Influence of the spacer region between the Shine–Dalgarno box and the start codon for fine-tuning of the translation efficiency in Escherichia coli

Translation efficiency contributes several orders of magnitude difference in the overall yield of exogenous gene expression in bacteria. In diverse bacteria, the translation initiation site, whose sequence is the primary determinant of the translation performance, is comprised of the start codon and the Shine–Dalgarno box located upstream. Here, we have examined how the sequence of a spacer between these main components of the translation initiation site contributes to the yield of synthesized protein. We have created a library of reporter constructs with the randomized spacer region, performed fluorescently activated cell sorting and applied next-generation sequencing analysis (the FlowSeq protocol). As a result, we have identified sequence motifs for the spacer region between the Shine–Dalgarno box and AUG start codon that may modulate the translation efficiency in a 100-fold range.     

Human HPRT1 gene and the Lesch–Nyhan disease: Substitution of alanine for glycine and inversely in the HGprt enzyme protein

Lesch–Nyhan disease (LND) is a rare X-linked inherited neurogenetic disorder of purine metabolism in which the enzyme, hypoxanthine-guanine phosphoribosyltransferase (HGprt) is defective. The authors report three novel independent mutations in the coding region of the HPRT1 gene from genomic DNA of (a) a carrier sister of two male patients with LND: c.569G>C, p.G190A in exon 8; and (b) two LND affected male patients unrelated to her who had two mutations: c.648delC, p.Y216X, and c.653C>G, p.A218G in exon 9. Molecular analysis reveals the heterogeneity of genetic mutation of the HPRT1 gene responsible for the HGprt deficiency. It allows fast, accurate detection of carriers and genetic counseling.     

Freeze–thaw processes and intense rainfall: the one-two punch for high sediment and nutrient loads from mid-Atlantic watersheds

Large runoff, sediment, and nutrient exports from watersheds could occur due to individual extreme climate events or a combination of multiple hydrologic and meteorological conditions. Using high-frequency hydrologic, sediment, and turbidity data we show that freeze–thaw episodes followed by intense winter (February) rainstorms can export very high concentrations and loads of suspended sediment and particulate organic carbon (POC) and nitrogen (PN) from mid-Atlantic watersheds in the US. Peak suspended sediment (> 5000 mg L^?1), POC (> 250 mg L^?1) and PN (> 15 mg L^?1) concentrations at our 12 and 79 ha forested watersheds for the February rainfall-runoff events were highest on record and the fluxes were comparable to those measured for tropical storms. Similar responses were observed for turbidity values (> 400 FNU) at larger USGS-monitored watersheds. Much of the sediments and particulate nutrients likely originated from erosion of stream bank sediments and/or channel storage. Currently, there is considerable uncertainty about the contribution of these sources to nonpoint source pollution, particularly, in watersheds with large legacy sediment deposits. Future climate projections indicate increased intensification of storm events and increased variability of winter temperatures. Freeze–thaw cycles coupled with winter rain events could increase erosion and transport of streambank sediments with detrimental consequences for water quality and health of downstream aquatic ecosystems.     

A Highlights from MBoC Selection: Combined computational and experimental analysis reveals mitogen-activated protein kinase–mediated feedback phosphorylation as a mechanism for signaling specificity

Different environmental stimuli often use the same set of signaling proteins to achieve very different physiological outcomes. The mating and invasive growth pathways in yeast each employ a mitogen-activated protein (MAP) kinase cascade that includes Ste20, Ste11, and Ste7. Whereas proper mating requires Ste7 activation of the MAP kinase Fus3, invasive growth requires activation of the alternate MAP kinase Kss1. To determine how MAP kinase specificity is achieved, we used a series of mathematical models to quantitatively characterize pheromone-stimulated kinase activation. In accordance with the computational analysis, MAP kinase feedback phosphorylation of Ste7 results in diminished activation of Kss1, but not Fus3. These findings reveal how feedback phosphorylation of a common pathway component can limit the activity of a competing MAP kinase through feedback phosphorylation of a common activator, and thereby promote signal fidelity.     

Applying new tools to cephalopod trophic dynamics and ecology: perspectives from the Southern Ocean Cephalopod Workshop, February 2–3, 2006

A two day workshop on Southern Ocean cephalopods was held in Hobart, Tasmania, Australia prior to the triennial 2006 Cephalopod International Advisory Council (CIAC) symposium. The workshop provided a second international forum to present the current state of research and new directions since the last Southern Ocean cephalopod meeting held in 1993. A major focus of the workshop was trophic ecology and the use of a variety of tools that can be applied in Southern Ocean trophic studies for both cephalopod and predator researchers. New tools that are being used as trophic indicators and tracers in food chain pathways include stable isotope, heavy metal and fatty acid signature analysis. Progress is also being made on understanding squid population dynamics in relation to other key components of the ecosystem by incorporating squid data in ecosystem models. Genetic barcoding is now of great value to fish taxonomy as well as other groups and it is expected that a cephalopod barcoding initiative will be an important tool for cephalopod taxonomy. There is a current initiative to produce a new cephalopod beak identification guide to assist predator biologists in identifying cephalopod prey items. There were also general discussions on specific taxonomic issues, Southern Ocean Cephalopod paralarvae and parasites, and suggestions for future CIAC workshop topics.     

Valorization of cruor slaughterhouse by-product by enzymatic hydrolysis for the production of antibacterial peptides: focus on α 1–32 family peptides mechanism and kinetics modeling

Bioprocess and Biosystems Engineering - Bovine hemoglobin is the major component of the cruor (slaughterhouse by-product) and can be considered as an important source of active peptides that could...     

Motifs specific for the ADR1 NBS–LRR protein family in <Emphasis Type="Italic">Arabidopsis</Emphasis> are conserved among NBS–LRR sequences from both dicotyledonous and monocotyledonous plants

The activated disease resistance (ADR) 1 gene encodes a protein that possesses an N-terminal coiled-coil (CC) motif, nucleotide-binding site (NBS) and C-terminal leucine-rich repeat (LRR) domains. ADR1 belongs to a small, atypical Arabidopsis thaliana sub-class containing four CC–NBS–LRR genes. The NBS region of most NBS–LRR proteins possesses numerous conserved motifs. In contrast, the LRR domain, which is subject to positive selection, is highly variable. Surprisingly, sequence analysis revealed that the LRR domain of the ADR1 sub-class was more conserved than the NBS region. Sequence analysis identified two novel conserved motifs, termed TVS and PKAE, specific for this CC–NBS–LRR sub-class. The TVS motif is adjacent to the P-loop, whereas the PKAE motif corresponded to the inter-domain region termed the NBS–LRR linker, which was conserved within the different CC–NBS–LRR classes but varied among classes. These ADR1-specific motifs were employed to identify putative ADR1 homologs in phylogenetically distant and agronomically important plant species. Putative ADR1 homologs were identified in 11 species including rice and in 3 further Poaceae species. The ADR1 sub-class of CC–NBS–LRR proteins is therefore conserved in both monocotyledonous and dicotyledonous plant species.     

Solution NMR structure of the helicase associated domain BVU_0683(627–691) from Bacteroides vulgatus provides first structural coverage for protein domain family PF03457 and indicates domain binding to DNA

A high-quality NMR structure of the helicase associated (HA) domain comprising residues 627–691 of the 753-residue protein BVU_0683 from Bacteroides vulgatus exhibits an all α-helical fold. The structure presented here is the first representative for the large protein domain family PF03457 (currently 742 members) of HA domains. Comparison with structurally similar proteins supports the hypothesis that HA domains bind to DNA and that binding specificity varies greatly within the family of HA domains constituting PF03457.     

Increase in survival for patients with mantle cell lymphoma in the era of novel agents in 1995–2013: Findings from Texas and national SEER areas

BackgroundOver the past 20 years, many novel agents and treatment regimens have been developed to treat mantle cell lymphoma (MCL). This study aimed to determine the impact of these new regimens on the survival of MCL patients from 1995 to 2013.MethodsAll newly diagnosed adult MCL patients in the Surveillance, Epidemiology, and End Results (SEER) and Texas Cancer Registry (TCR) databases were included. Patients were grouped into 4 calendar periods based on the time when new novel agents became available: chemotherapy-only (1995–1998, P1), rituximab + chemotherapy (1999–2004, P2), bortezomib and HyperCVAD (2005–2008, P3), bendamustine and Nordic regimen (2009–2013, P4). Associations between these time periods and survival outcomes were analyzed using the Kaplan-Meier method and Cox proportional hazard regressions.ResultsA total of 7,555 SEER patients and 2,055 TCR patients were identified. All-cause mortality rates decreased significantly from 1995 to 2013 (SEER, P < 0.001; TCR, P = 0.03). Multivariable analysis of SEER data showed that the risk of MCL-specific death decreased significantly over the study period with hazard ratios of 0.82 (P2 vs. P1), 0.66 (P3 vs. P1), and 0.58 (P4 vs. P1) (P < 0.0001). Similar results were observed for TCR data (P < 0.0001). In an analysis stratified by tumor stage, only patients with advanced- stage tumors showed a significantly decreased risk of death in both SEER (P < 0.0001) and TCR (P = 0.002) datasets.ConclusionSurvival outcome for MCL patients improved from 1995 to 2013, especially for patients with advanced-stage tumors, potentially reflecting the impact of the introduction of novel agents and new therapeutic regimens.     

Mössbauer spectra of the heme peptide (HP) 1–50 and the heme peptide:non-heme peptide (NHP) non-covalent complex 1–50:51–104 derived from cytochrome c: evidence for cytochrome c iron site solvation in aqueous solution

Mössbauer spectroscopic studies on a heme peptide (HP) derived from cytochrome c and on the HP recombined non-covalently with the remaining cleaved section are reported. The results suggest that the environment of the heme site in the known crystal structure of cytochrome c may differ in detail from the environment of the heme in the working protein.     

Disulfide bonds Cys9–Cys57, Cys34–Cys88 and Cys38–Cys90 of the β-subunit of human chorionic gonadotropin are crucial for heterodimer formation with the α-subunit: experimental evidence for the conclusions from the crystal structure of hCG

Human chorionic gonadotropin (hCG) is a heterodimeric glycoprotein hormone essential for the establishment and maintenance of pregnancy. The α- and β-subunits of hCG are highly cross-linked internally by disulfide bonds that seem to stabilize the tertiary structures required for the noncovalent association of the subunits to generate hormonal activity. This paper describes the results of our studies on the role of the disulfide bonds of hCG-β in heterodimer formation with the α-subunit. Six disulfide peptides incorporating each of the six disulfide bonds of hCG-β were screened, along with their linear counterparts, for their ability to competitively inhibit the recombination of α- and β-subunits. The disulfide peptides Cys (9–57), Cys (34–88) and Cys (38–90) were found to inhibit the α/β recombination whereas the remaining three disulfide peptides viz. Cys (23–72), Cys (26–110) and Cys (93–100) did not exhibit any inhibition activity. Interestingly, none of the linear peptides could inhibit the α/β recombination. Results clearly demonstrate that the disulfide bonds Cys⁹–Cys⁵⁷, Cys³⁴–Cys⁸⁸ and Cys³⁸–Cys⁹⁰ of the β-subunit of hCG are crucial for heterodimer formation with the α-subunit thus providing experimental confirmation of the conclusions from the crystal structure of the hormone.     

Comparing Methods for Assessing Chimpanzee (Pan troglodytes schweinfurthii) Party Size: Observations,Camera Traps,and Bed Counts from a Savanna–Woodland Mosaic in the Issa Valley,Tanzania

International Journal of Primatology - Studying animal grouping behavior is important for understanding the causes and consequences of sociality and has implications for conservation. Chimpanzee...     

Evidence for Parapatric Speciation in the Mormyrid Fish, Pollimyrus castelnaui (Boulenger, 1911), from the Okavango–Upper Zambezi River Systems: P. marianne sp. nov., Defined by Electric Organ Discharges, Morphology and Genetics

We report on parapatric speciation in the mormyrid fish, Pollimyrus castelnaui (Boulenger, 1911), from the Okavango and the Upper Zambezi River systems. We recognise samples from the Zambezi River as a distinct species, P. marianne, displaying an eastern phenotype of electric organ discharge (EOD) waveform (Type 3) that is distinct from the western EOD phenotype (Type 1) observed in P. castelnaui samples from the neighbouring Okavango. Samples from the geographically intermediate Kwando/Linyanti River (a tributary of the Zambezi that is also intermittently connected to the Okavango) presented a more variable third EOD phenotype (Type 2). In 13 out of 14 morphological characters studied, the Zambezi River samples differed significantly from P. castelnaui. Morphologically and in EOD characters, the Kwando/Linyanti fish are distinct from both P. castelnaui and P. marianne. Sequence analysis of the mitochondrial cytochrome b gene unambiguously reveals that specimens from the Zambezi River System form a well supported taxon which clearly differs from P. castelnaui from the Okavango (1.5–2.5% sequence divergence). Within specimens from the Kwando–Zambezi System some geographic differentiation can be detected (nucleotide substitutions up to 0.6%); but groups cannot be resolved with certainty. Significant allozyme differences were found between the Okavango and all other EOD types from the Upper Zambezi System, and, within the Zambezi System, between the Kwando (Type 2) and Zambezi (Type 3) individuals. The low Wright's fixation index values, the lack of fixed allele differences, and small genetic distances provide little evidence for speciation between groups within the Zambezi System, but moderate to great fixation index values and significant allele frequency differences were observed between the Okavango and the other fishes. It is concluded that within the Zambezi System, differentiation between Kwando/Linyanti and Zambezi populations (as revealed by morphology and EOD waveform comparisons) is so recent that substantial genetic (allozyme and mitochondrial sequence) differences could not have evolved, or were not detected.     

Findings from Integrated Behavioral and Biologic Survey among Males Who Inject Drugs (MWID) — Vietnam, 2009–2010: Evidence of the Need for an Integrated Response to HIV,Hepatitis B Virus,and Hepatitis C Virus

IntroductionGiven the overlapping modes of transmission of HIV, hepatitis B virus (HBV), and hepatitis C virus (HCV), understanding the burden and relationship of these infections is critical for an effective response. Representative data on these infections among males who inject drugs (MWID), the key high-risk population for HIV in Vietnam, are currently lacking.MethodsData and stored specimens from Vietnam’s 2009-2010 Integrated Biologic and Behavioral Survey, a cross-sectional study among high-risk populations, were used for this analysis. Plasma samples were tested for HIV, HBV, and HCV using commercial assays. A questionnaire was administered to provide demographic, behavior, and service-uptake information. Provincial-level analyses were conducted to profile MWID enrollees and to provide estimates on the prevalence of HIV, HBV, and HCV infection.ResultsAmong 3010 MWID sampled across 10 provinces, the median (range) HIV prevalence was 28.1% (1.0%-55.5%). Median prevalence for current HBV infection (HBsAg+) was 14.1% (11.7%-28.0%), for previous exposure to HBV (total anti-HBc+) was 71.4% (49.9%-83.1%), and for current or past HCV infection (HCV Ag/Ab+) was 53.8% (10.9%-80.8%). In adjusted analysis, HBsAg+ (aOR: 2.09, 1.01-4.34) and HCV Ag/Ab+ (aOR: 19.58, 13.07-29.33) status were significantly associated with HIV infection; the association with total anti-HBc+ approached significance (aOR: 1.29, 0.99-1.68).ConclusionThe prevalence and association between HIV, HBV, and HCV are high among MWID in Vietnam. These findings indicate the need for integrated policies and practice that for the surveillance, prevention, screening, and treatment of both HIV and viral hepatitis among MWID in Vietnam.