Internode elongation is an important agronomic trait in rice that determines culm length, which is related to lodging, panicle exsertion, and biomass. sui4 (shortened uppermost internode 4) mutants show reduced internode length and a dwarf phenotype due to shortened internodes; the uppermost internode is particularly severely affected. The present study was performed to identify the molecular nature and function of the SUI4 gene during internode elongation.

Arsenic (As) is an unwanted toxic mineral that threatens the major rice-growing regions in the world, especially in South Asia. Rice production in Bangladesh and India depends on As-contaminated groundwater sources for irrigating paddy fields, resulting in elevated amounts of As in the topsoil. Arsenic accumulating in rice plants has a significant negative effect on human and animal health. Here, we present a quantitative trait locus (QTL) mapping study to identify candidate genes conferring As toxicity tolerance and accumulation in rice (Oryza sativa L.) seedlings. An early backcross breeding population consisting of 194 lines derived from a cross between WTR1 (indica) and Hao-an-nong (japonica) was grown in hydroponics for 25 days, from the seventh day exposed to an environmentally relevant concentration of 10 ppm As.

Background The 5-year survival rate for extensive-disease small-cell lung carcinoma (ED-SCLC) is only 1%. Recently, apatinib exerted promising effects on cancer patients after failure of first-line chemotherapy. Methods This study enrolled 24 ED-SCLC patients to study the efficacy and toxicity of apatinib in combination with chemotherapy and maintenance therapy. The primary endpoints were overall survival (OS) and progression-free survival (PFS). The secondary endpoints included toxicity and safety. Apatinib was given 250 mg/day during the chemotherapy interval, and as maintenance therapy after 4-6 cycles until the patient progressed, died, or was intolerant to drug toxicity. The study further evaluated the cytotoxicity, cell-cycle arrest and apoptotic induction of apatinib in A549 and H446 cells. Results There was no difference in short-term efficacy between combined and chemotherapy groups. Long-term efficacy showed that the median PFS was 7.8 months and 4.9 months in combination and chemotherapy groups, respectively [p = 0.002, HR(95%CI): 0.18(0.06-0.60)]. The median OS was 12.1 months and 8.2 months in combination and chemotherapy groups, respectively [p = 0.023, HR(95%CI): 0.38 (0.16-0.90)]. Multivariate Cox regression analysis showed that apatinib combined with chemotherapy was an independent prognostic factor for OS and PFS. The ECOG score was an independent prognostic factor affecting OS. In vitro analysis showed that apatinib inhibited cell proliferation and caused cell-cycle arrest and apoptosis. Conclusion Apatinib combination/maintenance therapy showed promising efficacy and safety to extend OS/PFS in ED-SCLC and will be a potent therapeutic option in future practice. Although the scale of this study is small, further research on large sample sizes is needed.

Obesity and lack of physical activity among children and adolescents are public health problems in the United States. This Presidential Youth Fitness Program (PYFP) evaluation measured program implementation in 13 middle schools and its effect on physical education practices, student fitness knowledge, and student physical activity and fitness levels. PYFP, a free program with the potential to positively affect student health and fitness outcomes, was designed to improve fitness education practices that are easily integrated into existing physical education programs. We used a 2-group (13 PYFP and 13 comparison schools) quasi-experimental design to collect FitnessGram assessments, accelerometry data, and surveys of students, physical education teachers, and administrators. Although the program was positively associated with student cardiovascular endurance and physical activity gains during the semester, schools underused professional development courses and fitness recognition resources.

Natural products represent a rich reservoir of small molecule drug candidates utilized as antimicrobial drugs, anticancer therapies, and immunomodulatory agents. These molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The increase in full microbial genomes and similar resources has led to development of BGC prediction algorithms, although their precision and ability to identify novel BGC classes could be improved. Here we present a deep learning strategy (DeepBGC) that offers reduced false positive rates in BGC identification and an improved ability to extrapolate and identify novel BGC classes compared to existing machine-learning tools. We supplemented this with random forest classifiers that accurately predicted BGC product classes and potential chemical activity. Application of DeepBGC to bacterial genomes uncovered previously undetectable putative BGCs that may code for natural products with novel biologic activities. The improved accuracy and classification ability of DeepBGC represents a major addition to in-silico BGC identification.

Ubiquitous Structural Maintenance of Chromosomes (SMC) complexes use a proteinaceous ring-shaped architecture to organize and individualize chromosomes, thereby facilitating chromosome segregation. They utilize cycles of adenosine triphosphate (ATP) binding and hydrolysis to transport themselves rapidly with respect to DNA, a process requiring protein conformational changes and multiple DNA contact sites. By analysing changes in the architecture and stoichiometry of the Escherichia coli SMC complex, MukBEF, as a function of nucleotide binding to MukB and subsequent ATP hydrolysis, we demonstrate directly the formation of dimer of MukBEF dimer complexes, dependent on dimeric MukF kleisin. Using truncated and full length MukB, in combination with MukEF, we show that engagement of the MukB ATPase heads on nucleotide binding directs the formation of dimers of heads-engaged dimer complexes. Complex formation requires functional interactions between the C- and N-terminal domains of MukF with the MukB head and neck, respectively, and MukE, which organizes the complexes by stabilizing binding of MukB heads to MukF. In the absence of head engagement, a MukF dimer bound by MukE forms complexes containing only a dimer of MukB. Finally, we demonstrate that cells expressing MukBEF complexes in which MukF is monomeric are Muk-, with the complexes failing to associate with chromosomes.

Evolve and resequence (E&R) studies are frequently used to dissect the genetic basis of quantitative traits. By subjecting a population to truncating selection for several generations and estimating the allele frequency differences between selected and nonselected populations using next-generation sequencing (NGS), the loci contributing to the selected trait may be identified. The role of different parameters, such as, the population size or the number of replicate populations has been examined in previous works. However, the influence of the selection regime, that is the strength of truncating selection during the experiment, remains little explored. Using whole genome, individual based forward simulations of E&R studies, we found that the power to identify the causative alleles may be maximized by gradually increasing the strength of truncating selection during the experiment. Notably, such an optimal selection regime comes at no or little additional cost in terms of sequencing effort and experimental time. Interestingly, we also found that a selection regime which optimizes the power to identify the causative loci is not necessarily identical to a regime that maximizes the phenotypic response. Finally, our simulations suggest that an E&R study with an optimized selection regime may have a higher power to identify the genetic basis of quantitative traits than a genome-wide association study, highlighting that E&R is a powerful approach for finding the loci underlying complex traits.

Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.

Some parasites can manipulate the behavior of their animal hosts to increase transmission. An interesting area of research is understanding how host neurobiology is manipulated by microbes to the point of displaying such aberrant behaviors. Here, we characterize the metabolic profile of the brain of an insect at the moment of the behavioral manipulation by a parasitic microbe. Our model system are ants infected with the parasitic fungus Ophiocordyceps kimflemingiae (=unilateralis), which manipulates ants to climb and bite into plant substrates, before killing the host (i.e. zombie ants). At the moment of the behavioral manipulation by the fungus, the host's brain is not invaded by the fungus which is known to extensively invade muscle tissue. We found that, despite not being invaded by the parasite, the brains of manipulated ants are notably different, showing alterations in neuromodulatory substances, signs of neurodegeneration, changes in energy use, and antioxidant compound that signal stress reactions by the host. Ergothionine, a fungal derived compound with known neuronal cytoprotection functions was found to be highly elevated in zombie ant brains suggesting the fungus, which does not invade the central nervous system, is preserving the brain.

Adropin is a protein encoded by Energy Homeostasis Associated (Enho) gene which is expressed mainly in the liver and brain. There is evidence that biological effects of adropin are mediated via GPR19 activation. Animal studies showed that adropin modulates adiposity as well as lipid and glucose homeostasis. Adropin deficient animals have a phenotype closely resembling that of human metabolic syndrome with are obesity dyslipidemia and impaired glucose production. Animals treated with exogenous adropin lose weight, in addition to having reduced expression of lipogenic genes in the liver and fat tissue. While it was shown that adropin may contribute to energy homeostasis and body weight regulation, the role of this protein in controlling fat tissue formation is largely unknown. Thus, in the present study we investigated the effects of adropin on adipogenesis using 3T3-L1 cells and rat primary preadipocytes. We found a low Enho mRNA expression in 3T3-L1 cells and rat primary preadipocytes. Adropin stimulated proliferation of 3T3-L1 cells and rat primary preadipocytes. Stimulation of 3T3-L1 cell proliferation was mediated via ERK1/2 and AKT. Adropin reduced lipid accumulation as well as expression of proadipogenic genes in 3T3-L1 cells and rat preadipocytes, suggesting that this protein attenuates differentiation of preadipocytes into mature fat cells. In summary, these results show that adropin modulates proliferation and differentiation of preadipocytes.

MiR-126 has been shown to suppress malignant mesothelioma (MM) by targeting cancer-related genes without inducing toxicity or histopathological changes. Exosomes provide the opportunity to deliver therapeutic cargo to cancer stroma. Here, a tumour stromal model composed of endothelial cells (HUVECs), fibroblasts (IMR-90 cells), non-malignant mesothelial cells (Met-5A cells) and MM cells (H28 and MM-B1 cells) was used. The cells were treated with exosomes from HUVECs carrying endogenous (exo-HUVEC) and enriched miR-126 (exo-HUVECmiR-126), and the uptake/turnover of exosomes; miR-126 distribution within the stroma; and effect of miR-126 on cell signalling, angiogenesis and cell proliferation were evaluated. Based on the sensitivity of MM cells to exo-HUVEC miR-126 treatment, miR-126 was distributed differently across stromal cells. The reduced miR-126 content in fibroblasts in favour of endothelial cells reduced angiogenesis and suppressed cell growth in an miR-126-sensitive environment. Conversely, the accumulation of miR-126 in fibroblasts and the reduced level of miR-126 in endothelial cells induced tube formation in an miR-126-resistant environment via VEGF/EGFL7 upregulation and IRS1-mediated cell proliferation. These findings suggest that transfer of miR-126 via HUVEC-derived exosomes represents a novel strategy to inhibit angiogenesis and cell growth in MM.

Occupational exposure to trichloroethylene (TCE) has been associated with severe, generalized contact hypersensitivity (CHS) skin disorder, which is considered a delayed-type hypersensitivity reaction mediated by antigen-specific T cells. Transforming growth factor-β activated kinase-1 (TAK1) is essential for regulating the development and effector function of T cells. We hypothesized that disrupting TAK1 activity might inhibit TCE-induced CHS response. In this study, a local lymph node assay was employed to build a CHS model induced by TCE combined with the inducible-TAK1 deletion system to study the effect of TAK1 on it. It was observed that TAK1 deficiency ameliorated the TCE-induced CHS response and was associated with defective T cell expansion and activation and IFN-γ production in vivo. Furthermore, we investigated the effects of TCE and its metabolites trichloroacetic acid (TCA) and dichloroacetic acid (DCA) on CD4+ T cell function and the effect of TAK1 on it in vitro. The results showed that TCE, TCA and DCA augmented the proliferation, activation and differentiation of CD4+ T cells through Jnk MAPK and NF-κB pathways. TAK1 deletion significantly attenuated these effects induced by TCE, TCA or DCA on CD4+ T cells. In conclusion, it is suggested that TAK1 plays a critical role both in TCE-induced CHS response in vivo and in TCE and its metabolite-induced CD4+ T cell activation in vitro. Local inhibition of TAK1 might offer a promising alternative feasible strategy for TCE-induced CHS.

A promising strategy for treatment of EGFR-dependent tumours is EGFR signal transduction suppression via inhibition of HMG-CoA reductase using high doses of statins, popular cholesterol-lowering drugs. The main purpose of this study was to obtain targeted long circulating immunoliposomes containing simvastatin (tLCLS) with anti-EGFR antibody attached to their surface and to test whether they can be effective in treatment of TNBC. The designed tLCLS were characterized in terms of physicochemical properties and long-term stability. In vitro experiments conducted on MDA-MB-231 cells demonstrated that tLCLS induced apoptosis and are characterized by IC50 of 7.5 µM. Treatment of studied cells with tLCLS led to a decrease in membrane order and inhibited PI3K/Akt signalling. Analyses of efficacy of the tLCLS in in vivo experiments in model animals indicate that immunoliposomes were effectively delivered to tumours. Our results showed that regardless of whether tLCLS were administered before or after tumour formation, at the tested dose they inhibited tumour growth by an average of 25% in comparison to the control. However, the results were not statistically significant. The experiments described above allowed us to test the possibility of using immunoliposomes as simvastatin carriers delivering increased amounts of the drug to tumour cells.

One of the hallmarks of ageing is muscle wasting that may be preceded by morphological changes, such as capillary rarefaction. Muscle-specific changes in morphology in early ageing may differ between locomotor and respiratory muscles. To investigate this, we compared capillarization, fiber type composition, fiber cross-sectional area (FCSA) and oxidative capacity of individual fibers of the soleus (n = 6/5 for 20- and 79 weeks, respectively), extensor digitorum longus (EDL: n = 3/3) and diaphragm (n = 7/5) muscles in 20- (mature) and 79-week-old (early ageing) CD-1 female mice. There was no significant loss of soleus and EDL mass. The FCSA was larger and the capillary density lower at 79 than 20 weeks in the diaphragm, while in the EDL the opposite was found (both p ≤ 0.002) with no significant ageing-related differences in the soleus. The heterogeneity in capillary spacing, which may negatively impact on muscle oxygenation, was highest in muscles from 20-week-old mice, irrespective of muscle (p ≤ 0.011). Succinate dehydrogenase activity, indicative of oxidative capacity, and capillary to fiber ratio did not significantly change with age in any muscle. At all ages, the capillary supply to a fiber was positively related to FCSA in each muscle. We conclude that despite previously reported early age-related reductions in specific tension in both locomotor and respiratory muscles, morphological changes show a muscle-specific pattern in early ageing CD-1 mice. Specifically, early ageing was associated with 1) diaphragm hypertrophy 2) and fiber atrophy in the EDL that was not accompanied by angiogenesis, capillary rarefaction or reductions in oxidative capacity.

Escherichia coli is one of the primary causes of bacterial sepsis and meningitis in newborns. E. coli RS218, a prototype strain of neonatal meningitis E. coli (NMEC), is often used in research on the pathogenesis of NMEC. Phagocytes are crucial sentinels of immunity, and their antibacterial ability is largely determined by the capability to produce large amounts of ROS. The capacity of bacteria to endure oxidative pressure affects their colonization in the host. Here, we systematically screened the genes that plays key roles in the tolerance of the model of E. coli RS218 to peroxygen environment using a Tn5 mutant library. As a result, a gene encoding O antigen polymerase (O antigen ligase) that contains the Wzy_C superfamily domain (herein designated as Ocw) was identified in E. coli RS218. Furthermore, we constructed an isogenic deletion mutant of ocw gene and its complementary strain in E. coli. Our results revealed that ocw affects the lipopolysaccharide synthesis, ROS tolerance, and survival of E. coli in the host environment. The discovery of ocw provides important clues for better understanding the function of O-antigen.

Ingestion of microplastics can impair nutrition of marine invertebrates. In a laboratory study, we tested whether microplastics affect ingestion rates and gastrointestinal enzyme activities in the marine isopod Idotea emarginata. Isopods were fed for eight days with one out of four different food formulations: natural food (the brown alga Fucus vesiculosus) or synthetic diet consisting of freeze-dried algal powder embedded in agarose, both, with or without microplastic particles (fluorescent polymethyl methacrylate, 10-100 μm) at a concentration of 40 items per mg of food. The isopods accepted both types of food but consumed significantly more (average 3.1-fold) of the agar based synthetic food. I. emarginata responded to the reduced content of digestible organic matter in the synthetic food by a compensatory adjustment of the ingestion rates. Addition of microplastics had no effect on ingestion rates in natural food whereas the feeding rates for synthetic food varied in response to microplastics. Similarly, activity patterns of digestive enzymes, particularly those of esterases, changed significantly in the treatment with synthetic food. Isopods fed with synthetic food alone showed elevated esterase activities in the gut while those isopods fed with synthetic food and microplastics showed elevated esterase activities in the midgut gland but not in the gut. Apparently, not the exposure to microplastic alone, but the combined effects of reduced nutrient availability and microplastic ingestion caused considerable biochemical reactions in the digestive organs of the isopods.

Two-photon vision arises from the perception of pulsed infrared (IR) laser light as color corresponding to approximately half of the laser wavelength. The physical process responsible for two-photon vision in rods has been delineated and verified experimentally only recently. Here, we sought to determine whether IR light can also be perceived by mammalian cone photoreceptors via a similar activation mechanism. To investigate selectively mammalian cone signaling in mice, we used animals with disabled rod signal transduction. We found that, contrary to the expected progressive sensitivity decrease based on the one-photon cone visual pigment spectral template, the sensitivity of mouse cone photoreceptors decreases only up to 800 nm and then increases at 900 nm and 1000 nm. Similarly, in experiments with the parafoveal region of macaque retinas, we found that the spectral sensitivity of primate cones diverged above the predicted one-photon spectral sensitivity template beyond 800 nm. In both cases, efficient detection of IR light was dependent on minimizing the dispersion of the ultrashort light pulses, indicating a non-linear two-photon activation process. Together, our studies demonstrate that mammalian cones can be activated by near IR light by a nonlinear two-photon excitation. Our results pave the way for the creation of a two-photon IR-based ophthalmoscope for the simultaneous imaging and functional testing of human retinas as a novel tool for the diagnosis and treatment of a wide range of visual disorders.

Tumor-released extracellular vesicles (EVs) contain tumor-specific cargo distinguishing them from healthy EVs, and making them eligible as circulating biomarkers. Glypican 1 (GPC1)-positive exosome relevance as liquid biopsy elements is still debated. We carried out a prospective study to quantify GPC1-positive exosomes in sera from pancreatic ductal adenocarcinoma (PDAC) patients undergoing up-front surgery, as compared to controls including patients without cancer history and patients displaying pancreatic preneoplasic lesions. Sera were enriched in EVs, and exosomes were pulled down with anti-CD63 coupled magnetic beads. GPC1-positive bead percentages determined by flow cytometry were significantly higher in PDAC than in the control group. Diagnosis accuracy reached 78% (sensitivity 64% and specificity 90%), when results from peripheral and portal blood were combined. In association with echo-guided-ultrasound-fine-needle-aspiration (EUS-FNA) negative predictive value was 80% as compared to 33% for EUS-FNA only. This approach is clinically relevant as a companion test to the already available diagnostic tools, since patients with GPC1-positive exosomes in peripheral blood showed decreased tumor free survival.

The development of CRISPR/Cas9-mediated base editors (BEs) provided a versatile tool for precise genome editing. The recently developed xCas9-derived base editors (xBEs) that recognize the NG PAM substantially expand the targeting scope in the genome, while their editing efficiency needs to be improved. Here, we described an improved version of xBEs by fusing the BPNLS and Gam to the N terminus of xBEs (BPNLS-Gam-xBE3 and BPNLS-xABE), and this version of base editor displayed higher targeting efficiency for the majority of detected sites. By using this improved version of xBEs, we successfully created and corrected pathogenic mutations at genomic sites with the NGN protospacer-adjacent motif in human cells. Lastly, we used BPNLS-Gam-xBE3 to model pathogenic mutations in discarded human tripronuclear (3PN) zygotes, and no obvious off-targets and indels were detected. Taken together, the data in our study offer an efficient tool for precise genome editing and, thus, an enriched base editing toolkit.

Caudal-type homeobox 2 (.Cdx2) transcription factor is an essential regulator of differentiation to the intestinal epithelium, somatic mesoderm and trophectoderm function in the mouse. However, the regulation of Cdx2 in these processes is poorly understood. Separation of viable Cdx2 expressing cells during differentiation for downstream experiments is not possible due to its nuclear localization, limiting experimental possibilities and studying Cdx2 regulation. Here, we report generation of a Cdx2-mCherry knock-in reporter mouse embryonic stem cell line (TCMC), for modeling and studying in vitro differentiation of mESCs to intestinal epithelia, somatic mesoderm, and trophectoderm.