We found 33, 17, and 20 Alba genes in Gossypium hirsutum, Gossypium arboretum, and Gossypium raimondii, respectively. The Alba protein lengths ranged from 62 to 312 aa, the molecular weight (MW) from 7.003 to 34.55 kDa, grand average hydropathy values of -1.012 to 0.609 and isoelectric (pI) values of -3 to 11. Moreover, miRNAs such as gra-miR8770 targeted four genes, gra-miR8752 and gra-miR8666 targeted three genes, and each and gra-miR8657 a, b, c, d, e targeted 10 genes each, while the rests targeted 1 to 2 genes each. Similarly, various cis-regulatory elements were detected with significant roles in enhancing abiotic stress tolerance, such as CBFHV (RYCGAC) with a role in cold stress acclimation among others. Two genes, Gh_D01G0884 and Gh_D01G0922, were found to be highly induced under water deficit and salt stress conditions. Through virus-induced gene silencing (VIGS), the VIGS cotton plants were found to be highly susceptible to both water deficit and salt stresses; the VIGS plants exhibited a significant reduction in root growth, low cell membrane stability (CMS), saturated leaf weight (SLW), chlorophyll content levels, and higher excised leaf water loss (ELWL). Furthermore, the stress-responsive genes and ROS scavenging enzymes were significantly reduced in the VIGS plants compared to either the wild type (WT) and or the positively controlled plants. The VIGS plants registered higher concentration levels of hydrogen peroxide and malondialdehyde, with significantly lower levels of the various antioxidants evaluated an indication that the VIGS plants were highly affected by salt and drought stresses. This result provides a key foundation for future exploration of the Alba proteins in relation to abiotic stress.

Case-control genetic association studies are often used to examine the role of the genetic basis in complex diseases, such as cancer and neurodegenerative diseases. The role of the genetic basis might vary by nongenetic (environmental) measures, what is traditionally defined as gene-environment interactions (G×E). A commonly overlooked complication is that the set of clinically diagnosed cases might be contaminated by a subset with a nuisance pathologic state that presents with the same symptoms as the pathologic state of interest. The genetic basis of the pathologic state of interest might differ from that of the nuisance pathologic state. Often, frequencies of the pathologically defined states within the clinically diagnosed set of cases vary by the environment. We derive a simple and general approximation to bias in G×E parameter estimates when the presence of the nuisance pathologic state is ignored. We then perform extensive simulation studies to show that ignoring the presence of the nuisance pathologic state can result in substantial bias in G×E estimates and that the approximation we derived is reasonably accurate in finite samples. We demonstrate the applicability of the proposed approximation in a study of Alzheimer's disease.

More than 98% of the human genome does not encode proteins, and the vast majority of the noncoding regions have not been well studied. Some of these regions contain enhancers and functional non-coding RNAs. Previous research suggested that enhancer transcripts could be potent independent indicators of enhancer activity, and some enhancer lncRNAs (elncRNAs) have been proven to play critical roles in gene regulation. Here, we identified enhancer-promoter interactions from high-throughput chromosome conformation capture (Hi-C) data. We found that elncRNAs were highly enriched surrounding chromatin loop anchors. Additionally, the interaction frequency of elncRNA-associated enhancer-promoter pairs was significantly higher than the interaction frequency of other enhancer-promoter pairs, suggesting that elncRNAs may reinforce the interactions between enhancers and promoters. We also found that elncRNA expression levels were positively correlated with the interaction frequency of enhancer-promoter pairs. The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer-promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer-promoter pairs. Interestingly, G-quadruplexes were found to potentially mediate some enhancer-promoter interaction pairs, and the interaction frequency of these pairs was significantly higher than that of other enhancer-promoter pairs. We also found that the G-quadruplexes on enhancers were highly related to the expression of elncRNAs. G-quadruplexes located in the promoters of elncRNAs led to high expression of elncRNAs, whereas G-quadruplexes located in the gene bodies of elncRNAs generally resulted in low expression of elncRNAs.

Mitogen-activated protein kinases (MAPKs) play a regulatory role and influence various biological activities, such as cell proliferation, differentiation, and survival. Our group has demonstrated through functional studies that Schistosoma mansoni c-Jun N-terminal kinase (SmJNK) MAPK is involved in the parasite's development, reproduction, and survival. SmJNK can, therefore, be considered a potential target for the development of new drugs. Considering the importance of SmJNK in S. mansoni maturation, we aimed at understanding of SmJNK regulated signaling pathways in the parasite, correlating expression data with S. mansoni development. To better understand the role of SmJNK in S. mansoni intravertebrate host life stages, RNA interference knockdown was performed in adult worms and in schistosomula larval stage. SmJNK knocked-down in adult worms showed a decrease in oviposition and no significant alteration in their movement. RNASeq libraries of SmJNK knockdown schistosomula were sequenced. A total of 495 differentially expressed genes were observed in the SmJNK knockdown parasites, of which 373 were down-regulated and 122 up-regulated. Among the down-regulated genes, we found transcripts related to protein folding, purine nucleotide metabolism, the structural composition of ribosomes and cytoskeleton. Genes coding for proteins that bind to nucleic acids and proteins involved in the phagosome and spliceosome pathways were enriched. Additionally, we found that SmJNK and Smp38 MAPK signaling pathways converge regulating the expression of a large set of genes. C. elegans orthologous genes were enriched for genes related to sterility and oocyte maturation, corroborating the observed phenotype alteration. This work allowed an in-depth analysis of the SmJNK signaling pathway, elucidating gene targets of regulation and functional roles of this critical kinase for parasite maturation.

Tree aging is a new research area and has attracted research interest in recent years. Trees show extraordinary longevity; Platycladus orientalis L. (Cupressaceae) has a lifespan of thousands of years. Ancient trees are precious historical heritage and scientific research materials. However, tree aging and tree senescence have different definitions and are poorly understood. Since leaves are the most sensitive organ of a tree, we studied the structural response of leaves to tree age. Experiments investigating the leaf morphological structure, anatomical structure and ultrastructure were conducted in healthy P. orientalis at three different ages (ancient trees >2,000 years, 200 years < middle-aged trees <500 years, young trees <50 years) at the world's largest planted pure forest in the Mausoleum of the Yellow Emperor, Shaanxi Province, China. Interestingly, tree age did not significantly impact leaf cellular structure. Ancient P. orientalis trees in forests older than 2,000 years still have very strong vitality, and their leaves still maintained a perfect anatomical structure and ultrastructure. Our observations provide new evidence for the unique pattern of tree aging, especially healthy aging. Understanding the relationships between leaf structure and tree age will enhance the understanding of tree aging.

There is growing interest within regulatory agencies and toxicological research communities to develop, test, and apply new approaches, such as toxicogenomics, to more efficiently evaluate chemical hazards. Given the complexity of analyzing thousands of genes simultaneously, there is a need to identify reduced gene sets. Though several gene sets have been defined for toxicological applications, few of these were purposefully derived using toxicogenomics data. Here, we developed and applied a systematic approach to identify 1,000 genes (called Toxicogenomics-1000 or T1000) highly responsive to chemical exposures. First, a co-expression network of 11,210 genes was built by leveraging microarray data from the Open TG-GATEs program. This network was then re-weighted based on prior knowledge of their biological (KEGG, MSigDB) and toxicological (CTD) relevance. Finally, weighted correlation network analysis was applied to identify 258 gene clusters. T1000 was defined by selecting genes from each cluster that were most associated with outcome measures. For model evaluation, we compared the performance of T1000 to that of other gene sets (L1000, S1500, Genes selected by Limma, and random set) using two external datasets based on the rat model. Additionally, a smaller (T384) and a larger version (T1500) of T1000 were used for dose-response modeling to test the effect of gene set size. Our findings demonstrated that the T1000 gene set is predictive of apical outcomes across a range of conditions (e.g., in vitro and in vivo, dose-response, multiple species, tissues, and chemicals), and generally performs as well, or better than other gene sets available.

The number of people suffering from eye fatigue induced by visual display terminal (VDT) viewing is expected to increase in the modern world. Eye dysfunction is suggested to induce a decrease in cognitive function, at least in the long term. Furthermore, considering other previous findings, it may be reasonable to think that acute or relatively short-term eye dysfunction attenuates cognitive function for not only older but also young individuals. Hence, clarification of the effect of eye fatigue induced by VDT viewing on cognitive performance is essential in order to maintain and/or improve our quality of life in the modern world regardless of age. The present study investigated the effect of eye fatigue induced by 1-h VDT viewing on cognitive performance, to test the hypothesis that such eye fatigue impairs cognitive performance in young individuals. A total of 19 healthy female university students voluntarily participated in this study. Before and after the 1-h VDT viewing or resting, the degree of eye fatigue and cognitive performance were evaluated. Refractive error measurement was performed to assess the degree of eye fatigue using a binocular auto refractometer, and a memory recognition task and Go/NoGo task were used to estimate cognitive performance. Response accuracy and reaction time were evaluated in the two tasks. Due to difficulty in interpreting the data of refractive error for one participant from the perspective of eye fatigue, the data for 18 participants were used for further analysis. The refractive error was significantly lower after than before the VDT viewing, but a corresponding change was not found before and after resting. Regarding cognitive performance, only the reaction time in the memory recognition task varied with the VDT viewing or resting. The reaction time was significantly longer after than before resting, without a corresponding difference before and after the VDT viewing. Thus, the 1-h VDT viewing induced eye fatigue, but relatively improved rather than attenuated reaction time in the memory recognition task. These results suggest that the effect of the increase in arousal level induced by the present VDT viewing on memory recognition compensated for the negative effect of 1-h resting of the eyes. We conclude that the acute eye fatigue induced by the 1-h VDT viewing does not have detrimental effects on cognition in young females at least under the present conditions.

The immune environment in primary tumor has a profound impact on immunotherapy. However, the clinical relevance of immune environment in hepatocellular carcinoma (HCC) is largely unknown. Here, the immune profile and its clinical response in HCC were investigated. The gene expression profiles of 569 HCCs from three cohorts (The Cancer Genome Atlas, TCGA, n = 257; Gene Expression Omnibus, GEO, n = 170; International Cancer Genome Consortium, ICGC, n = 142) were used in the current study. Five gene expression subtypes (C1-C5) responsible for global immune genes were identified in HCCs at stage I/II. It was found that subtype C4 was associated with upregulation and subtype C5 was associated with downregulation of immune profiles in most metagenes. Immune-correlation analysis of the five subtypes demonstrated that C3 and C4 had higher immune score and better prognostic outcome, as compared with other subtypes. Moreover, the mutation frequencies of TP53, CTNNB1, and AXIN1 had significant difference in the five subgroups. Further, the expression of PDCD1, CD274, PDCD1LG2, CTLA4, CD86, and CD80 was higher in subtype C4 in comparison with the other subtypes. The WGCNA of immune-related genes in the five subtypes revealed that blue and turquoise modules were positively correlated with subtype C4 and were associated with 12 common pathways in the KEGG database. These results were validated in external cohorts from the NCI (National Cancer Institute) cohort (GSE14520) and the ICGC (International Cancer Genome Consortium) cohort. In summary, one immune-enhanced subtype and one immune-decreased subtype having different immune and clinical characteristics may provide guidance for developing novel treatment strategies for immune system malfunction-related cancer.

Acute myeloid leukemia (AML) requires refined risk stratification tools to drive decisions concerning effective therapeutic strategies. Here, genome-wide screening was carried out for identifying miRNA molecules capable of predicting treatment outcome in AML patients based on the TCGA dataset. We identified miR-340 as a prognostic factor for selecting treatment between chemotherapy and allogeneic transplantation (allo-HSCT). In multivariable analyses, low miR-340 expression independently predicted reduced OS (HR = 2.07, P = 0.004) and EFS (HR = 1.909, P = 0.01) independent of other well-known prognostic factors. Meanwhile, allo-HSCT overcome deleterious outcomes related to low miR-340. Cases administered allo-HSCT showed markedly improved OS (HR = 0.316, P < 0.0001) and EFS (HR = 0.391, P = 0.002) in comparison with those receiving chemotherapy in the low miR-340 group. Gene expression assessment revealed that elevated miR-340 amounts were negatively correlated with HOXA/HOXB cluster levels, as well as the amounts of the HOX cofactor MEIS1. Strikingly, in silico analysis pointing to HOXA10, HOXB2, and MEIS1 as miR-340 targets. The miR-340 expression may help identify cases requiring strategies for selecting the optimal therapeutic option between chemotherapy and allo-HCST. AML cases showing low miR-340 levels should be strongly considered for early allo-HSCT treatment.

Non-responsive subpopulation of tumor cells, and acquired resistance in initially responsive cells are major challenges for cancer therapy with molecularly-targeted drugs. While point mutations are considered the major contributing factor to acquired resistance, in this study we explored the role of heterogeneity and plasticity of selected human breast cancer cell lines (MDA-MB-231, MDA-MB-468, and AU565) in their initial and adjusted response, respectively, to ruxolitinib, everolimus, and erlotinib. After determination of lethal concentration for 50% cell death (LC50), cells were exposed to selected drugs using three different approaches: single exposure to 4 × LC50 and collection of surviving cells, multiple exposures to 1.5 × LC50 and monitoring the surviving population, and exposure to gradually increasing concentrations of selected drugs (range of concentrations equivalent to 10% of LC50 to 1.5 × LC50). Surviving cells were studied for adjustments in expression level of selected proteins using quantitative PCR and Western Blot. Our data indicated overexpression of a variety of proteins in resistant populations, which included cell membrane receptors EGFR and HER2, anti-apoptotic proteins Bcl-2 and BIRC8, and other proteins involved in cell signaling (e.g., Akt1, MAPK7, and RPS6KA5). Silencing the identified alternative proteins via siRNA resulted in significant drop in the LC50 of the selected molecularly-targeted drugs cells resistant to ruxolitinib (via targeting Akt), everolimus (via targeting EGFR, MAPK7, RPS6KA5, and HER2), and erlotinib (via silencing Bcl2 and BIRC8). Our data indicates that targeting well-selected alternative proteins could potentially sensitize the resistant cells to the effect of the molecularly-targeted treatment.

Early-stage ovarian serous carcinoma is usually difficult to detect in clinical practice. The profiling of protein expression in high-grade serous carcinoma (HGSC) and low-grade serous carcinoma (LGSC) would provide important information for diagnoses and chemotherapy. Here, we performed proteomic profiling of specimens from 13 HGSC and 7 LGSC patients by iTRAQ. A total of 323 proteins that were differentially expressed were identified. After immunohistochemical confirmation of expressed proteins in 166 clinical tissues, asparagine synthetase (ASNS) and filamin A (FLNA) were selected for further functional study. Cisplatin-sensitive (CS; ASNShigh and FLNAlow) and cisplatin-resistant (CR; ASNSlow and FLNAhigh) SKOV3 and OVCAR3 ovarian cancer cell lines were used for subsequent in vitro and in vivo experiments. Notably, ASNS overexpression (ASNS+) or FLNA knockdown (shFLNA) enabled cisplatin-induced apoptosis and autophagy in CR cells. However, ASNS+ and shFLNA promoted and attenuated tumor growth, respectively. In CS cells, ASNS knockdown (shASNS) attenuated clonogenicity, cell proliferation, and the epithelial-mesenchymal transition, whereas FLNA overexpression (FLNA+) protected cells from cisplatin. In vivo, cisplatin resistance was attenuated in mice xenografted with ASNS+, shFLNA, or ASNS+-shFLNA CR cells, whereas xenografts of shASNS or FLNA+ CS cells exhibited resistance to cisplatin. Clinically, all HGSC patients (83/83) responded to cisplatin, while 6 in 41 LGSC patients exhibited cisplatin resistance. These findings identify ASNS and FLNA as distinct biomarkers for HGSC and LGSC, which may have potential value in the prognosis and clinical treatment of serous carcinoma.

As a response to a diverse array of external stimuli, early growth response protein 1 (Egr-1) plays important roles in the transcriptional regulation of inflammation and the cellular immune response. However, a number of intracellular pathogens colonize immune cells and the implication of Egr-1 in the host-pathogen interplay has remained elusive. Here, we have characterized the Egr-1 responses of primary murine and human dendritic cells (DCs) upon challenge with the obligate intracellular parasite Toxoplasma gondii. We report that live intracellular parasites induce a sustained high expression of Egr-1 in DCs, different from the immediate-early Egr-1 response to parasite lysates, inactivated parasites or LPS. Moreover, a distinct nuclear localization of elevated amounts of Egr-1 protein was detected in infected DCs, but not in by-stander DCs. The ERK1/2 MAPK signaling pathway mediated the canonical immediate-early Egr-1 response to soluble antigens in a MyD88/TLR-dependent fashion. In contrast, a non-canonical extended Egr-1 response that relied primarily on p38 MAPK signaling was induced by intracellular parasites and was exhibited similarly by MyD88-deficient and wildtype DCs. The extended phase Egr-1 response was dramatically reduced upon challenge of DCs with T. gondii parasites deficient in GRA24, a secreted p38-interacting protein. Further, Egr-1-silenced primary DCs maintained their migratory responses upon T. gondii challenge. Importantly, Egr-1 silencing led to elevated expression of co-stimulatory molecules (CD40, CD80) in Toxoplasma-infected DCs and in LPS-challenged immature DCs, indicating that Egr-1 responses suppressed maturation of DCs. Moreover, the IL-12 and IL-2 responses of Toxoplasma-challenged DCs were modulated in a GRA24-dependent fashion. Jointly, the data show that the Egr-1 responses of DCs to microbial external stimuli and intracellular stimuli can be selectively mediated by ERK1/2 or p38 MAPK signaling, and that Egr-1 can act as an intrinsic negative modulator of maturation in primary DCs.

Intraspecific differences in biological traits between Neospora caninum isolates have been widely described and associated with variations in virulence. However, the molecular basis underlying these differences has been poorly studied. We demonstrated previously that Nc-Spain7 and Nc-Spain1H, high- and low-virulence isolates, respectively, show different invasion, proliferation and survival capabilities in bovine macrophages (boMØs), a key cell in the immune response against Neospora, and modulate the cell immune response in different ways. Here, we demonstrate that these differences are related to specific tachyzoite gene expression profiles. Specifically, the low-virulence Nc-Spain1H isolate showed enhanced expression of genes encoding for surface antigens and genes related to the bradyzoite stage. Among the primary up-regulated genes in Nc-Spain7, genes involved in parasite growth and redox homeostasis are particularly noteworthy because of their correlation with the enhanced proliferation and survival rates of Nc-Spain7 in boMØs relative to Nc-Spain1H. Genes potentially implicated in induction of proinflammatory immune responses were found to be up-regulated in the low-virulence isolate, whereas the high-virulence isolate showed enhanced expression of genes that may be involved in immune evasion. These results represent a further step in understanding the parasite effector molecules that may be associated to virulence and thus to disease traits as abortion and transmission.

A polyurethane based thermogelling system comprising poly(ω-pentadecalactone) (PPDL), poly(ethylene glycol) (PEG), and poly(propylene glycol) (PPG), termed as PDEP, was synthesized. The incorporation of PPDL lowers critical micelle concentration (CMC) as well as critical gelation concentration (CGC) of the novel copolymers compared to commercial Pluronic® F127. The thermogels showed excellent thermal stability at high temperature up to 80°C, fast response to temperature change in a time frame of less than second, as well as remarkable self-healing properties after being broken at high strain. In vitro drug release studies using docetaxel (DTX) and cell uptake studies using doxorubicin (DOX) show high potential of the hydrogel as drug reservoir for sustainable release profile of payloads, while the in vivo anti-tumor evaluation using mice model of hepatocellular carcinoma further demonstrated the significant inhibition on the growth of tumor. Together with its excellent biocompatibility in different organs, the novel PDPE thermogelling copolymers reported in this work could potentially be utilized as in situ-forming hydrogels for liver cancer therapy.

Neurodegenerative disorders are characterized by progressive degeneration of nerve cells resulting in functional decline of cognition and/or movement. As the prevalence of many of these disorders increases with the aging global population, there is an urgent need for disease-modifying drugs that will halt or slow the progression of these devastating diseases. A summary of the scientific information needed to guide the safe and effective use of a drug is provided in the product label in which the indication section should clearly state the treatment concept, e.g., distinguish between symptomatic, preventive, and curative treatments. However, a review of the United States (US) and European Union (EU) product labels for disease-modifying multiple sclerosis (MS) drugs reveals that the indications are not aligned with the regulatory guidance on labeling. Indication claims such as "delay of accumulation of disability" and "slowing of disease progression" were previously accepted by the US Food and Drug Administration (FDA) and the European Medicines Agency (EMA); however, all recently approved MS drugs include no such specification of the treatment concept in the label indication sections despite similar clinical data packages supporting the approvals. Coincidently, the FDA and EMA therapeutic guidelines pertaining to development of drugs for treatment of neurodegenerative disorders have changed from providing recommendations for specific disease modification label claims to a more general focus on the clinical development approach. Our analysis of MS drug labels could imply that the FDA and EMA may be unlikely to accept disease modification-related indication claims for drugs to treat neurodegenerative disorders in general. We envision that a potential disease-modifying effect is more likely to be inferred from the label descriptions of the mechanism of action, clinical efficacy data and trial design, and target patient population. This poses a challenge for communication of the clinical benefit in a language that can be easily understood by patients and prescribers.

Erythrocytes or red blood cells (RBCs) represent a promising cell-mediated drug delivery platform due to their inherent biocompatibility. Here, we developed an antigen delivery system based on the nanoerythrosomes derived from RBCs, inspired by the splenic antigen-presenting cell targeting capacity of senescent RBCs. Tumor antigens were loaded onto the nanoerythrosomes by fusing tumor cell membrane-associated antigens with nanoerythrosomes. This tumor antigen-loaded nanoerythrosomes (nano-Ag@erythrosome) elicited antigen responses in vivo and, in combination with the anti-programmed death ligand 1 (PD-L1) blockade, inhibited the tumor growth in B16F10 and 4T1 tumor models. We also generated a tumor model showing that "personalized nano-Ag@erythrosomes" could be achieved by fusing RBCs and surgically removed tumors, which effectively reduced tumor recurrence and metastasis after surgery.

Sodium channel NaV1.7 controls firing of nociceptors, and its role in human pain has been validated by genetic and functional studies. However, little is known about NaV1.7 trafficking or membrane distribution along sensory axons, which can be a meter or more in length. We show here with single-molecule resolution the first live visualization of NaV1.7 channels in dorsal root ganglia neurons, including long-distance microtubule-dependent vesicular transport in Rab6A-containing vesicles. We demonstrate nanoclusters that contain a median of 12.5 channels at the plasma membrane on axon termini. We also demonstrate that inflammatory mediators trigger an increase in the number of NaV1.7-carrying vesicles per axon, a threefold increase in the median number of NaV1.7 channels per vesicle and a ~50% increase in forward velocity. This remarkable enhancement of NaV1.7 vesicular trafficking and surface delivery under conditions that mimic a disease state provides new insights into the contribution of NaV1.7 to inflammatory pain.

Although management guidelines exist for several genes associated with a 2-fold to 5-fold increase in the relative risk for certain cancers, the value of testing for them remains controversial.

Consent rates for postmortem (PM) examination in the perinatal and paediatric setting have dropped significantly in the United Kingdom, the United States, and the Western Europe. We explored the factors that act as facilitators or barriers to consent and identified processes and practices that support parental decision-making.

Chikungunya virus (CHIKV), a mosquito-borne alphavirus, has become an important re-emerging pathogen with its rapid spread to many non-endemic areas. The lack of effective vaccines and antiviral agents is largely attributed to the elusive infection and dissemination dynamics in vivo. In this study, we designed and developed a novel, replication-competent, CHIKV reporter virus (CHIKV-iRFP) encoding a near infrared fluorescent protein (iRFP). In vitro and in vivo characterization demonstrated that CHIKV-iRFP retained similar replication and virulence phenotypes to its parental virus. Neonatal BABL/c mice and IFNAR-/- A129 mice were highly susceptible to CHIKV-iRFP infection. Following intracranial (i.c.) inoculation, CHIKV-iRFP efficiently replicated and disseminated into whole body, resulting in rapid death in an age-dependent manner. Remarkably, upon footpad injection, CHIKV-iRFP readily disseminated from footpad to head and whole skeleton, with a specific tropism for bone marrow. Taken together, this novel reporter virus provides a powerful tool to track real time CHIKV replication and to test the in vivo efficacy of vaccines and antiviral therapeutics.