Pepitope: epitope mapping from affinity-selected peptides

Identifying the epitope to which an antibody binds is central for many immunological applications such as drug design and vaccine development. The Pepitope server is a web-based tool that aims at predicting discontinuous epitopes based on a set of peptides that were affinity-selected against a monoclonal antibody of interest. The server implements three different algorithms for epitope mapping: PepSurf, Mapitope, and a combination of the two. The rationale behind these algorithms is that the set of peptides mimics the genuine epitope in terms of physicochemical properties and spatial organization. When the three-dimensional (3D) structure of the antigen is known, the information in these peptides can be used to computationally infer the corresponding epitope. A user-friendly web interface and a graphical tool that allows viewing the predicted epitopes were developed. Pepitope can also be applied for inferring other types of protein-protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure. AVAILABILITY: http://pepitope.tau.ac.il/     

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates

Distance-based methods for phylogeny reconstruction are the fastest and easiest to use, and their popularity is accordingly high. They are also the only known methods that can cope with huge datasets of thousands of sequences. These methods rely on evolutionary distance estimation and are sensitive to errors in such estimations. In this study, a novel Bayesian method for estimation of evolutionary distances is developed. The proposed method enables the use of a sophisticated evolutionary model that better accounts for among-site rate variation (ASRV), thereby improving the accuracy of distance estimation. Rate variations are estimated within a Bayesian framework by extracting information from the entire dataset of sequences, unlike standard methods that can only use one pair of sequences at a time. We compare the accuracy of a cascade of distance estimation methods, starting from commonly used methods and moving towards the more sophisticated novel method. Simulation studies show significant improvements in the accuracy of distance estimation by the novel method over the commonly used ones. We demonstrate the effect of the improved accuracy on tree reconstruction using both real and simulated protein sequence alignments. An implementation of this method is available as part of the SEMPHY package.     

Purification of the human alpha2 Isoform of Na,K-ATPase expressed in Pichia pastoris. Stabilization by lipids and FXYD1

Human alpha1 and alpha2 isoforms of Na,K-ATPase have been expressed with porcine 10*Histidine-tagged beta1 subunit in Pichia pastoris. Methanol-induced expression of alpha2 is optimal at 20 degrees C, whereas at 25 degrees C, which is optimal for expression of alpha1, alpha2 is not expressed. Detergent-soluble alpha2beta1 and alpha1beta1 complexes have been purified in a stable and functional state. alpha2beta1 shows a somewhat lower Na,K-ATPase activity and higher K0.5K compared to alpha1beta1, while values of K0.5Na and KmATP are similar. Ouabain inhibits both alpha1beta1 (K0.5 24.6 +/- 6 nM) and alpha2beta1 (K0.5 102 +/- 14 nM) with high affinity. A striking difference between the isoforms is that alpha2beta1 is unstable. Both alpha1beta1 and alpha2beta1 complexes, prepared in C12E8 with an added phosphatidyl serine, are active, but alpha2beta1 is rapidly inactivated at 0 degrees C. Addition of low concentrations of cholesterol with 1-stearoyl-2-oleoyl-sn-glycero-3-[phospho-l-serine] (SOPS) stabilizes strongly, maintaining alpha2beta1 active up to two weeks at 0 degrees C. By contrast, alpha1beta1 is stable at 0 degrees C without added cholesterol. Both alpha1beta1 and alpha2beta1 complexes are stabilized by cholesterol at 37 degrees C. Human FXYD1 spontaneously associates in vitro with either alpha1beta1 or alpha2beta1, to form alpha1beta1/FXYD1 and alpha2beta1/FXYD1 complexes. The reconstituted FXYD1 protects both alpha1beta1 and alpha2beta1 very strongly against thermal inactivation. Instability of alpha2 is attributable to suboptimal phophatidylserine-protein interactions. Residues within TM8, TM9 and TM10, near the alphabeta subunit interface, may play an important role in differential interactions of lipid with alpha1 and alpha2, and affect isoform stability. Possible physiological implications of isoform interactions with phospholipids and FXYD1 are discussed.     

Determination of the rotational barriers of atropisomeric polychlorinated biphenyls (PCBs) by a novel stopped-flow multidimensional gas chromatographic technique

The rotational barriers ΔG^‡ (T) of the four atropisomeric polychlorinated biphenyls (PCBs) 2,2′,3,5′,6-pentachlorobiphenyl (PCB 95), 2,2′3,3′,4,6′-hexachlorobiphenyl (PCB 132), 2,2′,3,3′,6,6′-hexachlorobiphenyl (PCB 136), and 2,2′,3,4′,5′,6-hexachlorobiphenyl (PCB 149) were determined via on-line enantiomerization kinetics by a new stopped-flow multidimensional gas chromatographic technique (stopped-flow MDGC) employing Chirasil-Dex as chiral stationary phase for enantiomer separation. The calculated rotational barriers ΔG^‡ (T) of the trichloro-ortho-substituted atropisomers are 184 ± 2 kJ/mol for PCB 95, 189 ± 4 kJ/mol for PCB 132, and 184 ± 1 kJ/mol for PCB 149 at 300°C. The rotational barrier ΔG^‡ (T) of tetrachloro-ortho-substituted PCB 136 is at least (or higher than) 210 kJ/mol at 320°C. Chirality 10:316–320, 1998. © 1998 Wiley-Liss, Inc.     

A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions

Insertions and deletions (indels) are common molecular evolutionary events. However, probabilistic models for indel evolution are under-developed due to their computational complexity. Here, we introduce several improvements to indel modeling: 1) While previous models for indel evolution assumed that the rates and length distributions of insertions and deletions are equal, here we propose a richer model that explicitly distinguishes between the two; 2) we introduce numerous summary statistics that allow approximate Bayesian computation-based parameter estimation; 3) we develop a method to correct for biases introduced by alignment programs, when inferring indel parameters from empirical data sets; and 4) using a model-selection scheme, we test whether the richer model better fits biological data compared with the simpler model. Our analyses suggest that both our inference scheme and the model-selection procedure achieve high accuracy on simulated data. We further demonstrate that our proposed richer model better fits a large number of empirical data sets and that, for the majority of these data sets, the deletion rate is higher than the insertion rate.     

Xylem Flow and its Driving Forces in a Tropical Liana: Concomitant Flow-Sensitive NMR Imaging and Pressure Probe Measurements

Abstract: Flow-sensitive NMR imaging and pressure probe techniques were used for measuring xylem water flow and its driving forces (i.e., xylem pressure as well as cell turgor and osmotic pressure gradients) in a tropical liana, Epipremnum aureum. Selection of tall specimens allowed continuous and simultaneous measurements of all parameters at various distances from the root under diurnally changing environmental conditions. Well hydrated plants exhibited exactly linearly correlated dynamic changes in xylem tension and flow velocity. Concomitant multiple-probe insertions along the plant shoot revealed xylem and turgor pressure gradients with changing magnitudes due to environmental changes and plant orientation (upright, apex-down, or horizontal). The data suggest that in upright and - to a lesser extent - in horizontal plants the transpirational water loss by the cells towards the apex during the day is not fully compensated by water uptake through the night. Thus, longitudinal cellular osmotic pressure gradients exist. Due to the tight hydraulic coupling of the xylem and the tissue cells these gradients represent (besides the transpiration-induced tension in the xylem) an additional tension component for anti-gravitational water movement from the roots through the vessels to the apex.     

Indian genetic heritage in Southeast Asian populations

The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, a cultural influence that is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA populations, we generated genome-wide SNP data (using the Affymetrix Human Origins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data using PCA, ADMIXTURE, and methods relying on f-statistics and on autosomal haplotypes. We found low levels of South Asian admixture in various MSEA populations for whom there is evidence of historical connections with the ancient Indian-influenced states but failed to find this genetic component in present-day hunter-gatherer groups and relatively isolated groups from the highlands of Northern Thailand. The results suggest that migration of Indian populations to MSEA may have been responsible for the spread of Indian culture in the region. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.     

Cortical signatures of auditory object binding in children with autism spectrum disorder are anomalous in concordance with behavior and diagnosis

Organizing sensory information into coherent perceptual objects is fundamental to everyday perception and communication. In the visual domain, indirect evidence from cortical responses suggests that children with autism spectrum disorder (ASD) have anomalous figure–ground segregation. While auditory processing abnormalities are common in ASD, especially in environments with multiple sound sources, to date, the question of scene segregation in ASD has not been directly investigated in audition. Using magnetoencephalography, we measured cortical responses to unattended (passively experienced) auditory stimuli while parametrically manipulating the degree of temporal coherence that facilitates auditory figure–ground segregation. Results from 21 children with ASD (aged 7–17 years) and 26 age- and IQ-matched typically developing children provide evidence that children with ASD show anomalous growth of cortical neural responses with increasing temporal coherence of the auditory figure. The documented neurophysiological abnormalities did not depend on age, and were reflected both in the response evoked by changes in temporal coherence of the auditory scene and in the associated induced gamma rhythms. Furthermore, the individual neural measures were predictive of diagnosis (83% accuracy) and also correlated with behavioral measures of ASD severity and auditory processing abnormalities. These findings offer new insight into the neural mechanisms underlying auditory perceptual deficits and sensory overload in ASD, and suggest that temporal-coherence-based auditory scene analysis and suprathreshold processing of coherent auditory objects may be atypical in ASD.

To navigate everyday environments, the auditory system must analyze the temporal coherence of sound elements scattered across different frequencies to organize them into discrete perceptual objects. This neuroimaging study reveals that this process is altered in autism, potentially explaining the often-experienced sensory overload.     

Genetic evidence for a recent origin by hybridization of red wolves

Genetic data suggest that red wolves ( Canis rufus ) resulted from a hybridization between coyotes ( C. latrans ) and grey wolves ( C. lupus ). The date of the hybridization, however, is uncertain. According to one hypothesis, the two species came into contact as coyotes increased their geographical range in conjunction with the advance of European settlers and as grey wolves were extirpated from the American south. Alternatively, the red wolves could have originated tens of thousands of years ago as a result of climate and habitat changes that disturbed the ecology of the two parent species. To obtain an upper limit on the date of hybridization that would help to distinguish the two scenarios, we compared microsatellite allele length distributions from red wolves, coyotes and grey wolves. Subject to the assumptions of our analysis, we conclude that the red wolves originated as a result of hybridizations that occurred during the past 12 800 years, and probably during the past 2500 years.     

Genome Scanning in Haemophilus influenzae for Identification of Essential Genes

We have developed a method for identifying essential genes by using an in vitro transposition system, with a small (975 bp) insertional element containing an antibiotic resistance cassette, and mapping these inserts relative to the deduced open reading frames of Haemophilus influenzae by PCR and Southern analysis. Putative essential genes are identified by two methods: mutation exclusion or zero time analysis. Mutation exclusion consists of growing an insertional library and identifying open reading frames that do not contain insertional elements: in a growing population of bacteria, insertions in essential genes are excluded. Zero time analysis consists of monitoring the fate of individual insertions after transformation in a growing culture: the loss of inserts in essential genes is observed over time. Both methods of analysis permit the identification of genes required for bacterial survival. Details of the mutant library construction and the mapping strategy, examples of mutant exclusion, and zero time analysis are presented.