in the bacteria Bacillus simplex and Brevibacterium frigoritolerans are found for the first time. Considering all the facts it becomes crucial to conduct studies in natural aquatic environments that could help depict the epidemiological situations in which the resistance mechanism might have clinical relevance.     

Exploring the role of copper and selenium in the maintenance of normal thyroid function among healthy Koreans

BackgroundSelenium and iodine are trace elements well known to have important roles in the synthesis and metabolism of thyroid hormones. However, the effects of other trace elements on thyroid hormones are still inconclusive. We investigated the association between several trace elements and thyroid hormones.MethodsThe data of 448 subjects who were measured for both, trace elements and TSH/free T4, at the Heath Checkup Center were retrospectively reviewed. The presence of thyroiditis (from thyroid echogenicity) and thyroid nodules were reviewed in the subjects who underwent thyroid ultrasonography.ResultsBlood concentrations of manganese, copper, selenium, and molybdenum were associated with TSH or free T4. After adjusting for age, sex, BMI, smoking, and alcohol consumption, blood copper levels were positively associated with free T4 in both sexes and selenium levels were positively associated with free T4 in women. There was no association between trace elements and thyroiditis. Blood copper concentration had a weak non-linear association with the presence of thyroid nodules.ConclusionsThis study demonstrated that blood concentrations of copper and selenium were significantly associated with free T4 in healthy Korean subjects with sufficient iodine intake suggesting their role in maintaining normal thyroid function.     

解磷菌对设施土壤金属元素有效含量及黄瓜秧苗金属元素吸收量的影响

通过向设施土壤中添加解磷菌和秸秆,达到活化土壤中作物所需金属元素的含量,促进作物对中微量元素吸收的目的。试验设置对照、秸秆、解磷菌、解磷菌+秸秆4个处理,在不同时间测试土壤及秧苗中钙、镁、铜、铁、锌等的含量,确定解磷菌及秸秆对设施土壤金属元素含量及黄瓜秧苗吸收量的影响。试验结果表明,秸秆、解磷菌、秸秆+解磷菌处理能明显增加黄瓜秧苗吸收钙、镁、铁、铜的能力,对锌的吸收没有影响,其中秸秆+解磷菌处理对黄瓜秧苗吸收钙、镁、铜影响最大,促进作用分别达到6.26%、8.25%和11.57%,3种处理对设施土壤中有效钙、镁、铁的含量没有影响,但是能明显提高土壤中有效铜、锌的含量,盛果后期有效铜含量分别比对照提高12.19%、15.41%、16.49%,盛果后期有效锌含量分别比对照区提高38.8%、33.26%、56.81%。     

Roadsides provide refuge for orchids: characteristic of the surrounding landscape

Seminatural habitats are declining throughout the world; thus, the role of small anthropogenic habitats in the preservation of plants is becoming increasingly appreciated. Here, we surveyed the orchid flora of roadside verges in five Central European countries (Austria, Hungary, Romania, Slovakia, and Slovenia) and tested how the surrounding landscape matrix affects the overall number of species and individuals, and also different functional groups of orchids. We found more than 2,000 individuals of 27 orchid species during our surveys. According to our results, the increasing coverage of agricultural and urban areas negatively affects both the number of orchid species and individuals on roadsides. Our study further suggests that differences in the surrounding habitats affect which species are found on roadsides, since the increasing coverage of grasslands or forested areas around orchid occurrences had a significant positive effect on the number of grassland or forest‐dwelling species and individuals, respectively. Most variance in orchid numerosity and diversity was explained by the cover of the suitable habitat types of the respective taxa in the surrounding landscape of the sampling points. This highlights the importance of roadsides acting as refugia for numerous species and valuable plant communities as well as in supporting biodiversity in general.