High Vcmax, Jmax and photosynthetic rates of Sonoran Desert species : using nitrogen and specific leaf area traits as predictors in biochemical models

Dryland ecosystems largely control the inter-annual variability of the global carbon cycle. Unfortunately, there is a paucity of data on key biochemical parameters, such as maximum carboxylation velocity (Vcmax25) and electron transport rate (Jmax25), from species in these ecosystems which limits our capacity to model photosynthesis across ecological scales. We studied six dominant C3 shrub and tree species from the Sonoran Desert with different leaf traits and phenological strategies. We characterized Vcmax25 and Jmax25 for each species and assessed which traits or trait combinations were the best predictors of these parameters for biochemical models of photosynthesis. All species had high values of Vcmax25 and Jmax25, mostly explained by high leaf nitrogen content (Narea) and high nitrogen allocation to photosynthetic enzymes comparable to those reported for herbs and crop species but higher than those of shrubs and other functional types in world databases. We found that the high values of Vcmax25 and Jmax25, by increasing rates of photosynthetic reactions, enhance photosynthetic water and nitrogen-use efficiencies and may favor carbon gain under typical conditions in drylands. Our findings improve the parameterization of photosynthesis models, and provide novel implications to common findings of high Narea in dryland species

Foliar C, N, and P stoichiometry characterize successful plant ecological strategies in the Sonoran Desert

Ecological processes are centered to water availability in drylands; however, less known nutrient stoichiometry can help explain much of their structure and ecological interactions. Here we look to the foliar stoichiometry of carbon (C), nitrogen (N), and phosphorus (P) of 38 dominant plant species from the Sonoran Desert, grouped in four different functional types to describe ecological characteristics and processes. We found that foliar N, C:N, C:P, and N:P stoichiometric ratios, but not P, were higher than those known to most other ecosystems and indicate P but not N limitations in leaves. Biological N fixers (BNF) had even higher leaf N concentrations, but bio-elemental concentrations and stoichiometry ratios were not different to other non-N-fixing legume species which underscores the need to understand the physiological mechanisms for high N, and to how costly BNF can succeed in P-limiting drylands environments. Stoichiometry ratios, and to lesser extent elemental concentrations, were able to characterize BNF and colonizing strategies in the Sonoran Desert, as well as explain leaf attribute differences, ecological processes, and biogeochemical niches in this dryland ecosystem, even when no direct reference is made to other water-limitation strategies

Rate of Isolation and Trends of Antimicrobial Resistance of Multidrug Resistant Pseudomonas Aeruginosa from Otorrhea in Chronic Suppurative Otitis Media

ObjectivesTo assess the rate of isolation of Pseudomonas aeruginosa (PA) and multidrug-resistant PA (MDR-PA) from patients with chronic suppurative otitis media (CSOM) otorrhea and the annual trend of antibiotic-resistance.MethodsOtorrhea samples were collected aseptically from 1,598 CSOM patients. The rate of bacterial isolation and the results of antibiotic susceptibility testing were evaluated retrospectively.ResultsThe PA isolation rate from CSOM otorrhea was 24.4%. Of the 398 isolated strains tested for their susceptibilities to 10 antibiotics, 395 strains showed definitive results. Of these, 183 (46.3%) were susceptible to whole antibiotics and 212 (53.7%) was resistant to more than 1 antibiotics, with the frequency of antibiotics-resistance increasing significantly over time. Although strains susceptible to all antibiotics decreased over time, the rate of isolation of MDR-PA did not change significantly. Resistance to aminoglycosides and quinolones was higher than to other antibiotics and significantly increased over time, whereas resistance to other antibiotics showed no trend.ConclusionMDR-PA, assessed using five individual antibiotics and six antibiotic-classes, showed no tendency to increase or decrease over time. This may have been due to increased concern about antibiotic-resistant bacterial strains, leading to improved infection control within hospitals and healthcare centers

Prospective identification of parasitic sequences in phage display screens

Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 10[superscript 9] random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the ‘parasites’), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 ‘parasites’. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ~10[superscript 6] diverse clones prevents the biased selection of parasitic clones

Aminoglycoside Resistance Rates, Phenotypes, and Mechanisms of Gram-Negative Bacteria from Infected Patients in Upper Egypt

With the re-emergence of older antibiotics as valuable choices for treatment of serious infections, we studied the aminoglycoside resistance of Gram-negative bacteria isolated from patients with ear, urinary tract, skin, and gastrointestinal tract infections at Minia university hospital in Egypt. Escherichia coli (mainly from urinary tract and gastrointestinal tract infections) was the most prevalent isolate (28.57%), followed by Pseudomonas aeruginosa (25.7%) (mainly from ear discharge and skin infections). Isolates exhibited maximal resistance against streptomycin (83.4%), and minimal resistance against amikacin (17.7%) and intermediate degrees of resistance against neomycin, kanamycin, gentamicin, and tobramycin. Resistance to older aminoglycosides was higher than newer aminoglycoides. The most common aminoglycoside resistance phenotype was that of streptomycin resistance, present as a single phenotype or in combination, followed by kanamycin-neomycin as determined by interpretative reading. The resistant Pseudomonas aeruginosa strains were capable of producing aminoglycoside-modifying enzymes and using efflux as mechanisms of resistance. Using checkerboard titration method, the most frequently-observed outcome in combinations of aminoglycosides with β-lactams or quinolones was synergism. The most effective combination was amikacin with ciprofloxacin (100% Synergism), whereas the least effective combination was gentamicin with amoxicillin (53.3% Synergistic, 26.7% additive, and 20% indifferent FIC indices). Whereas the studied combinations were additive and indifferent against few of the tested strains, antagonism was never observed. The high resistance rates to aminoglycosides exhibited by Gram-negative bacteria in this study could be attributed to the selective pressure of aminoglycoside usage which could be controlled by successful implementation of infection control measures

Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside–RNA hairpin loop interactions

Herein, we report the identification of RNA hairpin loops that bind derivatives of kanamycin A, tobramycin, neamine, and neomycin B via two-dimensional combinatorial screening, a method that screens chemical and RNA spaces simultaneously. An arrayed aminoglycoside library was probed for binding to a 6-nucleotide RNA hairpin loop library (4096 members). Members of the loop library that bound each aminoglycoside were excised from the array, amplified and sequenced. Sequences were analyzed with our newly developed RNA Privileged Space Predictor (RNA-PSP) program, which analyzes selected sequences to identify statistically significant trends. RNA-PSP identified the following unique trends: 5′UNNNC3′ loops for the kanamycin A derivative (where N is any nucleotide); 5′UNNC3′ loops for the tobramycin derivative; 5′UNC3′ loops for the neamine derivative; and 5′UNNG3′ loops for the neomycin B derivative. The affinities and selectivities of a subset of the ligand–hairpin loop interactions were determined. The selected interactions have Kd values ranging from 10 nM to 605 nM. Selectivities ranged from 0.4 to >200-fold. Interestingly, the results from RNA-PSP are able to qualitatively predict specificity based on overlap between the RNA sequences selected for the ligands. These studies expand the information available on small molecule–RNA motif interactions, which could be useful to design ligands targeting RNA

Quantitative Organization of GABAergic Synapses in the Molecular Layer of the Mouse Cerebellar Cortex

In the cerebellar cortex, interneurons of the molecular layer (stellate and basket cells) provide GABAergic input to Purkinje cells, as well as to each other and possibly to other interneurons. GABAergic inhibition in the molecular layer has mainly been investigated at the interneuron to Purkinje cell synapse. In this study, we used complementary subtractive strategies to quantitatively assess the ratio of GABAergic synapses on Purkinje cell dendrites versus those on interneurons. We generated a mouse model in which the GABAA receptor α1 subunit (GABAARα1) was selectively removed from Purkinje cells using the Cre/loxP system. Deletion of the α1 subunit resulted in a complete loss of GABAAR aggregates from Purkinje cells, allowing us to determine the density of GABAAR clusters in interneurons. In a complementary approach, we determined the density of GABA synapses impinging on Purkinje cells using α-dystroglycan as a specific marker of inhibitory postsynaptic sites. Combining these inverse approaches, we found that synapses received by interneurons represent approximately 40% of all GABAergic synapses in the molecular layer. Notably, this proportion was stable during postnatal development, indicating synchronized synaptogenesis. Based on the pure quantity of GABAergic synapses onto interneurons, we propose that mutual inhibition must play an important, yet largely neglected, computational role in the cerebellar cortex

Synthesis of Janus compounds for the recognition of G-U mismatched nucleobase pairs

The design and synthesis of two Janus-type heterocycles with the capacity to simultaneously recognize guanine and uracyl in G-U mismatched pairs through complementary hydrogen bond pairing is described. Both compounds were conveniently functionalized with a carboxylic function and efficiently attached to a tripeptide sequence by using solid-phase methodologies. Ligands based on the derivatization of such Janus compounds with a small aminoglycoside, neamine, and its guanidinylated analogue have been synthesized, and their interaction with Tau RNA has been investigated by using several biophysical techniques, including UV-monitored melting curves, fluorescence titration experiments, and 1H NMR. The overall results indicated that Janus-neamine/guanidinoneamine showed some preference for the +3 mutated RNA sequence associated with the development of some tauopathies, although preliminary NMR studies have not confirmed binding to G-U pairs. Moreover, a good correlation has been found between the RNA binding affinity of such Janus-containing ligands and their ability to stabilize this secondary structure upon complexation