Long-term dynamics of phytoplankton assemblages: Microcystis-domination in Lake Taihu, a large shallow lake in China

Long-term phytoplankton assemblages in a large shallow Chineselake, Lake Taihu, were presented using the monthly monitoringdata from October 1991 to December 1999. Earlier research results(1960, 1981 and 1988) were applied to discuss the differenttrophic stages of the lake. The species composition in the lakewas more closely related to eutrophication level than to lake-size,shallowness, or turbidity. Each summer, a single peak of phytoplanktonbiovolume appeared in Meiliang Bay. The results of principalcomponents analysis showed a distinct temporal shift in speciescomposition between summer and winter. A clear spatial differencein phytoplankton occurred between Meiliang Bay and the lakecentre. Wind speed and direction affected the horizontal distributionof phytoplankton, especially Microcystis, in the lake. Temperature,underwater light climate, nutrients and grazing by zooplanktonand by fish were discussed to explain the overwhelming dominanceof Microcystis. Four nutrient-phytoplankton stages were identifiedin the lake: an oligo-mesotrophic stage with low algal biomassuntil 1981, a eutrophic situation with blooms of Microcystisduring 1988–1995, hypertrophic conditions with the dominanceof Planctonema and total phosphorus up to 200 mg m^-3 from 1996to 1997 and the restoration period after 1997. The wax and waneof the phytoplankton assemblages were mainly controlled by temperature,wind and turbidity while long-term biomass dynamics were influencedby the level of nutrients.     

Purification of equine chorionic gonadotropin (eCG) using magnetic ion exchange adsorbents in combination with high‐gradient magnetic separation

Current purification of the glycoprotein equine chorionic gonadotropin (eCG) from horse serum includes consecutive precipitation steps beginning with metaphosphoric acid pH fractionation, two ethanol precipitation steps, and dialysis followed by a numerous of fixed‐bed chromatography steps up to the specific activity required. A promising procedure for a more economic purification procedure represents a simplified precipitation process requiring only onethird of the solvent, followed by the usage of magnetic ion exchange adsorbents employed together with a newly designed ‘rotor‐stator’ type High Gradient Magnetic Fishing (HGMF) system for large‐scale application, currently up to 100 g of magnetic adsorbents. Initially, the separation process design was optimized for binding and elution conditions for the target protein in mL scale. Subsequently, the magnetic filter for particle separation was characterized. Based on these results, a purification process for eCG was designed consisting of (i) pretreatment of the horse serum; (ii) binding of the target protein to magnetic ion exchange adsorbents in a batch reactor; (iii) recovery of loaded functionalized adsorbents from the pretreated solution using HGMF; (iv) washing of loaded adsorbents to remove unbound proteins; (v) elution of the target protein. Finally, the complete HGMF process was automated and conducted with either multiple single‐cycles or multicycle operation of four sequential cycles, using batches of pretreated serum of up to 20 L. eCG purification with yields of approximately 53% from single HGMF cycles and up to 80% from multicycle experiments were reached, with purification and concentration factors of around 2,500 and 6.7, respectively. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:78–89, 2015     

Health Concerns Versus Mobile Data Needs: Conjoint Measurement of Preferences for Mobile Communication Network Scenarios

As demands for mobile broadband services and ubiquitous network coverage in our societies are increasing, the mobile communication network infrastructure has to be expanded. Concurrently, the technical infrastructure of mobile communication technologies (base stations) raises the public's concerns about health risks due to electromagnetic fields (EMF). By applying conjoint analyses, the study empirically investigates the relationship between mobile data demands, different base station locations, the prevalence of perceived health complaints, and the impact of compensation payments. Findings show that health concerns are the most critical factor for mobile network communication scenario preferences, followed by data rate availability. In the decision scenarios, base station location and compensation payments played a minor role. Two user groups, cellphone and smart phone users who differ in their sensitivity regarding health concerns and data demands, were identified by segmentation analysis. By means of a sensitivity analysis, different mobile communication network scenarios were analyzed. Outcomes show the importance of integrating users’ preferences into the design of mobile communication networks. This especially refers to an increased sensitivity regarding health concerns in cellphone users and minimum requirements for data rates at least sufficient for the usage of mobile Internet services for smart phone users.     

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs.     

Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea

Submarine mud volcanoes are formed by expulsions of mud, fluids, and gases from deeply buried subsurface sources. They are highly reduced benthic habitats and often associated with intensive methane seepage. In this study, the microbial diversity and community structure in methane-rich sediments of the Haakon Mosby Mud Volcano (HMMV) were investigated by comparative sequence analysis of 16S rRNA genes and fluorescence in situ hybridization. In the active volcano center, which has a diameter of about 500 m, the main methane-consuming process was bacterial aerobic oxidation. In this zone, aerobic methanotrophs belonging to three bacterial clades closely affiliated with Methylobacter and Methylophaga species accounted for 56%+/-8% of total cells. In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation. ANME-3 archaea form cell aggregates mostly associated with sulfate-reducing bacteria of the Desulfobulbus (DBB) branch. These ANME-3/DBB aggregates were highly abundant and accounted for up to 94%+/-2% of total microbial biomass at 2 to 3 cm below the surface. ANME-3/DBB aggregates could be further enriched by flow cytometry to identify their phylogenetic relationships. At the outer rim of the mud volcano, the seafloor was colonized by tubeworms (Siboglinidae, formerly known as Pogonophora). Here, both aerobic and anaerobic methane oxidizers were found, however, in lower abundances. The level of microbial diversity at this site was higher than that at the central and Beggiatoa species-covered part of the HMMV. Analysis of methyl-coenzyme M-reductase alpha subunit (mcrA) genes showed a strong dominance of a novel lineage, mcrA group f, which could be assigned to ANME-3 archaea. Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and anaerobic methanotrophs.     

Investigation of metal sorption behavior of Slp1 from Lysinibacillus sphaericus JG-B53: a combined study using QCM-D,ICP-MS and AFM

Surface layer proteins (S-layer) of Lysinibacillus sphaericus JG-B53 are biological compounds with several bio-based technical applications such as biosorptive materials for metal removal or rare metals recovery from the environment. Despite their well-described applications, a deeper understanding of their metal sorption behavior still remains challenging. The metal sorption ability of Au³⁺, Pd²⁺, Pt²⁺ and Eu³⁺ was investigated by ICP-MS, AFM and QCM-D which enables the sorption detection in real-time during in situ experiments. Results indicate a high binding of Pd, followed by Au, Eu and Pt to the proteins. The comparison between different methods allowed a deeper understanding of the metal sorption of isolated S-layer either frees in liquid, adsorbed forming a protein layer or as the bacteria surface.     

Coding of sinusoidally amplitude modulated acoustic stimuli in the inferior colliculus of the rufous horseshoe bat,Rhinolophus rouxi

Summary Single neuron responses to sinusoidally amplitude modulated (SAM) signals were studied in the inferior colliculus of the horseshoe bat,Rhinolophus rouxi.57% of the neurons responded to SAM stimuli with periodical discharges synchronized to the modulation cycle. The proportion of cells driven by amplitude modulated signals was independent of the best frequency of the neurons. Best modulation frequencies were at or below 100 Hz in about 70% of the neurons. Synchronized activity could be elicited by modulation frequencies up to 400 Hz.Best SAM responses were observed at stimulus intensities 10 dB above threshold. Generally the BMF of a neuron did not change with intensity. The BMF decreased with decreasing modulation depth of the amplitude modulation.A trend for a topographical organization of neurons according to best modulation frequencies was detected. The results did not reveal any significant specialization of the bat's auditory system for coding of amplitude modulations as compared to other mammals.Abbreviations BF best frequency - BMF best modulation frequency - CF constant frequency - FM frequency modulation - IC inferior colliculus - SAM sinusoidal amplitude modulation - SFM sinusoidal frequency modulation     

Human ZBP1 induces cell death‐independent inflammatory signaling via RIPK3 and RIPK1

ZBP1 is an interferon‐induced cytosolic nucleic acid sensor that facilitates antiviral responses via RIPK3. Although ZBP1‐mediated programmed cell death is widely described, whether and how it promotes inflammatory signaling is unclear. Here, we report a ZBP1‐induced inflammatory signaling pathway mediated by K63‐ and M1‐linked ubiquitin chains, which depends on RIPK1 and RIPK3 as scaffolds independently of cell death. In human HT29 cells, ZBP1 associated with RIPK1 and RIPK3 as well as ubiquitin ligases cIAP1 and LUBAC. ZBP1‐induced K63‐ and M1‐linked ubiquitination of RIPK1 and ZBP1 to promote TAK1‐ and IKK‐mediated inflammatory signaling and cytokine production. Inhibition of caspase activity suppressed ZBP1‐induced cell death but enhanced cytokine production in a RIPK1‐ and RIPK3 kinase activity‐dependent manner. Lastly, we provide evidence that ZBP1 signaling contributes to SARS‐CoV‐2‐induced cytokine production. Taken together, we describe a ZBP1‐RIPK3‐RIPK1‐mediated inflammatory signaling pathway relayed by the scaffolding role of RIPKs and regulated by caspases, which may induce inflammation when ZBP1 is activated below the threshold needed to trigger a cell death response.     

Insights into RNA biology from an atlas of mammalian mRNA-binding proteins

RNA-binding proteins (RBPs) determine RNA fate from synthesis to decay. Employing two complementary protocols for covalent UV crosslinking of RBPs to RNA, we describe a systematic, unbiased, and comprehensive approach, termed "interactome capture," to define the mRNA interactome of proliferating human HeLa cells. We identify 860 proteins that qualify as RBPs by biochemical and statistical criteria, adding more than 300 RBPs to those previously known and shedding light on RBPs in disease, RNA-binding enzymes of intermediary metabolism, RNA-binding kinases, and RNA-binding architectures. Unexpectedly, we find that many proteins of the HeLa mRNA interactome are highly intrinsically disordered and enriched in short repetitive amino acid motifs. Interactome capture is broadly applicable to study mRNA interactome composition and dynamics in varied biological settings.