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A curved channel is a common flow form in nature, often hosting aquatic vegetation along rivers. The stem thickness of this vegetation affects its resistance to flow and subsequently influences flow characteristics. To explore the impact of stem thickness on river flow in curved channels, we developed a Reynolds stress model based on real river flow conditions and vegetation data. The flow characteristics were analyzed in terms of flow velocity, Reynolds stress and turbulence intensity by varying the stem thickness of the vegetation in the vegetated area. The results of the study reveal that: (1) Water velocity in the vegetated area is significantly reduced compared to the non-vegetated area, with a greater reduction observed for thicker stems. Increasing the vegetation diameter by 3 mm resulted in a velocity decrease of 2.31–26.55%. (2) Thicker vegetation stems lead to more intense energy exchange in water flow. A 3 mm increase in vegetation diameter increased Reynolds stress by 91.81–139.70%. (3) Turbulent kinetic energy in the vegetated area is significantly higher than in the non-vegetated area, with greater turbulence intensity observed for thicker vegetation stems. Increasing the vegetation diameter by 3 mm resulted in a turbulent kinetic energy increase of 115.19–218.55%. HIGHLIGHTS Less research has been done on the effect of vegetation stem thickness on water flow in curved channels.; The feasibility of studying the flow characteristics of curved river channels through simulation is verified.; Analysis of sedimentation by comparing concave and convex shores.; The results can guide the construction of river channels and the design of aquatic systems.; It can provide relevant data for the subsequent research on the influence of vegetation stem coarseness on water flow characteristics.;

Abstract The Middle Triassic Tredian Formation is well exposed in the western region of the Salt Range. It is mostly composed of sandstone with minor alternations of shales and dolomite. This is the first integrated attempt using petrographical and geochemical features to reveal palaeoclimate during deposition of the Tredian Formation. This work sheds light on the petrographical and geochemical properties of the Tredian sandstone in order to date various layers and evaluate the palaeoclimate. The formation was sampled at two distinct stratigraphic layers for petrographic and geochemical analysis of major and trace elements. The sandstone of the Tredian Formation is sub‐feldspathic to feldspathic arenite with sub‐angular to rounded grains that are moderately to extensively sorted. The relative proportions of the quartz, feldspars and lithoclasts in the examined sandstone samples shows that the Tredian sediments originated from the interior of the craton during a transitional continental regime. Chemical index of alteration values of 59, chemical index of weathering values of 67, and plagioclase index of alteration values of 74.5 indicate a low to moderate degree of weathering in the Tredian sediment source region. Based on the silica content, SiO2/Al2O3 ratios (2.7–6.1; mean 4.1), and chemical maturity index, it is deduced that the Tredian Formation was deposited in chemically immature to sub‐mature and dry to semi‐arid conditions. Geochemical proxies indicate the acidic source of sediment and deposition on the passive margin of the Indian Plate. The trace element characteristics of the sediments, especially the Rb/Sr, Cu/Zn, Ni/Co, V/Cr and Sr/Ba ratios, indicate that the sediments originated from the first weathering cycle and support the notion that they were deposited in an oxidising continental environment. A semi‐arid to arid palaeoclimate predominated through the Middle Triassic at the north‐western passive continental margin of the Indian Plate in the south‐eastern Neo‐Tethys.

Abstract A detailed sedimentological analysis of the Palaeocene Lockhart Limestone has been conducted to evaluate the depositional environment, diagenetic processes and hydrocarbon potential of the eastern margin of the Upper Indus Basin. From bottom to top, there are three microfacies recorded. The lower microfacies, composed of fine‐grained micrite and some diagenetic dolomite, reflect the low energy and calm palaeo‐current in the shallower section (1–2 m) of the inner shelf close to shore. The middle microfacies contain algae that suggest 5–15 m of water depth, especially along the inner‐middle shelf, but fractured and mixed bioclasts in micrite material indicate calm to moderately active water close to the wave base. Progressing from the lower microfacies to the middle microfacies, a gradual shift from orthochem to allochem components is observed. The top microfacies is dominated by massive benthic microfossils, indicating moderate energy‐water conditions with normal salinity. However, the presence of limestone intraclasts surrounded by microspar, miliolids and nummulites at the top indicates a high‐energy environment with increasing salinity and water depths from 20 to 130 m. These findings show that the Lockhart Limestone was deposited in a shallow shelf environment, spanning the inner‐mid shelf. Diagenetic processes observed include micritisation, cementation, dissolution, replacement, physical and chemical compaction, and fracture filling by calcite cement. The Lockhart Limestone represents a deepening upward sequence deposited below the shelf margin system tract and highstand systems tract in a regressive environment that could reflect good reservoir characteristics, has the potential to serve as an excellent hydrocarbon reservoir rock, and could be a primary target for future hydrocarbon exploration.

The nexus between green growth and ecological footprint is associated with crucial environmental implications. But this domain is not examined sufficiently and provides ambiguous findings. Furthermore, these studies have not addressed the role of natural resources, environmental innovation, and ICT in influencing ecological footprint. Our study analyzes the impact of green growth, ICT, environmental innovation, and natural resources on the ecological footprint ofemerging-7 and developed-7 economies. We employed CS-ARDL methodology to draw the long-run and short-run estimates of the said relationships. The obtained findings show that green growth, ICT, and environmental innovation reduce the ecological footprint in emerging economies in the long run. However, natural resources enhance the ecological footprint in emerging economies in the long run. Green growth, ICT, natural resources, and environmental innovation reduce the ecological footprint in the long run in developed economies. Based on these outcomes, the study recommends important policy suggestions.

Inrush of limestone karst water through the mine floor occurs frequently in the Carboniferous–Permian coalfield in northern China. The unascertained measurement evaluation and set pair analysis methods are proposed to evaluate water inflow, by using eight indices. Firstly, ordered binary comparison quantization method and interval number fuzzy decision matrix of EA-TOPSIS ordering were used to obtain weights for these eight factors. Secondly, conflicting evidence theory is applied to couple of these weights calculated by ordered binary comparison quantization and EA-TOPSIS ordering, to ensure the effective evaluation of the relative importance with respect to each indicator for the dynamic model. Lastly, the unapprehend measurement evaluation and set pair analysis methods were utilized to evaluate the risk of limestone karst water influx from coal seam floor. Based on the type of index value, the state classification is carried out through quantitative analysis, and single index measure functions including linear and non-linear patterns, are constructed. The process is described as follows: first, the 8 index values collected from 30 water inrush points in Xinwen coalfield are substituted into the measurement function to construct the multi index comprehensive evaluation matrix. Second, the credibility identification criterion is introduced to determine the risk level of water incurred point XiFinally, the general situation of water inflow risk from coal seam floor during coal mining in Xinwen coalfield is illustrated by using set pair potential analysis method. The production practice in Xinwen coalfield has proved that the evaluation results are consistent with the actual situation.

China has planned the Belt and Road Initiative to start collaborations among relevant economies in the technology innovation sector. This study examined the impact of technology innovation on environmental quality among the host economies of Belt and Road Initiative (BRI) countries by using panel data of 45 economies from 1991 to 2019. The study employed a fully modified ordinary least squares (FMOLS) panel to estimate the long-run associations among suggested variables. The outcomes validated a healthy cross-sectional dependence within the panel BRI economies. One estimated result of FMOLS specified that increases in patents and trademarks improved the quality of the environment in only Europe in the long run. Trademarks also enhanced the environment in BRI, MENA, and Central Asia. In the short run, the panel heterogeneous causality showed bi-directional causality among patents, trademarks, and CO2 emissions. The results of this study articulated the environment-friendly policies in technology innovation in BRI regions.

The current sedimentological and petrographical research of the Abbottabad Formation has been carried out in order to understand the formation and evolution of the Proto-Tethys Ocean during the Cambrian on the northern margin of the Indian Plate. The Muzaffarabad region is located east of the Upper Indus Basin and the southern part of the Hazara Kashmir Syntaxis. The geological history of the region varies from the Precambrian to the recent period. The Cambrian Abbottabad Formation is well exposed along the Hazara Kashmir Syntaxis at the core of the 500-m-thick Muzaffarabad anticline. The Abbottabad Formation is an unconformity-bounded allo-stratigraphic unit. It has an unconformable lower contact with the Late Precambrian Dogra Formation and an unconformable upper contact with the Paleocene Hangu Formation. The Abbottabad Formation has been divided into four lithofacies, from bottom to top, namely, thinly interbedded dolomite and shale, cherty-stromatolitic dolomite, oxidized limonitic-brecciated zone, and quartzite, with significant lithological changes. Petrographic studies revealed four types of dolomites: fine crystalline dolomite (Dol. I), dolomitic cryptocrystalline chert (Dol. II), algal mat-stromatolitic dolomite (Dol. III), and intraclastic-dolo-grain stone (Dol. IV). The mineral composition of dolostone was analyzed using X-ray diffraction (XRD) and found to be consistent with previous petrographic studies. The dolomite mineral content decreased from base to top, while chert increased towards the top. Elemental weight percentages through energy dispersive X-ray (EDX) analysis show different elements constitute the minerals found in the dolostone, as confirmed by petrographic and XRD analysis. Using outcrop data, facies information, and geochemical data, a modified depositional model of the Abbottabad Formation was developed. During the Early Cambrian period, the formation was deposited in a shallow subtidal to supratidal setting of the Proto-Tethys Ocean. The top of this deposit marks the Cambrian–Paleocene boundary. Because of the progressively coarsening outcrop sequences, this formation seems to be at the very top of the Proto-Tethys Ocean’s shallow marine system.

An integrated study based on field observation, petrography, and scanning electron microscopy (SEM) on the Early–Middle Eocene carbonate rocks has been carried out, which were deposited in the Ceno-Tethys Ocean. The study area of the Yadgaar Section lies on the eastern margin of the Upper Indus Basin, Pakistan. The Early–Middle Eocene Margalla Hill Limestone and Chorgali Formation act as reservoir rocks in other parts of the basin and are also present in the Yadgaar Section. The lack of comprehensive study in this area makes these reservoir rocks highly attractive for sedimentological evaluations and future exploration of hydrocarbons. The Early–Middle Eocene carbonate rocks are divided into nine microfacies: dolomicritic foraminiferal mudstone–wackestone microfacies (EMI); green algae dominated, mixed foraminiferal wackestone–packstone microfacies (EMII); ostracod, green algae and gypsum dominating mudstone–wackestone microfacies (EMIII); algae and mixed foraminiferal wackestone–packstone microfacies (EMIV); Nummulites dominating mudstone–wackestone microfacies (EMV); algal limestone mudstone microfacies (EMVI); Assilina bed wackestone–packstone microfacies (EMVII); micritized larger benthic foraminiferal wackestone–packstone microfacies (EMVIII); and algal limestone, mudstone microfacies (EMIX). The transgressive-regressive environment in the Ceno-Tethys Ocean leads to the deposition of these microfacies in the platform interior, open marine platform, platform edge, platform margin reef, toe of the slope apron, arid–humid platform interior, platform edge, open marine platform interior, and restricted marine platform interior, respectively. Initial post-depositional diagenetic stages are identified from the base to the top of the strata by their respective cement types, i.e., the base–lower middle part of the strata demonstrates an eogenetic sub-stage with the appearance of drusy cement, the middle section indicates a mesogenetic sub-stage by the appearance of blocky cement, while the top portion again reveals an eogenetic sub-stage of diagenesis by the presence of drusy and blocky types of cement. The ascending–descending hierarchy of cement generations is directly proportional to the grade of diagenesis from the base to the top of the carbonate strata. Variable diagenetic effects on the various microfacies also increase the secondary porosity range and enhance the reservoir characteristics of the Formations. The presence of foraminifera microfossils determined that these carbonate formations date from the Early–Middle Eocene.

Abstract Background The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent at the gene sequence level. Results A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella Typhi Ty2 (STY1), which were then grown in rich media. The locations of 234,152 and 53,556 integration sites, respectively, were mapped by sequencing. These data were compared to similar data available for a different Ty2 isolate (STY2) and essential genes identified in E. coli K-12 (ECO). Of 277 genes considered essential in ECO, all had syntenic homologs in STM1, STY1, and STY2, and all but nine genes were either devoid of transposon insertions or had very few. For three of these nine genes, part of the annotated gene lacked transposon integrations (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498, STM14_2872, STM14_3360, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. Conclusions Comparisons among transposon integration profiles from different members of a species and among related species, all grown in similar conditions, identify differences in gene contributions to fitness among syntenic homologs. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology.

Abstract Background The type III secretion system (TTSS) is an important virulence determinant of Gram-negative bacterial pathogens. It enables the injection of effector proteins into the cytosol of eukaryotic cells. These effectors ultimately manipulate the cellular functions of the infected organism. Salmonella enterica serovar Typhimurium encodes two virulence associated TTSSs encoded by the Salmonella Pathogenicity Islands (SPI) 1 and 2 that are required for the intestinal and systemic phases of the infection, respectively. However, recent studies suggest that the roles of these TTSSs are not restricted to these compartments. The regulation of TTSSs in Salmonella is very complex with several regulators operating to activate or to repress expression depending on the environmental conditions. Results We performed a systematic analysis of the regulation of type III effectors during growth in vitro. We have tested the ability of seven regulatory genes to regulate ten effector genes. Each regulator was expressed in the absence of the other six to avoid cascade effects. Our results confirm and extend the previously reported regulation of TTSS1 and TTSS2 effectors by InvF-SicA and SsrB respectively. Conclusion The set of strains constructed for this study can be used to quickly and systematically study the regulation of newly identified effector genes of Salmonella enterica. The approach we have used can also be applied to study complex regulatory cascades in other bacterial species.

The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This single-sample metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of clinically important bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, and West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. In addition, >99% inactivation, which increased with solvent exposure time, was also observed for pathogens without exposed lipid membranes including community-associated methicillin-resistant Staphylococcus aureus, Clostridium difficile spores and vegetative cells, and adenovirus type 5. The overall pipeline of inactivation and subsequent proteomic, metabolomic, and lipidomic analyses was evaluated using a human epithelial lung cell line infected with wild-type and mutant influenza H7N9 viruses, thereby demonstrating that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses. Based on these experimental results, we believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics measurements from a single specimen with high success for pathogens with exposed lipid membranes.

Proteins of the LuxR family detect the presence of N-acylhomoserine lactones (AHLs) and regulate transcription accordingly. When AHLs are synthesized by the same species that detects them, the system allows a bacterium to measure the population density of its own species, a phenomenon known as quorum sensing. The sdiA genes of Escherichia coli and Salmonella enterica serovar Typhimurium are predicted to encode LuxR homologs. However, these species do not appear to synthesize AHLs or any other molecule detected by SdiA. It has previously been demonstrated that overexpression of sdiA results in the activation of the ftsQAZ locus in E. coli and four other loci in Salmonella serovar Typhimurium. Here we report that transcriptional fusions to these five loci fall into two classes. The first class requires overexpression of sdiA for activation. The second class responds to sdiA expressed from its natural position in the chromosome if the appropriate AHLs are added to the culture. The only member of the second class is a series of Prck-luxCDABE fusions in Salmonella serovar Typhimurium. SdiA responds with highest sensitivity to AHLs that have a keto modification at the third carbon and an acyl chain length of 6 or 8 (half-maximal response between 1 and 5 nM). Growth of Salmonella in proximity to species known to synthesize these AHLs results in sdiA-dependent activation of the Prck-luxCDABE fusions. SdiA appears to be the first AHL receptor discovered that detects signals emanating exclusively from other species.

The sirA gene of Salmonella enterica serovar Typhimurium encodes a two-component response regulator of the FixJ family that has a positive regulatory influence on the expression of type III secretion genes involved with epithelial cell invasion and the elicitation of bovine gastroenteritis. SirA orthologs in Pseudomonas, Vibrio, and Erwinia control the expression of distinct virulence genes in these genera, but an evolutionarily conserved target of SirA regulation has never been identified. In this study we tested the hypothesis that sirA may be an ancient member of the flagellar regulon. We examined the effect of a sirA mutation on transcriptional fusions to flagellar promoters (flhD, fliE, fliF, flgA, flgB, fliC, fliD, motA, and fliA) while using fusions to the virulence gene sopB as a positive control. SirA had only small regulatory effects on all fusions in liquid medium (less than fivefold). However, in various types of motility agar plates, sirA was able to activate a sopB fusion by up to 63-fold while repressing flagellar fusions by values exceeding 100-fold. Mutations in the sirA orthologs of Escherichia coli, Vibrio cholerae, Pseudomonas fluorescens, and Pseudomonas aeruginosa result in defects in either motility or motility gene regulation, suggesting that control of flagellar regulons may be an evolutionarily conserved function of sirA orthologs. The implications for our understanding of virulence gene regulation in the gamma Proteobacteria are discussed.

SirA of Salmonella typhimurium is known to regulate the hilA and prgH genes within Salmonella pathogenicity island 1 (SPI1). To identify more members of the SirA regulon, we screened 10,000 random lacZY fusions (chromosomal MudJ insertions) for regulation by SirA and identified 10 positively regulated fusions. Three fusions were within the SPI1 genes hilA (an SPI1 transcriptional regulator), spaS (a component of the SPI1 type III export apparatus) and sipB (a substrate of the SPI1 export apparatus). Two fusions were within the sopB gene (also known as sigD). sopB is located within SPI5, but encodes a protein that is exported via the SPI1 export apparatus. In addition, five fusions were within genes of unknown function that are located in SPI4. As spaS and sipB were likely to be hilA dependent, we tested all of the fusions (except hilA) for hilA dependence. Surprisingly, we found that all of the fusions require hilA for expression and that plasmid-encoded SirA cannot bypass this requirement. Therefore, SirA regulates hilA, the product of which regulates genes within SPI1, SPI4 and SPI5. Both sirA and hilA mutants are dramatically attenuated in a bovine model of gastroenteritis, but have little or no effect in the mouse model of typhoid fever. This study establishes the SirA/HilA regulatory cascade as the primary regulon controlling enteropathogenic virulence functions in S. typhimurium. Because S. typhimurium causes gastroenteritis in both cattle and humans, we believe that this information may be directly applicable to the human disease.

Most isolates of Salmonella enterica serovar Typhimurium contain a 90-kb virulence plasmid. This plasmid is reported to be mobilizable but nonconjugative. However, we have determined that the virulence plasmid of strains LT2, 14028, and SR-11 is indeed self-transmissible. The plasmid of strain SL1344 is not. Optimal conjugation frequency requires filter matings on M9 minimal glucose plates with a recipient strain lacking the virulence plasmid. These conditions result in a frequency of 2.9 x 10(-4) transconjugants/donor. Matings on Luria-Bertani plates, liquid matings, or matings with a recipient strain carrying the virulence plasmid reduce the efficiency by up to 400-fold. Homologs of the F plasmid conjugation genes are physically located on the virulence plasmid and are required for the conjugative phenotype.

Quorum sensing is a phenomenon in which bacteria sense and respond to their own population density by releasing and sensing pheromones. In gram-negative bacteria, quorum sensing is often performed by the LuxR family of transcriptional regulators, which affect phenotypes as diverse as conjugation, bioluminescence, and virulence gene expression. The gene encoding one LuxR family member, named sdiA (suppressor of cell division inhibition), is present in the Escherichia coli genome. In this report, we have cloned the Salmonella typhimurium homolog of SdiA and performed a systematic screen for sdiA-regulated genes. A 4.4-kb fragment encoding the S. typhimurium sdiA gene was sequenced and found to encode the 3' end of YecC (homologous to amino acid transporters of the ABC family), all of SdiA and SirA (Salmonella invasion regulator), and the 5' end of UvrC. This gene organization is conserved between E. coli and S. typhimurium. We determined that the S. typhimurium sdiA gene was able to weakly complement the E. coli sdiA gene for activation of ftsQAZ at promoter 2 and for suppression of filamentation caused by an ftsZ(Ts) allele. To better understand the function of sdiA in S. typhimurium, we screened 10,000 random lacZY transcriptional fusions (MudJ transposon mutations) for regulation by sdiA. Ten positively regulated fusions were isolated. Seven of the fusions were within an apparent operon containing ORF8, ORF9, rck (resistance to complement killing), and ORF11 of the S. typhimurium virulence plasmid. The three ORFs have now been named srgA, srgB, and srgC (for sdiA-regulated gene), respectively. The DNA sequence adjacent to the remaining three fusions shared no similarity with previously described genes.

TonB, a cytoplasmic membrane protein, couples cytoplasmic membrane protonmotive force to active transport across the outer membrane of Escherichia coli. In vivo cross-linking studies were initiated to analyze TonB interactions with other cell envelope proteins. Four TonB-specific cross-linked complexes were detected with apparent molecular masses of 195, 77, 59, and 43.5 kDa. The 195-kDa complex was shown to contain both TonB and FepA, the outer membrane receptor for the siderophore enterochelin. The 195-kDa complex is absent in strains missing either TonB or FepA and can be detected by either TonB-specific or FepA-specific monoclonal antibodies. This is the first direct in vivo evidence that TonB can span the periplasmic space to interact physically with outer membrane receptors. Consistent with that observation, the outer membrane protease OmpT was shown to play a role in TonB turnover, both in the presence and absence of ExbB results in the rapid degradation of TonB. The absence of OmpT could be used to stabilize TonB in an exbB::Tn10 strain such that steady state levels of TonB protein are identical to a wild-type strain. Under those conditions, the absence of ExbB results in greatly reduced TonB activity, indicating that ExbB plays a direct role in energy transduction and probably secondarily protects TonB protein from proteolysis. The 59-kDa complex was absent in an exbB::Tn10 strain, suggesting either that ExbB is in the complex with TonB or that ExbB is required to form the 59-kDa complex. A tolQ nonsense mutation had no effect on the cross-linking profile observed, confirming that its participation in TonB-dependent phenomena is minor and most likely the result of evolutionary cross-talk.