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Background: Sorghum , the C4 dry-land cereal, important for food, fodder, feed and fuel, is a model crop for abiotic stress tolerance with smaller genome size, genetic diversity, and bio-energy traits. The heat shock proteins/chaperonin 60s (HSP60/Cpn60s) assist the plastid proteins, and participate in the folding and aggregation of proteins. However, the functions of HSP60s in abiotic stress tolerance in Sorghum remain unclear., Methods: Genome-wide screening and in silico characterization of SbHSP60s were carried out along with tissue and stress-specific expression analysis., Results: A total of 36 HSP60 genes were identified in Sorghum bicolor . They were subdivided into 2 groups, the HSP60 and HSP10 co-chaperonins encoded by 30 and 6 genes, respectively. The genes are distributed on all the chromosomes, chromosome 1 being the hot spot with 9 genes. All the HSP60s were found hydrophilic and highly unstable. The HSP60 genes showed a large number of introns, the majority of them with more than 10. Among the 12 paralogs, only 1 was tandem and the remaining 11 segmental, indicating their role in the expansion of SbHSP60s . Majority of the SbHSP60 genes expressed uniformly in leaf while a moderate expression was observed in the root tissues, with the highest expression displayed by SbHSP60-1 . From expression analysis, SbHSP60-3 for drought, SbHSP60-9 for salt, SbHSP60-9 and 24 for heat and SbHSP60-3, 9 and SbHSP10-2 have been found implicated for cold stress tolerance and appeared as the key regulatory genes., Conclusion: This work paves the way for the utilization of chaperonin family genes for achieving abiotic stress tolerance in plants., (© 2021 Bentham Science Publishers.)

Invasive lobular carcinoma of the breast (ILC) is strongly estrogen-driven and represents a unique context for estrogen receptor (ER) signaling. In ILC, ER controls the expression of the Wnt ligand WNT4, which is critical for endocrine response and anti-estrogen resistance. However, signaling mediated by WNT4 is cell type- and tissue-specific, and has not been explored in ILC. We utilized reverse phase protein array (RPPA) to characterize ER and WNT4-driven signaling in ILC cells and identified that WNT4 mediates downstream mTOR signaling via phosphorylation of S6 Kinase. Additionally, ER and WNT4 control levels of MCL-1, which is associated with regulation of mitochondrial function. In this context, WNT4 knockdown led to decreased ATP production and increased mitochondrial fragmentation. WNT4 regulation of both mTOR signaling and MCL-1 were also observed in anti-estrogen resistant models of ILC. We identified that high WNT4 expression is associated with similar mTOR pathway activation in ILC and serous ovarian cancer tumors, suggesting that WNT4 signaling is active in multiple tumor types. The identified downstream pathways offer insight into WNT4 signaling and represent potential targets to overcome anti-estrogen resistance for patients with ILC.

Porcupine O- acyltransferase (PORCN) is considered essential for Wnt secretion and signaling. However, we observed that PORCN inhibition does not phenocopy the effects of WNT4 knockdown in WNT4-dependent breast cancer cells. This suggests a unique relationship between PORCN and WNT4 signaling. To examine the role of PORCN in WNT4 signaling, here we overexpressed WNT4 or WNT3A in breast cancer, ovarian cancer, and fibrosarcoma cell lines. Conditioned media from these lines and co-culture systems were used to assess the dependence of Wnt secretion and activity on the critical Wnt secretion proteins PORCN and Wnt ligand secretion (WLS) mediator. We observed that WLS is universally required for Wnt secretion and paracrine signaling. In contrast, the dependence of WNT3A secretion and activity on PORCN varied across the cell lines, and WNT4 secretion was PORCN-independent in all models. Surprisingly, WNT4 did not exhibit paracrine activity in any tested context. Absent the expected paracrine activity of secreted WNT4, we identified cell-autonomous Wnt signaling activation by WNT4 and WNT3A, independent of PORCN or Wnt secretion. The PORCN-independent, cell-autonomous Wnt signaling demonstrated here may be critical in WNT4-driven cellular contexts or in those that are considered to have dysfunctional Wnt signaling., (© 2019 Rao et al.)

A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or do not provide sufficient forecast skill to be useful. We developed an open collaborative forecasting challenge to assess probabilistic forecasts for seasonal epidemics of dengue, a major global public health problem. Sixteen teams used a variety of methods and data to generate forecasts for 3 epidemiological targets (peak incidence, the week of the peak, and total incidence) over 8 dengue seasons in Iquitos, Peru and San Juan, Puerto Rico. Forecast skill was highly variable across teams and targets. While numerous forecasts showed high skill for midseason situational awareness, early season skill was low, and skill was generally lowest for high incidence seasons, those for which forecasts would be most valuable. A comparison of modeling approaches revealed that average forecast skill was lower for models including biologically meaningful data and mechanisms and that both multimodel and multiteam ensemble forecasts consistently outperformed individual model forecasts. Leveraging these insights, data, and the forecasting framework will be critical to improve forecast skill and the application of forecasts in real time for epidemic preparedness and response. Moreover, key components of this project-integration with public health needs, a common forecasting framework, shared and standardized data, and open participation-can help advance infectious disease forecasting beyond dengue., Competing Interests: The authors declare no competing interest., (Copyright © 2019 the Author(s). Published by PNAS.)

Over the past two decades, colloidal particles with a variety of shapes, sizes, and compositions have been synthesized and characterized successfully. One of the most important applications for colloidal building blocks is to engineer functional structures as mechanical, electrical, and optical metamaterials. However, complex interaction dynamics between the building blocks as well as sophisticated structure-property relationships make it challenging to design structures with predictable target properties. In this paper, we implement an inverse material design framework using Genetic Algorithm (GA)-based techniques to streamline the design of colloidal structures based on target properties. We investigate spherical particles as well as colloidal molecules of different sizes and shapes and evaluate a Geometric Landscape Accessibility parameter that identifies the size of feasible domains within the geometric phase space of each structure. Considering target photonic properties, our GA-assisted framework is further utilized to identify sets of building blocks and structures that lead to various target values for the size of the photonic band gaps. The proposed framework in this study will provide new insight for predictive computational material design approaches and help establish more efficient ways of understanding structure-property relations in sub-micrometer-scale materials.

Background: Although cigarette smoking (CS) is by far the most important risk factor of chronic obstructive pulmonary disease (COPD), repeated and sustained infections are clearly linked to disease pathogenesis and are responsible for acute inflammatory flares (i.e. COPD exacerbations). We have previously identified Fatty Acid Binding Protein 5 (FABP5) as an important anti-inflammatory protein in primary airway epithelial cells., Results: In this study we found decreased FABP5 mRNA and protein levels in peripheral blood mononuclear cells (PBMCs) of COPD patients, especially among those who reported episodes of COPD exacerbations. Using wildtype (WT) and FABP5 -/- mice, we examined the effects of FABP5 on CS and infection-induced inflammatory responses. Similarly to what we saw in airway epithelial cells, infection increased FABP5 expression while CS decreased FABP5 expression in mouse lung tissues. CS-exposed and P. aeruginosa-infected FABP5 -/- mice had significantly increased inflammation as shown by increased lung histopathological score, cell infiltration and inflammatory cytokine levels. Restoration of FABP5 in alveolar macrophages using a lentiviral approach attenuated the CS- and bacteria-induced pulmonary inflammation. And finally, while P. aeruginosa infection increased PPARγ activity, CS or FABP5 knockdown greatly reduced PPARγ activity., Conclusions: These findings support a model in which CS-induced FABP5 inhibition contributes to increased inflammation in COPD exacerbations. It is interesting to speculate that the increased inflammation is a result of decreased PPARγ activity.

Late embryogenesis abundant (LEA) proteins, the space fillers or molecular shields, are the hydrophilic protective proteins which play an important role during plant development and abiotic stress. The systematic survey and characterization revealed a total of 68 LEA genes, belonging to 8 families in Sorghum bicolor. The LEA-2, a typical hydrophobic family is the most abundant family. All of them are evenly distributed on all 10 chromosomes and chromosomes 1, 2, and 3 appear to be the hot spots. Majority of the S. bicolor LEA (SbLEA) genes are intron less or have fewer introns. A total of 22 paralogous events were observed and majority of them appear to be segmental duplications. Segmental duplication played an important role in SbLEA-2 family expansion. A total of 12 orthologs were observed with Arabidopsis and 13 with Oryza sativa. Majority of them are basic in nature, and targeted by chloroplast subcellular localization. Fifteen miRNAs targeted to 25 SbLEAs appear to participate in development, as well as in abiotic stress tolerance. Promoter analysis revealed the presence of abiotic stress-responsive DRE, MYB, MYC, and GT1, biotic stress-responsive W-Box, hormone-responsive ABA, ERE, and TGA, and development-responsive SKn cis-elements. This reveals that LEA proteins play a vital role during stress tolerance and developmental processes. Using microarray data, 65 SbLEA genes were analyzed in different tissues (roots, pith, rind, internode, shoot, and leaf) which show clear tissue specific expression. qRT-PCR analysis of 23 SbLEA genes revealed their abundant expression in various tissues like roots, stems and leaves. Higher expression was noticed in stems compared to roots and leaves. Majority of the SbLEA family members were up-regulated at least in one tissue under different stress conditions. The SbLEA3-2 is the regulator, which showed abundant expression under diverse stress conditions. Present study provides new insights into the formation of LEAs in S. bicolor and to understand their role in developmental processes under stress conditions, which may be a valuable source for future research., Competing Interests: The authors have declared that no competing interests exist.

To investigate the role of fatty acid-binding protein 5 (FABP5) in infectious diseases, FABP5-deficient mice were challenged with Listeria monocytogenes, a facultative intracellular bacterial pathogen. Interestingly, FABP5-deficient animals were able to clear the infection within 3 days whereas control wild-type (WT) animals showed comparatively higher bacterial burdens in the liver and spleen. Sections of infected tissues showed an increase in inflammatory foci in WT mice compared to FABP5-deficient mice. FABP5-deficient mice had lower circulating inflammatory cytokines and increased inducible nitric oxide synthase production. FABP5-deficient mouse bone marrow-derived macrophages produced higher levels of nitrite anion than their WT counterparts in response to various stimuli. Additionally, in contrast to FABP5-/- mice, transgenic mice overexpressing FABP5 in myeloid cells (LysM-Cre driven) showed decreased survival rates and increased bacterial burden and inflammatory cytokines. Overall, these findings suggest that increased FABP5 levels correlate with a higher L. monocytogenes bacterial burden and elevated subsequent inflammation., (© 2019 The Author(s) Published by S. Karger AG, Basel.)

Trisomy 21 (Down Syndrome, DS) is the most common chromosomal anomaly. Although DS is mostly perceived as affecting cognitive abilities and cardiac health, individuals with DS also exhibit dysregulated immune functions. Levels of pro-inflammatory cytokines are increased, but intrinsic alterations of innate immunity are understudied in DS. Furthermore, elevated Reactive Oxygen Species (ROS) are well documented in individuals with DS, further exacerbating inflammatory processes. Chronic inflammation and oxidative stress are often precursors of subsequent tissue destruction and pathologies, which affect a majority of persons with DS. Together with ROS, the second messenger ion Ca 2+ plays a central role in immune regulation. TRPM2 (Transient Receptor Potential Melastatin 2) is a Ca 2+ -permeable ion channel that is activated under conditions of oxidative stress. The Trpm2 gene is located on human Chromosome 21 (Hsa21). TRPM2 is strongly represented in innate immune cells, and numerous studies have documented its role in modulating inflammation. We have previously found that as a result of suboptimal cytokine production, TRPM2 -/- mice are highly susceptible to the bacterial pathogen Listeria monocytogenes (Lm). We therefore used Lm infection to trigger and characterize immune responsiveness in the DS mouse model Dp10(yey), and to investigate the potential contribution of TRPM2. In comparison to wildtype (WT), Dp10(yey) mice show an increased resistance against Lm infection and higher IFNγ serum concentrations. Using a gene elimination approach, we show that these effects correlate with Trpm2 gene copy number, supporting the notion that Trpm2 might promote hyperinflammation in DS., (Copyright © 2017. Published by Elsevier B.V.)

Gene mapping of inherited ophthalmic diseases such as congenital cataracts, retinal degeneration, glaucoma, age-related macular degeneration, myopia, optic atrophy, and eye malformations has shed more light on the disease pathology, identified targets for research on therapeutics, earlier detection, and treatment options for disease management and patient care. This article details the different approaches to gene identification for both Mendelian and complex eye disorders.

A genome-wide scanning of Sorghum bicolor resulted in the identification of 25 SbHsf genes. Phylogenetic analysis shows the ortholog genes that are clustered with only rice, representing a common ancestor. Promoter analysis revealed the identification of different cis-acting elements that are responsible for abiotic as well as biotic stresses. Hsf domains like DBD, NLS, NES, and AHA have been analyzed for their sequence similarity and functional characterization. Tissue specific expression patterns of Hsfs in different tissues like mature embryo, seedling, root, and panicle were studied using real-time PCR. While Hsfs4 and 22 are highly expressed in panicle, 4 and 9 are expressed in seedlings. Sorghum plants were exposed to different abiotic stress treatments but no expression of any Hsf was observed when seedlings were treated with ABA. High level expression of Hsf1 was noticed during high temperature as well as cold stresses, 4 and 6 during salt and 5, 6, 10, 13, 19, 23 and 25 during drought stress. This comprehensive analysis of SbHsf genes will provide an insight on how these genes are regulated in different tissues and also under different abiotic stresses and help to determine the functions of Hsfs during drought and temperature stress tolerance.

Background: Intercontinental migratory waterfowl are the primary vectors for dispersion of H5N1 viruses and have been implicated in several zoonotic epidemics and pandemics. Recent investigations have established that with a single mutation, the virus gains the ability to transmit between humans. Consequently, there is a heightened urgency to identify innovative approaches to proactively mitigate emergent epidemics. Accordingly, a novel methodology combining temporo-geospatial epidemiology and phylogeographic analysis of viral strains is proposed to identify critical epicenters and epidemic pathways along with high risk candidate regions for increased surveillance., Results: Epidemiological analysis was used to identify 91,245 candidate global infection transmission pathways between 22 high risk waterfowl species. Dominant infection pathways (25,625 and 54,500 in summering and wintering zones) were identified through annotation using phylogeographical data computed from the phylogram of 2417 H5N1 HA isolates (from GISAID EpiFlu database). Annotation of infection pathways in turn delineated 23 influential clades out of 130 clades in the phylogram., Conclusions: The phylogeographic analyses provides strong cross-validation of epidemic pathways and identifies the dominant pathways for use in other epidemiological and prophylactic studies. The temporo-geospatial characteristics of infection transmission provides corroborating, but novel evidence for rapid genesis of H5N1 lineages in S.E. Asia. The proposed method pinpoints several regions, particularly in the southern hemisphere, as candidates for increased surveillance.

Objective: The aim was to assess the accuracy of three-dimensional anatomical reductions achieved by open method of treatment in cases of displaced unilateral mandibular subcondylar fractures using preoperative (pre op) and postoperative (post op) computed tomography (CT) scans., Materials and Methods: In this prospective study, 10 patients with unilateral sub condylar fractures confirmed by an orthopantomogram were included. A pre op and post op CT after 1 week of surgical procedure was taken in axial, coronal and sagittal plane along with three-dimensional reconstruction. Standard anatomical parameters, which undergo changes due to fractures of the mandibular condyle were measured in pre and post op CT scans in three planes and statistically analysed for the accuracy of the reduction comparing the following variables: (a) Pre op fractured and nonfractured side (b) post op fractured and nonfractured side (c) pre op fractured and post op fractured side. P < 0.05 was considered as significant., Results: Three-dimensional anatomical reduction was possible in 9 out of 10 cases (90%). The statistical analysis of each parameter in three variables revealed (P < 0.05) that there was a gross change in the dimensions of the parameters obtained in pre op fractured and nonfractured side. When these parameters were assessed in post op CT for the three variables there was no statistical difference between the post op fractured side and non fractured side. The same parameters were analysed for the three variables in pre op fractured and post op fractured side and found significant statistical difference suggesting a considerable change in the dimensions of the fractured side post operatively., Conclusion: The statistical and clinical results in our study emphasised that it is possible to fix the condyle in three-dimensional anatomical positions with open method of treatment and avoid post op degenerative joint changes. CT is the ideal imaging tool and should be used on a regular basis for cases of condylar fractures.

The chemopreventive effect of ethanol root extract of Indigofera aspalathoides was evaluated in N-nitrosodiethylamine-induced experimental liver tumor in mice. Pretreatment with ethanol root extract (100 mg/kg, p.o.) for three weeks significantly reduced the impact of N-nitrosodiethylamine toxicity (50 mg/kg, i.p.) on the serum markers of liver damage, aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase and total bilirubin. Protective effect was reconfirmed the elevated serum total protein levels were significantly restored towards normalization by the extracts, and this was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Histological examination of the liver of animals treated with ethanol root extract of Indigofera aspalathoides showed the reduction of necrosis. These results suggest that ethanol root extract of Indigofera aspalathoides possess protective effect against N-nitrosodiethylamine-induced hepatocellular carcinogenesis.

Alzheimer's disease (AD) is a devastative neurodegenerative disorder which needs adequate studies on effective treatment options. The extracts of plants and their effect on the amelioration of AD symptoms have been extensively studied. This paper summarizes the mechanisms like acetylcholinesterase (AChE) inhibition, modification of monoamines, antiamyloid aggregation effect, and antioxidant activity which are actively entailed in the process of amelioration of AD symptoms. These effects are induced by extracts of a few plants of different origin like Yizhi Jiannao, Moringa oleifera (Drumstick tree), Ginkgo Biloba (Ginkgo/Maidenhair tree), Cassia obtisufolia (Sicklepod), Desmodium gangeticum (Sal Leaved Desmodium), Melissa officinalis (Lemon Balm), and Salvia officinalis (Garden sage, common sage).

We present PEACE, a stand-alone tool for high-throughput ab initio clustering of transcript fragment sequences produced by Next Generation or Sanger Sequencing technologies. It is freely available from www.peace-tools.org. Installed and managed through a downloadable user-friendly graphical user interface (GUI), PEACE can process large data sets of transcript fragments of length 50 bases or greater, grouping the fragments by gene associations with a sensitivity comparable to leading clustering tools. Once clustered, the user can employ the GUI's analysis functions, facilitating the easy collection of statistics and allowing them to single out specific clusters for more comprehensive study or assembly. Using a novel minimum spanning tree-based clustering method, PEACE is the equal of leading tools in the literature, with an interface making it accessible to any user. It produces results of quality virtually identical to those of the WCD tool when applied to Sanger sequences, significantly improved results over WCD and TGICL when applied to the products of Next Generation Sequencing Technology and significantly improved results over Cap3 in both cases. In short, PEACE provides an intuitive GUI and a feature-rich, parallel clustering engine that proves to be a valuable addition to the leading cDNA clustering tools.

Background: Alzheimers disease (AD) is a devastative neurodegenerative disorder. Lack of substantial animal model that can unravel molecular underpinnings has been a major lacuna which limited the understanding of the etiology of the disease in turn limiting the employment of potential therapeutic strategies to combat the disease for a few decades. Our studies for the first time provided substantial animal model and tattered the etiology of the disease at a molecular level., Methods: In this study DNA was isolated from Hippocampus (H), Midbrain (M) and Frontal Cortex (Fc) of control and aluminium maltolate (Al-M) treated aged New Zealand rabbit brain. DNA damage has been studied using Agarose gel electrophoresis, Ethidium Bromide (EtBr) binding and Melting temperature techniques., Results: Al-M treated aged New Zealand rabbit's H and M showed higher DNA damage compared to corresponding controls, where as Fc showed mild DNA damage compared to corresponding controls., Conclusions: This study tangibly provides substantial molecular level understanding of the disease in turn providing an adequate platform to streamline potential therapeutic strategies., Keywords: Alzheimer's disease; Aluminium maltolate; Animal model; DNA damage.

RET/papillary thyroid carcinoma (RET/PTC) oncoproteins result from the in-frame fusion of the RET receptor tyrosine kinase domain with protein dimerization motifs encoded by heterologous genes. Here, we show that RET/PTC stimulates the beta-catenin pathway. By stimulating PI3K/AKT and Ras/extracellular signal-regulated kinase (ERK), RET/PTC promotes glycogen synthase kinase 3beta (GSK3beta) phosphorylation, thereby reducing GSK3beta-mediated NH(2)-terminal beta-catenin (Ser33/Ser37/Thr41) phosphorylation. In addition, RET/PTC physically interacts with beta-catenin and increases its phosphotyrosine content. The increased free pool of S/T(nonphospho)/Y(phospho)beta-catenin is stabilized as a result of the reduced binding affinity for the Axin/GSK3beta complex and activates the transcription factor T-cell factor/lymphoid enhancer factor. Moreover, through the ERK pathway, RET/PTC stimulates cyclic AMP-responsive element binding protein (CREB) phosphorylation and promotes the formation of a beta-catenin-CREB-CREB-binding protein/p300 transcriptional complex. Transcriptional complexes containing beta-catenin are recruited to the cyclin D1 promoter and a cyclin D1 gene promoter reporter is active in RET/PTC-expressing cells. Silencing of beta-catenin by small interfering RNA inhibits proliferation of RET/PTC-transformed PC Cl3 thyrocytes, whereas a constitutively active form of beta-catenin stimulates autonomous proliferation of thyroid cells. Thus, multiple signaling events downstream from RET/PTC converge on beta-catenin to stimulate cell proliferation.

Chromosome studies were conducted on 117 men with primary infertility (54 with oligospermia and 63 with azoospermia) and 25 fertile volunteers who acted as controls. No chromosomal abnormalities were observed except for nine cases of Klinefelter's syndrome. From this study, it is apparent that chromosomal abnormalities other than Klinefelter's syndrome are not etiologic factors in the infertility of oligo- or azoospermic men.