Copper enrichment reduces thermal tolerance of the highly resistant Red Sea coral Stylophora pistillata

Coral Reefs - Corals in the Gulf of Aqaba (GoA) in the northern Red Sea show high thermal tolerance. The GoA has therefore been suggested as a coral reef refuge from climate change. However, as a...     

Modeling the anti-CEA antibody combining site by homology and conformational search.

A model for an antibody specific for the carcinoembryonic antigen (CEA) has been constructed using a method which combines the concept of canonical structures with conformational search. A conformational search technique is introduced which couples random generation of backbone loop conformations to a simulated annealing method for assigning side chain conformations. This technique was used both to verify conformations selected from the set of known canonical structures and to explore conformations available to the H3 loop in CEA ab initio. Canonical structures are not available for H3 due to its variability in length, sequence, and observed conformation in known antibody structures. Analysis of the results of conformational search resulted in three equally probable conformations for H3 loop in CEA. Force field energies, solvation free energies, exposure of charged residues and burial of hydrophobic residues, and packing of hydrophobic residues at the base of the loop were used as selection criteria. The existence of three equally plausible structures may reflect the high degree of flexibility expected for an exposed loop of this length. The nature of the combining site and features which could be important to interaction with antigen are discussed.     

Fab-based bispecific antibody formats with robust biophysical properties and biological activity

A myriad of innovative bispecific antibody (BsAb) platforms have been reported. Most require significant protein engineering to be viable from a development and manufacturing perspective. Single-chain variable fragments (scFvs) and diabodies that consist only of antibody variable domains have been used as building blocks for making BsAbs for decades. The drawback with Fv-only moieties is that they lack the native-like interactions with C_H1/C_L domains that make antibody Fab regions stable and soluble. Here, we utilize a redesigned Fab interface to explore 2 novel Fab-based BsAbs platforms. The redesigned Fab interface designs limit heavy and light chain mixing when 2 Fabs are co-expressed simultaneously, thus allowing the use of 2 different Fabs within a BsAb construct without the requirement of one or more scFvs. We describe the stability and activity of a HER2×HER2 IgG-Fab BsAb, and compare its biophysical and activity properties with those of an IgG-scFv that utilizes the variable domains of the same parental antibodies. We also generated an EGFR × CD3 tandem Fab protein with a similar format to a tandem scFv (otherwise known as a bispecific T cell engager or BiTE). We show that the Fab-based BsAbs have superior biophysical properties compared to the scFv-based BsAbs. Additionally, the Fab-based BsAbs do not simply recapitulate the activity of their scFv counterparts, but are shown to possess unique biological activity.     

Uptake of Cadmium by Hydroponically Grown,Mature Eucalyptus Camaldulensis Saplings and the Effect of Organic Ligands

The potential suitability of Eucalyptus camaldulensis for Cd phytoextraction was tested in a hydroponic study. Saplings were exposed to 4.5 and 89 μM Cd for one month, with and without EDTA and s,s-EDDS at 0.1, 1, and 5 mM. The saplings’ growth was not affected at the 4.5 μM Cd concentration, yet it decreased 3-fold at 89 μM, and almost all the Cd taken up was immobilized in the roots, reaching 360 and 5300 mg Cd kg^?1, respectively (approximately 75% of which was non-washable in acid). The respective Cd root-to-shoot translocation factors were 0.14 and ≈5*10^?4. At 0.1 mM concentration, EDTA and EDDS had no effect or even a positive effect on the saplings growth. This was reversed at 1 mM, and the chelants became lethal at the 5 mM concentration. At 89 μM Cd in the growth medium, 0.1 mM EDTA increased Cd translocation into the shoots by almost 10-fold, however it strongly reduced Cd content inside the roots. This hydroponic study indicates the feasibility of E. camaldulensis use for cleanup Cd-contaminated soils at environmental concentrations, both for site stabilization (phytostabilization) and gradual remediation (phytoextraction). EDTA was shown to be much more efficient in enhancing Cd translocation than s,s-EDDS.     

The Weight of the Hyphen: Freedom,Fusion and Responsibility Embodied by Young Muslim-American Women During a Time of Surveillance

This article reports on a qualitative investigation of 15 young Muslim-American women living in New York City, after 9/11 and in the midst of the Patriot Act. Participants completed surveys about identity, discrimination, and coping; drew “identity maps” to represent their multiple identities and alliances; and participated in focus groups on several college campuses in the New York metropolitan area. Focus groups were conducted to investigate collectively their sense of hyphenated identities, their experiences of surveillance and their responses to scrutiny in families, communities, on the streets and in the political public sphere. Implications for the theoretical and empirical study of immigrant youth “under siege” are developed, with a particular focus on the burdens and responsibilities embodied by daughters of the second generation of Muslim-Americans.     

Calls of the black drum (Pogonias cromis: Sciaenidae): geographical differences in sound production between northern and southern hemisphere populations

Because of apparent reproductive isolation between Northern and Southern hemisphere populations of the black drum Pogonius cromis, we tested the hypothesis that advertisement calls from a southern population would differ from known calls of North American populations. Additionally, we quantified disturbance and advertisement calls, their changes with fish size and sex, not previously examined in this species. Unlike most sciaenids, both sexes of P. cromis possess robust sonic muscles, and both produce disturbance calls when handled. However, only males produce an advertisement call used in courtship. The disturbance call consists of a variable train of short-duration pulses (average 23?ms). The duration, interpulse interval, and dominant frequency of pulses are similar in males and females and change developmentally: pulse duration and interpulse interval increase and dominant frequency decreases with fish size. Advertisement calls, recorded in the field and in captivity, are long-duration (average 184?ms) and tonal. Based on variation in fundamental frequency, which decreases with fish size, field choruses are composed of different-sized individuals. The duration of advertisement calls, about a third of those from Florida populations, suggests genetic differentiation between northern and southern populations.     

CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity

The ability to precisely modify endogenous genes can significantly facilitate biological studies and disease treatment, and the clustered regularly interspaced short palindromic repeats (CRISPR) systems have the potential to be powerful tools for genome engineering. However, the target specificity of CRISPR systems is largely unknown. Here we demonstrate that CRISPR/Cas9 systems targeting the human hemoglobin β and C-C chemokine receptor type 5 genes have substantial off-target cleavage, especially within the hemoglobin δ and C-C chemokine receptor type 2 genes, respectively, causing gross chromosomal deletions. The guide strands of the CRISPR/Cas9 systems were designed to have a range of mismatches with the sequences of potential off-target sites. Off-target analysis was performed using the T7 endonuclease I mutation detection assay and Sanger sequencing. We found that the repair of the on-and off-target cleavage resulted in a wide variety of insertions, deletions and point mutations. Therefore, CRISPR/Cas9 systems need to be carefully designed to avoid potential off-target cleavage sites, including those with mismatches to the 12-bases proximal to the guide strand protospacer-adjacent motif.     

A CFF 91-based Continuum Solvation Model: Solvation Free Energies of Small Organic Molecules and Conformations of the Alanine Dipeptide in Solution

Abstract

For molecular mechanics simulations of solvated molecules, it is important to use a consistent approach for calculating both the force field energy and the solvation free energy. A continuum solvation model based upon the atomic charges provided with the CFF91 force field is derived. The electrostatic component of the solvation free energy is described by the Poisson-Bolzmann equation while the nonpolar comonent of the solvation energy is assumed to be proportional to the solvent accessible surface area of the solute. Solute atomic radii used to describe the interface between the solute and solvent are fitted to reproduce the energies of small organic molecules. Data for 140 compounds are presented and compared to experiment and to the results from the well-characterized quantum mechanical solvation model AM1-SM2. In particular, accurate results are obtained for amino acid neutral analogues (mean unsigned error of 0.3 kcal/mol). The conformational energetics of the solvated alanine dipeptide is discussed.     

Determining an economic injury level for the persea mite,Oligonychus perseae,a new pest of avocado in Israel

The persea mite, Oligonychus perseae Tuttle, Baker & Abbatiello (Acari: Tetranychidae), a pest of avocado, was first discovered in Israel in the autumn of 2001. It has since spread to most avocado growing areas in Israel. To establish an economic injury level (EIL), based on the percentage of leaf area damaged (PLAD), we conducted an extensive field study. For three consecutive seasons we created distinct pest infestation levels on the Hass avocado cv., by applying acaricides (spirodiclofen and abamectin) at 50, 100, and 250 mites per leaf levels, along with non‐sprayed controls in a replicated block design. At harvest time we evaluated the level of leaf damage and fruit yields across treatments. In two out of the 3 years, trees sprayed at 50 and 100 mites per leaf levels had similar PLAD values, differing from trees treated at the 250 mites per leaf level and the non‐treated control, the latter pair also being similar. Over the 3 years, mean yield attained at the two higher infestation levels was reduced by 20% in comparison to the mean yields recorded for plots sprayed at the lower thresholds. Accordingly, we suggest that scouts adopt an action threshold (AT) of 50–100 mites per leaf. Future research is needed to refine this AT. Mean annual cumulative mite days (CMDs) of the two higher levels was ca. 13500 ± 700 per leaf. Using the linear regression equation PLAD = 0.0009CMDs + 2.42, describing leaf damage as a function of CMDs, we estimated an EIL of ca. 15 PLAD.