Chlorovirus PBCV-1 Multidomain Protein A111/114R Has Three Glycosyltransferase Functions Involved in the Synthesis of Atypical N-Glycans

The structures of the four N-linked glycans from the prototype chlorovirus PBCV-1 major capsid protein do not resemble any other glycans in the three domains of life. All known chloroviruses and antigenic variants (or mutants) share a unique conserved central glycan core consisting of five sugars, except for antigenic mutant virus P1L6, which has four of the five sugars. A combination of genetic and structural analyses indicates that the protein coded by PBCV-1 gene a111/114r, conserved in all chloroviruses, is a glycosyltransferase with three putative domains of approximately 300 amino acids each. Here, in addition to in silico sequence analysis and protein modeling, we measured the hydrolytic activity of protein A111/114R. The results suggest that domain 1 is a galactosyltransferase, domain 2 is a xylosyltransferase and domain 3 is a fucosyltransferase. Thus, A111/114R is the protein likely responsible for the attachment of three of the five conserved residues of the core region of this complex glycan, and, if biochemically corroborated, it would be the second three-domain protein coded by PBCV-1 that is involved in glycan synthesis. Importantly, these findings provide additional support that the chloroviruses do not use the canonical host endoplasmic reticulum–Golgi glycosylation pathway to glycosylate their glycoproteins; instead, they perform glycosylation independent of cellular organelles using virus-encoded enzymes.     

Enumeration of structure-sensitive graphical subsets: Theory

The necessary mathematical machinery is developed for enumeration of the following types of special subsets of the vertices or edges of a general graph: (i) independent sets, (ii) connected sets, (iii) point and line covers, (iv) externally stable sets, (v) kernels, and (vi) irredundant sets.     

Organelle DNA variation and systematic relationships in the genus Zea: Teosinte

Chloroplast and mitochondrial DNAs from six races of annual teosinte (Guatemala, Huehuetenango, Balsas, Central Plateau, Chalco, and Nobogame), perennial teosinte, and maize were compared and grouped by restriction endonuclease fragment analyses. Three groups of chloroplast DNAs were detected: (i) perennial teosinte and Guatemala; (ii) Balsas and Huehuetenango; and (iii) all other teosintes. Four groups of mitochondrial DNAs were separated: (i) perennial teosinte; (ii) Guatemala; (iii) Nobogame; and (iv) all other teosintes. Separation of the teosinte and maize organelle DNAs into five groups (Guatemala; perennial teosinte; Balsas and Huehuetenango; Central Plateau and Chalco; Nobogame and maize) approximated the biosystematic relationships of the taxa. It was suggested that the evolutions of the chloroplast and mitochondrial DNAs may be independent of each other, that variation of organelle DNA within a species complex of an organism may be the common condition, and that the DNAs of the organelle and nuclear systems evolve in reasonable harmony.     

Mechanism of four-level laser action in solution excimer and excited-state proton-transfer cases

Four-level laser energy level schemes are compared from the mechanistic spectroscopic viewpoint: (i) noble-gas excimer, (ii) solution molecular excimer, (iii) conventional dye laser, and (iv) intramolecular proton transfer. The lasing action of the chlorophyll special pair is discussed as an example of a solution excimer laser, and the lasing action of 3-hydroxyflavone and other molecules is discussed as an example of an intramolecular proton-transfer laser.     

Model for primary charge separation in reaction centers of photosynthetic bacteria

We present model calculations of the dynamics of primary electron transfer (ET) in reaction centers of photosynthetic bacteria. We obtain half times of [unk]1 ps and ≈5 ps for the first two ET processes, in excellent agreement with experimental observations. Our model is based on (i) a theoretical framework capable of describing ET in the presence of strong electronic interstate resonance coupling and (ii) energy parameters extracted from recent experimental data and molecular orbital calculations. Our analysis suggests that (i) strong electronic interstate mixing is crucial to the rapidity and efficiency of irreversible ET; (ii) possibly five rather than three electronic states participate in the transient ET prior to the reduction in vivo of the quinone complex; and (iii) conventional ET theories, which rely on weak electronic interstate mixing, are unfit for describing ET in reaction centers of photosynthetic bacteria.     

Non-enzymatic and enzymatic hydrolysis of alkyl halides: A haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an SN2 displacement reaction

The semiempirical PM3 method, calibrated against ab initio HF/6–31+G(d) theory, has been used to elucidate the reaction of 1,2-dichloroethane (DCE) with the carboxylate of Asp-124 at the active site of haloalkane dehalogenase of Xanthobacter autothropicus. Asp-124 and 13 other amino acid side chains that make up the active site cavity (Glu-56, Trp-125, Phe-128, Phe-172, Trp-175, Leu-179, Val-219, Phe-222, Pro-223, Val-226, Leu-262, Leu-263, and His-289) were included in the calculations. The three most significant observations of the present study are that: (i) the DCE substrate and Asp-124 carboxylate, in the reactive ES complex, are present as an ion-molecule complex with a structure similar to that seen in the gas-phase reaction of AcO⁻ with DCE; (ii) the structures of the transition states in the gas-phase and enzymatic reaction are much the same where the structure formed at the active site is somewhat exploded; and (iii) the enthalpies in going from ground states to transition states in the enzymatic and gas-phase reactions differ by only a couple kcal/mol. The dehalogenase derives its catalytic power from: (i) bringing the electrophile and nucleophile together in a low-dielectric environment in an orientation that allows the reaction to occur without much structural reorganization; (ii) desolvation; and (iii) stabilizing the leaving chloride anion by Trp-125 and Trp-175 through hydrogen bonding.     

Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution

Potential paleoclimatic driving mechanisms acting on human evolution present an open problem of cross-disciplinary scientific interest. The analysis of paleoclimate archives encoding the environmental variability in East Africa during the past 5 Ma has triggered an ongoing debate about possible candidate processes and evolutionary mechanisms. In this work, we apply a nonlinear statistical technique, recurrence network analysis, to three distinct marine records of terrigenous dust flux. Our method enables us to identify three epochs with transitions between qualitatively different types of environmental variability in North and East Africa during the (i) Middle Pliocene (3.35–3.15 Ma B.P.), (ii) Early Pleistocene (2.25–1.6 Ma B.P.), and (iii) Middle Pleistocene (1.1–0.7 Ma B.P.). A deeper examination of these transition periods reveals potential climatic drivers, including (i) large-scale changes in ocean currents due to a spatial shift of the Indonesian throughflow in combination with an intensification of Northern Hemisphere glaciation, (ii) a global reorganization of the atmospheric Walker circulation induced in the tropical Pacific and Indian Ocean, and (iii) shifts in the dominating temporal variability pattern of glacial activity during the Middle Pleistocene, respectively. A reexamination of the available fossil record demonstrates statistically significant coincidences between the detected transition periods and major steps in hominin evolution. This result suggests that the observed shifts between more regular and more erratic environmental variability may have acted as a trigger for rapid change in the development of humankind in Africa.     

High-resolution,noninvasive longitudinal live imaging of immune responses

Intravital imaging emerged as an indispensible tool in biological research, and a variety of imaging techniques have been developed to noninvasively monitor tissues in vivo. However, most of the current techniques lack the resolution to study events at the single-cell level. Although intravital multiphoton microscopy has addressed this limitation, the need for repeated noninvasive access to the same tissue in longitudinal in vivo studies remains largely unmet. We now report on a previously unexplored approach to study immune responses after transplantation of pancreatic islets into the anterior chamber of the mouse eye. This approach enabled (i) longitudinal, noninvasive imaging of transplanted tissues in vivo; (ii) in vivo cytolabeling to assess cellular phenotype and viability in situ; (iii) local intervention by topical application or intraocular injection; and (iv) real-time tracking of infiltrating immune cells in the target tissue.     

Threefolds whose canonical bundles are not numerically effective

Let X be an arbitrary nonsingular projective 3-fold whose canonical bundle is not numerically effective. Then we have: (i) X contains an exceptional divisor of several types, which we classify explicitly, (ii) X has a morphism to a projective nonsingular surface whose fibers are conics, (iii) X has a morphism to a projective nonsingular curve whose general fibers are Del Pezzo surfaces, or (iv) X is a Fano 3-fold with Picard number 1.     

Evidence for virus-encoded glycosylation specificity.

Four spontaneously derived serologically distinct classes of mutants of the Paramecium bursaria chlorella virus (PBCV-1) were isolated using polyclonal antiserum prepared against either intact PBCV-1 or PBCV-1-derived serotypes. The oligosaccharide(s) of the viral major capsid protein and two minor glycoproteins determined virus serological specificity. Normally, viral glycoproteins arise from host-specific glycosylation of viral proteins; the glycan portion can be altered only by growing the virus on another host or by mutations in glycosylation sites of the viral protein. Neither mechanism explains the changes in the glycan(s) of the PBCV-1 major capsid protein because all of the viruses were grown in the same host alga and the predicted amino acid sequence of the major capsid protein was identical in the PBCV-1 serotypes. PBCV-1 antiserum resistance is best explained by viral mutations that block specific steps in glycosylation, possibly by inactivating glycosyltransferases.     

Cytochemical studies on GERL, provacuoles, and vacuoles in root meristematic cells of Euphorbia

The genesis of plant vacuoles has been studied by high-voltage and conventional electron microscopy. Vacuole genesis is a lysosomal multistep process: (i) GERL (Golgi-associated Endoplasmic Reticulum from which Lysosomes apparently form) produces provacuoles into which lysosomal enzymes and probably other materials appear to be concentrated and packaged; (ii) GERL-derived provacuoles cooperate to drive a programmed cellular autophagy leading to young vacuoles; and (iii) the young vacuoles swell and fuse together into a few large mature vacuoles which continue to collect the GERL-derived provacuoles throughout the life of the cell.     

Soliton dynamics in polyacetylene

The equations of motion of the coupled electron-phonon system are integrated in real time for the model of polyacetylene recently proposed. To illustrate the physical behavior of this nonlinear system we consider the time evolution starting from three physically relevant configurations: (i) end generated soliton, (ii) electron-hole pair generation of a charged soliton-antisoliton pair, and (iii) the dressing of an injected electron. The calculations show that the system relaxes within a time of order 10^-13 sec, converting excited electron-hole pairs into soliton-antisoliton pairs.     

A biological rationale for musical consonance

The basis of musical consonance has been debated for centuries without resolution. Three interpretations have been considered: (i) that consonance derives from the mathematical simplicity of small integer ratios; (ii) that consonance derives from the physical absence of interference between harmonic spectra; and (iii) that consonance derives from the advantages of recognizing biological vocalization and human vocalization in particular. Whereas the mathematical and physical explanations are at odds with the evidence that has now accumulated, biology provides a plausible explanation for this central issue in music and audition.     

The structure and evolution of the major capsid protein of a large,lipid-containing DNA virus

Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-A resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel beta-barrel, "jelly-roll" domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-A diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus.     

Components of Adenovirus-Simian Virus 40 Hybrid Viruses

The DNA and protein components of the adenovirus 7-simian virus (SV)40 hybrid virus “E46⁺” have been investigated. The Ad.7-SV40 hybrid DNA genome could be distinguished from nonhybrid Ad. 7 genome on the basis of its molecular weight in an alkaline sucrose gradient. The hybrid genome could also be separated from nonhybrid adenovirus 2 DNA when purified transcapsidant adenovirus 2^+t7 (Ad.7-SV40 DNA within an Ad.2 capsid) was studied. The presence and amount of SV40 DNA in the hybrid virus genome was determined by DNA-RNA hybridization. The results presented suggest: (i) that about 10% of the particles in the E46⁺ preparations contained SV40 DNA covalently linked to adenovirus DNA; (ii) that the hybrid virus genome has a molecular weight 10-12% lower than that of nonhybrid virus, consistent with a deletion of adenovirus DNA; and (iii) that the hybrid virus contained only 40-50% of a total SV40 genome.     

Plasmodium falciparum antigenic diversity: Evidence of clonal population structure

Plasmodium falciparum, the agent of malignant malaria, is one of mankind’s most severe scourges. Efforts to develop preventive vaccines or remedial drugs are handicapped by the parasite’s rapid evolution of drug resistance and protective antigens. We examine 25 DNA sequences of the gene coding for the highly polymorphic antigenic circumsporozoite protein. We observe total absence of silent nucleotide variation in the two nonrepeated regions of the gene. We propose that this absence reflects a recent origin (within several thousand years) of the world populations of P. falciparum from a single individual; the amino acid polymorphisms observed in these nonrepeat regions would result from strong natural selection. Analysis of these polymorphisms indicates that: (i) the incidence of recombination events does not increase with nucleotide distance; (ii) the strength of linkage disequilibrium between nucleotides is also independent of distance; and (iii) haplotypes in the two nonrepeat regions are correlated with one another, but not with the central repeat region they span. We propose two hypotheses: (i) variation in the highly polymorphic central repeat region arises by mitotic intragenic recombination, and (ii) the population structure of P. falciparum is clonal—a state of affairs that persists in spite of the necessary stage of physiological sexuality that the parasite must sustain in the mosquito vector to complete its life cycle.     

ICP0 enables and monitors the function of D cyclins in herpes simplex virus 1 infected cells

The herpes simplex virus 1 ICP0 is a regulatory protein. Early in infection ICP0 localizes in ND10 bodies and performs two functions: As an E3 ligase in conjunction with E2 UbcH5a conjugating enzyme, it degrades the ND10 components PML and SP100. Concurrently, it suppresses the silencing of viral DNA by dispersing the HDAC1/CoREST/REST/LSD1 repressor complex. Subsequently, ICP0 is exported to the cytoplasm. In cells treated with HDAC inhibitors or transfected with irrelevant DNA, the export is delayed in a DNA dose-dependent fashion. Here, we follow up an observation that ICP0 binds cyclin D3 and that ICP0 mutants unable to bind cyclin D3 are not exported. Moreover, in infected cells cdk4 is activated, but cdk2 is not. We report that (i) cyclin D1, D2, or D3 colocalize with ND10 bodies and ICP0 early in infection and ultimately become incorporated into viral replication compartments, (ii) each of the D cyclins partially rescues ΔICP0 mutants, and (iii) inhibition of cdk4 by inhibitor I sequesters ICP0 in the nucleus. A key finding is that overexpression of cyclin D3 enables the transport of ICP0 to the cytoplasm. We conclude that (i) ICP0 facilitates the recruitment of cyclin D3 to the sites of viral DNA synthesis, (ii) until its functions are completed, ICP0 is retained in the nucleus, and (iii) a common signal that results in the export of ICP0 to the cytoplasm is the accumulation of a viral DNA-synthesis-dependent late protein.     

Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: The phenylacetyl-CoA catabolon

Fourteen different genes included in a DNA fragment of 18 kb are involved in the aerobic degradation of phenylacetic acid by Pseudomonas putida U. This catabolic pathway appears to be organized in three contiguous operons that contain the following functional units: (i) a transport system, (ii) a phenylacetic acid activating enzyme, (iii) a ring-hydroxylation complex, (iv) a ring-opening protein, (v) a β-oxidation-like system, and (vi) two regulatory genes. This pathway constitutes the common part (core) of a complex functional unit (catabolon) integrated by several routes that catalyze the transformation of structurally related molecules into a common intermediate (phenylacetyl-CoA).     

From the Cover: Explaining Asian Americans’ academic advantage over whites

The superior academic achievement of Asian Americans is a well-documented phenomenon that lacks a widely accepted explanation. Asian Americans’ advantage in this respect has been attributed to three groups of factors: (i) socio-demographic characteristics, (ii) cognitive ability, and (iii) academic effort as measured by characteristics such as attentiveness and work ethic. We combine data from two nationally representative cohort longitudinal surveys to compare Asian-American and white students in their educational trajectories from kindergarten through high school. We find that the Asian-American educational advantage is attributable mainly to Asian students exerting greater academic effort and not to advantages in tested cognitive abilities or socio-demographics. We test explanations for the Asian–white gap in academic effort and find that the gap can be further attributed to (i) cultural differences in beliefs regarding the connection between effort and achievement and (ii) immigration status. Finally, we highlight the potential psychological and social costs associated with Asian-American achievement success.Asian Americans have higher grades and standardized test scores, are more likely to finish high school and attend college, and are more likely to attend the most elite colleges relative to whites (1–4). Despite the vast research documenting their educational advantage, explanations for this remain uncertain. The main task of this study is to empirically test three widely proposed explanations for Asian Americans’ advantage in education: (i) family socio-demographic characteristics, (ii) cognitive skills, and (iii) academic effort as measured by characteristics such as attentiveness and work ethic. We combine data from two nationally representative cohort longitudinal surveys—the Early Childhood Longitudinal Study, Kindergarten Cohort (ECLS-K) and the Education Longitudinal Study (ELS)—to compare Asian American and white students in their educational trajectories from kindergarten through high school. Our findings show that the Asian-American advantage in academic achievement is primarily attributable to greater academic effort and not to advantages in tested cognitive ability or socio-demographic characteristics. In the second part of our study, we examine potential explanations for the observed Asian–white gap in academic effort. In the third part, we consider the potential psychological and social costs associated with Asian-American academic success. We close by summarizing and contextualizing our findings within the broader literature on Asian Americans.     

Density-dependent selection in a random environment: An evolutionary process that can maintain stable population dynamics

A theoretical analysis of natural selection is presented in which fitnesses depend on population density and randomly varying environmental processes. The theory is based on a general, heuristic analysis of a pair of coupled, nonlinear, stochastic difference equations that describe the joint dynamics of allele frequencies and population size. Four main conclusions emerge from the investigation of a particular class of models: (i) growth rates at low population densities tend to increase; (ii) individual selection, given sufficient genetic flexibility, will mold growth rates at higher densities so that in spite of i, stable deterministic population dynamics are maintained; (iii) “more fit” genotypes cannot be simply characterized—in particular, the mean population size need not be increased; and (iv) genetic polymorphisms can be maintained in both haploid and diploid organisms.