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We present results of dust continuum and [C  ii ] |$\, 158\, {\rm \mu m}$| emission line observations of a remarkably UV luminous (M UV = −21.6) galaxy at z = 10.603: GN-z11. Using the Northern Extended Millimeter Array (NOEMA), observations have been carried out over multiple observing cycles. We achieved a high sensitivity resulting in a |$\lambda _{\rm rest}=160\, {\rm \mu m}$| continuum |$1\, \sigma$| sensitivity of |$13.0\, \rm {\mu Jy \, beam}^{ -1}$| and a [C  ii ] emission line |$1\, \sigma$| sensitivity of |$31\, \rm {mJy\, beam^{ -1}\, km \, s}^{ -1}$| using |$50\, \rm {km \, s}^{ -1}$| binning with a |$\sim 2\, {\rm arcsec}$| synthesized beam. Neither dust continuum nor [C  ii ] |$\, 158\, {\rm \mu m}$| line emission are detected at the expected frequency of ν[C ii ] |$= 163.791\, \rm {GHz}$| and the sky location of GN-z11. The upper limits show that GN-z11 is neither luminous in L IR nor L [C ii ], with a dust mass |$3\, \sigma$| limit of |${\rm log}\, (M_{\rm dust}/{\rm {\rm M}_{\odot }}) \, \lt\, 6.5-6.9$| and with a [C  ii ] based molecular gas mass |$3\, \sigma$| limit of log (M mol, [C ii ] |$/{\rm {\rm M}_{\odot }}) \, \lt \, 9.3$|⁠. Together with radiative transfer calculations, we also investigated the possible cause of the dust poor nature of the GN-z11 showed by the blue colour in the UV continuum of GN-z11 (βUV = −2.4), and found that ≳3 × deeper observations are crucial to study dust production at very high-redshift. Nevertheless, our observations show the crucial role of deep mm/submm observations of very high-redshift galaxies to constrain multiple phases in the interstellar medium. [ABSTRACT FROM AUTHOR]

Microbial strategies for biomass deconstruction involve an incredible repertoire of enzymatic, structural, and regulatory proteins. From carbohydrate active enzymes to cellulosomes, bacteria, yeast, and filamentous fungi adapt their functional machinery to grow from alternative carbon sources such as lignocellulose and survive starvation. In that context, microbes must be able to sense, bind, degrade, and utilize lignin, cellulose, and hemicelluloses. Nature has developed specialized protein modules, RNA structures, and regulatory systems operating at a genomic, transcription, and translation level. This review briefly summarizes the main regulatory pathways involved in lignocellulose microbial degradation, including carbon catabolite repression; anti-sigma factors; regulatory RNA elements such as small RNAs, antisense RNA, RNA-binding proteins, and selective RNA processing and stabilization; and transcriptional regulators and unfolded protein response. Interplay with global regulators controlling pH response and nitrogen utilization is also revised. [ABSTRACT FROM AUTHOR]

Background: Sigma metrics is a quantitative management tool. This study assessed the Six Sigma score for 26 chemistry analytes, compared scores with different total allowable errors (TEa) and use of scores for internal quality control (IQC) rules in 4 Laboratories in Kwa-Zulu Natal, South Africa. Methods: Utilizing 6 months of IQC SD, CV, and bias data on albumin, alkaline phosphatase, alanine aminotransferase, amylase, aspartate aminotransferase, bicarbonate, calcium, total cholesterol, creatine kinase, chloride, creatinine, gamma glutamyl transferase, glucose, HDL-cholesterol, potassium, lactate dehydrogenase, magnesium, sodium, inorganic phosphate, direct bilirubin, total bilirubin, triglycerides, total protein, urea nitrogen, uric acid, and C-reactive protein (CRP) Six Sigma scores were calculated using Microsoft Excel 2016 and ideal IQC rules were determined. Six Sigma scores using Ricos et al. 2014, Royal College of Pathologists Australasia, and Clinical Laboratory Improvement Amendments TEas were compared. Results: For levels 1, 2, and 3 respectively, analytes scoring >3 sigma was 9 (35%), 12 (46%), and 14 (54%) in Laboratory A; Laboratory B had 15 (58%), 19 (73%), and 17 (65%); Laboratory C had 12 (46%), 13 (50%), and 15 (58%); and Laboratory D had 13 (50%), 18 (69%), and 18 (69%). Albumin, calcium, sodium, magnesium, bicarbonate, and chloride scored <3; CRP scored >6 for all. In Laboratories A, B, C, and D, 7 (27%), 7 (27%), 6 (23%), and 8 (31%) analytes, respectively, required only 1 IQC rule. One of 21 analytes for Laboratories C and D, 3 for Laboratory A, and 0 for Laboratory B had the same sigma score with all 3 databases. Conclusion: Despite South Africa being a developing nation, many analytes are able to achieve >3 sigma. [ABSTRACT FROM AUTHOR]

Motivation Promoter is a short region of DNA which is responsible for initiating transcription of specific genes. Development of computational tools for automatic identification of promoters is in high demand. According to the difference of functions, promoters can be of different types. Promoters may have both intra- and interclass variation and similarity in terms of consensus sequences. Accurate classification of various types of sigma promoters still remains a challenge. Results We present iPromoter-BnCNN for identification and accurate classification of six types of promoters— σ 24 , σ 28 , σ 32 , σ 38 , σ 54 , σ 70 ⁠. It is a CNN-based classifier which combines local features related to monomer nucleotide sequence, trimer nucleotide sequence, dimer structural properties and trimer structural properties through the use of parallel branching. We conducted experiments on a benchmark dataset and compared with six state-of-the-art tools to show our supremacy on 5-fold cross-validation. Moreover, we tested our classifier on an independent test dataset. Availability and implementation Our proposed tool iPromoter-BnCNN web server is freely available at http://103.109.52.8/iPromoter-BnCNN. The runnable source code can be found https://colab.research.google.com/drive/1yWWh7BXhsm8U4PODgPqlQRy23QGjF2DZ. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Acacia senegal is part of the natural diet of goats. Gum Arabica (GA) is a water-soluble complex polysaccharide antimicrobial, anti-inflammatory prebiotic, derived from Acacia Senegal. Its mechanism of action has not been defined. Galectins are secreted sugar-binding animal proteins involved in the regulation of innate and adaptive immunity. They function in microbe recognition and as regulators of inflammation. This study evaluated the effect of GA on Galectin transcription. Clinically healthy Boer X Spanish goats (n = 20) were randomly assigned to two groups of 10. Goats in the treatment group received 10 mL of GA in water daily for six weeks, controls received sterile water. Blood was collected weekly from the jugular vein using acid citrate dextrose as an anticoagulant. Subsequently, the blood was centrifuged to isolate the cells and plasma. Total RNA isolation was isolated from the cell pellet using Trizol (Sigma-Aldrich). The RNA concentration (ng/μL) and purity was assessed using a Nanodrop Spectrophotometer (Thermo Scientific Inc). Galectin-1, -3 and -9 transcription was conducted using goat specific primers and housekeeping genes for real-time PCR. Fold changes were calculated using the Livak method. The Log2FC values for Galectin 1, 3, and 9 expressions were 12.47, 0.29, and 2.22 respectively. Thus, GA had varying effects on structurally distinct galectins. Galectin 1 gene (Lgals1) is an important modulator of the immune response and was highly induced. Changes in Galectin transcription can impact microbial recognition and immune activation for goat health. Further analyses are needed to evaluate the functional effects of GA for application as a prebiotic and immune modulator lain goat health. [ABSTRACT FROM AUTHOR]

Chlorophyll accumulation and chloroplast development are regulated at multiple levels during plant development. The paralogous LLM-domain B-GATA transcription factors GNC and GNL contribute to chlorophyll biosynthesis and chloroplast formation in light-grown Arabidopsis thaliana seedlings. Whereas there is already ample knowledge about the transcriptional regulation of GNC and GNL , the identity of their downstream targets is largely unclear. Here, we identified genes controlling greening directly downstream of the GATAs by integrating data from RNA-sequencing and microarray data sets. We found that genes encoding subunits of the Mg-chelatase complex and 3,8-divinyl protochlorophyllide a 8-vinyl reductase (DVR) likely function directly downstream of the GATAs and that DVR expression is limiting in the pale-green gnc gnl mutants. The GATAs also regulate the nucleus-encoded SIGMA (SIG) factor genes, which control transcription in the chloroplast and suppress the greening defects of sig mutants. Furthermore, GNC and GNL act, at the gene expression level, in an additive manner with the GOLDEN2-LIKE1 (GLK1) and GLK2 transcription factor genes, which are also important for proper chlorophyll accumulation. We thus reveal that chlorophyll biosynthesis genes are directly controlled by LLM-domain B-GATAs and demonstrate that these transcription factors play an indirect role in the control of greening through regulating SIGMA factor genes. [ABSTRACT FROM AUTHOR]

Mutations in Sigma 1 receptor (SIGMAR1) have been previously identified in patients with amyotrophic lateral sclerosis and disruption of Sigmar1 in mouse leads to locomotor deficits. However, cellular mechanisms underlying motor phenotypes in human and mouse with disturbed SIGMAR1 function have not been described so far. Here we used a combination of in vivo and in vitro approaches to investigate the role of SIGMAR1 in motor neuron biology. Characterization of Sigmar 1-/- mice revealed that affected animals display locomotor deficits associated with muscle weakness, axonal degeneration and motor neuron loss. Using primary motor neuron cultures, we observed that pharmacological or genetic inactivation of SIGMAR1 led to motor neuron axonal degeneration followed by cell death. Disruption of SIGMAR1 function in motor neurons disturbed endoplasmic reticulum- mitochondria contacts, affected intracellular calcium signalling and was accompanied by activation of endoplasmic reticulum stress and defects in mitochondrial dynamics and transport. These defects were not observed in cultured sensory neurons, highlighting the exacerbated sensitivity of motor neurons to SIGMAR1 function. Interestingly, the inhibition of mitochondrial fission was sufficient to induce mitochondria axonal transport defects as well as axonal degeneration similar to the changes observed after SIGMAR1 inactivation or loss. Intracellular calcium scavenging and endoplasmic reticulum stress inhibition were able to restore mitochondrial function and consequently prevent motor neuron degeneration. These results uncover the cellular mechanisms underlying motor neuron degeneration mediated by loss of SIGMAR1 function and provide therapeutically relevant insight into motor neuronal diseases. [ABSTRACT FROM AUTHOR]

Sigma (σ) receptors have recently been identified as potential targets for the development of novel therapeutics aimed at mitigating the effects of methamphetamine. Particularly, σ receptors are believed to mitigate some of the neurotoxic effects of methamphetamine through modulation of dopamine, dopamine transporters and body temperature. Furthermore, recent evidence suggests that targeting σ receptors may prevent cognitive impairments produced by methamphetamine. In the present study, an optimized σ receptor antagonist, AZ66, was evaluated against methamphetamine-induced neurotoxicity and cognitive dysfunction. AZ66 was found to be highly selective for σ receptors compared to 64 other sites tested. Pretreatment of male, Swiss Webster mice with i.p. dosing of AZ66 significantly attenuated methamphetamine-induced striatal dopamine depletions, striatal dopamine transporter reductions and hyperthermia. Additionally, neurotoxic dosing with methamphetamine caused significant memory impairment in the object recognition test, which was attenuated when animals were pretreated with AZ66; similar trends were observed in the step-through passive avoidance test. Taken together, these results suggest that targeting σ receptors may provide neuroprotection against the neurotoxicity and cognitive impairments produced by methamphetamine. [ABSTRACT FROM PUBLISHER]

Necrotrophic pathogens are important plant pathogens that cause many devastating plant diseases. Despite their impact, our understanding of the plant defense response to necrotrophic pathogens is limited. The WRKY33 transcription factor is important for plant resistance to necrotrophic pathogens; therefore, elucidation of its functions will enhance our understanding of plant immunity to necrotrophic pathogens. Here, we report the identification of two WRKY33-interacting proteins, nuclear-encoded SIGMA FACTOR BINDING PROTEIN1 (SIB1) and SIB2, which also interact with plastid-encoded plastid RNA polymerase SIGMA FACTOR1. Both SIB1 and SIB2 contain an N-terminal chloroplast targeting signal and a putative nuclear localization signal, suggesting that they are dual targeted. Bimolecular fluorescence complementation indicates that WRKY33 interacts with SIBs in the nucleus of plant cells. Both SIB1 and SIB2 contain a short VQ motif that is important for interaction with WRKY33. The two VQ motif–containing proteins recognize the C-terminal WRKY domain and stimulate the DNA binding activity of WRKY33. Like WRKY33 , both SIB1 and SIB2 are rapidly and strongly induced by the necrotrophic pathogen Botrytis cinerea. Resistance to B. cinerea is compromised in the sib1 and sib2 mutants but enhanced in SIB1 -overexpressing transgenic plants. These results suggest that dual-targeted SIB1 and SIB2 function as activators of WRKY33 in plant defense against necrotrophic pathogens. [ABSTRACT FROM AUTHOR]

The article examines the heterologous expression of the Oceanobacillus iheyensis sigma factor SigW and its anti-protein RsiW in Bacillus subtilis. It explores the protein structure and gene organization of extra-cytoplasmic-function (EFC) sigma factors in the cytoplasmic membrane and periplasmic space and their genetic competence in manipulating the genome of Bacillus subtilis. It also notes the need to consider the mechanisms on protein translocation in designing heterologous gene expression.

During active growth of Escherichia coli, majority of the transcriptional activity is carried out by the housekeeping sigma factor (σ70), whose association with core RNAP is generally favoured because of its higher intracellular level and higher affinity to core RNAP. In order to facilitate transcription by alternative sigma factors during nutrient starvation, the bacterial cell uses multiple strategies by which the transcriptional ability of σ70 is diminished in a reversible manner. The facilitators of shifting the balance in favour of alternative sigma factors happen to be as diverse as a small molecule (p)ppGpp (represents ppGpp or pppGpp), proteins (DksA, Rsd) and a species of RNA (6S RNA). Although 6S RNA and (p)ppGpp were known in literature for a long time, their role in transcriptional switching has been understood only in recent years. With the elucidation of function of DksA, a new dimension has been added to the phenomenon of stringent response. As the final outcome of actions of (p)ppGpp, DksA, 6S RNA and Rsd is similar, there is a need to analyse these mechanisms in a collective manner. We review the recent trends in understanding the regulation of σ70 by (p)ppGpp, DksA, Rsd and 6S RNA and present a case for evolving a unified model of RNAP redistribution during starvation by modulation of σ70 activity in E. coli. [ABSTRACT FROM AUTHOR]

Aims: To examine the role of the alternative general stress sigma factor σB on the resistance of Staphylococcus aureus to stresses of relevance to food preservation, with special emphasis on emerging technologies such as pulsed electric fields (PEF) and high hydrostatic pressure (HHP). Methods and Results: S. aureus strain Newman and its isogenic Δ sigB mutant were grown to exponential and stationary growth phases and its resistance to various stresses was tested. The absence of the σB factor caused a decrease in the resistance to heat, PEF, HHP, alkali, acid and hydrogen peroxide. In the case of heat, the influence of the σB factor was particularly important, and decreases in decimal reduction time values of ninefold were observed as a result of its deficiency. The increased thermotolerance of the parental strain as compared with the sigB mutant could be attributed to a better capacity to sustain and repair sublethal damages caused by heat. Conclusions: σB factor provides S. aureus cells with resistance to multiple stresses, increasing survival to heat, PEF and HHP treatments. Significance and Impact of the Study: Results obtained in this work help in understanding the physiological mechanisms behind cell survival and death in food-processing environments. [ABSTRACT FROM AUTHOR]