Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data

<p>Abstract</p> <p>Background</p> <p>Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes.</p> <p>Results</p> <p>By the use of two distinct algorithms, implemented by <it>geNorm </it>and <it>NormFinder</it>, we have assessed the gene expression of nine candidate reference genes in cotton: <it>GhACT4, GhEF1α5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhβTUB3 </it>and <it>GhUBQ14</it>. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of <it>GhPP2A1 </it>and <it>GhUBQ14 </it>genes were the most stable across all samples and also when distinct plants organs are examined. <it>GhACT4 </it>and <it>GhUBQ14 </it>present more stable expression during flower development, <it>GhACT4 </it>and <it>GhFBX6 </it>in the floral verticils and <it>GhMZA </it>and <it>GhPTB </it>during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development.</p> <p>Conclusion</p> <p>We have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of <it>GhUBQ14 </it>and <it>GhPP2A1 </it>housekeeping genes as superior references for normalization of gene expression measures in different cotton plant organs; <it>GhACT4 </it>and <it>GhUBQ14 </it>for flower development, <it>GhACT4 </it>and <it>GhFBX6 </it>for the floral organs and <it>GhMZA </it>and <it>GhPTB </it>for fruit development. We also provide the primer sequences whose performance in qPCR experiments is demonstrated. These genes will enable more accurate and reliable normalization of qPCR results for gene expression studies in this important crop, the major source of natural fiber and also an important source of edible oil. The use of bona fide reference genes allowed a detailed and accurate characterization of the temporal and spatial expression pattern of two MADS-box genes in cotton.</p

Aspects of holography for theories with hyperscaling violation

We analyze various aspects of the recently proposed holographic theories with general dynamical critical exponent z and hyperscaling violation exponent $\theta$. We first find the basic constraints on $z, \theta$ from the gravity side, and compute the stress-energy tensor expectation values and scalar two-point functions. Massive correlators exhibit a nontrivial exponential behavior at long distances, controlled by $\theta$. At short distance, the two-point functions become power-law, with a universal form for $\theta > 0$. Next, the calculation of the holographic entanglement entropy reveals the existence of novel phases which violate the area law. The entropy in these phases has a behavior that interpolates between that of a Fermi surface and that exhibited by systems with extensive entanglement entropy. Finally, we describe microscopic embeddings of some $\theta \neq 0$ metrics into full string theory models -- these metrics characterize large regions of the parameter space of Dp-brane metrics for $p\neq 3$. For instance, the theory of N D2-branes in IIA supergravity has z=1 and $\theta = -1/3$ over a wide range of scales, at large $g_s N$.Comment: 35 pages; v2: new references added; v3: proper reference [14] added; v4: minor clarification

Egg development, hatching rhythm and moult patterns in Paralomos spinosissima (Decapoda: Anomura: Paguroidea: Lithodidae) from South Georgia waters (Southern Ocean)

Larval release, hatching rhythms and moult patterns were examined in a captive population of the subantarctic lithodid, Paralomis spinosissima from the South Georgia and Shag Rocks region. Larvae hatched throughout the year with the majority of females starting to release larvae at the end of the austral summer and beginning of autumn. Larval release continued over a period of up to 9 weeks with high variability in the numbers that hatched each day. A similar seasonal pattern to hatching was evident in the moulting of females. Intermoult period for two adult females (CL = 63 and 85 mm) ranged from 894 to 1,120 days while an intermoult period for males was estimated to be in excess of 832 days. The results are consistent with other species of Paralomis and are discussed in relation to physiological and environmental adaptations to the cold-water conditions south of the Antarctic Convergence

Identification of furfural resistant strains of Saccharomyces cerevisiae and Saccharomyces paradoxus from a collection of environmental and industrial isolates

Background Fermentation of bioethanol using lignocellulosic biomass as a raw material provides a sustainable alternative to current biofuel production methods by utilising waste food streams as raw material. Before lignocellulose can be fermented it requires physical, chemical and enzymatic treatment in order to release monosaccharides, a process that causes the chemical transformation of glucose and xylose into the cyclic aldehydes furfural and hydroxyfurfural. These furan compounds are potent inhibitors of Saccharomyces fermentation, and consequently furfural tolerant strains of Saccharomyces are required for lignocellulosic fermentation. Results This study investigated yeast tolerance to furfural and hydroxyfurfural using a collection of 71 environmental and industrial isolates of the baker’s yeast Saccharomyces cerevisiae and its closest relative Saccharomyces paradoxus. The Saccharomyces strains were initially screened for growth on media containing 100 mM glucose and 1.5 mg ml-1 furfural. Five strains were identified that showed a significant tolerance to growth in the presence of furfural and these were then screened for growth and ethanol production in the presence of increasing amounts (0.1-4 mg ml-1) of furfural. Conclusions Of the five furfural tolerant strains S. cerevisiae NCYC 3451 displayed the greatest furfural resistance, and was able to grow in the presence of up to 3.0 mg ml-1 furfural. Furthermore, ethanol production in this strain did not appear to be inhibited by furfural, with the highest ethanol yield observed at 3.0 mg ml-1 furfural. Although furfural resistance was not found to be a trait specific to any one particular lineage or population, three of the strains were isolated from environments where they might be continually exposed to low levels of furfural through the on-going natural degradation of lignocelluloses, and would therefore develop elevated levels of resistance to these furan compounds. Thus these strains represent good candidates for future studies of genetic variation relevant to understanding and manipulating furfural resistance and in the development of tolerant ethanologenic yeast strains for use in bioethanol production from lignocellulose processing

Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting

We present an analytical method to quantify clustering in super-resolution localization images of static surfaces in two dimensions. The method also describes how over-counting of labeled molecules contributes to apparent self-clustering and how the effective lateral resolution of an image can be determined. This treatment applies to clustering of proteins and lipids in membranes, where there is significant interest in using super-resolution localization techniques to probe membrane heterogeneity. When images are quantified using pair correlation functions, the magnitude of apparent clustering due to over-counting will vary inversely with the surface density of labeled molecules and does not depend on the number of times an average molecule is counted. Over-counting does not yield apparent co-clustering in double label experiments when pair cross-correlation functions are measured. We apply our analytical method to quantify the distribution of the IgE receptor (Fc{\epsilon}RI) on the plasma membranes of chemically fixed RBL-2H3 mast cells from images acquired using stochastic optical reconstruction microscopy (STORM) and scanning electron microscopy (SEM). We find that apparent clustering of labeled IgE bound to Fc{\epsilon}RI detected with both methods arises from over-counting of individual complexes. Thus our results indicate that these receptors are randomly distributed within the resolution and sensitivity limits of these experiments.Comment: 22 pages, 5 figure

The Role of Islamic Psychospiritual in Building Self-Resilience of Cancer Caregivers

The global community is increasingly recognizing the integration of health science with religion and spirituality. In Malaysia, the field of Islamic psychospiritual science, which combines psychology with spirituality and Islamic teachings, has garnered significant research attention, particularly in addressing the challenges faced by cancer caregivers. These caregivers, often referred to as "hidden patients," experience a range of difficulties including physical, emotional, spiritual, social, and financial burdens that adversely affect their quality of life. However, society tends to prioritize the health and well-being of the patients over that of the caregivers. In reality, caregivers place the needs of the patients above their own in all aspects. Spiritual, religious, and emotional distress are prevalent concerns for both patients and caregivers during the crisis of cancer, which is often associated with mortality. Hence, the objective of this article is to explore the role of Islamic psychospiritual knowledge in supporting cancer caregivers, specifically in addressing their spiritual, religious, and emotional well-being. The data collection process utilizes library methods based on key findings from previous studies, while data analysis is conducted using a thematic analysis approach. The findings of this study indicate that religious aspects emphasized in Islamic psychospiritual disciplines can enhance caregivers' resilience in effectively managing various cancer-related challenges, thereby improving their overall quality of life. Hence, the significance of the spiritual and religious dimension, which acts as a protective factor, should not be disregarded. Lastly, this article proposes the provision of spiritual and religious educational materials within medical settings as valuable resources for cancer caregivers to reinforce their own well-being

Evaluating the potential for the environmentally sustainable control of foot and mouth disease in Sub-Saharan Africa

Strategies to control transboundary diseases have in the past generated unintended negative consequences for both the environment and local human populations. Integrating perspectives from across disciplines, including livestock, veterinary and conservation sectors, is necessary for identifying disease control strategies that optimise environmental goods and services at the wildlife-livestock interface. Prompted by the recent development of a global strategy for the control and elimination of foot-and-mouth disease (FMD), this paper seeks insight into the consequences of, and rational options for potential FMD control measures in relation to environmental, conservation and human poverty considerations in Africa. We suggest a more environmentally nuanced process of FMD control that safe-guards the integrity of wild populations and the ecosystem dynamics on which human livelihoods depend while simultaneously improving socio-economic conditions of rural people. In particular, we outline five major issues that need to be considered: 1) improved understanding of the different FMD viral strains and how they circulate between domestic and wildlife populations; 2) an appreciation for the economic value of wildlife for many African countries whose presence might preclude the country from ever achieving an FMD-free status; 3) exploring ways in which livestock production can be improved without compromising wildlife such as implementing commodity-based trading schemes; 4) introducing a participatory approach involving local farmers and the national veterinary services in the control of FMD; and 5) finally the possibility that transfrontier conservation might offer new hope of integrating decision-making at the wildlife-livestock interface

Quantifying the burden of rhodesiense sleeping sickness in Urambo district, Tanzania

Sleeping sickness (human African trypanosomiasis - HAT) is a disease transmitted by tsetse flies and is always fatal if left untreated. The disease occurs in foci affecting poor communities with limited access to health service provision and as such the disease is often left undiagnosed, mistaken for more common afflictions. Even if diagnosed, sleeping sickness is costly to treat, both for health services and patients and their families in terms of costs of diagnosis, transport, hospital care, and the prolonged period of convalescence. Here we estimate the health burden of the acute form T. b. rhodesiense sleeping sickness in Urambo District, Tanzania in terms of Disability Adjusted Life Years (DALYs), the yardstick commonly used by policy makers to prioritize disease management practices, representing a year of healthy life lost to disease. In this single district, the burden of the disease over one year was estimated at 979 DALYs and the estimated monetary costs to health services for the 143 treated patients at US$11,841 and to the patients themselves at US$ 3,673 for direct medical costs and US$ 9,781 for indirect non-medical costs. Sleeping sickness thus places a considerable burden on the affected rural communities and health services

Cardiorespiratory fitness is associated with hard and light intensity physical activity but not time spent sedentary in 10–14 year old schoolchildren: the HAPPY study

Sedentary behaviour is a major risk factor for developing chronic diseases and is associated with low cardiorespiratory fitness in adults. It remains unclear how sedentary behaviour and different physical activity subcomponents are related to cardiorespiratory fitness in children. The purpose of this study was to assess how sedentary behaviour and different physical activity subcomponents are associated with 10–14 year-old schoolchildren's cardiorespiratory fitness